apollo.dataadapter.otter.parser
Class SequenceSetTagHandler

java.lang.Object
  apollo.dataadapter.otter.parser.TagHandler
      apollo.dataadapter.otter.parser.SequenceSetTagHandler

public class SequenceSetTagHandler
extends TagHandler

SequenceSets contain everything with a marker for an author - we map them to apollo GenericAnnotationSets

Field Summary

Fields inherited from class apollo.dataadapter.otter.parser.TagHandler

ACCESSION, ASSEMBLY_END, ASSEMBLY_START, ASSEMBLY_TYPE, AUTHOR, AUTHOR_EMAIL, CDS_END_NOT_FOUND, CDS_START_NOT_FOUND, CHROMOSOME, END, EVIDENCE, EXON, FRAGMENT_OFFSET, FRAGMENT_ORI, FRAME, ID, INDENT, KEYWORD, KNOWN, LEFT, LOCUS, LOCUS_TYPE, MRNA_END_NOT_FOUND, MRNA_START_NOT_FOUND, NAME, OTTER, REMARK, RETURN, RIGHT, SEQUENCE_FRAGMENT, SEQUENCE_SET, SLASH, STABLE_ID, START, STRAND, SYNONYM, TRANSCRIPT, TRANSCRIPT_CLASS, TRANSLATION_END, TRANSLATION_STABLE_ID, TRANSLATION_START, TYPE, VERSION

Constructor Summary

SequenceSetTagHandler()

Method Summary

java.lang.String	getFullName()
java.lang.String	getLeafName()
void	handleEndElement(OtterContentHandler theContentHandler, java.lang.String namespaceURI, java.lang.String localName, java.lang.String qualifiedName)
void	handleStartElement(OtterContentHandler theContentHandler, java.lang.String namespaceURI, java.lang.String localName, java.lang.String qualifiedName, org.xml.sax.Attributes attributes)

Methods inherited from class apollo.dataadapter.otter.parser.TagHandler

appendCharacterBuffer, getCharacterBuffer, getCharacters, handleCharacters, setCharacterBuffer

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

SequenceSetTagHandler

public SequenceSetTagHandler()

Method Detail

handleStartElement

public void handleStartElement(OtterContentHandler theContentHandler,
                               java.lang.String namespaceURI,
                               java.lang.String localName,
                               java.lang.String qualifiedName,
                               org.xml.sax.Attributes attributes)

Overrides:

handleStartElement in class TagHandler

handleEndElement

public void handleEndElement(OtterContentHandler theContentHandler,
                             java.lang.String namespaceURI,
                             java.lang.String localName,
                             java.lang.String qualifiedName)

Overrides:

handleEndElement in class TagHandler

getFullName

public java.lang.String getFullName()

Specified by:

getFullName in class TagHandler

getLeafName

public java.lang.String getLeafName()

Specified by:

getLeafName in class TagHandler