Uses of Interface
org.biojava.bio.seq.io.agave.StAXContentHandler
Packages that use StAXContentHandler
Package
Description
Classes for converting between AGAVE XML and BioJava objects.
-
Uses of StAXContentHandler in org.biojava.bio.seq.io.agave
Classes in org.biojava.bio.seq.io.agave that implement StAXContentHandlerModifier and TypeClassDescriptionclass
Deals with alternate sequence IDsclass
class
class
Handles the AGAVE <bio_sequence> elementclass
Handles the AGAVE <bio_sequence> elementclass
Handles the AGAVE <cds> elementclass
Handles the AGAVE <chromosome> elementclass
class
class
class
Handles the AGAVE <contig> elementclass
Deals with database crossreferencesclass
Deals with database crossreferencesclass
class
class
class
class
class
class
Handles the root AGAVE element modified for agave formatclass
class
Deals with AGAVE keywordsclass
class
class
Deals with match_alignclass
Deals with match_descclass
Deals with match_regionclass
Handles the AGAVE <mrna> elementclass
Deals with noteclass
Handles the AGAVE <predicted_protein> elementclass
class
class
class
class
class
sci_propertyclass
seq_featureclass
seq_locationclass
sequence_mapclass
Deals with sequence codeclass
transcriptclass
unordered_fragmentsclass
Moves view attributes into annotation properties.class
handle AGAVE xrefclass
xref_propertyclass
Deals with database crossreferences (xrefs)class
Simple implementation of theStAXContentHandler
interface, with empty implementations for all the methods.class
StAX handler shamelessly ripped off from Thomas Down's XFFFeatureSetHandler.class
StAX handler shamelessly ripped off from Thomas Down's XFFFeatureSetHandler.Methods in org.biojava.bio.seq.io.agave that return StAXContentHandlerModifier and TypeMethodDescriptionStAXHandlerFactory.getHandler
(StAXFeatureHandler staxenv) Return a suitable StAX content handler.Methods in org.biojava.bio.seq.io.agave with parameters of type StAXContentHandlerModifier and TypeMethodDescriptionvoid
DelegationManager.delegate
(StAXContentHandler handler) void
StAXContentHandler.endElement
(String nsURI, String localName, String qName, StAXContentHandler delegate) void
StAXContentHandlerBase.endElement
(String nsURI, String localName, String qName, StAXContentHandler delegate) void
StAXFeatureHandler.endElement
(String nsURI, String localName, String qName, StAXContentHandler handler) Handles basic exit processing.void
StAXPropertyHandler.endElement
(String nsURI, String localName, String qName, StAXContentHandler handler) void
AGAVEBioSeqHandler.endElementHandler
(String nsURI, String localName, String qName, StAXContentHandler handler) void
AGAVEChromosomeHandler.endElementHandler
(String nsURI, String localName, String qName, StAXContentHandler handler) void
AGAVEClassificationHandler.endElementHandler
(String nsURI, String localName, String qName, StAXContentHandler handler) void
AGAVEContigHandler.endElementHandler
(String nsURI, String localName, String qName, StAXContentHandler handler) void
AGAVEDbIdPropHandler.endElementHandler
(String nsURI, String localName, String qName, StAXContentHandler handler) void
AGAVEElementIdPropHandler.endElementHandler
(String nsURI, String localName, String qName, StAXContentHandler handler) void
AGAVEEvidenceHandler.endElementHandler
(String nsURI, String localName, String qName, StAXContentHandler handler) void
AGAVEIdAliasPropHandler.endElementHandler
(String nsURI, String localName, String qName, StAXContentHandler handler) void
AGAVEMapLocationPropHandler.endElementHandler
(String nsURI, String localName, String qName, StAXContentHandler handler) void
AGAVEMapPositionPropHandler.endElementHandler
(String nsURI, String localName, String qName, StAXContentHandler handler) void
AGAVEMatchRegionPropHandler.endElementHandler
(String nsURI, String localName, String qName, StAXContentHandler handler) void
AGAVEQualifierPropHandler.endElementHandler
(String nsURI, String localName, String qName, StAXContentHandler handler) void
AGAVEQueryRegionPropHandler.endElementHandler
(String nsURI, String localName, String qName, StAXContentHandler handler) void
AGAVERelatedAnnotPropHandler.endElementHandler
(String nsURI, String localName, String qName, StAXContentHandler handler) void
AGAVEResultPropertyPropHandler.endElementHandler
(String nsURI, String localName, String qName, StAXContentHandler handler) void
AGAVESciPropertyPropHandler.endElementHandler
(String nsURI, String localName, String qName, StAXContentHandler handler) void
AGAVESeqLocationPropHandler.endElementHandler
(String nsURI, String localName, String qName, StAXContentHandler handler) void
AGAVESeqPropHandler.endElementHandler
(String nsURI, String localName, String qName, StAXContentHandler handler) void
AGAVEXrefPropHandler.endElementHandler
(String nsURI, String localName, String qName, StAXContentHandler handler) void
AGAVEXrefPropPropHandler.endElementHandler
(String nsURI, String localName, String qName, StAXContentHandler handler) void
AGAVEXrefsPropHandler.endElementHandler
(String nsURI, String localName, String qName, StAXContentHandler handler) void
StAXFeatureHandler.endElementHandler
(String nsURI, String localName, String qName, StAXContentHandler handler) Element specific exit handler Subclass to do anything useful.void
StAXPropertyHandler.endElementHandler
(String nsURI, String localName, String qName, StAXContentHandler handler) Element specific exit handler Subclass to do anything useful.protected void
StAXFeatureHandler.push
(StAXContentHandler handler) Push StAXContentHandler object onto stackConstructors in org.biojava.bio.seq.io.agave with parameters of type StAXContentHandlerModifierConstructorDescriptionSAX2StAXAdaptor
(StAXContentHandler rootHandler) Construct a new SAX Content handler which wraps a StAX handler.