#/*****************************************************************************
##   Copyright (C) 1994-2008 by David Gordon.
##   All rights reserved.                           
##                                                                           
##   This software is part of a beta-test version of the Consed/Autofinish
##   package.  It should not be redistributed or
##   used for any commercial purpose, including commercially funded
##   sequencing, without written permission from the author and the
##   University of Washington.
##   
##   This software is provided ``AS IS'' and any express or implied
##   warranties, including, but not limited to, the implied warranties of
##   merchantability and fitness for a particular purpose, are disclaimed.
##   In no event shall the authors or the University of Washington be
##   liable for any direct, indirect, incidental, special, exemplary, or
##   consequential damages (including, but not limited to, procurement of
##   substitute goods or services; loss of use, data, or profits; or
##   business interruption) however caused and on any theory of liability,
##   whether in contract, strict liability, or tort (including negligence
##   or otherwise) arising in any way out of the use of this software, even
##   if advised of the possibility of such damage.
##
##   Building Consed from source is error prone and not simple which is
##   why I provide executables.  Due to time limitations I cannot
##   provide any assistance in building Consed.  Even if you do not
##   modify the source, you may introduce errors due to using a
##   different version of the compiler, a different version of motif,
##   different versions of other libraries than I used, etc.  For this
##   reason, if you discover Consed bugs, I can only offer help with
##   those bugs if you first reproduce those bugs with an executable
##   provided by me--not an executable you have built.
## 
##   Modifying Consed is also difficult.  Although Consed is modular,
##   some modules are used by many other modules.  Thus making a change
##   in one place can have unforeseen effects on many other features.
##   It may takes months for you to notice these other side-effects
##   which may not seen connected at all.  It is not feasable for me to
##   provide help with modifying Consed sources because of the
##   potentially huge amount of time involved.
##
##*****************************************************************************/
#
#  header file included in generated makefile
#  melakwa version (Linux and g++)
#

#
# compilation
#
CXX= g++
KRCC= gcc
CC=gcc 

#
#
CFLGS= -w -DINLINE_RWTPTRORDEREDVECTOR -DINLINE_RWTVALORDEREDVECTOR -DINLINE_MBTVALVECTOR -DLINUX_COMPILE -DSOCKLEN_T_DEFINED -D__BOOL_DEFINED -DANSI_C -DOFSTREAM_OPEN_WITHOUT_PERMISSIONS -fpermissive -DNO_POUND_POUND_MACROS -DUSE_USING_IN_PUBLIC_TEMPLATE_CLASSES -DINT_CHAR_OPERATOR -D_FILE_OFFSET_BITS=64

OPT= -O
#
# Include directory for template classes must be included
# in both compilation & link lines, even if .h file is
# found in default path.  C front, gotta love it.
#
INC=  -I/usr/X11R6/include

DEPENDENCIES=
#
#
# Linking
#
# A completely static link causes an immediate segmentation fault
# when errno is accessed.  A test program shows the shared library
# -lpthread is involved.  But the following build, which is close to
# static, does not segmentation fault.  It uses these shared libraries:
# > ldd consed
#         libstdc++.so.6 => /usr/lib/libstdc++.so.6 (0x00844000)
#         libm.so.6 => /lib/tls/libm.so.6 (0x00536000)
#         libgcc_s.so.1 => /lib/libgcc_s.so.1 (0x00818000)
#         libc.so.6 => /lib/tls/libc.so.6 (0x00408000)
#         /lib/ld-linux.so.2 (0x003ee000)
# 
# To fix cut/paste bug, I've made X11 always dynamic.
CLIBS= -lX11
LPATH= -L/usr/X11R6/lib
ARCHIVES= /usr/X11R6/lib/libXm.a \
/usr/X11R6/lib/libXt.a /usr/X11R6/lib/libSM.a \
/usr/X11R6/lib/libICE.a /usr/X11R6/lib/libXext.a /usr/X11R6/lib/libXmu.a \
/usr/X11R6/lib/libXp.a /usr/lib/libm.a



#
# debug, warning
#
#LDFLGS=	-g
# static linking
LDFLGS=	-g

# 
# the subdirectory used by cfront compilers gets cleaned
# out by "make clean"
#
#TEMPLATE_DIR= Templates.DB

#
# rules.  two different file extensions are used as a 
# workaround for (apparent) DEC cxx compiler bug
#
.SUFFIXES:	.o .cpp .cxx .c

#
# general compilation rules for .cpp, .cxx, .c  files
#
.cpp.o:		
	$(CXX) $(CFLGS) $(OPT) $(INC) -c $<
           
.c.o:	   
	$(CXX) $(CFLGS) $(OPT) $(INC) -c $<

#
# targets file included in generated makefile
#
# printAutoFinishMiscInfo must come after teditor and tedwin for sgi
# template instanciation

CONSED_OBJS = \
   guiEditResources.o \
   guiEditResourcesStandalone.o \
   addAlignedSequence.o \
   addNewReads.o \
   addNewReadsAutomated.o \
   addNewReadsWithExistingAlignments.o \
   addTearTagType.o \
   applyEditHistory.o \
   arrayOfFwdRevPairLines.o \
   arrayOfFwdRevPairSquares.o \
   arrayOfFwdRevPairTriangles.o \
   assembly.o \
   assembly2.o \
   assembly3.o \
   assembly4.o \
   assembly5.o \
   assemblyView.o \
   assemblyView2.o \
   assemblyView3.o \
   assemblyView4.o \
   assemblyViewRemoveReads.o \
   assert.o \
   autoEdit.o \
   autoFinish.o \
   autoFinishExpTag.o \
   autoFinishPCR.o \
   autoPCRAmplify.o \
   autoReport.o \
   automatedConsedInit.o \
   bDoPCRPrimersStickToEachOther.o \
   bEditHistoryFileExists.o \
   bErrorMessageIfNoPhd.o \
   bForwardReversePairIsConsistentWithContigOrder.o \
   bGuiGetAnswerYesNo.o \
   bInputEventToWrongWindow.o \
   bIsNumeric.o \
   bIsNumericDouble.o \
   bIsNumericFloat.o \
   bIsNumericLongMaybeWithWhitespace.o \
   bIsNumericMaybeWithWhitespace.o \
   bIsPCRPrimerPairOK.o \
   bIsPrimerStale.o \
   bIsTopStrandRead.o \
   bPrimerHasMatchesAgainstSequencesInFile.o \
   bPrimerHasMatchesElsewhere.o \
   basesAndQualitiesAndPeaks.o \
   basesegment.o \
   batchChangeConsensus.o \
   bigArrayOfLittleArraysOfDistributions.o \
   breakIntoShorterLines.o \
   busy_cursor.o \
   cGetProtein.o \
   calculatePrimerMeltingTemperatures.o \
   centerWidgetOnWidget.o \
   checkPrimersForACGT.o \
   checkPrimersForMononucleotideRepeats.o \
   checkVariableLengthLimit.o \
   choose_contig.o \
   chromatData.o \
   clScaffold.o \
   colorDefaults.o \
   colormode.o \
   compareContigs.o \
   compareContigs2.o \
   compareOnePrimerAndOneSequence.o \
   complementSequence.o \
   complement_so.o \
   consed.o \
   consedParameters.o \
   consedParameters2.o \
   consedParameters3.o \
   consedResources.o \
   consedResources2.o \
   consedResources3.o \
   contig.o \
   contig10.o \
   contig11.o \
   contig12.o \
   contig2.o \
   contig4.o \
   contig5.o \
   contig6.o \
   contig7.o \
   contig8.o \
   contig9.o \
   contigEndPair.o \
   contigEndReadList.o \
   contigview.o \
   contigwin.o \
   copyFiles.o \
   copyPrimerMatchesFromShorterToLongerPrimers.o \
   countsOfWhyPrimersAreNotAcceptable.o \
   createPrimerCandidate.o \
   createPrimerCandidates.o \
   createPrimerCandidatesWith3PrimeEnd.o \
   createTearTags.o \
   createUnalignedHighQualityNavigator.o \
   crossMatchInfoForRead.o \
   customNavigation.o \
   dGetPrimerMeltingTemperature.o \
   decisionbox.o \
   deleteFileIfItExists.o \
   deleteFileOrPopupErrorMessage.o \
   dictionary.o \
   diffChromosomes.o \
   digestForOneEnzyme.o \
   displayPrimers.o \
   distribution.o \
   dumpCore.o \
   editAddConsensusTag.o \
   editAddReadTag.o \
   editAddTagsToAllReadsAtConsPos.o \
   editCursor.o \
   editDeleteConsensusTag.o \
   editDeleteReadTag.o \
   editInsertColOfPads.o \
   editMakeHighQualityAndChangeConsensus.o \
   editOverstrikeAllReadsAtConsPos.o \
   editOverstrikeConsensus.o \
   edit_complement_contig.o \
   editaction.o \
   editedButNotNsGotoList.o \
   editedGotoList.o \
   evalExpCluster.o \
   experiment.o \
   extendAlignment.o \
   extendAlignmentBanded.o \
   filFindSolexaPrbFileFromSeqFile.o \
   filGetUniqueFilename.o \
   filePopupAndGetAceFilename.o \
   filePopupAndGetFilename.o \
   filename.o \
   fileselector.o \
   findAncestralTrees.o \
   findPrimerMatchesAgainstSequencesInFile.o \
   findPrimerMatchesElsewhere.o \
   findPrimerSelfMatches.o \
   findQueryWithinSubject.o \
   findRepeat.o \
   findStickiestSelfMatch.o \
   findTemplatesForPrimers.o \
   findTraceExtrema.o \
   fixContigEnd.o \
   fixContigEnds.o \
   fragment_and_contig.o \
   fullSmithWaterman.o \
   fwdRevPairLine.o \
   fwdRevPairSquare.o \
   fwdRevPairTriangle.o \
   geneClassifications.o \
   getAlignment.o \
   getAlignmentBanded.o \
   getAllSinglets.o \
   getAllTokens.o \
   getNextToken.o \
   gotoList.o \
   guiAddNewReads.o \
   guiAskUserToSelectReadListOptions.o \
   guiAssemblyViewIncludeContigs.o \
   guiAssemblyViewReadDepth.o \
   guiAssemblyViewShowTags.o \
   guiAssemblyViewWhatToShow.o \
   guiChangeColor.o \
   guiCheckPrimer.o \
   guiChoiceOfReadsForAlignedReads.o \
   guiChoiceOfSeqMatches.o \
   guiCompareContigs.o \
   guiDigestProblemNavigator.o \
   guiDisplayDigest.o \
   guiExportConsensusWithOptions.o \
   guiFindRestrictionEnzymeSites.o \
   guiGetCommentForTag.o \
   guiGetReferenceRead.o \
   guiGetTagType.o \
   guiGetUserDefinedTagInfo.o \
   guiHowToSortAlignedReads.o \
   guiMultiContigNavigator.o \
   guiNavigateByHighlyDiscrepantPositions.o \
   guiNavigateByReadDepth.o \
   guiPopupDocumentation.o \
   guiPopupTagInfo.o \
   guiPopupWholeReadItem.o \
   guiQuit.o \
   guiRemoveReads.o \
   guiReorderContigs.o \
   guiReorientContigs.o \
   guiSaveHighlightedReads.o \
   guiSearchForOligoTags.o \
   guiSearchForOpenReadingFrames.o \
   guiSearchForTagsByComment.o \
   guiSetGeneralPreferences.o \
   guiSetPrimerPickingPreferences.o \
   guiShowErrorInfoForARegion.o \
   guiTearContig.o \
   guiTopWindow.o \
   guiUndoEdit.o \
   guiWhatToDoWithSelection.o \
   gui_get_selection.o \
   gui_search_for_string.o \
   guiapp.o \
   guicolortext.o \
   guicontigwin.o \
   guidraw.o \
   guihighlight.o \
   guiinput.o \
   guiresize.o \
   guiteditor.o \
   guitedwin.o \
   handleWindowManagerDelete.o \
   handleWindowManagerDelete2.o \
   hideSomeTagTypes.o \
   highQualityDiscrepancyGotoList.o \
   infobutton.o \
   kimuraBranchProb.o \
   library.o \
   listOfLibraries.o \
   locatedFragment.o \
   lookForFalsePrimerMatchesOfOnePrimerInOneContig.o \
   lookForImperfect3Prime4MerFalsePrimerMatchesOfOnePrimerInOneContig.o \
   lookForPerfect4MerFalsePrimerMatchesOfOnePrimerInOneContig.o \
   lowconsqual.o \
   main.o \
   makeUpper.o \
   makeVectorLookupTables.o \
   maybeTerminateIfAnotherReadWriteConsed.o \
   mbtValOrderedVectorOfInt.o \
   mbtValVector.o \
   mbt_exception.o \
   messageAndFileSelector.o \
   miniassembly.o \
   miscProgram.o \
   motifutils.o \
   multiProblemGotoList.o \
   myAgrep.o \
   myAgrepAndFilter.o \
   nAmbiguityCodeToNumber2.o \
   nCompareContigsByName.o \
   nCreateSocket.o \
   nDeleteFile.o \
   nFindScoreOfMatch.o \
   nFindScoreOfSelfMatch.o \
   nGetLengthOfMononucleotideRepeat.o \
   nGetNumberOfTokens.o \
   nGetReadTypeFromReadName.o \
   nGetTrailingNumber.o \
   nStripTrailingWhitespace.o \
   nSystemReadALine.o \
   navigateByTagsInAllContigs.o \
   nextPhredPipeline.o \
   ntide.o \
   numutil.o \
   oligoTag.o \
   openAutoFinishOutputFiles.o \
   openLogFiles.o \
   ostream_overloads.o \
   pFindShortestAcceptablePrimer.o \
   paddedFromUnpadded.o \
   paddedPieceOfRead.o \
   paddedPieceOfSequence.o \
   parseAceFile.o \
   parseUserDefinedTagTypeLine.o \
   pcrPrimer.o \
   pcrPrimerrPair.o \
   perhapsCreateSocketToControlConsed.o \
   phaster2PhdBall.o \
   phdBall2Fasta.o \
   phredUtilities.o \
   pickCombinationsOfPCRPrimers.o \
   pickPCRPrimers.o \
   pickPCRPrimersForOneEndOfContig.o \
   pickPrimers.o \
   please_wait.o \
   popupErrorMessage.o \
   popupErrorMessage2.o \
   popupInfoMessage.o \
   popupInfoOrErrorMessageNoFormat.o \
   primateSpecies.o \
   primerStickiestFalseMatch.o \
   printAlignment.o \
   printAutoFinishMiscInfo.o \
   printAutoFinishParameters.o \
   printChangedAutoFinishParameters.o \
   printDefaultResources.o \
   printMemory.o \
   printPS.o \
   printSingleSignal.o \
   printTime.o \
   procToRunWhenSomeOtherProgramConnectsToConsed.o \
   readABI.o \
   readAndProcessReadPrefixFile.o \
   readData.o \
   readESD.o \
   readFileOfPhdFiles.o \
   readOneSffFile.o \
   readPHD.o \
   readPHDAgainForHighQualitySegment.o \
   readPHDOfSinglet.o \
   readPrimerScreenSequences.o \
   readSCF.o \
   readSCF2.o \
   readSCF3.o \
   readSCFUtil.o \
   readType.o \
   readWholeReadItem.o \
   regionOfSequenceArray.o \
   regionToAmplify.o \
   removeContigs.o \
   removeReads.o \
   renameFiles.o \
   restrictionFragment.o \
   rwUtil.o \
   rwcregexp.o \
   rwcstring.o \
   rwcsubstring.o \
   rwctokenizer.o \
   rwtptrorderedvector.o \
   rwtptrsortedvector.o \
   rwtvalorderedvector.o \
   saveTagTypes.o \
   saveTagTypesFromFile.o \
   searchForSingleStrandedRegions.o \
   searchForSingleSubcloneRegions.o \
   search_for_string.o \
   selection.o \
   seqMatch.o \
   sequence.o \
   setComplementBaseTable.o \
   setErrorRateFromQuality.o \
   setMatchLookupTable.o \
   setMatchMatrix.o \
   setNotACGTTable.o \
   setNumberFromBase4.o \
   setNumberFromBaseTable.o \
   setPrimerFalseMatchScoreArray.o \
   sff2PhdBall.o \
   singleStrandedRegionsGotoList.o \
   singleSubcloneRegionsGotoList.o \
   snpGenome.o \
   soAddCommas.o \
   soDecodePhasterBasesToGenomic.o \
   soDecodePhasterBasesToRead.o \
   soFindFlowCellFromPath.o \
   soGetChemistry.o \
   soGetDate.o \
   soGetDateTime.o \
   soGetErrno.o \
   soGetRequiredBases.o \
   soGetRestOfLine.o \
   solexa2PhdBall.o \
   someOtherProgramSentACommandToConsed.o \
   sortAcceptablePrimers.o \
   sortPrimersByEndPosition.o \
   sortPrimersByStartPosition.o \
   sortUnacceptablePrimers.o \
   subcloneTTemplate.o \
   szGetTime.o \
   tag.o \
   tagSNPs.o \
   tagTypes.o \
   tagsGotoList.o \
   teditor.o \
   tedwin.o \
   terminateIfDirectoryIsNotWritable.o \
   terminateIfNoPhdDir.o \
   testReadPhdBall.o \
   textbox.o \
   textfield.o \
   tracefile.o \
   transitionsTransversions.o \
   translateRWCString.o \
   uGetCRC_9_digits.o \
   ucGetReadType.o \
   unalignedHighQualityRegionsGotoList.o \
   universalPrimerAutoFinishExpTagsSortedByTemplateName.o \
   unpaddedFromPadded.o \
   userDefinedTagField.o \
   userDefinedTagFieldType.o \
   visibleLineForRestrictionFragments.o \
   waitUntilDialogIsVisible.o \
   whichPrimersAreAcceptable.o \
   whichPrimersHaveAcceptableMeltingTemp.o \
   whichPrimersHaveAcceptableSelfMatch.o \
   wholeAssemblyItem.o \
   wholeReadItem.o \
   writeNewAceFileNameToFile.o \
   xsynchronize.o

consed:	$(CONSED_OBJS) makefile checkLicenseKeyStub.o
	$(CXX) $(INC) $(LDFLGS) -o consed $(CONSED_OBJS) checkLicenseKeyStub.o \
		$(ARCHIVES) $(LPATH) $(CLIBS) $(XLIBS)

trial_consed: 	$(CONSED_OBJS) makefile checkLicenseKey.o
	$(CXX) $(INC) $(LDFLGS) -o trial_consed $(CONSED_OBJS) checkLicenseKey.o \
		$(ARCHIVES) $(LPATH) $(CLIBS) $(XLIBS)

pure:	$(CONSED_OBJS) makefile checkLicenseKeyStub.o
	$(PURIFY) $(CXX) $(INC) $(LDFLGS) -o consed $(CONSED_OBJS) checkLicenseKeyStub.o \
		$(ARCHIVES) $(LPATH) $(CLIBS) $(XLIBS)

clean:	
	rm -rf *.o core $(TEMPLATE_DIR)

dummy_dependencies:	$(CONSED_OBJS) checkLicenseKeyStub.o checkLicenseKey.o

# the Solaris 5.x compiler cannot optimize the following

consedResources.o:
	$(CXX) $(CFLGS) $(INC) $(DEPENDENCIES) -c consedResources.cpp

consedResources2.o:
	$(CXX) $(CFLGS) $(INC) $(DEPENDENCIES) -c consedResources2.cpp

# tlingit cannot optimize the following:

guiEditResources.o:
	$(CXX) $(CFLGS) $(INC) $(DEPENDENCIES) -c guiEditResources.cpp

guiEditResources.o : \
	 assemblyViewTagTypeAndLine.h assert.h bIsNumericDouble.h \
	 bIsNumericMaybeWithWhitespace.h bool.h consedParameters.h \
	 consedResources.h defaultResources.h filename.h \
	 guiEditResources.cpp guiEditResources.h guiTopWindow.h \
	 guiapp.h guicolortext.h handleWindowManagerDelete2.h \
	 hp_exception_kludge.h mbtPtrOrderedVector.h mbtValOrderedVectorOfRWCString.h \
	 mbt_exception.h motifutils.h please_wait.h \
	 popupErrorMessage.h popupInfoMessage.h restrictionEnzyme.h \
	 rwcstring.h rwcsubstring.h rwdefs.h \
	 rwtptrorderedvector.h rwtptrorderedvector_inc.cpp rwtvalorderedvector.h \
	 rwtvalorderedvector_inc.cpp soEmptyString.h soGetErrno.h \
	 sysdepend.h textbox.h waitUntilDialogIsVisible.h \
	 whatIsRunning.h

guiEditResourcesStandalone.o : \
	 abs.h assembly.h assemblyViewTagTypeAndLine.h \
	 assert.h autoFinishPurposes.h bIntersect.h \
	 bIntervalsIntersect.h basesegment.h blockOfLocationsOfA4MerType.h \
	 bool.h cComplementBase.h cComplementBaseTable.h \
	 compareContigs.h compareContigsCursor.h compareContigsTypes.h \
	 consed.h consedParameters.h consedResources.h \
	 contig.h contigEnd.h contigMatchTablesType.h \
	 contigSegment.h contigview.h contigwin.h \
	 dictionary.h distribution.h editCursor.h \
	 editaction.h experiment.h expidAndLocatedFragment.h \
	 filename.h gotoList.h gotoListType.h \
	 guiDisplayDigest.h guiEditResources.h guiEditResourcesStandalone.cpp \
	 guiEditResourcesStandalone.h guiMultiContigNavigator.h guiapp.h \
	 guicolortext.h listOfFragments.h locatedFragment.h \
	 matchWithinAssembly.h max.h mbtPtrOrderedVector.h \
	 mbtPtrVector.h mbtValOrderedVectorOfRWCString.h mbtValVector.h \
	 mbtValVectorOfBool.h mbtValVector_inc.cpp mbt_exception.h \
	 mbt_val_ord_offset_vec.h min.h motifutils.h \
	 multiProblemGotoList.h nMAX_QUALITY_LEVEL2.h ntide.h \
	 numutil.h paddedFromUnpadded.h primerType.h \
	 quality.h readTypes.h readsSortedByLeftEndPosition.h \
	 readsSortedByReadName.h readsSortedByTemplateName.h restrictionEnzyme.h \
	 restrictionFragment.h rwbtreedictionary.h rwcstring.h \
	 rwcsubstring.h rwdefs.h rwtptrorderedvector.h \
	 rwtptrorderedvector_inc.cpp rwtptrsortedvector.h rwtptrvector.h \
	 rwtvalorderedvector.h rwtvalorderedvector_inc.cpp rwtvalsortedvector.h \
	 rwtvalvector.h selection.h sequence.h \
	 singletInfo.h singletsSortedByTemplateName.h soEmptyString.h \
	 soGetErrno.h subcloneTTemplate.h sysdepend.h \
	 tag.h templatesSortedByName.h tracefile.h \
	 unpaddedFromPadded.h visibleLineForRestrictionFragments.h whatIsRunning.h \
	 wholeAssemblyItem.h wholeReadItem.h

addAlignedSequence.o : \
	 abs.h addAlignedSequence.cpp addAlignedSequence.h \
	 alignmentPiece.h assembly.h assemblyViewTagTypeAndLine.h \
	 assert.h autoFinishPurposes.h automatedConsedInit.h \
	 bIntersect.h bIntervalsIntersect.h bIsNumericMaybeWithWhitespace.h \
	 basesegment.h blockOfLocationsOfA4MerType.h bool.h \
	 cComplementBase.h cComplementBaseTable.h compareContigs.h \
	 compareContigsCursor.h compareContigsTypes.h consed.h \
	 consedParameters.h consedResources.h contig.h \
	 contigEnd.h contigMatchTablesType.h contigSegment.h \
	 contigview.h contigwin.h dictionary.h \
	 distribution.h editCursor.h editaction.h \
	 experiment.h expidAndLocatedFragment.h fileDefines.h \
	 filename.h gotoList.h gotoListType.h \
	 guiDisplayDigest.h guiMultiContigNavigator.h guiapp.h \
	 guicolortext.h library.h listOfFragments.h \
	 listOfLibraries.h locatedFragment.h matchWithinAssembly.h \
	 max.h maybeTerminateIfAnotherReadWriteConsed.h mbtPtrOrderedVector.h \
	 mbtPtrVector.h mbtValOrderedVectorOfRWCString.h mbtValVector.h \
	 mbtValVectorOfBool.h mbtValVector_inc.cpp mbt_exception.h \
	 mbt_val_ord_offset_vec.h min.h motifutils.h \
	 multiProblemGotoList.h nMAX_QUALITY_LEVEL2.h ntide.h \
	 numutil.h paddedFromUnpadded.h primerType.h \
	 quality.h readTypes.h readsSortedByLeftEndPosition.h \
	 readsSortedByReadName.h readsSortedByTemplateName.h restrictionEnzyme.h \
	 restrictionFragment.h rwbtreedictionary.h rwcstring.h \
	 rwcsubstring.h rwctokenizer.h rwdefs.h \
	 rwtptrorderedvector.h rwtptrorderedvector_inc.cpp rwtptrsortedvector.h \
	 rwtptrvector.h rwtvalorderedvector.h rwtvalorderedvector_inc.cpp \
	 rwtvalsortedvector.h rwtvalvector.h selection.h \
	 sequence.h singletInfo.h singletsSortedByTemplateName.h \
	 soEmptyString.h soGetDateTime.h soGetErrno.h \
	 soLine.h subcloneTTemplate.h sysdepend.h \
	 szGetTime.h tag.h templatesSortedByName.h \
	 terminateIfNoPhdDir.h tracefile.h unpaddedFromPadded.h \
	 visibleLineForRestrictionFragments.h whatIsRunning.h wholeAssemblyItem.h \
	 wholeReadItem.h

addNewReads.o : \
	 abs.h addNewReads.cpp addNewReads.h \
	 addNewReadsWithExistingAlignments.h assembly.h assemblyViewTagTypeAndLine.h \
	 assert.h autoFinishPurposes.h bGuiGetAnswerYesNo.h \
	 bIntersect.h bIntervalsIntersect.h bIsNumeric.h \
	 bIsNumericMaybeWithWhitespace.h basesegment.h blockOfLocationsOfA4MerType.h \
	 bool.h cComplementBase.h cComplementBaseTable.h \
	 choose_contig.h compareContigs.h compareContigsCursor.h \
	 compareContigsTypes.h consed.h consedParameters.h \
	 consedResources.h contig.h contigEnd.h \
	 contigEndReadList.h contigMatchTablesType.h contigSegment.h \
	 contigview.h contigwin.h crossMatchIndel.h \
	 crossMatchInfoForRead.h dictionary.h distribution.h \
	 editCursor.h editaction.h experiment.h \
	 expidAndLocatedFragment.h fileDefines.h filePopupAndGetFilename.h \
	 filename.h fragment_and_contig.h gotoList.h \
	 gotoListType.h guiAddNewReads.h guiDisplayDigest.h \
	 guiMultiContigNavigator.h guiTopWindow.h guiapp.h \
	 guicolortext.h listOfFragments.h locatedFragment.h \
	 matchWithinAssembly.h max.h maybeTerminateIfAnotherReadWriteConsed.h \
	 mbtPtrOrderedVector.h mbtPtrVector.h mbtValOrderedVectorOfRWCString.h \
	 mbtValVector.h mbtValVectorOfBool.h mbtValVector_inc.cpp \
	 mbt_errors.h mbt_exception.h mbt_val_ord_offset_vec.h \
	 min.h motifutils.h multiProblemGotoList.h \
	 nCountPadsAndConvertFormat.h nMAX_QUALITY_LEVEL2.h ntide.h \
	 numutil.h paddedFromUnpadded.h please_wait.h \
	 popupErrorMessage.h primerType.h printTime.h \
	 quality.h readPHD.h readTypes.h \
	 readsSortedByLeftEndPosition.h readsSortedByReadName.h readsSortedByTemplateName.h \
	 regionOfSequence.h regionOfSequenceArray.h restrictionEnzyme.h \
	 restrictionFragment.h rwbtreedictionary.h rwcstring.h \
	 rwcsubstring.h rwctokenizer.h rwdefs.h \
	 rwtptrorderedvector.h rwtptrorderedvector_inc.cpp rwtptrsortedvector.h \
	 rwtptrvector.h rwtvalorderedvector.h rwtvalorderedvector_inc.cpp \
	 rwtvalsortedvector.h rwtvalvector.h selection.h \
	 sequence.h singletInfo.h singletsSortedByTemplateName.h \
	 soAddCommas.h soEmptyString.h soFindFlowCellFromPath.h \
	 soGetChemistry.h soGetDateTime.h soGetErrno.h \
	 soLine.h subcloneTTemplate.h sysdepend.h \
	 szGetTime.h tag.h templatesSortedByName.h \
	 terminateIfDirectoryIsNotWritable.h textbox.h tracefile.h \
	 unpaddedFromPadded.h visibleLineForRestrictionFragments.h whatIsRunning.h \
	 wholeAssemblyItem.h wholeReadItem.h writeNewAceFileNameToFile.h

addNewReadsAutomated.o : \
	 abs.h addNewReads.h addNewReadsAutomated.cpp \
	 addNewReadsAutomated.h assembly.h assemblyViewTagTypeAndLine.h \
	 assert.h autoFinishPurposes.h bIntersect.h \
	 bIntervalsIntersect.h basesegment.h blockOfLocationsOfA4MerType.h \
	 bool.h cComplementBase.h cComplementBaseTable.h \
	 compareContigs.h compareContigsCursor.h compareContigsTypes.h \
	 consed.h consedParameters.h consedResources.h \
	 contig.h contigEnd.h contigMatchTablesType.h \
	 contigSegment.h contigview.h contigwin.h \
	 dictionary.h distribution.h editCursor.h \
	 editaction.h experiment.h expidAndLocatedFragment.h \
	 filGetUniqueFilename.h fileDefines.h filename.h \
	 gotoList.h gotoListType.h guiDisplayDigest.h \
	 guiMultiContigNavigator.h guiapp.h guicolortext.h \
	 listOfFragments.h locatedFragment.h matchWithinAssembly.h \
	 max.h maybeTerminateIfAnotherReadWriteConsed.h mbtPtrOrderedVector.h \
	 mbtPtrVector.h mbtValOrderedVectorOfRWCString.h mbtValVector.h \
	 mbtValVectorOfBool.h mbtValVector_inc.cpp mbt_exception.h \
	 mbt_val_ord_offset_vec.h min.h motifutils.h \
	 multiProblemGotoList.h nMAX_QUALITY_LEVEL2.h ntide.h \
	 numutil.h paddedFromUnpadded.h popupErrorMessage.h \
	 primerType.h quality.h readTypes.h \
	 readsSortedByLeftEndPosition.h readsSortedByReadName.h readsSortedByTemplateName.h \
	 restrictionEnzyme.h restrictionFragment.h rwbtreedictionary.h \
	 rwcregexp.h rwcstring.h rwcsubstring.h \
	 rwdefs.h rwtptrorderedvector.h rwtptrorderedvector_inc.cpp \
	 rwtptrsortedvector.h rwtptrvector.h rwtvalorderedvector.h \
	 rwtvalorderedvector_inc.cpp rwtvalsortedvector.h rwtvalvector.h \
	 selection.h sequence.h singletInfo.h \
	 singletsSortedByTemplateName.h soEmptyString.h soGetErrno.h \
	 subcloneTTemplate.h sysdepend.h tag.h \
	 templatesSortedByName.h terminateIfNoPhdDir.h tracefile.h \
	 unpaddedFromPadded.h visibleLineForRestrictionFragments.h whatIsRunning.h \
	 wholeAssemblyItem.h wholeReadItem.h

addNewReadsWithExistingAlignments.o : \
	 abs.h addNewReads.h addNewReadsWithExistingAlignments.cpp \
	 addNewReadsWithExistingAlignments.h assembly.h assemblyViewTagTypeAndLine.h \
	 assert.h autoFinishPurposes.h bIntersect.h \
	 bIntervalsIntersect.h bIsNumericFloat.h basesegment.h \
	 blockOfLocationsOfA4MerType.h bool.h cComplementBase.h \
	 cComplementBaseTable.h compareContigs.h compareContigsCursor.h \
	 compareContigsTypes.h consed.h consedParameters.h \
	 consedResources.h contig.h contigEnd.h \
	 contigMatchTablesType.h contigSegment.h contigview.h \
	 contigwin.h crossMatchIndel.h crossMatchInfoForRead.h \
	 dictionary.h distribution.h editCursor.h \
	 editaction.h experiment.h expidAndLocatedFragment.h \
	 filFindSolexaPrbFileFromSeqFile.h filGetUniqueFilename.h fileDefines.h \
	 filename.h gotoList.h gotoListType.h \
	 guiDisplayDigest.h guiMultiContigNavigator.h guiapp.h \
	 guicolortext.h listOfFragments.h locatedFragment.h \
	 matchWithinAssembly.h max.h maybeTerminateIfAnotherReadWriteConsed.h \
	 mbtPtrOrderedVector.h mbtPtrVector.h mbtValOrderedVectorOfRWCString.h \
	 mbtValVector.h mbtValVectorOfBool.h mbtValVector_inc.cpp \
	 mbt_exception.h mbt_val_ord_offset_vec.h min.h \
	 motifutils.h multiProblemGotoList.h nMAX_QUALITY_LEVEL2.h \
	 nNumberFromBase2.h ntide.h numutil.h \
	 paddedFromUnpadded.h primerType.h printTime.h \
	 quality.h readTypes.h readsSortedByLeftEndPosition.h \
	 readsSortedByReadName.h readsSortedByTemplateName.h restrictionEnzyme.h \
	 restrictionFragment.h rwbtreedictionary.h rwcregexp.h \
	 rwcstring.h rwcsubstring.h rwctokenizer.h \
	 rwdefs.h rwtptrorderedvector.h rwtptrorderedvector_inc.cpp \
	 rwtptrsortedvector.h rwtptrvector.h rwtvalorderedvector.h \
	 rwtvalorderedvector_inc.cpp rwtvalsortedvector.h rwtvalvector.h \
	 selection.h sequence.h singletInfo.h \
	 singletsSortedByTemplateName.h soEmptyString.h soGetChemistry.h \
	 soGetDateTime.h soGetErrno.h soLine.h \
	 subcloneTTemplate.h sysdepend.h szGetTime.h \
	 tag.h templatesSortedByName.h tracefile.h \
	 unpaddedFromPadded.h visibleLineForRestrictionFragments.h whatIsRunning.h \
	 wholeAssemblyItem.h wholeReadItem.h

addTearTagType.o : \
	 addTearTagType.cpp addTearTagType.h bool.h \
	 guicolortext.h mbt_exception.h rwcstring.h \
	 rwcsubstring.h rwdefs.h rwtptrorderedvector.h \
	 rwtptrorderedvector_inc.cpp rwtptrsortedvector.h soEmptyString.h \
	 soGetErrno.h sysdepend.h tagTypes.h \
	 userDefinedTagFieldType.h

applyEditHistory.o : \
	 abs.h applyEditHistory.cpp applyEditHistory.h \
	 assembly.h assemblyViewTagTypeAndLine.h assert.h \
	 autoFinishPurposes.h bIntersect.h bIntervalsIntersect.h \
	 bIsABase.h bIsNumeric.h bIsNumericMaybeWithWhitespace.h \
	 basesegment.h blockOfLocationsOfA4MerType.h bool.h \
	 cComplementBase.h cComplementBaseTable.h compareContigs.h \
	 compareContigsCursor.h compareContigsTypes.h consed.h \
	 consedParameters.h consedResources.h contig.h \
	 contigEnd.h contigMatchTablesType.h contigSegment.h \
	 contigview.h contigwin.h dictionary.h \
	 distribution.h editActionChangeRead.h editAddConsensusTag.h \
	 editAddReadTag.h editAddTagsToAllReadsAtConsPos.h editChangeToNs.h \
	 editChangeToNsToLeft.h editChangeToNsToRight.h editChangeToXs.h \
	 editCursor.h editDeleteConsensusTag.h editDeleteReadTag.h \
	 editInsertColOfPads.h editMakeHighQuality.h editMakeHighQualityAndChangeConsensus.h \
	 editMakeLowQuality.h editMakeLowQualityToLeft.h editMakeLowQualityToRight.h \
	 editOverstrike.h editOverstrikeAllReadsAtConsPos.h editOverstrikeConsensus.h \
	 edit_complement_contig.h editaction.h experiment.h \
	 expidAndLocatedFragment.h filename.h gotoList.h \
	 gotoListType.h guiDisplayDigest.h guiMultiContigNavigator.h \
	 guiapp.h guicolortext.h guitedwin.h \
	 infobutton.h listOfFragments.h locatedFragment.h \
	 matchWithinAssembly.h max.h mbtPtrOrderedVector.h \
	 mbtPtrVector.h mbtValOrderedVectorOfRWCString.h mbtValVector.h \
	 mbtValVectorOfBool.h mbtValVector_inc.cpp mbt_errors.h \
	 mbt_exception.h mbt_val_ord_offset_vec.h min.h \
	 motifutils.h multiProblemGotoList.h nMAX_QUALITY_LEVEL2.h \
	 ntide.h numutil.h oligoTag.h \
	 paddedFromUnpadded.h please_wait.h primerType.h \
	 quality.h readTypes.h readsSortedByLeftEndPosition.h \
	 readsSortedByReadName.h readsSortedByTemplateName.h restrictionEnzyme.h \
	 restrictionFragment.h rwbtreedictionary.h rwcregexp.h \
	 rwcstring.h rwcsubstring.h rwctokenizer.h \
	 rwdefs.h rwtptrorderedvector.h rwtptrorderedvector_inc.cpp \
	 rwtptrsortedvector.h rwtptrvector.h rwtvalorderedvector.h \
	 rwtvalorderedvector_inc.cpp rwtvalsortedvector.h rwtvalvector.h \
	 selection.h sequence.h singletInfo.h \
	 singletsSortedByTemplateName.h soEmptyString.h soGetErrno.h \
	 subcloneTTemplate.h sysdepend.h tag.h \
	 teditor_types.h tedwin.h templatesSortedByName.h \
	 textfield.h tracefile.h unpaddedFromPadded.h \
	 visibleLineForRestrictionFragments.h whatIsRunning.h whatToDoWithSelectionTypes.h \
	 wholeAssemblyItem.h wholeReadItem.h

arrayOfFwdRevPairLines.o : \
	 arrayOfFwdRevPairLines.cpp arrayOfFwdRevPairLines.h arrayOfFwdRevPairSquares.h \
	 arrayOfFwdRevPairTriangles.h assemblyView.h assemblyViewTagTypeAndLine.h \
	 assert.h bool.h consedParameters.h \
	 consedResources.h filename.h fwdRevPair2.h \
	 fwdRevPairLine.h fwdRevPairSquare.h fwdRevPairTriangle.h \
	 guiapp.h guicolortext.h max.h \
	 mbtPtrOrderedVector.h mbtValOrderedVectorOfRWCString.h mbt_exception.h \
	 min.h motifutils.h restrictionEnzyme.h \
	 rwcstring.h rwcsubstring.h rwdefs.h \
	 rwt2dptrvector.h rwtptrorderedvector.h rwtptrorderedvector_inc.cpp \
	 rwtvalorderedvector.h rwtvalorderedvector_inc.cpp seqMatch.h \
	 soEmptyString.h soGetErrno.h sysdepend.h \
	 whatIsRunning.h

arrayOfFwdRevPairSquares.o : \
	 arrayOfFwdRevPairLines.h arrayOfFwdRevPairSquares.cpp arrayOfFwdRevPairSquares.h \
	 arrayOfFwdRevPairTriangles.h assemblyView.h assemblyViewTagTypeAndLine.h \
	 assert.h bool.h consedParameters.h \
	 consedResources.h filename.h fwdRevPair2.h \
	 fwdRevPairLine.h fwdRevPairSquare.h fwdRevPairTriangle.h \
	 guiapp.h guicolortext.h max.h \
	 mbtPtrOrderedVector.h mbtValOrderedVectorOfRWCString.h mbt_exception.h \
	 min.h motifutils.h restrictionEnzyme.h \
	 rwcstring.h rwcsubstring.h rwdefs.h \
	 rwt2dptrvector.h rwtptrorderedvector.h rwtptrorderedvector_inc.cpp \
	 rwtvalorderedvector.h rwtvalorderedvector_inc.cpp seqMatch.h \
	 soEmptyString.h soGetErrno.h sysdepend.h \
	 whatIsRunning.h

arrayOfFwdRevPairTriangles.o : \
	 abs.h arrayOfFwdRevPairLines.h arrayOfFwdRevPairSquares.h \
	 arrayOfFwdRevPairTriangles.cpp arrayOfFwdRevPairTriangles.h assemblyView.h \
	 assemblyViewTagTypeAndLine.h assert.h bool.h \
	 cComplementBase.h cComplementBaseTable.h consedParameters.h \
	 consedResources.h filename.h fwdRevPair2.h \
	 fwdRevPairLine.h fwdRevPairSquare.h fwdRevPairTriangle.h \
	 guiapp.h guicolortext.h locatedFragment.h \
	 max.h mbtPtrOrderedVector.h mbtValOrderedVectorOfRWCString.h \
	 mbtValVector.h mbtValVector_inc.cpp mbt_exception.h \
	 mbt_val_ord_offset_vec.h min.h motifutils.h \
	 ntide.h quality.h readTypes.h \
	 restrictionEnzyme.h rwcstring.h rwcsubstring.h \
	 rwdefs.h rwt2dptrvector.h rwtptrorderedvector.h \
	 rwtptrorderedvector_inc.cpp rwtvalorderedvector.h rwtvalorderedvector_inc.cpp \
	 rwtvalvector.h seqMatch.h sequence.h \
	 soEmptyString.h soGetErrno.h sysdepend.h \
	 tag.h tracefile.h whatIsRunning.h \
	 wholeReadItem.h

assembly.o : \
	 abs.h assembly.cpp assembly.h \
	 assemblyViewTagTypeAndLine.h assert.h autoFinishPurposes.h \
	 bIntersect.h bIntervalsIntersect.h baseSegmentsToSort.h \
	 basesegment.h blockOfLocationsOfA4MerType.h bool.h \
	 cComplementBase.h cComplementBaseTable.h compareContigs.h \
	 compareContigsCursor.h compareContigsTypes.h consed.h \
	 consedParameters.h consedResources.h contig.h \
	 contigEnd.h contigMatchTablesType.h contigSegment.h \
	 contigview.h contigwin.h deleteFileIfItExists.h \
	 dictionary.h distribution.h editCursor.h \
	 editaction.h experiment.h expidAndLocatedFragment.h \
	 filename.h gotoList.h gotoListType.h \
	 guiDisplayDigest.h guiMultiContigNavigator.h guiapp.h \
	 guicolortext.h listOfFragments.h listOfFragmentsAndEndPositions.h \
	 locatedFragment.h matchWithinAssembly.h max.h \
	 mbtPtrOrderedVector.h mbtPtrVector.h mbtValOrderedVectorOfRWCString.h \
	 mbtValVector.h mbtValVectorOfBool.h mbtValVector_inc.cpp \
	 mbt_exception.h mbt_val_ord_offset_vec.h min.h \
	 motifutils.h multiProblemGotoList.h nMAX_QUALITY_LEVEL2.h \
	 ntide.h numutil.h paddedFromUnpadded.h \
	 primerType.h quality.h readTypes.h \
	 readsSortedByLeftEndPosition.h readsSortedByReadName.h readsSortedByTemplateName.h \
	 restrictionEnzyme.h restrictionFragment.h rwbtreedictionary.h \
	 rwcstring.h rwcsubstring.h rwctokenizer.h \
	 rwdefs.h rwtptrorderedvector.h rwtptrorderedvector_inc.cpp \
	 rwtptrsortedvector.h rwtptrvector.h rwtvalorderedvector.h \
	 rwtvalorderedvector_inc.cpp rwtvalsortedvector.h rwtvalvector.h \
	 selection.h sequence.h singletInfo.h \
	 singletsSortedByTemplateName.h soEmptyString.h soGetErrno.h \
	 subcloneTTemplate.h sysdepend.h tag.h \
	 templatesSortedByName.h tracefile.h unpaddedFromPadded.h \
	 visibleLineForRestrictionFragments.h whatIsRunning.h wholeAssemblyItem.h \
	 wholeReadItem.h

assembly2.o : \
	 abs.h assembly.h assembly2.cpp \
	 assemblyViewTagTypeAndLine.h assert.h autoFinishExpTag.h \
	 autoFinishPurposes.h bIntersect.h bIntervalsIntersect.h \
	 bIsNumeric.h bIsNumericMaybeWithWhitespace.h basesegment.h \
	 blockOfLocationsOfA4MerType.h bool.h cComplementBase.h \
	 cComplementBaseTable.h clScaffold.h compareContigs.h \
	 compareContigsCursor.h compareContigsTypes.h consed.h \
	 consedParameters.h consedResources.h contig.h \
	 contigEnd.h contigEndPair.h contigMatchTablesType.h \
	 contigSegment.h contigview.h contigwin.h \
	 copyFiles.h dErrorRateFromQuality.h dGetErrorsFixedAtBase.h \
	 deleteFileIfItExists.h dictionary.h distribution.h \
	 editCursor.h editaction.h evalExpCluster.h \
	 experiment.h expidAndLocatedFragment.h fileDefines.h \
	 filename.h findRepeat.h fwdRevPair.h \
	 gotoList.h gotoListType.h guiDisplayDigest.h \
	 guiMultiContigNavigator.h guiTopWindow.h guiapp.h \
	 guicolortext.h highQualityDiscrepancyGotoList.h hp_exception_kludge.h \
	 library.h listOfFragments.h listOfFragmentsAndEndPositions.h \
	 listOfLibraries.h locatedFragment.h lowconsqual.h \
	 matchWithinAssembly.h max.h mbtPtrOrderedVector.h \
	 mbtPtrVector.h mbtValOrderedVectorOfRWCString.h mbtValVector.h \
	 mbtValVectorOfBool.h mbtValVector_inc.cpp mbt_errors.h \
	 mbt_exception.h mbt_val_ord_offset_vec.h min.h \
	 motifutils.h multiProblemGotoList.h nGetReadTypeFromReadName.h \
	 nMAX_QUALITY_LEVEL2.h ntide.h numutil.h \
	 oligoTag.h paddedFromUnpadded.h please_wait.h \
	 popupErrorMessage.h popupErrorMessage2.h popupInfoMessage.h \
	 popupInfoOrErrorMessageNoFormat.h primerType.h printTime.h \
	 quality.h readFileOfPhdFiles.h readPHDOfSinglet.h \
	 readTypes.h readsSortedByLeftEndPosition.h readsSortedByReadName.h \
	 readsSortedByTemplateName.h renameFiles.h restrictionEnzyme.h \
	 restrictionFragment.h rwbtreedictionary.h rwcregexp.h \
	 rwcstring.h rwcsubstring.h rwctokenizer.h \
	 rwdefs.h rwtptrorderedvector.h rwtptrorderedvector_inc.cpp \
	 rwtptrsortedvector.h rwtptrvector.h rwtvalorderedvector.h \
	 rwtvalorderedvector_inc.cpp rwtvalsortedvector.h rwtvalvector.h \
	 selection.h sequence.h singletInfo.h \
	 singletsSortedByTemplateName.h soAddCommas.h soEmptyString.h \
	 soGetErrno.h subcloneTTemplate.h sysdepend.h \
	 tag.h templateForMinilibrary.h templatesSortedByLibrary.h \
	 templatesSortedByName.h textbox.h tracefile.h \
	 universalPrimerAutoFinishExpTagsSortedByTemplateName.h unpaddedFromPadded.h visibleLineForRestrictionFragments.h \
	 whatIsRunning.h wholeAssemblyItem.h wholeReadItem.h

assembly3.o : \
	 abs.h assembly.h assembly3.cpp \
	 assemblyViewTagTypeAndLine.h assert.h autoFinishPurposes.h \
	 bIntersect.h bIntervalsIntersect.h bIsNumericFloat.h \
	 bIsNumericMaybeWithWhitespace.h basesegment.h blockOfLocationsOfA4MerType.h \
	 bool.h cComplementBase.h cComplementBaseTable.h \
	 compareContigs.h compareContigsCursor.h compareContigsTypes.h \
	 consed.h consedParameters.h consedResources.h \
	 contig.h contigEnd.h contigMatchTablesType.h \
	 contigSegment.h contigview.h contigwin.h \
	 dictionary.h distribution.h editCursor.h \
	 editaction.h experiment.h expidAndLocatedFragment.h \
	 filFindSolexaPrbFileFromSeqFile.h fileDefines.h filename.h \
	 gotoList.h gotoListType.h guiDisplayDigest.h \
	 guiMultiContigNavigator.h guiapp.h guicolortext.h \
	 listOfFragments.h locatedFragment.h matchWithinAssembly.h \
	 max.h mbtPtrOrderedVector.h mbtPtrVector.h \
	 mbtValOrderedVectorOfRWCString.h mbtValVector.h mbtValVectorOfBool.h \
	 mbtValVector_inc.cpp mbt_exception.h mbt_val_ord_offset_vec.h \
	 min.h motifutils.h multiProblemGotoList.h \
	 nCompareContigsByName.h nGetTrailingNumber.h nMAX_QUALITY_LEVEL2.h \
	 nNumberFromBase2.h ntide.h numutil.h \
	 paddedFromUnpadded.h parseAceFile.h popupErrorMessage.h \
	 popupInfoOrErrorMessageNoFormat.h primerType.h quality.h \
	 readTypes.h readsSortedByLeftEndPosition.h readsSortedByReadName.h \
	 readsSortedByTemplateName.h restrictionEnzyme.h restrictionFragment.h \
	 rwbtreedictionary.h rwcregexp.h rwcstring.h \
	 rwcsubstring.h rwctokenizer.h rwdefs.h \
	 rwtptrorderedvector.h rwtptrorderedvector_inc.cpp rwtptrsortedvector.h \
	 rwtptrvector.h rwtvalorderedvector.h rwtvalorderedvector_inc.cpp \
	 rwtvalsortedvector.h rwtvalvector.h selection.h \
	 sequence.h singletInfo.h singletsSortedByTemplateName.h \
	 soAddCommas.h soEmptyString.h soFindFlowCellFromPath.h \
	 soGetErrno.h subcloneTTemplate.h sysdepend.h \
	 tag.h templatesSortedByName.h textbox.h \
	 tracefile.h unpaddedFromPadded.h visibleLineForRestrictionFragments.h \
	 whatIsRunning.h wholeAssemblyItem.h wholeReadItem.h

assembly4.o : \
	 assembly.h assembly4.cpp assemblyViewTagTypeAndLine.h \
	 assert.h autoFinishPurposes.h basesegment.h \
	 blockOfLocationsOfA4MerType.h bool.h cComplementBase.h \
	 cComplementBaseTable.h consedParameters.h consedResources.h \
	 contig.h contigEnd.h contigEndPair.h \
	 contigMatchTablesType.h dictionary.h distribution.h \
	 experiment.h expidAndLocatedFragment.h fileDefines.h \
	 filename.h listOfFragments.h locatedFragment.h \
	 matchWithinAssembly.h mbtPtrOrderedVector.h mbtPtrVector.h \
	 mbtValOrderedVectorOfRWCString.h mbtValVector.h mbtValVectorOfBool.h \
	 mbtValVector_inc.cpp mbt_exception.h mbt_val_ord_offset_vec.h \
	 min.h nMAX_QUALITY_LEVEL2.h ntide.h \
	 paddedFromUnpadded.h primerType.h quality.h \
	 readTypes.h readsSortedByLeftEndPosition.h readsSortedByReadName.h \
	 readsSortedByTemplateName.h restrictionEnzyme.h rwbtreedictionary.h \
	 rwcstring.h rwcsubstring.h rwdefs.h \
	 rwtptrorderedvector.h rwtptrorderedvector_inc.cpp rwtptrsortedvector.h \
	 rwtptrvector.h rwtvalorderedvector.h rwtvalorderedvector_inc.cpp \
	 rwtvalsortedvector.h rwtvalvector.h sequence.h \
	 singletInfo.h singletsSortedByTemplateName.h soEmptyString.h \
	 soGetErrno.h subcloneTTemplate.h sysdepend.h \
	 tag.h templatesSortedByName.h tracefile.h \
	 unpaddedFromPadded.h whatIsRunning.h wholeAssemblyItem.h \
	 wholeReadItem.h

assembly5.o : \
	 abs.h assembly.h assembly5.cpp \
	 assemblyViewTagTypeAndLine.h assert.h autoFinishPurposes.h \
	 bIntersect.h bIntervalsIntersect.h bIsNumeric.h \
	 bIsNumericMaybeWithWhitespace.h basesegment.h blockOfLocationsOfA4MerType.h \
	 bool.h cComplementBase.h cComplementBaseTable.h \
	 clScaffold.h compareContigs.h compareContigsCursor.h \
	 compareContigsTypes.h consed.h consedParameters.h \
	 consedResources.h contig.h contigEnd.h \
	 contigEndPair.h contigMatchTablesType.h contigSegment.h \
	 contigview.h contigwin.h dictionary.h \
	 distribution.h editCursor.h editaction.h \
	 experiment.h expidAndLocatedFragment.h fileDefines.h \
	 filename.h fwdRevPair.h gotoList.h \
	 gotoListType.h guiDisplayDigest.h guiMultiContigNavigator.h \
	 guiapp.h guicolortext.h highQualityDiscrepancyGotoList.h \
	 hp_exception_kludge.h listOfFragments.h locatedFragment.h \
	 matchWithinAssembly.h max.h mbtPtrOrderedVector.h \
	 mbtPtrVector.h mbtValOrderedVectorOfRWCString.h mbtValVector.h \
	 mbtValVectorOfBool.h mbtValVector_inc.cpp mbt_exception.h \
	 mbt_val_ord_offset_vec.h min.h motifutils.h \
	 multiProblemGotoList.h nMAX_QUALITY_LEVEL2.h ntide.h \
	 numutil.h oligoTag.h paddedFromUnpadded.h \
	 please_wait.h popupErrorMessage.h popupErrorMessage2.h \
	 popupInfoMessage.h primerType.h quality.h \
	 readTypes.h readsSortedByLeftEndPosition.h readsSortedByReadName.h \
	 readsSortedByTemplateName.h restrictionEnzyme.h restrictionFragment.h \
	 rwbtreedictionary.h rwcstring.h rwcsubstring.h \
	 rwctokenizer.h rwdefs.h rwtptrorderedvector.h \
	 rwtptrorderedvector_inc.cpp rwtptrsortedvector.h rwtptrvector.h \
	 rwtvalorderedvector.h rwtvalorderedvector_inc.cpp rwtvalsortedvector.h \
	 rwtvalvector.h selection.h sequence.h \
	 singletInfo.h singletsSortedByTemplateName.h soAddCommas.h \
	 soEmptyString.h soGetErrno.h subcloneTTemplate.h \
	 sysdepend.h tag.h templatesSortedByName.h \
	 textbox.h tracefile.h unpaddedFromPadded.h \
	 visibleLineForRestrictionFragments.h whatIsRunning.h wholeAssemblyItem.h \
	 wholeReadItem.h

assemblyView.o : \
	 abs.h arrayOfFwdRevPairLines.h arrayOfFwdRevPairSquares.h \
	 arrayOfFwdRevPairTriangles.h arrayOfRestrictionFragments.h assembly.h \
	 assemblyView.cpp assemblyView.h assemblyViewRemoveReads.h \
	 assemblyViewTagTypeAndLine.h assert.h autoFinishPurposes.h \
	 bForwardReversePairIsConsistentWithContigOrder.h bGuiGetAnswerYesNo.h bIntersect.h \
	 bIntervalsIntersect.h basesegment.h blockOfLocationsOfA4MerType.h \
	 bool.h cComplementBase.h cComplementBaseTable.h \
	 clScaffold.h colorDefaults.h compareContigs.h \
	 compareContigsCursor.h compareContigsTypes.h consed.h \
	 consedParameters.h consedResources.h contig.h \
	 contigEnd.h contigEndPair.h contigMatchTablesType.h \
	 contigSegment.h contigview.h contigwin.h \
	 dictionary.h digestForOneEnzyme.h distribution.h \
	 editAddConsensusTag.h editCursor.h editDeleteConsensusTag.h \
	 editaction.h experiment.h expidAndLocatedFragment.h \
	 fGetDistanceFromPointToLine.h fGetDistanceFromPointToPoint.h filename.h \
	 fwdRevPair.h fwdRevPair2.h fwdRevPairLine.h \
	 fwdRevPairSquare.h fwdRevPairTriangle.h gotoList.h \
	 gotoListType.h guiAssemblyViewIncludeContigs.h guiAssemblyViewReadDepth.h \
	 guiAssemblyViewShowTags.h guiAssemblyViewWhatToShow.h guiChoiceOfSeqMatches.h \
	 guiDisplayDigest.h guiMultiContigNavigator.h guiReorderContigs.h \
	 guiReorientContigs.h guiapp.h guicolortext.h \
	 handleWindowManagerDelete2.h hp_exception_kludge.h library.h \
	 listOfFragments.h locatedFragment.h matchWithinAssembly.h \
	 max.h mbtPtrOrderedVector.h mbtPtrVector.h \
	 mbtValOrderedVectorOfRWCString.h mbtValVector.h mbtValVectorOfBool.h \
	 mbtValVector_inc.cpp mbt_exception.h mbt_val_ord_offset_vec.h \
	 min.h motifutils.h multiProblemGotoList.h \
	 nMAX_QUALITY_LEVEL2.h ntide.h numutil.h \
	 paddedFromUnpadded.h please_wait.h popupErrorMessage.h \
	 popupErrorMessage2.h primerType.h printPS.h \
	 printTime.h quality.h readTypes.h \
	 readsSortedByLeftEndPosition.h readsSortedByReadName.h readsSortedByTemplateName.h \
	 restrictionEnzyme.h restrictionFragment.h rwbtreedictionary.h \
	 rwcregexp.h rwcstring.h rwcsubstring.h \
	 rwdefs.h rwt2dptrvector.h rwtptrorderedvector.h \
	 rwtptrorderedvector_inc.cpp rwtptrsortedvector.h rwtptrvector.h \
	 rwtvalorderedvector.h rwtvalorderedvector_inc.cpp rwtvalsortedvector.h \
	 rwtvalvector.h selection.h seqMatch.h \
	 sequence.h singletInfo.h singletsSortedByTemplateName.h \
	 soAddCommas.h soEmptyString.h soGetErrno.h \
	 subcloneTTemplate.h sysdepend.h tag.h \
	 templatesSortedByName.h textbox.h tracefile.h \
	 unpaddedFromPadded.h visibleLineForRestrictionFragments.h waitUntilDialogIsVisible.h \
	 whatIsRunning.h wholeAssemblyItem.h wholeReadItem.h

assemblyView2.o : \
	 abs.h arrayOfFwdRevPairLines.h arrayOfFwdRevPairSquares.h \
	 arrayOfFwdRevPairTriangles.h assembly.h assemblyView.h \
	 assemblyView2.cpp assemblyViewTagTypeAndLine.h assert.h \
	 autoFinishPurposes.h bIntersect.h bIntervalsIntersect.h \
	 bIsNumericFloat.h bIsNumericMaybeWithWhitespace.h basesegment.h \
	 blockOfLocationsOfA4MerType.h bool.h cComplementBase.h \
	 cComplementBaseTable.h clScaffold.h compareContigs.h \
	 compareContigsCursor.h compareContigsTypes.h consed.h \
	 consedParameters.h consedResources.h contig.h \
	 contigEnd.h contigMatchTablesType.h contigSegment.h \
	 contigview.h contigwin.h dictionary.h \
	 distribution.h editCursor.h editaction.h \
	 experiment.h expidAndLocatedFragment.h filename.h \
	 fwdRevPair2.h fwdRevPairLine.h fwdRevPairSquare.h \
	 fwdRevPairTriangle.h gotoList.h gotoListType.h \
	 guiDisplayDigest.h guiMultiContigNavigator.h guiapp.h \
	 guicolortext.h listOfFragments.h locatedFragment.h \
	 matchWithinAssembly.h max.h mbtPtrOrderedVector.h \
	 mbtPtrVector.h mbtValOrderedVectorOfRWCString.h mbtValVector.h \
	 mbtValVectorOfBool.h mbtValVector_inc.cpp mbt_exception.h \
	 mbt_val_ord_offset_vec.h min.h motifutils.h \
	 multiProblemGotoList.h nMAX_QUALITY_LEVEL2.h ntide.h \
	 numutil.h paddedFromUnpadded.h popupErrorMessage2.h \
	 primerType.h quality.h readTypes.h \
	 readsSortedByLeftEndPosition.h readsSortedByReadName.h readsSortedByTemplateName.h \
	 restrictionEnzyme.h restrictionFragment.h rwbtreedictionary.h \
	 rwcstring.h rwcsubstring.h rwctokenizer.h \
	 rwdefs.h rwt2dptrvector.h rwtptrorderedvector.h \
	 rwtptrorderedvector_inc.cpp rwtptrsortedvector.h rwtptrvector.h \
	 rwtvalorderedvector.h rwtvalorderedvector_inc.cpp rwtvalsortedvector.h \
	 rwtvalvector.h selection.h seqMatch.h \
	 sequence.h singletInfo.h singletsSortedByTemplateName.h \
	 soEmptyString.h soGetErrno.h subcloneTTemplate.h \
	 sysdepend.h tag.h templatesSortedByName.h \
	 tracefile.h unpaddedFromPadded.h visibleLineForRestrictionFragments.h \
	 whatIsRunning.h wholeAssemblyItem.h wholeReadItem.h

assemblyView3.o : \
	 arrayOfFwdRevPairLines.h arrayOfFwdRevPairSquares.h arrayOfFwdRevPairTriangles.h \
	 assemblyView.h assemblyView3.cpp assemblyViewTagTypeAndLine.h \
	 assert.h autoFinishPurposes.h bIntersect.h \
	 basesegment.h blockOfLocationsOfA4MerType.h bool.h \
	 cComplementBase.h cComplementBaseTable.h clScaffold.h \
	 consedParameters.h consedResources.h contig.h \
	 contigEnd.h contigMatchTablesType.h dictionary.h \
	 distribution.h experiment.h filename.h \
	 fwdRevPair2.h fwdRevPairLine.h fwdRevPairSquare.h \
	 fwdRevPairTriangle.h guiapp.h guicolortext.h \
	 locatedFragment.h max.h mbtPtrOrderedVector.h \
	 mbtPtrVector.h mbtValOrderedVectorOfRWCString.h mbtValVector.h \
	 mbtValVectorOfBool.h mbtValVector_inc.cpp mbt_exception.h \
	 mbt_val_ord_offset_vec.h min.h motifutils.h \
	 nMAX_QUALITY_LEVEL2.h ntide.h paddedFromUnpadded.h \
	 primerType.h quality.h readTypes.h \
	 readsSortedByLeftEndPosition.h readsSortedByReadName.h restrictionEnzyme.h \
	 rwbtreedictionary.h rwcstring.h rwcsubstring.h \
	 rwdefs.h rwt2dptrvector.h rwtptrorderedvector.h \
	 rwtptrorderedvector_inc.cpp rwtptrsortedvector.h rwtptrvector.h \
	 rwtvalorderedvector.h rwtvalorderedvector_inc.cpp rwtvalsortedvector.h \
	 rwtvalvector.h seqMatch.h sequence.h \
	 soEmptyString.h soGetErrno.h subcloneTTemplate.h \
	 sysdepend.h tag.h tagTypes.h \
	 tracefile.h unpaddedFromPadded.h whatIsRunning.h \
	 wholeReadItem.h

assemblyView4.o : \
	 abs.h arrayOfFwdRevPairLines.h arrayOfFwdRevPairSquares.h \
	 arrayOfFwdRevPairTriangles.h arrayOfRestrictionFragments.h assembly.h \
	 assemblyView.h assemblyView4.cpp assemblyViewTagTypeAndLine.h \
	 assert.h autoFinishPurposes.h bIntersect.h \
	 bIntervalsIntersect.h basesegment.h blockOfLocationsOfA4MerType.h \
	 bool.h cComplementBase.h cComplementBaseTable.h \
	 clScaffold.h compareContigs.h compareContigsCursor.h \
	 compareContigsTypes.h consed.h consedParameters.h \
	 consedResources.h contig.h contigEnd.h \
	 contigMatchTablesType.h contigSegment.h contigview.h \
	 contigwin.h dictionary.h digestForOneEnzyme.h \
	 distribution.h editCursor.h editaction.h \
	 experiment.h expidAndLocatedFragment.h filename.h \
	 fwdRevPair2.h fwdRevPairLine.h fwdRevPairSquare.h \
	 fwdRevPairTriangle.h gotoList.h gotoListType.h \
	 guiDisplayDigest.h guiMultiContigNavigator.h guiapp.h \
	 guicolortext.h listOfFragments.h locatedFragment.h \
	 matchWithinAssembly.h max.h mbtPtrOrderedVector.h \
	 mbtPtrVector.h mbtValOrderedVectorOfRWCString.h mbtValVector.h \
	 mbtValVectorOfBool.h mbtValVector_inc.cpp mbt_exception.h \
	 mbt_val_ord_offset_vec.h min.h motifutils.h \
	 multiProblemGotoList.h nMAX_QUALITY_LEVEL2.h ntide.h \
	 numutil.h paddedFromUnpadded.h popupErrorMessage.h \
	 primerType.h quality.h readTypes.h \
	 readsSortedByLeftEndPosition.h readsSortedByReadName.h readsSortedByTemplateName.h \
	 restrictionEnzyme.h restrictionFragment.h rwbtreedictionary.h \
	 rwcstring.h rwcsubstring.h rwdefs.h \
	 rwt2dptrvector.h rwtptrorderedvector.h rwtptrorderedvector_inc.cpp \
	 rwtptrsortedvector.h rwtptrvector.h rwtvalorderedvector.h \
	 rwtvalorderedvector_inc.cpp rwtvalsortedvector.h rwtvalvector.h \
	 selection.h seqMatch.h sequence.h \
	 singletInfo.h singletsSortedByTemplateName.h soEmptyString.h \
	 soGetErrno.h subcloneTTemplate.h sysdepend.h \
	 tag.h templatesSortedByName.h tracefile.h \
	 unpaddedFromPadded.h visibleLineForRestrictionFragments.h whatIsRunning.h \
	 wholeAssemblyItem.h wholeReadItem.h

assemblyViewRemoveReads.o : \
	 abs.h arrayOfFwdRevPairLines.h arrayOfFwdRevPairSquares.h \
	 arrayOfFwdRevPairTriangles.h assembly.h assemblyView.h \
	 assemblyViewRemoveReads.cpp assemblyViewRemoveReads.h assemblyViewTagTypeAndLine.h \
	 assert.h autoFinishPurposes.h bIntersect.h \
	 bIntervalsIntersect.h basesegment.h blockOfLocationsOfA4MerType.h \
	 bool.h breakIntoShorterLines.h cComplementBase.h \
	 cComplementBaseTable.h compareContigs.h compareContigsCursor.h \
	 compareContigsTypes.h consed.h consedParameters.h \
	 consedResources.h contig.h contigEnd.h \
	 contigMatchTablesType.h contigSegment.h contigview.h \
	 contigwin.h dictionary.h distribution.h \
	 editCursor.h editaction.h experiment.h \
	 expidAndLocatedFragment.h filename.h fwdRevPair2.h \
	 fwdRevPairLine.h fwdRevPairSquare.h fwdRevPairTriangle.h \
	 gotoList.h gotoListType.h guiDisplayDigest.h \
	 guiMultiContigNavigator.h guiRemoveReads.h guiapp.h \
	 guicolortext.h guicontigwin.h handleWindowManagerDelete2.h \
	 hp_exception_kludge.h infobutton.h listOfFragments.h \
	 locatedFragment.h matchWithinAssembly.h max.h \
	 mbtPtrOrderedVector.h mbtPtrVector.h mbtValOrderedVectorOfRWCString.h \
	 mbtValVector.h mbtValVectorOfBool.h mbtValVector_inc.cpp \
	 mbt_exception.h mbt_val_ord_offset_vec.h min.h \
	 motifutils.h multiProblemGotoList.h nMAX_QUALITY_LEVEL2.h \
	 ntide.h numutil.h paddedFromUnpadded.h \
	 popupErrorMessage.h primerType.h quality.h \
	 readTypes.h readsSortedByLeftEndPosition.h readsSortedByReadName.h \
	 readsSortedByTemplateName.h restrictionEnzyme.h restrictionFragment.h \
	 rwbtreedictionary.h rwcstring.h rwcsubstring.h \
	 rwdefs.h rwt2dptrvector.h rwtptrorderedvector.h \
	 rwtptrorderedvector_inc.cpp rwtptrsortedvector.h rwtptrvector.h \
	 rwtvalorderedvector.h rwtvalorderedvector_inc.cpp rwtvalsortedvector.h \
	 rwtvalvector.h selection.h seqMatch.h \
	 sequence.h singletInfo.h singletsSortedByTemplateName.h \
	 soEmptyString.h soGetErrno.h subcloneTTemplate.h \
	 sysdepend.h tag.h templatesSortedByName.h \
	 textfield.h tracefile.h unpaddedFromPadded.h \
	 visibleLineForRestrictionFragments.h whatIsRunning.h wholeAssemblyItem.h \
	 wholeReadItem.h

