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Packages that use StAXContentHandler | |
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org.biojava.bio.seq.io.agave | Classes for converting between AGAVE XML and BioJava objects. |
Uses of StAXContentHandler in org.biojava.bio.seq.io.agave |
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Classes in org.biojava.bio.seq.io.agave that implement StAXContentHandler | |
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class |
AGAVEAltIdsPropHandler
Deals with alternate sequence IDs |
class |
AGAVEAnnotationsHandler
|
class |
AGAVEAssemblyHandler
|
class |
AGAVEBioSeqHandler
Handles the AGAVE <bio_sequence> element |
class |
AGAVEBioSequenceHandler
Handles the AGAVE <bio_sequence> element |
class |
AGAVECdsHandler
Handles the AGAVE <cds> element |
class |
AGAVEChromosomeHandler
Handles the AGAVE <chromosome> element |
class |
AGAVEClassificationHandler
|
class |
AGAVECompResultHandler
|
class |
AGAVEComputationHandler
|
class |
AGAVEContigHandler
Handles the AGAVE <contig> element |
class |
AGAVEDbIdPropHandler
Deals with database crossreferences |
class |
AGAVEDescPropHandler
Deals with database crossreferences |
class |
AGAVEElementIdPropHandler
|
class |
AGAVEEvidenceHandler
|
class |
AGAVEExonsPropHandler
|
class |
AGAVEFragmentOrderHandler
|
class |
AGAVEFragmentOrientationHandler
|
class |
AGAVEGeneHandler
|
class |
AGAVEHandler
Handles the root AGAVE element modified for agave format |
class |
AGAVEIdAliasPropHandler
|
class |
AGAVEKeywordPropHandler
Deals with AGAVE keywords |
class |
AGAVEMapLocationPropHandler
|
class |
AGAVEMapPositionPropHandler
|
class |
AGAVEMatchAlignPropHandler
Deals with match_align |
class |
AGAVEMatchDescPropHandler
Deals with match_desc |
class |
AGAVEMatchRegionPropHandler
Deals with match_region |
class |
AGAVEMrnaHandler
Handles the AGAVE <mrna> element |
class |
AGAVENotePropHandler
Deals with note |
class |
AGAVEPredictedProteinHandler
Handles the AGAVE <predicted_protein> element |
class |
AGAVEQualifierPropHandler
|
class |
AGAVEQueryRegionPropHandler
|
class |
AGAVERelatedAnnotPropHandler
|
class |
AGAVEResultGroupHandler
|
class |
AGAVEResultPropertyPropHandler
|
class |
AGAVESciPropertyPropHandler
sci_property |
class |
AGAVESeqFeatureHandler
seq_feature |
class |
AGAVESeqLocationPropHandler
seq_location |
class |
AGAVESeqMapHandler
sequence_map |
class |
AGAVESeqPropHandler
Deals with sequence code |
class |
AGAVETranscriptHandler
transcript |
class |
AGAVEUnorderedFragmentsHandler
unordered_fragments |
class |
AGAVEViewPropHandler
Moves view attributes into annotation properties. |
class |
AGAVEXrefPropHandler
handle AGAVE xref |
class |
AGAVEXrefPropPropHandler
xref_property |
class |
AGAVEXrefsPropHandler
Deals with database crossreferences (xrefs) |
class |
StAXContentHandlerBase
Simple implementation of the StAXContentHandler
interface, with empty implementations for all the methods. |
class |
StAXFeatureHandler
StAX handler shamelessly ripped off from Thomas Down's XFFFeatureSetHandler. |
class |
StAXPropertyHandler
StAX handler shamelessly ripped off from Thomas Down's XFFFeatureSetHandler. |
Methods in org.biojava.bio.seq.io.agave that return StAXContentHandler | |
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StAXContentHandler |
StAXHandlerFactory.getHandler(StAXFeatureHandler staxenv)
Return a suitable StAX content handler. |
Methods in org.biojava.bio.seq.io.agave with parameters of type StAXContentHandler | |
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void |
DelegationManager.delegate(StAXContentHandler handler)
|
void |
StAXPropertyHandler.endElement(java.lang.String nsURI,
java.lang.String localName,
java.lang.String qName,
StAXContentHandler handler)
|
void |
StAXContentHandlerBase.endElement(java.lang.String nsURI,
java.lang.String localName,
java.lang.String qName,
StAXContentHandler delegate)
|
void |
StAXContentHandler.endElement(java.lang.String nsURI,
java.lang.String localName,
java.lang.String qName,
StAXContentHandler delegate)
|
void |
StAXFeatureHandler.endElement(java.lang.String nsURI,
java.lang.String localName,
java.lang.String qName,
