|
Definition at line 37 of file gnDefs.h.
Referenced by gnCompare::AddArrayEntry(), gnGenomeSpec::AddFeature(), gnSequence::addFeature(), gnFragmentSpec::AddFeature(), gnSequence::addHeader(), gnMultiSpec< SubSpec >::AddHeader(), gnBaseFeature::AddLocation(), gnMultiSpec< SubSpec >::AddSpec(), BaseCount(), gnSEQSource::BaseCount(), gnGenomeSpec::Clear(), gnFragmentSpec::Clear(), gnFileContig::Clear(), gnMultiSpec< SubSpec >::Clear(), gnGenomeSpec::CloneRange(), gnFragmentSpec::CloneRange(), ComplementLocation(), gnCompare::Contains(), gnBaseFeature::Contains(), gnSequence::contig(), gnSequence::contigByName(), gnSequence::contigIndexByBase(), gnSequence::contigIndexByName(), gnSequence::contigLength(), gnSequence::contigName(), gnSequence::contigStart(), gnFragmentSpec::CropEnd(), gnBaseFeature::CropEnd(), gnMultiSpec< SubSpec >::CropEnd(), gnFragmentSpec::CropStart(), gnBaseFeature::CropStart(), gnMultiSpec< SubSpec >::CropStart(), gnCompare::DelArrayEntry(), gnSourceFactory::DelPath(), gnSourceFactory::DelSource(), gnSequence::erase(), gnTranslator::Filter(), gnFilter::Filter(), gnFastTranslator::Filter(), gnBaseFeature::FirstIndexOfQualifier(), gnSEQSource::FormatString(), gnGBKSource::FormatString(), gnGenomeSpec::GetBrokenFeatures(), gnFragmentSpec::GetBrokenFeatures(), gnGenomeSpec::GetContainedFeatures(), gnFragmentSpec::GetContainedFeatures(), gnFASSource::GetContig(), gnSEQSource::GetContigID(), gnRAWSource::GetContigID(), gnGBKSource::GetContigID(), gnFASSource::GetContigID(), gnDNXSource::GetContigID(), gnABISource::GetContigID(), gnSEQSource::GetContigListLength(), gnRAWSource::GetContigListLength(), gnGBKSource::GetContigListLength(), gnFASSource::GetContigListLength(), gnDNXSource::GetContigListLength(), gnABISource::GetContigListLength(), gnSEQSource::GetContigName(), gnRAWSource::GetContigName(), gnGBKSource::GetContigName(), gnFASSource::GetContigName(), gnDNXSource::GetContigName(), gnABISource::GetContigName(), gnSEQSource::GetContigSeqLength(), gnRAWSource::GetContigSeqLength(), gnGBKSource::GetContigSeqLength(), gnFASSource::GetContigSeqLength(), gnDNXSource::GetContigSeqLength(), gnABISource::GetContigSeqLength(), gnTranslator::GetDefaultInputWidth(), gnGenomeSpec::GetFeature(), gnSequence::getFeature(), gnFragmentSpec::GetFeature(), gnGenomeSpec::GetFeatureListLength(), gnSequence::getFeatureListLength(), gnFragmentSpec::GetFeatureListLength(), gnSEQSource::GetFileContig(), gnRAWSource::GetFileContig(), gnGBKSource::GetFileContig(), gnFASSource::GetFileContig(), gnDNXSource::GetFileContig(), gnABISource::GetFileContig(), gnSequence::getHeader(), gnMultiSpec< SubSpec >::GetHeader(), gnSequence::getHeaderListLength(), gnMultiSpec< SubSpec >::GetHeaderListLength(), gnSourceHeader::GetHeaderStart(), gnBaseFeature::GetID(), gnExceptionCode::GetInt(), gnGenomeSpec::GetIntersectingFeatures(), gnFragmentSpec::GetIntersectingFeatures(), gnStringHeader::GetLength(), gnSourceHeader::GetLength(), gnMultiSpec< SubSpec >::GetLength(), gnBaseFeature::GetLocation(), gnBaseFeature::GetLocationListLength(), gnStringQualifier::GetNameLength(), gnSourceQualifier::GetNameLength(), GetNewExceptionCode(), gnSourceFactory::GetPath(), gnSourceFactory::GetPathListSize(), gnBaseFeature::GetQualifier(), gnBaseFeature::GetQualifierListLength(), gnBaseFeature::GetQualifierName(), gnBaseFeature::GetQualifierValue(), gnFileContig::GetSectLength(), gnFileContig::GetSectStartEnd(), gnSourceFactory::GetSource(), gnSourceFactory::GetSourceClassListSize(), gnContigSpec::GetSourceContigIndex(), gnSourceFactory::GetSourceListSize(), gnFASSource::GetSpec(), gnMultiSpec< SubSpec >::GetSpec(), gnMultiSpec< SubSpec >::GetSpecEndBase(), gnMultiSpec< SubSpec >::GetSpecIndexByBase(), gnMultiSpec< SubSpec >::GetSpecIndexByName(), gnMultiSpec< SubSpec >::GetSpecListLength(), gnMultiSpec< SubSpec >::GetSpecStartBase(), gnSourceFactory::GetURL(), gnStringQualifier::GetValueLength(), gnSourceQualifier::GetValueLength(), gnSourceQualifier::GetValueStart(), gnSequence::globalToLocal(), gnSequence::globalToSource(), gnBaseFeature::gnBaseFeature(), gnExceptionCode::gnExceptionCode(), gnFeature::gnFeature(), gnFileContig::gnFileContig(), gnFragmentSpec::gnFragmentSpec(), gnGenomeSpec::gnGenomeSpec(), gnSourceHeader::gnSourceHeader(), gnSourceQualifier::gnSourceQualifier(), gnSourceSpec::gnSourceSpec(), gnSEQSource::HasContig(), gnGBKSource::HasContig(), gnFASSource::HasContig(), gnDNXSource::HasContig(), gnSourceFactory::HasPath(), gnBaseFeature::HasQualifier(), gnSequence::insert(), gnSourceFactory::InsPath(), gnBaseFeature::Intersects(), gnBaseFeature::IsContainedBy(), gnSequence::isReverseComplement(), gnFilter::IsValid(), gnBaseFeature::LastIndexOfQualifier(), gnCompare::LessThan(), loc_binary_search(), gnSequence::localToGlobal(), gnSequence::localToSource(), main(), gnFilter::MakeValid(), map_coordinates(), gnSequence::mergeContigs(), gnGenomeSpec::MergeFragments(), gnBaseFeature::MoveNegative(), gnBaseFeature::MovePositive(), gnSEQSource::ParseStream(), gnRAWSource::ParseStream(), gnGBKSource::ParseStream(), gnFASSource::ParseStream(), gnDNXSource::ParseStream(), print_feature(), gnGenomeSpec::RemoveFeature(), gnSequence::removeFeature(), gnFragmentSpec::RemoveFeature(), gnSequence::removeHeader(), gnMultiSpec< SubSpec >::RemoveHeader(), gnBaseFeature::RemoveLocation(), gnTranslator::RemovePair(), gnBaseFeature::RemoveQualifier(), gnMultiSpec< SubSpec >::RemoveSpec(), gnFilter::ReverseFilter(), gnSEQSource::SeqRead(), gnRAWSource::SeqRead(), gnGBKSource::SeqRead(), gnFASSource::SeqRead(), gnContigSpec::SeqRead(), gnABISource::SeqRead(), gnMultiSpec< SubSpec >::SeqRead(), gnDNXSource::SeqRead(), gnSEQSource::SeqSeek(), gnGBKSource::SeqSeek(), gnFASSource::SeqSeek(), gnABISource::SeqSeek(), gnSEQSource::SeqStartPos(), gnGBKSource::SeqStartPos(), gnFASSource::SeqStartPos(), gnSequence::setContigName(), gnTranslator::SetDefaultInputWidth(), gnSourceHeader::SetHeaderLength(), gnSourceHeader::SetHeaderStart(), gnBaseFeature::SetID(), gnBaseFeature::SetLocation(), gnBaseFeature::SetQualifier(), gnBaseFeature::SetQualifierName(), gnBaseFeature::SetQualifierValue(), gnSequence::setReverseComplement(), gnGenomeSpec::SetReverseComplement(), gnFragmentSpec::SetReverseComplement(), gnFileContig::SetSectEnd(), gnFileContig::SetSectStart(), gnFileContig::SetSectStartEnd(), gnContigSpec::SetSourceContigIndex(), gnSourceQualifier::SetValueLength(), gnSourceQualifier::SetValueStart(), gnSequence::splitContig(), gnGBKSource::Write(), gnFASSource::Write(), gnDNXSource::Write(), WriteData(), WriteHeader(), and gnBaseFeature::~gnBaseFeature(). |