assert.o : \
	 assert.cpp

autoEdit.o : \
	 abs.h assembly.h assemblyViewTagTypeAndLine.h \
	 assert.h autoEdit.cpp autoEdit.h \
	 autoFinishPurposes.h bIntersect.h bIntervalsIntersect.h \
	 basesegment.h blockOfLocationsOfA4MerType.h bool.h \
	 cComplementBase.h cComplementBaseTable.h compareContigs.h \
	 compareContigsCursor.h compareContigsTypes.h consed.h \
	 consedParameters.h consedResources.h contig.h \
	 contigEnd.h contigMatchTablesType.h contigSegment.h \
	 contigview.h contigwin.h dictionary.h \
	 distribution.h editCursor.h editaction.h \
	 experiment.h expidAndLocatedFragment.h fileDefines.h \
	 filename.h gotoList.h gotoListType.h \
	 guiDisplayDigest.h guiMultiContigNavigator.h guiRemoveReads.h \
	 guiapp.h guicolortext.h library.h \
	 listOfFragments.h listOfLibraries.h locatedFragment.h \
	 matchWithinAssembly.h max.h maybeTerminateIfAnotherReadWriteConsed.h \
	 mbtPtrOrderedVector.h mbtPtrVector.h mbtValOrderedVectorOfRWCString.h \
	 mbtValVector.h mbtValVectorOfBool.h mbtValVector_inc.cpp \
	 mbt_exception.h mbt_val_ord_offset_vec.h min.h \
	 motifutils.h multiProblemGotoList.h nMAX_QUALITY_LEVEL2.h \
	 ntide.h numutil.h paddedFromUnpadded.h \
	 primerType.h quality.h readTypes.h \
	 readsSortedByLeftEndPosition.h readsSortedByReadName.h readsSortedByTemplateName.h \
	 restrictionEnzyme.h restrictionFragment.h rwbtreedictionary.h \
	 rwcregexp.h rwcstring.h rwcsubstring.h \
	 rwdefs.h rwtptrorderedvector.h rwtptrorderedvector_inc.cpp \
	 rwtptrsortedvector.h rwtptrvector.h rwtvalorderedvector.h \
	 rwtvalorderedvector_inc.cpp rwtvalsortedvector.h rwtvalvector.h \
	 selection.h sequence.h singletInfo.h \
	 singletsSortedByTemplateName.h soEmptyString.h soGetDateTime.h \
	 soGetErrno.h subcloneTTemplate.h sysdepend.h \
	 szGetTime.h tag.h templatesSortedByName.h \
	 terminateIfNoPhdDir.h tracefile.h unpaddedFromPadded.h \
	 visibleLineForRestrictionFragments.h whatIsRunning.h wholeAssemblyItem.h \
	 wholeReadItem.h

autoFinish.o : \
	 abs.h assembly.h assemblyViewTagTypeAndLine.h \
	 assert.h autoFinish.cpp autoFinishExpTag.h \
	 autoFinishPCR.h autoFinishPurposes.h bIntersect.h \
	 bIntervalsIntersect.h basesegment.h blockOfLocationsOfA4MerType.h \
	 bool.h cComplementBase.h cComplementBaseTable.h \
	 choose_contig.h compareContigs.h compareContigsCursor.h \
	 compareContigsTypes.h consed.h consedParameters.h \
	 consedResources.h contig.h contigEnd.h \
	 contigMatchTablesType.h contigSegment.h contigview.h \
	 contigwin.h dictionary.h distribution.h \
	 editCursor.h editaction.h experiment.h \
	 expidAndLocatedFragment.h fileDefines.h filename.h \
	 fragment_and_contig.h gotoList.h gotoListType.h \
	 guiDisplayDigest.h guiMultiContigNavigator.h guiapp.h \
	 guicolortext.h library.h listOfFragments.h \
	 listOfLibraries.h locatedFragment.h matchWithinAssembly.h \
	 max.h maybeTerminateIfAnotherReadWriteConsed.h mbtPtrOrderedVector.h \
	 mbtPtrVector.h mbtValOrderedVectorOfRWCString.h mbtValVector.h \
	 mbtValVectorOfBool.h mbtValVector_inc.cpp mbt_exception.h \
	 mbt_val_ord_offset_vec.h min.h motifutils.h \
	 multiProblemGotoList.h nMAX_QUALITY_LEVEL2.h ntide.h \
	 numutil.h openAutoFinishOutputFiles.h paddedFromUnpadded.h \
	 pickCombinationsOfPCRPrimers.h primerType.h printAutoFinishMiscInfo.h \
	 printMemory.h quality.h readTypes.h \
	 readsSortedByLeftEndPosition.h readsSortedByReadName.h readsSortedByTemplateName.h \
	 restrictionEnzyme.h restrictionFragment.h rwbtreedictionary.h \
	 rwcstring.h rwcsubstring.h rwdefs.h \
	 rwtptrorderedvector.h rwtptrorderedvector_inc.cpp rwtptrsortedvector.h \
	 rwtptrvector.h rwtvalorderedvector.h rwtvalorderedvector_inc.cpp \
	 rwtvalsortedvector.h rwtvalvector.h selection.h \
	 sequence.h singletInfo.h singletsSortedByTemplateName.h \
	 soEmptyString.h soGetErrno.h subcloneTTemplate.h \
	 sysdepend.h tag.h templatesSortedByName.h \
	 tracefile.h universalPrimerAutoFinishExpTagsSortedByTemplateName.h unpaddedFromPadded.h \
	 visibleLineForRestrictionFragments.h whatIsRunning.h wholeAssemblyItem.h \
	 wholeReadItem.h

autoFinishExpTag.o : \
	 assemblyViewTagTypeAndLine.h assert.h autoFinishExpTag.cpp \
	 autoFinishExpTag.h autoFinishPurposes.h bIntersect.h \
	 basesegment.h blockOfLocationsOfA4MerType.h bool.h \
	 cComplementBase.h cComplementBaseTable.h consedParameters.h \
	 consedResources.h contig.h contigEnd.h \
	 contigMatchTablesType.h dictionary.h distribution.h \
	 experiment.h fileDefines.h filename.h \
	 locatedFragment.h max.h mbtPtrOrderedVector.h \
	 mbtPtrVector.h mbtValOrderedVectorOfRWCString.h mbtValVector.h \
	 mbtValVectorOfBool.h mbtValVector_inc.cpp mbt_exception.h \
	 mbt_val_ord_offset_vec.h min.h nMAX_QUALITY_LEVEL2.h \
	 ntide.h paddedFromUnpadded.h primerType.h \
	 quality.h readTypes.h readsSortedByLeftEndPosition.h \
	 readsSortedByReadName.h restrictionEnzyme.h rwbtreedictionary.h \
	 rwcstring.h rwcsubstring.h rwdefs.h \
	 rwtptrorderedvector.h rwtptrorderedvector_inc.cpp rwtptrsortedvector.h \
	 rwtptrvector.h rwtvalorderedvector.h rwtvalorderedvector_inc.cpp \
	 rwtvalsortedvector.h rwtvalvector.h sequence.h \
	 soEmptyString.h soGetErrno.h subcloneTTemplate.h \
	 sysdepend.h tag.h tracefile.h \
	 unpaddedFromPadded.h whatIsRunning.h wholeReadItem.h

autoFinishPCR.o : \
	 abs.h assembly.h assemblyViewTagTypeAndLine.h \
	 assert.h autoFinishPCR.cpp autoFinishPCR.h \
	 autoFinishPurposes.h bIntersect.h bIntervalsIntersect.h \
	 basesegment.h blockOfLocationsOfA4MerType.h bool.h \
	 cComplementBase.h cComplementBaseTable.h compareContigs.h \
	 compareContigsCursor.h compareContigsTypes.h consed.h \
	 consedParameters.h consedResources.h contig.h \
	 contigEnd.h contigEndPair.h contigMatchTablesType.h \
	 contigSegment.h contigview.h contigwin.h \
	 dictionary.h distribution.h editCursor.h \
	 editaction.h experiment.h expidAndLocatedFragment.h \
	 fileDefines.h filename.h gotoList.h \
	 gotoListType.h guiDisplayDigest.h guiMultiContigNavigator.h \
	 guiapp.h guicolortext.h listOfFragments.h \
	 locatedFragment.h matchWithinAssembly.h max.h \
	 mbtPtrOrderedVector.h mbtPtrVector.h mbtValOrderedVectorOfRWCString.h \
	 mbtValVector.h mbtValVectorOfBool.h mbtValVector_inc.cpp \
	 mbt_exception.h mbt_val_ord_offset_vec.h min.h \
	 motifutils.h multiProblemGotoList.h nMAX_QUALITY_LEVEL2.h \
	 ntide.h numutil.h paddedFromUnpadded.h \
	 pcrPrimer.h pcrPrimerPairSubscripts.h pcrPrimerrPair.h \
	 pickCombinationsOfPCRPrimers.h primerType.h quality.h \
	 readTypes.h readsSortedByLeftEndPosition.h readsSortedByReadName.h \
	 readsSortedByTemplateName.h regionOfContig.h regionToAmplify.h \
	 restrictionEnzyme.h restrictionFragment.h rwbtreedictionary.h \
	 rwcstring.h rwcsubstring.h rwdefs.h \
	 rwtptrorderedvector.h rwtptrorderedvector_inc.cpp rwtptrsortedvector.h \
	 rwtptrvector.h rwtvalorderedvector.h rwtvalorderedvector_inc.cpp \
	 rwtvalsortedvector.h rwtvalvector.h selection.h \
	 sequence.h singletInfo.h singletsSortedByTemplateName.h \
	 soEmptyString.h soGetErrno.h subcloneTTemplate.h \
	 sysdepend.h tag.h templatesSortedByName.h \
	 tracefile.h unpaddedFromPadded.h visibleLineForRestrictionFragments.h \
	 whatIsRunning.h wholeAssemblyItem.h wholeReadItem.h

autoPCRAmplify.o : \
	 abs.h assembly.h assemblyViewTagTypeAndLine.h \
	 assert.h autoFinishPurposes.h autoPCRAmplify.cpp \
	 autoPCRAmplify.h bIntersect.h bIntervalsIntersect.h \
	 bIsNumericMaybeWithWhitespace.h basesegment.h blockOfLocationsOfA4MerType.h \
	 bool.h cComplementBase.h cComplementBaseTable.h \
	 compareContigs.h compareContigsCursor.h compareContigsTypes.h \
	 consed.h consedParameters.h consedResources.h \
	 contig.h contigEnd.h contigMatchTablesType.h \
	 contigSegment.h contigview.h contigwin.h \
	 dictionary.h distribution.h editCursor.h \
	 editaction.h experiment.h expidAndLocatedFragment.h \
	 fileDefines.h filename.h gotoList.h \
	 gotoListType.h guiDisplayDigest.h guiMultiContigNavigator.h \
	 guiapp.h guicolortext.h listOfFragments.h \
	 locatedFragment.h matchWithinAssembly.h max.h \
	 mbtPtrOrderedVector.h mbtPtrVector.h mbtValOrderedVectorOfRWCString.h \
	 mbtValVector.h mbtValVectorOfBool.h mbtValVector_inc.cpp \
	 mbt_exception.h mbt_val_ord_offset_vec.h min.h \
	 motifutils.h multiProblemGotoList.h nMAX_QUALITY_LEVEL2.h \
	 ntide.h numutil.h paddedFromUnpadded.h \
	 pcrPrimer.h pcrPrimerPairSubscripts.h pcrPrimerrPair.h \
	 primerType.h printAutoFinishMiscInfo.h quality.h \
	 readTypes.h readsSortedByLeftEndPosition.h readsSortedByReadName.h \
	 readsSortedByTemplateName.h regionOfContig.h regionToAmplify.h \
	 restrictionEnzyme.h restrictionFragment.h rwbtreedictionary.h \
	 rwcregexp.h rwcstring.h rwcsubstring.h \
	 rwctokenizer.h rwdefs.h rwtptrorderedvector.h \
	 rwtptrorderedvector_inc.cpp rwtptrsortedvector.h rwtptrvector.h \
	 rwtvalorderedvector.h rwtvalorderedvector_inc.cpp rwtvalsortedvector.h \
	 rwtvalvector.h selection.h sequence.h \
	 singletInfo.h singletsSortedByTemplateName.h soEmptyString.h \
	 soGetErrno.h subcloneTTemplate.h sysdepend.h \
	 tag.h templatesSortedByName.h terminateIfNoPhdDir.h \
	 tracefile.h unpaddedFromPadded.h visibleLineForRestrictionFragments.h \
	 whatIsRunning.h wholeAssemblyItem.h wholeReadItem.h

autoReport.o : \
	 abs.h assembly.h assemblyViewTagTypeAndLine.h \
	 assert.h autoFinishPurposes.h autoReport.cpp \
	 autoReport.h bIntersect.h bIntervalsIntersect.h \
	 basesegment.h blockOfLocationsOfA4MerType.h bool.h \
	 cComplementBase.h cComplementBaseTable.h compareContigs.h \
	 compareContigsCursor.h compareContigsTypes.h consed.h \
	 consedParameters.h consedResources.h contig.h \
	 contigEnd.h contigMatchTablesType.h contigSegment.h \
	 contigview.h contigwin.h dictionary.h \
	 distribution.h editCursor.h editaction.h \
	 experiment.h expidAndLocatedFragment.h fileDefines.h \
	 filename.h fwdRevPair.h fwdRevPair2.h \
	 gotoList.h gotoListType.h guiDisplayDigest.h \
	 guiMultiContigNavigator.h guiapp.h guicolortext.h \
	 highQualityDiscrepancyGotoList.h library.h listOfFragments.h \
	 listOfLibraries.h locatedFragment.h lowconsqual.h \
	 matchWithinAssembly.h max.h mbtPtrOrderedVector.h \
	 mbtPtrVector.h mbtValOrderedVectorOfRWCString.h mbtValVector.h \
	 mbtValVectorOfBool.h mbtValVector_inc.cpp mbt_exception.h \
	 mbt_val_ord_offset_vec.h min.h motifutils.h \
	 multiProblemGotoList.h nMAX_QUALITY_LEVEL2.h ntide.h \
	 numutil.h openLogFiles.h paddedFromUnpadded.h \
	 primateSpecies.h primerType.h printAutoFinishMiscInfo.h \
	 quality.h readTypes.h readsSortedByLeftEndPosition.h \
	 readsSortedByReadName.h readsSortedByTemplateName.h restrictionEnzyme.h \
	 restrictionFragment.h rwbtreedictionary.h rwcstring.h \
	 rwcsubstring.h rwctokenizer.h rwdefs.h \
	 rwtptrorderedvector.h rwtptrorderedvector_inc.cpp rwtptrsortedvector.h \
	 rwtptrvector.h rwtvalorderedvector.h rwtvalorderedvector_inc.cpp \
	 rwtvalsortedvector.h rwtvalvector.h selection.h \
	 sequence.h singleSubcloneRegionsGotoList.h singletInfo.h \
	 singletsSortedByTemplateName.h soAddCommas.h soEmptyString.h \
	 soGetErrno.h soLine.h subcloneTTemplate.h \
	 sysdepend.h tag.h templatesSortedByName.h \
	 terminateIfNoPhdDir.h tracefile.h unpaddedFromPadded.h \
	 visibleLineForRestrictionFragments.h whatIsRunning.h wholeAssemblyItem.h \
	 wholeReadItem.h

automatedConsedInit.o : \
	 abs.h assembly.h assemblyViewTagTypeAndLine.h \
	 assert.h autoFinishPurposes.h automatedConsedInit.cpp \
	 automatedConsedInit.h bIntersect.h bIntervalsIntersect.h \
	 basesegment.h blockOfLocationsOfA4MerType.h bool.h \
	 cComplementBase.h cComplementBaseTable.h compareContigs.h \
	 compareContigsCursor.h compareContigsTypes.h consed.h \
	 consedParameters.h consedResources.h contig.h \
	 contigEnd.h contigMatchTablesType.h contigSegment.h \
	 contigview.h contigwin.h dictionary.h \
	 distribution.h editCursor.h editaction.h \
	 experiment.h expidAndLocatedFragment.h fileDefines.h \
	 filename.h gotoList.h gotoListType.h \
	 guiDisplayDigest.h guiMultiContigNavigator.h guiapp.h \
	 guicolortext.h library.h listOfFragments.h \
	 listOfLibraries.h locatedFragment.h matchWithinAssembly.h \
	 max.h maybeTerminateIfAnotherReadWriteConsed.h mbtPtrOrderedVector.h \
	 mbtPtrVector.h mbtValOrderedVectorOfRWCString.h mbtValVector.h \
	 mbtValVectorOfBool.h mbtValVector_inc.cpp mbt_exception.h \
	 mbt_val_ord_offset_vec.h min.h motifutils.h \
	 multiProblemGotoList.h nMAX_QUALITY_LEVEL2.h ntide.h \
	 numutil.h paddedFromUnpadded.h primerType.h \
	 quality.h readTypes.h readsSortedByLeftEndPosition.h \
	 readsSortedByReadName.h readsSortedByTemplateName.h restrictionEnzyme.h \
	 restrictionFragment.h rwbtreedictionary.h rwcstring.h \
	 rwcsubstring.h rwdefs.h rwtptrorderedvector.h \
	 rwtptrorderedvector_inc.cpp rwtptrsortedvector.h rwtptrvector.h \
	 rwtvalorderedvector.h rwtvalorderedvector_inc.cpp rwtvalsortedvector.h \
	 rwtvalvector.h selection.h sequence.h \
	 singletInfo.h singletsSortedByTemplateName.h soEmptyString.h \
	 soGetErrno.h subcloneTTemplate.h sysdepend.h \
	 tag.h templatesSortedByName.h terminateIfNoPhdDir.h \
	 tracefile.h unpaddedFromPadded.h visibleLineForRestrictionFragments.h \
	 whatIsRunning.h wholeAssemblyItem.h wholeReadItem.h

bDoPCRPrimersStickToEachOther.o : \
	 assemblyViewTagTypeAndLine.h assert.h bDoPCRPrimersStickToEachOther.cpp \
	 bIntersect.h blockOfLocationsOfA4MerType.h bool.h \
	 consedParameters.h consedResources.h contigMatchTablesType.h \
	 filename.h matchScores.h max.h \
	 mbtPtrOrderedVector.h mbtValOrderedVectorOfRWCString.h mbt_exception.h \
	 min.h primerType.h restrictionEnzyme.h \
	 rwcstring.h rwcsubstring.h rwdefs.h \
	 rwtptrorderedvector.h rwtptrorderedvector_inc.cpp rwtvalorderedvector.h \
	 rwtvalorderedvector_inc.cpp soEmptyString.h soGetErrno.h \
	 sysdepend.h whatIsRunning.h

bEditHistoryFileExists.o : \
	 assert.h bEditHistoryFileExists.cpp bool.h \
	 filename.h guiapp.h guicolortext.h \
	 mbt_exception.h motifutils.h rwcstring.h \
	 rwcsubstring.h rwdefs.h rwtptrorderedvector.h \
	 rwtptrorderedvector_inc.cpp rwtvalorderedvector.h rwtvalorderedvector_inc.cpp \
	 soEmptyString.h soGetErrno.h sysdepend.h

bErrorMessageIfNoPhd.o : \
	 abs.h assembly.h assemblyViewTagTypeAndLine.h \
	 assert.h autoFinishPurposes.h bErrorMessageIfNoPhd.cpp \
	 bIntersect.h bIntervalsIntersect.h basesegment.h \
	 blockOfLocationsOfA4MerType.h bool.h cComplementBase.h \
	 cComplementBaseTable.h compareContigs.h compareContigsCursor.h \
	 compareContigsTypes.h consed.h consedParameters.h \
	 consedResources.h contig.h contigEnd.h \
	 contigMatchTablesType.h contigSegment.h contigview.h \
	 contigwin.h dictionary.h distribution.h \
	 editCursor.h editaction.h experiment.h \
	 expidAndLocatedFragment.h filename.h gotoList.h \
	 gotoListType.h guiDisplayDigest.h guiMultiContigNavigator.h \
	 guiapp.h guicolortext.h listOfFragments.h \
	 locatedFragment.h matchWithinAssembly.h max.h \
	 mbtPtrOrderedVector.h mbtPtrVector.h mbtValOrderedVectorOfRWCString.h \
	 mbtValVector.h mbtValVectorOfBool.h mbtValVector_inc.cpp \
	 mbt_exception.h mbt_val_ord_offset_vec.h min.h \
	 motifutils.h multiProblemGotoList.h nMAX_QUALITY_LEVEL2.h \
	 ntide.h numutil.h paddedFromUnpadded.h \
	 primerType.h quality.h readTypes.h \
	 readsSortedByLeftEndPosition.h readsSortedByReadName.h readsSortedByTemplateName.h \
	 restrictionEnzyme.h restrictionFragment.h rwbtreedictionary.h \
	 rwcstring.h rwcsubstring.h rwdefs.h \
	 rwtptrorderedvector.h rwtptrorderedvector_inc.cpp rwtptrsortedvector.h \
	 rwtptrvector.h rwtvalorderedvector.h rwtvalorderedvector_inc.cpp \
	 rwtvalsortedvector.h rwtvalvector.h selection.h \
	 sequence.h singletInfo.h singletsSortedByTemplateName.h \
	 soEmptyString.h soGetErrno.h subcloneTTemplate.h \
	 sysdepend.h tag.h templatesSortedByName.h \
	 tracefile.h unpaddedFromPadded.h visibleLineForRestrictionFragments.h \
	 whatIsRunning.h wholeAssemblyItem.h wholeReadItem.h

bForwardReversePairIsConsistentWithContigOrder.o : \
	 assemblyViewTagTypeAndLine.h assert.h autoFinishPurposes.h \
	 bForwardReversePairIsConsistentWithContigOrder.cpp bForwardReversePairIsConsistentWithContigOrder.h basesegment.h \
	 blockOfLocationsOfA4MerType.h bool.h cComplementBase.h \
	 cComplementBaseTable.h consedParameters.h consedResources.h \
	 contig.h contigEnd.h contigMatchTablesType.h \
	 dictionary.h distribution.h experiment.h \
	 filename.h fwdRevPair2.h locatedFragment.h \
	 mbtPtrOrderedVector.h mbtPtrVector.h mbtValOrderedVectorOfRWCString.h \
	 mbtValVector.h mbtValVectorOfBool.h mbtValVector_inc.cpp \
	 mbt_exception.h mbt_val_ord_offset_vec.h min.h \
	 nMAX_QUALITY_LEVEL2.h ntide.h paddedFromUnpadded.h \
	 primerType.h quality.h readTypes.h \
	 readsSortedByLeftEndPosition.h readsSortedByReadName.h restrictionEnzyme.h \
	 rwbtreedictionary.h rwcstring.h rwcsubstring.h \
	 rwdefs.h rwtptrorderedvector.h rwtptrorderedvector_inc.cpp \
	 rwtptrsortedvector.h rwtptrvector.h rwtvalorderedvector.h \
	 rwtvalorderedvector_inc.cpp rwtvalsortedvector.h rwtvalvector.h \
	 sequence.h soEmptyString.h soGetErrno.h \
	 subcloneTTemplate.h sysdepend.h tag.h \
	 tracefile.h unpaddedFromPadded.h whatIsRunning.h \
	 wholeReadItem.h

bGuiGetAnswerYesNo.o : \
	 assert.h bGuiGetAnswerYesNo.cpp bool.h \
	 breakIntoShorterLines.h filename.h guiapp.h \
	 guicolortext.h handleWindowManagerDelete.h mbt_exception.h \
	 motifutils.h rwcstring.h rwcsubstring.h \
	 rwdefs.h rwtptrorderedvector.h rwtptrorderedvector_inc.cpp \
	 rwtvalorderedvector.h rwtvalorderedvector_inc.cpp soEmptyString.h \
	 soGetErrno.h sysdepend.h

bInputEventToWrongWindow.o : \
	 assert.h bInputEventToWrongWindow.cpp bInputEventToWrongWindow.h \
	 bool.h filename.h guiapp.h \
	 guicolortext.h mbt_exception.h motifutils.h \
	 rwcstring.h rwcsubstring.h rwdefs.h \
	 rwtptrorderedvector.h rwtptrorderedvector_inc.cpp rwtvalorderedvector.h \
	 rwtvalorderedvector_inc.cpp soEmptyString.h soGetErrno.h \
	 sysdepend.h

bIsNumeric.o : \
	 bIsNumeric.cpp bool.h rwcstring.h \
	 rwcsubstring.h rwdefs.h sysdepend.h

bIsNumericDouble.o : \
	 bIsNumericDouble.cpp bool.h rwcregexp.h \
	 rwcstring.h rwcsubstring.h rwdefs.h

bIsNumericFloat.o : \
	 bIsNumericFloat.cpp bIsNumericFloat.h bool.h \
	 rwcregexp.h rwcstring.h rwcsubstring.h \
	 rwdefs.h

bIsNumericLongMaybeWithWhitespace.o : \
	 bIsNumericLongMaybeWithWhitespace.cpp bIsNumericLongMaybeWithWhitespace.h bool.h \
	 rwcregexp.h rwcstring.h rwcsubstring.h \
	 rwdefs.h

bIsNumericMaybeWithWhitespace.o : \
	 bIsNumericMaybeWithWhitespace.cpp bIsNumericMaybeWithWhitespace.h bool.h \
	 rwcregexp.h rwcstring.h rwcsubstring.h \
	 rwdefs.h

bIsPCRPrimerPairOK.o : \
	 abs.h assemblyViewTagTypeAndLine.h assert.h \
	 bDoPCRPrimersStickToEachOther.h bIsPCRPrimerPairOK.cpp bIsPCRPrimerPairOK.h \
	 blockOfLocationsOfA4MerType.h bool.h consedParameters.h \
	 consedResources.h contigMatchTablesType.h filename.h \
	 mbtPtrOrderedVector.h mbtValOrderedVectorOfRWCString.h mbt_exception.h \
	 primerType.h restrictionEnzyme.h rwcstring.h \
	 rwcsubstring.h rwdefs.h rwtptrorderedvector.h \
	 rwtptrorderedvector_inc.cpp rwtvalorderedvector.h rwtvalorderedvector_inc.cpp \
	 soEmptyString.h soGetErrno.h sysdepend.h \
	 whatIsRunning.h

bIsPrimerStale.o : \
	 abs.h assembly.h assemblyViewTagTypeAndLine.h \
	 assert.h autoFinishPurposes.h bIntersect.h \
	 bIntervalsIntersect.h bIsPrimerStale.cpp basesegment.h \
	 blockOfLocationsOfA4MerType.h bool.h cComplementBase.h \
	 cComplementBaseTable.h compareContigs.h compareContigsCursor.h \
	 compareContigsTypes.h consed.h consedParameters.h \
	 consedResources.h contig.h contigEnd.h \
	 contigMatchTablesType.h contigSegment.h contigview.h \
	 contigwin.h dictionary.h distribution.h \
	 editCursor.h editaction.h experiment.h \
	 expidAndLocatedFragment.h filename.h gotoList.h \
	 gotoListType.h guiDisplayDigest.h guiMultiContigNavigator.h \
	 guiapp.h guicolortext.h listOfFragments.h \
	 locatedFragment.h matchWithinAssembly.h max.h \
	 mbtPtrOrderedVector.h mbtPtrVector.h mbtValOrderedVectorOfRWCString.h \
	 mbtValVector.h mbtValVectorOfBool.h mbtValVector_inc.cpp \
	 mbt_exception.h mbt_val_ord_offset_vec.h min.h \
	 motifutils.h multiProblemGotoList.h nMAX_QUALITY_LEVEL2.h \
	 ntide.h numutil.h paddedFromUnpadded.h \
	 primerType.h quality.h readTypes.h \
	 readsSortedByLeftEndPosition.h readsSortedByReadName.h readsSortedByTemplateName.h \
	 restrictionEnzyme.h restrictionFragment.h rwbtreedictionary.h \
	 rwcstring.h rwcsubstring.h rwdefs.h \
	 rwtptrorderedvector.h rwtptrorderedvector_inc.cpp rwtptrsortedvector.h \
	 rwtptrvector.h rwtvalorderedvector.h rwtvalorderedvector_inc.cpp \
	 rwtvalsortedvector.h rwtvalvector.h selection.h \
	 sequence.h singletInfo.h singletsSortedByTemplateName.h \
	 soEmptyString.h soGetErrno.h subcloneTTemplate.h \
	 sysdepend.h tag.h templatesSortedByName.h \
	 tracefile.h unpaddedFromPadded.h visibleLineForRestrictionFragments.h \
	 whatIsRunning.h wholeAssemblyItem.h wholeReadItem.h

bIsTopStrandRead.o : \
	 assert.h bIsTopStrandRead.cpp bIsTopStrandRead.h \
	 bool.h mbt_exception.h readTypes.h \
	 rwcstring.h rwcsubstring.h rwdefs.h \
	 soGetErrno.h

bPrimerHasMatchesAgainstSequencesInFile.o : \
	 assemblyViewTagTypeAndLine.h assert.h bPrimerHasMatchesAgainstSequencesInFile.cpp \
	 bPrimerHasMatchesAgainstSequencesInFile.h blockOfLocationsOfA4MerType.h bool.h \
	 consedParameters.h consedResources.h contigMatchTablesType.h \
	 filename.h findPrimerMatchesAgainstSequencesInFile.h mbtPtrOrderedVector.h \
	 mbtValOrderedVectorOfRWCString.h mbt_exception.h primerType.h \
	 restrictionEnzyme.h rwcstring.h rwcsubstring.h \
	 rwdefs.h rwtptrorderedvector.h rwtptrorderedvector_inc.cpp \
	 rwtvalorderedvector.h rwtvalorderedvector_inc.cpp soEmptyString.h \
	 soGetErrno.h sysdepend.h whatIsRunning.h

bPrimerHasMatchesElsewhere.o : \
	 assemblyViewTagTypeAndLine.h assert.h bPrimerHasMatchesElsewhere.cpp \
	 bPrimerHasMatchesElsewhere.h blockOfLocationsOfA4MerType.h bool.h \
	 consedParameters.h consedResources.h contigMatchTablesType.h \
	 filename.h findPrimerMatchesElsewhere.h mbtPtrOrderedVector.h \
	 mbtValOrderedVectorOfRWCString.h mbt_exception.h primerType.h \
	 restrictionEnzyme.h rwcstring.h rwcsubstring.h \
	 rwdefs.h rwtptrorderedvector.h rwtptrorderedvector_inc.cpp \
	 rwtvalorderedvector.h rwtvalorderedvector_inc.cpp soEmptyString.h \
	 soGetErrno.h sysdepend.h whatIsRunning.h

basesAndQualitiesAndPeaks.o : \
	 assert.h basesAndQualitiesAndPeaks.cpp basesAndQualitiesAndPeaks.h \
	 bool.h complement_so.h mbt_exception.h \
	 rwcstring.h rwcsubstring.h rwdefs.h \
	 rwtvalorderedvector.h rwtvalorderedvector_inc.cpp soEmptyString.h \
	 soGetErrno.h

basesegment.o : \
	 abs.h assemblyViewTagTypeAndLine.h assert.h \
	 autoFinishPurposes.h bIntersect.h bIntervalsIntersect.h \
	 basesegment.cpp basesegment.h blockOfLocationsOfA4MerType.h \
	 bool.h cComplementBase.h cComplementBaseTable.h \
	 consedParameters.h consedResources.h contig.h \
	 contigEnd.h contigMatchTablesType.h dictionary.h \
	 distribution.h experiment.h fileDefines.h \
	 filename.h guicolortext.h locatedFragment.h \
	 max.h mbtPtrOrderedVector.h mbtPtrVector.h \
	 mbtValOrderedVectorOfRWCString.h mbtValVector.h mbtValVectorOfBool.h \
	 mbtValVector_inc.cpp mbt_exception.h mbt_val_ord_offset_vec.h \
	 min.h nMAX_QUALITY_LEVEL2.h ntide.h \
	 numutil.h paddedFromUnpadded.h primerType.h \
	 quality.h readTypes.h readsSortedByLeftEndPosition.h \
	 readsSortedByReadName.h restrictionEnzyme.h rwbtreedictionary.h \
	 rwcstring.h rwcsubstring.h rwdefs.h \
	 rwtptrorderedvector.h rwtptrorderedvector_inc.cpp rwtptrsortedvector.h \
	 rwtptrvector.h rwtvalorderedvector.h rwtvalorderedvector_inc.cpp \
	 rwtvalsortedvector.h rwtvalvector.h sequence.h \
	 soAddCommas.h soEmptyString.h soGetErrno.h \
	 subcloneTTemplate.h sysdepend.h tag.h \
	 tagTypes.h tracefile.h unpaddedFromPadded.h \
	 whatIsRunning.h wholeReadItem.h

batchChangeConsensus.o : \
	 abs.h assembly.h assemblyViewTagTypeAndLine.h \
	 assert.h autoFinishPurposes.h automatedConsedInit.h \
	 bIntersect.h bIntervalsIntersect.h bIsNumericMaybeWithWhitespace.h \
	 basesegment.h batchChangeConsensus.cpp batchChangeConsensus.h \
	 blockOfLocationsOfA4MerType.h bool.h cComplementBase.h \
	 cComplementBaseTable.h compareContigs.h compareContigsCursor.h \
	 compareContigsTypes.h consed.h consedParameters.h \
	 consedResources.h contig.h contigEnd.h \
	 contigMatchTablesType.h contigSegment.h contigview.h \
	 contigwin.h dictionary.h distribution.h \
	 editCursor.h editaction.h experiment.h \
	 expidAndLocatedFragment.h filename.h gotoList.h \
	 gotoListType.h guiDisplayDigest.h guiMultiContigNavigator.h \
	 guiapp.h guicolortext.h listOfFragments.h \
	 locatedFragment.h matchWithinAssembly.h max.h \
	 mbtPtrOrderedVector.h mbtPtrVector.h mbtValOrderedVectorOfRWCString.h \
	 mbtValVector.h mbtValVectorOfBool.h mbtValVector_inc.cpp \
	 mbt_exception.h mbt_val_ord_offset_vec.h min.h \
	 motifutils.h multiProblemGotoList.h nMAX_QUALITY_LEVEL2.h \
	 ntide.h numutil.h paddedFromUnpadded.h \
	 primerType.h quality.h readTypes.h \
	 readsSortedByLeftEndPosition.h readsSortedByReadName.h readsSortedByTemplateName.h \
	 restrictionEnzyme.h restrictionFragment.h rwbtreedictionary.h \
	 rwcstring.h rwcsubstring.h rwctokenizer.h \
	 rwdefs.h rwtptrorderedvector.h rwtptrorderedvector_inc.cpp \
	 rwtptrsortedvector.h rwtptrvector.h rwtvalorderedvector.h \
	 rwtvalorderedvector_inc.cpp rwtvalsortedvector.h rwtvalvector.h \
	 selection.h sequence.h singletInfo.h \
	 singletsSortedByTemplateName.h soAddCommas.h soEmptyString.h \
	 soGetErrno.h soLine.h subcloneTTemplate.h \
	 sysdepend.h tag.h templatesSortedByName.h \
	 tracefile.h unpaddedFromPadded.h visibleLineForRestrictionFragments.h \
	 whatIsRunning.h wholeAssemblyItem.h wholeReadItem.h \
	 writeNewAceFileNameToFile.h

bigArrayOfLittleArraysOfDistributions.o : \
	 assert.h bigArrayOfLittleArraysOfDistributions.cpp bigArrayOfLittleArraysOfDistributions.h \
	 bool.h distribution.h mbtValVector.h \
	 mbtValVector_inc.cpp mbt_exception.h min.h \
	 nMAX_QUALITY_LEVEL2.h rwcstring.h rwcsubstring.h \
	 rwdefs.h rwtptrorderedvector.h rwtptrorderedvector_inc.cpp \
	 rwtvalvector.h soEmptyString.h soGetErrno.h

breakIntoShorterLines.o : \
	 bool.h breakIntoShorterLines.cpp breakIntoShorterLines.h \
	 rwcstring.h rwcsubstring.h rwdefs.h

busy_cursor.o : \
	 assert.h bool.h busy_cursor.cpp \
	 filename.h guiapp.h guicolortext.h \
	 mbt_exception.h motifutils.h rwcstring.h \
	 rwcsubstring.h rwdefs.h rwtptrorderedvector.h \
	 rwtptrorderedvector_inc.cpp rwtvalorderedvector.h rwtvalorderedvector_inc.cpp \
	 soEmptyString.h soGetErrno.h sysdepend.h

cGetProtein.o : \
	 cGetProtein.cpp cGetProtein.h

calculatePrimerMeltingTemperatures.o : \
	 assemblyViewTagTypeAndLine.h assert.h blockOfLocationsOfA4MerType.h \
	 bool.h calculatePrimerMeltingTemperatures.cpp calculatePrimerMeltingTemperatures.h \
	 consedParameters.h consedResources.h contigMatchTablesType.h \
	 dGetPrimerMeltingTemperature.h filename.h mbtPtrOrderedVector.h \
	 mbtValOrderedVectorOfRWCString.h mbt_exception.h primerType.h \
	 restrictionEnzyme.h rwcstring.h rwcsubstring.h \
	 rwdefs.h rwtptrorderedvector.h rwtptrorderedvector_inc.cpp \
	 rwtvalorderedvector.h rwtvalorderedvector_inc.cpp soEmptyString.h \
	 soGetErrno.h sysdepend.h whatIsRunning.h \
	 whyIsPrimerNotAcceptableTypes.h

centerWidgetOnWidget.o : \
	 centerWidgetOnWidget.cpp

checkPrimersForACGT.o : \
	 assert.h bNotACGTTable.h blockOfLocationsOfA4MerType.h \
	 bool.h checkPrimersForACGT.cpp checkPrimersForACGT.h \
	 contigMatchTablesType.h mbt_exception.h primerType.h \
	 rwcstring.h rwcsubstring.h rwdefs.h \
	 soGetErrno.h whyIsPrimerNotAcceptableTypes.h

checkPrimersForMononucleotideRepeats.o : \
	 assemblyViewTagTypeAndLine.h assert.h blockOfLocationsOfA4MerType.h \
	 bool.h checkPrimersForMononucleotideRepeats.cpp checkPrimersForMononucleotideRepeats.h \
	 consedParameters.h consedResources.h contigMatchTablesType.h \
	 filename.h mbtPtrOrderedVector.h mbtValOrderedVectorOfRWCString.h \
	 mbt_exception.h nGetLengthOfMononucleotideRepeat.h primerType.h \
	 restrictionEnzyme.h rwcstring.h rwcsubstring.h \
	 rwdefs.h rwtptrorderedvector.h rwtptrorderedvector_inc.cpp \
	 rwtvalorderedvector.h rwtvalorderedvector_inc.cpp soEmptyString.h \
	 soGetErrno.h sysdepend.h whatIsRunning.h \
	 whichPrimersAreAcceptable.h whyIsPrimerNotAcceptableTypes.h

checkVariableLengthLimit.o : \
	 checkVariableLengthLimit.cpp

choose_contig.o : \
	 abs.h assembly.h assemblyViewTagTypeAndLine.h \
	 assert.h autoFinishPurposes.h bIntersect.h \
	 bIntervalsIntersect.h basesegment.h blockOfLocationsOfA4MerType.h \
	 bool.h cComplementBase.h cComplementBaseTable.h \
	 choose_contig.cpp choose_contig.h compareContigs.h \
	 compareContigsCursor.h compareContigsTypes.h consed.h \
	 consedParameters.h consedResources.h contig.h \
	 contigEnd.h contigMatchTablesType.h contigSegment.h \
	 contigview.h contigwin.h dictionary.h \
	 distribution.h editCursor.h editaction.h \
	 experiment.h expidAndLocatedFragment.h filename.h \
	 fragment_and_contig.h gotoList.h gotoListType.h \
	 guiDisplayDigest.h guiMultiContigNavigator.h guiTopWindow.h \
	 guiapp.h guicolortext.h listOfFragments.h \
	 locatedFragment.h matchWithinAssembly.h max.h \
	 mbtPtrOrderedVector.h mbtPtrVector.h mbtValOrderedVectorOfRWCString.h \
	 mbtValVector.h mbtValVectorOfBool.h mbtValVector_inc.cpp \
	 mbt_exception.h mbt_val_ord_offset_vec.h min.h \
	 motifutils.h multiProblemGotoList.h nMAX_QUALITY_LEVEL2.h \
	 ntide.h numutil.h paddedFromUnpadded.h \
	 primerType.h quality.h readTypes.h \
	 readsSortedByLeftEndPosition.h readsSortedByReadName.h readsSortedByTemplateName.h \
	 restrictionEnzyme.h restrictionFragment.h rwbtreedictionary.h \
	 rwcregexp.h rwcstring.h rwcsubstring.h \
	 rwdefs.h rwtptrorderedvector.h rwtptrorderedvector_inc.cpp \
	 rwtptrsortedvector.h rwtptrvector.h rwtvalorderedvector.h \
	 rwtvalorderedvector_inc.cpp rwtvalsortedvector.h rwtvalvector.h \
	 selection.h sequence.h singletInfo.h \
	 singletsSortedByTemplateName.h soEmptyString.h soGetErrno.h \
	 subcloneTTemplate.h sysdepend.h tag.h \
	 templatesSortedByName.h tracefile.h unpaddedFromPadded.h \
	 visibleLineForRestrictionFragments.h whatIsRunning.h wholeAssemblyItem.h \
	 wholeReadItem.h

chromatData.o : \
	 chromatData.c chromatData.h ourFree.h \
	 ourMalloc.h typeDef.h

clScaffold.o : \
	 abs.h assembly.h assemblyViewTagTypeAndLine.h \
	 assert.h autoFinishPurposes.h bIntersect.h \
	 bIntervalsIntersect.h basesegment.h blockOfLocationsOfA4MerType.h \
	 bool.h cComplementBase.h cComplementBaseTable.h \
	 clScaffold.cpp clScaffold.h compareContigs.h \
	 compareContigsCursor.h compareContigsTypes.h consed.h \
	 consedParameters.h consedResources.h contig.h \
	 contigEnd.h contigMatchTablesType.h contigSegment.h \
	 contigview.h contigwin.h dictionary.h \
	 distribution.h editCursor.h edit_complement_contig.h \
	 editaction.h experiment.h expidAndLocatedFragment.h \
	 filename.h gotoList.h gotoListType.h \
	 guiDisplayDigest.h guiMultiContigNavigator.h guiapp.h \
	 guicolortext.h listOfFragments.h locatedFragment.h \
	 matchWithinAssembly.h max.h mbtPtrOrderedVector.h \
	 mbtPtrVector.h mbtValOrderedVectorOfRWCString.h mbtValVector.h \
	 mbtValVectorOfBool.h mbtValVector_inc.cpp mbt_exception.h \
	 mbt_val_ord_offset_vec.h min.h motifutils.h \
	 multiProblemGotoList.h nMAX_QUALITY_LEVEL2.h ntide.h \
	 numutil.h paddedFromUnpadded.h please_wait.h \
	 primerType.h quality.h readTypes.h \
	 readsSortedByLeftEndPosition.h readsSortedByReadName.h readsSortedByTemplateName.h \
	 restrictionEnzyme.h restrictionFragment.h rwbtreedictionary.h \
	 rwcstring.h rwcsubstring.h rwdefs.h \
	 rwtptrorderedvector.h rwtptrorderedvector_inc.cpp rwtptrsortedvector.h \
	 rwtptrvector.h rwtvalorderedvector.h rwtvalorderedvector_inc.cpp \
	 rwtvalsortedvector.h rwtvalvector.h selection.h \
	 sequence.h singletInfo.h singletsSortedByTemplateName.h \
	 soEmptyString.h soGetErrno.h subcloneTTemplate.h \
	 sysdepend.h tag.h templatesSortedByName.h \
	 tracefile.h unpaddedFromPadded.h visibleLineForRestrictionFragments.h \
	 whatIsRunning.h wholeAssemblyItem.h wholeReadItem.h

colorDefaults.o : \
	 bool.h colorDefaults.cpp colorDefaults.h \
	 rwcstring.h rwcsubstring.h rwdefs.h \
	 sysdepend.h

colormode.o : \
	 assemblyViewTagTypeAndLine.h assert.h autoFinishPurposes.h \
	 basesegment.h blockOfLocationsOfA4MerType.h bool.h \
	 cComplementBase.h cComplementBaseTable.h colorDefaults.h \
	 colormode.cpp colormode.h consedParameters.h \
	 consedResources.h contig.h contigEnd.h \
	 contigMatchTablesType.h dictionary.h distribution.h \
	 experiment.h filename.h guiapp.h \
	 guicolortext.h locatedFragment.h mbtPtrOrderedVector.h \
	 mbtPtrVector.h mbtValOrderedVectorOfRWCString.h mbtValVector.h \
	 mbtValVectorOfBool.h mbtValVector_inc.cpp mbt_exception.h \
	 mbt_val_ord_offset_vec.h min.h motifutils.h \
	 nMAX_QUALITY_LEVEL2.h ntide.h paddedFromUnpadded.h \
	 primerType.h quality.h readTypes.h \
	 readsSortedByLeftEndPosition.h readsSortedByReadName.h restrictionEnzyme.h \
	 rwbtreedictionary.h rwcstring.h rwcsubstring.h \
	 rwdefs.h rwtptrorderedvector.h rwtptrorderedvector_inc.cpp \
	 rwtptrsortedvector.h rwtptrvector.h rwtvalorderedvector.h \
	 rwtvalorderedvector_inc.cpp rwtvalsortedvector.h rwtvalvector.h \
	 sequence.h soEmptyString.h soGetErrno.h \
	 subcloneTTemplate.h sysdepend.h tag.h \
	 tracefile.h unpaddedFromPadded.h whatIsRunning.h \
	 wholeReadItem.h

compareContigs.o : \
	 abs.h assembly.h assemblyViewTagTypeAndLine.h \
	 assert.h autoFinishPurposes.h bGuiGetAnswerYesNo.h \
	 bIntersect.h bIntervalsIntersect.h bIsAPad.h \
	 basesegment.h blockOfLocationsOfA4MerType.h bool.h \
	 cComplementBase.h cComplementBaseTable.h colormode.h \
	 compareContigs.cpp compareContigs.h compareContigsCursor.h \
	 compareContigsTypes.h consed.h consedParameters.h \
	 consedResources.h contig.h contigEnd.h \
	 contigMatchTablesType.h contigSegment.h contigview.h \
	 contigwin.h dictionary.h distribution.h \
	 editCursor.h editaction.h experiment.h \
	 expidAndLocatedFragment.h extendAlignment.h extendAlignmentBanded.h \
	 filename.h getAlignment.h getAlignmentBanded.h \
	 gotoList.h gotoListType.h guiCompareContigs.h \
	 guiDisplayDigest.h guiMultiContigNavigator.h guiapp.h \
	 guicolortext.h listOfFragments.h locatedFragment.h \
	 makeUpper.h matchWithinAssembly.h max.h \
	 mbtPtrOrderedVector.h mbtPtrVector.h mbtValOrderedVectorOfRWCString.h \
	 mbtValVector.h mbtValVectorOfBool.h mbtValVector_inc.cpp \
	 mbt_exception.h mbt_val_ord_offset_vec.h min.h \
	 motifutils.h multiProblemGotoList.h nMAX_QUALITY_LEVEL2.h \
	 ntide.h numutil.h paddedFromUnpadded.h \
	 paddedPieceOfRead.h please_wait.h popupErrorMessage.h \
	 primerType.h quality.h readTypes.h \
	 readsSortedByLeftEndPosition.h readsSortedByReadName.h readsSortedByTemplateName.h \
	 restrictionEnzyme.h restrictionFragment.h rwbtreedictionary.h \
	 rwcstring.h rwcsubstring.h rwdefs.h \
	 rwtptrorderedvector.h rwtptrorderedvector_inc.cpp rwtptrsortedvector.h \
	 rwtptrvector.h rwtvalorderedvector.h rwtvalorderedvector_inc.cpp \
	 rwtvalsortedvector.h rwtvalvector.h scaleTickSizes.h \
	 selection.h seqMatch.h sequence.h \
	 singletInfo.h singletsSortedByTemplateName.h soEmptyString.h \
	 soGetErrno.h subcloneTTemplate.h sysdepend.h \
	 tag.h templatesSortedByName.h tracefile.h \
	 translateRWCString.h unpaddedFromPadded.h visibleLineForRestrictionFragments.h \
	 whatIsRunning.h wholeAssemblyItem.h wholeReadItem.h

compareContigs2.o : \
	 abs.h assembly.h assemblyViewTagTypeAndLine.h \
	 assert.h autoFinishPurposes.h bIntersect.h \
	 bIntervalsIntersect.h bIsAPad.h basesegment.h \
	 blockOfLocationsOfA4MerType.h bool.h cComplementBase.h \
	 cComplementBaseTable.h compareContigs.h compareContigs2.cpp \
	 compareContigsCursor.h compareContigsTypes.h consed.h \
	 consedParameters.h consedResources.h contig.h \
	 contigEnd.h contigMatchTablesType.h contigSegment.h \
	 contigview.h contigwin.h dictionary.h \
	 distribution.h editCursor.h editaction.h \
	 experiment.h expidAndLocatedFragment.h extendAlignment.h \
	 filename.h getAlignment.h gotoList.h \
	 gotoListType.h guiCompareContigs.h guiDisplayDigest.h \
	 guiMultiContigNavigator.h guiapp.h guicolortext.h \
	 guicontigwin.h infobutton.h listOfFragments.h \
	 locatedFragment.h makeUpper.h matchWithinAssembly.h \
	 max.h mbtPtrOrderedVector.h mbtPtrVector.h \
	 mbtValOrderedVectorOfRWCString.h mbtValVector.h mbtValVectorOfBool.h \
	 mbtValVector_inc.cpp mbt_exception.h mbt_val_ord_offset_vec.h \
	 min.h motifutils.h multiProblemGotoList.h \
	 nMAX_QUALITY_LEVEL2.h ntide.h numutil.h \
	 paddedFromUnpadded.h paddedPieceOfRead.h please_wait.h \
	 popupErrorMessage.h popupInfoMessage.h primerType.h \
	 quality.h readTypes.h readsSortedByLeftEndPosition.h \
	 readsSortedByReadName.h readsSortedByTemplateName.h restrictionEnzyme.h \
	 restrictionFragment.h rwbtreedictionary.h rwcstring.h \
	 rwcsubstring.h rwdefs.h rwtptrorderedvector.h \
	 rwtptrorderedvector_inc.cpp rwtptrsortedvector.h rwtptrvector.h \
	 rwtvalorderedvector.h rwtvalorderedvector_inc.cpp rwtvalsortedvector.h \
	 rwtvalvector.h scaleTickSizes.h selection.h \
	 sequence.h singletInfo.h singletsSortedByTemplateName.h \
	 soAddCommas.h soEmptyString.h soGetDateTime.h \
	 soGetErrno.h subcloneTTemplate.h sysdepend.h \
	 szGetTime.h tag.h templatesSortedByName.h \
	 textfield.h tracefile.h translateRWCString.h \
	 unpaddedFromPadded.h visibleLineForRestrictionFragments.h whatIsRunning.h \
	 wholeAssemblyItem.h wholeReadItem.h

compareOnePrimerAndOneSequence.o : \
	 assemblyViewTagTypeAndLine.h assert.h blockOfLocationsOfA4MerType.h \
	 bool.h compareOnePrimerAndOneSequence.cpp compareOnePrimerAndOneSequence.h \
	 consedParameters.h consedResources.h contigMatchTablesType.h \
	 filename.h mbtPtrOrderedVector.h mbtValOrderedVectorOfRWCString.h \
	 mbt_exception.h nFindScoreOfMatch.h nLengthOf4Mer.h \
	 primerType.h restrictionEnzyme.h rwcstring.h \
	 rwcsubstring.h rwdefs.h rwtptrorderedvector.h \
	 rwtptrorderedvector_inc.cpp rwtvalorderedvector.h rwtvalorderedvector_inc.cpp \
	 soEmptyString.h soGetErrno.h sysdepend.h \
	 whatIsRunning.h whyIsPrimerNotAcceptableTypes.h

complementSequence.o : \
	 cComplementBase.h cComplementBaseTable.h complementSequence.cpp \
	 complementSequence.h

complement_so.o : \
	 bool.h cComplementBase.h cComplementBaseTable.h \
	 complement_so.cpp rwcstring.h rwcsubstring.h \
	 rwdefs.h

consed.o : \
	 abs.h applyEditHistory.h arrayOfFwdRevPairLines.h \
	 arrayOfFwdRevPairSquares.h arrayOfFwdRevPairTriangles.h assembly.h \
	 assemblyView.h assemblyViewTagTypeAndLine.h assert.h \
	 autoFinishPurposes.h bEditHistoryFileExists.h bGuiGetAnswerYesNo.h \
	 bIntersect.h bIntervalsIntersect.h bIsNumericMaybeWithWhitespace.h \
	 basesegment.h blockOfLocationsOfA4MerType.h bool.h \
	 cComplementBase.h cComplementBaseTable.h choose_contig.h \
	 compareContigs.h compareContigsCursor.h compareContigsTypes.h \
	 consed.cpp consed.h consedParameters.h \
	 consedResources.h consed_version.h contig.h \
	 contigEnd.h contigMatchTablesType.h contigSegment.h \
	 contigview.h contigwin.h customNavigation.h \
	 deleteFileIfItExists.h dictionary.h distribution.h \
	 editCursor.h editaction.h experiment.h \
	 expidAndLocatedFragment.h filePopupAndGetAceFilename.h filePopupAndGetFilename.h \
	 filename.h fragment_and_contig.h fwdRevPair2.h \
	 fwdRevPairLine.h fwdRevPairSquare.h fwdRevPairTriangle.h \
	 gotoList.h gotoListType.h guiDisplayDigest.h \
	 guiMultiContigNavigator.h guiQuit.h guiQuitTypes.h \
	 guiTopWindow.h gui_search_for_string.h guiapp.h \
	 guicolortext.h guitedwin.h infobutton.h \
	 listOfFragments.h locatedFragment.h matchWithinAssembly.h \
	 max.h mbtPtrOrderedVector.h mbtPtrVector.h \
	 mbtValOrderedVectorOfRWCString.h mbtValVector.h mbtValVectorOfBool.h \
	 mbtValVector_inc.cpp mbt_exception.h mbt_val_ord_offset_vec.h \
	 min.h motifutils.h multiProblemGotoList.h \
	 nMAX_QUALITY_LEVEL2.h ntide.h numutil.h \
	 paddedFromUnpadded.h perhapsCreateSocketToControlConsed.h please_wait.h \
	 popupErrorMessage.h popupInfoOrErrorMessageNoFormat.h primerType.h \
	 quality.h readTypes.h readsSortedByLeftEndPosition.h \
	 readsSortedByReadName.h readsSortedByTemplateName.h restrictionEnzyme.h \
	 restrictionFragment.h restrictionFragmentMobility.h rwbtreedictionary.h \
	 rwcregexp.h rwcstring.h rwcsubstring.h \
	 rwdefs.h rwt2dptrvector.h rwtptrorderedvector.h \
	 rwtptrorderedvector_inc.cpp rwtptrsortedvector.h rwtptrvector.h \
	 rwtvalorderedvector.h rwtvalorderedvector_inc.cpp rwtvalsortedvector.h \
	 rwtvalvector.h selection.h seqMatch.h \
	 sequence.h singletInfo.h singletsSortedByTemplateName.h \
	 soEmptyString.h soGetErrno.h subcloneTTemplate.h \
	 sysdepend.h tag.h teditor.h \
	 teditor_types.h tedwin.h templatesSortedByName.h \
	 textbox.h textfield.h tracefile.h \
	 unpaddedFromPadded.h visibleLineForRestrictionFragments.h whatIsRunning.h \
	 whatToDoWithSelectionTypes.h wholeAssemblyItem.h wholeReadItem.h

consedParameters.o : \
	 assemblyViewTagTypeAndLine.h assert.h bIsNumericMaybeWithWhitespace.h \
	 bool.h consedParameters.cpp consedParameters.h \
	 consedResources.h filename.h guiFindRestrictionEnzymeSites.h \
	 guicolortext.h mbtPtrOrderedVector.h mbtValOrderedVectorOfRWCString.h \
	 mbt_exception.h nPrimerFalseMatchScoreArray.h restrictionEnzyme.h \
	 rwcregexp.h rwcstring.h rwcsubstring.h \
	 rwctokenizer.h rwdefs.h rwtptrorderedvector.h \
	 rwtptrorderedvector_inc.cpp rwtptrsortedvector.h rwtvalorderedvector.h \
	 rwtvalorderedvector_inc.cpp soEmptyString.h soGetErrno.h \
	 soLine.h sysdepend.h tagTypes.h \
	 whatIsRunning.h

consedParameters2.o : \
	 assemblyViewTagTypeAndLine.h assert.h bool.h \
	 consedParameters.h consedParameters2.cpp consedResources.h \
	 filename.h mbtPtrOrderedVector.h mbtValOrderedVectorOfRWCString.h \
	 mbt_exception.h readme.h restrictionEnzyme.h \
	 rwcstring.h rwcsubstring.h rwdefs.h \
	 rwtptrorderedvector.h rwtptrorderedvector_inc.cpp rwtvalorderedvector.h \
	 rwtvalorderedvector_inc.cpp soEmptyString.h soGetErrno.h \
	 sysdepend.h whatIsRunning.h

consedParameters3.o : \
	 assemblyViewTagTypeAndLine.h assert.h bool.h \
	 consedParameters.h consedParameters3.cpp consedResources.h \
	 filename.h mbtPtrOrderedVector.h mbtValOrderedVectorOfRWCString.h \
	 mbt_exception.h popupErrorMessage.h restrictionEnzyme.h \
	 restrictionEnzymes.h rwcstring.h rwcsubstring.h \
	 rwctokenizer.h rwdefs.h rwtptrorderedvector.h \
	 rwtptrorderedvector_inc.cpp rwtvalorderedvector.h rwtvalorderedvector_inc.cpp \
	 soEmptyString.h soGetErrno.h sysdepend.h \
	 whatIsRunning.h

consedResources.o : \
	 assert.h bIsNumericDouble.h bIsNumericMaybeWithWhitespace.h \
	 bool.h consedResources.cpp consedResources.h \
	 consed_version.h fallbackConsedResources.h filename.h \
	 mbt_exception.h rwcregexp.h rwcstring.h \
	 rwcsubstring.h rwdefs.h soGetErrno.h \
	 sysdepend.h

consedResources2.o : \
	 bool.h consedResources.h consedResources2.cpp \
	 filename.h rwcstring.h rwcsubstring.h \
	 rwdefs.h sysdepend.h

consedResources3.o : \
	 bool.h consedResources.h consedResources3.cpp \
	 filename.h rwcregexp.h rwcstring.h \
	 rwcsubstring.h rwdefs.h sysdepend.h

contig.o : \
	 abs.h assembly.h assemblyViewTagTypeAndLine.h \
	 assert.h autoFinishPurposes.h bGuiGetAnswerYesNo.h \
	 bIntersect.h bIntervalsIntersect.h bIsNumericMaybeWithWhitespace.h \
	 basesegment.h blockOfLocationsOfA4MerType.h bool.h \
	 cComplementBase.h cComplementBaseTable.h compareContigs.h \
	 compareContigsCursor.h compareContigsTypes.h consed.h \
	 consedParameters.h consedResources.h contig.cpp \
	 contig.h contigEnd.h contigMatchTablesType.h \
	 contigSegment.h contigview.h contigwin.h \
	 dErrorRateFromQuality.h dictionary.h distribution.h \
	 editCursor.h editaction.h exclusive_or.h \
	 experiment.h expidAndLocatedFragment.h fileDefines.h \
	 filename.h findRepeat.h gotoList.h \
	 gotoListType.h guiDisplayDigest.h guiMultiContigNavigator.h \
	 guiapp.h guicolortext.h guicontigwin.h \
	 infobutton.h listOfFragments.h locatedFragment.h \
	 lowconsqual.h matchWithinAssembly.h max.h \
	 mbtPtrOrderedVector.h mbtPtrVector.h mbtValOrderedVectorOfInt.h \
	 mbtValOrderedVectorOfRWCString.h mbtValVector.h mbtValVectorOfBool.h \
	 mbtValVector_inc.cpp mbt_errors.h mbt_exception.h \
	 mbt_val_ord_offset_vec.h min.h motifutils.h \
	 multiProblemGotoList.h nConvertFrom4Mer.h nFindScoreOfMatch.h \
	 nLengthOf4Mer.h nMAX_QUALITY_LEVEL2.h nNumberFromBase.h \
	 nNumberFromBase3.h ntide.h numutil.h \
	 paddedFromUnpadded.h popupErrorMessage.h popupInfoMessage.h \
	 primerType.h quality.h readTypes.h \
	 readsSortedByLeftEndPosition.h readsSortedByReadName.h readsSortedByTemplateName.h \
	 restrictionEnzyme.h restrictionFragment.h rwbtreedictionary.h \
	 rwcregexp.h rwcstring.h rwcsubstring.h \
	 rwdefs.h rwt2dvalvector.h rwtptrorderedvector.h \
	 rwtptrorderedvector_inc.cpp rwtptrsortedvector.h rwtptrvector.h \
	 rwtvalorderedvector.h rwtvalorderedvector_inc.cpp rwtvalsortedvector.h \
	 rwtvalvector.h selection.h sequence.h \
	 setMatchLookupTable.h singletInfo.h singletsSortedByTemplateName.h \
	 soAddCommas.h soEmptyString.h soGetDateTime.h \
	 soGetErrno.h subcloneTTemplate.h sysdepend.h \
	 tag.h templatesSortedByName.h textfield.h \
	 tracefile.h unalignedHighQualityRegionsGotoList.h unpaddedFromPadded.h \
	 visibleLineForRestrictionFragments.h whatIsRunning.h wholeAssemblyItem.h \
	 wholeReadItem.h whyIsPrimerNotAcceptableTypes.h

contig10.o : \
	 abs.h assembly.h assemblyViewTagTypeAndLine.h \
	 assert.h autoFinishPurposes.h autoReport.h \
	 bIntersect.h bIntervalsIntersect.h basesegment.h \
	 blockOfLocationsOfA4MerType.h bool.h cComplementBase.h \
	 cComplementBaseTable.h compareContigs.h compareContigsCursor.h \
	 compareContigsTypes.h consed.h consedParameters.h \
	 consedResources.h contig.h contig10.cpp \
	 contigEnd.h contigMatchTablesType.h contigSegment.h \
	 contigview.h contigwin.h dErrorRateFromQuality.h \
	 dictionary.h distribution.h editCursor.h \
	 editaction.h experiment.h expidAndLocatedFragment.h \
	 fileDefines.h filename.h findAncestralTrees.h \
	 getAllSinglets.h gotoList.h gotoListType.h \
	 guiDisplayDigest.h guiMultiContigNavigator.h guiapp.h \
	 guicolortext.h listOfFragments.h locatedFragment.h \
	 matchWithinAssembly.h max.h mbtPtrOrderedVector.h \
	 mbtPtrVector.h mbtValOrderedVectorOfRWCString.h mbtValVector.h \
	 mbtValVectorOfBool.h mbtValVector_inc.cpp mbt_exception.h \
	 mbt_val_ord_offset_vec.h min.h motifutils.h \
	 multiProblemGotoList.h nMAX_QUALITY_LEVEL2.h nNumberFromBase.h \
	 ntide.h numutil.h paddedFromUnpadded.h \
	 primateSpecies.h primerType.h quality.h \
	 readPHDAgainForHighQualitySegment.h readTypes.h readsSortedByLeftEndPosition.h \
	 readsSortedByReadName.h readsSortedByTemplateName.h restrictionEnzyme.h \
	 restrictionFragment.h rwbtreedictionary.h rwcregexp.h \
	 rwcstring.h rwcsubstring.h rwctokenizer.h \
	 rwdefs.h rwtptrorderedvector.h rwtptrorderedvector_inc.cpp \
	 rwtptrsortedvector.h rwtptrvector.h rwtvalorderedvector.h \
	 rwtvalorderedvector_inc.cpp rwtvalsortedvector.h rwtvalvector.h \
	 selection.h sequence.h setErrorRateFromQuality.h \
	 singletInfo.h singletsSortedByTemplateName.h soAddCommas.h \
	 soEmptyString.h soGetBranchNameWithoutTree.h soGetErrno.h \
	 soLine.h subcloneTTemplate.h sysdepend.h \
	 tag.h templatesSortedByName.h tracefile.h \
	 transitionsTransversions.h unpaddedFromPadded.h visibleLineForRestrictionFragments.h \
	 whatIsRunning.h wholeAssemblyItem.h wholeReadItem.h

contig11.o : \
	 abs.h assembly.h assemblyViewTagTypeAndLine.h \
	 assert.h autoFinishPurposes.h autoReport.h \
	 bIntersect.h bIntervalsIntersect.h basesegment.h \
	 blockOfLocationsOfA4MerType.h bool.h cComplementBase.h \
	 cComplementBaseTable.h compareContigs.h compareContigsCursor.h \
	 compareContigsTypes.h consed.h consedParameters.h \
	 consedResources.h contig.h contig11.cpp \
	 contigEnd.h contigMatchTablesType.h contigSegment.h \
	 contigview.h contigwin.h dErrorRateFromQuality.h \
	 dictionary.h distribution.h editCursor.h \
	 editaction.h experiment.h expidAndLocatedFragment.h \
	 fileDefines.h filename.h findAncestralTrees.h \
	 getAllSinglets.h gotoList.h gotoListType.h \
	 guiDisplayDigest.h guiMultiContigNavigator.h guiapp.h \
	 guicolortext.h listOfFragments.h locatedFragment.h \
	 matchWithinAssembly.h max.h mbtPtrOrderedVector.h \
	 mbtPtrVector.h mbtValOrderedVectorOfRWCString.h mbtValVector.h \
	 mbtValVectorOfBool.h mbtValVector_inc.cpp mbt_exception.h \
	 mbt_val_ord_offset_vec.h min.h motifutils.h \
	 multiProblemGotoList.h nMAX_QUALITY_LEVEL2.h nNumberFromBase.h \
	 ntide.h numutil.h paddedFromUnpadded.h \
	 primerType.h quality.h readPHDAgainForHighQualitySegment.h \
	 readTypes.h readsSortedByLeftEndPosition.h readsSortedByReadName.h \
	 readsSortedByTemplateName.h restrictionEnzyme.h restrictionFragment.h \
	 rwbtreedictionary.h rwcregexp.h rwcstring.h \
	 rwcsubstring.h rwctokenizer.h rwdefs.h \
	 rwtptrorderedvector.h rwtptrorderedvector_inc.cpp rwtptrsortedvector.h \
	 rwtptrvector.h rwtvalorderedvector.h rwtvalorderedvector_inc.cpp \
	 rwtvalsortedvector.h rwtvalvector.h selection.h \
	 sequence.h setErrorRateFromQuality.h singletInfo.h \
	 singletsSortedByTemplateName.h soAddCommas.h soEmptyString.h \
	 soGetErrno.h soLine.h subcloneTTemplate.h \
	 sysdepend.h tag.h templatesSortedByName.h \
	 tracefile.h transitionsTransversions.h unpaddedFromPadded.h \
	 visibleLineForRestrictionFragments.h whatIsRunning.h wholeAssemblyItem.h \
	 wholeReadItem.h

contig12.o : \
	 abs.h assembly.h assemblyViewTagTypeAndLine.h \
	 assert.h autoFinishPurposes.h autoReport.h \
	 bAllNeededSpecies.h bIntersect.h bIntervalsIntersect.h \
	 basesegment.h blockOfLocationsOfA4MerType.h bool.h \
	 cComplementBase.h cComplementBaseTable.h compareContigs.h \
	 compareContigsCursor.h compareContigsTypes.h consed.h \
	 consedParameters.h consedResources.h contig.h \
	 contig12.cpp contigEnd.h contigMatchTablesType.h \
	 contigSegment.h contigview.h contigwin.h \
	 dErrorRateFromQuality.h dictionary.h distribution.h \
	 editCursor.h editaction.h experiment.h \
	 expidAndLocatedFragment.h fileDefines.h filename.h \
	 findAncestralTrees.h getAllSinglets.h gotoList.h \
	 gotoListType.h guiDisplayDigest.h guiMultiContigNavigator.h \
	 guiapp.h guicolortext.h listOfFragments.h \
	 locatedFragment.h matchWithinAssembly.h max.h \
	 mbtPtrOrderedVector.h mbtPtrVector.h mbtValOrderedVectorOfRWCString.h \
	 mbtValVector.h mbtValVectorOfBool.h mbtValVector_inc.cpp \
	 mbt_exception.h mbt_val_ord_offset_vec.h min.h \
	 motifutils.h multiProblemGotoList.h nMAX_QUALITY_LEVEL2.h \
	 nNumberFromBase.h ntide.h numutil.h \
	 paddedFromUnpadded.h primateSpecies.h primerType.h \
	 quality.h readPHDAgainForHighQualitySegment.h readTypes.h \
	 readsSortedByLeftEndPosition.h readsSortedByReadName.h readsSortedByTemplateName.h \
	 restrictionEnzyme.h restrictionFragment.h rwbtreedictionary.h \
	 rwcregexp.h rwcstring.h rwcsubstring.h \
	 rwctokenizer.h rwdefs.h rwtptrorderedvector.h \
	 rwtptrorderedvector_inc.cpp rwtptrsortedvector.h rwtptrvector.h \
	 rwtvalorderedvector.h rwtvalorderedvector_inc.cpp rwtvalsortedvector.h \
	 rwtvalvector.h selection.h sequence.h \
	 setErrorRateFromQuality.h singletInfo.h singletsSortedByTemplateName.h \
	 soAddCommas.h soEmptyString.h soGetErrno.h \
	 soGetRequiredBases.h soLine.h subcloneTTemplate.h \
	 sysdepend.h tag.h templatesSortedByName.h \
	 tracefile.h ucGetMaskForSpecies.h unpaddedFromPadded.h \
	 visibleLineForRestrictionFragments.h whatIsRunning.h wholeAssemblyItem.h \
	 wholeReadItem.h

