bio 0.7.0

data/doc/BioRuby.rd.ja

@@ -0,0 +1,225 @@
+=begin
+
+  $Id: BioRuby.rd.ja,v 1.10 2004/08/23 23:41:29 k Exp $
+
+  Copyright (C) 2001, 2002 KATAYAMA Toshiaki <k@bioruby.org>
+
+= BioRuby �ץ���������
+
+BioRuby �ϡ�Bioinformatics ��ɬ�פȤ���롢�ǡ����١����θ������ǡ�����
+�����ȥѡ�����������Ϥ���ѥ����������Ϥޤ��͡��ʷ׻����ʤɤ�ɬ�פȤʤ�
+�͡��ʵ�ǽ�� Ruby ����Ǽ���������ñ�˰�����褦�ˤ���ץ��������ȤǤ���
+
+¾����ԥץ��������ȤȤ��Ƥ� BioPerl, BioPython, BioJava �ʤ��͡��ʤ��
+������ޤ��������٤Ǥ���ˤ�Ĺ�� BioPerl ���Ǥ⽼�¤��Ƥ���Ȼפ��ޤ�����
+BioPerl ��������Τ�ʣ���ʹ�¤�ǡ��ǡ������󥿡��Ǥ����Ѥ�������ꤵ���
+����褦�˻פ��ޤ��������⤽�� Perl ��ʣ���ʥǡ�����¤�򰷤��ȥ���������
+�ɤ��ɤߤŤ餯�ʤ�ޤ������η�̡����ƥʥ󥹤���ɤ��񤷤��ʤ�ޤ���¾
+�Υץ��������Ȥˤ⤽�줾������������Ȼפ��ޤ�����������ˤ��Ƥ��ȯ�dz�
+ȯ�������ʳ��ˤ��뤳�Ȥ�ͤ���С���ʬ�λȤ��䤹�������ɬ�פʵ�ǽ�����
+���ƹԤäƤ⽽ʬ���ɤ��դ���Ȼפ��ޤ���
+
+BioRuby �Ǥϡ�����ץ�Ƕ��Ϥ� Ruby ����Υ��ɥХ�ơ�������������ʬ����
+�䤹�������ɤǥ���ɥ桼����ɬ�פʵ�ǽ��������Ƥ��������Ȼפ��ޤ����ä�
+Ruby �Τ����륪�֥������ȤȤ���ȯ�ۤϡ���Τ򰷤���ʪ�ؤˤ���ľ������
+�Ϥ�䤹�����󥻥ץȤǤ������ȥ饤�����顼�Ǻ�Ȥ�ʤ������Ǥ��륤�󥿡�
+�ץ꥿����� C �� Java ����٤ƥ����åȤʥ�ܤθ���Ԥˤ������ߤ䤹����
+�פ��ޤ���
+
+�ޤ���Ruby �Ǥ� Perl ����ζ��Ϥ�ʸ��������˲ä���Perl �θ�Ť��� OO ��
+��륪�ޥ��ʥ��䡢�ѽФ��� local, my �ʤɤ����פǡ�ʣ���ʥǡ�����¤�⥯
+�饹�Ǥ��ä����ɽ���Ǥ��뤿�ᡢ�ܼ�Ū����ʬ����ǰ���ƥ����ǥ��󥰤��뤳
+�Ȥ��Ǥ��ޤ�������ˤ�ꡢ��ȯ�θ�Ψ��⤯�ʤ뤿�ᡢ¾�Υץ��������Ȥ���
+�ݤ��Ƥ��ʤ��ΰ�ˤ⤤���᤯����Ȥ�Ǥ�����Ȼפ��ޤ���
+
+����ˡ�Ruby ���Τ����ܤdz�ȯ���줿����Ǥ���Τ˲ä� BioRuby �����ܽ��
+�����ץ�� Bio* �ץ��������ȤǤ������Τ��ᡢ�������ܸ������졢��ȯ��
+���ܸ�ǹԤʤ�������KEGG �ʤ������ȼ��Υ����ƥ�ؤ��б��ʤɤ�Ԥʤ��䤹
+������ BioRuby �Υ��åȤǤ��礦��
+
+BioRuby �Υ����֥����� ((<URL:http://bioruby.org/>)) �ǡ��ǿ��Τ��Τ餻��
+��������������ˡ���᡼��󥰥ꥹ�Ȥʤɤξ���ȡ�¾�Υɥ�����Ȥ䥳���
+�Ȥʤɤξ��������ޤ���
+
+== �Ȥ���
+
+BioRuby ��Ȥ�������ץȤ����
+
+  require 'bio'
+
+�Ȥ��Ƥ���������
+
+���ƤΥ��饹�� module Bio �β����ɲä���ޤ�����ɬ�פ˱�����
+
+  include Bio
+
+�Ȥ��뤳�Ȥǡ�Bio:: ��ʤ��Ƴƥ��饹��Ȥ������Ǥ��ޤ���
+
+== BioRuby �γ�ά
+
+bio.rb �� require ����ȡ��ʲ��Υ��饹������ʤɤ��Ȥ���褦�ˤʤ�ޤ���
+���߼�������Ƥ����ʵ�ǽ�ϡ�
+
+* ���ߥλ�������������Ρ������䥦����ɥ��������ʤɤ�ޤ���
+  ���ץ饤���󥰤ʤɤ�ɽ�� GenBank ������ location �ե����ޥåȤν���
+* BLAST/FASTA �ʤɤ��Ѥ�����Ʊ������
+* ���Υ�ͥå� ((<URL:http://www.genome.jp>)) �θ����ȥǡ�������
+* GenBank �� KEGG �ʤ��͡��ʥǡ����١����κ٤����ѡ���
+* PubMed/MEDLINE �ʤɤΰ���ʸ���ǡ����μ���������
+* �ѥ����������Ϥ�ɬ�פʥ���դȣ���ط������
+
+�ʤɤǤ����ܤ���������ˡ�ˤĤ��Ƥϡ��ġ��Υ��饹�˴ؤ���ɥ�����Ȥ䡢
+���塼�ȥꥢ��򻲾Ȥ��Ʋ�������
+
+¾�ˡ��ޤ�̤����Ǥ��� C ����ˤ�롢���饹����󥰤� Smith-Waterman ��
+�르�ꥺ��μ����ʤɤ�Ԥʤ��Ƥ��ޤ���
+
+=== ���饹����
