### Home Classes Methods

### In Files

- lib/bio/pathway.rb

### Parent

Object

### Methods

- ::new
- #append
- #bellman_ford
- #bfs
- #bfs_shortest_path
- #breadth_first_search
- #clear_relations!
- #clique
- #cliquishness
- #common_subgraph
- #delete
- #depth_first_search
- #dfs
- #dfs_topological_sort
- #dijkstra
- #directed
- #directed?
- #dump_list
- #dump_matrix
- #edges
- #nodes
- #small_world
- #subgraph
- #to_list
- #to_matrix
- #to_relations
- #undirected
- #undirected?

### Files

- ChangeLog
- KNOWN_ISSUES.rdoc
- LEGAL
- README.rdoc
- README_DEV.rdoc
- RELEASE_NOTES.rdoc
- Changes-1.3.rdoc
- RELEASE_NOTES-1.4.0.rdoc
- RELEASE_NOTES-1.4.1.rdoc
- RELEASE_NOTES-1.4.2.rdoc

### Class/Module Index

Quicksearch

- Bio
- Bio::AAindex
- Bio::AAindex1
- Bio::AAindex2
- Bio::Abif
- Bio::Abif::DirectoryEntry
- Bio::Alignment
- Bio::Alignment::ArrayExtension
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- Bio::Alignment::FactoryTemplate
- Bio::Alignment::FactoryTemplate::FileInFileOut
- Bio::Alignment::FactoryTemplate::FileInFileOutWithTree
- Bio::Alignment::FactoryTemplate::FileInStdoutOut
- Bio::Alignment::FactoryTemplate::Simple
- Bio::Alignment::FactoryTemplate::StdinInFileOut
- Bio::Alignment::FactoryTemplate::WrapInputStdin
- Bio::Alignment::FactoryTemplate::WrapInputTempfile
- Bio::Alignment::FactoryTemplate::WrapOutputStdout
- Bio::Alignment::FactoryTemplate::WrapOutputTempfile
- Bio::Alignment::GAP
- Bio::Alignment::HashExtension
- Bio::Alignment::MultiFastaFormat
- Bio::Alignment::OriginalAlignment
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- Bio::Alignment::Output
- Bio::Alignment::PropertyMethods
- Bio::Alignment::SequenceArray
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- Bio::Alignment::Site
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- Bio::AminoAcid
- Bio::AminoAcid::Data
- Bio::Blast
- Bio::Blast::Bl2seq
- Bio::Blast::Bl2seq::Report
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- Bio::Blast::RPSBlast::RPSBlastSplitter
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- Bio::Blat
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- Bio::ClustalW
- Bio::ClustalW::Report
- Bio::CodonTable
- Bio::ColorScheme
- Bio::Command
- Bio::Command::Tmpdir
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- Bio::ContingencyTable
- Bio::DAS
- Bio::DAS::DNA
- Bio::DAS::DSN
- Bio::DAS::ENTRY_POINT
- Bio::DAS::FEATURE
- Bio::DAS::GFF
- Bio::DAS::GROUP
- Bio::DAS::LINK
- Bio::DAS::SEGMENT
- Bio::DAS::SEQUENCE
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- Bio::DAS::TYPE
- Bio::DAS::TYPES
- Bio::DB
- Bio::DBGET
- Bio::DDBJ
- Bio::DDBJ::REST
- Bio::DDBJ::REST::Blast
- Bio::DDBJ::REST::ClustalW
- Bio::DDBJ::REST::DDBJ
- Bio::DDBJ::REST::Mafft
- Bio::DDBJ::REST::RequestManager
- Bio::DDBJ::REST::WABItemplate
- Bio::DDBJ::XML
- Bio::DDBJ::XML::Blast
- Bio::DDBJ::XML::ClustalW
- Bio::DDBJ::XML::DDBJ
- Bio::DDBJ::XML::Fasta
- Bio::DDBJ::XML::GetEntry
- Bio::DDBJ::XML::Gib
- Bio::DDBJ::XML::Gtop
- Bio::DDBJ::XML::PML
- Bio::DDBJ::XML::RequestManager
- Bio::DDBJ::XML::RequestManager::REST
- Bio::DDBJ::XML::SRS
- Bio::DDBJ::XML::TxSearch
- Bio::EBI
- Bio::EBI::SOAP
- Bio::EBI::SOAP::Citation
- Bio::EBI::SOAP::ClustalW
- Bio::EBI::SOAP::Dbfetch
- Bio::EBI::SOAP::Emboss
- Bio::EBI::SOAP::Fasta
- Bio::EBI::SOAP::InterProScan
- Bio::EBI::SOAP::MPsrch
- Bio::EBI::SOAP::MSD
- Bio::EBI::SOAP::Muscle
- Bio::EBI::SOAP::Ontology
- Bio::EBI::SOAP::ScanPS
- Bio::EBI::SOAP::TCoffee
- Bio::EBI::SOAP::WUBlast
- Bio::EMBL
- Bio::EMBLDB
- Bio::EMBLDB::Common
- Bio::EMBOSS
- Bio::Ensembl
- Bio::Ensembl::Base
- Bio::Ensembl::Human
- Bio::Ensembl::Mouse
- Bio::FANTOM
- Bio::FANTOM::MaXML
- Bio::FANTOM::MaXML::Annotation
- Bio::FANTOM::MaXML::Annotation::DataSrc
- Bio::FANTOM::MaXML::Annotations
- Bio::FANTOM::MaXML::Cluster
- Bio::FANTOM::MaXML::Sequence
- Bio::FANTOM::MaXML::Sequences
- Bio::Fasta
- Bio::Fasta::Report
- Bio::Fasta::Report::FLATFILE_SPLITTER
- Bio::Fasta::Report::FastaFormat10Splitter
- Bio::Fasta::Report::Hit
- Bio::Fasta::Report::Hit::Query
- Bio::Fasta::Report::Hit::Target
- Bio::Fasta::Report::Program
- Bio::FastaDefline
- Bio::FastaFormat
- Bio::FastaNumericFormat
- Bio::Fastq
- Bio::Fastq::Error
- Bio::Fastq::Error::Diff_ids
- Bio::Fastq::Error::Long_qual
- Bio::Fastq::Error::No_atmark
