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|
#
# bio/io/flatfile/bdb.rb - OBDA flatfile index by Berkley DB
#
# Copyright:: Copyright (C) 2002 GOTO Naohisa <ng@bioruby.org>
# License:: The Ruby License
#
# $Id: bdb.rb,v 1.10 2007/04/05 23:35:41 trevor Exp $
#
begin
require 'bdb'
rescue LoadError,NotImplementedError
end
require 'bio/io/flatfile/index'
require 'bio/io/flatfile/indexer'
module Bio
class FlatFileIndex
module BDBdefault
def permission
(0666 & (0777 ^ File.umask))
end
module_function :permission
def flag_read
BDB::RDONLY
end
module_function :flag_read
def flag_write
(BDB::CREATE | BDB::TRUNCATE)
end
module_function :flag_write
def flag_append
'r+'
end
module_function :flag_append
end #module BDBdefault
class BDBwrapper
def initialize(name, filename, *arg)
@dbname = name
@file = nil
@filename = filename
#self.open(*arg)
end
def filename
File.join(@dbname, @filename)
end
def open(flag = BDBdefault.flag_read,
permission = BDBdefault.permission)
unless @file then
DEBUG.print "BDBwrapper: open #{filename}\n"
@file = BDB::Btree.open(filename, nil, flag, permission)
end
true
end
def close
if @file
DEBUG.print "BDBwrapper: close #{filename}\n"
@file.close
@file = nil
end
nil
end
def [](arg)
#self.open
if @file then
@file[arg]
else
nil
end
end
def []=(key, val)
#self.open
@file[key.to_s] = val.to_s
end
def writeback_array(prefix, array, *arg)
self.close
self.open(*arg)
array.each_with_index do |val, key|
@file["#{prefix}#{key}"] = val.to_s
end
end
def keys
if @file then
@file.keys
else
[]
end
end
end #class BDBwrapper
module BDB_1
class BDBMappingFile
def self.open(*arg)
self.new(*arg)
end
def initialize(filename, flag = BDBdefault.flag_read,
permission = BDBdefault.permission)
@filename = filename
@flag = flag
@permission = permission
#@bdb = BDB::Btree.open(@filename, nil, @flag, @permission)
end
attr_reader :filename
attr_accessor :flag, :permission
def open
unless @bdb then
DEBUG.print "BDBMappingFile: open #{@filename}\n"
@bdb = BDB::Btree.open(@filename, nil, @flag, @permission)
true
else
nil
end
end
def close
if @bdb then
DEBUG.print "BDBMappingFile: close #{@filename}\n"
@bdb.close
@bdb = nil
end
nil
end
def records
@bdb.size
end
alias size records
# methods for writing
def add(key, val)
open
val = val.to_a.join("\t")
s = @bdb[key]
if s then
s << "\t"
s << val
val = s
end
@bdb[key] = val
#DEBUG.print "add: key=#{key.inspect}, val=#{val.inspect}\n"
val
end
def add_exclusive(key, val)
open
val = val.to_a.join("\t")
s = @bdb[key]
if s then
raise RuntimeError, "keys must be unique, but key #{key.inspect} already exists"
end
@bdb[key] = val
#DEBUG.print "add_exclusive: key=#{key.inspect}, val=#{val.inspect}\n"
val
end
def add_overwrite(key, val)
open
val = val.to_a.join("\t")
s = @bdb[key]
if s then
DEBUG.print "Warining: overwrote unique id #{key.inspect}\n"
end
@bdb[key] = val
#DEBUG.print "add_overwrite: key=#{key.inspect}, val=#{val.inspect}\n"
val
end
def add_nr(key, val)
open
s = @bdb[key]
if s then
a = s.split("\t")
else
a = []
end
a.concat val.to_a
a.sort!
a.uniq!
str = a.join("\t")
@bdb[key] = str
#DEBUG.print "add_nr: key=#{key.inspect}, val=#{str.inspect}\n"
str
end
# methods for searching
def search(key)
open
s = @bdb[key]
if s then
a = s.split("\t")
a
else
[]
end
end
end #class BDBMappingFile
class PrimaryNameSpace < Template::NameSpace
def mapping(filename)
BDBMappingFile.new(filename)
end
def filename
File.join(dbname, "key_#{name}")
end
def search(key)
r = super(key)
unless r.empty? then
[ r ]
else
r
end
end
end #class PrimaryNameSpace
class SecondaryNameSpace < Template::NameSpace
def mapping(filename)
BDBMappingFile.new(filename)
end
def filename
File.join(dbname, "id_#{name}")
end #class SecondaryNameSpaces
def search(key)
r = super(key)
file.close
r
end
end #class SecondaryNameSpace
end #module BDB_1
end #class FlatFileIndex
end #module Bio
=begin
* Classes/modules in this file are internal use only.
=end
|
