Copyright |
Copyright (C) 2001-2007 Toshiaki Katayama <k@bioruby.org> |
License |
The Ruby License |
$Id:$
+
Copyright |
Copyright (C) 2000-2006 Toshiaki Katayama <k@bioruby.org>, Yoshinori K. Okuji <okuji@enbug.org>, Naohisa Goto <ng@bioruby.org>, Ryan Raaum <ryan@raaum.org>, Jan Aerts <jan.aerts@bbsrc.ac.uk> |
License |
The Ruby License |
Ok Hilmar gives to me some clarification 1) "EMBL/GenBank/SwissProt" name in term table, is only a convention assuming data loaded by genbank embl ans swissprot formats.
If your features come from others ways for example blast or alignment ... whatever.. the user as to take care about the source.
TODO: 1) source_term_id => surce_term and check before if the source term is present or not and the level, the root should always be something "EMBL/GenBank/SwissProt" or contestualized. 2) Into DummyBase class delete connection there and use Bio::ArSQL.establish_connection which reads info from a yml file. 3) Chk Locations in Biofeatures ArSQL
Copyright (C) 2001-2006 Naohisa Goto <ng@bioruby.org>
License |
The Ruby License |
$Id:$
Bio::FlatFile is a helper and wrapper class to read a biological data file. It acts like a IO object. It can automatically detect data format, and users do not need to tell the class what the data is.
Copyright |
Copyright (C) 2001, 2005 Toshiaki Katayama <k@bioruby.org> 2006 Jan Aerts <jan.aerts@bbsrc.ac.uk> 2008 Naohisa Goto <ng@bioruby.org> |
License |
The Ruby License |
$Id:$
Copyright |
Copyright (C) 2008 Toshiaki Katayama <k@bioruby.org>, Ryan Raaum <ryan@raaum.org>, Jan Aerts <jandot@bioruby.org>, Naohisa Goto <ng@bioruby.org> |
License |
The Ruby License |
$Id: references.rb,v 1.1.2.1 2008/03/04 10:07:49 ngoto Exp $
The Bio::References class was obsoleted after BioRuby 1.2.1. To keep compatibility, some wrapper methods are provided in this file. As the compatibility methods (and Bio::References) will soon be removed, Please change your code not to use Bio::References.
Note that Bio::Reference is different from Bio::References. Bio::Reference still exists for storing a reference information in sequence entries.
Copyright |
Copyright (C) 2004-2006 Naohisa Goto <ng@bioruby.org> |
License |
The Ruby License |
This file contains formatter of Newick, NHX and Phylip distance matrix.
bio/util/color_scheme.rb - Popular color codings for nucleic and amino acids
Author |
Trevor Wennblom <trevor@corevx.com> |
Copyright |
Copyright (c) 2005-2007 Midwinter Laboratories, LLC (midwinterlabs.com) |
License |
The Ruby License |
$Id:$
bio/util/restriction_enzyme/sorted_num_array.rb - Internal data storage for Bio::RestrictionEnzyme::Range::SequenceRange
Copyright |
Copyright (C) 2011 Naohisa Goto <ng@bioruby.org> |
License |
The Ruby License |
bio/util/restriction_enzyme/cut_symbol.rb - Defines the symbol used to mark a cut in an enzyme sequence
Author |
Trevor Wennblom <trevor@corevx.com> |
Copyright |
Copyright (c) 2005-2007 Midwinter Laboratories, LLC (midwinterlabs.com) |
License |
The Ruby License |
bio/util/restriction_enzyme/string_formatting.rb - Useful functions for string manipulation
Author |
Trevor Wennblom <trevor@corevx.com> |
Copyright |
Copyright (c) 2005-2007 Midwinter Laboratories, LLC (midwinterlabs.com) |
License |
The Ruby License |
