/***************************************************************************** # 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. # #*****************************************************************************/ if ( soResourceName == "consed.colorHighlightBackground" ) { pRes->soColorHighlightBackground_ = soResourceValue; return; } if ( soResourceName == "consed.colorHighlightForegroundX" ) { pRes->soColorHighlightForegroundX_ = soResourceValue; return; } if ( soResourceName == "consed.colorMeansMatch_same" ) { pRes->soColorMeansMatch_same_ = soResourceValue; return; } if ( soResourceName == "consed.colorMeansMatch_different" ) { pRes->soColorMeansMatch_different_ = soResourceValue; return; } if ( soResourceName == "consed.colorMeansMatch_clippedEnds" ) { pRes->soColorMeansMatch_clippedEnds_ = soResourceValue; return; } if ( soResourceName == "consed.colorMeansMatch_consensus" ) { pRes->soColorMeansMatch_consensus_ = soResourceValue; return; } if ( soResourceName == "consed.colorMeansMatch_lowQualConsensus" ) { pRes->soColorMeansMatch_lowQualConsensus_ = soResourceValue; return; } if ( soResourceName == "consed.colorConsensusLabel" ) { pRes->soColorConsensusLabel_ = soResourceValue; return; } if ( soResourceName == "consed.colorConsensusLabelBackground" ) { pRes->soColorConsensusLabelBackground_ = soResourceValue; return; } if ( soResourceName == "consed.colorMeansQualityAgree" ) { pRes->soColorMeansQualityAgree_ = soResourceValue; return; } if ( soResourceName == "consed.colorMeansQualityDisagree" ) { pRes->soColorMeansQualityDisagree_ = soResourceValue; return; } if ( soResourceName == "consed.colorMeansQualityConsensusForeground" ) { pRes->soColorMeansQualityConsensusForeground_ = soResourceValue; return; } if ( soResourceName == "consed.colorMeansQuality0_4" ) { pRes->soColorMeansQuality0_4_ = soResourceValue; return; } if ( soResourceName == "consed.colorMeansQuality5_9" ) { pRes->soColorMeansQuality5_9_ = soResourceValue; return; } if ( soResourceName == "consed.colorMeansQuality10_14" ) { pRes->soColorMeansQuality10_14_ = soResourceValue; return; } if ( soResourceName == "consed.colorMeansQuality15_19" ) { pRes->soColorMeansQuality15_19_ = soResourceValue; return; } if ( soResourceName == "consed.colorMeansQuality20_24" ) { pRes->soColorMeansQuality20_24_ = soResourceValue; return; } if ( soResourceName == "consed.colorMeansQuality25_29" ) { pRes->soColorMeansQuality25_29_ = soResourceValue; return; } if ( soResourceName == "consed.colorMeansQuality30_34" ) { pRes->soColorMeansQuality30_34_ = soResourceValue; return; } if ( soResourceName == "consed.colorMeansQuality35_39" ) { pRes->soColorMeansQuality35_39_ = soResourceValue; return; } if ( soResourceName == "consed.colorMeansQuality40_97" ) { pRes->soColorMeansQuality40_97_ = soResourceValue; return; } if ( soResourceName == "consed.colorMeansQuality98" ) { pRes->soColorMeansQuality98_ = soResourceValue; return; } if ( soResourceName == "consed.colorMeansQuality99" ) { pRes->soColorMeansQuality99_ = soResourceValue; return; } if ( soResourceName == "consed.colorMeansEditedAgree" ) { pRes->soColorMeansEditedAgree_ = soResourceValue; return; } if ( soResourceName == "consed.colorMeansEditedDisagree" ) { pRes->soColorMeansEditedDisagree_ = soResourceValue; return; } if ( soResourceName == "consed.colorMeansEditedUnedited" ) { pRes->soColorMeansEditedUnedited_ = soResourceValue; return; } if ( soResourceName == "consed.colorMeansEdited98" ) { pRes->soColorMeansEdited98_ = soResourceValue; return; } if ( soResourceName == "consed.colorMeansEdited99" ) { pRes->soColorMeansEdited99_ = soResourceValue; return; } if ( soResourceName == "consed.colorVerticalScrollbarScrolledDown" ) { pRes->soColorVerticalScrollbarScrolledDown_ = soResourceValue; return; } if ( soResourceName == "consed.colorMode_editCursorForeground" ) { pRes->soColorMode_editCursorForeground_ = soResourceValue; return; } if ( soResourceName == "consed.colorMode_editCursorBackground" ) { pRes->soColorMode_editCursorBackground_ = soResourceValue; return; } if ( soResourceName == "consed.colorTracesA" ) { pRes->soColorTracesA_ = soResourceValue; return; } if ( soResourceName == "consed.colorTracesC" ) { pRes->soColorTracesC_ = soResourceValue; return; } if ( soResourceName == "consed.colorTracesG" ) { pRes->soColorTracesG_ = soResourceValue; return; } if ( soResourceName == "consed.colorTracesT" ) { pRes->soColorTracesT_ = soResourceValue; return; } if ( soResourceName == "consed.colorTracesN" ) { pRes->soColorTracesN_ = soResourceValue; return; } if ( soResourceName == "consed.colorTracesPad" ) { pRes->soColorTracesPad_ = soResourceValue; return; } if ( soResourceName == "consed.colorScale" ) { pRes->soColorScale_ = soResourceValue; return; } if ( soResourceName == "consed.colorScaleBackground" ) { pRes->soColorScaleBackground_ = soResourceValue; return; } if ( soResourceName == "consed.colorHighlightedReadNames" ) { pRes->soColorHighlightedReadNames_ = soResourceValue; return; } if ( soResourceName == "consed.colorSequencingDirectionArrow" ) { pRes->soColorSequencingDirectionArrow_ = soResourceValue; return; } if ( soResourceName == "consed.colorSequencingDirectionArrowTracesUp" ) { pRes->soColorSequencingDirectionArrowTracesUp_ = soResourceValue; return; } if ( soResourceName == "consed.colorVerticalLineAtCursor" ) { pRes->soColorVerticalLineAtCursor_ = soResourceValue; return; } if ( soResourceName == "consed.colorHorizontalLineAtCursor" ) { pRes->soColorHorizontalLineAtCursor_ = soResourceValue; return; } if ( soResourceName == "consed.colorProteinTranslation" ) { pRes->soColorProteinTranslation_ = soResourceValue; return; } if ( soResourceName == "consed.colorProteinTranslationLabels" ) { pRes->soColorProteinTranslationLabels_ = soResourceValue; return; } if ( soResourceName == "consed.colorProteinStartCodon" ) { pRes->soColorProteinStartCodon_ = soResourceValue; return; } if ( soResourceName == "consed.colorProteinStopCodon" ) { pRes->soColorProteinStopCodon_ = soResourceValue; return; } if ( soResourceName == "consed.colorUnmatchedRestrictionFragment" ) { pRes->soColorUnmatchedRestrictionFragment_ = soResourceValue; return; } if ( soResourceName == "consed.colorRestrictionFragmentPairTooFarApart" ) { pRes->soColorRestrictionFragmentPairTooFarApart_ = soResourceValue; return; } if ( soResourceName == "consed.colorRestrictionFragmentInContig" ) { pRes->soColorRestrictionFragmentInContig_ = soResourceValue; return; } if ( soResourceName == "consed.colorRestrictionFragmentPartlyOffContig" ) { pRes->soColorRestrictionFragmentPartlyOffContig_ = soResourceValue; return; } if ( soResourceName == "consed.colorRestrictionFragmentEntirelyOffContig" ) { pRes->soColorRestrictionFragmentEntirelyOffContig_ = soResourceValue; return; } if ( soResourceName == "consed.colorActualGelRestrictionFragment" ) { pRes->soColorActualGelRestrictionFragment_ = soResourceValue; return; } if ( soResourceName == "consed.colorRestrictionDigestScale" ) { pRes->soColorRestrictionDigestScale_ = soResourceValue; return; } if ( soResourceName == "consed.colorRestrictionDigestCursorIndicator" ) { pRes->soColorRestrictionDigestCursorIndicator_ = soResourceValue; return; } if ( soResourceName == "consed.colorRestrictionFragmentsOnTopOfEachOther" ) { pRes->soColorRestrictionFragmentsOnTopOfEachOther_ = soResourceValue; return; } if ( soResourceName == "consed.colorAssemblyViewScale" ) { pRes->soColorAssemblyViewScale_ = soResourceValue; return; } if ( soResourceName == "consed.colorAssemblyViewScaleNumbers" ) { pRes->soColorAssemblyViewScaleNumbers_ = soResourceValue; return; } if ( soResourceName == "consed.colorAssemblyViewContigs" ) { pRes->soColorAssemblyViewContigs_ = soResourceValue; return; } if ( soResourceName == "consed.colorAssemblyViewContigNamesForeground" ) { pRes->soColorAssemblyViewContigNamesForeground_ = soResourceValue; return; } if ( soResourceName == "consed.colorAssemblyViewContigNamesBackground" ) { pRes->soColorAssemblyViewContigNamesBackground_ = soResourceValue; return; } if ( soResourceName == "consed.colorAssemblyViewConsistentFwdRevPairs" ) { pRes->soColorAssemblyViewConsistentFwdRevPairs_ = soResourceValue; return; } if ( soResourceName == "consed.colorAssemblyViewConsistentFwdRevPairDepth" ) { pRes->soColorAssemblyViewConsistentFwdRevPairDepth_ = soResourceValue; return; } if ( soResourceName == "consed.colorAssemblyViewReadDepth" ) { pRes->soColorAssemblyViewReadDepth_ = soResourceValue; return; } if ( soResourceName == "consed.colorAssemblyViewDiscrepanciesNotIndels" ) { pRes->soColorAssemblyViewDiscrepanciesNotIndels_ = soResourceValue; return; } if ( soResourceName == "consed.colorAssemblyViewDiscrepanciesIndels" ) { pRes->soColorAssemblyViewDiscrepanciesIndels_ = soResourceValue; return; } if ( soResourceName == "consed.colorAssemblyViewTooFewConsistentFwdRevPairs" ) { pRes->soColorAssemblyViewTooFewConsistentFwdRevPairs_ = soResourceValue; return; } if ( soResourceName == "consed.colorAssemblyViewInconsistentFwdRevPair" ) { pRes->soColorAssemblyViewInconsistentFwdRevPair_ = soResourceValue; return; } if ( soResourceName == "consed.colorAssemblyViewConsistentGapSpanningFwdRevPair" ) { pRes->soColorAssemblyViewConsistentGapSpanningFwdRevPair_ = soResourceValue; return; } if ( soResourceName == "consed.colorAssemblyViewHighlight" ) { pRes->soColorAssemblyViewHighlight_ = soResourceValue; return; } if ( soResourceName == "consed.colorAssemblyViewMultipleItemsOnTopOfEachOther" ) { pRes->soColorAssemblyViewMultipleItemsOnTopOfEachOther_ = soResourceValue; return; } if ( soResourceName == "consed.colorAssemblyViewDirectSequenceMatches" ) { pRes->soColorAssemblyViewDirectSequenceMatches_ = soResourceValue; return; } if ( soResourceName == "consed.colorAssemblyViewInvertedSequenceMatches" ) { pRes->soColorAssemblyViewInvertedSequenceMatches_ = soResourceValue; return; } if ( soResourceName == "consed.colorAssemblyViewConsistentRestrictionDigestFragment1" ) { pRes->soColorAssemblyViewConsistentRestrictionDigestFragment1_ = soResourceValue; return; } if ( soResourceName == "consed.colorAssemblyViewConsistentRestrictionDigestFragment2" ) { pRes->soColorAssemblyViewConsistentRestrictionDigestFragment2_ = soResourceValue; return; } if ( soResourceName == "consed.colorAssemblyViewConsistentRestrictionDigestFragment3" ) { pRes->soColorAssemblyViewConsistentRestrictionDigestFragment3_ = soResourceValue; return; } if ( soResourceName == "consed.colorAssemblyViewConsistentRestrictionDigestFragment4" ) { pRes->soColorAssemblyViewConsistentRestrictionDigestFragment4_ = soResourceValue; return; } if ( soResourceName == "consed.colorAssemblyViewConsistentRestrictionDigestFragment5" ) { pRes->soColorAssemblyViewConsistentRestrictionDigestFragment5_ = soResourceValue; return; } if ( soResourceName == "consed.colorAssemblyViewConsistentRestrictionDigestFragment6" ) { pRes->soColorAssemblyViewConsistentRestrictionDigestFragment6_ = soResourceValue; return; } if ( soResourceName == "consed.colorAssemblyViewConsistentRestrictionDigestFragment7" ) { pRes->soColorAssemblyViewConsistentRestrictionDigestFragment7_ = soResourceValue; return; } if ( soResourceName == "consed.colorAssemblyViewConsistentRestrictionDigestFragment8" ) { pRes->soColorAssemblyViewConsistentRestrictionDigestFragment8_ = soResourceValue; return; } if ( soResourceName == "consed.colorAssemblyViewConsistentRestrictionDigestFragment9" ) { pRes->soColorAssemblyViewConsistentRestrictionDigestFragment9_ = soResourceValue; return; } if ( soResourceName == "consed.colorAssemblyViewConsistentRestrictionDigestFragment10" ) { pRes->soColorAssemblyViewConsistentRestrictionDigestFragment10_ = soResourceValue; return; } if ( soResourceName == "consed.colorAssemblyViewInconsistentRestrictionDigestFragment" ) { pRes->soColorAssemblyViewInconsistentRestrictionDigestFragment_ = soResourceValue; return; } if ( soResourceName == "consed.colorAssemblyViewCloneEnd" ) { pRes->soColorAssemblyViewCloneEnd_ = soResourceValue; return; } if ( soResourceName == "consed.colorReadPrefixDefault" ) { pRes->soColorReadPrefixDefault_ = soResourceValue; return; } if ( soResourceName == "consed.tagColorEdit" ) { pRes->soTagColorEdit_ = soResourceValue; return; } if ( soResourceName == "consed.tagColorBecomeConsensus" ) { pRes->soTagColorBecomeConsensus_ = soResourceValue; return; } if ( soResourceName == "consed.tagColorIgnoreMismatches" ) { pRes->soTagColorIgnoreMismatches_ = soResourceValue; return; } if ( soResourceName == "consed.tagColorIgnoreMatches" ) { pRes->soTagColorIgnoreMatches_ = soResourceValue; return; } if ( soResourceName == "consed.tagColorSignificantDiscrepancy" ) { pRes->soTagColorSignificantDiscrepancy_ = soResourceValue; return; } if ( soResourceName == "consed.tagColorCompression" ) { pRes->soTagColorCompression_ = soResourceValue; return; } if ( soResourceName == "consed.tagColorDataNeeded" ) { pRes->soTagColorDataNeeded_ = soResourceValue; return; } if ( soResourceName == "consed.tagColorComment" ) { pRes->soTagColorComment_ = soResourceValue; return; } if ( soResourceName == "consed.tagColorTagsOverlap" ) { pRes->soTagColorTagsOverlap_ = soResourceValue; return; } if ( soResourceName == "consed.tagColorSequencingVector" ) { pRes->soTagColorSequencingVector_ = soResourceValue; return; } if ( soResourceName == "consed.tagColorCloningVector" ) { pRes->soTagColorCloningVector_ = soResourceValue; return; } if ( soResourceName == "consed.tagColorVector" ) { pRes->soTagColorVector_ = soResourceValue; return; } if ( soResourceName == "consed.tagColorOligo" ) { pRes->soTagColorOligo_ = soResourceValue; return; } if ( soResourceName == "consed.tagColorOligo3PrimeEnd" ) { pRes->soTagColorOligo3PrimeEnd_ = soResourceValue; return; } if ( soResourceName == "consed.tagColorChimera" ) { pRes->soTagColorChimera_ = soResourceValue; return; } if ( soResourceName == "consed.tagColorContigName" ) { pRes->soTagColorContigName_ = soResourceValue; return; } if ( soResourceName == "consed.tagColorPolymorphism" ) { pRes->soTagColorPolymorphism_ = soResourceValue; return; } if ( soResourceName == "consed.tagColorHomozygoteAA" ) { pRes->soTagColorHomozygoteAA_ = soResourceValue; return; } if ( soResourceName == "consed.tagColorHomozygoteCC" ) { pRes->soTagColorHomozygoteCC_ = soResourceValue; return; } if ( soResourceName == "consed.tagColorHomozygoteGG" ) { pRes->soTagColorHomozygoteGG_ = soResourceValue; return; } if ( soResourceName == "consed.tagColorHomozygoteTT" ) { pRes->soTagColorHomozygoteTT_ = soResourceValue; return; } if ( soResourceName == "consed.tagColorHeterozygoteAC" ) { pRes->soTagColorHeterozygoteAC_ = soResourceValue; return; } if ( soResourceName == "consed.tagColorHeterozygoteAG" ) { pRes->soTagColorHeterozygoteAG_ = soResourceValue; return; } if ( soResourceName == "consed.tagColorHeterozygoteAT" ) { pRes->soTagColorHeterozygoteAT_ = soResourceValue; return; } if ( soResourceName == "consed.tagColorHeterozygoteCG" ) { pRes->soTagColorHeterozygoteCG_ = soResourceValue; return; } if ( soResourceName == "consed.tagColorHeterozygoteCT" ) { pRes->soTagColorHeterozygoteCT_ = soResourceValue; return; } if ( soResourceName == "consed.tagColorHeterozygoteGT" ) { pRes->soTagColorHeterozygoteGT_ = soResourceValue; return; } if ( soResourceName == "consed.tagColorRepeat" ) { pRes->soTagColorRepeat_ = soResourceValue; return; } if ( soResourceName == "consed.tagColorPolyPhredRank1" ) { pRes->soTagColorPolyPhredRank1_ = soResourceValue; return; } if ( soResourceName == "consed.tagColorPolyPhredRank2" ) { pRes->soTagColorPolyPhredRank2_ = soResourceValue; return; } if ( soResourceName == "consed.tagColorPolyPhredRank3" ) { pRes->soTagColorPolyPhredRank3_ = soResourceValue; return; } if ( soResourceName == "consed.tagColorPolyPhredRank4" ) { pRes->soTagColorPolyPhredRank4_ = soResourceValue; return; } if ( soResourceName == "consed.tagColorPolyPhredRank5" ) { pRes->soTagColorPolyPhredRank5_ = soResourceValue; return; } if ( soResourceName == "consed.tagColorPolyPhredRank6" ) { pRes->soTagColorPolyPhredRank6_ = soResourceValue; return; } if ( soResourceName == "consed.tagColorIndelSite" ) { pRes->soTagColorIndelSite_ = soResourceValue; return; } if ( soResourceName == "consed.tagColorHeterozygoteIndel" ) { pRes->soTagColorHeterozygoteIndel_ = soResourceValue; return; } if ( soResourceName == "consed.tagColorHomozygoteIndel" ) { pRes->soTagColorHomozygoteIndel_ = soResourceValue; return; } if ( soResourceName == "consed.tagColorPolymorphismConfirmed" ) { pRes->soTagColorPolymorphismConfirmed_ = soResourceValue; return; } if ( soResourceName == "consed.tagColorMatchElsewhereHighQual" ) { pRes->soTagColorMatchElsewhereHighQual_ = soResourceValue; return; } if ( soResourceName == "consed.tagColorMatchElsewhereLowQual" ) { pRes->soTagColorMatchElsewhereLowQual_ = soResourceValue; return; } if ( soResourceName == "consed.tagColorG_dropout" ) { pRes->soTagColorG_dropout_ = soResourceValue; return; } if ( soResourceName == "consed.tagColorMarkedHighQuality" ) { pRes->soTagColorMarkedHighQuality_ = soResourceValue; return; } if ( soResourceName == "consed.tagColorMarkedLowQuality" ) { pRes->soTagColorMarkedLowQuality_ = soResourceValue; return; } if ( soResourceName == "consed.tagColorAutoFinishExp" ) { pRes->soTagColorAutoFinishExp_ = soResourceValue; return; } if ( soResourceName == "consed.tagColorDoNotFinish" ) { pRes->soTagColorDoNotFinish_ = soResourceValue; return; } if ( soResourceName == "consed.tagColorDoNotDoPCR" ) { pRes->soTagColorDoNotDoPCR_ = soResourceValue; return; } if ( soResourceName == "consed.tagColorConsedFixedGoldenPath" ) { pRes->soTagColorConsedFixedGoldenPath_ = soResourceValue; return; } if ( soResourceName == "consed.tagColorCloneEnd" ) { pRes->soTagColorCloneEnd_ = soResourceValue; return; } if ( soResourceName == "consed.tagColorEditable" ) { pRes->soTagColorEditable_ = soResourceValue; return; } if ( soResourceName == "consed.tagColorContigEndPair" ) { pRes->soTagColorContigEndPair_ = soResourceValue; return; } if ( soResourceName == "consed.tagColorChangedGenotype" ) { pRes->soTagColorChangedGenotype_ = soResourceValue; return; } if ( soResourceName == "consed.tagColorStartNumberingConsensus" ) { pRes->soTagColorStartNumberingConsensus_ = soResourceValue; return; } if ( soResourceName == "consed.tagColorReferenceSequence" ) { pRes->soTagColorReferenceSequence_ = soResourceValue; return; } if ( soResourceName == "consed.tagColorJoin" ) { pRes->soTagColorJoin_ = soResourceValue; return; } if ( soResourceName == "consed.customTag1" ) { pRes->soCustomTag1_ = soResourceValue; return; } if ( soResourceName == "consed.tagColorCustomTag1" ) { pRes->soTagColorCustomTag1_ = soResourceValue; return; } if ( soResourceName == "consed.customTag2" ) { pRes->soCustomTag2_ = soResourceValue; return; } if ( soResourceName == "consed.tagColorCustomTag2" ) { pRes->soTagColorCustomTag2_ = soResourceValue; return; } if ( soResourceName == "consed.customTag3" ) { pRes->soCustomTag3_ = soResourceValue; return; } if ( soResourceName == "consed.tagColorCustomTag3" ) { pRes->soTagColorCustomTag3_ = soResourceValue; return; } if ( soResourceName == "consed.customTag4" ) { pRes->soCustomTag4_ = soResourceValue; return; } if ( soResourceName == "consed.tagColorCustomTag4" ) { pRes->soTagColorCustomTag4_ = soResourceValue; return; } if ( soResourceName == "consed.customTag5" ) { pRes->soCustomTag5_ = soResourceValue; return; } if ( soResourceName == "consed.tagColorCustomTag5" ) { pRes->soTagColorCustomTag5_ = soResourceValue; return; } if ( soResourceName == "consed.customTag6" ) { pRes->soCustomTag6_ = soResourceValue; return; } if ( soResourceName == "consed.tagColorCustomTag6" ) { pRes->soTagColorCustomTag6_ = soResourceValue; return; } if ( soResourceName == "consed.customTag7" ) { pRes->soCustomTag7_ = soResourceValue; return; } if ( soResourceName == "consed.tagColorCustomTag7" ) { pRes->soTagColorCustomTag7_ = soResourceValue; return; } if ( soResourceName == "consed.customTag8" ) { pRes->soCustomTag8_ = soResourceValue; return; } if ( soResourceName == "consed.tagColorCustomTag8" ) { pRes->soTagColorCustomTag8_ = soResourceValue; return; } if ( soResourceName == "consed.customTag9" ) { pRes->soCustomTag9_ = soResourceValue; return; } if ( soResourceName == "consed.tagColorCustomTag9" ) { pRes->soTagColorCustomTag9_ = soResourceValue; return; } if ( soResourceName == "consed.customTag10" ) { pRes->soCustomTag10_ = soResourceValue; return; } if ( soResourceName == "consed.tagColorCustomTag10" ) { pRes->soTagColorCustomTag10_ = soResourceValue; return; } if ( soResourceName == "consed.customTag11" ) { pRes->soCustomTag11_ = soResourceValue; return; } if ( soResourceName == "consed.tagColorCustomTag11" ) { pRes->soTagColorCustomTag11_ = soResourceValue; return; } if ( soResourceName == "consed.customTag12" ) { pRes->soCustomTag12_ = soResourceValue; return; } if ( soResourceName == "consed.tagColorCustomTag12" ) { pRes->soTagColorCustomTag12_ = soResourceValue; return; } if ( soResourceName == "consed.customTag13" ) { pRes->soCustomTag13_ = soResourceValue; return; } if ( soResourceName == "consed.tagColorCustomTag13" ) { pRes->soTagColorCustomTag13_ = soResourceValue; return; } if ( soResourceName == "consed.customTag14" ) { pRes->soCustomTag14_ = soResourceValue; return; } if ( soResourceName == "consed.tagColorCustomTag14" ) { pRes->soTagColorCustomTag14_ = soResourceValue; return; } if ( soResourceName == "consed.customTag15" ) { pRes->soCustomTag15_ = soResourceValue; return; } if ( soResourceName == "consed.tagColorCustomTag15" ) { pRes->soTagColorCustomTag15_ = soResourceValue; return; } if ( soResourceName == "consed.customConsensusTag1" ) { pRes->soCustomConsensusTag1_ = soResourceValue; return; } if ( soResourceName == "consed.tagColorCustomConsensusTag1" ) { pRes->soTagColorCustomConsensusTag1_ = soResourceValue; return; } if ( soResourceName == "consed.customConsensusTag2" ) { pRes->soCustomConsensusTag2_ = soResourceValue; return; } if ( soResourceName == "consed.tagColorCustomConsensusTag2" ) { pRes->soTagColorCustomConsensusTag2_ = soResourceValue; return; } if ( soResourceName == "consed.customConsensusTag3" ) { pRes->soCustomConsensusTag3_ = soResourceValue; return; } if ( soResourceName == "consed.tagColorCustomConsensusTag3" ) { pRes->soTagColorCustomConsensusTag3_ = soResourceValue; return; } if ( soResourceName == "consed.customConsensusTag4" ) { pRes->soCustomConsensusTag4_ = soResourceValue; return; } if ( soResourceName == "consed.tagColorCustomConsensusTag4" ) { pRes->soTagColorCustomConsensusTag4_ = soResourceValue; return; } if ( soResourceName == "consed.customConsensusTag5" ) { pRes->soCustomConsensusTag5_ = soResourceValue; return; } if ( soResourceName == "consed.tagColorCustomConsensusTag5" ) { pRes->soTagColorCustomConsensusTag5_ = soResourceValue; return; } if ( soResourceName == "consed.customConsensusTag6" ) { pRes->soCustomConsensusTag6_ = soResourceValue; return; } if ( soResourceName == "consed.tagColorCustomConsensusTag6" ) { pRes->soTagColorCustomConsensusTag6_ = soResourceValue; return; } if ( soResourceName == "consed.customConsensusTag7" ) { pRes->soCustomConsensusTag7_ = soResourceValue; return; } if ( soResourceName == "consed.tagColorCustomConsensusTag7" ) { pRes->soTagColorCustomConsensusTag7_ = soResourceValue; return; } if ( soResourceName == "consed.customConsensusTag8" ) { pRes->soCustomConsensusTag8_ = soResourceValue; return; } if ( soResourceName == "consed.tagColorCustomConsensusTag8" ) { pRes->soTagColorCustomConsensusTag8_ = soResourceValue; return; } if ( soResourceName == "consed.customConsensusTag9" ) { pRes->soCustomConsensusTag9_ = soResourceValue; return; } if ( soResourceName == "consed.tagColorCustomConsensusTag9" ) { pRes->soTagColorCustomConsensusTag9_ = soResourceValue; return; } if ( soResourceName == "consed.customConsensusTag10" ) { pRes->soCustomConsensusTag10_ = soResourceValue; return; } if ( soResourceName == "consed.tagColorCustomConsensusTag10" ) { pRes->soTagColorCustomConsensusTag10_ = soResourceValue; return; } if ( soResourceName == "consed.customConsensusTag11" ) { pRes->soCustomConsensusTag11_ = soResourceValue; return; } if ( soResourceName == "consed.tagColorCustomConsensusTag11" ) { pRes->soTagColorCustomConsensusTag11_ = soResourceValue; return; } if ( soResourceName == "consed.customConsensusTag12" ) { pRes->soCustomConsensusTag12_ = soResourceValue; return; } if ( soResourceName == "consed.tagColorCustomConsensusTag12" ) { pRes->soTagColorCustomConsensusTag12_ = soResourceValue; return; } if ( soResourceName == "consed.customConsensusTag13" ) { pRes->soCustomConsensusTag13_ = soResourceValue; return; } if ( soResourceName == "consed.tagColorCustomConsensusTag13" ) { pRes->soTagColorCustomConsensusTag13_ = soResourceValue; return; } if ( soResourceName == "consed.customConsensusTag14" ) { pRes->soCustomConsensusTag14_ = soResourceValue; return; } if ( soResourceName == "consed.tagColorCustomConsensusTag14" ) { pRes->soTagColorCustomConsensusTag14_ = soResourceValue; return; } if ( soResourceName == "consed.customConsensusTag15" ) { pRes->soCustomConsensusTag15_ = soResourceValue; return; } if ( soResourceName == "consed.tagColorCustomConsensusTag15" ) { pRes->soTagColorCustomConsensusTag15_ = soResourceValue; return; } if ( soResourceName == "consed.printPS" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bPrintPS_ = true; else if ( soResourceValue == "false" ) pRes->bPrintPS_ = false; else BAD_VALUE( "value for resource consed.printPS must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.defaultTagType" ) { pRes->soDefaultTagType_ = soResourceValue; return; } if ( soResourceName == "consed.defaultTagOnConsensusNotReads" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bDefaultTagOnConsensusNotReads_ = true; else if ( soResourceValue == "false" ) pRes->bDefaultTagOnConsensusNotReads_ = false; else BAD_VALUE( "value for resource consed.defaultTagOnConsensusNotReads must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.autoFinishMinNumberOfErrorsFixedByAnExp" ) { if ( !bIsNumericDouble( soResourceValue, pRes->dAutoFinishMinNumberOfErrorsFixedByAnExp_ ) ) BAD_VALUE( "value for resource consed.autoFinishMinNumberOfErrorsFixedByAnExp must be a decimal number", soResourceValue ) return; } if ( soResourceName == "consed.autoFinishRedundancy" ) { if ( !bIsNumericDouble( soResourceValue, pRes->dAutoFinishRedundancy_ ) ) BAD_VALUE( "value for resource consed.autoFinishRedundancy must be a decimal number", soResourceValue ) return; } if ( soResourceName == "consed.autoFinishAverageInsertSize" ) { if ( !bIsNumericMaybeWithWhitespace( soResourceValue, pRes->nAutoFinishAverageInsertSize_ ) ) BAD_VALUE( "value for resource consed.autoFinishAverageInsertSize must be numeric", soResourceValue ) return; } if ( soResourceName == "consed.primersMaxInsertSizeOfASubclone" ) { if ( !bIsNumericMaybeWithWhitespace( soResourceValue, pRes->nPrimersMaxInsertSizeOfASubclone_ ) ) BAD_VALUE( "value for resource consed.primersMaxInsertSizeOfASubclone must be numeric", soResourceValue ) return; } if ( soResourceName == "consed.primersMaxMeltingTemp" ) { if ( !bIsNumericMaybeWithWhitespace( soResourceValue, pRes->nPrimersMaxMeltingTemp_ ) ) BAD_VALUE( "value for resource consed.primersMaxMeltingTemp must be numeric", soResourceValue ) return; } if ( soResourceName == "consed.primersMaxMeltingTempForPCR" ) { if ( !bIsNumericMaybeWithWhitespace( soResourceValue, pRes->nPrimersMaxMeltingTempForPCR_ ) ) BAD_VALUE( "value for resource consed.primersMaxMeltingTempForPCR must be numeric", soResourceValue ) return; } if ( soResourceName == "consed.primersPickTemplatesForPrimers" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bPrimersPickTemplatesForPrimers_ = true; else if ( soResourceValue == "false" ) pRes->bPrimersPickTemplatesForPrimers_ = false; else BAD_VALUE( "value for resource consed.primersPickTemplatesForPrimers must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.primersSubcloneFullPathnameOfFileOfSequencesForScreening" ) { pRes->soPrimersSubcloneFullPathnameOfFileOfSequencesForScreening_ = soResourceValue; return; } if ( soResourceName == "consed.primersCloneFullPathnameOfFileOfSequencesForScreening" ) { pRes->soPrimersCloneFullPathnameOfFileOfSequencesForScreening_ = soResourceValue; return; } if ( soResourceName == "consed.primersMinMeltingTemp" ) { if ( !bIsNumericMaybeWithWhitespace( soResourceValue, pRes->nPrimersMinMeltingTemp_ ) ) BAD_VALUE( "value for resource consed.primersMinMeltingTemp must be numeric", soResourceValue ) return; } if ( soResourceName == "consed.primersMinMeltingTempForPCR" ) { if ( !bIsNumericMaybeWithWhitespace( soResourceValue, pRes->nPrimersMinMeltingTempForPCR_ ) ) BAD_VALUE( "value for resource consed.primersMinMeltingTempForPCR must be numeric", soResourceValue ) return; } if ( soResourceName == "consed.searchFunctionsUseUnalignedEndsOfReads" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bSearchFunctionsUseUnalignedEndsOfReads_ = true; else if ( soResourceValue == "false" ) pRes->bSearchFunctionsUseUnalignedEndsOfReads_ = false; else BAD_VALUE( "value for resource consed.searchFunctionsUseUnalignedEndsOfReads must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.searchFunctionsUseLowQualityEndsOfReads" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bSearchFunctionsUseLowQualityEndsOfReads_ = true; else if ( soResourceValue == "false" ) pRes->bSearchFunctionsUseLowQualityEndsOfReads_ = false; else BAD_VALUE( "value for resource consed.searchFunctionsUseLowQualityEndsOfReads must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.inexactSearchForStringMaxPerCentMismatch" ) { if ( !bIsNumericMaybeWithWhitespace( soResourceValue, pRes->nInexactSearchForStringMaxPerCentMismatch_ ) ) BAD_VALUE( "value for resource consed.inexactSearchForStringMaxPerCentMismatch must be numeric", soResourceValue ) return; } if ( soResourceName == "consed.onlyAllowOneReadWriteConsedAtATime" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bOnlyAllowOneReadWriteConsedAtATime_ = true; else if ( soResourceValue == "false" ) pRes->bOnlyAllowOneReadWriteConsedAtATime_ = false; else BAD_VALUE( "value for resource consed.onlyAllowOneReadWriteConsedAtATime must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.autoFinishAllowHighQualityDiscrepanciesInTemplateIfConsistentForwardReversePair" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bAutoFinishAllowHighQualityDiscrepanciesInTemplateIfConsistentForwardReversePair_ = true; else if ( soResourceValue == "false" ) pRes->bAutoFinishAllowHighQualityDiscrepanciesInTemplateIfConsistentForwardReversePair_ = false; else BAD_VALUE( "value for resource consed.autoFinishAllowHighQualityDiscrepanciesInTemplateIfConsistentForwardReversePair must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.printWindowCommand" ) { pRes->soPrintWindowCommand_ = soResourceValue; return; } if ( soResourceName == "consed.fileOfTagTypes" ) { pRes->filFileOfTagTypes_ = soResourceValue; return; } if ( soResourceName == "consed.assemblyViewShowConsistentFwdRevPairs" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bAssemblyViewShowConsistentFwdRevPairs_ = true; else if ( soResourceValue == "false" ) pRes->bAssemblyViewShowConsistentFwdRevPairs_ = false; else BAD_VALUE( "value for resource consed.assemblyViewShowConsistentFwdRevPairs must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.assemblyViewShowConsistentFwdRevPairDepth" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bAssemblyViewShowConsistentFwdRevPairDepth_ = true; else if ( soResourceValue == "false" ) pRes->bAssemblyViewShowConsistentFwdRevPairDepth_ = false; else BAD_VALUE( "value for resource consed.assemblyViewShowConsistentFwdRevPairDepth must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.assemblyViewShowConsistentFwdRevPairsBetweenDifferentScaffolds" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bAssemblyViewShowConsistentFwdRevPairsBetweenDifferentScaffolds_ = true; else if ( soResourceValue == "false" ) pRes->bAssemblyViewShowConsistentFwdRevPairsBetweenDifferentScaffolds_ = false; else BAD_VALUE( "value for resource consed.assemblyViewShowConsistentFwdRevPairsBetweenDifferentScaffolds must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.assemblyViewShowLegsOnSquaresForConsistentFwdRevPairs" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bAssemblyViewShowLegsOnSquaresForConsistentFwdRevPairs_ = true; else if ( soResourceValue == "false" ) pRes->bAssemblyViewShowLegsOnSquaresForConsistentFwdRevPairs_ = false; else BAD_VALUE( "value for resource consed.assemblyViewShowLegsOnSquaresForConsistentFwdRevPairs must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.assemblyViewShowGapSpanningFwdRevPairs" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bAssemblyViewShowGapSpanningFwdRevPairs_ = true; else if ( soResourceValue == "false" ) pRes->bAssemblyViewShowGapSpanningFwdRevPairs_ = false; else BAD_VALUE( "value for resource consed.assemblyViewShowGapSpanningFwdRevPairs must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.assemblyViewShowWhichInconsistentFwdRevPairs" ) { pRes->soAssemblyViewShowWhichInconsistentFwdRevPairs_ = soResourceValue; return; } if ( soResourceName == "consed.assemblyViewShowReadDepth" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bAssemblyViewShowReadDepth_ = true; else if ( soResourceValue == "false" ) pRes->bAssemblyViewShowReadDepth_ = false; else BAD_VALUE( "value for resource consed.assemblyViewShowReadDepth must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.assemblyViewShowMultipleHighQualityDiscrepancies" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bAssemblyViewShowMultipleHighQualityDiscrepancies_ = true; else if ( soResourceValue == "false" ) pRes->bAssemblyViewShowMultipleHighQualityDiscrepancies_ = false; else BAD_VALUE( "value for resource consed.assemblyViewShowMultipleHighQualityDiscrepancies must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.assemblyViewShowRestrictionDigestCutSites" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bAssemblyViewShowRestrictionDigestCutSites_ = true; else if ( soResourceValue == "false" ) pRes->bAssemblyViewShowRestrictionDigestCutSites_ = false; else BAD_VALUE( "value for resource consed.assemblyViewShowRestrictionDigestCutSites must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.assemblyViewFilterSequenceMatchesBySize" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bAssemblyViewFilterSequenceMatchesBySize_ = true; else if ( soResourceValue == "false" ) pRes->bAssemblyViewFilterSequenceMatchesBySize_ = false; else BAD_VALUE( "value for resource consed.assemblyViewFilterSequenceMatchesBySize must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.assemblyViewSequenceMatchesMinSize" ) { if ( !bIsNumericMaybeWithWhitespace( soResourceValue, pRes->nAssemblyViewSequenceMatchesMinSize_ ) ) BAD_VALUE( "value for resource consed.assemblyViewSequenceMatchesMinSize must be numeric", soResourceValue ) return; } if ( soResourceName == "consed.assemblyViewSequenceMatchesMaxSize" ) { if ( !bIsNumericMaybeWithWhitespace( soResourceValue, pRes->nAssemblyViewSequenceMatchesMaxSize_ ) ) BAD_VALUE( "value for resource consed.assemblyViewSequenceMatchesMaxSize must be numeric", soResourceValue ) return; } if ( soResourceName == "consed.assemblyViewAutomaticallyStartWithConsed" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bAssemblyViewAutomaticallyStartWithConsed_ = true; else if ( soResourceValue == "false" ) pRes->bAssemblyViewAutomaticallyStartWithConsed_ = false; else BAD_VALUE( "value for resource consed.assemblyViewAutomaticallyStartWithConsed must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.assemblyViewDisplayTheseTagTypesOnTheseLines" ) { pRes->soAssemblyViewDisplayTheseTagTypesOnTheseLines_ = soResourceValue; return; } if ( soResourceName == "consed.assemblyViewShowTags" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bAssemblyViewShowTags_ = true; else if ( soResourceValue == "false" ) pRes->bAssemblyViewShowTags_ = false; else BAD_VALUE( "value for resource consed.assemblyViewShowTags must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.autoEditRecalculateHighQualitySegmentsOfReads" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bAutoEditRecalculateHighQualitySegmentsOfReads_ = true; else if ( soResourceValue == "false" ) pRes->bAutoEditRecalculateHighQualitySegmentsOfReads_ = false; else BAD_VALUE( "value for resource consed.autoEditRecalculateHighQualitySegmentsOfReads must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.autoEditConvertCloneEndBasesToXs" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bAutoEditConvertCloneEndBasesToXs_ = true; else if ( soResourceValue == "false" ) pRes->bAutoEditConvertCloneEndBasesToXs_ = false; else BAD_VALUE( "value for resource consed.autoEditConvertCloneEndBasesToXs must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.autoEditTellPhrapNotToOverlapMultiplyDiscrepantReads" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bAutoEditTellPhrapNotToOverlapMultiplyDiscrepantReads_ = true; else if ( soResourceValue == "false" ) pRes->bAutoEditTellPhrapNotToOverlapMultiplyDiscrepantReads_ = false; else BAD_VALUE( "value for resource consed.autoEditTellPhrapNotToOverlapMultiplyDiscrepantReads must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.autoEditTagEditableLowConsensusQualityRegions" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bAutoEditTagEditableLowConsensusQualityRegions_ = true; else if ( soResourceValue == "false" ) pRes->bAutoEditTagEditableLowConsensusQualityRegions_ = false; else BAD_VALUE( "value for resource consed.autoEditTagEditableLowConsensusQualityRegions must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.autoEditMakeFakeRead" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bAutoEditMakeFakeRead_ = true; else if ( soResourceValue == "false" ) pRes->bAutoEditMakeFakeRead_ = false; else BAD_VALUE( "value for resource consed.autoEditMakeFakeRead must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.autoEditMakeFakeReadFromRead1" ) { pRes->soAutoEditMakeFakeReadFromRead1_ = soResourceValue; return; } if ( soResourceName == "consed.autoEditMakeFakeReadFromRead2" ) { pRes->soAutoEditMakeFakeReadFromRead2_ = soResourceValue; return; } if ( soResourceName == "consed.autoEditMakeFakeReadName" ) { pRes->soAutoEditMakeFakeReadName_ = soResourceValue; return; } if ( soResourceName == "consed.autoEditMakeFakeReadFastaFilename" ) { pRes->filAutoEditMakeFakeReadFastaFilename_ = soResourceValue; return; } if ( soResourceName == "consed.autoEditMergeAssembly" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bAutoEditMergeAssembly_ = true; else if ( soResourceValue == "false" ) pRes->bAutoEditMergeAssembly_ = false; else BAD_VALUE( "value for resource consed.autoEditMergeAssembly must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.autoEditSecondaryAceFile" ) { pRes->filAutoEditSecondaryAceFile_ = soResourceValue; return; } if ( soResourceName == "consed.autoEditFixRunsInConsensus" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bAutoEditFixRunsInConsensus_ = true; else if ( soResourceValue == "false" ) pRes->bAutoEditFixRunsInConsensus_ = false; else BAD_VALUE( "value