### Home Classes Methods

### In Files

- lib/bio/reference.rb

### Parent

Object

### Methods

- ::new
- #==
- #bibitem
- #bibtex
- #cell
- #current
- #embl
- #endnote
- #format
- #general
- #genome_biol
- #genome_res
- #nar
- #nature
- #pubmed_url
- #rd
- #science
- #trends

### 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
- Bio::Alignment::EnumerableExtension
- 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
- Bio::Alignment::OriginalPrivate
- Bio::Alignment::Output
- Bio::Alignment::PropertyMethods
- Bio::Alignment::SequenceArray
- Bio::Alignment::SequenceHash
- Bio::Alignment::Site
- Bio::Alignment::SiteMethods
- Bio::AminoAcid
- Bio::AminoAcid::Data
- Bio::Blast
- Bio::Blast::Bl2seq
- Bio::Blast::Bl2seq::Report
- Bio::Blast::Bl2seq::Report::HSP
- Bio::Blast::Bl2seq::Report::Hit
- Bio::Blast::Bl2seq::Report::Iteration
- Bio::Blast::Default
- Bio::Blast::Default::Report
- Bio::Blast::Default::Report::HSP
- Bio::Blast::Default::Report::Hit
- Bio::Blast::Default::Report::Iteration
- Bio::Blast::Default::Report_TBlast
- Bio::Blast::Fastacmd
- Bio::Blast::NCBIOptions
- Bio::Blast::RPSBlast
- Bio::Blast::RPSBlast::RPSBlastSplitter
- Bio::Blast::RPSBlast::Report
- Bio::Blast::RPSBlast::Report::FLATFILE_SPLITTER
- Bio::Blast::RPSBlast::Report::Iteration
- Bio::Blast::Remote
- Bio::Blast::Remote::DDBJ
- Bio::Blast::Remote::DDBJ::Information
- Bio::Blast::Remote::Ddbj
- Bio::Blast::Remote::GenomeNet
- Bio::Blast::Remote::GenomeNet::Information
- Bio::Blast::Remote::Genomenet
- Bio::Blast::Remote::Information
- Bio::Blast::Report
- Bio::Blast::Report::BlastXmlSplitter
- Bio::Blast::Report::FLATFILE_SPLITTER
- Bio::Blast::Report::Hit
- Bio::Blast::Report::Hsp
- Bio::Blast::Report::Iteration
- Bio::Blast::Report_tab
- Bio::Blast::WU
- Bio::Blast::WU::Report
- Bio::Blast::WU::Report::HSP
- Bio::Blast::WU::Report::Hit
- Bio::Blast::WU::Report::Iteration
- Bio::Blast::WU::Report_TBlast
- Bio::Blat
- Bio::Blat::Report
- Bio::Blat::Report::FLATFILE_SPLITTER
- Bio::Blat::Report::Hit
- Bio::Blat::Report::SegmentPair
- Bio::Blat::Report::SeqDesc
- Bio::ClustalW
- Bio::ClustalW::Report
- Bio::CodonTable
- Bio::ColorScheme
- Bio::Command
- Bio::Command::Tmpdir
- Bio::Command::Tmpdir::Remover
- 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
- Bio::DAS::TARGET
- 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::FLATFILE_SPLITTER
- 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::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::Reference

# DESCRIPTION

A class for journal reference information.

# USAGE

    hash = {'authors' => [ "Hoge, J.P.", "Fuga, F.B." ],
            'title' => "Title of the study.",
            'journal' => "Theor. J. Hoge",
            'volume' => 12,
            'issue' => 3,
            'pages' => "123-145",
            'year' => 2001,
            'pubmed' => 12345678,
            'medline' => 98765432,
            'abstract' => "Hoge fuga. ...",
            'url' => "http://example.com",
            'mesh' => [],
            'affiliations' => []}
    ref = Bio::Reference.new(hash)

    # Formats in the BiBTeX style.
    ref.format("bibtex")

    # Short-cut for Bio::Reference#format("bibtex")
    ref.bibtex

### Attributes

abstract[R]

Abstract text in String.

affiliations[R]

Affiliations in an Array.

authors[R]

Author names in an Array, [ "Hoge, J.P.", "Fuga, F.B." ].

comments[R]

Comments for the reference (typically Array of String, or nil)

doi[R]

