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## de.jstacs.data
Class Sample

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

All Implemented Interfaces:
  Iterable<Sequence>

Direct Known Subclasses:
  DNASample

    public class Sample

extends Object
implements Iterable<Sequence>

This is the class for any sample of `Sequence`s. All `Sequence`s in a `Sample` have to have the same `AlphabetContainer`. The `Sequence`s may have different lengths.
For the internal representation the class `Sequence` is used, where the external alphabet is converted to integral numerical values. The class `Sample` knows about this coding via instances of class `AlphabetContainer` and accordingly `Alphabet`.
There are different ways to access the elements of a `Sample`. If one needs random access there is the method `getElementAt(int)`. For fast sequential access it is recommended to use an `Sample.ElementEnumerator`.
`Sample` is immutable.

Author:
  Jens Keilwagen
See Also:
  `AlphabetContainer`, `Alphabet`, `Sequence`

Nested Class Summary
`static class` | `Sample.ElementEnumerator` This class can be used to have a fast sequential access to a `Sample`.
`static class` | `Sample.PartitionMethod` This `enum` defines different partition methods for a `Sample`.
`static class` | `Sample.WeightedSampleFactory` This class enables you to eliminate `Sequence`s that occur more than once in one or more `Sample`s.

Constructor Summary
`Sample(AlphabetContainer abc, AbstractStringExtractor se)` Creates a new `Sample` from a `StringExtractor` using the given `AlphabetContainer`.
`Sample(AlphabetContainer abc, AbstractStringExtractor se, int subsequenceLength)` Creates a new `Sample` from a `StringExtractor` using the given `AlphabetContainer` and all overlapping windows of length `subsequenceLength`.
`Sample(AlphabetContainer abc, AbstractStringExtractor se, String delim)` Creates a new `Sample` from a `StringExtractor` using the given `AlphabetContainer` and a delimiter `delim`.
`Sample(AlphabetContainer abc, AbstractStringExtractor se, String delim, int subsequenceLength)` Creates a new `Sample` from a `StringExtractor` using the given `AlphabetContainer`, the given delimiter `delim` and all overlapping windows of length `subsequenceLength`.
`Sample(Sample s, int subsequenceLength)` Creates a new `Sample` from a given `Sample` and a given length `subsequenceLength`.
`Sample(String annotation, Sequence... seqs)` Creates a new `Sample` from an array of `Sequence`s and a given annotation.

