Here is a list of all documented class members with links to the class documentation for each member:

- _ -

• __add__() : Bio::Restriction::Restriction::RestrictionType , Martel::Expression::Expression , Martel::Expression::Seq
• __and__() : Bio::EUtils::Datatypes::Expression
• __call__() : Bio::Affy::CelFile::CelParser
• __cmp__() : Bio::GA::Organism::Organism , Bio::SeqFeature::AbstractPosition
• __contains__() : Bio::Pathway::Rep::HashSet::HashSet
• __delitem__() : Bio::EUtils::MultiDict::OrderedMultiDict , Bio::EUtils::MultiDict::UnorderedMultiDict
• __div__() : Bio::Restriction::Restriction::RestrictionType
• __eq__() : Bio::Pathway::Reaction , Bio::Pathway::Rep::Graph::Graph , Bio::Pathway::Rep::HashSet::HashSet , Bio::Pathway::Rep::MultiGraph::MultiGraph , Bio::Restriction::Restriction::RestrictionType , Bio::EUtils::Datatypes::DBIds , Bio::EUtils::Datatypes::Date , Bio::EUtils::MultiDict::OrderedMultiDict , Bio::EUtils::MultiDict::UnorderedMultiDict
• __floordiv__() : Bio::Restriction::Restriction::RestrictionType
• __ge__() : Bio::Restriction::Restriction::RestrictionType
• __getattr__() : Bio::SeqFeature::FeatureLocation
• __getitem__() : Bio::SeqIO::Interfaces::InterlacedSequenceIterator , Bio::SeqIO::StockholmIO::StockholmIterator , Bio::SwissProt::SProt::ExPASyDictionary , biocorba_sql_server::BioSQLAdapterDictionary , Bio::EUtils::Datatypes::DBIds , Bio::EUtils::DBIdsClient::BaseDBIdsRecordSet , Bio::GenBank::NCBIDictionary , Bio::PDB::FragmentMapper::FragmentMapper , Bio::Prosite::ExPASyDictionary , Bio::Prosite::Prodoc::ExPASyDictionary , Bio::PubMed::Dictionary , Bio::SCOP::FileIndex::FileIndex
• __gt__() : Bio::Restriction::Restriction::RestrictionType
• __hash__() : Bio::Pathway::Reaction , Bio::Pathway::Interaction
• __init__() : Bio::config::DBRegistry::DBRegistry , Bio::HMM::MarkovModel::HiddenMarkovModel , Bio::SwissProt::SProt::_SequenceConsumer , BioSQL::Loader::DatabaseLoader , Bio::HMM::Trainer::TrainingSequence , BioSQL::Loader::DatabaseRemover , Martel::Expression::Alt , Bio::config::DBRegistry::DBObject , Bio::HMM::Trainer::BaumWelchTrainer , Martel::Expression::Seq , Martel::Parser::RecordParser , Bio::IntelliGenetics::Iterator , biocorba_sql_server::BioSQLAdapterDictionary , run_tests::RegressionTest , Bio::config::DBRegistry::DBGroup , Bio::IntelliGenetics::_Scanner , test_GAQueens::QueensRepair , test_GAQueens::QueensCrossover , Bio::IntelliGenetics::RecordParser , test_GAQueens::QueensMutation , Bio::config::DBRegistry::CGIDB , Bio::KEGG::Compound::Record , Bio::KEGG::Compound::Iterator , Bio::config::DBRegistry::EUtilsDB , Bio::KEGG::Enzyme::Record , Bio::KEGG::Enzyme::Iterator , Bio::config::DBRegistry::BioSQLDB , Bio::KEGG::Map::Iterator , Bio::kNN::kNN , Bio::config::DBRegistry::BioCorbaDB , Bio::LocusLink::Iterator , Bio::LocusLink::_Scanner , Bio::config::DBRegistry::IndexedFileDB , Bio::LocusLink::RecordParser , Bio::LogisticRegression::LogisticRegression , Bio::config::FormatRegistry::FormatObject , Bio::Medline::Iterator , Bio::Medline::NLMMedlineXML::_IndexerHandler , Bio::config::FormatRegistry::FormatGroup , Bio::MEME::Parser::MEMERecord , Bio::MEME::Parser::MEMEParser , Bio::config::Registry::Registry , Bio::MetaTool::Iterator , Bio::MetaTool::_Scanner , Bio::config::Registry::RegisterableObject , Bio::MetaTool::RecordParser , Bio::Mindy::SimpleSeqRecord::FixDocumentBuilder , Bio::config::Registry::RegisterableGroup , Bio::MultiProc::copen::_ProcHandle , Bio::MultiProc::copen::_PickleHandle , Bio::ECell::Iterator , Bio::MultiProc::Scheduler::Scheduler , Bio::MultiProc::Task::Task , Bio::Affy::CelFile::CelRecord , Bio::ECell::_Scanner , Bio::NBRF::Iterator , Bio::NBRF::_Scanner , Bio::ECell::RecordParser , Bio::NBRF::RecordParser , Bio::NeuralNetwork::BackPropagation::Layer::AbstractLayer , Bio::Affy::CelFile::CelParser , Bio::EUtils::Datatypes::DBIds , Bio::NeuralNetwork::BackPropagation::Network::BasicNetwork , Bio::NeuralNetwork::Gene::Motif::MotifFinder , Bio::EUtils::Datatypes::WithinNDays , Bio::NeuralNetwork::Gene::Motif::MotifCoder , Bio::NeuralNetwork::Gene::Pattern::PatternIO , Bio::Align::AlignInfo::SummaryInfo , Bio::EUtils::Datatypes::DateRange , Bio::NeuralNetwork::Gene::Pattern::PatternRepository , Bio::NeuralNetwork::Gene::Schema::Schema , Bio::EUtils::ThinClient::ThinClient , Bio::NeuralNetwork::Gene::Schema::GeneticAlgorithmFinder , Bio::NeuralNetwork::Gene::Schema::DifferentialSchemaFitness , Bio::Align::AlignInfo::PSSM , Bio::Fasta::Record , Bio::NeuralNetwork::Gene::Schema::MostCountSchemaFitness , Bio::NeuralNetwork::Gene::Schema::RandomMotifGenerator , Bio::Fasta::Iterator , Bio::NeuralNetwork::Gene::Schema::SimpleFinisher , Bio::NeuralNetwork::Gene::Schema::SchemaCoder , Bio::Align::FormatConvert::FormatConverter , Bio::Fasta::SequenceParser , Bio::NeuralNetwork::Gene::Schema::SchemaFactory , Bio::NeuralNetwork::Gene::Signature::SignatureFinder , Bio::Fasta::Dictionary , Bio::NeuralNetwork::Gene::Signature::SignatureCoder , Bio::NeuralNetwork::StopTraining::ValidationIncreaseStop , Bio::Align::Generic::Alignment , Bio::Fasta::FastaAlign::FastaAlignment , Bio::NeuralNetwork::Training::ExampleManager , Bio::Nexus::Nodes::Chain , Bio::File::SGMLHandle , Bio::Nexus::Nodes::Node , Bio::Nexus::Trees::Tree , Bio::AlignAce::Parser::AlignAceParser , Bio::GA::Crossover::General::SafeFitnessCrossover , Bio::ParserSupport::TaggingConsumer , Bio::ParserSupport::EventGenerator , Bio::GA::Crossover::GeneralPoint::GeneralPointCrossover , Bio::Pathway::Reaction , Bio::Pathway::System , Bio::AlignAce::Parser::CompareAceParser , Bio::GA::Crossover::Point::SinglePointCrossover , Bio::Pathway::Network , Bio::Pathway::Rep::Graph::Graph , Bio::GA::Crossover::TwoPoint::TwoPointCrossover , Bio::Pathway::Rep::HashSet::HashSet , Bio::Pathway::Rep::MultiGraph::MultiGraph , Bio::Application::ApplicationResult , Bio::GA::Crossover::Uniform::UniformCrossover , Bio::PDB::Atom::DisorderedAtom , Bio::PDB::DSSP::DSSP , Bio::GA::Evolver::GenerationEvolver , Bio::PDB::FragmentMapper::Fragment , Bio::PDB::FragmentMapper::FragmentMapper , Bio::Blast::NCBIStandalone::BlastParser , Bio::GA::Mutation::General::SafeFitnessMutation , Bio::PDB::HSExposure::_AbstractHSExposure , Bio::PDB::HSExposure::HSExposureCA , Bio::GA::Mutation::Simple::SinglePositionMutation , Bio::PDB::HSExposure::HSExposureCB , Bio::PDB::Model::Model , Bio::Blast::NCBIStandalone::PSIBlastParser , Bio::GA::Mutation::Simple::ConversionMutation , Bio::PDB::NeighborSearch::NeighborSearch , Bio::PDB::PDBIO::PDBIO , Bio::GA::Organism::Organism , Bio::PDB::PDBList::PDBList , Bio::PDB::PDBParser::PDBParser , Bio::Blast::NCBIStandalone::Iterator , Bio::GA::Repair::Stabilizing::AmbiguousRepair , Bio::PDB::Polypeptide::_PPBuilder , Bio::PDB::Polypeptide::CaPPBuilder , Bio::GA::Selection::Abstract::AbstractSelection , Bio::PDB::Polypeptide::PPBuilder , Bio::PDB::StructureAlignment::StructureAlignment , Bio::Blast::NCBIStandalone::BlastErrorParser , Bio::GA::Selection::Diversity::DiversitySelection , Bio::PopGen::Async::Async , Bio::PopGen::Async::Local::Local , Bio::GA::Selection::RouletteWheel::RouletteWheelSelection , Bio::PopGen::FDist::Async::FDistAsync , Bio::PopGen::FDist::Async::SplitFDist , Bio::Blast::NCBIWWW::BlastParser , Bio::GA::Selection::Tournament::TournamentSelection , Bio::Prosite::Iterator , Bio::Prosite::Dictionary , Bio::GenBank::Dictionary , Bio::Prosite::ExPASyDictionary , Bio::Prosite::Prodoc::Iterator , Bio::Blast::NCBIXML::_XMLparser , Bio::GenBank::Iterator , Bio::Prosite::Prodoc::Dictionary , Bio::Prosite::Prodoc::ExPASyDictionary , Bio::GenBank::FeatureParser , Bio::PubMed::Dictionary , Bio::Rebase::Record , Bio::Blast::NCBIXML::BlastParser , Bio::GenBank::RecordParser , Bio::Rebase::Iterator , Bio::Rebase::Dictionary , Bio::GenBank::NCBIDictionary , Bio::Restriction::_Update::RestrictionCompiler::TypeCompiler , Bio::Restriction::PrintFormat::PrintFormat , Bio::CAPS::DifferentialCutsite , Bio::GenBank::utils::FeatureValueCleaner , Bio::Restriction::Restriction::FormattedSeq , Bio::Restriction::Restriction::RestrictionType , Bio::Geo::Iterator , Bio::Saf::Iterator , Bio::Saf::_Scanner , Bio::CAPS::CAPSMap , Bio::Gobase::Record , Bio::Saf::RecordParser , Bio::SCOP::Scop , Bio::Gobase::SequenceRecord , Bio::SCOP::Node , Bio::SCOP::Domain , Bio::CDD::Iterator , Bio::Gobase::GeneRecord , Bio::SCOP::Astral , Bio::SCOP::Cla::Iterator , Bio::Gobase::ProteinRecord , Bio::SCOP::Des::Iterator , Bio::SCOP::Dom::Iterator , Bio::CDD::_Scanner , Bio::Gobase::Iterator , Bio::SCOP::FileIndex::FileIndex , Bio::SCOP::Hie::Iterator , Bio::Gobase::Dictionary , Bio::SCOP::Raf::Iterator , Bio::SeqFeature::SeqFeature , Bio::CDD::RecordParser , Bio::Graphics::BasicChromosome::_ChromosomeComponent , Bio::SeqFeature::FeatureLocation , Bio::SeqFeature::OneOfPosition , Bio::Graphics::BasicChromosome::Chromosome , Bio::SeqFeature::PositionGap , Bio::SeqIO::ClustalIO::ClustalWriter , Bio::Clustalw::ClustalAlignment , Bio::Graphics::BasicChromosome::ChromosomeSegment , Bio::SeqIO::FastaIO::FastaWriter , Bio::SeqIO::Interfaces::SequenceIterator , Bio::Graphics::BasicChromosome::TelomereSegment , Bio::SeqIO::Interfaces::InterlacedSequenceIterator , Bio::SeqIO::Interfaces::SequenceWriter , Bio::Clustalw::_AlignCreator , Bio::Graphics::DisplayRepresentation::ChromosomeCounts , Bio::SeqIO::Interfaces::SequentialSequenceWriter , Bio::SeqIO::PhylipIO::PhylipWriter , Bio::Graphics::Distribution::BarChartDistribution , Bio::SeqIO::StockholmIO::StockholmIterator , Bio::SeqIO::StockholmIO::StockholmWriter , Bio::Clustalw::MultipleAlignCL , Bio::HMM::DynamicProgramming::AbstractDPAlgorithms , Bio::SeqRecord::SeqRecord , Bio::Sequencing::Ace::Iterator , Bio::HMM::DynamicProgramming::ScaledDPAlgorithms , Bio::Sequencing::Phd::Iterator , Bio::SGMLExtractor::SGMLExtractorHandle , Bio::Cluster::Record , Bio::HMM::DynamicProgramming::LogDPAlgorithms , Bio::SwissProt::SProt::Iterator , Bio::SwissProt::SProt::Dictionary , Bio::HMM::MarkovModel::MarkovModelBuilder , Bio::SwissProt::SProt::ExPASyDictionary , Bio::SwissProt::SProt::SequenceParser
• __iter__() : Bio::Align::Generic::Alignment , Bio::EUtils::Datatypes::DBIds , Bio::EUtils::Datatypes::Expression , Bio::EUtils::Datatypes::Term , Bio::EUtils::Datatypes::BinaryOp , Bio::SeqIO::Interfaces::SequenceIterator , Bio::SeqIO::Interfaces::InterlacedSequenceIterator
• __le__() : Bio::Restriction::Restriction::RestrictionType
• __len__() : Bio::EUtils::Datatypes::DBIds , Bio::EUtils::DBIdsClient::BaseDBIdsRecordSet , Bio::Pathway::Rep::HashSet::HashSet , Bio::PDB::FragmentMapper::Fragment , Bio::Restriction::Restriction::RestrictionType , Bio::SeqIO::Interfaces::InterlacedSequenceIterator
• __lt__() : Bio::Restriction::Restriction::RestrictionType
• __mod__() : Bio::Restriction::Restriction::RestrictionType
• __mul__() : Bio::SubsMat::SeqMat
• __ne__() : Bio::Crystal::Hetero , Bio::EUtils::Datatypes::DBIds , Bio::EUtils::Datatypes::Date , Bio::EUtils::MultiDict::OrderedMultiDict , Bio::EUtils::MultiDict::UnorderedMultiDict , Bio::Pathway::Reaction , Bio::Pathway::Rep::Graph::Graph , Bio::Pathway::Rep::HashSet::HashSet , Bio::Pathway::Rep::MultiGraph::MultiGraph , Bio::Restriction::Restriction::RestrictionType
• __or__() : Martel::Expression::Expression , Bio::EUtils::Datatypes::Expression , Martel::Expression::Alt
• __rdiv__() : Bio::Restriction::Restriction::RestrictionType
• __repr__() : Bio::Pathway::Rep::HashSet::HashSet , Bio::Pathway::System , Bio::Pathway::Reaction , Bio::Pathway::Interaction , Bio::Pathway::Network , Bio::Pathway::Rep::Graph::Graph , Bio::Pathway::Rep::MultiGraph::MultiGraph , Bio::PDB::FragmentMapper::Fragment , Bio::PDB::Polypeptide::Polypeptide , Bio::Restriction::Restriction::RestrictionType , Bio::SeqRecord::SeqRecord
• __rfloordiv__() : Bio::Restriction::Restriction::RestrictionType
• __rshift__() : Bio::Restriction::Restriction::RestrictionType
• __rtruediv__() : Bio::Restriction::Restriction::RestrictionType
• __setitem__() : Bio::EUtils::MultiDict::OrderedMultiDict , Bio::EUtils::MultiDict::UnorderedMultiDict
• __str__() : Bio::AlignAce::Motif::Motif , Bio::Application::_Option , Bio::Clustalw::ClustalAlignment , Bio::Clustalw::MultipleAlignCL , Bio::GA::Organism::Organism , Bio::GenBank::Record::Record , Bio::KEGG::Compound::Record , Bio::KEGG::Enzyme::Record , Bio::NeuralNetwork::BackPropagation::Layer::AbstractLayer , Bio::Nexus::Trees::Tree , Bio::Pathway::Reaction , Bio::Pathway::Interaction , Bio::Pathway::Network , Bio::Pathway::Rep::Graph::Graph , Bio::Pathway::Rep::MultiGraph::MultiGraph , Bio::Restriction::Restriction::RestrictionType , Bio::SeqFeature::SeqFeature , Bio::SeqFeature::FeatureLocation , Bio::SeqRecord::SeqRecord , Martel::Expression::Expression , Martel::Expression::AtBeginning , Martel::Expression::AtEnd , Martel::Expression::Dot , Martel::Expression::AnyEol , Martel::Expression::Seq , Martel::Expression::Alt , Bio::Application::AbstractCommandline , Bio::Pathway::Rep::HashSet::HashSet , Bio::SeqFeature::Reference , Bio::Pathway::System , Bio::Fasta::FastaAlign::FastaAlignment
