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libGenome Compound Members a | b | c | d | e | f | g | h | i | l | m | n | o | p | r | s | t | u | v | w | ~ Here is a list of all class members with links to the class documentation for each member: - a - AddArrayEntry() : gnCompare AddCaller() : gnException AddFeature() : gnMultiSpec, gnGenomeSpec, gnFragmentSpec addFeature() : gnSequence AddHeader() : gnMultiSpec addHeader() : gnSequence AddLocation() : gnBaseFeature AddPath() : gnSourceFactory AddQualifier() : gnBaseFeature AddSource() : gnSourceFactory AddSpec() : gnMultiSpec, gnGenomeSpec, gnFragmentSpec AddToSeqLength() : gnFileContig allRegions : gnLocation alphabetCharacterFilter() : gnFilter alphabetCharacterFilterType : gnFilter append() : gnSequence assign() : gnSequence - b - BaseCount() : gnSEQSource basicDNASeqFilter() : gnFilter basicDNASeqFilterType : gnFilter basicRNASeqFilter() : gnFilter basicRNASeqFilterType : gnFilter - c - CacheTranslator() : gnFastTranslator Clear() : gnStringSpec, gnSourceSpec, gnMultiSpec, gnLocation, gnGenomeSpec, gnFragmentSpec, gnFileContig, gnContigSpec, gnBaseSpec Clone() : gnTranslator, gnStringSpec, gnStringQualifier, gnStringHeader, gnSourceSpec, gnSourceQualifier, gnSourceHeader, gnSequence, gnSEQSource, gnRAWSource, gnMultiSpec, gnLocation, gnGenomeSpec, gnGBKSource, gnFragmentSpec, gnFilter, gnFileSource, gnFileContig, gnFeature, gnFastTranslator, gnFASSource, gnDNXSource, gnDataBaseSource, gnContigSpec, gnCompare, gnClone, gnBaseSpec, gnBaseSource, gnBaseQualifier, gnBaseHeader, gnBaseFilter, gnBaseFeature, gnABISource CloneRange() : gnStringSpec, gnSourceSpec, gnGenomeSpec, gnFragmentSpec, gnContigSpec, gnBaseSpec Close() : gnFileSource, gnDataBaseSource, gnBaseSource comparator : gnSequence, gnRNASequence, gnProteinSequence, gnDNASequence compare : gnSequence, gnTranslator Contains() : gnLocation, gnCompare, gnBaseFeature contig() : gnSequence contigByBase() : gnSequence contigByName() : gnSequence contigIndexByBase() : gnSequence contigIndexByName() : gnSequence contigLength() : gnSequence contigListLength() : gnSequence contigListSize() : gnSequence contigName() : gnSequence contigStart() : gnSequence CreateAlphabetCharacterFilter() : gnFilter CreateBasicDNAFilter() : gnFilter CreateBasicRNAFilter() : gnFilter CreateDNAComparator() : gnCompare CreateDNAComplementFilter() : gnFilter CreateDNAProteinTranslator() : gnTranslator, gnFastTranslator CreateDNAtoRNAFilter() : gnFilter CreateFullDNAFilter() : gnFilter CreateFullRNAFilter() : gnFilter CreateNumberCharacterFilter() : gnFilter CreateProteinComparator() : gnCompare CreateProteinDNATranslator() : gnTranslator, gnFastTranslator CreateProteinFilter() : gnFilter CreateProteinRNATranslator() : gnTranslator CreateRNAComparator() : gnCompare CreateRNAComplementFilter() : gnFilter CreateRNAProteinTranslator() : gnTranslator CreateRNAtoDNAFilter() : gnFilter Crop() : gnBaseFeature CropEnd() : gnMultiSpec, gnLocation, gnFragmentSpec, gnContigSpec, gnBaseSpec, gnBaseFeature