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 some alphabets used in a sequence, sample, model or ... . The container enables the user to have at each position a different alphabet 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 Possible types of AlphabetContainers are discrete alphabets, continuous alphabets, or alphabets mixed of discrete and continuous symbols at different positions.

Constructor Summary

AlphabetContainer(Alphabet abc)
This constructor creates a simple AlphabetContainer.

AlphabetContainer(Alphabet[] abc)
This constructor creates an AlphabetContainer with different alphabets for each position.

AlphabetContainer(Alphabet[] abc, int[] assignment)
This constructor creates an AlphabetContainer that uses different alphabets.

AlphabetContainer(AlphabetContainer[] cons, int[] lengths)
This constructor creates an new sparse AlphabetContainer based on given AlphabetContainers.

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

AlphabetContainer(StringBuffer xml)
Extracts the AlphabetContainerParameterSet from a StringBuffer.

Method Summary

boolean	checkConsistency(AlphabetContainer abc) Checks whether two alphabets are consistent.
int	compareTo(AlphabetContainer abc)
Alphabet	getAlphabetAt(int pos) Returns the underlying alphabet of position pos.
double	getAlphabetLengthAt(int pos) Returns the length of the underlying alphabet of position pos.
double	getCode(int pos, String sym) Returns the encoded symbol sym for position pos .
AlphabetContainer	getCompositeContainer(int[] start, int[] length) This method returns a container of alphabets 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).
double	getMaximalAlphabetLength() Returns the maximal alphabet length of this container.
double	getMin(int pos) Returns the minimal value of the underlying alphabet of position pos.
double	getMinimalAlphabetLength() Returns the minimal alphabet length of this container.
int	getPossibleLength() Returns the possible length for sequences using this container.
static AlphabetContainer	getSimplifiedAlphabetContainer(Alphabet[] abc, int[] assignment) This method creates a new AlphabetContainer that uses as less as possible alphabets to describe the container.
AlphabetContainer	getSubContainer(int start, int length) This method returns a subcontainer for the positions starting at start and with length length.
String	getSymbol(int pos, double val) This method returns a String representation of val.
AlphabetContainer.AlphabetContainerType	getType() Returns the type of this AlphabetContainer.
boolean	ignoresCase() If this method returns true all used alphabets 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 alphabets into an existing AlphabetContainer.
boolean	isDiscrete() If this method returns true all positions use discrete values.
boolean	isDiscreteAt(int pos) Returns true if position pos is a discrete random variable.
boolean	isEncodedSymbol(int pos, double continuous) Returns true if continuous is a symbol of the alphabet used in position pos.
boolean	isReverseComplementable() This method helps to determine if the AlphabetContainer also computes the reverse complement of a sequence.
boolean	isSimple() This method answers the question whether all random variables are defined over the same range, i.e. all positions use the same (fixed) alphabet.
int	toDiscrete(int pos, double val) Returns the discrete value for val at a position pos.
String	toString()
StringBuffer	toXML() This method returns an XML-representation 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)

This constructor creates a simple AlphabetContainer. All positions use the same alphabet and therefore sequences of arbitrary length can be handled.

Parameters:

abc - the alphabet

AlphabetContainer

public AlphabetContainer(Alphabet[] abc)

This constructor creates an AlphabetContainer with different alphabets for each position. The assignment from the alphabets to the positions is given by the order in the alphabet array. This constructor should only be used if all alphabets are pairwise different.

Parameters:

abc - the alphabets

See Also:

AlphabetContainer(Alphabet[], int[])

AlphabetContainer

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

This constructor creates an new sparse AlphabetContainer based on given AlphabetContainers.

Parameters:

cons - the AlphabetContainers

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

This constructor creates an AlphabetContainer that uses different alphabets. The alphabets can be used more than once. The assignment for the alphabets to the positions is given by the assignment-array.

