Package 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
Format reader for GenBank XML files.
- Author:
- Alan Li - alanli[at]xyworks.com
- See Also:
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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
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionDeprecated.getDefaultFormat
returns the String identifier for the default format.boolean
readSequence
(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
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Constructor Details
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GenbankXmlFormat
public GenbankXmlFormat()Deprecated.
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Method Details
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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 interfaceSequenceFormat
- Overrides:
readSequence
in classGenbankFormat
- 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
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getDefaultFormat
Deprecated.Description copied from class:GenbankFormat
getDefaultFormat
returns the String identifier for the default format.- Specified by:
getDefaultFormat
in interfaceSequenceFormat
- Overrides:
getDefaultFormat
in classGenbankFormat
- Returns:
- a
String
.
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