/***************************************************************************** # 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. # #*****************************************************************************/ #ifndef consedResources_included #define consedResources_included #include "rwcstring.h" #include "bool.h" #include "filename.h" #define CONDEF consedResources::pDefaultResources_ class consedResources { public: static consedResources* pDefaultResources_; static consedResources* pEnvVariableResources_; static consedResources* pUsersHomeResources_; static consedResources* pCurrentDirectoryResources_; static consedResources* pCurrentResources_; static RWCString soConsedHome_; public: static void loadDefaultResources(); static void loadEnvVariableResources(); static void loadUsersHomeResources(); static void loadCurrentDirectoryResources(); static void getConsedResources(); static void parseResourceLine( consedResources* pRes, const RWCString& soResourceLine, const bool bAllowWhitespaceAndComments, const bool bAllowResourcesOtherThanConsed ); static void setConsedHome(); RWCString soGetResources(); void additionalChecksOnResources(); void translateCONSED_HOMEForAllResources(); void translateCONSED_HOMEForOneResource( RWCString& soResourceValue ); public: bool bShowProteinTranslation_; RWCString soColorHighlightBackground_; RWCString soColorHighlightForegroundX_; RWCString soColorMeansMatch_same_; RWCString soColorMeansMatch_different_; RWCString soColorMeansMatch_clippedEnds_; RWCString soColorMeansMatch_consensus_; RWCString soColorMeansMatch_lowQualConsensus_; RWCString soColorConsensusLabel_; RWCString soColorConsensusLabelBackground_; RWCString soColorMeansQualityAgree_; RWCString soColorMeansQualityDisagree_; RWCString soColorMeansQualityConsensusForeground_; RWCString soColorMeansQuality0_4_; RWCString soColorMeansQuality5_9_; RWCString soColorMeansQuality10_14_; RWCString soColorMeansQuality15_19_; RWCString soColorMeansQuality20_24_; RWCString soColorMeansQuality25_29_; RWCString soColorMeansQuality30_34_; RWCString soColorMeansQuality35_39_; RWCString soColorMeansQuality40_97_; RWCString soColorMeansQuality98_; RWCString soColorMeansQuality99_; RWCString soColorMeansEditedAgree_; RWCString soColorMeansEditedDisagree_; RWCString soColorMeansEditedUnedited_; RWCString soColorMeansEdited98_; RWCString soColorMeansEdited99_; RWCString soColorVerticalScrollbarScrolledDown_; RWCString soColorMode_editCursorForeground_; RWCString soColorMode_editCursorBackground_; RWCString soColorTracesA_; RWCString soColorTracesC_; RWCString soColorTracesG_; RWCString soColorTracesT_; RWCString soColorTracesN_; RWCString soColorTracesPad_; RWCString soColorScale_; RWCString soColorScaleBackground_; RWCString soColorHighlightedReadNames_; RWCString soColorSequencingDirectionArrow_; RWCString soColorSequencingDirectionArrowTracesUp_; RWCString soColorVerticalLineAtCursor_; RWCString soColorHorizontalLineAtCursor_; RWCString soColorProteinTranslation_; RWCString soColorProteinTranslationLabels_; RWCString soColorProteinStartCodon_; RWCString soColorProteinStopCodon_; RWCString soColorUnmatchedRestrictionFragment_; RWCString soColorRestrictionFragmentPairTooFarApart_; RWCString soColorRestrictionFragmentInContig_; RWCString soColorRestrictionFragmentPartlyOffContig_; RWCString soColorRestrictionFragmentEntirelyOffContig_; RWCString soColorActualGelRestrictionFragment_; RWCString soColorRestrictionDigestScale_; RWCString soColorRestrictionDigestCursorIndicator_; RWCString soColorRestrictionFragmentsOnTopOfEachOther_; RWCString soColorAssemblyViewScale_; RWCString soColorAssemblyViewScaleNumbers_; RWCString soColorAssemblyViewContigs_; RWCString