de.jstacs.data.alphabets

Class DiscreteAlphabet

java.lang.Object

de.jstacs.data.alphabets.Alphabet

de.jstacs.data.alphabets.DiscreteAlphabet

All Implemented Interfaces:

InstantiableFromParameterSet, Storable, Comparable<Alphabet>

Direct Known Subclasses:

ComplementableDiscreteAlphabet, ProteinAlphabet

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

Nested Classes

Modifier and Type	Class and Description
static class	DiscreteAlphabet.DiscreteAlphabetParameterSet Class for the ParameterSet of a DiscreteAlphabet.

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

Alphabet.AlphabetParameterSet<T extends Alphabet>

Field Summary

Fields

Modifier and Type	Field and Description
protected String[]	alphabet The alphabet as String array.
protected boolean	caseInsensitive Switch to decide whether the input should be treated case sensitive or insensitive.
protected Alphabet.AlphabetParameterSet	parameters The parameter set describing this DiscreteAlphabet .

Constructor Summary

Constructors

Constructor and Description
DiscreteAlphabet(boolean caseInsensitive, String... alphabet) Creates a new DiscreteAlphabet from a given alphabet as a String array.
DiscreteAlphabet(DiscreteAlphabet.DiscreteAlphabetParameterSet parameters) The constructor for the InstantiableFromParameterSet interface.
DiscreteAlphabet(int min, int max) Creates a new DiscreteAlphabet from a minimal and a maximal value, i.e.
DiscreteAlphabet(StringBuffer representation) The standard constructor for the interface Storable.

Method Summary

Modifier and Type	Method and Description
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 of theAlphabet.
String	getSymbolAt(int i) Returns the symbol at position i in the alphabet.
boolean	ignoresCase() Indicates if the alphabet ignores the case.
boolean	isEncodedSymbol(int candidate) Indicates 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 as StringBuffer of an instance of the implementing class.

Methods inherited from class de.jstacs.data.alphabets.Alphabet

checkConsistency

Methods inherited from class java.lang.Object

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

Field Detail

alphabet

protected String[] alphabet

The alphabet as String array.

caseInsensitive

protected boolean caseInsensitive

Switch to decide whether the input should be treated case sensitive or insensitive.

parameters

protected Alphabet.AlphabetParameterSet parameters

The parameter set describing this DiscreteAlphabet .

Constructor Detail

DiscreteAlphabet

public DiscreteAlphabet(StringBuffer representation)
                 throws NonParsableException

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

Parameters:

representation - the XML representation as StringBuffer

Throws:

NonParsableException - if the DiscreteAlphabet could not be reconstructed out of the XML representation (the StringBuffer representation could not be parsed)

See Also:

Storable

DiscreteAlphabet

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

The constructor for the InstantiableFromParameterSet interface. Creates a new DiscreteAlphabet from a given set of parameters.

Parameters:

parameters - the parameter set for the DiscreteAlphabet

Throws:

IllegalArgumentException - if space or tab will be used as symbols

DoubleSymbolException - if one of the symbols occurred more than once

See Also:

InstantiableFromParameterSet

DiscreteAlphabet

public DiscreteAlphabet(int min,
                        int max)
                 throws IllegalArgumentException

Creates a new DiscreteAlphabet from a minimal and a maximal value, i.e. in [min,max].

Parameters:

min - the minimal value (inclusive)

max - the maximal value (inclusive)

Throws:

IllegalArgumentException - if min > max

DiscreteAlphabet

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

Creates a new DiscreteAlphabet from a given alphabet as a String array. This String array is cloned internally.

Parameters:

alphabet - the alphabet as String array

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

Throws:

DoubleSymbolException - if one of the symbols occurred more than once

IllegalArgumentException - 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 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

Specified by:

getCurrentParameterSet in class Alphabet

Returns:

the current InstanceParameterSet

Throws:

Exception - if the InstanceParameterSet could not be returned

toXML

public StringBuffer toXML()

Description copied from interface: Storable

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

Returns:

the XML representation

compareTo

public int compareTo(Alphabet b)

getCode

public int getCode(String symbol)
            throws WrongAlphabetException

Returns the code of a given symbol.

Parameters:

symbol - the given symbol

Returns:

the code of a given symbol

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 of theAlphabet.

Specified by:

getMin in class Alphabet

Returns:

the minimal value of the Alphabet

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 at position i

ignoresCase

public final boolean ignoresCase()

Indicates if the alphabet ignores the case.

Returns:

true if the alphabet ignores the case, false otherwise

isEncodedSymbol

public final boolean isEncodedSymbol(int candidate)

Indicates 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, false otherwise

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, false otherwise

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 in the alphabet

toString

public String toString()

Specified by:

toString in class Alphabet