contig2.o : \
	 abs.h assembly.h assemblyViewTagTypeAndLine.h \
	 assert.h assignDistributions.h autoFinishPurposes.h \
	 bIntersect.h bIntervalsIntersect.h bIsTopStrandRead.h \
	 bPrimerHasMatchesAgainstSequencesInFile.h bPrimerHasMatchesElsewhere.h basesegment.h \
	 bigArrayOfLittleArraysOfDistributions.h blockOfLocationsOfA4MerType.h bool.h \
	 cComplementBase.h cComplementBaseTable.h checkPrimersForACGT.h \
	 checkPrimersForMononucleotideRepeats.h compareContigs.h compareContigsCursor.h \
	 compareContigsTypes.h consed.h consedParameters.h \
	 consedResources.h contig.h contig2.cpp \
	 contigEnd.h contigMatchTablesType.h contigSegment.h \
	 contigview.h contigwin.h createPrimerCandidatesWith3PrimeEnd.h \
	 dErrorRateFromQuality.h dGetErrorsFixedAtBase.h dictionary.h \
	 distribution.h dumpDistribution.h editCursor.h \
	 editaction.h experiment.h expidAndLocatedFragment.h \
	 fileDefines.h filename.h gotoList.h \
	 gotoListType.h guiDisplayDigest.h guiMultiContigNavigator.h \
	 guiapp.h guicolortext.h library.h \
	 listOfFragments.h locatedFragment.h makeDistributionAllOnes.h \
	 matchWithinAssembly.h max.h mbtPtrOrderedVector.h \
	 mbtPtrVector.h mbtValOrderedVectorOfRWCString.h mbtValVector.h \
	 mbtValVectorOfBool.h mbtValVector_inc.cpp mbt_exception.h \
	 mbt_val_ord_offset_vec.h min.h motifutils.h \
	 multiProblemGotoList.h multiplyDistributionWithMinimum.h multiplyDistributions.h \
	 multiplyDistributions2.h multiplyDistributions3.h nGetAmountOfOverlap.h \
	 nMAX_QUALITY_LEVEL2.h ntide.h numutil.h \
	 pFindShortestAcceptablePrimer.h paddedFromUnpadded.h please_wait.h \
	 primerType.h quality.h readTypes.h \
	 readsSortedByLeftEndPosition.h readsSortedByReadName.h readsSortedByTemplateName.h \
	 restrictionEnzyme.h restrictionFragment.h rwbtreedictionary.h \
	 rwcstring.h rwcsubstring.h rwdefs.h \
	 rwtptrorderedvector.h rwtptrorderedvector_inc.cpp rwtptrsortedvector.h \
	 rwtptrvector.h rwtvalorderedvector.h rwtvalorderedvector_inc.cpp \
	 rwtvalsortedvector.h rwtvalvector.h selection.h \
	 sequence.h singletInfo.h singletsSortedByTemplateName.h \
	 soEmptyString.h soGetErrno.h subcloneTTemplate.h \
	 sysdepend.h tag.h templatesSortedByName.h \
	 tracefile.h ucGetReadType.h unpaddedFromPadded.h \
	 visibleLineForRestrictionFragments.h whatIsRunning.h whichPrimersHaveAcceptableMeltingTemp.h \
	 whichPrimersHaveAcceptableSelfMatch.h wholeAssemblyItem.h wholeReadItem.h \
	 whyIsPrimerNotAcceptableTypes.h

contig4.o : \
	 abs.h assembly.h assemblyViewTagTypeAndLine.h \
	 assert.h autoFinishPurposes.h bIntersect.h \
	 bIntervalsIntersect.h basesegment.h blockOfLocationsOfA4MerType.h \
	 bool.h cComplementBase.h cComplementBaseTable.h \
	 compareContigs.h compareContigsCursor.h compareContigsTypes.h \
	 consed.h consedParameters.h consedResources.h \
	 contig.h contig4.cpp contigEnd.h \
	 contigMatchTablesType.h contigSegment.h contigview.h \
	 contigwin.h dictionary.h distribution.h \
	 editCursor.h editaction.h experiment.h \
	 expidAndLocatedFragment.h fileDefines.h filename.h \
	 gotoList.h gotoListType.h guiDisplayDigest.h \
	 guiMultiContigNavigator.h guiapp.h guicolortext.h \
	 listOfFragments.h locatedFragment.h matchWithinAssembly.h \
	 max.h mbtPtrOrderedVector.h mbtPtrVector.h \
	 mbtValOrderedVectorOfRWCString.h mbtValVector.h mbtValVectorOfBool.h \
	 mbtValVector_inc.cpp mbt_exception.h mbt_val_ord_offset_vec.h \
	 min.h motifutils.h multiProblemGotoList.h \
	 nMAX_QUALITY_LEVEL2.h ntide.h numutil.h \
	 paddedFromUnpadded.h primerType.h quality.h \
	 readTypes.h readsSortedByLeftEndPosition.h readsSortedByReadName.h \
	 readsSortedByTemplateName.h restrictionEnzyme.h restrictionFragment.h \
	 rwbtreedictionary.h rwcstring.h rwcsubstring.h \
	 rwdefs.h rwtptrorderedvector.h rwtptrorderedvector_inc.cpp \
	 rwtptrsortedvector.h rwtptrvector.h rwtvalorderedvector.h \
	 rwtvalorderedvector_inc.cpp rwtvalsortedvector.h rwtvalvector.h \
	 selection.h sequence.h singletInfo.h \
	 singletsSortedByTemplateName.h soEmptyString.h soGetErrno.h \
	 subcloneTTemplate.h sysdepend.h tag.h \
	 templatesSortedByName.h tracefile.h unpaddedFromPadded.h \
	 visibleLineForRestrictionFragments.h whatIsRunning.h wholeAssemblyItem.h \
	 wholeReadItem.h

contig5.o : \
	 abs.h assembly.h assemblyViewTagTypeAndLine.h \
	 assert.h autoFinishExpTag.h autoFinishPurposes.h \
	 bIntersect.h bIntervalsIntersect.h basesegment.h \
	 blockOfLocationsOfA4MerType.h bool.h cComplementBase.h \
	 cComplementBaseTable.h compareContigs.h compareContigsCursor.h \
	 compareContigsTypes.h consed.h consedParameters.h \
	 consedResources.h contig.h contig5.cpp \
	 contigEnd.h contigEndPair.h contigMatchTablesType.h \
	 contigSegment.h contigview.h contigwin.h \
	 dictionary.h distribution.h editCursor.h \
	 editaction.h experiment.h expidAndLocatedFragment.h \
	 fileDefines.h filename.h gotoList.h \
	 gotoListType.h guiDisplayDigest.h guiMultiContigNavigator.h \
	 guiapp.h guicolortext.h library.h \
	 listOfFragments.h listOfLibraries.h locatedFragment.h \
	 matchWithinAssembly.h max.h mbtPtrOrderedVector.h \
	 mbtPtrVector.h mbtValOrderedVectorOfRWCString.h mbtValVector.h \
	 mbtValVectorOfBool.h mbtValVector_inc.cpp mbt_exception.h \
	 mbt_val_ord_offset_vec.h min.h motifutils.h \
	 multiProblemGotoList.h nMAX_QUALITY_LEVEL2.h ntide.h \
	 numutil.h paddedFromUnpadded.h primerType.h \
	 quality.h readTypes.h readsSortedByLeftEndPosition.h \
	 readsSortedByReadName.h readsSortedByTemplateName.h restrictionEnzyme.h \
	 restrictionFragment.h rwbtreedictionary.h rwcstring.h \
	 rwcsubstring.h rwdefs.h rwtptrorderedvector.h \
	 rwtptrorderedvector_inc.cpp rwtptrsortedvector.h rwtptrvector.h \
	 rwtvalorderedvector.h rwtvalorderedvector_inc.cpp rwtvalsortedvector.h \
	 rwtvalvector.h selection.h sequence.h \
	 singletInfo.h singletsSortedByTemplateName.h soEmptyString.h \
	 soGetErrno.h subcloneTTemplate.h sysdepend.h \
	 tag.h templateForMinilibrary.h templatesSortedByName.h \
	 tracefile.h unpaddedFromPadded.h visibleLineForRestrictionFragments.h \
	 whatIsRunning.h wholeAssemblyItem.h wholeReadItem.h

contig6.o : \
	 abs.h assembly.h assemblyViewTagTypeAndLine.h \
	 assert.h autoFinishPurposes.h bGuiGetAnswerYesNo.h \
	 bIntersect.h bIntervalsIntersect.h basesegment.h \
	 blockOfLocationsOfA4MerType.h bool.h cComplementBase.h \
	 cComplementBaseTable.h compareContigs.h compareContigsCursor.h \
	 compareContigsTypes.h consed.h consedParameters.h \
	 consedResources.h contig.h contig6.cpp \
	 contigEnd.h contigMatchTablesType.h contigSegment.h \
	 contigview.h contigwin.h dictionary.h \
	 distribution.h editCursor.h editaction.h \
	 experiment.h expidAndLocatedFragment.h filename.h \
	 gotoList.h gotoListType.h guiDisplayDigest.h \
	 guiMultiContigNavigator.h guiapp.h guicolortext.h \
	 guicontigwin.h infobutton.h listOfFragments.h \
	 locatedFragment.h matchWithinAssembly.h max.h \
	 mbtPtrOrderedVector.h mbtPtrVector.h mbtValOrderedVectorOfRWCString.h \
	 mbtValVector.h mbtValVectorOfBool.h mbtValVector_inc.cpp \
	 mbt_exception.h mbt_val_ord_offset_vec.h min.h \
	 motifutils.h multiProblemGotoList.h nMAX_QUALITY_LEVEL2.h \
	 newContig.h ntide.h numutil.h \
	 paddedFromUnpadded.h please_wait.h popupErrorMessage.h \
	 popupInfoMessage.h primerType.h quality.h \
	 readTypes.h readsSortedByLeftEndPosition.h readsSortedByReadName.h \
	 readsSortedByTemplateName.h restrictionEnzyme.h restrictionFragment.h \
	 rwbtreedictionary.h rwcstring.h rwcsubstring.h \
	 rwdefs.h rwtptrorderedvector.h rwtptrorderedvector_inc.cpp \
	 rwtptrsortedvector.h rwtptrvector.h rwtvalorderedvector.h \
	 rwtvalorderedvector_inc.cpp rwtvalsortedvector.h rwtvalvector.h \
	 selection.h sequence.h singletInfo.h \
	 singletsSortedByTemplateName.h soEmptyString.h soGetErrno.h \
	 subcloneTTemplate.h sysdepend.h tag.h \
	 templatesSortedByName.h textfield.h tracefile.h \
	 unpaddedFromPadded.h visibleLineForRestrictionFragments.h whatIsRunning.h \
	 wholeAssemblyItem.h wholeReadItem.h

contig7.o : \
	 abs.h assembly.h assemblyViewTagTypeAndLine.h \
	 assert.h autoFinishPurposes.h autoReport.h \
	 bIntersect.h bIntervalsIntersect.h basesegment.h \
	 blockOfLocationsOfA4MerType.h bool.h cComplementBase.h \
	 cComplementBaseTable.h compareContigs.h compareContigsCursor.h \
	 compareContigsTypes.h consed.h consedParameters.h \
	 consedResources.h contig.h contig7.cpp \
	 contigEnd.h contigMatchTablesType.h contigSegment.h \
	 contigview.h contigwin.h dErrorRateFromQuality.h \
	 dictionary.h distribution.h editCursor.h \
	 editaction.h experiment.h expidAndLocatedFragment.h \
	 fileDefines.h filename.h getAllSinglets.h \
	 gotoList.h gotoListType.h guiDisplayDigest.h \
	 guiMultiContigNavigator.h guiapp.h guicolortext.h \
	 listOfFragments.h locatedFragment.h matchWithinAssembly.h \
	 max.h mbtPtrOrderedVector.h mbtPtrVector.h \
	 mbtValOrderedVectorOfRWCString.h mbtValVector.h mbtValVectorOfBool.h \
	 mbtValVector_inc.cpp mbt_exception.h mbt_val_ord_offset_vec.h \
	 min.h motifutils.h multiProblemGotoList.h \
	 nMAX_QUALITY_LEVEL2.h nNumberFromBase.h ntide.h \
	 numutil.h paddedFromUnpadded.h primerType.h \
	 quality.h readPHDAgainForHighQualitySegment.h readTypes.h \
	 readsSortedByLeftEndPosition.h readsSortedByReadName.h readsSortedByTemplateName.h \
	 restrictionEnzyme.h restrictionFragment.h rwbtreedictionary.h \
	 rwcregexp.h rwcstring.h rwcsubstring.h \
	 rwctokenizer.h rwdefs.h rwtptrorderedvector.h \
	 rwtptrorderedvector_inc.cpp rwtptrsortedvector.h rwtptrvector.h \
	 rwtvalorderedvector.h rwtvalorderedvector_inc.cpp rwtvalsortedvector.h \
	 rwtvalvector.h selection.h sequence.h \
	 setErrorRateFromQuality.h singletInfo.h singletsSortedByTemplateName.h \
	 soAddCommas.h soEmptyString.h soGetErrno.h \
	 soLine.h subcloneTTemplate.h sysdepend.h \
	 tag.h templatesSortedByName.h tracefile.h \
	 unpaddedFromPadded.h visibleLineForRestrictionFragments.h whatIsRunning.h \
	 wholeAssemblyItem.h wholeReadItem.h

contig8.o : \
	 abs.h assembly.h assemblyViewTagTypeAndLine.h \
	 assert.h autoFinishPurposes.h autoReport.h \
	 bAllNeededSpecies.h bIntersect.h bIntervalsIntersect.h \
	 basesegment.h blockOfLocationsOfA4MerType.h bool.h \
	 cComplementBase.h cComplementBaseTable.h compareContigs.h \
	 compareContigsCursor.h compareContigsTypes.h consed.h \
	 consedParameters.h consedResources.h contig.h \
	 contig8.cpp contigEnd.h contigMatchTablesType.h \
	 contigSegment.h contigview.h contigwin.h \
	 dErrorRateFromQuality.h dictionary.h distribution.h \
	 editCursor.h editaction.h experiment.h \
	 expidAndLocatedFragment.h fileDefines.h filename.h \
	 findAncestralTrees.h getAllSinglets.h gotoList.h \
	 gotoListType.h guiDisplayDigest.h guiMultiContigNavigator.h \
	 guiapp.h guicolortext.h listOfFragments.h \
	 locatedFragment.h matchWithinAssembly.h max.h \
	 mbtPtrOrderedVector.h mbtPtrVector.h mbtValOrderedVectorOfRWCString.h \
	 mbtValVector.h mbtValVectorOfBool.h mbtValVector_inc.cpp \
	 mbt_exception.h mbt_val_ord_offset_vec.h min.h \
	 motifutils.h multiProblemGotoList.h nMAX_QUALITY_LEVEL2.h \
	 nNumberFromBase.h ntide.h numutil.h \
	 paddedFromUnpadded.h primateSpecies.h primerType.h \
	 quality.h readPHDAgainForHighQualitySegment.h readTypes.h \
	 readsSortedByLeftEndPosition.h readsSortedByReadName.h readsSortedByTemplateName.h \
	 restrictionEnzyme.h restrictionFragment.h rwbtreedictionary.h \
	 rwcregexp.h rwcstring.h rwcsubstring.h \
	 rwctokenizer.h rwdefs.h rwtptrorderedvector.h \
	 rwtptrorderedvector_inc.cpp rwtptrsortedvector.h rwtptrvector.h \
	 rwtvalorderedvector.h rwtvalorderedvector_inc.cpp rwtvalsortedvector.h \
	 rwtvalvector.h selection.h sequence.h \
	 setErrorRateFromQuality.h singletInfo.h singletsSortedByTemplateName.h \
	 soAddCommas.h soEmptyString.h soGetErrno.h \
	 soLine.h subcloneTTemplate.h sysdepend.h \
	 tag.h templatesSortedByName.h tracefile.h \
	 ucGetMaskForSpecies.h unpaddedFromPadded.h visibleLineForRestrictionFragments.h \
	 whatIsRunning.h wholeAssemblyItem.h wholeReadItem.h

contig9.o : \
	 abs.h assembly.h assemblyViewTagTypeAndLine.h \
	 assert.h autoFinishPurposes.h autoReport.h \
	 bAllNeededSpecies.h bIntersect.h bIntervalsIntersect.h \
	 basesegment.h blockOfLocationsOfA4MerType.h bool.h \
	 cComplementBase.h cComplementBaseTable.h compareContigs.h \
	 compareContigsCursor.h compareContigsTypes.h consed.h \
	 consedParameters.h consedResources.h contig.h \
	 contig9.cpp contigEnd.h contigMatchTablesType.h \
	 contigSegment.h contigview.h contigwin.h \
	 dErrorRateFromQuality.h dictionary.h distribution.h \
	 editCursor.h editaction.h experiment.h \
	 expidAndLocatedFragment.h fileDefines.h filename.h \
	 findAncestralTrees.h getAllSinglets.h gotoList.h \
	 gotoListType.h guiDisplayDigest.h guiMultiContigNavigator.h \
	 guiapp.h guicolortext.h kimuraBranchProb.h \
	 listOfFragments.h locatedFragment.h matchWithinAssembly.h \
	 max.h mbtPtrOrderedVector.h mbtPtrVector.h \
	 mbtValOrderedVectorOfRWCString.h mbtValVector.h mbtValVectorOfBool.h \
	 mbtValVector_inc.cpp mbt_exception.h mbt_val_ord_offset_vec.h \
	 min.h motifutils.h multiProblemGotoList.h \
	 nMAX_QUALITY_LEVEL2.h nNumberFromBase.h ntide.h \
	 numutil.h paddedFromUnpadded.h primateSpecies.h \
	 primerType.h quality.h readPHDAgainForHighQualitySegment.h \
	 readTypes.h readsSortedByLeftEndPosition.h readsSortedByReadName.h \
	 readsSortedByTemplateName.h restrictionEnzyme.h restrictionFragment.h \
	 rwbtreedictionary.h rwcregexp.h rwcstring.h \
	 rwcsubstring.h rwctokenizer.h rwdefs.h \
	 rwtptrorderedvector.h rwtptrorderedvector_inc.cpp rwtptrsortedvector.h \
	 rwtptrvector.h rwtvalorderedvector.h rwtvalorderedvector_inc.cpp \
	 rwtvalsortedvector.h rwtvalvector.h selection.h \
	 sequence.h setErrorRateFromQuality.h singletInfo.h \
	 singletsSortedByTemplateName.h soAddCommas.h soEmptyString.h \
	 soGetBranchNameWithoutTree.h soGetErrno.h soLine.h \
	 subcloneTTemplate.h sysdepend.h tag.h \
	 templatesSortedByName.h tracefile.h ucGetMaskForSpecies.h \
	 unpaddedFromPadded.h visibleLineForRestrictionFragments.h whatIsRunning.h \
	 wholeAssemblyItem.h wholeReadItem.h

contigEndPair.o : \
	 assemblyViewTagTypeAndLine.h assert.h autoFinishPurposes.h \
	 basesegment.h blockOfLocationsOfA4MerType.h bool.h \
	 cComplementBase.h cComplementBaseTable.h consedParameters.h \
	 consedResources.h contig.h contigEnd.h \
	 contigEndPair.cpp contigEndPair.h contigMatchTablesType.h \
	 dictionary.h distribution.h experiment.h \
	 filename.h locatedFragment.h mbtPtrOrderedVector.h \
	 mbtPtrVector.h mbtValOrderedVectorOfRWCString.h mbtValVector.h \
	 mbtValVectorOfBool.h mbtValVector_inc.cpp mbt_exception.h \
	 mbt_val_ord_offset_vec.h min.h nMAX_QUALITY_LEVEL2.h \
	 ntide.h paddedFromUnpadded.h primerType.h \
	 quality.h readTypes.h readsSortedByLeftEndPosition.h \
	 readsSortedByReadName.h restrictionEnzyme.h rwbtreedictionary.h \
	 rwcstring.h rwcsubstring.h rwdefs.h \
	 rwtptrorderedvector.h rwtptrorderedvector_inc.cpp rwtptrsortedvector.h \
	 rwtptrvector.h rwtvalorderedvector.h rwtvalorderedvector_inc.cpp \
	 rwtvalsortedvector.h rwtvalvector.h sequence.h \
	 soEmptyString.h soGetErrno.h subcloneTTemplate.h \
	 sysdepend.h tag.h tracefile.h \
	 unpaddedFromPadded.h whatIsRunning.h wholeReadItem.h

contigEndReadList.o : \
	 assemblyViewTagTypeAndLine.h assert.h autoFinishPurposes.h \
	 basesegment.h blockOfLocationsOfA4MerType.h bool.h \
	 cComplementBase.h cComplementBaseTable.h consedParameters.h \
	 consedResources.h contig.h contigEnd.h \
	 contigEndReadList.cpp contigEndReadList.h contigMatchTablesType.h \
	 dictionary.h distribution.h experiment.h \
	 filename.h locatedFragment.h mbtPtrOrderedVector.h \
	 mbtPtrVector.h mbtValOrderedVectorOfRWCString.h mbtValVector.h \
	 mbtValVectorOfBool.h mbtValVector_inc.cpp mbt_exception.h \
	 mbt_val_ord_offset_vec.h min.h nMAX_QUALITY_LEVEL2.h \
	 ntide.h paddedFromUnpadded.h primerType.h \
	 quality.h readTypes.h readsSortedByLeftEndPosition.h \
	 readsSortedByReadName.h restrictionEnzyme.h rwbtreedictionary.h \
	 rwcstring.h rwcsubstring.h rwdefs.h \
	 rwtptrorderedvector.h rwtptrorderedvector_inc.cpp rwtptrsortedvector.h \
	 rwtptrvector.h rwtvalorderedvector.h rwtvalorderedvector_inc.cpp \
	 rwtvalsortedvector.h rwtvalvector.h sequence.h \
	 soEmptyString.h soGetErrno.h subcloneTTemplate.h \
	 sysdepend.h tag.h tracefile.h \
	 unpaddedFromPadded.h whatIsRunning.h wholeReadItem.h

contigview.o : \
	 abs.h assembly.h assemblyViewTagTypeAndLine.h \
	 assert.h autoFinishPurposes.h bIntersect.h \
	 bIntervalsIntersect.h basesegment.h blockOfLocationsOfA4MerType.h \
	 bool.h cComplementBase.h cComplementBaseTable.h \
	 cGetProtein.h compareContigs.h compareContigsCursor.h \
	 compareContigsTypes.h consed.h consedParameters.h \
	 consedResources.h contig.h contigEnd.h \
	 contigMatchTablesType.h contigSegment.h contigview.cpp \
	 contigview.h contigwin.h dictionary.h \
	 distribution.h editActionChangeRead.h editCursor.h \
	 editMakeHighQuality.h editaction.h experiment.h \
	 expidAndLocatedFragment.h filename.h gotoList.h \
	 gotoListType.h guiDisplayDigest.h guiMultiContigNavigator.h \
	 guiapp.h guicolortext.h guicontigwin.h \
	 infobutton.h listOfFragments.h locatedFragment.h \
	 matchWithinAssembly.h max.h mbtPtrOrderedVector.h \
	 mbtPtrVector.h mbtValOrderedVectorOfRWCString.h mbtValVector.h \
	 mbtValVectorOfBool.h mbtValVector_inc.cpp mbt_exception.h \
	 mbt_val_ord_offset_vec.h min.h motifutils.h \
	 multiProblemGotoList.h nMAX_QUALITY_LEVEL2.h ntide.h \
	 numutil.h paddedFromUnpadded.h popupErrorMessage2.h \
	 primerType.h quality.h readTypes.h \
	 readsSortedByLeftEndPosition.h readsSortedByReadName.h readsSortedByTemplateName.h \
	 restrictionEnzyme.h restrictionFragment.h rwbtreedictionary.h \
	 rwcstring.h rwcsubstring.h rwdefs.h \
	 rwtptrorderedvector.h rwtptrorderedvector_inc.cpp rwtptrsortedvector.h \
	 rwtptrvector.h rwtvalorderedvector.h rwtvalorderedvector_inc.cpp \
	 rwtvalsortedvector.h rwtvalvector.h selection.h \
	 sequence.h singletInfo.h singletsSortedByTemplateName.h \
	 soEmptyString.h soGetErrno.h subcloneTTemplate.h \
	 sysdepend.h tag.h templatesSortedByName.h \
	 textfield.h tracefile.h unpaddedFromPadded.h \
	 visibleLineForRestrictionFragments.h whatIsRunning.h wholeAssemblyItem.h \
	 wholeReadItem.h

contigwin.o : \
	 abs.h assembly.h assemblyViewTagTypeAndLine.h \
	 assert.h autoFinishPurposes.h bErrorMessageIfNoPhd.h \
	 bGuiGetAnswerYesNo.h bIntersect.h bIntervalsIntersect.h \
	 bIsNumericMaybeWithWhitespace.h basesegment.h blockOfLocationsOfA4MerType.h \
	 bool.h cComplementBase.h cComplementBaseTable.h \
	 colormode.h compareContigs.h compareContigsCursor.h \
	 compareContigsTypes.h consed.h consedParameters.h \
	 consedResources.h contig.h contigEnd.h \
	 contigMatchTablesType.h contigSegment.h contigview.h \
	 contigwin.cpp contigwin.h createUnalignedHighQualityNavigator.h \
	 dictionary.h distribution.h editActionChangeRead.h \
	 editAddConsensusTag.h editAddReadTag.h editAddTagsToAllReadsAtConsPos.h \
	 editChangeToNs.h editChangeToXs.h editCursor.h \
	 editMakeHighQuality.h editOverstrikeAllReadsAtConsPos.h editOverstrikeConsensus.h \
	 edit_complement_contig.h editaction.h editedButNotNsGotoList.h \
	 editedGotoList.h experiment.h expidAndLocatedFragment.h \
	 filePopupAndGetFilename.h filename.h fileselector.h \
	 gotoList.h gotoListType.h guiDisplayDigest.h \
	 guiGetReferenceRead.h guiGetTagType.h guiMultiContigNavigator.h \
	 guiPopupTagInfo.h guiTearContig.h guiapp.h \
	 guicolortext.h guicontigwin.h guiteditor.h \
	 guitedwin.h highQualityDiscrepancyGotoList.h infobutton.h \
	 library.h listOfFragments.h locatedFragment.h \
	 lowconsqual.h matchWithinAssembly.h max.h \
	 mbtPtrOrderedVector.h mbtPtrVector.h mbtValOrderedVectorOfRWCString.h \
	 mbtValVector.h mbtValVectorOfBool.h mbtValVector_inc.cpp \
	 mbt_errors.h mbt_exception.h mbt_val_ord_offset_vec.h \
	 min.h motifutils.h multiProblemGotoList.h \
	 nMAX_QUALITY_LEVEL2.h nNumberFromBase4.h ntide.h \
	 numutil.h oligoTag.h paddedFromUnpadded.h \
	 pickPrimers.h please_wait.h popupErrorMessage.h \
	 popupErrorMessage2.h popupInfoMessage.h primerType.h \
	 quality.h readTypes.h readsSortedByLeftEndPosition.h \
	 readsSortedByReadName.h readsSortedByTemplateName.h restrictionEnzyme.h \
	 restrictionFragment.h rwbtreedictionary.h rwcstring.h \
	 rwcsubstring.h rwdefs.h rwtptrorderedvector.h \
	 rwtptrorderedvector_inc.cpp rwtptrsortedvector.h rwtptrvector.h \
	 rwtvalorderedvector.h rwtvalorderedvector_inc.cpp rwtvalsortedvector.h \
	 rwtvalvector.h selection.h sequence.h \
	 singletInfo.h singletsSortedByTemplateName.h soAddCommas.h \
	 soEmptyString.h soGetErrno.h subcloneTTemplate.h \
	 sysdepend.h tag.h tagTypes.h \
	 tagsGotoList.h teditor.h teditor_types.h \
	 tedwin.h templatesSortedByName.h textbox.h \
	 textfield.h tracefile.h unpaddedFromPadded.h \
	 visibleLineForRestrictionFragments.h whatIsRunning.h whatToDoWithSelectionTypes.h \
	 wholeAssemblyItem.h wholeReadItem.h

copyFiles.o : \
	 bool.h copyFiles.cpp copyFiles.h \
	 filename.h mbt_exception.h rwcstring.h \
	 rwcsubstring.h rwdefs.h soGetErrno.h \
	 sysdepend.h

copyPrimerMatchesFromShorterToLongerPrimers.o : \
	 assemblyViewTagTypeAndLine.h assert.h blockOfLocationsOfA4MerType.h \
	 bool.h consedParameters.h consedResources.h \
	 contigMatchTablesType.h copyPrimerMatchesFromShorterToLongerPrimers.cpp copyPrimerMatchesFromShorterToLongerPrimers.h \
	 filename.h mbtPtrOrderedVector.h mbtValOrderedVectorOfRWCString.h \
	 mbt_exception.h primerType.h restrictionEnzyme.h \
	 rwcstring.h rwcsubstring.h rwdefs.h \
	 rwtptrorderedvector.h rwtptrorderedvector_inc.cpp rwtvalorderedvector.h \
	 rwtvalorderedvector_inc.cpp soEmptyString.h soGetErrno.h \
	 sortPrimersByEndPosition.h sortPrimersByStartPosition.h sysdepend.h \
	 whatIsRunning.h

countsOfWhyPrimersAreNotAcceptable.o : \
	 assert.h blockOfLocationsOfA4MerType.h bool.h \
	 contigMatchTablesType.h countsOfWhyPrimersAreNotAcceptable.cpp countsOfWhyPrimersAreNotAcceptable.h \
	 mbt_exception.h primerType.h rwcstring.h \
	 rwcsubstring.h rwdefs.h soGetErrno.h \
	 whyIsPrimerNotAcceptableTypes.h

createPrimerCandidate.o : \
	 assemblyViewTagTypeAndLine.h assert.h autoFinishPurposes.h \
	 basesegment.h blockOfLocationsOfA4MerType.h bool.h \
	 cComplementBase.h cComplementBaseTable.h complementSequence.h \
	 consedParameters.h consedResources.h contig.h \
	 contigEnd.h contigMatchTablesType.h createPrimerCandidate.cpp \
	 createPrimerCandidate.h dictionary.h distribution.h \
	 experiment.h filename.h locatedFragment.h \
	 mbtPtrOrderedVector.h mbtPtrVector.h mbtValOrderedVectorOfRWCString.h \
	 mbtValVector.h mbtValVectorOfBool.h mbtValVector_inc.cpp \
	 mbt_exception.h mbt_val_ord_offset_vec.h min.h \
	 nConvertFrom4Mer.h nLengthOf4Mer.h nMAX_QUALITY_LEVEL2.h \
	 nNumberFromBase.h ntide.h paddedFromUnpadded.h \
	 primerType.h quality.h readTypes.h \
	 readsSortedByLeftEndPosition.h readsSortedByReadName.h restrictionEnzyme.h \
	 rwbtreedictionary.h rwcstring.h rwcsubstring.h \
	 rwdefs.h rwtptrorderedvector.h rwtptrorderedvector_inc.cpp \
	 rwtptrsortedvector.h rwtptrvector.h rwtvalorderedvector.h \
	 rwtvalorderedvector_inc.cpp rwtvalsortedvector.h rwtvalvector.h \
	 sequence.h soEmptyString.h soGetErrno.h \
	 subcloneTTemplate.h sysdepend.h tag.h \
	 tracefile.h unpaddedFromPadded.h whatIsRunning.h \
	 wholeReadItem.h whyIsPrimerNotAcceptableTypes.h

createPrimerCandidates.o : \
	 abs.h assemblyViewTagTypeAndLine.h assert.h \
	 autoFinishPurposes.h bIntersect.h bIntervalsIntersect.h \
	 basesegment.h blockOfLocationsOfA4MerType.h bool.h \
	 cComplementBase.h cComplementBaseTable.h consedParameters.h \
	 consedResources.h contig.h contigEnd.h \
	 contigMatchTablesType.h createPrimerCandidate.h createPrimerCandidates.cpp \
	 dictionary.h distribution.h experiment.h \
	 filename.h locatedFragment.h max.h \
	 mbtPtrOrderedVector.h mbtPtrVector.h mbtValOrderedVectorOfRWCString.h \
	 mbtValVector.h mbtValVectorOfBool.h mbtValVector_inc.cpp \
	 mbt_exception.h mbt_val_ord_offset_vec.h min.h \
	 nMAX_QUALITY_LEVEL2.h ntide.h numutil.h \
	 paddedFromUnpadded.h primerType.h quality.h \
	 readTypes.h readsSortedByLeftEndPosition.h readsSortedByReadName.h \
	 restrictionEnzyme.h rwbtreedictionary.h rwcstring.h \
	 rwcsubstring.h rwdefs.h rwtptrorderedvector.h \
	 rwtptrorderedvector_inc.cpp rwtptrsortedvector.h rwtptrvector.h \
	 rwtvalorderedvector.h rwtvalorderedvector_inc.cpp rwtvalsortedvector.h \
	 rwtvalvector.h sequence.h soEmptyString.h \
	 soGetErrno.h subcloneTTemplate.h sysdepend.h \
	 tag.h tracefile.h unpaddedFromPadded.h \
	 whatIsRunning.h wholeReadItem.h

createPrimerCandidatesWith3PrimeEnd.o : \
	 abs.h assemblyViewTagTypeAndLine.h assert.h \
	 autoFinishPurposes.h bIntersect.h bIntervalsIntersect.h \
	 basesegment.h blockOfLocationsOfA4MerType.h bool.h \
	 cComplementBase.h cComplementBaseTable.h consedParameters.h \
	 consedResources.h contig.h contigEnd.h \
	 contigMatchTablesType.h createPrimerCandidate.h createPrimerCandidatesWith3PrimeEnd.cpp \
	 createPrimerCandidatesWith3PrimeEnd.h dictionary.h distribution.h \
	 experiment.h filename.h locatedFragment.h \
	 max.h mbtPtrOrderedVector.h mbtPtrVector.h \
	 mbtValOrderedVectorOfRWCString.h mbtValVector.h mbtValVectorOfBool.h \
	 mbtValVector_inc.cpp mbt_exception.h mbt_val_ord_offset_vec.h \
	 min.h nMAX_QUALITY_LEVEL2.h ntide.h \
	 numutil.h paddedFromUnpadded.h primerType.h \
	 quality.h readTypes.h readsSortedByLeftEndPosition.h \
	 readsSortedByReadName.h restrictionEnzyme.h rwbtreedictionary.h \
	 rwcstring.h rwcsubstring.h rwdefs.h \
	 rwtptrorderedvector.h rwtptrorderedvector_inc.cpp rwtptrsortedvector.h \
	 rwtptrvector.h rwtvalorderedvector.h rwtvalorderedvector_inc.cpp \
	 rwtvalsortedvector.h rwtvalvector.h sequence.h \
	 soEmptyString.h soGetErrno.h subcloneTTemplate.h \
	 sysdepend.h tag.h tracefile.h \
	 unpaddedFromPadded.h whatIsRunning.h wholeReadItem.h

createTearTags.o : \
	 abs.h assembly.h assemblyViewTagTypeAndLine.h \
	 assert.h autoFinishPurposes.h bIntersect.h \
	 bIntervalsIntersect.h basesegment.h blockOfLocationsOfA4MerType.h \
	 bool.h cComplementBase.h cComplementBaseTable.h \
	 compareContigs.h compareContigsCursor.h compareContigsTypes.h \
	 consed.h consedParameters.h consedResources.h \
	 contig.h contigEnd.h contigMatchTablesType.h \
	 contigSegment.h contigview.h contigwin.h \
	 createTearTags.cpp createTearTags.h dictionary.h \
	 distribution.h editCursor.h editaction.h \
	 experiment.h expidAndLocatedFragment.h filename.h \
	 gotoList.h gotoListType.h guiDisplayDigest.h \
	 guiMultiContigNavigator.h guiapp.h guicolortext.h \
	 listOfFragments.h locatedFragment.h matchWithinAssembly.h \
	 max.h mbtPtrOrderedVector.h mbtPtrVector.h \
	 mbtValOrderedVectorOfRWCString.h mbtValVector.h mbtValVectorOfBool.h \
	 mbtValVector_inc.cpp mbt_exception.h mbt_val_ord_offset_vec.h \
	 min.h motifutils.h multiProblemGotoList.h \
	 nMAX_QUALITY_LEVEL2.h ntide.h numutil.h \
	 paddedFromUnpadded.h primerType.h quality.h \
	 readTypes.h readsSortedByLeftEndPosition.h readsSortedByReadName.h \
	 readsSortedByTemplateName.h restrictionEnzyme.h restrictionFragment.h \
	 rwbtreedictionary.h rwcstring.h rwcsubstring.h \
	 rwdefs.h rwtptrorderedvector.h rwtptrorderedvector_inc.cpp \
	 rwtptrsortedvector.h rwtptrvector.h rwtvalorderedvector.h \
	 rwtvalorderedvector_inc.cpp rwtvalsortedvector.h rwtvalvector.h \
	 selection.h sequence.h singletInfo.h \
	 singletsSortedByTemplateName.h soEmptyString.h soGetErrno.h \
	 subcloneTTemplate.h sysdepend.h tag.h \
	 tagTypes.h templatesSortedByName.h tracefile.h \
	 unpaddedFromPadded.h userDefinedTagField.h userDefinedTagFieldType.h \
	 visibleLineForRestrictionFragments.h whatIsRunning.h wholeAssemblyItem.h \
	 wholeReadItem.h

createUnalignedHighQualityNavigator.o : \
	 abs.h assembly.h assemblyViewTagTypeAndLine.h \
	 assert.h autoFinishPurposes.h bIntersect.h \
	 bIntervalsIntersect.h basesegment.h blockOfLocationsOfA4MerType.h \
	 bool.h cComplementBase.h cComplementBaseTable.h \
	 consedParameters.h consedResources.h contig.h \
	 contigEnd.h contigMatchTablesType.h contigview.h \
	 contigwin.h createUnalignedHighQualityNavigator.cpp createUnalignedHighQualityNavigator.h \
	 dictionary.h distribution.h editCursor.h \
	 experiment.h expidAndLocatedFragment.h filename.h \
	 gotoList.h gotoListType.h guiMultiContigNavigator.h \
	 guiapp.h guicolortext.h listOfFragments.h \
	 locatedFragment.h matchWithinAssembly.h max.h \
	 mbtPtrOrderedVector.h mbtPtrVector.h mbtValOrderedVectorOfRWCString.h \
	 mbtValVector.h mbtValVectorOfBool.h mbtValVector_inc.cpp \
	 mbt_exception.h mbt_val_ord_offset_vec.h min.h \
	 motifutils.h multiProblemGotoList.h nMAX_QUALITY_LEVEL2.h \
	 ntide.h numutil.h paddedFromUnpadded.h \
	 primerType.h quality.h readTypes.h \
	 readsSortedByLeftEndPosition.h readsSortedByReadName.h readsSortedByTemplateName.h \
	 restrictionEnzyme.h rwbtreedictionary.h rwcregexp.h \
	 rwcstring.h rwcsubstring.h rwdefs.h \
	 rwtptrorderedvector.h rwtptrorderedvector_inc.cpp rwtptrsortedvector.h \
	 rwtptrvector.h rwtvalorderedvector.h rwtvalorderedvector_inc.cpp \
	 rwtvalsortedvector.h rwtvalvector.h sequence.h \
	 singletInfo.h singletsSortedByTemplateName.h soEmptyString.h \
	 soGetErrno.h subcloneTTemplate.h sysdepend.h \
	 tag.h templatesSortedByName.h tracefile.h \
	 unalignedHighQualityRegionsGotoList.h unpaddedFromPadded.h whatIsRunning.h \
	 wholeAssemblyItem.h wholeReadItem.h

crossMatchInfoForRead.o : \
	 assert.h bool.h cComplementBase.h \
	 cComplementBaseTable.h crossMatchIndel.h crossMatchInfoForRead.cpp \
	 crossMatchInfoForRead.h filename.h locatedFragment.h \
	 mbtPtrOrderedVector.h mbtValVector.h mbtValVector_inc.cpp \
	 mbt_exception.h mbt_val_ord_offset_vec.h min.h \
	 ntide.h quality.h readTypes.h \
	 rwcstring.h rwcsubstring.h rwdefs.h \
	 rwtptrorderedvector.h rwtptrorderedvector_inc.cpp rwtvalorderedvector.h \
	 rwtvalorderedvector_inc.cpp rwtvalvector.h sequence.h \
	 soEmptyString.h soGetErrno.h sysdepend.h \
	 tag.h tracefile.h wholeReadItem.h

customNavigation.o : \
	 abs.h assembly.h assemblyViewTagTypeAndLine.h \
	 assert.h autoFinishPurposes.h bIntersect.h \
	 bIntervalsIntersect.h bIsNumeric.h basesegment.h \
	 blockOfLocationsOfA4MerType.h bool.h cComplementBase.h \
	 cComplementBaseTable.h compareContigs.h compareContigsCursor.h \
	 compareContigsTypes.h consed.h consedParameters.h \
	 consedResources.h contig.h contigEnd.h \
	 contigMatchTablesType.h contigSegment.h contigview.h \
	 contigwin.h customNavigation.cpp customNavigation.h \
	 dictionary.h distribution.h editCursor.h \
	 editaction.h experiment.h expidAndLocatedFragment.h \
	 filePopupAndGetFilename.h filename.h gotoList.h \
	 gotoListType.h guiDisplayDigest.h guiMultiContigNavigator.h \
	 guiapp.h guicolortext.h listOfFragments.h \
	 locatedFragment.h matchWithinAssembly.h max.h \
	 mbtPtrOrderedVector.h mbtPtrVector.h mbtValOrderedVectorOfRWCString.h \
	 mbtValVector.h mbtValVectorOfBool.h mbtValVector_inc.cpp \
	 mbt_exception.h mbt_val_ord_offset_vec.h min.h \
	 motifutils.h multiProblemGotoList.h nMAX_QUALITY_LEVEL2.h \
	 ntide.h numutil.h paddedFromUnpadded.h \
	 please_wait.h primerType.h quality.h \
	 readTypes.h readsSortedByLeftEndPosition.h readsSortedByReadName.h \
	 readsSortedByTemplateName.h restrictionEnzyme.h restrictionFragment.h \
	 rwbtreedictionary.h rwcstring.h rwcsubstring.h \
	 rwctokenizer.h rwdefs.h rwtptrorderedvector.h \
	 rwtptrorderedvector_inc.cpp rwtptrsortedvector.h rwtptrvector.h \
	 rwtvalorderedvector.h rwtvalorderedvector_inc.cpp rwtvalsortedvector.h \
	 rwtvalvector.h selection.h sequence.h \
	 singletInfo.h singletsSortedByTemplateName.h soEmptyString.h \
	 soGetErrno.h soLine.h subcloneTTemplate.h \
	 sysdepend.h tag.h templatesSortedByName.h \
	 tracefile.h unpaddedFromPadded.h visibleLineForRestrictionFragments.h \
	 whatIsRunning.h wholeAssemblyItem.h wholeReadItem.h

dGetPrimerMeltingTemperature.o : \
	 assemblyViewTagTypeAndLine.h assert.h bool.h \
	 consedParameters.h consedResources.h dGetPrimerMeltingTemperature.cpp \
	 dGetPrimerMeltingTemperature.h filename.h mbtPtrOrderedVector.h \
	 mbtValOrderedVectorOfRWCString.h mbt_exception.h nNumberFromBase.h \
	 restrictionEnzyme.h rwcstring.h rwcsubstring.h \
	 rwdefs.h rwtptrorderedvector.h rwtptrorderedvector_inc.cpp \
	 rwtvalorderedvector.h rwtvalorderedvector_inc.cpp soEmptyString.h \
	 soGetErrno.h sysdepend.h whatIsRunning.h

decisionbox.o : \
	 assert.h bool.h decisionbox.cpp \
	 decisionbox.h filename.h guiapp.h \
	 guicolortext.h mbt_exception.h motifutils.h \
	 rwcstring.h rwcsubstring.h rwdefs.h \
	 rwtptrorderedvector.h rwtptrorderedvector_inc.cpp rwtvalorderedvector.h \
	 rwtvalorderedvector_inc.cpp soEmptyString.h soGetErrno.h \
	 sysdepend.h

deleteFileIfItExists.o : \
	 assert.h bool.h deleteFileIfItExists.cpp \
	 deleteFileOrPopupErrorMessage.h filename.h guiapp.h \
	 guicolortext.h mbt_exception.h motifutils.h \
	 rwcstring.h rwcsubstring.h rwdefs.h \
	 rwtptrorderedvector.h rwtptrorderedvector_inc.cpp rwtvalorderedvector.h \
	 rwtvalorderedvector_inc.cpp soEmptyString.h soGetErrno.h \
	 sysdepend.h

deleteFileOrPopupErrorMessage.o : \
	 assert.h bool.h deleteFileOrPopupErrorMessage.cpp \
	 filename.h guiapp.h guicolortext.h \
	 mbt_exception.h motifutils.h nDeleteFile.h \
	 rwcstring.h rwcsubstring.h rwdefs.h \
	 rwtptrorderedvector.h rwtptrorderedvector_inc.cpp rwtvalorderedvector.h \
	 rwtvalorderedvector_inc.cpp soEmptyString.h soGetErrno.h \
	 sysdepend.h

dictionary.o : \
	 bool.h dictionary.cpp dictionary.h \
	 rwcstring.h rwcsubstring.h rwdefs.h

diffChromosomes.o : \
	 assert.h bool.h diffChromosomes.cpp \
	 diffChromosomes.h filename.h max.h \
	 mbtPtrOrderedVector.h mbtValOrderedVectorOfRWCString.h mbt_exception.h \
	 min.h rwcstring.h rwcsubstring.h \
	 rwdefs.h rwtptrorderedvector.h rwtptrorderedvector_inc.cpp \
	 rwtvalorderedvector.h rwtvalorderedvector_inc.cpp soAddCommas.h \
	 soEmptyString.h soGetErrno.h soLine.h \
	 sysdepend.h

digestForOneEnzyme.o : \
	 abs.h arrayOfRestrictionFragments.h assembly.h \
	 assemblyViewTagTypeAndLine.h assert.h autoFinishPurposes.h \
	 bIntersect.h bIntervalsIntersect.h basesegment.h \
	 blockOfLocationsOfA4MerType.h bool.h cComplementBase.h \
	 cComplementBaseTable.h compareContigs.h compareContigsCursor.h \
	 compareContigsTypes.h consed.h consedParameters.h \
	 consedResources.h contig.h contigEnd.h \
	 contigMatchTablesType.h contigSegment.h contigview.h \
	 contigwin.h correspondingFragments.h dictionary.h \
	 digestForOneEnzyme.cpp digestForOneEnzyme.h distribution.h \
	 editCursor.h editaction.h experiment.h \
	 expidAndLocatedFragment.h filename.h gotoList.h \
	 gotoListType.h guiDisplayDigest.h guiMultiContigNavigator.h \
	 guiapp.h guicolortext.h listOfFragments.h \
	 locatedFragment.h matchWithinAssembly.h max.h \
	 mbtPtrOrderedVector.h mbtPtrVector.h mbtValOrderedVectorOfRWCString.h \
	 mbtValVector.h mbtValVectorOfBool.h mbtValVector_inc.cpp \
	 mbt_exception.h mbt_val_ord_offset_vec.h min.h \
	 motifutils.h multiProblemGotoList.h nMAX_QUALITY_LEVEL2.h \
	 ntide.h numutil.h paddedFromUnpadded.h \
	 popupErrorMessage.h primerType.h quality.h \
	 readTypes.h readsSortedByLeftEndPosition.h readsSortedByReadName.h \
	 readsSortedByTemplateName.h restrictionEnzyme.h restrictionFragment.h \
	 rwbtreedictionary.h rwcstring.h rwcsubstring.h \
	 rwdefs.h rwtptrorderedvector.h rwtptrorderedvector_inc.cpp \
	 rwtptrsortedvector.h rwtptrvector.h rwtvalorderedvector.h \
	 rwtvalorderedvector_inc.cpp rwtvalsortedvector.h rwtvalvector.h \
	 selection.h sequence.h singletInfo.h \
	 singletsSortedByTemplateName.h soEmptyString.h soGetErrno.h \
	 subcloneTTemplate.h sysdepend.h tag.h \
	 templatesSortedByName.h tracefile.h unpaddedFromPadded.h \
	 visibleLineForRestrictionFragments.h whatIsRunning.h wholeAssemblyItem.h \
	 wholeReadItem.h

displayPrimers.o : \
	 abs.h assembly.h assemblyViewTagTypeAndLine.h \
	 assert.h autoFinishPurposes.h bIntersect.h \
	 bIntervalsIntersect.h bIsPrimerStale.h basesegment.h \
	 blockOfLocationsOfA4MerType.h bool.h cComplementBase.h \
	 cComplementBaseTable.h compareContigs.h compareContigsCursor.h \
	 compareContigsTypes.h consed.h consedParameters.h \
	 consedResources.h contig.h contigEnd.h \
	 contigMatchTablesType.h contigSegment.h contigview.h \
	 contigwin.h dictionary.h displayPrimers.cpp \
	 displayPrimers.h distribution.h editAddConsensusTag.h \
	 editCursor.h editaction.h experiment.h \
	 expidAndLocatedFragment.h filename.h gotoList.h \
	 gotoListType.h guiDisplayDigest.h guiGetCommentForTag.h \
	 guiMultiContigNavigator.h guiapp.h guicolortext.h \
	 guicontigwin.h infobutton.h listOfFragments.h \
	 locatedFragment.h matchWithinAssembly.h max.h \
	 mbtPtrOrderedVector.h mbtPtrVector.h mbtValOrderedVectorOfRWCString.h \
	 mbtValVector.h mbtValVectorOfBool.h mbtValVector_inc.cpp \
	 mbt_exception.h mbt_val_ord_offset_vec.h min.h \
	 motifutils.h multiProblemGotoList.h nMAX_QUALITY_LEVEL2.h \
	 ntide.h numutil.h oligoTag.h \
	 paddedFromUnpadded.h popupErrorMessage2.h primerType.h \
	 quality.h readTypes.h readsSortedByLeftEndPosition.h \
	 readsSortedByReadName.h readsSortedByTemplateName.h restrictionEnzyme.h \
	 restrictionFragment.h rwbtreedictionary.h rwcstring.h \
	 rwcsubstring.h rwdefs.h rwtptrorderedvector.h \
	 rwtptrorderedvector_inc.cpp rwtptrsortedvector.h rwtptrvector.h \
	 rwtvalorderedvector.h rwtvalorderedvector_inc.cpp rwtvalsortedvector.h \
	 rwtvalvector.h selection.h sequence.h \
	 singletInfo.h singletsSortedByTemplateName.h soEmptyString.h \
	 soGetErrno.h subcloneTTemplate.h sysdepend.h \
	 tag.h templatesSortedByName.h textbox.h \
	 textfield.h tracefile.h unpaddedFromPadded.h \
	 visibleLineForRestrictionFragments.h whatIsRunning.h wholeAssemblyItem.h \
	 wholeReadItem.h whyIsPrimerNotAcceptableTypes.h

distribution.o : \
	 bool.h distribution.cpp distribution.h \
	 nMAX_QUALITY_LEVEL2.h

dumpCore.o : \
	 dumpCore.cpp

editAddConsensusTag.o : \
	 abs.h assembly.h assemblyViewTagTypeAndLine.h \
	 assert.h autoFinishPurposes.h bIntersect.h \
	 bIntervalsIntersect.h basesegment.h blockOfLocationsOfA4MerType.h \
	 bool.h cComplementBase.h cComplementBaseTable.h \
	 compareContigs.h compareContigsCursor.h compareContigsTypes.h \
	 consed.h consedParameters.h consedResources.h \
	 contig.h contigEnd.h contigMatchTablesType.h \
	 contigSegment.h contigview.h contigwin.h \
	 dictionary.h distribution.h editAddConsensusTag.cpp \
	 editAddConsensusTag.h editCursor.h editaction.h \
	 experiment.h expidAndLocatedFragment.h filename.h \
	 gotoList.h gotoListType.h guiDisplayDigest.h \
	 guiMultiContigNavigator.h guiapp.h guicolortext.h \
	 listOfFragments.h locatedFragment.h matchWithinAssembly.h \
	 max.h mbtPtrOrderedVector.h mbtPtrVector.h \
	 mbtValOrderedVectorOfRWCString.h mbtValVector.h mbtValVectorOfBool.h \
	 mbtValVector_inc.cpp mbt_exception.h mbt_val_ord_offset_vec.h \
	 min.h motifutils.h multiProblemGotoList.h \
	 nMAX_QUALITY_LEVEL2.h ntide.h numutil.h \
	 paddedFromUnpadded.h primerType.h quality.h \
	 readTypes.h readsSortedByLeftEndPosition.h readsSortedByReadName.h \
	 readsSortedByTemplateName.h restrictionEnzyme.h restrictionFragment.h \
	 rwbtreedictionary.h rwcstring.h rwcsubstring.h \
	 rwdefs.h rwtptrorderedvector.h rwtptrorderedvector_inc.cpp \
	 rwtptrsortedvector.h rwtptrvector.h rwtvalorderedvector.h \
	 rwtvalorderedvector_inc.cpp rwtvalsortedvector.h rwtvalvector.h \
	 selection.h sequence.h singletInfo.h \
	 singletsSortedByTemplateName.h soEmptyString.h soGetErrno.h \
	 subcloneTTemplate.h sysdepend.h tag.h \
	 templatesSortedByName.h tracefile.h unpaddedFromPadded.h \
	 visibleLineForRestrictionFragments.h whatIsRunning.h wholeAssemblyItem.h \
	 wholeReadItem.h

editAddReadTag.o : \
	 abs.h assembly.h assemblyViewTagTypeAndLine.h \
	 assert.h autoFinishPurposes.h bIntersect.h \
	 bIntervalsIntersect.h basesegment.h blockOfLocationsOfA4MerType.h \
	 bool.h cComplementBase.h cComplementBaseTable.h \
	 compareContigs.h compareContigsCursor.h compareContigsTypes.h \
	 consed.h consedParameters.h consedResources.h \
	 contig.h contigEnd.h contigMatchTablesType.h \
	 contigSegment.h contigview.h contigwin.h \
	 dictionary.h distribution.h editActionChangeRead.h \
	 editAddReadTag.cpp editAddReadTag.h editCursor.h \
	 editaction.h experiment.h expidAndLocatedFragment.h \
	 filename.h gotoList.h gotoListType.h \
	 guiDisplayDigest.h guiMultiContigNavigator.h guiapp.h \
	 guicolortext.h listOfFragments.h locatedFragment.h \
	 matchWithinAssembly.h max.h mbtPtrOrderedVector.h \
	 mbtPtrVector.h mbtValOrderedVectorOfRWCString.h mbtValVector.h \
	 mbtValVectorOfBool.h mbtValVector_inc.cpp mbt_exception.h \
	 mbt_val_ord_offset_vec.h min.h motifutils.h \
	 multiProblemGotoList.h nMAX_QUALITY_LEVEL2.h ntide.h \
	 numutil.h paddedFromUnpadded.h primerType.h \
	 quality.h readTypes.h readsSortedByLeftEndPosition.h \
	 readsSortedByReadName.h readsSortedByTemplateName.h restrictionEnzyme.h \
	 restrictionFragment.h rwbtreedictionary.h rwcstring.h \
	 rwcsubstring.h rwdefs.h rwtptrorderedvector.h \
	 rwtptrorderedvector_inc.cpp rwtptrsortedvector.h rwtptrvector.h \
	 rwtvalorderedvector.h rwtvalorderedvector_inc.cpp rwtvalsortedvector.h \
	 rwtvalvector.h selection.h sequence.h \
	 singletInfo.h singletsSortedByTemplateName.h soEmptyString.h \
	 soGetErrno.h subcloneTTemplate.h sysdepend.h \
	 tag.h templatesSortedByName.h tracefile.h \
	 unpaddedFromPadded.h visibleLineForRestrictionFragments.h whatIsRunning.h \
	 wholeAssemblyItem.h wholeReadItem.h

editAddTagsToAllReadsAtConsPos.o : \
	 abs.h assembly.h assemblyViewTagTypeAndLine.h \
	 assert.h autoFinishPurposes.h bIntersect.h \
	 bIntervalsIntersect.h basesegment.h blockOfLocationsOfA4MerType.h \
	 bool.h cComplementBase.h cComplementBaseTable.h \
	 compareContigs.h compareContigsCursor.h compareContigsTypes.h \
	 consed.h consedParameters.h consedResources.h \
	 contig.h contigEnd.h contigMatchTablesType.h \
	 contigSegment.h contigview.h contigwin.h \
	 dictionary.h distribution.h editAddTagsToAllReadsAtConsPos.cpp \
	 editAddTagsToAllReadsAtConsPos.h editCursor.h editaction.h \
	 experiment.h expidAndLocatedFragment.h filename.h \
	 gotoList.h gotoListType.h guiDisplayDigest.h \
	 guiMultiContigNavigator.h guiapp.h guicolortext.h \
	 listOfFragments.h locatedFragment.h matchWithinAssembly.h \
	 max.h mbtPtrOrderedVector.h mbtPtrVector.h \
	 mbtValOrderedVectorOfRWCString.h mbtValVector.h mbtValVectorOfBool.h \
	 mbtValVector_inc.cpp mbt_exception.h mbt_val_ord_offset_vec.h \
	 min.h motifutils.h multiProblemGotoList.h \
	 nMAX_QUALITY_LEVEL2.h ntide.h numutil.h \
	 paddedFromUnpadded.h primerType.h quality.h \
	 readTypes.h readsSortedByLeftEndPosition.h readsSortedByReadName.h \
	 readsSortedByTemplateName.h restrictionEnzyme.h restrictionFragment.h \
	 rwbtreedictionary.h rwcstring.h rwcsubstring.h \
	 rwdefs.h rwtptrorderedvector.h rwtptrorderedvector_inc.cpp \
	 rwtptrsortedvector.h rwtptrvector.h rwtvalorderedvector.h \
	 rwtvalorderedvector_inc.cpp rwtvalsortedvector.h rwtvalvector.h \
	 selection.h sequence.h singletInfo.h \
	 singletsSortedByTemplateName.h soEmptyString.h soGetErrno.h \
	 subcloneTTemplate.h sysdepend.h tag.h \
	 templatesSortedByName.h tracefile.h unpaddedFromPadded.h \
	 visibleLineForRestrictionFragments.h whatIsRunning.h wholeAssemblyItem.h \
	 wholeReadItem.h

editCursor.o : \
	 abs.h assembly.h assemblyViewTagTypeAndLine.h \
	 assert.h autoFinishPurposes.h bIntersect.h \
	 bIntervalsIntersect.h basesegment.h blockOfLocationsOfA4MerType.h \
	 bool.h cComplementBase.h cComplementBaseTable.h \
	 compareContigs.h compareContigsCursor.h compareContigsTypes.h \
	 consed.h consedParameters.h consedResources.h \
	 contig.h contigEnd.h contigMatchTablesType.h \
	 contigSegment.h contigview.h contigwin.h \
	 dictionary.h distribution.h editCursor.cpp \
	 editCursor.h editaction.h experiment.h \
	 expidAndLocatedFragment.h filename.h gotoList.h \
	 gotoListType.h guiDisplayDigest.h guiMultiContigNavigator.h \
	 guiapp.h guicolortext.h listOfFragments.h \
	 locatedFragment.h matchWithinAssembly.h max.h \
	 mbtPtrOrderedVector.h mbtPtrVector.h mbtValOrderedVectorOfRWCString.h \
	 mbtValVector.h mbtValVectorOfBool.h mbtValVector_inc.cpp \
	 mbt_exception.h mbt_val_ord_offset_vec.h min.h \
	 motifutils.h multiProblemGotoList.h nMAX_QUALITY_LEVEL2.h \
	 ntide.h numutil.h paddedFromUnpadded.h \
	 primerType.h quality.h readTypes.h \
	 readsSortedByLeftEndPosition.h readsSortedByReadName.h readsSortedByTemplateName.h \
	 restrictionEnzyme.h restrictionFragment.h rwbtreedictionary.h \
	 rwcstring.h rwcsubstring.h rwdefs.h \
	 rwtptrorderedvector.h rwtptrorderedvector_inc.cpp rwtptrsortedvector.h \
	 rwtptrvector.h rwtvalorderedvector.h rwtvalorderedvector_inc.cpp \
	 rwtvalsortedvector.h rwtvalvector.h selection.h \
	 sequence.h singletInfo.h singletsSortedByTemplateName.h \
	 soEmptyString.h soGetErrno.h subcloneTTemplate.h \
	 sysdepend.h tag.h templatesSortedByName.h \
	 tracefile.h unpaddedFromPadded.h visibleLineForRestrictionFragments.h \
	 whatIsRunning.h wholeAssemblyItem.h wholeReadItem.h

editDeleteConsensusTag.o : \
	 abs.h assembly.h assemblyViewTagTypeAndLine.h \
	 assert.h autoFinishPurposes.h bIntersect.h \
	 bIntervalsIntersect.h basesegment.h blockOfLocationsOfA4MerType.h \
	 bool.h cComplementBase.h cComplementBaseTable.h \
	 consedParameters.h consedResources.h contig.h \
	 contigEnd.h contigMatchTablesType.h contigview.h \
	 contigwin.h dictionary.h distribution.h \
	 editCursor.h editDeleteConsensusTag.cpp editDeleteConsensusTag.h \
	 editaction.h experiment.h expidAndLocatedFragment.h \
	 filename.h gotoList.h gotoListType.h \
	 guiapp.h guicolortext.h listOfFragments.h \
	 locatedFragment.h matchWithinAssembly.h max.h \
	 mbtPtrOrderedVector.h mbtPtrVector.h mbtValOrderedVectorOfRWCString.h \
	 mbtValVector.h mbtValVectorOfBool.h mbtValVector_inc.cpp \
	 mbt_exception.h mbt_val_ord_offset_vec.h min.h \
	 motifutils.h multiProblemGotoList.h nMAX_QUALITY_LEVEL2.h \
	 ntide.h numutil.h paddedFromUnpadded.h \
	 primerType.h quality.h readTypes.h \
	 readsSortedByLeftEndPosition.h readsSortedByReadName.h readsSortedByTemplateName.h \
	 restrictionEnzyme.h rwbtreedictionary.h rwcstring.h \
	 rwcsubstring.h rwdefs.h rwtptrorderedvector.h \
	 rwtptrorderedvector_inc.cpp rwtptrsortedvector.h rwtptrvector.h \
	 rwtvalorderedvector.h rwtvalorderedvector_inc.cpp rwtvalsortedvector.h \
	 rwtvalvector.h sequence.h singletInfo.h \
	 singletsSortedByTemplateName.h soEmptyString.h soGetErrno.h \
	 subcloneTTemplate.h sysdepend.h tag.h \
	 templatesSortedByName.h tracefile.h unpaddedFromPadded.h \
	 whatIsRunning.h wholeAssemblyItem.h wholeReadItem.h

editDeleteReadTag.o : \
	 abs.h assembly.h assemblyViewTagTypeAndLine.h \
	 assert.h autoFinishPurposes.h bIntersect.h \
	 bIntervalsIntersect.h basesegment.h blockOfLocationsOfA4MerType.h \
	 bool.h cComplementBase.h cComplementBaseTable.h \
	 compareContigs.h compareContigsCursor.h compareContigsTypes.h \
	 consed.h consedParameters.h consedResources.h \
	 contig.h contigEnd.h contigMatchTablesType.h \
	 contigSegment.h contigview.h contigwin.h \
	 dictionary.h distribution.h editActionChangeRead.h \
	 editCursor.h editDeleteReadTag.cpp editDeleteReadTag.h \
	 editaction.h experiment.h expidAndLocatedFragment.h \
	 filename.h gotoList.h gotoListType.h \
	 guiDisplayDigest.h guiMultiContigNavigator.h guiapp.h \
	 guicolortext.h listOfFragments.h locatedFragment.h \
	 matchWithinAssembly.h max.h mbtPtrOrderedVector.h \
	 mbtPtrVector.h mbtValOrderedVectorOfRWCString.h mbtValVector.h \
	 mbtValVectorOfBool.h mbtValVector_inc.cpp mbt_exception.h \
	 mbt_val_ord_offset_vec.h min.h motifutils.h \
	 multiProblemGotoList.h nMAX_QUALITY_LEVEL2.h ntide.h \
	 numutil.h paddedFromUnpadded.h primerType.h \
	 quality.h readTypes.h readsSortedByLeftEndPosition.h \
	 readsSortedByReadName.h readsSortedByTemplateName.h restrictionEnzyme.h \
	 restrictionFragment.h rwbtreedictionary.h rwcstring.h \
	 rwcsubstring.h rwdefs.h rwtptrorderedvector.h \
	 rwtptrorderedvector_inc.cpp rwtptrsortedvector.h rwtptrvector.h \
	 rwtvalorderedvector.h rwtvalorderedvector_inc.cpp rwtvalsortedvector.h \
	 rwtvalvector.h selection.h sequence.h \
	 singletInfo.h singletsSortedByTemplateName.h soEmptyString.h \
	 soGetErrno.h subcloneTTemplate.h sysdepend.h \
	 tag.h templatesSortedByName.h tracefile.h \
	 unpaddedFromPadded.h visibleLineForRestrictionFragments.h whatIsRunning.h \
	 wholeAssemblyItem.h wholeReadItem.h

editInsertColOfPads.o : \
	 abs.h assembly.h assemblyViewTagTypeAndLine.h \
	 assert.h autoFinishPurposes.h bIntersect.h \
	 bIntervalsIntersect.h basesegment.h blockOfLocationsOfA4MerType.h \
	 bool.h cComplementBase.h cComplementBaseTable.h \
	 compareContigs.h compareContigsCursor.h compareContigsTypes.h \
	 consed.h consedParameters.h consedResources.h \
	 contig.h contigEnd.h contigMatchTablesType.h \
	 contigSegment.h contigview.h contigwin.h \
	 dictionary.h distribution.h editCursor.h \
	 editInsertColOfPads.cpp editInsertColOfPads.h editaction.h \
	 experiment.h expidAndLocatedFragment.h filename.h \
	 gotoList.h gotoListType.h guiDisplayDigest.h \
	 guiMultiContigNavigator.h guiapp.h guicolortext.h \
	 guitedwin.h infobutton.h listOfFragments.h \
	 locatedFragment.h matchWithinAssembly.h max.h \
	 mbtPtrOrderedVector.h mbtPtrVector.h mbtValOrderedVectorOfRWCString.h \
	 mbtValVector.h mbtValVectorOfBool.h mbtValVector_inc.cpp \
	 mbt_exception.h mbt_val_ord_offset_vec.h min.h \
	 motifutils.h multiProblemGotoList.h nMAX_QUALITY_LEVEL2.h \
	 ntide.h numutil.h paddedFromUnpadded.h \
	 primerType.h quality.h readTypes.h \
	 readsSortedByLeftEndPosition.h readsSortedByReadName.h readsSortedByTemplateName.h \
	 restrictionEnzyme.h restrictionFragment.h rwbtreedictionary.h \
	 rwcstring.h rwcsubstring.h rwdefs.h \
	 rwtptrorderedvector.h rwtptrorderedvector_inc.cpp rwtptrsortedvector.h \
	 rwtptrvector.h rwtvalorderedvector.h rwtvalorderedvector_inc.cpp \
	 rwtvalsortedvector.h rwtvalvector.h selection.h \
	 sequence.h singletInfo.h singletsSortedByTemplateName.h \
	 soEmptyString.h soGetErrno.h subcloneTTemplate.h \
	 sysdepend.h tag.h teditor.h \
	 teditor_types.h tedwin.h templatesSortedByName.h \
	 textfield.h tracefile.h unpaddedFromPadded.h \
	 visibleLineForRestrictionFragments.h whatIsRunning.h whatToDoWithSelectionTypes.h \
	 wholeAssemblyItem.h wholeReadItem.h

editMakeHighQualityAndChangeConsensus.o : \
	 abs.h assembly.h assemblyViewTagTypeAndLine.h \
	 assert.h autoFinishPurposes.h bIntersect.h \
	 bIntervalsIntersect.h basesegment.h blockOfLocationsOfA4MerType.h \
	 bool.h cComplementBase.h cComplementBaseTable.h \
	 compareContigs.h compareContigsCursor.h compareContigsTypes.h \
	 consed.h consedParameters.h consedResources.h \
	 contig.h contigEnd.h contigMatchTablesType.h \
	 contigSegment.h contigview.h contigwin.h \
	 dictionary.h distribution.h editActionChangeRead.h \
	 editCursor.h editMakeHighQualityAndChangeConsensus.cpp editMakeHighQualityAndChangeConsensus.h \
	 editaction.h experiment.h expidAndLocatedFragment.h \
	 filename.h gotoList.h gotoListType.h \
	 guiDisplayDigest.h guiMultiContigNavigator.h guiapp.h \
	 guicolortext.h listOfFragments.h locatedFragment.h \
	 matchWithinAssembly.h max.h mbtPtrOrderedVector.h \
	 mbtPtrVector.h mbtValOrderedVectorOfRWCString.h mbtValVector.h \
	 mbtValVectorOfBool.h mbtValVector_inc.cpp mbt_exception.h \
	 mbt_val_ord_offset_vec.h min.h motifutils.h \
	 multiProblemGotoList.h nMAX_QUALITY_LEVEL2.h ntide.h \
	 numutil.h paddedFromUnpadded.h primerType.h \
	 quality.h readTypes.h readsSortedByLeftEndPosition.h \
	 readsSortedByReadName.h readsSortedByTemplateName.h restrictionEnzyme.h \
	 restrictionFragment.h rwbtreedictionary.h rwcstring.h \
	 rwcsubstring.h rwdefs.h rwtptrorderedvector.h \
	 rwtptrorderedvector_inc.cpp rwtptrsortedvector.h rwtptrvector.h \
	 rwtvalorderedvector.h rwtvalorderedvector_inc.cpp rwtvalsortedvector.h \
	 rwtvalvector.h selection.h sequence.h \
	 singletInfo.h singletsSortedByTemplateName.h soEmptyString.h \
	 soGetErrno.h subcloneTTemplate.h sysdepend.h \
	 tag.h templatesSortedByName.h tracefile.h \
	 unpaddedFromPadded.h visibleLineForRestrictionFragments.h whatIsRunning.h \
	 wholeAssemblyItem.h wholeReadItem.h