• __sub__() : Bio::EUtils::Datatypes::DBIds , Bio::PDB::FragmentMapper::Fragment , Bio::SubsMat::SeqMat
• __truediv__() : Bio::Restriction::Restriction::RestrictionType
• _accession_line() : Bio::GenBank::Record::Record
• _add_bioentry_dbxref() : BioSQL::Loader::DatabaseLoader
• _add_dbxref() : BioSQL::Loader::DatabaseLoader
• _add_feature() : Bio::GenBank::_FeatureConsumer , Bio::GenBank::_RecordConsumer
• _add_motif() : Bio::NeuralNetwork::Gene::Motif::MotifFinder
• _add_qualifier() : Bio::GenBank::_FeatureConsumer
• _add_seqfeature_dbxref() : BioSQL::Loader::DatabaseLoader
• _add_sig() : Bio::NeuralNetwork::Gene::Signature::SignatureFinder
• _add_star_info() : Bio::Clustalw::ClustalAlignment
• _add_subtree() : Bio::Nexus::Trees::Tree
• _add_version() : Bio::Clustalw::ClustalAlignment
• _all_blank() : Bio::HMM::MarkovModel::MarkovModelBuilder
• _all_pseudo() : Bio::HMM::MarkovModel::MarkovModelBuilder
• _always_mutate() : test_GAMutation::MutationHelper
• _authors_line() : Bio::GenBank::Record::Reference
• _backward_recursion() : Bio::HMM::DynamicProgramming::AbstractDPAlgorithms , Bio::HMM::DynamicProgramming::ScaledDPAlgorithms
• _base_count_line() : Bio::GenBank::Record::Record
• _calculate_from_transitions() : Bio::HMM::MarkovModel::HiddenMarkovModel
• _calculate_s_value() : Bio::HMM::DynamicProgramming::ScaledDPAlgorithms
• _check_value() : Bio::Application::AbstractCommandline
• _clean_location() : Bio::GenBank::_BaseGenBankConsumer
• _clean_translation() : Bio::GenBank::utils::FeatureValueCleaner
• _cleanup_child() : Bio::MultiProc::copen::_ProcHandle
• _color_from_count() : Bio::Graphics::DisplayRepresentation::ChromosomeCounts
• _comment_line() : Bio::GenBank::Record::Record
• _consrtm_line() : Bio::GenBank::Record::Reference
• _contig_line() : Bio::GenBank::Record::Record
• _convert_to() : Bio::config::DBRegistry::DBObject , Bio::config::DBRegistry::BioCorbaDB , Bio::config::DBRegistry::IndexedFileDB , Bio::config::DBRegistry::BioSQLDB
• _convert_to_python_numbers() : Bio::GenBank::_BaseGenBankConsumer
• _count_emissions() : Bio::HMM::Trainer::KnownStateTrainer
• _count_transitions() : Bio::HMM::Trainer::KnownStateTrainer
• _crossover() : Bio::GA::Crossover::GeneralPoint::GeneralPointCrossover , Bio::GA::Crossover::GeneralPoint::TwoCrossover , Bio::GA::Crossover::GeneralPoint::InterleaveCrossover
• _db_source_line() : Bio::GenBank::Record::Record
• _definition_line() : Bio::GenBank::Record::Record
• _determine_position() : Bio::Graphics::Distribution::BarChartDistribution
• _diagnose_error() : Bio::Blast::NCBIStandalone::BlastErrorParser
• _draw_distributions() : Bio::Graphics::Distribution::DistributionPage
• _draw_label() : Bio::Graphics::BasicChromosome::ChromosomeSegment , Bio::Graphics::BasicChromosome::Chromosome
• _draw_legend() : Bio::Graphics::Distribution::DistributionPage , Bio::Graphics::BasicChromosome::Organism
• _draw_scatter_plot() : Bio::Graphics::Comparative::ComparativeScatterPlot
