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Packages that use StAXContentHandler | |
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org.biojava.bio.program.sax.blastxml | Parsers for the XML output from NCBI blast. |
org.biojava.bio.program.ssbind | Creation of objects from SAX events using the BioJava BlastLikeDataSetCollection DTD. |
org.biojava.bio.program.xff | Event-driven parsing system for the Extensible Feature Format (XFF). |
org.biojava.bio.seq.io.filterxml | Tools for reading and writing an XML representation of BioJava's FeatureFilter language. |
org.biojava.bio.seq.io.game | Event-driven parsing system for the Gene Annotation Markup Elements (GAME). |
org.biojava.bio.seq.io.game12 | Event-driven parsing system for the Gene Annotation Markup Elements (GAME). |
org.biojava.utils.stax | The Stack API for XML (StAX). |
Uses of StAXContentHandler in org.biojava.bio.program.sax.blastxml |
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Classes in org.biojava.bio.program.sax.blastxml that implement StAXContentHandler | |
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class |
BlastXMLParser
This class parses NCBI Blast XML output. |
Methods in org.biojava.bio.program.sax.blastxml with parameters of type StAXContentHandler | |
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void |
BlastXMLParser.endElementHandler(String nsURI,
String localName,
String qName,
StAXContentHandler handler)
|
Uses of StAXContentHandler in org.biojava.bio.program.ssbind |
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Classes in org.biojava.bio.program.ssbind that implement StAXContentHandler | |
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class |
AlignmentStAXHandler
AlignmentStAXHandler handles the BlastLikeAlignment
element of BioJava BlastLike XML. |
class |
HeaderStAXHandler
HeaderStAXHandler handles the Header element of
BioJava BlastLike XML. |
class |
HitStAXHandler
AlignmentStAXHandler handles the Hit element of
BioJava BlastLike XML. |
class |
HSPStAXHandler
HSPStAXHandler handles the HSP element of BioJava
BlastLike XML. |
class |
HSPSummaryStAXHandler
HSPSummaryStAXHandler handles the HSPSummary element
of BioJava BlastLike XML. |
class |
SeqSimilarityStAXAdapter
SeqSimilarityStAXAdapter is a handler for XML
conforming to the BioJava BlastLike DTD. |
class |
SeqSimilarityStAXHandler
SeqSimilarityStAXHandler is a base class for creating
modular StAX handlers which send callbacks to a
SeqSimilarityStAXAdapter . |
Methods in org.biojava.bio.program.ssbind that return StAXContentHandler | |
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StAXContentHandler |
StAXHandlerFactory.getHandler(SeqSimilarityStAXAdapter ssContext)
getHandler returns an appropriate
StAXContentHandler implementation containing a
reference to a parent context. |
Methods in org.biojava.bio.program.ssbind with parameters of type StAXContentHandler | |
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void |
SeqSimilarityStAXHandler.endElement(String nsURI,
String localName,
String qName,
StAXContentHandler handler)
|
void |
SeqSimilarityStAXAdapter.endElement(String nsURI,
String localName,
String qName,
StAXContentHandler handler)
|
Uses of StAXContentHandler in org.biojava.bio.program.xff |
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Classes in org.biojava.bio.program.xff that implement StAXContentHandler | |
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class |
FeatureHandler
StAX handler for the basic feature type of XFF. |
class |
LocationHandlerBase
Handler to the XFF location type. |
class |
PropDetailHandler
StAX handler for xff:prop detail elements. |
class |
StrandedFeatureHandler
StAX handler for XFF strandedFeature type. |
class |
XFFFeatureSetHandler
StAX handler which converts and stream of parse events for an XFF featureSet element into BioJava SeqIO events. |
Methods in org.biojava.bio.program.xff that return StAXContentHandler | |
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protected StAXContentHandler |
FeatureHandler.getLocationHandler()
|
protected StAXContentHandler |
FeatureHandler.getOldIDHandler()
|
StAXContentHandler |
XFFPartHandlerFactory.getPartHandler(XFFFeatureSetHandler xffenv)
Return a suitable StAX content handler. |
protected StAXContentHandler |
FeatureHandler.getSourceHandler()
|
protected StAXContentHandler |
FeatureHandler.getTypeHandler()
|
Methods in org.biojava.bio.program.xff with parameters of type StAXContentHandler | |
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void |
XFFFeatureSetHandler.endElement(String nsURI,
String localName,
String qName,
StAXContentHandler handler)
|
void |
LocationHandlerBase.endElement(String nsURI,
String localName,
String qName,
StAXContentHandler handler)
|
void |
FeatureHandler.endElement(String nsURI,
String localName,
String qName,
StAXContentHandler handler)
StAX callback for element ends. |
Uses of StAXContentHandler in org.biojava.bio.seq.io.filterxml |
