### Home Classes Methods

### In Files

- lib/bio/alignment.rb

### Methods

- #alignment_collect
- #alignment_concat
- #alignment_length
- #alignment_lstrip!
- #alignment_normalize!
- #alignment_rstrip!
- #alignment_site
- #alignment_slice
- #alignment_strip!
- #alignment_subseq
- #alignment_window
- #collect_each_site
- #consensus_each_site
- #consensus_iupac
- #consensus_string
- #convert_match
- #convert_unmatch
- #each_seq
- #each_site
- #each_site_step
- #each_window
- #lstrip!
- #match_line
- #match_line_amino
- #match_line_nuc
- #normalize!
- #number_of_sequences
- #remove_all_gaps!
- #rstrip!
- #seq_length
- #seqclass
- #sequence_names
- #slice
- #strip!
- #subseq
- #window

### Included Modules

- Bio::Alignment::PropertyMethods
- Bio::Alignment::Output

### Files

- KNOWN_ISSUES.rdoc
- 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::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::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::Muscle::DEFAULT_PARSER
- 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::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::Alignment::EnumerableExtension

The module Bio::Alignment::EnumerableExtension is a set of useful methods for multiple sequence alignment. It can be included by any classes or can be extended to any objects. The classes or objects must have methods defined in Enumerable, and must have the `each` method which iterates over each sequence (or string) and yields a sequence (or string) object.

Optionally, if `each_seq` method is defined, which iterates over each sequence (or string) and yields each sequence (or string) object, it is used instead of `each`.

Note that the `each` or `each_seq` method would be called multiple times. This means that the module is not suitable for IO objects. In addition, `break` would be used in the given block and destructive methods would be used to the sequences.

For Array or Hash objects, you'd better using ArrayExtension or HashExtension modules, respectively. They would have built-in `each_seq` method and/or some methods would be redefined.

### Public Instance Methods

alignment_collect() click to toggle source

Iterates over each sequence and results running blocks are collected and returns a new alignment as a Bio::Alignment::SequenceArray object.

Note that it would be redefined if you want to change return value's class.

    # File lib/bio/alignment.rb, line 445
    def alignment_collect
      a = SequenceArray.new
      a.set_all_property(get_all_property)
      each_seq do |str|
        a << yield(str)
      end
      a
    end

alignment_concat(align) click to toggle source

Concatenates the given alignment. align must have `each_seq` or `each` method.

Returns self.

Note that it is a destructive method.

For Hash, please use it carefully because the order of the sequences is inconstant and key information is completely ignored.

    # File lib/bio/alignment.rb, line 849
    def alignment_concat(align)
      flag = nil
      a = []
      each_seq { |s| a << s }
      i = 0
      begin
        align.each_seq do |seq|
          flag = true
          a[i].concat(seq) if a[i] and seq
          i += 1
        end
        return self
      rescue NoMethodError, ArgumentError => evar
        raise evar if flag
      end
      align.each do |seq|
        a[i].concat(seq) if a[i] and seq
        i += 1
      end
      self
    end

alignment_length() click to toggle source

Returns the alignment length. Returns the longest length of the sequence in the alignment.

    # File lib/bio/alignment.rb, line 366
    def alignment_length
      maxlen = 0
      each_seq do |s|
        x = s.length
        maxlen = x if x > maxlen
      end
      maxlen
    end

Also aliased as: seq_length
alignment_lstrip!() click to toggle source

Removes excess gaps in the head of the sequences. If removes nothing, returns nil. Otherwise, returns self.

Note that it is a destructive method.

    # File lib/bio/alignment.rb, line 752
    def alignment_lstrip!
      #(String-like)
      pos = 0
      each_site do |a|
        a.remove_gaps!
        if a.empty?
          pos += 1
        else
          break
        end
      end
      return nil if pos <= 0
      each_seq { |s| s[0, pos] = '' }
      self
    end

Also aliased as: lstrip!
alignment_normalize!() click to toggle source

Fills gaps to the tail of each sequence if the length of the sequence is shorter than the alignment length.

Note that it is a destructive method.

    # File lib/bio/alignment.rb, line 712
    def alignment_normalize!
      #(original)
      len = alignment_length
      each_seq do |s|
        s << (gap_char * (len - s.length)) if s.length < len
      end
      self
    end

Also aliased as: normalize!
alignment_rstrip!() click to toggle source

Removes excess gaps in the tail of the sequences. If removes nothing, returns nil. Otherwise, returns self.

