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Class List

Here are the classes, structs, unions and interfaces with brief descriptions:
Bio::PDB::HSExposure::_AbstractHSExposure
Bio::Application::_AbstractParameter
Bio::Clustalw::_AlignCreator
Bio::Blast::NCBIStandalone::_AlignmentConsumer
Bio::Application::_Argument
Bio::EUtils::POM::_AttributeType
Bio::GenBank::_BaseGenBankConsumer
Bio::EUtils::MultiDict::_BaseMultiDict
Bio::Blast::NCBIStandalone::_BlastConsumer
Bio::Blast::NCBIStandalone::_BlastErrorConsumer
Martel::Generate::_call_call
Martel::Generate::_call_calltag
Bio::Graphics::BasicChromosome::_ChromosomeComponent
Bio::Compass::_Consumer
Bio::EUtils::POM::_ContentModelGenerator
Bio::Blast::NCBIStandalone::_DatabaseReportConsumer
Bio::Blast::NCBIStandalone::_DescriptionConsumer
Bio::Fasta::_FastaFunctionIndexer
Bio::Fasta::_FastaTitleIndexer
Bio::GenBank::_FeatureConsumer
Bio::Blast::NCBIStandalone::_HeaderConsumer
Bio::Blast::NCBIStandalone::_HSPConsumer
Bio::Medline::NLMMedlineXML::_IndexerHandler
Bio::Index::_InMemoryIndex
Martel::LAX::_IsIn
Bio::SwissProt::KeyWList::_ListConsumer
Bio::MEME::Parser::_MASTConsumer
Bio::MEME::Parser::_MASTScanner
Bio::MEME::Parser::_MEMEConsumer
Bio::MEME::Parser::_MEMEScanner
Bio::KDTree::CKDTree::_object
Bio::Application::_Option
Bio::Blast::NCBIStandalone::_ParametersConsumer
Bio::MultiProc::copen::_PickleHandle
Bio::PDB::Polypeptide::_PPBuilder
Bio::Emboss::Primer::_Primer3RecordConsumer
Bio::Emboss::Primer::_Primer3Scanner
Bio::Emboss::Primer::_PrimerSearchRecordConsumer
Bio::Emboss::Primer::_PrimerSearchScanner
Bio::MultiProc::copen::_ProcHandle
Bio::Blast::NCBIStandalone::_PSIBlastConsumer
Bio::IntelliGenetics::_RecordConsumer
Bio::LocusLink::_RecordConsumer
Bio::Medline::_RecordConsumer
Bio::MetaTool::_RecordConsumer
Bio::NBRF::_RecordConsumer
Bio::ECell::_RecordConsumer
Bio::PopGen::FDist::_RecordConsumer
Bio::CDD::_RecordConsumer
Bio::PopGen::GenePop::_RecordConsumer
Bio::Prosite::_RecordConsumer
Bio::Enzyme::_RecordConsumer
Bio::Prosite::Prodoc::_RecordConsumer
Bio::Rebase::_RecordConsumer
Bio::Saf::_RecordConsumer
Bio::GenBank::_RecordConsumer
Bio::Sequencing::Ace::_RecordConsumer
Bio::Sequencing::Phd::_RecordConsumer
Bio::SwissProt::SProt::_RecordConsumer
Bio::UniGene::_RecordConsumer
Bio::Gobase::_RecordConsumer
Bio::Medline::NLMMedlineXML::_SavedDataHandle
Bio::IntelliGenetics::_Scanner
Bio::Blast::NCBIWWW::_Scanner
Bio::LocusLink::_Scanner
Bio::Medline::_Scanner
Bio::MetaTool::_Scanner
Bio::NBRF::_Scanner
Bio::ECell::_Scanner
Bio::CDD::_Scanner
Bio::PopGen::FDist::_Scanner
Bio::PopGen::GenePop::_Scanner
Bio::Enzyme::_Scanner
Bio::Prosite::_Scanner
Bio::Prosite::Prodoc::_Scanner
Bio::Rebase::_Scanner
Bio::Saf::_Scanner
Bio::Compass::_Scanner
Bio::Blast::NCBIStandalone::_Scanner
Bio::Sequencing::Ace::_Scanner
Bio::Sequencing::Phd::_Scanner
Bio::SwissProt::KeyWList::_Scanner
Bio::SwissProt::SProt::_Scanner
Bio::UniGene::_Scanner
Bio::Gobase::_Scanner
Bio::Search::_SeqLength
Bio::SwissProt::SProt::_SequenceConsumer
Bio::Index::_ShelveIndex
_Transition
_Trie
Bio::Blast::NCBIXML::_XMLparser
Bio::GenBank::LocationParser::AbsoluteLocation
Bio::PDB::AbstractPropertyMap::AbstractAtomPropertyMap
Bio::Application::AbstractCommandline
Bio::ParserSupport::AbstractConsumer
Bio::Restriction::Restriction::AbstractCut
Bio::HMM::DynamicProgramming::AbstractDPAlgorithms
Bio::NeuralNetwork::BackPropagation::Layer::AbstractLayer
Bio::ParserSupport::AbstractParser
Bio::SeqFeature::AbstractPosition
Bio::PDB::AbstractPropertyMap::AbstractPropertyMap
Bio::PDB::AbstractPropertyMap::AbstractResiduePropertyMap
Bio::GA::Selection::Abstract::AbstractSelection
test_GASelection::AbstractSelectionTest
Bio::HMM::Trainer::AbstractTrainer
test_HMMGeneral::AbstractTrainerTest
Bio::Sequencing::Ace::ACEFileRecord
Bio::Sequencing::Ace::ACEParser
test_Ace::AceTestOne
BioSQL::BioSeqDatabase::Adaptor
Bio::Sequencing::Ace::af
Bio::pairwise2::affine_penalty
Bio::SeqFeature::AfterPosition
Bio::Search::Algorithm
Bio::pairwise2::align
Bio::FSSP::fssp_rec::align
Bio::AlignAce::Applications::AlignAceCommandline
Bio::AlignAce::Parser::AlignAceConsumer
Bio::AlignAce::Parser::AlignAceParser
Bio::AlignAce::Scanner::AlignAceScanner
Bio::Blast::Record::Alignment
Bio::Align::Generic::Alignment
Bio::Wise::psw::Alignment
Bio::pairwise2::align::alignment_function
Bio::Wise::psw::AlignmentColumn
Bio::Wise::psw::AlignmentColumnFullException
Bio::CAPS::AlignmentHasDifferentLengthsError
Bio::Alphabet::Alphabet
Bio::Alphabet::AlphabetEncoder
Martel::Expression::Alt
Bio::Restriction::Restriction::Ambiguous
Bio::Data::CodonTable::AmbiguousCodonTableDeal with ambiguous forward translations
Bio::Data::CodonTable::AmbiguousForwardTable
Bio::GA::Repair::Stabilizing::AmbiguousRepair
test_GARepair::AmbiguousRepairTest
Bio::Restriction::Restriction::Analysis
Bio::EUtils::Datatypes::And
Martel::Expression::Any
Martel::Expression::AnyEol
Bio::EUtils::DTDs::LinkOut::apad
Bio::GFF::GenericTools::AppendableListDictionary
Bio::Application::ApplicationResult
test_PopGen_FDist::AppTest
test_PopGen_SimCoal::AppTest
Bio::GFF::GenericTools::ArgsParser
Martel::Expression::Assert
Bio::SCOP::Astral
test_SCOP_Astral::AstralTests
Bio::PopGen::Async::Async
Martel::Expression::AtBeginning
Martel::Expression::AtEnd
