/***************************************************************************** # 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. # #*****************************************************************************/ makeWidgetTypeBool( consed.printPS, PrintPS ); makeWidgetTypeRWCString( consed.defaultTagType, DefaultTagType ); makeWidgetTypeBool( consed.defaultTagOnConsensusNotReads, DefaultTagOnConsensusNotReads ); makeWidgetTypeDouble( consed.autoFinishMinNumberOfErrorsFixedByAnExp, AutoFinishMinNumberOfErrorsFixedByAnExp ); makeWidgetTypeDouble( consed.autoFinishRedundancy, AutoFinishRedundancy ); makeWidgetTypeInt( consed.autoFinishAverageInsertSize, AutoFinishAverageInsertSize ); makeWidgetTypeInt( consed.primersMaxInsertSizeOfASubclone, PrimersMaxInsertSizeOfASubclone ); makeWidgetTypeInt( consed.primersMaxMeltingTemp, PrimersMaxMeltingTemp ); makeWidgetTypeInt( consed.primersMaxMeltingTempForPCR, PrimersMaxMeltingTempForPCR ); makeWidgetTypeBool( consed.primersPickTemplatesForPrimers, PrimersPickTemplatesForPrimers ); makeWidgetTypeRWCString( consed.primersSubcloneFullPathnameOfFileOfSequencesForScreening, PrimersSubcloneFullPathnameOfFileOfSequencesForScreening ); makeWidgetTypeRWCString( consed.primersCloneFullPathnameOfFileOfSequencesForScreening, PrimersCloneFullPathnameOfFileOfSequencesForScreening ); makeWidgetTypeInt( consed.primersMinMeltingTemp, PrimersMinMeltingTemp ); makeWidgetTypeInt( consed.primersMinMeltingTempForPCR, PrimersMinMeltingTempForPCR ); makeWidgetTypeBool( consed.searchFunctionsUseUnalignedEndsOfReads, SearchFunctionsUseUnalignedEndsOfReads ); makeWidgetTypeBool( consed.searchFunctionsUseLowQualityEndsOfReads, SearchFunctionsUseLowQualityEndsOfReads ); makeWidgetTypeInt( consed.inexactSearchForStringMaxPerCentMismatch, InexactSearchForStringMaxPerCentMismatch ); makeWidgetTypeBool( consed.onlyAllowOneReadWriteConsedAtATime, OnlyAllowOneReadWriteConsedAtATime ); makeWidgetTypeBool( consed.autoFinishAllowHighQualityDiscrepanciesInTemplateIfConsistentForwardReversePair, AutoFinishAllowHighQualityDiscrepanciesInTemplateIfConsistentForwardReversePair ); makeWidgetTypeRWCString( consed.printWindowCommand, PrintWindowCommand ); makeWidgetTypeFileName( consed.fileOfTagTypes, FileOfTagTypes ); makeWidgetTypeBool( consed.assemblyViewShowConsistentFwdRevPairs, AssemblyViewShowConsistentFwdRevPairs ); makeWidgetTypeBool( consed.assemblyViewShowConsistentFwdRevPairDepth, AssemblyViewShowConsistentFwdRevPairDepth ); makeWidgetTypeBool( consed.assemblyViewShowConsistentFwdRevPairsBetweenDifferentScaffolds, AssemblyViewShowConsistentFwdRevPairsBetweenDifferentScaffolds ); makeWidgetTypeBool( consed.assemblyViewShowLegsOnSquaresForConsistentFwdRevPairs, AssemblyViewShowLegsOnSquaresForConsistentFwdRevPairs ); makeWidgetTypeBool( consed.assemblyViewShowGapSpanningFwdRevPairs, AssemblyViewShowGapSpanningFwdRevPairs ); makeWidgetTypeRWCString( consed.assemblyViewShowWhichInconsistentFwdRevPairs, AssemblyViewShowWhichInconsistentFwdRevPairs ); makeWidgetTypeBool( consed.assemblyViewShowReadDepth, AssemblyViewShowReadDepth ); makeWidgetTypeBool( consed.assemblyViewShowMultipleHighQualityDiscrepancies, AssemblyViewShowMultipleHighQualityDiscrepancies ); makeWidgetTypeBool( consed.assemblyViewShowRestrictionDigestCutSites, AssemblyViewShowRestrictionDigestCutSites ); makeWidgetTypeBool( consed.assemblyViewFilterSequenceMatchesBySize, AssemblyViewFilterSequenceMatchesBySize ); makeWidgetTypeInt( consed.assemblyViewSequenceMatchesMinSize, AssemblyViewSequenceMatchesMinSize ); makeWidgetTypeInt( consed.assemblyViewSequenceMatchesMaxSize, AssemblyViewSequenceMatchesMaxSize ); makeWidgetTypeBool( consed.assemblyViewAutomaticallyStartWithConsed, AssemblyViewAutomaticallyStartWithConsed ); makeWidgetTypeRWCString( consed.assemblyViewDisplayTheseTagTypesOnTheseLines, AssemblyViewDisplayTheseTagTypesOnTheseLines ); makeWidgetTypeBool( consed.assemblyViewShowTags, AssemblyViewShowTags ); makeWidgetTypeBool( consed.autoEditRecalculateHighQualitySegmentsOfReads, AutoEditRecalculateHighQualitySegmentsOfReads ); makeWidgetTypeBool( consed.autoEditConvertCloneEndBasesToXs, AutoEditConvertCloneEndBasesToXs ); makeWidgetTypeBool( consed.autoEditTellPhrapNotToOverlapMultiplyDiscrepantReads, AutoEditTellPhrapNotToOverlapMultiplyDiscrepantReads ); makeWidgetTypeBool( consed.autoEditTagEditableLowConsensusQualityRegions, AutoEditTagEditableLowConsensusQualityRegions ); makeWidgetTypeBool( consed.autoEditMakeFakeRead, AutoEditMakeFakeRead ); makeWidgetTypeRWCString( consed.autoEditMakeFakeReadFromRead1, AutoEditMakeFakeReadFromRead1 ); makeWidgetTypeRWCString( consed.autoEditMakeFakeReadFromRead2, AutoEditMakeFakeReadFromRead2 ); makeWidgetTypeRWCString( consed.autoEditMakeFakeReadName, AutoEditMakeFakeReadName ); makeWidgetTypeFileName( consed.autoEditMakeFakeReadFastaFilename, AutoEditMakeFakeReadFastaFilename ); makeWidgetTypeBool( consed.autoEditMergeAssembly, AutoEditMergeAssembly ); makeWidgetTypeFileName( consed.autoEditSecondaryAceFile, AutoEditSecondaryAceFile ); makeWidgetTypeBool( consed.autoEditFixRunsInConsensus, AutoEditFixRunsInConsensus ); makeWidgetTypeBool( consed.showAllTracesJustShowGoodTraces, ShowAllTracesJustShowGoodTraces ); makeWidgetTypeInt( consed.addAlignedSequenceQualityOfBases, AddAlignedSequenceQualityOfBases ); makeWidgetTypeBool( consed.makeLightBackgroundInAlignedReadsWindowAndTracesWindow, MakeLightBackgroundInAlignedReadsWindowAndTracesWindow ); makeWidgetTypeBool( consed.putVerticalLineAtCursor, PutVerticalLineAtCursor ); makeWidgetTypeBool( consed.putHorizontalLineAtCursor, PutHorizontalLineAtCursor ); makeWidgetTypeFileName( consed.highlightedReadsFile, HighlightedReadsFile ); makeWidgetTypeBool( consed.autoReportPrintReadNamesInRegion, AutoReportPrintReadNamesInRegion ); makeWidgetTypeRWCString( consed.autoReportPrintReadNamesInRegionContig, AutoReportPrintReadNamesInRegionContig ); makeWidgetTypeInt( consed.autoReportPrintReadNamesInRegionLeftPos, AutoReportPrintReadNamesInRegionLeftPos ); makeWidgetTypeInt( consed.autoReportPrintReadNamesInRegionRightPos, AutoReportPrintReadNamesInRegionRightPos ); makeWidgetTypeBool( consed.autoReportPrintHighlyDiscrepantRegions, AutoReportPrintHighlyDiscrepantRegions ); makeWidgetTypeBool( consed.autoReportPrintScaffolds, AutoReportPrintScaffolds ); makeWidgetTypeBool( consed.numberUnpaddedConsensusAtUserDefined, NumberUnpaddedConsensusAtUserDefined ); makeWidgetTypeBool( consed.autoReportPrintHighQualityDiscrepancies, AutoReportPrintHighQualityDiscrepancies ); makeWidgetTypeBool( consed.autoReportHighQualityDiscrepanciesExcludeCompressionOrG_dropoutTags, AutoReportHighQualityDiscrepanciesExcludeCompressionOrG_dropoutTags ); makeWidgetTypeBool( consed.autoReportHighQualityDiscrepanciesExcludeMostPads, AutoReportHighQualityDiscrepanciesExcludeMostPads ); makeWidgetTypeBool( consed.autoReportPrintLowConsensusQualityRegions, AutoReportPrintLowConsensusQualityRegions ); makeWidgetTypeBool( consed.autoReportPrintSingleSubcloneRegions, AutoReportPrintSingleSubcloneRegions ); makeWidgetTypeBool( consed.autoReportPrintSingleStrandedRegions, AutoReportPrintSingleStrandedRegions ); makeWidgetTypeBool( consed.autoReportPrintLinkingForwardReversePairs, AutoReportPrintLinkingForwardReversePairs ); makeWidgetTypeBool( consed.autoReportPrintFilteredInconsistentForwardReversePairs, AutoReportPrintFilteredInconsistentForwardReversePairs ); makeWidgetTypeBool( consed.autoReportPrintAssemblySummary, AutoReportPrintAssemblySummary ); makeWidgetTypeRWCString( consed.showAllTracesDoNotShowTraceIfTheseTagsPresent, ShowAllTracesDoNotShowTraceIfTheseTagsPresent ); makeWidgetTypeBool( consed.nameOfFakeJoiningReadsIncludesAceFileName, NameOfFakeJoiningReadsIncludesAceFileName ); makeWidgetTypeInt( consed.whenUserScrollsOffWindowMillisecondsBetweenScrolling, WhenUserScrollsOffWindowMillisecondsBetweenScrolling ); makeWidgetTypeInt( consed.whenUserScrollsOffWindowBasesToScrollEachTime, WhenUserScrollsOffWindowBasesToScrollEachTime ); makeWidgetTypeBool( consed.compareContigsUseBandedRatherThanFullSmithWaterman, CompareContigsUseBandedRatherThanFullSmithWaterman ); makeWidgetTypeInt( consed.compareContigsBandSize, CompareContigsBandSize ); makeWidgetTypeInt( consed.assemblyViewShowFwdRevPairDepthsInRedIfOnlyThisMany, AssemblyViewShowFwdRevPairDepthsInRedIfOnlyThisMany ); makeWidgetTypeBool( consed.assemblyViewShowSequenceMatches, AssemblyViewShowSequenceMatches ); makeWidgetTypeBool( consed.assemblyViewOKToShowSequenceMatchesBetweenContigs, AssemblyViewOKToShowSequenceMatchesBetweenContigs ); makeWidgetTypeBool( consed.assemblyViewOKToShowSequenceMatchesWithinContigs, AssemblyViewOKToShowSequenceMatchesWithinContigs ); makeWidgetTypeBool( consed.assemblyViewOKToShowDirectSequenceMatches, AssemblyViewOKToShowDirectSequenceMatches ); makeWidgetTypeBool( consed.assemblyViewOKToShowInvertedSequenceMatches, AssemblyViewOKToShowInvertedSequenceMatches ); makeWidgetTypeBool( consed.assemblyViewOnlyShowSequenceMatchesToAParticularRegion, AssemblyViewOnlyShowSequenceMatchesToAParticularRegion ); makeWidgetTypeRWCString( consed.assemblyViewOnlyShowSequenceMatchesToThisContig, AssemblyViewOnlyShowSequenceMatchesToThisContig ); makeWidgetTypeInt( consed.assemblyViewOnlyShowSequenceMatchesToThisRegionLeft, AssemblyViewOnlyShowSequenceMatchesToThisRegionLeft ); makeWidgetTypeInt( consed.assemblyViewOnlyShowSequenceMatchesToThisRegionRight, AssemblyViewOnlyShowSequenceMatchesToThisRegionRight ); makeWidgetTypeBool( consed.assemblyViewOnlyShowSequenceMatchesToEndsOfContigs, AssemblyViewOnlyShowSequenceMatchesToEndsOfContigs ); makeWidgetTypeInt( consed.assemblyViewOnlyShowSequenceMatchesToEndsOfContigsThisFar, AssemblyViewOnlyShowSequenceMatchesToEndsOfContigsThisFar ); makeWidgetTypeRWCString( consed.defaultReadPrefix, DefaultReadPrefix ); makeWidgetTypeFileName( consed.readPrefixesFile, ReadPrefixesFile ); makeWidgetTypeInt( consed.maxCharsDisplayedForReadPrefix, MaxCharsDisplayedForReadPrefix ); makeWidgetTypeInt( consed.autoFinishDoNotDoPCRIfThisManyAvailableGapSpanningTemplates, AutoFinishDoNotDoPCRIfThisManyAvailableGapSpanningTemplates ); makeWidgetTypeInt( consed.autoFinishDoNotDoUnorientedPCRIfThisManyOrMoreUnorientedPCRReactions, AutoFinishDoNotDoUnorientedPCRIfThisManyOrMoreUnorientedPCRReactions ); makeWidgetTypeInt( consed.autoFinishDoNotDoOrientedPCRIfGapSizeLargerThanThis, AutoFinishDoNotDoOrientedPCRIfGapSizeLargerThanThis ); makeWidgetTypeBool( consed.autoFinishDoNotDoPCRIfEndIsExtendedByReads, AutoFinishDoNotDoPCRIfEndIsExtendedByReads ); makeWidgetTypeInt( consed.autoFinishMaxAcceptableErrorsPerMegabase, AutoFinishMaxAcceptableErrorsPerMegabase ); makeWidgetTypeInt( consed.autoFinishIfNotEnoughFwdRevPairsUseThisPerCentOfInsertSize, AutoFinishIfNotEnoughFwdRevPairsUseThisPerCentOfInsertSize ); makeWidgetTypeInt( consed.primersNumberOfBasesToBackUpToStartLooking, PrimersNumberOfBasesToBackUpToStartLooking ); makeWidgetTypeInt( consed.primersMakePCRPrimersThisManyBasesBackFromEndOfHighQualitySegment, PrimersMakePCRPrimersThisManyBasesBackFromEndOfHighQualitySegment ); makeWidgetTypeBool( consed.primersOKToChoosePrimersInSingleSubcloneRegion, PrimersOKToChoosePrimersInSingleSubcloneRegion ); makeWidgetTypeBool( consed.primersOKToChoosePrimersWhereHighQualityDiscrepancies, PrimersOKToChoosePrimersWhereHighQualityDiscrepancies ); makeWidgetTypeBool( consed.primersOKToChoosePrimersWhereUnalignedHighQualityRegion, PrimersOKToChoosePrimersWhereUnalignedHighQualityRegion ); makeWidgetTypeBool( consed.autoFinishCallReversesToFlankGaps, AutoFinishCallReversesToFlankGaps ); makeWidgetTypeBool( consed.autoFinishAllowWholeCloneReads, AutoFinishAllowWholeCloneReads ); makeWidgetTypeBool( consed.autoFinishAllowCustomPrimerSubcloneReads, AutoFinishAllowCustomPrimerSubcloneReads ); makeWidgetTypeBool( consed.autoFinishAllowResequencingReads, AutoFinishAllowResequencingReads ); makeWidgetTypeBool( consed.autoFinishAllowResequencingReadsOnlyForRunsAndStops, AutoFinishAllowResequencingReadsOnlyForRunsAndStops ); makeWidgetTypeBool( consed.autoFinishAllowDeNovoUniversalPrimerSubcloneReads, AutoFinishAllowDeNovoUniversalPrimerSubcloneReads ); makeWidgetTypeBool( consed.autoFinishAllowMinilibraries, AutoFinishAllowMinilibraries ); makeWidgetTypeBool( consed.autoFinishAllowPCR, AutoFinishAllowPCR ); makeWidgetTypeBool( consed.autoFinishAllowUnorientedPCRReactions, AutoFinishAllowUnorientedPCRReactions ); makeWidgetTypeBool( consed.autoFinishAllowResequencingAUniversalPrimerAutofinishRead, AutoFinishAllowResequencingAUniversalPrimerAutofinishRead ); makeWidgetTypeBool( consed.autoFinishAlwaysCloseGapsUsingMinilibraries, AutoFinishAlwaysCloseGapsUsingMinilibraries ); makeWidgetTypeInt( consed.autoFinishMaximumFinishingReadLength, AutoFinishMaximumFinishingReadLength ); makeWidgetTypeInt( consed.autoFinishSuggestMinilibraryIfGapThisManyBasesOrLarger, AutoFinishSuggestMinilibraryIfGapThisManyBasesOrLarger ); makeWidgetTypeBool( consed.autoFinishSuggestSpecialChemistryForRunsAndStops, AutoFinishSuggestSpecialChemistryForRunsAndStops ); makeWidgetTypeInt( consed.autoFinishSuggestThisManyMinilibrariesPerGap, AutoFinishSuggestThisManyMinilibrariesPerGap ); makeWidgetTypeInt( consed.primersWindowSizeInLooking, PrimersWindowSizeInLooking ); makeWidgetTypeBool( consed.primersAssumeTemplatesAreDoubleStrandedUnlessSpecified, PrimersAssumeTemplatesAreDoubleStrandedUnlessSpecified ); makeWidgetTypeInt( consed.alignedReadsWindowInitialCharsWide, AlignedReadsWindowInitialCharsWide ); makeWidgetTypeInt( consed.alignedReadsWindowInitialCharsHigh, AlignedReadsWindowInitialCharsHigh ); makeWidgetTypeInt( consed.alignedReadsWindowMaxCharsForReadNames, AlignedReadsWindowMaxCharsForReadNames ); makeWidgetTypeBool( consed.alignedReadsWindowAutomaticallyExpandRoomForReadNames, AlignedReadsWindowAutomaticallyExpandRoomForReadNames ); makeWidgetTypeBool( consed.autoFinishAllowResequencingReadsToExtendContigs, AutoFinishAllowResequencingReadsToExtendContigs ); makeWidgetTypeInt( consed.autoFinishCallHowManyReversesToFlankGaps, AutoFinishCallHowManyReversesToFlankGaps ); makeWidgetTypeBool( consed.autoFinishCloseGaps, AutoFinishCloseGaps ); makeWidgetTypeBool( consed.autoFinishContinueEvenThoughReadInfoDoesNotMakeSense, AutoFinishContinueEvenThoughReadInfoDoesNotMakeSense ); makeWidgetTypeDouble( consed.autoFinishCostOfResequencingUniversalPrimerSubcloneReaction, AutoFinishCostOfResequencingUniversalPrimerSubcloneReaction ); makeWidgetTypeDouble( consed.autoFinishCostOfCustomPrimerSubcloneReaction, AutoFinishCostOfCustomPrimerSubcloneReaction ); makeWidgetTypeDouble( consed.autoFinishCostOfCustomPrimerCloneReaction, AutoFinishCostOfCustomPrimerCloneReaction ); makeWidgetTypeDouble( consed.autoFinishCostOfDeNovoUniversalPrimerSubcloneReaction, AutoFinishCostOfDeNovoUniversalPrimerSubcloneReaction ); makeWidgetTypeDouble( consed.autoFinishCostOfMinilibrary, AutoFinishCostOfMinilibrary ); makeWidgetTypeBool( consed.autoFinishCoverSingleSubcloneRegions, AutoFinishCoverSingleSubcloneRegions ); makeWidgetTypeBool( consed.autoFinishCoverLowConsensusQualityRegions, AutoFinishCoverLowConsensusQualityRegions ); makeWidgetTypeFileName( consed.autoFinishDebugUniversalPrimerReadsFile, AutoFinishDebugUniversalPrimerReadsFile ); makeWidgetTypeFileName( consed.autoFinishDebugCustomPrimerReadsFile, AutoFinishDebugCustomPrimerReadsFile ); makeWidgetTypeInt( consed.autoFinishDoNotAllowSubcloneCustomPrimerReadsCloserThanThisManyBases, AutoFinishDoNotAllowSubcloneCustomPrimerReadsCloserThanThisManyBases ); makeWidgetTypeInt( consed.autoFinishDoNotAllowWholeCloneCustomPrimerReadsCloserThanThisManyBases, AutoFinishDoNotAllowWholeCloneCustomPrimerReadsCloserThanThisManyBases ); makeWidgetTypeRWCString( consed.autoFinishDoNotFinishWhereTheseTagsAre, AutoFinishDoNotFinishWhereTheseTagsAre ); makeWidgetTypeRWCString( consed.autoFinishDoNotExtendContigsWhereTheseTagsAre, AutoFinishDoNotExtendContigsWhereTheseTagsAre ); makeWidgetTypeInt( consed.autoFinishDoNotExtendContigsIfTagsAreThisCloseToContigEnd, AutoFinishDoNotExtendContigsIfTagsAreThisCloseToContigEnd ); makeWidgetTypeFileName( consed.dumpContigOrderAndOrientationInfoToThisFile, DumpContigOrderAndOrientationInfoToThisFile ); makeWidgetTypeBool( consed.autoFinishDumpTemplates, AutoFinishDumpTemplates ); makeWidgetTypeInt( consed.autoFinishExcludeContigIfOnlyThisManyReadsOrLess, AutoFinishExcludeContigIfOnlyThisManyReadsOrLess ); makeWidgetTypeDouble( consed.autoFinishExcludeContigIfDepthOfCoverageGreaterThanThis, AutoFinishExcludeContigIfDepthOfCoverageGreaterThanThis ); makeWidgetTypeInt( consed.autoFinishExcludeContigIfThisManyBasesOrLess, AutoFinishExcludeContigIfThisManyBasesOrLess ); makeWidgetTypeInt( consed.autoFinishHowManyTemplatesYouIntendToUseForCustomPrimerSubcloneReactions, AutoFinishHowManyTemplatesYouIntendToUseForCustomPrimerSubcloneReactions ); makeWidgetTypeInt( consed.primersMinNumberOfTemplatesForPrimers, PrimersMinNumberOfTemplatesForPrimers ); makeWidgetTypeInt( consed.autoFinishMinBaseOverlapBetweenAReadAndHighQualitySegmentOfConsensus, AutoFinishMinBaseOverlapBetweenAReadAndHighQualitySegmentOfConsensus ); makeWidgetTypeInt( consed.autoFinishNumberOfVectorBasesAtBeginningOfAUniveralPrimerRead, AutoFinishNumberOfVectorBasesAtBeginningOfAUniveralPrimerRead ); makeWidgetTypeBool( consed.autoFinishCDNANotGenomic, AutoFinishCDNANotGenomic ); makeWidgetTypeInt( consed.autoFinishConfidenceThatReadWillCoverSingleSubcloneRegion, AutoFinishConfidenceThatReadWillCoverSingleSubcloneRegion ); makeWidgetTypeBool( consed.autoFinishPrintForwardOrReverseStrandWhenPrintingSubcloneTemplatesForCustomPrimerReads, AutoFinishPrintForwardOrReverseStrandWhenPrintingSubcloneTemplatesForCustomPrimerReads ); makeWidgetTypeBool( consed.autoFinishPrintMinilibrariesSummaryFile, AutoFinishPrintMinilibrariesSummaryFile ); makeWidgetTypeBool( consed.autoFinishNearGapsSuggestEachMissingReadOfReadPairs, AutoFinishNearGapsSuggestEachMissingReadOfReadPairs ); makeWidgetTypeInt( consed.autoFinishDoNotIgnoreLCQIfThisManyBasesFromEndOfContigForLCQTagger, AutoFinishDoNotIgnoreLCQIfThisManyBasesFromEndOfContigForLCQTagger ); makeWidgetTypeBool( consed.checkIfTooManyWalks, CheckIfTooManyWalks ); makeWidgetTypeInt( consed.numberOfColumnsBeforeReadNameInAlignedReadsWindow, NumberOfColumnsBeforeReadNameInAlignedReadsWindow ); makeWidgetTypeInt( consed.compareContigsAlignsThisManyBasesMax, CompareContigsAlignsThisManyBasesMax ); makeWidgetTypeRWCString( consed.compressedChromatExtension, CompressedChromatExtension ); makeWidgetTypeBool( consed.dimLowQualityEndsOfReads, DimLowQualityEndsOfReads ); makeWidgetTypeBool( consed.dimUnalignedEndsOfReads, DimUnalignedEndsOfReads ); makeWidgetTypeBool( consed.fakeReadsSpecifiedByFilenameExtension, FakeReadsSpecifiedByFilenameExtension ); makeWidgetTypeFileName( consed.fullPathnameOfAddReads2ConsedScript, FullPathnameOfAddReads2ConsedScript ); makeWidgetTypeFileName( consed.fullPathnameOfFixContigEndScript, FullPathnameOfFixContigEndScript ); makeWidgetTypeBool( consed.fixContigEndsCleanUpTemporaryFiles, FixContigEndsCleanUpTemporaryFiles ); makeWidgetTypeInt( consed.fixContigEndsMinSmithWatermanScoreToMakeJoin, FixContigEndsMinSmithWatermanScoreToMakeJoin ); makeWidgetTypeInt( consed.fixContigEndsMinNumberOfReadsInContig, FixContigEndsMinNumberOfReadsInContig ); makeWidgetTypeFileName( consed.fullPathnameOfCrossMatch, FullPathnameOfCrossMatch ); makeWidgetTypeFileName( consed.fullPathnameOfPhred, FullPathnameOfPhred ); makeWidgetTypeFileName( consed.fullPathnameOfMiniassemblyScript, FullPathnameOfMiniassemblyScript ); makeWidgetTypeRWCString( consed.gunzipFullPath, GunzipFullPath ); makeWidgetTypeFileName( consed.fullPathnameOfFilter454ReadsScript, FullPathnameOfFilter454ReadsScript ); makeWidgetTypeFileName( consed.filter454ReadsAgainstThis, Filter454ReadsAgainstThis ); makeWidgetTypeFileName( consed.454LinkerSequences, 454LinkerSequences ); makeWidgetTypeBool( consed.hideSomeTagTypesAtStartup, HideSomeTagTypesAtStartup ); makeWidgetTypeInt( consed.maximumNumberOfTracesShown, MaximumNumberOfTracesShown ); makeWidgetTypeBool( consed.navigateAutomaticTracePopup, NavigateAutomaticTracePopup ); makeWidgetTypeBool( consed.navigateAutomaticAllTracesPopup, NavigateAutomaticAllTracesPopup ); makeWidgetTypeInt( consed.primersMinimumLengthOfAPrimer, PrimersMinimumLengthOfAPrimer ); makeWidgetTypeInt( consed.primersMaximumLengthOfAPrimer, PrimersMaximumLengthOfAPrimer ); makeWidgetTypeInt( consed.primersMinimumLengthOfAPrimerForPCR, PrimersMinimumLengthOfAPrimerForPCR ); makeWidgetTypeInt( consed.primersMaximumLengthOfAPrimerForPCR, PrimersMaximumLengthOfAPrimerForPCR ); makeWidgetTypeDouble( consed.primersMaxMeltingTempDifferenceForPCR, PrimersMaxMeltingTempDifferenceForPCR ); makeWidgetTypeInt( consed.primersMaxPCRPrimerPairsToDisplay, PrimersMaxPCRPrimerPairsToDisplay ); makeWidgetTypeBool( consed.primersCheckJustSomePCRPrimerPairsRatherThanAll, PrimersCheckJustSomePCRPrimerPairsRatherThanAll ); makeWidgetTypeInt( consed.primersNumberOfTemplatesToDisplayInFront, PrimersNumberOfTemplatesToDisplayInFront ); makeWidgetTypeInt( consed.primersMaxLengthOfMononucleotideRepeat, PrimersMaxLengthOfMononucleotideRepeat ); makeWidgetTypeFileName( consed.primersBadLibrariesFile, PrimersBadLibrariesFile ); makeWidgetTypeFileName( consed.primersLibrariesInfoFile, PrimersLibrariesInfoFile ); makeWidgetTypeFileName( consed.primersBadTemplatesFile, PrimersBadTemplatesFile ); makeWidgetTypeBool( consed.primersChooseTemplatesByPositionInsteadOfQuality, PrimersChooseTemplatesByPositionInsteadOfQuality ); makeWidgetTypeInt( consed.primersWhenChoosingATemplateMinPotentialReadLength, PrimersWhenChoosingATemplateMinPotentialReadLength ); makeWidgetTypeInt( consed.primersWindowSizeInLookingForPCR, PrimersWindowSizeInLookingForPCR ); makeWidgetTypeInt( consed.qualityThresholdForFindingHighQualityDiscrepancies, QualityThresholdForFindingHighQualityDiscrepancies ); makeWidgetTypeInt( consed.qualityThresholdForNavigateByDepthOfCoverage, QualityThresholdForNavigateByDepthOfCoverage ); makeWidgetTypeBool( consed.navigateByHighDepthOfCoverageNotLow, NavigateByHighDepthOfCoverageNotLow ); makeWidgetTypeInt( consed.MinDepthForNavigateByDepthOfCoverage, MinDepthForNavigateByDepthOfCoverage ); makeWidgetTypeFileName( consed.defaultVectorPathnameForRestrictionFragments, DefaultVectorPathnameForRestrictionFragments ); makeWidgetTypeFileName( consed.fileOfAdditionalRestrictionEnzymes, FileOfAdditionalRestrictionEnzymes ); makeWidgetTypeRWCString( consed.commonRestrictionEnzymes, CommonRestrictionEnzymes ); makeWidgetTypeRWCString( consed.defaultSelectedRestrictionEnzymes, DefaultSelectedRestrictionEnzymes ); makeWidgetTypeFileName( consed.restrictionEnzymesActualFragmentsFile, RestrictionEnzymesActualFragmentsFile ); makeWidgetTypeInt( consed.restrictionDigestInitialWindowSizeInTextRows, RestrictionDigestInitialWindowSizeInTextRows ); makeWidgetTypeInt( consed.restrictionDigestDoNoShowAreaOfFragmentsOverThisSize, RestrictionDigestDoNoShowAreaOfFragmentsOverThisSize ); makeWidgetTypeBool( consed.showReadsAlphabetically, ShowReadsAlphabetically ); makeWidgetTypeBool( consed.showReadsInAlignedReadsWindowOrderedByFile, ShowReadsInAlignedReadsWindowOrderedByFile ); makeWidgetTypeFileName( consed.showReadsInAlignedReadsWindowOrderedByThisFile, ShowReadsInAlignedReadsWindowOrderedByThisFile ); makeWidgetTypeRWCString( consed.showReadsAtCursorSortedHow, ShowReadsAtCursorSortedHow ); makeWidgetTypeBool( consed.showABIBasesInTraceWindow, ShowABIBasesInTraceWindow ); makeWidgetTypeInt( consed.tracesWindowInitialPixelHeight, TracesWindowInitialPixelHeight ); makeWidgetTypeInt( consed.assemblyViewWindowInitialPixelHeight, AssemblyViewWindowInitialPixelHeight ); makeWidgetTypeFileName( consed.assemblyViewFileOfTemplatesToNotShow, AssemblyViewFileOfTemplatesToNotShow ); makeWidgetTypeInt( consed.assemblyViewCrossMatchMinmatch, AssemblyViewCrossMatchMinmatch ); makeWidgetTypeInt( consed.assemblyViewCrossMatchMinscore, AssemblyViewCrossMatchMinscore ); makeWidgetTypeFileName( consed.assemblyViewFindSequenceMatchesForConsedScript, AssemblyViewFindSequenceMatchesForConsedScript ); makeWidgetTypeInt( consed.assemblyViewCrossmatchMinmatch, AssemblyViewCrossmatchMinmatch ); makeWidgetTypeInt( consed.assemblyViewCrossmatchMinscore, AssemblyViewCrossmatchMinscore ); makeWidgetTypeInt( consed.assemblyViewSequenceMatchesMinimumSimilarity, AssemblyViewSequenceMatchesMinimumSimilarity ); makeWidgetTypeInt( consed.tracesWindowInitialPixelWidth, TracesWindowInitialPixelWidth ); makeWidgetTypeInt( consed.assemblyViewWindowInitialPixelWidth, AssemblyViewWindowInitialPixelWidth ); makeWidgetTypeBool( consed.automaticallyScaleTraces, AutomaticallyScaleTraces ); makeWidgetTypeDouble( consed.automaticallyScaleTracesSamplePeakHeightFractionOfWindowHeight, AutomaticallyScaleTracesSamplePeakHeightFractionOfWindowHeight ); makeWidgetTypeInt( consed.automaticallyScaleTracesSamplePeakPercentile, AutomaticallyScaleTracesSamplePeakPercentile ); makeWidgetTypeInt( consed.verticalTraceMagnification, VerticalTraceMagnification ); makeWidgetTypeRWCString( consed.userDefinedKeys, UserDefinedKeys ); makeWidgetTypeRWCString( consed.programsForUserDefinedKeys, ProgramsForUserDefinedKeys ); makeWidgetTypeRWCString( consed.argumentsToPassToUserDefinedPrograms, ArgumentsToPassToUserDefinedPrograms ); makeWidgetTypeRWCString( consed.tagsToApplyWithUserDefinedKeys, TagsToApplyWithUserDefinedKeys ); makeWidgetTypeBool( consed.snpGenomeUseInsertionPolymorphisms, SnpGenomeUseInsertionPolymorphisms ); makeWidgetTypeRWCString( consed.listOfTagTypesToHide, ListOfTagTypesToHide ); makeWidgetTypeRWCString( consed.listOfOptionalWordsToSaveInListOfReadNames, ListOfOptionalWordsToSaveInListOfReadNames ); makeWidgetTypeBool( consed.extendConsensusWithHighQuality, ExtendConsensusWithHighQuality ); makeWidgetTypeBool( consed.fastStartup, FastStartup ); makeWidgetTypeFileName( consed.fastStartupFile, FastStartupFile ); makeWidgetTypeRWCString( consed.alwaysRunProgramToGetChromats, AlwaysRunProgramToGetChromats ); makeWidgetTypeFileName( consed.programToRunToGetChromats, ProgramToRunToGetChromats ); makeWidgetTypeFileName( consed.programToRunToGetChromatsOf454Reads, ProgramToRunToGetChromatsOf454Reads ); makeWidgetTypeBool( consed.createFakeChromatsForSolexaReads, CreateFakeChromatsForSolexaReads ); makeWidgetTypeBool( consed.autoFinishUseLongModelReadRatherThanShort, AutoFinishUseLongModelReadRatherThanShort ); makeWidgetTypeInt( consed.askAgainIfWantToQuitConsedIfThisManyReads, AskAgainIfWantToQuitConsedIfThisManyReads ); makeWidgetTypeRWCString( consed.printWindowInstructions, PrintWindowInstructions ); makeWidgetTypeBool( consed.allowMultipleSearchForStringWindows, AllowMultipleSearchForStringWindows ); makeWidgetTypeInt( consed.autoPCRAmplifyFalseProductsOKIfLargerThanThis, AutoPCRAmplifyFalseProductsOKIfLargerThanThis ); makeWidgetTypeBool( consed.autoPCRAmplifyMakePrimerOutOfFirstRegion, AutoPCRAmplifyMakePrimerOutOfFirstRegion ); makeWidgetTypeInt( consed.autoPCRAmplifyMaybeRejectPrimerIfThisCloseToDesiredProduct, AutoPCRAmplifyMaybeRejectPrimerIfThisCloseToDesiredProduct ); makeWidgetTypeBool( consed.addNewReadsRecalculateConsensusQuality, AddNewReadsRecalculateConsensusQuality ); makeWidgetTypeRWCString( consed.addNewReadsPutReadIntoItsOwnContig, AddNewReadsPutReadIntoItsOwnContig ); makeWidgetTypeBool( consed.addNewReadsCheckThatCrossMatchRunCorrectly, AddNewReadsCheckThatCrossMatchRunCorrectly ); makeWidgetTypeInt( consed.assemblyViewNumberOfRowsOfTags, AssemblyViewNumberOfRowsOfTags ); makeWidgetTypeBool( consed.warnUserWhenTryingToEditAllReads, WarnUserWhenTryingToEditAllReads ); makeWidgetTypeFileName( consed.maybeXKEYSYMDBPath, MaybeXKEYSYMDBPath ); makeWidgetTypeFileName( consed.maybeXKEYSYMDBPath2, MaybeXKEYSYMDBPath2 ); makeWidgetTypeInt( consed.amountToMoveWithBigLeftAndRightArrows, AmountToMoveWithBigLeftAndRightArrows ); makeWidgetTypeInt( consed.navigateByHighlyDiscrepantPositionsMinDiscrepantReads, NavigateByHighlyDiscrepantPositionsMinDiscrepantReads ); makeWidgetTypeInt( consed.navigateByHighlyDiscrepantPositionsMaxDepthOfCoverage, NavigateByHighlyDiscrepantPositionsMaxDepthOfCoverage ); makeWidgetTypeInt( consed.navigateByHighlyDiscrepantPositionsIgnoreBasesBelowThisQuality, NavigateByHighlyDiscrepantPositionsIgnoreBasesBelowThisQuality ); makeWidgetTypeBool( consed.navigateByHighlyDiscrepantPositionsJustListIndels, NavigateByHighlyDiscrepantPositionsJustListIndels ); makeWidgetTypeBool( consed.navigateByHighlyDiscrepantPositionsIgnoreOtherReadsStartingAtSameLocation, NavigateByHighlyDiscrepantPositionsIgnoreOtherReadsStartingAtSameLocation ); makeWidgetTypeBool( consed.navigateByHighlyDiscrepantPositionsIgnoreIfListedBasesInConsensus, NavigateByHighlyDiscrepantPositionsIgnoreIfListedBasesInConsensus ); makeWidgetTypeRWCString( consed.navigateByHighlyDiscrepantPositionsIgnoreIfTheseBasesInConsensus, NavigateByHighlyDiscrepantPositionsIgnoreIfTheseBasesInConsensus ); makeWidgetTypeFileName( consed.phdBallDirectory, PhdBallDirectory ); makeWidgetTypeFileName( consed.newAceFileFOF, NewAceFileFOF ); makeWidgetTypeInt( consed.navigateByHighOrLowDepthCoalesceRegionsIfThisClose, NavigateByHighOrLowDepthCoalesceRegionsIfThisClose ); makeWidgetTypeBool( consed.removeReadsDeleteNotJustPutInOwnContig, RemoveReadsDeleteNotJustPutInOwnContig ); makeWidgetTypeRWCString( consed.paired454LeftReadExtension, Paired454LeftReadExtension ); makeWidgetTypeRWCString( consed.paired454RightReadExtension, Paired454RightReadExtension ); makeWidgetTypeFileName( consed.snpGenome1MSnps, SnpGenome1MSnps ); makeWidgetTypeBool( consed.diffChromosomesExcludeDeletions, DiffChromosomesExcludeDeletions ); makeWidgetTypeBool( consed.snpGenomeFilterByWeight, SnpGenomeFilterByWeight ); makeWidgetTypeInt( consed.wantReadsUpToThisFarFromSnps, WantReadsUpToThisFarFromSnps ); makeWidgetTypeRWCString( consed.phaster2PhdBallSaveWhichMate, Phaster2PhdBallSaveWhichMate ); makeWidgetTypeBool( consed.phaster2PhdBallSaveInPhasterFormat, Phaster2PhdBallSaveInPhasterFormat ); makeWidgetTypeBool( consed.phaster2PhdBallCalculateNewLocationsFile, Phaster2PhdBallCalculateNewLocationsFile ); makeWidgetTypeBool( consed.phdBall2FastaIgnoreLowQualityReads, PhdBall2FastaIgnoreLowQualityReads ); makeWidgetTypeInt( consed.phdBall2FastaLowestAverageQuality, PhdBall2FastaLowestAverageQuality ); makeWidgetTypeFileName( consed.nextPhredPipelineControlFile, NextPhredPipelineControlFile ); makeWidgetTypeFileName( consed.nextPhredPipelineTiffPerlScript, NextPhredPipelineTiffPerlScript ); makeWidgetTypeFileName( consed.nextPhredPipelinePhasterPerlScript, NextPhredPipelinePhasterPerlScript ); makeWidgetTypeRWCString( consed.nextPhredPipelineVersion, NextPhredPipelineVersion ); makeWidgetTypeRWCString( consed.nextPhredPipelineMainDirectory, NextPhredPipelineMainDirectory ); makeWidgetTypeInt( consed.maxNumberOfReadsPerPhdBall, MaxNumberOfReadsPerPhdBall ); makeWidgetTypeFileName( consed.userWantsToSaveToThisAceFile, UserWantsToSaveToThisAceFile ); makeWidgetTypeBool( consed.autoFinishEmulate9_66Behavior, AutoFinishEmulate9_66Behavior ); makeWidgetTypeInt( consed.primersPCRPrimersGroupedIntoWindowOfThisManyBases, PrimersPCRPrimersGroupedIntoWindowOfThisManyBases ); makeWidgetTypeInt( consed.primersLookForThisManyPCRPrimerPairsPerPairOfGroups, PrimersLookForThisManyPCRPrimerPairsPerPairOfGroups ); makeWidgetTypeDouble( consed.autoFinishStandardDeviationsFromMeanFromGapToLookForTemplatesForSuggestingEachMissingReadOfReadPairs, AutoFinishStandardDeviationsFromMeanFromGapToLookForTemplatesForSuggestingEachMissingReadOfReadPairs ); makeWidgetTypeBool( consed.autoFinishCheckThatReadsFromTheSameTemplateAreConsistent, AutoFinishCheckThatReadsFromTheSameTemplateAreConsistent ); makeWidgetTypeBool( consed.autoFinishDoNotAllowSubcloneCustomPrimerReadsCloseTogether, AutoFinishDoNotAllowSubcloneCustomPrimerReadsCloseTogether ); makeWidgetTypeBool( consed.autoFinishDoNotAllowWholeCloneCustomPrimerReadsCloseTogether, AutoFinishDoNotAllowWholeCloneCustomPrimerReadsCloseTogether ); makeWidgetTypeDouble( consed.autoFinishMinilibrariesPreferTemplateIfSizeThisManyStdDevsFromMean, AutoFinishMinilibrariesPreferTemplateIfSizeThisManyStdDevsFromMean ); makeWidgetTypeInt( consed.autoFinishMinNumberOfForwardReversePairsInLibraryToCalculateAverageInsertSize, AutoFinishMinNumberOfForwardReversePairsInLibraryToCalculateAverageInsertSize ); makeWidgetTypeDouble( consed.autoFinishIfEnoughFwdRevPairsUseThisManyStdDevBelowMeanForInsertSize, AutoFinishIfEnoughFwdRevPairsUseThisManyStdDevBelowMeanForInsertSize ); makeWidgetTypeInt( consed.autoFinishNewCustomPrimerReadThisFarFromOldCustomPrimerRead, AutoFinishNewCustomPrimerReadThisFarFromOldCustomPrimerRead ); makeWidgetTypeInt( consed.autoFinishMinNumberOfSingleSubcloneBasesFixedByAnExp, AutoFinishMinNumberOfSingleSubcloneBasesFixedByAnExp ); makeWidgetTypeInt( consed.autoFinishNumberOfBasesBetweenContigsAssumed, AutoFinishNumberOfBasesBetweenContigsAssumed ); makeWidgetTypeInt( consed.autoFinishPotentialHighQualityPartOfReadStart, AutoFinishPotentialHighQualityPartOfReadStart ); makeWidgetTypeInt( consed.autoFinishPotentialHighQualityPartOfReadEnd, AutoFinishPotentialHighQualityPartOfReadEnd ); makeWidgetTypeBool( consed.autoFinishPrintCustomNavigationFileForChosenReads, AutoFinishPrintCustomNavigationFileForChosenReads ); makeWidgetTypeInt( consed.autoFinishReversesForFlankingGapsTemplateMustProtrudeFromContigThisMuch, AutoFinishReversesForFlankingGapsTemplateMustProtrudeFromContigThisMuch ); makeWidgetTypeBool( consed.autoFinishTagOligosWhenDoExperiments, AutoFinishTagOligosWhenDoExperiments ); makeWidgetTypeBool( consed.countPads, CountPads ); makeWidgetTypeInt( consed.debugging, Debugging ); makeWidgetTypeInt( consed.debugging2, Debugging2 ); makeWidgetTypeInt( consed.debugging3, Debugging3 ); makeWidgetTypeRWCString( consed.debuggingString, DebuggingString ); makeWidgetTypeInt( consed.ignoreHighQualityDiscrepanciesThisManyBasesFromEndOfAlignedRegion, IgnoreHighQualityDiscrepanciesThisManyBasesFromEndOfAlignedRegion ); makeWidgetTypeInt( consed.ignoreUnalignedHighQualitySegmentsShorterThanThis, IgnoreUnalignedHighQualitySegmentsShorterThanThis ); makeWidgetTypeInt( consed.primersLookThisFarForForwardVectorInsertJunction, PrimersLookThisFarForForwardVectorInsertJunction ); makeWidgetTypeDouble( consed.primersDNAConcentrationNanomolar, PrimersDNAConcentrationNanomolar ); makeWidgetTypeInt( consed.primersMaxMatchElsewhereScore, PrimersMaxMatchElsewhereScore ); makeWidgetTypeInt( consed.primersMaxMatchElsewhereScoreForPCR, PrimersMaxMatchElsewhereScoreForPCR ); makeWidgetTypeInt( consed.primersMaxSelfMatchScore, PrimersMaxSelfMatchScore ); makeWidgetTypeInt( consed.primersMaxPrimerDimerScoreForPCR, PrimersMaxPrimerDimerScoreForPCR ); makeWidgetTypeInt( consed.primersMinQuality, PrimersMinQuality ); makeWidgetTypeBool( consed.primersPrintInfoOnRejectedTemplates, PrimersPrintInfoOnRejectedTemplates ); makeWidgetTypeDouble( consed.primersSaltConcentrationMillimolar, PrimersSaltConcentrationMillimolar ); makeWidgetTypeBool( consed.primersScreenForVector, PrimersScreenForVector ); makeWidgetTypeInt( consed.primersToleranceForDifferentBeginningLocationOfUniversalPrimerReads, PrimersToleranceForDifferentBeginningLocationOfUniversalPrimerReads ); makeWidgetTypeInt( consed.primersTooManyVectorBasesInWalkingRead, PrimersTooManyVectorBasesInWalkingRead ); makeWidgetTypeInt( consed.qualityThresholdForLowConsensusQuality, QualityThresholdForLowConsensusQuality ); makeWidgetTypeInt( consed.tagColorPerCentOfBase, TagColorPerCentOfBase ); makeWidgetTypeRWCString( consed.uncompressedChromatDirectory, UncompressedChromatDirectory ); makeWidgetTypeFileName( consed.454sff2scfDirectory, 454sff2scfDirectory ); makeWidgetTypeInt( consed.whenMakingFakeReadToJoinContigsAddThisManyBasesOnEitherSideOfAlignedRegion, WhenMakingFakeReadToJoinContigsAddThisManyBasesOnEitherSideOfAlignedRegion ); makeWidgetTypeInt( consed.writeThisAceFormat, WriteThisAceFormat ); makeWidgetTypeBool( consed.dumpCoreIfBoundsError, DumpCoreIfBoundsError ); makeWidgetTypeInt( consed.autoFinishMinSmithWatermanScoreOfARun, AutoFinishMinSmithWatermanScoreOfARun ); makeWidgetTypeDouble( consed.autoFinishDoNotComparePCRPrimersMoreThanThisManyTimes, AutoFinishDoNotComparePCRPrimersMoreThanThisManyTimes ); makeWidgetTypeInt( consed.restrictionDigestMaximumBasesToCompareToVector, RestrictionDigestMaximumBasesToCompareToVector ); makeWidgetTypeDouble( consed.restrictionDigestZoomFactor, RestrictionDigestZoomFactor ); makeWidgetTypeDouble( consed.restrictionDigestZoomFactorForNavigate, RestrictionDigestZoomFactorForNavigate ); makeWidgetTypeInt( consed.restrictionDigestToleranceInPositionUnits, RestrictionDigestToleranceInPositionUnits ); makeWidgetTypeInt( consed.autoPCRAmplifyTooManySeriousFalseMatches, AutoPCRAmplifyTooManySeriousFalseMatches ); makeWidgetTypeDouble( consed.assemblyViewZoomFactor, AssemblyViewZoomFactor ); makeWidgetTypeInt( consed.assemblyViewFilterInconsistentFwdRevPairsIfThisClose, AssemblyViewFilterInconsistentFwdRevPairsIfThisClose ); makeWidgetTypeDouble( consed.assemblyViewGridCellWidthInPixels, AssemblyViewGridCellWidthInPixels ); makeWidgetTypeInt( consed.assemblyViewCursorSensitivityInPixels, AssemblyViewCursorSensitivityInPixels ); makeWidgetTypeInt( consed.assemblyViewReadDepthQuality, AssemblyViewReadDepthQuality ); makeWidgetTypeInt( consed.showAllTracesMaxNumberOfTracesToShowAtOnce, ShowAllTracesMaxNumberOfTracesToShowAtOnce ); makeWidgetTypeInt( consed.allowFwdRevPairScaffoldsToBeMergedIfThisManyBasesIntersectionOrLess, AllowFwdRevPairScaffoldsToBeMergedIfThisManyBasesIntersectionOrLess ); makeWidgetTypeBool( consed.justForPrimateProject, JustForPrimateProject ); makeWidgetTypeFileName( consed.solexaFilesAreAssumedToBeHere, SolexaFilesAreAssumedToBeHere ); makeWidgetTypeInt( consed.solexaAlignmentFilesPerInsertingPadsCycle, SolexaAlignmentFilesPerInsertingPadsCycle ); makeWidgetTypeInt( consed.solexaAlignmentsPerAlignmentFile, SolexaAlignmentsPerAlignmentFile ); makeWidgetTypeBool( consed.solexaFastqFilesArePhredQualityNotSolexaQuality, SolexaFastqFilesArePhredQualityNotSolexaQuality ); makeWidgetTypeRWCString( consed.solexa64FastqOrSanger33Fastq, Solexa64FastqOrSanger33Fastq ); makeWidgetTypeInt( consed.maximumReadsInReadList, MaximumReadsInReadList ); makeWidgetTypeInt( consed.maxLengthOfReadsInapLocatedFragment2, MaxLengthOfReadsInapLocatedFragment2 ); makeWidgetTypeInt( consed.maximumStartupErrorsToReport, MaximumStartupErrorsToReport ); makeWidgetTypeInt( consed.454LinkerAlignmentMatchScore, 454LinkerAlignmentMatchScore ); makeWidgetTypeInt( consed.454LinkerAlignmentMismatchScore, 454LinkerAlignmentMismatchScore ); makeWidgetTypeInt( consed.454LinkerAlignmentIndelScore, 454LinkerAlignmentIndelScore ); makeWidgetTypeBool( consed.filter454ReadsDeleteCrossMatchOutput, Filter454ReadsDeleteCrossMatchOutput ); makeWidgetTypeInt( consed.autoReportAllNeededSpeciesCode, AutoReportAllNeededSpeciesCode ); makeWidgetTypeBool( consed.autoReportUseCommasInBigNumbers, AutoReportUseCommasInBigNumbers ); makeWidgetTypeBool( consed.autoReportPrintToCompareToReich, AutoReportPrintToCompareToReich ); makeWidgetTypeBool( consed.autoReportOnlyAllowSitesThatAreBetweenAcceptableSites, AutoReportOnlyAllowSitesThatAreBetweenAcceptableSites ); makeWidgetTypeBool( consed.autoReportDeaminationMutationsDeterminedByMoreAccurateMethod, AutoReportDeaminationMutationsDeterminedByMoreAccurateMethod ); makeWidgetTypeBool( consed.autoReportChooseTreesUsingBadData, AutoReportChooseTreesUsingBadData ); makeWidgetTypeBool( consed.autoReportChooseTreesByCountingDeaminationMutations, AutoReportChooseTreesByCountingDeaminationMutations ); makeWidgetTypeBool( consed.autoReportChooseTreesUsingKimura, AutoReportChooseTreesUsingKimura ); makeWidgetTypeBool( consed.autoReportPrintCrudeChimpHumanMutations, AutoReportPrintCrudeChimpHumanMutations ); makeWidgetTypeBool( consed.autoReportPrintPositionsForGraham, AutoReportPrintPositionsForGraham ); makeWidgetTypeBool( consed.autoReportPrintAncestralCpGs, AutoReportPrintAncestralCpGs ); makeWidgetTypeBool( consed.autoReportPrintCpGMutations, AutoReportPrintCpGMutations ); makeWidgetTypeBool( consed.autoReportPrintMutationsWithContext, AutoReportPrintMutationsWithContext ); makeWidgetTypeBool( consed.autoReportCountAllMutationsML, AutoReportCountAllMutationsML ); makeWidgetTypeBool( consed.autoReportCountAllMutations, AutoReportCountAllMutations ); makeWidgetTypeBool( consed.autoReportIgnoreMultipleTrees, AutoReportIgnoreMultipleTrees ); makeWidgetTypeBool( consed.autoReportCountAcceptableColumnsWithNoneOnLeft, AutoReportCountAcceptableColumnsWithNoneOnLeft ); makeWidgetTypeBool( consed.autoReportPrintFlankedColumns4, AutoReportPrintFlankedColumns4 ); makeWidgetTypeBool( consed.autoReportUseAnnotationFormat, AutoReportUseAnnotationFormat ); makeWidgetTypeBool( consed.autoReportPrintFlankedColumns3, AutoReportPrintFlankedColumns3 ); makeWidgetTypeBool( consed.autoReportPrintFlankedColumns2, AutoReportPrintFlankedColumns2 ); makeWidgetTypeBool( consed.autoReportPrintFlankedColumns, AutoReportPrintFlankedColumns ); makeWidgetTypeBool( consed.autoReportHighQualitySegmentData, AutoReportHighQualitySegmentData ); makeWidgetTypeBool( consed.autoReportGoodReadsBug, AutoReportGoodReadsBug ); makeWidgetTypeBool( consed.autoReportDiscrepancyRateInFlankedRegions, AutoReportDiscrepancyRateInFlankedRegions ); makeWidgetTypeBool( consed.autoReportDiscrepancyRateInFlankedRegions2, AutoReportDiscrepancyRateInFlankedRegions2 ); makeWidgetTypeBool( consed.autoReportDiscrepancyRateInFlankedRegions4, AutoReportDiscrepancyRateInFlankedRegions4 ); makeWidgetTypeBool( consed.autoReportDiscrepancyRateInFlankedRegions5, AutoReportDiscrepancyRateInFlankedRegions5 ); makeWidgetTypeBool( consed.autoReportSingleSignalOrQuality, AutoReportSingleSignalOrQuality ); makeWidgetTypeBool( consed.autoReportLowQualityBasesInHQS, AutoReportLowQualityBasesInHQS ); makeWidgetTypeBool( consed.autoReportCompareHQSWithLQS, AutoReportCompareHQSWithLQS ); makeWidgetTypeBool( consed.autoReportCountColumnsForGroupsOfSpecies, AutoReportCountColumnsForGroupsOfSpecies ); makeWidgetTypeBool( consed.autoReportSingleSignalInfo, AutoReportSingleSignalInfo ); makeWidgetTypeBool( consed.autoReportSingleSignalInfo2, AutoReportSingleSignalInfo2 ); makeWidgetTypeBool( consed.autoReportCompareTopAndBottomStrands, AutoReportCompareTopAndBottomStrands ); makeWidgetTypeBool( consed.autoReportCompareTopAndBottomStrandsNoHuman, AutoReportCompareTopAndBottomStrandsNoHuman ); makeWidgetTypeBool( consed.autoReportCompareTopAndBottomStrands2, AutoReportCompareTopAndBottomStrands2 ); makeWidgetTypeBool( consed.autoReportCompareTopAndBottomStrands3, AutoReportCompareTopAndBottomStrands3 ); makeWidgetTypeBool( consed.autoReportCompareTopAndBottomStrands4, AutoReportCompareTopAndBottomStrands4 ); makeWidgetTypeInt( consed.autoReportTopStrandPinnedPosition, AutoReportTopStrandPinnedPosition ); makeWidgetTypeInt( consed.autoReportBottomStrandPinnedPosition, AutoReportBottomStrandPinnedPosition ); makeWidgetTypeBool( consed.autoReportCompareTopAndBottomStrandsWithHuman, AutoReportCompareTopAndBottomStrandsWithHuman ); makeWidgetTypeBool( consed.autoReportPrintLengthsOfAlignedSegmentsOfReads, AutoReportPrintLengthsOfAlignedSegmentsOfReads ); makeWidgetTypeBool( consed.autoReportPrintLengthsOfUnalignedHighQualitySegmentsOfReads, AutoReportPrintLengthsOfUnalignedHighQualitySegmentsOfReads ); makeWidgetTypeBool( consed.autoReportPrintIfReadsAreCorrectlyAligned, AutoReportPrintIfReadsAreCorrectlyAligned ); makeWidgetTypeBool( consed.autoReportCalculateErrorProbabilitiesByComparingPTroPPan, AutoReportCalculateErrorProbabilitiesByComparingPTroPPan ); makeWidgetTypeBool( consed.autoReportPrintAgreeDisagreeBetweenPairsOfSpecies, AutoReportPrintAgreeDisagreeBetweenPairsOfSpecies ); makeWidgetTypeBool( consed.autoReportPrintAgreeDisagreeBetweenPairsOfSpecies2, AutoReportPrintAgreeDisagreeBetweenPairsOfSpecies2 ); makeWidgetTypeBool( consed.autoReportFilterSingleSignal, AutoReportFilterSingleSignal ); makeWidgetTypeFileName( consed.autoReportGoodHitReads, AutoReportGoodHitReads ); makeWidgetTypeInt( consed.autoReportQualityWindowLow, AutoReportQualityWindowLow ); makeWidgetTypeInt( consed.autoReportQualityWindowHigh, AutoReportQualityWindowHigh ); makeWidgetTypeBool( consed.autoReportPrintNumberOfIsolatedPadsForEachSpecies, AutoReportPrintNumberOfIsolatedPadsForEachSpecies ); makeWidgetTypeBool( consed.autoReportPrintNumberOfIsolatedPads, AutoReportPrintNumberOfIsolatedPads ); makeWidgetTypeRWCString( consed.autoReportIsolatedPadsOfReadsWithThisPattern, AutoReportIsolatedPadsOfReadsWithThisPattern ); makeWidgetTypeInt( consed.autoReportMinNumberOfPerfectlyAlignedBasesBeforeDiscrepancy, AutoReportMinNumberOfPerfectlyAlignedBasesBeforeDiscrepancy ); makeWidgetTypeInt( consed.autoReportMaxSizeOfDiscrepantRegion, AutoReportMaxSizeOfDiscrepantRegion ); makeWidgetTypeInt( consed.autoReportSizeOfDiscrepantRegion, AutoReportSizeOfDiscrepantRegion ); makeWidgetTypeBool( consed.autoReportPrintMinimumQualityHistogram, AutoReportPrintMinimumQualityHistogram ); makeWidgetTypeBool( consed.autoReportPrintDiscrepantRegions, AutoReportPrintDiscrepantRegions ); makeWidgetTypeBool( consed.autoReportPrintBasesInDiscrepantRegions, AutoReportPrintBasesInDiscrepantRegions ); makeWidgetTypeRWCString( consed.autoReportPrintDiscrepantRegionsButIgnoreReadsContainingThis, AutoReportPrintDiscrepantRegionsButIgnoreReadsContainingThis ); makeWidgetTypeRWCString( consed.autoReportBackboneReadHasThisStringInIt, AutoReportBackboneReadHasThisStringInIt ); makeWidgetTypeBool( consed.autoReportPrintDiscrepantRegionsButOnlyIfAboveQualityThreshold, AutoReportPrintDiscrepantRegionsButOnlyIfAboveQualityThreshold ); makeWidgetTypeBool( consed.autoReportPrintSpeciesAlignment, AutoReportPrintSpeciesAlignment ); makeWidgetTypeBool( consed.autoReportPrintReadAlignment, AutoReportPrintReadAlignment ); makeWidgetTypeFileName( consed.autoReportPrintTheseReads, AutoReportPrintTheseReads ); makeWidgetTypeBool( consed.autoReportPrintReadPositions, AutoReportPrintReadPositions ); makeWidgetTypeBool( consed.autoReportPrintChosenReadName, AutoReportPrintChosenReadName ); makeWidgetTypeInt( consed.autoReportNumbersOfCharactersOfChosenReadNameToBePrinted, AutoReportNumbersOfCharactersOfChosenReadNameToBePrinted ); makeWidgetTypeRWCString( consed.autoReportPrefix, AutoReportPrefix ); makeWidgetTypeBool( consed.autoReportUseOldCriteriaForDeletingColumnsOfPads, AutoReportUseOldCriteriaForDeletingColumnsOfPads ); makeWidgetTypeBool( consed.autoReportDeleteColumnsOfPadsBeforeAdjustingReadQualityValues, AutoReportDeleteColumnsOfPadsBeforeAdjustingReadQualityValues ); makeWidgetTypeBool( consed.autoReportFlankingBasesMustBeSingleSignal, AutoReportFlankingBasesMustBeSingleSignal ); makeWidgetTypeInt( consed.autoReportMinimumQualityOfFlankingBases, AutoReportMinimumQualityOfFlankingBases ); makeWidgetTypeBool( consed.autoReportFlankingBasesMustBeInHighQualitySegment, AutoReportFlankingBasesMustBeInHighQualitySegment ); makeWidgetTypeRWCString( consed.autoReportSpecies, AutoReportSpecies );