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Subinterfaces of StAXContentHandler in org.biojava.bio.seq.io.filterxml | |
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static interface |
XMLAnnotationTypeHandler.CollectionConstraintHandler
Handler for an individual CollectionConstraint in an AnnotationType. |
static interface |
XMLAnnotationTypeHandler.PropertyConstraintHandler
Handler for an individual PropertyConstraint in an AnnotationType. |
static interface |
XMLFilterHandler.FilterHandler
StAXContentHandler for a particular type of FeatureFilter. |
Classes in org.biojava.bio.seq.io.filterxml that implement StAXContentHandler | |
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class |
XMLAnnotationTypeHandler
StAX handler for parsing AnnotationTypes in FilterXML documents. |
Methods in org.biojava.bio.seq.io.filterxml with parameters of type StAXContentHandler | |
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void |
XMLAnnotationTypeHandler.endElement(String nsURI,
String localName,
String qName,
StAXContentHandler delegate)
|
Uses of StAXContentHandler in org.biojava.bio.seq.io.game |
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Classes in org.biojava.bio.seq.io.game that implement StAXContentHandler | |
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class |
GAMEAnnotationHandler
Handles the GAME <annotation> element |
class |
GAMEAspectPropHandler
Handles the GAME <aspect> element |
class |
GAMEDbxrefPropHandler
Deals with database crossreferences |
class |
GAMEDescriptionPropHandler
StAX handler for GAME <description> elements. |
class |
GAMEFeatureSetHandler
Handles the <feature_set> element |
class |
GAMEFeatureSetPropHandler
Handles the GAME |
class |
GAMEFeatureSpanHandler
Handles the <feature_span> element |
class |
GAMEGenePropHandler
Handles the GAME <gene> element |
class |
GAMEHandler
Handles the root GAME element |
class |
GAMEMapPosPropHandler
Handles the GAME <map_position> element Currently, it just ignores it! |
class |
GAMENamePropHandler
StAX handler for the GAME <name> element. |
class |
GAMEResiduesPropHandler
StAX handler for GAME <residues> elements. |
class |
GAMESeqPropHandler
Handles the GAME <seq> element |
class |
GAMESeqRelPropHandler
Handles the GAME <aspect> element |
class |
GAMESpanPropHandler
Handles the GAME <span> element Currently, it just ignores it! |
class |
GAMETypePropHandler
StAX handler for GAME <type> elements. |
class |
SequenceContentHandlerBase
StAX handler for elements containing sequence |
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.game 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.game with parameters of type StAXContentHandler | |
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void |
StAXPropertyHandler.endElement(String nsURI,
String localName,
String qName,
StAXContentHandler handler)
|
void |
StAXFeatureHandler.endElement(String nsURI,
String localName,
String qName,
StAXContentHandler handler)
Handles basic exit processing. |
void |
SequenceContentHandlerBase.endElement(String nsURI,
String localName,
String qName,
StAXContentHandler handler)
|
void |
StAXPropertyHandler.endElementHandler(String nsURI,
String localName,
String qName,
StAXContentHandler handler)
Element specific exit handler Subclass to do anything useful. |
void |
StAXFeatureHandler.endElementHandler(String nsURI,
String localName,
String qName,
StAXContentHandler handler)
Element specific exit handler Subclass to do anything useful. |
void |
GAMESpanPropHandler.endElementHandler(String nsURI,
String localName,
String qName,
StAXContentHandler handler)
|
void |
GAMEFeatureSpanHandler.endElementHandler(String nsURI,
String localName,
String qName,
StAXContentHandler handler)
|
void |
GAMEFeatureSetHandler.endElementHandler(String nsURI,
String localName,
String qName,
StAXContentHandler handler)
|
void |
GAMEDbxrefPropHandler.endElementHandler(String nsURI,
String localName,
String qName,
StAXContentHandler handler)
when exiting, put the DbXrefElement into the annotation bundle |
void |
GAMEAnnotationHandler.endElementHandler(String nsURI,
String localName,
String qName,
StAXContentHandler handler)
|
protected void |
StAXFeatureHandler.push(StAXContentHandler handler)
Push StAXContentHandler object onto stack |
Uses of StAXContentHandler in org.biojava.bio.seq.io.game12 |
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Classes in org.biojava.bio.seq.io.game12 that implement StAXContentHandler | |
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class |
GAMEAspectHandler
Handles the GAME <aspect> element |
class |
GAMEDbxrefHandler
Handles the GAME <dbxref> element |
class |
GAMEFeatureSpanHandler.SeqRelHandler
|
class |
GAMEGeneHandler
Handles the GAME <annotation> element |
class |
GAMEPropertyHandler
Handles the GAME <dbxref> element |
class |
GAMESeqHandler
Handles the GAME <seq> element |
class |
GAMESeqRelHandler
