Package apollo.dataadapter.otter.parser

Class Summary

EvidenceNameTagHandler
EvidenceTagHandler	I will create a new Evidence element when my tag is found.
EvidenceTypeTagHandler
ExonEndTagHandler
ExonFrameTagHandler
ExonStableIdTagHandler
ExonStartTagHandler
ExonStrandTagHandler
ExonTagHandler	I will create a new Exon when my tag is found.
GenericTagHandler	SequenceSets contain everything with a marker for an author - we map them to apollo GenericAnnotationSets
LocusAuthorEmailTagHandler
LocusAuthorTagHandler
LocusKnownTagHandler
LocusNameTagHandler
LocusRemarkTagHandler
LocusStableIdTagHandler
LocusSynonymTagHandler
LocusTagHandler	I will create a new Locus when my tag is found.
LocusTypeTagHandler
OtterContentHandler	I am the ContentHandler used when SyntenyAdaptor parses the result of a call for annotations on the synteny regions in question.
OtterTagHandler	General do-nothing tag for the root of the document
OtterXMLRenderingVisitor	I visit elements of the Apollo datamodel, converting each them into XML with my visit() methods.
ResponseTagHandler	Responses are returned from the server when the user does an update.
SequenceFragmentAccessionTagHandler	I add on the name of the current sequence fragment.
SequenceFragmentAssemblyEndTagHandler
SequenceFragmentAssemblyStartTagHandler	I add on the assembly start of the current sequence fragment.
SequenceFragmentAuthorEmailTagHandler
SequenceFragmentAuthorTagHandler
SequenceFragmentChromosomeTagHandler	I add on the name of the current sequence fragment.
SequenceFragmentFragmentOffsetTagHandler	I add on the assembly start of the current sequence fragment.
SequenceFragmentFragmentOrientationTagHandler	I add on the assembly start of the current sequence fragment.
SequenceFragmentIdTagHandler	I add on the name of the current sequence fragment.
SequenceFragmentKeywordTagHandler
SequenceFragmentRemarkTagHandler
SequenceFragmentTagHandler	SequenceFragments will be mapped to Apollo GenericAnnotations: this handler will create a new GenericAnnotation when the start tag is found, set its attributes as each subcomponent is found (assembly_start etc) and add it to the set of sequence fragments (of the geneset) when the end tag is hit.
SequenceFragmentVersionTagHandler	I add on the assembly start of the current sequence fragment.
SequenceSetAssemblyTypeTagHandler	I add on the assembly start of the current sequence fragment.
SequenceSetAuthorTagHandler	I add on the assembly start of the current sequence fragment.
SequenceSetTagHandler	SequenceSets contain everything with a marker for an author - we map them to apollo GenericAnnotationSets
TagHandler	General superclass of the command-objects which are used by the OtterContentHandler.
TranscriptAuthorEmailTagHandler
TranscriptAuthorTagHandler
TranscriptCdsEndNotFoundTagHandler
TranscriptCdsStartNotFoundTagHandler
TranscriptClassTagHandler
TranscriptMRNAEndNotFoundTagHandler
TranscriptMRNAStartNotFoundTagHandler
TranscriptNameTagHandler
TranscriptRemarkTagHandler
TranscriptStableIdTagHandler
TranscriptTagHandler	I will create a new Gene when my tag is found.
TranscriptTranslationEndTagHandler
TranscriptTranslationStableIdTagHandler
TranscriptTranslationStartTagHandler