soColorAssemblyViewContigNamesForeground_; RWCString soColorAssemblyViewContigNamesBackground_; RWCString soColorAssemblyViewConsistentFwdRevPairs_; RWCString soColorAssemblyViewConsistentFwdRevPairDepth_; RWCString soColorAssemblyViewReadDepth_; RWCString soColorAssemblyViewDiscrepanciesNotIndels_; RWCString soColorAssemblyViewDiscrepanciesIndels_; RWCString soColorAssemblyViewTooFewConsistentFwdRevPairs_; RWCString soColorAssemblyViewInconsistentFwdRevPair_; RWCString soColorAssemblyViewConsistentGapSpanningFwdRevPair_; RWCString soColorAssemblyViewHighlight_; RWCString soColorAssemblyViewMultipleItemsOnTopOfEachOther_; RWCString soColorAssemblyViewDirectSequenceMatches_; RWCString soColorAssemblyViewInvertedSequenceMatches_; RWCString soColorAssemblyViewConsistentRestrictionDigestFragment1_; RWCString soColorAssemblyViewConsistentRestrictionDigestFragment2_; RWCString soColorAssemblyViewConsistentRestrictionDigestFragment3_; RWCString soColorAssemblyViewConsistentRestrictionDigestFragment4_; RWCString soColorAssemblyViewConsistentRestrictionDigestFragment5_; RWCString soColorAssemblyViewConsistentRestrictionDigestFragment6_; RWCString soColorAssemblyViewConsistentRestrictionDigestFragment7_; RWCString soColorAssemblyViewConsistentRestrictionDigestFragment8_; RWCString soColorAssemblyViewConsistentRestrictionDigestFragment9_; RWCString soColorAssemblyViewConsistentRestrictionDigestFragment10_; RWCString soColorAssemblyViewInconsistentRestrictionDigestFragment_; RWCString soColorAssemblyViewCloneEnd_; RWCString soColorReadPrefixDefault_; RWCString soTagColorEdit_; RWCString soTagColorBecomeConsensus_; RWCString soTagColorIgnoreMismatches_; RWCString soTagColorIgnoreMatches_; RWCString soTagColorSignificantDiscrepancy_; RWCString soTagColorCompression_; RWCString soTagColorDataNeeded_; RWCString soTagColorComment_; RWCString soTagColorTagsOverlap_; RWCString soTagColorSequencingVector_; RWCString soTagColorCloningVector_; RWCString soTagColorVector_; RWCString soTagColorOligo_; RWCString soTagColorOligo3PrimeEnd_; RWCString soTagColorChimera_; RWCString soTagColorContigName_; RWCString soTagColorPolymorphism_; RWCString soTagColorHomozygoteAA_; RWCString soTagColorHomozygoteCC_; RWCString soTagColorHomozygoteGG_; RWCString soTagColorHomozygoteTT_; RWCString soTagColorHeterozygoteAC_; RWCString soTagColorHeterozygoteAG_; RWCString soTagColorHeterozygoteAT_; RWCString soTagColorHeterozygoteCG_; RWCString soTagColorHeterozygoteCT_; RWCString soTagColorHeterozygoteGT_; RWCString soTagColorRepeat_; RWCString soTagColorPolyPhredRank1_; RWCString soTagColorPolyPhredRank2_; RWCString soTagColorPolyPhredRank3_; RWCString soTagColorPolyPhredRank4_; RWCString soTagColorPolyPhredRank5_; RWCString soTagColorPolyPhredRank6_; RWCString soTagColorIndelSite_; RWCString soTagColorHeterozygoteIndel_; RWCString soTagColorHomozygoteIndel_; RWCString soTagColorPolymorphismConfirmed_; RWCString soTagColorMatchElsewhereHighQual_; RWCString soTagColorMatchElsewhereLowQual_; RWCString soTagColorG_dropout_; RWCString soTagColorMarkedHighQuality_; RWCString soTagColorMarkedLowQuality_; RWCString soTagColorAutoFinishExp_; RWCString soTagColorDoNotFinish_; RWCString soTagColorDoNotDoPCR_; RWCString soTagColorConsedFixedGoldenPath_; RWCString soTagColorCloneEnd_; RWCString soTagColorEditable_; RWCString soTagColorContigEndPair_; RWCString soTagColorChangedGenotype_; RWCString soTagColorStartNumberingConsensus_; RWCString soTagColorReferenceSequence_; RWCString soTagColorJoin_; RWCString soCustomTag1_; RWCString soTagColorCustomTag1_; RWCString soCustomTag2_; RWCString soTagColorCustomTag2_; RWCString soCustomTag3_; RWCString soTagColorCustomTag3_; RWCString soCustomTag4_; RWCString soTagColorCustomTag4_; RWCString