• _draw_segment() : Bio::Graphics::BasicChromosome::ChromosomeSegment , Bio::Graphics::BasicChromosome::TelomereSegment
• _draw_subcomponents() : Bio::Graphics::BasicChromosome::ChromosomeSegment
• _draw_title() : Bio::Graphics::BasicChromosome::Organism , Bio::Graphics::Comparative::ComparativeScatterPlot , Bio::Graphics::Distribution::BarChartDistribution , Bio::Graphics::Distribution::DistributionPage
• _drop() : Bio::Restriction::Restriction::Defined , Bio::Restriction::Restriction::Ambiguous , Bio::Restriction::Restriction::NotDefined
• _end_BlastOutput_db() : Bio::Blast::NCBIXML::BlastParser
• _end_BlastOutput_program() : Bio::Blast::NCBIXML::BlastParser
• _end_BlastOutput_query_def() : Bio::Blast::NCBIXML::BlastParser
• _end_BlastOutput_query_ID() : Bio::Blast::NCBIXML::BlastParser
• _end_BlastOutput_query_len() : Bio::Blast::NCBIXML::BlastParser
• _end_BlastOutput_reference() : Bio::Blast::NCBIXML::BlastParser
• _end_BlastOutput_version() : Bio::Blast::NCBIXML::BlastParser
• _end_Iteration_query_def() : Bio::Blast::NCBIXML::BlastParser
• _end_Iteration_query_ID() : Bio::Blast::NCBIXML::BlastParser
• _end_Iteration_query_len() : Bio::Blast::NCBIXML::BlastParser
• _features_line() : Bio::GenBank::Record::Record
• _feed_feature_table() : Bio::GenBank::Scanner::InsdcScanner
• _feed_first_line() : Bio::GenBank::Scanner::EmblScanner , Bio::GenBank::Scanner::GenBankScanner , Bio::GenBank::Scanner::InsdcScanner
• _feed_header_lines() : Bio::GenBank::Scanner::GenBankScanner , Bio::GenBank::Scanner::InsdcScanner , Bio::GenBank::Scanner::EmblScanner
• _feed_misc_lines() : Bio::GenBank::Scanner::InsdcScanner , Bio::GenBank::Scanner::EmblScanner , Bio::GenBank::Scanner::GenBankScanner
• _find_best_region() : test_GAQueens::QueensCrossover
• _find_groups() : Martel::Expression::Expression , Martel::Expression::ExpressionList
• _find_min_max() : Bio::Graphics::Comparative::ComparativeScatterPlot
• _fitness_cmp() : Bio::GA::Selection::Tournament::TournamentSelection
• _fix_varsplic_sequences() : Bio::SwissProt::SProt::_RecordConsumer
• _fixup_query() : Bio::EUtils::ThinClient::ThinClient
• _forward_recursion() : Bio::HMM::DynamicProgramming::ScaledDPAlgorithms
• _foward_recursion() : Bio::HMM::DynamicProgramming::AbstractDPAlgorithms
• _full_to_half() : Bio::SubsMat::SeqMat
• _generate_locs() : Bio::GA::Crossover::GeneralPoint::InterleaveCrossover , Bio::GA::Crossover::GeneralPoint::GeneralPointCrossover , Bio::GA::Crossover::GeneralPoint::TwoCrossover
• _get() : Bio::config::DBRegistry::CGIDB , Bio::EUtils::ThinClient::ThinClient , Bio::config::DBRegistry::BioSQLDB , Bio::config::DBRegistry::EUtilsDB , Bio::config::DBRegistry::BioCorbaDB , Bio::config::DBRegistry::IndexedFileDB , Bio::config::DBRegistry::DBObject
• _get_atom_line() : Bio::PDB::PDBIO::PDBIO
• _get_base_info() : Bio::Align::FormatConvert::FormatConverter
• _get_base_letters() : Bio::Align::AlignInfo::SummaryInfo
• _get_base_replacements() : Bio::Align::AlignInfo::SummaryInfo
• _get_bioentry_dbxref() : BioSQL::Loader::DatabaseLoader
• _get_cb() : Bio::PDB::HSExposure::HSExposureCB , Bio::PDB::HSExposure::HSExposureCA
• _get_check_names() : Bio::config::DBRegistry::IndexedFileDB
