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Package apollo.dataadapter.otter.parser
| Class Summary | |
| EvidenceDBXrefDbTagHandler | |
| EvidenceDBXrefIdTagHandler | |
| EvidenceNameTagHandler | |
| EvidenceTagHandler | I will create a new Gene when my tag is found. |
| EvidenceTypeTagHandler | |
| ExonEndTagHandler | |
| ExonFrameTagHandler | |
| ExonStableIdTagHandler | |
| ExonStartTagHandler | |
| ExonStrandTagHandler | |
| ExonTagHandler | I will create a new Gene when my tag is found. |
| GenericTagHandler | SequenceSets contain everything with a marker for an author - we map them to apollo GenericAnnotationSets |
| LocusAuthorEmailTagHandler | |
| LocusAuthorTagHandler | |
| LocusNameTagHandler | |
| LocusRemarkTagHandler | |
| LocusStableIdTagHandler | I add on the assembly start of the current sequence fragment. |
| 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 | I add on the assembly start of the current sequence fragment. |
| SequenceFragmentAssemblyOffsetTagHandler | I add on the assembly start of the current sequence fragment. |
| SequenceFragmentAssemblyOrientationTagHandler | I add on the assembly start of the current sequence fragment. |
| SequenceFragmentAssemblyStartTagHandler | I add on the assembly start of the current sequence fragment. |
| SequenceFragmentChromosomeTagHandler | I add on the name of the current sequence fragment. |
| SequenceFragmentIdTagHandler | I add on the name of the current sequence fragment. |
| SequenceFragmentKeywordTagHandler | |
| SequenceFragmentNameTagHandler | I add on the name of the current sequence fragment. |
| 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 (assemblystart 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. |
| TranscriptCdsEndNotFoundTagHandler | |
| TranscriptCdsStartNotFoundTagHandler | |
| TranscriptClassTagHandler | |
| TranscriptMRNAEndNotFoundTagHandler | |
| TranscriptMRNAStartNotFoundTagHandler | |
| TranscriptNameTagHandler | |
| TranscriptRemarkTagHandler | |
| TranscriptStableIdTagHandler | |
| TranscriptTagHandler | I will create a new Gene when my tag is found. |
| TranscriptTranslationEndTagHandler | |
| TranscriptTranslationStartTagHandler | |
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