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

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

Method Summary

protected void

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

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

addToAnnotation, clearAnnotation, getCurrentAnnotation, parseAnnotationToComment

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)
                                  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