org.biojava.bio.seq.io
Class GenbankXmlFormat
java.lang.Object
org.biojava.bio.seq.io.GenbankFormat
org.biojava.bio.seq.io.GenbankXmlFormat
- All Implemented Interfaces:
- Serializable, 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
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 |
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
GenbankXmlFormat
public GenbankXmlFormat()
- Deprecated.
readSequence
public boolean readSequence(BufferedReader reader,
SymbolTokenization symParser,
SeqIOListener listener)
throws IllegalSymbolException,
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.
IOException
- if an error occurs while reading from the
stream.
ParseException
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
.