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

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.

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)