[BioRuby-cvs] bioruby/lib bio.rb,1.44,1.45
Katayama Toshiaki
k at pub.open-bio.org
Wed Sep 7 21:15:54 EDT 2005
Update of /home/repository/bioruby/bioruby/lib
In directory pub.open-bio.org:/tmp/cvs-serv8937/lib
Modified Files:
bio.rb
Log Message:
* require -> autoload (lost compatibility with Ruby 1.6 but runs
at least 3 times faster by Ruby 1.8)
Index: bio.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio.rb,v
retrieving revision 1.44
retrieving revision 1.45
diff -C2 -d -r1.44 -r1.45
*** bio.rb 10 Aug 2005 12:56:37 -0000 1.44
--- bio.rb 8 Sep 2005 01:15:52 -0000 1.45
***************
*** 22,156 ****
module Bio
- BIORUBY_VERSION = [0, 6, 4].extend(Comparable)
- end
! ### Basic data type modules
! ## Sequence
! require 'bio/sequence'
! ## Locations/Location
! require 'bio/location'
! ## Features/Feature
! require 'bio/feature'
! ## References/Reference
! require 'bio/reference'
! ## Pathway/Relation
! require 'bio/pathway'
! ## Alignment
! require 'bio/alignment'
! ### Constants
! require 'bio/data/na'
! require 'bio/data/aa'
! require 'bio/data/codontable'
! ### DB parsers
! require 'bio/db'
! ## GenBank/RefSeq/DDBJ
! require 'bio/db/genbank'
! ## EMBL/TrEMBL/Swiss-Prot/SPTR
! require 'bio/db/embl'
! ## KEGG
! require 'bio/db/kegg/genome'
! require 'bio/db/kegg/genes'
! require 'bio/db/kegg/enzyme'
! require 'bio/db/kegg/compound'
! require 'bio/db/kegg/glycan'
! require 'bio/db/kegg/reaction'
! require 'bio/db/kegg/brite'
! require 'bio/db/kegg/cell'
! require 'bio/db/kegg/microarray'
! require 'bio/db/kegg/keggtab'
! require 'bio/db/kegg/ko'
- ## other formats
! require 'bio/db/fasta'
! require 'bio/db/gff'
! require 'bio/db/aaindex'
! require 'bio/db/transfac'
! require 'bio/db/prosite'
! require 'bio/db/litdb'
! require 'bio/db/medline'
! require 'bio/db/fantom'
! require 'bio/db/go'
! require 'bio/db/pdb'
! require 'bio/db/nbrf'
! ### IO interface modules
! require 'bio/io/registry'
! require 'bio/io/flatfile'
! require 'bio/io/flatfile/indexer'
! require 'bio/io/flatfile/index'
! require 'bio/io/flatfile/bdb'
! require 'bio/io/fastacmd'
! require 'bio/io/fetch'
! require 'bio/io/sql'
- require 'bio/io/dbget'
- require 'bio/io/keggapi'
- require 'bio/io/pubmed'
- require 'bio/io/das'
- require 'bio/io/ddbjxml'
- require 'bio/io/higet'
- #require 'bio/io/esoap'
- #require 'bio/io/brdb'
! ### Applications
! require 'bio/appl/fasta'
! require 'bio/appl/fasta/format10'
! require 'bio/appl/blast'
! require 'bio/appl/blast/report'
! require 'bio/appl/blast/format0'
! require 'bio/appl/blast/wublast'
! require 'bio/appl/blast/rexml'
! require 'bio/appl/blast/xmlparser'
! require 'bio/appl/blast/format8'
! require 'bio/appl/bl2seq/report'
! require 'bio/appl/hmmer'
! require 'bio/appl/hmmer/report'
! require 'bio/appl/emboss'
