Modifier and Type | Field and Description |
---|---|
protected IntList[][] |
DiffSSBasedOptimizableFunction.iList
These
IntList s are used during the parallel computation of the gradient. |
Modifier and Type | Method and Description |
---|---|
<S> ClusterTree<S> |
ClusterTree.dropBelow(IntList rootOriginalIndexes,
S[] newElements)
Removes all sub-trees below the inner nodes identified by the original indexes supplied
and creates new leaf nodes instead, which obtain the supplied leaf elements.
|
Modifier and Type | Method and Description |
---|---|
IntList |
SignificantMotifOccurrencesFinder.getStartPositions(int startPos,
DataSet data,
int motifIndex,
int addMax)
This method returns a list of start positions of binding sites.
|
Modifier and Type | Method and Description |
---|---|
double |
DifferentiableSequenceScore.getLogScoreAndPartialDerivation(Sequence seq,
int start,
int end,
IntList indices,
DoubleList partialDer)
|
double |
AbstractDifferentiableSequenceScore.getLogScoreAndPartialDerivation(Sequence seq,
int startpos,
int endpos,
IntList indices,
DoubleList partialDer) |
double |
UniformDiffSS.getLogScoreAndPartialDerivation(Sequence seq,
int start,
IntList indices,
DoubleList dList) |
double |
MultiDimensionalSequenceWrapperDiffSS.getLogScoreAndPartialDerivation(Sequence seq,
int start,
IntList indices,
DoubleList partialDer) |
double |
IndependentProductDiffSS.getLogScoreAndPartialDerivation(Sequence seq,
int start,
IntList indices,
DoubleList partialDer) |
double |
DifferentiableSequenceScore.getLogScoreAndPartialDerivation(Sequence seq,
int start,
IntList indices,
DoubleList partialDer)
|
double |
DifferentiableSequenceScore.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 |
AbstractDifferentiableSequenceScore.getLogScoreAndPartialDerivation(Sequence seq,
IntList indices,
DoubleList partialDer) |
Modifier and Type | Method and Description |
---|---|
double |
LogisticDiffSS.getLogScoreAndPartialDerivation(Sequence seq,
int start,
IntList indices,
DoubleList partialDer) |
Modifier and Type | Method and Description |
---|---|
double |
VariableLengthDiffSM.getLogScoreAndPartialDerivation(Sequence seq,
int startpos,
int endpos,
IntList indices,
DoubleList partialDer) |
double |
CyclicMarkovModelDiffSM.getLogScoreAndPartialDerivation(Sequence seq,
int start,
int end,
IntList indices,
DoubleList dList) |
abstract double |
AbstractVariableLengthDiffSM.getLogScoreAndPartialDerivation(Sequence seq,
int startpos,
int endpos,
IntList indices,
DoubleList partialDer) |
double |
UniformDiffSM.getLogScoreAndPartialDerivation(Sequence seq,
int start,
IntList indices,
DoubleList dList) |
double |
NormalizedDiffSM.getLogScoreAndPartialDerivation(Sequence seq,
int start,
IntList indices,
DoubleList partialDer) |
double |
MarkovRandomFieldDiffSM.getLogScoreAndPartialDerivation(Sequence seq,
int start,
IntList indices,
DoubleList partialDer) |
double |
MappingDiffSM.getLogScoreAndPartialDerivation(Sequence seq,
int start,
IntList indices,
DoubleList partialDer) |
double |
AbstractVariableLengthDiffSM.getLogScoreAndPartialDerivation(Sequence seq,
int start,
IntList indices,
DoubleList dList) |
Modifier and Type | Method and Description |
---|---|
double |
BayesianNetworkDiffSM.getLogScoreAndPartialDerivation(Sequence seq,
int start,
IntList indices,
DoubleList partialDer) |
Modifier and Type | Method and Description |
---|---|
double |
UniformHomogeneousDiffSM.getLogScoreAndPartialDerivation(Sequence seq,
int start,
