#/***************************************************************************** ## 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. ## ##*****************************************************************************/ # # 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