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Packages that use Sequence | |
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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.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.homogeneous | |
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.mixture.motif | |
de.jstacs.models.utils | |
de.jstacs.motifDiscovery | This package provides the framework including the interface for any de novo motif discoverer |
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. |
de.jstacs.scoringFunctions.mix.motifSearch |
Uses of Sequence in de.jstacs.algorithms |
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Methods in de.jstacs.algorithms with parameters of type Sequence | |
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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 | |
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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 |
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Methods in de.jstacs.classifier with parameters of type Sequence | |
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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 of
the class to which the sequence is assigned with
0 < i < getNumberOfClasses() . |
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 |
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Methods in de.jstacs.classifier.modelBased with parameters of type Sequence | |
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protected double |
ModelBasedClassifier.getScore(Sequence seq,
int i,
boolean check)
|
Uses of Sequence in de.jstacs.classifier.scoringFunctionBased |
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Methods in de.jstacs.classifier.scoringFunctionBased with parameters of type Sequence | |
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protected double |
ScoreClassifier.getScore(Sequence seq,
int i,
boolean check)
|
Uses of Sequence in de.jstacs.data |
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Subclasses of Sequence in de.jstacs.data | |
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protected static class |
Sequence.CompositeSequence
The class handles composite Sequence s. |
protected static class |
Sequence.SubSequence
This class handles subsequences. |
Fields in de.jstacs.data declared as Sequence | |
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protected Sequence |
Sequence.rc
The pointer to the reverse complement of the Sequence.CompositeSequence . |
Methods in de.jstacs.data that return Sequence | |
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Sequence |
Sequence.annotate(boolean add,
SequenceAnnotation... annotation)
This method allows to append annotation to a Sequence.CompositeSequence . |
Sequence |
Sequence.complement()
This method returns a new instance of Sequence.CompositeSequence containing the
complementary current Sequence.CompositeSequence . |
Sequence |
Sequence.complement(int start,
int end)
This method returns a new instance of Sequence.CompositeSequence containing a part
of the complementary current Sequence.CompositeSequence . |
static Sequence |
Sequence.create(AlphabetContainer con,
SequenceAnnotation[] annotation,
String sequence,
String delim)
Creates a Sequence.CompositeSequence from a String based on the given
AlphabetContainer using the given delimiter delim
and some annotation for the Sequence.CompositeSequence . |
static Sequence |
Sequence.create(AlphabetContainer con,
String sequence)
Creates a Sequence.CompositeSequence 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.CompositeSequence from a String based on the given
AlphabetContainer using the given delimiter delim . |
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 Sequence s containing all elements of this
Sample . |
Sequence |
Sequence.getCompositeSequence(AlphabetContainer abc,
int[] starts,
int[] lengths)
This method should be used if one wants to create a Sample of
Sequence.CompositeSequence s. |
Sequence |
Sequence.getCompositeSequence(int[] starts,
int[] lengths)
This is a very efficient way to create a Sequence.CompositeSequence for
sequences with a simple AlphabetContainer . |
Sequence |
Sample.getElementAt(int i)
This method returns the element, i.e. the Sequence , 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 a very efficient way to create a subsequence/suffix for Sequence.CompositeSequence s with a simple AlphabetContainer . |
Sequence |
Sequence.getSubSequence(int start,
int length)
This is a very efficient way to create a subsequence of defined length for Sequence.CompositeSequence s with a simple AlphabetContainer . |
Sequence |
Sample.ElementEnumerator.nextElement()
|
Sequence |
DiscreteSequenceEnumerator.nextElement()
|
Sequence |
Sequence.reverse()
This method returns a new instance of Sequence.CompositeSequence containing the
reverse current Sequence.CompositeSequence . |
Sequence |
Sequence.reverse(int start,
int end)
This method returns a new instance of Sequence.CompositeSequence containing a part
of the reverse current Sequence.CompositeSequence . |
Sequence |
Sequence.reverseComplement()
This method returns a new instance of Sequence.CompositeSequence containing the
reverse complementary current Sequence.CompositeSequence . |
Sequence |
Sequence.reverseComplement(int start,
int end)
This method returns a new instance of Sequence.CompositeSequence containing a