int end,
IntList indices,
DoubleList dList) |
double |
HomogeneousMMDiffSM.getLogScoreAndPartialDerivation(Sequence seq,
int start,
int end,
IntList indices,
DoubleList dList) |
double |
HomogeneousMM0DiffSM.getLogScoreAndPartialDerivation(Sequence seq,
int start,
int end,
IntList indices,
DoubleList dList) |
Modifier and Type | Method and Description |
---|---|
double |
LimitedSparseLocalInhomogeneousMixtureDiffSM_higherOrder.getLogScoreAndPartialDerivation(Sequence seq,
int start,
IntList indices,
DoubleList partialDer) |
Modifier and Type | Field and Description |
---|---|
protected IntList[] |
AbstractMixtureDiffSM.iList
This array contains some
IntList s that are used while computing
the partial derivation. |
Modifier and Type | Method and Description |
---|---|
double |
VariableLengthMixtureDiffSM.getLogScoreAndPartialDerivation(Sequence seq,
int start,
int end,
IntList indices,
DoubleList partialDer) |
double |
StrandDiffSM.getLogScoreAndPartialDerivation(Sequence seq,
int start,
IntList indices,
DoubleList partialDer) |
double |
MixtureDiffSM.getLogScoreAndPartialDerivation(Sequence seq,
int start,
IntList indices,
DoubleList partialDer) |
Modifier and Type | Method and Description |
---|---|
double |
UniformDurationDiffSM.getLogScoreAndPartialDerivation(IntList indices,
DoubleList partialDer,
int... values) |
double |
SkewNormalLikeDurationDiffSM.getLogScoreAndPartialDerivation(IntList indices,
DoubleList partialDer,
int... values) |
abstract double |
PositionDiffSM.getLogScoreAndPartialDerivation(IntList indices,
DoubleList partialDer,
int... values)
This method enables the user to get the log-score and the partial derivations without using a sequence object.
|
double |
MixtureDurationDiffSM.getLogScoreAndPartialDerivation(IntList indices,
DoubleList partialDer,
int... values) |
double |
PositionDiffSM.getLogScoreAndPartialDerivation(Sequence seq,
int start,
IntList indices,
DoubleList partialDer) |
double |
ExtendedZOOPSDiffSM.getLogScoreAndPartialDerivation(Sequence seq,
int start,
IntList indices,
DoubleList partialDer) |
double |
PositionDiffSM.getLogScoreAndPartialDerivationForInternal(IntList indices,
DoubleList partialDer)
This method enables the user to get the log-score and the partial derivations without using a sequence object by using the internal iterator.
|
Modifier and Type | Method and Description |
---|---|
void |
MEMConstraint.addParameters(int offset,
IntList list,
MEMConstraint[] constraint,
double[] params,
int[] start)
This method implements a heuristic to modify a constraint if a number of constraints should be delete.
|
Modifier and Type | Method and Description |
---|---|
abstract Pair<IntList,Double> |
AbstractHMM.getViterbiPathFor(int startPos,
int endPos,
Sequence seq) |
Pair<IntList,Double> |
AbstractHMM.getViterbiPathFor(Sequence seq) |
Modifier and Type | Method and Description |
---|---|
String[] |
AbstractHMM.decodePath(IntList path)
This method decodes any path of the HMM, i.e.
|
abstract double |
AbstractHMM.getLogProbForPath(IntList path,
int startPos,
Sequence seq) |
Modifier and Type | Field and Description |
---|---|
protected IntList[] |
DifferentiableHigherOrderHMM.indicesState
Help array for the indexes of the parameters of the states
|
protected IntList[] |
DifferentiableHigherOrderHMM.indicesTransition
Help array for the indexes of the parameters of the transition
|
protected IntList |
HigherOrderHMM.stateList
Helper variable = only for internal use.
