Package org.biojava.bio.seq.io

Class FastaDescriptionLineParser

java.lang.Object

org.biojava.bio.seq.io.SequenceBuilderFilter

org.biojava.bio.seq.io.FastaDescriptionLineParser

All Implemented Interfaces:

SeqIOListener, SequenceBuilder

public class FastaDescriptionLineParser
extends SequenceBuilderFilter

Deprecated.

Use org.biojavax.bio.seq.io.FastaFormat

Simple filter which performs a default extraction of data from the description lines of FASTA files. Behaviour is similar to DefaultDescriptionReader in the old I/O framework.

Since:

1.1

Author:

Thomas Down

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	FastaDescriptionLineParser.Factory	Deprecated. Factory which wraps SequenceBuilders in a FastaDescriptionLineParser

Constructor Summary

Constructors

Constructor	Description
FastaDescriptionLineParser(SequenceBuilder delegate)	Deprecated.

Method Summary

Modifier and Type	Method	Description
void	addSequenceProperty(Object key, Object value)	Deprecated. Notify the listener of a sequence-wide property.

Methods inherited from class org.biojava.bio.seq.io.SequenceBuilderFilter

addFeatureProperty, addSymbols, endFeature, endSequence, getDelegate, makeSequence, setName, setURI, startFeature, startSequence

Methods inherited from class java.lang.Object

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

Constructor Detail

FastaDescriptionLineParser

public FastaDescriptionLineParser(SequenceBuilder delegate)

Deprecated.

Method Detail

addSequenceProperty

public void addSequenceProperty(Object key,
                                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