Bio::PDB::Atom::Atom
Bio::PDB::NeighborSearch::Atom
Bio::EUtils::DTDs::eLink_020511::Attribute
Bio::EUtils::DTDs::LinkOut::Attribute
Bio::EUtils::POM::AttributeList
Bio::SubsMat::BadMatrix
Bio::Graphics::Distribution::BarChartDistribution
test_GraphicsDistribution::BarChartTest
Bio::EUtils::DTDs::LinkOut::Base
Bio::EUtils::DBIdsClient::BaseDBIdsRecordSet
Bio::Mindy::FlatDB::BaseFlatDB
unittestgui::BaseGUITestRunnerGUI framework classes
Bio::EUtils::HistoryClient::BaseHistoryRecordSet
Bio::Mindy::SimpleSeqRecord::BaseSeqRecordIndexer
Bio::NeuralNetwork::BackPropagation::Network::BasicNetwork
Bio::HMM::Trainer::BaumWelchTrainer
Bio::SeqFeature::BeforePosition
Bio::Mindy::BerkeleyDB::BerkeleyDB
Bio::GenBank::LocationParser::Between
Bio::SeqFeature::BetweenPosition
Bio::biblio::Biblio
Bio::biblio::BiblioCollection
Bio::EUtils::Datatypes::BinaryOp
Bio::config::DBRegistry::BioCorbaDB
Bio::DBXRef::BioformatDBName
BioSQL::BioSeqDatabase::BioSeqDatabase
biocorba_sql_server::BioSQLAdapterDictionary
Bio::config::DBRegistry::BioSQLDB
Bio::Mindy::FlatDB::BisectFile
Bio::Blast::Record::Blast
Bio::Blast::Applications::BlastallCommandline
xbb_blastbg::BlastDisplayer
Bio::Blast::NCBIStandalone::BlastErrorParser
xbb_blast::BlastIt
Bio::Blast::NCBIWWW::BlastParser
Bio::Blast::NCBIXML::BlastParser
Bio::Blast::NCBIStandalone::BlastParser
Bio::Blast::ParseBlastTable::BlastTableEntry
Bio::Blast::ParseBlastTable::BlastTableReader
Bio::Blast::ParseBlastTable::BlastTableRec
xbb_blastbg::BlastWorker
Bio::Nexus::Nexus::Block
Bio::Restriction::Restriction::Blunt
Bio::EUtils::DTDs::LinkOut::Brief
Bio::Sequencing::Ace::bs
setup::build_ext_biopython
setup::build_py_biopython
Bio::builders::Search::search::BuildSearch
Bio::builders::SeqRecord::sequence::BuildSeqRecord
Martel::Dispatch::Callback
Bio::PDB::Polypeptide::CaPPBuilder
Bio::CAPS::CAPSMap
Martel::test::test_macros::Capture
Martel::test::test_delimiter::CatchFields
Bio::EUtils::POM::CDATA
Bio::Affy::CelFile::CelConsumer
Bio::Affy::CelFile::CelParser
Bio::Affy::CelFile::CelRecord
Bio::Affy::CelFile::CelScanner
Bio::config::DBRegistry::CGIDB
Bio::Crystal::Chain
Bio::Nexus::Nodes::Chain
Bio::PDB::Chain::Chain
Bio::Nexus::Nodes::ChainException
Bio::PDB::Dice::ChainSelector
test_Crystal::ChainTestCase
Bio::Nexus::Nexus::CharBuffer
Martel::Generate::CheckAssert
Martel::Generate::CheckAssertNot
Martel::test::support::CheckGood
martel_support::CheckGood
Martel::Generate::CheckGroupRef
Bio::EUtils::Datatypes::CheckLinkSet
Bio::Graphics::BasicChromosome::Chromosome
Bio::Graphics::DisplayRepresentation::ChromosomeCounts
test_GraphicsChromosome::ChromosomeCountTest
Bio::Graphics::BasicChromosome::ChromosomeSegment
Bio::Medline::NLMMedlineXML::Citation
Bio::Medline::NLMMedlineXML::CitationParser
Bio::EUtils::sourcegen::ClassHolder
test_SCOP_Cla::ClaTests
Bio::Clustalw::ClustalAlignment
Bio::SeqIO::generic::ClustalFormat
Bio::SeqIO::ClustalIO::ClustalWriter
Bio::SeqUtils::CodonUsage::CodonAdaptationIndex
Bio::Data::CodonTable::CodonTable
Bio::Wise::psw::ColumnUnit
Bio::Nexus::Nexus::Commandline
Bio::EUtils::POM::Comment
Bio::Restriction::Restriction::Commercially_available
Bio::Graphics::Comparative::ComparativeScatterPlot
test_GraphicsGeneral::ComparativeTest
Bio::AlignAce::Applications::CompareAceCommandline
Bio::AlignAce::Parser::CompareAceConsumer
Bio::AlignAce::Parser::CompareAceParser
Bio::AlignAce::Scanner::CompareAceScanner
test_Compass::CompassTest
Bio::GFF::Connection
Bio::Restriction::_Update::Update::ConnectionError
Bio::EUtils::POM::ContentModel
Bio::Sequencing::Ace::Contig
Bio::GA::Mutation::Simple::ConversionMutation
test_GAMutation::ConversionTest
test_PopGen_FDist_nodepend::ConversionTest
Bio::StdHandler::ConvertDispatchHandler
Bio::StdHandler::ConvertHandler
Bio::EUtils::DTDs::eSearch_020511::Count
Bio::EUtils::DTDs::eInfo_020511::Count
Martel::test::test_Parser::CountErrors
Martel::RecordReader::CountLines
Martel::test::test_Parser::CountRecords
setup::CplusplusExtension
Bio::DocSQL::Create
Bio::PropertyManager::CreateDict
test_GAOrganism::CreatePopulationTest
Bio::Crystal::Crystal
Bio::Crystal::CrystalError
test_Crystal::CrystalTestCase
test_Crystal::CrystalTestSuite
Bio::Sequencing::Ace::ct
Bio::EUtils::DTDs::LinkOut::Database
Bio::Search::Database
Bio::EUtils::Config::DatabaseDict
Bio::EUtils::Config::DatabaseInfo
BioSQL::Loader::DatabaseLoader
BioSQL::Loader::DatabaseRemover
Bio::Blast::Record::DatabaseReport
Bio::Cluster::DataFile
DataPoint
Bio::Enzyme::DataRecord
Bio::EUtils::Datatypes::Date
Bio::EUtils::Datatypes::DateRange
getgene::DB_Index
Bio::EUtils::DTDs::eLink_020511::DbFrom
Bio::config::DBRegistry::DBGroup
Bio::EUtils::Datatypes::DBIds
Bio::EUtils::DBIdsClient::DBIdsClient
Bio::EUtils::DBIdsClient::DBIdsLookup
Bio::EUtils::DBIdsClient::DBIdsRecord
Bio::EUtils::DTDs::eInfo_020511::DbInfo
Bio::EUtils::DTDs::eInfo_020511::DbList
Bio::EUtils::DTDs::eInfo_020511::DbName
Bio::config::DBRegistry::DBObject
Bio::config::DBRegistry::DBRegistry
BioSQL::BioSeq::DBSeq
BioSQL::BioSeq::DBSeqRecord
BioSQL::BioSeqDatabase::DBServer
Bio::EUtils::DTDs::eLink_020511::DbTo
Bio::EUtils::DTDs::eInfo_020511::DbTo
Bio::DBXRef::DBXRef
Martel::Expression::Debug
debug_blast_parser::DebuggingConsumer
Bio::SCOP::FileIndex::defaultdict
Bio::Restriction::Restriction::Defined