for resource consed.autoEditFixRunsInConsensus must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.showAllTracesJustShowGoodTraces" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bShowAllTracesJustShowGoodTraces_ = true; else if ( soResourceValue == "false" ) pRes->bShowAllTracesJustShowGoodTraces_ = false; else BAD_VALUE( "value for resource consed.showAllTracesJustShowGoodTraces must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.addAlignedSequenceQualityOfBases" ) { if ( !bIsNumericMaybeWithWhitespace( soResourceValue, pRes->nAddAlignedSequenceQualityOfBases_ ) ) BAD_VALUE( "value for resource consed.addAlignedSequenceQualityOfBases must be numeric", soResourceValue ) return; } if ( soResourceName == "consed.makeLightBackgroundInAlignedReadsWindowAndTracesWindow" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bMakeLightBackgroundInAlignedReadsWindowAndTracesWindow_ = true; else if ( soResourceValue == "false" ) pRes->bMakeLightBackgroundInAlignedReadsWindowAndTracesWindow_ = false; else BAD_VALUE( "value for resource consed.makeLightBackgroundInAlignedReadsWindowAndTracesWindow must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.putVerticalLineAtCursor" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bPutVerticalLineAtCursor_ = true; else if ( soResourceValue == "false" ) pRes->bPutVerticalLineAtCursor_ = false; else BAD_VALUE( "value for resource consed.putVerticalLineAtCursor must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.putHorizontalLineAtCursor" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bPutHorizontalLineAtCursor_ = true; else if ( soResourceValue == "false" ) pRes->bPutHorizontalLineAtCursor_ = false; else BAD_VALUE( "value for resource consed.putHorizontalLineAtCursor must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.highlightedReadsFile" ) { pRes->filHighlightedReadsFile_ = soResourceValue; return; } if ( soResourceName == "consed.autoReportPrintReadNamesInRegion" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bAutoReportPrintReadNamesInRegion_ = true; else if ( soResourceValue == "false" ) pRes->bAutoReportPrintReadNamesInRegion_ = false; else BAD_VALUE( "value for resource consed.autoReportPrintReadNamesInRegion must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.autoReportPrintReadNamesInRegionContig" ) { pRes->soAutoReportPrintReadNamesInRegionContig_ = soResourceValue; return; } if ( soResourceName == "consed.autoReportPrintReadNamesInRegionLeftPos" ) { if ( !bIsNumericMaybeWithWhitespace( soResourceValue, pRes->nAutoReportPrintReadNamesInRegionLeftPos_ ) ) BAD_VALUE( "value for resource consed.autoReportPrintReadNamesInRegionLeftPos must be numeric", soResourceValue ) return; } if ( soResourceName == "consed.autoReportPrintReadNamesInRegionRightPos" ) { if ( !bIsNumericMaybeWithWhitespace( soResourceValue, pRes->nAutoReportPrintReadNamesInRegionRightPos_ ) ) BAD_VALUE( "value for resource consed.autoReportPrintReadNamesInRegionRightPos must be numeric", soResourceValue ) return; } if ( soResourceName == "consed.autoReportPrintHighlyDiscrepantRegions" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bAutoReportPrintHighlyDiscrepantRegions_ = true; else if ( soResourceValue == "false" ) pRes->bAutoReportPrintHighlyDiscrepantRegions_ = false; else BAD_VALUE( "value for resource consed.autoReportPrintHighlyDiscrepantRegions must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.autoReportPrintScaffolds" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bAutoReportPrintScaffolds_ = true; else if ( soResourceValue == "false" ) pRes->bAutoReportPrintScaffolds_ = false; else BAD_VALUE( "value for resource consed.autoReportPrintScaffolds must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.numberUnpaddedConsensusAtUserDefined" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bNumberUnpaddedConsensusAtUserDefined_ = true; else if ( soResourceValue == "false" ) pRes->bNumberUnpaddedConsensusAtUserDefined_ = false; else BAD_VALUE( "value for resource consed.numberUnpaddedConsensusAtUserDefined must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.autoReportPrintHighQualityDiscrepancies" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bAutoReportPrintHighQualityDiscrepancies_ = true; else if ( soResourceValue == "false" ) pRes->bAutoReportPrintHighQualityDiscrepancies_ = false; else BAD_VALUE( "value for resource consed.autoReportPrintHighQualityDiscrepancies must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.autoReportHighQualityDiscrepanciesExcludeCompressionOrG_dropoutTags" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bAutoReportHighQualityDiscrepanciesExcludeCompressionOrG_dropoutTags_ = true; else if ( soResourceValue == "false" ) pRes->bAutoReportHighQualityDiscrepanciesExcludeCompressionOrG_dropoutTags_ = false; else BAD_VALUE( "value for resource consed.autoReportHighQualityDiscrepanciesExcludeCompressionOrG_dropoutTags must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.autoReportHighQualityDiscrepanciesExcludeMostPads" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bAutoReportHighQualityDiscrepanciesExcludeMostPads_ = true; else if ( soResourceValue == "false" ) pRes->bAutoReportHighQualityDiscrepanciesExcludeMostPads_ = false; else BAD_VALUE( "value for resource consed.autoReportHighQualityDiscrepanciesExcludeMostPads must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.autoReportPrintLowConsensusQualityRegions" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bAutoReportPrintLowConsensusQualityRegions_ = true; else if ( soResourceValue == "false" ) pRes->bAutoReportPrintLowConsensusQualityRegions_ = false; else BAD_VALUE( "value for resource consed.autoReportPrintLowConsensusQualityRegions must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.autoReportPrintSingleSubcloneRegions" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bAutoReportPrintSingleSubcloneRegions_ = true; else if ( soResourceValue == "false" ) pRes->bAutoReportPrintSingleSubcloneRegions_ = false; else BAD_VALUE( "value for resource consed.autoReportPrintSingleSubcloneRegions must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.autoReportPrintSingleStrandedRegions" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bAutoReportPrintSingleStrandedRegions_ = true; else if ( soResourceValue == "false" ) pRes->bAutoReportPrintSingleStrandedRegions_ = false; else BAD_VALUE( "value for resource consed.autoReportPrintSingleStrandedRegions must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.autoReportPrintLinkingForwardReversePairs" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bAutoReportPrintLinkingForwardReversePairs_ = true; else if ( soResourceValue == "false" ) pRes->bAutoReportPrintLinkingForwardReversePairs_ = false; else BAD_VALUE( "value for resource consed.autoReportPrintLinkingForwardReversePairs must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.autoReportPrintFilteredInconsistentForwardReversePairs" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bAutoReportPrintFilteredInconsistentForwardReversePairs_ = true; else if ( soResourceValue == "false" ) pRes->bAutoReportPrintFilteredInconsistentForwardReversePairs_ = false; else BAD_VALUE( "value for resource consed.autoReportPrintFilteredInconsistentForwardReversePairs must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.autoReportPrintAssemblySummary" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bAutoReportPrintAssemblySummary_ = true; else if ( soResourceValue == "false" ) pRes->bAutoReportPrintAssemblySummary_ = false; else BAD_VALUE( "value for resource consed.autoReportPrintAssemblySummary must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.showAllTracesDoNotShowTraceIfTheseTagsPresent" ) { pRes->soShowAllTracesDoNotShowTraceIfTheseTagsPresent_ = soResourceValue; return; } if ( soResourceName == "consed.nameOfFakeJoiningReadsIncludesAceFileName" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bNameOfFakeJoiningReadsIncludesAceFileName_ = true; else if ( soResourceValue == "false" ) pRes->bNameOfFakeJoiningReadsIncludesAceFileName_ = false; else BAD_VALUE( "value for resource consed.nameOfFakeJoiningReadsIncludesAceFileName must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.whenUserScrollsOffWindowMillisecondsBetweenScrolling" ) { if ( !bIsNumericMaybeWithWhitespace( soResourceValue, pRes->nWhenUserScrollsOffWindowMillisecondsBetweenScrolling_ ) ) BAD_VALUE( "value for resource consed.whenUserScrollsOffWindowMillisecondsBetweenScrolling must be numeric", soResourceValue ) return; } if ( soResourceName == "consed.whenUserScrollsOffWindowBasesToScrollEachTime" ) { if ( !bIsNumericMaybeWithWhitespace( soResourceValue, pRes->nWhenUserScrollsOffWindowBasesToScrollEachTime_ ) ) BAD_VALUE( "value for resource consed.whenUserScrollsOffWindowBasesToScrollEachTime must be numeric", soResourceValue ) return; } if ( soResourceName == "consed.compareContigsUseBandedRatherThanFullSmithWaterman" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bCompareContigsUseBandedRatherThanFullSmithWaterman_ = true; else if ( soResourceValue == "false" ) pRes->bCompareContigsUseBandedRatherThanFullSmithWaterman_ = false; else BAD_VALUE( "value for resource consed.compareContigsUseBandedRatherThanFullSmithWaterman must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.compareContigsBandSize" ) { if ( !bIsNumericMaybeWithWhitespace( soResourceValue, pRes->nCompareContigsBandSize_ ) ) BAD_VALUE( "value for resource consed.compareContigsBandSize must be numeric", soResourceValue ) return; } if ( soResourceName == "consed.assemblyViewShowFwdRevPairDepthsInRedIfOnlyThisMany" ) { if ( !bIsNumericMaybeWithWhitespace( soResourceValue, pRes->nAssemblyViewShowFwdRevPairDepthsInRedIfOnlyThisMany_ ) ) BAD_VALUE( "value for resource consed.assemblyViewShowFwdRevPairDepthsInRedIfOnlyThisMany must be numeric", soResourceValue ) return; } if ( soResourceName == "consed.assemblyViewShowSequenceMatches" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bAssemblyViewShowSequenceMatches_ = true; else if ( soResourceValue == "false" ) pRes->bAssemblyViewShowSequenceMatches_ = false; else BAD_VALUE( "value for resource consed.assemblyViewShowSequenceMatches must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.assemblyViewOKToShowSequenceMatchesBetweenContigs" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bAssemblyViewOKToShowSequenceMatchesBetweenContigs_ = true; else if ( soResourceValue == "false" ) pRes->bAssemblyViewOKToShowSequenceMatchesBetweenContigs_ = false; else BAD_VALUE( "value for resource consed.assemblyViewOKToShowSequenceMatchesBetweenContigs must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.assemblyViewOKToShowSequenceMatchesWithinContigs" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bAssemblyViewOKToShowSequenceMatchesWithinContigs_ = true; else if ( soResourceValue == "false" ) pRes->bAssemblyViewOKToShowSequenceMatchesWithinContigs_ = false; else BAD_VALUE( "value for resource consed.assemblyViewOKToShowSequenceMatchesWithinContigs must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.assemblyViewOKToShowDirectSequenceMatches" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bAssemblyViewOKToShowDirectSequenceMatches_ = true; else if ( soResourceValue == "false" ) pRes->bAssemblyViewOKToShowDirectSequenceMatches_ = false; else BAD_VALUE( "value for resource consed.assemblyViewOKToShowDirectSequenceMatches must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.assemblyViewOKToShowInvertedSequenceMatches" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bAssemblyViewOKToShowInvertedSequenceMatches_ = true; else if ( soResourceValue == "false" ) pRes->bAssemblyViewOKToShowInvertedSequenceMatches_ = false; else BAD_VALUE( "value for resource consed.assemblyViewOKToShowInvertedSequenceMatches must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.assemblyViewOnlyShowSequenceMatchesToAParticularRegion" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bAssemblyViewOnlyShowSequenceMatchesToAParticularRegion_ = true; else if ( soResourceValue == "false" ) pRes->bAssemblyViewOnlyShowSequenceMatchesToAParticularRegion_ = false; else BAD_VALUE( "value for resource consed.assemblyViewOnlyShowSequenceMatchesToAParticularRegion must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.assemblyViewOnlyShowSequenceMatchesToThisContig" ) { pRes->soAssemblyViewOnlyShowSequenceMatchesToThisContig_ = soResourceValue; return; } if ( soResourceName == "consed.assemblyViewOnlyShowSequenceMatchesToThisRegionLeft" ) { if ( !bIsNumericMaybeWithWhitespace( soResourceValue, pRes->nAssemblyViewOnlyShowSequenceMatchesToThisRegionLeft_ ) ) BAD_VALUE( "value for resource consed.assemblyViewOnlyShowSequenceMatchesToThisRegionLeft must be numeric", soResourceValue ) return; } if ( soResourceName == "consed.assemblyViewOnlyShowSequenceMatchesToThisRegionRight" ) { if ( !bIsNumericMaybeWithWhitespace( soResourceValue, pRes->nAssemblyViewOnlyShowSequenceMatchesToThisRegionRight_ ) ) BAD_VALUE( "value for resource consed.assemblyViewOnlyShowSequenceMatchesToThisRegionRight must be numeric", soResourceValue ) return; } if ( soResourceName == "consed.assemblyViewOnlyShowSequenceMatchesToEndsOfContigs" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bAssemblyViewOnlyShowSequenceMatchesToEndsOfContigs_ = true; else if ( soResourceValue == "false" ) pRes->bAssemblyViewOnlyShowSequenceMatchesToEndsOfContigs_ = false; else BAD_VALUE( "value for resource consed.assemblyViewOnlyShowSequenceMatchesToEndsOfContigs must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.assemblyViewOnlyShowSequenceMatchesToEndsOfContigsThisFar" ) { if ( !bIsNumericMaybeWithWhitespace( soResourceValue, pRes->nAssemblyViewOnlyShowSequenceMatchesToEndsOfContigsThisFar_ ) ) BAD_VALUE( "value for resource consed.assemblyViewOnlyShowSequenceMatchesToEndsOfContigsThisFar must be numeric", soResourceValue ) return; } if ( soResourceName == "consed.defaultReadPrefix" ) { pRes->soDefaultReadPrefix_ = soResourceValue; return; } if ( soResourceName == "consed.readPrefixesFile" ) { pRes->filReadPrefixesFile_ = soResourceValue; return; } if ( soResourceName == "consed.maxCharsDisplayedForReadPrefix" ) { if ( !bIsNumericMaybeWithWhitespace( soResourceValue, pRes->nMaxCharsDisplayedForReadPrefix_ ) ) BAD_VALUE( "value for resource consed.maxCharsDisplayedForReadPrefix must be numeric", soResourceValue ) return; } if ( soResourceName == "consed.autoFinishDoNotDoPCRIfThisManyAvailableGapSpanningTemplates" ) { if ( !bIsNumericMaybeWithWhitespace( soResourceValue, pRes->nAutoFinishDoNotDoPCRIfThisManyAvailableGapSpanningTemplates_ ) ) BAD_VALUE( "value for resource consed.autoFinishDoNotDoPCRIfThisManyAvailableGapSpanningTemplates must be numeric", soResourceValue ) return; } if ( soResourceName == "consed.autoFinishDoNotDoUnorientedPCRIfThisManyOrMoreUnorientedPCRReactions" ) { if ( !bIsNumericMaybeWithWhitespace( soResourceValue, pRes->nAutoFinishDoNotDoUnorientedPCRIfThisManyOrMoreUnorientedPCRReactions_ ) ) BAD_VALUE( "value for resource consed.autoFinishDoNotDoUnorientedPCRIfThisManyOrMoreUnorientedPCRReactions must be numeric", soResourceValue ) return; } if ( soResourceName == "consed.autoFinishDoNotDoOrientedPCRIfGapSizeLargerThanThis" ) { if ( !bIsNumericMaybeWithWhitespace( soResourceValue, pRes->nAutoFinishDoNotDoOrientedPCRIfGapSizeLargerThanThis_ ) ) BAD_VALUE( "value for resource consed.autoFinishDoNotDoOrientedPCRIfGapSizeLargerThanThis must be numeric", soResourceValue ) return; } if ( soResourceName == "consed.autoFinishDoNotDoPCRIfEndIsExtendedByReads" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bAutoFinishDoNotDoPCRIfEndIsExtendedByReads_ = true; else if ( soResourceValue == "false" ) pRes->bAutoFinishDoNotDoPCRIfEndIsExtendedByReads_ = false; else BAD_VALUE( "value for resource consed.autoFinishDoNotDoPCRIfEndIsExtendedByReads must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.autoFinishMaxAcceptableErrorsPerMegabase" ) { if ( !bIsNumericMaybeWithWhitespace( soResourceValue, pRes->nAutoFinishMaxAcceptableErrorsPerMegabase_ ) ) BAD_VALUE( "value for resource consed.autoFinishMaxAcceptableErrorsPerMegabase must be numeric", soResourceValue ) return; } if ( soResourceName == "consed.autoFinishIfNotEnoughFwdRevPairsUseThisPerCentOfInsertSize" ) { if ( !bIsNumericMaybeWithWhitespace( soResourceValue, pRes->nAutoFinishIfNotEnoughFwdRevPairsUseThisPerCentOfInsertSize_ ) ) BAD_VALUE( "value for resource consed.autoFinishIfNotEnoughFwdRevPairsUseThisPerCentOfInsertSize must be numeric", soResourceValue ) return; } if ( soResourceName == "consed.primersNumberOfBasesToBackUpToStartLooking" ) { if ( !bIsNumericMaybeWithWhitespace( soResourceValue, pRes->nPrimersNumberOfBasesToBackUpToStartLooking_ ) ) BAD_VALUE( "value for resource consed.primersNumberOfBasesToBackUpToStartLooking must be numeric", soResourceValue ) return; } if ( soResourceName == "consed.primersMakePCRPrimersThisManyBasesBackFromEndOfHighQualitySegment" ) { if ( !bIsNumericMaybeWithWhitespace( soResourceValue, pRes->nPrimersMakePCRPrimersThisManyBasesBackFromEndOfHighQualitySegment_ ) ) BAD_VALUE( "value for resource consed.primersMakePCRPrimersThisManyBasesBackFromEndOfHighQualitySegment must be numeric", soResourceValue ) return; } if ( soResourceName == "consed.primersOKToChoosePrimersInSingleSubcloneRegion" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bPrimersOKToChoosePrimersInSingleSubcloneRegion_ = true; else if ( soResourceValue == "false" ) pRes->bPrimersOKToChoosePrimersInSingleSubcloneRegion_ = false; else BAD_VALUE( "value for resource consed.primersOKToChoosePrimersInSingleSubcloneRegion must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.primersOKToChoosePrimersWhereHighQualityDiscrepancies" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bPrimersOKToChoosePrimersWhereHighQualityDiscrepancies_ = true; else if ( soResourceValue == "false" ) pRes->bPrimersOKToChoosePrimersWhereHighQualityDiscrepancies_ = false; else BAD_VALUE( "value for resource consed.primersOKToChoosePrimersWhereHighQualityDiscrepancies must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.primersOKToChoosePrimersWhereUnalignedHighQualityRegion" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bPrimersOKToChoosePrimersWhereUnalignedHighQualityRegion_ = true; else if ( soResourceValue == "false" ) pRes->bPrimersOKToChoosePrimersWhereUnalignedHighQualityRegion_ = false; else BAD_VALUE( "value for resource consed.primersOKToChoosePrimersWhereUnalignedHighQualityRegion must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.autoFinishCallReversesToFlankGaps" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bAutoFinishCallReversesToFlankGaps_ = true; else if ( soResourceValue == "false" ) pRes->bAutoFinishCallReversesToFlankGaps_ = false; else BAD_VALUE( "value for resource consed.autoFinishCallReversesToFlankGaps must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.autoFinishAllowWholeCloneReads" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bAutoFinishAllowWholeCloneReads_ = true; else if ( soResourceValue == "false" ) pRes->bAutoFinishAllowWholeCloneReads_ = false; else BAD_VALUE( "value for resource consed.autoFinishAllowWholeCloneReads must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.autoFinishAllowCustomPrimerSubcloneReads" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bAutoFinishAllowCustomPrimerSubcloneReads_ = true; else if ( soResourceValue == "false" ) pRes->bAutoFinishAllowCustomPrimerSubcloneReads_ = false; else BAD_VALUE( "value for resource consed.autoFinishAllowCustomPrimerSubcloneReads