org.biojava.bio.seq.io
Class OrganismParser
java.lang.Object
org.biojava.bio.seq.io.SequenceBuilderFilter
org.biojava.bio.seq.io.OrganismParser
- All Implemented Interfaces:
- SeqIOListener, SequenceBuilder
Deprecated. Use org.biojavax.bio.taxa framework instead
public class OrganismParser
- extends SequenceBuilderFilter
A parser that is able to generate Taxon entries for sequence
builder event streams.
- Author:
- Matthew Pocock
Nested Class Summary |
static class |
OrganismParser.Factory
Deprecated. Factory which wraps SequenceBuilders in an OrganismParser. |
Method Summary |
void |
addSequenceProperty(java.lang.Object sciNameKey,
java.lang.Object value)
Deprecated. Notify the listener of a sequence-wide property. |
void |
endSequence()
Deprecated. Notify the listener that processing of the sequence is complete. |
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
PROPERTY_ORGANISM
public static final java.lang.String PROPERTY_ORGANISM
- Deprecated.
OrganismParser
public OrganismParser(SequenceBuilder delegate,
TaxonFactory taxonFactory,
TaxonParser taxonParser,
java.lang.String sciNameKey,
java.lang.String commonNameKey,
java.lang.String ncbiTaxonKey)
- Deprecated.
addSequenceProperty
public void addSequenceProperty(java.lang.Object sciNameKey,
java.lang.Object value)
throws ParseException
- Deprecated.
- Description copied from interface:
SeqIOListener
- Notify the listener of a sequence-wide property. This might
be stored as an entry in the sequence's annotation bundle.
- Specified by:
addSequenceProperty
in interface SeqIOListener
- Overrides:
addSequenceProperty
in class SequenceBuilderFilter
- Throws:
ParseException
endSequence
public void endSequence()
throws ParseException
- Deprecated.
- Description copied from interface:
SeqIOListener
- Notify the listener that processing of the sequence is complete.
- Specified by:
endSequence
in interface SeqIOListener
- Overrides:
endSequence
in class SequenceBuilderFilter
- Throws:
ParseException