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# Copyright 2001 by Gavin E. Crooks. All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
# This functionality may be of general use, in which case this module should
# be moved out of the SCOP package.
class defaultdict(dict):
def __init__(self, default=None):
dict.__init__(self)
self.default = default
def __getitem__(self, key):
try:
return dict.__getitem__(self, key)
except KeyError:
return self.default
class FileIndex(dict) :
""" An in memory index that allows rapid random access into a file.
The class can be used to turn a file into a read-only
database.
"""
def __init__(self, filename, iterator_gen, key_gen ) :
"""
Arguments:
filename -- The file to index
iterator_gen -- A function that eats a file handle, and returns
a file iterator. The iterator has a method next()
that returns the next item to be indexed from the file.
key_gen -- A function that generates an index key from the items
created by the iterator.
"""
dict.__init__(self)
self.filename = filename
self.iterator_gen = iterator_gen
f = open(self.filename)
try:
loc = 0
i = self.iterator_gen(f)
while 1 :
next_thing = i.next()
if next_thing is None : break
key = key_gen(next_thing)
if key != None :
self[key]=loc
loc = f.tell()
finally :
f.close()
def __getitem__(self, key) :
""" Return an item from the indexed file. """
loc = dict.__getitem__(self,key)
f = open(self.filename)
try:
f.seek(loc)
thing = self.iterator_gen(f).next()
finally:
f.close()
return thing
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