Package org.biojava.bio.program.xff

Event-driven parsing system for the Extensible Feature Format (XFF). This is currently targetted at the XFF 0.2 proposal. For more information, see The XFF proposal page.

XFF is an experimental format, and both the format and the APIs in this package may change in the future.

The main class in this package is XFFFeatureSetHandler, which is intended as a content handler for XFF featureSet elements. By default, this class handles the XFF feature and strandedFeature types. Any other feature types are treated as one of these. It is, however, possible to plug in additional handlers to cope with sub-types of feature. The only detail type recognized is xff:prop -- all others are silently ignored. But again, it is easy to plug in extra StAX handlers for other detail types.

When writing a handler, for a new feature type, you will normally want to sub-class the existing FeatureHandler or StrandedFeatureHanlder classes.

Interface Summary

Interface	Description
ElementRecognizer	Simple interface for filtering SAX/StAX startElement events.
XFFHelper
XFFPartHandlerFactory	Factory for StAX content handlers.

Class Summary

Class	Description
BasicXFFHelper
ElementRecognizer.AllElementRecognizer
ElementRecognizer.ByLocalName	Filter elements by local name (not recommended).
ElementRecognizer.ByNSName	Filter elements by name and namespace.
ElementRecognizer.HasAttribute	Filter elements on the existence of a specified attribute.
FeatureHandler	StAX handler for the basic feature type of XFF.
LocationHandlerBase	Handler to the XFF location type.
PropDetailHandler	StAX handler for xff:prop detail elements.
PropertyWriter
StrandedFeatureHandler	StAX handler for XFF strandedFeature type.
XFFFeatureSetHandler	StAX handler which converts and stream of parse events for an XFF featureSet element into BioJava SeqIO events.
XFFTools	Common functionality for manipulating XFF.
XFFWriter	Simple XFF writing code, ripped off from Dazzle 0.08.