must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.autoFinishAllowResequencingReads" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bAutoFinishAllowResequencingReads_ = true; else if ( soResourceValue == "false" ) pRes->bAutoFinishAllowResequencingReads_ = false; else BAD_VALUE( "value for resource consed.autoFinishAllowResequencingReads must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.autoFinishAllowResequencingReadsOnlyForRunsAndStops" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bAutoFinishAllowResequencingReadsOnlyForRunsAndStops_ = true; else if ( soResourceValue == "false" ) pRes->bAutoFinishAllowResequencingReadsOnlyForRunsAndStops_ = false; else BAD_VALUE( "value for resource consed.autoFinishAllowResequencingReadsOnlyForRunsAndStops must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.autoFinishAllowDeNovoUniversalPrimerSubcloneReads" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bAutoFinishAllowDeNovoUniversalPrimerSubcloneReads_ = true; else if ( soResourceValue == "false" ) pRes->bAutoFinishAllowDeNovoUniversalPrimerSubcloneReads_ = false; else BAD_VALUE( "value for resource consed.autoFinishAllowDeNovoUniversalPrimerSubcloneReads must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.autoFinishAllowMinilibraries" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bAutoFinishAllowMinilibraries_ = true; else if ( soResourceValue == "false" ) pRes->bAutoFinishAllowMinilibraries_ = false; else BAD_VALUE( "value for resource consed.autoFinishAllowMinilibraries must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.autoFinishAllowPCR" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bAutoFinishAllowPCR_ = true; else if ( soResourceValue == "false" ) pRes->bAutoFinishAllowPCR_ = false; else BAD_VALUE( "value for resource consed.autoFinishAllowPCR must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.autoFinishAllowUnorientedPCRReactions" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bAutoFinishAllowUnorientedPCRReactions_ = true; else if ( soResourceValue == "false" ) pRes->bAutoFinishAllowUnorientedPCRReactions_ = false; else BAD_VALUE( "value for resource consed.autoFinishAllowUnorientedPCRReactions must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.autoFinishAllowResequencingAUniversalPrimerAutofinishRead" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bAutoFinishAllowResequencingAUniversalPrimerAutofinishRead_ = true; else if ( soResourceValue == "false" ) pRes->bAutoFinishAllowResequencingAUniversalPrimerAutofinishRead_ = false; else BAD_VALUE( "value for resource consed.autoFinishAllowResequencingAUniversalPrimerAutofinishRead must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.autoFinishAlwaysCloseGapsUsingMinilibraries" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bAutoFinishAlwaysCloseGapsUsingMinilibraries_ = true; else if ( soResourceValue == "false" ) pRes->bAutoFinishAlwaysCloseGapsUsingMinilibraries_ = false; else BAD_VALUE( "value for resource consed.autoFinishAlwaysCloseGapsUsingMinilibraries must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.autoFinishMaximumFinishingReadLength" ) { if ( !bIsNumericMaybeWithWhitespace( soResourceValue, pRes->nAutoFinishMaximumFinishingReadLength_ ) ) BAD_VALUE( "value for resource consed.autoFinishMaximumFinishingReadLength must be numeric", soResourceValue ) return; } if ( soResourceName == "consed.autoFinishSuggestMinilibraryIfGapThisManyBasesOrLarger" ) { if ( !bIsNumericMaybeWithWhitespace( soResourceValue, pRes->nAutoFinishSuggestMinilibraryIfGapThisManyBasesOrLarger_ ) ) BAD_VALUE( "value for resource consed.autoFinishSuggestMinilibraryIfGapThisManyBasesOrLarger must be numeric", soResourceValue ) return; } if ( soResourceName == "consed.autoFinishSuggestSpecialChemistryForRunsAndStops" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bAutoFinishSuggestSpecialChemistryForRunsAndStops_ = true; else if ( soResourceValue == "false" ) pRes->bAutoFinishSuggestSpecialChemistryForRunsAndStops_ = false; else BAD_VALUE( "value for resource consed.autoFinishSuggestSpecialChemistryForRunsAndStops must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.autoFinishSuggestThisManyMinilibrariesPerGap" ) { if ( !bIsNumericMaybeWithWhitespace( soResourceValue, pRes->nAutoFinishSuggestThisManyMinilibrariesPerGap_ ) ) BAD_VALUE( "value for resource consed.autoFinishSuggestThisManyMinilibrariesPerGap must be numeric", soResourceValue ) return; } if ( soResourceName == "consed.primersWindowSizeInLooking" ) { if ( !bIsNumericMaybeWithWhitespace( soResourceValue, pRes->nPrimersWindowSizeInLooking_ ) ) BAD_VALUE( "value for resource consed.primersWindowSizeInLooking must be numeric", soResourceValue ) return; } if ( soResourceName == "consed.primersAssumeTemplatesAreDoubleStrandedUnlessSpecified" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bPrimersAssumeTemplatesAreDoubleStrandedUnlessSpecified_ = true; else if ( soResourceValue == "false" ) pRes->bPrimersAssumeTemplatesAreDoubleStrandedUnlessSpecified_ = false; else BAD_VALUE( "value for resource consed.primersAssumeTemplatesAreDoubleStrandedUnlessSpecified must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.alignedReadsWindowInitialCharsWide" ) { if ( !bIsNumericMaybeWithWhitespace( soResourceValue, pRes->nAlignedReadsWindowInitialCharsWide_ ) ) BAD_VALUE( "value for resource consed.alignedReadsWindowInitialCharsWide must be numeric", soResourceValue ) return; } if ( soResourceName == "consed.alignedReadsWindowInitialCharsHigh" ) { if ( !bIsNumericMaybeWithWhitespace( soResourceValue, pRes->nAlignedReadsWindowInitialCharsHigh_ ) ) BAD_VALUE( "value for resource consed.alignedReadsWindowInitialCharsHigh must be numeric", soResourceValue ) return; } if ( soResourceName == "consed.alignedReadsWindowMaxCharsForReadNames" ) { if ( !bIsNumericMaybeWithWhitespace( soResourceValue, pRes->nAlignedReadsWindowMaxCharsForReadNames_ ) ) BAD_VALUE( "value for resource consed.alignedReadsWindowMaxCharsForReadNames must be numeric", soResourceValue ) return; } if ( soResourceName == "consed.alignedReadsWindowAutomaticallyExpandRoomForReadNames" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bAlignedReadsWindowAutomaticallyExpandRoomForReadNames_ = true; else if ( soResourceValue == "false" ) pRes->bAlignedReadsWindowAutomaticallyExpandRoomForReadNames_ = false; else BAD_VALUE( "value for resource consed.alignedReadsWindowAutomaticallyExpandRoomForReadNames must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.autoFinishAllowResequencingReadsToExtendContigs" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bAutoFinishAllowResequencingReadsToExtendContigs_ = true; else if ( soResourceValue == "false" ) pRes->bAutoFinishAllowResequencingReadsToExtendContigs_ = false; else BAD_VALUE( "value for resource consed.autoFinishAllowResequencingReadsToExtendContigs must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.autoFinishCallHowManyReversesToFlankGaps" ) { if ( !bIsNumericMaybeWithWhitespace( soResourceValue, pRes->nAutoFinishCallHowManyReversesToFlankGaps_ ) ) BAD_VALUE( "value for resource consed.autoFinishCallHowManyReversesToFlankGaps must be numeric", soResourceValue ) return; } if ( soResourceName == "consed.autoFinishCloseGaps" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bAutoFinishCloseGaps_ = true; else if ( soResourceValue == "false" ) pRes->bAutoFinishCloseGaps_ = false; else BAD_VALUE( "value for resource consed.autoFinishCloseGaps must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.autoFinishContinueEvenThoughReadInfoDoesNotMakeSense" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bAutoFinishContinueEvenThoughReadInfoDoesNotMakeSense_ = true; else if ( soResourceValue == "false" ) pRes->bAutoFinishContinueEvenThoughReadInfoDoesNotMakeSense_ = false; else BAD_VALUE( "value for resource consed.autoFinishContinueEvenThoughReadInfoDoesNotMakeSense must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.autoFinishCostOfResequencingUniversalPrimerSubcloneReaction" ) { if ( !bIsNumericDouble( soResourceValue, pRes->dAutoFinishCostOfResequencingUniversalPrimerSubcloneReaction_ ) ) BAD_VALUE( "value for resource consed.autoFinishCostOfResequencingUniversalPrimerSubcloneReaction must be a decimal number", soResourceValue ) return; } if ( soResourceName == "consed.autoFinishCostOfCustomPrimerSubcloneReaction" ) { if ( !bIsNumericDouble( soResourceValue, pRes->dAutoFinishCostOfCustomPrimerSubcloneReaction_ ) ) BAD_VALUE( "value for resource consed.autoFinishCostOfCustomPrimerSubcloneReaction must be a decimal number", soResourceValue ) return; } if ( soResourceName == "consed.autoFinishCostOfCustomPrimerCloneReaction" ) { if ( !bIsNumericDouble( soResourceValue, pRes->dAutoFinishCostOfCustomPrimerCloneReaction_ ) ) BAD_VALUE( "value for resource consed.autoFinishCostOfCustomPrimerCloneReaction must be a decimal number", soResourceValue ) return; } if ( soResourceName == "consed.autoFinishCostOfDeNovoUniversalPrimerSubcloneReaction" ) { if ( !bIsNumericDouble( soResourceValue, pRes->dAutoFinishCostOfDeNovoUniversalPrimerSubcloneReaction_ ) ) BAD_VALUE( "value for resource consed.autoFinishCostOfDeNovoUniversalPrimerSubcloneReaction must be a decimal number", soResourceValue ) return; } if ( soResourceName == "consed.autoFinishCostOfMinilibrary" ) { if ( !bIsNumericDouble( soResourceValue, pRes->dAutoFinishCostOfMinilibrary_ ) ) BAD_VALUE( "value for resource consed.autoFinishCostOfMinilibrary must be a decimal number", soResourceValue ) return; } if ( soResourceName == "consed.autoFinishCoverSingleSubcloneRegions" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bAutoFinishCoverSingleSubcloneRegions_ = true; else if ( soResourceValue == "false" ) pRes->bAutoFinishCoverSingleSubcloneRegions_ = false; else BAD_VALUE( "value for resource consed.autoFinishCoverSingleSubcloneRegions must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.autoFinishCoverLowConsensusQualityRegions" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bAutoFinishCoverLowConsensusQualityRegions_ = true; else if ( soResourceValue == "false" ) pRes->bAutoFinishCoverLowConsensusQualityRegions_ = false; else BAD_VALUE( "value for resource consed.autoFinishCoverLowConsensusQualityRegions must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.autoFinishDebugUniversalPrimerReadsFile" ) { pRes->filAutoFinishDebugUniversalPrimerReadsFile_ = soResourceValue; return; } if ( soResourceName == "consed.autoFinishDebugCustomPrimerReadsFile" ) { pRes->filAutoFinishDebugCustomPrimerReadsFile_ = soResourceValue; return; } if ( soResourceName == "consed.autoFinishDoNotAllowSubcloneCustomPrimerReadsCloserThanThisManyBases" ) { if ( !bIsNumericMaybeWithWhitespace( soResourceValue, pRes->nAutoFinishDoNotAllowSubcloneCustomPrimerReadsCloserThanThisManyBases_ ) ) BAD_VALUE( "value for resource consed.autoFinishDoNotAllowSubcloneCustomPrimerReadsCloserThanThisManyBases must be numeric", soResourceValue ) return; } if ( soResourceName == "consed.autoFinishDoNotAllowWholeCloneCustomPrimerReadsCloserThanThisManyBases" ) { if ( !bIsNumericMaybeWithWhitespace( soResourceValue, pRes->nAutoFinishDoNotAllowWholeCloneCustomPrimerReadsCloserThanThisManyBases_ ) ) BAD_VALUE( "value for resource consed.autoFinishDoNotAllowWholeCloneCustomPrimerReadsCloserThanThisManyBases must be numeric", soResourceValue ) return; } if ( soResourceName == "consed.autoFinishDoNotFinishWhereTheseTagsAre" ) { pRes->soAutoFinishDoNotFinishWhereTheseTagsAre_ = soResourceValue; return; } if ( soResourceName == "consed.autoFinishDoNotExtendContigsWhereTheseTagsAre" ) { pRes->soAutoFinishDoNotExtendContigsWhereTheseTagsAre_ = soResourceValue; return; } if ( soResourceName == "consed.autoFinishDoNotExtendContigsIfTagsAreThisCloseToContigEnd" ) { if ( !bIsNumericMaybeWithWhitespace( soResourceValue, pRes->nAutoFinishDoNotExtendContigsIfTagsAreThisCloseToContigEnd_ ) ) BAD_VALUE( "value for resource consed.autoFinishDoNotExtendContigsIfTagsAreThisCloseToContigEnd must be numeric", soResourceValue ) return; } if ( soResourceName == "consed.dumpContigOrderAndOrientationInfoToThisFile" ) { pRes->filDumpContigOrderAndOrientationInfoToThisFile_ = soResourceValue; return; } if ( soResourceName == "consed.autoFinishDumpTemplates" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bAutoFinishDumpTemplates_ = true; else if ( soResourceValue == "false" ) pRes->bAutoFinishDumpTemplates_ = false; else BAD_VALUE( "value for resource consed.autoFinishDumpTemplates must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.autoFinishExcludeContigIfOnlyThisManyReadsOrLess" ) { if ( !bIsNumericMaybeWithWhitespace( soResourceValue, pRes->nAutoFinishExcludeContigIfOnlyThisManyReadsOrLess_ ) ) BAD_VALUE( "value for resource consed.autoFinishExcludeContigIfOnlyThisManyReadsOrLess must be numeric", soResourceValue ) return; } if ( soResourceName == "consed.autoFinishExcludeContigIfDepthOfCoverageGreaterThanThis" ) { if ( !bIsNumericDouble( soResourceValue, pRes->dAutoFinishExcludeContigIfDepthOfCoverageGreaterThanThis_ ) ) BAD_VALUE( "value for resource consed.autoFinishExcludeContigIfDepthOfCoverageGreaterThanThis must be a decimal number", soResourceValue ) return; } if ( soResourceName == "consed.autoFinishExcludeContigIfThisManyBasesOrLess" ) { if ( !bIsNumericMaybeWithWhitespace( soResourceValue, pRes->nAutoFinishExcludeContigIfThisManyBasesOrLess_ ) ) BAD_VALUE( "value for resource consed.autoFinishExcludeContigIfThisManyBasesOrLess must be numeric", soResourceValue ) return; } if ( soResourceName == "consed.autoFinishHowManyTemplatesYouIntendToUseForCustomPrimerSubcloneReactions" ) { if ( !bIsNumericMaybeWithWhitespace( soResourceValue, pRes->nAutoFinishHowManyTemplatesYouIntendToUseForCustomPrimerSubcloneReactions_ ) ) BAD_VALUE( "value for resource consed.autoFinishHowManyTemplatesYouIntendToUseForCustomPrimerSubcloneReactions must be numeric", soResourceValue ) return; } if ( soResourceName == "consed.primersMinNumberOfTemplatesForPrimers" ) { if ( !bIsNumericMaybeWithWhitespace( soResourceValue, pRes->nPrimersMinNumberOfTemplatesForPrimers_ ) ) BAD_VALUE( "value for resource consed.primersMinNumberOfTemplatesForPrimers must be numeric", soResourceValue ) return; } if ( soResourceName == "consed.autoFinishMinBaseOverlapBetweenAReadAndHighQualitySegmentOfConsensus" ) { if ( !bIsNumericMaybeWithWhitespace( soResourceValue, pRes->nAutoFinishMinBaseOverlapBetweenAReadAndHighQualitySegmentOfConsensus_ ) ) BAD_VALUE( "value for resource consed.autoFinishMinBaseOverlapBetweenAReadAndHighQualitySegmentOfConsensus must be numeric", soResourceValue ) return; } if ( soResourceName == "consed.autoFinishNumberOfVectorBasesAtBeginningOfAUniveralPrimerRead" ) { if ( !bIsNumericMaybeWithWhitespace( soResourceValue, pRes->nAutoFinishNumberOfVectorBasesAtBeginningOfAUniveralPrimerRead_ ) ) BAD_VALUE( "value for resource consed.autoFinishNumberOfVectorBasesAtBeginningOfAUniveralPrimerRead must be numeric", soResourceValue ) return; } if ( soResourceName == "consed.autoFinishCDNANotGenomic" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bAutoFinishCDNANotGenomic_ = true; else if ( soResourceValue == "false" ) pRes->bAutoFinishCDNANotGenomic_ = false; else BAD_VALUE( "value for resource consed.autoFinishCDNANotGenomic must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.autoFinishConfidenceThatReadWillCoverSingleSubcloneRegion" ) { if ( !bIsNumericMaybeWithWhitespace( soResourceValue, pRes->nAutoFinishConfidenceThatReadWillCoverSingleSubcloneRegion_ ) ) BAD_VALUE( "value for resource consed.autoFinishConfidenceThatReadWillCoverSingleSubcloneRegion must be numeric", soResourceValue ) return; } if ( soResourceName == "consed.autoFinishPrintForwardOrReverseStrandWhenPrintingSubcloneTemplatesForCustomPrimerReads" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bAutoFinishPrintForwardOrReverseStrandWhenPrintingSubcloneTemplatesForCustomPrimerReads_ = true; else if ( soResourceValue == "false" ) pRes->bAutoFinishPrintForwardOrReverseStrandWhenPrintingSubcloneTemplatesForCustomPrimerReads_ = false; else BAD_VALUE( "value for resource consed.autoFinishPrintForwardOrReverseStrandWhenPrintingSubcloneTemplatesForCustomPrimerReads must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.autoFinishPrintMinilibrariesSummaryFile" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bAutoFinishPrintMinilibrariesSummaryFile_ = true; else if ( soResourceValue == "false" ) pRes->bAutoFinishPrintMinilibrariesSummaryFile_ = false; else BAD_VALUE( "value for resource consed.autoFinishPrintMinilibrariesSummaryFile must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.autoFinishNearGapsSuggestEachMissingReadOfReadPairs" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bAutoFinishNearGapsSuggestEachMissingReadOfReadPairs_ = true; else if ( soResourceValue == "false" ) pRes->bAutoFinishNearGapsSuggestEachMissingReadOfReadPairs_ = false; else BAD_VALUE( "value for resource consed.autoFinishNearGapsSuggestEachMissingReadOfReadPairs must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.autoFinishDoNotIgnoreLCQIfThisManyBasesFromEndOfContigForLCQTagger" ) { if ( !bIsNumericMaybeWithWhitespace( soResourceValue, pRes->nAutoFinishDoNotIgnoreLCQIfThisManyBasesFromEndOfContigForLCQTagger_ ) ) BAD_VALUE( "value for resource consed.autoFinishDoNotIgnoreLCQIfThisManyBasesFromEndOfContigForLCQTagger must be numeric", soResourceValue ) return; } if ( soResourceName == "consed.checkIfTooManyWalks" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bCheckIfTooManyWalks_ = true; else if ( soResourceValue == "false" ) pRes->bCheckIfTooManyWalks_ = false; else BAD_VALUE( "value for resource consed.checkIfTooManyWalks must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.numberOfColumnsBeforeReadNameInAlignedReadsWindow" ) { if ( !bIsNumericMaybeWithWhitespace( soResourceValue, pRes->nNumberOfColumnsBeforeReadNameInAlignedReadsWindow_ ) ) BAD_VALUE( "value for resource consed.numberOfColumnsBeforeReadNameInAlignedReadsWindow must be numeric", soResourceValue ) return; } if ( soResourceName == "consed.compareContigsAlignsThisManyBasesMax" ) { if ( !bIsNumericMaybeWithWhitespace( soResourceValue, pRes->nCompareContigsAlignsThisManyBasesMax_ ) ) BAD_VALUE( "value for resource consed.compareContigsAlignsThisManyBasesMax must be numeric", soResourceValue ) return; } if ( soResourceName == "consed.compressedChromatExtension" ) { pRes->soCompressedChromatExtension_ = soResourceValue; return; } if ( soResourceName == "consed.dimLowQualityEndsOfReads" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bDimLowQualityEndsOfReads_ = true; else if ( soResourceValue == "false" ) pRes->bDimLowQualityEndsOfReads_ = false; else BAD_VALUE( "value for resource consed.dimLowQualityEndsOfReads must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.dimUnalignedEndsOfReads" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bDimUnalignedEndsOfReads_ = true; else if ( soResourceValue == "false" ) pRes->bDimUnalignedEndsOfReads_ = false; else BAD_VALUE( "value for resource consed.dimUnalignedEndsOfReads must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.fakeReadsSpecifiedByFilenameExtension" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bFakeReadsSpecifiedByFilenameExtension_ = true; else if ( soResourceValue == "false" ) pRes->bFakeReadsSpecifiedByFilenameExtension_ = false; else BAD_VALUE( "value for resource consed.fakeReadsSpecifiedByFilenameExtension must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.fullPathnameOfAddReads2ConsedScript" ) { pRes->filFullPathnameOfAddReads2ConsedScript_ = soResourceValue; return; } if ( soResourceName == "consed.fullPathnameOfFixContigEndScript" ) { pRes->filFullPathnameOfFixContigEndScript_ = soResourceValue; return; } if ( soResourceName == "consed.fixContigEndsCleanUpTemporaryFiles" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bFixContigEndsCleanUpTemporaryFiles_ = true; else if ( soResourceValue == "false" ) pRes->bFixContigEndsCleanUpTemporaryFiles_ = false; else BAD_VALUE( "value for resource consed.fixContigEndsCleanUpTemporaryFiles must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.fixContigEndsMinSmithWatermanScoreToMakeJoin" ) { if ( !bIsNumericMaybeWithWhitespace( soResourceValue, pRes->nFixContigEndsMinSmithWatermanScoreToMakeJoin_ ) ) BAD_VALUE( "value for resource consed.fixContigEndsMinSmithWatermanScoreToMakeJoin must be numeric", soResourceValue ) return; } if ( soResourceName == "consed.fixContigEndsMinNumberOfReadsInContig" ) { if ( !bIsNumericMaybeWithWhitespace( soResourceValue, pRes->nFixContigEndsMinNumberOfReadsInContig_ ) ) BAD_VALUE( "value for resource consed.fixContigEndsMinNumberOfReadsInContig must be numeric", soResourceValue ) return; } if ( soResourceName == "consed.fullPathnameOfCrossMatch" ) { pRes->filFullPathnameOfCrossMatch_ = soResourceValue; return; } if ( soResourceName == "consed.fullPathnameOfPhred" ) { pRes->filFullPathnameOfPhred_ = soResourceValue; return; } if ( soResourceName == "consed.fullPathnameOfMiniassemblyScript" ) { pRes->filFullPathnameOfMiniassemblyScript_ = soResourceValue; return; } if ( soResourceName == "consed.gunzipFullPath" ) { pRes->soGunzipFullPath_ = soResourceValue; return; } if ( soResourceName == "consed.fullPathnameOfFilter454ReadsScript" ) { pRes->filFullPathnameOfFilter454ReadsScript_ = soResourceValue; return; } if ( soResourceName == "consed.filter454ReadsAgainstThis" ) { pRes->filFilter454ReadsAgainstThis_ = soResourceValue; return; } if ( soResourceName == "consed.454LinkerSequences" ) { pRes->fil454LinkerSequences_ = soResourceValue; return; } if ( soResourceName == "consed.hideSomeTagTypesAtStartup" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bHideSomeTagTypesAtStartup_ = true; else if ( soResourceValue == "false" ) pRes->bHideSomeTagTypesAtStartup_ = false; else BAD_VALUE( "value for resource consed.hideSomeTagTypesAtStartup must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.maximumNumberOfTracesShown" ) { if ( !bIsNumericMaybeWithWhitespace( soResourceValue, pRes->nMaximumNumberOfTracesShown_ ) ) BAD_VALUE( "value for resource consed.maximumNumberOfTracesShown must be numeric", soResourceValue ) return; } if ( soResourceName == "consed.navigateAutomaticTracePopup" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bNavigateAutomaticTracePopup_ = true; else if ( soResourceValue == "false" ) pRes->bNavigateAutomaticTracePopup_ = false; else BAD_VALUE( "value for resource consed.navigateAutomaticTracePopup must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.navigateAutomaticAllTracesPopup" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bNavigateAutomaticAllTracesPopup_ = true; else if ( soResourceValue == "false" ) pRes->bNavigateAutomaticAllTracesPopup_ = false; else BAD_VALUE( "value for resource consed.navigateAutomaticAllTracesPopup must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.primersMinimumLengthOfAPrimer" ) { if ( !bIsNumericMaybeWithWhitespace( soResourceValue, pRes->nPrimersMinimumLengthOfAPrimer_ ) ) BAD_VALUE( "value for resource consed.primersMinimumLengthOfAPrimer must be numeric", soResourceValue ) return; } if ( soResourceName == "consed.primersMaximumLengthOfAPrimer" ) { if ( !bIsNumericMaybeWithWhitespace( soResourceValue, pRes->nPrimersMaximumLengthOfAPrimer_ ) ) BAD_VALUE( "value for resource consed.primersMaximumLengthOfAPrimer must be numeric", soResourceValue ) return; } if ( soResourceName == "consed.primersMinimumLengthOfAPrimerForPCR" ) { if ( !bIsNumericMaybeWithWhitespace( soResourceValue, pRes->nPrimersMinimumLengthOfAPrimerForPCR_ ) ) BAD_VALUE( "value for resource consed.primersMinimumLengthOfAPrimerForPCR must be numeric", soResourceValue ) return; } if ( soResourceName == "consed.primersMaximumLengthOfAPrimerForPCR" ) { if ( !bIsNumericMaybeWithWhitespace( soResourceValue, pRes->nPrimersMaximumLengthOfAPrimerForPCR_ ) ) BAD_VALUE( "value for resource consed.primersMaximumLengthOfAPrimerForPCR must be numeric", soResourceValue ) return; } if ( soResourceName == "consed.primersMaxMeltingTempDifferenceForPCR" ) { if ( !bIsNumericDouble( soResourceValue, pRes->dPrimersMaxMeltingTempDifferenceForPCR_ ) ) BAD_VALUE( "value for resource consed.primersMaxMeltingTempDifferenceForPCR must be a decimal number", soResourceValue ) return; } if ( soResourceName == "consed.primersMaxPCRPrimerPairsToDisplay" ) { if ( !bIsNumericMaybeWithWhitespace( soResourceValue, pRes->nPrimersMaxPCRPrimerPairsToDisplay_ ) ) BAD_VALUE( "value for resource consed.primersMaxPCRPrimerPairsToDisplay must be numeric", soResourceValue ) return; } if ( soResourceName == "consed.primersCheckJustSomePCRPrimerPairsRatherThanAll" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bPrimersCheckJustSomePCRPrimerPairsRatherThanAll_ = true; else if ( soResourceValue == "false" ) pRes->bPrimersCheckJustSomePCRPrimerPairsRatherThanAll_ = false; else BAD_VALUE( "value for resource consed.primersCheckJustSomePCRPrimerPairsRatherThanAll must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.primersNumberOfTemplatesToDisplayInFront" ) { if ( !bIsNumericMaybeWithWhitespace( soResourceValue, pRes->nPrimersNumberOfTemplatesToDisplayInFront_ ) ) BAD_VALUE( "value for resource consed.primersNumberOfTemplatesToDisplayInFront must be numeric", soResourceValue ) return; } if ( soResourceName == "consed.primersMaxLengthOfMononucleotideRepeat" ) { if ( !bIsNumericMaybeWithWhitespace( soResourceValue, pRes->nPrimersMaxLengthOfMononucleotideRepeat_ ) ) BAD_VALUE( "value for resource consed.primersMaxLengthOfMononucleotideRepeat must be numeric", soResourceValue ) return; } if ( soResourceName == "consed.primersBadLibrariesFile" ) { pRes->filPrimersBadLibrariesFile_ = soResourceValue; return; } if ( soResourceName == "consed.primersLibrariesInfoFile" ) { pRes->filPrimersLibrariesInfoFile_ = soResourceValue; return; } if ( soResourceName == "consed.primersBadTemplatesFile" ) { pRes->filPrimersBadTemplatesFile_ = soResourceValue; return; } if ( soResourceName == "consed.primersChooseTemplatesByPositionInsteadOfQuality" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bPrimersChooseTemplatesByPositionInsteadOfQuality_ = true; else if ( soResourceValue == "false" ) pRes->bPrimersChooseTemplatesByPositionInsteadOfQuality_ = false; else BAD_VALUE( "value for resource consed.primersChooseTemplatesByPositionInsteadOfQuality must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.primersWhenChoosingATemplateMinPotentialReadLength" ) { if ( !bIsNumericMaybeWithWhitespace( soResourceValue, pRes->nPrimersWhenChoosingATemplateMinPotentialReadLength_ ) ) BAD_VALUE( "value for resource consed.primersWhenChoosingATemplateMinPotentialReadLength must be numeric", soResourceValue ) return; } if ( soResourceName == "consed.primersWindowSizeInLookingForPCR" ) { if ( !bIsNumericMaybeWithWhitespace( soResourceValue, pRes->nPrimersWindowSizeInLookingForPCR_ ) ) BAD_VALUE( "value for resource consed.primersWindowSizeInLookingForPCR must be numeric", soResourceValue ) return; } if ( soResourceName == "consed.qualityThresholdForFindingHighQualityDiscrepancies" ) { if ( !bIsNumericMaybeWithWhitespace( soResourceValue, pRes->nQualityThresholdForFindingHighQualityDiscrepancies_ ) ) BAD_VALUE( "value for resource consed.qualityThresholdForFindingHighQualityDiscrepancies must be numeric", soResourceValue ) return; } if ( soResourceName == "consed.qualityThresholdForNavigateByDepthOfCoverage" ) { if ( !bIsNumericMaybeWithWhitespace( soResourceValue, pRes->nQualityThresholdForNavigateByDepthOfCoverage_ ) ) BAD_VALUE( "value for resource consed.qualityThresholdForNavigateByDepthOfCoverage must be numeric", soResourceValue ) return; } if ( soResourceName == "consed.navigateByHighDepthOfCoverageNotLow" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bNavigateByHighDepthOfCoverageNotLow_ = true; else if ( soResourceValue == "false" ) pRes->bNavigateByHighDepthOfCoverageNotLow_ = false; else BAD_VALUE( "value for resource consed.navigateByHighDepthOfCoverageNotLow must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.MinDepthForNavigateByDepthOfCoverage" ) { if ( !bIsNumericMaybeWithWhitespace( soResourceValue, pRes->nMinDepthForNavigateByDepthOfCoverage_ ) ) BAD_VALUE( "value for resource consed.MinDepthForNavigateByDepthOfCoverage must be numeric", soResourceValue ) return; } if ( soResourceName == "consed.defaultVectorPathnameForRestrictionFragments" ) { pRes->filDefaultVectorPathnameForRestrictionFragments_ = soResourceValue; return; } if ( soResourceName == "consed.fileOfAdditionalRestrictionEnzymes" ) { pRes->filFileOfAdditionalRestrictionEnzymes_ = soResourceValue; return; } if ( soResourceName == "consed.commonRestrictionEnzymes" ) { pRes->soCommonRestrictionEnzymes_ = soResourceValue; return; } if ( soResourceName == "consed.defaultSelectedRestrictionEnzymes" ) { pRes->soDefaultSelectedRestrictionEnzymes_ = soResourceValue; return; } if ( soResourceName == "consed.restrictionEnzymesActualFragmentsFile" ) { pRes->filRestrictionEnzymesActualFragmentsFile_ = soResourceValue; return; } if ( soResourceName == "consed.restrictionDigestInitialWindowSizeInTextRows" ) { if ( !bIsNumericMaybeWithWhitespace( soResourceValue, pRes->nRestrictionDigestInitialWindowSizeInTextRows_ ) ) BAD_VALUE( "value for resource consed.restrictionDigestInitialWindowSizeInTextRows must be numeric", soResourceValue ) return; } if ( soResourceName == "consed.restrictionDigestDoNoShowAreaOfFragmentsOverThisSize" ) { if ( !bIsNumericMaybeWithWhitespace( soResourceValue, pRes->nRestrictionDigestDoNoShowAreaOfFragmentsOverThisSize_ ) ) BAD_VALUE( "value for resource consed.restrictionDigestDoNoShowAreaOfFragmentsOverThisSize must be numeric", soResourceValue ) return; } if ( soResourceName == "consed.showReadsAlphabetically" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bShowReadsAlphabetically_ = true; else if ( soResourceValue == "false" ) pRes->bShowReadsAlphabetically_ = false; else BAD_VALUE( "value for resource consed.showReadsAlphabetically must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.showReadsInAlignedReadsWindowOrderedByFile" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bShowReadsInAlignedReadsWindowOrderedByFile_ = true; else if ( soResourceValue == "false" ) pRes->bShowReadsInAlignedReadsWindowOrderedByFile_ = false; else BAD_VALUE( "value for resource consed.showReadsInAlignedReadsWindowOrderedByFile must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.showReadsInAlignedReadsWindowOrderedByThisFile" ) { pRes->filShowReadsInAlignedReadsWindowOrderedByThisFile_ = soResourceValue; return; } if ( soResourceName == "consed.showReadsAtCursorSortedHow" ) { pRes->soShowReadsAtCursorSortedHow_ = soResourceValue; return; } if ( soResourceName == "consed.showABIBasesInTraceWindow" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bShowABIBasesInTraceWindow_ = true; else if ( soResourceValue == "false" ) pRes->bShowABIBasesInTraceWindow_ = false; else BAD_VALUE( "value for resource consed.showABIBasesInTraceWindow must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.tracesWindowInitialPixelHeight" ) { if ( !bIsNumericMaybeWithWhitespace( soResourceValue, pRes->nTracesWindowInitialPixelHeight_ ) ) BAD_VALUE( "value for resource consed.tracesWindowInitialPixelHeight must be numeric", soResourceValue ) return; } if ( soResourceName == "consed.assemblyViewWindowInitialPixelHeight" ) { if ( !bIsNumericMaybeWithWhitespace( soResourceValue, pRes->nAssemblyViewWindowInitialPixelHeight_ ) ) BAD_VALUE( "value for resource consed.assemblyViewWindowInitialPixelHeight must be numeric", soResourceValue ) return; } if ( soResourceName == "consed.assemblyViewFileOfTemplatesToNotShow" ) { pRes->filAssemblyViewFileOfTemplatesToNotShow_ = soResourceValue; return; } if ( soResourceName == "consed.assemblyViewCrossMatchMinmatch" ) { if ( !bIsNumericMaybeWithWhitespace( soResourceValue, pRes->nAssemblyViewCrossMatchMinmatch_ ) ) BAD_VALUE( "value for resource consed.assemblyViewCrossMatchMinmatch must be numeric", soResourceValue ) return; } if ( soResourceName == "consed.assemblyViewCrossMatchMinscore" ) { if ( !bIsNumericMaybeWithWhitespace( soResourceValue, pRes->nAssemblyViewCrossMatchMinscore_ ) ) BAD_VALUE( "value for resource consed.assemblyViewCrossMatchMinscore must be numeric", soResourceValue ) return; } if ( soResourceName == "consed.assemblyViewFindSequenceMatchesForConsedScript" ) { pRes->filAssemblyViewFindSequenceMatchesForConsedScript_ = soResourceValue; return; } if ( soResourceName == "consed.assemblyViewCrossmatchMinmatch" ) { if ( !bIsNumericMaybeWithWhitespace( soResourceValue, pRes->nAssemblyViewCrossmatchMinmatch_ ) ) BAD_VALUE( "value for resource consed.assemblyViewCrossmatchMinmatch must be numeric", soResourceValue ) return; } if ( soResourceName == "consed.assemblyViewCrossmatchMinscore" ) { if ( !bIsNumericMaybeWithWhitespace( soResourceValue, pRes->nAssemblyViewCrossmatchMinscore_ ) ) BAD_VALUE( "value for resource consed.assemblyViewCrossmatchMinscore must be numeric", soResourceValue ) return; } if ( soResourceName == "consed.assemblyViewSequenceMatchesMinimumSimilarity" ) { if ( !bIsNumericMaybeWithWhitespace( soResourceValue, pRes->nAssemblyViewSequenceMatchesMinimumSimilarity_ ) ) BAD_VALUE( "value for resource consed.assemblyViewSequenceMatchesMinimumSimilarity must be numeric", soResourceValue ) return; } if ( soResourceName == "consed.tracesWindowInitialPixelWidth" ) { if ( !bIsNumericMaybeWithWhitespace( soResourceValue, pRes->nTracesWindowInitialPixelWidth_ ) ) BAD_VALUE( "value for resource consed.tracesWindowInitialPixelWidth must be numeric", soResourceValue ) return; } if ( soResourceName == "consed.assemblyViewWindowInitialPixelWidth" ) { if ( !bIsNumericMaybeWithWhitespace( soResourceValue, pRes->nAssemblyViewWindowInitialPixelWidth_ ) ) BAD_VALUE( "value for resource consed.assemblyViewWindowInitialPixelWidth must be numeric", soResourceValue ) return; } if ( soResourceName == "consed.automaticallyScaleTraces" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bAutomaticallyScaleTraces_ = true; else if ( soResourceValue == "false" ) pRes->bAutomaticallyScaleTraces_ = false; else BAD_VALUE( "value for resource consed.automaticallyScaleTraces must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.automaticallyScaleTracesSamplePeakHeightFractionOfWindowHeight" ) { if ( !bIsNumericDouble( soResourceValue, pRes->dAutomaticallyScaleTracesSamplePeakHeightFractionOfWindowHeight_ ) ) BAD_VALUE( "value for resource consed.automaticallyScaleTracesSamplePeakHeightFractionOfWindowHeight must be a decimal number", soResourceValue ) return; } if ( soResourceName == "consed.automaticallyScaleTracesSamplePeakPercentile" ) { if ( !bIsNumericMaybeWithWhitespace( soResourceValue, pRes->nAutomaticallyScaleTracesSamplePeakPercentile_ ) ) BAD_VALUE( "value for resource consed.automaticallyScaleTracesSamplePeakPercentile must be numeric", soResourceValue ) return; } if ( soResourceName == "consed.verticalTraceMagnification" ) { if ( !bIsNumericMaybeWithWhitespace( soResourceValue, pRes->nVerticalTraceMagnification_ ) ) BAD_VALUE( "value for resource consed.verticalTraceMagnification must be numeric", soResourceValue ) return; } if ( soResourceName == "consed.userDefinedKeys" ) { pRes->soUserDefinedKeys_ = soResourceValue; return; } if ( soResourceName == "consed.programsForUserDefinedKeys" ) { pRes->soProgramsForUserDefinedKeys_ = soResourceValue; return; } if ( soResourceName == "consed.argumentsToPassToUserDefinedPrograms" ) { pRes->soArgumentsToPassToUserDefinedPrograms_ = soResourceValue; return; } if ( soResourceName == "consed.tagsToApplyWithUserDefinedKeys" ) { pRes->soTagsToApplyWithUserDefinedKeys_ = soResourceValue; return; } if ( soResourceName == "consed.snpGenomeUseInsertionPolymorphisms" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bSnpGenomeUseInsertionPolymorphisms_ = true; else if ( soResourceValue == "false" ) pRes->bSnpGenomeUseInsertionPolymorphisms_ = false; else BAD_VALUE( "value for resource consed.snpGenomeUseInsertionPolymorphisms must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.listOfTagTypesToHide" ) { pRes->soListOfTagTypesToHide_ = soResourceValue; return; } if ( soResourceName == "consed.listOfOptionalWordsToSaveInListOfReadNames" ) { pRes->soListOfOptionalWordsToSaveInListOfReadNames_ = soResourceValue; return; } if ( soResourceName == "consed.extendConsensusWithHighQuality" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bExtendConsensusWithHighQuality_ = true; else if ( soResourceValue == "false" ) pRes->bExtendConsensusWithHighQuality_ = false; else BAD_VALUE( "value for resource consed.extendConsensusWithHighQuality must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.fastStartup" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bFastStartup_ = true; else if ( soResourceValue == "false" ) pRes->bFastStartup_ = false; else BAD_VALUE( "value for resource consed.fastStartup must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.fastStartupFile" ) { pRes->filFastStartupFile_ = soResourceValue; return; } if ( soResourceName == "consed.alwaysRunProgramToGetChromats" ) { pRes->soAlwaysRunProgramToGetChromats_ = soResourceValue; return; } if ( soResourceName == "consed.programToRunToGetChromats" ) { pRes->filProgramToRunToGetChromats_ = soResourceValue; return; } if ( soResourceName == "consed.programToRunToGetChromatsOf454Reads" ) { pRes->filProgramToRunToGetChromatsOf454Reads_ = soResourceValue; return; } if ( soResourceName == "consed.createFakeChromatsForSolexaReads" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bCreateFakeChromatsForSolexaReads_ = true; else if ( soResourceValue == "false" ) pRes->bCreateFakeChromatsForSolexaReads_ = false; else BAD_VALUE( "value for resource consed.createFakeChromatsForSolexaReads must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.autoFinishUseLongModelReadRatherThanShort" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bAutoFinishUseLongModelReadRatherThanShort_ = true; else if ( soResourceValue == "false" ) pRes->bAutoFinishUseLongModelReadRatherThanShort_ = false; else BAD_VALUE( "value for resource consed.autoFinishUseLongModelReadRatherThanShort must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.askAgainIfWantToQuitConsedIfThisManyReads" ) { if ( !bIsNumericMaybeWithWhitespace( soResourceValue, pRes->nAskAgainIfWantToQuitConsedIfThisManyReads_ ) ) BAD_VALUE( "value for resource consed.askAgainIfWantToQuitConsedIfThisManyReads must be numeric", soResourceValue ) return; } if ( soResourceName == "consed.printWindowInstructions" ) { pRes->soPrintWindowInstructions_ = soResourceValue; return; } if ( soResourceName == "consed.allowMultipleSearchForStringWindows" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bAllowMultipleSearchForStringWindows_ = true; else if ( soResourceValue == "false" ) pRes->bAllowMultipleSearchForStringWindows_ = false; else BAD_VALUE( "value for resource consed.allowMultipleSearchForStringWindows must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.autoPCRAmplifyFalseProductsOKIfLargerThanThis" ) { if ( !bIsNumericMaybeWithWhitespace( soResourceValue, pRes->nAutoPCRAmplifyFalseProductsOKIfLargerThanThis_ ) ) BAD_VALUE( "value for resource consed.autoPCRAmplifyFalseProductsOKIfLargerThanThis must be numeric", soResourceValue ) return; } if ( soResourceName == "consed.autoPCRAmplifyMakePrimerOutOfFirstRegion" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bAutoPCRAmplifyMakePrimerOutOfFirstRegion_ = true; else if ( soResourceValue == "false" ) pRes->bAutoPCRAmplifyMakePrimerOutOfFirstRegion_ = false; else BAD_VALUE( "value for resource consed.autoPCRAmplifyMakePrimerOutOfFirstRegion must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.autoPCRAmplifyMaybeRejectPrimerIfThisCloseToDesiredProduct" ) { if ( !bIsNumericMaybeWithWhitespace( soResourceValue, pRes->nAutoPCRAmplifyMaybeRejectPrimerIfThisCloseToDesiredProduct_ ) ) BAD_VALUE( "value for resource consed.autoPCRAmplifyMaybeRejectPrimerIfThisCloseToDesiredProduct must be numeric", soResourceValue ) return; } if ( soResourceName == "consed.addNewReadsRecalculateConsensusQuality" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bAddNewReadsRecalculateConsensusQuality_ = true; else if ( soResourceValue == "false" ) pRes->bAddNewReadsRecalculateConsensusQuality_ = false; else BAD_VALUE( "value for resource consed.addNewReadsRecalculateConsensusQuality must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.addNewReadsPutReadIntoItsOwnContig" ) { pRes->soAddNewReadsPutReadIntoItsOwnContig_ = soResourceValue; return; } if ( soResourceName == "consed.addNewReadsCheckThatCrossMatchRunCorrectly" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bAddNewReadsCheckThatCrossMatchRunCorrectly_ = true; else if ( soResourceValue == "false" ) pRes->bAddNewReadsCheckThatCrossMatchRunCorrectly_ = false; else BAD_VALUE( "value for resource consed.addNewReadsCheckThatCrossMatchRunCorrectly must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.assemblyViewNumberOfRowsOfTags" ) { if ( !bIsNumericMaybeWithWhitespace( soResourceValue, pRes->nAssemblyViewNumberOfRowsOfTags_ ) ) BAD_VALUE( "value for resource consed.assemblyViewNumberOfRowsOfTags must be numeric", soResourceValue ) return; } if ( soResourceName == "consed.warnUserWhenTryingToEditAllReads" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bWarnUserWhenTryingToEditAllReads_ = true; else if ( soResourceValue == "false" ) pRes->bWarnUserWhenTryingToEditAllReads_ = false; else BAD_VALUE( "value for resource consed.warnUserWhenTryingToEditAllReads must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.maybeXKEYSYMDBPath" ) { pRes->filMaybeXKEYSYMDBPath_ = soResourceValue; return; } if ( soResourceName == "consed.maybeXKEYSYMDBPath2" ) { pRes->filMaybeXKEYSYMDBPath2_ = soResourceValue; return; } if ( soResourceName == "consed.amountToMoveWithBigLeftAndRightArrows" ) { if ( !bIsNumericMaybeWithWhitespace( soResourceValue, pRes->nAmountToMoveWithBigLeftAndRightArrows_ ) ) BAD_VALUE( "value for resource consed.amountToMoveWithBigLeftAndRightArrows must be numeric", soResourceValue ) return; } if ( soResourceName == "consed.navigateByHighlyDiscrepantPositionsMinDiscrepantReads" ) { if ( !bIsNumericMaybeWithWhitespace( soResourceValue, pRes->nNavigateByHighlyDiscrepantPositionsMinDiscrepantReads_ ) ) BAD_VALUE( "value for resource consed.navigateByHighlyDiscrepantPositionsMinDiscrepantReads must be numeric", soResourceValue ) return; } if ( soResourceName == "consed.navigateByHighlyDiscrepantPositionsMaxDepthOfCoverage" ) { if ( !bIsNumericMaybeWithWhitespace( soResourceValue, pRes->nNavigateByHighlyDiscrepantPositionsMaxDepthOfCoverage_ ) ) BAD_VALUE( "value for resource consed.navigateByHighlyDiscrepantPositionsMaxDepthOfCoverage must be numeric", soResourceValue ) return; } if ( soResourceName == "consed.navigateByHighlyDiscrepantPositionsIgnoreBasesBelowThisQuality" ) { if ( !bIsNumericMaybeWithWhitespace( soResourceValue, pRes->nNavigateByHighlyDiscrepantPositionsIgnoreBasesBelowThisQuality_ ) ) BAD_VALUE( "value for resource consed.navigateByHighlyDiscrepantPositionsIgnoreBasesBelowThisQuality must be numeric", soResourceValue ) return; } if ( soResourceName == "consed.navigateByHighlyDiscrepantPositionsJustListIndels" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bNavigateByHighlyDiscrepantPositionsJustListIndels_ = true; else if ( soResourceValue == "false" ) pRes->bNavigateByHighlyDiscrepantPositionsJustListIndels_ = false; else BAD_VALUE( "value for resource consed.navigateByHighlyDiscrepantPositionsJustListIndels must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.navigateByHighlyDiscrepantPositionsIgnoreOtherReadsStartingAtSameLocation" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bNavigateByHighlyDiscrepantPositionsIgnoreOtherReadsStartingAtSameLocation_ = true; else if ( soResourceValue == "false" ) pRes->bNavigateByHighlyDiscrepantPositionsIgnoreOtherReadsStartingAtSameLocation_ = false; else BAD_VALUE( "value for resource consed.navigateByHighlyDiscrepantPositionsIgnoreOtherReadsStartingAtSameLocation must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.navigateByHighlyDiscrepantPositionsIgnoreIfListedBasesInConsensus" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bNavigateByHighlyDiscrepantPositionsIgnoreIfListedBasesInConsensus_ = true; else if ( soResourceValue == "false" ) pRes->bNavigateByHighlyDiscrepantPositionsIgnoreIfListedBasesInConsensus_ = false; else BAD_VALUE( "value for resource consed.navigateByHighlyDiscrepantPositionsIgnoreIfListedBasesInConsensus must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.navigateByHighlyDiscrepantPositionsIgnoreIfTheseBasesInConsensus" ) { pRes->soNavigateByHighlyDiscrepantPositionsIgnoreIfTheseBasesInConsensus_ = soResourceValue; return; } if ( soResourceName == "consed.phdBallDirectory" ) { pRes->filPhdBallDirectory_ = soResourceValue; return; } if ( soResourceName == "consed.newAceFileFOF" ) { pRes->filNewAceFileFOF_ = soResourceValue; return; } if ( soResourceName == "consed.navigateByHighOrLowDepthCoalesceRegionsIfThisClose" ) { if ( !bIsNumericMaybeWithWhitespace( soResourceValue, pRes->nNavigateByHighOrLowDepthCoalesceRegionsIfThisClose_ ) ) BAD_VALUE( "value for resource consed.navigateByHighOrLowDepthCoalesceRegionsIfThisClose must be numeric", soResourceValue ) return; } if ( soResourceName == "consed.removeReadsDeleteNotJustPutInOwnContig" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bRemoveReadsDeleteNotJustPutInOwnContig_ = true; else if ( soResourceValue == "false" ) pRes->bRemoveReadsDeleteNotJustPutInOwnContig_ = false; else BAD_VALUE( "value for resource consed.removeReadsDeleteNotJustPutInOwnContig must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.paired454LeftReadExtension" ) { pRes->soPaired454LeftReadExtension_ = soResourceValue; return; } if ( soResourceName == "consed.paired454RightReadExtension" ) { pRes->soPaired454RightReadExtension_ = soResourceValue; return; } if ( soResourceName == "consed.snpGenome1MSnps" ) { pRes->filSnpGenome1MSnps_ = soResourceValue; return; } if ( soResourceName == "consed.diffChromosomesExcludeDeletions" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bDiffChromosomesExcludeDeletions_ = true; else if ( soResourceValue == "false" ) pRes->bDiffChromosomesExcludeDeletions_ = false; else BAD_VALUE( "value for resource consed.diffChromosomesExcludeDeletions must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.snpGenomeFilterByWeight" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bSnpGenomeFilterByWeight_ = true; else if ( soResourceValue == "false" ) pRes->bSnpGenomeFilterByWeight_ = false; else BAD_VALUE( "value for resource consed.snpGenomeFilterByWeight must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.wantReadsUpToThisFarFromSnps" ) { if ( !bIsNumericMaybeWithWhitespace( soResourceValue, pRes->nWantReadsUpToThisFarFromSnps_ ) ) BAD_VALUE( "value for resource consed.wantReadsUpToThisFarFromSnps must be numeric", soResourceValue ) return; } if ( soResourceName == "consed.phaster2PhdBallSaveWhichMate" ) { pRes->soPhaster2PhdBallSaveWhichMate_ = soResourceValue; return; } if ( soResourceName == "consed.phaster2PhdBallSaveInPhasterFormat" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bPhaster2PhdBallSaveInPhasterFormat_ = true; else if ( soResourceValue == "false" ) pRes->bPhaster2PhdBallSaveInPhasterFormat_ = false; else BAD_VALUE( "value for resource consed.phaster2PhdBallSaveInPhasterFormat must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.phaster2PhdBallCalculateNewLocationsFile" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bPhaster2PhdBallCalculateNewLocationsFile_ = true; else if ( soResourceValue == "false" ) pRes->bPhaster2PhdBallCalculateNewLocationsFile_ = false; else BAD_VALUE( "value for resource consed.phaster2PhdBallCalculateNewLocationsFile must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.phdBall2FastaIgnoreLowQualityReads" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bPhdBall2FastaIgnoreLowQualityReads_ = true; else if ( soResourceValue == "false" ) pRes->bPhdBall2FastaIgnoreLowQualityReads_ = false; else BAD_VALUE( "value for resource consed.phdBall2FastaIgnoreLowQualityReads must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.phdBall2FastaLowestAverageQuality" ) { if ( !bIsNumericMaybeWithWhitespace( soResourceValue, pRes->nPhdBall2FastaLowestAverageQuality_ ) ) BAD_VALUE( "value for resource consed.phdBall2FastaLowestAverageQuality must be numeric", soResourceValue ) return; } if ( soResourceName == "consed.nextPhredPipelineControlFile" ) { pRes->filNextPhredPipelineControlFile_ = soResourceValue; return; } if ( soResourceName == "consed.nextPhredPipelineTiffPerlScript" ) { pRes->filNextPhredPipelineTiffPerlScript_ = soResourceValue; return; } if ( soResourceName == "consed.nextPhredPipelinePhasterPerlScript" ) { pRes->filNextPhredPipelinePhasterPerlScript_ = soResourceValue; return; } if ( soResourceName == "consed.nextPhredPipelineVersion" ) { pRes->soNextPhredPipelineVersion_ = soResourceValue; return; } if ( soResourceName == "consed.nextPhredPipelineMainDirectory" ) { pRes->soNextPhredPipelineMainDirectory_ = soResourceValue; return; } if ( soResourceName == "consed.maxNumberOfReadsPerPhdBall" ) { if ( !bIsNumericMaybeWithWhitespace( soResourceValue, pRes->nMaxNumberOfReadsPerPhdBall_ ) ) BAD_VALUE( "value for resource consed.maxNumberOfReadsPerPhdBall must be numeric", soResourceValue ) return; } if ( soResourceName == "consed.userWantsToSaveToThisAceFile" ) { pRes->filUserWantsToSaveToThisAceFile_ = soResourceValue; return; } if ( soResourceName == "consed.autoFinishEmulate9_66Behavior" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bAutoFinishEmulate9_66Behavior_ = true; else if ( soResourceValue == "false" ) pRes->bAutoFinishEmulate9_66Behavior_ = false; else BAD_VALUE( "value for resource consed.autoFinishEmulate9_66Behavior must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.primersPCRPrimersGroupedIntoWindowOfThisManyBases" ) { if ( !bIsNumericMaybeWithWhitespace( soResourceValue, pRes->nPrimersPCRPrimersGroupedIntoWindowOfThisManyBases_ ) ) BAD_VALUE( "value for resource consed.primersPCRPrimersGroupedIntoWindowOfThisManyBases must be numeric", soResourceValue ) return; } if ( soResourceName == "consed.primersLookForThisManyPCRPrimerPairsPerPairOfGroups" ) { if ( !bIsNumericMaybeWithWhitespace( soResourceValue, pRes->nPrimersLookForThisManyPCRPrimerPairsPerPairOfGroups_ ) ) BAD_VALUE( "value for resource consed.primersLookForThisManyPCRPrimerPairsPerPairOfGroups must be numeric", soResourceValue ) return; } if ( soResourceName == "consed.autoFinishStandardDeviationsFromMeanFromGapToLookForTemplatesForSuggestingEachMissingReadOfReadPairs" ) { if ( !bIsNumericDouble( soResourceValue, pRes->dAutoFinishStandardDeviationsFromMeanFromGapToLookForTemplatesForSuggestingEachMissingReadOfReadPairs_ ) ) BAD_VALUE( "value for resource consed.autoFinishStandardDeviationsFromMeanFromGapToLookForTemplatesForSuggestingEachMissingReadOfReadPairs must be a decimal number", soResourceValue ) return; } if ( soResourceName == "consed.autoFinishCheckThatReadsFromTheSameTemplateAreConsistent" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bAutoFinishCheckThatReadsFromTheSameTemplateAreConsistent_ = true; else if ( soResourceValue == "false" ) pRes->bAutoFinishCheckThatReadsFromTheSameTemplateAreConsistent_ = false; else BAD_VALUE( "value for resource consed.autoFinishCheckThatReadsFromTheSameTemplateAreConsistent must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.autoFinishDoNotAllowSubcloneCustomPrimerReadsCloseTogether" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bAutoFinishDoNotAllowSubcloneCustomPrimerReadsCloseTogether_ = true; else if ( soResourceValue == "false" ) pRes->bAutoFinishDoNotAllowSubcloneCustomPrimerReadsCloseTogether_ = false; else BAD_VALUE( "value for resource consed.autoFinishDoNotAllowSubcloneCustomPrimerReadsCloseTogether must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.autoFinishDoNotAllowWholeCloneCustomPrimerReadsCloseTogether" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bAutoFinishDoNotAllowWholeCloneCustomPrimerReadsCloseTogether_ = true; else if ( soResourceValue == "false" ) pRes->bAutoFinishDoNotAllowWholeCloneCustomPrimerReadsCloseTogether_ = false; else BAD_VALUE( "value for resource consed.autoFinishDoNotAllowWholeCloneCustomPrimerReadsCloseTogether must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.autoFinishMinilibrariesPreferTemplateIfSizeThisManyStdDevsFromMean" ) { if ( !bIsNumericDouble( soResourceValue, pRes->dAutoFinishMinilibrariesPreferTemplateIfSizeThisManyStdDevsFromMean_ ) ) BAD_VALUE( "value for resource consed.autoFinishMinilibrariesPreferTemplateIfSizeThisManyStdDevsFromMean must be a decimal number", soResourceValue ) return; } if ( soResourceName == "consed.autoFinishMinNumberOfForwardReversePairsInLibraryToCalculateAverageInsertSize" ) { if ( !bIsNumericMaybeWithWhitespace( soResourceValue, pRes->nAutoFinishMinNumberOfForwardReversePairsInLibraryToCalculateAverageInsertSize_ ) ) BAD_VALUE( "value for resource consed.autoFinishMinNumberOfForwardReversePairsInLibraryToCalculateAverageInsertSize must be numeric", soResourceValue ) return; } if ( soResourceName == "consed.autoFinishIfEnoughFwdRevPairsUseThisManyStdDevBelowMeanForInsertSize" ) { if ( !bIsNumericDouble( soResourceValue, pRes->dAutoFinishIfEnoughFwdRevPairsUseThisManyStdDevBelowMeanForInsertSize_ ) ) BAD_VALUE( "value for resource consed.autoFinishIfEnoughFwdRevPairsUseThisManyStdDevBelowMeanForInsertSize must be a decimal number", soResourceValue ) return; } if ( soResourceName == "consed.autoFinishNewCustomPrimerReadThisFarFromOldCustomPrimerRead" ) { if ( !bIsNumericMaybeWithWhitespace( soResourceValue, pRes->nAutoFinishNewCustomPrimerReadThisFarFromOldCustomPrimerRead_ ) ) BAD_VALUE( "value for resource consed.autoFinishNewCustomPrimerReadThisFarFromOldCustomPrimerRead must be numeric", soResourceValue ) return; } if ( soResourceName == "consed.autoFinishMinNumberOfSingleSubcloneBasesFixedByAnExp" ) { if ( !bIsNumericMaybeWithWhitespace( soResourceValue, pRes->nAutoFinishMinNumberOfSingleSubcloneBasesFixedByAnExp_ ) ) BAD_VALUE( "value for resource consed.autoFinishMinNumberOfSingleSubcloneBasesFixedByAnExp must be numeric", soResourceValue ) return; } if ( soResourceName == "consed.autoFinishNumberOfBasesBetweenContigsAssumed" ) { if ( !bIsNumericMaybeWithWhitespace( soResourceValue, pRes->nAutoFinishNumberOfBasesBetweenContigsAssumed_ ) ) BAD_VALUE( "value for resource consed.autoFinishNumberOfBasesBetweenContigsAssumed must be numeric", soResourceValue ) return; } if ( soResourceName == "consed.autoFinishPotentialHighQualityPartOfReadStart" ) { if ( !bIsNumericMaybeWithWhitespace( soResourceValue, pRes->nAutoFinishPotentialHighQualityPartOfReadStart_ ) ) BAD_VALUE( "value for resource consed.autoFinishPotentialHighQualityPartOfReadStart must be numeric", soResourceValue ) return; } if ( soResourceName == "consed.autoFinishPotentialHighQualityPartOfReadEnd" ) { if ( !bIsNumericMaybeWithWhitespace( soResourceValue, pRes->nAutoFinishPotentialHighQualityPartOfReadEnd_ ) ) BAD_VALUE( "value for resource consed.autoFinishPotentialHighQualityPartOfReadEnd must be numeric", soResourceValue ) return; } if ( soResourceName == "consed.autoFinishPrintCustomNavigationFileForChosenReads" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bAutoFinishPrintCustomNavigationFileForChosenReads_ = true; else if ( soResourceValue == "false" ) pRes->bAutoFinishPrintCustomNavigationFileForChosenReads_ = false; else BAD_VALUE( "value for resource consed.autoFinishPrintCustomNavigationFileForChosenReads must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.autoFinishReversesForFlankingGapsTemplateMustProtrudeFromContigThisMuch" ) { if ( !bIsNumericMaybeWithWhitespace( soResourceValue, pRes->nAutoFinishReversesForFlankingGapsTemplateMustProtrudeFromContigThisMuch_ ) ) BAD_VALUE( "value for resource consed.autoFinishReversesForFlankingGapsTemplateMustProtrudeFromContigThisMuch must be numeric", soResourceValue ) return; } if ( soResourceName == "consed.autoFinishTagOligosWhenDoExperiments" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bAutoFinishTagOligosWhenDoExperiments_ = true; else if ( soResourceValue == "false" ) pRes->bAutoFinishTagOligosWhenDoExperiments_ = false; else BAD_VALUE( "value for resource consed.autoFinishTagOligosWhenDoExperiments must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.countPads" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bCountPads_ = true; else if ( soResourceValue == "false" ) pRes->bCountPads_ = false; else BAD_VALUE( "value for resource consed.countPads must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.debugging" ) { if ( !bIsNumericMaybeWithWhitespace( soResourceValue, pRes->nDebugging_ ) ) BAD_VALUE( "value for resource consed.debugging must be numeric", soResourceValue ) return; } if ( soResourceName == "consed.debugging2" ) { if ( !bIsNumericMaybeWithWhitespace( soResourceValue, pRes->nDebugging2_ ) ) BAD_VALUE( "value for resource consed.debugging2 must be numeric", soResourceValue ) return; } if ( soResourceName == "consed.debugging3" ) { if ( !bIsNumericMaybeWithWhitespace( soResourceValue, pRes->nDebugging3_ ) ) BAD_VALUE( "value for resource consed.debugging3 must be numeric", soResourceValue ) return; } if ( soResourceName == "consed.debuggingString" ) { pRes->soDebuggingString_ = soResourceValue; return; } if ( soResourceName == "consed.ignoreHighQualityDiscrepanciesThisManyBasesFromEndOfAlignedRegion" ) { if ( !bIsNumericMaybeWithWhitespace( soResourceValue, pRes->nIgnoreHighQualityDiscrepanciesThisManyBasesFromEndOfAlignedRegion_ ) ) BAD_VALUE( "value for resource consed.ignoreHighQualityDiscrepanciesThisManyBasesFromEndOfAlignedRegion must be numeric", soResourceValue ) return; } if ( soResourceName == "consed.ignoreUnalignedHighQualitySegmentsShorterThanThis" ) { if ( !bIsNumericMaybeWithWhitespace( soResourceValue, pRes->nIgnoreUnalignedHighQualitySegmentsShorterThanThis_ ) ) BAD_VALUE( "value for resource consed.ignoreUnalignedHighQualitySegmentsShorterThanThis must be numeric", soResourceValue ) return; } if ( soResourceName == "consed.primersLookThisFarForForwardVectorInsertJunction" ) { if ( !bIsNumericMaybeWithWhitespace( soResourceValue, pRes->nPrimersLookThisFarForForwardVectorInsertJunction_ ) ) BAD_VALUE( "value for resource consed.primersLookThisFarForForwardVectorInsertJunction must be numeric", soResourceValue ) return; } if ( soResourceName == "consed.primersDNAConcentrationNanomolar" ) { if ( !bIsNumericDouble( soResourceValue, pRes->dPrimersDNAConcentrationNanomolar_ ) ) BAD_VALUE( "value for resource