Module | Bio

In:

lib/bio.rb
lib/bio/sequence/common.rb
lib/bio/sequence/format.rb
lib/bio/sequence/adapter.rb
lib/bio/sequence/generic.rb
lib/bio/sequence/quality_score.rb
lib/bio/sequence/sequence_masker.rb
lib/bio/sequence/na.rb
lib/bio/sequence/compat.rb
lib/bio/sequence/dblink.rb
lib/bio/sequence/aa.rb
lib/bio/compat/references.rb
lib/bio/compat/features.rb
lib/bio/tree.rb
lib/bio/db/kegg/brite.rb
lib/bio/db/kegg/genome.rb
lib/bio/db/kegg/compound.rb
lib/bio/db/kegg/pathway.rb
lib/bio/db/kegg/enzyme.rb
lib/bio/db/kegg/module.rb
lib/bio/db/kegg/common.rb
lib/bio/db/kegg/glycan.rb
lib/bio/db/kegg/genes.rb
lib/bio/db/kegg/keggtab.rb
lib/bio/db/kegg/orthology.rb
lib/bio/db/kegg/drug.rb
lib/bio/db/kegg/taxonomy.rb
lib/bio/db/kegg/kgml.rb
lib/bio/db/kegg/reaction.rb
lib/bio/db/kegg/expression.rb
lib/bio/db/soft.rb
lib/bio/db/nexus.rb
lib/bio/db/medline.rb
lib/bio/db/newick.rb
lib/bio/db/rebase.rb
lib/bio/db/phyloxml/phyloxml_parser.rb
lib/bio/db/phyloxml/phyloxml_writer.rb
lib/bio/db/phyloxml/phyloxml_elements.rb
lib/bio/db/fasta/defline.rb
lib/bio/db/fasta/qual.rb
lib/bio/db/genbank/genbank.rb
lib/bio/db/genbank/common.rb
lib/bio/db/genbank/ddbj.rb
lib/bio/db/genbank/genpept.rb
lib/bio/db/genbank/refseq.rb
lib/bio/db/sanger_chromatogram/chromatogram.rb
lib/bio/db/sanger_chromatogram/abif.rb
lib/bio/db/sanger_chromatogram/scf.rb
lib/bio/db/pdb.rb
lib/bio/db/go.rb
lib/bio/db/lasergene.rb
lib/bio/db/fastq.rb
lib/bio/db/gff.rb
lib/bio/db/prosite.rb
lib/bio/db/pdb/residue.rb
lib/bio/db/pdb/chemicalcomponent.rb
lib/bio/db/pdb/atom.rb
lib/bio/db/pdb/chain.rb
lib/bio/db/pdb/utils.rb
lib/bio/db/pdb/model.rb
lib/bio/db/pdb/pdb.rb
lib/bio/db/aaindex.rb
lib/bio/db/embl/swissprot.rb
lib/bio/db/embl/common.rb
lib/bio/db/embl/uniprot.rb
lib/bio/db/embl/embl.rb
lib/bio/db/embl/trembl.rb
lib/bio/db/embl/sptr.rb
lib/bio/db/biosql/sequence.rb
lib/bio/db/transfac.rb
lib/bio/db/nbrf.rb
lib/bio/db/fantom.rb
lib/bio/db/litdb.rb
lib/bio/db/fasta.rb
lib/bio/data/aa.rb
lib/bio/data/na.rb
lib/bio/data/codontable.rb
lib/bio/appl/meme/mast/report.rb
lib/bio/appl/meme/mast.rb
lib/bio/appl/meme/motif.rb
lib/bio/appl/iprscan/report.rb
lib/bio/appl/muscle.rb
lib/bio/appl/gcg/seq.rb
lib/bio/appl/gcg/msf.rb
lib/bio/appl/hmmer/report.rb
lib/bio/appl/tcoffee.rb
lib/bio/appl/hmmer.rb
lib/bio/appl/blast.rb
lib/bio/appl/tmhmm/report.rb
lib/bio/appl/mafft/report.rb
lib/bio/appl/emboss.rb
lib/bio/appl/pts1.rb
lib/bio/appl/spidey/report.rb
lib/bio/appl/paml/codeml.rb
lib/bio/appl/paml/common.rb
lib/bio/appl/genscan/report.rb
lib/bio/appl/fasta.rb
lib/bio/appl/targetp/report.rb
lib/bio/appl/clustalw.rb
lib/bio/appl/clustalw/report.rb
lib/bio/appl/blast/rexml.rb
lib/bio/appl/blast/xmlparser.rb
lib/bio/appl/blast/wublast.rb
lib/bio/appl/blast/remote.rb
lib/bio/appl/blast/format8.rb
lib/bio/appl/blast/format0.rb
