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Packages that use StAXContentHandlerBase | |
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.bio.seq.ragbag | The Ragbag package is a set of classes for setting up a virtual sequence contig without the need for writing Biojava code. |
org.biojava.utils.stax | The Stack API for XML (StAX). |
Uses of StAXContentHandlerBase in org.biojava.bio.program.sax.blastxml |
Subclasses of StAXContentHandlerBase in org.biojava.bio.program.sax.blastxml | |
class |
BlastXMLParser
This class parses NCBI Blast XML output. |
(package private) class |
org.biojava.bio.program.sax.blastxml.StAXFeatureHandler
StAX handler shamelessly ripped off from Thomas Down's XFFFeatureSetHandler. |
Uses of StAXContentHandlerBase in org.biojava.bio.program.ssbind |
Subclasses of StAXContentHandlerBase in org.biojava.bio.program.ssbind | |
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 . |
Uses of StAXContentHandlerBase in org.biojava.bio.program.xff |
Subclasses of StAXContentHandlerBase in org.biojava.bio.program.xff | |
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 StAXContentHandlerBase | |
StAXContentHandlerBase |
XFFFeatureSetHandler.getDetailsHandler()
Return a handler for the XFF details element. |
Uses of StAXContentHandlerBase in org.biojava.bio.seq.io.filterxml |
Subclasses of StAXContentHandlerBase in org.biojava.bio.seq.io.filterxml | |
class |
XMLAnnotationTypeHandler
StAX handler for parsing AnnotationTypes in FilterXML documents. |
Uses of StAXContentHandlerBase in org.biojava.bio.seq.io.game |
Subclasses of StAXContentHandlerBase in org.biojava.bio.seq.io.game | |
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 |
StAXPropertyHandler
StAX handler shamelessly ripped off from Thomas Down's XFFFeatureSetHandler. |
Uses of StAXContentHandlerBase in org.biojava.bio.seq.io.game12 |
Subclasses of StAXContentHandlerBase in org.biojava.bio.seq.io.game12 | |
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. |
Uses of StAXContentHandlerBase in org.biojava.bio.seq.ragbag |
Subclasses of StAXContentHandlerBase in org.biojava.bio.seq.ragbag | |
class |
RagbagMap
This class is an object that encapsulates all information present in a Map file in a Ragbag directory. |
Uses of StAXContentHandlerBase in org.biojava.utils.stax |
Subclasses of StAXContentHandlerBase in org.biojava.utils.stax | |
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 |
StringElementHandlerBase
StAX handler for any element which just contains a string. |
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