consed.primersDNAConcentrationNanomolar must be a decimal number", soResourceValue ) return; } if ( soResourceName == "consed.primersMaxMatchElsewhereScore" ) { if ( !bIsNumericMaybeWithWhitespace( soResourceValue, pRes->nPrimersMaxMatchElsewhereScore_ ) ) BAD_VALUE( "value for resource consed.primersMaxMatchElsewhereScore must be numeric", soResourceValue ) return; } if ( soResourceName == "consed.primersMaxMatchElsewhereScoreForPCR" ) { if ( !bIsNumericMaybeWithWhitespace( soResourceValue, pRes->nPrimersMaxMatchElsewhereScoreForPCR_ ) ) BAD_VALUE( "value for resource consed.primersMaxMatchElsewhereScoreForPCR must be numeric", soResourceValue ) return; } if ( soResourceName == "consed.primersMaxSelfMatchScore" ) { if ( !bIsNumericMaybeWithWhitespace( soResourceValue, pRes->nPrimersMaxSelfMatchScore_ ) ) BAD_VALUE( "value for resource consed.primersMaxSelfMatchScore must be numeric", soResourceValue ) return; } if ( soResourceName == "consed.primersMaxPrimerDimerScoreForPCR" ) { if ( !bIsNumericMaybeWithWhitespace( soResourceValue, pRes->nPrimersMaxPrimerDimerScoreForPCR_ ) ) BAD_VALUE( "value for resource consed.primersMaxPrimerDimerScoreForPCR must be numeric", soResourceValue ) return; } if ( soResourceName == "consed.primersMinQuality" ) { if ( !bIsNumericMaybeWithWhitespace( soResourceValue, pRes->nPrimersMinQuality_ ) ) BAD_VALUE( "value for resource consed.primersMinQuality must be numeric", soResourceValue ) return; } if ( soResourceName == "consed.primersPrintInfoOnRejectedTemplates" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bPrimersPrintInfoOnRejectedTemplates_ = true; else if ( soResourceValue == "false" ) pRes->bPrimersPrintInfoOnRejectedTemplates_ = false; else BAD_VALUE( "value for resource consed.primersPrintInfoOnRejectedTemplates must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.primersSaltConcentrationMillimolar" ) { if ( !bIsNumericDouble( soResourceValue, pRes->dPrimersSaltConcentrationMillimolar_ ) ) BAD_VALUE( "value for resource consed.primersSaltConcentrationMillimolar must be a decimal number", soResourceValue ) return; } if ( soResourceName == "consed.primersScreenForVector" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bPrimersScreenForVector_ = true; else if ( soResourceValue == "false" ) pRes->bPrimersScreenForVector_ = false; else BAD_VALUE( "value for resource consed.primersScreenForVector must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.primersToleranceForDifferentBeginningLocationOfUniversalPrimerReads" ) { if ( !bIsNumericMaybeWithWhitespace( soResourceValue, pRes->nPrimersToleranceForDifferentBeginningLocationOfUniversalPrimerReads_ ) ) BAD_VALUE( "value for resource consed.primersToleranceForDifferentBeginningLocationOfUniversalPrimerReads must be numeric", soResourceValue ) return; } if ( soResourceName == "consed.primersTooManyVectorBasesInWalkingRead" ) { if ( !bIsNumericMaybeWithWhitespace( soResourceValue, pRes->nPrimersTooManyVectorBasesInWalkingRead_ ) ) BAD_VALUE( "value for resource consed.primersTooManyVectorBasesInWalkingRead must be numeric", soResourceValue ) return; } if ( soResourceName == "consed.qualityThresholdForLowConsensusQuality" ) { if ( !bIsNumericMaybeWithWhitespace( soResourceValue, pRes->nQualityThresholdForLowConsensusQuality_ ) ) BAD_VALUE( "value for resource consed.qualityThresholdForLowConsensusQuality must be numeric", soResourceValue ) return; } if ( soResourceName == "consed.tagColorPerCentOfBase" ) { if ( !bIsNumericMaybeWithWhitespace( soResourceValue, pRes->nTagColorPerCentOfBase_ ) ) BAD_VALUE( "value for resource consed.tagColorPerCentOfBase must be numeric", soResourceValue ) return; } if ( soResourceName == "consed.uncompressedChromatDirectory" ) { pRes->soUncompressedChromatDirectory_ = soResourceValue; return; } if ( soResourceName == "consed.454sff2scfDirectory" ) { pRes->fil454sff2scfDirectory_ = soResourceValue; return; } if ( soResourceName == "consed.whenMakingFakeReadToJoinContigsAddThisManyBasesOnEitherSideOfAlignedRegion" ) { if ( !bIsNumericMaybeWithWhitespace( soResourceValue, pRes->nWhenMakingFakeReadToJoinContigsAddThisManyBasesOnEitherSideOfAlignedRegion_ ) ) BAD_VALUE( "value for resource consed.whenMakingFakeReadToJoinContigsAddThisManyBasesOnEitherSideOfAlignedRegion must be numeric", soResourceValue ) return; } if ( soResourceName == "consed.writeThisAceFormat" ) { if ( !bIsNumericMaybeWithWhitespace( soResourceValue, pRes->nWriteThisAceFormat_ ) ) BAD_VALUE( "value for resource consed.writeThisAceFormat must be numeric", soResourceValue ) return; } if ( soResourceName == "consed.dumpCoreIfBoundsError" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bDumpCoreIfBoundsError_ = true; else if ( soResourceValue == "false" ) pRes->bDumpCoreIfBoundsError_ = false; else BAD_VALUE( "value for resource consed.dumpCoreIfBoundsError must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.autoFinishMinSmithWatermanScoreOfARun" ) { if ( !bIsNumericMaybeWithWhitespace( soResourceValue, pRes->nAutoFinishMinSmithWatermanScoreOfARun_ ) ) BAD_VALUE( "value for resource consed.autoFinishMinSmithWatermanScoreOfARun must be numeric", soResourceValue ) return; } if ( soResourceName == "consed.autoFinishDoNotComparePCRPrimersMoreThanThisManyTimes" ) { if ( !bIsNumericDouble( soResourceValue, pRes->dAutoFinishDoNotComparePCRPrimersMoreThanThisManyTimes_ ) ) BAD_VALUE( "value for resource consed.autoFinishDoNotComparePCRPrimersMoreThanThisManyTimes must be a decimal number", soResourceValue ) return; } if ( soResourceName == "consed.restrictionDigestMaximumBasesToCompareToVector" ) { if ( !bIsNumericMaybeWithWhitespace( soResourceValue, pRes->nRestrictionDigestMaximumBasesToCompareToVector_ ) ) BAD_VALUE( "value for resource consed.restrictionDigestMaximumBasesToCompareToVector must be numeric", soResourceValue ) return; } if ( soResourceName == "consed.restrictionDigestZoomFactor" ) { if ( !bIsNumericDouble( soResourceValue, pRes->dRestrictionDigestZoomFactor_ ) ) BAD_VALUE( "value for resource consed.restrictionDigestZoomFactor must be a decimal number", soResourceValue ) return; } if ( soResourceName == "consed.restrictionDigestZoomFactorForNavigate" ) { if ( !bIsNumericDouble( soResourceValue, pRes->dRestrictionDigestZoomFactorForNavigate_ ) ) BAD_VALUE( "value for resource consed.restrictionDigestZoomFactorForNavigate must be a decimal number", soResourceValue ) return; } if ( soResourceName == "consed.restrictionDigestToleranceInPositionUnits" ) { if ( !bIsNumericMaybeWithWhitespace( soResourceValue, pRes->nRestrictionDigestToleranceInPositionUnits_ ) ) BAD_VALUE( "value for resource consed.restrictionDigestToleranceInPositionUnits must be numeric", soResourceValue ) return; } if ( soResourceName == "consed.autoPCRAmplifyTooManySeriousFalseMatches" ) { if ( !bIsNumericMaybeWithWhitespace( soResourceValue, pRes->nAutoPCRAmplifyTooManySeriousFalseMatches_ ) ) BAD_VALUE( "value for resource consed.autoPCRAmplifyTooManySeriousFalseMatches must be numeric", soResourceValue ) return; } if ( soResourceName == "consed.assemblyViewZoomFactor" ) { if ( !bIsNumericDouble( soResourceValue, pRes->dAssemblyViewZoomFactor_ ) ) BAD_VALUE( "value for resource consed.assemblyViewZoomFactor must be a decimal number", soResourceValue ) return; } if ( soResourceName == "consed.assemblyViewFilterInconsistentFwdRevPairsIfThisClose" ) { if ( !bIsNumericMaybeWithWhitespace( soResourceValue, pRes->nAssemblyViewFilterInconsistentFwdRevPairsIfThisClose_ ) ) BAD_VALUE( "value for resource consed.assemblyViewFilterInconsistentFwdRevPairsIfThisClose must be numeric", soResourceValue ) return; } if ( soResourceName == "consed.assemblyViewGridCellWidthInPixels" ) { if ( !bIsNumericDouble( soResourceValue, pRes->dAssemblyViewGridCellWidthInPixels_ ) ) BAD_VALUE( "value for resource consed.assemblyViewGridCellWidthInPixels must be a decimal number", soResourceValue ) return; } if ( soResourceName == "consed.assemblyViewCursorSensitivityInPixels" ) { if ( !bIsNumericMaybeWithWhitespace( soResourceValue, pRes->nAssemblyViewCursorSensitivityInPixels_ ) ) BAD_VALUE( "value for resource consed.assemblyViewCursorSensitivityInPixels must be numeric", soResourceValue ) return; } if ( soResourceName == "consed.assemblyViewReadDepthQuality" ) { if ( !bIsNumericMaybeWithWhitespace( soResourceValue, pRes->nAssemblyViewReadDepthQuality_ ) ) BAD_VALUE( "value for resource consed.assemblyViewReadDepthQuality must be numeric", soResourceValue ) return; } if ( soResourceName == "consed.showAllTracesMaxNumberOfTracesToShowAtOnce" ) { if ( !bIsNumericMaybeWithWhitespace( soResourceValue, pRes->nShowAllTracesMaxNumberOfTracesToShowAtOnce_ ) ) BAD_VALUE( "value for resource consed.showAllTracesMaxNumberOfTracesToShowAtOnce must be numeric", soResourceValue ) return; } if ( soResourceName == "consed.allowFwdRevPairScaffoldsToBeMergedIfThisManyBasesIntersectionOrLess" ) { if ( !bIsNumericMaybeWithWhitespace( soResourceValue, pRes->nAllowFwdRevPairScaffoldsToBeMergedIfThisManyBasesIntersectionOrLess_ ) ) BAD_VALUE( "value for resource consed.allowFwdRevPairScaffoldsToBeMergedIfThisManyBasesIntersectionOrLess must be numeric", soResourceValue ) return; } if ( soResourceName == "consed.justForPrimateProject" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bJustForPrimateProject_ = true; else if ( soResourceValue == "false" ) pRes->bJustForPrimateProject_ = false; else BAD_VALUE( "value for resource consed.justForPrimateProject must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.solexaFilesAreAssumedToBeHere" ) { pRes->filSolexaFilesAreAssumedToBeHere_ = soResourceValue; return; } if ( soResourceName == "consed.solexaAlignmentFilesPerInsertingPadsCycle" ) { if ( !bIsNumericMaybeWithWhitespace( soResourceValue, pRes->nSolexaAlignmentFilesPerInsertingPadsCycle_ ) ) BAD_VALUE( "value for resource consed.solexaAlignmentFilesPerInsertingPadsCycle must be numeric", soResourceValue ) return; } if ( soResourceName == "consed.solexaAlignmentsPerAlignmentFile" ) { if ( !bIsNumericMaybeWithWhitespace( soResourceValue, pRes->nSolexaAlignmentsPerAlignmentFile_ ) ) BAD_VALUE( "value for resource consed.solexaAlignmentsPerAlignmentFile must be numeric", soResourceValue ) return; } if ( soResourceName == "consed.solexaFastqFilesArePhredQualityNotSolexaQuality" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bSolexaFastqFilesArePhredQualityNotSolexaQuality_ = true; else if ( soResourceValue == "false" ) pRes->bSolexaFastqFilesArePhredQualityNotSolexaQuality_ = false; else BAD_VALUE( "value for resource consed.solexaFastqFilesArePhredQualityNotSolexaQuality must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.solexa64FastqOrSanger33Fastq" ) { pRes->soSolexa64FastqOrSanger33Fastq_ = soResourceValue; return; } if ( soResourceName == "consed.maximumReadsInReadList" ) { if ( !bIsNumericMaybeWithWhitespace( soResourceValue, pRes->nMaximumReadsInReadList_ ) ) BAD_VALUE( "value for resource consed.maximumReadsInReadList must be numeric", soResourceValue ) return; } if ( soResourceName == "consed.maxLengthOfReadsInapLocatedFragment2" ) { if ( !bIsNumericMaybeWithWhitespace( soResourceValue, pRes->nMaxLengthOfReadsInapLocatedFragment2_ ) ) BAD_VALUE( "value for resource consed.maxLengthOfReadsInapLocatedFragment2 must be numeric", soResourceValue ) return; } if ( soResourceName == "consed.maximumStartupErrorsToReport" ) { if ( !bIsNumericMaybeWithWhitespace( soResourceValue, pRes->nMaximumStartupErrorsToReport_ ) ) BAD_VALUE( "value for resource consed.maximumStartupErrorsToReport must be numeric", soResourceValue ) return; } if ( soResourceName == "consed.454LinkerAlignmentMatchScore" ) { if ( !bIsNumericMaybeWithWhitespace( soResourceValue, pRes->n454LinkerAlignmentMatchScore_ ) ) BAD_VALUE( "value for resource consed.454LinkerAlignmentMatchScore must be numeric", soResourceValue ) return; } if ( soResourceName == "consed.454LinkerAlignmentMismatchScore" ) { if ( !bIsNumericMaybeWithWhitespace( soResourceValue, pRes->n454LinkerAlignmentMismatchScore_ ) ) BAD_VALUE( "value for resource consed.454LinkerAlignmentMismatchScore must be numeric", soResourceValue ) return; } if ( soResourceName == "consed.454LinkerAlignmentIndelScore" ) { if ( !bIsNumericMaybeWithWhitespace( soResourceValue, pRes->n454LinkerAlignmentIndelScore_ ) ) BAD_VALUE( "value for resource consed.454LinkerAlignmentIndelScore must be numeric", soResourceValue ) return; } if ( soResourceName == "consed.filter454ReadsDeleteCrossMatchOutput" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bFilter454ReadsDeleteCrossMatchOutput_ = true; else if ( soResourceValue == "false" ) pRes->bFilter454ReadsDeleteCrossMatchOutput_ = false; else BAD_VALUE( "value for resource consed.filter454ReadsDeleteCrossMatchOutput must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.autoReportAllNeededSpeciesCode" ) { if ( !bIsNumericMaybeWithWhitespace( soResourceValue, pRes->nAutoReportAllNeededSpeciesCode_ ) ) BAD_VALUE( "value for resource consed.autoReportAllNeededSpeciesCode must be numeric", soResourceValue ) return; } if ( soResourceName == "consed.autoReportUseCommasInBigNumbers" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bAutoReportUseCommasInBigNumbers_ = true; else if ( soResourceValue == "false" ) pRes->bAutoReportUseCommasInBigNumbers_ = false; else BAD_VALUE( "value for resource consed.autoReportUseCommasInBigNumbers must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.autoReportPrintToCompareToReich" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bAutoReportPrintToCompareToReich_ = true; else if ( soResourceValue == "false" ) pRes->bAutoReportPrintToCompareToReich_ = false; else BAD_VALUE( "value for resource consed.autoReportPrintToCompareToReich must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.autoReportOnlyAllowSitesThatAreBetweenAcceptableSites" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bAutoReportOnlyAllowSitesThatAreBetweenAcceptableSites_ = true; else if ( soResourceValue == "false" ) pRes->bAutoReportOnlyAllowSitesThatAreBetweenAcceptableSites_ = false; else BAD_VALUE( "value for resource consed.autoReportOnlyAllowSitesThatAreBetweenAcceptableSites must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.autoReportDeaminationMutationsDeterminedByMoreAccurateMethod" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bAutoReportDeaminationMutationsDeterminedByMoreAccurateMethod_ = true; else if ( soResourceValue == "false" ) pRes->bAutoReportDeaminationMutationsDeterminedByMoreAccurateMethod_ = false; else BAD_VALUE( "value for resource consed.autoReportDeaminationMutationsDeterminedByMoreAccurateMethod must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.autoReportChooseTreesUsingBadData" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bAutoReportChooseTreesUsingBadData_ = true; else if ( soResourceValue == "false" ) pRes->bAutoReportChooseTreesUsingBadData_ = false; else BAD_VALUE( "value for resource consed.autoReportChooseTreesUsingBadData must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.autoReportChooseTreesByCountingDeaminationMutations" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bAutoReportChooseTreesByCountingDeaminationMutations_ = true; else if ( soResourceValue == "false" ) pRes->bAutoReportChooseTreesByCountingDeaminationMutations_ = false; else BAD_VALUE( "value for resource consed.autoReportChooseTreesByCountingDeaminationMutations must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.autoReportChooseTreesUsingKimura" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bAutoReportChooseTreesUsingKimura_ = true; else if ( soResourceValue == "false" ) pRes->bAutoReportChooseTreesUsingKimura_ = false; else BAD_VALUE( "value for resource consed.autoReportChooseTreesUsingKimura must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.autoReportPrintCrudeChimpHumanMutations" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bAutoReportPrintCrudeChimpHumanMutations_ = true; else if ( soResourceValue == "false" ) pRes->bAutoReportPrintCrudeChimpHumanMutations_ = false; else BAD_VALUE( "value for resource consed.autoReportPrintCrudeChimpHumanMutations must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.autoReportPrintPositionsForGraham" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bAutoReportPrintPositionsForGraham_ = true; else if ( soResourceValue == "false" ) pRes->bAutoReportPrintPositionsForGraham_ = false; else BAD_VALUE( "value for resource consed.autoReportPrintPositionsForGraham must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.autoReportPrintAncestralCpGs" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bAutoReportPrintAncestralCpGs_ = true; else if ( soResourceValue == "false" ) pRes->bAutoReportPrintAncestralCpGs_ = false; else BAD_VALUE( "value for resource consed.autoReportPrintAncestralCpGs must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.autoReportPrintCpGMutations" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bAutoReportPrintCpGMutations_ = true; else if ( soResourceValue == "false" ) pRes->bAutoReportPrintCpGMutations_ = false; else BAD_VALUE( "value for resource consed.autoReportPrintCpGMutations must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.autoReportPrintMutationsWithContext" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bAutoReportPrintMutationsWithContext_ = true; else if ( soResourceValue == "false" ) pRes->bAutoReportPrintMutationsWithContext_ = false; else BAD_VALUE( "value for resource consed.autoReportPrintMutationsWithContext must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.autoReportCountAllMutationsML" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bAutoReportCountAllMutationsML_ = true; else if ( soResourceValue == "false" ) pRes->bAutoReportCountAllMutationsML_ = false; else BAD_VALUE( "value for resource consed.autoReportCountAllMutationsML must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.autoReportCountAllMutations" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bAutoReportCountAllMutations_ = true; else if ( soResourceValue == "false" ) pRes->bAutoReportCountAllMutations_ = false; else BAD_VALUE( "value for resource consed.autoReportCountAllMutations must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.autoReportIgnoreMultipleTrees" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bAutoReportIgnoreMultipleTrees_ = true; else if ( soResourceValue == "false" ) pRes->bAutoReportIgnoreMultipleTrees_ = false; else BAD_VALUE( "value for resource consed.autoReportIgnoreMultipleTrees must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.autoReportCountAcceptableColumnsWithNoneOnLeft" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bAutoReportCountAcceptableColumnsWithNoneOnLeft_ = true; else if ( soResourceValue == "false" ) pRes->bAutoReportCountAcceptableColumnsWithNoneOnLeft_ = false; else BAD_VALUE( "value for resource consed.autoReportCountAcceptableColumnsWithNoneOnLeft must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.autoReportPrintFlankedColumns4" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bAutoReportPrintFlankedColumns4_ = true; else if ( soResourceValue == "false" ) pRes->bAutoReportPrintFlankedColumns4_ = false; else BAD_VALUE( "value for resource consed.autoReportPrintFlankedColumns4 must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.autoReportUseAnnotationFormat" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bAutoReportUseAnnotationFormat_ = true; else if ( soResourceValue == "false" ) pRes->bAutoReportUseAnnotationFormat_ = false; else BAD_VALUE( "value for resource consed.autoReportUseAnnotationFormat