Package Bio :: Package SearchIO :: Package ExonerateIO :: Module exonerate_text :: Class ExonerateTextIndexer

Class ExonerateTextIndexer

               object --+            
                        |            
File._IndexedSeqFileProxy --+        
                            |        
         _index.SearchIndexer --+    
                                |    
      _base._BaseExonerateIndexer --+
                                    |
                                   ExonerateTextIndexer

Indexer class for Exonerate plain text.

Nested Classes

[hide private]

_parser
Parser for Exonerate plain text output.

Instance Methods

[hide private]

get_qresult_id(self, pos)
Returns the query ID from the nearest "Query:" line.

source code

get_raw(self, offset)
Returns the raw string of a QueryResult object from the given offset.

source code

Inherited from _base._BaseExonerateIndexer: __iter__

Inherited from _index.SearchIndexer: __init__, get

Inherited from _index.SearchIndexer (private): _parse

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

Class Variables

[hide private]

_query_mark = 'C4 Alignment'

Properties

[hide private]

Inherited from object: __class__

Method Details

[hide private]

get_qresult_id(self, pos)

source code

Returns the query ID from the nearest "Query:" line.

Overrides: _base._BaseExonerateIndexer.get_qresult_id

get_raw(self, offset)

source code

Returns the raw string of a QueryResult object from the given offset.

Overrides: File._IndexedSeqFileProxy.get_raw