Bio::Blast::Record::Description
Bio::EUtils::DTDs::eInfo_020511::Descriptor
test_SCOP_Des::DesTests
test_HMMCasino::DiceRollAlphabet
test_HMMCasino::DiceTypeAlphabet
Bio::Prosite::Dictionary
Bio::Prosite::Prodoc::Dictionary
Bio::PubMed::Dictionary
Bio::Rebase::Dictionary
Bio::Fasta::Dictionary
Bio::GenBank::Dictionary
Bio::SwissProt::SProt::Dictionary
Bio::Gobase::Dictionary
Bio::pairwise2::dictionary_match
Bio::Restriction::_Update::RestrictionCompiler::DictionaryBuilder
Bio::Mindy::BaseDB::DictLookup
Bio::CAPS::DifferentialCutsite
Bio::NeuralNetwork::Gene::Schema::DifferentialSchemaFitness
Bio::PopGen::Async::DirectoryRetriever
Bio::Mindy::FlatDB::DiskFlatDB
Bio::PDB::Atom::DisorderedAtom
Bio::PDB::Entity::DisorderedEntityWrapper
Bio::PDB::Residue::DisorderedResidue
Martel::Dispatch::Dispatcher
Martel::Dispatch::DispatchHandler
Bio::Graphics::Distribution::DistributionPage
Bio::GA::Selection::Diversity::DiversitySelection
test_GASelection::DiversitySelectionTest
Bio::Alphabet::DNAAlphabet
xbb_search::DNAsearch
test_MarkovModel::DNAStrandStates = [ "state0", "state1", "state2", "state3", ] alphabet = ["a", "c", "g", "t"]
Bio::EUtils::DTDs::eSummary_020511::DocSum
Bio::SCOP::Domain
test_SCOP_Dom::DomTests
Martel::Expression::Dot
Bio::Sequencing::Ace::ds
Bio::PDB::DSSP::DSSP
Bio::EUtils::POM::DTDConsumerForSourceGeneration
Martel::test::support::Dump
martel_support::Dump
Bio::ECell::ECellError
Bio::Emboss::Applications::EConsenseCommandline
Bio::EUtils::DTDs::eInfo_020511::eInfoResult
Bio::Emboss::Applications::EInvertedCommandline
Martel::LAX::ElementInfo
Bio::EUtils::POM::ElementNode
Bio::EUtils::DTDs::eLink_020511::eLinkResult
Bio::SeqIO::generic::EMBLFormat
Bio::GenBank::Scanner::EmblScanner
Martel::RecordReader::EndsWith
Bio::Emboss::Applications::ENeighborCommandline
Bio::EUtils::POM::ENTITIES
Bio::PDB::Entity::Entity
Bio::EUtils::POM::ENTITY
Bio::EUtils::POM::Enumeration
test_Restriction::EnzymeComparison
Bio::Enzyme::EnzymeRecord
Bio::EUtils::DTDs::ePost_020511::ePostResult
Bio::Emboss::Applications::EProtDistCommandline
Bio::Emboss::Applications::EProtParsCommandline
Bio::EUtils::DTDs::eLink_020511::ERROR
Martel::msre_constants::error
Bio::Crystal::Error
Bio::EUtils::DTDs::ePost_020511::ERROR
Bio::ECell::Error
Bio::EUtils::DTDs::eSummary_020511::ERROR
Bio::EUtils::DTDs::eSearch_020511::ERROR
Bio::EUtils::DTDs::eInfo_020511::ERROR
Bio::EUtils::DTDs::eSearch_020511::ErrorList
Bio::EUtils::Datatypes::ErrorProblem
Bio::EUtils::DTDs::eSearch_020511::eSearchResult
Bio::Emboss::Applications::ESeqBootCommandline
Bio::Emboss::Applications::Est2GenomeCommandline
Bio::EUtils::DTDs::eSummary_020511::eSummaryResult
Bio::Emboss::Applications::ETandemCommandline
Bio::config::DBRegistry::EUtilsDB
Bio::EUtils::Datatypes::EUtilsError
Bio::EUtils::Datatypes::EUtilsSearchError
Bio::ParserSupport::EventGenerator
test_ParserSupport::EventGeneratorTest
Martel::Iterator::EventStream
Martel::RecordReader::Everything
Bio::SeqFeature::ExactPosition
test_CAPS::Example1
Bio::NeuralNetwork::Training::ExampleManager
test_NNGeneral::ExampleManagerTest
Bio::EUtils::DTDs::LinkOut::ExclQuery
Bio::Prosite::ExPASyDictionary
Bio::Prosite::Prodoc::ExPASyDictionary
Bio::SwissProt::SProt::ExPASyDictionary
Bio::EUtils::DTDs::eSearch_020511::Explode
Bio::PDB::HSExposure::ExposureCN
Bio::EUtils::Datatypes::Expression
Martel::Expression::Expression
Martel::Expression::ExpressionList
Bio::Alphabet::IUPAC::ExtendedIUPACDNA
Bio::Alphabet::IUPAC::ExtendedIUPACProtein
Bio::NetCatch::ExtractUrls
Bio::Fasta::FastaAlign::FastaAlignment
test_CAPS::FastaAlignmentTest
Bio::Blast::Applications::FastacmdCommandline
Bio::SeqIO::generic::FastaFormat
Bio::SeqIO::FASTA::FastaReader
Bio::SeqIO::FASTA::FastaWriter
Bio::SeqIO::FastaIO::FastaWriter
Martel::Expression::FastFeature
Bio::PopGen::FDist::Async::FDistAsync
Bio::PopGen::FDist::Controller::FDistController
Bio::StdHandler::Feature
Bio::GenBank::Record::Feature
Bio::GFF::Feature
Bio::GFF::FeatureAggregate
Bio::GFF::easy::FeatureDict
Bio::SeqFeature::FeatureLocation
Bio::GenBank::LocationParser::FeatureName
Bio::GenBank::FeatureParser
Bio::GFF::FeatureQuery
Bio::GFF::FeatureQueryRow
Bio::GenBank::utils::FeatureValueCleaner
Bio::FSSP::fssp_rec::fff_rec
Bio::EUtils::DTDs::eSearch_020511::Field
Bio::EUtils::DTDs::eInfo_020511::Field
Bio::EUtils::DTDs::eSearch_020511::FieldNotFound
Bio::EUtils::Datatypes::FieldNotFound
Bio::EUtils::DTDs::eInfo_020511::FiledList
Bio::SCOP::FileIndex::FileIndex
Bio::PopGen::Async::FileRetriever
Bio::FilteredReader::FilteredReader
Bio::Mindy::SimpleSeqRecord::FixDocumentBuilder
Bio::GFF::GenericTools::ForgivingDictionary
Bio::Align::FormatConvert::FormatConverter
Bio::config::FormatRegistry::FormatGroup
Bio::config::FormatRegistry::FormatObject
Bio::config::FormatRegistry::FormatRegistry
Bio::Restriction::Restriction::FormattedSeq
test_GACrossover::FourPointTest
Bio::PDB::FragmentMapper::Fragment
Bio::PDB::FragmentMapper::FragmentMapper
Bio::EUtils::POM::Fragments
Bio::SubsMat::FreqTable::FreqTableA class to handle frequency tables Copyright Iddo Friedberg idoerg@cc.huji.ac.il Biopython (http://biopython.org) license applies Methods to read a letter frequency or a letter count file: Example files for a DNA alphabet:
Bio::EUtils::DTDs::eSearch_020511::From
