Class StAXFeatureHandler

java.lang.Object
org.biojava.bio.seq.io.agave.StAXContentHandlerBase
org.biojava.bio.seq.io.agave.StAXFeatureHandler
All Implemented Interfaces:
StAXContentHandler
Direct Known Subclasses:
AGAVEAssemblyHandler, AGAVEBioSeqHandler, AGAVEBioSequenceHandler, AGAVECdsHandler, AGAVEChromosomeHandler, AGAVEClassificationHandler, AGAVECompResultHandler, AGAVEComputationHandler, AGAVEContigHandler, AGAVEEvidenceHandler, AGAVEFragmentOrderHandler, AGAVEFragmentOrientationHandler, AGAVEGeneHandler, AGAVEHandler, AGAVEMrnaHandler, AGAVEPredictedProteinHandler, AGAVEQueryRegionPropHandler, AGAVEResultGroupHandler, AGAVESeqFeatureHandler, AGAVESeqMapHandler, AGAVETranscriptHandler, AGAVEUnorderedFragmentsHandler

StAX handler shamelessly ripped off from Thomas Down's XFFFeatureSetHandler. It was modified for greater generality. NOTE This class is not thread-safe -- it must only be used for one parse at any time.

Because AGAVE has nested feature and each feature must attached to some parent feature-holder in biojava, which means we need to generate parents first, so we have to keep the tree structure of features in memory, which is really bad. anyway, we still saved a lot of memory compared with DOM tree . Hanning Ni)

Author:
copied from Thomas Down, copied from David Huen, Hanning Ni Doubletwist Inc