bio/util/restriction_enzyme/analysis.rb - Does the work of fragmenting the DNA from the enzymes
Author |
Trevor Wennblom <trevor@corevx.com> |
Copyright |
Copyright (c) 2005-2007 Midwinter Laboratories, LLC (midwinterlabs.com) |
License |
The Ruby License |
bio/util/restriction_enzyme/double_stranded.rb - DoubleStranded restriction enzyme sequence
Author |
Trevor Wennblom <trevor@corevx.com> |
Copyright |
Copyright (c) 2005-2007 Midwinter Laboratories, LLC (midwinterlabs.com) |
License |
The Ruby License |
bio/util/restriction_enzyme/single_strand/cut_locations_in_enzyme_notation.rb - The cut locations, in enzyme notation
Author |
Trevor Wennblom <trevor@corevx.com> |
Copyright |
Copyright (c) 2005-2007 Midwinter Laboratories, LLC (midwinterlabs.com) |
License |
The Ruby License |
bio/util/restriction_enzyme/double_stranded/cut_locations_in_enzyme_notation.rb - Inherits from DoubleStrand::CutLocations
Author |
Trevor Wennblom <trevor@corevx.com> |
Copyright |
Copyright (c) 2005-2007 Midwinter Laboratories, LLC (midwinterlabs.com) |
License |
The Ruby License |
bio/util/restriction_enzyme/double_stranded/cut_location_pair.rb - Stores a cut location pair in 0-based index notation
Author |
Trevor Wennblom <trevor@corevx.com> |
Copyright |
Copyright (c) 2005-2007 Midwinter Laboratories, LLC (midwinterlabs.com) |
License |
The Ruby License |
bio/util/restriction_enzyme/double_stranded/cut_location_pair_in_enzyme_notation.rb - Inherits from DoubleStranded::CutLocationPair
Author |
Trevor Wennblom <trevor@corevx.com> |
Copyright |
Copyright (c) 2005-2007 Midwinter Laboratories, LLC (midwinterlabs.com) |
License |
The Ruby License |
bio/util/restriction_enzyme/double_stranded/cut_locations.rb - Contains an Array of CutLocationPair objects
Author |
Trevor Wennblom <trevor@corevx.com> |
Copyright |
Copyright (c) 2005-2007 Midwinter Laboratories, LLC (midwinterlabs.com) |
License |
The Ruby License |
bio/util/restriction_enzyme/double_stranded/aligned_strands.rb - Align two SingleStrand objects
Author |
Trevor Wennblom <trevor@corevx.com> |
Copyright |
Copyright (c) 2005-2007 Midwinter Laboratories, LLC (midwinterlabs.com) |
License |
The Ruby License |
bio/util/restriction_enzyme/dense_int_array.rb - Internal data storage for Bio::RestrictionEnzyme::Range::SequenceRange
Copyright |
Copyright (C) 2011 Naohisa Goto <ng@bioruby.org> Tomoaki NISHIYAMA |
License |
The Ruby License |
bio/util/restriction_enzyme/range/vertical_cut_range.rb -
Author |
Trevor Wennblom <trevor@corevx.com> |
Copyright |
Copyright (c) 2005-2007 Midwinter Laboratories, LLC (midwinterlabs.com) |
License |
The Ruby License |
bio/util/restriction_enzyme/range/cut_range.rb - Abstract base class for HorizontalCutRange and VerticalCutRange
Author |
Trevor Wennblom <trevor@corevx.com> |
Copyright |
Copyright (c) 2005-2007 Midwinter Laboratories, LLC (midwinterlabs.com) |
License |
The Ruby License |
bio/util/restriction_enzyme/range/horizontal_cut_range.rb -
Author |
Trevor Wennblom <trevor@corevx.com> |
Copyright |
Copyright (c) 2005-2007 Midwinter Laboratories, LLC (midwinterlabs.com) |
License |
The Ruby License |
bio/util/restriction_enzyme/range/cut_ranges.rb - Container for many CutRange objects or CutRange child objects.