Bio::FSSP::FSSPTools::FSSPAlign
Bio::FSSP::FSSPAlignDict
Bio::FSSP::FSSPAlignRec
Bio::FSSP::FSSPHeader
Bio::FSSP::FSSPTools::FSSPMultAlign
Bio::FSSP::FSSPSumDict
Bio::FSSP::FSSPSumRec
Bio::Restriction::_Update::Update::FtpNameError
Bio::Restriction::_Update::Update::FtpPasswordError
Bio::GenBank::LocationParser::Function
Bio::EUtils::sourcegen::FunctionHolder
Bio::Mindy::SimpleSeqRecord::FunctionIndexer
Bio::Emboss::Applications::FuzznucCommandline
Bio::Alphabet::Gapped
Bio::SeqIO::generic::GCGFormat
test_Registry::GenBankRetrievalTest
Bio::GenBank::Scanner::GenBankScanner
Bio::GA::Crossover::GeneralPoint::GeneralPointCrossover
Bio::GA::Evolver::GenerationEvolver
Martel::Generate::GeneratorState
Bio::Gobase::GeneRecord
BioSQL::DBUtils::Generic_dbutils
Bio::Parsers::spark::GenericASTBuilder
Bio::Parsers::spark::GenericASTMatcher
Bio::Parsers::spark::GenericASTTraversal
Bio::Parsers::spark::GenericASTTraversalPruningException
Bio::SeqIO::generic::GenericFormat
Bio::Parsers::spark::GenericParser
Bio::Parsers::spark::GenericScanner
Bio::NeuralNetwork::Gene::Schema::GeneticAlgorithmFinder
Martel::test::test_optimize::GetErrorPos
Bio::EUtils::parse::GetObject
Martel::test::test_attrs::GrabElements
Bio::Pathway::Rep::Graph::Graph
test_Pathway::GraphTestCase
Martel::Expression::Group
Martel::convert_re::GroupNames
Martel::Expression::GroupRef
unittestgui::GUITestResult
Bio::StdHandler::Handle_dbid
Bio::StdHandler::Handle_dbxref
Bio::StdHandler::Handle_description
Bio::StdHandler::Handle_feature_location
Bio::StdHandler::Handle_feature_qualifier
Bio::StdHandler::Handle_features
Bio::StdHandler::Handle_hsp
Bio::StdHandler::Handle_hsp_seqalign
Bio::StdHandler::Handle_search_header
Bio::StdHandler::Handle_search_info
Bio::StdHandler::Handle_search_table
Bio::StdHandler::Handle_sequence
Martel::Generate::HandleRepeatCount
Bio::Pathway::Rep::HashSet::HashSet
test_Pathway::HashSetTestCase
Bio::Alphabet::HasStopCodon
Bio::Blast::Record::Header
Martel::Expression::HeaderFooter
Martel::Iterator::HeaderFooterEventStream
Martel::Parser::HeaderFooterParser
Bio::Crystal::Hetero
test_Crystal::HeteroTestCase
test_HotRand::HexConversionTest
Bio::NeuralNetwork::BackPropagation::Layer::HiddenLayer
Bio::HMM::MarkovModel::HiddenMarkovModel
test_HMMGeneral::HiddenMarkovModelTest
Bio::EUtils::DTDs::eInfo_020511::Hierarchy
test_SCOP_Hie::HieTests
Bio::GenBank::LocationParser::HighBound
Bio::EUtils::HistoryClient::HistoryClient
test_EUtils::HistoryClientTest
Bio::EUtils::HistoryClient::HistoryCookie
Bio::EUtils::HistoryClient::HistoryLookup
Bio::EUtils::HistoryClient::HistoryRecord
Bio::Search::Hit
Bio::Search::HomologySeq
Bio::HotRand::HotCache
Bio::HotRand::HotRandom
Bio::Alphabet::Reduced::HPModel
Bio::PDB::HSExposure::HSExposureCA
Bio::PDB::HSExposure::HSExposureCB
Bio::Blast::Record::HSP
Bio::Search::HSP
Bio::Search::HSPSeq
Bio::EUtils::DTDs::eLink_020511::IconUrl
Bio::EUtils::DTDs::LinkOut::IconUrl
Bio::EUtils::DTDs::eLink_020511::Id
Bio::EUtils::DTDs::ePost_020511::Id
Bio::EUtils::DTDs::eSearch_020511::Id
Bio::EUtils::DTDs::eSummary_020511::Id
Bio::EUtils::POM::ID
Bio::EUtils::Datatypes::IdCheck
Bio::EUtils::DTDs::eLink_020511::IdCheckList
Bio::pairwise2::identity_match
Bio::EUtils::DTDs::eSearch_020511::IdList
Bio::EUtils::DTDs::eLink_020511::IdList
Bio::EUtils::POM::IDREF
Bio::EUtils::POM::IDREFS
Bio::EUtils::DTDs::eLink_020511::IdUrlList
Bio::EUtils::DTDs::eLink_020511::IdUrlSet
Bio::EUtils::Datatypes::IdUrlSet
Bio::Ais::Immune
Bio::EUtils::DTDs::LinkOut::InclQuery
Bio::EUtils::POM::IndentedText
test_BioSQL::InDepthLoadTest
Bio::SCOP::Cla::Index
Bio::config::DBRegistry::IndexedFileDB
IndexList
Bio::EUtils::DTDs::eLink_020511::Info
Bio::NeuralNetwork::BackPropagation::Layer::InputLayer
Bio::GenBank::Scanner::InsdcScanner
Bio::DocSQL::Insert
setup::install_biopython
setup::install_data_biopython
Bio::MEME::Motif::Instance
Bio::GenBank::LocationParser::Integer
Bio::IntelliGenetics::IntelliGeneticsReader
Bio::Pathway::Interaction
Bio::SeqIO::Interfaces::InterlacedSequenceIterator
Bio::GA::Crossover::GeneralPoint::InterleaveCrossover
test_GACrossover::InterleaveTest
Bio::InterPro::InterProParser
Bio::EUtils::DTDs::ePost_020511::InvalidIdList
Bio::EUtils::DTDs::eInfo_020511::IsDate
Bio::EUtils::DTDs::eInfo_020511::IsNumerical
Bio::SeqUtils::IsoelectricPoint::IsoelectricPoint
Bio::EUtils::DTDs::eSummary_020511::Item
Martel::Iterator::Iterate
Bio::DocSQL::IterationCursor
Bio::Gobase::Iterator
Bio::IntelliGenetics::Iterator
Bio::KEGG::Compound::Iterator
Bio::KEGG::Enzyme::Iterator
Bio::KEGG::Map::Iterator
Bio::LocusLink::Iterator
Bio::Medline::Iterator
Bio::Blast::NCBIStandalone::Iterator
Bio::MetaTool::Iterator
Bio::NBRF::Iterator
Bio::ECell::Iterator
Bio::CDD::Iterator
Bio::Prosite::Iterator
Bio::Prosite::Prodoc::Iterator
Bio::Rebase::Iterator
Bio::Enzyme::Iterator
Martel::Iterator::Iterator
Bio::Fasta::Iterator
Bio::Saf::Iterator
Bio::SCOP::Cla::Iterator
Bio::SCOP::Des::Iterator
Bio::SCOP::Dom::Iterator
Bio::SCOP::Hie::Iterator
Bio::SCOP::Raf::Iterator
Bio::Compass::Iterator
Bio::GenBank::Iterator
Bio::Sequencing::Ace::Iterator
Bio::Sequencing::Phd::Iterator
Bio::SwissProt::SProt::Iterator
Bio::Geo::Iterator
Bio::UniGene::Iterator
Martel::Iterator::IteratorHeaderFooter
Martel::Iterator::IteratorRecords
test_Fasta::IteratorTest
