org.biojava.bio.seq.io
Class GenbankXmlFormat

java.lang.Object
  extended by org.biojava.bio.seq.io.GenbankFormat
      extended by org.biojava.bio.seq.io.GenbankXmlFormat
All Implemented Interfaces:
java.io.Serializable, java.util.EventListener, SequenceFormat, ParseErrorListener, ParseErrorSource

Deprecated. Use org.biojavax.bio.seq.io.INSDseqFormat

public class GenbankXmlFormat
extends GenbankFormat

Format reader for GenBank XML files.

Author:
Alan Li - alanli[at]xyworks.com
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
GenbankXmlFormat()
          Deprecated.  
 
Method Summary
 java.lang.String getDefaultFormat()
          Deprecated. getDefaultFormat returns the String identifier for the default format.
 boolean readSequence(java.io.BufferedReader reader, SymbolTokenization symParser, SeqIOListener listener)
          Deprecated. Reads a sequence from the specified reader using the Symbol parser and Sequence Factory provided.
 
Methods inherited from class org.biojava.bio.seq.io.GenbankFormat
addParseErrorListener, BadLineParsed, getElideSymbols, notifyParseErrorEvent, removeParseErrorListener, setElideSymbols, writeSequence, writeSequence
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

GenbankXmlFormat

public GenbankXmlFormat()
Deprecated. 
Method Detail

readSequence

public boolean readSequence(java.io.BufferedReader reader,
                            SymbolTokenization symParser,
                            SeqIOListener listener)
                     throws IllegalSymbolException,
                            java.io.IOException,
                            ParseException
Deprecated. 
Description copied from class: GenbankFormat
Reads a sequence from the specified reader using the Symbol parser and Sequence Factory provided. The sequence read in must be in Genbank format.

Specified by:
readSequence in interface SequenceFormat
Overrides:
readSequence in class GenbankFormat
Parameters:
reader - The stream of data to parse.
symParser - A SymbolParser defining a mapping from character data to Symbols.
listener - A listener to notify when data is extracted from the stream.
Returns:
boolean True if there is another sequence in the file; false otherwise
Throws:
IllegalSymbolException - if it is not possible to translate character data from the stream into valid BioJava symbols.
java.io.IOException - if an error occurs while reading from the stream.
ParseException

getDefaultFormat

public java.lang.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.