org.biojava.bio.seq.io
Class GenpeptFormat

java.lang.Object
  extended by org.biojava.bio.seq.io.GenbankFormat
      extended by 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
GenpeptFormat()
          Deprecated.  
 
Method Summary
 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.


Copyright © 2012 BioJava. All Rights Reserved.