- Bio::Fastq::Error::No_ids
- Bio::Fastq::Error::No_qual
- Bio::Fastq::Error::No_seq
- Bio::Fastq::Error::Qual_char
- Bio::Fastq::Error::Qual_range
- Bio::Fastq::Error::Seq_char
- Bio::Fastq::Error::Short_qual
- Bio::Fastq::Error::Skipped_unformatted_lines
- Bio::Fastq::FormatData
- Bio::Fastq::FormatData::FASTQ_ILLUMINA
- Bio::Fastq::FormatData::FASTQ_SANGER
- Bio::Fastq::FormatData::FASTQ_SOLEXA
- Bio::Feature
- Bio::Feature::Qualifier
- Bio::Features
- Bio::Fetch
- Bio::FlatFile
- Bio::FlatFile::AutoDetect
- Bio::FlatFile::AutoDetect::RuleDebug
- Bio::FlatFile::AutoDetect::RuleProc
- Bio::FlatFile::AutoDetect::RuleRegexp
- Bio::FlatFile::AutoDetect::RuleRegexp2
- Bio::FlatFile::AutoDetect::RuleSpecial
- Bio::FlatFile::AutoDetect::RuleTemplate
- Bio::FlatFile::AutoDetect::RulesArray
- Bio::FlatFile::BufferedInputStream
- Bio::FlatFile::Splitter
- Bio::FlatFile::Splitter::Default
- Bio::FlatFile::Splitter::LineOriented
- Bio::FlatFile::Splitter::Template
- Bio::FlatFile::UnknownDataFormatError
- Bio::FlatFileIndex
- Bio::FlatFileIndex::BDB_1
- Bio::FlatFileIndex::BDB_1::BDBMappingFile
- Bio::FlatFileIndex::BDB_1::PrimaryNameSpace
- Bio::FlatFileIndex::BDB_1::SecondaryNameSpace
- Bio::FlatFileIndex::BDBdefault
- Bio::FlatFileIndex::BDBwrapper
- Bio::FlatFileIndex::DEBUG
- Bio::FlatFileIndex::DataBank
- Bio::FlatFileIndex::FileID
- Bio::FlatFileIndex::FileIDs
- Bio::FlatFileIndex::Flat_1
- Bio::FlatFileIndex::Flat_1::FlatMappingFile
- Bio::FlatFileIndex::Flat_1::PrimaryNameSpace
- Bio::FlatFileIndex::Flat_1::Record
- Bio::FlatFileIndex::Flat_1::SecondaryNameSpace
- Bio::FlatFileIndex::Indexer
- Bio::FlatFileIndex::Indexer::NameSpace
- Bio::FlatFileIndex::Indexer::NameSpaces
- Bio::FlatFileIndex::Indexer::Parser
- Bio::FlatFileIndex::Indexer::Parser::BlastDefaultParser
- Bio::FlatFileIndex::Indexer::Parser::EMBLParser
- Bio::FlatFileIndex::Indexer::Parser::FastaFormatParser
- Bio::FlatFileIndex::Indexer::Parser::GenBankParser
- Bio::FlatFileIndex::Indexer::Parser::GenPeptParser
- Bio::FlatFileIndex::Indexer::Parser::MaXMLClusterParser
- Bio::FlatFileIndex::Indexer::Parser::MaXMLSequenceParser
- Bio::FlatFileIndex::Indexer::Parser::PDBChemicalComponentParser
- Bio::FlatFileIndex::Indexer::Parser::SPTRParser
- Bio::FlatFileIndex::Indexer::Parser::TemplateParser
- Bio::FlatFileIndex::NameSpaces
- Bio::FlatFileIndex::Results
- Bio::FlatFileIndex::Template
- Bio::FlatFileIndex::Template::NameSpace
- Bio::GCG
- Bio::GCG::Msf
- Bio::GCG::Seq
- Bio::GFF
- Bio::GFF::GFF2
- Bio::GFF::GFF2::Escape
- Bio::GFF::GFF2::MetaData
- Bio::GFF::GFF2::Record
- Bio::GFF::GFF2::Record::Value
- Bio::GFF::GFF3
- Bio::GFF::GFF3::Escape
- Bio::GFF::GFF3::Record
- Bio::GFF::GFF3::Record::Gap
- Bio::GFF::GFF3::Record::Gap::Code
- Bio::GFF::GFF3::Record::Target
- Bio::GFF::GFF3::RecordBoundary
- Bio::GFF::GFF3::SequenceRegion
- Bio::GFF::Record
- Bio::GO
- Bio::GO::External2go
- Bio::GO::GeneAssociation
- Bio::GO::Ontology
- Bio::GenBank
- Bio::GenBank::Locus
- Bio::GenPept
- Bio::GenPept::Locus
- Bio::Genscan
- Bio::Genscan::Report
- Bio::Genscan::Report::Exon
- Bio::Genscan::Report::Gene
- Bio::HGC
- Bio::HGC::HiGet
- Bio::HMMER
- Bio::HMMER::Report
- Bio::HMMER::Report::Hit
- Bio::HMMER::Report::Hsp
- Bio::Hinv
- Bio::Hinv::Acc2hit
- Bio::Hinv::Common
- Bio::Hinv::Hit2acc
- Bio::Hinv::HitCnt
- Bio::Hinv::HitDefinition
- Bio::Hinv::HitPubmedId
- Bio::Hinv::HitXML
- Bio::Hinv::Hix2hit
- Bio::Hinv::HixCnt
- Bio::Hinv::HixRepresent
- Bio::Hinv::HixXML
- Bio::Hinv::IdSearch
- Bio::Hinv::KeywordSearch
- Bio::Iprscan
- Bio::Iprscan::Report
- Bio::Iprscan::Report::Match
- Bio::KEGG
- Bio::KEGG::API
- Bio::KEGG::BRITE
- Bio::KEGG::COMPOUND
- Bio::KEGG::Common
- Bio::KEGG::Common::DblinksAsHash
- Bio::KEGG::Common::GenesAsHash
- Bio::KEGG::Common::ModulesAsHash
- Bio::KEGG::Common::OrthologsAsHash
- Bio::KEGG::Common::PathwaysAsHash
- Bio::KEGG::Common::References
- Bio::KEGG::Common::StringsAsHash
- Bio::KEGG::DRUG
- Bio::KEGG::ENZYME
- Bio::KEGG::EXPRESSION
- Bio::KEGG::GENES
- Bio::KEGG::GENOME
- Bio::KEGG::GLYCAN
- Bio::KEGG::KGML
- Bio::KEGG::KGML::Entry
- Bio::KEGG::KGML::Graphics
- Bio::KEGG::KGML::Product
- Bio::KEGG::KGML::Reaction
- Bio::KEGG::KGML::Relation
- Bio::KEGG::KGML::Substrate
- Bio::KEGG::KGML::SubstrateProduct
- Bio::KEGG::Keggtab
- Bio::KEGG::Keggtab::DB