Martel::IterParser::IterHeaderFooter
Martel::IterParser::IterRecords
Bio::Alphabet::IUPAC::IUPACAmbiguousDNADNA
Bio::Alphabet::IUPAC::IUPACAmbiguousRNARNA
Bio::Alphabet::IUPAC::IUPACProteinProtein
Bio::Alphabet::IUPAC::IUPACUnambiguousDNA
Bio::Alphabet::IUPAC::IUPACUnambiguousRNA
Bio::KDTree::CKDTree::KDTree
KDTree
Bio::KDTree::KDTree::KDTree
Bio::KDTree::CKDTree::KDTreePtr
Bio::kNN::kNN
Bio::HMM::Trainer::KnownStateTrainer
Bio::SeqIO::generic::LargeFastaFormat
Martel::LAX::LAX
Martel::LAX::LAXAttrs
Martel::LAX::LAXPositions
test_HMMGeneral::LetterAlphabet
Bio::Graphics::Distribution::LineDistribution
Bio::EUtils::DTDs::LinkOut::Link
Bio::EUtils::DTDs::eInfo_020511::Link
Bio::EUtils::Datatypes::Link
Bio::EUtils::DTDs::eLink_020511::Link
Bio::EUtils::DTDs::LinkOut::LinkId
Bio::EUtils::DTDs::eInfo_020511::LinkList
Bio::EUtils::Mixins::LinkMixin
Bio::EUtils::DTDs::eLink_020511::LinkName
Bio::EUtils::DTDs::LinkOut::LinkSet
Bio::EUtils::DTDs::eLink_020511::LinkSet
Bio::EUtils::DTDs::eLink_020511::LinkSetDb
Bio::EUtils::Datatypes::LinkSetDb
Bio::EUtils::Datatypes::LinksLinkSet
Bio::SwissProt::KeyWList::ListParser
Martel::Expression::Literal
test_BioSQL::LoaderTest
Bio::PopGen::Async::Local::Local
Bio::SGMLExtractor::SGMLExtractor::LocalParser
Bio::Mindy::Location::Location
Bio::GFF::easy::Location
Bio::GFF::easy::LocationFromCoords
Bio::GFF::easy::LocationFromString
Bio::GFF::easy::LocationJoin
Bio::GenBank::LocationParser::LocationParser
Bio::GenBank::LocationParserError
Bio::GenBank::LocationParser::LocationScanner
Bio::LocusLink::web_parse::LocusLinkParser
Bio::HMM::DynamicProgramming::LogDPAlgorithms
Bio::LogisticRegression::LogisticRegression
Bio::GenBank::LocationParser::LowBound
Bio::Blast::NCBIStandalone::LowQualityBlastError
Bio::Ais::Lymphocyte
Bio::config::_support::make_cached_expression
Bio::config::_support::make_rate_limited_function
Bio::config::_support::make_timed_function
Bio::MarkovModel::MarkovModel
Bio::HMM::MarkovModel::MarkovModelBuilder
test_HMMGeneral::MarkovModelBuilderTest
Bio::MarkupEditor::MarkupEditor
Martel::Parser::MartelAttributeList
Bio::MEME::Parser::MASTParser
Bio::MEME::Parser::MASTRecord
Bio::MaxEntropy::MaxEntropy
Martel::Expression::MaxRepeat
Bio::MEME::Motif::MEMEMotif
Bio::MEME::Parser::MEMEParser
Bio::MEME::Parser::MEMERecord
Bio::Mindy::FlatDB::MemoryFlatDB
Bio::EUtils::DTDs::eInfo_020511::Menu
Bio::EUtils::DTDs::eInfo_020511::MenuName
Bio::GFF::binning::Meta
Bio::MetaTool::Record::Metabolite
Bio::MetaTool::Record::MetaboliteRole
Bio::Restriction::Restriction::Meth_Dep
Bio::Restriction::Restriction::Meth_Undep
Bio::EUtils::sourcegen::MethodHolder
Bio::MarkupEditor::MidPoint
Bio::MissingExternalDependencyError
nextorf::MissingTable
Bio::SeqUtils::MissingTable
Bio::PDB::MMCIF2Dict::MMCIF2Dict
Bio::PDB::MMCIFParser::MMCIFParser
Bio::PDB::Model::Model
Bio::NeuralNetwork::Gene::Schema::MostCountSchemaFitness
Bio::MEME::Motif::Motif
Bio::AlignAce::Motif::Motif
Bio::NeuralNetwork::Gene::Motif::MotifCoder
test_NNGene::MotifCoderTest
Bio::NeuralNetwork::Gene::Motif::MotifFinder
test_NNGene::MotifFinderTest
Martel::Dispatch::Multicall
Martel::Dispatch::MulticallEnd
Martel::Dispatch::MulticallStart
Bio::Pathway::Rep::MultiGraph::MultiGraph
test_Pathway::MultiGraphTestCase
Bio::Clustalw::MultipleAlignCL
Bio::Blast::Record::MultipleAlignment
Bio::Alphabet::Reduced::Murphy10
Bio::Alphabet::Reduced::Murphy15
Bio::Alphabet::Reduced::Murphy4
Bio::Alphabet::Reduced::Murphy8
Bio::Seq::MutableSeq
test_GAMutation::MutationHelper
Martel::setup::my_install
SeqGui::MyApp
test_KeyWList::MyConsumer
test_MyModule::MyModuleTestOne
Bio::File::SGMLStripper::MyParser
BioSQL::DBUtils::Mysql_dbutils
Bio::PDB::NACCESS::NACCESS
Bio::PDB::NACCESS::NACCESS_atomic
Bio::NaiveBayes::NaiveBayes
Bio::EUtils::DTDs::eLink_020511::Name
Bio::EUtils::DTDs::LinkOut::Name
Bio::EUtils::DTDs::eInfo_020511::Name
Bio::EUtils::DTDs::eLink_020511::NameAbbr
Bio::EUtils::DTDs::LinkOut::NameAbbr
Bio::Data::CodonTable::NCBICodonTable
Bio::Data::CodonTable::NCBICodonTableDNA
Bio::Data::CodonTable::NCBICodonTableRNA
Bio::GenBank::NCBIDictionary
Bio::Ndb::NdbParser
Bio::EUtils::Datatypes::NeighborLinkSet
Bio::PDB::NeighborSearch::NeighborSearch
Bio::NetCatch::NetCatch
Bio::Pathway::Network
Bio::Restriction::_Update::RestrictionCompiler::newenzyme
nextorf::NextOrf
Bio::Nexus::Nexus::Nexus
Bio::Nexus::Nexus::NexusError
Bio::SeqIO::generic::NexusFormat
test_Nexus::NexusTest1
Bio::EUtils::POM::NMTOKEN
Bio::EUtils::POM::NMTOKENS
test_GASelection::NoCrossover
Bio::Restriction::Restriction::NoCut
Bio::Nexus::Nodes::Node
Node
Bio::SCOP::Node
Bio::Nexus::Trees::NodeData
Bio::Nexus::Nodes::NodeException
Bio::DocSQL::NoInsertionError
test_GASelection::NoMutation
test_CAPS::NonExample
Bio::Restriction::Restriction::NonPalindromic
test_GASelection::NoRepair
Bio::EUtils::DTDs::LinkOut::normalize
test_GASelection::NoSelection
Bio::EUtils::Datatypes::Not
Bio::Restriction::Restriction::Not_available
Bio::Restriction::Restriction::NotDefined
xbb_utils::NotePad
Martel::RecordReader::Nothing
Bio::Alphabet::NucleotideAlphabetDNA
Martel::Expression::NullOp
test_HMMGeneral::NumberAlphabet
Bio::EUtils::DTDs::LinkOut::ObjectList
Bio::EUtils::POM::ObjectParserHandler
Bio::EUtils::DTDs::LinkOut::ObjectSelector