editOverstrikeAllReadsAtConsPos.o : \
	 abs.h assembly.h assemblyViewTagTypeAndLine.h \
	 assert.h autoFinishPurposes.h bIntersect.h \
	 bIntervalsIntersect.h basesegment.h blockOfLocationsOfA4MerType.h \
	 bool.h cComplementBase.h cComplementBaseTable.h \
	 compareContigs.h compareContigsCursor.h compareContigsTypes.h \
	 consed.h consedParameters.h consedResources.h \
	 contig.h contigEnd.h contigMatchTablesType.h \
	 contigSegment.h contigview.h contigwin.h \
	 dictionary.h distribution.h editCursor.h \
	 editOverstrikeAllReadsAtConsPos.cpp editOverstrikeAllReadsAtConsPos.h editaction.h \
	 experiment.h expidAndLocatedFragment.h filename.h \
	 gotoList.h gotoListType.h guiDisplayDigest.h \
	 guiMultiContigNavigator.h guiapp.h guicolortext.h \
	 listOfFragments.h locatedFragment.h matchWithinAssembly.h \
	 max.h mbtPtrOrderedVector.h mbtPtrVector.h \
	 mbtValOrderedVectorOfRWCString.h mbtValVector.h mbtValVectorOfBool.h \
	 mbtValVector_inc.cpp mbt_exception.h mbt_val_ord_offset_vec.h \
	 min.h motifutils.h multiProblemGotoList.h \
	 nMAX_QUALITY_LEVEL2.h ntide.h numutil.h \
	 paddedFromUnpadded.h primerType.h quality.h \
	 readTypes.h readsSortedByLeftEndPosition.h readsSortedByReadName.h \
	 readsSortedByTemplateName.h restrictionEnzyme.h restrictionFragment.h \
	 rwbtreedictionary.h rwcstring.h rwcsubstring.h \
	 rwdefs.h rwtptrorderedvector.h rwtptrorderedvector_inc.cpp \
	 rwtptrsortedvector.h rwtptrvector.h rwtvalorderedvector.h \
	 rwtvalorderedvector_inc.cpp rwtvalsortedvector.h rwtvalvector.h \
	 selection.h sequence.h singletInfo.h \
	 singletsSortedByTemplateName.h soEmptyString.h soGetErrno.h \
	 subcloneTTemplate.h sysdepend.h tag.h \
	 templatesSortedByName.h tracefile.h unpaddedFromPadded.h \
	 visibleLineForRestrictionFragments.h whatIsRunning.h wholeAssemblyItem.h \
	 wholeReadItem.h

editOverstrikeConsensus.o : \
	 abs.h assembly.h assemblyViewTagTypeAndLine.h \
	 assert.h autoFinishPurposes.h bIntersect.h \
	 bIntervalsIntersect.h basesegment.h blockOfLocationsOfA4MerType.h \
	 bool.h cComplementBase.h cComplementBaseTable.h \
	 compareContigs.h compareContigsCursor.h compareContigsTypes.h \
	 consed.h consedParameters.h consedResources.h \
	 contig.h contigEnd.h contigMatchTablesType.h \
	 contigSegment.h contigview.h contigwin.h \
	 dictionary.h distribution.h editCursor.h \
	 editOverstrikeConsensus.cpp editOverstrikeConsensus.h editaction.h \
	 experiment.h expidAndLocatedFragment.h filename.h \
	 gotoList.h gotoListType.h guiDisplayDigest.h \
	 guiMultiContigNavigator.h guiapp.h guicolortext.h \
	 listOfFragments.h locatedFragment.h matchWithinAssembly.h \
	 max.h mbtPtrOrderedVector.h mbtPtrVector.h \
	 mbtValOrderedVectorOfRWCString.h mbtValVector.h mbtValVectorOfBool.h \
	 mbtValVector_inc.cpp mbt_exception.h mbt_val_ord_offset_vec.h \
	 min.h motifutils.h multiProblemGotoList.h \
	 nMAX_QUALITY_LEVEL2.h ntide.h numutil.h \
	 paddedFromUnpadded.h primerType.h quality.h \
	 readTypes.h readsSortedByLeftEndPosition.h readsSortedByReadName.h \
	 readsSortedByTemplateName.h restrictionEnzyme.h restrictionFragment.h \
	 rwbtreedictionary.h rwcstring.h rwcsubstring.h \
	 rwdefs.h rwtptrorderedvector.h rwtptrorderedvector_inc.cpp \
	 rwtptrsortedvector.h rwtptrvector.h rwtvalorderedvector.h \
	 rwtvalorderedvector_inc.cpp rwtvalsortedvector.h rwtvalvector.h \
	 selection.h sequence.h singletInfo.h \
	 singletsSortedByTemplateName.h soEmptyString.h soGetErrno.h \
	 subcloneTTemplate.h sysdepend.h tag.h \
	 templatesSortedByName.h tracefile.h unpaddedFromPadded.h \
	 visibleLineForRestrictionFragments.h whatIsRunning.h wholeAssemblyItem.h \
	 wholeReadItem.h

edit_complement_contig.o : \
	 abs.h assembly.h assemblyViewTagTypeAndLine.h \
	 assert.h autoFinishPurposes.h bIntersect.h \
	 bIntervalsIntersect.h basesegment.h blockOfLocationsOfA4MerType.h \
	 bool.h cComplementBase.h cComplementBaseTable.h \
	 compareContigs.h compareContigsCursor.h compareContigsTypes.h \
	 consed.h consedParameters.h consedResources.h \
	 contig.h contigEnd.h contigMatchTablesType.h \
	 contigSegment.h contigview.h contigwin.h \
	 dictionary.h distribution.h editCursor.h \
	 edit_complement_contig.cpp edit_complement_contig.h editaction.h \
	 experiment.h expidAndLocatedFragment.h filename.h \
	 gotoList.h gotoListType.h guiDisplayDigest.h \
	 guiMultiContigNavigator.h guiapp.h guicolortext.h \
	 guitedwin.h infobutton.h listOfFragments.h \
	 locatedFragment.h matchWithinAssembly.h max.h \
	 mbtPtrOrderedVector.h mbtPtrVector.h mbtValOrderedVectorOfRWCString.h \
	 mbtValVector.h mbtValVectorOfBool.h mbtValVector_inc.cpp \
	 mbt_exception.h mbt_val_ord_offset_vec.h min.h \
	 motifutils.h multiProblemGotoList.h nMAX_QUALITY_LEVEL2.h \
	 ntide.h numutil.h paddedFromUnpadded.h \
	 please_wait.h primerType.h quality.h \
	 readTypes.h readsSortedByLeftEndPosition.h readsSortedByReadName.h \
	 readsSortedByTemplateName.h restrictionEnzyme.h restrictionFragment.h \
	 rwbtreedictionary.h rwcstring.h rwcsubstring.h \
	 rwdefs.h rwtptrorderedvector.h rwtptrorderedvector_inc.cpp \
	 rwtptrsortedvector.h rwtptrvector.h rwtvalorderedvector.h \
	 rwtvalorderedvector_inc.cpp rwtvalsortedvector.h rwtvalvector.h \
	 selection.h sequence.h singletInfo.h \
	 singletsSortedByTemplateName.h soEmptyString.h soGetErrno.h \
	 subcloneTTemplate.h sysdepend.h tag.h \
	 teditor.h teditor_types.h tedwin.h \
	 templatesSortedByName.h textfield.h tracefile.h \
	 unpaddedFromPadded.h visibleLineForRestrictionFragments.h whatIsRunning.h \
	 whatToDoWithSelectionTypes.h wholeAssemblyItem.h wholeReadItem.h

editaction.o : \
	 abs.h assembly.h assemblyViewTagTypeAndLine.h \
	 assert.h autoFinishPurposes.h bIntersect.h \
	 bIntervalsIntersect.h basesegment.h blockOfLocationsOfA4MerType.h \
	 bool.h cComplementBase.h cComplementBaseTable.h \
	 compareContigs.h compareContigsCursor.h compareContigsTypes.h \
	 consed.h consedParameters.h consedResources.h \
	 contig.h contigEnd.h contigMatchTablesType.h \
	 contigSegment.h contigview.h contigwin.h \
	 dictionary.h distribution.h editCursor.h \
	 editaction.cpp editaction.h experiment.h \
	 expidAndLocatedFragment.h filename.h gotoList.h \
	 gotoListType.h guiDisplayDigest.h guiMultiContigNavigator.h \
	 guiapp.h guicolortext.h guitedwin.h \
	 infobutton.h listOfFragments.h locatedFragment.h \
	 matchWithinAssembly.h max.h mbtPtrOrderedVector.h \
	 mbtPtrVector.h mbtValOrderedVectorOfRWCString.h mbtValVector.h \
	 mbtValVectorOfBool.h mbtValVector_inc.cpp mbt_exception.h \
	 mbt_val_ord_offset_vec.h min.h motifutils.h \
	 multiProblemGotoList.h nMAX_QUALITY_LEVEL2.h ntide.h \
	 numutil.h paddedFromUnpadded.h primerType.h \
	 quality.h readTypes.h readsSortedByLeftEndPosition.h \
	 readsSortedByReadName.h readsSortedByTemplateName.h restrictionEnzyme.h \
	 restrictionFragment.h rwbtreedictionary.h rwcstring.h \
	 rwcsubstring.h rwdefs.h rwtptrorderedvector.h \
	 rwtptrorderedvector_inc.cpp rwtptrsortedvector.h rwtptrvector.h \
	 rwtvalorderedvector.h rwtvalorderedvector_inc.cpp rwtvalsortedvector.h \
	 rwtvalvector.h selection.h sequence.h \
	 singletInfo.h singletsSortedByTemplateName.h soEmptyString.h \
	 soGetErrno.h subcloneTTemplate.h sysdepend.h \
	 tag.h teditor.h teditor_types.h \
	 tedwin.h templatesSortedByName.h textfield.h \
	 tracefile.h unpaddedFromPadded.h visibleLineForRestrictionFragments.h \
	 whatIsRunning.h whatToDoWithSelectionTypes.h wholeAssemblyItem.h \
	 wholeReadItem.h

editedButNotNsGotoList.o : \
	 assemblyViewTagTypeAndLine.h assert.h autoFinishPurposes.h \
	 basesegment.h blockOfLocationsOfA4MerType.h bool.h \
	 cComplementBase.h cComplementBaseTable.h consedParameters.h \
	 consedResources.h contig.h contigEnd.h \
	 contigMatchTablesType.h dictionary.h distribution.h \
	 editedButNotNsGotoList.cpp editedButNotNsGotoList.h experiment.h \
	 filename.h gotoList.h locatedFragment.h \
	 mbtPtrOrderedVector.h mbtPtrVector.h mbtValOrderedVectorOfRWCString.h \
	 mbtValVector.h mbtValVectorOfBool.h mbtValVector_inc.cpp \
	 mbt_exception.h mbt_val_ord_offset_vec.h min.h \
	 nMAX_QUALITY_LEVEL2.h ntide.h paddedFromUnpadded.h \
	 primerType.h quality.h readTypes.h \
	 readsSortedByLeftEndPosition.h readsSortedByReadName.h restrictionEnzyme.h \
	 rwbtreedictionary.h rwcstring.h rwcsubstring.h \
	 rwdefs.h rwtptrorderedvector.h rwtptrorderedvector_inc.cpp \
	 rwtptrsortedvector.h rwtptrvector.h rwtvalorderedvector.h \
	 rwtvalorderedvector_inc.cpp rwtvalsortedvector.h rwtvalvector.h \
	 sequence.h soEmptyString.h soGetErrno.h \
	 subcloneTTemplate.h sysdepend.h tag.h \
	 tracefile.h unpaddedFromPadded.h whatIsRunning.h \
	 wholeReadItem.h

editedGotoList.o : \
	 assemblyViewTagTypeAndLine.h assert.h autoFinishPurposes.h \
	 basesegment.h blockOfLocationsOfA4MerType.h bool.h \
	 cComplementBase.h cComplementBaseTable.h consedParameters.h \
	 consedResources.h contig.h contigEnd.h \
	 contigMatchTablesType.h dictionary.h distribution.h \
	 editedGotoList.cpp editedGotoList.h experiment.h \
	 filename.h gotoList.h locatedFragment.h \
	 mbtPtrOrderedVector.h mbtPtrVector.h mbtValOrderedVectorOfRWCString.h \
	 mbtValVector.h mbtValVectorOfBool.h mbtValVector_inc.cpp \
	 mbt_exception.h mbt_val_ord_offset_vec.h min.h \
	 nMAX_QUALITY_LEVEL2.h ntide.h paddedFromUnpadded.h \
	 primerType.h quality.h readTypes.h \
	 readsSortedByLeftEndPosition.h readsSortedByReadName.h restrictionEnzyme.h \
	 rwbtreedictionary.h rwcstring.h rwcsubstring.h \
	 rwdefs.h rwtptrorderedvector.h rwtptrorderedvector_inc.cpp \
	 rwtptrsortedvector.h rwtptrvector.h rwtvalorderedvector.h \
	 rwtvalorderedvector_inc.cpp rwtvalsortedvector.h rwtvalvector.h \
	 sequence.h soEmptyString.h soGetErrno.h \
	 subcloneTTemplate.h sysdepend.h tag.h \
	 tracefile.h unpaddedFromPadded.h whatIsRunning.h \
	 wholeReadItem.h

evalExpCluster.o : \
	 abs.h assembly.h assemblyViewTagTypeAndLine.h \
	 assert.h autoFinishExpTag.h autoFinishPurposes.h \
	 bIntersect.h bIntervalsIntersect.h basesegment.h \
	 blockOfLocationsOfA4MerType.h bool.h cComplementBase.h \
	 cComplementBaseTable.h compareContigs.h compareContigsCursor.h \
	 compareContigsTypes.h consed.h consedParameters.h \
	 consedResources.h contig.h contigEnd.h \
	 contigMatchTablesType.h contigSegment.h contigview.h \
	 contigwin.h dictionary.h distribution.h \
	 editCursor.h editaction.h evalExpCluster.cpp \
	 evalExpCluster.h experiment.h expidAndLocatedFragment.h \
	 fileDefines.h filename.h gotoList.h \
	 gotoListType.h guiDisplayDigest.h guiMultiContigNavigator.h \
	 guiapp.h guicolortext.h listOfFragments.h \
	 locatedFragment.h matchWithinAssembly.h max.h \
	 mbtPtrOrderedVector.h mbtPtrVector.h mbtValOrderedVectorOfRWCString.h \
	 mbtValVector.h mbtValVectorOfBool.h mbtValVector_inc.cpp \
	 mbt_exception.h mbt_val_ord_offset_vec.h min.h \
	 motifutils.h multiProblemGotoList.h nMAX_QUALITY_LEVEL2.h \
	 ntide.h numutil.h paddedFromUnpadded.h \
	 primerType.h quality.h readTypes.h \
	 readsSortedByLeftEndPosition.h readsSortedByReadName.h readsSortedByTemplateName.h \
	 restrictionEnzyme.h restrictionFragment.h rwbtreedictionary.h \
	 rwcregexp.h rwcstring.h rwcsubstring.h \
	 rwctokenizer.h rwdefs.h rwtptrorderedvector.h \
	 rwtptrorderedvector_inc.cpp rwtptrsortedvector.h rwtptrvector.h \
	 rwtvalorderedvector.h rwtvalorderedvector_inc.cpp rwtvalsortedvector.h \
	 rwtvalvector.h selection.h sequence.h \
	 singletInfo.h singletsSortedByTemplateName.h soEmptyString.h \
	 soGetErrno.h subcloneTTemplate.h sysdepend.h \
	 tag.h templatesSortedByName.h tracefile.h \
	 unpaddedFromPadded.h visibleLineForRestrictionFragments.h whatIsRunning.h \
	 wholeAssemblyItem.h wholeReadItem.h

experiment.o : \
	 abs.h assembly.h assemblyViewTagTypeAndLine.h \
	 assert.h autoFinishExpTag.h autoFinishPurposes.h \
	 bIntersect.h bIntervalsIntersect.h bIsDyePrimerNotDyeTerminator.h \
	 basesegment.h blockOfLocationsOfA4MerType.h bool.h \
	 cComplementBase.h cComplementBaseTable.h compareContigs.h \
	 compareContigsCursor.h compareContigsTypes.h consed.h \
	 consedParameters.h consedResources.h contig.h \
	 contigEnd.h contigMatchTablesType.h contigSegment.h \
	 contigview.h contigwin.h dictionary.h \
	 distribution.h editCursor.h editaction.h \
	 experiment.cpp experiment.h expidAndLocatedFragment.h \
	 fileDefines.h filename.h gotoList.h \
	 gotoListType.h guiDisplayDigest.h guiMultiContigNavigator.h \
	 guiapp.h guicolortext.h listOfFragments.h \
	 locatedFragment.h matchWithinAssembly.h max.h \
	 mbtPtrOrderedVector.h mbtPtrVector.h mbtValOrderedVectorOfRWCString.h \
	 mbtValVector.h mbtValVectorOfBool.h mbtValVector_inc.cpp \
	 mbt_exception.h mbt_val_ord_offset_vec.h min.h \
	 motifutils.h multiProblemGotoList.h nMAX_QUALITY_LEVEL2.h \
	 ntide.h numutil.h paddedFromUnpadded.h \
	 primerType.h quality.h readTypes.h \
	 readsSortedByLeftEndPosition.h readsSortedByReadName.h readsSortedByTemplateName.h \
	 restrictionEnzyme.h restrictionFragment.h rwbtreedictionary.h \
	 rwcstring.h rwcsubstring.h rwdefs.h \
	 rwtptrorderedvector.h rwtptrorderedvector_inc.cpp rwtptrsortedvector.h \
	 rwtptrvector.h rwtvalorderedvector.h rwtvalorderedvector_inc.cpp \
	 rwtvalsortedvector.h rwtvalvector.h selection.h \
	 sequence.h singletInfo.h singletsSortedByTemplateName.h \
	 soEmptyString.h soGetErrno.h subcloneTTemplate.h \
	 sysdepend.h tag.h templatesSortedByName.h \
	 tracefile.h unpaddedFromPadded.h visibleLineForRestrictionFragments.h \
	 whatIsRunning.h wholeAssemblyItem.h wholeReadItem.h

extendAlignment.o : \
	 abs.h assert.h bIntersect.h \
	 bIntervalsIntersect.h bool.h extendAlignment.cpp \
	 extendAlignment.h max.h mbt_exception.h \
	 min.h numutil.h rwcstring.h \
	 rwcsubstring.h rwdefs.h soGetErrno.h \
	 sysdepend.h

extendAlignmentBanded.o : \
	 abs.h assemblyViewTagTypeAndLine.h assert.h \
	 bIntersect.h bIntervalsIntersect.h bool.h \
	 consedParameters.h consedResources.h extendAlignmentBanded.cpp \
	 extendAlignmentBanded.h filename.h max.h \
	 mbtPtrOrderedVector.h mbtValOrderedVectorOfRWCString.h mbt_exception.h \
	 min.h numutil.h restrictionEnzyme.h \
	 rwcstring.h rwcsubstring.h rwdefs.h \
	 rwtptrorderedvector.h rwtptrorderedvector_inc.cpp rwtvalorderedvector.h \
	 rwtvalorderedvector_inc.cpp setMatchMatrix.h soEmptyString.h \
	 soGetErrno.h sysdepend.h whatIsRunning.h

filFindSolexaPrbFileFromSeqFile.o : \
	 bool.h filFindSolexaPrbFileFromSeqFile.cpp filFindSolexaPrbFileFromSeqFile.h \
	 filename.h rwcregexp.h rwcstring.h \
	 rwcsubstring.h rwdefs.h sysdepend.h

filGetUniqueFilename.o : \
	 bool.h filGetUniqueFilename.cpp filGetUniqueFilename.h \
	 filename.h rwcstring.h rwcsubstring.h \
	 rwdefs.h sysdepend.h

filePopupAndGetAceFilename.o : \
	 abs.h assembly.h assemblyViewTagTypeAndLine.h \
	 assert.h autoFinishPurposes.h bIntersect.h \
	 bIntervalsIntersect.h basesegment.h blockOfLocationsOfA4MerType.h \
	 bool.h cComplementBase.h cComplementBaseTable.h \
	 compareContigs.h compareContigsCursor.h compareContigsTypes.h \
	 consed.h consedParameters.h consedResources.h \
	 contig.h contigEnd.h contigMatchTablesType.h \
	 contigSegment.h contigview.h contigwin.h \
	 dictionary.h distribution.h editCursor.h \
	 editaction.h experiment.h expidAndLocatedFragment.h \
	 filePopupAndGetAceFilename.cpp filePopupAndGetAceFilename.h filename.h \
	 filenamePlus.h gotoList.h gotoListType.h \
	 guiDisplayDigest.h guiMultiContigNavigator.h guiapp.h \
	 guicolortext.h handleWindowManagerDelete2.h hp_exception_kludge.h \
	 listOfFragments.h locatedFragment.h matchWithinAssembly.h \
	 max.h mbtPtrOrderedVector.h mbtPtrVector.h \
	 mbtValOrderedVectorOfRWCString.h mbtValVector.h mbtValVectorOfBool.h \
	 mbtValVector_inc.cpp mbt_exception.h mbt_val_ord_offset_vec.h \
	 min.h motifutils.h multiProblemGotoList.h \
	 nMAX_QUALITY_LEVEL2.h ntide.h numutil.h \
	 paddedFromUnpadded.h popupErrorMessage.h primerType.h \
	 quality.h readTypes.h readsSortedByLeftEndPosition.h \
	 readsSortedByReadName.h readsSortedByTemplateName.h restrictionEnzyme.h \
	 restrictionFragment.h rwbtreedictionary.h rwcregexp.h \
	 rwcstring.h rwcsubstring.h rwdefs.h \
	 rwtptrorderedvector.h rwtptrorderedvector_inc.cpp rwtptrsortedvector.h \
	 rwtptrvector.h rwtvalorderedvector.h rwtvalorderedvector_inc.cpp \
	 rwtvalsortedvector.h rwtvalvector.h selection.h \
	 sequence.h singletInfo.h singletsSortedByTemplateName.h \
	 soEmptyString.h soGetErrno.h subcloneTTemplate.h \
	 sysdepend.h tag.h templatesSortedByName.h \
	 tracefile.h unpaddedFromPadded.h visibleLineForRestrictionFragments.h \
	 whatIsRunning.h wholeAssemblyItem.h wholeReadItem.h

filePopupAndGetFilename.o : \
	 assert.h bool.h filePopupAndGetFilename.cpp \
	 filename.h mbt_exception.h messageAndFileSelector.h \
	 rwcstring.h rwcsubstring.h rwdefs.h \
	 soGetErrno.h sysdepend.h

filename.o : \
	 assert.h bool.h filename.cpp \
	 filename.h mbt_exception.h rwcregexp.h \
	 rwcstring.h rwcsubstring.h rwdefs.h \
	 soGetErrno.h sysdepend.h

fileselector.o : \
	 assert.h bool.h filename.h \
	 fileselector.cpp fileselector.h guiapp.h \
	 guicolortext.h mbt_exception.h motifutils.h \
	 rwcstring.h rwcsubstring.h rwdefs.h \
	 rwtptrorderedvector.h rwtptrorderedvector_inc.cpp rwtvalorderedvector.h \
	 rwtvalorderedvector_inc.cpp soEmptyString.h soGetErrno.h \
	 sysdepend.h

findAncestralTrees.o : \
	 assemblyViewTagTypeAndLine.h assert.h bool.h \
	 consedParameters.h consedResources.h filename.h \
	 findAncestralTrees.cpp findAncestralTrees.h mbtPtrOrderedVector.h \
	 mbtValOrderedVectorOfRWCString.h mbt_exception.h restrictionEnzyme.h \
	 rwcstring.h rwcsubstring.h rwdefs.h \
	 rwtptrorderedvector.h rwtptrorderedvector_inc.cpp rwtptrvector.h \
	 rwtvalorderedvector.h rwtvalorderedvector_inc.cpp soEmptyString.h \
	 soGetErrno.h sysdepend.h whatIsRunning.h

findPrimerMatchesAgainstSequencesInFile.o : \
	 assemblyViewTagTypeAndLine.h assert.h blockOfLocationsOfA4MerType.h \
	 bool.h compareOnePrimerAndOneSequence.h complementSequence.h \
	 consedParameters.h consedResources.h contigMatchTablesType.h \
	 filename.h findPrimerMatchesAgainstSequencesInFile.cpp findPrimerMatchesAgainstSequencesInFile.h \
	 makeVectorLookupTables.h mbtPtrOrderedVector.h mbtValOrderedVectorOfRWCString.h \
	 mbt_exception.h primerType.h readPrimerScreenSequences.h \
	 restrictionEnzyme.h rwcstring.h rwcsubstring.h \
	 rwdefs.h rwtptrorderedvector.h rwtptrorderedvector_inc.cpp \
	 rwtvalorderedvector.h rwtvalorderedvector_inc.cpp setPrimerFalseMatchScoreArray.h \
	 soEmptyString.h soGetErrno.h sysdepend.h \
	 whatIsRunning.h

findPrimerMatchesElsewhere.o : \
	 abs.h assembly.h assemblyViewTagTypeAndLine.h \
	 assert.h autoFinishPurposes.h bIntersect.h \
	 bIntervalsIntersect.h basesegment.h blockOfLocationsOfA4MerType.h \
	 bool.h cComplementBase.h cComplementBaseTable.h \
	 compareContigs.h compareContigsCursor.h compareContigsTypes.h \
	 consed.h consedParameters.h consedResources.h \
	 contig.h contigEnd.h contigMatchTablesType.h \
	 contigSegment.h contigview.h contigwin.h \
	 dictionary.h distribution.h editCursor.h \
	 editaction.h experiment.h expidAndLocatedFragment.h \
	 filename.h findPrimerMatchesElsewhere.cpp findPrimerMatchesElsewhere.h \
	 gotoList.h gotoListType.h guiDisplayDigest.h \
	 guiMultiContigNavigator.h guiapp.h guicolortext.h \
	 listOfFragments.h locatedFragment.h lookForFalsePrimerMatchesOfOnePrimerInOneContig.h \
	 matchWithinAssembly.h max.h mbtPtrOrderedVector.h \
	 mbtPtrVector.h mbtValOrderedVectorOfRWCString.h mbtValVector.h \
	 mbtValVectorOfBool.h mbtValVector_inc.cpp mbt_exception.h \
	 mbt_val_ord_offset_vec.h min.h motifutils.h \
	 multiProblemGotoList.h nMAX_QUALITY_LEVEL2.h ntide.h \
	 numutil.h paddedFromUnpadded.h primerType.h \
	 quality.h readTypes.h readsSortedByLeftEndPosition.h \
	 readsSortedByReadName.h readsSortedByTemplateName.h restrictionEnzyme.h \
	 restrictionFragment.h rwbtreedictionary.h rwcstring.h \
	 rwcsubstring.h rwdefs.h rwtptrorderedvector.h \
	 rwtptrorderedvector_inc.cpp rwtptrsortedvector.h rwtptrvector.h \
	 rwtvalorderedvector.h rwtvalorderedvector_inc.cpp rwtvalsortedvector.h \
	 rwtvalvector.h selection.h sequence.h \
	 setPrimerFalseMatchScoreArray.h singletInfo.h singletsSortedByTemplateName.h \
	 soEmptyString.h soGetErrno.h subcloneTTemplate.h \
	 sysdepend.h tag.h templatesSortedByName.h \
	 tracefile.h unpaddedFromPadded.h visibleLineForRestrictionFragments.h \
	 whatIsRunning.h wholeAssemblyItem.h wholeReadItem.h

findPrimerSelfMatches.o : \
	 blockOfLocationsOfA4MerType.h bool.h contigMatchTablesType.h \
	 findPrimerSelfMatches.cpp findPrimerSelfMatches.h findStickiestSelfMatch.h \
	 primerType.h

findQueryWithinSubject.o : \
	 abs.h assemblyViewTagTypeAndLine.h assert.h \
	 bIntersect.h bIntervalsIntersect.h bool.h \
	 consedParameters.h consedResources.h filename.h \
	 findQueryWithinSubject.cpp findQueryWithinSubject.h getAlignment.h \
	 max.h mbtPtrOrderedVector.h mbtValOrderedVectorOfRWCString.h \
	 mbt_exception.h min.h numutil.h \
	 restrictionEnzyme.h rwcstring.h rwcsubstring.h \
	 rwdefs.h rwtptrorderedvector.h rwtptrorderedvector_inc.cpp \
	 rwtvalorderedvector.h rwtvalorderedvector_inc.cpp soEmptyString.h \
	 soGetErrno.h sysdepend.h whatIsRunning.h

findRepeat.o : \
	 assemblyViewTagTypeAndLine.h assert.h bool.h \
	 consedParameters.h consedResources.h filename.h \
	 findRepeat.cpp findRepeat.h max.h \
	 mbtPtrOrderedVector.h mbtValOrderedVectorOfRWCString.h mbt_exception.h \
	 min.h restrictionEnzyme.h rwcstring.h \
	 rwcsubstring.h rwdefs.h rwtptrorderedvector.h \
	 rwtptrorderedvector_inc.cpp rwtvalorderedvector.h rwtvalorderedvector_inc.cpp \
	 setMatchMatrix.h soEmptyString.h soGetErrno.h \
	 sysdepend.h whatIsRunning.h

findStickiestSelfMatch.o : \
	 abs.h assemblyViewTagTypeAndLine.h assert.h \
	 bIntersect.h bIntervalsIntersect.h blockOfLocationsOfA4MerType.h \
	 bool.h complementSequence.h consedParameters.h \
	 consedResources.h contigMatchTablesType.h filename.h \
	 findStickiestSelfMatch.cpp max.h mbtPtrOrderedVector.h \
	 mbtValOrderedVectorOfRWCString.h mbt_exception.h min.h \
	 nFindScoreOfSelfMatch.h numutil.h primerType.h \
	 restrictionEnzyme.h rwcstring.h rwcsubstring.h \
	 rwdefs.h rwtptrorderedvector.h rwtptrorderedvector_inc.cpp \
	 rwtvalorderedvector.h rwtvalorderedvector_inc.cpp setPrimerFalseMatchScoreArray.h \
	 soEmptyString.h soGetErrno.h sysdepend.h \
	 whatIsRunning.h

findTemplatesForPrimers.o : \
	 assemblyViewTagTypeAndLine.h assert.h autoFinishPurposes.h \
	 basesegment.h blockOfLocationsOfA4MerType.h bool.h \
	 cComplementBase.h cComplementBaseTable.h consedParameters.h \
	 consedResources.h contig.h contigEnd.h \
	 contigMatchTablesType.h dictionary.h distribution.h \
	 experiment.h filename.h findTemplatesForPrimers.cpp \
	 findTemplatesForPrimers.h locatedFragment.h mbtPtrOrderedVector.h \
	 mbtPtrVector.h mbtValOrderedVectorOfRWCString.h mbtValVector.h \
	 mbtValVectorOfBool.h mbtValVector_inc.cpp mbt_exception.h \
	 mbt_val_ord_offset_vec.h min.h nMAX_QUALITY_LEVEL2.h \
	 ntide.h paddedFromUnpadded.h primerType.h \
	 quality.h readTypes.h readsSortedByLeftEndPosition.h \
	 readsSortedByReadName.h restrictionEnzyme.h rwbtreedictionary.h \
	 rwcstring.h rwcsubstring.h rwdefs.h \
	 rwtptrorderedvector.h rwtptrorderedvector_inc.cpp rwtptrsortedvector.h \
	 rwtptrvector.h rwtvalorderedvector.h rwtvalorderedvector_inc.cpp \
	 rwtvalsortedvector.h rwtvalvector.h sequence.h \
	 soEmptyString.h soGetErrno.h subcloneTTemplate.h \
	 sysdepend.h tag.h tracefile.h \
	 unpaddedFromPadded.h whatIsRunning.h wholeReadItem.h

findTraceExtrema.o : \
	 chromatData.h findTraceExtrema.c typeDef.h

fixContigEnd.o : \
	 abs.h assembly.h assemblyViewTagTypeAndLine.h \
	 assert.h autoFinishPurposes.h bIntersect.h \
	 bIntervalsIntersect.h basesegment.h blockOfLocationsOfA4MerType.h \
	 bool.h cComplementBase.h cComplementBaseTable.h \
	 compareContigs.h compareContigsCursor.h compareContigsTypes.h \
	 consed.h consedParameters.h consedResources.h \
	 contig.h contigEnd.h contigMatchTablesType.h \
	 contigSegment.h contigview.h contigwin.h \
	 dictionary.h distribution.h editCursor.h \
	 editaction.h experiment.h expidAndLocatedFragment.h \
	 fileDefines.h filename.h fixContigEnd.cpp \
	 fixContigEnd.h fullSmithWaterman.h getAlignment.h \
	 gotoList.h gotoListType.h guiDisplayDigest.h \
	 guiMultiContigNavigator.h guiapp.h guicolortext.h \
	 listOfFragments.h locatedFragment.h matchWithinAssembly.h \
	 max.h mbtPtrOrderedVector.h mbtPtrVector.h \
	 mbtValOrderedVectorOfRWCString.h mbtValVector.h mbtValVectorOfBool.h \
	 mbtValVector_inc.cpp mbt_exception.h mbt_val_ord_offset_vec.h \
	 min.h motifutils.h multiProblemGotoList.h \
	 nMAX_QUALITY_LEVEL2.h ntide.h numutil.h \
	 paddedFromUnpadded.h paddedPieceOfRead.h primerType.h \
	 quality.h readTypes.h readsSortedByLeftEndPosition.h \
	 readsSortedByReadName.h readsSortedByTemplateName.h restrictionEnzyme.h \
	 restrictionFragment.h rwbtreedictionary.h rwcstring.h \
	 rwcsubstring.h rwdefs.h rwtptrorderedvector.h \
	 rwtptrorderedvector_inc.cpp rwtptrsortedvector.h rwtptrvector.h \
	 rwtvalorderedvector.h rwtvalorderedvector_inc.cpp rwtvalsortedvector.h \
	 rwtvalvector.h selection.h sequence.h \
	 singletInfo.h singletsSortedByTemplateName.h soAddCommas.h \
	 soEmptyString.h soGetErrno.h subcloneTTemplate.h \
	 sysdepend.h szGetTime.h tag.h \
	 templatesSortedByName.h tracefile.h unpaddedFromPadded.h \
	 visibleLineForRestrictionFragments.h whatIsRunning.h wholeAssemblyItem.h \
	 wholeReadItem.h

fixContigEnds.o : \
	 abs.h assembly.h assemblyViewTagTypeAndLine.h \
	 assert.h autoFinishPurposes.h bIntersect.h \
	 bIntervalsIntersect.h basesegment.h blockOfLocationsOfA4MerType.h \
	 bool.h cComplementBase.h cComplementBaseTable.h \
	 compareContigs.h compareContigsCursor.h compareContigsTypes.h \
	 consed.h consedParameters.h consedResources.h \
	 contig.h contigEnd.h contigMatchTablesType.h \
	 contigSegment.h contigview.h contigwin.h \
	 dictionary.h distribution.h editCursor.h \
	 editaction.h experiment.h expidAndLocatedFragment.h \
	 fileDefines.h filename.h fixContigEnd.h \
	 fixContigEnds.cpp fixContigEnds.h gotoList.h \
	 gotoListType.h guiDisplayDigest.h guiMultiContigNavigator.h \
	 guiapp.h guicolortext.h library.h \
	 listOfFragments.h listOfLibraries.h locatedFragment.h \
	 matchWithinAssembly.h max.h maybeTerminateIfAnotherReadWriteConsed.h \
	 mbtPtrOrderedVector.h mbtPtrVector.h mbtValOrderedVectorOfRWCString.h \
	 mbtValVector.h mbtValVectorOfBool.h mbtValVector_inc.cpp \
	 mbt_exception.h mbt_val_ord_offset_vec.h min.h \
	 motifutils.h multiProblemGotoList.h nMAX_QUALITY_LEVEL2.h \
	 ntide.h numutil.h openLogFiles.h \
	 paddedFromUnpadded.h primerType.h quality.h \
	 readTypes.h readsSortedByLeftEndPosition.h readsSortedByReadName.h \
	 readsSortedByTemplateName.h restrictionEnzyme.h restrictionFragment.h \
	 rwbtreedictionary.h rwcstring.h rwcsubstring.h \
	 rwctokenizer.h rwdefs.h rwtptrorderedvector.h \
	 rwtptrorderedvector_inc.cpp rwtptrsortedvector.h rwtptrvector.h \
	 rwtvalorderedvector.h rwtvalorderedvector_inc.cpp rwtvalsortedvector.h \
	 rwtvalvector.h selection.h sequence.h \
	 singletInfo.h singletsSortedByTemplateName.h soEmptyString.h \
	 soGetDateTime.h soGetErrno.h soLine.h \
	 subcloneTTemplate.h sysdepend.h szGetTime.h \
	 tag.h templatesSortedByName.h terminateIfNoPhdDir.h \
	 tracefile.h unpaddedFromPadded.h visibleLineForRestrictionFragments.h \
	 whatIsRunning.h wholeAssemblyItem.h wholeReadItem.h

fragment_and_contig.o : \
	 assemblyViewTagTypeAndLine.h assert.h autoFinishPurposes.h \
	 basesegment.h blockOfLocationsOfA4MerType.h bool.h \
	 cComplementBase.h cComplementBaseTable.h consedParameters.h \
	 consedResources.h contig.h contigEnd.h \
	 contigMatchTablesType.h dictionary.h distribution.h \
	 experiment.h filename.h fragment_and_contig.cpp \
	 fragment_and_contig.h locatedFragment.h mbtPtrOrderedVector.h \
	 mbtPtrVector.h mbtValOrderedVectorOfRWCString.h mbtValVector.h \
	 mbtValVectorOfBool.h mbtValVector_inc.cpp mbt_exception.h \
	 mbt_val_ord_offset_vec.h min.h nMAX_QUALITY_LEVEL2.h \
	 ntide.h paddedFromUnpadded.h primerType.h \
	 quality.h readTypes.h readsSortedByLeftEndPosition.h \
	 readsSortedByReadName.h restrictionEnzyme.h rwbtreedictionary.h \
	 rwcstring.h rwcsubstring.h rwdefs.h \
	 rwtptrorderedvector.h rwtptrorderedvector_inc.cpp rwtptrsortedvector.h \
	 rwtptrvector.h rwtvalorderedvector.h rwtvalorderedvector_inc.cpp \
	 rwtvalsortedvector.h rwtvalvector.h sequence.h \
	 soEmptyString.h soGetErrno.h subcloneTTemplate.h \
	 sysdepend.h tag.h tracefile.h \
	 unpaddedFromPadded.h whatIsRunning.h wholeReadItem.h

fullSmithWaterman.o : \
	 assemblyViewTagTypeAndLine.h assert.h bool.h \
	 consedParameters.h consedResources.h fileDefines.h \
	 filename.h fullSmithWaterman.cpp fullSmithWaterman.h \
	 mbtPtrOrderedVector.h mbtValOrderedVectorOfRWCString.h mbt_exception.h \
	 restrictionEnzyme.h rwcstring.h rwcsubstring.h \
	 rwdefs.h rwtptrorderedvector.h rwtptrorderedvector_inc.cpp \
	 rwtvalorderedvector.h rwtvalorderedvector_inc.cpp soEmptyString.h \
	 soGetErrno.h sysdepend.h whatIsRunning.h

fwdRevPairLine.o : \
	 arrayOfFwdRevPairLines.h arrayOfFwdRevPairSquares.h arrayOfFwdRevPairTriangles.h \
	 assemblyView.h assemblyViewTagTypeAndLine.h assert.h \
	 bool.h consedParameters.h consedResources.h \
	 filename.h fwdRevPair2.h fwdRevPairLine.cpp \
	 fwdRevPairLine.h fwdRevPairSquare.h fwdRevPairTriangle.h \
	 guiapp.h guicolortext.h max.h \
	 mbtPtrOrderedVector.h mbtValOrderedVectorOfRWCString.h mbt_exception.h \
	 min.h motifutils.h restrictionEnzyme.h \
	 rwcstring.h rwcsubstring.h rwdefs.h \
	 rwt2dptrvector.h rwtptrorderedvector.h rwtptrorderedvector_inc.cpp \
	 rwtvalorderedvector.h rwtvalorderedvector_inc.cpp seqMatch.h \
	 soEmptyString.h soGetErrno.h sysdepend.h \
	 whatIsRunning.h

fwdRevPairSquare.o : \
	 arrayOfFwdRevPairLines.h arrayOfFwdRevPairSquares.h arrayOfFwdRevPairTriangles.h \
	 assemblyView.h assemblyViewTagTypeAndLine.h assert.h \
	 bool.h consedParameters.h consedResources.h \
	 filename.h fwdRevPair2.h fwdRevPairLine.h \
	 fwdRevPairSquare.cpp fwdRevPairSquare.h fwdRevPairTriangle.h \
	 guiapp.h guicolortext.h max.h \
	 mbtPtrOrderedVector.h mbtValOrderedVectorOfRWCString.h mbt_exception.h \
	 min.h motifutils.h restrictionEnzyme.h \
	 rwcstring.h rwcsubstring.h rwdefs.h \
	 rwt2dptrvector.h rwtptrorderedvector.h rwtptrorderedvector_inc.cpp \
	 rwtvalorderedvector.h rwtvalorderedvector_inc.cpp seqMatch.h \
	 soEmptyString.h soGetErrno.h sysdepend.h \
	 whatIsRunning.h

fwdRevPairTriangle.o : \
	 arrayOfFwdRevPairLines.h arrayOfFwdRevPairSquares.h arrayOfFwdRevPairTriangles.h \
	 assemblyView.h assemblyViewTagTypeAndLine.h assert.h \
	 bool.h consedParameters.h consedResources.h \
	 filename.h fwdRevPair2.h fwdRevPairLine.h \
	 fwdRevPairSquare.h fwdRevPairTriangle.cpp fwdRevPairTriangle.h \
	 guiapp.h guicolortext.h max.h \
	 mbtPtrOrderedVector.h mbtValOrderedVectorOfRWCString.h mbt_exception.h \
	 min.h motifutils.h restrictionEnzyme.h \
	 rwcstring.h rwcsubstring.h rwdefs.h \
	 rwt2dptrvector.h rwtptrorderedvector.h rwtptrorderedvector_inc.cpp \
	 rwtvalorderedvector.h rwtvalorderedvector_inc.cpp seqMatch.h \
	 soEmptyString.h soGetErrno.h sysdepend.h \
	 whatIsRunning.h

geneClassifications.o : \
	 assert.h bIntersect.h bool.h \
	 cComplementBase.h cComplementBaseTable.h cGetProtein.h \
	 filename.h geneClassifications.cpp geneClassifications.h \
	 max.h mbt_exception.h min.h \
	 rwcstring.h rwcsubstring.h rwctokenizer.h \
	 rwdefs.h rwtvalorderedvector.h rwtvalorderedvector_inc.cpp \
	 soAddCommas.h soEmptyString.h soGetDateTime.h \
	 soGetErrno.h soLine.h sysdepend.h

getAlignment.o : \
	 assert.h bool.h getAlignment.cpp \
	 mbtValOrderedVectorOfInt.h mbt_exception.h printAlignment.h \
	 rwcstring.h rwcsubstring.h rwdefs.h \
	 rwtvalorderedvector.h rwtvalorderedvector_inc.cpp soEmptyString.h \
	 soGetErrno.h

getAlignmentBanded.o : \
	 assert.h bool.h getAlignmentBanded.cpp \
	 getAlignmentBanded.h max.h mbt_exception.h \
	 min.h rwcstring.h rwcsubstring.h \
	 rwdefs.h setMatchMatrix.h soGetErrno.h

getAllSinglets.o : \
	 abs.h assembly.h assemblyViewTagTypeAndLine.h \
	 assert.h autoFinishPurposes.h bIntersect.h \
	 bIntervalsIntersect.h basesegment.h blockOfLocationsOfA4MerType.h \
	 bool.h cComplementBase.h cComplementBaseTable.h \
	 compareContigs.h compareContigsCursor.h compareContigsTypes.h \
	 consed.h consedParameters.h consedResources.h \
	 contig.h contigEnd.h contigMatchTablesType.h \
	 contigSegment.h contigview.h contigwin.h \
	 dictionary.h distribution.h editCursor.h \
	 editaction.h experiment.h expidAndLocatedFragment.h \
	 filename.h getAllSinglets.cpp getAllSinglets.h \
	 gotoList.h gotoListType.h guiDisplayDigest.h \
	 guiMultiContigNavigator.h guiapp.h guicolortext.h \
	 listOfFragments.h locatedFragment.h matchWithinAssembly.h \
	 max.h mbtPtrOrderedVector.h mbtPtrVector.h \
	 mbtValOrderedVectorOfRWCString.h mbtValVector.h mbtValVectorOfBool.h \
	 mbtValVector_inc.cpp mbt_exception.h mbt_val_ord_offset_vec.h \
	 min.h motifutils.h multiProblemGotoList.h \
	 nMAX_QUALITY_LEVEL2.h ntide.h numutil.h \
	 paddedFromUnpadded.h primerType.h quality.h \
	 readTypes.h readsSortedByLeftEndPosition.h readsSortedByReadName.h \
	 readsSortedByTemplateName.h restrictionEnzyme.h restrictionFragment.h \
	 rwbtreedictionary.h rwcregexp.h rwcstring.h \
	 rwcsubstring.h rwdefs.h rwtptrorderedvector.h \
	 rwtptrorderedvector_inc.cpp rwtptrsortedvector.h rwtptrvector.h \
	 rwtvalorderedvector.h rwtvalorderedvector_inc.cpp rwtvalsortedvector.h \
	 rwtvalvector.h selection.h sequence.h \
	 singletInfo.h singletsSortedByTemplateName.h soEmptyString.h \
	 soGetErrno.h subcloneTTemplate.h sysdepend.h \
	 tag.h templatesSortedByName.h tracefile.h \
	 unpaddedFromPadded.h visibleLineForRestrictionFragments.h whatIsRunning.h \
	 wholeAssemblyItem.h wholeReadItem.h

getAllTokens.o : \
	 assert.h bool.h getAllTokens.cpp \
	 getAllTokens.h mbtValOrderedVectorOfRWCString.h mbt_exception.h \
	 rwcstring.h rwcsubstring.h rwctokenizer.h \
	 rwdefs.h rwtvalorderedvector.h rwtvalorderedvector_inc.cpp \
	 soEmptyString.h soGetErrno.h

getNextToken.o : \
	 bool.h getNextToken.cpp getNextToken.h

gotoList.o : \
	 abs.h assemblyViewTagTypeAndLine.h assert.h \
	 autoFinishPurposes.h bIntervalsIntersect.h bIsNumeric.h \
	 basesegment.h blockOfLocationsOfA4MerType.h bool.h \
	 cComplementBase.h cComplementBaseTable.h consedParameters.h \
	 consedResources.h contig.h contigEnd.h \
	 contigMatchTablesType.h dictionary.h distribution.h \
	 experiment.h filename.h gotoList.cpp \
	 gotoList.h locatedFragment.h mbtPtrOrderedVector.h \
	 mbtPtrVector.h mbtValOrderedVectorOfRWCString.h mbtValVector.h \
	 mbtValVectorOfBool.h mbtValVector_inc.cpp mbt_exception.h \
	 mbt_val_ord_offset_vec.h min.h nMAX_QUALITY_LEVEL2.h \
	 ntide.h paddedFromUnpadded.h primerType.h \
	 quality.h readTypes.h readsSortedByLeftEndPosition.h \
	 readsSortedByReadName.h restrictionEnzyme.h rwbtreedictionary.h \
	 rwcstring.h rwcsubstring.h rwdefs.h \
	 rwtptrorderedvector.h rwtptrorderedvector_inc.cpp rwtptrsortedvector.h \
	 rwtptrvector.h rwtvalorderedvector.h rwtvalorderedvector_inc.cpp \
	 rwtvalsortedvector.h rwtvalvector.h sequence.h \
	 soEmptyString.h soGetErrno.h subcloneTTemplate.h \
	 sysdepend.h tag.h tracefile.h \
	 unpaddedFromPadded.h whatIsRunning.h wholeReadItem.h

guiAddNewReads.o : \
	 assert.h bInputEventToWrongWindow.h bool.h \
	 filename.h guiAddNewReads.cpp guiAddNewReads.h \
	 guiapp.h guicolortext.h handleWindowManagerDelete2.h \
	 hp_exception_kludge.h mbt_exception.h motifutils.h \
	 popupErrorMessage2.h rwcstring.h rwcsubstring.h \
	 rwdefs.h rwtptrorderedvector.h rwtptrorderedvector_inc.cpp \
	 rwtvalorderedvector.h rwtvalorderedvector_inc.cpp soEmptyString.h \
	 soGetErrno.h sysdepend.h

guiAskUserToSelectReadListOptions.o : \
	 assemblyViewTagTypeAndLine.h assert.h bool.h \
	 consedParameters.h consedResources.h filename.h \
	 guiAskUserToSelectReadListOptions.cpp guiAskUserToSelectReadListOptions.h guiapp.h \
	 guicolortext.h handleWindowManagerDelete.h mbtPtrOrderedVector.h \
	 mbtValOrderedVectorOfRWCString.h mbt_exception.h motifutils.h \
	 restrictionEnzyme.h rwcstring.h rwcsubstring.h \
	 rwctokenizer.h rwdefs.h rwtptrorderedvector.h \
	 rwtptrorderedvector_inc.cpp rwtvalorderedvector.h rwtvalorderedvector_inc.cpp \
	 soEmptyString.h soGetErrno.h sysdepend.h \
	 whatIsRunning.h

guiAssemblyViewIncludeContigs.o : \
	 abs.h arrayOfFwdRevPairLines.h arrayOfFwdRevPairSquares.h \
	 arrayOfFwdRevPairTriangles.h assembly.h assemblyView.h \
	 assemblyViewTagTypeAndLine.h assert.h autoFinishPurposes.h \
	 bIntersect.h bIntervalsIntersect.h bIsNumericDouble.h \
	 bIsNumericMaybeWithWhitespace.h basesegment.h blockOfLocationsOfA4MerType.h \
	 bool.h cComplementBase.h cComplementBaseTable.h \
	 compareContigs.h compareContigsCursor.h compareContigsTypes.h \
	 consed.h consedParameters.h consedResources.h \
	 contig.h contigEnd.h contigMatchTablesType.h \
	 contigSegment.h contigview.h contigwin.h \
	 dictionary.h distribution.h editCursor.h \
	 editaction.h experiment.h expidAndLocatedFragment.h \
	 filename.h fwdRevPair2.h fwdRevPairLine.h \
	 fwdRevPairSquare.h fwdRevPairTriangle.h gotoList.h \
	 gotoListType.h guiAssemblyViewIncludeContigs.cpp guiAssemblyViewIncludeContigs.h \
	 guiDisplayDigest.h guiMultiContigNavigator.h guiapp.h \
	 guicolortext.h handleWindowManagerDelete2.h hp_exception_kludge.h \
	 listOfFragments.h locatedFragment.h matchWithinAssembly.h \
	 max.h mbtPtrOrderedVector.h mbtPtrVector.h \
	 mbtValOrderedVectorOfRWCString.h mbtValVector.h mbtValVectorOfBool.h \
	 mbtValVector_inc.cpp mbt_exception.h mbt_val_ord_offset_vec.h \
	 min.h motifutils.h multiProblemGotoList.h \
	 nMAX_QUALITY_LEVEL2.h ntide.h numutil.h \
	 paddedFromUnpadded.h popupErrorMessage.h primerType.h \
	 quality.h readTypes.h readsSortedByLeftEndPosition.h \
	 readsSortedByReadName.h readsSortedByTemplateName.h restrictionEnzyme.h \
	 restrictionFragment.h rwbtreedictionary.h rwcstring.h \
	 rwcsubstring.h rwctokenizer.h rwdefs.h \
	 rwt2dptrvector.h rwtptrorderedvector.h rwtptrorderedvector_inc.cpp \
	 rwtptrsortedvector.h rwtptrvector.h rwtvalorderedvector.h \
	 rwtvalorderedvector_inc.cpp rwtvalsortedvector.h rwtvalvector.h \
	 selection.h seqMatch.h sequence.h \
	 singletInfo.h singletsSortedByTemplateName.h soEmptyString.h \
	 soGetErrno.h subcloneTTemplate.h sysdepend.h \
	 tag.h templatesSortedByName.h tracefile.h \
	 unpaddedFromPadded.h visibleLineForRestrictionFragments.h whatIsRunning.h \
	 wholeAssemblyItem.h wholeReadItem.h

guiAssemblyViewReadDepth.o : \
	 arrayOfFwdRevPairLines.h arrayOfFwdRevPairSquares.h arrayOfFwdRevPairTriangles.h \
	 assemblyView.h assemblyViewTagTypeAndLine.h assert.h \
	 bIsNumericMaybeWithWhitespace.h bool.h consedParameters.h \
	 consedResources.h filename.h fwdRevPair2.h \
	 fwdRevPairLine.h fwdRevPairSquare.h fwdRevPairTriangle.h \
	 guiAssemblyViewReadDepth.cpp guiAssemblyViewReadDepth.h guiapp.h \
	 guicolortext.h handleWindowManagerDelete2.h hp_exception_kludge.h \
	 max.h mbtPtrOrderedVector.h mbtValOrderedVectorOfRWCString.h \
	 mbt_exception.h min.h motifutils.h \
	 popupErrorMessage.h restrictionEnzyme.h rwcstring.h \
	 rwcsubstring.h rwdefs.h rwt2dptrvector.h \
	 rwtptrorderedvector.h rwtptrorderedvector_inc.cpp rwtvalorderedvector.h \
	 rwtvalorderedvector_inc.cpp seqMatch.h soEmptyString.h \
	 soGetErrno.h sysdepend.h whatIsRunning.h

guiAssemblyViewShowTags.o : \
	 arrayOfFwdRevPairLines.h arrayOfFwdRevPairSquares.h arrayOfFwdRevPairTriangles.h \
	 assemblyView.h assemblyViewTagTypeAndLine.h assert.h \
	 bIsNumericMaybeWithWhitespace.h bool.h breakIntoShorterLines.h \
	 consedParameters.h consedResources.h filename.h \
	 fwdRevPair2.h fwdRevPairLine.h fwdRevPairSquare.h \
	 fwdRevPairTriangle.h guiAssemblyViewShowTags.cpp guiAssemblyViewShowTags.h \
	 guiapp.h guicolortext.h handleWindowManagerDelete2.h \
	 hp_exception_kludge.h max.h mbtPtrOrderedVector.h \
	 mbtValOrderedVectorOfRWCString.h mbt_exception.h min.h \
	 motifutils.h popupErrorMessage.h restrictionEnzyme.h \
	 rwcstring.h rwcsubstring.h rwdefs.h \
	 rwt2dptrvector.h rwtptrorderedvector.h rwtptrorderedvector_inc.cpp \
	 rwtptrsortedvector.h rwtvalorderedvector.h rwtvalorderedvector_inc.cpp \
	 seqMatch.h soEmptyString.h soGetErrno.h \
	 sysdepend.h tagTypes.h whatIsRunning.h

guiAssemblyViewWhatToShow.o : \
	 abs.h arrayOfFwdRevPairLines.h arrayOfFwdRevPairSquares.h \
	 arrayOfFwdRevPairTriangles.h assembly.h assemblyView.h \
	 assemblyViewTagTypeAndLine.h assert.h autoFinishPurposes.h \
	 bIntersect.h bIntervalsIntersect.h bIsNumericMaybeWithWhitespace.h \
	 basesegment.h blockOfLocationsOfA4MerType.h bool.h \
	 cComplementBase.h cComplementBaseTable.h compareContigs.h \
	 compareContigsCursor.h compareContigsTypes.h consed.h \
	 consedParameters.h consedResources.h contig.h \
	 contigEnd.h contigMatchTablesType.h contigSegment.h \
	 contigview.h contigwin.h dictionary.h \
	 distribution.h editCursor.h editaction.h \
	 experiment.h expidAndLocatedFragment.h filename.h \
	 fwdRevPair2.h fwdRevPairLine.h fwdRevPairSquare.h \
	 fwdRevPairTriangle.h gotoList.h gotoListType.h \
	 guiAssemblyViewWhatToShow.cpp guiAssemblyViewWhatToShow.h guiDisplayDigest.h \
	 guiMultiContigNavigator.h guiapp.h guicolortext.h \
	 handleWindowManagerDelete2.h hp_exception_kludge.h listOfFragments.h \
	 locatedFragment.h matchWithinAssembly.h max.h \
	 mbtPtrOrderedVector.h mbtPtrVector.h mbtValOrderedVectorOfRWCString.h \
	 mbtValVector.h mbtValVectorOfBool.h mbtValVector_inc.cpp \
	 mbt_exception.h mbt_val_ord_offset_vec.h min.h \
	 motifutils.h multiProblemGotoList.h nMAX_QUALITY_LEVEL2.h \
	 ntide.h numutil.h paddedFromUnpadded.h \
	 popupErrorMessage.h popupErrorMessage2.h primerType.h \
	 quality.h readTypes.h readsSortedByLeftEndPosition.h \
	 readsSortedByReadName.h readsSortedByTemplateName.h restrictionEnzyme.h \
	 restrictionFragment.h rwbtreedictionary.h rwcstring.h \
	 rwcsubstring.h rwdefs.h rwt2dptrvector.h \
	 rwtptrorderedvector.h rwtptrorderedvector_inc.cpp rwtptrsortedvector.h \
	 rwtptrvector.h rwtvalorderedvector.h rwtvalorderedvector_inc.cpp \
	 rwtvalsortedvector.h rwtvalvector.h selection.h \
	 seqMatch.h sequence.h singletInfo.h \
	 singletsSortedByTemplateName.h soEmptyString.h soGetErrno.h \
	 subcloneTTemplate.h sysdepend.h tag.h \
	 templatesSortedByName.h tracefile.h unpaddedFromPadded.h \
	 visibleLineForRestrictionFragments.h whatIsRunning.h wholeAssemblyItem.h \
	 wholeReadItem.h

guiChangeColor.o : \
	 abs.h assembly.h assemblyViewTagTypeAndLine.h \
	 assert.h autoFinishPurposes.h bIntersect.h \
	 bIntervalsIntersect.h basesegment.h blockOfLocationsOfA4MerType.h \
	 bool.h cComplementBase.h cComplementBaseTable.h \
	 colorDefaults.h colormode.h consedParameters.h \
	 consedResources.h contig.h contigEnd.h \
	 contigMatchTablesType.h contigview.h contigwin.h \
	 dictionary.h distribution.h editCursor.h \
	 experiment.h expidAndLocatedFragment.h filename.h \
	 gotoList.h gotoListType.h guiChangeColor.cpp \
	 guiChangeColor.h guiapp.h guicolortext.h \
	 guicontigwin.h handleWindowManagerDelete2.h hp_exception_kludge.h \
	 infobutton.h listOfFragments.h locatedFragment.h \
	 matchWithinAssembly.h max.h mbtPtrOrderedVector.h \
	 mbtPtrVector.h mbtValOrderedVectorOfRWCString.h mbtValVector.h \
	 mbtValVectorOfBool.h mbtValVector_inc.cpp mbt_exception.h \
	 mbt_val_ord_offset_vec.h min.h motifutils.h \
	 multiProblemGotoList.h nMAX_QUALITY_LEVEL2.h ntide.h \
	 numutil.h paddedFromUnpadded.h primerType.h \
	 quality.h readTypes.h readsSortedByLeftEndPosition.h \
	 readsSortedByReadName.h readsSortedByTemplateName.h restrictionEnzyme.h \
	 rwbtreedictionary.h rwcstring.h rwcsubstring.h \
	 rwdefs.h rwtptrorderedvector.h rwtptrorderedvector_inc.cpp \
	 rwtptrsortedvector.h rwtptrvector.h rwtvalorderedvector.h \
	 rwtvalorderedvector_inc.cpp rwtvalsortedvector.h rwtvalvector.h \
	 sequence.h singletInfo.h singletsSortedByTemplateName.h \
	 soEmptyString.h soGetErrno.h subcloneTTemplate.h \
	 sysdepend.h tag.h tagTypes.h \
	 templatesSortedByName.h textfield.h tracefile.h \
	 unpaddedFromPadded.h whatIsRunning.h wholeAssemblyItem.h \
	 wholeReadItem.h

guiCheckPrimer.o : \
	 abs.h assembly.h assemblyViewTagTypeAndLine.h \
	 assert.h autoFinishPurposes.h bIntersect.h \
	 bIntervalsIntersect.h bIsNumericMaybeWithWhitespace.h basesegment.h \
	 blockOfLocationsOfA4MerType.h bool.h cComplementBase.h \
	 cComplementBaseTable.h calculatePrimerMeltingTemperatures.h checkPrimersForACGT.h \
	 checkPrimersForMononucleotideRepeats.h compareContigs.h compareContigsCursor.h \
	 compareContigsTypes.h complement_so.h consed.h \
	 consedParameters.h consedResources.h contig.h \
	 contigEnd.h contigMatchTablesType.h contigSegment.h \
	 contigview.h contigwin.h createPrimerCandidate.h \
	 dictionary.h distribution.h editCursor.h \
	 editaction.h experiment.h expidAndLocatedFragment.h \
	 filename.h findPrimerMatchesAgainstSequencesInFile.h findPrimerMatchesElsewhere.h \
	 findPrimerSelfMatches.h findStickiestSelfMatch.h findTemplatesForPrimers.h \
	 gotoList.h gotoListType.h guiCheckPrimer.cpp \
	 guiCheckPrimer.h guiDisplayDigest.h guiMultiContigNavigator.h \
	 guiapp.h guicolortext.h handleWindowManagerDelete2.h \
	 hp_exception_kludge.h listOfFragments.h locatedFragment.h \
	 matchWithinAssembly.h max.h mbtPtrOrderedVector.h \
	 mbtPtrVector.h mbtValOrderedVectorOfRWCString.h mbtValVector.h \
	 mbtValVectorOfBool.h mbtValVector_inc.cpp mbt_exception.h \
	 mbt_val_ord_offset_vec.h min.h motifutils.h \
	 multiProblemGotoList.h nMAX_QUALITY_LEVEL2.h ntide.h \
	 numutil.h paddedFromUnpadded.h please_wait.h \
	 popupErrorMessage.h primerStickiestFalseMatch.h primerType.h \
	 quality.h readTypes.h readsSortedByLeftEndPosition.h \
	 readsSortedByReadName.h readsSortedByTemplateName.h restrictionEnzyme.h \
	 restrictionFragment.h rwbtreedictionary.h rwcstring.h \
	 rwcsubstring.h rwdefs.h rwtptrorderedvector.h \
	 rwtptrorderedvector_inc.cpp rwtptrsortedvector.h rwtptrvector.h \
	 rwtvalorderedvector.h rwtvalorderedvector_inc.cpp rwtvalsortedvector.h \
	 rwtvalvector.h selection.h sequence.h \
	 singletInfo.h singletsSortedByTemplateName.h soEmptyString.h \
	 soGetErrno.h subcloneTTemplate.h sysdepend.h \
	 tag.h templatesSortedByName.h textbox.h \
	 tracefile.h unpaddedFromPadded.h visibleLineForRestrictionFragments.h \
	 whatIsRunning.h wholeAssemblyItem.h wholeReadItem.h \
	 whyIsPrimerNotAcceptableTypes.h

guiChoiceOfReadsForAlignedReads.o : \
	 abs.h assembly.h assemblyViewTagTypeAndLine.h \
	 assert.h autoFinishPurposes.h bIntersect.h \
	 bIntervalsIntersect.h basesegment.h blockOfLocationsOfA4MerType.h \
	 bool.h cComplementBase.h cComplementBaseTable.h \
	 choose_contig.h compareContigs.h compareContigsCursor.h \
	 compareContigsTypes.h consed.h consedParameters.h \
	 consedResources.h contig.h contigEnd.h \
	 contigMatchTablesType.h contigSegment.h contigview.h \
	 contigwin.h dictionary.h distribution.h \
	 editCursor.h editaction.h experiment.h \
	 expidAndLocatedFragment.h filename.h fragment_and_contig.h \
	 gotoList.h gotoListType.h guiChoiceOfReadsForAlignedReads.cpp \
	 guiChoiceOfReadsForAlignedReads.h guiDisplayDigest.h guiMultiContigNavigator.h \
	 guiapp.h guicolortext.h handleWindowManagerDelete2.h \
	 hp_exception_kludge.h listOfFragments.h locatedFragment.h \
	 matchWithinAssembly.h max.h mbtPtrOrderedVector.h \
	 mbtPtrVector.h mbtValOrderedVectorOfRWCString.h mbtValVector.h \
	 mbtValVectorOfBool.h mbtValVector_inc.cpp mbt_exception.h \
	 mbt_val_ord_offset_vec.h min.h motifutils.h \
	 multiProblemGotoList.h nMAX_QUALITY_LEVEL2.h ntide.h \
	 numutil.h paddedFromUnpadded.h primerType.h \
	 quality.h readTypes.h readsSortedByLeftEndPosition.h \
	 readsSortedByReadName.h readsSortedByTemplateName.h restrictionEnzyme.h \
	 restrictionFragment.h rwbtreedictionary.h rwcstring.h \
	 rwcsubstring.h rwdefs.h rwtptrorderedvector.h \
	 rwtptrorderedvector_inc.cpp rwtptrsortedvector.h rwtptrvector.h \
	 rwtvalorderedvector.h rwtvalorderedvector_inc.cpp rwtvalsortedvector.h \
	 rwtvalvector.h selection.h sequence.h \
	 singletInfo.h singletsSortedByTemplateName.h soEmptyString.h \
	 soGetErrno.h subcloneTTemplate.h sysdepend.h \
	 tag.h templatesSortedByName.h tracefile.h \
	 unpaddedFromPadded.h visibleLineForRestrictionFragments.h whatIsRunning.h \
	 wholeAssemblyItem.h wholeReadItem.h

guiChoiceOfSeqMatches.o : \
	 abs.h arrayOfFwdRevPairLines.h arrayOfFwdRevPairSquares.h \
	 arrayOfFwdRevPairTriangles.h assembly.h assemblyView.h \
	 assemblyViewTagTypeAndLine.h assert.h autoFinishPurposes.h \
	 bIntersect.h bIntervalsIntersect.h basesegment.h \
	 blockOfLocationsOfA4MerType.h bool.h cComplementBase.h \
	 cComplementBaseTable.h compareContigs.h compareContigsCursor.h \
	 compareContigsTypes.h consed.h consedParameters.h \
	 consedResources.h contig.h contigEnd.h \
	 contigMatchTablesType.h contigSegment.h contigview.h \
	 contigwin.h dictionary.h distribution.h \
	 editCursor.h editaction.h experiment.h \
	 expidAndLocatedFragment.h filename.h fwdRevPair2.h \
	 fwdRevPairLine.h fwdRevPairSquare.h fwdRevPairTriangle.h \
	 gotoList.h gotoListType.h guiChoiceOfSeqMatches.cpp \
	 guiChoiceOfSeqMatches.h guiDisplayDigest.h guiMultiContigNavigator.h \
	 guiapp.h guicolortext.h handleWindowManagerDelete2.h \
	 hp_exception_kludge.h listOfFragments.h locatedFragment.h \
	 matchWithinAssembly.h max.h mbtPtrOrderedVector.h \
	 mbtPtrVector.h mbtValOrderedVectorOfRWCString.h mbtValVector.h \
	 mbtValVectorOfBool.h mbtValVector_inc.cpp mbt_exception.h \
	 mbt_val_ord_offset_vec.h min.h motifutils.h \
	 multiProblemGotoList.h nMAX_QUALITY_LEVEL2.h ntide.h \
	 numutil.h paddedFromUnpadded.h popupErrorMessage2.h \
	 primerType.h quality.h readTypes.h \
	 readsSortedByLeftEndPosition.h readsSortedByReadName.h readsSortedByTemplateName.h \
	 restrictionEnzyme.h restrictionFragment.h rwbtreedictionary.h \
	 rwcstring.h rwcsubstring.h rwdefs.h \
	 rwt2dptrvector.h rwtptrorderedvector.h rwtptrorderedvector_inc.cpp \
	 rwtptrsortedvector.h rwtptrvector.h rwtvalorderedvector.h \
	 rwtvalorderedvector_inc.cpp rwtvalsortedvector.h rwtvalvector.h \
	 selection.h seqMatch.h sequence.h \
	 singletInfo.h singletsSortedByTemplateName.h soEmptyString.h \
	 soGetErrno.h subcloneTTemplate.h sysdepend.h \
	 tag.h templatesSortedByName.h tracefile.h \
	 unpaddedFromPadded.h visibleLineForRestrictionFragments.h whatIsRunning.h \
	 wholeAssemblyItem.h wholeReadItem.h