! require 'bio/appl/psort'
! require 'bio/appl/tmhmm/report'
! require 'bio/appl/targetp/report'
! require 'bio/appl/sosui/report'
! require 'bio/appl/genscan/report'
! require 'bio/appl/clustalw'
! require 'bio/appl/clustalw/report'
! require 'bio/appl/mafft'
! require 'bio/appl/mafft/report'
! require 'bio/appl/sim4'
! require 'bio/appl/sim4/report'
! require 'bio/appl/spidey/report'
! require 'bio/appl/blat/report'
! ### Utilities
! require 'bio/util/sirna'
--- 22,234 ----
module Bio
+ BIORUBY_VERSION = [0, 7, 0].extend(Comparable)
! ### Basic data types
! ## Sequence
! autoload :Seq, 'bio/sequence'
! autoload :Sequence, 'bio/sequence'
! ## Locations/Location
! autoload :Location, 'bio/location'
! autoload :Locations, 'bio/location'
! ## Features/Feature
! autoload :Feature, 'bio/feature'
! autoload :Features, 'bio/feature' # to_gff
! ## References/Reference
! autoload :Reference, 'bio/reference'
! autoload :References, 'bio/reference'
! ## Pathway/Relation
! autoload :Pathway, 'bio/pathway'
! autoload :Relation, 'bio/pathway'
! ## Alignment
! autoload :Alignment, 'bio/alignment'
! ### Constants
! autoload :NucleicAcid, 'bio/data/na'
! autoload :AminoAcid, 'bio/data/aa'
! autoload :CodonTable, 'bio/data/codontable'
! ### DB parsers
! autoload :DB, 'bio/db'
! autoload :NCBIDB, 'bio/db'
! autoload :KEGGDB, 'bio/db'
! autoload :EMBLDB, 'bio/db'
! ## GenBank/RefSeq/DDBJ
! # module Bio
! # autoload :NCBIDB, 'bio/db'
! # class GenBank < NCBIDB
! # autoload :Common, 'bio/db/genbank/common'
! # include Bio::GenBank::Common
! # module Bio
! # autoload :NCBIDB, 'bio/db'
! # end
! # class Bio::GenBank < Bio::NCBIDB
! # autoload :Common, 'bio/db/genbank/common'
! # include Bio::GenBank::Common
! autoload :GenBank, 'bio/db/genbank/genbank'
! autoload :GenPept, 'bio/db/genbank/genpept'
! autoload :RefSeq, 'bio/db/genbank/refseq'
! autoload :DDBJ, 'bio/db/genbank/ddbj'
! ## EMBL/TrEMBL/Swiss-Prot/SPTR
! autoload :EMBL, 'bio/db/embl/embl'
! autoload :SPTR, 'bio/db/embl/sptr'
! autoload :TrEMBL, 'bio/db/embl/trembl'
! autoload :UniProt, 'bio/db/embl/uniprot'
! autoload :SwissProt, 'bio/db/embl/swissprot'
! ## KEGG
+ class KEGG
+ autoload :GENOME, 'bio/db/kegg/genome'
+ autoload :GENES, 'bio/db/kegg/genes'
+ autoload :ENZYME, 'bio/db/kegg/enzyme'
+ autoload :COMPOUND, 'bio/db/kegg/compound'
+ autoload :GLYCAN, 'bio/db/kegg/glycan'
+ autoload :REACTION, 'bio/db/kegg/reaction'
+ autoload :BRITE, 'bio/db/kegg/brite'
+ autoload :CELL, 'bio/db/kegg/cell'
+ autoload :Microarray, 'bio/db/kegg/microarray'
+ autoload :Microarrays, 'bio/db/kegg/microarray'
+ autoload :Keggtab, 'bio/db/kegg/keggtab'
+ autoload :KO, 'bio/db/kegg/ko'
+ end
! ## other formats
! autoload :FastaFormat, 'bio/db/fasta'
! autoload :FastaNumericFormat, 'bio/db/fasta' # change to FastaFormat::Numeric ?