Note that it is a destructive method.

    # File lib/bio/alignment.rb, line 727
    def alignment_rstrip!
      #(String-like)
      len = alignment_length
      newlen = len
      each_site_step(len - 1, 0, -1) do |a|
        a.remove_gaps!
        if a.empty? then
          newlen -= 1
        else
          break
        end
      end
      return nil if newlen >= len
      each_seq do |s|
        s[newlen..-1] = '' if s.length > newlen
      end
      self
    end

Also aliased as: rstrip!
alignment_site(position) click to toggle source

Gets a site of the position. Returns a Bio::Alignment::Site object.

If the position is out of range, it returns the site of which all are gaps.

    # File lib/bio/alignment.rb, line 403
    def alignment_site(position)
      site = _alignment_site(position)
      site.set_all_property(get_all_property)
      site
    end

alignment_slice(*arg) click to toggle source

Returns the specified range of the alignment. For each sequence, the 'slice' method (it may be String#slice, which is the same as String#[]) is executed, and returns a new alignment as a Bio::Alignment::SequenceArray object.

Unlike alignment_window method, the result alignment might contain nil.

If you want to change return value's class, you should redefine alignment_collect method.

    # File lib/bio/alignment.rb, line 807
    def alignment_slice(*arg)
      #(String-like)
      #(BioPerl) AlignI::slice like method
      alignment_collect do |s|
        s.slice(*arg)
      end
    end

Also aliased as: slice
alignment_strip!() click to toggle source

Removes excess gaps in the sequences. If removes nothing, returns nil. Otherwise, returns self.

Note that it is a destructive method.

    # File lib/bio/alignment.rb, line 774
    def alignment_strip!
      #(String-like)
      r = alignment_rstrip!
      l = alignment_lstrip!
      (r or l)
    end

Also aliased as: strip!
alignment_subseq(*arg) click to toggle source

For each sequence, the 'subseq' method (Bio::Seqeunce::Common#subseq is expected) is executed, and returns a new alignment as a Bio::Alignment::SequenceArray object.

All sequences in the alignment are expected to be kind of Bio::Sequence::NA or Bio::Sequence::AA objects.

Unlike alignment_window method, the result alignment might contain nil.

If you want to change return value's class, you should redefine alignment_collect method.

    # File lib/bio/alignment.rb, line 829
    def alignment_subseq(*arg)
      #(original)
      alignment_collect do |s|
        s.subseq(*arg)
      end
    end

Also aliased as: subseq
alignment_window(*arg) click to toggle source

Returns specified range of the alignment. For each sequence, the '[]' method (it may be String#[]) is executed, and returns a new alignment as a Bio::Alignment::SequenceArray object.

Unlike alignment_slice method, the result alignment are guaranteed to contain String object if the range specified is out of range.

If you want to change return value's class, you should redefine alignment_collect method.

    # File lib/bio/alignment.rb, line 466
    def alignment_window(*arg)
      alignment_collect do |s|
        s[*arg] or seqclass.new('')
      end
    end

Also aliased as: window
collect_each_site() click to toggle source

Iterates over each site of the alignment and results running the block are collected and returns an array. It yields a Bio::Alignment::Site object.

    # File lib/bio/alignment.rb, line 503
    def collect_each_site
      ary = []
      each_site do |site|
        ary << yield(site)
      end
      ary
    end

consensus_each_site(opt = {}) click to toggle source

Helper method for calculating consensus sequence. It iterates over each site of the alignment. In each site, gaps will be removed if specified with opt. It yields a Bio::Alignment::Site object. Results running the block (String objects are expected) are joined to a string and it returns the string.

    opt[:gap_mode] ==> 0 -- gaps are regarded as normal characters
                       1 -- a site within gaps is regarded as a gap
                      -1 -- gaps are eliminated from consensus calculation
        default: 0

    # File lib/bio/alignment.rb, line 523
    def consensus_each_site(opt = {})
      mchar = (opt[:missing_char] or self.missing_char)
      gap_mode = opt[:gap_mode]
      case gap_mode
      when 0, nil
        collect_each_site do |a|
          yield(a) or mchar
        end.join('')
      when 1
        collect_each_site do |a|
          a.has_gap? ? gap_char : (yield(a) or mchar)
        end.join('')
      when -1
        collect_each_site do |a|
          a.remove_gaps!
          a.empty? ? gap_char : (yield(a) or mchar)
        end.join('')
      else
        raise ':gap_mode must be 0, 1 or -1'
      end
    end

consensus_iupac(opt = {}) click to toggle source

Returns the IUPAC consensus string of the alignment of nucleic-acid sequences.

