|
||||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | |||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |
java.lang.Objectorg.biojava.bio.seq.io.GenbankFormat
org.biojava.bio.seq.io.GenbankXmlFormat
public class GenbankXmlFormat
Format reader for GenBank XML files.
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 |
---|
public GenbankXmlFormat()
Method Detail |
---|
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
.
|
||||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | |||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |