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## de.jstacs.data
Class AlphabetContainer

    java.lang.Object
      de.jstacs.data.AlphabetContainer

All Implemented Interfaces:
  InstantiableFromParameterSet, Storable, Comparable<AlphabetContainer>

    public class AlphabetContainer

extends Object
implements Storable, InstantiableFromParameterSet, Comparable<AlphabetContainer>

The container for `Alphabet`s used in a `Sequence`, `Sample`, `AbstractModel` or ... . The container enables the user to have a different `Alphabet` at each position or at least not the same `Alphabet` at all positions. This is impossible if you use only instances of `Alphabet`. The container maps the given `Alphabet` objects to the positions.
`AlphabetContainer` is immutable.

Author:
  Jens Keilwagen
See Also:
  `Alphabet`

Nested Class Summary
`static class` | `AlphabetContainer.AlphabetContainerType` This `enum` defines types of `AlphabetContainer`s.

Constructor Summary
`AlphabetContainer(Alphabet abc)` Creates a new simple `AlphabetContainer`.
`AlphabetContainer(Alphabet[] abc)` Creates a new `AlphabetContainer` with different `Alphabet`s for each position.
`AlphabetContainer(Alphabet[] abc, int[] assignment)` Creates a new `AlphabetContainer` that uses different `Alphabet`s.
`AlphabetContainer(AlphabetContainer[] cons, int[] lengths)` Creates an new sparse `AlphabetContainer` based on given `AlphabetContainer`s.
`AlphabetContainer(AlphabetContainerParameterSet parameters)` Creates a new `AlphabetContainer` from an `AlphabetContainerParameterSet` that contains all necessary parameters.
`AlphabetContainer(StringBuffer xml)` The standard constructor for the interface `Storable`.

Method Summary
`boolean` | `checkConsistency(AlphabetContainer abc)` Checks if this `AlphabetContainer` is consistent consistent with another `AlphabetContainer`.
`int` | `compareTo(AlphabetContainer abc)`
`Alphabet` | `getAlphabetAt(int pos)` Returns the underlying `Alphabet` of position `pos`.
`int` | `getAlphabetIndexForPosition(int pos)` This method returns the index of the `Alphabet` that is used for the given position.
`double` | `getAlphabetLengthAt(int pos)` Returns the length of the underlying `Alphabet` of position `pos`.
`double` | `getCode(int pos, String sym)` Returns the encoded symbol for `sym` of the `Alphabet` of position `pos` of this `AlphabetContainer`.
`AlphabetContainer` | `getCompositeContainer(int[] start, int[] length)` Returns an `AlphabetContainer` of `Alphabet`s e.g. for composite motifs/sequences.
`AlphabetContainerParameterSet` | `getCurrentParameterSet()` Returns the `InstanceParameterSet` that has been used to instantiate the current instance of the implementing class.
`String` | `getDelim()` Returns the delimiter that should be used (for writing e.g. a sequence).
`int[]` | `getIndexForAlphabets()` This method returns an object that is used for assigning the positions of the `Sequence`s to specific `Alphabet`s.
`double` | `getMaximalAlphabetLength()` Returns the maximal `Alphabet` length of this `AlphabetContainer`.
`double` | `getMin(int pos)` Returns the minimal value of the underlying `Alphabet` of position `pos`.
`double` | `getMinimalAlphabetLength()` Returns the minimal `Alphabet` length of this `AlphabetContainer`.
`int` | `getNumberOfAlphabets()` This method returns the number of `Alphabet`s used in the current `AlphabetContainer`.
`int` | `getPossibleLength()` Returns the possible length for `Sequence`s using this `AlphabetContainer`.
`static AlphabetContainer` | `getSimplifiedAlphabetContainer(Alphabet[] abc, int[] assignment)` This method creates a new `AlphabetContainer` that uses as less as possible `Alphabet`s to describe the container.
`AlphabetContainer` | `getSubContainer(int start, int length)` Returns a sub-container with the `Alphabet`s for the positions starting at `start` and with length `length`.
`String` | `getSymbol(int pos, double val)` Returns a `String` representation of the encoded symbol `val` of the `Alphabet` of position `pos` of this `AlphabetContainer`.
`AlphabetContainer.AlphabetContainerType` | `getType()` Returns the type of this `AlphabetContainer`.
`boolean` | `ignoresCase()` Indicates if all used `Alphabet`s ignore the case.
`static AlphabetContainer` | `insertAlphabet(AlphabetContainer aC, Alphabet a, boolean[] useNewAlphabet)` This method may be used to construct a new `AlphabetContainer` by incorporating additional `Alphabet`s into an existing `AlphabetContainer`.
`boolean` | `isDiscrete()` Indicates if all positions use discrete `Alphabet`s.
`boolean` | `isDiscreteAt(int pos)` Indicates if position `pos` is a discrete random variable, i.e. if the `Alphabet` of position `pos` is discrete.
`boolean` | `isEncodedSymbol(int pos, double continuous)` Indicates if `continuous` is a symbol of the `Alphabet` used at position `pos` of the `AlphabetContainer`.
`boolean` | `isReverseComplementable()` This method helps to determine if the `AlphabetContainer` also computes the reverse complement of a `Sequence`.
`boolean` | `isSimple()` Indicates whether all random variables are defined over the same range, i.e. if the `AlphabetContainer` is simple and all positions use the same (fixed) `Alphabet`.
`int` | `toDiscrete(int pos, double val)` Returns the discrete value for `val` of the `Alphabet` of position `pos` in the `AlphabetContainer`.
`String` | `toString()`
`StringBuffer` | `toXML()` This method returns an XML representation as `StringBuffer` of an instance of the implementing class.

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

Constructor Detail

### AlphabetContainer

    public AlphabetContainer(Alphabet abc)

  Creates a new simple `AlphabetContainer`. All positions use the same `Alphabet` and therefore sequences of arbitrary length can be handled.

  Parameters:
    `abc` - the `Alphabet` for all positions

### AlphabetContainer

    public AlphabetContainer(Alphabet[] abc)

  Creates a new `AlphabetContainer` with different `Alphabet`s for each position. The assignment of the `Alphabet`s to the positions is given by the order in the `Alphabet` array. This constructor should only be used if all `Alphabet`s are pairwise different.

  Parameters:
    `abc` - the different `Alphabet`s for each position
  See Also:
    `AlphabetContainer(Alphabet[], int[])`

### AlphabetContainer

    public AlphabetContainer(AlphabetContainer[] cons,
                             int[] lengths)
                      throws IllegalArgumentException

  Creates an new sparse `AlphabetContainer` based on given `AlphabetContainer`s.

  Parameters:
    `cons` - the given `AlphabetContainer`s
    `lengths` - the corresponding lengths of each `AlphabetContainer` that is used
  Throws:
    `IllegalArgumentException` - if the given length for an `AlphabetContainer` is not possible

### AlphabetContainer

    public AlphabetContainer(Alphabet[] abc,
                             int[] assignment)
                      throws IllegalArgumentException

  Creates a new `AlphabetContainer` that uses different `Alphabet`s. The `Alphabet`s can be used more than once. The assignment for the `Alphabet`s to the positions is given by the array `assignment`.

  Parameters:
    `abc` - the `Alphabet`s
    `assignment` - the assignment array
  Throws:
    `IllegalArgumentException` - if the assignment of the `Alphabet`s to the positions is not correct

### AlphabetContainer

    public AlphabetContainer(AlphabetContainerParameterSet parameters)
                      throws IllegalArgumentException,
                             DoubleSymbolException,
                             ParameterSetParser.NotInstantiableException

  Creates a new `AlphabetContainer` from an `AlphabetContainerParameterSet` that contains all necessary parameters.

  Parameters:
    `parameters` - the parameter set
  Throws:
    `IllegalArgumentException` - if something is wrong with the parameters in the `AlphabetContainerParameterSet`
    `DoubleSymbolException` - if the definitions within `parameters` contains a symbol twice
    `ParameterSetParser.NotInstantiableException` - if an instance could not be created

### AlphabetContainer

    public AlphabetContainer(StringBuffer xml)
                      throws NonParsableException

  The standard constructor for the interface `Storable`. Creates a new `AlphabetContainer` out of its XML representation.

  Parameters:
    `xml` - the XML representation as `StringBuffer`
  Throws:
    `NonParsableException` - if the `AlphabetContainer` could not be reconstructed out of the XML representation (the `StringBuffer` could not be parsed)
  See Also:
    `Storable`

Method Detail

### getSimplifiedAlphabetContainer

    public static AlphabetContainer getSimplifiedAlphabetContainer(Alphabet[] abc,
                                                                   int[] assignment)

  This method creates a new `AlphabetContainer` that uses as less as possible `Alphabet`s to describe the container. So, if possible, `Alphabet`s will be reused.

  Parameters:
    `abc` - the `Alphabet`s
    `assignment` - the assignment of the `Alphabet`s to the positions
  Returns:
    an `AlphabetContainer` that uses as less as possible `Alphabet`s
  See Also:
    `AlphabetContainer(Alphabet[], int[])`

### insertAlphabet

    public static AlphabetContainer insertAlphabet(AlphabetContainer aC,
                                                   Alphabet a,
                                                   boolean[] useNewAlphabet)
                                            throws IllegalArgumentException

  This method may be used to construct a new `AlphabetContainer` by incorporating additional `Alphabet`s into an existing `AlphabetContainer`.

