|
||||||||||
PREV NEXT | FRAMES NO FRAMES |
Packages that use Alphabet | |
---|---|
de.jstacs.data | Provides classes for the representation of data. |
de.jstacs.data.alphabets | Provides classes for the representation of discrete and continuous alphabets, including a DNAAlphabet for the most common case of DNA-sequences |
Uses of Alphabet in de.jstacs.data |
---|
Methods in de.jstacs.data that return Alphabet | |
---|---|
Alphabet |
AlphabetContainer.getAlphabetAt(int pos)
Returns the underlying alphabet of position pos . |
Methods in de.jstacs.data with parameters of type Alphabet | |
---|---|
boolean |
Alphabet.checkConsistency(Alphabet a)
Checks if two alphabets are consistent, i.e. both alphabets use the same symbols. |
static AlphabetContainer |
AlphabetContainer.getSimplifiedAlphabetContainer(Alphabet[] abc,
int[] assignment)
This method creates a new AlphabetContainer that used as less as possible alphabets to describe the container. |
static AlphabetContainer |
AlphabetContainer.insertAlphabet(AlphabetContainer aC,
Alphabet a,
boolean[] useNewAlphabet)
This method may be used to construct a new AlphabetContainer by incorporating additional alphabets
into an exsisting AlphabetContainer . |
Constructors in de.jstacs.data with parameters of type Alphabet | |
---|---|
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. |
|
AlphabetContainerParameterSet.AlphabetArrayParameterSet(Alphabet[] alphabets,
boolean discrete)
Creates a new AlphabetArrayParameterSet from an array of Alphabet s and the
information if all alphabets are discrete |
|
AlphabetContainerParameterSet.SectionDefinedAlphabetParameterSet(Alphabet[] alphabets,
int[] indexes,
boolean discrete)
Creates a new SectionDefinedAlphabetParameterSet from an array of Alphabet s,
an array of indexes that define the index of the Alphabet<>/code> in |
|
AlphabetContainerParameterSet(Alphabet alph)
Creates a new AlphabetContainerParameterSet from a single Alphabet . |
|
AlphabetContainerParameterSet(Alphabet[] alphabets)
Creates a new AlphabetContainerParameterSet from an array of Alphabet s. |
|
AlphabetContainerParameterSet(Alphabet[] alphabets,
int[] indexes)
Creates a new AlphabetContainerParameterSet from an array of Alphabet s and an
array of int s defining the number of the alphabet in alphabets that is used for
that position in indexes . |
Constructor parameters in de.jstacs.data with type arguments of type Alphabet | |
---|---|
Alphabet.AlphabetParameterSet(Class<? extends Alphabet> instanceClass)
Creates a new AlphabetParameterSet . |
Uses of Alphabet in de.jstacs.data.alphabets |
---|
Subclasses of Alphabet in de.jstacs.data.alphabets | |
---|---|
class |
ComplementableDiscreteAlphabet
This abstract class indicates that an alphabet can be used for to compute the complement. |
class |
ContinuousAlphabet
Class for a continuous alphabet. |
class |
DiscreteAlphabet
Class for an alphabet that consists of arbitrary Strings. |
class |
DNAAlphabet
This class implements the alphabet that is used for DNA. |
Methods in de.jstacs.data.alphabets with parameters of type Alphabet | |
---|---|
int |
DiscreteAlphabet.compareTo(Alphabet b)
|
int |
ContinuousAlphabet.compareTo(Alphabet a)
|
|
||||||||||
PREV NEXT | FRAMES NO FRAMES |