It resembles the BioPerl's AlignI::consensus_iupac method.

Please refer to the consensus_each_site method for opt.

    # File lib/bio/alignment.rb, line 565
    def consensus_iupac(opt = {})
      consensus_each_site(opt) do |a|
        a.consensus_iupac
      end
    end

consensus_string(threshold = 1.0, opt = {}) click to toggle source

Returns the consensus string of the alignment. 0.0 <= threshold <= 1.0 is expected.

It resembles the BioPerl's AlignI::consensus_string method.

Please refer to the consensus_each_site method for opt.

    # File lib/bio/alignment.rb, line 552
    def consensus_string(threshold = 1.0, opt = {})
      consensus_each_site(opt) do |a|
        a.consensus_string(threshold)
      end
    end

convert_match(match_char = '.') click to toggle source

This is the BioPerl's AlignI::match like method.

Changes second to last sequences' sites to match_char(default: '.') when a site is equeal to the first sequence's corresponding site.

Note that it is a destructive method.

For Hash, please use it carefully because the order of the sequences is inconstant.

    # File lib/bio/alignment.rb, line 662
    def convert_match(match_char = '.')
      #(BioPerl) AlignI::match like method
      len = alignment_length
      firstseq = nil
      each_seq do |s|
        unless firstseq then
          firstseq = s
        else
          (0...len).each do |i|
            if s[i] and firstseq[i] == s[i] and !is_gap?(firstseq[i..i])
              s[i..i] = match_char
            end
          end
        end
      end
      self
    end

convert_unmatch(match_char = '.') click to toggle source

This is the BioPerl's AlignI::unmatch like method.

Changes second to last sequences' sites match_char(default: '.') to original sites' characters.

Note that it is a destructive method.

For Hash, please use it carefully because the order of the sequences is inconstant.

    # File lib/bio/alignment.rb, line 690
    def convert_unmatch(match_char = '.')
      #(BioPerl) AlignI::unmatch like method
      len = alignment_length
      firstseq = nil
      each_seq do |s|
        unless firstseq then
          firstseq = s
        else
          (0...len).each do |i|
            if s[i..i] == match_char then
              s[i..i] = (firstseq[i..i] or match_char)
            end
          end
        end
      end
      self
    end

each_seq() click to toggle source

Iterates over each sequences. Yields a sequence. It acts the same as Enumerable#each.

You would redefine the method suitable for the class/object.

    # File lib/bio/alignment.rb, line 340
    def each_seq(&block) #:yields: seq
      each(&block)
    end

each_site() click to toggle source

Iterates over each site of the alignment. It yields a Bio::Alignment::Site object (which inherits Array). It returns self.

    # File lib/bio/alignment.rb, line 412
    def each_site
      cp = get_all_property
      (0...alignment_length).each do |i|
        site = _alignment_site(i)
        site.set_all_property(cp)
        yield(site)
      end
      self
    end

each_site_step(start, stop, step = 1) click to toggle source

Iterates over each site of the alignment, with specifying start, stop positions and step. It yields Bio::Alignment::Site object (which inherits Array). It returns self. It is same as `start.step(stop, step) { |i| yield alignment_site(i) }`.

    # File lib/bio/alignment.rb, line 428
    def each_site_step(start, stop, step = 1)
      cp = get_all_property
      start.step(stop, step) do |i|
        site = _alignment_site(i)
        site.set_all_property(cp)
        yield(site)
      end
      self
    end

each_window(window_size, step_size = 1) click to toggle source

Iterates over each sliding window of the alignment. window_size is the size of sliding window. step is the step of each sliding. It yields a Bio::Alignment::SequenceArray object which contains each sliding window. It returns a Bio::Alignment::SequenceArray object which contains remainder alignment at the terminal end. If window_size is smaller than 0, it returns nil.

    # File lib/bio/alignment.rb, line 481
    def each_window(window_size, step_size = 1)
      return nil if window_size < 0
      if step_size >= 0 then
        last_step = nil
        0.step(alignment_length - window_size, step_size) do |i|
          yield alignment_window(i, window_size)
          last_step = i
        end
        alignment_window((last_step + window_size)..-1)
      else
        i = alignment_length - window_size
        while i >= 0
          yield alignment_window(i, window_size)
          i += step_size
        end
        alignment_window(0...(i-step_size))
      end
    end

lstrip!() click to toggle source
Alias for: alignment_lstrip!
match_line(opt = {}) click to toggle source

Returns the match line stirng of the alignment of nucleic- or amino-acid sequences. The type of the sequence is automatically determined or you can specify with opt.

