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Package Bio :: Package Mindy :: Module SimpleSeqRecord :: Class FixDocumentBuilder
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Class FixDocumentBuilder

 ContentHandler --+        
                  |        
DispatchHandler --+        
                  |        
         Dispatcher --+    
                      |    
         BuildSeqRecord --+
                          |
                         FixDocumentBuilder

A SAX builder-style class to make a parsed SeqRecord available.

This class does a lot of trickery to make things fit in the SAX framework and still have the flexibility to use a built SeqRecord object.

You shouldn't really need to use this class unless you are doing something really fancy-pants; otherwise, just use the BaseSeqRecordIndexer interfaces.
Method Summary
  __init__(self, get_ids_callback)
Intialize with a callback function to gets id info from a SeqRecord.
  end_record(self, tag)
Overrride the builder function to muck with the document attribute.
    Inherited from BuildSeqRecord
  add_dbid(self, text, attrs)
  add_dbxref(self, dbname_style, dbname, idtype, dbid, negate)
Store all id cross references.
  add_dbxref_dbids(self, dbname_style, dbname, idtype, dbid, negate)
Handle setting name and id attributes from the dbxref ids.
  add_description(self, text)
  add_features(self, features)
  add_sequence(self, (alphabet, seq, gapchar, stopchar))
  start_record(self, tag, attrs)
    Inherited from Dispatcher
  acquire(self, obj, prefix)
  characters(self, s)
  endDocument(self)
Receive notification of the end of a document.
  endElement(self, tag)
  get_characters(self)
  save_characters(self)
  startDocument(self)
Receive notification of the beginning of a document.
  startElement(self, tag, attrs)
  uses_tags(self)
    Inherited from ContentHandler
  endElementNS(self, name, qname)
Signals the end of an element in namespace mode.
  endPrefixMapping(self, prefix)
End the scope of a prefix-URI mapping.
  ignorableWhitespace(self, whitespace)
Receive notification of ignorable whitespace in element content.
  processingInstruction(self, target, data)
Receive notification of a processing instruction.
  setDocumentLocator(self, locator)
Called by the parser to give the application a locator for locating the origin of document events.
  skippedEntity(self, name)
Receive notification of a skipped entity.
  startElementNS(self, name, qname, attrs)
Signals the start of an element in namespace mode.
  startPrefixMapping(self, prefix, uri)
Begin the scope of a prefix-URI Namespace mapping.
    Inherited from DispatchHandler
  get_supported_features(self)
  setCharacterSaver(self, saver)

Method Details

__init__(self, get_ids_callback)
(Constructor)

Intialize with a callback function to gets id info from a SeqRecord.

get_ids_callback should be a callable function that will take a SeqRecord object and return a dictionary mapping id names to the valid ids for these names.
Overrides:
Bio.builders.SeqRecord.sequence.BuildSeqRecord.__init__

end_record(self, tag)

Overrride the builder function to muck with the document attribute.
Overrides:
Bio.builders.SeqRecord.sequence.BuildSeqRecord.end_record

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