Bio.ParserSupport.EventGenerator

Class EventGenerator

xml.sax.handler.ContentHandler --+ | EventGenerator

Handler to generate events associated with a Martel parsed file. This acts like a normal SAX handler, and accepts XML generated by Martel during parsing. These events are then converted into 'Biopython events', which can then be caught by a standard biopython consumer. Note that Martel is now DEPRECATED.

Instance Methods

[hide private]

__init__(self, consumer, interest_tags, callback_finalizer=None, exempt_tags=[])
Initialize to begin catching and firing off events. source code

startElement(self, name, attrs)
Determine if we should collect characters from this tag.

source code

characters(self, content)
Extract the information if we are interested in it.

source code

endElement(self, name)
Send the information to the consumer.

source code

_make_callback(self, name)
Call the callback function with the info with the given name.

source code

endDocument(self)
Make sure all of our information has been passed.

source code

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

init(self, consumer, interest_tags, callback_finalizer=None, exempt_tags=`[]`)
(Constructor)

source code

Initialize to begin catching and firing off events.

Arguments:
o consumer - The consumer that we'll send Biopython events to.

o interest_tags - A listing of all the tags we are interested in.

o callback_finalizer - A function to deal with the collected
information before passing it on to the consumer. By default
the collected information is a list of all of the lines read
for a particular tag -- if there are multiple tags in a row
like:

<some_info>Spam<some_info>
<some_info>More Spam<some_info>

In this case the list of information would be:

['Spam', 'More Spam']

This list of lines will be passed to the callback finalizer if
it is present. Otherwise the consumer will be called with the
list of content information.

o exempt_tags - A listing of particular tags that are exempt from
being processed by the callback_finalizer. This allows you to
use a finalizer to deal with most tags, but leave those you don't
want touched.

Overrides: xml.sax.handler.ContentHandler.__init__

startElement(self, name, attrs)

source code

Determine if we should collect characters from this tag.

Overrides: xml.sax.handler.ContentHandler.startElement

characters(self, content)

source code

Extract the information if we are interested in it.

Overrides: xml.sax.handler.ContentHandler.characters

endElement(self, name)

source code

Send the information to the consumer.

Once we've got the end element we've collected up all of the
character information we need, and we need to send this on to
the consumer to do something with it.

We have a delay of one tag on doing this, so that we can collect
all of the info from multiple calls to the same element at once.

Overrides: xml.sax.handler.ContentHandler.endElement

endDocument(self)

source code

Make sure all of our information has been passed.

This just flushes out any stored tags that need to be passed.

Overrides: xml.sax.handler.ContentHandler.endDocument

Class EventGenerator

__init__(self, consumer, interest_tags, callback_finalizer=None, exempt_tags=[]) (Constructor)

startElement(self, name, attrs)

characters(self, content)

endElement(self, name)

endDocument(self)

init(self, consumer, interest_tags, callback_finalizer=None, exempt_tags=`[]`)
(Constructor)