DOI identifier (typically String, e.g. "10.1126/science.1110418")

embl_gb_record_number[R]

Sequence number in EMBL/GenBank records

issue[R]

issue number (typically Fixnum)

journal[R]

String with journal name

medline[R]

medline identifier (typically Fixnum)

mesh[R]

MeSH terms in an Array.

pages[R]

page range (typically String, e.g. "123-145")

pubmed[R]

pubmed identifier (typically Fixnum)

sequence_position[R]

Position in a sequence that this reference refers to

title[R]

String with title of the study

url[R]

An URL String.

volume[R]

volume number (typically Fixnum)

year[R]

year of publication (typically Fixnum)

### Public Class Methods

new(hash) click to toggle source

Create a new Bio::Reference object from a Hash of values. Data is extracted from the values for keys:

- authors - expected value: Array of Strings

- title - expected value: String

- journal - expected value: String

- volume - expected value: Fixnum or String

- issue - expected value: Fixnum or String

- pages - expected value: String

- year - expected value: Fixnum or String

- pubmed - expected value: Fixnum or String

- medline - expected value: Fixnum or String

- abstract - expected value: String

- url - expected value: String

- mesh - expected value: Array of Strings

- affiliations - expected value: Array of Strings

      hash = {'authors' => [ "Hoge, J.P.", "Fuga, F.B." ],
              'title' => "Title of the study.",
              'journal' => "Theor. J. Hoge",
              'volume' => 12,
              'issue' => 3,
              'pages' => "123-145",
              'year' => 2001,
              'pubmed' => 12345678,
              'medline' => 98765432,
              'abstract' => "Hoge fuga. ...",
              'url' => "http://example.com",
              'mesh' => [],
              'affiliations' => []}
      ref = Bio::Reference.new(hash)

Arguments:

- (required) hash: Hash

Returns | Bio::Reference object

    # File lib/bio/reference.rb, line 133
    def initialize(hash)
      @authors  = hash['authors'] || [] # [ "Hoge, J.P.", "Fuga, F.B." ]
      @title    = hash['title']   || '' # "Title of the study."
      @journal  = hash['journal'] || '' # "Theor. J. Hoge"
      @volume   = hash['volume']  || '' # 12
      @issue    = hash['issue']   || '' # 3
      @pages    = hash['pages']   || '' # 123-145
      @year     = hash['year']    || '' # 2001
      @pubmed   = hash['pubmed']  || '' # 12345678
      @medline  = hash['medline'] || '' # 98765432
      @doi      = hash['doi']
      @abstract = hash['abstract'] || ''
      @url      = hash['url']
      @mesh     = hash['mesh'] || []
      @embl_gb_record_number = hash['embl_gb_record_number'] || nil
      @sequence_position = hash['sequence_position'] || nil
      @comments  = hash['comments']
      @affiliations = hash['affiliations'] || []
    end

### Public Instance Methods

==(other) click to toggle source

If other is equal with the self, returns true. Otherwise, returns false.

Arguments:

- (required) other: any object

Returns | true or false

    # File lib/bio/reference.rb, line 159
    def ==(other)
      return true if super(other)
      return false unless other.instance_of?(self.class)
      flag = false
      [ :authors, :title, :journal, :volume, :issue, :pages,
        :year, :pubmed, :medline, :doi, :abstract,
        :url, :mesh, :embl_gb_record_number,
        :sequence_position, :comments, :affiliations ].each do |m|
        begin
          flag = (self.__send__(m) == other.__send__(m))
        rescue NoMethodError, ArgumentError, NameError
          flag = false
        end
        break unless flag
      end
      flag
    end

bibitem(item = nil) click to toggle source

Returns reference formatted in the bibitem style

    # ref is a Bio::Reference object
    puts ref.bibitem

      \bibitem{PMID:12345678}
      Hoge, J.P., Fuga, F.B.
      Title of the study.,
      {\em Theor. J. Hoge}, 12(3):123--145, 2001.

Arguments:

- (optional) item: label string (default: `"PMID:#{pubmed}"`).

Returns | String

    # File lib/bio/reference.rb, line 316
    def bibitem(item = nil)
      item  = "PMID:#{@pubmed}" unless item
      pages = @pages.sub('-', '--')
      return         \\bibitem{#{item}}        #{@authors.join(', ')}        #{@title},        {\\em #{@journal}}, #{@volume}(#{@issue}):#{pages}, #{@year}..enum_for(:each_line).collect {|line| line.strip}.join("\n")
    end

bibtex(section = nil, label = nil, keywords = {}) click to toggle source

Returns reference formatted in the BiBTeX style.