soCustomTag5_; RWCString soTagColorCustomTag5_; RWCString soCustomTag6_; RWCString soTagColorCustomTag6_; RWCString soCustomTag7_; RWCString soTagColorCustomTag7_; RWCString soCustomTag8_; RWCString soTagColorCustomTag8_; RWCString soCustomTag9_; RWCString soTagColorCustomTag9_; RWCString soCustomTag10_; RWCString soTagColorCustomTag10_; RWCString soCustomTag11_; RWCString soTagColorCustomTag11_; RWCString soCustomTag12_; RWCString soTagColorCustomTag12_; RWCString soCustomTag13_; RWCString soTagColorCustomTag13_; RWCString soCustomTag14_; RWCString soTagColorCustomTag14_; RWCString soCustomTag15_; RWCString soTagColorCustomTag15_; RWCString soCustomConsensusTag1_; RWCString soTagColorCustomConsensusTag1_; RWCString soCustomConsensusTag2_; RWCString soTagColorCustomConsensusTag2_; RWCString soCustomConsensusTag3_; RWCString soTagColorCustomConsensusTag3_; RWCString soCustomConsensusTag4_; RWCString soTagColorCustomConsensusTag4_; RWCString soCustomConsensusTag5_; RWCString soTagColorCustomConsensusTag5_; RWCString soCustomConsensusTag6_; RWCString soTagColorCustomConsensusTag6_; RWCString soCustomConsensusTag7_; RWCString soTagColorCustomConsensusTag7_; RWCString soCustomConsensusTag8_; RWCString soTagColorCustomConsensusTag8_; RWCString soCustomConsensusTag9_; RWCString soTagColorCustomConsensusTag9_; RWCString soCustomConsensusTag10_; RWCString soTagColorCustomConsensusTag10_; RWCString soCustomConsensusTag11_; RWCString soTagColorCustomConsensusTag11_; RWCString soCustomConsensusTag12_; RWCString soTagColorCustomConsensusTag12_; RWCString soCustomConsensusTag13_; RWCString soTagColorCustomConsensusTag13_; RWCString soCustomConsensusTag14_; RWCString soTagColorCustomConsensusTag14_; RWCString soCustomConsensusTag15_; RWCString soTagColorCustomConsensusTag15_; bool bPrintPS_; RWCString soDefaultTagType_; bool bDefaultTagOnConsensusNotReads_; double dAutoFinishMinNumberOfErrorsFixedByAnExp_; double dAutoFinishRedundancy_; int nAutoFinishAverageInsertSize_; int nPrimersMaxInsertSizeOfASubclone_; int nPrimersMaxMeltingTemp_; int nPrimersMaxMeltingTempForPCR_; bool bPrimersPickTemplatesForPrimers_; RWCString soPrimersSubcloneFullPathnameOfFileOfSequencesForScreening_; RWCString soPrimersCloneFullPathnameOfFileOfSequencesForScreening_; int nPrimersMinMeltingTemp_; int nPrimersMinMeltingTempForPCR_; bool bSearchFunctionsUseUnalignedEndsOfReads_; bool bSearchFunctionsUseLowQualityEndsOfReads_; int nInexactSearchForStringMaxPerCentMismatch_; bool bOnlyAllowOneReadWriteConsedAtATime_; bool bAutoFinishAllowHighQualityDiscrepanciesInTemplateIfConsistentForwardReversePair_; RWCString soPrintWindowCommand_; FileName filFileOfTagTypes_; bool bAssemblyViewShowConsistentFwdRevPairs_; bool bAssemblyViewShowConsistentFwdRevPairDepth_; bool bAssemblyViewShowConsistentFwdRevPairsBetweenDifferentScaffolds_; bool bAssemblyViewShowLegsOnSquaresForConsistentFwdRevPairs_; bool bAssemblyViewShowGapSpanningFwdRevPairs_; RWCString soAssemblyViewShowWhichInconsistentFwdRevPairs_; bool bAssemblyViewShowReadDepth_; bool bAssemblyViewShowMultipleHighQualityDiscrepancies_; bool bAssemblyViewShowRestrictionDigestCutSites_; bool bAssemblyViewFilterSequenceMatchesBySize_; int nAssemblyViewSequenceMatchesMinSize_; int nAssemblyViewSequenceMatchesMaxSize_; bool bAssemblyViewAutomaticallyStartWithConsed_; RWCString soAssemblyViewDisplayTheseTagTypesOnTheseLines_; bool bAssemblyViewShowTags_; bool bAutoEditRecalculateHighQualitySegmentsOfReads_; bool bAutoEditConvertCloneEndBasesToXs_; bool bAutoEditTellPhrapNotToOverlapMultiplyDiscrepantReads_; bool bAutoEditTagEditableLowConsensusQualityRegions_; bool bAutoEditMakeFakeRead_; RWCString soAutoEditMakeFakeReadFromRead1_; RWCString soAutoEditMakeFakeReadFromRead2_; RWCString