[BioRuby-cvs] bioruby/lib/bio/db/embl sptr.rb,1.32,1.33

[Mitsuteru C. Nakao]

Update of /home/repository/bioruby/bioruby/lib/bio/db/embl
In directory dev.open-bio.org:/tmp/cvs-serv25655/lib/bio/db/embl

Modified Files:
	sptr.rb 
Log Message:
* Added codes for "Changes concerning the copyright statement"
  (http://www.expasy.org/sprot/relnotes/sp_news.html#rel7).


Index: sptr.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/db/embl/sptr.rb,v
retrieving revision 1.32
retrieving revision 1.33
diff -C2 -d -r1.32 -r1.33
*** sptr.rb	16 Jun 2006 17:01:01 -0000	1.32
--- sptr.rb	11 Jul 2006 15:52:51 -0000	1.33
***************
*** 354,362 ****
  
  
!   @@cc_topics = ['ALTERNATIVE PRODUCTS','CATALYTIC ACTIVITY','CAUTION',
!     'COFACTOR','DATABASE','DEVELOPMENTAL STAGE','DISEASE','DOMAIN',
!     'ENZYME REGULATION','FUNCTION','INDUCTION','MASS SPECTROMETRY',
!     'MISCELLANEOUS','PATHWAY','PHARMACEUTICAL','POLYMORPHISM','PTM',
!     'SIMILARITY','SUBCELLULAR LOCATION','SUBUNIT','TISSUE SPECIFICITY']
    # returns contents in the CC lines.
    # * Bio::SPTR#cc -> Hash
--- 354,384 ----
  
  
!   @@cc_topics = ['PHARMACEUTICAL',
!                  'BIOTECHNOLOGY',
!                  'TOXIC DOSE', 
!                  'ALLERGEN',   
!                  'RNA EDITING',
!                  'POLYMORPHISM',
!                  'BIOPHYSICOCHEMICAL PROPERTIES',
!                  'MASS SPECTROMETRY',
!                  'WEB RESOURCE', 
!                  'ENZYME REGULATION',
!                  'DISEASE',
!                  'INTERACTION',
!                  'DEVELOPMENTAL STAGE',
!                  'INDUCTION',
!                  'CAUTION',
!                  'ALTERNATIVE PRODUCTS',
!                  'DOMAIN',
!                  'PTM',
!                  'MISCELLANEOUS',
!                  'TISSUE SPECIFICITY',
!                  'COFACTOR',
!                  'PATHWAY',
!                  'SUBUNIT',
!                  'CATALYTIC ACTIVITY',
!                  'SUBCELLULAR LOCATION',
!                  'FUNCTION',
!                  'SIMILARITY']
    # returns contents in the CC lines.
    # * Bio::SPTR#cc -> Hash
***************
*** 398,401 ****
--- 420,425 ----
    #   CC       SECOND AND SUBSEQUENT LINES OF A COMMENT BLOCK.
    #
+   # See also http://www.expasy.org/sprot/userman.html#CC_line
+   #
    def cc(tag = nil)
      unless @data['CC']
***************
*** 404,411 ****
        dlm = /-!- /
  
!       return cc if get('CC').size == 0 # 12KD_MYCSM has no CC lines.
  
        begin
!         fetch('CC').split(/#{cmt}/)[0].sub(dlm,'').split(dlm).each do |tmp|
            if /(^[A-Z ]+[A-Z]): (.+)/ =~ tmp
              key  = $1
--- 428,443 ----
        dlm = /-!- /
  
!       # 12KD_MYCSM has no CC lines.
!       return cc if get('CC').size == 0
!       
!       cc_raw = fetch('CC')
! 
!       cc_raw.sub!(/ *---.+---/m, '')
!       # Not any CC Lines without the copyright statement.
!       return cc if cc_raw == ''
! 
  
        begin
!         cc_raw.split(/#{cmt}/)[0].sub(dlm,'').split(dlm).each do |tmp|
            if /(^[A-Z ]+[A-Z]): (.+)/ =~ tmp
              key  = $1