Package | Description |
---|---|
de.jstacs.data |
Provides classes for the representation of data.
The base classes to represent data are Alphabet and AlphabetContainer for representing alphabets,
Sequence and its sub-classes to represent continuous and discrete sequences, and
DataSet to represent data sets comprising a set of sequences. |
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. |
Modifier and Type | Method and Description |
---|---|
Alphabet |
AlphabetContainer.getAlphabetAt(int pos)
Returns the underlying
Alphabet of position pos . |
Modifier and Type | Method and Description |
---|---|
static AlphabetContainer |
AlphabetContainer.getSimplifiedAlphabetContainer(Alphabet[] abc,
int[] assignment)
This method creates a new
AlphabetContainer that uses as less as
possible Alphabet s 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 Alphabet s into an existing
AlphabetContainer . |
Constructor and Description |
---|
AlphabetArrayParameterSet(Alphabet[] alphabets,
AlphabetContainer.AlphabetContainerType type)
Creates a new
AlphabetContainerParameterSet.AlphabetArrayParameterSet from an array of
Alphabet s and the information about the type of
the Alphabet s. |
AlphabetContainer(Alphabet... abc)
Creates a new
AlphabetContainer with different Alphabet s
for each position. |
AlphabetContainer(Alphabet abc)
Creates a new simple
AlphabetContainer . |
AlphabetContainer(Alphabet[] abc,
int[] assignment)
Creates a new
AlphabetContainer that uses different
Alphabet s. |
AlphabetContainerParameterSet(Alphabet alph)
|
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
Alphabet index i in alphabets
that is used for position i . |
AlphabetContainerParameterSet(Class<? extends AlphabetContainer> instanceClass,
Alphabet... alphabets)
/**
Creates a new
AlphabetContainerParameterSet from an array of
Alphabet s for a given sub-class of AlphabetContainer . |
SectionDefinedAlphabetParameterSet(Alphabet[] alphabets,
int[] indexes)
Creates a new
AlphabetContainerParameterSet.SectionDefinedAlphabetParameterSet from an
array of Alphabet s and an array of indexes that define the
index of the Alphabet in alphabets belonging to
that position in indexes . |
Modifier and Type | Class and Description |
---|---|
static class |
Alphabet.AlphabetParameterSet<T extends Alphabet>
The super class for the
InstanceParameterSet of any
Alphabet . |
Modifier and Type | Class and Description |
---|---|
class |
ComplementableDiscreteAlphabet
This abstract class indicates that an alphabet can be used to compute the
complement.
|
class |
ContinuousAlphabet
Class for a continuous alphabet.
|
class |
DiscreteAlphabet
Class for an alphabet that consists of arbitrary
String s. |
class |
DNAAlphabet
This class implements the discrete alphabet that is used for DNA.
|
class |
GenericComplementableDiscreteAlphabet
This class implements an generic complementable discrete alphabet.
|
class |
IUPACDNAAlphabet
This class implements a discrete alphabet for the IUPAC DNA code.
|
class |
ProteinAlphabet
This class implements the discrete alphabet that is used for proteins (one letter code).
|
Modifier and Type | Method and Description |
---|---|
abstract InstanceParameterSet<? extends Alphabet> |
Alphabet.getCurrentParameterSet() |
Modifier and Type | Method and Description |
---|---|
boolean |
Alphabet.checkConsistency(Alphabet a)
|
int |
DiscreteAlphabet.compareTo(Alphabet b) |
int |
ContinuousAlphabet.compareTo(Alphabet a) |