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## de.jstacs.data.sequences.annotation
Class MotifAnnotationParser

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

All Implemented Interfaces:
  SequenceAnnotationParser

    public class MotifAnnotationParser

extends SplitSequenceAnnotationParser

Annotation parser for `MotifAnnotation`s.

Author:
  Jan Grau

Field Summary

Fields inherited from class de.jstacs.data.sequences.annotation.SplitSequenceAnnotationParser
`annot, annotationDelimiter, keyValueDelimiter`

Constructor Summary
`MotifAnnotationParser()` Creates a new `MotifAnnotationParser` with default delimiters.
`MotifAnnotationParser(String keyValueDelimiter, String annotationDelimiter)` Creates a new `MotifAnnotationParser` with the supplied delimiters

Method Summary
`protected void` | `add(String identifier, int position, int length, StrandedLocatedSequenceAnnotationWithLength.Strand strandedness)` Adds the motif with identifier `identifier` at position `position` with length `length` and `StrandedLocatedSequenceAnnotationWithLength.Strand` `strandedness`
`void` | `addToAnnotation(String unparsed)` This method adds the `unparsed` `String` in some way to the `SequenceAnnotation`.
`String` | `parseAnnotationToComment(char commentChar, SequenceAnnotation... annotations)` This method returns a `String` representation of the given `SequenceAnnotation`s that can be used as comment line in a file.

Methods inherited from class de.jstacs.data.sequences.annotation.SplitSequenceAnnotationParser
`add, clearAnnotation, getCurrentAnnotation`

Methods inherited from class java.lang.Object
`clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait`

Constructor Detail

### MotifAnnotationParser

    public MotifAnnotationParser()

  Creates a new `MotifAnnotationParser` with default delimiters.

  See Also:
    `SplitSequenceAnnotationParser.SplitSequenceAnnotationParser()`

### MotifAnnotationParser

    public MotifAnnotationParser(String keyValueDelimiter,
                                 String annotationDelimiter)

  Creates a new `MotifAnnotationParser` with the supplied delimiters

  Parameters:
    `keyValueDelimiter` - the delimiter between key and value
    `annotationDelimiter` - the delimiter between different annotations

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`
  Overrides:
    `addToAnnotation` in class `SplitSequenceAnnotationParser`
  Parameters:
    `unparsed` - the String containing the annotation

### add

    protected void add(String identifier,
                       int position,
                       int length,
                       StrandedLocatedSequenceAnnotationWithLength.Strand strandedness)

  Adds the motif with identifier `identifier` at position `position` with length `length` and `StrandedLocatedSequenceAnnotationWithLength.Strand` `strandedness`

  Parameters:
    `identifier` - the identifier of the motif
    `position` - the position of the motif
    `length` - the length of the motif
    `strandedness` - the strand of the motif

### parseAnnotationToComment

    public String parseAnnotationToComment(char commentChar,
                                           SequenceAnnotation... annotations)

  Description copied from interface: `SequenceAnnotationParser`
  This method returns a `String` representation of the given `SequenceAnnotation`s 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 `SequenceAnnotation`s to be parsed
  Returns:
    a String representing the given `SequenceAnnotation`s
  See Also:
    `Sample.save(java.io.OutputStream, char, SequenceAnnotationParser)`

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