reverse part of the complementary current Sequence.CompositeSequence . |
Sequence |
Sequence.SubSequence.reverseComplement(int start,
int end)
|
Methods in de.jstacs.data with parameters of type Sequence | |
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int |
Sequence.compareTo(Sequence s)
|
Constructors in de.jstacs.data with parameters of type Sequence | |
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Sample(String annotation,
Sequence... seqs)
Creates a new Sample from an array of Sequence s and a
given annotation. |
|
Sequence.CompositeSequence(AlphabetContainer abc,
Sequence seq,
int[] starts,
int[] lengths)
This constructor should be used if one wants to create a Sample of Sequence.CompositeSequence s. |
|
Sequence.CompositeSequence(Sequence seq,
int[] starts,
int[] lengths)
This is a very efficient way to create a Sequence.CompositeSequence
for Sequence s 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 Sequence.SubSequence s of defined length. |
|
Sequence.SubSequence(Sequence seq,
int start,
int length)
This is a very efficient way to create a Sequence.SubSequence of
defined length for Sequence s with a simple
AlphabetContainer . |
Uses of Sequence in de.jstacs.data.sequences |
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Subclasses of Sequence in de.jstacs.data.sequences | |
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class |
ArbitrarySequence
This class is for any continuous or hybrid sequence. |
class |
ByteSequence
This class is for sequences with the alphabet symbols encoded as byte s and can therefore be used for discrete
AlphabetContainer s with alphabets that use only few symbols. |
class |
DiscreteSequence
This is the main class for any discrete sequence. |
class |
IntSequence
This class is for sequences with the alphabet symbols encoded as int s and can therefore be used for discrete
AlphabetContainer s with alphabets that use a huge number of symbols. |
class |
PermutedSequence
This class is for permuted sequences. |
class |
RecursiveSequence
This is the main class for subsequences, composite sequences, ... . |
class |
ShortSequence
This class is for sequences with the alphabet symbols encoded as shorts s and can therefore be used for discrete
AlphabetContainer s with alphabets that use many different symbols. |
class |
SparseSequence
This class is an implementation for sequences on one alphabet with length 4. |
Fields in de.jstacs.data.sequences declared as Sequence | |
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protected Sequence |
RecursiveSequence.content
The internal sequence. |
Methods in de.jstacs.data.sequences that return Sequence | |
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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 | |
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PermutedSequence(Sequence seq)
Creates a new PermutedSequence by shuffling the symbols of a
given Sequence . |
|
RecursiveSequence(AlphabetContainer alphabet,
Sequence seq)
Creates a new RecursiveSequence on the Sequence
seq with the AlphabetContainer alphabet
using the annotation of the given Sequence . |
|
RecursiveSequence(AlphabetContainer alphabet,
SequenceAnnotation[] annotation,
Sequence seq)
Creates a new RecursiveSequence on the Sequence
seq with the AlphabetContainer alphabet
and the annotation annotation . |
Uses of Sequence in de.jstacs.models |
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Methods in de.jstacs.models with parameters of type Sequence | |
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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 (a part 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 (a part 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 (a part 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 (a part of) the given sequence given the model. |
double |
CompositeModel.getProbFor(Sequence sequence,
int startpos,
int endpos)
|
Uses of Sequence in de.jstacs.models.discrete |
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Methods in de.jstacs.models.discrete with parameters of type Sequence | |
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void |
Constraint.add(Sequence seq,
int start,
double weight)
This method determines the specific constraint that is fulfilled by the Sequence seq 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 fulfilled by the Sequence seq beginning at position
start . |
abstract int |
Constraint.satisfiesSpecificConstraint(Sequence seq,
int start)
This method returns the index of the specific constraint that is fulfilled by the Sequence seq beginning at position
start . |
Uses of Sequence in de.jstacs.models.discrete.homogeneous |
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Methods in de.jstacs.models.discrete.homogeneous that return Sequence | |
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protected abstract Sequence |
HomogeneousModel.getRandomSequence(Random r,
int length)
This method creates a random Sequence from a trained homogeneous
model. |
protected Sequence |
HomogeneousMM.getRandomSequence(Random r,
int length)
|
Methods in de.jstacs.models.discrete.homogeneous with parameters of type Sequence | |
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void |
HomogeneousModel.HomCondProb.addAll(Sequence seq,
double weight,
int start,
int prevIndex)
Adds the given weight to the counts corresponding to the
Sequence seq from start to the end
of the Sequence . |