Method Summary
`static Sample` | `diff(Sample data, Sample... samples)` This method computes the difference between the `Sample` `data` and the `Sample`s `samples`.
`Sequence[]` | `getAllElements()` Returns an array of `Sequence`s containing all elements of this `Sample`.
`AlphabetContainer` | `getAlphabetContainer()` Returns the `AlphabetContainer` of this `Sample`.
`String` | `getAnnotation()` Returns some annotation of the `Sample`.
`static String` | `getAnnotation(Sample... s)` Returns the annotation for an array of `Sample`s.
`Hashtable<String,HashSet<String>>` | `getAnnotationTypesAndIdentifier()` This method returns all `SequenceAnnotation` types and the corresponding identifier which occur in this `Sample`.
`Sample` | `getCompositeSample(int[] starts, int[] lengths)` This method enables you to use only composite `Sequence`s of all elements in the current `Sample`.
`Sequence` | `getElementAt(int i)` This method returns the element, i.e. the `Sequence`, with index `i`.
`int` | `getElementLength()` Returns the length of the elements, i.e. the `Sequence`s, in this `Sample`.
`Sample` | `getInfixSample(int start, int length)` This method enables you to use only an infix of all elements, i.e. the `Sequence`s, in the current `Sample`.
`int` | `getMaximalElementLength()` Returns the maximal length of an element, i.e. a `Sequence`, in this `Sample`.
`int` | `getMinimalElementLength()` Returns the minimal length of an element, i.e. a `Sequence`, in this `Sample`.
`int` | `getNumberOfElements()` Returns the number of elements, i.e. the `Sequence`s, in this `Sample`.
`int` | `getNumberOfElementsWithLength(int len)` Returns the number of overlapping elements that can be extracted.
`double` | `getNumberOfElementsWithLength(int len, double[] weights)` Returns the weighted number of overlapping elements that can be extracted.
`int[][]` | `getSequenceAnnotationIndexMatrix(String rowType, Hashtable<String,Integer> rowHash, String columnType, Hashtable<String,Integer> columnHash)` This method creates a matrix which contains the index of the `Sequence` with specific `SequenceAnnotation` combination or -1 if the `Sample` does not contain any `Sequence` with such a combination.
`Sample` | `getSuffixSample(int start)` This method enables you to use only a suffix of all elements, i.e. the `Sequence`, in the current `Sample`.
`static Sample` | `intersection(Sample... samples)` This method computes the intersection between all elements/`Sample` s of the array, i.e. it returns a `Sample` containing only `Sequence`s that are contained in all `Sample`s of the array.
`boolean` | `isDiscreteSample()` This method indicates if all positions use discrete values.
`boolean` | `isSimpleSample()` This method indicates whether all random variables are defined over the same range, i.e. all positions use the same (fixed) alphabet.
`Iterator<Sequence>` | `iterator()`
`Sample[]` | `partition(double p, Sample.PartitionMethod method, int subsequenceLength)` This method partitions the elements, i.e. the `Sequence`s, of the `Sample` in two distinct parts.
`Sample[]` | `partition(int k, Sample.PartitionMethod method)` This method partitions the elements, i.e. the `Sequence`s, of the `Sample` in `k` distinct parts.
`Sample[]` | `partition(Sample.PartitionMethod method, double... percentage)` This method partitions the elements, i.e. the `Sequence`s, of the `Sample` in distinct parts where each part holds the corresponding percentage given in the array `percentage`.
`void` | `save(File f)` This method writes the `Sample` to a file `f`.
`void` | `save(OutputStream stream, char commentChar, SequenceAnnotationParser p)` This method allows to write all `Sequence`s including their `SequenceAnnotation`s into a `OutputStream`.
`Sample` | `subSampling(int number)` Randomly samples elements, i.e.
`String` | `toString()`
`static Sample` | `union(Sample... s)` Unites all `Sample`s of the array `s`.
`static Sample` | `union(Sample[] s, boolean[] in)` This method unites all `Sample`s of the array `s` regarding the array `in`.
`static Sample` | `union(Sample[] s, boolean[] in, int subsequenceLength)` This method unites all `Sample`s of the array `s` regarding the array `in` and sets the element length in the united `Sample` to `subsequenceLength`.
`static Sample` | `union(Sample[] s, int subsequenceLength)` This method unites all `Sample`s of the array `s` and sets the element length in the united sample to `subsequenceLength`.

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

Constructor Detail

### Sample

    public Sample(AlphabetContainer abc,
                  AbstractStringExtractor se)
           throws WrongAlphabetException,
                  EmptySampleException,
                  WrongLengthException

  Creates a new `Sample` from a `StringExtractor` using the given `AlphabetContainer`.

  Parameters:
    `abc` - the `AlphabetContainer`
    `se` - the `StringExtractor`
  Throws:
    `WrongAlphabetException` - if the `AlphabetContainer` is not suitable
    `EmptySampleException` - if the `Sample` would be empty
    `WrongLengthException` - never happens (forwarded from `Sample(AlphabetContainer, AbstractStringExtractor, String, int)` )
  See Also:
    `Sample(AlphabetContainer, AbstractStringExtractor, String, int)`

### Sample

    public Sample(AlphabetContainer abc,
                  AbstractStringExtractor se,
                  int subsequenceLength)
           throws WrongAlphabetException,
                  WrongLengthException,
                  EmptySampleException

  Creates a new `Sample` from a `StringExtractor` using the given `AlphabetContainer` and all overlapping windows of length `subsequenceLength`.