• _get_column_info_content() : Bio::Align::AlignInfo::SummaryInfo
• _get_corba_client() : Bio::config::DBRegistry::BioCorbaDB
• _get_db_module() : Bio::config::DBRegistry::BioSQLDB
• _get_dbxref_id() : BioSQL::Loader::DatabaseLoader
• _get_duplicates() : test_GAQueens::QueensRepair
• _get_gly_cb_vector() : Bio::PDB::HSExposure::_AbstractHSExposure
• _get_id() : Bio::Nexus::Nodes::Chain
• _get_letter_freqs() : Bio::Align::AlignInfo::SummaryInfo
• _get_location() : Bio::GenBank::_FeatureConsumer
• _get_meta_data() : Bio::SeqIO::StockholmIO::StockholmIterator
• _get_motif_dict() : Bio::NeuralNetwork::Gene::Motif::MotifFinder
• _get_new_organism() : Bio::GA::Selection::Diversity::DiversitySelection
• _get_num_motifs() : Bio::NeuralNetwork::Gene::Schema::SchemaFactory
• _get_position() : Bio::GenBank::_FeatureConsumer
• _get_retriever() : Bio::config::DBRegistry::BioCorbaDB
• _get_seqfeature_dbxref() : BioSQL::Loader::DatabaseLoader
• _get_signature_dict() : Bio::NeuralNetwork::Gene::Signature::SignatureFinder
• _get_taxon_id() : BioSQL::Loader::DatabaseLoader
• _get_term_id() : BioSQL::Loader::DatabaseLoader
• _get_unique_schema() : Bio::NeuralNetwork::Gene::Schema::SchemaFactory
• _get_unused() : test_GAQueens::QueensRepair
• _get_values() : Bio::Nexus::Trees::Tree
• _guess_consensus_alphabet() : Bio::Align::AlignInfo::SummaryInfo
• _handle_PDB_exception() : Bio::PDB::PDBParser::PDBParser
• _identifier_split() : Bio::SeqIO::StockholmIO::StockholmIterator
• _insert_seqfeature_location() : BioSQL::Loader::DatabaseLoader
• _journal_line() : Bio::GenBank::Record::Reference
• _keywords_line() : Bio::GenBank::Record::Record
• _kill() : Bio::MultiProc::copen::_ProcHandle
• _load_annotations() : BioSQL::Loader::DatabaseLoader
• _load_bioentry_date() : BioSQL::Loader::DatabaseLoader
• _load_bioentry_table() : BioSQL::Loader::DatabaseLoader
• _load_biosequence() : BioSQL::Loader::DatabaseLoader
• _load_database() : Bio::config::DBRegistry::IndexedFileDB
• _load_dbxrefs() : BioSQL::Loader::DatabaseLoader
• _load_schema_repository() : test_NNGene::SchemaFactoryTest
• _load_seqfeature() : BioSQL::Loader::DatabaseLoader
• _load_seqfeature_basic() : BioSQL::Loader::DatabaseLoader
• _load_seqfeature_dbxref() : BioSQL::Loader::DatabaseLoader
• _load_seqfeature_locations() : BioSQL::Loader::DatabaseLoader
• _load_seqfeature_qualifiers() : BioSQL::Loader::DatabaseLoader
• _locus_line() : Bio::GenBank::Record::Record
• _log_transform() : Bio::HMM::MarkovModel::HiddenMarkovModel
• _make_callback() : Bio::ParserSupport::EventGenerator
• _make_pickleable() : Bio::config::DBRegistry::DBObject , Bio::config::DBRegistry::BioSQLDB , Bio::config::DBRegistry::CGIDB
• _make_random_points() : test_GraphicsGeneral::ComparativeTest
• _map() : Bio::PDB::FragmentMapper::FragmentMapper
• _medline_line() : Bio::GenBank::Record::Reference
• _mod1() : Bio::Restriction::Restriction::Blunt , Bio::Restriction::Restriction::Ov5 , Bio::Restriction::Restriction::Unknown , Bio::Restriction::Restriction::Ov3
• _mod2() : Bio::Restriction::Restriction::Ambiguous , Bio::Restriction::Restriction::NotDefined , Bio::Restriction::Restriction::Defined