soAutoEditMakeFakeReadName_; FileName filAutoEditMakeFakeReadFastaFilename_; bool bAutoEditMergeAssembly_; FileName filAutoEditSecondaryAceFile_; bool bAutoEditFixRunsInConsensus_; bool bShowAllTracesJustShowGoodTraces_; int nAddAlignedSequenceQualityOfBases_; bool bMakeLightBackgroundInAlignedReadsWindowAndTracesWindow_; bool bPutVerticalLineAtCursor_; bool bPutHorizontalLineAtCursor_; FileName filHighlightedReadsFile_; bool bAutoReportPrintReadNamesInRegion_; RWCString soAutoReportPrintReadNamesInRegionContig_; int nAutoReportPrintReadNamesInRegionLeftPos_; int nAutoReportPrintReadNamesInRegionRightPos_; bool bAutoReportPrintHighlyDiscrepantRegions_; bool bAutoReportPrintScaffolds_; bool bNumberUnpaddedConsensusAtUserDefined_; bool bAutoReportPrintHighQualityDiscrepancies_; bool bAutoReportHighQualityDiscrepanciesExcludeCompressionOrG_dropoutTags_; bool bAutoReportHighQualityDiscrepanciesExcludeMostPads_; bool bAutoReportPrintLowConsensusQualityRegions_; bool bAutoReportPrintSingleSubcloneRegions_; bool bAutoReportPrintSingleStrandedRegions_; bool bAutoReportPrintLinkingForwardReversePairs_; bool bAutoReportPrintFilteredInconsistentForwardReversePairs_; bool bAutoReportPrintAssemblySummary_; RWCString soShowAllTracesDoNotShowTraceIfTheseTagsPresent_; bool bNameOfFakeJoiningReadsIncludesAceFileName_; int nWhenUserScrollsOffWindowMillisecondsBetweenScrolling_; int nWhenUserScrollsOffWindowBasesToScrollEachTime_; bool bCompareContigsUseBandedRatherThanFullSmithWaterman_; int nCompareContigsBandSize_; int nAssemblyViewShowFwdRevPairDepthsInRedIfOnlyThisMany_; bool bAssemblyViewShowSequenceMatches_; bool bAssemblyViewOKToShowSequenceMatchesBetweenContigs_; bool bAssemblyViewOKToShowSequenceMatchesWithinContigs_; bool bAssemblyViewOKToShowDirectSequenceMatches_; bool bAssemblyViewOKToShowInvertedSequenceMatches_; bool bAssemblyViewOnlyShowSequenceMatchesToAParticularRegion_; RWCString soAssemblyViewOnlyShowSequenceMatchesToThisContig_; int nAssemblyViewOnlyShowSequenceMatchesToThisRegionLeft_; int nAssemblyViewOnlyShowSequenceMatchesToThisRegionRight_; bool bAssemblyViewOnlyShowSequenceMatchesToEndsOfContigs_; int nAssemblyViewOnlyShowSequenceMatchesToEndsOfContigsThisFar_; RWCString soDefaultReadPrefix_; FileName filReadPrefixesFile_; int nMaxCharsDisplayedForReadPrefix_; int nAutoFinishDoNotDoPCRIfThisManyAvailableGapSpanningTemplates_; int nAutoFinishDoNotDoUnorientedPCRIfThisManyOrMoreUnorientedPCRReactions_; int nAutoFinishDoNotDoOrientedPCRIfGapSizeLargerThanThis_; bool bAutoFinishDoNotDoPCRIfEndIsExtendedByReads_; int nAutoFinishMaxAcceptableErrorsPerMegabase_; int nAutoFinishIfNotEnoughFwdRevPairsUseThisPerCentOfInsertSize_; int nPrimersNumberOfBasesToBackUpToStartLooking_; int nPrimersMakePCRPrimersThisManyBasesBackFromEndOfHighQualitySegment_; bool bPrimersOKToChoosePrimersInSingleSubcloneRegion_; bool bPrimersOKToChoosePrimersWhereHighQualityDiscrepancies_; bool bPrimersOKToChoosePrimersWhereUnalignedHighQualityRegion_; bool bAutoFinishCallReversesToFlankGaps_; bool bAutoFinishAllowWholeCloneReads_; bool bAutoFinishAllowCustomPrimerSubcloneReads_; bool bAutoFinishAllowResequencingReads_; bool bAutoFinishAllowResequencingReadsOnlyForRunsAndStops_; bool bAutoFinishAllowDeNovoUniversalPrimerSubcloneReads_; bool bAutoFinishAllowMinilibraries_; bool bAutoFinishAllowPCR_; bool bAutoFinishAllowUnorientedPCRReactions_; bool bAutoFinishAllowResequencingAUniversalPrimerAutofinishRead_; bool bAutoFinishAlwaysCloseGapsUsingMinilibraries_; int nAutoFinishMaximumFinishingReadLength_; int nAutoFinishSuggestMinilibraryIfGapThisManyBasesOrLarger_; bool bAutoFinishSuggestSpecialChemistryForRunsAndStops_; int nAutoFinishSuggestThisManyMinilibrariesPerGap_; int