- Bio::KEGG::MODULE
- Bio::KEGG::ORTHOLOGY
- Bio::KEGG::PATHWAY
- Bio::KEGG::REACTION
- Bio::KEGG::Taxonomy
- Bio::KEGGDB
- Bio::LITDB
- Bio::Lasergene
- Bio::Location
- Bio::Locations
- Bio::MAFFT
- Bio::MAFFT::Report
- Bio::MEDLINE
- Bio::Map
- Bio::Map::ActsLikeMap
- Bio::Map::ActsLikeMarker
- Bio::Map::Mapping
- Bio::Map::Marker
- Bio::Map::SimpleMap
- Bio::Meme
- Bio::Meme::Mast
- Bio::Meme::Mast::Report
- Bio::Meme::Motif
- Bio::Muscle
- Bio::NBRF
- Bio::NCBI
- Bio::NCBI::REST
- Bio::NCBI::REST::EFetch
- Bio::NCBI::REST::EFetch::Methods
- Bio::NCBI::REST::ESearch
- Bio::NCBI::REST::ESearch::Methods
- Bio::NCBI::SOAP
- Bio::NCBI::SOAP::EFetch
- Bio::NCBI::SOAP::EFetchLite
- Bio::NCBI::SOAP::EUtils
- Bio::NCBI::SOAP::EUtilsLite
- Bio::NCBIDB
- Bio::NCBIDB::Common
- Bio::Newick
- Bio::Newick::Edge
- Bio::Newick::Node
- Bio::Newick::ParseError
- Bio::Nexus
- Bio::Nexus::CharactersBlock
- Bio::Nexus::DataBlock
- Bio::Nexus::DistancesBlock
- Bio::Nexus::GenericBlock
- Bio::Nexus::NexusMatrix
- Bio::Nexus::NexusMatrix::NexusMatrixError
- Bio::Nexus::NexusParseError
- Bio::Nexus::TaxaBlock
- Bio::Nexus::TreesBlock
- Bio::Nexus::Util
- Bio::NucleicAcid
- Bio::NucleicAcid::Data
- Bio::PAML
- Bio::PAML::Baseml
- Bio::PAML::Baseml::Report
- Bio::PAML::Codeml
- Bio::PAML::Codeml::Model
- Bio::PAML::Codeml::PositiveSite
- Bio::PAML::Codeml::PositiveSites
- Bio::PAML::Codeml::Rates
- Bio::PAML::Codeml::Report
- Bio::PAML::Codeml::ReportError
- Bio::PAML::Codeml::ReportSingle
- Bio::PAML::Common
- Bio::PAML::Common::Report
- Bio::PAML::Yn00
- Bio::PAML::Yn00::Report
- Bio::PDB
- Bio::PDB::AtomFinder
- Bio::PDB::Chain
- Bio::PDB::ChainFinder
- Bio::PDB::ChemicalComponent
- Bio::PDB::ChemicalComponent::Record
- Bio::PDB::Coordinate
- Bio::PDB::DataType
- Bio::PDB::DataType::ConstLikeMethod
- Bio::PDB::DataType::Pdb_AChar
- Bio::PDB::DataType::Pdb_Atom
- Bio::PDB::DataType::Pdb_Character
- Bio::PDB::DataType::Pdb_Date
- Bio::PDB::DataType::Pdb_IDcode
- Bio::PDB::DataType::Pdb_Integer
- Bio::PDB::DataType::Pdb_LString
- Bio::PDB::DataType::Pdb_List
- Bio::PDB::DataType::Pdb_Real
- Bio::PDB::DataType::Pdb_Residue_name
- Bio::PDB::DataType::Pdb_SList
- Bio::PDB::DataType::Pdb_Specification_list
- Bio::PDB::DataType::Pdb_String
- Bio::PDB::DataType::Pdb_StringRJ
- Bio::PDB::DataType::Pdb_SymOP
- Bio::PDB::HetatmFinder
- Bio::PDB::Heterogen
- Bio::PDB::HeterogenFinder
- Bio::PDB::Model
- Bio::PDB::ModelFinder
- Bio::PDB::Record
- Bio::PDB::Record::ANISOU
- Bio::PDB::Record::ATOM
- Bio::PDB::Record::HETATM
- Bio::PDB::Record::Jrnl
- Bio::PDB::Record::Remark1
- Bio::PDB::Record::Remark2
- Bio::PDB::Residue
- Bio::PDB::ResidueFinder
- Bio::PDB::Utils
- Bio::PROSITE
- Bio::PSORT
- Bio::PSORT::CGIDriver
- Bio::PSORT::IPSORT
- Bio::PSORT::PSORT1
- Bio::PSORT::PSORT1::Remote
- Bio::PSORT::PSORT1::Report
- Bio::PSORT::PSORT2
- Bio::PSORT::PSORT2::Remote
- Bio::PSORT::PSORT2::Report
- Bio::PSORT::PSORTB
- Bio::PSORT::WoLF_PSORT
- Bio::PTS1
- Bio::PTS1::Report
- Bio::Pathway
- Bio::Phylip
- Bio::Phylip::DistanceMatrix
- Bio::Phylip::PhylipFormat
- Bio::PhyloXML
- Bio::PhyloXML::Accession
- Bio::PhyloXML::Annotation
- Bio::PhyloXML::BinaryCharacters
- Bio::PhyloXML::BranchColor
- Bio::PhyloXML::CladeRelation
- Bio::PhyloXML::Confidence
- Bio::PhyloXML::Date
- Bio::PhyloXML::Distribution
- Bio::PhyloXML::DomainArchitecture
- Bio::PhyloXML::Events
- Bio::PhyloXML::Id
- Bio::PhyloXML::Node
- Bio::PhyloXML::Other
- Bio::PhyloXML::Parser
- Bio::PhyloXML::Point
- Bio::PhyloXML::Polygon
- Bio::PhyloXML::Property
- Bio::PhyloXML::ProteinDomain
- Bio::PhyloXML::Reference
- Bio::PhyloXML::Sequence
- Bio::PhyloXML::SequenceRelation
- Bio::PhyloXML::Taxonomy
- Bio::PhyloXML::Tree
- Bio::PhyloXML::Uri
- Bio::PhyloXML::Writer
- Bio::Probcons
- Bio::Probcons::DEFAULT_PARSER
- Bio::PubMed
- Bio::REBASE
- Bio::RefSeq
- Bio::Reference
- Bio::References
- Bio::Registry
- Bio::Registry::DB
- Bio::RestrictionEnzyme
- Bio::RestrictionEnzyme::Analysis
- Bio::RestrictionEnzyme::CutSymbol
- Bio::RestrictionEnzyme::CutSymbol::CutSymbol__
- Bio::RestrictionEnzyme::DenseIntArray
- Bio::RestrictionEnzyme::DoubleStranded
- Bio::RestrictionEnzyme::DoubleStranded::AlignedStrands
- Bio::RestrictionEnzyme::DoubleStranded::CutLocationPair
- Bio::RestrictionEnzyme::DoubleStranded::CutLocationPairInEnzymeNotation
