de.jstacs.data.sequences.annotation

Class SimpleSequenceAnnotationParser

java.lang.Object

de.jstacs.data.sequences.annotation.SimpleSequenceAnnotationParser

All Implemented Interfaces:

SequenceAnnotationParser

public class SimpleSequenceAnnotationParser
extends Object
implements SequenceAnnotationParser

This class implements a naive SequenceAnnotationParser which simply paste the comments into SequenceAnnotation.

Author:

Jens Keilwagen

Constructor Summary

Constructors

Constructor and Description
SimpleSequenceAnnotationParser() The constructor of a SimpleSequenceAnnotationParser which simply paste the comments into SequenceAnnotation.

Method Summary

Modifier and Type	Method and Description
void	addToAnnotation(String unparsed) This method adds the unparsed String in some way to the SequenceAnnotation.
void	clearAnnotation() This method reset the current SequenceAnnotation.
SequenceAnnotation[]	getCurrentAnnotation() This method returns the current 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 java.lang.Object

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

Constructor Detail

SimpleSequenceAnnotationParser

public SimpleSequenceAnnotationParser()

The constructor of a SimpleSequenceAnnotationParser which simply paste the comments into SequenceAnnotation.

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

Parameters:

unparsed - the String containing the annotation

clearAnnotation

public void clearAnnotation()

Description copied from interface: SequenceAnnotationParser

This method reset the current SequenceAnnotation.

Specified by:

clearAnnotation in interface SequenceAnnotationParser

getCurrentAnnotation

public SequenceAnnotation[] getCurrentAnnotation()

Description copied from interface: SequenceAnnotationParser

This method returns the current SequenceAnnotation.

Specified by:

getCurrentAnnotation in interface SequenceAnnotationParser

Returns:

the current SequenceAnnotation

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

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)