CropStart() : gnMultiSpec, gnLocation, gnFragmentSpec, gnContigSpec, gnBaseSpec, gnBaseFeature CropTo() : gnLocation - d - Defined : gnLocation DelArrayEntry() : gnCompare DelPath() : gnSourceFactory DelSource() : gnSourceFactory DelSourceClass() : gnSourceFactory determinedRegions : gnLocation DNAComplementFilter() : gnFilter DNAComplementFilterType : gnFilter DNAProteinTranslator() : gnTranslator, gnFastTranslator DNAProteinTranslatorType : gnTranslator, gnFastTranslator DNASeqCompare() : gnCompare DNASeqCompareType : gnCompare DNAtoRNAFilter() : gnFilter DNAtoRNAFilterType : gnFilter - e - erase() : gnSequence ex_start : ExMem - f - Filler() : gnSEQSource, gnGBKSource Filter() : gnTranslator, gnFilter, gnFastTranslator, gnBaseFilter filter_list : gnSequence, gnRNASequence, gnProteinSequence, gnDNASequence find() : gnSequence FirstIndexOfQualifier() : gnBaseFeature FormatString() : gnSEQSource, gnGBKSource fullDNASeqFilter() : gnFilter fullDNASeqFilterType : gnFilter fullRNASeqFilter() : gnFilter fullRNASeqFilterType : gnFilter function_trace : gnException - g - GetBounds() : gnLocation GetBrokenFeatures() : gnMultiSpec, gnGenomeSpec, gnFragmentSpec getBrokenFeatures() : gnSequence GetCode() : gnException GetContainedFeatures() : gnMultiSpec, gnGenomeSpec, gnFragmentSpec getContainedFeatures() : gnSequence GetContig() : gnFASSource, gnABISource GetContigID() : gnSEQSource, gnRAWSource, gnGBKSource, gnFASSource, gnDNXSource, gnDataBaseSource, gnBaseSource, gnABISource GetContigListLength() : gnSEQSource, gnRAWSource, gnGBKSource, gnFASSource, gnDNXSource, gnDataBaseSource, gnBaseSource, gnABISource GetContigName() : gnSEQSource, gnRAWSource, gnGBKSource, gnFASSource, gnDNXSource, gnDataBaseSource, gnBaseSource, gnABISource GetContigSeqLength() : gnSEQSource, gnRAWSource, gnGBKSource, gnFASSource, gnDNXSource, gnDataBaseSource, gnBaseSource, gnABISource GetDefaultChar() : gnTranslator, gnFilter, gnFastTranslator GetDefaultInputWidth() : gnTranslator GetDefaultSourceClass() : gnSourceFactory GetEnd() : gnLocation GetEndLength() : gnLocation GetFeature() : gnMultiSpec, gnGenomeSpec, gnFragmentSpec getFeature() : gnSequence GetFeatureListLength() : gnMultiSpec, gnGenomeSpec, gnFragmentSpec getFeatureListLength() : gnSequence GetFileContig() : gnSEQSource, gnRAWSource, gnGBKSource, gnFileSource, gnFASSource, gnDNXSource, gnABISource GetFileLength() : gnFileContig GetFileStartEnd() : gnFileContig GetFilter() : gnFileSource, gnDataBaseSource, gnBaseSource getFilterList() : gnSequence GetFirst() : gnLocation GetHeader() : gnStringHeader, gnSourceHeader, gnMultiSpec, gnBaseHeader getHeader() : gnSequence GetHeaderListLength() : gnMultiSpec getHeaderListLength() : gnSequence GetHeaderLoc() : gnSourceHeader GetHeaderName() : gnStringHeader, gnSourceHeader, gnBaseHeader GetHeaderStart() : gnSourceHeader GetID() : gnBaseFeature GetInt() : gnExceptionCode GetIntersectingFeatures() : gnMultiSpec, gnGenomeSpec, gnFragmentSpec getIntersectingFeatures() : gnSequence GetIntersection() : gnLocation GetLast() : gnLocation