protected void |
HomogeneousModel.check(Sequence sequence,
int startpos,
int endpos)
Checks some constraints, these are in general conditions on the AlphabetContainer of a (sub)Sequence
between startpos und endpos . |
double |
HomogeneousModel.getLogProbFor(Sequence sequence,
int startpos,
int endpos)
|
double |
HomogeneousModel.getProbFor(Sequence sequence,
int startpos,
int endpos)
|
protected abstract double |
HomogeneousModel.logProbFor(Sequence sequence,
int startpos,
int endpos)
This method computes the logarithm of the probability of the given Sequence in the given interval. |
protected double |
HomogeneousMM.logProbFor(Sequence sequence,
int startpos,
int endpos)
|
protected abstract double |
HomogeneousModel.probFor(Sequence sequence,
int startpos,
int endpos)
This method computes the probability of the given Sequence in the
given interval. |
protected double |
HomogeneousMM.probFor(Sequence sequence,
int startpos,
int endpos)
|
int |
HomogeneousModel.HomCondProb.satisfiesSpecificConstraint(Sequence seq,
int start)
|
Uses of Sequence in de.jstacs.models.discrete.inhomogeneous |
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Methods in de.jstacs.models.discrete.inhomogeneous with parameters of type Sequence | |
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protected void |
InhomogeneousDGM.check(Sequence sequence,
int startpos,
int endpos)
|
double |
InhCondProb.getLnFreq(Sequence s,
int start)
Returns the logarithm of the relative frequency (=probability) with the position in the distribution given by the index of the specific constraint that is fulfilled by the Sequence s
beginning at start . |
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 |
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Methods in de.jstacs.models.mixture that return Sequence | |
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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 | |
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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 logarithmic 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 logarithmic 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.mixture.motif |
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Methods in de.jstacs.models.mixture.motif that return Sequence | |
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protected Sequence[] |
HiddenMotifMixture.emitSampleUsingCurrentParameterSet(int n,
int... lengths)
Standard implementation throwing an OperationNotSupportedException . |
Methods in de.jstacs.models.mixture.motif with parameters of type Sequence | |
---|---|
protected double |
SingleHiddenMotifMixture.getLogProbUsingCurrentParameterSetFor(int component,
Sequence seq,
int start,
int end)
|
double[] |
SingleHiddenMotifMixture.getProfileOfScoresFor(int component,
int motif,
Sequence sequence,
int startpos,
MotifDiscoverer.KindOfProfile kind)
|
StrandedLocatedSequenceAnnotationWithLength.Strand |
SingleHiddenMotifMixture.getStrandFor(int component,
int motif,
Sequence sequence,
int startpos)
|
Uses of Sequence in de.jstacs.models.utils |
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Methods in de.jstacs.models.utils that return Sequence | |
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static Sequence |
ModelTester.getMostProbableSequence(Model m,
int length)
Returns one most probable sequence for the discrete model m . |
Uses of Sequence in de.jstacs.motifDiscovery |
---|
Methods in de.jstacs.motifDiscovery that return Sequence | |
---|---|
static Sequence |
MutableMotifDiscovererToolbox.enumerate(Sample[] data,
ScoringFunction[] funs,
int classIndex,
int motifIndex,
double weight,
OptimizableFunction opt,
OutputStream out)
This method allows to enumerate all possible seeds for a motif in the HiddenMotifsMixture of a specific class. |
Methods in de.jstacs.motifDiscovery with parameters of type Sequence | |
---|---|
MotifAnnotation[] |
SignificantMotifOccurrencesFinder.findSignificantMotifOccurrences(int motif,
Sequence seq,
int start)
This method finds the significant motif occurrences in the sequence. |
int |
MotifDiscoverer.getIndexOfMaximalComponentFor(Sequence sequence)
Returns the index of the component with the maximal score for the sequence sequence . |
double[] |
MotifDiscoverer.getProfileOfScoresFor(int component,
int motif,
Sequence sequence,
int startpos,
MotifDiscoverer.KindOfProfile kind)
Returns the profile of the scores for component component
and motif motif at all possible start positions of the motif
in the sequence sequence beginning at startpos . |
StrandedLocatedSequenceAnnotationWithLength.Strand |
MotifDiscoverer.getStrandFor(int component,
int motif,
Sequence sequence,
int startpos)
This method returns the strand for a given subsequence if it is considered as site of the motif model in a specific component. |
static ImageResult |
MotifDiscovererToolBox.plot(MotifDiscoverer motifDisc,
int component,
int motif,
Sequence sequence,
int startpos,
REnvironment r,
int width,
int height,
MotifDiscoverer.KindOfProfile kind)
This method creates a simple plot of the profile of scores for a sequence and a start position. |
static ImageResult |
MotifDiscovererToolBox.plotAndAnnotate(MotifDiscoverer motifDisc,
int component,
int motif,
Sequence sequence,
int startpos,
REnvironment r,
int width,
int height,
double yMin,
double yMax,
double threshold,
MotifDiscoverer.KindOfProfile kind)