lib/bio/appl/blast/rpsblast.rb
lib/bio/appl/blast/ncbioptions.rb
lib/bio/appl/blast/report.rb
lib/bio/appl/psort.rb
lib/bio/appl/phylip/distance_matrix.rb
lib/bio/appl/phylip/alignment.rb
lib/bio/appl/fasta/format10.rb
lib/bio/appl/sim4.rb
lib/bio/appl/sosui/report.rb
lib/bio/appl/sim4/report.rb
lib/bio/appl/psort/report.rb
lib/bio/appl/bl2seq/report.rb
lib/bio/appl/blat/report.rb
lib/bio/appl/probcons.rb
lib/bio/appl/mafft.rb
lib/bio/reference.rb
lib/bio/alignment.rb
lib/bio/map.rb
lib/bio/version.rb
lib/bio/db.rb
lib/bio/shell/plugin/das.rb
lib/bio/feature.rb
lib/bio/sequence.rb
lib/bio/io/soapwsdl.rb
lib/bio/io/ebisoap.rb
lib/bio/io/das.rb
lib/bio/io/registry.rb
lib/bio/io/flatfile/autodetection.rb
lib/bio/io/flatfile/index.rb
lib/bio/io/flatfile/buffer.rb
lib/bio/io/flatfile/splitter.rb
lib/bio/io/flatfile/indexer.rb
lib/bio/io/flatfile/bdb.rb
lib/bio/io/ncbirest.rb
lib/bio/io/ddbjxml.rb
lib/bio/io/fetch.rb
lib/bio/io/sql.rb
lib/bio/io/fastacmd.rb
lib/bio/io/ensembl.rb
lib/bio/io/keggapi.rb
lib/bio/io/flatfile.rb
lib/bio/io/togows.rb
lib/bio/io/hinv.rb
lib/bio/io/dbget.rb
lib/bio/io/ncbisoap.rb
lib/bio/io/pubmed.rb
lib/bio/io/biosql/biosql.rb
lib/bio/io/biosql/ar-biosql.rb
lib/bio/io/ddbjrest.rb
lib/bio/io/higet.rb
lib/bio/command.rb
lib/bio/pathway.rb
lib/bio/location.rb
lib/bio/util/restriction_enzyme.rb
lib/bio/util/sirna.rb
lib/bio/util/color_scheme.rb
lib/bio/util/restriction_enzyme/single_strand/cut_locations_in_enzyme_notation.rb
lib/bio/util/restriction_enzyme/analysis_basic.rb
lib/bio/util/restriction_enzyme/analysis.rb
lib/bio/util/restriction_enzyme/double_stranded/cut_locations_in_enzyme_notation.rb
lib/bio/util/restriction_enzyme/double_stranded/aligned_strands.rb
lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair_in_enzyme_notation.rb
lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair.rb
lib/bio/util/restriction_enzyme/double_stranded/cut_locations.rb
lib/bio/util/restriction_enzyme/single_strand_complement.rb
lib/bio/util/restriction_enzyme/range/cut_ranges.rb
lib/bio/util/restriction_enzyme/range/sequence_range.rb
lib/bio/util/restriction_enzyme/range/sequence_range/fragments.rb
lib/bio/util/restriction_enzyme/range/sequence_range/fragment.rb
lib/bio/util/restriction_enzyme/range/sequence_range/calculated_cuts.rb
lib/bio/util/restriction_enzyme/range/vertical_cut_range.rb
lib/bio/util/restriction_enzyme/range/cut_range.rb
lib/bio/util/restriction_enzyme/range/horizontal_cut_range.rb
lib/bio/util/restriction_enzyme/double_stranded.rb
lib/bio/util/restriction_enzyme/cut_symbol.rb
lib/bio/util/restriction_enzyme/single_strand.rb
lib/bio/util/restriction_enzyme/dense_int_array.rb
lib/bio/util/restriction_enzyme/sorted_num_array.rb
lib/bio/util/restriction_enzyme/string_formatting.rb
lib/bio/util/contingency_table.rb
lib/bio/tree/output.rb