Author |
Trevor Wennblom <trevor@corevx.com> |
Copyright |
Copyright (c) 2005-2007 Midwinter Laboratories, LLC (midwinterlabs.com) |
License |
The Ruby License |
bio/util/restriction_enzyme/range/sequence_range/fragment.rb -
Author |
Trevor Wennblom <trevor@corevx.com> |
Copyright |
Copyright (c) 2005-2007 Midwinter Laboratories, LLC (midwinterlabs.com) |
License |
The Ruby License |
bio/util/restriction_enzyme/range/sequence_range/calculated_cuts.rb -
Author |
Trevor Wennblom <trevor@corevx.com> |
Copyright |
Copyright (c) 2005-2007 Midwinter Laboratories, LLC (midwinterlabs.com) |
License |
The Ruby License |
bio/util/restriction_enzyme/analysis/fragments.rb -
Author |
Trevor Wennblom <trevor@corevx.com> |
Copyright |
Copyright (c) 2005-2007 Midwinter Laboratories, LLC (midwinterlabs.com) |
License |
The Ruby License |
bio/util/restriction_enzyme/range/sequence_range.rb - A defined range over a nucleotide sequence
Author |
Trevor Wennblom <trevor@corevx.com> |
Copyright |
Copyright (c) 2005-2007 Midwinter Laboratories, LLC (midwinterlabs.com) |
License |
The Ruby License |
bio/util/restriction_enzyme/single_strand_complement.rb - Single strand restriction enzyme sequence in complement orientation
Author |
Trevor Wennblom <trevor@corevx.com> |
Copyright |
Copyright (c) 2005-2007 Midwinter Laboratories, LLC (midwinterlabs.com) |
License |
The Ruby License |
bio/util/restriction_enzyme.rb - Digests DNA based on restriction enzyme cut patterns
Author |
Trevor Wennblom <trevor@corevx.com> |
Copyright |
Copyright (c) 2005-2007 Midwinter Laboratories, LLC (midwinterlabs.com) |
License |
The Ruby License |
bio/util/contingency_table.rb - Statistical contingency table analysis for aligned sequences
Author |
Trevor Wennblom <trevor@corevx.com> |
Copyright |
Copyright (c) 2005-2007 Midwinter Laboratories, LLC (midwinterlabs.com) |
License |
The Ruby License |
$Id:$
Copyright |
Copyright (C) 2001, 2004 Toshiaki Katayama <k@bioruby.org> |
License |
The Ruby License |
$Id:$
Data in this class is converted from the NCBI's genetic codes page.
* ((<URL:http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?mode=t>))
Obtain a codon table No.1 -- Standard (Eukaryote)
table = Bio::CodonTable[1]
Obtain a copy of the codon table No.1 to modify. In this example, reassign a seleno cystein ('U') to the 'tga' codon.
table = Bio::CodonTable.copy(1) table['tga'] = 'U'
Create a new codon table by your own from the Hash which contains pairs of codon and amino acid. You can also define the table name in the second argument.
hash = { 'ttt' => 'F', 'ttc' => 'ttc', ... } table = Bio::CodonTable.new(hash, "my codon table")
Obtain a translated amino acid by codon.
table = Bio::CodonTable[1] table['ttt'] # => F
Reverse translation of a amino acid into a list of relevant codons.
table = Bio::CodonTable[1] table.revtrans("A") # => ["gcg", "gct", "gca", "gcc"]
Copyright |
Copyright (C) 2001, 2005 Toshiaki Katayama <k@bioruby.org> |
License |
The Ruby License |
$Id:$
Copyright |
Copyright (C) 2001, 2005 Toshiaki Katayama <k@bioruby.org> |
License |
The Ruby License |
$Id:$
Bio::NucleicAcid class contains data related to nucleic acids.
Examples:
require 'bio' puts "### na = Bio::NucleicAcid.new" na = Bio::NucleicAcid.new puts "# na.to_re('yrwskmbdhvnatgc')" p na.to_re('yrwskmbdhvnatgc') puts "# Bio::NucleicAcid.to_re('yrwskmbdhvnatgc')" p Bio::NucleicAcid.to_re('yrwskmbdhvnatgc') puts "# na.weight('A')" p na.weight('A') puts "# Bio::NucleicAcid.weight('A')" p Bio::NucleicAcid.weight('A') puts "# na.weight('atgc')" p na.weight('atgc') puts "# Bio::NucleicAcid.weight('atgc')" p Bio::NucleicAcid.weight('atgc')
Copyright |
Copyright (C) 2001-2012 Toshiaki Katayama <k@bioruby.org>, Naohisa Goto <ng@bioruby.org> |
License |
The Ruby License |
Copyright |
Copyright (c) 2002, 2005 Toshiaki Katayama <k@bioruby.org> 2006 Jan Aerts <jan.aerts@bbsrc.ac.uk> |
License |
The Ruby License |
Copyright |
Copyright (C) 2005 Naohisa Goto <ng@bioruby.org> |
License |
The Ruby License |
Bio::Blast::Bl2seq::Report is a NCBI bl2seq (BLAST 2 sequences) output parser.
Thanks to Tomoaki NISHIYAMA <tomoakin __at__ kenroku.kanazawa-u.ac.jp> for providing bl2seq parser patches based on lib/bio/appl/blast/format0.rb.
Copyright |
Copyright (C) 2002, 2003, 2007 Toshiaki Katayama <k@bioruby.org> |
License |
The Ruby License |
$Id:$
This file is automatically loaded by bio/appl/blast/report.rb
Copyright |
Copyright (C) 2008 Naohisa Goto <ng@bioruby.org> |
License |
The Ruby License |
Copyright |
Copyright (C) 2003, 2008 Naohisa GOTO <ng@bioruby.org> |
License |
The Ruby License |
WU-BLAST default output parser.