  Parameters:
    `abc` - the `AlphabetContainer`
    `se` - the `StringExtractor`
    `subsequenceLength` - the length of the window sliding on the `String` of `se`, if `len` is 0 (zero) then the `Sequence`s are used as given from the `StringExtractor`
  Throws:
    `WrongAlphabetException` - if the `AlphabetContainer` is not suitable
    `WrongLengthException` - if the subsequence length is not supported
    `EmptySampleException` - if the `Sample` would be empty
  See Also:
    `Sample(AlphabetContainer, AbstractStringExtractor, String, int)`

### Sample

    public Sample(AlphabetContainer abc,
                  AbstractStringExtractor se,
                  String delim)
           throws WrongAlphabetException,
                  EmptySampleException,
                  WrongLengthException

  Creates a new `Sample` from a `StringExtractor` using the given `AlphabetContainer` and a delimiter `delim`.

  Parameters:
    `abc` - the `AlphabetContainer`
    `se` - the `StringExtractor`
    `delim` - the delimiter for parsing the `String`s
  Throws:
    `WrongAlphabetException` - if the `AlphabetContainer` is not suitable
    `EmptySampleException` - if the `Sample` would be empty
    `WrongLengthException` - never happens (forwarded from `Sample(AlphabetContainer, AbstractStringExtractor, String, int)` )
  See Also:
    `Sample(AlphabetContainer, AbstractStringExtractor, String, int)`

### Sample

    public Sample(AlphabetContainer abc,
                  AbstractStringExtractor se,
                  String delim,
                  int subsequenceLength)
           throws EmptySampleException,
                  WrongAlphabetException,
                  WrongLengthException

  Creates a new `Sample` from a `StringExtractor` using the given `AlphabetContainer`, the given delimiter `delim` and all overlapping windows of length `subsequenceLength`.

  Parameters:
    `abc` - the `AlphabetContainer`
    `se` - the `StringExtractor`
    `delim` - the delimiter for parsing the `String`s
    `subsequenceLength` - the length of the window sliding on the `String` of `se`, if `len` is 0 (zero) then the `Sequence`s are used as given from the `StringExtractor`
  Throws:
    `WrongAlphabetException` - if the `AlphabetContainer` is not suitable
    `EmptySampleException` - if the `Sample` would be empty
    `WrongLengthException` - if the subsequence length is not supported

### Sample

    public Sample(Sample s,
                  int subsequenceLength)
           throws WrongLengthException

  Creates a new `Sample` from a given `Sample` and a given length `subsequenceLength`.
  This constructor enables you to use subsequences of the elements of a `Sample`.
  It can also be used to ensure that all sequences that can be accessed by `getElementAt(int)` are real objects and do not have to be created at the invocation of the method. (The same holds for the `Sample.ElementEnumerator`. In those cases both ways to access the `Sequence` are approximately equally fast.)

  Parameters:
    `s` - the given `Sample`
    `subsequenceLength` - the new element length
  Throws:
    `WrongLengthException` - if something is wrong with `subsequenceLength`

### Sample

    public Sample(String annotation,
                  Sequence... seqs)
           throws EmptySampleException,
                  WrongAlphabetException

  Creates a new `Sample` from an array of `Sequence`s and a given annotation.
  This constructor is specially designed for the method `Model.emitSample(int, int...)`.

  Parameters:
    `annotation` - the annotation of the `Sample`
    `seqs` - the `Sequence`(s)
  Throws:
    `EmptySampleException` - if the array `seqs` is `null` or the length is 0
    `WrongAlphabetException` - if the `AlphabetContainer`s do not match

Method Detail

### getAnnotation

    public static final String getAnnotation(Sample... s)

  Returns the annotation for an array of `Sample`s.