+
+  class Object				�ե�����			��٥�
+  |- class String
+  |  `- class Bio::Sequence		bio/sequence.rb			stable
+  |	|- class Bio::Sequence::AA	bio/sequence.rb			stable
+  |	`- class Bio::Sequence::NA	bio/sequence.rb			stable
+  |- class Bio::Location		bio/location.rb			stable
+  |- class Bio::Locations		bio/location.rb			stable
+  |- class Bio::Feature			bio/feature.rb			stable
+  |- class Bio::Features		bio/feature.rb			stable
+  |- class Bio::Reference		bio/reference.rb		stable
+  |- class Bio::References		bio/reference.rb		stable
+  |- class Bio::Pathway			bio/pathway.rb			stable
+  |- class Bio::Relation		bio/pathway.rb			stable
+  |- class Bio::FlatFile		bio/io/flatfile.rb		stable
+  |- class Bio::Registry		bio/io/registry.rb		beta
+  |- class Bio::Fetch			bio/io/fetch.rb			stable
+  |- class Bio::SQL			bio/io/sql.rb			beta
+  |- class Bio::DBGET			bio/io/dbget.rb			stable
+  |- class Bio::PubMed			bio/io/pubmed.rb		stable
+  |- class Bio::BRDB			bio/io/brdb.rb			alpha
+  |- class Bio::Fasta			bio/appl/fasta.rb		stable
+  |- class Bio::Fasta::Report::*	bio/appl/fasta/*.rb		stable
+  |- class Bio::Blast			bio/appl/blast.rb		stable
+  |- class Bio::Blast::Report::*	bio/appl/blast/*.rb		stable
+  |- class Bio::DB			bio/db.rb			stable
+  |  |- class Bio::FastaFormat		bio/db/fasta.rb			stable
+  |  |- class Bio::NCBIDB		bio/db.rb			stable
+  |  |	|- class Bio::GenBank		bio/db/genbank/genbank.rb	stable
+  |  |	|  |- class Bio::GenPept	bio/db/genbank/genpept.rb	stable
+  |  |	|  |- class Bio::RefSeq		bio/db/genbank/refseq.rb	stable
+  |  |	|  `- class Bio::DDBJ		bio/db/genbank/ddbj.rb		stable
+  |  |	|- class Bio::MEDLINE		bio/db/medline.rb		stable
+  |  |	|- class Bio::LITDB		bio/db/litdb.rb			stable
+  |  |	`- class Bio::KEGGDB		bio/db.rb			beta
+  |  |	   |- class Bio::AAindex	bio/db/aaindex.rb		beta
+  |  |	   |  |- class Bio::AAindex1	bio/db/aaindex.rb		beta
+  |  |	   |  `- class Bio::AAindex2	bio/db/aaindex.rb		beta
+  |  |	   |- class Bio::KEGG::GENES	bio/db/kegg/genes.rb		stable
+  |  |	   |- class Bio::KEGG::GENOME	bio/db/kegg/genome.rb		stable
+  |  |	   |- class Bio::KEGG::BRITE	bio/db/kegg/brite.rb		alpha
+  |  |	   |- class Bio::KEGG::CELL	bio/db/kegg/cell.rb		beta
+  |  |	   |- class Bio::KEGG::ENZYME	bio/db/kegg/enzyme.rb		alpha
+  |  |	   `- class Bio::KEGG::COMPOUND bio/db/kegg/compound.rb		alpha
+  |  `- class Bio::EMBLDB		bio/db.rb			stable
+  |     |- class Bio::EMBL		bio/db/embl/embl.rb		beta
+  |     |- class Bio::SPTR		bio/db/embl/sptr.rb		beta