- Bio::RestrictionEnzyme::DoubleStranded::CutLocations
- Bio::RestrictionEnzyme::DoubleStranded::CutLocationsInEnzymeNotation
- Bio::RestrictionEnzyme::DoubleStranded::EnzymeAction
- Bio::RestrictionEnzyme::Fragments
- Bio::RestrictionEnzyme::Range
- Bio::RestrictionEnzyme::Range::CutRange
- Bio::RestrictionEnzyme::Range::CutRanges
- Bio::RestrictionEnzyme::Range::HorizontalCutRange
- Bio::RestrictionEnzyme::Range::SequenceRange
- Bio::RestrictionEnzyme::Range::SequenceRange::CalculatedCuts
- Bio::RestrictionEnzyme::Range::SequenceRange::Fragment
- Bio::RestrictionEnzyme::Range::SequenceRange::Fragments
- Bio::RestrictionEnzyme::Range::VerticalCutRange
- Bio::RestrictionEnzyme::SingleStrand
- Bio::RestrictionEnzyme::SingleStrand::CutLocationsInEnzymeNotation
- Bio::RestrictionEnzyme::SingleStrandComplement
- Bio::RestrictionEnzyme::SortedNumArray
- Bio::RestrictionEnzyme::StringFormatting
- Bio::SOAPWSDL
- Bio::SOFT
- Bio::SOSUI
- Bio::SOSUI::Report
- Bio::SOSUI::Report::TMH
- Bio::SPTR
- Bio::SQL
- Bio::SQL::Biodatabase
- Bio::SQL::Bioentry
- Bio::SQL::BioentryDbxref
- Bio::SQL::BioentryPath
- Bio::SQL::BioentryQualifierValue
- Bio::SQL::BioentryReference
- Bio::SQL::BioentryRelationship
- Bio::SQL::Biosequence
- Bio::SQL::Comment
- Bio::SQL::Dbxref
- Bio::SQL::DbxrefQualifierValue
- Bio::SQL::DummyBase
- Bio::SQL::Location
- Bio::SQL::LocationQualifierValue
- Bio::SQL::Ontology
- Bio::SQL::Reference
- Bio::SQL::Seqfeature
- Bio::SQL::SeqfeatureDbxref
- Bio::SQL::SeqfeaturePath
- Bio::SQL::SeqfeatureQualifierValue
- Bio::SQL::SeqfeatureRelationship
- Bio::SQL::Sequence
- Bio::SQL::Taxon
- Bio::SQL::TaxonName
- Bio::SQL::Term
- Bio::SQL::TermDbxref
- Bio::SQL::TermPath
- Bio::SQL::TermRelationship
- Bio::SQL::TermRelationshipTerm
- Bio::SQL::TermSynonym
- Bio::SangerChromatogram
- Bio::Scf
- Bio::Sequence
- Bio::Sequence::AA
- Bio::Sequence::Adapter
- Bio::Sequence::Adapter::BioSQL
- Bio::Sequence::Adapter::EMBL
- Bio::Sequence::Adapter::FastaFormat
- Bio::Sequence::Adapter::FastaNumericFormat
- Bio::Sequence::Adapter::Fastq
- Bio::Sequence::Adapter::GenBank
- Bio::Sequence::Adapter::SangerChromatogram
- Bio::Sequence::Common
- Bio::Sequence::DBLink
- Bio::Sequence::Format
- Bio::Sequence::Format::AminoFormatter
- Bio::Sequence::Format::Formatter
- Bio::Sequence::Format::Formatter::Fasta
- Bio::Sequence::Format::Formatter::Fasta_ncbi
- Bio::Sequence::Format::Formatter::Fasta_numeric
- Bio::Sequence::Format::Formatter::Fastq
- Bio::Sequence::Format::Formatter::Fastq_illumina
- Bio::Sequence::Format::Formatter::Fastq_sanger
- Bio::Sequence::Format::Formatter::Fastq_solexa
- Bio::Sequence::Format::Formatter::Qual
- Bio::Sequence::Format::Formatter::Raw
- Bio::Sequence::Format::FormatterBase
- Bio::Sequence::Format::INSDFeatureHelper
- Bio::Sequence::Format::NucFormatter
- Bio::Sequence::Format::NucFormatter::Embl
- Bio::Sequence::Format::NucFormatter::Genbank
- Bio::Sequence::NA
- Bio::Sequence::NA::MidiTrack
- Bio::Sequence::QualityScore
- Bio::Sequence::QualityScore::Converter
- Bio::Sequence::QualityScore::Phred
- Bio::Sequence::QualityScore::Solexa
- Bio::Sequence::SequenceMasker
- Bio::Shell
- Bio::Shell::ColoredCodonTable
- Bio::Shell::Core
- Bio::Shell::Demo
- Bio::Shell::Ghost
- Bio::Shell::Irb
- Bio::Shell::Private
- Bio::Shell::Script
- Bio::Shell::Setup
- Bio::Shell::Web
- Bio::Shell::Web::Results
- Bio::SiRNA
- Bio::SiRNA::Pair
- Bio::SiRNA::ShRNA
- Bio::Sim4
- Bio::Sim4::Report
- Bio::Sim4::Report::Hit
- Bio::Sim4::Report::Segment
- Bio::Sim4::Report::SegmentPair
- Bio::Sim4::Report::SeqDesc
- Bio::Spidey
- Bio::Spidey::Report
- Bio::Spidey::Report::Hit
- Bio::Spidey::Report::Segment
- Bio::Spidey::Report::SegmentPair
- Bio::Spidey::Report::SeqDesc
- Bio::SwissProt
- Bio::TMHMM
- Bio::TMHMM::Report
- Bio::TMHMM::TMH
- Bio::TRANSFAC
- Bio::TRANSFAC::CELL
- Bio::TRANSFAC::CLASS
- Bio::TRANSFAC::FACTOR
- Bio::TRANSFAC::GENE
- Bio::TRANSFAC::MATRIX
- Bio::TRANSFAC::SITE
- Bio::TargetP
- Bio::TargetP::Report
- Bio::Taxonomy
- Bio::Tcoffee
- Bio::Tcoffee::DEFAULT_PARSER
- Bio::TogoWS
- Bio::TogoWS::AccessWait
- Bio::TogoWS::REST
- Bio::TrEMBL
- Bio::Tree
- Bio::Tree::Edge
- Bio::Tree::NoPathError
- Bio::Tree::Node
- Bio::UniProt
- BiorubyController
- BiorubyGenerator
- BiorubyHelper
- Hash
- Object
- String

