apollo.dataadapter.otter.parser
Class TagHandler

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

Direct Known Subclasses:

EvidenceNameTagHandler, EvidenceTagHandler, EvidenceTypeTagHandler, ExonEndTagHandler, ExonFrameTagHandler, ExonStableIdTagHandler, ExonStartTagHandler, ExonStrandTagHandler, ExonTagHandler, GenericTagHandler, LocusAuthorEmailTagHandler, LocusAuthorTagHandler, LocusKnownTagHandler, LocusNameTagHandler, LocusRemarkTagHandler, LocusStableIdTagHandler, LocusSynonymTagHandler, LocusTagHandler, LocusTypeTagHandler, OtterTagHandler, ResponseTagHandler, SequenceFragmentAccessionTagHandler, SequenceFragmentAssemblyEndTagHandler, SequenceFragmentAssemblyStartTagHandler, SequenceFragmentAuthorEmailTagHandler, SequenceFragmentAuthorTagHandler, SequenceFragmentChromosomeTagHandler, SequenceFragmentFragmentOffsetTagHandler, SequenceFragmentFragmentOrientationTagHandler, SequenceFragmentIdTagHandler, SequenceFragmentKeywordTagHandler, SequenceFragmentRemarkTagHandler, SequenceFragmentTagHandler, SequenceFragmentVersionTagHandler, SequenceSetAssemblyTypeTagHandler, SequenceSetAuthorTagHandler, SequenceSetTagHandler, TranscriptAuthorEmailTagHandler, TranscriptAuthorTagHandler, TranscriptCdsEndNotFoundTagHandler, TranscriptCdsStartNotFoundTagHandler, TranscriptClassTagHandler, TranscriptMRNAEndNotFoundTagHandler, TranscriptMRNAStartNotFoundTagHandler, TranscriptNameTagHandler, TranscriptRemarkTagHandler, TranscriptStableIdTagHandler, TranscriptTagHandler, TranscriptTranslationEndTagHandler, TranscriptTranslationStableIdTagHandler, TranscriptTranslationStartTagHandler

public abstract class TagHandler
extends java.lang.Object

General superclass of the command-objects which are used by the OtterContentHandler.

Field Summary

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

Constructor Summary

TagHandler()

Method Summary

protected void	appendCharacterBuffer(java.lang.String value)
protected java.lang.StringBuffer	getCharacterBuffer()
protected java.lang.String	getCharacters()
abstract java.lang.String	getFullName()
abstract java.lang.String	getLeafName()
void	handleCharacters(OtterContentHandler theContentHandler, char[] text, int start, int length)
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)
protected void	setCharacterBuffer(java.lang.StringBuffer newValue)

Methods inherited from class java.lang.Object

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

Field Detail

LEFT

public static java.lang.String LEFT

RIGHT

public static java.lang.String RIGHT

SLASH

public static java.lang.String SLASH

OTTER

public static java.lang.String OTTER

SEQUENCE_SET

public static java.lang.String SEQUENCE_SET

INDENT

public static java.lang.String INDENT

RETURN

public static java.lang.String RETURN

AUTHOR

public static java.lang.String AUTHOR

AUTHOR_EMAIL

public static java.lang.String AUTHOR_EMAIL

ASSEMBLY_TYPE

public static java.lang.String ASSEMBLY_TYPE

SEQUENCE_FRAGMENT

public static java.lang.String SEQUENCE_FRAGMENT

ID

public static java.lang.String ID

KEYWORD

public static java.lang.String KEYWORD

REMARK

public static java.lang.String REMARK

ACCESSION

public static java.lang.String ACCESSION

VERSION

public static java.lang.String VERSION

CHROMOSOME

public static java.lang.String CHROMOSOME

ASSEMBLY_START

public static java.lang.String ASSEMBLY_START

ASSEMBLY_END

public static java.lang.String ASSEMBLY_END

FRAGMENT_ORI

public static java.lang.String FRAGMENT_ORI

FRAGMENT_OFFSET

public static java.lang.String FRAGMENT_OFFSET

LOCUS

public static java.lang.String LOCUS

NAME

public static java.lang.String NAME

LOCUS_TYPE

public static java.lang.String LOCUS_TYPE

STABLE_ID

public static java.lang.String STABLE_ID

SYNONYM

public static java.lang.String SYNONYM

KNOWN

public static java.lang.String KNOWN

TRANSCRIPT

public static java.lang.String TRANSCRIPT

CDS_START_NOT_FOUND

public static java.lang.String CDS_START_NOT_FOUND

CDS_END_NOT_FOUND

public static java.lang.String CDS_END_NOT_FOUND

MRNA_START_NOT_FOUND

public static java.lang.String MRNA_START_NOT_FOUND

MRNA_END_NOT_FOUND

public static java.lang.String MRNA_END_NOT_FOUND

TRANSLATION_START

public static java.lang.String TRANSLATION_START

TRANSLATION_END

public static java.lang.String TRANSLATION_END

TRANSLATION_STABLE_ID

public static java.lang.String TRANSLATION_STABLE_ID

TRANSCRIPT_CLASS

public static java.lang.String TRANSCRIPT_CLASS

EXON

public static java.lang.String EXON

START

public static java.lang.String START

END

public static java.lang.String END

FRAME

public static java.lang.String FRAME

STRAND

public static java.lang.String STRAND

EVIDENCE

public static java.lang.String EVIDENCE

TYPE

public static java.lang.String TYPE

Constructor Detail

TagHandler

public TagHandler()

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)

handleEndElement

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

handleCharacters

public void handleCharacters(OtterContentHandler theContentHandler,
                             char[] text,
                             int start,
                             int length)

getFullName

public abstract java.lang.String getFullName()

getLeafName

public abstract java.lang.String getLeafName()

getCharacters

protected java.lang.String getCharacters()

getCharacterBuffer

protected java.lang.StringBuffer getCharacterBuffer()

appendCharacterBuffer

protected void appendCharacterBuffer(java.lang.String value)

setCharacterBuffer

protected void setCharacterBuffer(java.lang.StringBuffer newValue)