de.jstacs.data.sequences.annotation
Interface SequenceAnnotationParser

All Known Implementing Classes:

MotifAnnotationParser, NullSequenceAnnotationParser, ReferenceSequenceAnnotationParser, SimpleSequenceAnnotationParser, SplitSequenceAnnotationParser

public interface SequenceAnnotationParser

This interface declares the methods which are used by AbstractStringExtractor to annotate a String which will be parsed to a Sequence.

Author:

Jens Keilwagen

Method Summary

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.

Method Detail

getCurrentAnnotation

SequenceAnnotation[] getCurrentAnnotation()

This method returns the current SequenceAnnotation.

Returns:

the current SequenceAnnotation

addToAnnotation

void addToAnnotation(String unparsed)

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

Parameters:

unparsed - the String containing the annotation

clearAnnotation

void clearAnnotation()

This method reset the current SequenceAnnotation.

parseAnnotationToComment

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.
Normally, the method should do the opposite of addToAnnotation(String).

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)