nPrimersWindowSizeInLooking_; bool bPrimersAssumeTemplatesAreDoubleStrandedUnlessSpecified_; int nAlignedReadsWindowInitialCharsWide_; int nAlignedReadsWindowInitialCharsHigh_; int nAlignedReadsWindowMaxCharsForReadNames_; bool bAlignedReadsWindowAutomaticallyExpandRoomForReadNames_; bool bAutoFinishAllowResequencingReadsToExtendContigs_; int nAutoFinishCallHowManyReversesToFlankGaps_; bool bAutoFinishCloseGaps_; bool bAutoFinishContinueEvenThoughReadInfoDoesNotMakeSense_; double dAutoFinishCostOfResequencingUniversalPrimerSubcloneReaction_; double dAutoFinishCostOfCustomPrimerSubcloneReaction_; double dAutoFinishCostOfCustomPrimerCloneReaction_; double dAutoFinishCostOfDeNovoUniversalPrimerSubcloneReaction_; double dAutoFinishCostOfMinilibrary_; bool bAutoFinishCoverSingleSubcloneRegions_; bool bAutoFinishCoverLowConsensusQualityRegions_; FileName filAutoFinishDebugUniversalPrimerReadsFile_; FileName filAutoFinishDebugCustomPrimerReadsFile_; int nAutoFinishDoNotAllowSubcloneCustomPrimerReadsCloserThanThisManyBases_; int nAutoFinishDoNotAllowWholeCloneCustomPrimerReadsCloserThanThisManyBases_; RWCString soAutoFinishDoNotFinishWhereTheseTagsAre_; RWCString soAutoFinishDoNotExtendContigsWhereTheseTagsAre_; int nAutoFinishDoNotExtendContigsIfTagsAreThisCloseToContigEnd_; FileName filDumpContigOrderAndOrientationInfoToThisFile_; bool bAutoFinishDumpTemplates_; int nAutoFinishExcludeContigIfOnlyThisManyReadsOrLess_; double dAutoFinishExcludeContigIfDepthOfCoverageGreaterThanThis_; int nAutoFinishExcludeContigIfThisManyBasesOrLess_; int nAutoFinishHowManyTemplatesYouIntendToUseForCustomPrimerSubcloneReactions_; int nPrimersMinNumberOfTemplatesForPrimers_; int nAutoFinishMinBaseOverlapBetweenAReadAndHighQualitySegmentOfConsensus_; int nAutoFinishNumberOfVectorBasesAtBeginningOfAUniveralPrimerRead_; bool bAutoFinishCDNANotGenomic_; int nAutoFinishConfidenceThatReadWillCoverSingleSubcloneRegion_; bool bAutoFinishPrintForwardOrReverseStrandWhenPrintingSubcloneTemplatesForCustomPrimerReads_; bool bAutoFinishPrintMinilibrariesSummaryFile_; bool bAutoFinishNearGapsSuggestEachMissingReadOfReadPairs_; int nAutoFinishDoNotIgnoreLCQIfThisManyBasesFromEndOfContigForLCQTagger_; bool bCheckIfTooManyWalks_; int nNumberOfColumnsBeforeReadNameInAlignedReadsWindow_; int nCompareContigsAlignsThisManyBasesMax_; RWCString soCompressedChromatExtension_; bool bDimLowQualityEndsOfReads_; bool bDimUnalignedEndsOfReads_; bool bFakeReadsSpecifiedByFilenameExtension_; FileName filFullPathnameOfAddReads2ConsedScript_; FileName filFullPathnameOfFixContigEndScript_; bool bFixContigEndsCleanUpTemporaryFiles_; int nFixContigEndsMinSmithWatermanScoreToMakeJoin_; int nFixContigEndsMinNumberOfReadsInContig_; FileName filFullPathnameOfCrossMatch_; FileName filFullPathnameOfPhred_; FileName filFullPathnameOfMiniassemblyScript_; RWCString soGunzipFullPath_; FileName filFullPathnameOfFilter454ReadsScript_; FileName filFilter454ReadsAgainstThis_; FileName fil454LinkerSequences_; bool bHideSomeTagTypesAtStartup_; int nMaximumNumberOfTracesShown_; bool bNavigateAutomaticTracePopup_; bool bNavigateAutomaticAllTracesPopup_; int nPrimersMinimumLengthOfAPrimer_; int nPrimersMaximumLengthOfAPrimer_; int nPrimersMinimumLengthOfAPrimerForPCR_; int nPrimersMaximumLengthOfAPrimerForPCR_; double dPrimersMaxMeltingTempDifferenceForPCR_; int nPrimersMaxPCRPrimerPairsToDisplay_; bool bPrimersCheckJustSomePCRPrimerPairsRatherThanAll_; int nPrimersNumberOfTemplatesToDisplayInFront_; int nPrimersMaxLengthOfMononucleotideRepeat_; FileName filPrimersBadLibrariesFile_; FileName filPrimersLibrariesInfoFile_; FileName filPrimersBadTemplatesFile_; bool bPrimersChooseTemplatesByPositionInsteadOfQuality_; int