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## de.jstacs.data
Class DNASample

    java.lang.Object
      de.jstacs.data.Sample
          de.jstacs.data.DNASample

All Implemented Interfaces:
  Iterable<Sequence>

    public class DNASample

extends Sample

This class exist for convenience to allow the user an easy creation of `Sample`s of DNA `Sequence`s.

Author:
  Jan Grau, Jens Keilwagen

Nested Class Summary

Nested classes/interfaces inherited from class de.jstacs.data.Sample
`Sample.ElementEnumerator, Sample.PartitionMethod, Sample.WeightedSampleFactory`

Constructor Summary
`DNASample(String fName)` Creates a new sample of DNA sequence from a FASTA file with file name `fName`.
`DNASample(String fName, char ignore)` Creates a new sample of DNA sequence from a file with file name `fName`.
`DNASample(String fName, char ignore, SequenceAnnotationParser parser)` Creates a new sample of DNA sequence from a file with file name `fName` using the given `parser`.

Method Summary

Methods inherited from class de.jstacs.data.Sample
`diff, getAllElements, getAlphabetContainer, getAnnotation, getAnnotation, getAnnotationTypesAndIdentifier, getCompositeSample, getElementAt, getElementLength, getInfixSample, getMaximalElementLength, getMinimalElementLength, getNumberOfElements, getNumberOfElementsWithLength, getNumberOfElementsWithLength, getReverseComplementarySample, getSequenceAnnotationIndexMatrix, getSuffixSample, intersection, isDiscreteSample, isSimpleSample, iterator, partition, partition, partition, partition, partition, save, save, subSampling, toString, union, union, union, union`

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

Constructor Detail

### DNASample

    public DNASample(String fName)
              throws FileNotFoundException,
                     WrongAlphabetException,
                     EmptySampleException,
                     WrongLengthException,
                     IOException

  Creates a new sample of DNA sequence from a FASTA file with file name `fName`.

  Parameters:
    `fName` - the file name
  Throws:
    `IOException` - if the `File` could not be read
    `FileNotFoundException` - if the `File` could not be found
    `WrongAlphabetException` - if the DNA `AlphabetContainer` is not suitable
    `EmptySampleException` - if the `Sample` would be empty
    `WrongLengthException` - never happens (forwarded from `Sample.Sample(AlphabetContainer, de.jstacs.io.AbstractStringExtractor, String, int)` )
  See Also:
    `AbstractStringExtractor.FASTA`, `DNASample(String, char)`

### DNASample

    public DNASample(String fName,
                     char ignore)
              throws FileNotFoundException,
                     WrongAlphabetException,
                     EmptySampleException,
                     WrongLengthException,
                     IOException

  Creates a new sample of DNA sequence from a file with file name `fName`.

  Parameters:
    `fName` - the file name
    `ignore` - the first character of lines that should be treated as comments
  Throws:
    `IOException` - if the `File` could not be read
    `FileNotFoundException` - if the `File` could not be found
    `WrongAlphabetException` - if the DNA `AlphabetContainer` is not suitable
    `EmptySampleException` - if the `Sample` would be empty
    `WrongLengthException` - never happens (forwarded from `Sample.Sample(AlphabetContainer, de.jstacs.io.AbstractStringExtractor, String, int)` )
  See Also:
    `SparseStringExtractor`, `AbstractStringExtractor.FASTA`, `AbstractStringExtractor.USUALLY`, `DNASample(String, char, SequenceAnnotationParser)`

### DNASample

    public DNASample(String fName,
                     char ignore,
                     SequenceAnnotationParser parser)
              throws FileNotFoundException,
                     WrongAlphabetException,
                     EmptySampleException,
                     WrongLengthException,
                     IOException

  Creates a new sample of DNA sequence from a file with file name `fName` using the given `parser`.

  Parameters:
    `fName` - the file name
    `ignore` - the first character of lines that should be treated as comments
    `parser` - the parser for the `SequenceAnnotation`
  Throws:
    `IOException` - if the `File` could not be read
    `FileNotFoundException` - if the `File` could not be found
    `WrongAlphabetException` - if the DNA `AlphabetContainer` is not suitable
    `EmptySampleException` - if the `Sample` would be empty
    `WrongLengthException` - never happens (forwarded from `Sample.Sample(AlphabetContainer, de.jstacs.io.AbstractStringExtractor, String, int)` )
  See Also:
    `SparseStringExtractor`, `AbstractStringExtractor.FASTA`, `AbstractStringExtractor.USUALLY`, `Sample.Sample(AlphabetContainer, de.jstacs.io.AbstractStringExtractor)`

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