No matching classes.

# Bio::Pathway

Bio::Pathway is a general graph object initially constructed by the list of the ((<Bio::Relation>)) objects. The basic concept of the Bio::Pathway object is to store a graph as an adjacency list (in the instance variable @graph), and converting the list into an adjacency matrix by calling to_matrix method on demand. However, in some cases, it is convenient to have the original list of the ((<Bio::Relation>))s, Bio::Pathway object also stores the list (as the instance variable @relations) redundantly.

Note: you can clear the @relations list by calling clear_relations! method to reduce the memory usage, and the content of the @relations can be re-generated from the @graph by to_relations method.

### Attributes

graph[R]

Read-only accessor for the adjacency list of the graph.

index[R]

Read-only accessor for the row/column index (@index) of the adjacency matrix. Contents of the hash @index is created by calling to_matrix method.

label[RW]

Accessor for the hash of the label assigned to the each node. You can label some of the nodes in the graph by passing a hash to the label and select subgraphs which contain labeled nodes only by subgraph method.

    hash = { 1 => 'red', 2 => 'green', 5 => 'black' }
    g.label = hash
    g.label
    g.subgraph    # => new graph consists of the node 1, 2, 5 only

relations[R]

Read-only accessor for the internal list of the Bio::Relation objects

### Public Class Methods

new(relations, undirected = false) click to toggle source

Initial graph (adjacency list) generation from the list of Relation.