guiCompareContigs.o : \
	 abs.h assembly.h assemblyViewTagTypeAndLine.h \
	 assert.h autoFinishPurposes.h bIntersect.h \
	 bIntervalsIntersect.h basesegment.h blockOfLocationsOfA4MerType.h \
	 bool.h cComplementBase.h cComplementBaseTable.h \
	 centerWidgetOnWidget.h colorDefaults.h compareContigs.h \
	 compareContigsCursor.h compareContigsTypes.h consedParameters.h \
	 consedResources.h contig.h contigEnd.h \
	 contigMatchTablesType.h contigSegment.h contigview.h \
	 contigwin.h dictionary.h distribution.h \
	 editCursor.h experiment.h expidAndLocatedFragment.h \
	 filename.h gotoList.h gotoListType.h \
	 guiCompareContigs.cpp guiCompareContigs.h guiapp.h \
	 guicolortext.h guicontigwin.h handleWindowManagerDelete.h \
	 hp_exception_kludge.h infobutton.h listOfFragments.h \
	 locatedFragment.h matchWithinAssembly.h max.h \
	 mbtPtrOrderedVector.h mbtPtrVector.h mbtValOrderedVectorOfRWCString.h \
	 mbtValVector.h mbtValVectorOfBool.h mbtValVector_inc.cpp \
	 mbt_exception.h mbt_val_ord_offset_vec.h min.h \
	 motifutils.h multiProblemGotoList.h nMAX_QUALITY_LEVEL2.h \
	 ntide.h numutil.h paddedFromUnpadded.h \
	 primerType.h quality.h readTypes.h \
	 readsSortedByLeftEndPosition.h readsSortedByReadName.h readsSortedByTemplateName.h \
	 restrictionEnzyme.h rwbtreedictionary.h rwcstring.h \
	 rwcsubstring.h rwdefs.h rwtptrorderedvector.h \
	 rwtptrorderedvector_inc.cpp rwtptrsortedvector.h rwtptrvector.h \
	 rwtvalorderedvector.h rwtvalorderedvector_inc.cpp rwtvalsortedvector.h \
	 rwtvalvector.h scaleTickSizes.h sequence.h \
	 singletInfo.h singletsSortedByTemplateName.h soEmptyString.h \
	 soGetErrno.h subcloneTTemplate.h sysdepend.h \
	 tag.h templatesSortedByName.h textfield.h \
	 tracefile.h unpaddedFromPadded.h whatIsRunning.h \
	 wholeAssemblyItem.h wholeReadItem.h

guiDigestProblemNavigator.o : \
	 assert.h bool.h filename.h \
	 guiDigestProblemNavigator.cpp guiDigestProblemNavigator.h guiDisplayDigest.h \
	 guiapp.h guicolortext.h handleWindowManagerDelete2.h \
	 hp_exception_kludge.h mbt_exception.h motifutils.h \
	 popupErrorMessage.h restrictionFragment.h rwcstring.h \
	 rwcsubstring.h rwdefs.h rwtptrorderedvector.h \
	 rwtptrorderedvector_inc.cpp rwtvalorderedvector.h rwtvalorderedvector_inc.cpp \
	 soEmptyString.h soGetErrno.h sysdepend.h \
	 visibleLineForRestrictionFragments.h

guiDisplayDigest.o : \
	 abs.h arrayOfFwdRevPairLines.h arrayOfFwdRevPairSquares.h \
	 arrayOfFwdRevPairTriangles.h arrayOfRestrictionFragments.h assembly.h \
	 assemblyView.h assemblyViewTagTypeAndLine.h assert.h \
	 autoFinishPurposes.h bIntersect.h bIntervalsIntersect.h \
	 basesegment.h blockOfLocationsOfA4MerType.h bool.h \
	 cComplementBase.h cComplementBaseTable.h clScaffold.h \
	 colorDefaults.h compareContigs.h compareContigsCursor.h \
	 compareContigsTypes.h consed.h consedParameters.h \
	 consedResources.h contig.h contigEnd.h \
	 contigMatchTablesType.h contigSegment.h contigview.h \
	 contigwin.h dictionary.h digestForOneEnzyme.h \
	 distribution.h editCursor.h editaction.h \
	 experiment.h expidAndLocatedFragment.h filename.h \
	 fwdRevPair2.h fwdRevPairLine.h fwdRevPairSquare.h \
	 fwdRevPairTriangle.h gotoList.h gotoListType.h \
	 guiDigestProblemNavigator.h guiDisplayDigest.cpp guiDisplayDigest.h \
	 guiFindRestrictionEnzymeSites.h guiMultiContigNavigator.h guiapp.h \
	 guicolortext.h handleWindowManagerDelete2.h hp_exception_kludge.h \
	 listOfFragments.h locatedFragment.h matchWithinAssembly.h \
	 max.h mbtPtrOrderedVector.h mbtPtrVector.h \
	 mbtValOrderedVectorOfRWCString.h mbtValVector.h mbtValVectorOfBool.h \
	 mbtValVector_inc.cpp mbt_exception.h mbt_val_ord_offset_vec.h \
	 min.h motifutils.h multiProblemGotoList.h \
	 nMAX_QUALITY_LEVEL2.h ntide.h numutil.h \
	 paddedFromUnpadded.h popupErrorMessage.h popupErrorMessage2.h \
	 primerType.h quality.h readTypes.h \
	 readsSortedByLeftEndPosition.h readsSortedByReadName.h readsSortedByTemplateName.h \
	 restrictionEnzyme.h restrictionFragment.h rwbtreedictionary.h \
	 rwcstring.h rwcsubstring.h rwdefs.h \
	 rwt2dptrvector.h rwtptrorderedvector.h rwtptrorderedvector_inc.cpp \
	 rwtptrsortedvector.h rwtptrvector.h rwtvalorderedvector.h \
	 rwtvalorderedvector_inc.cpp rwtvalsortedvector.h rwtvalvector.h \
	 selection.h seqMatch.h sequence.h \
	 singletInfo.h singletsSortedByTemplateName.h soEmptyString.h \
	 soGetErrno.h subcloneTTemplate.h sysdepend.h \
	 tag.h templatesSortedByName.h textbox.h \
	 tracefile.h unpaddedFromPadded.h visibleLineForRestrictionFragments.h \
	 waitUntilDialogIsVisible.h whatIsRunning.h wholeAssemblyItem.h \
	 wholeReadItem.h

guiExportConsensusWithOptions.o : \
	 abs.h assembly.h assemblyViewTagTypeAndLine.h \
	 assert.h autoFinishPurposes.h bIntersect.h \
	 bIntervalsIntersect.h bIsNumericMaybeWithWhitespace.h basesegment.h \
	 blockOfLocationsOfA4MerType.h bool.h cComplementBase.h \
	 cComplementBaseTable.h compareContigs.h compareContigsCursor.h \
	 compareContigsTypes.h consed.h consedParameters.h \
	 consedResources.h contig.h contigEnd.h \
	 contigMatchTablesType.h contigSegment.h contigview.h \
	 contigwin.h dictionary.h distribution.h \
	 editCursor.h editaction.h experiment.h \
	 expidAndLocatedFragment.h filename.h gotoList.h \
	 gotoListType.h guiDisplayDigest.h guiExportConsensusWithOptions.cpp \
	 guiExportConsensusWithOptions.h guiMultiContigNavigator.h guiapp.h \
	 guicolortext.h handleWindowManagerDelete2.h hp_exception_kludge.h \
	 listOfFragments.h locatedFragment.h matchWithinAssembly.h \
	 max.h mbtPtrOrderedVector.h mbtPtrVector.h \
	 mbtValOrderedVectorOfRWCString.h mbtValVector.h mbtValVectorOfBool.h \
	 mbtValVector_inc.cpp mbt_exception.h mbt_val_ord_offset_vec.h \
	 min.h motifutils.h multiProblemGotoList.h \
	 nMAX_QUALITY_LEVEL2.h ntide.h numutil.h \
	 paddedFromUnpadded.h popupErrorMessage.h primerType.h \
	 quality.h readTypes.h readsSortedByLeftEndPosition.h \
	 readsSortedByReadName.h readsSortedByTemplateName.h restrictionEnzyme.h \
	 restrictionFragment.h rwbtreedictionary.h rwcstring.h \
	 rwcsubstring.h rwdefs.h rwtptrorderedvector.h \
	 rwtptrorderedvector_inc.cpp rwtptrsortedvector.h rwtptrvector.h \
	 rwtvalorderedvector.h rwtvalorderedvector_inc.cpp rwtvalsortedvector.h \
	 rwtvalvector.h selection.h sequence.h \
	 singletInfo.h singletsSortedByTemplateName.h soEmptyString.h \
	 soGetErrno.h subcloneTTemplate.h sysdepend.h \
	 tag.h templatesSortedByName.h tracefile.h \
	 unpaddedFromPadded.h visibleLineForRestrictionFragments.h whatIsRunning.h \
	 wholeAssemblyItem.h wholeReadItem.h

guiFindRestrictionEnzymeSites.o : \
	 abs.h arrayOfRestrictionFragments.h assembly.h \
	 assemblyViewTagTypeAndLine.h assert.h autoFinishPurposes.h \
	 bGuiGetAnswerYesNo.h bIntersect.h bIntervalsIntersect.h \
	 bIsNumericMaybeWithWhitespace.h basesegment.h blockOfLocationsOfA4MerType.h \
	 bool.h cComplementBase.h cComplementBaseTable.h \
	 clScaffold.h compareContigs.h compareContigsCursor.h \
	 compareContigsTypes.h complement_so.h consed.h \
	 consedParameters.h consedResources.h contig.h \
	 contigEnd.h contigMatchTablesType.h contigSegment.h \
	 contigview.h contigwin.h dictionary.h \
	 digestForOneEnzyme.h distribution.h editCursor.h \
	 editaction.h experiment.h expidAndLocatedFragment.h \
	 filename.h gotoList.h gotoListType.h \
	 guiDisplayDigest.h guiFindRestrictionEnzymeSites.cpp guiFindRestrictionEnzymeSites.h \
	 guiMultiContigNavigator.h guiapp.h guicolortext.h \
	 handleWindowManagerDelete2.h hp_exception_kludge.h listOfFragments.h \
	 locatedFragment.h matchWithinAssembly.h max.h \
	 mbtPtrOrderedVector.h mbtPtrVector.h mbtValOrderedVectorOfRWCString.h \
	 mbtValVector.h mbtValVectorOfBool.h mbtValVector_inc.cpp \
	 mbt_exception.h mbt_val_ord_offset_vec.h min.h \
	 motifutils.h multiProblemGotoList.h nMAX_QUALITY_LEVEL2.h \
	 ntide.h numutil.h paddedFromUnpadded.h \
	 please_wait.h popupErrorMessage.h popupErrorMessage2.h \
	 primerType.h quality.h readTypes.h \
	 readsSortedByLeftEndPosition.h readsSortedByReadName.h readsSortedByTemplateName.h \
	 restrictionEnzyme.h restrictionFragment.h rwbtreedictionary.h \
	 rwcstring.h rwcsubstring.h rwctokenizer.h \
	 rwdefs.h rwtptrorderedvector.h rwtptrorderedvector_inc.cpp \
	 rwtptrsortedvector.h rwtptrvector.h rwtvalorderedvector.h \
	 rwtvalorderedvector_inc.cpp rwtvalsortedvector.h rwtvalvector.h \
	 selection.h sequence.h singletInfo.h \
	 singletsSortedByTemplateName.h soEmptyString.h soGetErrno.h \
	 subcloneTTemplate.h sysdepend.h tag.h \
	 templatesSortedByName.h tracefile.h unpaddedFromPadded.h \
	 visibleLineForRestrictionFragments.h whatIsRunning.h wholeAssemblyItem.h \
	 wholeReadItem.h

guiGetCommentForTag.o : \
	 abs.h assembly.h assemblyViewTagTypeAndLine.h \
	 assert.h autoFinishPurposes.h bIntersect.h \
	 bIntervalsIntersect.h bIsNumericMaybeWithWhitespace.h basesegment.h \
	 blockOfLocationsOfA4MerType.h bool.h cComplementBase.h \
	 cComplementBaseTable.h consedParameters.h consedResources.h \
	 contig.h contigEnd.h contigMatchTablesType.h \
	 contigview.h contigwin.h dictionary.h \
	 distribution.h editCursor.h experiment.h \
	 expidAndLocatedFragment.h filename.h gotoList.h \
	 gotoListType.h guiGetCommentForTag.cpp guiGetCommentForTag.h \
	 guiapp.h guicolortext.h guicontigwin.h \
	 handleWindowManagerDelete2.h infobutton.h listOfFragments.h \
	 locatedFragment.h matchWithinAssembly.h max.h \
	 mbtPtrOrderedVector.h mbtPtrVector.h mbtValOrderedVectorOfRWCString.h \
	 mbtValVector.h mbtValVectorOfBool.h mbtValVector_inc.cpp \
	 mbt_exception.h mbt_val_ord_offset_vec.h min.h \
	 motifutils.h multiProblemGotoList.h nMAX_QUALITY_LEVEL2.h \
	 ntide.h numutil.h paddedFromUnpadded.h \
	 primerType.h quality.h readTypes.h \
	 readsSortedByLeftEndPosition.h readsSortedByReadName.h readsSortedByTemplateName.h \
	 restrictionEnzyme.h rwbtreedictionary.h rwcregexp.h \
	 rwcstring.h rwcsubstring.h rwdefs.h \
	 rwtptrorderedvector.h rwtptrorderedvector_inc.cpp rwtptrsortedvector.h \
	 rwtptrvector.h rwtvalorderedvector.h rwtvalorderedvector_inc.cpp \
	 rwtvalsortedvector.h rwtvalvector.h sequence.h \
	 singletInfo.h singletsSortedByTemplateName.h soEmptyString.h \
	 soGetErrno.h subcloneTTemplate.h sysdepend.h \
	 tag.h templatesSortedByName.h textfield.h \
	 tracefile.h unpaddedFromPadded.h whatIsRunning.h \
	 wholeAssemblyItem.h wholeReadItem.h

guiGetReferenceRead.o : \
	 abs.h assembly.h assemblyViewTagTypeAndLine.h \
	 assert.h autoFinishPurposes.h bIntersect.h \
	 bIntervalsIntersect.h bIsNumericMaybeWithWhitespace.h basesegment.h \
	 blockOfLocationsOfA4MerType.h bool.h cComplementBase.h \
	 cComplementBaseTable.h consedParameters.h consedResources.h \
	 contig.h contigEnd.h contigMatchTablesType.h \
	 contigview.h contigwin.h dictionary.h \
	 distribution.h editCursor.h experiment.h \
	 expidAndLocatedFragment.h filename.h gotoList.h \
	 gotoListType.h guiGetCommentForTag.h guiGetReferenceRead.cpp \
	 guiGetReferenceRead.h guiMultiContigNavigator.h guiapp.h \
	 guicolortext.h guicontigwin.h handleWindowManagerDelete2.h \
	 hp_exception_kludge.h infobutton.h listOfFragments.h \
	 locatedFragment.h matchWithinAssembly.h max.h \
	 mbtPtrOrderedVector.h mbtPtrVector.h mbtValOrderedVectorOfRWCString.h \
	 mbtValVector.h mbtValVectorOfBool.h mbtValVector_inc.cpp \
	 mbt_exception.h mbt_val_ord_offset_vec.h min.h \
	 motifutils.h multiProblemGotoList.h nMAX_QUALITY_LEVEL2.h \
	 ntide.h numutil.h paddedFromUnpadded.h \
	 popupErrorMessage.h primerType.h quality.h \
	 readTypes.h readsSortedByLeftEndPosition.h readsSortedByReadName.h \
	 readsSortedByTemplateName.h restrictionEnzyme.h rwbtreedictionary.h \
	 rwcregexp.h rwcstring.h rwcsubstring.h \
	 rwdefs.h rwtptrorderedvector.h rwtptrorderedvector_inc.cpp \
	 rwtptrsortedvector.h rwtptrvector.h rwtvalorderedvector.h \
	 rwtvalorderedvector_inc.cpp rwtvalsortedvector.h rwtvalvector.h \
	 sequence.h singletInfo.h singletsSortedByTemplateName.h \
	 soEmptyString.h soGetErrno.h subcloneTTemplate.h \
	 sysdepend.h tag.h templatesSortedByName.h \
	 textfield.h tracefile.h unpaddedFromPadded.h \
	 whatIsRunning.h wholeAssemblyItem.h wholeReadItem.h

guiGetTagType.o : \
	 assemblyViewTagTypeAndLine.h assert.h bIsNumericMaybeWithWhitespace.h \
	 bool.h consedParameters.h consedResources.h \
	 filename.h guiGetTagType.cpp guiGetTagType.h \
	 guiapp.h guicolortext.h handleWindowManagerDelete.h \
	 hp_exception_kludge.h mbtPtrOrderedVector.h mbtValOrderedVectorOfRWCString.h \
	 mbt_exception.h min.h motifutils.h \
	 popupErrorMessage.h popupErrorMessage2.h restrictionEnzyme.h \
	 rwcregexp.h rwcstring.h rwcsubstring.h \
	 rwdefs.h rwtptrorderedvector.h rwtptrorderedvector_inc.cpp \
	 rwtptrsortedvector.h rwtvalorderedvector.h rwtvalorderedvector_inc.cpp \
	 rwtvalvector.h soEmptyString.h soGetErrno.h \
	 sysdepend.h tagTypes.h whatIsRunning.h

guiGetUserDefinedTagInfo.o : \
	 abs.h assembly.h assemblyViewTagTypeAndLine.h \
	 assert.h autoFinishPurposes.h bInputEventToWrongWindow.h \
	 bIntersect.h bIntervalsIntersect.h bIsNumericLongMaybeWithWhitespace.h \
	 basesegment.h blockOfLocationsOfA4MerType.h bool.h \
	 cComplementBase.h cComplementBaseTable.h compareContigs.h \
	 compareContigsCursor.h compareContigsTypes.h consed.h \
	 consedParameters.h consedResources.h contig.h \
	 contigEnd.h contigMatchTablesType.h contigSegment.h \
	 contigview.h contigwin.h dictionary.h \
	 distribution.h editCursor.h editaction.h \
	 experiment.h expidAndLocatedFragment.h filename.h \
	 gotoList.h gotoListType.h guiDisplayDigest.h \
	 guiGetUserDefinedTagInfo.cpp guiGetUserDefinedTagInfo.h guiMultiContigNavigator.h \
	 guiapp.h guicolortext.h handleWindowManagerDelete2.h \
	 hp_exception_kludge.h listOfFragments.h locatedFragment.h \
	 matchWithinAssembly.h max.h mbtPtrOrderedVector.h \
	 mbtPtrVector.h mbtValOrderedVectorOfRWCString.h mbtValVector.h \
	 mbtValVectorOfBool.h mbtValVector_inc.cpp mbt_exception.h \
	 mbt_val_ord_offset_vec.h min.h motifutils.h \
	 multiProblemGotoList.h nMAX_QUALITY_LEVEL2.h ntide.h \
	 numutil.h paddedFromUnpadded.h popupErrorMessage2.h \
	 primerType.h quality.h readTypes.h \
	 readsSortedByLeftEndPosition.h readsSortedByReadName.h readsSortedByTemplateName.h \
	 restrictionEnzyme.h restrictionFragment.h rwbtreedictionary.h \
	 rwcstring.h rwcsubstring.h rwdefs.h \
	 rwtptrorderedvector.h rwtptrorderedvector_inc.cpp rwtptrsortedvector.h \
	 rwtptrvector.h rwtvalorderedvector.h rwtvalorderedvector_inc.cpp \
	 rwtvalsortedvector.h rwtvalvector.h selection.h \
	 sequence.h singletInfo.h singletsSortedByTemplateName.h \
	 soEmptyString.h soGetErrno.h subcloneTTemplate.h \
	 sysdepend.h tag.h tagTypes.h \
	 templatesSortedByName.h tracefile.h unpaddedFromPadded.h \
	 userDefinedTagFieldType.h visibleLineForRestrictionFragments.h whatIsRunning.h \
	 wholeAssemblyItem.h wholeReadItem.h

guiHowToSortAlignedReads.o : \
	 abs.h assembly.h assemblyViewTagTypeAndLine.h \
	 assert.h autoFinishPurposes.h bIntersect.h \
	 bIntervalsIntersect.h basesegment.h blockOfLocationsOfA4MerType.h \
	 bool.h cComplementBase.h cComplementBaseTable.h \
	 centerWidgetOnWidget.h consedParameters.h consedResources.h \
	 contig.h contigEnd.h contigMatchTablesType.h \
	 contigview.h contigwin.h dictionary.h \
	 distribution.h editCursor.h experiment.h \
	 expidAndLocatedFragment.h filename.h gotoList.h \
	 gotoListType.h guiHowToSortAlignedReads.cpp guiHowToSortAlignedReads.h \
	 guiapp.h guicolortext.h guicontigwin.h \
	 handleWindowManagerDelete2.h hp_exception_kludge.h infobutton.h \
	 listOfFragments.h locatedFragment.h matchWithinAssembly.h \
	 max.h mbtPtrOrderedVector.h mbtPtrVector.h \
	 mbtValOrderedVectorOfRWCString.h mbtValVector.h mbtValVectorOfBool.h \
	 mbtValVector_inc.cpp mbt_exception.h mbt_val_ord_offset_vec.h \
	 min.h motifutils.h multiProblemGotoList.h \
	 nMAX_QUALITY_LEVEL2.h ntide.h numutil.h \
	 paddedFromUnpadded.h primerType.h quality.h \
	 readTypes.h readsSortedByLeftEndPosition.h readsSortedByReadName.h \
	 readsSortedByTemplateName.h restrictionEnzyme.h rwbtreedictionary.h \
	 rwcstring.h rwcsubstring.h rwdefs.h \
	 rwtptrorderedvector.h rwtptrorderedvector_inc.cpp rwtptrsortedvector.h \
	 rwtptrvector.h rwtvalorderedvector.h rwtvalorderedvector_inc.cpp \
	 rwtvalsortedvector.h rwtvalvector.h sequence.h \
	 singletInfo.h singletsSortedByTemplateName.h soEmptyString.h \
	 soGetErrno.h subcloneTTemplate.h sysdepend.h \
	 tag.h templatesSortedByName.h textfield.h \
	 tracefile.h unpaddedFromPadded.h whatIsRunning.h \
	 wholeAssemblyItem.h wholeReadItem.h

guiMultiContigNavigator.o : \
	 abs.h arrayOfFwdRevPairLines.h arrayOfFwdRevPairSquares.h \
	 arrayOfFwdRevPairTriangles.h assembly.h assemblyView.h \
	 assemblyViewTagTypeAndLine.h assert.h autoFinishPurposes.h \
	 bIntersect.h bIntervalsIntersect.h basesegment.h \
	 blockOfLocationsOfA4MerType.h bool.h cComplementBase.h \
	 cComplementBaseTable.h compareContigs.h compareContigsCursor.h \
	 compareContigsTypes.h consed.h consedParameters.h \
	 consedResources.h contig.h contigEnd.h \
	 contigMatchTablesType.h contigSegment.h contigview.h \
	 contigwin.h dictionary.h distribution.h \
	 editCursor.h editaction.h experiment.h \
	 expidAndLocatedFragment.h filename.h fwdRevPair2.h \
	 fwdRevPairLine.h fwdRevPairSquare.h fwdRevPairTriangle.h \
	 gotoList.h gotoListType.h guiDisplayDigest.h \
	 guiMultiContigNavigator.cpp guiMultiContigNavigator.h guiapp.h \
	 guicolortext.h guicontigwin.h handleWindowManagerDelete.h \
	 hp_exception_kludge.h infobutton.h listOfFragments.h \
	 locatedFragment.h matchWithinAssembly.h max.h \
	 mbtPtrOrderedVector.h mbtPtrVector.h mbtValOrderedVectorOfRWCString.h \
	 mbtValVector.h mbtValVectorOfBool.h mbtValVector_inc.cpp \
	 mbt_exception.h mbt_val_ord_offset_vec.h min.h \
	 motifutils.h multiProblemGotoList.h nMAX_QUALITY_LEVEL2.h \
	 ntide.h numutil.h paddedFromUnpadded.h \
	 primerType.h quality.h readTypes.h \
	 readsSortedByLeftEndPosition.h readsSortedByReadName.h readsSortedByTemplateName.h \
	 restrictionEnzyme.h restrictionFragment.h rwbtreedictionary.h \
	 rwcstring.h rwcsubstring.h rwdefs.h \
	 rwt2dptrvector.h rwtptrorderedvector.h rwtptrorderedvector_inc.cpp \
	 rwtptrsortedvector.h rwtptrvector.h rwtvalorderedvector.h \
	 rwtvalorderedvector_inc.cpp rwtvalsortedvector.h rwtvalvector.h \
	 selection.h seqMatch.h sequence.h \
	 singletInfo.h singletsSortedByTemplateName.h soEmptyString.h \
	 soGetErrno.h subcloneTTemplate.h sysdepend.h \
	 tag.h templatesSortedByName.h textfield.h \
	 tracefile.h unpaddedFromPadded.h visibleLineForRestrictionFragments.h \
	 whatIsRunning.h wholeAssemblyItem.h wholeReadItem.h

guiNavigateByHighlyDiscrepantPositions.o : \
	 abs.h assembly.h assemblyViewTagTypeAndLine.h \
	 assert.h autoFinishPurposes.h bIntersect.h \
	 bIntervalsIntersect.h bIsNumericDouble.h bIsNumericMaybeWithWhitespace.h \
	 basesegment.h blockOfLocationsOfA4MerType.h bool.h \
	 cComplementBase.h cComplementBaseTable.h compareContigs.h \
	 compareContigsCursor.h compareContigsTypes.h consed.h \
	 consedParameters.h consedResources.h contig.h \
	 contigEnd.h contigMatchTablesType.h contigSegment.h \
	 contigview.h contigwin.h dictionary.h \
	 distribution.h editCursor.h editaction.h \
	 experiment.h expidAndLocatedFragment.h filename.h \
	 gotoList.h gotoListType.h guiDisplayDigest.h \
	 guiMultiContigNavigator.h guiNavigateByHighlyDiscrepantPositions.cpp guiNavigateByHighlyDiscrepantPositions.h \
	 guiapp.h guicolortext.h handleWindowManagerDelete2.h \
	 hp_exception_kludge.h listOfFragments.h locatedFragment.h \
	 matchWithinAssembly.h max.h mbtPtrOrderedVector.h \
	 mbtPtrVector.h mbtValOrderedVectorOfRWCString.h mbtValVector.h \
	 mbtValVectorOfBool.h mbtValVector_inc.cpp mbt_exception.h \
	 mbt_val_ord_offset_vec.h min.h motifutils.h \
	 multiProblemGotoList.h nMAX_QUALITY_LEVEL2.h ntide.h \
	 numutil.h paddedFromUnpadded.h please_wait.h \
	 popupErrorMessage.h primerType.h quality.h \
	 readTypes.h readsSortedByLeftEndPosition.h readsSortedByReadName.h \
	 readsSortedByTemplateName.h restrictionEnzyme.h restrictionFragment.h \
	 rwbtreedictionary.h rwcstring.h rwcsubstring.h \
	 rwdefs.h rwtptrorderedvector.h rwtptrorderedvector_inc.cpp \
	 rwtptrsortedvector.h rwtptrvector.h rwtvalorderedvector.h \
	 rwtvalorderedvector_inc.cpp rwtvalsortedvector.h rwtvalvector.h \
	 selection.h sequence.h singletInfo.h \
	 singletsSortedByTemplateName.h soEmptyString.h soGetErrno.h \
	 subcloneTTemplate.h sysdepend.h tag.h \
	 templatesSortedByName.h tracefile.h unpaddedFromPadded.h \
	 visibleLineForRestrictionFragments.h whatIsRunning.h wholeAssemblyItem.h \
	 wholeReadItem.h

guiNavigateByReadDepth.o : \
	 abs.h assembly.h assemblyViewTagTypeAndLine.h \
	 assert.h autoFinishPurposes.h bIntersect.h \
	 bIntervalsIntersect.h bIsNumericMaybeWithWhitespace.h basesegment.h \
	 blockOfLocationsOfA4MerType.h bool.h cComplementBase.h \
	 cComplementBaseTable.h compareContigs.h compareContigsCursor.h \
	 compareContigsTypes.h consed.h consedParameters.h \
	 consedResources.h contig.h contigEnd.h \
	 contigMatchTablesType.h contigSegment.h contigview.h \
	 contigwin.h dictionary.h distribution.h \
	 editCursor.h editaction.h experiment.h \
	 expidAndLocatedFragment.h filename.h gotoList.h \
	 gotoListType.h guiDisplayDigest.h guiMultiContigNavigator.h \
	 guiNavigateByReadDepth.cpp guiNavigateByReadDepth.h guiapp.h \
	 guicolortext.h handleWindowManagerDelete2.h hp_exception_kludge.h \
	 listOfFragments.h locatedFragment.h matchWithinAssembly.h \
	 max.h mbtPtrOrderedVector.h mbtPtrVector.h \
	 mbtValOrderedVectorOfRWCString.h mbtValVector.h mbtValVectorOfBool.h \
	 mbtValVector_inc.cpp mbt_exception.h mbt_val_ord_offset_vec.h \
	 min.h motifutils.h multiProblemGotoList.h \
	 nMAX_QUALITY_LEVEL2.h ntide.h numutil.h \
	 paddedFromUnpadded.h popupErrorMessage.h primerType.h \
	 quality.h readTypes.h readsSortedByLeftEndPosition.h \
	 readsSortedByReadName.h readsSortedByTemplateName.h restrictionEnzyme.h \
	 restrictionFragment.h rwbtreedictionary.h rwcstring.h \
	 rwcsubstring.h rwdefs.h rwtptrorderedvector.h \
	 rwtptrorderedvector_inc.cpp rwtptrsortedvector.h rwtptrvector.h \
	 rwtvalorderedvector.h rwtvalorderedvector_inc.cpp rwtvalsortedvector.h \
	 rwtvalvector.h selection.h sequence.h \
	 singletInfo.h singletsSortedByTemplateName.h soEmptyString.h \
	 soGetErrno.h subcloneTTemplate.h sysdepend.h \
	 tag.h templatesSortedByName.h tracefile.h \
	 unpaddedFromPadded.h visibleLineForRestrictionFragments.h whatIsRunning.h \
	 wholeAssemblyItem.h wholeReadItem.h

guiPopupDocumentation.o : \
	 assemblyViewTagTypeAndLine.h assert.h bool.h \
	 consedParameters.h consedResources.h filename.h \
	 guiPopupDocumentation.cpp guiPopupDocumentation.h guiapp.h \
	 guicolortext.h mbtPtrOrderedVector.h mbtValOrderedVectorOfRWCString.h \
	 mbt_exception.h motifutils.h readme.h \
	 restrictionEnzyme.h rwcstring.h rwcsubstring.h \
	 rwdefs.h rwtptrorderedvector.h rwtptrorderedvector_inc.cpp \
	 rwtvalorderedvector.h rwtvalorderedvector_inc.cpp soEmptyString.h \
	 soGetErrno.h sysdepend.h textbox.h \
	 whatIsRunning.h

guiPopupTagInfo.o : \
	 abs.h assembly.h assemblyViewTagTypeAndLine.h \
	 assert.h autoFinishPurposes.h bGuiGetAnswerYesNo.h \
	 bIntersect.h bIntervalsIntersect.h bIsNumericMaybeWithWhitespace.h \
	 basesegment.h blockOfLocationsOfA4MerType.h bool.h \
	 cComplementBase.h cComplementBaseTable.h compareContigs.h \
	 compareContigsCursor.h compareContigsTypes.h consed.h \
	 consedParameters.h consedResources.h contig.h \
	 contigEnd.h contigMatchTablesType.h contigSegment.h \
	 contigview.h contigwin.h dictionary.h \
	 distribution.h editActionChangeRead.h editCursor.h \
	 editDeleteConsensusTag.h editDeleteReadTag.h editaction.h \
	 experiment.h expidAndLocatedFragment.h filename.h \
	 gotoList.h gotoListType.h guiDisplayDigest.h \
	 guiMultiContigNavigator.h guiPopupTagInfo.cpp guiPopupTagInfo.h \
	 guiapp.h guicolortext.h guicontigwin.h \
	 guiteditor.h handleWindowManagerDelete.h hp_exception_kludge.h \
	 infobutton.h listOfFragments.h locatedFragment.h \
	 matchWithinAssembly.h max.h mbtPtrOrderedVector.h \
	 mbtPtrVector.h mbtValOrderedVectorOfRWCString.h mbtValVector.h \
	 mbtValVectorOfBool.h mbtValVector_inc.cpp mbt_exception.h \
	 mbt_val_ord_offset_vec.h min.h motifutils.h \
	 multiProblemGotoList.h nMAX_QUALITY_LEVEL2.h ntide.h \
	 numutil.h oligoTag.h paddedFromUnpadded.h \
	 popupErrorMessage.h primerType.h quality.h \
	 readTypes.h readsSortedByLeftEndPosition.h readsSortedByReadName.h \
	 readsSortedByTemplateName.h restrictionEnzyme.h restrictionFragment.h \
	 rwbtreedictionary.h rwcregexp.h rwcstring.h \
	 rwcsubstring.h rwdefs.h rwtptrorderedvector.h \
	 rwtptrorderedvector_inc.cpp rwtptrsortedvector.h rwtptrvector.h \
	 rwtvalorderedvector.h rwtvalorderedvector_inc.cpp rwtvalsortedvector.h \
	 rwtvalvector.h selection.h sequence.h \
	 singletInfo.h singletsSortedByTemplateName.h soEmptyString.h \
	 soGetErrno.h subcloneTTemplate.h sysdepend.h \
	 tag.h tagTypes.h templatesSortedByName.h \
	 textfield.h tracefile.h unpaddedFromPadded.h \
	 userDefinedTagField.h userDefinedTagFieldType.h visibleLineForRestrictionFragments.h \
	 whatIsRunning.h wholeAssemblyItem.h wholeReadItem.h

guiPopupWholeReadItem.o : \
	 assert.h bool.h filename.h \
	 guiPopupWholeReadItem.cpp guiPopupWholeReadItem.h guiapp.h \
	 guicolortext.h handleWindowManagerDelete2.h hp_exception_kludge.h \
	 mbt_exception.h motifutils.h rwcstring.h \
	 rwcsubstring.h rwdefs.h rwtptrorderedvector.h \
	 rwtptrorderedvector_inc.cpp rwtvalorderedvector.h rwtvalorderedvector_inc.cpp \
	 soEmptyString.h soGetErrno.h sysdepend.h \
	 wholeReadItem.h

guiQuit.o : \
	 assert.h bool.h filename.h \
	 guiQuit.cpp guiQuit.h guiQuitTypes.h \
	 guiapp.h guicolortext.h handleWindowManagerDelete.h \
	 mbt_exception.h motifutils.h rwcstring.h \
	 rwcsubstring.h rwdefs.h rwtptrorderedvector.h \
	 rwtptrorderedvector_inc.cpp rwtvalorderedvector.h rwtvalorderedvector_inc.cpp \
	 soEmptyString.h soGetErrno.h sysdepend.h

guiRemoveReads.o : \
	 abs.h assembly.h assemblyViewTagTypeAndLine.h \
	 assert.h autoFinishPurposes.h bIntersect.h \
	 bIntervalsIntersect.h basesegment.h blockOfLocationsOfA4MerType.h \
	 bool.h cComplementBase.h cComplementBaseTable.h \
	 compareContigs.h compareContigsCursor.h compareContigsTypes.h \
	 consed.h consedParameters.h consedResources.h \
	 contig.h contigEnd.h contigMatchTablesType.h \
	 contigSegment.h contigview.h contigwin.h \
	 dictionary.h distribution.h editCursor.h \
	 editaction.h experiment.h expidAndLocatedFragment.h \
	 filename.h gotoList.h gotoListType.h \
	 guiDisplayDigest.h guiMultiContigNavigator.h guiRemoveReads.cpp \
	 guiRemoveReads.h guiapp.h guicolortext.h \
	 handleWindowManagerDelete2.h hp_exception_kludge.h listOfFragments.h \
	 locatedFragment.h matchWithinAssembly.h max.h \
	 mbtPtrOrderedVector.h mbtPtrVector.h mbtValOrderedVectorOfRWCString.h \
	 mbtValVector.h mbtValVectorOfBool.h mbtValVector_inc.cpp \
	 mbt_exception.h mbt_val_ord_offset_vec.h min.h \
	 motifutils.h multiProblemGotoList.h nMAX_QUALITY_LEVEL2.h \
	 ntide.h numutil.h paddedFromUnpadded.h \
	 please_wait.h popupErrorMessage.h popupErrorMessage2.h \
	 popupInfoMessage.h primerType.h quality.h \
	 readTypes.h readsSortedByLeftEndPosition.h readsSortedByReadName.h \
	 readsSortedByTemplateName.h restrictionEnzyme.h restrictionFragment.h \
	 rwbtreedictionary.h rwcstring.h rwcsubstring.h \
	 rwdefs.h rwtptrorderedvector.h rwtptrorderedvector_inc.cpp \
	 rwtptrsortedvector.h rwtptrvector.h rwtvalorderedvector.h \
	 rwtvalorderedvector_inc.cpp rwtvalsortedvector.h rwtvalvector.h \
	 selection.h sequence.h singletInfo.h \
	 singletsSortedByTemplateName.h soAddCommas.h soEmptyString.h \
	 soGetErrno.h subcloneTTemplate.h sysdepend.h \
	 tag.h templatesSortedByName.h textbox.h \
	 tracefile.h unpaddedFromPadded.h visibleLineForRestrictionFragments.h \
	 whatIsRunning.h wholeAssemblyItem.h wholeReadItem.h

guiReorderContigs.o : \
	 abs.h arrayOfFwdRevPairLines.h arrayOfFwdRevPairSquares.h \
	 arrayOfFwdRevPairTriangles.h assembly.h assemblyView.h \
	 assemblyViewTagTypeAndLine.h assert.h autoFinishPurposes.h \
	 bGuiGetAnswerYesNo.h bIntersect.h bIntervalsIntersect.h \
	 basesegment.h blockOfLocationsOfA4MerType.h bool.h \
	 cComplementBase.h cComplementBaseTable.h compareContigs.h \
	 compareContigsCursor.h compareContigsTypes.h consed.h \
	 consedParameters.h consedResources.h contig.h \
	 contigEnd.h contigEndPair.h contigMatchTablesType.h \
	 contigSegment.h contigview.h contigwin.h \
	 dictionary.h distribution.h editAddConsensusTag.h \
	 editCursor.h editDeleteConsensusTag.h editaction.h \
	 experiment.h expidAndLocatedFragment.h filename.h \
	 fwdRevPair2.h fwdRevPairLine.h fwdRevPairSquare.h \
	 fwdRevPairTriangle.h gotoList.h gotoListType.h \
	 guiDisplayDigest.h guiMultiContigNavigator.h guiReorderContigs.cpp \
	 guiReorderContigs.h guiapp.h guicolortext.h \
	 handleWindowManagerDelete2.h hp_exception_kludge.h listOfFragments.h \
	 locatedFragment.h matchWithinAssembly.h max.h \
	 mbtPtrOrderedVector.h mbtPtrVector.h mbtValOrderedVectorOfRWCString.h \
	 mbtValVector.h mbtValVectorOfBool.h mbtValVector_inc.cpp \
	 mbt_exception.h mbt_val_ord_offset_vec.h min.h \
	 motifutils.h multiProblemGotoList.h nMAX_QUALITY_LEVEL2.h \
	 ntide.h numutil.h paddedFromUnpadded.h \
	 popupErrorMessage2.h primerType.h quality.h \
	 readTypes.h readsSortedByLeftEndPosition.h readsSortedByReadName.h \
	 readsSortedByTemplateName.h restrictionEnzyme.h restrictionFragment.h \
	 rwbtreedictionary.h rwcstring.h rwcsubstring.h \
	 rwdefs.h rwt2dptrvector.h rwtptrorderedvector.h \
	 rwtptrorderedvector_inc.cpp rwtptrsortedvector.h rwtptrvector.h \
	 rwtvalorderedvector.h rwtvalorderedvector_inc.cpp rwtvalsortedvector.h \
	 rwtvalvector.h selection.h seqMatch.h \
	 sequence.h singletInfo.h singletsSortedByTemplateName.h \
	 soEmptyString.h soGetErrno.h subcloneTTemplate.h \
	 sysdepend.h tag.h templatesSortedByName.h \
	 tracefile.h unpaddedFromPadded.h visibleLineForRestrictionFragments.h \
	 whatIsRunning.h wholeAssemblyItem.h wholeReadItem.h

guiReorientContigs.o : \
	 abs.h arrayOfFwdRevPairLines.h arrayOfFwdRevPairSquares.h \
	 arrayOfFwdRevPairTriangles.h assembly.h assemblyView.h \
	 assemblyViewTagTypeAndLine.h assert.h autoFinishPurposes.h \
	 bIntersect.h bIntervalsIntersect.h basesegment.h \
	 blockOfLocationsOfA4MerType.h bool.h breakIntoShorterLines.h \
	 cComplementBase.h cComplementBaseTable.h clScaffold.h \
	 compareContigs.h compareContigsCursor.h compareContigsTypes.h \
	 consed.h consedParameters.h consedResources.h \
	 contig.h contigEnd.h contigMatchTablesType.h \
	 contigSegment.h contigview.h contigwin.h \
	 dictionary.h distribution.h editCursor.h \
	 editaction.h experiment.h expidAndLocatedFragment.h \
	 filename.h fwdRevPair2.h fwdRevPairLine.h \
	 fwdRevPairSquare.h fwdRevPairTriangle.h gotoList.h \
	 gotoListType.h guiDisplayDigest.h guiMultiContigNavigator.h \
	 guiReorientContigs.cpp guiReorientContigs.h guiapp.h \
	 guicolortext.h handleWindowManagerDelete2.h hp_exception_kludge.h \
	 listOfFragments.h locatedFragment.h matchWithinAssembly.h \
	 max.h mbtPtrOrderedVector.h mbtPtrVector.h \
	 mbtValOrderedVectorOfRWCString.h mbtValVector.h mbtValVectorOfBool.h \
	 mbtValVector_inc.cpp mbt_exception.h mbt_val_ord_offset_vec.h \
	 min.h motifutils.h multiProblemGotoList.h \
	 nMAX_QUALITY_LEVEL2.h ntide.h numutil.h \
	 paddedFromUnpadded.h popupErrorMessage2.h primerType.h \
	 quality.h readTypes.h readsSortedByLeftEndPosition.h \
	 readsSortedByReadName.h readsSortedByTemplateName.h restrictionEnzyme.h \
	 restrictionFragment.h rwbtreedictionary.h rwcstring.h \
	 rwcsubstring.h rwdefs.h rwt2dptrvector.h \
	 rwtptrorderedvector.h rwtptrorderedvector_inc.cpp rwtptrsortedvector.h \
	 rwtptrvector.h rwtvalorderedvector.h rwtvalorderedvector_inc.cpp \
	 rwtvalsortedvector.h rwtvalvector.h selection.h \
	 seqMatch.h sequence.h singletInfo.h \
	 singletsSortedByTemplateName.h soEmptyString.h soGetErrno.h \
	 subcloneTTemplate.h sysdepend.h tag.h \
	 templatesSortedByName.h tracefile.h unpaddedFromPadded.h \
	 visibleLineForRestrictionFragments.h whatIsRunning.h wholeAssemblyItem.h \
	 wholeReadItem.h

guiSaveHighlightedReads.o : \
	 abs.h assembly.h assemblyViewTagTypeAndLine.h \
	 assert.h autoFinishPurposes.h bGuiGetAnswerYesNo.h \
	 bIntersect.h bIntervalsIntersect.h basesegment.h \
	 blockOfLocationsOfA4MerType.h bool.h cComplementBase.h \
	 cComplementBaseTable.h compareContigs.h compareContigsCursor.h \
	 compareContigsTypes.h consed.h consedParameters.h \
	 consedResources.h contig.h contigEnd.h \
	 contigMatchTablesType.h contigSegment.h contigview.h \
	 contigwin.h dictionary.h distribution.h \
	 editCursor.h editaction.h experiment.h \
	 expidAndLocatedFragment.h filePopupAndGetFilename.h filename.h \
	 gotoList.h gotoListType.h guiDisplayDigest.h \
	 guiMultiContigNavigator.h guiSaveHighlightedReads.cpp guiSaveHighlightedReads.h \
	 guiapp.h guicolortext.h guicontigwin.h \
	 handleWindowManagerDelete2.h hp_exception_kludge.h infobutton.h \
	 listOfFragments.h locatedFragment.h matchWithinAssembly.h \
	 max.h mbtPtrOrderedVector.h mbtPtrVector.h \
	 mbtValOrderedVectorOfRWCString.h mbtValVector.h mbtValVectorOfBool.h \
	 mbtValVector_inc.cpp mbt_exception.h mbt_val_ord_offset_vec.h \
	 min.h motifutils.h multiProblemGotoList.h \
	 nMAX_QUALITY_LEVEL2.h ntide.h numutil.h \
	 paddedFromUnpadded.h please_wait.h popupInfoMessage.h \
	 primerType.h quality.h readTypes.h \
	 readsSortedByLeftEndPosition.h readsSortedByReadName.h readsSortedByTemplateName.h \
	 restrictionEnzyme.h restrictionFragment.h rwbtreedictionary.h \
	 rwcstring.h rwcsubstring.h rwdefs.h \
	 rwtptrorderedvector.h rwtptrorderedvector_inc.cpp rwtptrsortedvector.h \
	 rwtptrvector.h rwtvalorderedvector.h rwtvalorderedvector_inc.cpp \
	 rwtvalsortedvector.h rwtvalvector.h selection.h \
	 sequence.h singletInfo.h singletsSortedByTemplateName.h \
	 soEmptyString.h soGetErrno.h subcloneTTemplate.h \
	 sysdepend.h tag.h templatesSortedByName.h \
	 textfield.h tracefile.h unpaddedFromPadded.h \
	 visibleLineForRestrictionFragments.h whatIsRunning.h wholeAssemblyItem.h \
	 wholeReadItem.h

guiSearchForOligoTags.o : \
	 abs.h assembly.h assemblyViewTagTypeAndLine.h \
	 assert.h autoFinishPurposes.h bIntersect.h \
	 bIntervalsIntersect.h basesegment.h blockOfLocationsOfA4MerType.h \
	 bool.h cComplementBase.h cComplementBaseTable.h \
	 compareContigs.h compareContigsCursor.h compareContigsTypes.h \
	 consed.h consedParameters.h consedResources.h \
	 contig.h contigEnd.h contigMatchTablesType.h \
	 contigSegment.h contigview.h contigwin.h \
	 dictionary.h distribution.h editCursor.h \
	 editaction.h experiment.h expidAndLocatedFragment.h \
	 filename.h gotoList.h gotoListType.h \
	 guiDisplayDigest.h guiMultiContigNavigator.h guiSearchForOligoTags.cpp \
	 guiSearchForOligoTags.h guiapp.h guicolortext.h \
	 handleWindowManagerDelete2.h hp_exception_kludge.h listOfFragments.h \
	 locatedFragment.h matchWithinAssembly.h max.h \
	 mbtPtrOrderedVector.h mbtPtrVector.h mbtValOrderedVectorOfRWCString.h \
	 mbtValVector.h mbtValVectorOfBool.h mbtValVector_inc.cpp \
	 mbt_exception.h mbt_val_ord_offset_vec.h min.h \
	 motifutils.h multiProblemGotoList.h nMAX_QUALITY_LEVEL2.h \
	 ntide.h numutil.h paddedFromUnpadded.h \
	 primerType.h quality.h readTypes.h \
	 readsSortedByLeftEndPosition.h readsSortedByReadName.h readsSortedByTemplateName.h \
	 restrictionEnzyme.h restrictionFragment.h rwbtreedictionary.h \
	 rwcstring.h rwcsubstring.h rwdefs.h \
	 rwtptrorderedvector.h rwtptrorderedvector_inc.cpp rwtptrsortedvector.h \
	 rwtptrvector.h rwtvalorderedvector.h rwtvalorderedvector_inc.cpp \
	 rwtvalsortedvector.h rwtvalvector.h selection.h \
	 sequence.h singletInfo.h singletsSortedByTemplateName.h \
	 soEmptyString.h soGetErrno.h subcloneTTemplate.h \
	 sysdepend.h tag.h templatesSortedByName.h \
	 tracefile.h unpaddedFromPadded.h visibleLineForRestrictionFragments.h \
	 whatIsRunning.h wholeAssemblyItem.h wholeReadItem.h

guiSearchForOpenReadingFrames.o : \
	 abs.h assemblyViewTagTypeAndLine.h assert.h \
	 autoFinishPurposes.h bIsStartCodon.h bIsStopCodon.h \
	 basesegment.h blockOfLocationsOfA4MerType.h bool.h \
	 cComplementBase.h cComplementBaseTable.h complementSequence.h \
	 consedParameters.h consedResources.h contig.h \
	 contigEnd.h contigMatchTablesType.h dictionary.h \
	 distribution.h experiment.h filename.h \
	 gotoList.h guiMultiContigNavigator.h guiSearchForOpenReadingFrames.cpp \
	 guiSearchForOpenReadingFrames.h guiapp.h guicolortext.h \
	 locatedFragment.h mbtPtrOrderedVector.h mbtPtrVector.h \
	 mbtValOrderedVectorOfRWCString.h mbtValVector.h mbtValVectorOfBool.h \
	 mbtValVector_inc.cpp mbt_exception.h mbt_val_ord_offset_vec.h \
	 min.h motifutils.h nMAX_QUALITY_LEVEL2.h \
	 ntide.h paddedFromUnpadded.h please_wait.h \
	 primerType.h quality.h readTypes.h \
	 readsSortedByLeftEndPosition.h readsSortedByReadName.h restrictionEnzyme.h \
	 rwbtreedictionary.h rwcstring.h rwcsubstring.h \
	 rwdefs.h rwtptrorderedvector.h rwtptrorderedvector_inc.cpp \
	 rwtptrsortedvector.h rwtptrvector.h rwtvalorderedvector.h \
	 rwtvalorderedvector_inc.cpp rwtvalsortedvector.h rwtvalvector.h \
	 sequence.h soEmptyString.h soGetErrno.h \
	 subcloneTTemplate.h sysdepend.h tag.h \
	 tracefile.h unpaddedFromPadded.h whatIsRunning.h \
	 wholeReadItem.h

guiSearchForTagsByComment.o : \
	 abs.h assembly.h assemblyViewTagTypeAndLine.h \
	 assert.h autoFinishPurposes.h bIntersect.h \
	 bIntervalsIntersect.h basesegment.h blockOfLocationsOfA4MerType.h \
	 bool.h cComplementBase.h cComplementBaseTable.h \
	 compareContigs.h compareContigsCursor.h compareContigsTypes.h \
	 consed.h consedParameters.h consedResources.h \
	 contig.h contigEnd.h contigMatchTablesType.h \
	 contigSegment.h contigview.h contigwin.h \
	 dictionary.h distribution.h editCursor.h \
	 editaction.h experiment.h expidAndLocatedFragment.h \
	 filename.h gotoList.h gotoListType.h \
	 guiDisplayDigest.h guiMultiContigNavigator.h guiSearchForTagsByComment.cpp \
	 guiSearchForTagsByComment.h guiapp.h guicolortext.h \
	 handleWindowManagerDelete2.h hp_exception_kludge.h listOfFragments.h \
	 locatedFragment.h matchWithinAssembly.h max.h \
	 mbtPtrOrderedVector.h mbtPtrVector.h mbtValOrderedVectorOfRWCString.h \
	 mbtValVector.h mbtValVectorOfBool.h mbtValVector_inc.cpp \
	 mbt_exception.h mbt_val_ord_offset_vec.h min.h \
	 motifutils.h multiProblemGotoList.h nMAX_QUALITY_LEVEL2.h \
	 ntide.h numutil.h paddedFromUnpadded.h \
	 primerType.h quality.h readTypes.h \
	 readsSortedByLeftEndPosition.h readsSortedByReadName.h readsSortedByTemplateName.h \
	 restrictionEnzyme.h restrictionFragment.h rwbtreedictionary.h \
	 rwcstring.h rwcsubstring.h rwdefs.h \
	 rwtptrorderedvector.h rwtptrorderedvector_inc.cpp rwtptrsortedvector.h \
	 rwtptrvector.h rwtvalorderedvector.h rwtvalorderedvector_inc.cpp \
	 rwtvalsortedvector.h rwtvalvector.h selection.h \
	 sequence.h singletInfo.h singletsSortedByTemplateName.h \
	 soEmptyString.h soGetErrno.h subcloneTTemplate.h \
	 sysdepend.h tag.h templatesSortedByName.h \
	 tracefile.h unpaddedFromPadded.h visibleLineForRestrictionFragments.h \
	 whatIsRunning.h wholeAssemblyItem.h wholeReadItem.h

guiSetGeneralPreferences.o : \
	 abs.h assembly.h assemblyViewTagTypeAndLine.h \
	 assert.h autoFinishPurposes.h bIntersect.h \
	 bIntervalsIntersect.h bIsNumericMaybeWithWhitespace.h basesegment.h \
	 blockOfLocationsOfA4MerType.h bool.h cComplementBase.h \
	 cComplementBaseTable.h compareContigs.h compareContigsCursor.h \
	 compareContigsTypes.h consed.h consedParameters.h \
	 consedResources.h contig.h contigEnd.h \
	 contigMatchTablesType.h contigSegment.h contigview.h \
	 contigwin.h dictionary.h distribution.h \
	 editCursor.h editaction.h experiment.h \
	 expidAndLocatedFragment.h filename.h gotoList.h \
	 gotoListType.h guiDisplayDigest.h guiMultiContigNavigator.h \
	 guiSetGeneralPreferences.cpp guiSetGeneralPreferences.h guiapp.h \
	 guicolortext.h handleWindowManagerDelete2.h hp_exception_kludge.h \
	 listOfFragments.h locatedFragment.h matchWithinAssembly.h \
	 max.h mbtPtrOrderedVector.h mbtPtrVector.h \
	 mbtValOrderedVectorOfRWCString.h mbtValVector.h mbtValVectorOfBool.h \
	 mbtValVector_inc.cpp mbt_exception.h mbt_val_ord_offset_vec.h \
	 min.h motifutils.h multiProblemGotoList.h \
	 nMAX_QUALITY_LEVEL2.h ntide.h numutil.h \
	 paddedFromUnpadded.h popupErrorMessage.h primerType.h \
	 quality.h readTypes.h readsSortedByLeftEndPosition.h \
	 readsSortedByReadName.h readsSortedByTemplateName.h restrictionEnzyme.h \
	 restrictionFragment.h rwbtreedictionary.h rwcregexp.h \
	 rwcstring.h rwcsubstring.h rwdefs.h \
	 rwtptrorderedvector.h rwtptrorderedvector_inc.cpp rwtptrsortedvector.h \
	 rwtptrvector.h rwtvalorderedvector.h rwtvalorderedvector_inc.cpp \
	 rwtvalsortedvector.h rwtvalvector.h selection.h \
	 sequence.h singletInfo.h singletsSortedByTemplateName.h \
	 soEmptyString.h soGetErrno.h subcloneTTemplate.h \
	 sysdepend.h tag.h templatesSortedByName.h \
	 tracefile.h unpaddedFromPadded.h visibleLineForRestrictionFragments.h \
	 whatIsRunning.h wholeAssemblyItem.h wholeReadItem.h

guiSetPrimerPickingPreferences.o : \
	 abs.h assembly.h assemblyViewTagTypeAndLine.h \
	 assert.h autoFinishPurposes.h bIntersect.h \
	 bIntervalsIntersect.h bIsNumericDouble.h bIsNumericMaybeWithWhitespace.h \
	 basesegment.h blockOfLocationsOfA4MerType.h bool.h \
	 cComplementBase.h cComplementBaseTable.h compareContigs.h \
	 compareContigsCursor.h compareContigsTypes.h consed.h \
	 consedParameters.h consedResources.h contig.h \
	 contigEnd.h contigMatchTablesType.h contigSegment.h \
	 contigview.h contigwin.h dictionary.h \
	 distribution.h editCursor.h editaction.h \
	 experiment.h expidAndLocatedFragment.h filename.h \
	 gotoList.h gotoListType.h guiDisplayDigest.h \
	 guiMultiContigNavigator.h guiSetPrimerPickingPreferences.cpp guiSetPrimerPickingPreferences.h \
	 guiapp.h guicolortext.h handleWindowManagerDelete2.h \
	 hp_exception_kludge.h listOfFragments.h locatedFragment.h \
	 matchWithinAssembly.h max.h mbtPtrOrderedVector.h \
	 mbtPtrVector.h mbtValOrderedVectorOfRWCString.h mbtValVector.h \
	 mbtValVectorOfBool.h mbtValVector_inc.cpp mbt_exception.h \
	 mbt_val_ord_offset_vec.h min.h motifutils.h \
	 multiProblemGotoList.h nMAX_QUALITY_LEVEL2.h nPrimerFalseMatchScoreArray.h \
	 ntide.h numutil.h paddedFromUnpadded.h \
	 popupErrorMessage.h primerType.h quality.h \
	 readTypes.h readsSortedByLeftEndPosition.h readsSortedByReadName.h \
	 readsSortedByTemplateName.h restrictionEnzyme.h restrictionFragment.h \
	 rwbtreedictionary.h rwcregexp.h rwcstring.h \
	 rwcsubstring.h rwdefs.h rwtptrorderedvector.h \
	 rwtptrorderedvector_inc.cpp rwtptrsortedvector.h rwtptrvector.h \
	 rwtvalorderedvector.h rwtvalorderedvector_inc.cpp rwtvalsortedvector.h \
	 rwtvalvector.h selection.h sequence.h \
	 singletInfo.h singletsSortedByTemplateName.h soEmptyString.h \
	 soGetErrno.h subcloneTTemplate.h sysdepend.h \
	 tag.h templatesSortedByName.h tracefile.h \
	 unpaddedFromPadded.h visibleLineForRestrictionFragments.h whatIsRunning.h \
	 wholeAssemblyItem.h wholeReadItem.h

guiShowErrorInfoForARegion.o : \
	 assemblyViewTagTypeAndLine.h assert.h autoFinishPurposes.h \
	 bIsNumericMaybeWithWhitespace.h basesegment.h blockOfLocationsOfA4MerType.h \
	 bool.h cComplementBase.h cComplementBaseTable.h \
	 consedParameters.h consedResources.h contig.h \
	 contigEnd.h contigMatchTablesType.h dictionary.h \
	 distribution.h experiment.h filename.h \
	 guiShowErrorInfoForARegion.cpp guiShowErrorInfoForARegion.h guiapp.h \
	 guicolortext.h handleWindowManagerDelete2.h hp_exception_kludge.h \
	 locatedFragment.h mbtPtrOrderedVector.h mbtPtrVector.h \
	 mbtValOrderedVectorOfRWCString.h mbtValVector.h mbtValVectorOfBool.h \
	 mbtValVector_inc.cpp mbt_exception.h mbt_val_ord_offset_vec.h \
	 min.h motifutils.h nMAX_QUALITY_LEVEL2.h \
	 ntide.h paddedFromUnpadded.h please_wait.h \
	 popupErrorMessage.h primerType.h quality.h \
	 readTypes.h readsSortedByLeftEndPosition.h readsSortedByReadName.h \
	 restrictionEnzyme.h rwbtreedictionary.h rwcstring.h \
	 rwcsubstring.h rwdefs.h rwtptrorderedvector.h \
	 rwtptrorderedvector_inc.cpp rwtptrsortedvector.h rwtptrvector.h \
	 rwtvalorderedvector.h rwtvalorderedvector_inc.cpp rwtvalsortedvector.h \
	 rwtvalvector.h sequence.h soEmptyString.h \
	 soGetErrno.h subcloneTTemplate.h sysdepend.h \
	 tag.h tracefile.h unpaddedFromPadded.h \
	 whatIsRunning.h wholeReadItem.h

guiTearContig.o : \
	 abs.h assembly.h assemblyViewTagTypeAndLine.h \
	 assert.h autoFinishPurposes.h bGuiGetAnswerYesNo.h \
	 bIntersect.h bIntervalsIntersect.h basesegment.h \
	 blockOfLocationsOfA4MerType.h bool.h breakIntoShorterLines.h \
	 cComplementBase.h cComplementBaseTable.h compareContigs.h \
	 compareContigsCursor.h compareContigsTypes.h consed.h \
	 consedParameters.h consedResources.h contig.h \
	 contigEnd.h contigMatchTablesType.h contigSegment.h \
	 contigview.h contigwin.h createTearTags.h \
	 dictionary.h distribution.h editCursor.h \
	 editaction.h experiment.h expidAndLocatedFragment.h \
	 filename.h gotoList.h gotoListType.h \
	 guiDisplayDigest.h guiMultiContigNavigator.h guiTearContig.cpp \
	 guiTearContig.h guiapp.h guicolortext.h \
	 guicontigwin.h handleWindowManagerDelete2.h hp_exception_kludge.h \
	 infobutton.h listOfFragments.h locatedFragment.h \
	 matchWithinAssembly.h max.h mbtPtrOrderedVector.h \
	 mbtPtrVector.h mbtValOrderedVectorOfRWCString.h mbtValVector.h \
	 mbtValVectorOfBool.h mbtValVector_inc.cpp mbt_exception.h \
	 mbt_val_ord_offset_vec.h min.h motifutils.h \
	 multiProblemGotoList.h nMAX_QUALITY_LEVEL2.h ntide.h \
	 numutil.h paddedFromUnpadded.h popupErrorMessage.h \
	 popupInfoMessage.h primerType.h quality.h \
	 readTypes.h readsSortedByLeftEndPosition.h readsSortedByReadName.h \
	 readsSortedByTemplateName.h restrictionEnzyme.h restrictionFragment.h \
	 rwbtreedictionary.h rwcstring.h rwcsubstring.h \
	 rwdefs.h rwtptrorderedvector.h rwtptrorderedvector_inc.cpp \
	 rwtptrsortedvector.h rwtptrvector.h rwtvalorderedvector.h \
	 rwtvalorderedvector_inc.cpp rwtvalsortedvector.h rwtvalvector.h \
	 selection.h sequence.h singletInfo.h \
	 singletsSortedByTemplateName.h soAddCommas.h soEmptyString.h \
	 soGetDateTime.h soGetErrno.h subcloneTTemplate.h \
	 sysdepend.h tag.h tagTypes.h \
	 templatesSortedByName.h textfield.h tracefile.h \
	 ucNormalQualityFrom9899Quality.h unpaddedFromPadded.h visibleLineForRestrictionFragments.h \
	 whatIsRunning.h wholeAssemblyItem.h wholeReadItem.h

guiTopWindow.o : \
	 abs.h addNewReads.h arrayOfFwdRevPairLines.h \
	 arrayOfFwdRevPairSquares.h arrayOfFwdRevPairTriangles.h assembly.h \
	 assemblyView.h assemblyViewTagTypeAndLine.h assert.h \
	 autoFinishPurposes.h bGuiGetAnswerYesNo.h bIntersect.h \
	 bIntervalsIntersect.h basesegment.h blockOfLocationsOfA4MerType.h \
	 bool.h cComplementBase.h cComplementBaseTable.h \
	 choose_contig.h compareContigs.h compareContigsCursor.h \
	 compareContigsTypes.h consed.h consedParameters.h \
	 consedResources.h contig.h contigEnd.h \
	 contigMatchTablesType.h contigSegment.h contigview.h \
	 contigwin.h customNavigation.h dErrorRateFromQuality.h \
	 dGetErrorsFixedAtBase.h dictionary.h distribution.h \
	 editCursor.h editaction.h experiment.h \
	 expidAndLocatedFragment.h filename.h fragment_and_contig.h \
	 fwdRevPair2.h fwdRevPairLine.h fwdRevPairSquare.h \
	 fwdRevPairTriangle.h gotoList.h gotoListType.h \
	 guiChoiceOfReadsForAlignedReads.h guiDisplayDigest.h guiEditResources.h \
	 guiFindRestrictionEnzymeSites.h guiMultiContigNavigator.h guiNavigateByHighlyDiscrepantPositions.h \
	 guiNavigateByReadDepth.h guiPopupDocumentation.h guiRemoveReads.h \
	 guiSearchForOligoTags.h guiSearchForTagsByComment.h guiSetGeneralPreferences.h \
	 guiSetPrimerPickingPreferences.h guiTopWindow.cpp guiTopWindow.h \
	 guiUndoEdit.h guiapp.h guicolortext.h \
	 hideSomeTagTypes.h hp_exception_kludge.h listOfFragments.h \
	 locatedFragment.h matchWithinAssembly.h max.h \
	 mbtPtrOrderedVector.h mbtPtrVector.h mbtValOrderedVectorOfRWCString.h \
	 mbtValVector.h mbtValVectorOfBool.h mbtValVector_inc.cpp \
	 mbt_exception.h mbt_val_ord_offset_vec.h min.h \
	 miniassembly.h motifutils.h multiProblemGotoList.h \
	 nMAX_QUALITY_LEVEL2.h navigateByTagsInAllContigs.h ntide.h \
	 numutil.h paddedFromUnpadded.h please_wait.h \
	 popupErrorMessage.h primerType.h quality.h \
	 readTypes.h readsSortedByLeftEndPosition.h readsSortedByReadName.h \
	 readsSortedByTemplateName.h restrictionEnzyme.h restrictionFragment.h \
	 rwbtreedictionary.h rwcregexp.h rwcstring.h \
	 rwcsubstring.h rwdefs.h rwt2dptrvector.h \
	 rwtptrorderedvector.h rwtptrorderedvector_inc.cpp rwtptrsortedvector.h \
	 rwtptrvector.h rwtvalorderedvector.h rwtvalorderedvector_inc.cpp \
	 rwtvalsortedvector.h rwtvalvector.h selection.h \
	 seqMatch.h sequence.h singletInfo.h \
	 singletsSortedByTemplateName.h soAddCommas.h soEmptyString.h \
	 soGetErrno.h subcloneTTemplate.h sysdepend.h \
	 tag.h templatesSortedByName.h textbox.h \
	 tracefile.h unpaddedFromPadded.h visibleLineForRestrictionFragments.h \
	 whatIsRunning.h wholeAssemblyItem.h wholeReadItem.h

guiUndoEdit.o : \
	 abs.h assembly.h assemblyViewTagTypeAndLine.h \
	 assert.h autoFinishPurposes.h bIntersect.h \
	 bIntervalsIntersect.h basesegment.h blockOfLocationsOfA4MerType.h \
	 bool.h cComplementBase.h cComplementBaseTable.h \
	 compareContigs.h compareContigsCursor.h compareContigsTypes.h \
	 consed.h consedParameters.h consedResources.h \
	 contig.h contigEnd.h contigMatchTablesType.h \
	 contigSegment.h contigview.h contigwin.h \
	 dictionary.h distribution.h editCursor.h \
	 editaction.h experiment.h expidAndLocatedFragment.h \
	 filename.h gotoList.h gotoListType.h \
	 guiDisplayDigest.h guiMultiContigNavigator.h guiUndoEdit.cpp \
	 guiUndoEdit.h guiapp.h guicolortext.h \
	 handleWindowManagerDelete.h hp_exception_kludge.h listOfFragments.h \
	 locatedFragment.h matchWithinAssembly.h max.h \
	 mbtPtrOrderedVector.h mbtPtrVector.h mbtValOrderedVectorOfRWCString.h \
	 mbtValVector.h mbtValVectorOfBool.h mbtValVector_inc.cpp \
	 mbt_exception.h mbt_val_ord_offset_vec.h min.h \
	 motifutils.h multiProblemGotoList.h nMAX_QUALITY_LEVEL2.h \
	 ntide.h numutil.h paddedFromUnpadded.h \
	 primerType.h quality.h readTypes.h \
	 readsSortedByLeftEndPosition.h readsSortedByReadName.h readsSortedByTemplateName.h \
	 restrictionEnzyme.h restrictionFragment.h rwbtreedictionary.h \
	 rwcstring.h rwcsubstring.h rwdefs.h \
	 rwtptrorderedvector.h rwtptrorderedvector_inc.cpp rwtptrsortedvector.h \
	 rwtptrvector.h rwtvalorderedvector.h rwtvalorderedvector_inc.cpp \
	 rwtvalsortedvector.h rwtvalvector.h selection.h \
	 sequence.h singletInfo.h singletsSortedByTemplateName.h \
	 soEmptyString.h soGetErrno.h subcloneTTemplate.h \
	 sysdepend.h tag.h templatesSortedByName.h \
	 tracefile.h unpaddedFromPadded.h visibleLineForRestrictionFragments.h \
	 whatIsRunning.h wholeAssemblyItem.h wholeReadItem.h

guiWhatToDoWithSelection.o : \
	 assert.h bool.h filename.h \
	 guiWhatToDoWithSelection.cpp guiWhatToDoWithSelection.h guiapp.h \
	 guicolortext.h handleWindowManagerDelete.h mbt_exception.h \
	 motifutils.h rwcstring.h rwcsubstring.h \
	 rwdefs.h rwtptrorderedvector.h rwtptrorderedvector_inc.cpp \
	 rwtvalorderedvector.h rwtvalorderedvector_inc.cpp soEmptyString.h \
	 soGetErrno.h sysdepend.h whatToDoWithSelectionTypes.h

gui_get_selection.o : \
	 assert.h bool.h filename.h \
	 gui_get_selection.cpp guiapp.h guicolortext.h \
	 mbt_exception.h motifutils.h rwcstring.h \
	 rwcsubstring.h rwdefs.h rwtptrorderedvector.h \
	 rwtptrorderedvector_inc.cpp rwtvalorderedvector.h rwtvalorderedvector_inc.cpp \
	 soEmptyString.h soGetErrno.h sysdepend.h