The parser is still incomplete and may contain many bugs, because I didn't have WU-BLAST license. It was tested under web-based WU-BLAST results and obsolete version downloaded from blast.wustl.edu/ .
Copyright |
Copyright (C) 2008 Adam Kraut <adamnkraut@gmail.com>, |
License |
The Ruby License |
This file contains a minimal class to represent meme motifs
Copyright |
Copyright (C) 2006 Mitsuteru C. Nakao <mn@kazusa.or.jp> |
License |
The Ruby License |
$Id: report.rb,v 1.9 2007/07/18 11:11:57 nakao Exp $
Copyright |
Copyright (C) 2003 Mitsuteru C. Nakao <n@bioruby.org> |
License |
The Ruby License |
$Id:$
Copyright |
Copyright (C) 2006-2007 Jeffrey Blakeslee and John Conery University of Oregon <jeffb@uoregon.edu> Naohisa Goto <ng@bioruby.org> |
License |
The Ruby License |
$Id: tcoffee.rb,v 1.1 2007/07/16 12:25:50 ngoto Exp $
Bio::Tcoffee is a wrapper class to execute T-Coffee.
Notredame, C., Higgins, D.G. and Heringa, J. T-Coffee: A novel method for fast and accurate multiple sequence alignment. J. Mol. Biol. 302: 205-217, 2000.
Copyright |
Copyright (C) 2006 GOTO Naohisa <ng@bioruby.org> |
License |
The Ruby License |
$Id: alignment.rb,v 1.2 2007/04/05 23:35:40 trevor Exp $
Please refer document of Bio::Phylip::PhylipFormat class.
Copyright |
Copyright (C) 2003 Mitsuteru C. Nakao <n@bioruby.org> |
License |
The Ruby License |
$Id:$
TargetP class for www.cbs.dtu.dk/services/TargetP/
Copyright |
Copyright (C) 2002, 2005 Toshiaki Katayama<k@bioruby.org> |
Copyright |
Copyright (C) 2006 Jan Aerts <jan.aerts@bbsrc.ac.uk> |
License |
The Ruby License |
$Id: emboss.rb,v 1.9 2008/01/10 03:51:06 ngoto Exp $
Copyright |
Copyright (C) 2003, 2006 Naohisa Goto <ng@bioruby.org> |
License |
The Ruby License |
$Id: seq.rb,v 1.3 2007/04/05 23:35:39 trevor Exp $
Please refer document of Bio::GCG::Seq.
+
Copyright |
Copyright (C) 2004 GOTO Naohisa <ng@bioruby.org> |
License |
The Ruby License |
$Id:$
The sim4 report parser classes.
Florea, L., et al., A Computer program for aligning a cDNA sequence with a genomic DNA sequence, Genome Research, 8, 967--974, 1998. www.genome.org/cgi/content/abstract/8/9/967
Copyright |
Copyright (C) 2006-2007 Jeffrey Blakeslee and John Conery University of Oregon <jeffb@uoregon.edu> Naohisa Goto <ng@bioruby.org> |
License |
The Ruby License |
$Id: muscle.rb,v 1.1 2007/07/16 12:25:50 ngoto Exp $
Bio::Muscle is a wrapper class to execute MUSCLE.
Edgar R.C. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32: 1792-1797, 2004.
Edgar, R.C. MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics 5: 113, 2004.
Copyright |
Copyright (C) 2006-2007 Jeffrey Blakeslee and John Conery University of Oregon <jeffb@uoregon.edu> Naohisa Goto <ng@bioruby.org> |
License |
The Ruby License |
$Id: probcons.rb,v 1.1 2007/07/16 12:25:50 ngoto Exp $
Bio::Probcons is a wrapper class to execute ProbCons (Probabilistic Consistency-based Multiple Alignment of Amino Acid Sequences).
Do, C.B., Mahabhashyam, M.S.P., Brudno, M., and Batzoglou, S. ProbCons: Probabilistic Consistency-based Multiple Sequence Alignment. Genome Research 15: 330-340, 2005.
bio/db/lasergene.rb - Interface for DNAStar Lasergene sequence file format
Author |
Trevor Wennblom <trevor@corevx.com> |
Copyright |
Copyright (c) 2007 Center for Biomedical Research Informatics, University of Minnesota (cbri.umn.edu) |
License |
The Ruby License |
$Id:$
Autoload definition
Copyright |
Copyright (C) 2006 GOTO Naohisa <ngoto@gen-info.osaka-u.ac.jp> |
License |
The Ruby License |
Please refer Bio::PDB::ChemicalComponent.