    # ref is a Bio::Reference object
    puts ref.bibtex

      @article{PMID:12345678,
        author  = {Hoge, J.P. and Fuga, F.B.},
        title   = {Title of the study.},
        journal = {Theor. J. Hoge},
        year    = {2001},
        volume  = {12},
        number  = {3},
        pages   = {123--145},
      }

    # using a different section (e.g. "book")
    # (but not really configured for anything other than articles)
    puts ref.bibtex("book")

      @book{PMID:12345678,
        author  = {Hoge, J.P. and Fuga, F.B.},
        title   = {Title of the study.},
        journal = {Theor. J. Hoge},
        year    = {2001},
        volume  = {12},
        number  = {3},
        pages   = {123--145},
      }

Arguments:

- (optional) section: BiBTeX section as String

- (optional) label: Label string cited by LaTeX documents.

      Default is <tt>"PMID:#{pubmed}"</tt>.

- (optional) keywords: Hash of additional keywords,

      e.g. { 'abstract' => 'This is abstract.' }.
      You can also override default keywords.
      To disable default keywords, specify false as
      value, e.g. { 'url' => false, 'year' => false }.

Returns | String

    # File lib/bio/reference.rb, line 366
    def bibtex(section = nil, label = nil, keywords = {})
      section = "article" unless section
      authors = authors_join(' and ', ' and ')
      thepages = pages.to_s.empty? ? nil : pages.sub(/\-/, '--')
      unless label then
        label = "PMID:#{pubmed}"
      end
      theurl = if !(url.to_s.empty?) then
                 url
               elsif pmurl = pubmed_url and !(pmurl.to_s.empty?) then
                 pmurl
               else
                 nil
               end
      hash = {
        'author'  => authors.empty?    ? nil : authors,
        'title'   => title.to_s.empty? ? nil : title,
        'number'  => issue.to_s.empty? ? nil : issue,
        'pages'   => thepages,
        'url'     => theurl
      }
      keys = %( author title journal year volume number pages url )
      keys.each do |k|
        hash[k] = self.__send__(k.intern) unless hash.has_key?(k)
      end
      hash.merge!(keywords) { |k, v1, v2| v2.nil? ? v1 : v2 }
      bib = [ "@#{section}{#{label}," ]
      keys.concat((hash.keys - keys).sort)
      keys.each do |kw|
        ref = hash[kw]
        bib.push "  #{kw.ljust(12)} = {#{ref}}," if ref
      end
      bib.push "}\n"
      return bib.join("\n")
    end

cell() click to toggle source

Returns reference formatted in the CELL Press style.

    # ref is a Bio::Reference object
    puts ref.cell

      Hoge, J.P. and Fuga, F.B. (2001). Title of the study. Theor. J. Hoge 12, 123-145.

Returns | String

    # File lib/bio/reference.rb, line 560
    def cell
      authors = authors_join(' and ')
      "#{authors} (#{@year}). #{@title} #{@journal} #{@volume}, #{pages}."
    end

current() click to toggle source

Returns reference formatted in the Current Biology (current-biology.com) style. (Same as the Genome Biology style)

    # ref is a Bio::Reference object
    puts ref.current

      Hoge JP, Fuga FB: Title of the study. Theor J Hoge 2001, 12:123-145.

Returns | String

    # File lib/bio/reference.rb, line 518
    def current
      self.genome_biol
    end

embl() click to toggle source

Returns reference formatted in the EMBL style.

    # ref is a Bio::Reference object
    puts ref.embl

      RP   1-1859
      RX   PUBMED; 1907511.
      RA   Oxtoby E., Dunn M.A., Pancoro A., Hughes M.A.;
      RT   "Nucleotide and derived amino acid sequence of the cyanogenic
      RT   beta-glucosidase (linamarase) from white clover (Trifolium repens L.)";
      RL   Plant Mol. Biol. 17(2):209-219(1991).

    # File lib/bio/reference.rb, line 296
    def embl
      r = self
      Bio::Sequence::Format::NucFormatter::Embl.new('').instance_eval {
        reference_format_embl(r)
      }
    end

endnote() click to toggle source

Returns reference formatted in the Endnote style.