gui_search_for_string.o : \
	 abs.h assembly.h assemblyViewTagTypeAndLine.h \
	 assert.h autoFinishPurposes.h bIntersect.h \
	 bIntervalsIntersect.h bIsNumericMaybeWithWhitespace.h basesegment.h \
	 blockOfLocationsOfA4MerType.h bool.h cComplementBase.h \
	 cComplementBaseTable.h compareContigs.h compareContigsCursor.h \
	 compareContigsTypes.h consed.h consedParameters.h \
	 consedResources.h contig.h contigEnd.h \
	 contigMatchTablesType.h contigSegment.h contigview.h \
	 contigwin.h dictionary.h distribution.h \
	 editCursor.h editaction.h experiment.h \
	 expidAndLocatedFragment.h filename.h gotoList.h \
	 gotoListType.h guiDisplayDigest.h guiMultiContigNavigator.h \
	 gui_get_selection.h gui_search_for_string.cpp gui_search_for_string.h \
	 guiapp.h guicolortext.h handleWindowManagerDelete.h \
	 hp_exception_kludge.h listOfFragments.h locatedFragment.h \
	 matchWithinAssembly.h max.h mbtPtrOrderedVector.h \
	 mbtPtrVector.h mbtValOrderedVectorOfRWCString.h mbtValVector.h \
	 mbtValVectorOfBool.h mbtValVector_inc.cpp mbt_exception.h \
	 mbt_val_ord_offset_vec.h min.h motifutils.h \
	 multiProblemGotoList.h nMAX_QUALITY_LEVEL2.h ntide.h \
	 numutil.h paddedFromUnpadded.h popupErrorMessage.h \
	 primerType.h quality.h readTypes.h \
	 readsSortedByLeftEndPosition.h readsSortedByReadName.h readsSortedByTemplateName.h \
	 restrictionEnzyme.h restrictionFragment.h rwbtreedictionary.h \
	 rwcregexp.h rwcstring.h rwcsubstring.h \
	 rwdefs.h rwtptrorderedvector.h rwtptrorderedvector_inc.cpp \
	 rwtptrsortedvector.h rwtptrvector.h rwtvalorderedvector.h \
	 rwtvalorderedvector_inc.cpp rwtvalsortedvector.h rwtvalvector.h \
	 searchMethods.h search_for_string.h selection.h \
	 sequence.h singletInfo.h singletsSortedByTemplateName.h \
	 soEmptyString.h soGetErrno.h subcloneTTemplate.h \
	 sysdepend.h tag.h templatesSortedByName.h \
	 tracefile.h unpaddedFromPadded.h visibleLineForRestrictionFragments.h \
	 whatIsRunning.h wholeAssemblyItem.h wholeReadItem.h

guiapp.o : \
	 abs.h assembly.h assemblyViewTagTypeAndLine.h \
	 assert.h autoFinishPurposes.h bGuiGetAnswerYesNo.h \
	 bIntersect.h bIntervalsIntersect.h basesegment.h \
	 blockOfLocationsOfA4MerType.h bool.h cComplementBase.h \
	 cComplementBaseTable.h colorDefaults.h colormode.h \
	 compareContigs.h compareContigsCursor.h compareContigsTypes.h \
	 consed.h consedParameters.h consedResources.h \
	 contig.h contigEnd.h contigMatchTablesType.h \
	 contigSegment.h contigview.h contigwin.h \
	 decisionbox.h dictionary.h distribution.h \
	 editCursor.h editaction.h experiment.h \
	 expidAndLocatedFragment.h filename.h fileselector.h \
	 gotoList.h gotoListType.h guiDisplayDigest.h \
	 guiMultiContigNavigator.h guiTopWindow.h guiapp.cpp \
	 guiapp.h guicolortext.h guitedwin.h \
	 hp_exception_kludge.h infobutton.h listOfFragments.h \
	 locatedFragment.h matchWithinAssembly.h max.h \
	 mbtPtrOrderedVector.h mbtPtrVector.h mbtValOrderedVectorOfRWCString.h \
	 mbtValVector.h mbtValVectorOfBool.h mbtValVector_inc.cpp \
	 mbt_exception.h mbt_val_ord_offset_vec.h min.h \
	 motifutils.h multiProblemGotoList.h nMAX_QUALITY_LEVEL2.h \
	 nPrimerFalseMatchScoreArray.h ntide.h numutil.h \
	 paddedFromUnpadded.h popupInfoOrErrorMessageNoFormat.h primerType.h \
	 quality.h readTypes.h readsSortedByLeftEndPosition.h \
	 readsSortedByReadName.h readsSortedByTemplateName.h restrictionEnzyme.h \
	 restrictionFragment.h rwbtreedictionary.h rwcstring.h \
	 rwcsubstring.h rwdefs.h rwtptrorderedvector.h \
	 rwtptrorderedvector_inc.cpp rwtptrsortedvector.h rwtptrvector.h \
	 rwtvalorderedvector.h rwtvalorderedvector_inc.cpp rwtvalsortedvector.h \
	 rwtvalvector.h saveColors.cpp.part2 selection.h \
	 sequence.h singletInfo.h singletsSortedByTemplateName.h \
	 soEmptyString.h soGetErrno.h subcloneTTemplate.h \
	 sysdepend.h tag.h tagTypes.h \
	 teditor_types.h templatesSortedByName.h textfield.h \
	 tracefile.h unpaddedFromPadded.h visibleLineForRestrictionFragments.h \
	 whatIsRunning.h wholeAssemblyItem.h wholeReadItem.h

guicolortext.o : \
	 assert.h bool.h filename.h \
	 guiapp.h guicolortext.cpp guicolortext.h \
	 mbt_exception.h motifutils.h rwcstring.h \
	 rwcsubstring.h rwdefs.h rwtptrorderedvector.h \
	 rwtptrorderedvector_inc.cpp rwtvalorderedvector.h rwtvalorderedvector_inc.cpp \
	 soEmptyString.h soGetErrno.h sysdepend.h

guicontigwin.o : \
	 abs.h arrayOfFwdRevPairLines.h arrayOfFwdRevPairSquares.h \
	 arrayOfFwdRevPairTriangles.h assembly.h assemblyView.h \
	 assemblyViewTagTypeAndLine.h assert.h autoFinishPurposes.h \
	 bGuiGetAnswerYesNo.h bIntersect.h bIntervalsIntersect.h \
	 basesegment.h blockOfLocationsOfA4MerType.h bool.h \
	 cComplementBase.h cComplementBaseTable.h colorDefaults.h \
	 compareContigs.h compareContigsCursor.h compareContigsTypes.h \
	 consed.h consedParameters.h consedResources.h \
	 contig.h contigEnd.h contigMatchTablesType.h \
	 contigSegment.h contigview.h contigwin.h \
	 dictionary.h distribution.h editCursor.h \
	 editaction.h experiment.h expidAndLocatedFragment.h \
	 filename.h fwdRevPair2.h fwdRevPairLine.h \
	 fwdRevPairSquare.h fwdRevPairTriangle.h gotoList.h \
	 gotoListType.h guiAskUserToSelectReadListOptions.h guiChangeColor.h \
	 guiCheckPrimer.h guiDisplayDigest.h guiExportConsensusWithOptions.h \
	 guiHowToSortAlignedReads.h guiMultiContigNavigator.h guiPopupDocumentation.h \
	 guiPopupTagInfo.h guiPopupWholeReadItem.h guiSaveHighlightedReads.h \
	 guiSearchForOpenReadingFrames.h guiShowErrorInfoForARegion.h guiTopWindow.h \
	 guiapp.h guicolortext.h guicontigwin.cpp \
	 guicontigwin.h handleWindowManagerDelete2.h hp_exception_kludge.h \
	 infobutton.h listOfFragments.h locatedFragment.h \
	 matchWithinAssembly.h max.h mbtPtrOrderedVector.h \
	 mbtPtrVector.h mbtValOrderedVectorOfRWCString.h mbtValVector.h \
	 mbtValVectorOfBool.h mbtValVector_inc.cpp mbt_errors.h \
	 mbt_exception.h mbt_val_ord_offset_vec.h min.h \
	 motifutils.h multiProblemGotoList.h nMAX_QUALITY_LEVEL2.h \
	 ntide.h numutil.h paddedFromUnpadded.h \
	 pcrPrimerPair.h pickPCRPrimers.h primerType.h \
	 quality.h readTypes.h readsSortedByLeftEndPosition.h \
	 readsSortedByReadName.h readsSortedByTemplateName.h restrictionEnzyme.h \
	 restrictionFragment.h rwbtreedictionary.h rwcstring.h \
	 rwcsubstring.h rwdefs.h rwt2dptrvector.h \
	 rwtptrorderedvector.h rwtptrorderedvector_inc.cpp rwtptrsortedvector.h \
	 rwtptrvector.h rwtvalorderedvector.h rwtvalorderedvector_inc.cpp \
	 rwtvalsortedvector.h rwtvalvector.h searchForSingleStrandedRegions.h \
	 searchForSingleSubcloneRegions.h selection.h seqMatch.h \
	 sequence.h singletInfo.h singletsSortedByTemplateName.h \
	 soEmptyString.h soGetErrno.h subcloneTTemplate.h \
	 sysdepend.h tag.h tagTypes.h \
	 templatesSortedByName.h textfield.h tracefile.h \
	 unpaddedFromPadded.h visibleLineForRestrictionFragments.h whatIsRunning.h \
	 wholeAssemblyItem.h wholeReadItem.h xsynchronize.h

guidraw.o : \
	 abs.h assembly.h assemblyViewTagTypeAndLine.h \
	 assert.h autoFinishPurposes.h bIntersect.h \
	 bIntervalsIntersect.h basesegment.h blockOfLocationsOfA4MerType.h \
	 bool.h cComplementBase.h cComplementBaseTable.h \
	 compareContigs.h compareContigsCursor.h compareContigsTypes.h \
	 consed.h consedParameters.h consedResources.h \
	 contig.h contigEnd.h contigMatchTablesType.h \
	 contigSegment.h contigview.h contigwin.h \
	 dictionary.h distribution.h editCursor.h \
	 editaction.h experiment.h expidAndLocatedFragment.h \
	 filename.h gotoList.h gotoListType.h \
	 guiDisplayDigest.h guiMultiContigNavigator.h guiapp.h \
	 guicolortext.h guicontigwin.h guidraw.cpp \
	 infobutton.h listOfFragments.h locatedFragment.h \
	 matchWithinAssembly.h max.h mbtPtrOrderedVector.h \
	 mbtPtrVector.h mbtValOrderedVectorOfRWCString.h mbtValVector.h \
	 mbtValVectorOfBool.h mbtValVector_inc.cpp mbt_errors.h \
	 mbt_exception.h mbt_val_ord_offset_vec.h min.h \
	 motifutils.h multiProblemGotoList.h nMAX_QUALITY_LEVEL2.h \
	 ntide.h numutil.h paddedFromUnpadded.h \
	 primerType.h quality.h readTypes.h \
	 readsSortedByLeftEndPosition.h readsSortedByReadName.h readsSortedByTemplateName.h \
	 restrictionEnzyme.h restrictionFragment.h rwbtreedictionary.h \
	 rwcstring.h rwcsubstring.h rwdefs.h \
	 rwtptrorderedvector.h rwtptrorderedvector_inc.cpp rwtptrsortedvector.h \
	 rwtptrvector.h rwtvalorderedvector.h rwtvalorderedvector_inc.cpp \
	 rwtvalsortedvector.h rwtvalvector.h selection.h \
	 sequence.h singletInfo.h singletsSortedByTemplateName.h \
	 soEmptyString.h soGetErrno.h subcloneTTemplate.h \
	 sysdepend.h tag.h templatesSortedByName.h \
	 textfield.h tracefile.h unpaddedFromPadded.h \
	 visibleLineForRestrictionFragments.h whatIsRunning.h wholeAssemblyItem.h \
	 wholeReadItem.h

guihighlight.o : \
	 abs.h assembly.h assemblyViewTagTypeAndLine.h \
	 assert.h autoFinishPurposes.h bIntersect.h \
	 bIntervalsIntersect.h basesegment.h blockOfLocationsOfA4MerType.h \
	 bool.h cComplementBase.h cComplementBaseTable.h \
	 compareContigs.h compareContigsCursor.h compareContigsTypes.h \
	 consed.h consedParameters.h consedResources.h \
	 contig.h contigEnd.h contigMatchTablesType.h \
	 contigSegment.h contigview.h contigwin.h \
	 dictionary.h distribution.h editCursor.h \
	 editaction.h experiment.h expidAndLocatedFragment.h \
	 filename.h gotoList.h gotoListType.h \
	 guiDisplayDigest.h guiMultiContigNavigator.h guiapp.h \
	 guicolortext.h guihighlight.cpp guiteditor.h \
	 guitedwin.h hp_exception_kludge.h infobutton.h \
	 listOfFragments.h locatedFragment.h matchWithinAssembly.h \
	 max.h mbtPtrOrderedVector.h mbtPtrVector.h \
	 mbtValOrderedVectorOfRWCString.h mbtValVector.h mbtValVectorOfBool.h \
	 mbtValVector_inc.cpp mbt_exception.h mbt_val_ord_offset_vec.h \
	 min.h motifutils.h multiProblemGotoList.h \
	 nMAX_QUALITY_LEVEL2.h ntide.h numutil.h \
	 paddedFromUnpadded.h primerType.h quality.h \
	 readTypes.h readsSortedByLeftEndPosition.h readsSortedByReadName.h \
	 readsSortedByTemplateName.h restrictionEnzyme.h restrictionFragment.h \
	 rwbtreedictionary.h rwcstring.h rwcsubstring.h \
	 rwdefs.h rwtptrorderedvector.h rwtptrorderedvector_inc.cpp \
	 rwtptrsortedvector.h rwtptrvector.h rwtvalorderedvector.h \
	 rwtvalorderedvector_inc.cpp rwtvalsortedvector.h rwtvalvector.h \
	 selection.h sequence.h singletInfo.h \
	 singletsSortedByTemplateName.h soEmptyString.h soGetErrno.h \
	 subcloneTTemplate.h sysdepend.h tag.h \
	 teditor.h teditor_types.h tedwin.h \
	 templatesSortedByName.h textfield.h tracefile.h \
	 unpaddedFromPadded.h visibleLineForRestrictionFragments.h whatIsRunning.h \
	 whatToDoWithSelectionTypes.h wholeAssemblyItem.h wholeReadItem.h

guiinput.o : \
	 abs.h assembly.h assemblyViewTagTypeAndLine.h \
	 assert.h autoFinishPurposes.h bIntersect.h \
	 bIntervalsIntersect.h basesegment.h blockOfLocationsOfA4MerType.h \
	 bool.h cComplementBase.h cComplementBaseTable.h \
	 compareContigs.h compareContigsCursor.h compareContigsTypes.h \
	 consed.h consedParameters.h consedResources.h \
	 contig.h contigEnd.h contigMatchTablesType.h \
	 contigSegment.h contigview.h contigwin.h \
	 dictionary.h distribution.h editCursor.h \
	 editaction.h experiment.h expidAndLocatedFragment.h \
	 filename.h gotoList.h gotoListType.h \
	 guiDisplayDigest.h guiMultiContigNavigator.h guiapp.h \
	 guicolortext.h guicontigwin.h guiinput.cpp \
	 hp_exception_kludge.h infobutton.h listOfFragments.h \
	 locatedFragment.h matchWithinAssembly.h max.h \
	 mbtPtrOrderedVector.h mbtPtrVector.h mbtValOrderedVectorOfRWCString.h \
	 mbtValVector.h mbtValVectorOfBool.h mbtValVector_inc.cpp \
	 mbt_errors.h mbt_exception.h mbt_val_ord_offset_vec.h \
	 min.h motifutils.h multiProblemGotoList.h \
	 nMAX_QUALITY_LEVEL2.h ntide.h numutil.h \
	 paddedFromUnpadded.h primerType.h quality.h \
	 readTypes.h readsSortedByLeftEndPosition.h readsSortedByReadName.h \
	 readsSortedByTemplateName.h restrictionEnzyme.h restrictionFragment.h \
	 rwbtreedictionary.h rwcstring.h rwcsubstring.h \
	 rwdefs.h rwtptrorderedvector.h rwtptrorderedvector_inc.cpp \
	 rwtptrsortedvector.h rwtptrvector.h rwtvalorderedvector.h \
	 rwtvalorderedvector_inc.cpp rwtvalsortedvector.h rwtvalvector.h \
	 selection.h sequence.h singletInfo.h \
	 singletsSortedByTemplateName.h soEmptyString.h soGetErrno.h \
	 subcloneTTemplate.h sysdepend.h tag.h \
	 templatesSortedByName.h textfield.h tracefile.h \
	 unpaddedFromPadded.h visibleLineForRestrictionFragments.h whatIsRunning.h \
	 wholeAssemblyItem.h wholeReadItem.h

guiresize.o : \
	 abs.h assembly.h assemblyViewTagTypeAndLine.h \
	 assert.h autoFinishPurposes.h bIntersect.h \
	 bIntervalsIntersect.h basesegment.h blockOfLocationsOfA4MerType.h \
	 bool.h cComplementBase.h cComplementBaseTable.h \
	 compareContigs.h compareContigsCursor.h compareContigsTypes.h \
	 consed.h consedParameters.h consedResources.h \
	 contig.h contigEnd.h contigMatchTablesType.h \
	 contigSegment.h contigview.h contigwin.h \
	 dictionary.h distribution.h editCursor.h \
	 editaction.h experiment.h expidAndLocatedFragment.h \
	 filename.h gotoList.h gotoListType.h \
	 guiDisplayDigest.h guiMultiContigNavigator.h guiapp.h \
	 guicolortext.h guicontigwin.h guiresize.cpp \
	 hp_exception_kludge.h infobutton.h listOfFragments.h \
	 locatedFragment.h matchWithinAssembly.h max.h \
	 mbtPtrOrderedVector.h mbtPtrVector.h mbtValOrderedVectorOfRWCString.h \
	 mbtValVector.h mbtValVectorOfBool.h mbtValVector_inc.cpp \
	 mbt_errors.h mbt_exception.h mbt_val_ord_offset_vec.h \
	 min.h motifutils.h multiProblemGotoList.h \
	 nMAX_QUALITY_LEVEL2.h ntide.h numutil.h \
	 paddedFromUnpadded.h primerType.h quality.h \
	 readTypes.h readsSortedByLeftEndPosition.h readsSortedByReadName.h \
	 readsSortedByTemplateName.h restrictionEnzyme.h restrictionFragment.h \
	 rwbtreedictionary.h rwcstring.h rwcsubstring.h \
	 rwdefs.h rwtptrorderedvector.h rwtptrorderedvector_inc.cpp \
	 rwtptrsortedvector.h rwtptrvector.h rwtvalorderedvector.h \
	 rwtvalorderedvector_inc.cpp rwtvalsortedvector.h rwtvalvector.h \
	 selection.h sequence.h singletInfo.h \
	 singletsSortedByTemplateName.h soEmptyString.h soGetErrno.h \
	 subcloneTTemplate.h sysdepend.h tag.h \
	 templatesSortedByName.h textfield.h tracefile.h \
	 unpaddedFromPadded.h visibleLineForRestrictionFragments.h whatIsRunning.h \
	 wholeAssemblyItem.h wholeReadItem.h

guiteditor.o : \
	 abs.h assembly.h assemblyViewTagTypeAndLine.h \
	 assert.h autoFinishPurposes.h bIntersect.h \
	 bIntervalsIntersect.h basesegment.h blockOfLocationsOfA4MerType.h \
	 bool.h cComplementBase.h cComplementBaseTable.h \
	 consedParameters.h consedResources.h contig.h \
	 contigEnd.h contigMatchTablesType.h contigview.h \
	 contigwin.h dictionary.h distribution.h \
	 editCursor.h experiment.h expidAndLocatedFragment.h \
	 filename.h gotoList.h gotoListType.h \
	 guiapp.h guicolortext.h guicontigwin.h \
	 guiteditor.cpp guiteditor.h guitedwin.h \
	 handleWindowManagerDelete.h hp_exception_kludge.h infobutton.h \
	 listOfFragments.h locatedFragment.h matchWithinAssembly.h \
	 max.h mbtPtrOrderedVector.h mbtPtrVector.h \
	 mbtValOrderedVectorOfRWCString.h mbtValVector.h mbtValVectorOfBool.h \
	 mbtValVector_inc.cpp mbt_exception.h mbt_val_ord_offset_vec.h \
	 min.h motifutils.h multiProblemGotoList.h \
	 nMAX_QUALITY_LEVEL2.h ntide.h numutil.h \
	 paddedFromUnpadded.h popupInfoMessage.h primerType.h \
	 quality.h readTypes.h readsSortedByLeftEndPosition.h \
	 readsSortedByReadName.h readsSortedByTemplateName.h restrictionEnzyme.h \
	 rwbtreedictionary.h rwcstring.h rwcsubstring.h \
	 rwdefs.h rwtptrorderedvector.h rwtptrorderedvector_inc.cpp \
	 rwtptrsortedvector.h rwtptrvector.h rwtvalorderedvector.h \
	 rwtvalorderedvector_inc.cpp rwtvalsortedvector.h rwtvalvector.h \
	 sequence.h singletInfo.h singletsSortedByTemplateName.h \
	 soEmptyString.h soGetErrno.h subcloneTTemplate.h \
	 sysdepend.h tag.h teditor.h \
	 teditor_types.h tedwin.h templatesSortedByName.h \
	 textfield.h tracefile.h unpaddedFromPadded.h \
	 waitUntilDialogIsVisible.h whatIsRunning.h whatToDoWithSelectionTypes.h \
	 wholeAssemblyItem.h wholeReadItem.h

guitedwin.o : \
	 abs.h assembly.h assemblyViewTagTypeAndLine.h \
	 assert.h autoFinishPurposes.h bIntersect.h \
	 bIntervalsIntersect.h basesegment.h blockOfLocationsOfA4MerType.h \
	 bool.h cComplementBase.h cComplementBaseTable.h \
	 colorDefaults.h compareContigs.h compareContigsCursor.h \
	 compareContigsTypes.h consed.h consedParameters.h \
	 consedResources.h contig.h contigEnd.h \
	 contigMatchTablesType.h contigSegment.h contigview.h \
	 contigwin.h dictionary.h distribution.h \
	 editCursor.h editaction.h experiment.h \
	 expidAndLocatedFragment.h filename.h gotoList.h \
	 gotoListType.h guiDisplayDigest.h guiMultiContigNavigator.h \
	 guiapp.h guicolortext.h guihighlight.h \
	 guiteditor.h guitedwin.cpp guitedwin.h \
	 hp_exception_kludge.h infobutton.h listOfFragments.h \
	 locatedFragment.h matchWithinAssembly.h max.h \
	 mbtPtrOrderedVector.h mbtPtrVector.h mbtValOrderedVectorOfInt.h \
	 mbtValOrderedVectorOfRWCString.h mbtValVector.h mbtValVectorOfBool.h \
	 mbtValVector_inc.cpp mbt_exception.h mbt_val_ord_offset_vec.h \
	 min.h motifutils.h multiProblemGotoList.h \
	 nMAX_QUALITY_LEVEL2.h ntide.h numutil.h \
	 paddedFromUnpadded.h primerType.h quality.h \
	 readTypes.h readsSortedByLeftEndPosition.h readsSortedByReadName.h \
	 readsSortedByTemplateName.h readsense_bitmaps.h restrictionEnzyme.h \
	 restrictionFragment.h rwbtreedictionary.h rwcstring.h \
	 rwcsubstring.h rwdefs.h rwtptrorderedvector.h \
	 rwtptrorderedvector_inc.cpp rwtptrsortedvector.h rwtptrvector.h \
	 rwtvalorderedvector.h rwtvalorderedvector_inc.cpp rwtvalsortedvector.h \
	 rwtvalvector.h selection.h sequence.h \
	 singletInfo.h singletsSortedByTemplateName.h soEmptyString.h \
	 soGetErrno.h subcloneTTemplate.h sysdepend.h \
	 tag.h teditor.h teditor_types.h \
	 tedwin.h templatesSortedByName.h textfield.h \
	 tracefile.h unpaddedFromPadded.h visibleLineForRestrictionFragments.h \
	 whatIsRunning.h whatToDoWithSelectionTypes.h wholeAssemblyItem.h \
	 wholeReadItem.h xsynchronize.h

handleWindowManagerDelete.o : \
	 assert.h bool.h filename.h \
	 guiapp.h guicolortext.h handleWindowManagerDelete.cpp \
	 mbt_exception.h motifutils.h rwcstring.h \
	 rwcsubstring.h rwdefs.h rwtptrorderedvector.h \
	 rwtptrorderedvector_inc.cpp rwtvalorderedvector.h rwtvalorderedvector_inc.cpp \
	 soEmptyString.h soGetErrno.h sysdepend.h

handleWindowManagerDelete2.o : \
	 assert.h bool.h filename.h \
	 guiapp.h guicolortext.h handleWindowManagerDelete2.cpp \
	 mbt_exception.h motifutils.h rwcstring.h \
	 rwcsubstring.h rwdefs.h rwtptrorderedvector.h \
	 rwtptrorderedvector_inc.cpp rwtvalorderedvector.h rwtvalorderedvector_inc.cpp \
	 soEmptyString.h soGetErrno.h sysdepend.h

hideSomeTagTypes.o : \
	 abs.h assembly.h assemblyViewTagTypeAndLine.h \
	 assert.h autoFinishPurposes.h bIntersect.h \
	 bIntervalsIntersect.h basesegment.h blockOfLocationsOfA4MerType.h \
	 bool.h cComplementBase.h cComplementBaseTable.h \
	 compareContigs.h compareContigsCursor.h compareContigsTypes.h \
	 consed.h consedParameters.h consedResources.h \
	 contig.h contigEnd.h contigMatchTablesType.h \
	 contigSegment.h contigview.h contigwin.h \
	 dictionary.h distribution.h editCursor.h \
	 editaction.h experiment.h expidAndLocatedFragment.h \
	 filename.h gotoList.h gotoListType.h \
	 guiDisplayDigest.h guiMultiContigNavigator.h guiapp.h \
	 guicolortext.h handleWindowManagerDelete2.h hideSomeTagTypes.cpp \
	 hideSomeTagTypes.h hp_exception_kludge.h listOfFragments.h \
	 locatedFragment.h matchWithinAssembly.h max.h \
	 mbtPtrOrderedVector.h mbtPtrVector.h mbtValOrderedVectorOfRWCString.h \
	 mbtValVector.h mbtValVectorOfBool.h mbtValVector_inc.cpp \
	 mbt_exception.h mbt_val_ord_offset_vec.h min.h \
	 motifutils.h multiProblemGotoList.h nMAX_QUALITY_LEVEL2.h \
	 ntide.h numutil.h paddedFromUnpadded.h \
	 primerType.h quality.h readTypes.h \
	 readsSortedByLeftEndPosition.h readsSortedByReadName.h readsSortedByTemplateName.h \
	 restrictionEnzyme.h restrictionFragment.h rwbtreedictionary.h \
	 rwcstring.h rwcsubstring.h rwdefs.h \
	 rwtptrorderedvector.h rwtptrorderedvector_inc.cpp rwtptrsortedvector.h \
	 rwtptrvector.h rwtvalorderedvector.h rwtvalorderedvector_inc.cpp \
	 rwtvalsortedvector.h rwtvalvector.h selection.h \
	 sequence.h singletInfo.h singletsSortedByTemplateName.h \
	 soEmptyString.h soGetErrno.h subcloneTTemplate.h \
	 sysdepend.h tag.h tagTypes.h \
	 templatesSortedByName.h tracefile.h unpaddedFromPadded.h \
	 visibleLineForRestrictionFragments.h whatIsRunning.h wholeAssemblyItem.h \
	 wholeReadItem.h

highQualityDiscrepancyGotoList.o : \
	 assemblyViewTagTypeAndLine.h assert.h autoFinishPurposes.h \
	 basesegment.h blockOfLocationsOfA4MerType.h bool.h \
	 cComplementBase.h cComplementBaseTable.h consedParameters.h \
	 consedResources.h contig.h contigEnd.h \
	 contigMatchTablesType.h dictionary.h distribution.h \
	 experiment.h filename.h gotoList.h \
	 highQualityDiscrepancyGotoList.cpp highQualityDiscrepancyGotoList.h locatedFragment.h \
	 mbtPtrOrderedVector.h mbtPtrVector.h mbtValOrderedVectorOfRWCString.h \
	 mbtValVector.h mbtValVectorOfBool.h mbtValVector_inc.cpp \
	 mbt_exception.h mbt_val_ord_offset_vec.h min.h \
	 nMAX_QUALITY_LEVEL2.h ntide.h paddedFromUnpadded.h \
	 primerType.h quality.h readTypes.h \
	 readsSortedByLeftEndPosition.h readsSortedByReadName.h restrictionEnzyme.h \
	 rwbtreedictionary.h rwcstring.h rwcsubstring.h \
	 rwdefs.h rwtptrorderedvector.h rwtptrorderedvector_inc.cpp \
	 rwtptrsortedvector.h rwtptrvector.h rwtvalorderedvector.h \
	 rwtvalorderedvector_inc.cpp rwtvalsortedvector.h rwtvalvector.h \
	 sequence.h soEmptyString.h soGetErrno.h \
	 subcloneTTemplate.h sysdepend.h tag.h \
	 tracefile.h unpaddedFromPadded.h whatIsRunning.h \
	 wholeReadItem.h

infobutton.o : \
	 assert.h bool.h filename.h \
	 guiapp.h guicolortext.h hp_exception_kludge.h \
	 infobutton.cpp infobutton.h mbt_exception.h \
	 motifutils.h rwcstring.h rwcsubstring.h \
	 rwdefs.h rwtptrorderedvector.h rwtptrorderedvector_inc.cpp \
	 rwtvalorderedvector.h rwtvalorderedvector_inc.cpp soEmptyString.h \
	 soGetErrno.h sysdepend.h

kimuraBranchProb.o : \
	 assert.h bool.h kimuraBranchProb.cpp \
	 kimuraBranchProb.h mbt_exception.h rwcstring.h \
	 rwcsubstring.h rwdefs.h soGetErrno.h \
	 transitionsTransversions.h

library.o : \
	 assemblyViewTagTypeAndLine.h assert.h bool.h \
	 consedParameters.h consedResources.h fileDefines.h \
	 filename.h library.cpp library.h \
	 mbtPtrOrderedVector.h mbtValOrderedVectorOfRWCString.h mbt_exception.h \
	 restrictionEnzyme.h rwcstring.h rwcsubstring.h \
	 rwdefs.h rwtptrorderedvector.h rwtptrorderedvector_inc.cpp \
	 rwtvalorderedvector.h rwtvalorderedvector_inc.cpp soEmptyString.h \
	 soGetErrno.h sysdepend.h whatIsRunning.h

listOfLibraries.o : \
	 assemblyViewTagTypeAndLine.h assert.h bIsNumericDouble.h \
	 bIsNumericMaybeWithWhitespace.h bool.h consedParameters.h \
	 consedResources.h fileDefines.h filename.h \
	 library.h listOfLibraries.cpp listOfLibraries.h \
	 mbtPtrOrderedVector.h mbtValOrderedVectorOfRWCString.h mbt_exception.h \
	 restrictionEnzyme.h rwcstring.h rwcsubstring.h \
	 rwctokenizer.h rwdefs.h rwtptrorderedvector.h \
	 rwtptrorderedvector_inc.cpp rwtvalorderedvector.h rwtvalorderedvector_inc.cpp \
	 soEmptyString.h soGetErrno.h sysdepend.h \
	 whatIsRunning.h

locatedFragment.o : \
	 abs.h assembly.h assemblyViewTagTypeAndLine.h \
	 assert.h autoFinishPurposes.h bIntersect.h \
	 bIntervalsIntersect.h bIsNumeric.h bIsNumericFloat.h \
	 basesegment.h blockOfLocationsOfA4MerType.h bool.h \
	 cComplementBase.h cComplementBaseTable.h choose_contig.h \
	 compareContigs.h compareContigsCursor.h compareContigsTypes.h \
	 complement_so.h consed.h consedParameters.h \
	 consedResources.h contig.h contigEnd.h \
	 contigMatchTablesType.h contigSegment.h contigview.h \
	 contigwin.h dErrorRateFromQuality.h dictionary.h \
	 distribution.h editCursor.h editaction.h \
	 experiment.h expidAndLocatedFragment.h extendAlignment.h \
	 fileDefines.h filename.h fragment_and_contig.h \
	 getAlignment.h gotoList.h gotoListType.h \
	 guiDisplayDigest.h guiMultiContigNavigator.h guiapp.h \
	 guicolortext.h library.h listOfFragments.h \
	 locatedFragment.cpp locatedFragment.h matchWithinAssembly.h \
	 max.h mbtPtrOrderedVector.h mbtPtrVector.h \
	 mbtValOrderedVectorOfRWCString.h mbtValVector.h mbtValVectorOfBool.h \
	 mbtValVector_inc.cpp mbt_errors.h mbt_exception.h \
	 mbt_val_ord_offset_vec.h min.h motifutils.h \
	 multiProblemGotoList.h nGetReadTypeFromReadName.h nMAX_QUALITY_LEVEL2.h \
	 nNumberFromBase2.h ntide.h numutil.h \
	 paddedFromUnpadded.h primerType.h printAlignment.h \
	 quality.h readPHD.h readTypes.h \
	 readsSortedByLeftEndPosition.h readsSortedByReadName.h readsSortedByTemplateName.h \
	 restrictionEnzyme.h restrictionFragment.h rwbtreedictionary.h \
	 rwcregexp.h rwcstring.h rwcsubstring.h \
	 rwctokenizer.h rwdefs.h rwtptrorderedvector.h \
	 rwtptrorderedvector_inc.cpp rwtptrsortedvector.h rwtptrvector.h \
	 rwtvalorderedvector.h rwtvalorderedvector_inc.cpp rwtvalsortedvector.h \
	 rwtvalvector.h selection.h sequence.h \
	 singletInfo.h singletsSortedByTemplateName.h soAddCommas.h \
	 soEmptyString.h soGetErrno.h soLine.h \
	 subcloneTTemplate.h sysdepend.h tag.h \
	 templatesSortedByName.h tracefile.h unpaddedFromPadded.h \
	 visibleLineForRestrictionFragments.h whatIsRunning.h wholeAssemblyItem.h \
	 wholeReadItem.h

lookForFalsePrimerMatchesOfOnePrimerInOneContig.o : \
	 assemblyViewTagTypeAndLine.h assert.h autoFinishPurposes.h \
	 basesegment.h blockOfLocationsOfA4MerType.h bool.h \
	 cComplementBase.h cComplementBaseTable.h consedParameters.h \
	 consedResources.h contig.h contigEnd.h \
	 contigMatchTablesType.h dictionary.h distribution.h \
	 experiment.h filename.h locatedFragment.h \
	 lookForFalsePrimerMatchesOfOnePrimerInOneContig.cpp lookForFalsePrimerMatchesOfOnePrimerInOneContig.h lookForImperfect3Prime4MerFalsePrimerMatchesOfOnePrimerInOneContig.h \
	 lookForPerfect4MerFalsePrimerMatchesOfOnePrimerInOneContig.h mbtPtrOrderedVector.h mbtPtrVector.h \
	 mbtValOrderedVectorOfRWCString.h mbtValVector.h mbtValVectorOfBool.h \
	 mbtValVector_inc.cpp mbt_exception.h mbt_val_ord_offset_vec.h \
	 min.h nMAX_QUALITY_LEVEL2.h ntide.h \
	 paddedFromUnpadded.h primerType.h quality.h \
	 readTypes.h readsSortedByLeftEndPosition.h readsSortedByReadName.h \
	 restrictionEnzyme.h rwbtreedictionary.h rwcstring.h \
	 rwcsubstring.h rwdefs.h rwtptrorderedvector.h \
	 rwtptrorderedvector_inc.cpp rwtptrsortedvector.h rwtptrvector.h \
	 rwtvalorderedvector.h rwtvalorderedvector_inc.cpp rwtvalsortedvector.h \
	 rwtvalvector.h sequence.h soEmptyString.h \
	 soGetErrno.h subcloneTTemplate.h sysdepend.h \
	 tag.h tracefile.h unpaddedFromPadded.h \
	 whatIsRunning.h wholeReadItem.h

lookForImperfect3Prime4MerFalsePrimerMatchesOfOnePrimerInOneContig.o : \
	 assemblyViewTagTypeAndLine.h assert.h autoFinishPurposes.h \
	 basesegment.h blockOfLocationsOfA4MerType.h bool.h \
	 cComplementBase.h cComplementBaseTable.h consedParameters.h \
	 consedResources.h contig.h contigEnd.h \
	 contigMatchTablesType.h dictionary.h distribution.h \
	 experiment.h filename.h locatedFragment.h \
	 lookForImperfect3Prime4MerFalsePrimerMatchesOfOnePrimerInOneContig.cpp lookForImperfect3Prime4MerFalsePrimerMatchesOfOnePrimerInOneContig.h mbtPtrOrderedVector.h \
	 mbtPtrVector.h mbtValOrderedVectorOfRWCString.h mbtValVector.h \
	 mbtValVectorOfBool.h mbtValVector_inc.cpp mbt_exception.h \
	 mbt_val_ord_offset_vec.h min.h nConvertFrom4Mer.h \
	 nFindScoreOfMatch.h nLengthOf4Mer.h nMAX_QUALITY_LEVEL2.h \
	 nNumberFromBase.h ntide.h paddedFromUnpadded.h \
	 primerType.h quality.h readTypes.h \
	 readsSortedByLeftEndPosition.h readsSortedByReadName.h restrictionEnzyme.h \
	 rwbtreedictionary.h rwcstring.h rwcsubstring.h \
	 rwdefs.h rwtptrorderedvector.h rwtptrorderedvector_inc.cpp \
	 rwtptrsortedvector.h rwtptrvector.h rwtvalorderedvector.h \
	 rwtvalorderedvector_inc.cpp rwtvalsortedvector.h rwtvalvector.h \
	 sequence.h soEmptyString.h soGetErrno.h \
	 subcloneTTemplate.h sysdepend.h tag.h \
	 tracefile.h unpaddedFromPadded.h whatIsRunning.h \
	 wholeReadItem.h whyIsPrimerNotAcceptableTypes.h

lookForPerfect4MerFalsePrimerMatchesOfOnePrimerInOneContig.o : \
	 assemblyViewTagTypeAndLine.h assert.h autoFinishPurposes.h \
	 basesegment.h blockOfLocationsOfA4MerType.h bool.h \
	 cComplementBase.h cComplementBaseTable.h consedParameters.h \
	 consedResources.h contig.h contigEnd.h \
	 contigMatchTablesType.h dictionary.h distribution.h \
	 experiment.h filename.h locatedFragment.h \
	 lookForPerfect4MerFalsePrimerMatchesOfOnePrimerInOneContig.cpp lookForPerfect4MerFalsePrimerMatchesOfOnePrimerInOneContig.h mbtPtrOrderedVector.h \
	 mbtPtrVector.h mbtValOrderedVectorOfRWCString.h mbtValVector.h \
	 mbtValVectorOfBool.h mbtValVector_inc.cpp mbt_exception.h \
	 mbt_val_ord_offset_vec.h min.h nFindScoreOfMatch.h \
	 nLengthOf4Mer.h nMAX_QUALITY_LEVEL2.h ntide.h \
	 paddedFromUnpadded.h primerType.h quality.h \
	 readTypes.h readsSortedByLeftEndPosition.h readsSortedByReadName.h \
	 restrictionEnzyme.h rwbtreedictionary.h rwcstring.h \
	 rwcsubstring.h rwdefs.h rwtptrorderedvector.h \
	 rwtptrorderedvector_inc.cpp rwtptrsortedvector.h rwtptrvector.h \
	 rwtvalorderedvector.h rwtvalorderedvector_inc.cpp rwtvalsortedvector.h \
	 rwtvalvector.h sequence.h soEmptyString.h \
	 soGetErrno.h subcloneTTemplate.h sysdepend.h \
	 tag.h tracefile.h unpaddedFromPadded.h \
	 whatIsRunning.h wholeReadItem.h whyIsPrimerNotAcceptableTypes.h

lowconsqual.o : \
	 assemblyViewTagTypeAndLine.h assert.h autoFinishPurposes.h \
	 basesegment.h blockOfLocationsOfA4MerType.h bool.h \
	 cComplementBase.h cComplementBaseTable.h consedParameters.h \
	 consedResources.h contig.h contigEnd.h \
	 contigMatchTablesType.h dictionary.h distribution.h \
	 experiment.h filename.h gotoList.h \
	 locatedFragment.h lowconsqual.cpp lowconsqual.h \
	 mbtPtrOrderedVector.h mbtPtrVector.h mbtValOrderedVectorOfRWCString.h \
	 mbtValVector.h mbtValVectorOfBool.h mbtValVector_inc.cpp \
	 mbt_exception.h mbt_val_ord_offset_vec.h min.h \
	 nMAX_QUALITY_LEVEL2.h ntide.h paddedFromUnpadded.h \
	 primerType.h quality.h readTypes.h \
	 readsSortedByLeftEndPosition.h readsSortedByReadName.h restrictionEnzyme.h \
	 rwbtreedictionary.h rwcstring.h rwcsubstring.h \
	 rwdefs.h rwtptrorderedvector.h rwtptrorderedvector_inc.cpp \
	 rwtptrsortedvector.h rwtptrvector.h rwtvalorderedvector.h \
	 rwtvalorderedvector_inc.cpp rwtvalsortedvector.h rwtvalvector.h \
	 sequence.h soEmptyString.h soGetErrno.h \
	 subcloneTTemplate.h sysdepend.h tag.h \
	 tracefile.h unpaddedFromPadded.h whatIsRunning.h \
	 wholeReadItem.h

main.o : \
	 abs.h addAlignedSequence.h addNewReads.h \
	 addNewReadsAutomated.h addNewReadsWithExistingAlignments.h arrayOfFwdRevPairLines.h \
	 arrayOfFwdRevPairSquares.h arrayOfFwdRevPairTriangles.h assembly.h \
	 assemblyView.h assemblyViewTagTypeAndLine.h assert.h \
	 autoEdit.h autoFinish.h autoFinishPurposes.h \
	 autoPCRAmplify.h autoReport.h bIntersect.h \
	 bIntervalsIntersect.h bIsNumericMaybeWithWhitespace.h basesegment.h \
	 batchChangeConsensus.h blockOfLocationsOfA4MerType.h bool.h \
	 cComplementBase.h cComplementBaseTable.h checkLicenseKey.h \
	 checkVariableLengthLimit.h compareContigs.h compareContigsCursor.h \
	 compareContigsTypes.h consed.h consedParameters.h \
	 consedResources.h consed_version.h contig.h \
	 contigEnd.h contigMatchTablesType.h contigSegment.h \
	 contigview.h contigwin.h defaultResourcesDefinition.h \
	 dictionary.h diffChromosomes.h distribution.h \
	 editCursor.h editaction.h experiment.h \
	 expidAndLocatedFragment.h fileDefines.h filename.h \
	 fixContigEnds.h fwdRevPair2.h fwdRevPairLine.h \
	 fwdRevPairSquare.h fwdRevPairTriangle.h geneClassifications.h \
	 gotoList.h gotoListType.h guiDisplayDigest.h \
	 guiEditResourcesStandalone.h guiMultiContigNavigator.h guiTopWindow.h \
	 guiapp.h guicolortext.h library.h \
	 listOfFragments.h listOfLibraries.h locatedFragment.h \
	 main.cpp matchWithinAssembly.h max.h \
	 maybeTerminateIfAnotherReadWriteConsed.h mbtPtrOrderedVector.h mbtPtrVector.h \
	 mbtValOrderedVectorOfLong.h mbtValOrderedVectorOfRWCString.h mbtValVector.h \
	 mbtValVectorOfBool.h mbtValVector_inc.cpp mbt_exception.h \
	 mbt_val_ord_offset_vec.h min.h miscProgram.h \
	 motifutils.h multiProblemGotoList.h nMAX_QUALITY_LEVEL2.h \
	 nextPhredPipeline.h ntide.h numutil.h \
	 paddedFromUnpadded.h perhapsCreateSocketToControlConsed.h phaster2PhdBall.h \
	 phdBall2Fasta.h primerType.h printDefaultResources.h \
	 printMemory.h printSingleSignal.h printTime.h \
	 quality.h readAndProcessReadPrefixFile.h readTypes.h \
	 readsSortedByLeftEndPosition.h readsSortedByReadName.h readsSortedByTemplateName.h \
	 removeContigs.h removeReads.h restrictionEnzyme.h \
	 restrictionFragment.h rwbtreedictionary.h rwcstring.h \
	 rwcsubstring.h rwctokenizer.h rwdefs.h \
	 rwt2dptrvector.h rwtptrorderedvector.h rwtptrorderedvector_inc.cpp \
	 rwtptrsortedvector.h rwtptrvector.h rwtvalorderedvector.h \
	 rwtvalorderedvector_inc.cpp rwtvalsortedvector.h rwtvalvector.h \
	 saveTagTypes.h selection.h seqMatch.h \
	 sequence.h setComplementBaseTable.h setErrorRateFromQuality.h \
	 setNotACGTTable.h setNumberFromBaseTable.h sff2PhdBall.h \
	 singletInfo.h singletsSortedByTemplateName.h snpGenome.h \
	 soEmptyString.h soGetErrno.h solexa2PhdBall.h \
	 subcloneTTemplate.h sysdepend.h tag.h \
	 tagSNPs.h templatesSortedByName.h terminateIfNoPhdDir.h \
	 testReadPhdBall.h tracefile.h unpaddedFromPadded.h \
	 visibleLineForRestrictionFragments.h whatIsRunning.h wholeAssemblyItem.h \
	 wholeReadItem.h

makeUpper.o : \
	 makeUpper.c

makeVectorLookupTables.o : \
	 assert.h blockOfLocationsOfA4MerType.h bool.h \
	 contigMatchTablesType.h makeVectorLookupTables.cpp makeVectorLookupTables.h \
	 mbt_exception.h rwcstring.h rwcsubstring.h \
	 rwdefs.h setMatchLookupTable.h soGetErrno.h

maybeTerminateIfAnotherReadWriteConsed.o : \
	 assemblyViewTagTypeAndLine.h assert.h bool.h \
	 consedParameters.h consedResources.h filename.h \
	 maybeTerminateIfAnotherReadWriteConsed.cpp maybeTerminateIfAnotherReadWriteConsed.h mbtPtrOrderedVector.h \
	 mbtValOrderedVectorOfRWCString.h mbt_exception.h restrictionEnzyme.h \
	 rwcstring.h rwcsubstring.h rwdefs.h \
	 rwtptrorderedvector.h rwtptrorderedvector_inc.cpp rwtvalorderedvector.h \
	 rwtvalorderedvector_inc.cpp soEmptyString.h soGetErrno.h \
	 sysdepend.h whatIsRunning.h

mbtValOrderedVectorOfInt.o : \
	 assert.h bool.h mbtValOrderedVectorOfInt.cpp \
	 mbtValOrderedVectorOfInt.h mbt_exception.h rwcstring.h \
	 rwcsubstring.h rwdefs.h rwtvalorderedvector.h \
	 rwtvalorderedvector_inc.cpp soEmptyString.h soGetErrno.h

mbtValVector.o : \
	 mbtValVector.cpp

mbt_exception.o : \
	 abs.h assembly.h assemblyViewTagTypeAndLine.h \
	 assert.h autoFinishPurposes.h bIntersect.h \
	 bIntervalsIntersect.h basesegment.h blockOfLocationsOfA4MerType.h \
	 bool.h cComplementBase.h cComplementBaseTable.h \
	 compareContigs.h compareContigsCursor.h compareContigsTypes.h \
	 consed.h consedParameters.h consedResources.h \
	 contig.h contigEnd.h contigMatchTablesType.h \
	 contigSegment.h contigview.h contigwin.h \
	 dictionary.h distribution.h dumpCore.h \
	 editCursor.h editaction.h experiment.h \
	 expidAndLocatedFragment.h filename.h gotoList.h \
	 gotoListType.h guiDisplayDigest.h guiMultiContigNavigator.h \
	 guiapp.h guicolortext.h listOfFragments.h \
	 locatedFragment.h matchWithinAssembly.h max.h \
	 mbtPtrOrderedVector.h mbtPtrVector.h mbtValOrderedVectorOfRWCString.h \
	 mbtValVector.h mbtValVectorOfBool.h mbtValVector_inc.cpp \
	 mbt_exception.cpp mbt_exception.h mbt_val_ord_offset_vec.h \
	 min.h motifutils.h multiProblemGotoList.h \
	 nMAX_QUALITY_LEVEL2.h ntide.h numutil.h \
	 paddedFromUnpadded.h primerType.h quality.h \
	 readTypes.h readsSortedByLeftEndPosition.h readsSortedByReadName.h \
	 readsSortedByTemplateName.h restrictionEnzyme.h restrictionFragment.h \
	 rwbtreedictionary.h rwcstring.h rwcsubstring.h \
	 rwdefs.h rwtptrorderedvector.h rwtptrorderedvector_inc.cpp \
	 rwtptrsortedvector.h rwtptrvector.h rwtvalorderedvector.h \
	 rwtvalorderedvector_inc.cpp rwtvalsortedvector.h rwtvalvector.h \
	 selection.h sequence.h singletInfo.h \
	 singletsSortedByTemplateName.h soEmptyString.h soGetErrno.h \
	 subcloneTTemplate.h sysdepend.h tag.h \
	 templatesSortedByName.h tracefile.h unpaddedFromPadded.h \
	 visibleLineForRestrictionFragments.h whatIsRunning.h wholeAssemblyItem.h \
	 wholeReadItem.h

messageAndFileSelector.o : \
	 assert.h bool.h filename.h \
	 guiapp.h guicolortext.h handleWindowManagerDelete.h \
	 hp_exception_kludge.h mbt_exception.h messageAndFileSelector.cpp \
	 messageAndFileSelector.h motifutils.h rwcstring.h \
	 rwcsubstring.h rwdefs.h rwtptrorderedvector.h \
	 rwtptrorderedvector_inc.cpp rwtvalorderedvector.h rwtvalorderedvector_inc.cpp \
	 soEmptyString.h soGetErrno.h sysdepend.h

miniassembly.o : \
	 abs.h assembly.h assemblyViewTagTypeAndLine.h \
	 assert.h autoFinishPurposes.h bGuiGetAnswerYesNo.h \
	 bIntersect.h bIntervalsIntersect.h bIsNumeric.h \
	 bIsNumericMaybeWithWhitespace.h basesegment.h blockOfLocationsOfA4MerType.h \
	 bool.h cComplementBase.h cComplementBaseTable.h \
	 compareContigs.h compareContigsCursor.h compareContigsTypes.h \
	 consed.h consedParameters.h consedResources.h \
	 contig.h contigEnd.h contigMatchTablesType.h \
	 contigSegment.h contigview.h contigwin.h \
	 dictionary.h distribution.h editCursor.h \
	 editaction.h experiment.h expidAndLocatedFragment.h \
	 filGetUniqueFilename.h filename.h gotoList.h \
	 gotoListType.h guiDisplayDigest.h guiMultiContigNavigator.h \
	 guiapp.h guicolortext.h handleWindowManagerDelete2.h \
	 hp_exception_kludge.h intXtPointerUnion.h listOfFragments.h \
	 locatedFragment.h matchWithinAssembly.h max.h \
	 mbtPtrOrderedVector.h mbtPtrVector.h mbtValOrderedVectorOfRWCString.h \
	 mbtValVector.h mbtValVectorOfBool.h mbtValVector_inc.cpp \
	 mbt_exception.h mbt_val_ord_offset_vec.h min.h \
	 miniassembly.cpp miniassembly.h motifutils.h \
	 multiProblemGotoList.h nCompareContigsByName.h nMAX_QUALITY_LEVEL2.h \
	 ntide.h numutil.h paddedFromUnpadded.h \
	 phdBall2Fasta.h popupErrorMessage.h popupErrorMessage2.h \
	 popupInfoMessage.h primerType.h quality.h \
	 readTypes.h readsSortedByLeftEndPosition.h readsSortedByReadName.h \
	 readsSortedByTemplateName.h restrictionEnzyme.h restrictionFragment.h \
	 rwbtreedictionary.h rwcstring.h rwcsubstring.h \
	 rwctokenizer.h rwdefs.h rwtptrorderedvector.h \
	 rwtptrorderedvector_inc.cpp rwtptrsortedvector.h rwtptrvector.h \
	 rwtvalorderedvector.h rwtvalorderedvector_inc.cpp rwtvalsortedvector.h \
	 rwtvalvector.h selection.h sequence.h \
	 singletInfo.h singletsSortedByTemplateName.h soEmptyString.h \
	 soGetErrno.h subcloneTTemplate.h sysdepend.h \
	 tag.h templatesSortedByName.h textbox.h \
	 tracefile.h unpaddedFromPadded.h visibleLineForRestrictionFragments.h \
	 whatIsRunning.h wholeAssemblyItem.h wholeReadItem.h

miscProgram.o : \
	 miscProgram.cpp miscProgram.h

motifutils.o : \
	 assert.h bool.h filename.h \
	 guiapp.h guicolortext.h mbt_exception.h \
	 motifutils.cpp motifutils.h rwcstring.h \
	 rwcsubstring.h rwdefs.h rwtptrorderedvector.h \
	 rwtptrorderedvector_inc.cpp rwtvalorderedvector.h rwtvalorderedvector_inc.cpp \
	 soEmptyString.h soGetErrno.h sysdepend.h

multiProblemGotoList.o : \
	 assemblyViewTagTypeAndLine.h assert.h autoFinishPurposes.h \
	 basesegment.h blockOfLocationsOfA4MerType.h bool.h \
	 cComplementBase.h cComplementBaseTable.h consedParameters.h \
	 consedResources.h contig.h contigEnd.h \
	 contigMatchTablesType.h dictionary.h distribution.h \
	 experiment.h filename.h gotoList.h \
	 gotoListType.h highQualityDiscrepancyGotoList.h locatedFragment.h \
	 lowconsqual.h mbtPtrOrderedVector.h mbtPtrVector.h \
	 mbtValOrderedVectorOfRWCString.h mbtValVector.h mbtValVectorOfBool.h \
	 mbtValVector_inc.cpp mbt_exception.h mbt_val_ord_offset_vec.h \
	 min.h multiProblemGotoList.cpp multiProblemGotoList.h \
	 nMAX_QUALITY_LEVEL2.h ntide.h paddedFromUnpadded.h \
	 primerType.h quality.h readTypes.h \
	 readsSortedByLeftEndPosition.h readsSortedByReadName.h restrictionEnzyme.h \
	 rwbtreedictionary.h rwcstring.h rwcsubstring.h \
	 rwdefs.h rwtptrorderedvector.h rwtptrorderedvector_inc.cpp \
	 rwtptrsortedvector.h rwtptrvector.h rwtvalorderedvector.h \
	 rwtvalorderedvector_inc.cpp rwtvalsortedvector.h rwtvalvector.h \
	 sequence.h singleStrandedRegionsGotoList.h singleSubcloneRegionsGotoList.h \
	 soEmptyString.h soGetErrno.h subcloneTTemplate.h \
	 sysdepend.h tag.h tracefile.h \
	 unalignedHighQualityRegionsGotoList.h unpaddedFromPadded.h whatIsRunning.h \
	 wholeReadItem.h

myAgrep.o : \
	 assemblyViewTagTypeAndLine.h assert.h bool.h \
	 consedParameters.h consedResources.h filename.h \
	 mbtPtrOrderedVector.h mbtValOrderedVectorOfRWCString.h mbt_exception.h \
	 myAgrep.cpp myAgrep.h nNumberFromBase2.h \
	 restrictionEnzyme.h rwcstring.h rwcsubstring.h \
	 rwdefs.h rwtptrorderedvector.h rwtptrorderedvector_inc.cpp \
	 rwtvalorderedvector.h rwtvalorderedvector_inc.cpp soEmptyString.h \
	 soGetErrno.h sysdepend.h whatIsRunning.h

myAgrepAndFilter.o : \
	 abs.h assert.h bool.h \
	 mbt_exception.h myAgrep.h myAgrepAndFilter.cpp \
	 myAgrepAndFilter.h rwcstring.h rwcsubstring.h \
	 rwdefs.h rwtvalorderedvector.h rwtvalorderedvector_inc.cpp \
	 soEmptyString.h soGetErrno.h

nAmbiguityCodeToNumber2.o : \
	 assert.h bool.h mbt_exception.h \
	 nAmbiguityCodeToNumber2.cpp nAmbiguityCodeToNumber2.h rwcstring.h \
	 rwcsubstring.h rwdefs.h soGetErrno.h

nCompareContigsByName.o : \
	 assemblyViewTagTypeAndLine.h assert.h autoFinishPurposes.h \
	 bIsNumericMaybeWithWhitespace.h basesegment.h blockOfLocationsOfA4MerType.h \
	 bool.h cComplementBase.h cComplementBaseTable.h \
	 consedParameters.h consedResources.h contig.h \
	 contigEnd.h contigMatchTablesType.h dictionary.h \
	 distribution.h experiment.h filename.h \
	 locatedFragment.h mbtPtrOrderedVector.h mbtPtrVector.h \
	 mbtValOrderedVectorOfRWCString.h mbtValVector.h mbtValVectorOfBool.h \
	 mbtValVector_inc.cpp mbt_exception.h mbt_val_ord_offset_vec.h \
	 min.h nCompareContigsByName.cpp nCompareContigsByName.h \
	 nMAX_QUALITY_LEVEL2.h ntide.h paddedFromUnpadded.h \
	 primerType.h quality.h readTypes.h \
	 readsSortedByLeftEndPosition.h readsSortedByReadName.h restrictionEnzyme.h \
	 rwbtreedictionary.h rwcstring.h rwcsubstring.h \
	 rwdefs.h rwtptrorderedvector.h rwtptrorderedvector_inc.cpp \
	 rwtptrsortedvector.h rwtptrvector.h rwtvalorderedvector.h \
	 rwtvalorderedvector_inc.cpp rwtvalsortedvector.h rwtvalvector.h \
	 sequence.h soEmptyString.h soGetErrno.h \
	 subcloneTTemplate.h sysdepend.h tag.h \
	 tracefile.h unpaddedFromPadded.h whatIsRunning.h \
	 wholeReadItem.h

nCreateSocket.o : \
	 assert.h bool.h filename.h \
	 guiapp.h guicolortext.h mbt_exception.h \
	 motifutils.h nCreateSocket.cpp rwcstring.h \
	 rwcsubstring.h rwdefs.h rwtptrorderedvector.h \
	 rwtptrorderedvector_inc.cpp rwtvalorderedvector.h rwtvalorderedvector_inc.cpp \
	 soEmptyString.h soGetErrno.h sysdepend.h

nDeleteFile.o : \
	 bool.h nDeleteFile.cpp rwcstring.h \
	 rwcsubstring.h rwdefs.h

nFindScoreOfMatch.o : \
	 nFindScoreOfMatch.cpp nFindScoreOfMatch.h nNumberFromBase.h \
	 nPrimerFalseMatchScoreArray.h

nFindScoreOfSelfMatch.o : \
	 nFindScoreOfSelfMatch.cpp nFindScoreOfSelfMatch.h nNumberFromBase.h \
	 nPrimerFalseMatchScoreArray.h

nGetLengthOfMononucleotideRepeat.o : \
	 nGetLengthOfMononucleotideRepeat.cpp nGetLengthOfMononucleotideRepeat.h

nGetNumberOfTokens.o : \
	 bool.h nGetNumberOfTokens.cpp nGetNumberOfTokens.h

nGetReadTypeFromReadName.o : \
	 assert.h bool.h mbt_exception.h \
	 nGetReadTypeFromReadName.cpp nGetReadTypeFromReadName.h readTypes.h \
	 rwcstring.h rwcsubstring.h rwdefs.h \
	 soGetErrno.h

nGetTrailingNumber.o : \
	 bool.h nGetTrailingNumber.cpp nGetTrailingNumber.h \
	 rwcstring.h rwcsubstring.h rwdefs.h

nStripTrailingWhitespace.o : \
	 nStripTrailingWhitespace.cpp nStripTrailingWhitespace.h

nSystemReadALine.o : \
	 nSystemReadALine.cpp nSystemReadALine.h

navigateByTagsInAllContigs.o : \
	 abs.h assembly.h assemblyViewTagTypeAndLine.h \
	 assert.h autoFinishPurposes.h bIntersect.h \
	 bIntervalsIntersect.h basesegment.h blockOfLocationsOfA4MerType.h \
	 bool.h cComplementBase.h cComplementBaseTable.h \
	 compareContigs.h compareContigsCursor.h compareContigsTypes.h \
	 consed.h consedParameters.h consedResources.h \
	 contig.h contigEnd.h contigMatchTablesType.h \
	 contigSegment.h contigview.h contigwin.h \
	 dictionary.h distribution.h editCursor.h \
	 editaction.h experiment.h expidAndLocatedFragment.h \
	 filename.h gotoList.h gotoListType.h \
	 guiDisplayDigest.h guiGetTagType.h guiMultiContigNavigator.h \
	 guiapp.h guicolortext.h listOfFragments.h \
	 locatedFragment.h matchWithinAssembly.h max.h \
	 mbtPtrOrderedVector.h mbtPtrVector.h mbtValOrderedVectorOfRWCString.h \
	 mbtValVector.h mbtValVectorOfBool.h mbtValVector_inc.cpp \
	 mbt_exception.h mbt_val_ord_offset_vec.h min.h \
	 motifutils.h multiProblemGotoList.h nMAX_QUALITY_LEVEL2.h \
	 navigateByTagsInAllContigs.cpp ntide.h numutil.h \
	 paddedFromUnpadded.h primerType.h quality.h \
	 readTypes.h readsSortedByLeftEndPosition.h readsSortedByReadName.h \
	 readsSortedByTemplateName.h restrictionEnzyme.h restrictionFragment.h \
	 rwbtreedictionary.h rwcstring.h rwcsubstring.h \
	 rwdefs.h rwtptrorderedvector.h rwtptrorderedvector_inc.cpp \
	 rwtptrsortedvector.h rwtptrvector.h rwtvalorderedvector.h \
	 rwtvalorderedvector_inc.cpp rwtvalsortedvector.h rwtvalvector.h \
	 selection.h sequence.h singletInfo.h \
	 singletsSortedByTemplateName.h soEmptyString.h soGetErrno.h \
	 subcloneTTemplate.h sysdepend.h tag.h \
	 tagTypes.h tagsGotoList.h templatesSortedByName.h \
	 tracefile.h unpaddedFromPadded.h visibleLineForRestrictionFragments.h \
	 whatIsRunning.h wholeAssemblyItem.h wholeReadItem.h

nextPhredPipeline.o : \
	 assert.h bIsNumericMaybeWithWhitespace.h bool.h \
	 filename.h mbtValOrderedVectorOfInt.h mbtValOrderedVectorOfRWCString.h \
	 mbtValVector.h mbtValVectorOfBool.h mbtValVector_inc.cpp \
	 mbt_exception.h min.h nextPhredPipeline.cpp \
	 nextPhredPipeline.h rwcstring.h rwcsubstring.h \
	 rwctokenizer.h rwdefs.h rwtvalorderedvector.h \
	 rwtvalorderedvector_inc.cpp rwtvalvector.h soEmptyString.h \
	 soGetDateTime.h soGetErrno.h soLine.h \
	 sysdepend.h

ntide.o : \
	 assemblyViewTagTypeAndLine.h assert.h bool.h \
	 cComplementBase.h cComplementBaseTable.h consedParameters.h \
	 consedResources.h filename.h mbtPtrOrderedVector.h \
	 mbtValOrderedVectorOfRWCString.h mbt_exception.h ntide.cpp \
	 ntide.h quality.h restrictionEnzyme.h \
	 rwcstring.h rwcsubstring.h rwdefs.h \
	 rwtptrorderedvector.h rwtptrorderedvector_inc.cpp rwtvalorderedvector.h \
	 rwtvalorderedvector_inc.cpp soEmptyString.h soGetErrno.h \
	 sysdepend.h whatIsRunning.h

numutil.o : \
	 abs.h assert.h bIntersect.h \
	 bIntervalsIntersect.h bool.h max.h \
	 mbt_errors.h mbt_exception.h min.h \
	 numutil.cpp numutil.h rwcstring.h \
	 rwcsubstring.h rwdefs.h soGetErrno.h \
	 sysdepend.h

oligoTag.o : \
	 abs.h assembly.h assemblyViewTagTypeAndLine.h \
	 assert.h autoFinishPurposes.h bIntersect.h \
	 bIntervalsIntersect.h basesegment.h blockOfLocationsOfA4MerType.h \
	 bool.h cComplementBase.h cComplementBaseTable.h \
	 centerWidgetOnWidget.h compareContigs.h compareContigsCursor.h \
	 compareContigsTypes.h complement_so.h consed.h \
	 consedParameters.h consedResources.h contig.h \
	 contigEnd.h contigMatchTablesType.h contigSegment.h \
	 contigview.h contigwin.h dictionary.h \
	 distribution.h editCursor.h editaction.h \
	 experiment.h expidAndLocatedFragment.h filename.h \
	 gotoList.h gotoListType.h guiDisplayDigest.h \
	 guiMultiContigNavigator.h guiapp.h guicolortext.h \
	 hp_exception_kludge.h listOfFragments.h locatedFragment.h \
	 matchWithinAssembly.h max.h mbtPtrOrderedVector.h \
	 mbtPtrVector.h mbtValOrderedVectorOfRWCString.h mbtValVector.h \
	 mbtValVectorOfBool.h mbtValVector_inc.cpp mbt_exception.h \
	 mbt_val_ord_offset_vec.h min.h motifutils.h \
	 multiProblemGotoList.h nMAX_QUALITY_LEVEL2.h ntide.h \
	 numutil.h oligoTag.cpp oligoTag.h \
	 paddedFromUnpadded.h popupErrorMessage.h primerType.h \
	 quality.h readTypes.h readsSortedByLeftEndPosition.h \
	 readsSortedByReadName.h readsSortedByTemplateName.h restrictionEnzyme.h \
	 restrictionFragment.h rwbtreedictionary.h rwcregexp.h \
	 rwcstring.h rwcsubstring.h rwdefs.h \
	 rwtptrorderedvector.h rwtptrorderedvector_inc.cpp rwtptrsortedvector.h \
	 rwtptrvector.h rwtvalorderedvector.h rwtvalorderedvector_inc.cpp \
	 rwtvalsortedvector.h rwtvalvector.h searchMethods.h \
	 search_for_string.h selection.h sequence.h \
	 singletInfo.h singletsSortedByTemplateName.h soEmptyString.h \
	 soGetErrno.h subcloneTTemplate.h sysdepend.h \
	 tag.h templatesSortedByName.h tracefile.h \
	 unpaddedFromPadded.h visibleLineForRestrictionFragments.h whatIsRunning.h \
	 wholeAssemblyItem.h wholeReadItem.h

openAutoFinishOutputFiles.o : \
	 assemblyViewTagTypeAndLine.h assert.h bool.h \
	 consedParameters.h consedResources.h filGetUniqueFilename.h \
	 fileDefines.h filename.h mbtPtrOrderedVector.h \
	 mbtValOrderedVectorOfRWCString.h mbt_exception.h openAutoFinishOutputFiles.cpp \
	 restrictionEnzyme.h rwcregexp.h rwcstring.h \
	 rwcsubstring.h rwdefs.h rwtptrorderedvector.h \
	 rwtptrorderedvector_inc.cpp rwtvalorderedvector.h rwtvalorderedvector_inc.cpp \
	 soEmptyString.h soGetErrno.h sysdepend.h \
	 whatIsRunning.h

openLogFiles.o : \
	 assemblyViewTagTypeAndLine.h assert.h bool.h \
	 consedParameters.h consedResources.h fileDefines.h \
	 filename.h mbtPtrOrderedVector.h mbtValOrderedVectorOfRWCString.h \
	 mbt_exception.h openLogFiles.cpp openLogFiles.h \
	 restrictionEnzyme.h rwcregexp.h rwcstring.h \
	 rwcsubstring.h rwdefs.h rwtptrorderedvector.h \
	 rwtptrorderedvector_inc.cpp rwtvalorderedvector.h rwtvalorderedvector_inc.cpp \
	 soEmptyString.h soGetErrno.h sysdepend.h \
	 whatIsRunning.h

ostream_overloads.o : \
	 assert.h basesegment.h bool.h \
	 cComplementBase.h cComplementBaseTable.h filename.h \
	 locatedFragment.h mbtValVector.h mbtValVector_inc.cpp \
	 mbt_exception.h mbt_val_ord_offset_vec.h min.h \
	 ntide.h ostream_overloads.cpp quality.h \
	 readTypes.h rwcstring.h rwcsubstring.h \
	 rwdefs.h rwtptrorderedvector.h rwtptrorderedvector_inc.cpp \
	 rwtptrsortedvector.h rwtvalorderedvector.h rwtvalorderedvector_inc.cpp \
	 rwtvalsortedvector.h rwtvalvector.h sequence.h \
	 soEmptyString.h soGetErrno.h sysdepend.h \
	 tag.h tracefile.h wholeReadItem.h

pFindShortestAcceptablePrimer.o : \
	 blockOfLocationsOfA4MerType.h bool.h contigMatchTablesType.h \
	 pFindShortestAcceptablePrimer.cpp pFindShortestAcceptablePrimer.h primerType.h