  Parameters:
    `aC` - the `AlphabetContainer` used as template for the returned `AlphabetContainer`
    `a` - the `Alphabet` that should be inserted
    `useNewAlphabet` - an array to define, which `Alphabet`s are used for which positions
    - the length of this array defines the length of the `Sequence`s the returned `AlphabetContainer` is capable to handle
    - for each position `false` forces to use the `Alphabet` given by the given `AlphabetContainer`
    - for each position `true` forces to use the given `Alphabet`
    Incorporation of the additional `Alphabet` must be understood as defining new additional positions for which the given `Alphabet` should be used. For example: let the given `AlphabetContainer` contain three `Alphabet` s `A0,A1,A2` (`Ai` for position `i`) and therefore have a possible length of three. Calling this method using this `AlphabetContainer`, an additional `Alphabet` `A3` and an assignment array of `[false`, `true`, `true`, `false`, `false]` returns a new `AlphabetContainer` having a possible length of five and using the following alphabets for those positions: `A0,A3,A3,A1,A2`. If the given `AlphabetContainer` has a possible length not equal zero, then the assignment array must contain as many `false`-values as the length of the given `AlphabetContainer`.
  Returns:
    a new `AlphabetContainer` as described above
  Throws:
    `IllegalArgumentException` - if `useNewAlphabet` is `null` or has length 0
  See Also:
    `AlphabetContainer(Alphabet[], int[])`

### checkConsistency

    public boolean checkConsistency(AlphabetContainer abc)

  Checks if this `AlphabetContainer` is consistent consistent with another `AlphabetContainer`.

  Parameters:
    `abc` - the second `AlphabetContainer`
  Returns:
    `true` if the `AlphabetContainer`s are consistent, `false` otherwise
  See Also:
    `Comparable.compareTo(Object)`

### compareTo

    public int compareTo(AlphabetContainer abc)

  Specified by:
    `compareTo` in interface `Comparable<AlphabetContainer>`

### getAlphabetAt

    public Alphabet getAlphabetAt(int pos)

  Returns the underlying `Alphabet` of position `pos`. Please note that the `Alphabet` is returned as reference, so take care of what you are doing with it!

  Parameters:
    `pos` - the position
  Returns:
    the `Alphabet` of the given position

### getAlphabetLengthAt

    public double getAlphabetLengthAt(int pos)

  Returns the length of the underlying `Alphabet` of position `pos`.

  Parameters:
    `pos` - the position
  Returns:
    the length of the underlying `Alphabet` of position `pos`

### getCode

    public double getCode(int pos,
                          String sym)
                   throws WrongAlphabetException

  Returns the encoded symbol for `sym` of the `Alphabet` of position `pos` of this `AlphabetContainer`.

  Parameters:
    `pos` - the position of the `Alphabet`
    `sym` - the symbol that should be returned encoded
  Returns:
    the encoded symbol
  Throws:
    `WrongAlphabetException` - if the symbol is not defined in the `Alphabet` of the given position
  See Also:
    `getAlphabetAt(int)`

### getCompositeContainer

    public AlphabetContainer getCompositeContainer(int[] start,
                                                   int[] length)

  Returns an `AlphabetContainer` of `Alphabet`s e.g. for composite motifs/sequences.

  Parameters:
    `start` - the array of start indices
    `length` - the array of lengths
  Returns:
    the `AlphabetContainer`
  See Also:
    `getSubContainer(int, int)`

### getCurrentParameterSet

    public AlphabetContainerParameterSet getCurrentParameterSet()
                                                         throws Exception

  Description copied from interface: `InstantiableFromParameterSet`
  Returns the `InstanceParameterSet` that has been used to instantiate the current instance of the implementing class. If the current instance was not created using an `InstanceParameterSet`, an equivalent `InstanceParameterSet` should be returned, so that an instance created using this `InstanceParameterSet` would be in principle equal to the current instance.

  Specified by:
    `getCurrentParameterSet` in interface `InstantiableFromParameterSet`
  Returns:
    the current `InstanceParameterSet`
  Throws:
    `Exception` - if the `InstanceParameterSet` could not be returned

### getDelim

    public String getDelim()

  Returns the delimiter that should be used (for writing e.g. a sequence).

  Returns:
    the delimiter

### getMaximalAlphabetLength

    public double getMaximalAlphabetLength()

  Returns the maximal `Alphabet` length of this `AlphabetContainer`.

  Returns:
    the maximal `Alphabet` length

### getMin

    public double getMin(int pos)

  Returns the minimal value of the underlying `Alphabet` of position `pos`.

