|
||||||||||
PREV NEXT | FRAMES NO FRAMES |
Packages that use Sequence | |
---|---|
de.jstacs.algorithms | Provides classes for algorithms on graphs. |
de.jstacs.classifier | This package provides the framework for any classifier. |
de.jstacs.classifier.modelBased | Provides the classes for Classifier s that are based on Model s |
de.jstacs.classifier.scoringFunctionBased | Provides the classes for Classifier s that are based on ScoringFunction s. |
de.jstacs.classifier.scoringFunctionBased.cll | Provides the implementation of the log conditional likelihood as an OptimizableFunction and a classifier that uses log conditional likelihood or supervised posterior
to learn the parameters of a set of ScoringFunctions |
de.jstacs.data | Provides classes for the representation of data. |
de.jstacs.data.sequences | Provides classes for representing sequences. |
de.jstacs.models | Provides the interface Model and its abstract implementation AbstractModel , which is the super class of all other models. |
de.jstacs.models.discrete | |
de.jstacs.models.discrete.inhomogeneous | This package contains various inhomogeneous models. |
de.jstacs.models.mixture | This package is the super package for any mixture model. |
de.jstacs.models.utils | |
de.jstacs.scoringFunctions | Provides ScoringFunction s that can be used in a ScoreClassifier . |
de.jstacs.scoringFunctions.directedGraphicalModels | Provides ScoringFunction s that are equivalent to directed graphical models. |
de.jstacs.scoringFunctions.homogeneous | Provides ScoringFunction s that are homogeneous, i.e. model probabilities or scores independent of the position within a sequence |
de.jstacs.scoringFunctions.mix | Provides ScoringFunction s that are mixtures of other ScoringFunction s. |
Uses of Sequence in de.jstacs.algorithms |
---|
Methods in de.jstacs.algorithms with parameters of type Sequence | |
---|---|
double |
Alignment.SimpleCosts.getCostFor(Sequence s1,
Sequence s2,
int i,
int j,
Alignment.Costs.Direction from)
|
double |
Alignment.Costs.getCostFor(Sequence s1,
Sequence s2,
int i,
int j,
Alignment.Costs.Direction from)
Returns the costs for the alignment if s1(i) and s2(j) coming from from . |
Constructors in de.jstacs.algorithms with parameters of type Sequence | |
---|---|
Alignment(Sequence s1,
Sequence s2,
Alignment.Costs costs)
Creates a new Alignment.StringAlignment instance that aligns the sequences
s1 and s2 using the costs defined in
costs . |
Uses of Sequence in de.jstacs.classifier |
---|
Methods in de.jstacs.classifier with parameters of type Sequence | |
---|---|
protected void |
AbstractScoreBasedClassifier.check(Sequence seq)
This method checks if the given sequence can be used. |
byte |
AbstractScoreBasedClassifier.classify(Sequence seq)
|
abstract byte |
AbstractClassifier.classify(Sequence seq)
This method classifies a sequence and returns the index i , with
0 < i < getNumberOfClasses() , of the class to which the sequence is assigned. |
protected byte |
AbstractScoreBasedClassifier.classify(Sequence seq,
boolean check)
This method classifies a sequence. |
double |
AbstractScoreBasedClassifier.getPValue(Sequence candidate,
Sample bg)
Returns the p-value for a sequence candidate with respect to a given background sample. |
double |
AbstractScoreBasedClassifier.getScore(Sequence seq,
int i)
This method returns the score for a given sequence and a given class. |
protected double |
MappingClassifier.getScore(Sequence seq,
int i,
boolean check)
|
protected abstract double |
AbstractScoreBasedClassifier.getScore(Sequence seq,
int i,
boolean check)
This method returns the score for a given sequence and a given class. |
Uses of Sequence in de.jstacs.classifier.modelBased |
---|
Methods in de.jstacs.classifier.modelBased with parameters of type Sequence | |
---|---|
protected double |
ModelBasedClassifier.getScore(Sequence seq,
int i,
boolean check)
|
Uses of Sequence in de.jstacs.classifier.scoringFunctionBased |
---|
Methods in de.jstacs.classifier.scoringFunctionBased with parameters of type Sequence | |
---|---|
protected double |
ScoreClassifier.getScore(Sequence seq,
int i,
boolean check)
|
Uses of Sequence in de.jstacs.classifier.scoringFunctionBased.cll |