+  |     |  |- class Bio::SwissProt	bio/db/embl/swissprot.rb	beta
+  |     |  `- class Bio::TrEMBL		bio/db/embl/swissprot.rb	beta
+  |	|- class Bio::PROSITE		bio/db/prosite.rb		beta
+  |	`- class Bio::TRANSFAC		bio/db/transfac.rb		beta
+  |	    |- class Bio::TFMATRIX	bio/db/transfac.rb		beta
+  |	    |- class Bio::TFSITE	bio/db/transfac.rb		beta
+  |	    |- class Bio::TFFACTOR	bio/db/transfac.rb		beta
+  |	    |- class Bio::TFCELL	bio/db/transfac.rb		beta
+  |	    |- class Bio::TFCLASS	bio/db/transfac.rb		beta
+  |	    `- class Bio::TFGENE	bio/db/transfac.rb		beta
+  |- class Bio::KEGG::DBname		bio/db/kegg/keggtab.rb		beta
+  |- class Bio::KEGG::Keggtab		bio/db/kegg/keggtab.rb		beta
+  |- class Bio::KEGG::Microarray	bio/db/kegg/microarray.rb	alpha
+  `- class Bio::KEGG::Microarrays	bio/db/kegg/microarray.rb	alpha
+
+=== ɸ�९�饹�ؤΥ᥽�å��ɲ�
+
+  class Matrix				bio/matrix.rb			alpha
+  class Vector				bio/matrix.rb			alpha
+  class String				bio/extend.rb			beta
+  class Array				bio/extend.rb			beta
+
+=== �����̾�����֤γ���
+
+  module Bio				�ե�����			������
+  |- AAindex				bio/db/aaindex.rb		class
+  |- AAindex1				bio/db/aaindex.rb		class
+  |- AAindex2				bio/db/aaindex.rb		class
+  |- AminoAcid				bio/data/aa.rb			constant
+  |- AminoAcid_weight			bio/data/aa.rb			constant
+  |- BIORUBY_VERSION			bio.rb				constant
+  |- Blast				bio/appl/blast.rb		class
+  |  `- Report::*			bio/appl/blast/*.rb		class
+  |- BRDB				bio/io/brdb.rb			class
+  |- CodonTable				bio/data/codontable.rb		constant
+  |- DB					bio/db.rb			class
+  |- DBGET				bio/io/dbget.rb			class
+  |- DDBJ				bio/db/genbank/ddbj.rb		class
+  |- EMBL_COMMON			bio/db/embl.rb			module
+  |- EMBL				bio/db/embl/embl.rb		class
+  |- EMBLDB				bio/db.rb			class
+  |- Fasta				bio/appl/fasta.rb		class
+  |  `- Report::*			bio/appl/fasta/*.rb		class
+  |- FastaFormat			bio/db/fasta.rb			class
+  |- FastaNumericFormat			bio/db/fasta.rb			class
+  |- Fetch				bio/io/fetch.rb			class
+  |- FlatFile				bio/io/flatfile.rb		class
+  |- GENBANK_COMMON			bio/db/genbank.rb		module
+  |- GenBank				bio/db/genbank/genbank.rb	class
+  |- GenPept				bio/db/genbank/genpept.rb	class
+  |- KEGG				bio/db/kegg/			class
+  |  |- BRITE				bio/db/kegg/brite.rb		class
+  |  |- CELL				bio/db/kegg/cell.rb		class
+  |  |- COMPOUND			bio/db/kegg/compound.rb		class
+  |  |- ENZYME				bio/db/kegg/enzyme.rb		class
+  |  |- GENES				bio/db/kegg/genes.rb		class
+  |  |- GENOME				bio/db/kegg/genome.rb		class