Generate Bio::Pathway object from the list of Bio::Relation objects. If the second argument is true, undirected graph is generated.

    r1 = Bio::Relation.new('a', 'b', 1)
    r2 = Bio::Relation.new('a', 'c', 5)
    r3 = Bio::Relation.new('b', 'c', 3)
    list = [ r1, r2, r3 ]
    g = Bio::Pathway.new(list, 'undirected')

    # File lib/bio/pathway.rb, line 41
    def initialize(relations, undirected = false)
      @undirected = undirected
      @relations = relations
      @graph = {}         # adjacency list expression of the graph
      @index = {}         # numbering each node in matrix
      @label = {}         # additional information on each node
      self.to_list                # generate adjacency list
    end

### Public Instance Methods

append(rel, add_rel = true) click to toggle source

Add an Bio::Relation object 'rel' to the @graph and @relations. If the second argument is false, @relations is not modified (only useful when genarating @graph from @relations internally).

    # File lib/bio/pathway.rb, line 144
    def append(rel, add_rel = true)
      @relations.push(rel) if add_rel
      if @graph[rel.from].nil?
        @graph[rel.from] = {}
      end
      if @graph[rel.to].nil?
        @graph[rel.to] = {}
      end
      @graph[rel.from][rel.to] = rel.relation
      @graph[rel.to][rel.from] = rel.relation if @undirected
    end

bellman_ford(root) click to toggle source

Bellman-Ford method for solving the single-source shortest-paths problem in the graph in which edge weights can be negative.

    # File lib/bio/pathway.rb, line 592
    def bellman_ford(root)
      distance, predecessor = initialize_single_source(root)
      for i in 1 ..(self.nodes - 1) do
        @graph.each_key do |u|
          @graph[u].each do |v, w|
            # relaxing procedure of root -> 'u' -> 'v'
            if distance[v] > distance[u] + w
              distance[v] = distance[u] + w
              predecessor[v] = u
            end
          end

bfs(root) click to toggle source

Alias for the breadth_first_search method.

Alias for: breadth_first_search
bfs_shortest_path(node1, node2) click to toggle source

Calculates the shortest path between two nodes by using breadth_first_search method and returns steps and the path as Array.

    # File lib/bio/pathway.rb, line 450
    def bfs_shortest_path(node1, node2)
      distance, route = breadth_first_search(node1)
      step = distance[node2]
      node = node2
      path = [ node2 ]
      while node != node1 and route[node]
        node = route[node]
        path.unshift(node)
      end
      return step, path
    end

breadth_first_search(root) click to toggle source

Breadth first search solves steps and path to the each node and forms a tree contains all reachable vertices from the root node. This method returns the result in 2 hashes - 1st one shows the steps from root node and 2nd hash shows the structure of the tree.

The weight of the edges are not considered in this method.

    # File lib/bio/pathway.rb, line 419
    def breadth_first_search(root)
      visited = {}
      distance = {}
      predecessor = {}

      visited[root] = true
      distance[root] = 0
      predecessor[root] = nil

      queue = [ root ]

      while from = queue.shift
        next unless @graph[from]
        @graph[from].each_key do |to|
          unless visited[to]
            visited[to] = true
            distance[to] = distance[from] + 1
            predecessor[to] = from
            queue.push(to)
          end
        end
      end
      return distance, predecessor
    end

Also aliased as: bfs
clear_relations!() click to toggle source

Clear @relations array to reduce the memory usage.

    # File lib/bio/pathway.rb, line 114
    def clear_relations!
      @relations.clear
    end

clique() click to toggle source

Not implemented yet.

    # File lib/bio/pathway.rb, line 370
    def clique
      raise NotImplementedError
    end

cliquishness(node) click to toggle source

Returns completeness of the edge density among the surrounded nodes.

Calculates the value of cliquishness around the 'node'. This value indicates completeness of the edge density among the surrounded nodes.

Note: cliquishness (clustering coefficient) for a directed graph is also calculated. Reference: en.wikipedia.org/wiki/Clustering_coefficient

Note: Cliquishness (clustering coefficient) for a node that has only one neighbor node is undefined. Currently, it returns NaN, but the behavior may be changed in the future.

    # File lib/bio/pathway.rb, line 388
    def cliquishness(node)
      neighbors = @graph[node].keys
      sg = subgraph(neighbors)
      if sg.graph.size != 0
        edges = sg.edges
        nodes = neighbors.size
        complete = (nodes * (nodes - 1))
        return edges.quo(complete)
      else
        return 0.0
      end
    end

common_subgraph(graph) click to toggle source

Not implemented yet.

    # File lib/bio/pathway.rb, line 364
    def common_subgraph(graph)
      raise NotImplementedError
    end

delete(rel) click to toggle source

Remove an edge indicated by the Bio::Relation object 'rel' from the @graph and the @relations.

    # File lib/bio/pathway.rb, line 158
    def delete(rel)
      @relations.delete_if do |x|
        x === rel
      end
      @graph[rel.from].delete(rel.to)
      @graph[rel.to].delete(rel.from) if @undirected
    end

depth_first_search() click to toggle source

Depth first search yields much information about the structure of the graph especially on the classification of the edges. This method returns 5 hashes - 1st one shows the timestamps of each node containing the first discoverd time and the search finished time in an array. The 2nd, 3rd, 4th, and 5th hashes contain 'tree edges', 'back edges', 'cross edges', 'forward edges' respectively.

If $DEBUG is true (e.g. ruby -d), this method prints the progression of the search.

The weight of the edges are not considered in this method.

Note: The result of this method depends on the order of Hash#each (and each_key, etc.), which may be variable with Ruby version and Ruby interpreter variations (JRuby, etc.). For a workaround to remove such dependency, you can use @index to set order of Hash keys. Note that this bahavior might be changed in the future.