  Parameters:
    `s` - an array of `Sample`s
  Returns:
    the annotation
  See Also:
    `getAnnotation()`

### diff

    public static final Sample diff(Sample data,
                                    Sample... samples)
                             throws EmptySampleException,
                                    WrongAlphabetException

  This method computes the difference between the `Sample` `data` and the `Sample`s `samples`.

  Parameters:
    `data` - the minuend
    `samples` - the subtrahends
  Returns:
    the difference
  Throws:
    `WrongAlphabetException` - if the `AlphabetContainer`s do not match, i.e., if the Samples are from different domains
    `EmptySampleException` - if the difference is empty

### intersection

    public static final Sample intersection(Sample... samples)
                                     throws IllegalArgumentException,
                                            EmptySampleException

  This method computes the intersection between all elements/`Sample` s of the array, i.e. it returns a `Sample` containing only `Sequence`s that are contained in all `Sample`s of the array.

  Parameters:
    `samples` - the array of `Sample`s
  Returns:
    the intersection of the elements/`Sample`s in the array
  Throws:
    `IllegalArgumentException` - if the elements of the array are from different domains
    `EmptySampleException` - if the intersection is empty

### union

    public static final Sample union(Sample[] s,
                                     boolean[] in)
                              throws IllegalArgumentException,
                                     EmptySampleException

  This method unites all `Sample`s of the array `s` regarding the array `in`.

  Parameters:
    `s` - the array of `Sample`s
    `in` - an array indicating which `Sample` is used in the union, if `in[i]==true` the `Sample` `s[i]` is used
  Returns:
    the united `Sample`
  Throws:
    `IllegalArgumentException` - if `s.length != in.length` or the `Alphabet` s do not match
    `EmptySampleException` - if the union is empty
  See Also:
    `union(Sample[], boolean[], int)`

### union

    public static final Sample union(Sample... s)
                              throws IllegalArgumentException

  Unites all `Sample`s of the array `s`.

  Parameters:
    `s` - the array of `Sample`s
  Returns:
    the united `Sample`
  Throws:
    `IllegalArgumentException` - if the `Alphabet`s do not match
  See Also:
    `union(Sample[], boolean[])`

### union

    public static final Sample union(Sample[] s,
                                     boolean[] in,
                                     int subsequenceLength)
                              throws IllegalArgumentException,
                                     EmptySampleException,
                                     WrongLengthException

  This method unites all `Sample`s of the array `s` regarding the array `in` and sets the element length in the united `Sample` to `subsequenceLength`.

  Parameters:
    `s` - the array of `Sample`s
    `in` - an array indicating which `Sample` is used in the union, if `in[i]==true` the `Sample` `s[i]` is used
    `subsequenceLength` - the length of the elements in the united `Sample`
  Returns:
    the united `Sample`
  Throws:
    `IllegalArgumentException` - if `s.length != in.length` or the `Alphabet` s do not match
    `EmptySampleException` - if the union is empty
    `WrongLengthException` - if the united `Sample` does not support this `subsequenceLength`

### union

    public static final Sample union(Sample[] s,
                                     int subsequenceLength)
                              throws IllegalArgumentException,
                                     WrongLengthException

  This method unites all `Sample`s of the array `s` and sets the element length in the united sample to `subsequenceLength`.

  Parameters:
    `s` - the array of `Sample`s
    `subsequenceLength` - the length of the elements in the united `Sample`
  Returns:
    the united `Sample`
  Throws:
    `IllegalArgumentException` - if the `Alphabet`s do not match
    `WrongLengthException` - if the united `Sample` does not support this `subsequenceLength`
  See Also:
    `union(Sample[], boolean[], int)`

### getAllElements

    public Sequence[] getAllElements()

  Returns an array of `Sequence`s containing all elements of this `Sample`.

  Returns:
    all elements (`Sequence`s) of this `Sample`
  See Also:
    `Sample.ElementEnumerator`

### getAlphabetContainer

    public final AlphabetContainer getAlphabetContainer()

  Returns the `AlphabetContainer` of this `Sample`.