paddedFromUnpadded.o : \
	 assemblyViewTagTypeAndLine.h assert.h autoFinishPurposes.h \
	 basesegment.h blockOfLocationsOfA4MerType.h bool.h \
	 cComplementBase.h cComplementBaseTable.h consedParameters.h \
	 consedResources.h contig.h contigEnd.h \
	 contigMatchTablesType.h dictionary.h distribution.h \
	 experiment.h filename.h locatedFragment.h \
	 mbtPtrOrderedVector.h mbtPtrVector.h mbtValOrderedVectorOfRWCString.h \
	 mbtValVector.h mbtValVectorOfBool.h mbtValVector_inc.cpp \
	 mbt_exception.h mbt_val_ord_offset_vec.h min.h \
	 nMAX_QUALITY_LEVEL2.h ntide.h paddedFromUnpadded.cpp \
	 paddedFromUnpadded.h primerType.h quality.h \
	 readTypes.h readsSortedByLeftEndPosition.h readsSortedByReadName.h \
	 restrictionEnzyme.h rwbtreedictionary.h rwcstring.h \
	 rwcsubstring.h rwdefs.h rwtptrorderedvector.h \
	 rwtptrorderedvector_inc.cpp rwtptrsortedvector.h rwtptrvector.h \
	 rwtvalorderedvector.h rwtvalorderedvector_inc.cpp rwtvalsortedvector.h \
	 rwtvalvector.h sequence.h soEmptyString.h \
	 soGetErrno.h subcloneTTemplate.h sysdepend.h \
	 tag.h tracefile.h unpaddedFromPadded.h \
	 whatIsRunning.h wholeReadItem.h

paddedPieceOfRead.o : \
	 assemblyViewTagTypeAndLine.h assert.h autoFinishPurposes.h \
	 bIsAPad.h basesegment.h blockOfLocationsOfA4MerType.h \
	 bool.h cComplementBase.h cComplementBaseTable.h \
	 consedParameters.h consedResources.h contig.h \
	 contigEnd.h contigMatchTablesType.h dictionary.h \
	 distribution.h experiment.h filename.h \
	 locatedFragment.h mbtPtrOrderedVector.h mbtPtrVector.h \
	 mbtValOrderedVectorOfRWCString.h mbtValVector.h mbtValVectorOfBool.h \
	 mbtValVector_inc.cpp mbt_exception.h mbt_val_ord_offset_vec.h \
	 min.h nMAX_QUALITY_LEVEL2.h ntide.h \
	 paddedFromUnpadded.h paddedPieceOfRead.cpp paddedPieceOfRead.h \
	 primerType.h quality.h readTypes.h \
	 readsSortedByLeftEndPosition.h readsSortedByReadName.h restrictionEnzyme.h \
	 rwbtreedictionary.h rwcstring.h rwcsubstring.h \
	 rwdefs.h rwtptrorderedvector.h rwtptrorderedvector_inc.cpp \
	 rwtptrsortedvector.h rwtptrvector.h rwtvalorderedvector.h \
	 rwtvalorderedvector_inc.cpp rwtvalsortedvector.h rwtvalvector.h \
	 sequence.h soEmptyString.h soGetErrno.h \
	 subcloneTTemplate.h sysdepend.h tag.h \
	 tracefile.h unpaddedFromPadded.h whatIsRunning.h \
	 wholeReadItem.h

paddedPieceOfSequence.o : \
	 assert.h bool.h mbt_exception.h \
	 paddedPieceOfSequence.cpp paddedPieceOfSequence.h rwcstring.h \
	 rwcsubstring.h rwdefs.h soGetErrno.h

parseAceFile.o : \
	 abs.h assembly.h assemblyViewTagTypeAndLine.h \
	 assert.h autoFinishExpTag.h autoFinishPurposes.h \
	 bIntersect.h bIntervalsIntersect.h bIsNumeric.h \
	 bIsNumericDouble.h bIsNumericLongMaybeWithWhitespace.h bIsNumericMaybeWithWhitespace.h \
	 basesegment.h blockOfLocationsOfA4MerType.h bool.h \
	 cComplementBase.h cComplementBaseTable.h compareContigs.h \
	 compareContigsCursor.h compareContigsTypes.h consed.h \
	 consedParameters.h consedResources.h contig.h \
	 contigEnd.h contigMatchTablesType.h contigSegment.h \
	 contigview.h contigwin.h dictionary.h \
	 distribution.h editCursor.h editaction.h \
	 experiment.h expidAndLocatedFragment.h filename.h \
	 gotoList.h gotoListType.h guiDisplayDigest.h \
	 guiMultiContigNavigator.h guiapp.h guicolortext.h \
	 listOfFragments.h locatedFragment.h matchWithinAssembly.h \
	 max.h mbtPtrOrderedVector.h mbtPtrVector.h \
	 mbtValOrderedVectorOfRWCString.h mbtValVector.h mbtValVectorOfBool.h \
	 mbtValVector_inc.cpp mbt_errors.h mbt_exception.h \
	 mbt_val_ord_offset_vec.h min.h motifutils.h \
	 multiProblemGotoList.h nMAX_QUALITY_LEVEL2.h ntide.h \
	 numutil.h oligoTag.h paddedFromUnpadded.h \
	 parseAceFile.cpp parseUserDefinedTagTypeLine.h popupErrorMessage.h \
	 primerType.h quality.h readTypes.h \
	 readsSortedByLeftEndPosition.h readsSortedByReadName.h readsSortedByTemplateName.h \
	 restrictionEnzyme.h restrictionFragment.h rwbtreedictionary.h \
	 rwcstring.h rwcsubstring.h rwctokenizer.h \
	 rwdefs.h rwtptrorderedvector.h rwtptrorderedvector_inc.cpp \
	 rwtptrsortedvector.h rwtptrvector.h rwtvalorderedvector.h \
	 rwtvalorderedvector_inc.cpp rwtvalsortedvector.h rwtvalvector.h \
	 selection.h sequence.h singletInfo.h \
	 singletsSortedByTemplateName.h soAddCommas.h soEmptyString.h \
	 soGetErrno.h subcloneTTemplate.h sysdepend.h \
	 tag.h tagTypes.h templatesSortedByName.h \
	 tracefile.h trimWhitespace.h unpaddedFromPadded.h \
	 userDefinedTagField.h userDefinedTagFieldType.h visibleLineForRestrictionFragments.h \
	 whatIsRunning.h wholeAssemblyItem.h wholeReadItem.h

parseUserDefinedTagTypeLine.o : \
	 abs.h assembly.h assemblyViewTagTypeAndLine.h \
	 assert.h autoFinishPurposes.h bIntersect.h \
	 bIntervalsIntersect.h bIsNumericDouble.h bIsNumericLongMaybeWithWhitespace.h \
	 bIsNumericMaybeWithWhitespace.h basesegment.h blockOfLocationsOfA4MerType.h \
	 bool.h cComplementBase.h cComplementBaseTable.h \
	 compareContigs.h compareContigsCursor.h compareContigsTypes.h \
	 consed.h consedParameters.h consedResources.h \
	 contig.h contigEnd.h contigMatchTablesType.h \
	 contigSegment.h contigview.h contigwin.h \
	 dictionary.h distribution.h editCursor.h \
	 editaction.h experiment.h expidAndLocatedFragment.h \
	 filename.h gotoList.h gotoListType.h \
	 guiDisplayDigest.h guiMultiContigNavigator.h guiapp.h \
	 guicolortext.h listOfFragments.h locatedFragment.h \
	 matchWithinAssembly.h max.h mbtPtrOrderedVector.h \
	 mbtPtrVector.h mbtValOrderedVectorOfRWCString.h mbtValVector.h \
	 mbtValVectorOfBool.h mbtValVector_inc.cpp mbt_exception.h \
	 mbt_val_ord_offset_vec.h min.h motifutils.h \
	 multiProblemGotoList.h nMAX_QUALITY_LEVEL2.h ntide.h \
	 numutil.h paddedFromUnpadded.h parseUserDefinedTagTypeLine.cpp \
	 parseUserDefinedTagTypeLine.h primerType.h quality.h \
	 readTypes.h readsSortedByLeftEndPosition.h readsSortedByReadName.h \
	 readsSortedByTemplateName.h restrictionEnzyme.h restrictionFragment.h \
	 rwbtreedictionary.h rwcstring.h rwcsubstring.h \
	 rwctokenizer.h rwdefs.h rwtptrorderedvector.h \
	 rwtptrorderedvector_inc.cpp rwtptrsortedvector.h rwtptrvector.h \
	 rwtvalorderedvector.h rwtvalorderedvector_inc.cpp rwtvalsortedvector.h \
	 rwtvalvector.h selection.h sequence.h \
	 singletInfo.h singletsSortedByTemplateName.h soEmptyString.h \
	 soGetErrno.h subcloneTTemplate.h sysdepend.h \
	 tag.h tagTypes.h templatesSortedByName.h \
	 tracefile.h unpaddedFromPadded.h userDefinedTagField.h \
	 userDefinedTagFieldType.h visibleLineForRestrictionFragments.h whatIsRunning.h \
	 wholeAssemblyItem.h wholeReadItem.h

pcrPrimer.o : \
	 abs.h assembly.h assemblyViewTagTypeAndLine.h \
	 assert.h autoFinishPurposes.h bIntersect.h \
	 bIntervalsIntersect.h basesegment.h blockOfLocationsOfA4MerType.h \
	 bool.h cComplementBase.h cComplementBaseTable.h \
	 compareContigs.h compareContigsCursor.h compareContigsTypes.h \
	 consed.h consedParameters.h consedResources.h \
	 contig.h contigEnd.h contigMatchTablesType.h \
	 contigSegment.h contigview.h contigwin.h \
	 dictionary.h distribution.h editCursor.h \
	 editaction.h experiment.h expidAndLocatedFragment.h \
	 filename.h gotoList.h gotoListType.h \
	 guiDisplayDigest.h guiMultiContigNavigator.h guiapp.h \
	 guicolortext.h listOfFragments.h locatedFragment.h \
	 matchWithinAssembly.h max.h mbtPtrOrderedVector.h \
	 mbtPtrVector.h mbtValOrderedVectorOfRWCString.h mbtValVector.h \
	 mbtValVectorOfBool.h mbtValVector_inc.cpp mbt_exception.h \
	 mbt_val_ord_offset_vec.h min.h motifutils.h \
	 multiProblemGotoList.h nMAX_QUALITY_LEVEL2.h ntide.h \
	 numutil.h paddedFromUnpadded.h pcrPrimer.cpp \
	 pcrPrimer.h primerType.h quality.h \
	 readTypes.h readsSortedByLeftEndPosition.h readsSortedByReadName.h \
	 readsSortedByTemplateName.h restrictionEnzyme.h restrictionFragment.h \
	 rwbtreedictionary.h rwcstring.h rwcsubstring.h \
	 rwdefs.h rwtptrorderedvector.h rwtptrorderedvector_inc.cpp \
	 rwtptrsortedvector.h rwtptrvector.h rwtvalorderedvector.h \
	 rwtvalorderedvector_inc.cpp rwtvalsortedvector.h rwtvalvector.h \
	 selection.h sequence.h setPrimerFalseMatchScoreArray.h \
	 singletInfo.h singletsSortedByTemplateName.h soEmptyString.h \
	 soGetErrno.h subcloneTTemplate.h sysdepend.h \
	 tag.h templatesSortedByName.h tracefile.h \
	 unpaddedFromPadded.h visibleLineForRestrictionFragments.h whatIsRunning.h \
	 wholeAssemblyItem.h wholeReadItem.h

pcrPrimerrPair.o : \
	 abs.h assemblyViewTagTypeAndLine.h assert.h \
	 autoFinishPurposes.h bIsPCRPrimerPairOK.h basesegment.h \
	 blockOfLocationsOfA4MerType.h bool.h cComplementBase.h \
	 cComplementBaseTable.h consedParameters.h consedResources.h \
	 contig.h contigEnd.h contigMatchTablesType.h \
	 dictionary.h distribution.h experiment.h \
	 fileDefines.h filename.h locatedFragment.h \
	 mbtPtrOrderedVector.h mbtPtrVector.h mbtValOrderedVectorOfRWCString.h \
	 mbtValVector.h mbtValVectorOfBool.h mbtValVector_inc.cpp \
	 mbt_exception.h mbt_val_ord_offset_vec.h min.h \
	 nMAX_QUALITY_LEVEL2.h ntide.h paddedFromUnpadded.h \
	 pcrPrimer.h pcrPrimerrPair.cpp pcrPrimerrPair.h \
	 primerType.h quality.h readTypes.h \
	 readsSortedByLeftEndPosition.h readsSortedByReadName.h restrictionEnzyme.h \
	 rwbtreedictionary.h rwcstring.h rwcsubstring.h \
	 rwdefs.h rwtptrorderedvector.h rwtptrorderedvector_inc.cpp \
	 rwtptrsortedvector.h rwtptrvector.h rwtvalorderedvector.h \
	 rwtvalorderedvector_inc.cpp rwtvalsortedvector.h rwtvalvector.h \
	 sequence.h soEmptyString.h soGetErrno.h \
	 subcloneTTemplate.h sysdepend.h szWhichStrand.h \
	 tag.h tracefile.h unpaddedFromPadded.h \
	 whatIsRunning.h wholeReadItem.h whyIsPrimerNotAcceptableTypes.h

perhapsCreateSocketToControlConsed.o : \
	 assemblyViewTagTypeAndLine.h assert.h bool.h \
	 consedParameters.h consedResources.h filename.h \
	 guiapp.h guicolortext.h mbtPtrOrderedVector.h \
	 mbtValOrderedVectorOfRWCString.h mbt_exception.h motifutils.h \
	 nCreateSocket.h perhapsCreateSocketToControlConsed.cpp perhapsCreateSocketToControlConsed.h \
	 procToRunWhenSomeOtherProgramConnectsToConsed.h restrictionEnzyme.h rwcstring.h \
	 rwcsubstring.h rwdefs.h rwtptrorderedvector.h \
	 rwtptrorderedvector_inc.cpp rwtvalorderedvector.h rwtvalorderedvector_inc.cpp \
	 soEmptyString.h soGetErrno.h sysdepend.h \
	 whatIsRunning.h

phaster2PhdBall.o : \
	 assemblyViewTagTypeAndLine.h assert.h bIntersectLong.h \
	 bIntervalsIntersectLong.h bIsNumeric.h bool.h \
	 complement_so.h consedParameters.h consedResources.h \
	 filename.h getAllTokens.h max.h \
	 mbtPtrOrderedVector.h mbtValOrderedVectorOfInt.h mbtValOrderedVectorOfLong.h \
	 mbtValOrderedVectorOfRWCString.h mbt_exception.h min.h \
	 nAmbiguityCodeToNumber2.h phaster2PhdBall.cpp phaster2PhdBall.h \
	 restrictionEnzyme.h rwcregexp.h rwcstring.h \
	 rwcsubstring.h rwctokenizer.h rwdefs.h \
	 rwtptrorderedvector.h rwtptrorderedvector_inc.cpp rwtvalorderedvector.h \
	 rwtvalorderedvector_inc.cpp rwtvalvector.h soAddCommas.h \
	 soDecodePhasterBasesToGenomic.h soDecodePhasterBasesToRead.h soEmptyString.h \
	 soGetDateTime.h soGetErrno.h sysdepend.h \
	 szGetTime.h whatIsRunning.h

phdBall2Fasta.o : \
	 assemblyViewTagTypeAndLine.h assert.h bool.h \
	 consedParameters.h consedResources.h filename.h \
	 mbtPtrOrderedVector.h mbtValOrderedVectorOfRWCString.h mbt_exception.h \
	 phdBall2Fasta.cpp phdBall2Fasta.h restrictionEnzyme.h \
	 rwcstring.h rwcsubstring.h rwdefs.h \
	 rwtptrorderedvector.h rwtptrorderedvector_inc.cpp rwtvalorderedvector.h \
	 rwtvalorderedvector_inc.cpp soEmptyString.h soGetErrno.h \
	 sysdepend.h whatIsRunning.h

phredUtilities.o : \
	 phredUtilities.c typeDef.h

pickCombinationsOfPCRPrimers.o : \
	 abs.h assembly.h assemblyViewTagTypeAndLine.h \
	 assert.h autoFinishPurposes.h bIntersect.h \
	 bIntervalsIntersect.h bIsPCRPrimerPairOK.h basesegment.h \
	 blockOfLocationsOfA4MerType.h bool.h cComplementBase.h \
	 cComplementBaseTable.h compareContigs.h compareContigsCursor.h \
	 compareContigsTypes.h consed.h consedParameters.h \
	 consedResources.h contig.h contigEnd.h \
	 contigMatchTablesType.h contigSegment.h contigview.h \
	 contigwin.h dictionary.h distribution.h \
	 editCursor.h editaction.h exclusive_or.h \
	 experiment.h expidAndLocatedFragment.h fileDefines.h \
	 filename.h gotoList.h gotoListType.h \
	 guiDisplayDigest.h guiMultiContigNavigator.h guiapp.h \
	 guicolortext.h listOfFragments.h locatedFragment.h \
	 matchWithinAssembly.h max.h mbtPtrOrderedVector.h \
	 mbtPtrVector.h mbtValOrderedVectorOfRWCString.h mbtValVector.h \
	 mbtValVectorOfBool.h mbtValVector_inc.cpp mbt_exception.h \
	 mbt_val_ord_offset_vec.h min.h motifutils.h \
	 multiProblemGotoList.h nMAX_QUALITY_LEVEL2.h ntide.h \
	 numutil.h oligoTag.h paddedFromUnpadded.h \
	 pcrPrimer.h pcrPrimerPairSubscripts.h pcrPrimerrPair.h \
	 pickCombinationsOfPCRPrimers.cpp pickCombinationsOfPCRPrimers.h pickPCRPrimersForOneEndOfContig.h \
	 primerType.h quality.h readTypes.h \
	 readsSortedByLeftEndPosition.h readsSortedByReadName.h readsSortedByTemplateName.h \
	 regionOfContig.h regionToAmplify.h restrictionEnzyme.h \
	 restrictionFragment.h rwbtreedictionary.h rwcstring.h \
	 rwcsubstring.h rwdefs.h rwtptrorderedvector.h \
	 rwtptrorderedvector_inc.cpp rwtptrsortedvector.h rwtptrvector.h \
	 rwtvalorderedvector.h rwtvalorderedvector_inc.cpp rwtvalsortedvector.h \
	 rwtvalvector.h selection.h sequence.h \
	 singletInfo.h singletsSortedByTemplateName.h soEmptyString.h \
	 soGetErrno.h subcloneTTemplate.h sysdepend.h \
	 tag.h templatesSortedByName.h tracefile.h \
	 unpaddedFromPadded.h visibleLineForRestrictionFragments.h whatIsRunning.h \
	 wholeAssemblyItem.h wholeReadItem.h

pickPCRPrimers.o : \
	 abs.h assembly.h assemblyViewTagTypeAndLine.h \
	 assert.h autoFinishPurposes.h bIntersect.h \
	 bIntervalsIntersect.h bIsPCRPrimerPairOK.h bIsPrimerStale.h \
	 basesegment.h blockOfLocationsOfA4MerType.h bool.h \
	 cComplementBase.h cComplementBaseTable.h calculatePrimerMeltingTemperatures.h \
	 checkPrimersForACGT.h checkPrimersForMononucleotideRepeats.h compareContigs.h \
	 compareContigsCursor.h compareContigsTypes.h consed.h \
	 consedParameters.h consedResources.h contig.h \
	 contigEnd.h contigMatchTablesType.h contigSegment.h \
	 contigview.h contigwin.h copyPrimerMatchesFromShorterToLongerPrimers.h \
	 createPrimerCandidates.h dictionary.h distribution.h \
	 editAddConsensusTag.h editCursor.h editaction.h \
	 experiment.h expidAndLocatedFragment.h filename.h \
	 findPrimerMatchesAgainstSequencesInFile.h findPrimerMatchesElsewhere.h findPrimerSelfMatches.h \
	 gotoList.h gotoListType.h groupOfPrimers.h \
	 guiDisplayDigest.h guiMultiContigNavigator.h guiapp.h \
	 guicolortext.h guicontigwin.h infobutton.h \
	 listOfFragments.h locatedFragment.h matchScores.h \
	 matchWithinAssembly.h max.h mbtPtrOrderedVector.h \
	 mbtPtrVector.h mbtValOrderedVectorOfRWCString.h mbtValVector.h \
	 mbtValVectorOfBool.h mbtValVector_inc.cpp mbt_exception.h \
	 mbt_val_ord_offset_vec.h min.h motifutils.h \
	 multiProblemGotoList.h nMAX_QUALITY_LEVEL2.h ntide.h \
	 numutil.h oligoTag.h paddedFromUnpadded.h \
	 pcrPrimerPair.h pickPCRPrimers.cpp pickPCRPrimers.h \
	 please_wait.h popupErrorMessage.h popupInfoMessage.h \
	 primerType.h quality.h readTypes.h \
	 readsSortedByLeftEndPosition.h readsSortedByReadName.h readsSortedByTemplateName.h \
	 restrictionEnzyme.h restrictionFragment.h rwbtreedictionary.h \
	 rwcstring.h rwcsubstring.h rwdefs.h \
	 rwtptrorderedvector.h rwtptrorderedvector_inc.cpp rwtptrsortedvector.h \
	 rwtptrvector.h rwtvalorderedvector.h rwtvalorderedvector_inc.cpp \
	 rwtvalsortedvector.h rwtvalvector.h selection.h \
	 sequence.h singletInfo.h singletsSortedByTemplateName.h \
	 soEmptyString.h soGetErrno.h subcloneTTemplate.h \
	 sysdepend.h tag.h templatesSortedByName.h \
	 textbox.h textfield.h tracefile.h \
	 unpaddedFromPadded.h visibleLineForRestrictionFragments.h whatIsRunning.h \
	 whichPrimersAreAcceptable.h wholeAssemblyItem.h wholeReadItem.h \
	 whyIsPrimerNotAcceptableTypes.h

pickPCRPrimersForOneEndOfContig.o : \
	 assemblyViewTagTypeAndLine.h assert.h autoFinishPurposes.h \
	 basesegment.h blockOfLocationsOfA4MerType.h bool.h \
	 cComplementBase.h cComplementBaseTable.h calculatePrimerMeltingTemperatures.h \
	 checkPrimersForACGT.h checkPrimersForMononucleotideRepeats.h consedParameters.h \
	 consedResources.h contig.h contigEnd.h \
	 contigMatchTablesType.h copyPrimerMatchesFromShorterToLongerPrimers.h createPrimerCandidates.h \
	 dictionary.h distribution.h experiment.h \
	 fileDefines.h filename.h findPrimerMatchesAgainstSequencesInFile.h \
	 findPrimerMatchesElsewhere.h findPrimerSelfMatches.h locatedFragment.h \
	 mbtPtrOrderedVector.h mbtPtrVector.h mbtValOrderedVectorOfRWCString.h \
	 mbtValVector.h mbtValVectorOfBool.h mbtValVector_inc.cpp \
	 mbt_exception.h mbt_val_ord_offset_vec.h min.h \
	 nMAX_QUALITY_LEVEL2.h ntide.h paddedFromUnpadded.h \
	 pickPCRPrimersForOneEndOfContig.cpp pickPCRPrimersForOneEndOfContig.h primerType.h \
	 quality.h readTypes.h readsSortedByLeftEndPosition.h \
	 readsSortedByReadName.h restrictionEnzyme.h rwbtreedictionary.h \
	 rwcstring.h rwcsubstring.h rwdefs.h \
	 rwtptrorderedvector.h rwtptrorderedvector_inc.cpp rwtptrsortedvector.h \
	 rwtptrvector.h rwtvalorderedvector.h rwtvalorderedvector_inc.cpp \
	 rwtvalsortedvector.h rwtvalvector.h sequence.h \
	 soEmptyString.h soGetErrno.h subcloneTTemplate.h \
	 sysdepend.h tag.h tracefile.h \
	 unpaddedFromPadded.h whatIsRunning.h whichPrimersAreAcceptable.h \
	 wholeReadItem.h

pickPrimers.o : \
	 abs.h assembly.h assemblyViewTagTypeAndLine.h \
	 assert.h autoFinishPurposes.h bIntersect.h \
	 bIntervalsIntersect.h basesegment.h blockOfLocationsOfA4MerType.h \
	 bool.h cComplementBase.h cComplementBaseTable.h \
	 calculatePrimerMeltingTemperatures.h checkPrimersForACGT.h checkPrimersForMononucleotideRepeats.h \
	 compareContigs.h compareContigsCursor.h compareContigsTypes.h \
	 consed.h consedParameters.h consedResources.h \
	 contig.h contigEnd.h contigMatchTablesType.h \
	 contigSegment.h contigview.h contigwin.h \
	 copyPrimerMatchesFromShorterToLongerPrimers.h countsOfWhyPrimersAreNotAcceptable.h createPrimerCandidates.h \
	 dictionary.h displayPrimers.h distribution.h \
	 editCursor.h editaction.h experiment.h \
	 expidAndLocatedFragment.h filename.h findPrimerMatchesAgainstSequencesInFile.h \
	 findPrimerMatchesElsewhere.h findPrimerSelfMatches.h findTemplatesForPrimers.h \
	 gotoList.h gotoListType.h guiDisplayDigest.h \
	 guiMultiContigNavigator.h guiapp.h guicolortext.h \
	 listOfFragments.h locatedFragment.h matchWithinAssembly.h \
	 max.h mbtPtrOrderedVector.h mbtPtrVector.h \
	 mbtValOrderedVectorOfRWCString.h mbtValVector.h mbtValVectorOfBool.h \
	 mbtValVector_inc.cpp mbt_exception.h mbt_val_ord_offset_vec.h \
	 min.h motifutils.h multiProblemGotoList.h \
	 nMAX_QUALITY_LEVEL2.h ntide.h numutil.h \
	 paddedFromUnpadded.h pickPrimers.cpp popupErrorMessage.h \
	 primerType.h quality.h readTypes.h \
	 readsSortedByLeftEndPosition.h readsSortedByReadName.h readsSortedByTemplateName.h \
	 restrictionEnzyme.h restrictionFragment.h rwbtreedictionary.h \
	 rwcstring.h rwcsubstring.h rwdefs.h \
	 rwtptrorderedvector.h rwtptrorderedvector_inc.cpp rwtptrsortedvector.h \
	 rwtptrvector.h rwtvalorderedvector.h rwtvalorderedvector_inc.cpp \
	 rwtvalsortedvector.h rwtvalvector.h selection.h \
	 sequence.h singletInfo.h singletsSortedByTemplateName.h \
	 soEmptyString.h soGetErrno.h sortAcceptablePrimers.h \
	 sortUnacceptablePrimers.h subcloneTTemplate.h sysdepend.h \
	 tag.h templatesSortedByName.h textbox.h \
	 tracefile.h unpaddedFromPadded.h visibleLineForRestrictionFragments.h \
	 whatIsRunning.h whichPrimersAreAcceptable.h wholeAssemblyItem.h \
	 wholeReadItem.h

please_wait.o : \
	 assert.h bool.h busy_cursor.h \
	 filename.h guiapp.h guicolortext.h \
	 mbt_exception.h motifutils.h please_wait.cpp \
	 please_wait.h rwcstring.h rwcsubstring.h \
	 rwdefs.h rwtptrorderedvector.h rwtptrorderedvector_inc.cpp \
	 rwtvalorderedvector.h rwtvalorderedvector_inc.cpp soEmptyString.h \
	 soGetErrno.h sysdepend.h

popupErrorMessage.o : \
	 abs.h assembly.h assemblyViewTagTypeAndLine.h \
	 assert.h autoFinishPurposes.h bIntersect.h \
	 bIntervalsIntersect.h basesegment.h blockOfLocationsOfA4MerType.h \
	 bool.h cComplementBase.h cComplementBaseTable.h \
	 compareContigs.h compareContigsCursor.h compareContigsTypes.h \
	 consed.h consedParameters.h consedResources.h \
	 contig.h contigEnd.h contigMatchTablesType.h \
	 contigSegment.h contigview.h contigwin.h \
	 dictionary.h distribution.h editCursor.h \
	 editaction.h experiment.h expidAndLocatedFragment.h \
	 filename.h gotoList.h gotoListType.h \
	 guiDisplayDigest.h guiMultiContigNavigator.h guiapp.h \
	 guicolortext.h listOfFragments.h locatedFragment.h \
	 matchWithinAssembly.h max.h mbtPtrOrderedVector.h \
	 mbtPtrVector.h mbtValOrderedVectorOfRWCString.h mbtValVector.h \
	 mbtValVectorOfBool.h mbtValVector_inc.cpp mbt_exception.h \
	 mbt_val_ord_offset_vec.h min.h motifutils.h \
	 multiProblemGotoList.h nMAX_QUALITY_LEVEL2.h ntide.h \
	 numutil.h paddedFromUnpadded.h popupErrorMessage.cpp \
	 popupErrorMessage.h popupInfoOrErrorMessageNoFormat.h primerType.h \
	 quality.h readTypes.h readsSortedByLeftEndPosition.h \
	 readsSortedByReadName.h readsSortedByTemplateName.h restrictionEnzyme.h \
	 restrictionFragment.h rwbtreedictionary.h rwcstring.h \
	 rwcsubstring.h rwdefs.h rwtptrorderedvector.h \
	 rwtptrorderedvector_inc.cpp rwtptrsortedvector.h rwtptrvector.h \
	 rwtvalorderedvector.h rwtvalorderedvector_inc.cpp rwtvalsortedvector.h \
	 rwtvalvector.h selection.h sequence.h \
	 singletInfo.h singletsSortedByTemplateName.h soEmptyString.h \
	 soGetErrno.h subcloneTTemplate.h sysdepend.h \
	 tag.h templatesSortedByName.h tracefile.h \
	 unpaddedFromPadded.h visibleLineForRestrictionFragments.h whatIsRunning.h \
	 wholeAssemblyItem.h wholeReadItem.h

popupErrorMessage2.o : \
	 abs.h assembly.h assemblyViewTagTypeAndLine.h \
	 assert.h autoFinishPurposes.h bIntersect.h \
	 bIntervalsIntersect.h basesegment.h blockOfLocationsOfA4MerType.h \
	 bool.h cComplementBase.h cComplementBaseTable.h \
	 compareContigs.h compareContigsCursor.h compareContigsTypes.h \
	 consed.h consedParameters.h consedResources.h \
	 contig.h contigEnd.h contigMatchTablesType.h \
	 contigSegment.h contigview.h contigwin.h \
	 dictionary.h distribution.h editCursor.h \
	 editaction.h experiment.h expidAndLocatedFragment.h \
	 filename.h gotoList.h gotoListType.h \
	 guiDisplayDigest.h guiMultiContigNavigator.h guiapp.h \
	 guicolortext.h listOfFragments.h locatedFragment.h \
	 matchWithinAssembly.h max.h mbtPtrOrderedVector.h \
	 mbtPtrVector.h mbtValOrderedVectorOfRWCString.h mbtValVector.h \
	 mbtValVectorOfBool.h mbtValVector_inc.cpp mbt_exception.h \
	 mbt_val_ord_offset_vec.h min.h motifutils.h \
	 multiProblemGotoList.h nMAX_QUALITY_LEVEL2.h ntide.h \
	 numutil.h paddedFromUnpadded.h popupErrorMessage.h \
	 popupErrorMessage2.cpp popupInfoOrErrorMessageNoFormat.h primerType.h \
	 quality.h readTypes.h readsSortedByLeftEndPosition.h \
	 readsSortedByReadName.h readsSortedByTemplateName.h restrictionEnzyme.h \
	 restrictionFragment.h rwbtreedictionary.h rwcstring.h \
	 rwcsubstring.h rwdefs.h rwtptrorderedvector.h \
	 rwtptrorderedvector_inc.cpp rwtptrsortedvector.h rwtptrvector.h \
	 rwtvalorderedvector.h rwtvalorderedvector_inc.cpp rwtvalsortedvector.h \
	 rwtvalvector.h selection.h sequence.h \
	 singletInfo.h singletsSortedByTemplateName.h soEmptyString.h \
	 soGetErrno.h subcloneTTemplate.h sysdepend.h \
	 tag.h templatesSortedByName.h tracefile.h \
	 unpaddedFromPadded.h visibleLineForRestrictionFragments.h whatIsRunning.h \
	 wholeAssemblyItem.h wholeReadItem.h

popupInfoMessage.o : \
	 abs.h assembly.h assemblyViewTagTypeAndLine.h \
	 assert.h autoFinishPurposes.h bIntersect.h \
	 bIntervalsIntersect.h basesegment.h blockOfLocationsOfA4MerType.h \
	 bool.h cComplementBase.h cComplementBaseTable.h \
	 compareContigs.h compareContigsCursor.h compareContigsTypes.h \
	 consed.h consedParameters.h consedResources.h \
	 contig.h contigEnd.h contigMatchTablesType.h \
	 contigSegment.h contigview.h contigwin.h \
	 dictionary.h distribution.h editCursor.h \
	 editaction.h experiment.h expidAndLocatedFragment.h \
	 filename.h gotoList.h gotoListType.h \
	 guiDisplayDigest.h guiMultiContigNavigator.h guiapp.h \
	 guicolortext.h listOfFragments.h locatedFragment.h \
	 matchWithinAssembly.h max.h mbtPtrOrderedVector.h \
	 mbtPtrVector.h mbtValOrderedVectorOfRWCString.h mbtValVector.h \
	 mbtValVectorOfBool.h mbtValVector_inc.cpp mbt_exception.h \
	 mbt_val_ord_offset_vec.h min.h motifutils.h \
	 multiProblemGotoList.h nMAX_QUALITY_LEVEL2.h ntide.h \
	 numutil.h paddedFromUnpadded.h popupInfoMessage.cpp \
	 popupInfoMessage.h popupInfoOrErrorMessageNoFormat.h primerType.h \
	 quality.h readTypes.h readsSortedByLeftEndPosition.h \
	 readsSortedByReadName.h readsSortedByTemplateName.h restrictionEnzyme.h \
	 restrictionFragment.h rwbtreedictionary.h rwcstring.h \
	 rwcsubstring.h rwdefs.h rwtptrorderedvector.h \
	 rwtptrorderedvector_inc.cpp rwtptrsortedvector.h rwtptrvector.h \
	 rwtvalorderedvector.h rwtvalorderedvector_inc.cpp rwtvalsortedvector.h \
	 rwtvalvector.h selection.h sequence.h \
	 singletInfo.h singletsSortedByTemplateName.h soEmptyString.h \
	 soGetErrno.h subcloneTTemplate.h sysdepend.h \
	 tag.h templatesSortedByName.h tracefile.h \
	 unpaddedFromPadded.h visibleLineForRestrictionFragments.h whatIsRunning.h \
	 wholeAssemblyItem.h wholeReadItem.h

popupInfoOrErrorMessageNoFormat.o : \
	 abs.h assembly.h assemblyViewTagTypeAndLine.h \
	 assert.h autoFinishPurposes.h bIntersect.h \
	 bIntervalsIntersect.h basesegment.h blockOfLocationsOfA4MerType.h \
	 bool.h breakIntoShorterLines.h cComplementBase.h \
	 cComplementBaseTable.h compareContigs.h compareContigsCursor.h \
	 compareContigsTypes.h consed.h consedParameters.h \
	 consedResources.h contig.h contigEnd.h \
	 contigMatchTablesType.h contigSegment.h contigview.h \
	 contigwin.h dictionary.h distribution.h \
	 editCursor.h editaction.h experiment.h \
	 expidAndLocatedFragment.h fileDefines.h filename.h \
	 gotoList.h gotoListType.h guiDisplayDigest.h \
	 guiMultiContigNavigator.h guiapp.h guicolortext.h \
	 listOfFragments.h locatedFragment.h matchWithinAssembly.h \
	 max.h mbtPtrOrderedVector.h mbtPtrVector.h \
	 mbtValOrderedVectorOfRWCString.h mbtValVector.h mbtValVectorOfBool.h \
	 mbtValVector_inc.cpp mbt_exception.h mbt_val_ord_offset_vec.h \
	 min.h motifutils.h multiProblemGotoList.h \
	 nMAX_QUALITY_LEVEL2.h ntide.h numutil.h \
	 paddedFromUnpadded.h popupErrorMessage.h popupInfoOrErrorMessageNoFormat.cpp \
	 primerType.h quality.h readTypes.h \
	 readsSortedByLeftEndPosition.h readsSortedByReadName.h readsSortedByTemplateName.h \
	 restrictionEnzyme.h restrictionFragment.h rwbtreedictionary.h \
	 rwcstring.h rwcsubstring.h rwdefs.h \
	 rwtptrorderedvector.h rwtptrorderedvector_inc.cpp rwtptrsortedvector.h \
	 rwtptrvector.h rwtvalorderedvector.h rwtvalorderedvector_inc.cpp \
	 rwtvalsortedvector.h rwtvalvector.h selection.h \
	 sequence.h singletInfo.h singletsSortedByTemplateName.h \
	 soEmptyString.h soGetErrno.h subcloneTTemplate.h \
	 sysdepend.h tag.h templatesSortedByName.h \
	 tracefile.h unpaddedFromPadded.h visibleLineForRestrictionFragments.h \
	 waitUntilDialogIsVisible.h whatIsRunning.h wholeAssemblyItem.h \
	 wholeReadItem.h

primateSpecies.o : \
	 assert.h autoReport.h bool.h \
	 filename.h mbtValOrderedVectorOfRWCString.h mbtValVector.h \
	 mbtValVectorOfBool.h mbtValVector_inc.cpp mbt_exception.h \
	 min.h primateSpecies.cpp primateSpecies.h \
	 rwcstring.h rwcsubstring.h rwdefs.h \
	 rwtptrorderedvector.h rwtptrorderedvector_inc.cpp rwtptrvector.h \
	 rwtvalorderedvector.h rwtvalorderedvector_inc.cpp rwtvalvector.h \
	 soEmptyString.h soGetErrno.h sysdepend.h

primerStickiestFalseMatch.o : \
	 abs.h assemblyViewTagTypeAndLine.h assert.h \
	 autoFinishPurposes.h basesegment.h blockOfLocationsOfA4MerType.h \
	 bool.h cComplementBase.h cComplementBaseTable.h \
	 consedParameters.h consedResources.h contig.h \
	 contigEnd.h contigMatchTablesType.h dictionary.h \
	 distribution.h experiment.h filename.h \
	 locatedFragment.h mbtPtrOrderedVector.h mbtPtrVector.h \
	 mbtValOrderedVectorOfRWCString.h mbtValVector.h mbtValVectorOfBool.h \
	 mbtValVector_inc.cpp mbt_exception.h mbt_val_ord_offset_vec.h \
	 min.h nMAX_QUALITY_LEVEL2.h ntide.h \
	 paddedFromUnpadded.h primerStickiestFalseMatch.cpp primerStickiestFalseMatch.h \
	 primerType.h quality.h readTypes.h \
	 readsSortedByLeftEndPosition.h readsSortedByReadName.h restrictionEnzyme.h \
	 rwbtreedictionary.h rwcstring.h rwcsubstring.h \
	 rwdefs.h rwtptrorderedvector.h rwtptrorderedvector_inc.cpp \
	 rwtptrsortedvector.h rwtptrvector.h rwtvalorderedvector.h \
	 rwtvalorderedvector_inc.cpp rwtvalsortedvector.h rwtvalvector.h \
	 sequence.h soEmptyString.h soGetErrno.h \
	 subcloneTTemplate.h sysdepend.h tag.h \
	 tracefile.h unpaddedFromPadded.h whatIsRunning.h \
	 wholeReadItem.h

printAlignment.o : \
	 bool.h printAlignment.cpp printAlignment.h \
	 rwcstring.h rwcsubstring.h rwdefs.h

printAutoFinishMiscInfo.o : \
	 abs.h assembly.h assemblyViewTagTypeAndLine.h \
	 assert.h autoFinishPurposes.h bIntersect.h \
	 bIntervalsIntersect.h basesegment.h blockOfLocationsOfA4MerType.h \
	 bool.h cComplementBase.h cComplementBaseTable.h \
	 compareContigs.h compareContigsCursor.h compareContigsTypes.h \
	 consed.h consedParameters.h consedResources.h \
	 contig.h contigEnd.h contigMatchTablesType.h \
	 contigSegment.h contigview.h contigwin.h \
	 dictionary.h distribution.h editCursor.h \
	 editaction.h experiment.h expidAndLocatedFragment.h \
	 fileDefines.h filename.h gotoList.h \
	 gotoListType.h guiDisplayDigest.h guiMultiContigNavigator.h \
	 guiapp.h guicolortext.h listOfFragments.h \
	 locatedFragment.h matchWithinAssembly.h max.h \
	 mbtPtrOrderedVector.h mbtPtrVector.h mbtValOrderedVectorOfRWCString.h \
	 mbtValVector.h mbtValVectorOfBool.h mbtValVector_inc.cpp \
	 mbt_exception.h mbt_val_ord_offset_vec.h min.h \
	 motifutils.h multiProblemGotoList.h nMAX_QUALITY_LEVEL2.h \
	 ntide.h numutil.h paddedFromUnpadded.h \
	 primerType.h printAutoFinishMiscInfo.cpp printAutoFinishParameters.h \
	 printChangedAutoFinishParameters.h quality.h readTypes.h \
	 readsSortedByLeftEndPosition.h readsSortedByReadName.h readsSortedByTemplateName.h \
	 restrictionEnzyme.h restrictionFragment.h rwbtreedictionary.h \
	 rwcstring.h rwcsubstring.h rwdefs.h \
	 rwtptrorderedvector.h rwtptrorderedvector_inc.cpp rwtptrsortedvector.h \
	 rwtptrvector.h rwtvalorderedvector.h rwtvalorderedvector_inc.cpp \
	 rwtvalsortedvector.h rwtvalvector.h selection.h \
	 sequence.h singletInfo.h singletsSortedByTemplateName.h \
	 soEmptyString.h soGetDateTime.h soGetErrno.h \
	 subcloneTTemplate.h sysdepend.h tag.h \
	 templatesSortedByName.h tracefile.h unpaddedFromPadded.h \
	 visibleLineForRestrictionFragments.h whatIsRunning.h wholeAssemblyItem.h \
	 wholeReadItem.h

printAutoFinishParameters.o : \
	 assemblyViewTagTypeAndLine.h assert.h bool.h \
	 consedParameters.h consedResources.h fileDefines.h \
	 filename.h mbtPtrOrderedVector.h mbtValOrderedVectorOfRWCString.h \
	 mbt_exception.h printAutoFinishParameters.cpp printAutoFinishParameters.h \
	 restrictionEnzyme.h rwcstring.h rwcsubstring.h \
	 rwdefs.h rwtptrorderedvector.h rwtptrorderedvector_inc.cpp \
	 rwtvalorderedvector.h rwtvalorderedvector_inc.cpp soEmptyString.h \
	 soGetErrno.h sysdepend.h whatIsRunning.h

printChangedAutoFinishParameters.o : \
	 assemblyViewTagTypeAndLine.h assert.h bool.h \
	 consedParameters.h consedResources.h fileDefines.h \
	 filename.h mbtPtrOrderedVector.h mbtValOrderedVectorOfRWCString.h \
	 mbt_exception.h printChangedAutoFinishParameters.cpp printChangedAutoFinishParameters.h \
	 restrictionEnzyme.h rwcstring.h rwcsubstring.h \
	 rwdefs.h rwtptrorderedvector.h rwtptrorderedvector_inc.cpp \
	 rwtvalorderedvector.h rwtvalorderedvector_inc.cpp soEmptyString.h \
	 soGetErrno.h sysdepend.h whatIsRunning.h

printDefaultResources.o : \
	 defaultResources.h printDefaultResources.cpp printDefaultResources.h

printMemory.o : \
	 assemblyViewTagTypeAndLine.h assert.h bool.h \
	 consedParameters.h consedResources.h fileDefines.h \
	 filename.h mbtPtrOrderedVector.h mbtValOrderedVectorOfRWCString.h \
	 mbt_exception.h printMemory.cpp printMemory.h \
	 restrictionEnzyme.h rwcstring.h rwcsubstring.h \
	 rwdefs.h rwtptrorderedvector.h rwtptrorderedvector_inc.cpp \
	 rwtvalorderedvector.h rwtvalorderedvector_inc.cpp soEmptyString.h \
	 soGetErrno.h sysdepend.h whatIsRunning.h

printPS.o : \
	 assert.h bool.h mbt_exception.h \
	 printPS.cpp printPS.h rwcstring.h \
	 rwcsubstring.h rwdefs.h soGetErrno.h \
	 soLine.h

printSingleSignal.o : \
	 abs.h assembly.h assemblyViewTagTypeAndLine.h \
	 assert.h autoFinishPurposes.h bIntersect.h \
	 bIntervalsIntersect.h bIsNumericMaybeWithWhitespace.h basesegment.h \
	 blockOfLocationsOfA4MerType.h bool.h cComplementBase.h \
	 cComplementBaseTable.h compareContigs.h compareContigsCursor.h \
	 compareContigsTypes.h consed.h consedParameters.h \
	 consedResources.h contig.h contigEnd.h \
	 contigMatchTablesType.h contigSegment.h contigview.h \
	 contigwin.h dictionary.h distribution.h \
	 editCursor.h editaction.h experiment.h \
	 expidAndLocatedFragment.h fileDefines.h filename.h \
	 gotoList.h gotoListType.h guiDisplayDigest.h \
	 guiMultiContigNavigator.h guiapp.h guicolortext.h \
	 library.h listOfFragments.h listOfLibraries.h \
	 locatedFragment.h matchWithinAssembly.h max.h \
	 mbtPtrOrderedVector.h mbtPtrVector.h mbtValOrderedVectorOfRWCString.h \
	 mbtValVector.h mbtValVectorOfBool.h mbtValVector_inc.cpp \
	 mbt_exception.h mbt_val_ord_offset_vec.h min.h \
	 motifutils.h multiProblemGotoList.h nMAX_QUALITY_LEVEL2.h \
	 ntide.h numutil.h paddedFromUnpadded.h \
	 primerType.h printSingleSignal.cpp printSingleSignal.h \
	 quality.h readTypes.h readsSortedByLeftEndPosition.h \
	 readsSortedByReadName.h readsSortedByTemplateName.h restrictionEnzyme.h \
	 restrictionFragment.h rwbtreedictionary.h rwcstring.h \
	 rwcsubstring.h rwdefs.h rwtptrorderedvector.h \
	 rwtptrorderedvector_inc.cpp rwtptrsortedvector.h rwtptrvector.h \
	 rwtvalorderedvector.h rwtvalorderedvector_inc.cpp rwtvalsortedvector.h \
	 rwtvalvector.h selection.h sequence.h \
	 singletInfo.h singletsSortedByTemplateName.h soEmptyString.h \
	 soGetErrno.h subcloneTTemplate.h sysdepend.h \
	 tag.h templatesSortedByName.h terminateIfNoPhdDir.h \
	 tracefile.h unpaddedFromPadded.h visibleLineForRestrictionFragments.h \
	 whatIsRunning.h wholeAssemblyItem.h wholeReadItem.h

printTime.o : \
	 assemblyViewTagTypeAndLine.h assert.h bool.h \
	 consedParameters.h consedResources.h filename.h \
	 mbtPtrOrderedVector.h mbtValOrderedVectorOfRWCString.h mbt_exception.h \
	 printTime.cpp printTime.h restrictionEnzyme.h \
	 rwcstring.h rwcsubstring.h rwdefs.h \
	 rwtptrorderedvector.h rwtptrorderedvector_inc.cpp rwtvalorderedvector.h \
	 rwtvalorderedvector_inc.cpp soEmptyString.h soGetErrno.h \
	 sysdepend.h whatIsRunning.h

procToRunWhenSomeOtherProgramConnectsToConsed.o : \
	 assert.h bool.h filename.h \
	 guiapp.h guicolortext.h intXtPointerUnion.h \
	 mbt_exception.h motifutils.h procToRunWhenSomeOtherProgramConnectsToConsed.cpp \
	 rwcstring.h rwcsubstring.h rwdefs.h \
	 rwtptrorderedvector.h rwtptrorderedvector_inc.cpp rwtvalorderedvector.h \
	 rwtvalorderedvector_inc.cpp soEmptyString.h soGetErrno.h \
	 socketConnection.h someOtherProgramSentACommandToConsed.h sysdepend.h

readABI.o : \
	 chromatData.h findTraceExtrema.h readABI.c \
	 readABI.h rwUtil.h typeDef.h

readAndProcessReadPrefixFile.o : \
	 abs.h assembly.h assemblyViewTagTypeAndLine.h \
	 assert.h autoFinishPurposes.h bIntersect.h \
	 bIntervalsIntersect.h basesegment.h blockOfLocationsOfA4MerType.h \
	 bool.h cComplementBase.h cComplementBaseTable.h \
	 colorDefaults.h compareContigs.h compareContigsCursor.h \
	 compareContigsTypes.h consed.h consedParameters.h \
	 consedResources.h contig.h contigEnd.h \
	 contigMatchTablesType.h contigSegment.h contigview.h \
	 contigwin.h dictionary.h distribution.h \
	 editCursor.h editaction.h experiment.h \
	 expidAndLocatedFragment.h filename.h gotoList.h \
	 gotoListType.h guiDisplayDigest.h guiMultiContigNavigator.h \
	 guiapp.h guicolortext.h listOfFragments.h \
	 locatedFragment.h matchWithinAssembly.h max.h \
	 mbtPtrOrderedVector.h mbtPtrVector.h mbtValOrderedVectorOfRWCString.h \
	 mbtValVector.h mbtValVectorOfBool.h mbtValVector_inc.cpp \
	 mbt_exception.h mbt_val_ord_offset_vec.h min.h \
	 motifutils.h multiProblemGotoList.h nMAX_QUALITY_LEVEL2.h \
	 ntide.h numutil.h paddedFromUnpadded.h \
	 primerType.h quality.h readAndProcessReadPrefixFile.cpp \
	 readTypes.h readsSortedByLeftEndPosition.h readsSortedByReadName.h \
	 readsSortedByTemplateName.h restrictionEnzyme.h restrictionFragment.h \
	 rwbtreedictionary.h rwcstring.h rwcsubstring.h \
	 rwctokenizer.h rwdefs.h rwtptrorderedvector.h \
	 rwtptrorderedvector_inc.cpp rwtptrsortedvector.h rwtptrvector.h \
	 rwtvalorderedvector.h rwtvalorderedvector_inc.cpp rwtvalsortedvector.h \
	 rwtvalvector.h selection.h sequence.h \
	 singletInfo.h singletsSortedByTemplateName.h soEmptyString.h \
	 soGetErrno.h subcloneTTemplate.h sysdepend.h \
	 tag.h templatesSortedByName.h tracefile.h \
	 unpaddedFromPadded.h visibleLineForRestrictionFragments.h whatIsRunning.h \
	 wholeAssemblyItem.h wholeReadItem.h

readData.o : \
	 chromatData.h readABI.h readData.c \
	 readESD.h readSCF.h readType.h \
	 typeDef.h

readESD.o : \
	 chromatData.h findTraceExtrema.h readESD.c \
	 readESD.h typeDef.h

readFileOfPhdFiles.o : \
	 abs.h assembly.h assemblyViewTagTypeAndLine.h \
	 assert.h autoFinishPurposes.h bIntersect.h \
	 bIntervalsIntersect.h bIsNumeric.h bIsNumericLongMaybeWithWhitespace.h \
	 bIsNumericMaybeWithWhitespace.h basesegment.h blockOfLocationsOfA4MerType.h \
	 bool.h cComplementBase.h cComplementBaseTable.h \
	 compareContigs.h compareContigsCursor.h compareContigsTypes.h \
	 consed.h consedParameters.h consedResources.h \
	 contig.h contigEnd.h contigMatchTablesType.h \
	 contigSegment.h contigview.h contigwin.h \
	 dictionary.h distribution.h editCursor.h \
	 editaction.h experiment.h expidAndLocatedFragment.h \
	 filename.h gotoList.h gotoListType.h \
	 guiDisplayDigest.h guiMultiContigNavigator.h guiapp.h \
	 guicolortext.h listOfFragments.h locatedFragment.h \
	 matchWithinAssembly.h max.h mbtPtrOrderedVector.h \
	 mbtPtrVector.h mbtValOrderedVectorOfRWCString.h mbtValVector.h \
	 mbtValVectorOfBool.h mbtValVector_inc.cpp mbt_exception.h \
	 mbt_val_ord_offset_vec.h min.h motifutils.h \
	 multiProblemGotoList.h nLine.h nMAX_QUALITY_LEVEL2.h \
	 ntide.h numutil.h paddedFromUnpadded.h \
	 phdBall2Fasta.h primerType.h quality.h \
	 readFileOfPhdFiles.cpp readPHD.h readTypes.h \
	 readWholeReadItem.h readsSortedByLeftEndPosition.h readsSortedByReadName.h \
	 readsSortedByTemplateName.h restrictionEnzyme.h restrictionFragment.h \
	 rwbtreedictionary.h rwcregexp.h rwcstring.h \
	 rwcsubstring.h rwctokenizer.h rwdefs.h \
	 rwtptrorderedvector.h rwtptrorderedvector_inc.cpp rwtptrsortedvector.h \
	 rwtptrvector.h rwtvalorderedvector.h rwtvalorderedvector_inc.cpp \
	 rwtvalsortedvector.h rwtvalvector.h selection.h \
	 sequence.h singletInfo.h singletsSortedByTemplateName.h \
	 soAddCommas.h soEmptyString.h soGetErrno.h \
	 soGetRestOfLine.h subcloneTTemplate.h sysdepend.h \
	 tag.h tagTypes.h templatesSortedByName.h \
	 tracefile.h unpaddedFromPadded.h visibleLineForRestrictionFragments.h \
	 whatIsRunning.h wholeAssemblyItem.h wholeReadItem.h

readOneSffFile.o : \
	 assert.h basesAndQualitiesAndPeaks.h bool.h \
	 mbtValOrderedVectorOfRWCString.h mbt_exception.h readOneSffFile.cpp \
	 rwcstring.h rwcsubstring.h rwdefs.h \
	 rwtptrorderedvector.h rwtptrorderedvector_inc.cpp rwtvalorderedvector.h \
	 rwtvalorderedvector_inc.cpp soEmptyString.h soGetErrno.h

readPHD.o : \
	 abs.h assembly.h assemblyViewTagTypeAndLine.h \
	 assert.h autoFinishPurposes.h bIntersect.h \
	 bIntervalsIntersect.h bIsNumeric.h bIsNumericLongMaybeWithWhitespace.h \
	 bIsNumericMaybeWithWhitespace.h basesegment.h blockOfLocationsOfA4MerType.h \
	 bool.h cComplementBase.h cComplementBaseTable.h \
	 compareContigs.h compareContigsCursor.h compareContigsTypes.h \
	 consed.h consedParameters.h consedResources.h \
	 contig.h contigEnd.h contigMatchTablesType.h \
	 contigSegment.h contigview.h contigwin.h \
	 dictionary.h distribution.h editCursor.h \
	 editaction.h experiment.h expidAndLocatedFragment.h \
	 filename.h gotoList.h gotoListType.h \
	 guiDisplayDigest.h guiMultiContigNavigator.h guiapp.h \
	 guicolortext.h listOfFragments.h locatedFragment.h \
	 matchWithinAssembly.h max.h mbtPtrOrderedVector.h \
	 mbtPtrVector.h mbtValOrderedVectorOfRWCString.h mbtValVector.h \
	 mbtValVectorOfBool.h mbtValVector_inc.cpp mbt_exception.h \
	 mbt_val_ord_offset_vec.h min.h motifutils.h \
	 multiProblemGotoList.h nLine.h nMAX_QUALITY_LEVEL2.h \
	 ntide.h numutil.h paddedFromUnpadded.h \
	 parseUserDefinedTagTypeLine.h primerType.h quality.h \
	 readPHD.cpp readPHD.h readTypes.h \
	 readWholeReadItem.h readsSortedByLeftEndPosition.h readsSortedByReadName.h \
	 readsSortedByTemplateName.h restrictionEnzyme.h restrictionFragment.h \
	 rwbtreedictionary.h rwcregexp.h rwcstring.h \
	 rwcsubstring.h rwctokenizer.h rwdefs.h \
	 rwtptrorderedvector.h rwtptrorderedvector_inc.cpp rwtptrsortedvector.h \
	 rwtptrvector.h rwtvalorderedvector.h rwtvalorderedvector_inc.cpp \
	 rwtvalsortedvector.h rwtvalvector.h selection.h \
	 sequence.h singletInfo.h singletsSortedByTemplateName.h \
	 soEmptyString.h soGetErrno.h soGetRestOfLine.h \
	 subcloneTTemplate.h sysdepend.h tag.h \
	 tagTypes.h templatesSortedByName.h tracefile.h \
	 unpaddedFromPadded.h visibleLineForRestrictionFragments.h whatIsRunning.h \
	 wholeAssemblyItem.h wholeReadItem.h

readPHDAgainForHighQualitySegment.o : \
	 assert.h bool.h filename.h \
	 mbt_exception.h readPHDAgainForHighQualitySegment.cpp readPHDAgainForHighQualitySegment.h \
	 rwcstring.h rwcsubstring.h rwdefs.h \
	 singletInfo.h soGetErrno.h sysdepend.h

readPHDOfSinglet.o : \
	 abs.h assembly.h assemblyViewTagTypeAndLine.h \
	 assert.h autoFinishPurposes.h bIntersect.h \
	 bIntervalsIntersect.h basesegment.h blockOfLocationsOfA4MerType.h \
	 bool.h cComplementBase.h cComplementBaseTable.h \
	 compareContigs.h compareContigsCursor.h compareContigsTypes.h \
	 consed.h consedParameters.h consedResources.h \
	 contig.h contigEnd.h contigMatchTablesType.h \
	 contigSegment.h contigview.h contigwin.h \
	 dictionary.h distribution.h editCursor.h \
	 editaction.h experiment.h expidAndLocatedFragment.h \
	 filename.h gotoList.h gotoListType.h \
	 guiDisplayDigest.h guiMultiContigNavigator.h guiapp.h \
	 guicolortext.h listOfFragments.h locatedFragment.h \
	 matchWithinAssembly.h max.h mbtPtrOrderedVector.h \
	 mbtPtrVector.h mbtValOrderedVectorOfRWCString.h mbtValVector.h \
	 mbtValVectorOfBool.h mbtValVector_inc.cpp mbt_exception.h \
	 mbt_val_ord_offset_vec.h min.h motifutils.h \
	 multiProblemGotoList.h nGetReadTypeFromReadName.h nMAX_QUALITY_LEVEL2.h \
	 ntide.h numutil.h paddedFromUnpadded.h \
	 primerType.h quality.h readPHDAgainForHighQualitySegment.h \
	 readPHDOfSinglet.cpp readPHDOfSinglet.h readTypes.h \
	 readsSortedByLeftEndPosition.h readsSortedByReadName.h readsSortedByTemplateName.h \
	 restrictionEnzyme.h restrictionFragment.h rwbtreedictionary.h \
	 rwcstring.h rwcsubstring.h rwdefs.h \
	 rwtptrorderedvector.h rwtptrorderedvector_inc.cpp rwtptrsortedvector.h \
	 rwtptrvector.h rwtvalorderedvector.h rwtvalorderedvector_inc.cpp \
	 rwtvalsortedvector.h rwtvalvector.h selection.h \
	 sequence.h singletInfo.h singletsSortedByTemplateName.h \
	 soEmptyString.h soGetErrno.h subcloneTTemplate.h \
	 sysdepend.h tag.h templatesSortedByName.h \
	 tracefile.h unpaddedFromPadded.h visibleLineForRestrictionFragments.h \
	 whatIsRunning.h wholeAssemblyItem.h wholeReadItem.h

readPrimerScreenSequences.o : \
	 bool.h readPrimerScreenSequences.cpp readPrimerScreenSequences.h \
	 rwcstring.h rwcsubstring.h rwdefs.h

readSCF.o : \
	 chromatData.h freeChromatData.h readSCF.c \
	 readSCF.h rwUtil.h typeDef.h

readSCF2.o : \
	 chromatData.h findTraceExtrema.h freeChromatData.h \
	 readSCF.h readSCF2.c rwUtil.h \
	 typeDef.h

readSCF3.o : \
	 chromatData.h findTraceExtrema.h freeChromatData.h \
	 readSCF.h readSCF3.c rwUtil.h \
	 typeDef.h

readSCFUtil.o : \
	 chromatData.h freeChromatData.h readSCF.h \
	 readSCFUtil.c rwUtil.h typeDef.h

readType.o : \
	 chromatData.h readType.c typeDef.h

readWholeReadItem.o : \
	 abs.h assembly.h assemblyViewTagTypeAndLine.h \
	 assert.h autoFinishPurposes.h bIntersect.h \
	 bIntervalsIntersect.h bIsNumericMaybeWithWhitespace.h basesegment.h \
	 blockOfLocationsOfA4MerType.h bool.h cComplementBase.h \
	 cComplementBaseTable.h compareContigs.h compareContigsCursor.h \
	 compareContigsTypes.h consed.h consedParameters.h \
	 consedResources.h contig.h contigEnd.h \
	 contigMatchTablesType.h contigSegment.h contigview.h \
	 contigwin.h dictionary.h distribution.h \
	 editCursor.h editaction.h experiment.h \
	 expidAndLocatedFragment.h filename.h gotoList.h \
	 gotoListType.h guiDisplayDigest.h guiMultiContigNavigator.h \
	 guiapp.h guicolortext.h listOfFragments.h \
	 locatedFragment.h matchWithinAssembly.h max.h \
	 mbtPtrOrderedVector.h mbtPtrVector.h mbtValOrderedVectorOfRWCString.h \
	 mbtValVector.h mbtValVectorOfBool.h mbtValVector_inc.cpp \
	 mbt_exception.h mbt_val_ord_offset_vec.h min.h \
	 motifutils.h multiProblemGotoList.h nLine.h \
	 nMAX_QUALITY_LEVEL2.h ntide.h numutil.h \
	 paddedFromUnpadded.h phdBall2Fasta.h primerType.h \
	 quality.h readTypes.h readWholeReadItem.cpp \
	 readWholeReadItem.h readsSortedByLeftEndPosition.h readsSortedByReadName.h \
	 readsSortedByTemplateName.h restrictionEnzyme.h restrictionFragment.h \
	 rwbtreedictionary.h rwcstring.h rwcsubstring.h \
	 rwdefs.h rwtptrorderedvector.h rwtptrorderedvector_inc.cpp \
	 rwtptrsortedvector.h rwtptrvector.h rwtvalorderedvector.h \
	 rwtvalorderedvector_inc.cpp rwtvalsortedvector.h rwtvalvector.h \
	 selection.h sequence.h singletInfo.h \
	 singletsSortedByTemplateName.h soEmptyString.h soGetErrno.h \
	 subcloneTTemplate.h sysdepend.h tag.h \
	 templatesSortedByName.h tracefile.h unpaddedFromPadded.h \
	 visibleLineForRestrictionFragments.h whatIsRunning.h wholeAssemblyItem.h \
	 wholeReadItem.h

regionOfSequenceArray.o : \
	 assemblyViewTagTypeAndLine.h assert.h bIntervalsIntersect.h \
	 bool.h consedParameters.h consedResources.h \
	 filename.h mbtPtrOrderedVector.h mbtValOrderedVectorOfRWCString.h \
	 mbt_exception.h regionOfSequence.h regionOfSequenceArray.cpp \
	 regionOfSequenceArray.h restrictionEnzyme.h rwcstring.h \
	 rwcsubstring.h rwdefs.h rwtptrorderedvector.h \
	 rwtptrorderedvector_inc.cpp rwtvalorderedvector.h rwtvalorderedvector_inc.cpp \
	 soEmptyString.h soGetErrno.h sysdepend.h \
	 whatIsRunning.h

regionToAmplify.o : \
	 abs.h assembly.h assemblyViewTagTypeAndLine.h \
	 assert.h autoFinishPurposes.h bIntersect.h \
	 bIntervalsIntersect.h basesegment.h blockOfLocationsOfA4MerType.h \
	 bool.h cComplementBase.h cComplementBaseTable.h \
	 checkPrimersForACGT.h checkPrimersForMononucleotideRepeats.h compareContigs.h \
	 compareContigsCursor.h compareContigsTypes.h consed.h \
	 consedParameters.h consedResources.h contig.h \
	 contigEnd.h contigMatchTablesType.h contigSegment.h \
	 contigview.h contigwin.h createPrimerCandidate.h \
	 createPrimerCandidatesWith3PrimeEnd.h dGetPrimerMeltingTemperature.h dictionary.h \
	 distribution.h editCursor.h editaction.h \
	 exclusive_or.h experiment.h expidAndLocatedFragment.h \
	 fileDefines.h filename.h gotoList.h \
	 gotoListType.h guiDisplayDigest.h guiMultiContigNavigator.h \
	 guiapp.h guicolortext.h listOfFragments.h \
	 locatedFragment.h matchWithinAssembly.h max.h \
	 mbtPtrOrderedVector.h mbtPtrVector.h mbtValOrderedVectorOfRWCString.h \
	 mbtValVector.h mbtValVectorOfBool.h mbtValVector_inc.cpp \
	 mbt_exception.h mbt_val_ord_offset_vec.h min.h \
	 motifutils.h multiProblemGotoList.h nMAX_QUALITY_LEVEL2.h \
	 ntide.h numutil.h oligoTag.h \
	 paddedFromUnpadded.h pcrPrimer.h pcrPrimerPairSubscripts.h \
	 pcrPrimerrPair.h primerType.h quality.h \
	 readTypes.h readsSortedByLeftEndPosition.h readsSortedByReadName.h \
	 readsSortedByTemplateName.h regionOfContig.h regionToAmplify.cpp \
	 regionToAmplify.h restrictionEnzyme.h restrictionFragment.h \
	 rwbtreedictionary.h rwcstring.h rwcsubstring.h \
	 rwdefs.h rwtptrorderedvector.h rwtptrorderedvector_inc.cpp \
	 rwtptrsortedvector.h rwtptrvector.h rwtvalorderedvector.h \
	 rwtvalorderedvector_inc.cpp rwtvalsortedvector.h rwtvalvector.h \
	 selection.h sequence.h setPrimerFalseMatchScoreArray.h \
	 singletInfo.h singletsSortedByTemplateName.h soEmptyString.h \
	 soGetErrno.h subcloneTTemplate.h sysdepend.h \
	 tag.h templatesSortedByName.h tracefile.h \
	 unpaddedFromPadded.h visibleLineForRestrictionFragments.h whatIsRunning.h \
	 whichPrimersHaveAcceptableMeltingTemp.h whichPrimersHaveAcceptableSelfMatch.h wholeAssemblyItem.h \
	 wholeReadItem.h whyIsPrimerNotAcceptableTypes.h

removeContigs.o : \
	 abs.h assembly.h assemblyViewTagTypeAndLine.h \
	 assert.h autoFinishPurposes.h automatedConsedInit.h \
	 bIntersect.h bIntervalsIntersect.h basesegment.h \
	 blockOfLocationsOfA4MerType.h bool.h cComplementBase.h \
	 cComplementBaseTable.h compareContigs.h compareContigsCursor.h \
	 compareContigsTypes.h consed.h consedParameters.h \
	 consedResources.h contig.h contigEnd.h \
	 contigMatchTablesType.h contigSegment.h contigview.h \
	 contigwin.h dictionary.h distribution.h \
	 editCursor.h editaction.h experiment.h \
	 expidAndLocatedFragment.h filename.h gotoList.h \
	 gotoListType.h guiDisplayDigest.h guiMultiContigNavigator.h \
	 guiRemoveReads.h guiapp.h guicolortext.h \
	 listOfFragments.h locatedFragment.h matchWithinAssembly.h \
	 max.h mbtPtrOrderedVector.h mbtPtrVector.h \
	 mbtValOrderedVectorOfRWCString.h mbtValVector.h mbtValVectorOfBool.h \
	 mbtValVector_inc.cpp mbt_exception.h mbt_val_ord_offset_vec.h \
	 min.h motifutils.h multiProblemGotoList.h \
	 nMAX_QUALITY_LEVEL2.h ntide.h numutil.h \
	 paddedFromUnpadded.h primerType.h quality.h \
	 readTypes.h readsSortedByLeftEndPosition.h readsSortedByReadName.h \
	 readsSortedByTemplateName.h removeContigs.cpp removeContigs.h \
	 restrictionEnzyme.h restrictionFragment.h rwbtreedictionary.h \
	 rwcstring.h rwcsubstring.h rwdefs.h \
	 rwtptrorderedvector.h rwtptrorderedvector_inc.cpp rwtptrsortedvector.h \
	 rwtptrvector.h rwtvalorderedvector.h rwtvalorderedvector_inc.cpp \
	 rwtvalsortedvector.h rwtvalvector.h selection.h \
	 sequence.h singletInfo.h singletsSortedByTemplateName.h \
	 soEmptyString.h soGetErrno.h soLine.h \
	 subcloneTTemplate.h sysdepend.h tag.h \
	 templatesSortedByName.h tracefile.h unpaddedFromPadded.h \
	 visibleLineForRestrictionFragments.h whatIsRunning.h wholeAssemblyItem.h \
	 wholeReadItem.h