nPrimersWhenChoosingATemplateMinPotentialReadLength_; int nPrimersWindowSizeInLookingForPCR_; int nQualityThresholdForFindingHighQualityDiscrepancies_; int nQualityThresholdForNavigateByDepthOfCoverage_; bool bNavigateByHighDepthOfCoverageNotLow_; int nMinDepthForNavigateByDepthOfCoverage_; FileName filDefaultVectorPathnameForRestrictionFragments_; FileName filFileOfAdditionalRestrictionEnzymes_; RWCString soCommonRestrictionEnzymes_; RWCString soDefaultSelectedRestrictionEnzymes_; FileName filRestrictionEnzymesActualFragmentsFile_; int nRestrictionDigestInitialWindowSizeInTextRows_; int nRestrictionDigestDoNoShowAreaOfFragmentsOverThisSize_; bool bShowReadsAlphabetically_; bool bShowReadsInAlignedReadsWindowOrderedByFile_; FileName filShowReadsInAlignedReadsWindowOrderedByThisFile_; RWCString soShowReadsAtCursorSortedHow_; bool bShowABIBasesInTraceWindow_; int nTracesWindowInitialPixelHeight_; int nAssemblyViewWindowInitialPixelHeight_; FileName filAssemblyViewFileOfTemplatesToNotShow_; int nAssemblyViewCrossMatchMinmatch_; int nAssemblyViewCrossMatchMinscore_; FileName filAssemblyViewFindSequenceMatchesForConsedScript_; int nAssemblyViewCrossmatchMinmatch_; int nAssemblyViewCrossmatchMinscore_; int nAssemblyViewSequenceMatchesMinimumSimilarity_; int nTracesWindowInitialPixelWidth_; int nAssemblyViewWindowInitialPixelWidth_; bool bAutomaticallyScaleTraces_; double dAutomaticallyScaleTracesSamplePeakHeightFractionOfWindowHeight_; int nAutomaticallyScaleTracesSamplePeakPercentile_; int nVerticalTraceMagnification_; RWCString soUserDefinedKeys_; RWCString soProgramsForUserDefinedKeys_; RWCString soArgumentsToPassToUserDefinedPrograms_; RWCString soTagsToApplyWithUserDefinedKeys_; bool bSnpGenomeUseInsertionPolymorphisms_; RWCString soListOfTagTypesToHide_; RWCString soListOfOptionalWordsToSaveInListOfReadNames_; bool bExtendConsensusWithHighQuality_; bool bFastStartup_; FileName filFastStartupFile_; RWCString soAlwaysRunProgramToGetChromats_; FileName filProgramToRunToGetChromats_; FileName filProgramToRunToGetChromatsOf454Reads_; bool bCreateFakeChromatsForSolexaReads_; bool bAutoFinishUseLongModelReadRatherThanShort_; int nAskAgainIfWantToQuitConsedIfThisManyReads_; RWCString soPrintWindowInstructions_; bool bAllowMultipleSearchForStringWindows_; int nAutoPCRAmplifyFalseProductsOKIfLargerThanThis_; bool bAutoPCRAmplifyMakePrimerOutOfFirstRegion_; int nAutoPCRAmplifyMaybeRejectPrimerIfThisCloseToDesiredProduct_; bool bAddNewReadsRecalculateConsensusQuality_; RWCString soAddNewReadsPutReadIntoItsOwnContig_; bool bAddNewReadsCheckThatCrossMatchRunCorrectly_; int nAssemblyViewNumberOfRowsOfTags_; bool bWarnUserWhenTryingToEditAllReads_; FileName filMaybeXKEYSYMDBPath_; FileName filMaybeXKEYSYMDBPath2_; int nAmountToMoveWithBigLeftAndRightArrows_; int nNavigateByHighlyDiscrepantPositionsMinDiscrepantReads_; int nNavigateByHighlyDiscrepantPositionsMaxDepthOfCoverage_; int nNavigateByHighlyDiscrepantPositionsIgnoreBasesBelowThisQuality_; bool bNavigateByHighlyDiscrepantPositionsJustListIndels_; bool bNavigateByHighlyDiscrepantPositionsIgnoreOtherReadsStartingAtSameLocation_; bool bNavigateByHighlyDiscrepantPositionsIgnoreIfListedBasesInConsensus_; RWCString soNavigateByHighlyDiscrepantPositionsIgnoreIfTheseBasesInConsensus_; FileName filPhdBallDirectory_; FileName filNewAceFileFOF_; int nNavigateByHighOrLowDepthCoalesceRegionsIfThisClose_; bool bRemoveReadsDeleteNotJustPutInOwnContig_; RWCString soPaired454LeftReadExtension_; RWCString soPaired454RightReadExtension_; FileName filSnpGenome1MSnps_; bool bDiffChromosomesExcludeDeletions_; bool bSnpGenomeFilterByWeight_; int nWantReadsUpToThisFarFromSnps_; RWCString soPhaster2PhdBallSaveWhichMate_; bool bPhaster2PhdBallSaveInPhasterFormat_; bool