public class GenbankXmlFormat extends 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 and Description |
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GenbankXmlFormat()
Deprecated.
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Modifier and Type | Method and Description |
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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.
|
addParseErrorListener, BadLineParsed, getElideSymbols, notifyParseErrorEvent, removeParseErrorListener, setElideSymbols, writeSequence, writeSequence
public boolean readSequence(java.io.BufferedReader reader, SymbolTokenization symParser, SeqIOListener listener) throws IllegalSymbolException, java.io.IOException, ParseException
GenbankFormat
readSequence
in interface SequenceFormat
readSequence
in class GenbankFormat
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.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
public java.lang.String getDefaultFormat()
GenbankFormat
getDefaultFormat
returns the String identifier for
the default format.getDefaultFormat
in interface SequenceFormat
getDefaultFormat
in class GenbankFormat
String
.