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•	apollo.dataadapter.otter.parser.* (51)

• apollo.dataadapter.otter: Javadoc index of package apollo.dataadapter.otter.


Package Samples:

• apollo.dataadapter.otter.parser

Classes:

• OtterXMLRenderingVisitor: I visit elements of the Apollo datamodel, converting each them into XML with my visit() methods. I am typically invoked with a call like: GenericAnnotationSet set = ... OtterXMLRenderingVisitor visitor = new OtterXMLRenderingVisitor(); set.visit(visitor); //will create XML for all features in the set String xml = visitor.getReturnBuffer().toString();
• 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.
• ResponseTagHandler: Responses are returned from the server when the user does an update. contain everything with a marker for an author. They are added to the returned objects on the controller as a string.
• OtterContentHandler: I am the ContentHandler used when SyntenyAdaptor parses the result of a call for annotations on the synteny regions in question.
• OtterAdapterGUI: I am a very simple test interface for the otter adapter. I am NOT a production-strength interface to fetch/write otter-format annotations.
• OtterAdapter: I am a test adapter (along with a simple test interface) which drives the fetching/writing of annotations from an xml-based format.
• LocusTagHandler: I will create a new Locus when my tag is found. When I am closed, I will add myself to the current GenericAnnotationSet.
• ExonTagHandler: I will create a new Gene when my tag is found. When I am closed, I will add myself to the current GenericAnnotationSet.
• EvidenceTagHandler: I will create a new Gene when my tag is found. When I am closed, I will add myself to the current GenericAnnotationSet.
• TranscriptTagHandler: I will create a new Gene when my tag is found. When I am closed, I will add myself to the current GenericAnnotationSet.
• SequenceSetTagHandler: SequenceSets contain everything with a marker for an author - we map them to apollo GenericAnnotationSets
• GenericTagHandler: 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.
• SequenceFragmentAssemblyOffsetTagHandler: I add on the assembly start of the current sequence fragment.
• SequenceFragmentAssemblyOrientationTagHandler: I add on the assembly start of the current sequence fragment.
• SequenceSetAuthorTagHandler: I add on the assembly start of the current sequence fragment.
• SequenceFragmentAssemblyEndTagHandler: I add on the assembly start of the current sequence fragment.
• SequenceFragmentVersionTagHandler: I add on the assembly start of the current sequence fragment.
• SequenceSetAssemblyTypeTagHandler: I add on the assembly start of the current sequence fragment.
• LocusStableIdTagHandler: I add on the assembly start of the current sequence fragment.
• SequenceFragmentAssemblyStartTagHandler: I add on the assembly start of the current sequence fragment.
• OtterTagHandler: General do-nothing tag for the root of the document
• SequenceFragmentIdTagHandler: I add on the name of the current sequence fragment.
• SequenceFragmentChromosomeTagHandler: I add on the name of the current sequence fragment.
• SequenceFragmentAccessionTagHandler: I add on the name of the current sequence fragment.

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