---|
Methods in de.jstacs.classifier.scoringFunctionBased.cll with parameters of type Sequence | |
---|---|
protected double |
CLLClassifier.getScore(Sequence seq,
int i,
boolean check)
|
Uses of Sequence in de.jstacs.data |
---|
Subclasses of Sequence in de.jstacs.data | |
---|---|
protected static class |
Sequence.CompositeSequence
The class handles composite sequences. |
protected static class |
Sequence.SubSequence
This class handles subsequences. |
Fields in de.jstacs.data declared as Sequence | |
---|---|
protected Sequence |
Sequence.rc
The pointer to the reverse complement |
Methods in de.jstacs.data that return Sequence | |
---|---|
Sequence |
Sequence.annotate(boolean add,
SequenceAnnotation... annotation)
This method allows to append annotation to a sequence. |
Sequence |
Sequence.complement()
This method returns a new instance of sequence containing the complementary current sequence. |
Sequence |
Sequence.complement(int start,
int end)
This method returns a new instance of sequence containing a part of the complementary current sequence. |
static Sequence |
Sequence.create(AlphabetContainer con,
SequenceAnnotation[] annotation,
String sequence,
String delim)
Creates a sequence from a string based on the given AlphabetContainer using the given delimiter. |
static Sequence |
Sequence.create(AlphabetContainer con,
String sequence)
Creates a sequence from a string based on the given AlphabetContainer using the standard delimiter for this AlphabetContainer. |
static Sequence |
Sequence.create(AlphabetContainer con,
String sequence,
String delim)
Creates a sequence from a string based on the given AlphabetContainer using the given delimiter. |
protected abstract Sequence |
Sequence.flatCloneWithoutAnnotation()
Works in analogy to Object.clone() , but does not clone the annotation. |
protected Sequence |
Sequence.CompositeSequence.flatCloneWithoutAnnotation()
|
protected Sequence |
Sequence.SubSequence.flatCloneWithoutAnnotation()
|
Sequence[] |
Sample.getAllElements()
Returns an array of sequences containing all elements of this Sample. |
Sequence |
Sequence.getCompositeSequence(AlphabetContainer abc,
int[] starts,
int[] lengths)
This constructor should be used if one wants to create a sample of composite sequences. |
Sequence |
Sequence.getCompositeSequence(int[] starts,
int[] lengths)
This is an very efficient way to create a composite sequence for sequences with a simple AlphabetContainer. |
Sequence |
Sample.getElementAt(int i)
This method returns the element with index i . |
Sequence |
Sample.WeightedSampleFactory.getElementAt(int index)
Returns the sequence with index index . |
Sequence |
Sequence.getSubSequence(AlphabetContainer abc,
int start)
This method should be used if one wants to create a sample of subsequences of defined length. |
Sequence |
Sequence.getSubSequence(AlphabetContainer abc,
int start,
int length)
This method should be used if one wants to create a sample of subsequences of defined length. |
Sequence |
Sequence.getSubSequence(int start)
This is an very efficient way to create a subsequence/suffix for sequences with a simple AlphabetContainer. |
Sequence |
Sequence.getSubSequence(int start,
int length)
This is an very efficient way to create a subsequence of defined length for sequences with a simple AlphabetContainer. |
Sequence |
Sample.ElementEnumerator.nextElement()
|
Sequence |
DiscreteSequenceEnumerator.nextElement()
|
Sequence |
Sequence.reverse()
This method returns a new instance of sequence containing the reverse current sequence. |
Sequence |
Sequence.reverse(int start,
int end)
This method returns a new instance of sequence containing a part of the reverse current sequence. |
Sequence |
Sequence.reverseComplement()
This method returns a new sequence instance containing the complementary current sequence. |
Sequence |
Sequence.reverseComplement(int start,
int end)
This method returns a new sequence instance containing a part of the complementary current sequence. |
Sequence |
Sequence.SubSequence.reverseComplement(int start,
int end)
|
Methods in de.jstacs.data with parameters of type Sequence | |
---|---|
int |
Sequence.compareTo(Sequence s)
|
