Class: SwissprotDatabase

Inherits:
Object
  • Object
show all
Defined in:
lib/protk/swissprot_database.rb

Overview

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

Instance Method Summary collapse

Constructor Details

#initialize(datfile_path, skip_indexing = false) ⇒ SwissprotDatabase

Returns a new instance of SwissprotDatabase.



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# 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

Instance Method Details

#get_entry_for_name(name) ⇒ Object 



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# 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