+++ /dev/null
-# Copyright 1999 by Jeffrey Chang. 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.
-
-"""Index.py
-
-This module provides a way to create indexes to text files.
-
-Classes:
-Index Dictionary-like class used to store index information.
-
-_ShelveIndex An Index class based on the shelve module.
-_InMemoryIndex An in-memory Index class.
-
-"""
-import os
-import array
-import cPickle
-import shelve
-
-class _ShelveIndex(dict):
- """An index file wrapped around shelve.
-
- """
- # Without a good dbm module installed, this is pretty slow and
- # generates large files. When generating an index on a FASTA-
- # formatted file with 82000 sequences (37Mb), the
- # index 'dat' file is 42Mb and 'dir' file is 8Mb.
-
- __version = 2
- __version_key = '__version'
-
- def __init__(self, indexname, truncate=None):
- dict.__init__(self)
- try:
- if truncate:
- # In python 1.52 and before, dumbdbm (under shelve)
- # doesn't clear the old database.
- files = [indexname + '.dir',
- indexname + '.dat',
- indexname + '.bak'
- ]
- for file in files:
- if os.path.exists(file):
- os.unlink(file)
- raise Exception("open a new shelf")
- self.data = shelve.open(indexname, flag='r')
- except:
- # No database exists.
- self.data = shelve.open(indexname, flag='n')
- self.data[self.__version_key] = self.__version
- else:
- # Check to make sure the database is the correct version.
- version = self.data.get(self.__version_key, None)
- if version is None:
- raise IOError("Unrecognized index format")
- elif version != self.__version:
- raise IOError("Version %s doesn't match my version %s" \
- % (version, self.__version))
-
- def __del__(self):
- if self.__dict__.has_key('data'):
- self.data.close()
-
-class _InMemoryIndex(dict):
- """This creates an in-memory index file.
-
- """
- # File Format:
- # version
- # key value
- # [...]
-
- __version = 3
- __version_key = '__version'
-
- def __init__(self, indexname, truncate=None):
- self._indexname = indexname
- dict.__init__(self)
- self.__changed = 0 # the index hasn't changed
-
- # Remove the database if truncate is true.
- if truncate and os.path.exists(indexname):
- os.unlink(indexname)
- self.__changed = 1
-
- # Load the database if it exists
- if os.path.exists(indexname):
- handle = open(indexname)
- version = self._toobj(handle.readline().rstrip())
- if version != self.__version:
- raise IOError("Version %s doesn't match my version %s" \
- % (version, self.__version))
- for line in handle:
- key, value = line.split()
- key, value = self._toobj(key), self._toobj(value)
- self[key] = value
- self.__changed = 0
-
- def update(self, dict):
- self.__changed = 1
- dict.update(self, dict)
- def __setitem__(self, key, value):
- self.__changed = 1
- dict.__setitem__(self, key, value)
- def __delitem__(self, key):
- self.__changed = 1
- dict.__delitem__(self, key)
- def clear(self):
- self.__changed = 1
- dict.clear(self)
-
- def __del__(self):
- if self.__changed:
- handle = open(self._indexname, 'w')
- handle.write("%s\n" % self._tostr(self.__version))
- for key, value in self.items():
- handle.write("%s %s\n" %
- (self._tostr(key), self._tostr(value)))
- handle.close()
-
- def _tostr(self, obj):
- # I need a representation of the object that's saveable to
- # a file that uses whitespace as delimiters. Thus, I'm
- # going to pickle the object, and then convert each character of
- # the string to its ASCII integer value. Then, I'm going to convert
- # the integers into strings and join them together with commas.
- # It's not the most efficient way of storing things, but it's
- # relatively fast.
- s = cPickle.dumps(obj)
- intlist = array.array('b', s)
- strlist = map(str, intlist)
- return ','.join(strlist)
-
- def _toobj(self, str):
- intlist = map(int, str.split(','))
- intlist = array.array('b', intlist)
- strlist = map(chr, intlist)
- return cPickle.loads(''.join(strlist))
-
-Index = _InMemoryIndex
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