Package Bio :: Package SearchIO :: Package BlastIO :: Module blast_xml :: Class BlastXmlIndexer

Class BlastXmlIndexer

               object --+        
                        |        
File._IndexedSeqFileProxy --+    
                            |    
         _index.SearchIndexer --+
                                |
                               BlastXmlIndexer

Indexer class for BLAST XML output.

Nested Classes

[hide private]

_parser
Parser for the BLAST XML format

Instance Methods

[hide private]

__init__(self, filename)
x.__init__(...) initializes x; see x.__class__.__doc__ for signature

source code

__iter__(self)
Returns (identifier, offset, length in bytes) tuples.

source code

_parse(self, handle)

source code

get_raw(self, offset)
Returns bytes string (if implemented for this file format).

source code

Inherited from _index.SearchIndexer: get

Inherited from object: __delattr__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __str__

Class Variables

[hide private]

qstart_mark = '<Iteration>'

qend_mark = '</Iteration>'

block_size = 16384

Properties

[hide private]

Inherited from object: __class__

Method Details

[hide private]

init(self, filename)
(Constructor)

source code

x.__init__(...) initializes x; see x.__class__.__doc__ for signature

Overrides: object.__init__: (inherited documentation)

iter(self)

source code

Returns (identifier, offset, length in bytes) tuples.

The length can be zero where it is not implemented or not
possible for a particular file format.

Overrides: File._IndexedSeqFileProxy.__iter__: (inherited documentation)

_parse(self, handle)

source code

Overrides: _index.SearchIndexer._parse

get_raw(self, offset)

source code

Returns bytes string (if implemented for this file format).

Overrides: File._IndexedSeqFileProxy.get_raw: (inherited documentation)

Class BlastXmlIndexer

__init__(self, filename) (Constructor)

__iter__(self)

_parse(self, handle)

get_raw(self, offset)

init(self, filename)
(Constructor)

iter(self)