Package Bio :: Package builders :: Package SeqRecord :: Module sequence :: Class BuildSeqRecord

Class BuildSeqRecord

 xml.sax.handler.ContentHandler --+    
                                  |    
Martel.Dispatch.DispatchHandler --+    
                                  |    
         Martel.Dispatch.Dispatcher --+
                                      |
                                     BuildSeqRecord

Known Subclasses:

Mindy.SimpleSeqRecord.FixDocumentBuilder

Instance Methods

[hide private]

__init__(self)

source code

start_record(self, tag, attrs)

source code

add_dbid(self, text, attrs)

source code

add_dbxref_dbids(self, dbname_style, dbname, idtype, dbid, negate)
Handle setting name and id attributes from the dbxref ids.

source code

add_description(self, text)

source code

add_sequence(self, (alphabet, seq, gapchar, stopchar))

source code

add_dbxref(self, dbname_style, dbname, idtype, dbid, negate)
Store all id cross references.

source code

add_features(self, features)

source code

end_record(self, tag)

source code

Inherited from Martel.Dispatch.Dispatcher: acquire, characters, endDocument, endElement, get_characters, save_characters, startDocument, startElement, uses_tags

Inherited from xml.sax.handler.ContentHandler: endElementNS, endPrefixMapping, ignorableWhitespace, processingInstruction, setDocumentLocator, skippedEntity, startElementNS, startPrefixMapping

Inherited from Martel.Dispatch.DispatchHandler: get_supported_features, setCharacterSaver

Method Details

[hide private]

init(self)
(Constructor)

source code

Overrides: Martel.Dispatch.DispatchHandler.__init__

add_dbxref_dbids(self, dbname_style, dbname, idtype, dbid, negate)

source code

Handle setting name and id attributes from the dbxref ids.

Likely we'll either have a dbid or dbxref dbids to use. We default to using the dbid if it exists.

Class BuildSeqRecord

__init__(self) (Constructor)

add_dbxref_dbids(self, dbname_style, dbname, idtype, dbid, negate)

init(self)
(Constructor)