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java.lang.Object | +--uk.ac.man.bioinf.io.parsers.AbstractProteinAlignmentInputParser | +--uk.ac.man.bioinf.io.parsers.PIRProteinAlignmentParser
A filter that reads an alignment in PIR/NBRF protein sequence format and returns a sequence alignment object. This parser has no state attached to it, and may be re-entered (ie it is thread safe). Created: Fri May 26 10:18:02 2000
Constructor Summary | |
PIRProteinAlignmentParser()
|
Method Summary | |
String |
getDescription()
Returns that this is a PIR/NBRF protein sequence parser. |
SequenceAlignment |
parse(Identifier ident,
Reader r,
ParserExceptionHandler eh)
|
SequenceAlignment |
parse(Reader r,
ParserExceptionHandler eh)
This function parses an input reader which contains a (set of) PIR/NBRF sequence(s), and returns an alignment containing them. |
Writer |
write(SequenceAlignment sa,
Writer writer,
ParserExceptionHandler eh)
This method parses a sequence alignment and writes it out to the supplied writer. |
Methods inherited from class uk.ac.man.bioinf.io.parsers.AbstractProteinAlignmentInputParser |
toSequence |
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
public PIRProteinAlignmentParser()
Method Detail |
public SequenceAlignment parse(Reader r, ParserExceptionHandler eh) throws IOException
parse
in interface AlignmentInputParser
r
- the input readereh
- the exception handler
IOException
- if there is an error in the readerpublic SequenceAlignment parse(Identifier ident, Reader r, ParserExceptionHandler eh) throws IOException
parse
in interface AlignmentInputParser
IOException
public Writer write(SequenceAlignment sa, Writer writer, ParserExceptionHandler eh)
N.B., this method does nothing with the writer other than write output to it - i.e. it does not close the writer.
write
in interface AlignmentOutputParser
sa
- the sequence alignment to be written.writer
- the writer to which the sequence is to be writteneh
- the exception handler to which exceptions are parsed.
public String getDescription()
getDescription
in interface AlignmentOutputParser
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