+  |  |- Keggtab				bio/db/kegg/keggtab.rb		class
+  |  |- DBname				bio/db/kegg/keggtab.rb		class
+  |  |- Microarray			bio/db/kegg/microarray.rb	class
+  |  `- Microarrays			bio/db/kegg/microarray.rb	class
+  |- KEGGDB				bio/db.rb			class
+  |- KEGGORG				bio/data/keggorg.rb		constant
+  |- LITDB				bio/db/litdb.rb			class
+  |- Location				bio/location.rb			class
+  |- Locations				bio/location.rb			class
+  |- MEDLINE				bio/db/medline.rb		class
+  |- NCBIDB				bio/db.rb			class
+  |- NucleicAcid			bio/data/na.rb			constant
+  |- NucleicAcid_weight			bio/data/na.rb			constant
+  |- Pathway				bio/pathway.rb			class
+  |- PROSITE				bio/db/prosite.rb		class
+  |- PubMed				bio/io/pubmed.rb		class
+  |- Reference				bio/reference.rb		class
+  |- RefSeq				bio/db/genbank/refseq.rb	class
+  |- Registry				bio/db/registry.rb		class
+  |- Relation				bio/pathway.rb			class
+  |- Seq				bio/sequence.rb			class
+  |  |- AA				bio/sequence.rb			class
+  |  `- NA				bio/sequence.rb			class
+  |- Sequence				bio/sequence.rb			class
+  |  |- AA				bio/sequence.rb			class
+  |  `- NA				bio/sequence.rb			class
+  |- SwissProt				bio/db/embl/swissprot.rb	class
+  |- SPTR				bio/db/embl/sptr.rb		class
+  |- SQL				bio/io/sql.rb			class
+  |- TFCELL				bio/db/transfac.rb		class
+  |- TFCLASS				bio/db/transfac.rb		class
+  |- TFFACTOR				bio/db/transfac.rb		class
+  |- TFGENE				bio/db/transfac.rb		class
+  |- TFMATRIX				bio/db/transfac.rb		class
+  |- TFSITE				bio/db/transfac.rb		class
+  |- TRANSFAC				bio/db/transfac.rb		class
+  `- TrEMBL				bio/db/embl/trembl.rb		class
+
+=== �ե����볬��
+
+BioRuby �Υե����빽���ˤĤ��Ƥ� Design.rd.ja �򻲾Ȥ��Ƥ���������
+
+=end
+

data/doc/Changes-0.7.rd

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+= Incompatible and important changes since the BioRuby 0.6.4 release
+
+A lot of changes have been made to the BioRuby after the version 0.6.4
+is released.
+
+--- Ruby 1.6 series are no longer supported.
+
+We use autoload functionality and many other libraries bundled in
+Ruby 1.8.2 (such as SOAP, open-uri, pp etc.) by default.
+
+--- BioRuby will be loaded about 30 times faster than before.
+
+As we changed to use autoload instead of require, time required
+to start up the BioRuby library made surprisingly faster.
+
+Other changes (including exciting BioRuby shell etc.) made in this release
+is described in this file.
+
+== New features
+
+--- BioRuby shell
+
+Command line user interface for the BioRuby is included.