    # ref is a Bio::Reference object
    puts ref.endnote

      %0 Journal Article
      %A Hoge, J.P.
      %A Fuga, F.B.
      %D 2001
      %T Title of the study.
      %J Theor. J. Hoge
      %V 12
      %N 3
      %P 123-145
      %M 12345678
      %U http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12345678
      %X Hoge fuga. ...

Returns | String

    # File lib/bio/reference.rb, line 262
    def endnote
      lines = []
      lines << "%0 Journal Article"
      @authors.each do |author|
        lines << "%A #{author}"
      end
      lines << "%D #{@year}" unless @year.to_s.empty?
      lines << "%T #{@title}" unless @title.empty?
      lines << "%J #{@journal}" unless @journal.empty?
      lines << "%V #{@volume}" unless @volume.to_s.empty?
      lines << "%N #{@issue}" unless @issue.to_s.empty?
      lines << "%P #{@pages}" unless @pages.empty?
      lines << "%M #{@pubmed}" unless @pubmed.to_s.empty?
      u = @url.to_s.empty? ? pubmed_url : @url
      lines << "%U #{u}" unless u.empty?
      lines << "%X #{@abstract}" unless @abstract.empty?
      @mesh.each do |term|
        lines << "%K #{term}"
      end
      lines << "%+ #{@affiliations.join(' ')}" unless @affiliations.empty?
      return lines.join("\n")
    end

format(style = nil, *options) click to toggle source

Formats the reference in a given style.

Styles:

1. nil - general

2. endnote - Endnote

3. bibitem - Bibitem (option available)

4. bibtex - BiBTeX (option available)

5. rd - rd (option available)

6. nature - Nature (option available)

7. science - Science

8. genome_biol - Genome Biology

9. genome_res - Genome Research

10. nar - Nucleic Acids Research

11. current - Current Biology

12. trends - Trends in *

13. cell - Cell Press

See individual methods for details. Basic usage is:

    # ref is Bio::Reference object
    # using simplest possible call (for general style)
    puts ref.format

    # output in Nature style
    puts ref.format("nature")      # alternatively, puts ref.nature

    # output in Nature short style (see Bio::Reference#nature)
    puts ref.format("nature",true) # alternatively, puts ref.nature(true)

Arguments:

- (optional) style: String with style identifier

- (optional) options: Options for styles accepting one

Returns | String

    # File lib/bio/reference.rb, line 210
    def format(style = nil, *options)
      case style
      when 'embl'
        return embl
      when 'endnote'
        return endnote
      when 'bibitem'
        return bibitem(*options)
      when 'bibtex'
        return bibtex(*options)
      when 'rd'
        return rd(*options)
      when /^nature$/
        return nature(*options)
      when /^science$/
        return science
      when /^genome\s*_*biol/
        return genome_biol
      when /^genome\s*_*res/
        return genome_res
      when /^nar$/
        return nar
      when /^current/
        return current
      when /^trends/
        return trends
      when /^cell$/
        return cell
      else
        return general
      end
    end

general() click to toggle source

Returns reference formatted in a general/generic style.

    # ref is a Bio::Reference object
    puts ref.general

      Hoge, J.P., Fuga, F.B. (2001). "Title of the study." Theor. J. Hoge 12:123-145.

Returns | String

    # File lib/bio/reference.rb, line 410
    def general
      authors = @authors.join(', ')
      "#{authors} (#{@year}). \"#{@title}\" #{@journal} #{@volume}:#{@pages}."
    end

genome_biol() click to toggle source

Returns reference formatted in the Genome Biology (genomebiology.com) style.

    # ref is a Bio::Reference object
    puts ref.genome_biol

      Hoge JP, Fuga FB: Title of the study. Theor J Hoge 2001, 12:123-145.

Returns | String

    # File lib/bio/reference.rb, line 503
    def genome_biol
      authors = @authors.collect {|name| strip_dots(name)}.join(', ')
      journal = strip_dots(@journal)
      "#{authors}: #{@title} #{journal} #{@year}, #{@volume}:#{@pages}."
    end

genome_res() click to toggle source

Returns reference formatted in the Genome Research (genome.org) style.

