uk.ac.man.bioinf.io.parsers
Class MotProteinParser
java.lang.Object
|
+--uk.ac.man.bioinf.io.parsers.MotProteinParser
- All Implemented Interfaces:
- AlignmentOutputParser
- public class MotProteinParser
- extends Object
- implements AlignmentOutputParser
MotProteinParser.java
Mot files are used by several of the applications that are used to
produce PRINTS. Its a very simple format. One line per sequence
(motif files tend to be fairly short alignments). Comments are
designated with a #. PRINTS motif's can't contain gaps so by
definition here this parser does not like gaps and will not write
them out.
Created: Mon Jan 22 16:44:15 2001
- Version:
- $Id: MotProteinParser.java,v 1.3 2001/04/11 17:04:43 lord Exp $
- Author:
- Phillip Lord
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
MotProteinParser
public MotProteinParser()
write
public Writer write(SequenceAlignment sa,
Writer writer,
ParserExceptionHandler eh)
- Description copied from interface:
AlignmentOutputParser
- Returns a writer for output, when provided with a sequence
alignment. Exceptions are handled by the supplied exception
handler.
- Specified by:
write
in interface AlignmentOutputParser
- Parameters:
sa
- the sequence alignmenteh
- the exception handler
- Returns:
- the writer for output
getDescription
public String getDescription()
- Description copied from interface:
AlignmentOutputParser
- Returns the description of this alignment output parser, and
should be human readable/understandable.
- Specified by:
getDescription
in interface AlignmentOutputParser
- Returns:
- the description