Modifier and Type | Field and Description |
---|---|
protected DoubleList[][] |
DiffSSBasedOptimizableFunction.dList
These
DoubleList s are used during the parallel computation of the gradient. |
Modifier and Type | Method and Description |
---|---|
Pair<double[][],double[]> |
SignificantMotifOccurrencesFinder.getPWMAndPosDist(int motif,
DataSet data,
double[] weights,
double[] mean,
int addLeft,
int addRight,
LinkedList<Sequence> bs,
DoubleList bsWeight,
DoubleList bsScores)
Returns the position weight matrix and standard deviation of the position distribution using the given mean.
|
protected double[][] |
SignificantMotifOccurrencesFinder.getPWMAndPositions(int motif,
DataSet data,
double[] weights,
int addLeft,
int addRight,
int[][] positions,
double[][] pvals,
double[] mean,
double[] sd,
LinkedList<Sequence> bs,
DoubleList bsWeights,
DoubleList bsScores)
Returns the Position weight matrix (PWM) of the binding sites of motif
motif
in the data set data of the MotifDiscoverer of this SignificantMotifOccurrencesFinder
and fills with the positions of the binding sites within the sequences of data and the corresponding p-values into the corresponding arrays. |
Modifier and Type | Field and Description |
---|---|
protected DoubleList[] |
AbstractBurnInTest.values
This array contains all values that will be set via
BurnInTest.setValue(double) . |
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 DoubleList[] |
AbstractMixtureDiffSM.dList
This array contains some
DoubleList 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 | Field and Description |
---|---|
protected DoubleList[] |
DifferentiableHigherOrderHMM.partDerState
Help array for the derivatives of the parameters of the states
|
protected DoubleList[] |
DifferentiableHigherOrderHMM.partDerTransition
Help array for the derivatives of the parameters of the transition
|
Modifier and Type | Method and Description |
---|---|
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) |
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 |
---|---|
DoubleList |
DoubleList.clone() |
Modifier and Type | Method and Description |
---|---|
void |
DoubleList.addAll(DoubleList list2)
This method adds all elements of
DoubleList list2 to the current list. |