de.jstacs.data.sequences.annotation

Class ReferenceSequenceAnnotationParser

java.lang.Object

de.jstacs.data.sequences.annotation.SplitSequenceAnnotationParser

de.jstacs.data.sequences.annotation.ReferenceSequenceAnnotationParser

All Implemented Interfaces:

SequenceAnnotationParser

public class ReferenceSequenceAnnotationParser
extends SplitSequenceAnnotationParser

This class implements an SequenceAnnotationParser that parses a ReferenceSequenceAnnotation from the comment lines of a sequence.

Author:

Jan Grau

Field Summary

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

annot, annotationDelimiter, keyValueDelimiter

Constructor Summary

Constructors

Constructor and Description
ReferenceSequenceAnnotationParser(String key, AlphabetContainer alphabet, String keyValueDelimiter, String annotationDelimiter) Creates a new ReferenceSequenceAnnotationParser with user-specified delimiters.
ReferenceSequenceAnnotationParser(String key, AlphabetContainer alphabet, String keyValueDelimiter, String annotationDelimiter, String delim) Creates a new ReferenceSequenceAnnotationParser with user-specified delimiters.

Method Summary

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

addToAnnotation, clearAnnotation, getCurrentAnnotation

Methods inherited from class java.lang.Object

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

Constructor Detail

ReferenceSequenceAnnotationParser

public ReferenceSequenceAnnotationParser(String key,
                                         AlphabetContainer alphabet,
                                         String keyValueDelimiter,
                                         String annotationDelimiter,
                                         String delim)
                                  throws IllegalArgumentException

Creates a new ReferenceSequenceAnnotationParser with user-specified delimiters.

Parameters:

key - the key for the ReferenceSequenceAnnotation

alphabet - the AlphabetContainer of the reference sequence

keyValueDelimiter - the delimiter between key and corresponding value

annotationDelimiter - the delimiter between different SequenceAnnotations

delim - the delimiter between symbols a the reference sequence

Throws:

IllegalArgumentException - if the delimiters are identical

ReferenceSequenceAnnotationParser

public ReferenceSequenceAnnotationParser(String key,
                                         AlphabetContainer alphabet,
                                         String keyValueDelimiter,
                                         String annotationDelimiter)
                                  throws IllegalArgumentException

Creates a new ReferenceSequenceAnnotationParser with user-specified delimiters.

Parameters:

key - the key for the ReferenceSequenceAnnotation

alphabet - the AlphabetContainer of the reference sequence

keyValueDelimiter - the delimiter between key and corresponding value

annotationDelimiter - the delimiter between different SequenceAnnotations

Throws:

IllegalArgumentException - if the delimiters are identical

Method Detail

add

protected void add(String type,
                   String identifier)

Description copied from class: SplitSequenceAnnotationParser

This method actually adds a SequenceAnnotation to the internal list.

Overrides:

add in class SplitSequenceAnnotationParser

Parameters:

type - the type of the SequenceAnnotation

identifier - the identifier of the 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

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)