Bio::EUtils::DTDs::LinkOut::ObjectUrl
Bio::EUtils::DTDs::LinkOut::ObjId
Bio::EUtils::Datatypes::ObjUrl
Bio::EUtils::DTDs::eLink_020511::ObjUrl
Bio::Restriction::Restriction::OneCut
Bio::SeqFeature::OneOfPosition
Bio::EUtils::DTDs::eSearch_020511::OP
Bio::Mindy::BaseDB::OpenDB
Bio::EUtils::Datatypes::Or
Bio::EUtils::MultiDict::OrderedMultiDict
Bio::Graphics::BasicChromosome::Organism
Bio::GA::Organism::Organism
test_GraphicsChromosome::OrganismGraphicTest
test_GAOrganism::OrganismTest
Bio::NeuralNetwork::BackPropagation::Layer::OutputLayer
Bio::EUtils::DTDs::eSearch_020511::OutputMessage
Bio::EUtils::Datatypes::OutputMessage
Bio::Restriction::Restriction::Ov3
Bio::Restriction::Restriction::Ov5
Bio::Restriction::_Update::RestrictionCompiler::OverhangError
Bio::EUtils::DTDs::LinkOut::pad
Bio::Emboss::Applications::PalindromeCommandline
Bio::Restriction::Restriction::Palindromic
Bio::Blast::Record::Parameters
SeqGui::ParamsPanel
Bio::SCOP::Des::Parser
Martel::Parser::Parser
Bio::SCOP::Hie::Parser
Bio::SCOP::Cla::Parser
Bio::SCOP::Raf::Parser
Bio::SCOP::Dom::Parser
Martel::Expression::ParseRecords
Martel::Parser::ParserException
Bio::GenBank::ParserFailureError
Martel::Parser::ParserIncompleteException
Martel::Parser::ParserPositionException
Martel::Parser::ParserRecordException
test_Fasta::ParserTest
test_PopGen_FDist_nodepend::ParserTest
test_PopGen_GenePop::ParserTest
Martel::Expression::PassThrough
Bio::GenBank::LocationParser::Path
test_Pathway::PathwayTestSuite
Bio::MetaTool::Record::PathwayTransform
Martel::msre_parse::Pattern
Bio::Prosite::PatternHit
Bio::NeuralNetwork::Gene::Pattern::PatternIO
test_NNGene::PatternIOTest
Bio::NeuralNetwork::Gene::Pattern::PatternRepository
test_NNGene::PatternRepositoryTest
Bio::Alphabet::Reduced::PC5
Bio::PDB::PDBIO::PDBIO
Bio::PDB::PDBList::PDBList
Bio::PDB::PDBParser::PDBParser
Bio::NMR::xpktools::Peaklist
BioSQL::DBUtils::Pgdb_dbutils
test_Phd::PhdTestOne
Bio::EUtils::DTDs::eSearch_020511::PhraseIgnored
Bio::EUtils::Datatypes::PhraseIgnored
Bio::EUtils::DTDs::eSearch_020511::PhraseNotFound
Bio::EUtils::Datatypes::PhraseNotFound
Bio::SeqIO::PhylipIO::PhylipWriter
Bio::SeqIO::generic::PirFormat
Bio::PDB::Polypeptide::Polypeptide
Bio::EUtils::POM::POMDocument
Bio::FSSP::PosAlign
Bio::SeqFeature::PositionGap
Bio::EUtils::Datatypes::PostResult
Bio::PDB::Polypeptide::PPBuilder
Bio::Mindy::FlatDB::PrimaryNamespace
Bio::Mindy::BerkeleyDB::PrimaryNamespace
Bio::Mindy::FlatDB::PrimaryTable
Bio::Emboss::Applications::Primer3Commandline
Bio::Emboss::Primer::Primer3Parser
test_EmbossPrimer::Primer3ParseTest
Bio::Emboss::Primer::Primer3Primers
Bio::Emboss::Primer::Primer3Record
Bio::Emboss::Primer::PrimerSearchAmplifier
Bio::Emboss::Applications::PrimerSearchCommandline
Bio::Emboss::Primer::PrimerSearchInputRecord
test_EmbossPrimer::PrimerSearchInputTest
Bio::Emboss::Primer::PrimerSearchOutputRecord
Bio::Emboss::Primer::PrimerSearchParser
test_EmbossPrimer::PrimersearchParseTest
Martel::Generate::print_debug
Martel::Generate::print_info
Bio::Restriction::PrintFormat::PrintFormat
Bio::EUtils::Datatypes::Problem
unittestgui::ProgressBar
Bio::PropertyManager::PropertyManager
Bio::Prosite::Pattern::Prosite
Bio::Prosite::Pattern::PrositeAlphabet
Bio::Prosite::Pattern::PrositeMatch
Bio::Prosite::Pattern::PrositeTerm
Bio::Alphabet::ProteinAlphabetProtein
Bio::SeqUtils::ProtParam::ProteinAnalysis
Bio::Gobase::ProteinRecord
Bio::SeqUtils::ProteinXProtein
nextorf::ProteinX
Bio::EUtils::DTDs::eLink_020511::Provider
Bio::EUtils::DTDs::LinkOut::Provider
Bio::EUtils::Datatypes::Provider
Bio::EUtils::DTDs::LinkOut::ProviderId
Bio::PDB::PSEA::PSEA
Bio::Blast::Record::PSIBlast
Bio::Blast::NCBIStandalone::PSIBlastParser
Bio::Align::AlignInfo::PSSM
BioSQL::DBUtils::Psycopg_dbutils
Bio::EUtils::DBIdsClient::PublicationDBIdsFetchMixin
Bio::EUtils::DBIdsClient::PublicationDBIdsRecord
Bio::EUtils::DBIdsClient::PublicationDBIdsRecordSet
Bio::EUtils::Mixins::PublicationFetchMixinShould turn this into a Bio.SeqRecord object Could do that using the XML code, but GenBank/GenPept is better
Bio::EUtils::HistoryClient::PublicationHistoryFetchMixin
Bio::EUtils::HistoryClient::PublicationHistoryRecord
Bio::EUtils::HistoryClient::PublicationHistoryRecordSet
PyNode
PyTree
Bio::Sequencing::Ace::qa
Bio::GenBank::Record::Qualifier
test_GAQueens::QueensAlphabet
test_GAQueens::QueensCrossover
test_GAQueens::QueensMutation
test_GAQueens::QueensRepair
Bio::Search::Query
Bio::DocSQL::Query
Bio::EUtils::DTDs::LinkOut::Query
Bio::DocSQL::QueryAll
Bio::DocSQL::QueryAllFirstItem
Bio::DocSQL::QueryGeneric
Bio::EUtils::DTDs::ePost_020511::QueryKey
Bio::EUtils::DTDs::eSearch_020511::QueryKey
Bio::DocSQL::QueryRow
Bio::DocSQL::QuerySingle
Bio::EUtils::DTDs::eSearch_020511::QueryTranslation
Bio::EUtils::DTDs::eSearch_020511::QuotedPhraseNotFound
Bio::EUtils::Datatypes::QuotedPhraseNotFound
test_SCOP_Raf::RafTests
Bio::NeuralNetwork::Gene::Schema::RandomMotifGenerator
test_HotRand::RandomSequenceTest
Bio::GenBank::LocationParser::Range
Bio::EUtils::Datatypes::Range
Bio::Sequencing::Ace::rd
Bio::Pathway::Reaction
test_Pathway::ReactionTestCase
Martel::RecordReader::ReaderError
Bio::Sequencing::Ace::Reads
Bio::SeqIO::generic::ReadSeq
test_BioSQL::ReadTest
Bio::Restriction::_Update::Update::RebaseUpdate
Bio::StdHandler::RecognizeHandler