Parameters:

abc - the alphabets

assignment - the assignment-array

Throws:

IllegalArgumentException - if the assignment from the alphabets 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 parameters

Throws:

IllegalArgumentException - is thrown if the AlphabetContainerParameterSet is not cloneable

DoubleSymbolException - is thrown 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

Extracts the AlphabetContainerParameterSet from a StringBuffer.

Parameters:

xml - the XML stream

Throws:

NonParsableException - if the stream is not parsable

Method Detail

getSimplifiedAlphabetContainer

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

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

Parameters:

abc - the alphabets

assignment - the assignment of the alphabets to the positions

Returns:

an AlphabetContainer that uses as less as possible alphabets

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 alphabets into an existing AlphabetContainer.

Parameters:

aC - the AlphabetContainer used as template for the returned AlphabetContainer

a - this Alphabet should be inserted

useNewAlphabet - This array is used to define, which Alphabets are used for which positions.

• the length of this array defines the length of Sequences 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 to which the given alphabet should be used. For example: let the given AlphabetContainer contain three alphabets A0,A1,A2 (Ai for position i) and 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 position: 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

checkConsistency

public boolean checkConsistency(AlphabetContainer abc)

Checks whether two alphabets are consistent.

Parameters:

abc - the second alphabet

Returns:

whether two alphabets are consistent

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

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 sym for position pos .

Parameters:

pos - the position

sym - the symbol

Returns:

the encoded symbol

Throws:

WrongAlphabetException - if the symbol is not defined in the alphabet

getCompositeContainer

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

This method returns a container of alphabets e.g. for composite motifs/sequences.

Parameters:

start - the array of start indices

length - the array of lengths

Returns:

the container

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 a InstanceParameterSet, an equivalent InstanceParameterSet should be returned, such 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 - is thrown 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 container.

Returns:

the maximal alphabet length of this container

getMin

public double getMin(int pos)

Returns the minimal value of the underlying alphabet of position pos.

Parameters:

pos - the position

Returns:

the minimal value

getMinimalAlphabetLength

public double getMinimalAlphabetLength()

Returns the minimal alphabet length of this container.

Returns:

the minimal alphabet length of this container

getPossibleLength

public int getPossibleLength()

Returns the possible length for sequences using this container. If 0 (zero) is returned, all lengths are possible.

Returns:

the possible length using this container

getSubContainer

public AlphabetContainer getSubContainer(int start,
                                         int length)

This method returns a subcontainer 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 subcontainer of alphabets

See Also:

getCompositeContainer(int[], int[])

getSymbol

public String getSymbol(int pos,
                        double val)

This method returns a String representation of val.

Parameters:

pos - the position

val - the value

Returns:

a String representation for val at position pos

ignoresCase

public final boolean ignoresCase()

If this method returns true all used alphabets ignore the case.

Returns:

true if all used alphabets ignore the case

isDiscrete

public final boolean isDiscrete()

If this method returns true all positions use discrete values.

Returns:

true if all positions use discrete values

isDiscreteAt

public boolean isDiscreteAt(int pos)

Returns true if position pos is a discrete random variable.

Parameters:

pos - the position

Returns:

true if position pos is a discrete random variable

isEncodedSymbol

public boolean isEncodedSymbol(int pos,
                               double continuous)

Returns true if continuous is a symbol of the alphabet used in position pos.

Parameters:

pos - the position

continuous - the continuous value

Returns:

true if continuous is a symbol of the alphabet used in position pos

isSimple

public final boolean isSimple()

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

Returns:

whether all random variables are defined over the same range

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

toDiscrete

public int toDiscrete(int pos,
                      double val)

Returns the discrete value for val at a position pos.

Parameters:

pos - the position

val - the value

Returns:

a discrete value for val at position pos

toString

public String toString()

Overrides:

toString in class Object

toXML

public StringBuffer toXML()

Description copied from interface: Storable

This method returns an XML-representation 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