    # ref is a Bio::Reference object
    puts ref.genome_res

      Hoge, J.P. and Fuga, F.B. 2001.
        Title of the study. Theor. J. Hoge 12: 123-145.

Returns | String

    # File lib/bio/reference.rb, line 532
    def genome_res
      authors = authors_join(' and ')
      "#{authors} #{@year}.\n  #{@title} #{@journal} #{@volume}: #{@pages}."
    end

nar() click to toggle source

Returns reference formatted in the Nucleic Acids Reseach (nar.oxfordjournals.org) style.

    # ref is a Bio::Reference object
    puts ref.nar

      Hoge, J.P. and Fuga, F.B. (2001) Title of the study. Theor. J. Hoge, 12, 123-145.

Returns | String

    # File lib/bio/reference.rb, line 546
    def nar
      authors = authors_join(' and ')
      "#{authors} (#{@year}) #{@title} #{@journal}, #{@volume}, #{@pages}."
    end

nature(short = false) click to toggle source

Formats in the Nature Publishing Group (www.nature.com) style.

    # ref is a Bio::Reference object
    puts ref.nature

      Hoge, J.P. & Fuga, F.B. Title of the study. Theor. J. Hoge 12, 123-145 (2001).

    # optionally, output short version
    puts ref.nature(true)  # or puts ref.nature(short=true)

      Hoge, J.P. & Fuga, F.B. Theor. J. Hoge 12, 123-145 (2001).

Arguments:

- (optional) short: Boolean (default false)

Returns | String

    # File lib/bio/reference.rb, line 459
    def nature(short = false)
      if short
        if @authors.size > 4
          authors = "#{@authors[0]} et al."
        elsif @authors.size == 1
          authors = "#{@authors[0]}"
        else
          authors = authors_join(' & ')
        end
        "#{authors} #{@journal} #{@volume}, #{@pages} (#{@year})."
      else
        authors = authors_join(' & ')
        "#{authors} #{@title} #{@journal} #{@volume}, #{@pages} (#{@year})."
      end
    end

pubmed_url() click to toggle source

Returns a valid URL for pubmed records

Returns | String

    # File lib/bio/reference.rb, line 588
    def pubmed_url
      unless @pubmed.to_s.empty?
        head = "http://www.ncbi.nlm.nih.gov/pubmed"
        return "#{head}/#{@pubmed}"
      end
      ''
    end

rd(str = nil) click to toggle source

Return reference formatted in the RD style.

    # ref is a Bio::Reference object
    puts ref.rd

      == Title of the study.

      * Hoge, J.P. and Fuga, F.B.

      * Theor. J. Hoge 2001 12:123-145 [PMID:12345678]

      Hoge fuga. ...

An optional string argument can be supplied, but does nothing.

Arguments:

- (optional) str: String (default nil)

Returns | String

    # File lib/bio/reference.rb, line 433
    def rd(str = nil)
      @abstract ||= str
      lines = []
      lines << "== " + @title
      lines << "* " + authors_join(' and ')
      lines << "* #{@journal} #{@year} #{@volume}:#{@pages} [PMID:#{@pubmed}]"
      lines << @abstract
      return lines.join("\n\n")
    end

science() click to toggle source

Returns reference formatted in the Science style.

    # ref is a Bio::Reference object
    puts ref.science

      J.P. Hoge, F.B. Fuga, Theor. J. Hoge 12 123 (2001).

Returns | String

    # File lib/bio/reference.rb, line 484
    def science
      if @authors.size > 4
        authors = rev_name(@authors[0]) + " et al."
      else
        authors = @authors.collect {|name| rev_name(name)}.join(', ')
      end
      page_from, = @pages.split('-')
      "#{authors}, #{@journal} #{@volume} #{page_from} (#{@year})."
    end

trends() click to toggle source

Returns reference formatted in the TRENDS style.

    # ref is a Bio::Reference object
    puts ref.trends

      Hoge, J.P. and Fuga, F.B. (2001) Title of the study. Theor. J. Hoge 12, 123-145

Returns | String

    # File lib/bio/reference.rb, line 574
    def trends
      if @authors.size > 2
        authors = "#{@authors[0]} et al."
      elsif @authors.size == 1
        authors = "#{@authors[0]}"
      else
        authors = authors_join(' and ')
      end
      "#{authors} (#{@year}) #{@title} #{@journal} #{@volume}, #{@pages}"
    end

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