org.biojava.bio.seq.io

Class GenpeptFormat

java.lang.Object

org.biojava.bio.seq.io.GenbankFormat

org.biojava.bio.seq.io.GenpeptFormat

All Implemented Interfaces:

Serializable, EventListener, SequenceFormat, ParseErrorListener, ParseErrorSource

Deprecated.

Use org.biojavax.bio.seq.io framework instead

public class GenpeptFormat
extends GenbankFormat

This class is necessitated by the deprecation of writeSequence(Sequence seq, String format, PrintStream os) method. Now the format object must be intimately associated to the format it is handling.

Author:

David Huen

See Also:

Serialized Form

Field Summary

Fields inherited from class org.biojava.bio.seq.io.GenbankFormat

ACCESSION_TAG, AUTHORS_TAG, BASE_COUNT_TAG, CIRCULAR_TAG, COMMENT_TAG, COORDINATE_TAG, DATE_TAG, DEFAULT, DEFINITION_TAG, DIVISION_TAG, END_SEQUENCE_TAG, FEATURE_FLAG, FEATURE_LINE_PREFIX, FEATURE_TAG, GI_TAG, JOURNAL_TAG, KEYWORDS_TAG, LOCUS_TAG, MEDLINE_TAG, ORGANISM_TAG, PUBMED_TAG, REF_ACCESSION_TAG, REFERENCE_TAG, SIZE_TAG, SOURCE_TAG, START_SEQUENCE_TAG, STRAND_NUMBER_TAG, TITLE_TAG, TYPE_TAG, VERSION_TAG

Constructor Summary

Constructors

Constructor and Description
GenpeptFormat() Deprecated.

Method Summary

Modifier and Type	Method and Description
String	getDefaultFormat() Deprecated. getDefaultFormat returns the String identifier for the default format.

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

addParseErrorListener, BadLineParsed, getElideSymbols, notifyParseErrorEvent, readSequence, removeParseErrorListener, setElideSymbols, writeSequence, writeSequence

Methods inherited from class java.lang.Object

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

Constructor Detail

GenpeptFormat

public GenpeptFormat()

Deprecated.

Method Detail

getDefaultFormat

public String getDefaultFormat()

Deprecated.

Description copied from class: GenbankFormat

getDefaultFormat returns the String identifier for the default format.

Specified by:

getDefaultFormat in interface SequenceFormat

Overrides:

getDefaultFormat in class GenbankFormat

Returns:

a String.