removeReads.o : \
	 abs.h assembly.h assemblyViewTagTypeAndLine.h \
	 assert.h autoFinishPurposes.h automatedConsedInit.h \
	 bIntersect.h bIntervalsIntersect.h basesegment.h \
	 blockOfLocationsOfA4MerType.h bool.h cComplementBase.h \
	 cComplementBaseTable.h compareContigs.h compareContigsCursor.h \
	 compareContigsTypes.h consed.h consedParameters.h \
	 consedResources.h contig.h contigEnd.h \
	 contigMatchTablesType.h contigSegment.h contigview.h \
	 contigwin.h dictionary.h distribution.h \
	 editCursor.h editaction.h experiment.h \
	 expidAndLocatedFragment.h filename.h gotoList.h \
	 gotoListType.h guiDisplayDigest.h guiMultiContigNavigator.h \
	 guiRemoveReads.h guiapp.h guicolortext.h \
	 listOfFragments.h locatedFragment.h matchWithinAssembly.h \
	 max.h mbtPtrOrderedVector.h mbtPtrVector.h \
	 mbtValOrderedVectorOfRWCString.h mbtValVector.h mbtValVectorOfBool.h \
	 mbtValVector_inc.cpp mbt_exception.h mbt_val_ord_offset_vec.h \
	 min.h motifutils.h multiProblemGotoList.h \
	 nMAX_QUALITY_LEVEL2.h ntide.h numutil.h \
	 paddedFromUnpadded.h primerType.h quality.h \
	 readTypes.h readsSortedByLeftEndPosition.h readsSortedByReadName.h \
	 readsSortedByTemplateName.h removeReads.cpp removeReads.h \
	 restrictionEnzyme.h restrictionFragment.h rwbtreedictionary.h \
	 rwcstring.h rwcsubstring.h rwdefs.h \
	 rwtptrorderedvector.h rwtptrorderedvector_inc.cpp rwtptrsortedvector.h \
	 rwtptrvector.h rwtvalorderedvector.h rwtvalorderedvector_inc.cpp \
	 rwtvalsortedvector.h rwtvalvector.h selection.h \
	 sequence.h singletInfo.h singletsSortedByTemplateName.h \
	 soEmptyString.h soGetErrno.h soLine.h \
	 subcloneTTemplate.h sysdepend.h tag.h \
	 templatesSortedByName.h tracefile.h unpaddedFromPadded.h \
	 visibleLineForRestrictionFragments.h whatIsRunning.h wholeAssemblyItem.h \
	 wholeReadItem.h

renameFiles.o : \
	 bool.h filename.h mbt_exception.h \
	 renameFiles.cpp renameFiles.h rwcstring.h \
	 rwcsubstring.h rwdefs.h soGetErrno.h \
	 sysdepend.h

restrictionFragment.o : \
	 abs.h assemblyViewTagTypeAndLine.h assert.h \
	 autoFinishPurposes.h basesegment.h blockOfLocationsOfA4MerType.h \
	 bool.h cComplementBase.h cComplementBaseTable.h \
	 consedParameters.h consedResources.h contig.h \
	 contigEnd.h contigMatchTablesType.h dictionary.h \
	 distribution.h experiment.h filename.h \
	 guiapp.h guicolortext.h locatedFragment.h \
	 mbtPtrOrderedVector.h mbtPtrVector.h mbtValOrderedVectorOfRWCString.h \
	 mbtValVector.h mbtValVectorOfBool.h mbtValVector_inc.cpp \
	 mbt_exception.h mbt_val_ord_offset_vec.h min.h \
	 motifutils.h nMAX_QUALITY_LEVEL2.h ntide.h \
	 paddedFromUnpadded.h primerType.h quality.h \
	 readTypes.h readsSortedByLeftEndPosition.h readsSortedByReadName.h \
	 restrictionEnzyme.h restrictionFragment.cpp restrictionFragment.h \
	 rwbtreedictionary.h rwcstring.h rwcsubstring.h \
	 rwdefs.h rwtptrorderedvector.h rwtptrorderedvector_inc.cpp \
	 rwtptrsortedvector.h rwtptrvector.h rwtvalorderedvector.h \
	 rwtvalorderedvector_inc.cpp rwtvalsortedvector.h rwtvalvector.h \
	 sequence.h soEmptyString.h soGetErrno.h \
	 subcloneTTemplate.h sysdepend.h tag.h \
	 tracefile.h unpaddedFromPadded.h whatIsRunning.h \
	 wholeReadItem.h

rwUtil.o : \
	 rwUtil.c rwUtil.h typeDef.h

rwcregexp.o : \
	 bool.h mbt_exception.h rwcregexp.cpp \
	 rwcregexp.h rwcstring.h rwcsubstring.h \
	 rwdefs.h soGetErrno.h

rwcstring.o : \
	 assert.h bool.h max.h \
	 mbt_exception.h rwcregexp.h rwcstring.cpp \
	 rwcstring.h rwcsubstring.h rwdefs.h \
	 soEmptyString.h soGetErrno.h

rwcsubstring.o : \
	 bool.h rwcstring.h rwcsubstring.cpp \
	 rwcsubstring.h rwdefs.h

rwctokenizer.o : \
	 bool.h rwcstring.h rwcsubstring.h \
	 rwctokenizer.cpp rwctokenizer.h rwdefs.h

rwtptrorderedvector.o : \
	 rwtptrorderedvector.cpp

rwtptrsortedvector.o : \
	 bool.h mbt_exception.h rwcstring.h \
	 rwcsubstring.h rwdefs.h rwtptrorderedvector.h \
	 rwtptrorderedvector_inc.cpp rwtptrsortedvector.cpp rwtptrsortedvector.h \
	 soEmptyString.h soGetErrno.h

rwtvalorderedvector.o : \
	 rwtvalorderedvector.cpp

saveTagTypes.o : \
	 addTearTagType.h bool.h consedResources.h \
	 filename.h guicolortext.h mbt_exception.h \
	 rwcstring.h rwcsubstring.h rwdefs.h \
	 rwtptrorderedvector.h rwtptrorderedvector_inc.cpp rwtptrsortedvector.h \
	 saveTagTypes.cpp saveTagTypes.h saveTagTypesFromFile.h \
	 soEmptyString.h soGetErrno.h sysdepend.h \
	 tagTypes.h

saveTagTypesFromFile.o : \
	 assemblyViewTagTypeAndLine.h assert.h bool.h \
	 consedParameters.h consedResources.h fileDefines.h \
	 filename.h guicolortext.h mbtPtrOrderedVector.h \
	 mbtValOrderedVectorOfRWCString.h mbt_exception.h restrictionEnzyme.h \
	 rwcstring.h rwcsubstring.h rwctokenizer.h \
	 rwdefs.h rwtptrorderedvector.h rwtptrorderedvector_inc.cpp \
	 rwtptrsortedvector.h rwtvalorderedvector.h rwtvalorderedvector_inc.cpp \
	 saveTagTypesFromFile.cpp saveTagTypesFromFile.h soEmptyString.h \
	 soGetErrno.h sysdepend.h tagTypes.h \
	 userDefinedTagFieldType.h whatIsRunning.h

searchForSingleStrandedRegions.o : \
	 assemblyViewTagTypeAndLine.h assert.h autoFinishPurposes.h \
	 basesegment.h blockOfLocationsOfA4MerType.h bool.h \
	 cComplementBase.h cComplementBaseTable.h consedParameters.h \
	 consedResources.h contig.h contigEnd.h \
	 contigMatchTablesType.h dictionary.h distribution.h \
	 experiment.h filename.h gotoList.h \
	 guiMultiContigNavigator.h guiapp.h guicolortext.h \
	 locatedFragment.h mbtPtrOrderedVector.h mbtPtrVector.h \
	 mbtValOrderedVectorOfRWCString.h mbtValVector.h mbtValVectorOfBool.h \
	 mbtValVector_inc.cpp mbt_exception.h mbt_val_ord_offset_vec.h \
	 min.h motifutils.h nMAX_QUALITY_LEVEL2.h \
	 ntide.h paddedFromUnpadded.h primerType.h \
	 quality.h readTypes.h readsSortedByLeftEndPosition.h \
	 readsSortedByReadName.h restrictionEnzyme.h rwbtreedictionary.h \
	 rwcstring.h rwcsubstring.h rwdefs.h \
	 rwtptrorderedvector.h rwtptrorderedvector_inc.cpp rwtptrsortedvector.h \
	 rwtptrvector.h rwtvalorderedvector.h rwtvalorderedvector_inc.cpp \
	 rwtvalsortedvector.h rwtvalvector.h searchForSingleStrandedRegions.cpp \
	 searchForSingleStrandedRegions.h sequence.h soEmptyString.h \
	 soGetErrno.h subcloneTTemplate.h sysdepend.h \
	 tag.h tracefile.h unpaddedFromPadded.h \
	 whatIsRunning.h wholeReadItem.h

searchForSingleSubcloneRegions.o : \
	 assemblyViewTagTypeAndLine.h assert.h autoFinishPurposes.h \
	 basesegment.h blockOfLocationsOfA4MerType.h bool.h \
	 cComplementBase.h cComplementBaseTable.h consedParameters.h \
	 consedResources.h contig.h contigEnd.h \
	 contigMatchTablesType.h dictionary.h distribution.h \
	 experiment.h filename.h gotoList.h \
	 guiMultiContigNavigator.h guiapp.h guicolortext.h \
	 locatedFragment.h mbtPtrOrderedVector.h mbtPtrVector.h \
	 mbtValOrderedVectorOfRWCString.h mbtValVector.h mbtValVectorOfBool.h \
	 mbtValVector_inc.cpp mbt_exception.h mbt_val_ord_offset_vec.h \
	 min.h motifutils.h nMAX_QUALITY_LEVEL2.h \
	 ntide.h paddedFromUnpadded.h primerType.h \
	 quality.h readTypes.h readsSortedByLeftEndPosition.h \
	 readsSortedByReadName.h restrictionEnzyme.h rwbtreedictionary.h \
	 rwcstring.h rwcsubstring.h rwdefs.h \
	 rwtptrorderedvector.h rwtptrorderedvector_inc.cpp rwtptrsortedvector.h \
	 rwtptrvector.h rwtvalorderedvector.h rwtvalorderedvector_inc.cpp \
	 rwtvalsortedvector.h rwtvalvector.h searchForSingleSubcloneRegions.cpp \
	 searchForSingleSubcloneRegions.h sequence.h soEmptyString.h \
	 soGetErrno.h subcloneTTemplate.h sysdepend.h \
	 tag.h tracefile.h unpaddedFromPadded.h \
	 whatIsRunning.h wholeReadItem.h

search_for_string.o : \
	 abs.h assembly.h assemblyViewTagTypeAndLine.h \
	 assert.h autoFinishPurposes.h bIntersect.h \
	 bIntervalsIntersect.h basesegment.h blockOfLocationsOfA4MerType.h \
	 bool.h cComplementBase.h cComplementBaseTable.h \
	 compareContigs.h compareContigsCursor.h compareContigsTypes.h \
	 complement_so.h consed.h consedParameters.h \
	 consedResources.h contig.h contigEnd.h \
	 contigMatchTablesType.h contigSegment.h contigview.h \
	 contigwin.h dictionary.h distribution.h \
	 editCursor.h editaction.h experiment.h \
	 expidAndLocatedFragment.h filePopupAndGetFilename.h filename.h \
	 getAlignment.h gotoList.h gotoListType.h \
	 guiDisplayDigest.h guiMultiContigNavigator.h gui_search_for_string.h \
	 guiapp.h guicolortext.h listOfFragments.h \
	 locatedFragment.h matchWithinAssembly.h max.h \
	 mbtPtrOrderedVector.h mbtPtrVector.h mbtValOrderedVectorOfRWCString.h \
	 mbtValVector.h mbtValVectorOfBool.h mbtValVector_inc.cpp \
	 mbt_exception.h mbt_val_ord_offset_vec.h min.h \
	 motifutils.h multiProblemGotoList.h myAgrepAndFilter.h \
	 nMAX_QUALITY_LEVEL2.h nNumberFromBase.h ntide.h \
	 numutil.h paddedFromUnpadded.h please_wait.h \
	 popupErrorMessage.h popupErrorMessage2.h primerType.h \
	 quality.h readTypes.h readsSortedByLeftEndPosition.h \
	 readsSortedByReadName.h readsSortedByTemplateName.h restrictionEnzyme.h \
	 restrictionFragment.h rwbtreedictionary.h rwcregexp.h \
	 rwcstring.h rwcsubstring.h rwctokenizer.h \
	 rwdefs.h rwtptrorderedvector.h rwtptrorderedvector_inc.cpp \
	 rwtptrsortedvector.h rwtptrvector.h rwtvalorderedvector.h \
	 rwtvalorderedvector_inc.cpp rwtvalsortedvector.h rwtvalvector.h \
	 searchMethods.h search_for_string.cpp search_for_string.h \
	 selection.h sequence.h singletInfo.h \
	 singletsSortedByTemplateName.h soEmptyString.h soGetErrno.h \
	 subcloneTTemplate.h sysdepend.h tag.h \
	 templatesSortedByName.h tracefile.h unpaddedFromPadded.h \
	 visibleLineForRestrictionFragments.h whatIsRunning.h wholeAssemblyItem.h \
	 wholeReadItem.h

selection.o : \
	 assert.h bool.h cComplementBase.h \
	 cComplementBaseTable.h filename.h locatedFragment.h \
	 mbtValVector.h mbtValVector_inc.cpp mbt_errors.h \
	 mbt_exception.h mbt_val_ord_offset_vec.h min.h \
	 ntide.h quality.h readTypes.h \
	 rwcstring.h rwcsubstring.h rwdefs.h \
	 rwtptrorderedvector.h rwtptrorderedvector_inc.cpp rwtvalorderedvector.h \
	 rwtvalorderedvector_inc.cpp rwtvalvector.h selection.cpp \
	 selection.h sequence.h soEmptyString.h \
	 soGetErrno.h sysdepend.h tag.h \
	 tracefile.h wholeReadItem.h

seqMatch.o : \
	 abs.h assemblyViewTagTypeAndLine.h assert.h \
	 autoFinishPurposes.h bIntervalsIntersect.h basesegment.h \
	 blockOfLocationsOfA4MerType.h bool.h cComplementBase.h \
	 cComplementBaseTable.h consedParameters.h consedResources.h \
	 contig.h contigEnd.h contigMatchTablesType.h \
	 dictionary.h distribution.h experiment.h \
	 filename.h locatedFragment.h mbtPtrOrderedVector.h \
	 mbtPtrVector.h mbtValOrderedVectorOfRWCString.h mbtValVector.h \
	 mbtValVectorOfBool.h mbtValVector_inc.cpp mbt_exception.h \
	 mbt_val_ord_offset_vec.h min.h nCompareContigsByName.h \
	 nMAX_QUALITY_LEVEL2.h ntide.h paddedFromUnpadded.h \
	 primerType.h quality.h readTypes.h \
	 readsSortedByLeftEndPosition.h readsSortedByReadName.h restrictionEnzyme.h \
	 rwbtreedictionary.h rwcstring.h rwcsubstring.h \
	 rwdefs.h rwtptrorderedvector.h rwtptrorderedvector_inc.cpp \
	 rwtptrsortedvector.h rwtptrvector.h rwtvalorderedvector.h \
	 rwtvalorderedvector_inc.cpp rwtvalsortedvector.h rwtvalvector.h \
	 seqMatch.cpp seqMatch.h sequence.h \
	 soEmptyString.h soGetErrno.h subcloneTTemplate.h \
	 sysdepend.h tag.h tracefile.h \
	 unpaddedFromPadded.h whatIsRunning.h wholeReadItem.h

sequence.o : \
	 assemblyViewTagTypeAndLine.h assert.h bool.h \
	 cComplementBase.h cComplementBaseTable.h consedParameters.h \
	 consedResources.h dErrorRateFromQuality.h filename.h \
	 guiapp.h guicolortext.h mbtPtrOrderedVector.h \
	 mbtValOrderedVectorOfRWCString.h mbt_exception.h mbt_val_ord_offset_vec.h \
	 motifutils.h ntide.h popupErrorMessage.h \
	 quality.h restrictionEnzyme.h rwcstring.h \
	 rwcsubstring.h rwdefs.h rwtptrorderedvector.h \
	 rwtptrorderedvector_inc.cpp rwtvalorderedvector.h rwtvalorderedvector_inc.cpp \
	 sequence.cpp sequence.h soEmptyString.h \
	 soGetErrno.h sysdepend.h whatIsRunning.h

setComplementBaseTable.o : \
	 cComplementBaseTable.h setComplementBaseTable.cpp

setErrorRateFromQuality.o : \
	 dErrorRateFromQuality.h setErrorRateFromQuality.cpp

setMatchLookupTable.o : \
	 assert.h blockOfLocationsOfA4MerType.h bool.h \
	 contigMatchTablesType.h mbt_exception.h nConvertFrom4Mer.h \
	 nLengthOf4Mer.h nNumberFromBase.h rwcstring.h \
	 rwcsubstring.h rwdefs.h setMatchLookupTable.cpp \
	 soGetErrno.h

setMatchMatrix.o : \
	 bool.h setMatchMatrix.cpp setMatchMatrix.h

setNotACGTTable.o : \
	 bNotACGTTable.h bool.h setNotACGTTable.cpp \
	 setNotACGTTable.h

setNumberFromBase4.o : \
	 nNumberFromBase4.h setNumberFromBase4.cpp

setNumberFromBaseTable.o : \
	 nNumberFromBase.h setNumberFromBaseTable.cpp setNumberFromBaseTable.h

setPrimerFalseMatchScoreArray.o : \
	 assemblyViewTagTypeAndLine.h assert.h autoFinishPurposes.h \
	 basesegment.h blockOfLocationsOfA4MerType.h bool.h \
	 cComplementBase.h cComplementBaseTable.h consedParameters.h \
	 consedResources.h contig.h contigEnd.h \
	 contigMatchTablesType.h dictionary.h distribution.h \
	 experiment.h filename.h locatedFragment.h \
	 matchScores.h mbtPtrOrderedVector.h mbtPtrVector.h \
	 mbtValOrderedVectorOfRWCString.h mbtValVector.h mbtValVectorOfBool.h \
	 mbtValVector_inc.cpp mbt_exception.h mbt_val_ord_offset_vec.h \
	 min.h nMAX_QUALITY_LEVEL2.h nNumberFromBase.h \
	 nPrimerFalseMatchScoreArray.h ntide.h paddedFromUnpadded.h \
	 primerType.h quality.h readTypes.h \
	 readsSortedByLeftEndPosition.h readsSortedByReadName.h restrictionEnzyme.h \
	 rwbtreedictionary.h rwcstring.h rwcsubstring.h \
	 rwdefs.h rwtptrorderedvector.h rwtptrorderedvector_inc.cpp \
	 rwtptrsortedvector.h rwtptrvector.h rwtvalorderedvector.h \
	 rwtvalorderedvector_inc.cpp rwtvalsortedvector.h rwtvalvector.h \
	 sequence.h setPrimerFalseMatchScoreArray.cpp setPrimerFalseMatchScoreArray.h \
	 soEmptyString.h soGetErrno.h subcloneTTemplate.h \
	 sysdepend.h tag.h tracefile.h \
	 unpaddedFromPadded.h whatIsRunning.h wholeReadItem.h

sff2PhdBall.o : \
	 assemblyViewTagTypeAndLine.h assert.h bIntersect.h \
	 basesAndQualitiesAndPeaks.h bool.h complement_so.h \
	 consedParameters.h consedResources.h filename.h \
	 findQueryWithinSubject.h getNextToken.h matchLinker.h \
	 max.h mbtPtrOrderedVector.h mbtValOrderedVectorOfRWCString.h \
	 mbt_exception.h min.h readOneSffFile.h \
	 restrictionEnzyme.h rwcstring.h rwcsubstring.h \
	 rwctokenizer.h rwdefs.h rwtptrorderedvector.h \
	 rwtptrorderedvector_inc.cpp rwtvalorderedvector.h rwtvalorderedvector_inc.cpp \
	 rwtvalvector.h seqJustBases.h sff2PhdBall.cpp \
	 sff2PhdBall.h soAddCommas.h soEmptyString.h \
	 soGetDateTime.h soGetErrno.h soLine.h \
	 sysdepend.h szGetTime.h whatIsRunning.h

singleStrandedRegionsGotoList.o : \
	 assemblyViewTagTypeAndLine.h assert.h autoFinishPurposes.h \
	 basesegment.h blockOfLocationsOfA4MerType.h bool.h \
	 cComplementBase.h cComplementBaseTable.h consedParameters.h \
	 consedResources.h contig.h contigEnd.h \
	 contigMatchTablesType.h dictionary.h distribution.h \
	 experiment.h filename.h gotoList.h \
	 locatedFragment.h mbtPtrOrderedVector.h mbtPtrVector.h \
	 mbtValOrderedVectorOfRWCString.h mbtValVector.h mbtValVectorOfBool.h \
	 mbtValVector_inc.cpp mbt_exception.h mbt_val_ord_offset_vec.h \
	 min.h nMAX_QUALITY_LEVEL2.h ntide.h \
	 paddedFromUnpadded.h primerType.h quality.h \
	 readTypes.h readsSortedByLeftEndPosition.h readsSortedByReadName.h \
	 restrictionEnzyme.h rwbtreedictionary.h rwcstring.h \
	 rwcsubstring.h rwdefs.h rwtptrorderedvector.h \
	 rwtptrorderedvector_inc.cpp rwtptrsortedvector.h rwtptrvector.h \
	 rwtvalorderedvector.h rwtvalorderedvector_inc.cpp rwtvalsortedvector.h \
	 rwtvalvector.h sequence.h singleStrandedRegionsGotoList.cpp \
	 singleStrandedRegionsGotoList.h soEmptyString.h soGetErrno.h \
	 subcloneTTemplate.h sysdepend.h tag.h \
	 tracefile.h unpaddedFromPadded.h whatIsRunning.h \
	 wholeReadItem.h

singleSubcloneRegionsGotoList.o : \
	 assemblyViewTagTypeAndLine.h assert.h autoFinishPurposes.h \
	 basesegment.h blockOfLocationsOfA4MerType.h bool.h \
	 cComplementBase.h cComplementBaseTable.h consedParameters.h \
	 consedResources.h contig.h contigEnd.h \
	 contigMatchTablesType.h dictionary.h distribution.h \
	 experiment.h filename.h gotoList.h \
	 locatedFragment.h mbtPtrOrderedVector.h mbtPtrVector.h \
	 mbtValOrderedVectorOfRWCString.h mbtValVector.h mbtValVectorOfBool.h \
	 mbtValVector_inc.cpp mbt_exception.h mbt_val_ord_offset_vec.h \
	 min.h nMAX_QUALITY_LEVEL2.h ntide.h \
	 paddedFromUnpadded.h primerType.h quality.h \
	 readTypes.h readsSortedByLeftEndPosition.h readsSortedByReadName.h \
	 restrictionEnzyme.h rwbtreedictionary.h rwcstring.h \
	 rwcsubstring.h rwdefs.h rwtptrorderedvector.h \
	 rwtptrorderedvector_inc.cpp rwtptrsortedvector.h rwtptrvector.h \
	 rwtvalorderedvector.h rwtvalorderedvector_inc.cpp rwtvalsortedvector.h \
	 rwtvalvector.h sequence.h singleSubcloneRegionsGotoList.cpp \
	 singleSubcloneRegionsGotoList.h soEmptyString.h soGetErrno.h \
	 subcloneTTemplate.h sysdepend.h tag.h \
	 tracefile.h unpaddedFromPadded.h whatIsRunning.h \
	 wholeReadItem.h

snpGenome.o : \
	 assemblyViewTagTypeAndLine.h assert.h bIsNumericMaybeWithWhitespace.h \
	 bool.h complement_so.h consedParameters.h \
	 consedResources.h filename.h mbtPtrOrderedVector.h \
	 mbtValOrderedVectorOfRWCString.h mbt_exception.h min.h \
	 restrictionEnzyme.h rwcstring.h rwcsubstring.h \
	 rwctokenizer.h rwdefs.h rwtptrorderedvector.h \
	 rwtptrorderedvector_inc.cpp rwtvalorderedvector.h rwtvalorderedvector_inc.cpp \
	 rwtvalvector.h snpGenome.cpp snpGenome.h \
	 soAddCommas.h soEmptyString.h soGetErrno.h \
	 soLine.h sysdepend.h whatIsRunning.h

soAddCommas.o : \
	 bool.h rwcregexp.h rwcstring.h \
	 rwcsubstring.h rwdefs.h soAddCommas.cpp \
	 soAddCommas.h

soDecodePhasterBasesToGenomic.o : \
	 bool.h rwcstring.h rwcsubstring.h \
	 rwdefs.h soDecodePhasterBasesToGenomic.cpp soDecodePhasterBasesToGenomic.h

soDecodePhasterBasesToRead.o : \
	 bool.h rwcstring.h rwcsubstring.h \
	 rwdefs.h soDecodePhasterBasesToRead.cpp soDecodePhasterBasesToRead.h

soFindFlowCellFromPath.o : \
	 assert.h bool.h mbt_exception.h \
	 rwcregexp.h rwcstring.h rwcsubstring.h \
	 rwdefs.h soFindFlowCellFromPath.cpp soFindFlowCellFromPath.h \
	 soGetErrno.h

soGetChemistry.o : \
	 bool.h rwcstring.h rwcsubstring.h \
	 rwdefs.h soGetChemistry.cpp soGetChemistry.h

soGetDate.o : \
	 bool.h rwcstring.h rwcsubstring.h \
	 rwdefs.h soGetDate.cpp

soGetDateTime.o : \
	 bool.h rwcstring.h rwcsubstring.h \
	 rwdefs.h soGetDateTime.cpp soGetDateTime.h

soGetErrno.o : \
	 bool.h rwcstring.h rwcsubstring.h \
	 rwdefs.h soGetErrno.cpp soGetErrno.h

soGetRequiredBases.o : \
	 bool.h primateSpecies.h rwcstring.h \
	 rwcsubstring.h rwdefs.h soGetRequiredBases.cpp \
	 soGetRequiredBases.h

soGetRestOfLine.o : \
	 bool.h rwcstring.h rwcsubstring.h \
	 rwdefs.h soGetRestOfLine.cpp

solexa2PhdBall.o : \
	 assemblyViewTagTypeAndLine.h assert.h bIsNumeric.h \
	 bool.h consedParameters.h consedResources.h \
	 consed_version.h filename.h getNextToken.h \
	 mbtPtrOrderedVector.h mbtValOrderedVectorOfRWCString.h mbt_exception.h \
	 nGetNumberOfTokens.h nNumberFromBase2.h nStripTrailingWhitespace.h \
	 restrictionEnzyme.h rwcstring.h rwcsubstring.h \
	 rwctokenizer.h rwdefs.h rwtptrorderedvector.h \
	 rwtptrorderedvector_inc.cpp rwtvalorderedvector.h rwtvalorderedvector_inc.cpp \
	 soEmptyString.h soGetDateTime.h soGetErrno.h \
	 solexa2PhdBall.cpp solexa2PhdBall.h sysdepend.h \
	 szGetTime.h whatIsRunning.h

someOtherProgramSentACommandToConsed.o : \
	 abs.h assembly.h assemblyViewTagTypeAndLine.h \
	 assert.h autoFinishPurposes.h bIntersect.h \
	 bIntervalsIntersect.h bIsNumericMaybeWithWhitespace.h basesegment.h \
	 blockOfLocationsOfA4MerType.h bool.h cComplementBase.h \
	 cComplementBaseTable.h compareContigs.h compareContigsCursor.h \
	 compareContigsTypes.h consed.h consedParameters.h \
	 consedResources.h contig.h contigEnd.h \
	 contigMatchTablesType.h contigSegment.h contigview.h \
	 contigwin.h dictionary.h distribution.h \
	 editCursor.h editaction.h experiment.h \
	 expidAndLocatedFragment.h filename.h gotoList.h \
	 gotoListType.h guiDisplayDigest.h guiMultiContigNavigator.h \
	 guiapp.h guicolortext.h listOfFragments.h \
	 locatedFragment.h matchWithinAssembly.h max.h \
	 mbtPtrOrderedVector.h mbtPtrVector.h mbtValOrderedVectorOfRWCString.h \
	 mbtValVector.h mbtValVectorOfBool.h mbtValVector_inc.cpp \
	 mbt_exception.h mbt_val_ord_offset_vec.h min.h \
	 motifutils.h multiProblemGotoList.h nMAX_QUALITY_LEVEL2.h \
	 nSystemReadALine.h ntide.h numutil.h \
	 paddedFromUnpadded.h popupErrorMessage.h primerType.h \
	 quality.h readTypes.h readsSortedByLeftEndPosition.h \
	 readsSortedByReadName.h readsSortedByTemplateName.h restrictionEnzyme.h \
	 restrictionFragment.h rwbtreedictionary.h rwcstring.h \
	 rwcsubstring.h rwctokenizer.h rwdefs.h \
	 rwtptrorderedvector.h rwtptrorderedvector_inc.cpp rwtptrsortedvector.h \
	 rwtptrvector.h rwtvalorderedvector.h rwtvalorderedvector_inc.cpp \
	 rwtvalsortedvector.h rwtvalvector.h selection.h \
	 sequence.h singletInfo.h singletsSortedByTemplateName.h \
	 soEmptyString.h soGetErrno.h socketConnection.h \
	 someOtherProgramSentACommandToConsed.cpp someOtherProgramSentACommandToConsed.h subcloneTTemplate.h \
	 sysdepend.h tag.h templatesSortedByName.h \
	 tracefile.h unpaddedFromPadded.h visibleLineForRestrictionFragments.h \
	 whatIsRunning.h wholeAssemblyItem.h wholeReadItem.h

sortAcceptablePrimers.o : \
	 blockOfLocationsOfA4MerType.h bool.h contigMatchTablesType.h \
	 primerType.h sortAcceptablePrimers.cpp sortAcceptablePrimers.h

sortPrimersByEndPosition.o : \
	 blockOfLocationsOfA4MerType.h bool.h contigMatchTablesType.h \
	 primerType.h sortPrimersByEndPosition.cpp sortPrimersByEndPosition.h

sortPrimersByStartPosition.o : \
	 blockOfLocationsOfA4MerType.h bool.h contigMatchTablesType.h \
	 primerType.h sortPrimersByStartPosition.cpp sortPrimersByStartPosition.h

sortUnacceptablePrimers.o : \
	 blockOfLocationsOfA4MerType.h bool.h contigMatchTablesType.h \
	 primerType.h sortUnacceptablePrimers.cpp sortUnacceptablePrimers.h

subcloneTTemplate.o : \
	 abs.h assembly.h assemblyViewTagTypeAndLine.h \
	 assert.h autoFinishPurposes.h bIntersect.h \
	 bIntervalsIntersect.h basesegment.h blockOfLocationsOfA4MerType.h \
	 bool.h cComplementBase.h cComplementBaseTable.h \
	 compareContigs.h compareContigsCursor.h compareContigsTypes.h \
	 consed.h consedParameters.h consedResources.h \
	 contig.h contigEnd.h contigMatchTablesType.h \
	 contigSegment.h contigview.h contigwin.h \
	 dErrorRateFromQuality.h dictionary.h distribution.h \
	 editCursor.h editaction.h experiment.h \
	 expidAndLocatedFragment.h fileDefines.h filename.h \
	 fwdRevPair2.h gotoList.h gotoListType.h \
	 guiDisplayDigest.h guiMultiContigNavigator.h guiapp.h \
	 guicolortext.h library.h listOfFragments.h \
	 locatedFragment.h matchWithinAssembly.h max.h \
	 mbtPtrOrderedVector.h mbtPtrVector.h mbtValOrderedVectorOfRWCString.h \
	 mbtValVector.h mbtValVectorOfBool.h mbtValVector_inc.cpp \
	 mbt_exception.h mbt_val_ord_offset_vec.h min.h \
	 motifutils.h multiProblemGotoList.h nMAX_QUALITY_LEVEL2.h \
	 ntide.h numutil.h paddedFromUnpadded.h \
	 popupErrorMessage.h primerType.h quality.h \
	 readTypes.h readsSortedByLeftEndPosition.h readsSortedByReadName.h \
	 readsSortedByTemplateName.h restrictionEnzyme.h restrictionFragment.h \
	 rwbtreedictionary.h rwcstring.h rwcsubstring.h \
	 rwdefs.h rwtptrorderedvector.h rwtptrorderedvector_inc.cpp \
	 rwtptrsortedvector.h rwtptrvector.h rwtvalorderedvector.h \
	 rwtvalorderedvector_inc.cpp rwtvalsortedvector.h rwtvalvector.h \
	 selection.h sequence.h singletInfo.h \
	 singletsSortedByTemplateName.h soEmptyString.h soGetErrno.h \
	 subcloneTTemplate.cpp subcloneTTemplate.h sysdepend.h \
	 tag.h templatesSortedByName.h tracefile.h \
	 unpaddedFromPadded.h visibleLineForRestrictionFragments.h whatIsRunning.h \
	 wholeAssemblyItem.h wholeReadItem.h

szGetTime.o : \
	 szGetTime.c szGetTime.h

tag.o : \
	 abs.h assembly.h assemblyViewTagTypeAndLine.h \
	 assert.h autoFinishPurposes.h bIntersect.h \
	 bIntervalsIntersect.h basesegment.h blockOfLocationsOfA4MerType.h \
	 bool.h cComplementBase.h cComplementBaseTable.h \
	 compareContigs.h compareContigsCursor.h compareContigsTypes.h \
	 consed.h consedParameters.h consedResources.h \
	 contig.h contigEnd.h contigMatchTablesType.h \
	 contigSegment.h contigview.h contigwin.h \
	 dictionary.h distribution.h editCursor.h \
	 editaction.h experiment.h expidAndLocatedFragment.h \
	 filename.h gotoList.h gotoListType.h \
	 guiDisplayDigest.h guiGetUserDefinedTagInfo.h guiMultiContigNavigator.h \
	 guiPopupTagInfo.h guiapp.h guicolortext.h \
	 hp_exception_kludge.h listOfFragments.h locatedFragment.h \
	 matchWithinAssembly.h max.h mbtPtrOrderedVector.h \
	 mbtPtrVector.h mbtValOrderedVectorOfRWCString.h mbtValVector.h \
	 mbtValVectorOfBool.h mbtValVector_inc.cpp mbt_exception.h \
	 mbt_val_ord_offset_vec.h min.h motifutils.h \
	 multiProblemGotoList.h nMAX_QUALITY_LEVEL2.h ntide.h \
	 numutil.h paddedFromUnpadded.h primerType.h \
	 quality.h readTypes.h readsSortedByLeftEndPosition.h \
	 readsSortedByReadName.h readsSortedByTemplateName.h restrictionEnzyme.h \
	 restrictionFragment.h rwbtreedictionary.h rwcregexp.h \
	 rwcstring.h rwcsubstring.h rwdefs.h \
	 rwtptrorderedvector.h rwtptrorderedvector_inc.cpp rwtptrsortedvector.h \
	 rwtptrvector.h rwtvalorderedvector.h rwtvalorderedvector_inc.cpp \
	 rwtvalsortedvector.h rwtvalvector.h searchMethods.h \
	 search_for_string.h selection.h sequence.h \
	 singletInfo.h singletsSortedByTemplateName.h soEmptyString.h \
	 soGetDate.h soGetDateTime.h soGetErrno.h \
	 subcloneTTemplate.h sysdepend.h tag.cpp \
	 tag.h tagTypes.h templatesSortedByName.h \
	 tracefile.h unpaddedFromPadded.h userDefinedTagField.h \
	 userDefinedTagFieldType.h visibleLineForRestrictionFragments.h whatIsRunning.h \
	 wholeAssemblyItem.h wholeReadItem.h

tagSNPs.o : \
	 abs.h addNewReads.h assembly.h \
	 assemblyViewTagTypeAndLine.h assert.h autoFinishPurposes.h \
	 automatedConsedInit.h bIntersect.h bIntervalsIntersect.h \
	 basesegment.h blockOfLocationsOfA4MerType.h bool.h \
	 cComplementBase.h cComplementBaseTable.h compareContigs.h \
	 compareContigsCursor.h compareContigsTypes.h consed.h \
	 consedParameters.h consedResources.h contig.h \
	 contigEnd.h contigMatchTablesType.h contigSegment.h \
	 contigview.h contigwin.h crossMatchIndel.h \
	 crossMatchInfoForRead.h dictionary.h distribution.h \
	 editCursor.h editaction.h experiment.h \
	 expidAndLocatedFragment.h filGetUniqueFilename.h fileDefines.h \
	 filename.h gotoList.h gotoListType.h \
	 guiDisplayDigest.h guiMultiContigNavigator.h guiRemoveReads.h \
	 guiapp.h guicolortext.h listOfFragments.h \
	 locatedFragment.h matchWithinAssembly.h max.h \
	 mbtPtrOrderedVector.h mbtPtrVector.h mbtValOrderedVectorOfRWCString.h \
	 mbtValVector.h mbtValVectorOfBool.h mbtValVector_inc.cpp \
	 mbt_exception.h mbt_val_ord_offset_vec.h min.h \
	 motifutils.h multiProblemGotoList.h nMAX_QUALITY_LEVEL2.h \
	 ntide.h numutil.h paddedFromUnpadded.h \
	 primerType.h quality.h readTypes.h \
	 readsSortedByLeftEndPosition.h readsSortedByReadName.h readsSortedByTemplateName.h \
	 restrictionEnzyme.h restrictionFragment.h rwbtreedictionary.h \
	 rwcstring.h rwcsubstring.h rwdefs.h \
	 rwtptrorderedvector.h rwtptrorderedvector_inc.cpp rwtptrsortedvector.h \
	 rwtptrvector.h rwtvalorderedvector.h rwtvalorderedvector_inc.cpp \
	 rwtvalsortedvector.h rwtvalvector.h selection.h \
	 sequence.h singletInfo.h singletsSortedByTemplateName.h \
	 soEmptyString.h soGetErrno.h subcloneTTemplate.h \
	 sysdepend.h tag.h tagSNPs.cpp \
	 tagSNPs.h templatesSortedByName.h tracefile.h \
	 unpaddedFromPadded.h visibleLineForRestrictionFragments.h whatIsRunning.h \
	 wholeAssemblyItem.h wholeReadItem.h

tagTypes.o : \
	 abs.h assembly.h assemblyViewTagTypeAndLine.h \
	 assert.h autoFinishExpTag.h autoFinishPurposes.h \
	 bIntersect.h bIntervalsIntersect.h basesegment.h \
	 blockOfLocationsOfA4MerType.h bool.h cComplementBase.h \
	 cComplementBaseTable.h compareContigs.h compareContigsCursor.h \
	 compareContigsTypes.h consed.h consedParameters.h \
	 consedResources.h contig.h contigEnd.h \
	 contigMatchTablesType.h contigSegment.h contigview.h \
	 contigwin.h dictionary.h distribution.h \
	 editCursor.h editaction.h experiment.h \
	 expidAndLocatedFragment.h filename.h gotoList.h \
	 gotoListType.h guiDisplayDigest.h guiMultiContigNavigator.h \
	 guiapp.h guicolortext.h listOfFragments.h \
	 locatedFragment.h matchWithinAssembly.h max.h \
	 mbtPtrOrderedVector.h mbtPtrVector.h mbtValOrderedVectorOfRWCString.h \
	 mbtValVector.h mbtValVectorOfBool.h mbtValVector_inc.cpp \
	 mbt_exception.h mbt_val_ord_offset_vec.h min.h \
	 motifutils.h multiProblemGotoList.h nMAX_QUALITY_LEVEL2.h \
	 ntide.h numutil.h oligoTag.h \
	 paddedFromUnpadded.h popupErrorMessage.h primerType.h \
	 quality.h readTypes.h readsSortedByLeftEndPosition.h \
	 readsSortedByReadName.h readsSortedByTemplateName.h restrictionEnzyme.h \
	 restrictionFragment.h rwbtreedictionary.h rwcstring.h \
	 rwcsubstring.h rwctokenizer.h rwdefs.h \
	 rwtptrorderedvector.h rwtptrorderedvector_inc.cpp rwtptrsortedvector.h \
	 rwtptrvector.h rwtvalorderedvector.h rwtvalorderedvector_inc.cpp \
	 rwtvalsortedvector.h rwtvalvector.h selection.h \
	 sequence.h singletInfo.h singletsSortedByTemplateName.h \
	 soEmptyString.h soGetErrno.h subcloneTTemplate.h \
	 sysdepend.h tag.h tagTypes.cpp \
	 tagTypes.h templatesSortedByName.h tracefile.h \
	 unpaddedFromPadded.h userDefinedTagField.h userDefinedTagFieldType.h \
	 visibleLineForRestrictionFragments.h whatIsRunning.h wholeAssemblyItem.h \
	 wholeReadItem.h

tagsGotoList.o : \
	 assemblyViewTagTypeAndLine.h assert.h autoFinishPurposes.h \
	 basesegment.h blockOfLocationsOfA4MerType.h bool.h \
	 cComplementBase.h cComplementBaseTable.h consedParameters.h \
	 consedResources.h contig.h contigEnd.h \
	 contigMatchTablesType.h dictionary.h distribution.h \
	 experiment.h filename.h gotoList.h \
	 locatedFragment.h mbtPtrOrderedVector.h mbtPtrVector.h \
	 mbtValOrderedVectorOfRWCString.h mbtValVector.h mbtValVectorOfBool.h \
	 mbtValVector_inc.cpp mbt_exception.h mbt_val_ord_offset_vec.h \
	 min.h nMAX_QUALITY_LEVEL2.h ntide.h \
	 paddedFromUnpadded.h primerType.h quality.h \
	 readTypes.h readsSortedByLeftEndPosition.h readsSortedByReadName.h \
	 restrictionEnzyme.h rwbtreedictionary.h rwcstring.h \
	 rwcsubstring.h rwdefs.h rwtptrorderedvector.h \
	 rwtptrorderedvector_inc.cpp rwtptrsortedvector.h rwtptrvector.h \
	 rwtvalorderedvector.h rwtvalorderedvector_inc.cpp rwtvalsortedvector.h \
	 rwtvalvector.h sequence.h soEmptyString.h \
	 soGetErrno.h subcloneTTemplate.h sysdepend.h \
	 tag.h tagsGotoList.cpp tagsGotoList.h \
	 tracefile.h unpaddedFromPadded.h whatIsRunning.h \
	 wholeReadItem.h

teditor.o : \
	 abs.h assembly.h assemblyViewTagTypeAndLine.h \
	 assert.h autoFinishPurposes.h bIntersect.h \
	 bIntervalsIntersect.h basesegment.h blockOfLocationsOfA4MerType.h \
	 bool.h cComplementBase.h cComplementBaseTable.h \
	 compareContigs.h compareContigsCursor.h compareContigsTypes.h \
	 consed.h consedParameters.h consedResources.h \
	 contig.h contigEnd.h contigMatchTablesType.h \
	 contigSegment.h contigview.h contigwin.h \
	 dictionary.h distribution.h editCursor.h \
	 editaction.h experiment.h expidAndLocatedFragment.h \
	 filename.h gotoList.h gotoListType.h \
	 guiDisplayDigest.h guiMultiContigNavigator.h guiapp.h \
	 guicolortext.h guiteditor.h guitedwin.h \
	 infobutton.h listOfFragments.h locatedFragment.h \
	 matchWithinAssembly.h max.h mbtPtrOrderedVector.h \
	 mbtPtrVector.h mbtValOrderedVectorOfRWCString.h mbtValVector.h \
	 mbtValVectorOfBool.h mbtValVector_inc.cpp mbt_errors.h \
	 mbt_exception.h mbt_val_ord_offset_vec.h min.h \
	 motifutils.h multiProblemGotoList.h nMAX_QUALITY_LEVEL2.h \
	 ntide.h numutil.h oligoTag.h \
	 paddedFromUnpadded.h popupErrorMessage.h primerType.h \
	 quality.h readTypes.h readsSortedByLeftEndPosition.h \
	 readsSortedByReadName.h readsSortedByTemplateName.h restrictionEnzyme.h \
	 restrictionFragment.h rwbtreedictionary.h rwcstring.h \
	 rwcsubstring.h rwdefs.h rwtptrorderedvector.h \
	 rwtptrorderedvector_inc.cpp rwtptrsortedvector.h rwtptrvector.h \
	 rwtvalorderedvector.h rwtvalorderedvector_inc.cpp rwtvalsortedvector.h \
	 rwtvalvector.h selection.h sequence.h \
	 singletInfo.h singletsSortedByTemplateName.h soEmptyString.h \
	 soGetErrno.h subcloneTTemplate.h sysdepend.h \
	 tag.h tagTypes.h teditor.cpp \
	 teditor.h teditor_types.h tedwin.h \
	 templatesSortedByName.h textfield.h tracefile.h \
	 unpaddedFromPadded.h visibleLineForRestrictionFragments.h whatIsRunning.h \
	 whatToDoWithSelectionTypes.h wholeAssemblyItem.h wholeReadItem.h

tedwin.o : \
	 abs.h assembly.h assemblyViewTagTypeAndLine.h \
	 assert.h autoFinishPurposes.h bGuiGetAnswerYesNo.h \
	 bIntersect.h bIntervalsIntersect.h basesegment.h \
	 blockOfLocationsOfA4MerType.h bool.h cComplementBase.h \
	 cComplementBaseTable.h colormode.h compareContigs.h \
	 compareContigsCursor.h compareContigsTypes.h consed.h \
	 consedParameters.h consedResources.h contig.h \
	 contigEnd.h contigMatchTablesType.h contigSegment.h \
	 contigview.h contigwin.h dictionary.h \
	 distribution.h editActionChangeRead.h editAddReadTag.h \
	 editChangeToNs.h editChangeToNsToLeft.h editChangeToNsToRight.h \
	 editChangeToXs.h editCursor.h editInsertColOfPads.h \
	 editMakeHighQuality.h editMakeHighQualityAndChangeConsensus.h editMakeLowQuality.h \
	 editMakeLowQualityToLeft.h editMakeLowQualityToRight.h editOverstrike.h \
	 editaction.h experiment.h expidAndLocatedFragment.h \
	 filename.h gotoList.h gotoListType.h \
	 guiDisplayDigest.h guiGetTagType.h guiMultiContigNavigator.h \
	 guiWhatToDoWithSelection.h guiapp.h guicolortext.h \
	 guiteditor.h guitedwin.h infobutton.h \
	 listOfFragments.h locatedFragment.h matchWithinAssembly.h \
	 max.h mbtPtrOrderedVector.h mbtPtrVector.h \
	 mbtValOrderedVectorOfRWCString.h mbtValVector.h mbtValVectorOfBool.h \
	 mbtValVector_inc.cpp mbt_errors.h mbt_exception.h \
	 mbt_val_ord_offset_vec.h min.h motifutils.h \
	 multiProblemGotoList.h nMAX_QUALITY_LEVEL2.h ntide.h \
	 numutil.h paddedFromUnpadded.h popupInfoMessage.h \
	 primerType.h quality.h readTypes.h \
	 readsSortedByLeftEndPosition.h readsSortedByReadName.h readsSortedByTemplateName.h \
	 restrictionEnzyme.h restrictionFragment.h rwbtreedictionary.h \
	 rwcstring.h rwcsubstring.h rwdefs.h \
	 rwtptrorderedvector.h rwtptrorderedvector_inc.cpp rwtptrsortedvector.h \
	 rwtptrvector.h rwtvalorderedvector.h rwtvalorderedvector_inc.cpp \
	 rwtvalsortedvector.h rwtvalvector.h selection.h \
	 sequence.h singletInfo.h singletsSortedByTemplateName.h \
	 soEmptyString.h soGetErrno.h subcloneTTemplate.h \
	 sysdepend.h tag.h tagTypes.h \
	 teditor.h teditor_types.h tedwin.cpp \
	 tedwin.h templatesSortedByName.h textfield.h \
	 tracefile.h unpaddedFromPadded.h visibleLineForRestrictionFragments.h \
	 whatIsRunning.h whatToDoWithSelectionTypes.h wholeAssemblyItem.h \
	 wholeReadItem.h

terminateIfDirectoryIsNotWritable.o : \
	 assert.h bool.h filename.h \
	 mbt_exception.h rwcstring.h rwcsubstring.h \
	 rwdefs.h soGetErrno.h sysdepend.h \
	 terminateIfDirectoryIsNotWritable.cpp terminateIfDirectoryIsNotWritable.h

terminateIfNoPhdDir.o : \
	 popupErrorMessage.h terminateIfNoPhdDir.cpp terminateIfNoPhdDir.h

testReadPhdBall.o : \
	 assert.h bool.h cComplementBase.h \
	 cComplementBaseTable.h filename.h findQueryWithinSubject.h \
	 locatedFragment.h mbtValOrderedVectorOfRWCString.h mbtValVector.h \
	 mbtValVector_inc.cpp mbt_exception.h mbt_val_ord_offset_vec.h \
	 min.h ntide.h quality.h \
	 readTypes.h readsSortedByReadName.h rwcstring.h \
	 rwcsubstring.h rwdefs.h rwtptrorderedvector.h \
	 rwtptrorderedvector_inc.cpp rwtvalorderedvector.h rwtvalorderedvector_inc.cpp \
	 rwtvalvector.h sequence.h soEmptyString.h \
	 soGetErrno.h soLine.h sysdepend.h \
	 tag.h testReadPhdBall.cpp testReadPhdBall.h \
	 tracefile.h wholeReadItem.h

textbox.o : \
	 assert.h bool.h filename.h \
	 guiapp.h guicolortext.h handleWindowManagerDelete2.h \
	 hp_exception_kludge.h mbt_exception.h motifutils.h \
	 popupErrorMessage.h rwcstring.h rwcsubstring.h \
	 rwdefs.h rwtptrorderedvector.h rwtptrorderedvector_inc.cpp \
	 rwtvalorderedvector.h rwtvalorderedvector_inc.cpp soEmptyString.h \
	 soGetErrno.h sysdepend.h textbox.cpp \
	 textbox.h

textfield.o : \
	 assert.h bool.h mbt_exception.h \
	 motifutils.h rwcstring.h rwcsubstring.h \
	 rwdefs.h soGetErrno.h sysdepend.h \
	 textfield.cpp textfield.h

tracefile.o : \
	 abs.h assembly.h assemblyViewTagTypeAndLine.h \
	 assert.h autoFinishPurposes.h bIntersect.h \
	 bIntervalsIntersect.h basesegment.h blockOfLocationsOfA4MerType.h \
	 bool.h cComplementBase.h cComplementBaseTable.h \
	 chromatData.h compareContigs.h compareContigsCursor.h \
	 compareContigsTypes.h consed.h consedParameters.h \
	 consedResources.h contig.h contigEnd.h \
	 contigMatchTablesType.h contigSegment.h contigview.h \
	 contigwin.h dictionary.h distribution.h \
	 editCursor.h editaction.h experiment.h \
	 expidAndLocatedFragment.h filePopupAndGetFilename.h filename.h \
	 freeChromatData.h gotoList.h gotoListType.h \
	 guiDisplayDigest.h guiMultiContigNavigator.h guiapp.h \
	 guicolortext.h listOfFragments.h locatedFragment.h \
	 matchWithinAssembly.h max.h mbtPtrOrderedVector.h \
	 mbtPtrVector.h mbtValOrderedVectorOfRWCString.h mbtValVector.h \
	 mbtValVectorOfBool.h mbtValVector_inc.cpp mbt_exception.h \
	 mbt_val_ord_offset_vec.h min.h motifutils.h \
	 multiProblemGotoList.h nMAX_QUALITY_LEVEL2.h nNumberFromBase.h \
	 ntide.h numutil.h paddedFromUnpadded.h \
	 primerType.h quality.h readData.h \
	 readPHD.h readTypes.h readsSortedByLeftEndPosition.h \
	 readsSortedByReadName.h readsSortedByTemplateName.h restrictionEnzyme.h \
	 restrictionFragment.h rwbtreedictionary.h rwcstring.h \
	 rwcsubstring.h rwdefs.h rwtptrorderedvector.h \
	 rwtptrorderedvector_inc.cpp rwtptrsortedvector.h rwtptrvector.h \
	 rwtvalorderedvector.h rwtvalorderedvector_inc.cpp rwtvalsortedvector.h \
	 rwtvalvector.h selection.h sequence.h \
	 singletInfo.h singletsSortedByTemplateName.h soEmptyString.h \
	 soGetErrno.h subcloneTTemplate.h sysdepend.h \
	 tag.h templatesSortedByName.h tracefile.cpp \
	 tracefile.h unpaddedFromPadded.h visibleLineForRestrictionFragments.h \
	 whatIsRunning.h wholeAssemblyItem.h wholeReadItem.h

transitionsTransversions.o : \
	 bool.h transitionsTransversions.cpp transitionsTransversions.h

translateRWCString.o : \
	 bool.h rwcstring.h rwcsubstring.h \
	 rwdefs.h translateRWCString.cpp

uGetCRC_9_digits.o : \
	 uGetCRC_9_digits.cpp

ucGetReadType.o : \
	 assert.h bool.h mbt_exception.h \
	 readTypes.h rwcstring.h rwcsubstring.h \
	 rwdefs.h soGetErrno.h ucGetReadType.cpp \
	 ucGetReadType.h

unalignedHighQualityRegionsGotoList.o : \
	 assemblyViewTagTypeAndLine.h assert.h autoFinishPurposes.h \
	 basesegment.h blockOfLocationsOfA4MerType.h bool.h \
	 cComplementBase.h cComplementBaseTable.h consedParameters.h \
	 consedResources.h contig.h contigEnd.h \
	 contigMatchTablesType.h dictionary.h distribution.h \
	 experiment.h filename.h gotoList.h \
	 locatedFragment.h mbtPtrOrderedVector.h mbtPtrVector.h \
	 mbtValOrderedVectorOfRWCString.h mbtValVector.h mbtValVectorOfBool.h \
	 mbtValVector_inc.cpp mbt_exception.h mbt_val_ord_offset_vec.h \
	 min.h nMAX_QUALITY_LEVEL2.h ntide.h \
	 paddedFromUnpadded.h primerType.h quality.h \
	 readTypes.h readsSortedByLeftEndPosition.h readsSortedByReadName.h \
	 restrictionEnzyme.h rwbtreedictionary.h rwcstring.h \
	 rwcsubstring.h rwdefs.h rwtptrorderedvector.h \
	 rwtptrorderedvector_inc.cpp rwtptrsortedvector.h rwtptrvector.h \
	 rwtvalorderedvector.h rwtvalorderedvector_inc.cpp rwtvalsortedvector.h \
	 rwtvalvector.h sequence.h soEmptyString.h \
	 soGetErrno.h subcloneTTemplate.h sysdepend.h \
	 tag.h tracefile.h unalignedHighQualityRegionsGotoList.cpp \
	 unalignedHighQualityRegionsGotoList.h unpaddedFromPadded.h whatIsRunning.h \
	 wholeReadItem.h

universalPrimerAutoFinishExpTagsSortedByTemplateName.o : \
	 abs.h assembly.h assemblyViewTagTypeAndLine.h \
	 assert.h autoFinishExpTag.h autoFinishPurposes.h \
	 bIntersect.h bIntervalsIntersect.h basesegment.h \
	 blockOfLocationsOfA4MerType.h bool.h cComplementBase.h \
	 cComplementBaseTable.h compareContigs.h compareContigsCursor.h \
	 compareContigsTypes.h consed.h consedParameters.h \
	 consedResources.h contig.h contigEnd.h \
	 contigMatchTablesType.h contigSegment.h contigview.h \
	 contigwin.h dictionary.h distribution.h \
	 editCursor.h editaction.h experiment.h \
	 expidAndLocatedFragment.h filename.h gotoList.h \
	 gotoListType.h guiDisplayDigest.h guiMultiContigNavigator.h \
	 guiapp.h guicolortext.h listOfFragments.h \
	 locatedFragment.h matchWithinAssembly.h max.h \
	 mbtPtrOrderedVector.h mbtPtrVector.h mbtValOrderedVectorOfRWCString.h \
	 mbtValVector.h mbtValVectorOfBool.h mbtValVector_inc.cpp \
	 mbt_exception.h mbt_val_ord_offset_vec.h min.h \
	 motifutils.h multiProblemGotoList.h nMAX_QUALITY_LEVEL2.h \
	 ntide.h numutil.h paddedFromUnpadded.h \
	 primerType.h quality.h readTypes.h \
	 readsSortedByLeftEndPosition.h readsSortedByReadName.h readsSortedByTemplateName.h \
	 restrictionEnzyme.h restrictionFragment.h rwbtreedictionary.h \
	 rwcstring.h rwcsubstring.h rwdefs.h \
	 rwtptrorderedvector.h rwtptrorderedvector_inc.cpp rwtptrsortedvector.h \
	 rwtptrvector.h rwtvalorderedvector.h rwtvalorderedvector_inc.cpp \
	 rwtvalsortedvector.h rwtvalvector.h selection.h \
	 sequence.h singletInfo.h singletsSortedByTemplateName.h \
	 soEmptyString.h soGetErrno.h subcloneTTemplate.h \
	 sysdepend.h tag.h templatesSortedByName.h \
	 tracefile.h universalPrimerAutoFinishExpTagsSortedByTemplateName.cpp universalPrimerAutoFinishExpTagsSortedByTemplateName.h \
	 unpaddedFromPadded.h visibleLineForRestrictionFragments.h whatIsRunning.h \
	 wholeAssemblyItem.h wholeReadItem.h

unpaddedFromPadded.o : \
	 assemblyViewTagTypeAndLine.h assert.h autoFinishPurposes.h \
	 basesegment.h blockOfLocationsOfA4MerType.h bool.h \
	 cComplementBase.h cComplementBaseTable.h consedParameters.h \
	 consedResources.h contig.h contigEnd.h \
	 contigMatchTablesType.h dictionary.h distribution.h \
	 experiment.h filename.h locatedFragment.h \
	 mbtPtrOrderedVector.h mbtPtrVector.h mbtValOrderedVectorOfRWCString.h \
	 mbtValVector.h mbtValVectorOfBool.h mbtValVector_inc.cpp \
	 mbt_exception.h mbt_val_ord_offset_vec.h min.h \
	 nMAX_QUALITY_LEVEL2.h ntide.h paddedFromUnpadded.h \
	 primerType.h quality.h readTypes.h \
	 readsSortedByLeftEndPosition.h readsSortedByReadName.h restrictionEnzyme.h \
	 rwbtreedictionary.h rwcstring.h rwcsubstring.h \
	 rwdefs.h rwtptrorderedvector.h rwtptrorderedvector_inc.cpp \
	 rwtptrsortedvector.h rwtptrvector.h rwtvalorderedvector.h \
	 rwtvalorderedvector_inc.cpp rwtvalsortedvector.h rwtvalvector.h \
	 sequence.h soEmptyString.h soGetErrno.h \
	 subcloneTTemplate.h sysdepend.h tag.h \
	 tracefile.h unpaddedFromPadded.cpp unpaddedFromPadded.h \
	 whatIsRunning.h wholeReadItem.h

userDefinedTagField.o : \
	 abs.h assembly.h assemblyViewTagTypeAndLine.h \
	 assert.h autoFinishPurposes.h bIntersect.h \
	 bIntervalsIntersect.h basesegment.h blockOfLocationsOfA4MerType.h \
	 bool.h cComplementBase.h cComplementBaseTable.h \
	 compareContigs.h compareContigsCursor.h compareContigsTypes.h \
	 consed.h consedParameters.h consedResources.h \
	 contig.h contigEnd.h contigMatchTablesType.h \
	 contigSegment.h contigview.h contigwin.h \
	 dictionary.h distribution.h editCursor.h \
	 editaction.h experiment.h expidAndLocatedFragment.h \
	 filename.h gotoList.h gotoListType.h \
	 guiDisplayDigest.h guiMultiContigNavigator.h guiapp.h \
	 guicolortext.h listOfFragments.h locatedFragment.h \
	 matchWithinAssembly.h max.h mbtPtrOrderedVector.h \
	 mbtPtrVector.h mbtValOrderedVectorOfRWCString.h mbtValVector.h \
	 mbtValVectorOfBool.h mbtValVector_inc.cpp mbt_exception.h \
	 mbt_val_ord_offset_vec.h min.h motifutils.h \
	 multiProblemGotoList.h nMAX_QUALITY_LEVEL2.h ntide.h \
	 numutil.h paddedFromUnpadded.h primerType.h \
	 quality.h readTypes.h readsSortedByLeftEndPosition.h \
	 readsSortedByReadName.h readsSortedByTemplateName.h restrictionEnzyme.h \
	 restrictionFragment.h rwbtreedictionary.h rwcstring.h \
	 rwcsubstring.h rwdefs.h rwtptrorderedvector.h \
	 rwtptrorderedvector_inc.cpp rwtptrsortedvector.h rwtptrvector.h \
	 rwtvalorderedvector.h rwtvalorderedvector_inc.cpp rwtvalsortedvector.h \
	 rwtvalvector.h selection.h sequence.h \
	 singletInfo.h singletsSortedByTemplateName.h soEmptyString.h \
	 soGetErrno.h subcloneTTemplate.h sysdepend.h \
	 tag.h tagTypes.h templatesSortedByName.h \
	 tracefile.h unpaddedFromPadded.h userDefinedTagField.cpp \
	 userDefinedTagField.h userDefinedTagFieldType.h visibleLineForRestrictionFragments.h \
	 whatIsRunning.h wholeAssemblyItem.h wholeReadItem.h

userDefinedTagFieldType.o : \
	 abs.h assembly.h assemblyViewTagTypeAndLine.h \
	 assert.h autoFinishPurposes.h bIntersect.h \
	 bIntervalsIntersect.h bIsNumericDouble.h bIsNumericLongMaybeWithWhitespace.h \
	 basesegment.h blockOfLocationsOfA4MerType.h bool.h \
	 cComplementBase.h cComplementBaseTable.h compareContigs.h \
	 compareContigsCursor.h compareContigsTypes.h consed.h \
	 consedParameters.h consedResources.h contig.h \
	 contigEnd.h contigMatchTablesType.h contigSegment.h \
	 contigview.h contigwin.h dictionary.h \
	 distribution.h editCursor.h editaction.h \
	 experiment.h expidAndLocatedFragment.h filename.h \
	 gotoList.h gotoListType.h guiDisplayDigest.h \
	 guiMultiContigNavigator.h guiapp.h guicolortext.h \
	 listOfFragments.h locatedFragment.h matchWithinAssembly.h \
	 max.h mbtPtrOrderedVector.h mbtPtrVector.h \
	 mbtValOrderedVectorOfRWCString.h mbtValVector.h mbtValVectorOfBool.h \
	 mbtValVector_inc.cpp mbt_exception.h mbt_val_ord_offset_vec.h \
	 min.h motifutils.h multiProblemGotoList.h \
	 nMAX_QUALITY_LEVEL2.h ntide.h numutil.h \
	 paddedFromUnpadded.h primerType.h quality.h \
	 readTypes.h readsSortedByLeftEndPosition.h readsSortedByReadName.h \
	 readsSortedByTemplateName.h restrictionEnzyme.h restrictionFragment.h \
	 rwbtreedictionary.h rwcstring.h rwcsubstring.h \
	 rwdefs.h rwtptrorderedvector.h rwtptrorderedvector_inc.cpp \
	 rwtptrsortedvector.h rwtptrvector.h rwtvalorderedvector.h \
	 rwtvalorderedvector_inc.cpp rwtvalsortedvector.h rwtvalvector.h \
	 selection.h sequence.h singletInfo.h \
	 singletsSortedByTemplateName.h soEmptyString.h soGetErrno.h \
	 subcloneTTemplate.h sysdepend.h tag.h \
	 tagTypes.h templatesSortedByName.h tracefile.h \
	 unpaddedFromPadded.h userDefinedTagField.h userDefinedTagFieldType.cpp \
	 userDefinedTagFieldType.h visibleLineForRestrictionFragments.h whatIsRunning.h \
	 wholeAssemblyItem.h wholeReadItem.h

visibleLineForRestrictionFragments.o : \
	 assert.h bool.h filename.h \
	 guiapp.h guicolortext.h mbt_exception.h \
	 motifutils.h restrictionFragment.h rwcstring.h \
	 rwcsubstring.h rwdefs.h rwtptrorderedvector.h \
	 rwtptrorderedvector_inc.cpp rwtvalorderedvector.h rwtvalorderedvector_inc.cpp \
	 soEmptyString.h soGetErrno.h sysdepend.h \
	 visibleLineForRestrictionFragments.cpp visibleLineForRestrictionFragments.h

waitUntilDialogIsVisible.o : \
	 assert.h bool.h filename.h \
	 guiapp.h guicolortext.h mbt_exception.h \
	 motifutils.h rwcstring.h rwcsubstring.h \
	 rwdefs.h rwtptrorderedvector.h rwtptrorderedvector_inc.cpp \
	 rwtvalorderedvector.h rwtvalorderedvector_inc.cpp soEmptyString.h \
	 soGetErrno.h sysdepend.h waitUntilDialogIsVisible.cpp

whichPrimersAreAcceptable.o : \
	 assemblyViewTagTypeAndLine.h assert.h blockOfLocationsOfA4MerType.h \
	 bool.h consedParameters.h consedResources.h \
	 contigMatchTablesType.h filename.h mbtPtrOrderedVector.h \
	 mbtValOrderedVectorOfRWCString.h mbt_exception.h primerType.h \
	 restrictionEnzyme.h rwcstring.h rwcsubstring.h \
	 rwdefs.h rwtptrorderedvector.h rwtptrorderedvector_inc.cpp \
	 rwtvalorderedvector.h rwtvalorderedvector_inc.cpp soEmptyString.h \
	 soGetErrno.h sysdepend.h whatIsRunning.h \
	 whichPrimersAreAcceptable.cpp whichPrimersAreAcceptable.h whyIsPrimerNotAcceptableTypes.h

whichPrimersHaveAcceptableMeltingTemp.o : \
	 assemblyViewTagTypeAndLine.h assert.h blockOfLocationsOfA4MerType.h \
	 bool.h consedParameters.h consedResources.h \
	 contigMatchTablesType.h dGetPrimerMeltingTemperature.h filename.h \
	 mbtPtrOrderedVector.h mbtValOrderedVectorOfRWCString.h mbt_exception.h \
	 primerType.h restrictionEnzyme.h rwcstring.h \
	 rwcsubstring.h rwdefs.h rwtptrorderedvector.h \
	 rwtptrorderedvector_inc.cpp rwtvalorderedvector.h rwtvalorderedvector_inc.cpp \
	 soEmptyString.h soGetErrno.h sysdepend.h \
	 whatIsRunning.h whichPrimersHaveAcceptableMeltingTemp.cpp whichPrimersHaveAcceptableMeltingTemp.h \
	 whyIsPrimerNotAcceptableTypes.h

whichPrimersHaveAcceptableSelfMatch.o : \
	 assemblyViewTagTypeAndLine.h assert.h blockOfLocationsOfA4MerType.h \
	 bool.h consedParameters.h consedResources.h \
	 contigMatchTablesType.h filename.h findStickiestSelfMatch.h \
	 mbtPtrOrderedVector.h mbtValOrderedVectorOfRWCString.h mbt_exception.h \
	 primerType.h restrictionEnzyme.h rwcstring.h \
	 rwcsubstring.h rwdefs.h rwtptrorderedvector.h \
	 rwtptrorderedvector_inc.cpp rwtvalorderedvector.h rwtvalorderedvector_inc.cpp \
	 soEmptyString.h soGetErrno.h sysdepend.h \
	 whatIsRunning.h whichPrimersHaveAcceptableSelfMatch.cpp whichPrimersHaveAcceptableSelfMatch.h

wholeAssemblyItem.o : \
	 bool.h rwcstring.h rwcsubstring.h \
	 rwdefs.h wholeAssemblyItem.cpp wholeAssemblyItem.h

wholeReadItem.o : \
	 assemblyViewTagTypeAndLine.h assert.h autoFinishPurposes.h \
	 basesegment.h blockOfLocationsOfA4MerType.h bool.h \
	 cComplementBase.h cComplementBaseTable.h consedParameters.h \
	 consedResources.h contig.h contigEnd.h \
	 contigMatchTablesType.h dictionary.h distribution.h \
	 experiment.h filename.h locatedFragment.h \
	 mbtPtrOrderedVector.h mbtPtrVector.h mbtValOrderedVectorOfRWCString.h \
	 mbtValVector.h mbtValVectorOfBool.h mbtValVector_inc.cpp \
	 mbt_exception.h mbt_val_ord_offset_vec.h min.h \
	 nMAX_QUALITY_LEVEL2.h ntide.h paddedFromUnpadded.h \
	 primerType.h quality.h readTypes.h \
	 readsSortedByLeftEndPosition.h readsSortedByReadName.h restrictionEnzyme.h \
	 rwbtreedictionary.h rwcstring.h rwcsubstring.h \
	 rwdefs.h rwtptrorderedvector.h rwtptrorderedvector_inc.cpp \
	 rwtptrsortedvector.h rwtptrvector.h rwtvalorderedvector.h \
	 rwtvalorderedvector_inc.cpp rwtvalsortedvector.h rwtvalvector.h \
	 sequence.h soEmptyString.h soGetErrno.h \
	 subcloneTTemplate.h sysdepend.h tag.h \
	 tracefile.h unpaddedFromPadded.h whatIsRunning.h \
	 wholeReadItem.cpp wholeReadItem.h

writeNewAceFileNameToFile.o : \
	 assemblyViewTagTypeAndLine.h assert.h bool.h \
	 consedParameters.h consedResources.h filename.h \
	 mbtPtrOrderedVector.h mbtValOrderedVectorOfRWCString.h mbt_exception.h \
	 restrictionEnzyme.h rwcstring.h rwcsubstring.h \
	 rwdefs.h rwtptrorderedvector.h rwtptrorderedvector_inc.cpp \
	 rwtvalorderedvector.h rwtvalorderedvector_inc.cpp soEmptyString.h \
	 soGetErrno.h sysdepend.h whatIsRunning.h \
	 writeNewAceFileNameToFile.cpp writeNewAceFileNameToFile.h

xsynchronize.o : \
	 assert.h bool.h filename.h \
	 guiapp.h guicolortext.h mbt_exception.h \
	 motifutils.h rwcstring.h rwcsubstring.h \
	 rwdefs.h rwtptrorderedvector.h rwtptrorderedvector_inc.cpp \
	 rwtvalorderedvector.h rwtvalorderedvector_inc.cpp soEmptyString.h \
	 soGetErrno.h sysdepend.h xsynchronize.cpp

checkLicenseKeyStub.o : \
	 checkLicenseKeyStub.cpp

checkLicenseKey.o : \
	 assert.h bool.h checkLicenseKey.cpp \
	 mbt_exception.h rwcregexp.h rwcstring.h \
	 rwcsubstring.h rwdefs.h soGetErrno.h \
	 uGetCRC_9_digits.h