class SwissprotDatabase

Provides fast indexed access to a swissprot database in a flat .dat file

Public Class Methods

new(datfile_path,skip_indexing=false) click to toggle source
# File lib/protk/swissprot_database.rb, line 10
def initialize(datfile_path,skip_indexing=false)

  dbpath=Pathname.new(datfile_path)
  dbclass=Bio::SPTR

  unless skip_indexing
    parser = Bio::FlatFileIndex::Indexer::Parser.new(dbclass, nil, nil)
    Bio::FlatFileIndex::Indexer::makeindexFlat(dbpath.realpath.dirname.to_s, parser, {}, \
      dbpath.realpath.to_s)
  end
    
  @db_object=Bio::FlatFileIndex.new("#{dbpath.realpath.dirname.to_s}")
  
  @db_object.always_check_consistency=false
end

Public Instance Methods

get_entry_for_name(name) click to toggle source
# File lib/protk/swissprot_database.rb, line 27
def get_entry_for_name(name)
  result=@db_object.get_by_id(name)
  if result==""
    return nil
  else
    Bio::SPTR.new(result)
  end
end