apollo.dataadapter.otter.parser
Class SequenceFragmentTagHandler

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

public class SequenceFragmentTagHandler
extends TagHandler

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.

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

SequenceFragmentTagHandler()

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

SequenceFragmentTagHandler

public SequenceFragmentTagHandler()

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