  Returns:
    the `AlphabetContainer` of this `Sample`

### getAnnotation

    public final String getAnnotation()

  Returns some annotation of the `Sample`.

  Returns:
    some annotation of the `Sample`

### getCompositeSample

    public final Sample getCompositeSample(int[] starts,
                                           int[] lengths)
                                    throws IllegalArgumentException

  This method enables you to use only composite `Sequence`s of all elements in the current `Sample`. Each composite `Sequence` will be build from one corresponding `Sequence` in this `Sample` and all composite `Sequence`s will be returned in a new `Sample`.

  Parameters:
    `starts` - the start positions of the chunks
    `lengths` - the lengths of the chunks
  Returns:
    a composite `Sample`
  Throws:
    `IllegalArgumentException` - if either `starts` or `lengths` or both in combination are not suitable
  See Also:
    `Sequence.getCompositeSequence(AlphabetContainer, int[], int[])`

### getElementAt

    public Sequence getElementAt(int i)

  This method returns the element, i.e. the `Sequence`, with index `i`. See also this comment.

  Parameters:
    `i` - the index of the element, i.e. the `Sequence`
  Returns:
    the element, i.e. the `Sequence`, with index `i`

### getElementLength

    public int getElementLength()

  Returns the length of the elements, i.e. the `Sequence`s, in this `Sample`.

  Returns:
    the length of the elements, i.e. the `Sequence`s, in this `Sample`

### getInfixSample

    public final Sample getInfixSample(int start,
                                       int length)
                                throws IllegalArgumentException

  This method enables you to use only an infix of all elements, i.e. the `Sequence`s, in the current `Sample`. The subsequences will be returned in an new `Sample`.
  This method can also be used to create a `Sample` of prefixes if the element length is not zero.

  Parameters:
    `start` - the start position of the infix
    `length` - the length of the infix, has to be positive
  Returns:
    a `Sample` of the specified infixes
  Throws:
    `IllegalArgumentException` - if either `start` or `length` or both in combination are not suitable

### getMinimalElementLength

    public int getMinimalElementLength()

  Returns the minimal length of an element, i.e. a `Sequence`, in this `Sample`.

  Returns:
    the minimal length of an element, i.e. a `Sequence`, in this `Sample`

### getMaximalElementLength

    public int getMaximalElementLength()

  Returns the maximal length of an element, i.e. a `Sequence`, in this `Sample`.

  Returns:
    the maximal length of an element, i.e. a `Sequence`, in this `Sample`

### getNumberOfElements

    public int getNumberOfElements()

  Returns the number of elements, i.e. the `Sequence`s, in this `Sample`.

  Returns:
    the number of elements, i.e. the `Sequence`s, in this `Sample`

### iterator

    public Iterator<Sequence> iterator()

  Specified by:
    `iterator` in interface `Iterable<Sequence>`

### getNumberOfElementsWithLength

    public int getNumberOfElementsWithLength(int len)
                                      throws WrongLengthException

  Returns the number of overlapping elements that can be extracted.

  Parameters:
    `len` - the length of the elements
  Returns:
    the number of elements with the specified length
  Throws:
    `WrongLengthException` - if the given length is bigger than the minimal element length
  See Also:
    `getNumberOfElementsWithLength(int, double[])`

### getNumberOfElementsWithLength

    public double getNumberOfElementsWithLength(int len,
                                                double[] weights)
                                         throws WrongLengthException,
                                                IllegalArgumentException

  Returns the weighted number of overlapping elements that can be extracted.