+You can invoke the shell by
+
+  % bioruby
+
+--- UnitTest
+
+Test::Unit now covers wide range of the BioRuby library.
+You can run them by
+
+  % ruby test/runner.rb
+
+or
+
+  % ruby install.rb config
+  % ruby install.rb setup
+  % ruby install.rb test
+
+during the installation procedure.
+
+--- Documents
+
+README, README.DEV, doc/Tutorial.rd, doc/Tutorial.rd.ja etc. are updated
+or newly added.
+
+== Incompatible changes
+
+--- Bio::Sequence
+
+* Bio::Sequence::NA#gc_percent returns integer instead of float
+* Bio::Sequence::NA#gc (was aliased to gc_percent) is removed
+
+Previously, GC% is rounded to one decimal place.  However, how many digits
+should be left when rounding the value is not clear and as the GC% is an
+rough measure by its nature, we have changed to return integer part only.
+If you need a precise value, you can calculate it by values from the
+'composition' method by your own criteria.
+
+Also, the 'gc' method is removed as the method name doesn't represent
+its value is ambiguous.
+
+* Bio::Sequence#blast
+* Bio::Sequence#fasta
+
+These two methods are removed.  Use Bio::Blast and Bio::Fasta to execute
+BLAST and FASTA search.
+
+--- Bio::NucleicAcid
+
+Bio::NucleicAcid::Names and Bio::NucleicAcid::Weight no longer exists.
+
+Bio::NucleicAcid::Names is renamed to Bio::NucleicAcid::Data::NAMES and
+can be accessed by Bio::NucleicAcid#names, Bio::NucleicAcid.names methods
+and Bio::NucleicAcid::WEIGHT hash as the Data module is included.
+
+Bio::NucleicAcid::Weight is renamed to Bio::NucleicAcid::Data::Weight and
+can be accessed by Bio::NucleicAcid#weight, Bio::NucleicAcid.weight methods
+and Bio::NucleicAcid::WEIGHT hash as the Data module is included.
+
+--- Bio::AminoAcid
+
+Bio::AminoAcid::Names and Bio::AminoAcid::Weight no longer exists.
+
+Bio::AminoAcid::Names is renamed to Bio::AminoAcid::Data::NAMES and
+can be accessed by Bio::AminoAcid#names, Bio::AminoAcid.names methods
+and Bio::AminoAcid::WEIGHT hash as the Data module is included.
+
+Bio::AminoAcid::Weight is renamed to Bio::AminoAcid::Data::Weight and
+can be accessed by Bio::AminoAcid#weight, Bio::AminoAcid.weight methods
+and Bio::AminoAcid::WEIGHT hash as the Data module is included.
+
+--- Bio::CodonTable
+
+Bio::CodonTable::Tables, Bio::CodonTable::Definitions,
+Bio::CodonTable::Starts, and Bio::CodonTable::Stops
+are renamed to
+Bio::CodonTable::TABLES, Bio::CodonTable::DEFINITIONS,
+Bio::CodonTable::STARTS, and Bio::CodonTable::STOPS
+respectively.
+
+--- Bio::KEGG::Microarrays, Bio::KEGG::Microarray
+
+* lib/bio/db/kegg/microarray.rb is renamed to lib/bio/db/kegg/expression.rb
+* Bio::KEGG::Microarray is renamed to Bio::KEGG::EXPRESSION
+* Bio::KEGG::Microarrays is removed
+
+Bio::KEGG::Microarrays was intended to store a series of microarray
+expressions as a Hash of Array -like data structure,
+
+  gene1 => [exp1, exp2, exp3, ... ]
+  gene2 => [exp1, exp2, exp3, ... ]
+
+however, it is not utilized well and more suitable container class
+can be proposed.  Until then, this class is removed.
+
+#
+# Following changes are suspended for a while (not yet introduced for now)
+#
+# --- Bio::Pathway
+#
+# * Bio::Pathway#nodes returns an Array of the node objects instead of
+#   the number of the node objects.
+# * Bio::Pathway#edges returns an Array of the edge objects instead of
+#   the number of the edge objects.
+#
+
+--- Bio::GenBank
+
+Bio::GenBank#gc is removed as the value can be calculated by the
+Bio::Sequence::NA#gc method and the method is also changed to
+return integer instead of float.