# bio/tree/output.rb - Phylogenetic tree formatter

Copyright: | Copyright (C) 2004-2006 Naohisa Goto <ng@bioruby.org>
License: | The Ruby License

## Description

This file contains formatter of Newick, NHX and Phylip distance matrix.

## References

- evolution.genetics.washington.edu/phylip/newick_doc.html
- www.phylosoft.org/forester/NHX.html

### Methods

method_missing

### Classes and Modules

Module Bio::Alignment
Module Bio::ColorScheme
Module Bio::Command
Module Bio::FANTOM
Module Bio::GCG
Module Bio::Map
Module Bio::Meme
Module Bio::PAML
Module Bio::Phylip
Module Bio::PhyloXML
Module Bio::Shell
Module Bio::TogoWS
Class Bio::AAindex
Class Bio::AAindex1
Class Bio::AAindex2
Class Bio::Abif
Class Bio::AminoAcid
Class Bio::Blast
Class Bio::Blat
Class Bio::ClustalW
Class Bio::CodonTable
Class Bio::ContingencyTable
Class Bio::DAS
Class Bio::DB
Class Bio::DBGET
Class Bio::DDBJ
Class Bio::EBI
Class Bio::EMBL
Class Bio::EMBLDB
Class Bio::EMBOSS
Class Bio::Ensembl
Class Bio::Fasta
Class Bio::FastaDefline
Class Bio::FastaFormat
Class Bio::FastaNumericFormat
Class Bio::Fastq
Class Bio::Feature
Class Bio::Features
Class Bio::Fetch
Class Bio::FlatFile
Class Bio::FlatFileIndex
Class Bio::GFF
Class Bio::GO
Class Bio::GenBank
Class Bio::GenPept
Class Bio::Genscan
Class Bio::HGC
Class Bio::HMMER
Class Bio::Hinv
Class Bio::Iprscan
Class Bio::KEGG
Class Bio::KEGGDB
Class Bio::LITDB
Class Bio::Lasergene
Class Bio::Location
Class Bio::Locations
Class Bio::MAFFT
Class Bio::MEDLINE
Class Bio::Muscle
Class Bio::NBRF
Class Bio::NCBI
Class Bio::NCBIDB
Class Bio::Newick
Class Bio::Nexus
Class Bio::NucleicAcid
Class Bio::PDB
Class Bio::PROSITE
Class Bio::PSORT
Class Bio::PTS1
Class Bio::Pathway
Class Bio::Probcons
Class Bio::PubMed
Class Bio::REBASE
Class Bio::RefSeq
Class Bio::Reference
Class Bio::References
Class Bio::Registry
Class Bio::RestrictionEnzyme
Class Bio::SOAPWSDL
Class Bio::SOFT
Class Bio::SOSUI
Class Bio::SPTR
Class Bio::SQL
Class Bio::SangerChromatogram
Class Bio::Scf
Class Bio::Sequence
Class Bio::SiRNA
Class Bio::Sim4
Class Bio::Spidey
Class Bio::SwissProt
Class Bio::TMHMM
Class Bio::TRANSFAC
Class Bio::TargetP
Class Bio::Taxonomy
Class Bio::Tcoffee
Class Bio::TrEMBL
Class Bio::Tree
Class Bio::UniProt

### Constants

BIORUBY_VERSION | = | [1, 4, 3].extend(Comparable).freeze |  | BioRuby version (Array containing Integer)

BIORUBY_EXTRA_VERSION

=

nil

Extra version specifier (String or nil). Existance of the value indicates pre-release version or modified version.

nil : | Release version.
".0000"..".4999" : | Release version with patches.
".5000" : | Development unstable version.
".5001"..".8999" : | Pre-alpha version.
"-alphaN" (N=0..99) : | Alpha version.
"-preN" (N=0..99) : | Pre-release test version.
"-rcN" (N=0..99) : | Release candidate version.

BIORUBY_VERSION_ID | = | (BIORUBY_VERSION.join('.') + BIORUBY_EXTRA_VERSION.to_s).freeze |  | Version identifier, including extra version string (String) Unlike BIORUBY_VERSION, it is not comparable.

### Public Class methods

method_missing(*args)

Provide BioRuby shell ‘command’ also as ‘Bio.command’ (like ChemRuby)

[Source]

         # File lib/bio.rb, line 309
    309:   def self.method_missing(*args)
    310:     require 'bio/shell'
    311:     extend Bio::Shell
    312:     public_class_method(*Bio::Shell.private_instance_methods)
    313:     if Bio.respond_to?(args.first)
    314:       Bio.send(*args)
    315:     else
    316:       raise NameError
    317:     end
    318:   end

[Validate]