GetLength() : gnStringHeader, gnSourceHeader, gnMultiSpec, gnContigSpec, gnBaseSpec, gnBaseHeader GetLocation() : gnBaseFeature GetLocationListLength() : gnBaseFeature GetLocationType() : gnBaseFeature GetMessage() : gnException GetName() : gnStringQualifier, gnSourceQualifier, gnFileContig, gnExceptionCode, gnCompare, gnBaseSpec, gnBaseQualifier, gnBaseFilter, gnBaseFeature GetNameLength() : gnStringQualifier, gnSourceQualifier, gnBaseQualifier GetOpenString() : gnFileSource, gnDataBaseSource, gnBaseSource GetPath() : gnSourceFactory GetPathListSize() : gnSourceFactory GetQualifier() : gnBaseFeature GetQualifierListLength() : gnBaseFeature GetQualifierName() : gnBaseFeature GetQualifierValue() : gnBaseFeature GetRDefaultChar() : gnFilter GetRepeatSeqGapSize() : gnFileContig GetSectLength() : gnFileContig GetSectStartEnd() : gnFileContig GetSeqC() : gnSequence GetSeqLength() : gnFileContig GetSource() : gnStringSpec, gnSourceSpec, gnSourceFactory GetSourceClass() : gnSourceFactory GetSourceClassListSize() : gnSourceFactory GetSourceContigIndex() : gnContigSpec GetSourceFactory() : gnSourceFactory GetSourceLength() : gnStringSpec, gnSourceSpec, gnContigSpec GetSourceListSize() : gnSourceFactory GetSourceName() : gnMultiSpec, gnContigSpec GetSpec() : gnSequence, gnSEQSource, gnRAWSource, gnMultiSpec, gnGenomeSpec, gnGBKSource, gnFragmentSpec, gnFASSource, gnDNXSource, gnDataBaseSource, gnBaseSource, gnBaseFeature, gnABISource GetSpecByBase() : gnMultiSpec, gnGenomeSpec, gnFragmentSpec GetSpecEndBase() : gnMultiSpec GetSpecIndexByBase() : gnMultiSpec GetSpecIndexByName() : gnMultiSpec GetSpecListLength() : gnMultiSpec, gnGenomeSpec, gnFragmentSpec GetSpecStartBase() : gnMultiSpec GetStart() : gnLocation, gnContigSpec GetStartLength() : gnLocation GetType() : gnLocation GetUnion() : gnLocation GetURL() : gnSourceFactory GetValue() : gnStringQualifier, gnSourceQualifier, gnBaseQualifier GetValueLength() : gnStringQualifier, gnSourceQualifier, gnBaseQualifier GetValueLoc() : gnSourceQualifier GetValueStart() : gnSourceQualifier globalToLocal() : gnSequence globalToSource() : gnSequence gnABISource() : gnABISource gnBaseFeature() : gnBaseFeature gnBaseHeader() : gnBaseHeader gnBaseQualifier() : gnBaseQualifier gnBaseSource() : gnBaseSource gnBaseSpec() : gnBaseSpec gnClone() : gnClone gnCompare() : gnCompare gnCompareType : gnCompare gnContigSpec() : gnContigSpec gnDataBaseSource() : gnDataBaseSource gnDNASequence() : gnDNASequence gnDNXSource() : gnDNXSource gnException() : gnException gnExceptionCode() : gnExceptionCode gnFASSource() : gnFASSource gnFastTranslator() : gnFastTranslator gnFeature() : gnFeature gnFileContig() : gnFileContig gnFileSource() : gnFileSource gnFilter() : gnFilter gnFilterType : gnFilter gnFragmentSpec() : gnFragmentSpec gnGBKSource() : gnGBKSource gnGenomeSpec() : gnGenomeSpec gnLocation() : gnLocation gnLocationType : gnLocation gnMultiSpec() : gnMultiSpec gnProteinSequence() : gnProteinSequence gnRAWSource() : gnRAWSource gnRNASequence() : gnRNASequence gnSEQSource() : gnSEQSource gnSequence() : gnSequence