de.jstacs.data.sequences.annotation

Class MotifAnnotationParser

java.lang.Object

de.jstacs.data.sequences.annotation.SplitSequenceAnnotationParser

de.jstacs.data.sequences.annotation.MotifAnnotationParser

All Implemented Interfaces:

SequenceAnnotationParser

public class MotifAnnotationParser
extends SplitSequenceAnnotationParser

Annotation parser for MotifAnnotations.

Author:

Jan Grau

Field Summary

Fields inherited from class de.jstacs.data.sequences.annotation.SplitSequenceAnnotationParser

annot, annotationDelimiter, keyValueDelimiter

Constructor Summary

Constructors

Constructor and Description
MotifAnnotationParser() Creates a new MotifAnnotationParser with default delimiters.
MotifAnnotationParser(String keyValueDelimiter, String annotationDelimiter) Creates a new MotifAnnotationParser with the supplied delimiters

Method Summary

Modifier and Type	Method and Description
protected void	add(String identifier, int position, int length, StrandedLocatedSequenceAnnotationWithLength.Strand strandedness) Adds the motif with identifier identifier at position position with length length and StrandedLocatedSequenceAnnotationWithLength.Strand strandedness
void	addToAnnotation(String unparsed) This method adds the unparsed String in some way to the SequenceAnnotation.
String	parseAnnotationToComment(char commentChar, SequenceAnnotation... annotations) This method returns a String representation of the given SequenceAnnotations that can be used as comment line in a file.

Methods inherited from class de.jstacs.data.sequences.annotation.SplitSequenceAnnotationParser

add, clearAnnotation, getCurrentAnnotation

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

MotifAnnotationParser

public MotifAnnotationParser()

Creates a new MotifAnnotationParser with default delimiters.

See Also:

SplitSequenceAnnotationParser.SplitSequenceAnnotationParser()

MotifAnnotationParser

public MotifAnnotationParser(String keyValueDelimiter,
                             String annotationDelimiter)

Creates a new MotifAnnotationParser with the supplied delimiters

Parameters:

keyValueDelimiter - the delimiter between key and value

annotationDelimiter - the delimiter between different annotations

Method Detail

addToAnnotation

public void addToAnnotation(String unparsed)

Description copied from interface: SequenceAnnotationParser

This method adds the unparsed String in some way to the SequenceAnnotation.

Specified by:

addToAnnotation in interface SequenceAnnotationParser

Overrides:

addToAnnotation in class SplitSequenceAnnotationParser

Parameters:

unparsed - the String containing the annotation

add

protected void add(String identifier,
                   int position,
                   int length,
                   StrandedLocatedSequenceAnnotationWithLength.Strand strandedness)

Adds the motif with identifier identifier at position position with length length and StrandedLocatedSequenceAnnotationWithLength.Strand strandedness

Parameters:

identifier - the identifier of the motif

position - the position of the motif

length - the length of the motif

strandedness - the strand of the motif

parseAnnotationToComment

public String parseAnnotationToComment(char commentChar,
                                       SequenceAnnotation... annotations)

Description copied from interface: SequenceAnnotationParser

This method returns a String representation of the given SequenceAnnotations that can be used as comment line in a file.
Normally, the method should do the opposite of SequenceAnnotationParser.addToAnnotation(String).

Specified by:

parseAnnotationToComment in interface SequenceAnnotationParser

Overrides:

parseAnnotationToComment in class SplitSequenceAnnotationParser

Parameters:

commentChar - the char at the beginning of comment lines

annotations - the SequenceAnnotations to be parsed

Returns:

a String representing the given SequenceAnnotations

See Also:

DataSet.save(java.io.OutputStream, char, SequenceAnnotationParser)