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

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

All Implemented Interfaces:
  SequenceAnnotationParser

Direct Known Subclasses:
  MotifAnnotationParser, ReferenceSequenceAnnotationParser

    public class SplitSequenceAnnotationParser

extends Object
implements SequenceAnnotationParser

This class implements a simple `SequenceAnnotationParser` which simply splits the comments by specific delimiters.

Author:
  Jens Keilwagen

Field Summary
`protected LinkedList<SequenceAnnotation>` | `annot` The internal list of current `SequenceAnnotation`s.
`protected String` | `annotationDelimiter` The delimiter between different annotations
`protected String` | `keyValueDelimiter` The delimiter between key and value

Constructor Summary
`SplitSequenceAnnotationParser()` Creates a new `SplitSequenceAnnotationParser` with specific delimiters, i.e., key value delimiter "=" and annotation delimiter ";".
`SplitSequenceAnnotationParser(String keyValueDelimiter, String annotationDelimiter)` Creates a new `SplitSequenceAnnotationParser` with user-specified delimiters.

Method Summary
`protected void` | `add(String type, String identifier)` This method actually adds a `SequenceAnnotation` to the internal list.
`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.

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

Field Detail

### keyValueDelimiter

    protected String keyValueDelimiter

  The delimiter between key and value

### annotationDelimiter

    protected String annotationDelimiter

  The delimiter between different annotations

### annot

    protected LinkedList<SequenceAnnotation> annot

  The internal list of current `SequenceAnnotation`s.

Constructor Detail

### SplitSequenceAnnotationParser

    public SplitSequenceAnnotationParser()

  Creates a new `SplitSequenceAnnotationParser` with specific delimiters, i.e., key value delimiter "=" and annotation delimiter ";".

  See Also:
    `SplitSequenceAnnotationParser(String, String)`

### SplitSequenceAnnotationParser

    public SplitSequenceAnnotationParser(String keyValueDelimiter,
                                         String annotationDelimiter)

  Creates a new `SplitSequenceAnnotationParser` with user-specified delimiters.

  Parameters:
    `keyValueDelimiter` - the delimiter between key and corresponding value
    `annotationDelimiter` - the delimiter between different `SequenceAnnotation`s
  Throws:
    `IllegalArgumentException` - if the delimiters are identical

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`
  Parameters:
    `unparsed` - the String containing the annotation

### add

    protected void add(String type,
                       String identifier)

  This method actually adds a `SequenceAnnotation` to the internal list.

  Parameters:
    `type` - the type of the `SequenceAnnotation`
    `identifier` - the identifier of the `SequenceAnnotation`

### clearAnnotation

    public void clearAnnotation()

  Description copied from interface: `SequenceAnnotationParser`
  This method reset the current `SequenceAnnotation`.

  Specified by:
    `clearAnnotation` in interface `SequenceAnnotationParser`

### getCurrentAnnotation

    public SequenceAnnotation[] getCurrentAnnotation()

  Description copied from interface: `SequenceAnnotationParser`
  This method returns the current `SequenceAnnotation`.

  Specified by:
    `getCurrentAnnotation` in interface `SequenceAnnotationParser`
  Returns:
    the current `SequenceAnnotation`

### 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`
  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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