StAXContentHandler handler)
Handles basic exit processing. |
void |
AGAVERelatedAnnotPropHandler.endElementHandler(java.lang.String nsURI,
java.lang.String localName,
java.lang.String qName,
StAXContentHandler handler)
|
void |
AGAVESeqPropHandler.endElementHandler(java.lang.String nsURI,
java.lang.String localName,
java.lang.String qName,
StAXContentHandler handler)
|
void |
AGAVEQualifierPropHandler.endElementHandler(java.lang.String nsURI,
java.lang.String localName,
java.lang.String qName,
StAXContentHandler handler)
|
void |
AGAVEDbIdPropHandler.endElementHandler(java.lang.String nsURI,
java.lang.String localName,
java.lang.String qName,
StAXContentHandler handler)
|
void |
AGAVEMapLocationPropHandler.endElementHandler(java.lang.String nsURI,
java.lang.String localName,
java.lang.String qName,
StAXContentHandler handler)
|
void |
AGAVEMatchRegionPropHandler.endElementHandler(java.lang.String nsURI,
java.lang.String localName,
java.lang.String qName,
StAXContentHandler handler)
|
void |
AGAVEBioSeqHandler.endElementHandler(java.lang.String nsURI,
java.lang.String localName,
java.lang.String qName,
StAXContentHandler handler)
|
void |
StAXPropertyHandler.endElementHandler(java.lang.String nsURI,
java.lang.String localName,
java.lang.String qName,
StAXContentHandler handler)
Element specific exit handler Subclass to do anything useful. |
void |
AGAVEXrefsPropHandler.endElementHandler(java.lang.String nsURI,
java.lang.String localName,
java.lang.String qName,
StAXContentHandler handler)
|
void |
AGAVEQueryRegionPropHandler.endElementHandler(java.lang.String nsURI,
java.lang.String localName,
java.lang.String qName,
StAXContentHandler handler)
|
void |
AGAVESciPropertyPropHandler.endElementHandler(java.lang.String nsURI,
java.lang.String localName,
java.lang.String qName,
StAXContentHandler handler)
|
void |
AGAVEResultPropertyPropHandler.endElementHandler(java.lang.String nsURI,
java.lang.String localName,
java.lang.String qName,
StAXContentHandler handler)
|
void |
AGAVEMapPositionPropHandler.endElementHandler(java.lang.String nsURI,
java.lang.String localName,
java.lang.String qName,
StAXContentHandler handler)
|
void |
AGAVEXrefPropPropHandler.endElementHandler(java.lang.String nsURI,
java.lang.String localName,
java.lang.String qName,
StAXContentHandler handler)
|
void |
AGAVEEvidenceHandler.endElementHandler(java.lang.String nsURI,
java.lang.String localName,
java.lang.String qName,
StAXContentHandler handler)
|
void |
AGAVEElementIdPropHandler.endElementHandler(java.lang.String nsURI,
java.lang.String localName,
java.lang.String qName,
StAXContentHandler handler)
|
void |
AGAVEClassificationHandler.endElementHandler(java.lang.String nsURI,
java.lang.String localName,
java.lang.String qName,
StAXContentHandler handler)
|
void |
AGAVEContigHandler.endElementHandler(java.lang.String nsURI,
java.lang.String localName,
java.lang.String qName,
StAXContentHandler handler)
|
void |
AGAVEIdAliasPropHandler.endElementHandler(java.lang.String nsURI,
java.lang.String localName,
java.lang.String qName,
StAXContentHandler handler)
|
void |
AGAVEXrefPropHandler.endElementHandler(java.lang.String nsURI,
java.lang.String localName,
java.lang.String qName,
StAXContentHandler handler)
|
void |
AGAVESeqLocationPropHandler.endElementHandler(java.lang.String nsURI,
java.lang.String localName,
java.lang.String qName,
StAXContentHandler handler)
|
void |
StAXFeatureHandler.endElementHandler(java.lang.String nsURI,
java.lang.String localName,
java.lang.String qName,
StAXContentHandler handler)
Element specific exit handler Subclass to do anything useful. |
void |
AGAVEChromosomeHandler.endElementHandler(java.lang.String nsURI,
java.lang.String localName,
java.lang.String qName,
StAXContentHandler handler)
|
protected void |
StAXFeatureHandler.push(StAXContentHandler handler)
Push StAXContentHandler object onto stack |
Constructors in org.biojava.bio.seq.io.agave with parameters of type StAXContentHandler | |
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SAX2StAXAdaptor(StAXContentHandler rootHandler)
Construct a new SAX Content handler which wraps a StAX handler. |
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