Constructors in de.jstacs.data with parameters of type Sequence | |
---|---|
Sample(String annotation,
Sequence... seqs)
This constructor is specially designed for the method Model.emitSample(int, int...) . |
|
Sequence.CompositeSequence(AlphabetContainer abc,
Sequence seq,
int[] starts,
int[] lengths)
This constructor should be used if one wants to create a sample of composite sequences. |
|
Sequence.CompositeSequence(Sequence seq,
int[] starts,
int[] lengths)
This is an very effient way to create a composite sequence for sequences with a simple AlphabetContainer. |
|
Sequence.SubSequence(AlphabetContainer abc,
Sequence seq,
int start,
int length)
This constructor should be used if one wants to create a sample of subsequences of defined length. |
|
Sequence.SubSequence(Sequence seq,
int start,
int length)
This is an very efficient way to create a subsequence of defined length for sequences with a simple AlphabetContainer. |
Uses of Sequence in de.jstacs.data.sequences |
---|
Subclasses of Sequence in de.jstacs.data.sequences | |
---|---|
class |
ArbitrarySequence
The class for any continuous or hybrid sequence. |
class |
ByteSequence
This class can be used for discrete AlphabetContainer with alphabets that use only few symbols. |
class |
DiscreteSequence
The main class for any discrete sequence. |
class |
IntSequence
This class can be used for discrete AlphabetContainer with alphabets that use a huge number of symbols. |
class |
PermutedSequence
Class for a permuted sequence. |
class |
RecursiveSequence
This is the main class for subsequences, composite sequences, ... . |
class |
ShortSequence
This class can be used for discrete AlphabetContainer with alphabets that use many different symbols. |
class |
SparseSequence
This class is an implementation for sequence on one alphabet with length 4. |
Fields in de.jstacs.data.sequences declared as Sequence | |
---|---|
protected Sequence |
RecursiveSequence.content
The internal sequence |
Methods in de.jstacs.data.sequences that return Sequence | |
---|---|
protected Sequence |
SparseSequence.flatCloneWithoutAnnotation()
|
protected Sequence |
ShortSequence.flatCloneWithoutAnnotation()
|
protected Sequence |
PermutedSequence.flatCloneWithoutAnnotation()
|
protected Sequence |
IntSequence.flatCloneWithoutAnnotation()
|
protected Sequence |
ByteSequence.flatCloneWithoutAnnotation()
|
protected Sequence |
ArbitrarySequence.flatCloneWithoutAnnotation()
|
Constructors in de.jstacs.data.sequences with parameters of type Sequence | |
---|---|
PermutedSequence(Sequence seq)
This constructor creates an instance by shuffling the symbols. |
|
RecursiveSequence(AlphabetContainer alphabet,
Sequence seq)
This constructor creates a recursive sequence using the annotation of the given sequence. |
|
RecursiveSequence(AlphabetContainer alphabet,
SequenceAnnotation[] annotation,
Sequence seq)
This constructor creates a recursive sequence. |
Uses of Sequence in de.jstacs.models |
---|
Methods in de.jstacs.models with parameters of type Sequence | |
---|---|
double |
Model.getLogProbFor(Sequence sequence)
Returns the logarithm of the probability of the given sequence given the model. |
double |
AbstractModel.getLogProbFor(Sequence sequence)
|
double |
Model.getLogProbFor(Sequence sequence,
int startpos)
Returns the logarithm of the probability of the given sequence given the model. |
double |
AbstractModel.getLogProbFor(Sequence sequence,
int startpos)
|
double |
Model.getLogProbFor(Sequence sequence,
int startpos,
int endpos)
Returns the logarithm of the probability of the given sequence given the model. |
double |
CompositeModel.getLogProbFor(Sequence sequence,
int startpos,
int endpos)
|
double |
AbstractModel.getLogProbFor(Sequence sequence,
int startpos,
int endpos)
|
double |
Model.getProbFor(Sequence sequence)
Returns the probability of the given sequence given the model. |
double |
AbstractModel.getProbFor(Sequence sequence)
|
double |
Model.getProbFor(Sequence sequence,
int startpos)
Returns the probability of the given sequence given the model. |
double |
AbstractModel.getProbFor(Sequence sequence,
int startpos)
|
double |
UniformModel.getProbFor(Sequence sequence,
int startpos,