It resembles the BioPerl's AlignI::match_line method.

    opt[:type] ==> :na or :aa (or determined by sequence class)
    opt[:match_line_char]   ==> 100% equal    default: '*'
    opt[:strong_match_char] ==> strong match  default: ':'
    opt[:weak_match_char]   ==> weak match    default: '.'
    opt[:mismatch_char]     ==> mismatch      default: ' '
      :strong_ and :weak_match_char are used only in amino mode (:aa)

More opt can be accepted. Please refer to the consensus_each_site method for opt.

    # File lib/bio/alignment.rb, line 624
    def match_line(opt = {})
      case opt[:type]
      when :aa
        amino = true
      when :na, :dna, :rna
        amino = false
      else
        if seqclass == Bio::Sequence::AA then
          amino = true
        elsif seqclass == Bio::Sequence::NA then
          amino = false
        else
          amino = nil
          self.each_seq do |x|
            if /[EFILPQ]/ =~ x
              amino = true
              break
            end
          end
        end
      end
      if amino then
        match_line_amino(opt)
      else
        match_line_nuc(opt)
      end
    end

match_line_amino(opt = {}) click to toggle source

Returns the match line stirng of the alignment of amino-acid sequences.

It resembles the BioPerl's AlignI::match_line method.

    opt[:match_line_char]   ==> 100% equal    default: '*'
    opt[:strong_match_char] ==> strong match  default: ':'
    opt[:weak_match_char]   ==> weak match    default: '.'
    opt[:mismatch_char]     ==> mismatch      default: ' '

More opt can be accepted. Please refer to the consensus_each_site method for opt.

    # File lib/bio/alignment.rb, line 584
    def match_line_amino(opt = {})
      collect_each_site do |a|
        a.match_line_amino(opt)
      end.join('')
    end

match_line_nuc(opt = {}) click to toggle source

Returns the match line stirng of the alignment of nucleic-acid sequences.

It resembles the BioPerl's AlignI::match_line method.

    opt[:match_line_char]   ==> 100% equal    default: '*'
    opt[:mismatch_char]     ==> mismatch      default: ' '

More opt can be accepted. Please refer to the consensus_each_site method for opt.

    # File lib/bio/alignment.rb, line 601
    def match_line_nuc(opt = {})
      collect_each_site do |a|
        a.match_line_nuc(opt)
      end.join('')
    end

normalize!() click to toggle source
Alias for: alignment_normalize!
number_of_sequences() click to toggle source

Returns number of sequences in this alignment.

    # File lib/bio/alignment.rb, line 1315
    def number_of_sequences
      i = 0
      self.each_seq { |s| i += 1 }
      i
    end

remove_all_gaps!() click to toggle source

Completely removes ALL gaps in the sequences. If removes nothing, returns nil. Otherwise, returns self.

Note that it is a destructive method.

    # File lib/bio/alignment.rb, line 787
    def remove_all_gaps!
      ret = nil
      each_seq do |s|
        x = s.gsub!(gap_regexp, '')
        ret ||= x
      end
      ret ? self : nil
    end

rstrip!() click to toggle source
Alias for: alignment_rstrip!
seq_length() click to toggle source
Alias for: alignment_length
seqclass() click to toggle source

Returns class of the sequence. If instance variable @seqclass (which can be set by 'seqclass=' method) is set, simply returns the value. Otherwise, returns the first sequence's class. If no sequences are found, returns nil.

    # File lib/bio/alignment.rb, line 349
    def seqclass
      if (defined? @seqclass) and @seqclass then
        @seqclass
      else
        klass = nil
        each_seq do |s|
          if s then
            klass = s.class
            break if klass
          end
        end
        (klass or String)
      end
    end

sequence_names() click to toggle source

Returns an array of sequence names. The order of the names must be the same as the order of `each_seq`.

    # File lib/bio/alignment.rb, line 1324
    def sequence_names
      (0...(self.number_of_sequences)).to_a
    end

slice(*arg) click to toggle source
Alias for: alignment_slice
strip!() click to toggle source
Alias for: alignment_strip!
subseq(*arg) click to toggle source
Alias for: alignment_subseq
window(*arg) click to toggle source
Alias for: alignment_window

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