    # File lib/bio/pathway.rb, line 481
    def depth_first_search
      visited = {}
      timestamp = {}
      tree_edges = {}
      back_edges = {}
      cross_edges = {}
      forward_edges = {}
      count = 0

      # begin workaround removing depencency to order of Hash#each
      if @index.empty? then
        preference_of_nodes = nil
      else
        preference_of_nodes = {}.merge(@index)
        i = preference_of_nodes.values.max
        @graph.each_key do |node0|
          preference_of_nodes[node0] ||= (i += 1)
        end
      end
      # end workaround removing depencency to order of Hash#each

      dfs_visit = Proc.new { |from|
        visited[from] = true
        timestamp[from] = [count += 1]
        ary = @graph[from].keys
        # begin workaround removing depencency to order of Hash#each
        if preference_of_nodes then
          ary = ary.sort_by { |node0| preference_of_nodes[node0] }
        end
        # end workaround removing depencency to order of Hash#each
        ary.each do |to|
          if visited[to]
            if timestamp[to].size > 1
              if timestamp[from].first < timestamp[to].first
          # forward edge (black)
          p "#{from} -> #{to} : forward edge" if $DEBUG
          forward_edges[from] = to
              else
          # cross edge (black)
          p "#{from} -> #{to} : cross edge" if $DEBUG
          cross_edges[from] = to
              end
            else
              # back edge (gray)
              p "#{from} -> #{to} : back edge" if $DEBUG
              back_edges[from] = to
            end
          else
            # tree edge (white)
            p "#{from} -> #{to} : tree edge" if $DEBUG
            tree_edges[to] = from
            dfs_visit.call(to)
          end
        end
        timestamp[from].push(count += 1)
      }

      ary = @graph.keys
      # begin workaround removing depencency to order of Hash#each
      if preference_of_nodes then
        ary = ary.sort_by { |node0| preference_of_nodes[node0] }
      end
      # end workaround removing depencency to order of Hash#each
      ary.each do |node|
        unless visited[node]
          dfs_visit.call(node)
        end
      end
      return timestamp, tree_edges, back_edges, cross_edges, forward_edges
    end

Also aliased as: dfs
dfs() click to toggle source

Alias for the depth_first_search method.

Alias for: depth_first_search
dfs_topological_sort() click to toggle source

Topological sort of the directed acyclic graphs ("dags") by using depth_first_search.

    # File lib/bio/pathway.rb, line 558
    def dfs_topological_sort
      # sorted by finished time reversely and collect node names only
      timestamp, = self.depth_first_search
      timestamp.sort {|a,b| b[1][1] <=> a[1][1]}.collect {|x| x.first }
    end

dijkstra(root) click to toggle source

Dijkstra method to solve the shortest path problem in the weighted graph.

    # File lib/bio/pathway.rb, line 566
    def dijkstra(root)
      distance, predecessor = initialize_single_source(root)
      @graph[root].each do |k, v|
        distance[k] = v
        predecessor[k] = root
      end
      queue = distance.dup
      queue.delete(root)

      while queue.size != 0
        min = queue.min {|a, b| a[1] <=> b[1]}
        u = min[0]                # extranct a node having minimal distance
        @graph[u].each do |k, v|
          # relaxing procedure of root -> 'u' -> 'k'
          if distance[k] > distance[u] + v
            distance[k] = distance[u] + v
            predecessor[k] = u
          end
        end
        queue.delete(u)
      end
      return distance, predecessor
    end

directed() click to toggle source

Changes the internal state of the graph from 'undirected' to 'directed' and re-generate adjacency list. The undirected graph can be converted to directed graph, however, the edge between two nodes will be simply doubled to both ends.

Note: this method can not be used without the list of the Bio::Relation objects (internally stored in @relations variable). Thus if you already called clear_relations! method, call to_relations first.

    # File lib/bio/pathway.rb, line 92
    def directed
      if undirected?
        @undirected = false
        self.to_list
      end
    end

directed?() click to toggle source

Returns true or false respond to the internal state of the graph.

    # File lib/bio/pathway.rb, line 74
    def directed?
      @undirected ? false : true
    end

dump_list() click to toggle source

Pretty printer of the adjacency list.

Useful when you want to check the internal state of the adjacency list (for debug purpose etc.) easily.

The result of this method depends on the order of Hash#each (and each_key, etc.), which may be variable with Ruby version and Ruby interpreter variations (JRuby, etc.). For a workaround to remove such dependency, you can use @index to set order of Hash keys. Note that this behavior might be changed in the future.

    # File lib/bio/pathway.rb, line 293
    def dump_list
      # begin workaround removing depencency to order of Hash#each
      if @index.empty? then
        pref = nil
        enum = @graph
      else
        pref = {}.merge(@index)
        i = pref.values.max
        @graph.each_key do |node|
          pref[node] ||= (i += 1)
        end
        graph_to_a = @graph.to_a
        graph_to_a.sort! { |x, y| pref[x[0]] <=> pref[y[0]] }
        enum = graph_to_a
      end
      # end workaround removing depencency to order of Hash#each

      list = ""
      enum.each do |from, hash|
        list << "#{from} => "
        # begin workaround removing depencency to order of Hash#each
        if pref then
          ary = hash.to_a
          ary.sort! { |x,y| pref[x[0]] <=> pref[y[0]] }
          hash = ary
        end
        # end workaround removing depencency to order of Hash#each
        a = []
        hash.each do |to, relation|
          a.push("#{to} (#{relation})")
        end
        list << a.join(", ") + "\n"
      end
      list
    end

dump_matrix(*arg) click to toggle source

Pretty printer of the adjacency matrix.

The dump_matrix method accepts the same arguments as to_matrix. Useful when you want to check the internal state of the matrix (for debug purpose etc.) easily.

This method internally calls to_matrix method. Read documents of to_matrix for important informations.