+
+Bio::GenBank#varnacular_name is renamed to Bio::GenBank#vernacular_name
+as it was a typo.
+
+--- Bio::GenBank::Common
+
+* lib/bio/db/genbank/common.rb is removed.
+
+Renamed to Bio::NCBIDB::Common for the simple autoload dependency.
+
+--- Bio::EMBL::Common
+
+* lib/bio/db/embl/common.rb is removed.
+
+Renamed to Bio::EMBLDB::Common for the simple autoload dependency.
+
+--- Bio::KEGG::GENES
+
+* lib/bio/db/kegg/genes.rb
+
+linkdb method is changed to return a Hash of an Array of entry IDs
+instead of a Hash of a entry ID string.
+
+--- Bio::TRANSFAC
+
+* Bio::TFMATRIX is renamed to Bio::TRANSFAC::MATRIX
+* Bio::TFSITE   is renamed to Bio::TRANSFAC::SITE
+* Bio::TFFACTOR is renamed to Bio::TRANSFAC::FACTOR
+* Bio::TFCELL   is renamed to Bio::TRANSFAC::CELL
+* Bio::TFCLASS  is renamed to Bio::TRANSFAC::CLASS
+* Bio::TFGENE   is renamed to Bio::TRANSFAC::GENE
+
+--- Bio::GFF
+
+* Bio::GFF2 is renamed to Bio::GFF::GFF2
+* Bio::GFF3 is renamed to Bio::GFF::GFF3
+
+--- Bio::Alignment
+
+* Old Bio::Alignment class is renamed to Bio::Alignment::OriginalAlignment.
+  Now, new Bio::Alignment is a module. However, you don't mind so much
+  because most of the class methods previously existed are defined
+  to delegate to the new Bio::Alignment::OriginalAlignment class,
+  for keeping backward compatibility.
+* New classes and modules are introduced. Please refer RDoc.
+* each_site and some methods changed to return Bio::Alignment::Site,
+  which inherits Array (previously returned Array).
+* consensus_iupac now returns only standard bases
+  'a', 'c', 'g', 't', 'm', 'r', 'w', 's', 'y', 'k', 'v',
+  'h', 'd', 'b', 'n', or nil (in SiteMethods#consensus_iupac) or
+  '?' (or missing_char, in EnumerableExtension#consensus_iupac).
+  Note that consensus_iupac now does not return u and invalid letters
+  not defined in IUPAC standard even if all bases are equal.
+* There are more and more changes to be written...
+
+--- Bio::PDB
+
+* Bio::PDB::Atom is removed. Instead, please use Bio::PDB::Record::ATOM and
+  Bio::PDB::Record::HETATM.
+* Bio::PDB::FieldDef is removed and Bio::PDB::Record is completely
+  changed. Now, Record is changed from hash to Struct, and
+  method_missing is no longer used.
+* In the "MODEL" record, model_serial is changed to serial.
+* In records, record_type is changed to record_name.
+* In any records, record_type is changed to record_name.
+* In most records contains real numbers, changed to return
+  float values instead of strings.
+* Pdb_AChar, Pdb_Atom, Pdb_Character, Pdb_Continuation,
+  Pdb_Date, Pdb_IDcode, Pdb_Integer, Pdb_LString, Pdb_List,
+  Pdb_Real, Pdb_Residue_name, Pdb_SList, Pdb_Specification_list,
+  Pdb_String, Pdb_StringRJ and Pdb_SymOP are moved under
+  Bio::PDB::DataType.
+* There are more and more changes to be written...
+
+=== Deleted files
+
+: lib/bio/db/genbank.rb
+: lib/bio/db/embl.rb
+
+These files are removed as we changed to use autoload.  You can safely
+replace
+
+  require 'bio/db/genbank'
+
+or
+
+  require 'bio/db/embl'
+
+in your code to
+
+  require 'bio'
+
+and this change will also speeds up loading time if you only need
+one of the sub classes under the genbank/ or embl/ directory.
+
+: lib/bio/extend.rb
+
+This file contained some additional methods to String and Array classes.
+The methods added to Array are already included in Ruby itself since the
+version 1.8, and the methods added to String are moved to the BioRuby shell
+(lib/bio/shell/plugin/seq.rb).
+
+