must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.autoReportPrintFlankedColumns3" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bAutoReportPrintFlankedColumns3_ = true; else if ( soResourceValue == "false" ) pRes->bAutoReportPrintFlankedColumns3_ = false; else BAD_VALUE( "value for resource consed.autoReportPrintFlankedColumns3 must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.autoReportPrintFlankedColumns2" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bAutoReportPrintFlankedColumns2_ = true; else if ( soResourceValue == "false" ) pRes->bAutoReportPrintFlankedColumns2_ = false; else BAD_VALUE( "value for resource consed.autoReportPrintFlankedColumns2 must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.autoReportPrintFlankedColumns" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bAutoReportPrintFlankedColumns_ = true; else if ( soResourceValue == "false" ) pRes->bAutoReportPrintFlankedColumns_ = false; else BAD_VALUE( "value for resource consed.autoReportPrintFlankedColumns must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.autoReportHighQualitySegmentData" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bAutoReportHighQualitySegmentData_ = true; else if ( soResourceValue == "false" ) pRes->bAutoReportHighQualitySegmentData_ = false; else BAD_VALUE( "value for resource consed.autoReportHighQualitySegmentData must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.autoReportGoodReadsBug" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bAutoReportGoodReadsBug_ = true; else if ( soResourceValue == "false" ) pRes->bAutoReportGoodReadsBug_ = false; else BAD_VALUE( "value for resource consed.autoReportGoodReadsBug must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.autoReportDiscrepancyRateInFlankedRegions" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bAutoReportDiscrepancyRateInFlankedRegions_ = true; else if ( soResourceValue == "false" ) pRes->bAutoReportDiscrepancyRateInFlankedRegions_ = false; else BAD_VALUE( "value for resource consed.autoReportDiscrepancyRateInFlankedRegions must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.autoReportDiscrepancyRateInFlankedRegions2" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bAutoReportDiscrepancyRateInFlankedRegions2_ = true; else if ( soResourceValue == "false" ) pRes->bAutoReportDiscrepancyRateInFlankedRegions2_ = false; else BAD_VALUE( "value for resource consed.autoReportDiscrepancyRateInFlankedRegions2 must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.autoReportDiscrepancyRateInFlankedRegions4" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bAutoReportDiscrepancyRateInFlankedRegions4_ = true; else if ( soResourceValue == "false" ) pRes->bAutoReportDiscrepancyRateInFlankedRegions4_ = false; else BAD_VALUE( "value for resource consed.autoReportDiscrepancyRateInFlankedRegions4 must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.autoReportDiscrepancyRateInFlankedRegions5" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bAutoReportDiscrepancyRateInFlankedRegions5_ = true; else if ( soResourceValue == "false" ) pRes->bAutoReportDiscrepancyRateInFlankedRegions5_ = false; else BAD_VALUE( "value for resource consed.autoReportDiscrepancyRateInFlankedRegions5 must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.autoReportSingleSignalOrQuality" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bAutoReportSingleSignalOrQuality_ = true; else if ( soResourceValue == "false" ) pRes->bAutoReportSingleSignalOrQuality_ = false; else BAD_VALUE( "value for resource consed.autoReportSingleSignalOrQuality must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.autoReportLowQualityBasesInHQS" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bAutoReportLowQualityBasesInHQS_ = true; else if ( soResourceValue == "false" ) pRes->bAutoReportLowQualityBasesInHQS_ = false; else BAD_VALUE( "value for resource consed.autoReportLowQualityBasesInHQS must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.autoReportCompareHQSWithLQS" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bAutoReportCompareHQSWithLQS_ = true; else if ( soResourceValue == "false" ) pRes->bAutoReportCompareHQSWithLQS_ = false; else BAD_VALUE( "value for resource consed.autoReportCompareHQSWithLQS must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.autoReportCountColumnsForGroupsOfSpecies" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bAutoReportCountColumnsForGroupsOfSpecies_ = true; else if ( soResourceValue == "false" ) pRes->bAutoReportCountColumnsForGroupsOfSpecies_ = false; else BAD_VALUE( "value for resource consed.autoReportCountColumnsForGroupsOfSpecies must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.autoReportSingleSignalInfo" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bAutoReportSingleSignalInfo_ = true; else if ( soResourceValue == "false" ) pRes->bAutoReportSingleSignalInfo_ = false; else BAD_VALUE( "value for resource consed.autoReportSingleSignalInfo must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.autoReportSingleSignalInfo2" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bAutoReportSingleSignalInfo2_ = true; else if ( soResourceValue == "false" ) pRes->bAutoReportSingleSignalInfo2_ = false; else BAD_VALUE( "value for resource consed.autoReportSingleSignalInfo2 must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.autoReportCompareTopAndBottomStrands" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bAutoReportCompareTopAndBottomStrands_ = true; else if ( soResourceValue == "false" ) pRes->bAutoReportCompareTopAndBottomStrands_ = false; else BAD_VALUE( "value for resource consed.autoReportCompareTopAndBottomStrands must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.autoReportCompareTopAndBottomStrandsNoHuman" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bAutoReportCompareTopAndBottomStrandsNoHuman_ = true; else if ( soResourceValue == "false" ) pRes->bAutoReportCompareTopAndBottomStrandsNoHuman_ = false; else BAD_VALUE( "value for resource consed.autoReportCompareTopAndBottomStrandsNoHuman must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.autoReportCompareTopAndBottomStrands2" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bAutoReportCompareTopAndBottomStrands2_ = true; else if ( soResourceValue == "false" ) pRes->bAutoReportCompareTopAndBottomStrands2_ = false; else BAD_VALUE( "value for resource consed.autoReportCompareTopAndBottomStrands2 must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.autoReportCompareTopAndBottomStrands3" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bAutoReportCompareTopAndBottomStrands3_ = true; else if ( soResourceValue == "false" ) pRes->bAutoReportCompareTopAndBottomStrands3_ = false; else BAD_VALUE( "value for resource consed.autoReportCompareTopAndBottomStrands3 must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.autoReportCompareTopAndBottomStrands4" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bAutoReportCompareTopAndBottomStrands4_ = true; else if ( soResourceValue == "false" ) pRes->bAutoReportCompareTopAndBottomStrands4_ = false; else BAD_VALUE( "value for resource consed.autoReportCompareTopAndBottomStrands4 must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.autoReportTopStrandPinnedPosition" ) { if ( !bIsNumericMaybeWithWhitespace( soResourceValue, pRes->nAutoReportTopStrandPinnedPosition_ ) ) BAD_VALUE( "value for resource consed.autoReportTopStrandPinnedPosition must be numeric", soResourceValue ) return; } if ( soResourceName == "consed.autoReportBottomStrandPinnedPosition" ) { if ( !bIsNumericMaybeWithWhitespace( soResourceValue, pRes->nAutoReportBottomStrandPinnedPosition_ ) ) BAD_VALUE( "value for resource consed.autoReportBottomStrandPinnedPosition must be numeric", soResourceValue ) return; } if ( soResourceName == "consed.autoReportCompareTopAndBottomStrandsWithHuman" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bAutoReportCompareTopAndBottomStrandsWithHuman_ = true; else if ( soResourceValue == "false" ) pRes->bAutoReportCompareTopAndBottomStrandsWithHuman_ = false; else BAD_VALUE( "value for resource consed.autoReportCompareTopAndBottomStrandsWithHuman must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.autoReportPrintLengthsOfAlignedSegmentsOfReads" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bAutoReportPrintLengthsOfAlignedSegmentsOfReads_ = true; else if ( soResourceValue == "false" ) pRes->bAutoReportPrintLengthsOfAlignedSegmentsOfReads_ = false; else BAD_VALUE( "value for resource consed.autoReportPrintLengthsOfAlignedSegmentsOfReads must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.autoReportPrintLengthsOfUnalignedHighQualitySegmentsOfReads" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bAutoReportPrintLengthsOfUnalignedHighQualitySegmentsOfReads_ = true; else if ( soResourceValue == "false" ) pRes->bAutoReportPrintLengthsOfUnalignedHighQualitySegmentsOfReads_ = false; else BAD_VALUE( "value for resource consed.autoReportPrintLengthsOfUnalignedHighQualitySegmentsOfReads must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.autoReportPrintIfReadsAreCorrectlyAligned" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bAutoReportPrintIfReadsAreCorrectlyAligned_ = true; else if ( soResourceValue == "false" ) pRes->bAutoReportPrintIfReadsAreCorrectlyAligned_ = false; else BAD_VALUE( "value for resource consed.autoReportPrintIfReadsAreCorrectlyAligned must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.autoReportCalculateErrorProbabilitiesByComparingPTroPPan" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bAutoReportCalculateErrorProbabilitiesByComparingPTroPPan_ = true; else if ( soResourceValue == "false" ) pRes->bAutoReportCalculateErrorProbabilitiesByComparingPTroPPan_ = false; else BAD_VALUE( "value for resource consed.autoReportCalculateErrorProbabilitiesByComparingPTroPPan must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.autoReportPrintAgreeDisagreeBetweenPairsOfSpecies" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bAutoReportPrintAgreeDisagreeBetweenPairsOfSpecies_ = true; else if ( soResourceValue == "false" ) pRes->bAutoReportPrintAgreeDisagreeBetweenPairsOfSpecies_ = false; else BAD_VALUE( "value for resource consed.autoReportPrintAgreeDisagreeBetweenPairsOfSpecies must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.autoReportPrintAgreeDisagreeBetweenPairsOfSpecies2" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bAutoReportPrintAgreeDisagreeBetweenPairsOfSpecies2_ = true; else if ( soResourceValue == "false" ) pRes->bAutoReportPrintAgreeDisagreeBetweenPairsOfSpecies2_ = false; else BAD_VALUE( "value for resource consed.autoReportPrintAgreeDisagreeBetweenPairsOfSpecies2 must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.autoReportFilterSingleSignal" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bAutoReportFilterSingleSignal_ = true; else if ( soResourceValue == "false" ) pRes->bAutoReportFilterSingleSignal_ = false; else BAD_VALUE( "value for resource consed.autoReportFilterSingleSignal must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.autoReportGoodHitReads" ) { pRes->filAutoReportGoodHitReads_ = soResourceValue; return; } if ( soResourceName == "consed.autoReportQualityWindowLow" ) { if ( !bIsNumericMaybeWithWhitespace( soResourceValue, pRes->nAutoReportQualityWindowLow_ ) ) BAD_VALUE( "value for resource consed.autoReportQualityWindowLow must be numeric", soResourceValue ) return; } if ( soResourceName == "consed.autoReportQualityWindowHigh" ) { if ( !bIsNumericMaybeWithWhitespace( soResourceValue, pRes->nAutoReportQualityWindowHigh_ ) ) BAD_VALUE( "value for resource consed.autoReportQualityWindowHigh must be numeric", soResourceValue ) return; } if ( soResourceName == "consed.autoReportPrintNumberOfIsolatedPadsForEachSpecies" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bAutoReportPrintNumberOfIsolatedPadsForEachSpecies_ = true; else if ( soResourceValue == "false" ) pRes->bAutoReportPrintNumberOfIsolatedPadsForEachSpecies_ = false; else BAD_VALUE( "value for resource consed.autoReportPrintNumberOfIsolatedPadsForEachSpecies must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.autoReportPrintNumberOfIsolatedPads" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bAutoReportPrintNumberOfIsolatedPads_ = true; else if ( soResourceValue == "false" ) pRes->bAutoReportPrintNumberOfIsolatedPads_ = false; else BAD_VALUE( "value for resource consed.autoReportPrintNumberOfIsolatedPads must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.autoReportIsolatedPadsOfReadsWithThisPattern" ) { pRes->soAutoReportIsolatedPadsOfReadsWithThisPattern_ = soResourceValue; return; } if ( soResourceName == "consed.autoReportMinNumberOfPerfectlyAlignedBasesBeforeDiscrepancy" ) { if ( !bIsNumericMaybeWithWhitespace( soResourceValue, pRes->nAutoReportMinNumberOfPerfectlyAlignedBasesBeforeDiscrepancy_ ) ) BAD_VALUE( "value for resource consed.autoReportMinNumberOfPerfectlyAlignedBasesBeforeDiscrepancy must be numeric", soResourceValue ) return; } if ( soResourceName == "consed.autoReportMaxSizeOfDiscrepantRegion" ) { if ( !bIsNumericMaybeWithWhitespace( soResourceValue, pRes->nAutoReportMaxSizeOfDiscrepantRegion_ ) ) BAD_VALUE( "value for resource consed.autoReportMaxSizeOfDiscrepantRegion must be numeric", soResourceValue ) return; } if ( soResourceName == "consed.autoReportSizeOfDiscrepantRegion" ) { if ( !bIsNumericMaybeWithWhitespace( soResourceValue, pRes->nAutoReportSizeOfDiscrepantRegion_ ) ) BAD_VALUE( "value for resource consed.autoReportSizeOfDiscrepantRegion must be numeric", soResourceValue ) return; } if ( soResourceName == "consed.autoReportPrintMinimumQualityHistogram" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bAutoReportPrintMinimumQualityHistogram_ = true; else if ( soResourceValue == "false" ) pRes->bAutoReportPrintMinimumQualityHistogram_ = false; else BAD_VALUE( "value for resource consed.autoReportPrintMinimumQualityHistogram must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.autoReportPrintDiscrepantRegions" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bAutoReportPrintDiscrepantRegions_ = true; else if ( soResourceValue == "false" ) pRes->bAutoReportPrintDiscrepantRegions_ = false; else BAD_VALUE( "value for resource consed.autoReportPrintDiscrepantRegions must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.autoReportPrintBasesInDiscrepantRegions" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bAutoReportPrintBasesInDiscrepantRegions_ = true; else if ( soResourceValue == "false" ) pRes->bAutoReportPrintBasesInDiscrepantRegions_ = false; else BAD_VALUE( "value for resource consed.autoReportPrintBasesInDiscrepantRegions must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.autoReportPrintDiscrepantRegionsButIgnoreReadsContainingThis" ) { pRes->soAutoReportPrintDiscrepantRegionsButIgnoreReadsContainingThis_ = soResourceValue; return; } if ( soResourceName == "consed.autoReportBackboneReadHasThisStringInIt" ) { pRes->soAutoReportBackboneReadHasThisStringInIt_ = soResourceValue; return; } if ( soResourceName == "consed.autoReportPrintDiscrepantRegionsButOnlyIfAboveQualityThreshold" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bAutoReportPrintDiscrepantRegionsButOnlyIfAboveQualityThreshold_ = true; else if ( soResourceValue == "false" ) pRes->bAutoReportPrintDiscrepantRegionsButOnlyIfAboveQualityThreshold_ = false; else BAD_VALUE( "value for resource consed.autoReportPrintDiscrepantRegionsButOnlyIfAboveQualityThreshold must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.autoReportPrintSpeciesAlignment" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bAutoReportPrintSpeciesAlignment_ = true; else if ( soResourceValue == "false" ) pRes->bAutoReportPrintSpeciesAlignment_ = false; else BAD_VALUE( "value for resource consed.autoReportPrintSpeciesAlignment must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.autoReportPrintReadAlignment" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bAutoReportPrintReadAlignment_ = true; else if ( soResourceValue == "false" ) pRes->bAutoReportPrintReadAlignment_ = false; else BAD_VALUE( "value for resource consed.autoReportPrintReadAlignment must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.autoReportPrintTheseReads" ) { pRes->filAutoReportPrintTheseReads_ = soResourceValue; return; } if ( soResourceName == "consed.autoReportPrintReadPositions" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bAutoReportPrintReadPositions_ = true; else if ( soResourceValue == "false" ) pRes->bAutoReportPrintReadPositions_ = false; else BAD_VALUE( "value for resource consed.autoReportPrintReadPositions must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.autoReportPrintChosenReadName" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bAutoReportPrintChosenReadName_ = true; else if ( soResourceValue == "false" ) pRes->bAutoReportPrintChosenReadName_ = false; else BAD_VALUE( "value for resource consed.autoReportPrintChosenReadName must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.autoReportNumbersOfCharactersOfChosenReadNameToBePrinted" ) { if ( !bIsNumericMaybeWithWhitespace( soResourceValue, pRes->nAutoReportNumbersOfCharactersOfChosenReadNameToBePrinted_ ) ) BAD_VALUE( "value for resource consed.autoReportNumbersOfCharactersOfChosenReadNameToBePrinted must be numeric", soResourceValue ) return; } if ( soResourceName == "consed.autoReportPrefix" ) { pRes->soAutoReportPrefix_ = soResourceValue; return; } if ( soResourceName == "consed.autoReportUseOldCriteriaForDeletingColumnsOfPads" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bAutoReportUseOldCriteriaForDeletingColumnsOfPads_ = true; else if ( soResourceValue == "false" ) pRes->bAutoReportUseOldCriteriaForDeletingColumnsOfPads_ = false; else BAD_VALUE( "value for resource consed.autoReportUseOldCriteriaForDeletingColumnsOfPads must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.autoReportDeleteColumnsOfPadsBeforeAdjustingReadQualityValues" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bAutoReportDeleteColumnsOfPadsBeforeAdjustingReadQualityValues_ = true; else if ( soResourceValue == "false" ) pRes->bAutoReportDeleteColumnsOfPadsBeforeAdjustingReadQualityValues_ = false; else BAD_VALUE( "value for resource consed.autoReportDeleteColumnsOfPadsBeforeAdjustingReadQualityValues must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.autoReportFlankingBasesMustBeSingleSignal" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bAutoReportFlankingBasesMustBeSingleSignal_ = true; else if ( soResourceValue == "false" ) pRes->bAutoReportFlankingBasesMustBeSingleSignal_ = false; else BAD_VALUE( "value for resource consed.autoReportFlankingBasesMustBeSingleSignal must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.autoReportMinimumQualityOfFlankingBases" ) { if ( !bIsNumericMaybeWithWhitespace( soResourceValue, pRes->nAutoReportMinimumQualityOfFlankingBases_ ) ) BAD_VALUE( "value for resource consed.autoReportMinimumQualityOfFlankingBases must be numeric", soResourceValue ) return; } if ( soResourceName == "consed.autoReportFlankingBasesMustBeInHighQualitySegment" ) { soResourceValue.toLower(); if ( soResourceValue == "true" ) pRes->bAutoReportFlankingBasesMustBeInHighQualitySegment_ = true; else if ( soResourceValue == "false" ) pRes->bAutoReportFlankingBasesMustBeInHighQualitySegment_ = false; else BAD_VALUE( "value for resource consed.autoReportFlankingBasesMustBeInHighQualitySegment must be true or false", soResourceValue ) return; } if ( soResourceName == "consed.autoReportSpecies" ) { pRes->soAutoReportSpecies_ = soResourceValue; return; }