This method creates a plot of the profile of scores for a sequence and a start position and annotates bindings sites in the plot that have a higher score than threshold . |
Uses of Sequence in de.jstacs.scoringFunctions |
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Methods in de.jstacs.scoringFunctions with parameters of type Sequence | |
---|---|
int |
IndependentProductScoringFunction.getIndexOfMaximalComponentFor(Sequence sequence)
|
double |
ScoringFunction.getLogScore(Sequence seq)
Returns the logarithmic score for the Sequence seq . |
double |
AbstractNormalizableScoringFunction.getLogScore(Sequence seq)
Returns the logarithmic score for a given Sequence . |
double |
VariableLengthScoringFunction.getLogScore(Sequence seq,
int start)
|
double |
UniformScoringFunction.getLogScore(Sequence seq,
int start)
|
double |
ScoringFunction.getLogScore(Sequence seq,
int start)
Returns the logarithmic score for the Sequence seq
beginning at position start in the Sequence . |
double |
NormalizedScoringFunction.getLogScore(Sequence seq,
int start)
|
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 logarithmic score for a Sequence beginning at
position start in the Sequence and fills lists with
the indices and the partial derivations. |
double |
NormalizedScoringFunction.getLogScoreAndPartialDerivation(Sequence seq,
int start,
IntList indices,
DoubleList partialDer)
|
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 logarithmic score for a Sequence seq and
fills lists with the indices and the partial derivations. |
double |
AbstractNormalizableScoringFunction.getLogScoreAndPartialDerivation(Sequence seq,
IntList indices,
DoubleList partialDer)
|
double[] |
IndependentProductScoringFunction.getProfileOfScoresFor(int component,
int motif,
Sequence sequence,
int startpos,
MotifDiscoverer.KindOfProfile dist)
|
StrandedLocatedSequenceAnnotationWithLength.Strand |
NormalizedScoringFunction.getStrand(Sequence seq,
int startPos)
This method return the preferred StrandedLocatedSequenceAnnotationWithLength.Strand for a Sequence beginning at startPos . |
StrandedLocatedSequenceAnnotationWithLength.Strand |
IndependentProductScoringFunction.getStrandFor(int component,
int motif,
Sequence sequence,
int startpos)
|
Uses of Sequence in de.jstacs.scoringFunctions.directedGraphicalModels |
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Methods in de.jstacs.scoringFunctions.directedGraphicalModels with parameters of type Sequence | |
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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)
Indicates if the Sequence seq fulfills all
requirements defined in the 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 |
StrandScoringFunction.fillComponentScores(Sequence seq,
int start)
|
protected void |
MixtureScoringFunction.fillComponentScores(Sequence seq,
int start)
|
protected abstract void |
AbstractMixtureScoringFunction.fillComponentScores(Sequence seq,
int start)
Fills the internal array AbstractMixtureScoringFunction.componentScore with the logarithmic
scores of the components given a Sequence . |
int |
AbstractMixtureScoringFunction.getIndexOfMaximalComponentFor(Sequence seq,
int start)
Returns the index of the component that has the greatest impact on the complete score for a Sequence . |
double |
AbstractMixtureScoringFunction.getLogScore(Sequence seq,
int start)
|
double |
StrandScoringFunction.getLogScoreAndPartialDerivation(Sequence seq,
int start,
IntList indices,
DoubleList partialDer)
|
double |
MixtureScoringFunction.getLogScoreAndPartialDerivation(Sequence seq,
int start,
IntList indices,
DoubleList partialDer)
|
double[] |
AbstractMixtureScoringFunction.getProbsForComponent(Sequence seq)
Returns the probabilities for each component given a Sequence . |
StrandedLocatedSequenceAnnotationWithLength.Strand |
StrandScoringFunction.getStrand(Sequence seq,
int startPos)
This method returns the preferred StrandedLocatedSequenceAnnotationWithLength.Strand for a given subsequence. |
Uses of Sequence in de.jstacs.scoringFunctions.mix.motifSearch |
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Methods in de.jstacs.scoringFunctions.mix.motifSearch with parameters of type Sequence | |
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protected int |
HiddenMotifsMixture.fillComponentScoreOf(int i,
Sequence seq,
int start)
This method fills an internal array with the partial scores. |
protected void |
HiddenMotifsMixture.fillComponentScores(Sequence seq,
int start)
|
int |
HiddenMotifsMixture.getIndexOfMaximalComponentFor(Sequence sequence)
|
double |
PositionScoringFunction.getLogScore(Sequence seq,
int start)
|
double |
HiddenMotifsMixture.getLogScore(Sequence seq,
int start)
|
double |
PositionScoringFunction.getLogScoreAndPartialDerivation(Sequence seq,
int start,
IntList indices,
DoubleList partialDer)
|
double |
HiddenMotifsMixture.getLogScoreAndPartialDerivation(Sequence seq,
int start,
IntList indices,
DoubleList partialDer)
|
double[] |
HiddenMotifsMixture.getProfileOfScoresFor(int component,
int motif,
Sequence sequence,
int startpos,
MotifDiscoverer.KindOfProfile dist)
|
StrandedLocatedSequenceAnnotationWithLength.Strand |
HiddenMotifsMixture.getStrandFor(int component,
int motif,
Sequence sequence,
int startpos)
|
protected int[] |
PositionScoringFunction.getValuesFromSequence(Sequence seq,
int start)
This method extracts the values form a sequence. |
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