gnSourceFactory() : gnSourceFactory gnSourceHeader() : gnSourceHeader gnSourceQualifier() : gnSourceQualifier gnSourceSpec() : gnSourceSpec gnStringHeader() : gnStringHeader gnStringQualifier() : gnStringQualifier gnStringSpec() : gnStringSpec gnTranslator() : gnTranslator gnTranslatorType : gnTranslator, gnFastTranslator - h - HasContig() : gnSEQSource, gnRAWSource, gnGBKSource, gnFASSource, gnDNXSource, gnDataBaseSource, gnBaseSource, gnABISource HasPath() : gnSourceFactory HasQualifier() : gnBaseFeature HasRepeatSeqGap() : gnFileContig HasSource() : gnSourceFactory HasSourceClass() : gnSourceFactory - i - in_start : ExMem insert() : gnSequence InsPath() : gnSourceFactory intersectRestriction : gnLocation Intersects() : gnLocation, gnBaseFeature IsBroken() : gnBaseFeature isCircular() : gnSequence IsCircular() : gnBaseSpec IsContainedBy() : gnBaseFeature IsEndBoundLonger() : gnLocation IsEndBoundShorter() : gnLocation IsReverseComplement() : gnBaseSpec isReverseComplement() : gnSequence IsStartBoundLonger() : gnLocation IsStartBoundShorter() : gnLocation IsValid() : gnFilter - l - LastIndexOfQualifier() : gnBaseFeature length : gnSequence, ExMem LessThan() : gnCompare LoadSource() : gnSequence localToGlobal() : gnSequence localToSource() : gnSequence LT_BetweenBases : gnLocation LT_Complement : gnLocation LT_Group : gnLocation LT_Nothing : gnLocation LT_OneOf : gnLocation LT_Order : gnLocation LT_Standard : gnLocation - m - m_broken : gnBaseFeature m_circular : gnBaseSpec m_code : gnExceptionCode, gnException m_containArray : gnCompare m_contig : gnRAWSource m_contigList : gnSEQSource, gnGBKSource, gnFASSource, gnABISource m_defaultChar : gnTranslator, gnFilter, gnFastTranslator m_defaultInputWidth : gnTranslator m_DNXSpec : gnDNXSource m_end : gnLocation m_endLength : gnLocation m_featureList : gnFragmentSpec m_file : gnException m_fileStartEnd : gnFileContig m_header : gnStringHeader m_headerList : gnMultiSpec m_id : gnBaseFeature m_ifstream : gnFileSource m_ignoreCase : gnCompare m_inputTable : gnTranslator m_length : gnSourceQualifier, gnSourceHeader, gnContigSpec m_line : gnException m_locationList : gnBaseFeature m_locationType : gnBaseFeature m_message : gnException m_name : gnTranslator, gnStringQualifier, gnStringHeader, gnSourceQualifier, gnSourceHeader, gnLocation, gnFilter, gnFileContig, gnFastTranslator, gnExceptionCode, gnCompare, gnBaseSpec, gnBaseFilter, gnBaseFeature m_newlineSize : gnFileSource m_newlineType : gnFileSource m_openString : gnFileSource m_outputTable : gnTranslator m_pairArray : gnFilter, gnCompare m_pathList : gnSourceFactory m_pDefaultSourceClass : gnSourceFactory m_pFilter : gnFileSource m_pSource : gnSourceSpec m_qualifierList : gnBaseFeature m_rDefaultChar : gnFilter m_repeatSeqGap : gnFileContig m_repeatSeqGapSize : gnFileContig m_reverseComplement : gnBaseSpec m_seqLength : gnFileContig m_seqString : gnStringSpec m_source : gnSourceQualifier, gnSourceHeader m_sourceClassList : gnSourceFactory m_SourceContigIndex : gnContigSpec m_sourceList : gnSourceFactory