int endpos)
|
double |
Model.getProbFor(Sequence sequence,
int startpos,
int endpos)
Returns the probability of the given sequence given the model. |
double |
CompositeModel.getProbFor(Sequence sequence,
int startpos,
int endpos)
|
Uses of Sequence in de.jstacs.models.discrete |
---|
Methods in de.jstacs.models.discrete with parameters of type Sequence | |
---|---|
void |
Constraint.add(Sequence seq,
int start,
double weight)
This method determines the specific constraint that is fulfilled by the sequence and adds the weight
to the specific counter. |
protected void |
DiscreteGraphicalModel.check(Sequence sequence,
int startpos,
int endpos)
Checks some conditions on a sequence. |
double |
Constraint.getFreq(Sequence seq,
int start)
This method determines the specific constraint that is fullfilled by the sequence beginning at start . |
abstract int |
Constraint.satisfiesSpecificConstraint(Sequence seq,
int start)
This method returns the index of the specific constraint that is fullfilled by the sequence beginning at start . |
Uses of Sequence in de.jstacs.models.discrete.inhomogeneous |
---|
Methods in de.jstacs.models.discrete.inhomogeneous with parameters of type Sequence | |
---|---|
protected void |
InhomogeneousDGM.check(Sequence sequence,
int startpos,
int endpos)
|
double |
InhCondProb.getLnFreq(Sequence s,
int start)
Returns the logarithmic frequency. |
double |
DAGModel.getLogProbFor(Sequence sequence,
int startpos,
int endpos)
|
double |
DAGModel.getProbFor(Sequence sequence,
int startpos,
int endpos)
|
int |
InhConstraint.satisfiesSpecificConstraint(Sequence s,
int start)
|
Uses of Sequence in de.jstacs.models.mixture |
---|
Methods in de.jstacs.models.mixture that return Sequence | |
---|---|
protected Sequence[] |
StrandModel.emitSampleUsingCurrentParameterSet(int n,
int... lengths)
|
protected Sequence[] |
MixtureModel.emitSampleUsingCurrentParameterSet(int n,
int... lengths)
|
protected abstract Sequence[] |
AbstractMixtureModel.emitSampleUsingCurrentParameterSet(int n,
int... lengths)
The method returns an array of sequences using the current parameter set. |
Methods in de.jstacs.models.mixture with parameters of type Sequence | |
---|---|
int |
AbstractMixtureModel.getIndexOfMaximalComponentFor(Sequence s)
Returns the index i of the component with
P(i|s) |
double |
AbstractMixtureModel.getLogProbFor(int component,
Sequence s)
Returns the log probability for the sequence and the given component. |
double |
AbstractMixtureModel.getLogProbFor(Sequence sequence,
int startpos,
int endpos)
|
protected double |
StrandModel.getLogProbUsingCurrentParameterSetFor(int component,
Sequence s,
int start,
int end)
|
protected double |
MixtureModel.getLogProbUsingCurrentParameterSetFor(int component,
Sequence s,
int start,
int end)
|
protected abstract double |
AbstractMixtureModel.getLogProbUsingCurrentParameterSetFor(int component,
Sequence s,
int start,
int end)
Returns the log probability for the sequence and the given component using the current parameter set. |
double |
AbstractMixtureModel.getProbFor(Sequence sequence,
int startpos,
int endpos)
|
Uses of Sequence in de.jstacs.models.utils |
---|
Methods in de.jstacs.models.utils that return Sequence | |
---|---|
static Sequence |
ModelTester.getMostProbableSequence(Model m,
int length)
Returns one most probable sequence for the discrete model m . |
Sequence |
ModelTester.SeqIterator.getSequence()
|
Uses of Sequence in de.jstacs.scoringFunctions |
---|
Methods in de.jstacs.scoringFunctions with parameters of type Sequence | |
---|---|
double |
ScoringFunction.getLogScore(Sequence seq)
Returns the log score for the sequence |
double |
AbstractNormalizableScoringFunction.getLogScore(Sequence seq)
Returns the log score for the sequence |
double |
VariableLengthScoringFunction.getLogScore(Sequence seq,
int start)
|
double |
UniformScoringFunction.getLogScore(Sequence seq,
int start)
|
double |
ScoringFunction.getLogScore(Sequence seq,
int start)
Returns the log score for the sequence |
double |
MRFScoringFunction.getLogScore(Sequence seq,
int start)
|
double |
IndependentProductScoringFunction.getLogScore(Sequence seq,
int start)
|
abstract double |