  Parameters:
    `pos` - the given position
  Returns:
    the minimal value of the `Alphabet` of the given position
  See Also:
    `Alphabet.getMin()`

### getMinimalAlphabetLength

    public double getMinimalAlphabetLength()

  Returns the minimal `Alphabet` length of this `AlphabetContainer`.

  Returns:
    the minimal `Alphabet` length of this `AlphabetContainer`

### getPossibleLength

    public int getPossibleLength()

  Returns the possible length for `Sequence`s using this `AlphabetContainer`. If 0 (zero) is returned, all lengths are possible.

  Returns:
    the possible length using this `AlphabetContainer`

### getSubContainer

    public AlphabetContainer getSubContainer(int start,
                                             int length)

  Returns a sub-container with the `Alphabet`s for the positions starting at `start` and with length `length`. The method can be used for subsequences, ... .

  Parameters:
    `start` - the index of the start position
    `length` - the length
  Returns:
    the sub-container of `Alphabet`s
  See Also:
    `getCompositeContainer(int[], int[])`

### getSymbol

    public String getSymbol(int pos,
                            double val)

  Returns a `String` representation of the encoded symbol `val` of the `Alphabet` of position `pos` of this `AlphabetContainer`.

  Parameters:
    `pos` - the position of the `Alphabet`
    `val` - the value of the encoded symbol
  Returns:
    a `String` representation for the encoded symbol `val` of the `Alphabet` of position `pos`

### ignoresCase

    public final boolean ignoresCase()

  Indicates if all used `Alphabet`s ignore the case.

  Returns:
    `true` if all used alphabets ignore the case, `false` otherwise

### isDiscrete

    public final boolean isDiscrete()

  Indicates if all positions use discrete `Alphabet`s.

  Returns:
    `true` if all positions use discrete `Alphabet`s, otherwise `false`

### isDiscreteAt

    public boolean isDiscreteAt(int pos)

  Indicates if position `pos` is a discrete random variable, i.e. if the `Alphabet` of position `pos` is discrete.

  Parameters:
    `pos` - the position
  Returns:
    `true` if position `pos` is a discrete random variable, `false` otherwise

### isEncodedSymbol

    public boolean isEncodedSymbol(int pos,
                                   double continuous)

  Indicates if `continuous` is a symbol of the `Alphabet` used at position `pos` of the `AlphabetContainer`.

  Parameters:
    `pos` - the position
    `continuous` - the continuous value
  Returns:
    `true` if `continuous` is a symbol of the `Alphabet` used in position `pos`, `false` otherwise

### isSimple

    public final boolean isSimple()

  Indicates whether all random variables are defined over the same range, i.e. if the `AlphabetContainer` is simple and all positions use the same (fixed) `Alphabet`.

  Returns:
    whether all random variables are defined over the same range, i.e. if the `AlphabetContainer` is simple

### isReverseComplementable

    public final boolean isReverseComplementable()

  This method helps to determine if the `AlphabetContainer` also computes the reverse complement of a `Sequence`.

  Returns:
    `true` if the `AlphabetContainer` also computes the reverse complement of a `Sequence`, `false` otherwise

### toDiscrete

    public int toDiscrete(int pos,
                          double val)

  Returns the discrete value for `val` of the `Alphabet` of position `pos` in the `AlphabetContainer`.

  Parameters:
    `pos` - the position
    `val` - the value
  Returns:
    the discrete value for `val` of the `Alphabet` of position `pos`
  See Also:
    `isDiscreteAt(int)`

### toString

    public String toString()

  Overrides:
    `toString` in class `Object`

### toXML

    public StringBuffer toXML()

  Description copied from interface: `Storable`
  This method returns an XML representation as `StringBuffer` of an instance of the implementing class.

  Specified by:
    `toXML` in interface `Storable`
  Returns:
    the XML representation

### getType

    public final AlphabetContainer.AlphabetContainerType getType()

  Returns the type of this `AlphabetContainer`.

  Returns:
    the type
  See Also:
    `AlphabetContainer.AlphabetContainerType`

### getAlphabetIndexForPosition

    public int getAlphabetIndexForPosition(int pos)

  This method returns the index of the `Alphabet` that is used for the given position.

  Parameters:
    `pos` - the position
  Returns:
    the index of the used `Alphabet`

### getNumberOfAlphabets

    public int getNumberOfAlphabets()

  This method returns the number of `Alphabet`s used in the current `AlphabetContainer`.

  Returns:
    the number of used `Alphabet`s

### getIndexForAlphabets

    public int[] getIndexForAlphabets()

  This method returns an object that is used for assigning the positions of the `Sequence`s to specific `Alphabet`s.

  Returns:
    `null` or an int array

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