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## 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 `SequenceAnnotation`s 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 `SequenceAnnotation`s 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 `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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