  Parameters:
    `len` - the length of the elements
    `weights` - the weights of each element of the sample (see `getElementAt(int)`), can be `null`
  Returns:
    the weighted number of elements with the specified length
  Throws:
    `WrongLengthException` - if the given length is bigger than the minimal element length
    `IllegalArgumentException` - if the weights have a wrong dimension

### getSuffixSample

    public final Sample getSuffixSample(int start)
                                 throws IllegalArgumentException

  This method enables you to use only a suffix of all elements, i.e. the `Sequence`, in the current `Sample`. The subsequences will be returned in an new `Sample`.

  Parameters:
    `start` - the start position of the suffix
  Returns:
    a `Sample` of specified suffixes
  Throws:
    `IllegalArgumentException` - if `start` is not suitable

### isSimpleSample

    public final boolean isSimpleSample()

  This method indicates whether all random variables are defined over the same range, i.e. all positions use the same (fixed) alphabet.

  Returns:
    `true` if the `Sample` is simple, `false` otherwise
  See Also:
    `AlphabetContainer.isSimple()`

### isDiscreteSample

    public final boolean isDiscreteSample()

  This method indicates if all positions use discrete values.

  Returns:
    `true` if the `Sample` is discrete, `false` otherwise
  See Also:
    `AlphabetContainer.isDiscrete()`

### partition

    public Sample[] partition(double p,
                              Sample.PartitionMethod method,
                              int subsequenceLength)
                       throws WrongLengthException,
                              UnsupportedOperationException,
                              EmptySampleException

  This method partitions the elements, i.e. the `Sequence`s, of the `Sample` in two distinct parts. The second part (test sample) holds the percentage of `p`, the first the rest (train sample). The first part has element length as the current `Sample`, the second has element length `subsequenceLength`, which might be necessary for testing.

  Parameters:
    `p` - the percentage for the second part, the second part holds at least this percentage of the full `Sample`
    `method` - the method how to partition the sample (partitioning criterion)
    `subsequenceLength` - the element length of the second part, if 0 (zero) then the sequences are used as given in this `Sample`
  Returns:
    the array of partitioned `Sample`s
  Throws:
    `WrongLengthException` - if something is wrong with `subsequenceLength`
    `UnsupportedOperationException` - if the `Sample` is not simple
    `EmptySampleException` - if at least one of the created partitions is empty
  See Also:
    `Sample.PartitionMethod`, `Sample.PartitionMethod.PARTITION_BY_NUMBER_OF_ELEMENTS`, `Sample.PartitionMethod.PARTITION_BY_NUMBER_OF_SYMBOLS`, `partition(PartitionMethod, double...)`

### partition

    public Sample[] partition(Sample.PartitionMethod method,
                              double... percentage)
                       throws IllegalArgumentException,
                              EmptySampleException

  This method partitions the elements, i.e. the `Sequence`s, of the `Sample` in distinct parts where each part holds the corresponding percentage given in the array `percentage`.

  Parameters:
    `method` - the method how to partition the `Sample` (partitioning criterion)
    `percentage` - the array of percentages for each "subsample"
  Returns:
    the array of partitioned `Sample`s
  Throws:
    `IllegalArgumentException` - if something with the percentages is not correct ( `sum != 1` or one value is not in `[0,1]`)
    `EmptySampleException` - if at least one of the created partitions is empty
  See Also:
    `Sample.PartitionMethod`, `Sample.PartitionMethod.PARTITION_BY_NUMBER_OF_ELEMENTS`, `Sample.PartitionMethod.PARTITION_BY_NUMBER_OF_SYMBOLS`

### partition

    public Sample[] partition(int k,
                              Sample.PartitionMethod method)
                       throws IllegalArgumentException,
                              EmptySampleException

  This method partitions the elements, i.e. the `Sequence`s, of the `Sample` in `k` distinct parts.