bPhaster2PhdBallCalculateNewLocationsFile_; bool bPhdBall2FastaIgnoreLowQualityReads_; int nPhdBall2FastaLowestAverageQuality_; FileName filNextPhredPipelineControlFile_; FileName filNextPhredPipelineTiffPerlScript_; FileName filNextPhredPipelinePhasterPerlScript_; RWCString soNextPhredPipelineVersion_; RWCString soNextPhredPipelineMainDirectory_; int nMaxNumberOfReadsPerPhdBall_; FileName filUserWantsToSaveToThisAceFile_; bool bAutoFinishEmulate9_66Behavior_; int nPrimersPCRPrimersGroupedIntoWindowOfThisManyBases_; int nPrimersLookForThisManyPCRPrimerPairsPerPairOfGroups_; double dAutoFinishStandardDeviationsFromMeanFromGapToLookForTemplatesForSuggestingEachMissingReadOfReadPairs_; bool bAutoFinishCheckThatReadsFromTheSameTemplateAreConsistent_; bool bAutoFinishDoNotAllowSubcloneCustomPrimerReadsCloseTogether_; bool bAutoFinishDoNotAllowWholeCloneCustomPrimerReadsCloseTogether_; double dAutoFinishMinilibrariesPreferTemplateIfSizeThisManyStdDevsFromMean_; int nAutoFinishMinNumberOfForwardReversePairsInLibraryToCalculateAverageInsertSize_; double dAutoFinishIfEnoughFwdRevPairsUseThisManyStdDevBelowMeanForInsertSize_; int nAutoFinishNewCustomPrimerReadThisFarFromOldCustomPrimerRead_; int nAutoFinishMinNumberOfSingleSubcloneBasesFixedByAnExp_; int nAutoFinishNumberOfBasesBetweenContigsAssumed_; int nAutoFinishPotentialHighQualityPartOfReadStart_; int nAutoFinishPotentialHighQualityPartOfReadEnd_; bool bAutoFinishPrintCustomNavigationFileForChosenReads_; int nAutoFinishReversesForFlankingGapsTemplateMustProtrudeFromContigThisMuch_; bool bAutoFinishTagOligosWhenDoExperiments_; bool bCountPads_; int nDebugging_; int nDebugging2_; int nDebugging3_; RWCString soDebuggingString_; int nIgnoreHighQualityDiscrepanciesThisManyBasesFromEndOfAlignedRegion_; int nIgnoreUnalignedHighQualitySegmentsShorterThanThis_; int nPrimersLookThisFarForForwardVectorInsertJunction_; double dPrimersDNAConcentrationNanomolar_; int nPrimersMaxMatchElsewhereScore_; int nPrimersMaxMatchElsewhereScoreForPCR_; int nPrimersMaxSelfMatchScore_; int nPrimersMaxPrimerDimerScoreForPCR_; int nPrimersMinQuality_; bool bPrimersPrintInfoOnRejectedTemplates_; double dPrimersSaltConcentrationMillimolar_; bool bPrimersScreenForVector_; int nPrimersToleranceForDifferentBeginningLocationOfUniversalPrimerReads_; int nPrimersTooManyVectorBasesInWalkingRead_; int nQualityThresholdForLowConsensusQuality_; int nTagColorPerCentOfBase_; RWCString soUncompressedChromatDirectory_; FileName fil454sff2scfDirectory_; int nWhenMakingFakeReadToJoinContigsAddThisManyBasesOnEitherSideOfAlignedRegion_; int nWriteThisAceFormat_; bool bDumpCoreIfBoundsError_; int nAutoFinishMinSmithWatermanScoreOfARun_; double dAutoFinishDoNotComparePCRPrimersMoreThanThisManyTimes_; int nRestrictionDigestMaximumBasesToCompareToVector_; double dRestrictionDigestZoomFactor_; double dRestrictionDigestZoomFactorForNavigate_; int nRestrictionDigestToleranceInPositionUnits_; int nAutoPCRAmplifyTooManySeriousFalseMatches_; double dAssemblyViewZoomFactor_; int nAssemblyViewFilterInconsistentFwdRevPairsIfThisClose_; double dAssemblyViewGridCellWidthInPixels_; int nAssemblyViewCursorSensitivityInPixels_; int nAssemblyViewReadDepthQuality_; int nShowAllTracesMaxNumberOfTracesToShowAtOnce_; int nAllowFwdRevPairScaffoldsToBeMergedIfThisManyBasesIntersectionOrLess_; bool bJustForPrimateProject_; FileName filSolexaFilesAreAssumedToBeHere_; int nSolexaAlignmentFilesPerInsertingPadsCycle_; int nSolexaAlignmentsPerAlignmentFile_; bool bSolexaFastqFilesArePhredQualityNotSolexaQuality_; RWCString soSolexa64FastqOrSanger33Fastq_; int nMaximumReadsInReadList_; int nMaxLengthOfReadsInapLocatedFragment2_; int nMaximumStartupErrorsToReport_; int n454LinkerAlignmentMatchScore_; int