    # File lib/bio/pathway.rb, line 274
    def dump_matrix(*arg)
      matrix = self.to_matrix(*arg)
      sorted = @index.sort {|a,b| a[1] <=> b[1]}
      "[# " + sorted.collect{|x| x[0]}.join(", ") + "\n" +
        matrix.to_a.collect{|row| ' ' + row.inspect}.join(",\n") + "\n]"
    end

edges() click to toggle source

Returns the number of the edges in the graph.

    # File lib/bio/pathway.rb, line 172
    def edges
      edges = 0
      @graph.each_value do |v|
        edges += v.size
      end
      edges
    end

nodes() click to toggle source

Returns the number of the nodes in the graph.

    # File lib/bio/pathway.rb, line 167
    def nodes
      @graph.keys.length
    end

small_world() click to toggle source

Returns frequency of the nodes having same number of edges as hash

Calculates the frequency of the nodes having the same number of edges and returns the value as Hash.

    # File lib/bio/pathway.rb, line 405
    def small_world
      freq = Hash.new(0)
      @graph.each_value do |v|
        freq[v.size] += 1
      end
      return freq
    end

subgraph(list = nil) click to toggle source

Select labeled nodes and generate subgraph

This method select some nodes and returns new Bio::Pathway object consists of selected nodes only. If the list of the nodes (as Array) is assigned as the argument, use the list to select the nodes from the graph. If no argument is assigned, internal property of the graph @label is used to select the nodes.

    hash = { 'a' => 'secret', 'b' => 'important', 'c' => 'important' }
    g.label = hash
    g.subgraph
    list = [ 'a', 'b', 'c' ]
     g.subgraph(list)

    # File lib/bio/pathway.rb, line 343
    def subgraph(list = nil)
      if list
        @label.clear
        list.each do |node|
          @label[node] = true
        end
      end
      sub_graph = Pathway.new([], @undirected)
      @graph.each do |from, hash|
        next unless @label[from]
        sub_graph.graph[from] ||= {}
        hash.each do |to, relation|
          next unless @label[to]
          sub_graph.append(Relation.new(from, to, relation))
        end
      end
      return sub_graph
    end

to_list() click to toggle source

Graph (adjacency list) generation from the Relations

Generate the adjcancecy list @graph from @relations (called by initialize and in some other cases when @relations has been changed).

    # File lib/bio/pathway.rb, line 134
    def to_list
      @graph.clear
      @relations.each do |rel|
        append(rel, false)        # append to @graph without push to @relations
      end
    end

to_matrix(default_value = nil, diagonal_value = nil) click to toggle source

Convert adjacency list to adjacency matrix

Returns the adjacency matrix expression of the graph as a Matrix object. If the first argument was assigned, the matrix will be filled with the given value. The second argument indicates the value of the diagonal constituents of the matrix besides the above.

The result of this method depends on the order of Hash#each (and each_key, etc.), which may be variable with Ruby version and Ruby interpreter variations (JRuby, etc.). For a workaround to remove such dependency, you can use @index to set order of Hash keys. Note that this behavior might be changed in the future. Be careful that @index is overwritten by this method.

    # File lib/bio/pathway.rb, line 196
    def to_matrix(default_value = nil, diagonal_value = nil)

      #--
      # Note: following code only fills the outer Array with the reference
      # to the same inner Array object.
      #
      #   matrix = Array.new(nodes, Array.new(nodes))
      #
      # so create a new Array object for each row as follows:
      #++

      matrix = Array.new
      nodes.times do
        matrix.push(Array.new(nodes, default_value))
      end

      if diagonal_value
        nodes.times do |i|
          matrix[i][i] = diagonal_value
        end
      end

      # assign index number
      if @index.empty? then
        # assign index number for each node
        @graph.keys.each_with_index do |k, i|
          @index[k] = i
        end
      else
        # begin workaround removing depencency to order of Hash#each
        # assign index number from the preset @index
        indices = @index.to_a
        indices.sort! { |i0, i1| i0[1] <=> i1[1] }
        indices.collect! { |i0| i0[0] }
        @index.clear
        v = 0
        indices.each do |k, i|
          if @graph[k] and !@index[k] then
            @index[k] = v; v += 1
          end
        end
        @graph.each_key do |k|
          unless @index[k] then
            @index[k] = v; v += 1
          end
        end
        # end workaround removing depencency to order of Hash#each
      end

      if @relations.empty?                # only used after clear_relations!
        @graph.each do |from, hash|
          hash.each do |to, relation|
            x = @index[from]
            y = @index[to]
            matrix[x][y] = relation
          end
        end
      else
        @relations.each do |rel|
          x = @index[rel.from]
          y = @index[rel.to]
          matrix[x][y] = rel.relation
          matrix[y][x] = rel.relation if @undirected
        end
      end
      Matrix[*matrix]
    end

to_relations() click to toggle source

Reconstruct @relations from the adjacency list @graph.

    # File lib/bio/pathway.rb, line 119
    def to_relations
      @relations.clear
      @graph.each_key do |from|
        @graph[from].each do |to, w|
          @relations << Relation.new(from, to, w)
        end
      end
      return @relations
    end

undirected() click to toggle source

Changes the internal state of the graph from 'directed' to 'undirected' and re-generate adjacency list.

Note: this method can not be used without the list of the Bio::Relation objects (internally stored in @relations variable). Thus if you already called clear_relations! method, call to_relations first.

    # File lib/bio/pathway.rb, line 106
    def undirected
      if directed?
        @undirected = true
        self.to_list
      end
    end

undirected?() click to toggle source

Returns true or false respond to the internal state of the graph.

    # File lib/bio/pathway.rb, line 79
    def undirected?
      @undirected ? true : false
    end

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