m_sourceName : gnMultiSpec, gnBaseSpec m_spec : gnSEQSource, gnRAWSource, gnGBKSource, gnBaseFeature, gnABISource m_SpecList : gnGenomeSpec, gnFragmentSpec m_start : gnSourceQualifier, gnSourceHeader, gnLocation, gnContigSpec m_startEndArray : gnFileContig m_startLength : gnLocation m_transCache : gnFastTranslator m_translator : gnFastTranslator m_type : gnLocation m_value : gnStringQualifier MakeValid() : gnFilter MatchSourceClass() : gnSourceFactory merge() : gnSequence mergeContigs() : gnSequence MergeFragments() : gnGenomeSpec MoveNegative() : gnLocation, gnBaseFeature MovePositive() : gnLocation, gnBaseFeature MoveTo() : gnLocation - n - numberCharacterFilter() : gnFilter numberCharacterFilterType : gnFilter - o - Open() : gnFileSource, gnDataBaseSource, gnBaseSource operator!=() : gnSequence, gnExceptionCode operator+() : gnSequence operator+=() : gnSequence operator<() : gnSequence operator<< : gnSequence, gnException operator<=() : gnSequence operator=() : gnSourceFactory, gnSequence, gnFastTranslator, gnExceptionCode operator==() : gnSequence, gnExceptionCode operator>() : gnSequence operator>=() : gnSequence operator>> : gnSequence operator[]() : gnSequence - p - ParseStream() : gnSEQSource, gnRAWSource, gnGBKSource, gnFileSource, gnFASSource, gnDNXSource, gnABISource PathExists() : gnSourceFactory ProteinDNATranslator() : gnTranslator, gnFastTranslator ProteinDNATranslatorType : gnTranslator, gnFastTranslator ProteinRNATranslator() : gnTranslator ProteinRNATranslatorType : gnTranslator ProteinSeqCompare() : gnCompare ProteinSeqCompareType : gnCompare proteinSeqFilter() : gnFilter proteinSeqFilterType : gnFilter - r - Read() : gnStringSpec, gnSourceSpec, gnFileSource, gnDataBaseSource, gnContigSpec, gnBaseSource RemoveContained() : gnCompare removeFeature() : gnSequence RemoveFeature() : gnMultiSpec, gnGenomeSpec, gnFragmentSpec removeHeader() : gnSequence RemoveHeader() : gnMultiSpec RemoveLocation() : gnBaseFeature RemovePair() : gnTranslator, gnFilter, gnFastTranslator, gnCompare RemoveQualifier() : gnBaseFeature RemoveSingle() : gnFilter, gnCompare RemoveSpec() : gnMultiSpec, gnGenomeSpec, gnFragmentSpec ReverseFilter() : gnFilter RNAComplementFilter() : gnFilter RNAComplementFilterType : gnFilter RNAProteinTranslator() : gnTranslator RNAProteinTranslatorType : gnTranslator RNASeqCompare() : gnCompare RNASeqCompareType : gnCompare RNAtoDNAFilter() : gnFilter RNAtoDNAFilterType : gnFilter - s - SeqRead() : gnSEQSource, gnRAWSource, gnMultiSpec, gnGBKSource, gnFASSource, gnDNXSource, gnDataBaseSource, gnContigSpec, gnBaseSpec, gnBaseSource, gnABISource SeqSeek() : gnSEQSource, gnRAWSource, gnGBKSource, gnFASSource, gnABISource SeqStartPos() : gnSEQSource, gnRAWSource, gnGBKSource, gnFASSource, gnABISource SetBounds() : gnLocation SetBroken() : gnBaseFeature setCircular() : gnSequence SetCircular() : gnBaseSpec SetCompare() : gnTranslator SetContained() : gnCompare setContigName() : gnSequence SetDefaultChar() : gnTranslator, gnFilter, gnFastTranslator SetDefaultInputWidth() : gnTranslator