[BioRuby-cvs] bioruby/lib/bio/io/flatfile indexer.rb,1.21,1.22

[Naohisa Goto]

Update of /home/repository/bioruby/bioruby/lib/bio/io/flatfile
In directory pub.open-bio.org:/tmp/cvs-serv7939/io/flatfile

Modified Files:
	indexer.rb 
Log Message:
* In lib/bio/db/pdb/chemicalcomponent.rb, added a new class Bio::PDB::ChemicalComponent to parse the PDB Chemical Component Dictionary (PDB style format).
* Added file format autodetection for Bio::PDB::ChemicalComponent.
* Added flatfile indexer for Bio::PDB::ChemicalComponent.


Index: indexer.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/io/flatfile/indexer.rb,v
retrieving revision 1.21
retrieving revision 1.22
diff -C2 -d -r1.21 -r1.22
*** indexer.rb	26 Sep 2005 13:00:08 -0000	1.21
--- indexer.rb	29 Jan 2006 06:54:14 -0000	1.22
***************
*** 81,84 ****
--- 81,86 ----
            when 'Bio::Blast::WU::Report_TBlast'
              BlastDefaultParser.new(Bio::Blast::WU::Report_TBlast, *arg)
+           when 'Bio::PDB::ChemicalComponent'
+             PDBChemicalComponentParser.new(Bio::PDB::ChemicalComponent, *arg)
            else
              raise 'unknown or unsupported format'
***************
*** 437,440 ****
--- 439,471 ----
            end
          end #class BlastDefaultReportParser
+ 
+         class PDBChemicalComponentParser < TemplateParser
+           NAMESTYLE = NameSpaces.new(
+              NameSpace.new( 'UNIQUE', Proc.new { |x| x.entry_id } )
+                                      )
+           PRIMARY = 'UNIQUE'
+           def initialize(klass, pri_name = nil, sec_names = nil)
+             super()
+             self.format = 'raw'
+             self.dbclass = Bio::PDB::ChemicalComponent
+             self.set_primary_namespace((pri_name or PRIMARY))
+             unless sec_names then
+               sec_names = []
+               @namestyle.each_value do |x|
+                 sec_names << x.name if x.name != self.primary.name
+               end
+             end
+             self.add_secondary_namespaces(*sec_names)
+           end
+           def open_flatfile(fileid, file)
+             super
+             @flatfile.pos = 0
+             begin
+               pos = @flatfile.pos
+               line = @flatfile.gets
+             end until (!line or line =~ /^RESIDUE /)
+             @flatfile.pos = pos
+           end
+         end #class PDBChemicalComponentParser
  
        end #module Parser