• _modify() : Bio::Restriction::Restriction::OneCut , Bio::Restriction::Restriction::TwoCuts , Bio::Restriction::Restriction::NoCut
• _modify_leaves() : Martel::Expression::ExpressionList , Martel::Expression::Expression
• _never_mutate() : test_GAMutation::MutationHelper
• _nid_line() : Bio::GenBank::Record::Record
• _normalize_spaces() : Bio::GenBank::_BaseGenBankConsumer
• _organism_line() : Bio::GenBank::Record::Record
• _origin_line() : Bio::GenBank::Record::Record
• _pair_replacement() : Bio::Align::AlignInfo::SummaryInfo
• _parse() : Bio::Nexus::Trees::Tree
• _parse_buffer() : Bio::MEME::Parser::_MASTConsumer
• _pid_line() : Bio::GenBank::Record::Record
• _populate_meta_data() : Bio::SeqIO::StockholmIO::StockholmIterator
• _pubmed_line() : Bio::GenBank::Record::Reference
• _reference_line() : Bio::GenBank::Record::Reference
• _remark_line() : Bio::GenBank::Record::Reference
• _remove_newlines() : Bio::GenBank::_BaseGenBankConsumer
• _remove_spaces() : Bio::GenBank::_BaseGenBankConsumer
• _rev_modify() : Bio::Restriction::Restriction::OneCut , Bio::Restriction::Restriction::TwoCuts , Bio::Restriction::Restriction::NoCut
• _run_program() : Bio::PopGen::Async::Local::Local
• _scan_alignment() : Bio::Compass::_Scanner
• _scan_bq_data() : Bio::Sequencing::Ace::_Scanner
• _scan_bracket_tags() : Bio::Sequencing::Ace::_Scanner
• _scan_lengths() : Bio::Compass::_Scanner
• _scan_names() : Bio::Compass::_Scanner
• _scan_profilewidth() : Bio::Compass::_Scanner
• _scan_scores() : Bio::Compass::_Scanner
• _scan_sequence_data() : Bio::Sequencing::Ace::_Scanner
• _scan_threshold() : Bio::Compass::_Scanner
• _schema_from_motif() : Bio::NeuralNetwork::Gene::Schema::SchemaFactory
• _search() : Bio::Restriction::Restriction::Palindromic , Bio::Restriction::Restriction::NonPalindromic
• _secure_name() : Bio::Blast::NCBIXML::_XMLparser
• _segment_line() : Bio::GenBank::Record::Record
• _select_names() : Martel::Expression::Expression , Martel::Expression::ExpressionList
• _sequence_line() : Bio::GenBank::Record::Record
• _set() : Bio::config::DBRegistry::DBObject
• _set_colors_and_shapes() : Bio::Graphics::Comparative::ComparativeScatterPlot
• _set_function() : Bio::GenBank::_FeatureConsumer
• _set_location() : Bio::GenBank::_FeatureConsumer
• _set_location_info() : Bio::GenBank::_FeatureConsumer
• _set_ordering_info() : Bio::GenBank::_FeatureConsumer
• _set_up_genetic_algorithm() : Bio::NeuralNetwork::Gene::Schema::GeneticAlgorithmFinder
• _set_up_wheel() : Bio::GA::Selection::RouletteWheel::RouletteWheelSelection
• _skip_starstar() : Bio::SwissProt::SProt::_Scanner
• _sort() : Bio::PDB::Residue::Residue , Bio::PDB::Model::Model , Bio::PDB::Structure::Structure
• _source_line() : Bio::GenBank::Record::Record
• _split_accessions() : Bio::GenBank::_BaseGenBankConsumer
• _split_keywords() : Bio::GenBank::_BaseGenBankConsumer
• _split_reference_locations() : Bio::GenBank::_FeatureConsumer
• _split_taxonomy() : Bio::GenBank::_BaseGenBankConsumer
• _title_line() : Bio::GenBank::Record::Reference
• _unmake_pickleable() : Bio::config::DBRegistry::CGIDB , Bio::config::DBRegistry::BioSQLDB , Bio::config::DBRegistry::DBObject
• _version_line() : Bio::GenBank::Record::Record
• _walk() : Bio::Nexus::Trees::Tree