de.jstacs.data.alphabets
Class DiscreteAlphabet

java.lang.Object
  de.jstacs.data.Alphabet
      de.jstacs.data.alphabets.DiscreteAlphabet

All Implemented Interfaces:

InstantiableFromParameterSet, Storable, Comparable<Alphabet>

Direct Known Subclasses:

ComplementableDiscreteAlphabet

public class DiscreteAlphabet
extends Alphabet

Class for an alphabet that consists of arbitrary Strings. For DNA alphabets, the class DNAAlphabet should be used.

Author:

Jan Grau, Jens Keilwagen

Nested Class Summary

static class

DiscreteAlphabet.DiscreteAlphabetParameterSet Class for the ParameterSet of a DiscreteAlphabet.

Nested classes/interfaces inherited from class de.jstacs.data.Alphabet

Alphabet.AlphabetParameterSet

Field Summary

protected Alphabet.AlphabetParameterSet

parameters The ParameterSet describing this DiscreteAlphabet.

Constructor Summary

DiscreteAlphabet(DiscreteAlphabet.DiscreteAlphabetParameterSet parameters)
The constructor for the InstantiableFromParameterSet interface.

DiscreteAlphabet(int min, int max)
Constructor for a discrete alphabet in [min,max].

DiscreteAlphabet(String[] alphabet, boolean caseInsensitive)
Constructor for a discrete alphabet.

DiscreteAlphabet(StringBuffer representation)
Extracts the alphabet from the StringBuffer.

Method Summary

int	compareTo(Alphabet b)
int	getCode(String symbol) Returns the code of a given symbol.
Alphabet.AlphabetParameterSet	getCurrentParameterSet() Returns the InstanceParameterSet that has been used to instantiate the current instance of the implementing class.
int	getMaximalSymbolLength() Returns the length of the longest "symbol" in the alphabet.
double	getMin() Returns the minimal value.
String	getSymbolAt(int i) Returns the symbol at position i in the alphabet.
boolean	ignoresCase() If this method returns true the alphabet ignores the case.
boolean	isEncodedSymbol(int candidate) Returns true if candidate is an element of the internal interval.
boolean	isSymbol(String candidat) Tests if a given symbol is contained in the alphabet.
double	length() Returns the number of symbols in the calling alphabet.
String	toString()
StringBuffer	toXML() This method returns an XML-representation of an instance of the implementing class.

Methods inherited from class de.jstacs.data.Alphabet

checkConsistency

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail

parameters

protected Alphabet.AlphabetParameterSet parameters

The ParameterSet describing this DiscreteAlphabet.

Constructor Detail

DiscreteAlphabet

public DiscreteAlphabet(StringBuffer representation)
                 throws NonParsableException

Extracts the alphabet from the StringBuffer.

Parameters:

representation - the XML stream

Throws:

NonParsableException - if the stream is not parsable

DiscreteAlphabet

public DiscreteAlphabet(DiscreteAlphabet.DiscreteAlphabetParameterSet parameters)
                 throws IllegalArgumentException,
                        DoubleSymbolException

The constructor for the InstantiableFromParameterSet interface.

Parameters:

parameters - the ParameterSet

Throws:

IllegalArgumentException - is thrown if space or tab will be used as symbols

DoubleSymbolException - is thrown if one of the symbols occurred more than once

DiscreteAlphabet

public DiscreteAlphabet(int min,
                        int max)
                 throws IllegalArgumentException

Constructor for a discrete alphabet in [min,max].

Parameters:

min - the minimal value (inclusive)

max - the maximal value (inclusive)

Throws:

IllegalArgumentException - is thrown if min>max

DiscreteAlphabet

public DiscreteAlphabet(String[] alphabet,
                        boolean caseInsensitive)
                 throws DoubleSymbolException,
                        IllegalArgumentException

Constructor for a discrete alphabet. The String array is cloned internally.

Parameters:

alphabet - the alphabet as String array

caseInsensitive - if true then there will be no difference between lowercase and uppercase letters/symbols in the alphabet (no case sensivity)

Throws:

DoubleSymbolException - is thrown if one of the symbols occurred more than once

IllegalArgumentException - is thrown if one of the symbols is either empty or a white-space character

Method Detail

getCurrentParameterSet

public Alphabet.AlphabetParameterSet 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.

Returns:

the current InstanceParameterSet

Throws:

Exception - is thrown if the InstanceParameterSet could not be returned

toXML

public StringBuffer toXML()

Description copied from interface: Storable

This method returns an XML-representation of an instance of the implementing class.

Returns:

the XML-representation

compareTo

public int compareTo(Alphabet b)

getCode

public final int getCode(String symbol)
                  throws WrongAlphabetException

Returns the code of a given symbol.

Parameters:

symbol - the symbol

Returns:

the code

Throws:

WrongAlphabetException - if the symbol is not defined in the alphabet

getMaximalSymbolLength

public final int getMaximalSymbolLength()

Returns the length of the longest "symbol" in the alphabet.

Returns:

the length of the longest "symbol"

getMin

public double getMin()

Description copied from class: Alphabet

Returns the minimal value.

Specified by:

getMin in class Alphabet

Returns:

the minimal value

getSymbolAt

public final String getSymbolAt(int i)

Returns the symbol at position i in the alphabet.

Parameters:

i - the position in the alphabet

Returns:

the symbol

ignoresCase

public final boolean ignoresCase()

If this method returns true the alphabet ignores the case.

Returns:

true if the alphabet ignores the case

isEncodedSymbol

public final boolean isEncodedSymbol(int candidate)

Returns true if candidate is an element of the internal interval.

Parameters:

candidate - the value to be tested

Returns:

true if candidate is an element of the internal interval

isSymbol

public final boolean isSymbol(String candidat)

Tests if a given symbol is contained in the alphabet.

Parameters:

candidat - the candidat symbol

Returns:

true if the candidat is a symbol of the alphabet

length

public final double length()

Returns the number of symbols in the calling alphabet.

Specified by:

length in class Alphabet

Returns:

the number of symbols

toString

public String toString()

Specified by:

toString in class Alphabet