[BioRuby-cvs] bioruby/lib/bio/db/embl sptr.rb,1.26,1.27

[Mitsuteru C. Nakao]

Update of /home/repository/bioruby/bioruby/lib/bio/db/embl
In directory pub.open-bio.org:/tmp/cvs-serv4056/lib/bio/db/embl

Modified Files:
	sptr.rb 
Log Message:
* Updated RDoc documents.
* Chaged Bio::EMBL::Common to Bio::EMBLDB::Common. 


Index: sptr.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/db/embl/sptr.rb,v
retrieving revision 1.26
retrieving revision 1.27
diff -C2 -d -r1.26 -r1.27
*** sptr.rb	23 Oct 2005 08:59:43 -0000	1.26
--- sptr.rb	27 Oct 2005 09:30:42 -0000	1.27
***************
*** 106,110 ****
  
  
!   # Bio::EMBL::Common#ac  -> ary
    #                  #accessions  -> ary
    #                  #accession  -> String (accessions.first)
--- 106,110 ----
  
  
!   # Bio::EMBLDB::Common#ac  -> ary
    #                  #accessions  -> ary
    #                  #accession  -> String (accessions.first)
***************
*** 206,209 ****
--- 206,210 ----
    end
  
+   # returns contents in the old style GN line.
    # GN Line: Gene name(s) (>=0, optional)
    #  GN   HNS OR DRDX OR OSMZ OR BGLY.
***************
*** 230,234 ****
    private :gn_old_parser
  
! 
    # The new format of the GN line is:
    #  GN   Name=; Synonyms=[, ...]; OrderedLocusNames=[, ...];
--- 231,235 ----
    private :gn_old_parser
  
!   # returns contents in the structured GN line.
    # The new format of the GN line is:
    #  GN   Name=; Synonyms=[, ...]; OrderedLocusNames=[, ...];
***************
*** 323,327 ****
    
  
!   # Bio::EMBL::Common#og -> Array
    # OG Line; organella (0 or 1/entry)
    # ["MITOCHONDRION", "CHLOROPLAST", "Cyanelle", "Plasmid"]
--- 324,328 ----
    
  
!   # Bio::EMBLDB::Common#og -> Array
    # OG Line; organella (0 or 1/entry)
    # ["MITOCHONDRION", "CHLOROPLAST", "Cyanelle", "Plasmid"]
***************
*** 329,333 ****
  
  
!   # Bio::EMBL::Common#oc -> Array
    # OC Line; organism classification (>=1)
    # "OC   Eukaryota; Alveolata; Apicomplexa; Piroplasmida; Theileriidae;"
--- 330,334 ----
  
  
!   # Bio::EMBLDB::Common#oc -> Array
    # OC Line; organism classification (>=1)
    # "OC   Eukaryota; Alveolata; Apicomplexa; Piroplasmida; Theileriidae;"
***************
*** 357,361 ****
  
    
!   # Bio::EMBL::Common#ref -> Array
    # R Lines
    # RN RC RP RX RA RT RL
--- 358,362 ----
  
    
!   # Bio::EMBLDB::Common#ref -> Array
    # R Lines
    # RN RC RP RX RA RT RL
***************
*** 513,516 ****
--- 514,520 ----
        return tmp
  
+     when 'INTERACTION'
+       return cc_interaction_parse(@data['CC']['INTERACTION'].to_s)
+ 
      when nil
        return @data['CC']	
***************
*** 522,525 ****
--- 526,530 ----
  
  
+ 
    def cc_ap_variants_parse(ent)
      hsh = {}
***************
*** 536,539 ****
--- 541,556 ----
  
  
+   # returns conteins in a line of the CC INTERACTION section.
+   #
+   #  CC       P46527:CDKN1B; NbExp=1; IntAct=EBI-359815, EBI-519280;
+   def cc_interaction_parse(str)
+     it = str.scan(/(.+?); NbExp=(.+?); IntAct=(.+?);/)
+     it.map {|ent|
+       {:partner_id => ent[0].strip,
+        :nbexp => ent[1].strip, 
+        :intact_acc => ent[2].split(', ') }
+     }
+   end
+   private :cc_interaction_parse
  
    # returns databases cross-references in the DR lines.
***************
*** 550,555 ****
      'SWISS-2DPAGE','TIGR','TRANSFAC','TUBERCULIST','WORMPEP','YEPD','ZFIN']
  
!   # Bio::EMBL::Common#kw - Array
!   #            #keywords  -> Array
    #
    # KW Line; keyword (>=1)
--- 567,572 ----
      'SWISS-2DPAGE','TIGR','TRANSFAC','TUBERCULIST','WORMPEP','YEPD','ZFIN']
  
!   # Bio::EMBLDB::Common#kw - Array
!   #                    #keywords  -> Array
    #
    # KW Line; keyword (>=1)