Class: Bio::FlatFileIndex::Indexer::Parser::PDBChemicalComponentParser
- Inherits:
-
TemplateParser
- Object
- TemplateParser
- Bio::FlatFileIndex::Indexer::Parser::PDBChemicalComponentParser
- Defined in:
- lib/bio/io/flatfile/indexer.rb
Overview
class BlastDefaultReportParser
Constant Summary collapse
- NAMESTYLE =
NameSpaces.new( NameSpace.new( 'UNIQUE', Proc.new { |x| x.entry_id } ) )
- PRIMARY =
'UNIQUE'
Instance Attribute Summary
Attributes inherited from TemplateParser
#dbclass, #errorlog, #fileid, #format, #primary, #secondary
Instance Method Summary collapse
-
#initialize(klass, pri_name = nil, sec_names = nil) ⇒ PDBChemicalComponentParser
constructor
A new instance of PDBChemicalComponentParser.
- #open_flatfile(fileid, file) ⇒ Object
Methods inherited from TemplateParser
#add_secondary_namespaces, #close_flatfile, #each, #parse_primary, #parse_secondary, #set_primary_namespace
Constructor Details
#initialize(klass, pri_name = nil, sec_names = nil) ⇒ PDBChemicalComponentParser
Returns a new instance of PDBChemicalComponentParser.
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# File 'lib/bio/io/flatfile/indexer.rb', line 425 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 |
Instance Method Details
#open_flatfile(fileid, file) ⇒ Object
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# File 'lib/bio/io/flatfile/indexer.rb', line 438 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 |