Copyright |
Copyright (C) 2004, 2006 Alex Gutteridge <alexg@ebi.ac.uk> Naohisa Goto <ng@bioruby.org> |
License |
The Ruby License |
Please refer Bio::PDB::Model.
Copyright |
Copyright (C) 2004, 2006 Alex Gutteridge <alexg@ebi.ac.uk> Naohisa Goto <ng@bioruby.org> |
License |
The Ruby License |
Copyright |
Copyright (C) 2004, 2006 Alex Gutteridge <alexg@ebi.ac.uk> Naohisa Goto <ng@bioruby.org> |
License |
The Ruby License |
Please refer Bio::PDB::Chain.
definition of the PDB class
TODO save on db reading from a genbank or embl object
bio/db/soft.rb - Interface for SOFT formatted files
Author |
Trevor Wennblom <trevor@corevx.com> |
Copyright |
Copyright (c) 2007 Midwinter Laboratories, LLC (midwinterlabs.com) |
License |
The Ruby License |
$Id:$
Copyright |
Copyright (C) 2007 Toshiaki Katayama <k@bioruby.org> |
License |
The Ruby License |
$Id:$
Copyright |
Copyright (C) 2001-2007 Toshiaki Katayama <k@bioruby.org> |
Copyright |
Copyright (C) 2003 Masumi Itoh <m@bioruby.org> |
Copyright |
Copyright (C) 2009 Kozo Nishida <kozo-ni@is.naist.jp> |
License |
The Ruby License |
Note that the modules in this file are intended to be Bio::KEGG::* internal use only.
This file contains modules that implement methods commonly used from KEGG database parser classes.
Copyright |
Copyright (C) 2001, 2002, 2006, 2010 Toshiaki Katayama <k@bioruby.org> |
License |
The Ruby License |
$Id:$
See www.genome.jp/kegg/genes.html
require 'bio/io/fetch' entry_string = Bio::Fetch.query('genes', 'b0002') entry = Bio::KEGG::GENES.new(entry_string) # ENTRY p entry.entry # => Hash p entry.entry_id # => String p entry.division # => String p entry.organism # => String # NAME p entry.name # => String p entry.names # => Array # DEFINITION p entry.definition # => String p entry.eclinks # => Array # PATHWAY p entry.pathway # => String p entry.pathways # => Hash # POSITION p entry.position # => String p entry.chromosome # => String p entry.gbposition # => String p entry.locations # => Bio::Locations # MOTIF p entry.motifs # => Hash of Array # DBLINKS p entry.dblinks # => Hash of Array # STRUCTURE p entry.structure # => Array # CODON_USAGE p entry.codon_usage # => Hash p entry.cu_list # => Array # AASEQ p entry.aaseq # => Bio::Sequence::AA p entry.aalen # => Fixnum # NTSEQ p entry.ntseq # => Bio::Sequence::NA p entry.naseq # => Bio::Sequence::NA p entry.ntlen # => Fixnum p entry.nalen # => Fixnum
Copyright |
Copyright (C) 2001 Mitsuteru C. Nakao <n@bioruby.org> Copyright (C) 2003, 2006 Toshiaki Katayama <k@bioruby.org> |
License |
The Ruby License |
$Id: keggtab.rb,v 1.10 2007/04/05 23:35:41 trevor Exp $
require 'bio/sequence'
Copyright |
Copyright (C) 2001, 2002 GOTO Naohisa <ngoto@gen-info.osaka-u.ac.jp>, Toshiaki Katayama <k@bioruby.org> |
License |
The Ruby License |
$Id: defline.rb,v 1.1.2.1 2008/06/20 13:22:32 ngoto Exp $
Bio::FastaDefline is a parser class for definition line (defline) of the FASTA format.