n454LinkerAlignmentMismatchScore_; int n454LinkerAlignmentIndelScore_; bool bFilter454ReadsDeleteCrossMatchOutput_; int nAutoReportAllNeededSpeciesCode_; bool bAutoReportUseCommasInBigNumbers_; bool bAutoReportPrintToCompareToReich_; bool bAutoReportOnlyAllowSitesThatAreBetweenAcceptableSites_; bool bAutoReportDeaminationMutationsDeterminedByMoreAccurateMethod_; bool bAutoReportChooseTreesUsingBadData_; bool bAutoReportChooseTreesByCountingDeaminationMutations_; bool bAutoReportChooseTreesUsingKimura_; bool bAutoReportPrintCrudeChimpHumanMutations_; bool bAutoReportPrintPositionsForGraham_; bool bAutoReportPrintAncestralCpGs_; bool bAutoReportPrintCpGMutations_; bool bAutoReportPrintMutationsWithContext_; bool bAutoReportCountAllMutationsML_; bool bAutoReportCountAllMutations_; bool bAutoReportIgnoreMultipleTrees_; bool bAutoReportCountAcceptableColumnsWithNoneOnLeft_; bool bAutoReportPrintFlankedColumns4_; bool bAutoReportUseAnnotationFormat_; bool bAutoReportPrintFlankedColumns3_; bool bAutoReportPrintFlankedColumns2_; bool bAutoReportPrintFlankedColumns_; bool bAutoReportHighQualitySegmentData_; bool bAutoReportGoodReadsBug_; bool bAutoReportDiscrepancyRateInFlankedRegions_; bool bAutoReportDiscrepancyRateInFlankedRegions2_; bool bAutoReportDiscrepancyRateInFlankedRegions4_; bool bAutoReportDiscrepancyRateInFlankedRegions5_; bool bAutoReportSingleSignalOrQuality_; bool bAutoReportLowQualityBasesInHQS_; bool bAutoReportCompareHQSWithLQS_; bool bAutoReportCountColumnsForGroupsOfSpecies_; bool bAutoReportSingleSignalInfo_; bool bAutoReportSingleSignalInfo2_; bool bAutoReportCompareTopAndBottomStrands_; bool bAutoReportCompareTopAndBottomStrandsNoHuman_; bool bAutoReportCompareTopAndBottomStrands2_; bool bAutoReportCompareTopAndBottomStrands3_; bool bAutoReportCompareTopAndBottomStrands4_; int nAutoReportTopStrandPinnedPosition_; int nAutoReportBottomStrandPinnedPosition_; bool bAutoReportCompareTopAndBottomStrandsWithHuman_; bool bAutoReportPrintLengthsOfAlignedSegmentsOfReads_; bool bAutoReportPrintLengthsOfUnalignedHighQualitySegmentsOfReads_; bool bAutoReportPrintIfReadsAreCorrectlyAligned_; bool bAutoReportCalculateErrorProbabilitiesByComparingPTroPPan_; bool bAutoReportPrintAgreeDisagreeBetweenPairsOfSpecies_; bool bAutoReportPrintAgreeDisagreeBetweenPairsOfSpecies2_; bool bAutoReportFilterSingleSignal_; FileName filAutoReportGoodHitReads_; int nAutoReportQualityWindowLow_; int nAutoReportQualityWindowHigh_; bool bAutoReportPrintNumberOfIsolatedPadsForEachSpecies_; bool bAutoReportPrintNumberOfIsolatedPads_; RWCString soAutoReportIsolatedPadsOfReadsWithThisPattern_; int nAutoReportMinNumberOfPerfectlyAlignedBasesBeforeDiscrepancy_; int nAutoReportMaxSizeOfDiscrepantRegion_; int nAutoReportSizeOfDiscrepantRegion_; bool bAutoReportPrintMinimumQualityHistogram_; bool bAutoReportPrintDiscrepantRegions_; bool bAutoReportPrintBasesInDiscrepantRegions_; RWCString soAutoReportPrintDiscrepantRegionsButIgnoreReadsContainingThis_; RWCString soAutoReportBackboneReadHasThisStringInIt_; bool bAutoReportPrintDiscrepantRegionsButOnlyIfAboveQualityThreshold_; bool bAutoReportPrintSpeciesAlignment_; bool bAutoReportPrintReadAlignment_; FileName filAutoReportPrintTheseReads_; bool bAutoReportPrintReadPositions_; bool bAutoReportPrintChosenReadName_; int nAutoReportNumbersOfCharactersOfChosenReadNameToBePrinted_; RWCString soAutoReportPrefix_; bool bAutoReportUseOldCriteriaForDeletingColumnsOfPads_; bool bAutoReportDeleteColumnsOfPadsBeforeAdjustingReadQualityValues_; bool bAutoReportFlankingBasesMustBeSingleSignal_; int nAutoReportMinimumQualityOfFlankingBases_; bool bAutoReportFlankingBasesMustBeInHighQualitySegment_; RWCString soAutoReportSpecies_; }; #endif