|
Modifier and Type | Method and Description |
---|---|
Pair<IntList,Double> |
SamplingHigherOrderHMM.getViterbiPath(int startPos,
int endPos,
Sequence seq,
SamplingHigherOrderHMM.ViterbiComputation compute)
This method returns a viterbi path that is the optimum for the choosen ViterbiComputation method
|
Pair<IntList,Double> |
SamplingHigherOrderHMM.getViterbiPathFor(int startPos,
int endPos,
Sequence seq) |
Pair<IntList,Double> |
HigherOrderHMM.getViterbiPathFor(int startPos,
int endPos,
Sequence seq) |
Modifier and Type | Method and Description |
---|---|
double |
SamplingHigherOrderHMM.getLogProbForPath(IntList path,
int startPos,
Sequence seq) |
double |
HigherOrderHMM.getLogProbForPath(IntList path,
int startPos,
Sequence seq) |
double |
DifferentiableHigherOrderHMM.getLogScoreAndPartialDerivation(Sequence seq,
int startPos,
int endPos,
IntList indices,
DoubleList partialDer) |
double |
DifferentiableHigherOrderHMM.getLogScoreAndPartialDerivation(Sequence seq,
int startPos,
IntList indices,
DoubleList partialDer) |
double |
DifferentiableHigherOrderHMM.getLogScoreAndPartialDerivation(Sequence seq,
IntList indices,
DoubleList partialDer) |
void |
HigherOrderHMM.samplePath(IntList path,
int startPos,
int endPos,
Sequence seq)
This method samples a valid path for the given sequence
seq using the internal parameters. |
protected double |
HigherOrderHMM.viterbi(IntList path,
int startPos,
int endPos,
double weight,
Sequence seq)
This method computes the viterbi score of a given sequence
seq . |
Modifier and Type | Method and Description |
---|---|
double |
SimpleDifferentiableState.getLogScoreAndPartialDerivation(int startPos,
int endPos,
IntList indices,
DoubleList partDer,
Sequence seq) |
double |
DifferentiableState.getLogScoreAndPartialDerivation(int startPos,
int endPos,
IntList indices,
DoubleList partDer,
Sequence seq)
This method allows to compute the logarithm of the score and the gradient for the given subsequences.
|
Modifier and Type | Method and Description |
---|---|
double |
UniformEmission.getLogProbAndPartialDerivationFor(boolean forward,
int startPos,
int endPos,
IntList indices,
DoubleList partDer,
Sequence seq) |
double |
SilentEmission.getLogProbAndPartialDerivationFor(boolean forward,
int startPos,
int endPos,
IntList indices,
DoubleList partDer,
Sequence seq) |
double |
DifferentiableEmission.getLogProbAndPartialDerivationFor(boolean forward,
int startPos,
int endPos,
IntList indices,
DoubleList partDer,
Sequence seq)
|
Modifier and Type | Method and Description |
---|---|
double |
GaussianEmission.getLogProbAndPartialDerivationFor(boolean forward,
int startPos,
int endPos,
IntList indices,
DoubleList partDer,
Sequence seq) |
Modifier and Type | Method and Description |
---|---|
double |
PhyloDiscreteEmission.getLogProbAndPartialDerivationFor(boolean forward,
int startPos,
int endPos,
IntList indices,
DoubleList partDer,
Sequence seq) |
double |
AbstractConditionalDiscreteEmission.getLogProbAndPartialDerivationFor(boolean forward,
int startPos,
int endPos,
IntList indices,
DoubleList partDer,
Sequence seq) |
Modifier and Type | Method and Description |
---|---|
double |
HigherOrderTransition.getLogScoreAndPartialDerivation(int layer,
int index,
int childIdx,
IntList indices,
DoubleList partDer,
Sequence sequence,
int sequencePosition) |
double |
DifferentiableTransition.getLogScoreAndPartialDerivation(int layer,
int index,
int childIdx,
IntList indices,
DoubleList partDer,
Sequence sequence,
int sequencePosition)
This method allows to compute the logarithm of the score and the gradient for a specific transition.
|
Modifier and Type | Method and Description |
---|---|
double |
TransitionElement.getLogScoreAndPartialDerivation(int childIdx,
IntList indices,
DoubleList partialDer,
Sequence sequence,
int sequencePosition)
Returns the logarithmic score and fills lists with
the indices and the partial derivations.
|
Modifier and Type | Method and Description |
---|---|
IntList |
IntList.clone() |