de.jstacs.data.sequences.annotation
Class SplitSequenceAnnotationParser

java.lang.Object
  de.jstacs.data.sequences.annotation.SplitSequenceAnnotationParser

All Implemented Interfaces:

SequenceAnnotationParser

Direct Known Subclasses:

MotifAnnotationParser, ReferenceSequenceAnnotationParser

public class SplitSequenceAnnotationParser
extends Object
implements SequenceAnnotationParser

This class implements a simple SequenceAnnotationParser which simply splits the comments by specific delimiters.

Author:

Jens Keilwagen

Field Summary

protected LinkedList<SequenceAnnotation>	annot The internal list of current SequenceAnnotations.
protected String	annotationDelimiter The delimiter between different annotations
protected String	keyValueDelimiter The delimiter between key and value

Constructor Summary

SplitSequenceAnnotationParser()
Creates a new SplitSequenceAnnotationParser with specific delimiters, i.e., key value delimiter "=" and annotation delimiter ";".

SplitSequenceAnnotationParser(String keyValueDelimiter, String annotationDelimiter)
Creates a new SplitSequenceAnnotationParser with user-specified delimiters.

Method Summary

protected void	add(String type, String identifier) This method actually adds a SequenceAnnotation to the internal list.
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

Field Detail

keyValueDelimiter

protected String keyValueDelimiter

The delimiter between key and value

annotationDelimiter

protected String annotationDelimiter

The delimiter between different annotations

annot

protected LinkedList<SequenceAnnotation> annot

The internal list of current SequenceAnnotations.

Constructor Detail

SplitSequenceAnnotationParser

public SplitSequenceAnnotationParser()

Creates a new SplitSequenceAnnotationParser with specific delimiters, i.e., key value delimiter "=" and annotation delimiter ";".

See Also:

SplitSequenceAnnotationParser(String, String)

SplitSequenceAnnotationParser

public SplitSequenceAnnotationParser(String keyValueDelimiter,
                                     String annotationDelimiter)

Creates a new SplitSequenceAnnotationParser with user-specified delimiters.

Parameters:

keyValueDelimiter - the delimiter between key and corresponding value

annotationDelimiter - the delimiter between different SequenceAnnotations

Throws:

IllegalArgumentException - if the delimiters are identical

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

add

protected void add(String type,
                   String identifier)

This method actually adds a SequenceAnnotation to the internal list.

Parameters:

type - the type of the SequenceAnnotation

identifier - the identifier of the SequenceAnnotation

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)