VariableLengthScoringFunction.getLogScore(Sequence seq,
int start,
int length)
This method computes the logarithm of the score for a given subsequence. |
abstract double |
VariableLengthScoringFunction.getLogScoreAndPartialDerivation(Sequence seq,
int start,
int length,
IntList indices,
DoubleList dList)
This method computes the logarithm of the score and the partial derivations for a given subsequence. |
double |
VariableLengthScoringFunction.getLogScoreAndPartialDerivation(Sequence seq,
int start,
IntList indices,
DoubleList dList)
|
double |
UniformScoringFunction.getLogScoreAndPartialDerivation(Sequence seq,
int start,
IntList indices,
DoubleList dList)
|
double |
ScoringFunction.getLogScoreAndPartialDerivation(Sequence seq,
int start,
IntList indices,
DoubleList partialDer)
Returns the log score for the sequence and fills the list with the indices and the partial derivations. |
double |
MRFScoringFunction.getLogScoreAndPartialDerivation(Sequence seq,
int start,
IntList indices,
DoubleList partialDer)
|
double |
IndependentProductScoringFunction.getLogScoreAndPartialDerivation(Sequence seq,
int start,
IntList indices,
DoubleList partialDer)
|
double |
ScoringFunction.getLogScoreAndPartialDerivation(Sequence seq,
IntList indices,
DoubleList partialDer)
Returns the log score for the sequence and fills the list with the indices and the partial derivations. |
double |
AbstractNormalizableScoringFunction.getLogScoreAndPartialDerivation(Sequence seq,
IntList indices,
DoubleList partialDer)
|
Uses of Sequence in de.jstacs.scoringFunctions.directedGraphicalModels |
---|
Methods in de.jstacs.scoringFunctions.directedGraphicalModels with parameters of type Sequence | |
---|---|
void |
ParameterTree.addCount(Sequence seq,
int start,
double count)
Adds count to the parameter as returned by ParameterTree.getParameterFor(Sequence, int) . |
double |
Parameter.doesApplyFor(Sequence seq)
Returns true if seq fulfills all requirements defined in the context (Parameter.context }). |
double |
BayesianNetworkScoringFunction.getLogScore(Sequence seq,
int start)
|
double |
BayesianNetworkScoringFunction.getLogScoreAndPartialDerivation(Sequence seq,
int start,
IntList indices,
DoubleList partialDer)
|
Parameter |
ParameterTree.getParameterFor(Sequence seq,
int start)
Returns the Parameter that is responsible for the suffix of sequence seq starting at position start . |
Uses of Sequence in de.jstacs.scoringFunctions.homogeneous |
---|
Methods in de.jstacs.scoringFunctions.homogeneous with parameters of type Sequence | |
---|---|
double |
UniformHomogeneousScoringFunction.getLogScore(Sequence seq,
int start,
int length)
|
double |
HMMScoringFunction.getLogScore(Sequence seq,
int start,
int length)
|
double |
HMM0ScoringFunction.getLogScore(Sequence seq,
int start,
int length)
|
double |
UniformHomogeneousScoringFunction.getLogScoreAndPartialDerivation(Sequence seq,
int start,
int length,
IntList indices,
DoubleList dList)
|
double |
HMMScoringFunction.getLogScoreAndPartialDerivation(Sequence seq,
int start,
int length,
IntList indices,
DoubleList dList)
|
double |
HMM0ScoringFunction.getLogScoreAndPartialDerivation(Sequence seq,
int start,
int length,
IntList indices,
DoubleList dList)
|
Uses of Sequence in de.jstacs.scoringFunctions.mix |
---|
Methods in de.jstacs.scoringFunctions.mix with parameters of type Sequence | |
---|---|
protected void |
MixtureScoringFunction.fillComponentScores(Sequence seq,
int start)
|
protected abstract void |
AbstractMixtureScoringFunction.fillComponentScores(Sequence seq,
int start)
Fills the internal array componentScore with the log scores of the components. |
int |
AbstractMixtureScoringFunction.getIndexOfMaximalComponentFor(Sequence seq,
int start)
Returns the index of the component that has the greatest impact on the complete score |
double |
AbstractMixtureScoringFunction.getLogScore(Sequence seq,
int start)
|
double |
MixtureScoringFunction.getLogScoreAndPartialDerivation(Sequence seq,
int start,
IntList indices,
DoubleList partialDer)
|
double[] |
AbstractMixtureScoringFunction.getProbsForComponent(Sequence seq)
Returns the probabilities for each component |
|
||||||||||
PREV NEXT | FRAMES NO FRAMES |