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java.lang.Object de.jstacs.data.Alphabet de.jstacs.data.alphabets.DiscreteAlphabet
public class DiscreteAlphabet
Class for an alphabet that consists of arbitrary String
s. For DNA
alphabets, the class DNAAlphabet
should be used.
Nested Class Summary | |
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static class |
DiscreteAlphabet.DiscreteAlphabetParameterSet
Class for the ParameterSet of a
DiscreteAlphabet . |
Nested classes/interfaces inherited from class de.jstacs.data.Alphabet |
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Alphabet.AlphabetParameterSet |
Field Summary | |
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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 | |
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DiscreteAlphabet(boolean caseInsensitive,
String... alphabet)
Creates a new DiscreteAlphabet from a given alphabet as a
String array. |
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DiscreteAlphabet(DiscreteAlphabet.DiscreteAlphabetParameterSet parameters)
The constructor for the InstantiableFromParameterSet
interface. |
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DiscreteAlphabet(int min,
int max)
Creates a new DiscreteAlphabet from a minimal and a maximal
value, i.e. in [min,max] . |
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DiscreteAlphabet(StringBuffer representation)
The standard constructor for the interface Storable . |
Method Summary | |
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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 the Alphabet . |
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.Alphabet |
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checkConsistency |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
Field Detail |
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protected String[] alphabet
String
array.
protected boolean caseInsensitive
protected Alphabet.AlphabetParameterSet parameters
DiscreteAlphabet
.
Constructor Detail |
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public DiscreteAlphabet(StringBuffer representation) throws NonParsableException
Storable
.
Creates a new DiscreteAlphabet
out of its XML representation.
representation
- the XML representation as StringBuffer
NonParsableException
- if the DiscreteAlphabet
could not be reconstructed
out of the XML representation (the StringBuffer
representation
could not be parsed)Storable
public DiscreteAlphabet(DiscreteAlphabet.DiscreteAlphabetParameterSet parameters) throws IllegalArgumentException, DoubleSymbolException
InstantiableFromParameterSet
interface. Creates a new DiscreteAlphabet
from a given set of
parameters.
parameters
- the parameter set for the DiscreteAlphabet
IllegalArgumentException
- if space or tab will be used as symbols
DoubleSymbolException
- if one of the symbols occurred more than onceInstantiableFromParameterSet
public DiscreteAlphabet(int min, int max) throws IllegalArgumentException
DiscreteAlphabet
from a minimal and a maximal
value, i.e. in [min,max]
.
min
- the minimal value (inclusive)max
- the maximal value (inclusive)
IllegalArgumentException
- if min > max
public DiscreteAlphabet(boolean caseInsensitive, String... alphabet) throws DoubleSymbolException, IllegalArgumentException
DiscreteAlphabet
from a given alphabet as a
String
array. This String
array is cloned internally.
alphabet
- the alphabet as String
arraycaseInsensitive
- indicates if there will be no difference between lowercase and
uppercase letters/symbols in the alphabet (no case sensitivity)
DoubleSymbolException
- if one of the symbols occurred more than once
IllegalArgumentException
- if one of the symbols is either empty or a white-space
characterMethod Detail |
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public Alphabet.AlphabetParameterSet getCurrentParameterSet() throws Exception
InstantiableFromParameterSet
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.
InstanceParameterSet
Exception
- if the InstanceParameterSet
could not be returnedpublic StringBuffer toXML()
Storable
StringBuffer
of an
instance of the implementing class.
public int compareTo(Alphabet b)
public final int getCode(String symbol) throws WrongAlphabetException
symbol
- the given symbol
WrongAlphabetException
- if the symbol is not defined in the alphabetpublic final int getMaximalSymbolLength()
public double getMin()
Alphabet
Alphabet
.
getMin
in class Alphabet
Alphabet
public final String getSymbolAt(int i)
i
in the alphabet.
i
- the position in the alphabet
i
public final boolean ignoresCase()
true
if the alphabet ignores the case,
false
otherwisepublic final boolean isEncodedSymbol(int candidate)
candidate
is an element of the internal
interval.
candidate
- the value to be tested
true
if candidate
is an element of the
internal interval, false
otherwisepublic final boolean isSymbol(String candidat)
candidat
- the candidat symbol
true
if the candidat
is a symbol of the
alphabet, false
otherwisepublic final double length()
length
in class Alphabet
public String toString()
toString
in class Alphabet
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