! autoload :FastaDefline, 'bio/db/fasta' # change to FastaFormat::Defline
! autoload :GFF, 'bio/db/gff'
! autoload :GFF2, 'bio/db/gff' # change to GFF::GFF2, improve
! autoload :GFF3, 'bio/db/gff' # change to GFF::GFF3, improve
! autoload :AAindex, 'bio/db/aaindex'
! autoload :TRANSFAC, 'bio/db/transfac'
! autoload :TFMATRIX, 'bio/db/transfac' # change to TRANSFAC::MATRIX
! autoload :TFSITE, 'bio/db/transfac' # change to TRANSFAC::SITE
! autoload :TFFACTOR, 'bio/db/transfac' # change to TRANSFAC::FACTOR
! autoload :TFCELL, 'bio/db/transfac' # change to TRANSFAC::CELL
! autoload :TFCLASS, 'bio/db/transfac' # change to TRANSFAC::CLASS
! autoload :TFGENE, 'bio/db/transfac' # change to TRANSFAC::GENE
! autoload :PROSITE, 'bio/db/prosite'
! autoload :LITDB, 'bio/db/litdb'
! autoload :MEDLINE, 'bio/db/medline'
! autoload :FANTOM, 'bio/db/fantom'
! autoload :GO, 'bio/db/go'
! autoload :PDB, 'bio/db/pdb'
! autoload :NBRF, 'bio/db/nbrf'
+ ### IO interface modules
! autoload :Registry, 'bio/io/registry'
! autoload :Fetch, 'bio/io/fetch'
! autoload :SQL, 'bio/io/sql'
! autoload :FlatFile, 'bio/io/flatfile'
! autoload :FlatFileIndex, 'bio/io/flatfile/index' # chage to FlatFile::Index ?
! class FlatFileIndex
! autoload :Indexer, 'bio/io/flatfile/indexer' # require 'flatfile/index'
! autoload :BDBdefault, 'bio/io/flatfile/bdb' # require 'flatfile/index'
! end
! autoload :PubMed, 'bio/io/pubmed'
! autoload :DAS, 'bio/io/das'
! autoload :DBGET, 'bio/io/dbget'
! class Blast
! autoload :Fastacmd, 'bio/io/fastacmd'
! end
! class KEGG
! autoload :API, 'bio/io/keggapi'
! end
+ class DDBJ
+ autoload :XML, 'bio/io/ddbjxml'
+ end
+
+ class HGC
+ autoload :HiGet, 'bio/io/higet'
+ end
+
+ # autoload :ESOAP, 'bio/io/esoap' # NCBI::ESOAP ?
+ # autoload :BRDB, 'bio/io/brdb' # remove
+
+
+ ### Applications
+
+ autoload :Fasta, 'bio/appl/fasta'
+ autoload :Report, 'bio/appl/fasta/format10' # improve format6
+
+ autoload :Blast, 'bio/appl/blast'
+ class Blast
+ autoload :Report, 'bio/appl/blast/report'
+ autoload :Default, 'bio/appl/blast/format0'
+ autoload :WU, 'bio/appl/blast/wublast'
+ autoload :Bl2seq, 'bio/appl/bl2seq/report'
+ end
+
+ autoload :HMMER, 'bio/appl/hmmer'
+ class HMMER
+ autoload :Report, 'bio/appl/hmmer/report'
+ end
+
+ # autoload :EMBOSS, 'bio/appl/emboss' # use bio/command, improve
+
+ autoload :PSORT, 'bio/appl/psort'
+ class PSORT
+ autoload :PSORT1, 'bio/appl/psort'
+ autoload :PSORT2, 'bio/appl/psort'
+ end
+
+ autoload :TMHMM, 'bio/appl/tmhmm/report'
+ autoload :TargetP, 'bio/appl/targetp/report'
+ autoload :SOSUI, 'bio/appl/sosui/report'
+ autoload :Genscan, 'bio/appl/genscan/report'
+
+ autoload :ClustalW, 'bio/appl/clustalw'
+ class ClustalW
+ autoload :Report, 'bio/appl/clustalw/report'
+ end
+
+ autoload :MAFFT, 'bio/appl/mafft'
+ class MAFFT
+ autoload :Report, 'bio/appl/mafft/report'
+ end
+
+ autoload :Sim4, 'bio/appl/sim4'
+ class Sim4
+ autoload :Report, 'bio/appl/sim4/report'
+ end
+
+ autoload :Spidey, 'bio/appl/spidey/report'
+ autoload :Blat, 'bio/appl/blat/report'
+
+
+ ### Utilities
+
+ autoload :SiRNA, 'bio/util/sirna'
+
+ end
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