Bio::KEGG::Enzyme::Record
Bio::SCOP::Hie::Record
Bio::Gobase::Record
Bio::SCOP::Dom::Record
Bio::Compass::Record
Bio::Medline::Record
Bio::MetaTool::Record::Record
Bio::NBRF::Record::Record
Bio::CDD::Record::Record
Bio::ECell::Record::Record
Bio::Sequencing::Phd::Record
Bio::IntelliGenetics::Record::Record
Bio::PopGen::GenePop::Record
Bio::SCOP::Des::Record
Bio::Prosite::Record
Bio::Rebase::Record
Bio::Cluster::Record
Bio::Fasta::Record
Bio::SCOP::Cla::Record
Bio::Prosite::Prodoc::Record
Bio::LocusLink::web_parse::Record
Bio::GenBank::Record::Record
Bio::PopGen::FDist::Record
Bio::Geo::Record::Record
Bio::Saf::Record::Record
Bio::SwissProt::SProt::Record
Bio::LocusLink::Record
Bio::InterPro::Record
Bio::KEGG::Compound::Record
Bio::Ndb::Record
Martel::Iterator::RecordEventStream
Bio::Sequencing::Ace::RecordParser
Bio::Medline::RecordParser
Bio::Prosite::RecordParser
Bio::Sequencing::Phd::RecordParser
Bio::UniGene::RecordParser
Martel::Parser::RecordParser
Bio::IntelliGenetics::RecordParser
Bio::NBRF::RecordParser
Bio::ECell::RecordParser
Bio::SwissProt::SProt::RecordParser
Bio::Prosite::Prodoc::RecordParser
Bio::Compass::RecordParser
Bio::LocusLink::RecordParser
Bio::PopGen::FDist::RecordParser
Bio::CDD::RecordParser
Bio::Enzyme::RecordParser
Bio::GenBank::RecordParser
Bio::Fasta::RecordParser
Bio::Saf::RecordParser
Bio::PopGen::GenePop::RecordParser
Bio::Rebase::RecordParser
Bio::MetaTool::RecordParser
Bio::Gobase::RecordParser
Martel::RecordReader::RecordReader
test_PopGen_FDist_nodepend::RecordTest
test_Fasta::RecordTest
test_PopGen_GenePop::RecordTest
Bio::GenBank::Record::Reference
Bio::Prosite::Prodoc::Reference
Bio::SeqFeature::Reference
Bio::SwissProt::SProt::Reference
Region
Bio::config::Registry::RegisterableGroup
Bio::config::Registry::RegisterableObject
Bio::config::Registry::Registry
run_tests::RegressionTest
Martel::Dispatch::RemapEnd
Martel::Dispatch::RemapStart
test_Pathway::RepTestSuite
Bio::WWW::RequestLimiter
Bio::SCOP::Raf::Res
Bio::EUtils::ReseekFile::ReseekFile
Bio::PDB::Residue::Residue
Bio::PDB::ResidueDepth::ResidueDepth
Bio::SCOP::Residues::Residues
test_SCOP_Residues::ResiduesTests
Bio::Restriction::Restriction::RestrictionBatch
test_Restriction::RestrictionBatches
Bio::Restriction::Restriction::RestrictionType
test_CAPS::ResultChecker
Bio::EUtils::DTDs::eSearch_020511::RetMax
Bio::GFF::RetrieveSeqname
Bio::EUtils::DTDs::eSearch_020511::RetStart
Bio::Alphabet::RNAAlphabetRNA
unittestgui::RollbackImporter
Bio::GA::Selection::RouletteWheel::RouletteWheelSelection
test_GASelection::RouletteWheelSelectionTest
Bio::Blast::Record::Round
Bio::Sequencing::Ace::rt
Bio::EUtils::DTDs::LinkOut::Rule
Bio::EUtils::DTDs::LinkOut::RuleToMany
Martel::setup::run_install_tests
Martel::setup::run_local_tests
Bio::GA::Crossover::General::SafeFitnessCrossover
Bio::GA::Mutation::General::SafeFitnessMutation
test_GAMutation::SafeFitnessTest
test_GACrossover::SafeFitnessTest
Bio::HMM::DynamicProgramming::ScaledDPAlgorithms
test_HMMGeneral::ScaledDPAlgorithmsTest
Bio::MultiProc::Scheduler::Scheduler
Bio::NeuralNetwork::Gene::Schema::Schema
Bio::NeuralNetwork::Gene::Schema::SchemaCoder
test_NNGene::SchemaCoderTest
Bio::NeuralNetwork::Gene::Schema::SchemaDNAAlphabet
Bio::NeuralNetwork::Gene::Schema::SchemaFactory
test_NNGene::SchemaFactoryTest
Bio::NeuralNetwork::Gene::Schema::SchemaFinder
test_NNGene::SchemaFinderTest
test_NNGene::SchemaMatchingTest
test_NNGene::SchemaTest
Bio::SCOP::Scop
test_SCOP_Scop::ScopTests
Bio::EUtils::DTDs::eLink_020511::Score
Bio::Search::Search
Bio::EUtils::Datatypes::SearchResult
Bio::Mindy::BerkeleyDB::SecondaryNamespace
Bio::Mindy::FlatDB::SecondaryNamespace
Bio::Alphabet::SecondaryStructureOther per-sequence encodings
Bio::Mindy::FlatDB::SecondaryTable
Bio::GFF::Segment
Bio::PDB::PDBIO::Select
Bio::EUtils::DTDs::LinkOut::Separator
Bio::Seq::Seq
Martel::Expression::Seq
Bio::config::SeqDBRegistry::SeqDBRegistry
Bio::SeqFeature::SeqFeature
SeqGui::SeqFrame
test_BioSQL::SeqInterfaceTest
Bio::SCOP::Raf::SeqMap
Bio::SCOP::Raf::SeqMapIndex
Bio::SubsMat::SeqMat
SeqGui::SeqPanel
Bio::SeqRecord::SeqRecord
Bio::SeqIO::generic::SeqRecord
Bio::EUtils::DBIdsClient::SequenceDBIdsFetchMixin
Bio::EUtils::DBIdsClient::SequenceDBIdsRecord
Bio::EUtils::DBIdsClient::SequenceDBIdsRecordSet
Bio::EUtils::Mixins::SequenceFetchMixin
Bio::EUtils::HistoryClient::SequenceHistoryFetchMixin
Bio::EUtils::HistoryClient::SequenceHistoryRecord
Bio::EUtils::HistoryClient::SequenceHistoryRecordSet
Bio::SeqIO::Interfaces::SequenceIterator
Bio::Fasta::SequenceParser
Bio::SwissProt::SProt::SequenceParser
Bio::Gobase::SequenceRecord
Bio::SeqIO::Interfaces::SequenceWriter
Bio::SeqIO::Interfaces::SequentialSequenceWriter
Martel::Generate::SetGroupValue
Bio::SGMLExtractor::SGMLExtractor
Bio::SGMLExtractor::SGMLExtractorHandle
Bio::File::SGMLHandle
Bio::File::SGMLStripper
Bio::ParserSupport::SGMLStrippingConsumer
Bio::Blast::NCBIStandalone::ShortQueryBlastError
Bio::NeuralNetwork::Gene::Signature::SignatureCoder
test_NNGene::SignatureCoderTest
Bio::NeuralNetwork::Gene::Signature::SignatureFinder
test_NNGene::SignatureFinderTest
Bio::PopGen::SimCoal::Cache::SimCoalCache
Bio::PopGen::SimCoal::Async::SimCoalCache
Bio::PopGen::SimCoal::Controller::SimCoalController
test_Restriction::SimpleEnzyme
