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# Copyright 2012 by Wibowo Arindrarto. All rights reserved.
# Revisions copyright 2012-2016 by Peter Cock. All rights reserved.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""Custom indexing for Bio.SearchIO objects."""
from io import StringIO
from Bio.File import _IndexedSeqFileProxy
from Bio.File import _open_for_random_access
class SearchIndexer(_IndexedSeqFileProxy):
"""Base class for file format specific random access.
Subclasses for each file format should define '_parser' and optionally
'get_raw' methods.
"""
def __init__(self, filename, **kwargs):
"""Initialize the class."""
self._handle = _open_for_random_access(filename)
self._kwargs = kwargs
def _parse(self, handle):
"""Pass handle and arguments to the next iterable (PRIVATE)."""
return next(iter(self._parser(handle, **self._kwargs)))
def get(self, offset):
"""Get offset and convert it from bytes to string."""
return self._parse(StringIO(self.get_raw(offset).decode()))
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