rub = Bio::FastaDefline.new('>gi|671595|emb|CAA85678.1| rubisco large subunit [Perovskia abrotanoides]') rub.entry_id ==> 'gi|671595' rub.get('emb') ==> 'CAA85678.1' rub.emb ==> 'CAA85678.1' rub.gi ==> '671595' rub.accession ==> 'CAA85678' rub.accessions ==> [ 'CAA85678' ] rub.acc_version ==> 'CAA85678.1' rub.locus ==> nil rub.list_ids ==> [["gi", "671595"], ["emb", "CAA85678.1", nil], ["Perovskia abrotanoides"]] ckr = Bio::FastaDefline.new(">gi|2495000|sp|Q63931|CCKR_CAVPO CHOLECYSTOKININ TYPE A RECEPTOR (CCK-A RECEPTOR) (CCK-AR)\001gi|2147182|pir||I51898 cholecystokinin A receptor - guinea pig\001gi|544724|gb|AAB29504.1| cholecystokinin A receptor; CCK-A receptor [Cavia]") ckr.entry_id ==> "gi|2495000" ckr.sp ==> "CCKR_CAVPO" ckr.pir ==> "I51898" ckr.gb ==> "AAB29504.1" ckr.gi ==> "2495000" ckr.accession ==> "AAB29504" ckr.accessions ==> ["Q63931", "AAB29504"] ckr.acc_version ==> "AAB29504.1" ckr.locus ==> nil ckr.description ==> "CHOLECYSTOKININ TYPE A RECEPTOR (CCK-A RECEPTOR) (CCK-AR)" ckr.descriptions ==> ["CHOLECYSTOKININ TYPE A RECEPTOR (CCK-A RECEPTOR) (CCK-AR)", "cholecystokinin A receptor - guinea pig", "cholecystokinin A receptor; CCK-A receptor [Cavia]"] ckr.words ==> ["cavia", "cck-a", "cck-ar", "cholecystokinin", "guinea", "pig", "receptor", "type"] ckr.id_strings ==> ["2495000", "Q63931", "CCKR_CAVPO", "2147182", "I51898", "544724", "AAB29504.1", "Cavia"] ckr.list_ids ==> [["gi", "2495000"], ["sp", "Q63931", "CCKR_CAVPO"], ["gi", "2147182"], ["pir", nil, "I51898"], ["gi", "544724"], ["gb", "AAB29504.1", nil], ["Cavia"]]
FASTA format (WikiPedia) en.wikipedia.org/wiki/FASTA_format
Fasta format description (NCBI) www.ncbi.nlm.nih.gov/BLAST/fasta.shtml
Copyright |
Copyright (C) 2006 Toshiaki Katayama <k@bioruby.org> |
License |
The Ruby License |
$Id: das.rb,v 1.3 2007/04/05 23:35:41 trevor Exp $
Copyright |
Copyright (C) 2006 Toshiaki Katayama <k@bioruby.org> |
License |
The Ruby License |
Copyright |
Copyright (C) 2006 Toshiaki Katayama <k@bioruby.org>, Ryan Raaum <ryan@raaum.org> |
License |
The Ruby License |
Copyright |
Copyright (C) 2009 Naohisa Goto <ng@bioruby.org> |
License |
The Ruby License |
Sequence quality score manipulation modules, mainly used by Bio::Fastq and related classes.
FASTQ format specification maq.sourceforge.net/fastq.shtml
Copyright |
Copyright (C) 2008 Naohisa Goto <ng@bioruby.org>, |
License |
The Ruby License |
Copyright |
Copyright (C) 2010 Naohisa Goto <ng@bioruby.org> |
License |
The Ruby License |
Bio::Sequence::SequenceMasker is a mix-in module to provide helpful methods for masking a sequence.
For details, see documentation of Bio::Sequence::SequenceMasker.
Copyright |
Copyright (C) 2008 Naohisa Goto <ng@bioruby.org> |
License |
The Ruby License |
Copyright |
Copyright (C) 2006 Toshiaki Katayama <k@bioruby.org>, Ryan Raaum <ryan@raaum.org> |
License |
The Ruby License |
Copyright |
Copyright (C) 2006 Toshiaki Katayama <k@bioruby.org>, Ryan Raaum <ryan@raaum.org> |
License |
The Ruby License |
Copyright |
Copyright (C) 2006 Toshiaki Katayama <k@bioruby.org>, Ryan Raaum <ryan@raaum.org> |
License |
The Ruby License |
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 (Array containing Integer)
Version identifier, including extra version string (String) Unlike BIORUBY_VERSION, it is not comparable.
Provide BioRuby shell 'command' also as 'Bio.command' (like ChemRuby)
# File lib/bio.rb, line 309 def self.method_missing(*args) require 'bio/shell' extend Bio::Shell public_class_method(*Bio::Shell.private_instance_methods) if Bio.respond_to?(args.first) Bio.send(*args) else raise NameError end end
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