Bio::NeuralNetwork::Gene::Schema::SimpleFinisher
Bio::Mindy::SimpleSeqRecord::SimpleIndexer
Bio::Alphabet::SingleLetterAlphabet
Bio::GA::Crossover::Point::SinglePointCrossover
test_GACrossover::SinglePointTest
Bio::GA::Mutation::Simple::SinglePositionMutation
test_GAMutation::SinglePositionTest
Bio::EUtils::DTDs::eInfo_020511::SingleToken
Bio::EUtils::sourcegen::SourceFile
Bio::EUtils::sourcegen::SourceGen
Bio::PopGen::FDist::Async::SplitFDist
Bio::config::_stanzaformat::Stanza
Bio::config::_stanzaformat::StanzaFormat
Martel::RecordReader::StartsWith
Bio::Wise::dnal::Statistics
Bio::Std::StdTerm
Bio::GA::Evolver::SteadyStateEvolver
Bio::Nexus::Nexus::StepMatrix
Bio::SeqIO::StockholmIO::StockholmIterator
Bio::SeqIO::StockholmIO::StockholmWriter
test_NNGeneral::StopTrainingTest
Martel::test::support::Storage
martel_support::Storage
Martel::Iterator::StoreEvents
Martel::Expression::Str
Bio::EUtils::DTDs::LinkOut::strip
Bio::PDB::Structure::Structure
Bio::PDB::StructureAlignment::StructureAlignment
Bio::PDB::StructureBuilder::StructureBuilder
Bio::EUtils::sourcegen::SUBCLASS
Bio::EUtils::DTDs::eLink_020511::SubjectType
Bio::EUtils::DTDs::LinkOut::SubjectType
Bio::EUtils::DTDs::LinkOut::SubObjectSelector
Martel::msre_parse::SubPattern
Bio::EUtils::DTDs::LinkOut::SubProvider
Bio::EUtils::DTDs::LinkOut::subs
Bio::EUtils::Datatypes::Summary
Bio::Align::AlignInfo::SummaryInfo
Bio::PDB::Superimposer::Superimposer
Bio::GFF::GenericTools::Surrogate
Bio::GFF::GenericTools::SurrogateNotInitedError
Bio::SVDSuperimposer::SVDSuperimposer::SVDSuperimposer
swig_const_info
swig_globalvar
swig_type_info
swig_varlinkobject
Bio::GenBank::LocationParser::Symbol
Bio::Pathway::System
Bio::Search::TableInfo
Bio::ParserSupport::TaggingConsumer
Bio::MultiProc::Task::Task
Bio::Graphics::BasicChromosome::TelomereSegment
Bio::GFF::GenericTools::TempFile
test_PopGen_SimCoal_nodepend::TemplateTest
Bio::EUtils::Datatypes::Term
Bio::EUtils::DTDs::eSearch_020511::Term
Bio::EUtils::DTDs::eInfo_020511::TermCount
Bio::EUtils::DTDs::eSearch_020511::TermSet
setup::test_biopython
test_GAMutation::TestAlphabet
test_GACrossover::TestAlphabet
test_GAOrganism::TestAlphabet
test_GASelection::TestAlphabet
test_GARepair::TestAlphabet
test_ParserSupport::TestConsumer
test_GACrossover::TestCrossover
test_ParserSupport::TestHandleTaggingConsumer
test_GAMutation::TestMutator
test_psw::TestPSW
test_Wise::TestWise
test_Wise::TestWiseDryRun
Bio::EUtils::POM::Text
Bio::config::DBRegistry::TextLikeMixin
test_PDB::TheVoid
Bio::EUtils::ThinClient::ThinClient
Bio::Alphabet::ThreeLetterProtein
unittestgui::TkTestRunner
Bio::EUtils::DTDs::eSearch_020511::To
Bio::LocusLink::web_parse::Token
Bio::GenBank::LocationParser::Token
Martel::msre_parse::Tokenizer
Bio::EUtils::DTDs::LinkOut::tolower
Bio::EUtils::DTDs::LinkOut::toupper
Bio::GA::Selection::Tournament::TournamentSelection
test_GASelection::TournamentSelectionTest
Bio::NeuralNetwork::Training::TrainingExample
Bio::HMM::Trainer::TrainingSequence
Bio::Emboss::Applications::TranalignCommandline
Bio::Transcribe::Transcribe
Bio::EUtils::DTDs::eSearch_020511::Translation
Bio::Data::CodonTable::TranslationError
Bio::EUtils::DTDs::eSearch_020511::TranslationSet
Bio::EUtils::DTDs::eSearch_020511::TranslationStack
Bio::Translate::Translator
Bio::Nexus::Trees::Tree
Bio::Nexus::Trees::TreeError
trieobject
test_CAPS::TrivialExample
Bio::GenBank::LocationParser::TwoBound
Bio::GA::Crossover::GeneralPoint::TwoCrossover
Bio::Restriction::Restriction::TwoCuts
Bio::GA::Crossover::TwoPoint::TwoPointCrossover
test_GACrossover::TwoPointTest
Bio::Restriction::_Update::RestrictionCompiler::TypeCompiler
Bio::File::UndoHandle
test_CAPS::UnevenAlignment
Bio::GA::Crossover::Uniform::UniformCrossover
test_GACrossover::UniformTest
Bio::UniGene::UnigeneProtsimRecord
Bio::UniGene::UnigeneRecord
Bio::UniGene::UnigeneSequenceRecord
Bio::UniGene::UnigeneSTSRecord
Bio::Restriction::Restriction::Unknown
Bio::DBXRef::UnknownDBName
Bio::EUtils::MultiDict::UnorderedMultiDict
Bio::GenBank::LocationParser::UnsignedInteger
Martel::RecordReader::Until
Bio::DocSQL::Update
Bio::LocusLink::web_parse::Url
Bio::EUtils::DTDs::eLink_020511::Url
Bio::EUtils::DTDs::LinkOut::Url
Bio::NetCatch::Url
Bio::EUtils::DTDs::LinkOut::UrlName
Bio::EUtils::parse::UsePOMParser
test_PopGen_GenePop::UtilsTest
Bio::EUtils::POM::ValidationError
Bio::NeuralNetwork::StopTraining::ValidationIncreaseStop
Bio::PDB::Vector::Vector
Bio::GFF::GenericTools::VerboseDict
Bio::GFF::GenericTools::VerboseList
Bio::Sequencing::Ace::wa
Bio::EUtils::DTDs::eSearch_020511::WarningList
Bio::EUtils::Datatypes::WarningProblem
Bio::Emboss::Applications::WaterCommandline
Bio::EUtils::DTDs::eSearch_020511::WebEnv
Bio::EUtils::DTDs::ePost_020511::WebEnv
Bio::EUtils::Datatypes::WithinNDays
Bio::SeqFeature::WithinPosition
Bio::Sequencing::Ace::wr
Bio::Mindy::BaseDB::WriteDB
Bio::writers::SeqRecord::embl::WriteEmbl
Bio::writers::SeqRecord::empty::WriteEmpty
Bio::writers::SeqRecord::fasta::WriteFasta
Bio::Writer::Writer
xbb_io::xbb_io
xbb_sequence::xbb_sequence
xbb_translations::xbb_translations
xbb_widget::xbb_widget
xbb_help::xbbtools_help
xbb_search::XDNAsearch
Bio::EUtils::POM::XMLAttribute
Bio::NMR::xpktools::XpkEntry
yy_buffer_state

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