  Parameters:
    `k` - the number of distinct parts
    `method` - the method how to partition the `Sample` (partitioning criterion)
  Returns:
    the array of partitioned `Sample`s
  Throws:
    `IllegalArgumentException` - if `k` is not correct
    `EmptySampleException` - if at least one of the created partitions is empty
  See Also:
    `Sample.PartitionMethod`, `Sample.PartitionMethod.PARTITION_BY_NUMBER_OF_ELEMENTS`, `Sample.PartitionMethod.PARTITION_BY_NUMBER_OF_SYMBOLS`

### subSampling

    public Sample subSampling(int number)
                       throws EmptySampleException

  Randomly samples elements, i.e. `Sequence`s, from the set of all elements, i.e. the `Sequence`s, contained in this `Sample`.
  Depending on whether this `Sample` is chosen to contain overlapping elements (windows of length `subsequenceLength`) or not, those elements (overlapping windows, whole sequences) are subsampled.

  Parameters:
    `number` - the number of `Sequence`s that should be drawn from the contained set of `Sequence`s (with replacement)
  Returns:
    a new `Sample` containing the drawn `Sequence`s
  Throws:
    `EmptySampleException` - if `number` is not positive

### save

    public final void save(File f)
                    throws IOException

  This method writes the `Sample` to a file `f`.

  Parameters:
    `f` - the `File`
  Throws:
    `IOException` - if something went wrong with the file
  See Also:
    `save(OutputStream, char, SequenceAnnotationParser)`

### save

    public final void save(OutputStream stream,
                           char commentChar,
                           SequenceAnnotationParser p)
                    throws IOException

  This method allows to write all `Sequence`s including their `SequenceAnnotation`s into a `OutputStream`. The `SequenceAnnotation`s are parsed using the `SequenceAnnotationParser`.

  Parameters:
    `stream` - the stream which is used to write the `Sample`
    `commentChar` - the character that marks comment lines
    `p` - the parser for the `SequenceAnnotation`s of the `Sequence`s
  Throws:
    `IOException` - if something went wrong while writing into the stream.
  See Also:
    `SequenceAnnotationParser.parseAnnotationToComment(char, SequenceAnnotation...)`

### toString

    public String toString()

  Overrides:
    `toString` in class `Object`

### getAnnotationTypesAndIdentifier

    public Hashtable<String,HashSet<String>> getAnnotationTypesAndIdentifier()

  This method returns all `SequenceAnnotation` types and the corresponding identifier which occur in this `Sample`.

  Returns:
    a `Hashtable` with key = `SequenceAnnotation` type and identifier = `SequenceAnnotation` identifier
  See Also:
    `SequenceAnnotation`

### getSequenceAnnotationIndexMatrix

    public int[][] getSequenceAnnotationIndexMatrix(String rowType,
                                                    Hashtable<String,Integer> rowHash,
                                                    String columnType,
                                                    Hashtable<String,Integer> columnHash)

  This method creates a matrix which contains the index of the `Sequence` with specific `SequenceAnnotation` combination or -1 if the `Sample` does not contain any `Sequence` with such a combination. The rows and columns are indexed according to the `Hashtable`s.
  Here is a short example, how to interpret the returned matrix: `

       int[][] matrix = s.getSequenceAnnotationIndexMatrix( rowType, rowHash, columnType, columnHash )

       if( matrix[i][j] < 0 ) {
              System.out.println( "There is no Sequence in the Sample with this SequenceAnnotation combination");
       } else {
              System.out.println( "This is the Sequence: " + s.getElementAt( matrix[i][j] ) );
       }

  `

  Parameters:
    `rowType` - the `SequenceAnnotation` type for the rows
    `rowHash` - a `Hashtable` of `SequenceAnnotation` identifier and indices for the rows
    `columnType` - the `SequenceAnnotation` type for the columns
    `columnHash` - a `Hashtable` of `SequenceAnnotation` identifier and indices for the columns
  Returns:
    a matrix with the indices of the `Sequence`s with each specific combination of `SequenceAnnotation` for code>rowType and `columnType` and -1 if this combination does not exist in the `Sample`
  See Also:
    `getAnnotationTypesAndIdentifier()`, `ToolBox.parseHashSet2IndexHashtable(HashSet)`

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