Handles the GAME < |
class |
GAMESpanHandler
Handles the GAME <> element. |
Methods in org.biojava.bio.seq.io.game12 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.game12 with parameters of type StAXContentHandler | |
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void |
StAXFeatureHandler.endElement(String nsURI,
String localName,
String qName,
StAXContentHandler handler)
Handles basic exit processing. |
void |
StAXFeatureHandler.endElementHandler(String nsURI,
String localName,
String qName,
StAXContentHandler handler)
Element specific exit handler Subclass to do anything useful. |
void |
GAMESpanHandler.endElementHandler(String nsURI,
String localName,
String qName,
StAXContentHandler contentHandler)
|
void |
GAMESeqRelHandler.endElementHandler(String nsURI,
String localName,
String qName,
StAXContentHandler contentHandler)
|
void |
GAMESeqHandler.endElementHandler(String nsURI,
String localName,
String qName,
StAXContentHandler staxHandler)
|
void |
GAMEPropertyHandler.endElementHandler(String nsURI,
String localName,
String qName,
StAXContentHandler contentHandler)
|
void |
GAMEHandler.endElementHandler(String nsURI,
String localName,
String qName,
StAXContentHandler contentHandler)
|
void |
GAMEGeneHandler.endElementHandler(String nsURI,
String localName,
String qName,
StAXContentHandler contentHandler)
|
void |
GAMEFeatureSpanHandler.endElementHandler(String nsURI,
String localName,
String qName,
StAXContentHandler contentHandler)
|
void |
GAMEFeatureSpanHandler.SeqRelHandler.endElementHandler(String nsURI,
String localName,
String qName,
StAXContentHandler contentHandler)
|
void |
GAMEFeatureSetHandler.endElementHandler(String nsURI,
String localName,
String qName,
StAXContentHandler contentHandler)
|
void |
GAMEDbxrefHandler.endElementHandler(String nsURI,
String localName,
String qName,
StAXContentHandler contentHandler)
|
void |
GAMEAspectHandler.endElementHandler(String nsURI,
String localName,
String qName,
StAXContentHandler contentHandler)
|
void |
GAMEAnnotationHandler.endElementHandler(String nsURI,
String localName,
String qName,
StAXContentHandler contentHandler)
|
Uses of StAXContentHandler in org.biojava.utils.stax |
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Classes in org.biojava.utils.stax that implement StAXContentHandler | |
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class |
BooleanElementHandlerBase
StAX handler for any element which just contains a string representation of an boolean. |
class |
ByteElementHandlerBase
StAX handler for any element which just contains a string representation of a byte. |
class |
CharElementHandlerBase
StAX handler for any element which just contains a string representation of a char. |
class |
DoubleElementHandlerBase
StAX handler for any element which just contains a string representation of a double. |
class |
FloatElementHandlerBase
StAX handler for any element which just contains a string representation of a float. |
class |
IntElementHandlerBase
StAX handler for any element which just contains a string representation of an integer. |
class |
LongElementHandlerBase
StAX handler for any element which just contains a string representation of a long. |
class |
StAXContentHandlerBase
Simple implementation of the StAXContentHandler
interface, with empty implementations for all the methods. |
class |
StringElementHandlerBase
StAX handler for any element which just contains a string. |
Methods in org.biojava.utils.stax with parameters of type StAXContentHandler | |
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void |
DelegationManager.delegate(StAXContentHandler handler)
|
void |
StringElementHandlerBase.endElement(String nsURI,
String localName,
String qName,
StAXContentHandler handler)
|
void |
StAXContentHandlerBase.endElement(String nsURI,
String localName,
String qName,
StAXContentHandler delegate)
|
void |
StAXContentHandler.endElement(String nsURI,
String localName,
String qName,
StAXContentHandler delegate)
|
void |
LongElementHandlerBase.endElement(String nsURI,
String localName,
String qName,
StAXContentHandler handler)
|
void |
IntElementHandlerBase.endElement(String nsURI,
String localName,
String qName,
StAXContentHandler handler)
|
void |
FloatElementHandlerBase.endElement(String nsURI,
String localName,
String qName,
StAXContentHandler handler)
|
void |
DoubleElementHandlerBase.endElement(String nsURI,
String localName,
String qName,
StAXContentHandler handler)
|
void |
CharElementHandlerBase.endElement(String nsURI,
String localName,
String qName,
StAXContentHandler handler)
|
void |
ByteElementHandlerBase.endElement(String nsURI,
String localName,
String qName,
StAXContentHandler handler)
|
void |
BooleanElementHandlerBase.endElement(String nsURI,
String localName,
String qName,
StAXContentHandler handler)
|
Constructors in org.biojava.utils.stax 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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