SetDefaultSourceClass() : gnSourceFactory SetEnd() : gnLocation SetEndLength() : gnLocation SetFileEnd() : gnFileContig SetFileStart() : gnFileContig SetFileStartEnd() : gnFileContig SetFilter() : gnFileSource, gnDataBaseSource, gnBaseSource setFilter() : gnSequence setFilterList() : gnSequence SetHeader() : gnStringHeader SetHeaderLength() : gnSourceHeader SetHeaderLoc() : gnSourceHeader SetHeaderName() : gnStringHeader SetHeaderStart() : gnSourceHeader SetID() : gnBaseFeature SetLength() : gnContigSpec SetLocation() : gnBaseFeature SetLocationType() : gnBaseFeature SetName() : gnStringQualifier, gnFileContig, gnCompare, gnBaseSpec, gnBaseFilter, gnBaseFeature SetPair() : gnTranslator, gnFilter, gnFastTranslator, gnCompare SetQualifier() : gnBaseFeature SetQualifierName() : gnBaseFeature SetQualifierValue() : gnBaseFeature SetRepeatGapSize() : gnFileContig SetRepeatSeqGap() : gnFileContig SetRepeatSeqGapSize() : gnFileContig SetRepeatSeqSize() : gnFileContig SetReverseComplement() : gnGenomeSpec, gnFragmentSpec, gnContigSpec, gnBaseSpec setReverseComplement() : gnSequence SetSectEnd() : gnFileContig SetSectStart() : gnFileContig SetSectStartEnd() : gnFileContig SetSeqLength() : gnFileContig SetSingle() : gnFilter, gnCompare SetSourceClass() : gnSourceFactory SetSourceContigIndex() : gnContigSpec SetSourceName() : gnMultiSpec, gnContigSpec SetSpec() : gnSequence, gnBaseFeature SetStart() : gnLocation, gnContigSpec SetStartLength() : gnLocation SetType() : gnLocation SetValue() : gnStringQualifier SetValueLength() : gnSourceQualifier SetValueLoc() : gnSourceQualifier SetValueStart() : gnSourceQualifier size() : gnSequence spec : gnSequence, gnRNASequence, gnProteinSequence, gnDNASequence splitContig() : gnSequence subseq() : gnSequence - t - ToArray() : gnSequence ToString() : gnSequence - u - undeterminedRegions : gnLocation Unknown : gnLocation use_default : gnTranslator, gnFastTranslator UseDefaultChar() : gnTranslator, gnFastTranslator - v - ValidateName() : gnDNXSource - w - Write() : gnSEQSource, gnRAWSource, gnGBKSource, gnFASSource, gnDNXSource, gnABISource WriteHeader() : gnGBKSource - ~ - ~gnABISource() : gnABISource ~gnBaseFeature() : gnBaseFeature ~gnBaseHeader() : gnBaseHeader ~gnBaseQualifier() : gnBaseQualifier ~gnBaseSource() : gnBaseSource ~gnBaseSpec() : gnBaseSpec ~gnClone() : gnClone ~gnCompare() : gnCompare ~gnContigSpec() : gnContigSpec ~gnDataBaseSourcee() : gnDataBaseSource ~gnDNXSource() : gnDNXSource ~gnFASSource() : gnFASSource ~gnFeature() : gnFeature ~gnFileContig() : gnFileContig ~gnFileSource() : gnFileSource ~gnFilter() : gnFilter ~gnFragmentSpec() : gnFragmentSpec ~gnGBKSource() : gnGBKSource ~gnGenomeSpec() : gnGenomeSpec ~gnMultiSpec() : gnMultiSpec ~gnRAWSource() : gnRAWSource ~gnSEQSource() : gnSEQSource ~gnSequence() : gnSequence ~gnSourceFactory() : gnSourceFactory ~gnSourceHeader() : gnSourceHeader ~gnSourceQualifier() : gnSourceQualifier ~gnSourceSpec() : gnSourceSpec ~gnStringHeader() : gnStringHeader ~gnStringQualifier() : gnStringQualifier ~gnStringSpec() : gnStringSpec