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java.lang.Objectde.jstacs.sequenceScores.differentiable.AbstractDifferentiableSequenceScore
de.jstacs.sequenceScores.statisticalModels.differentiable.AbstractDifferentiableStatisticalModel
de.jstacs.sequenceScores.statisticalModels.differentiable.mixture.AbstractMixtureDiffSM
de.jstacs.sequenceScores.statisticalModels.differentiable.mixture.MixtureDiffSM
public class MixtureDiffSM
This class implements a real mixture model.
Nested Class Summary |
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Nested classes/interfaces inherited from interface de.jstacs.motifDiscovery.MotifDiscoverer |
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MotifDiscoverer.KindOfProfile |
Field Summary |
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Fields inherited from class de.jstacs.sequenceScores.statisticalModels.differentiable.mixture.AbstractMixtureDiffSM |
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componentScore, dList, freeParams, function, hiddenParameter, hiddenPotential, iList, logGammaSum, logHiddenNorm, logHiddenPotential, norm, optimizeHidden, paramRef, partNorm |
Fields inherited from class de.jstacs.sequenceScores.differentiable.AbstractDifferentiableSequenceScore |
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alphabets, length, r |
Fields inherited from interface de.jstacs.sequenceScores.differentiable.DifferentiableSequenceScore |
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UNKNOWN |
Constructor Summary | |
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MixtureDiffSM(int starts,
boolean plugIn,
DifferentiableStatisticalModel... component)
This constructor creates a new MixtureDiffSM . |
|
MixtureDiffSM(StringBuffer xml)
This is the constructor for the interface Storable . |
Method Summary | |
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void |
adjustHiddenParameters(int index,
DataSet[] data,
double[][] weights)
Adjusts all hidden parameters including duration and mixture parameters according to the current values of the remaining parameters. |
MixtureDiffSM |
clone()
Creates a clone (deep copy) of the current DifferentiableSequenceScore
instance. |
protected void |
fillComponentScores(Sequence seq,
int start)
Fills the internal array AbstractMixtureDiffSM.componentScore with the logarithmic
scores of the components given a Sequence . |
double |
getESS()
Returns the equivalent sample size (ess) of this model, i.e. the equivalent sample size for the class or component that is represented by this model. |
int |
getGlobalIndexOfMotifInComponent(int component,
int motif)
Returns the global index of the motif used in
component . |
double |
getHyperparameterForHiddenParameter(int index)
This method returns the hyperparameter for the hidden parameter with index index . |
int |
getIndexOfMaximalComponentFor(Sequence sequence)
Returns the index of the component with the maximal score for the sequence sequence . |
String |
getInstanceName()
Should return a short instance name such as iMM(0), BN(2), ... |
protected double |
getLogNormalizationConstantForComponent(int i)
Computes the logarithm of the normalization constant for the component i . |
double |
getLogPartialNormalizationConstant(int parameterIndex)
Returns the logarithm of the partial normalization constant for the parameter with index parameterIndex . |
double |
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. |
int |
getMotifLength(int motif)
This method returns the length of the motif with index motif
. |
int |
getNumberOfMotifs()
Returns the number of motifs for this MotifDiscoverer . |
int |
getNumberOfMotifsInComponent(int component)
Returns the number of motifs that are used in the component component of this MotifDiscoverer . |
double[] |
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 . |
double[] |
getStrandProbabilitiesFor(int component,
int motif,
Sequence sequence,
int startpos)
This method returns the probabilities of the strand orientations for a given subsequence if it is considered as site of the motif model in a specific component. |
void |
initializeMotif(int motifIndex,
DataSet data,
double[] weights)
This method allows to initialize the model of a motif manually using a weighted sample. |
void |
initializeMotifRandomly(int motif)
This method initializes the motif with index motif randomly using for instance DifferentiableSequenceScore.initializeFunctionRandomly(boolean) . |
protected void |
initializeUsingPlugIn(int index,
boolean freeParams,
DataSet[] data,
double[][] weights)
This method initializes the functions using the data in some way. |
boolean |
modifyMotif(int motifIndex,
int offsetLeft,
int offsetRight)
Manually modifies the motif model with index motifIndex . |
String |
toString()
|
Methods inherited from class de.jstacs.sequenceScores.statisticalModels.differentiable.AbstractDifferentiableStatisticalModel |
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emitDataSet, getInitialClassParam, getLogProbFor, getLogProbFor, getLogProbFor, getLogScoreFor, getLogScoreFor, getMaximalMarkovOrder, isNormalized |
Methods inherited from class de.jstacs.sequenceScores.differentiable.AbstractDifferentiableSequenceScore |
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getAlphabetContainer, getCharacteristics, getLength, getLogScoreAndPartialDerivation, getLogScoreAndPartialDerivation, getLogScoreFor, getLogScoreFor, getNumberOfStarts, getNumericalCharacteristics |
Methods inherited from class java.lang.Object |
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equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
Methods inherited from interface de.jstacs.motifDiscovery.MotifDiscoverer |
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getNumberOfComponents |
Methods inherited from interface de.jstacs.Storable |
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toXML |
Methods inherited from interface de.jstacs.sequenceScores.differentiable.DifferentiableSequenceScore |
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getInitialClassParam, getLogScoreAndPartialDerivation, getLogScoreAndPartialDerivation |
Methods inherited from interface de.jstacs.sequenceScores.statisticalModels.StatisticalModel |
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emitDataSet, getLogProbFor, getLogProbFor, getLogProbFor, getMaximalMarkovOrder |
Methods inherited from interface de.jstacs.sequenceScores.SequenceScore |
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getAlphabetContainer, getCharacteristics, getLength, getLogScoreFor, getLogScoreFor, getLogScoreFor, getLogScoreFor, getNumericalCharacteristics |
Constructor Detail |
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public MixtureDiffSM(int starts, boolean plugIn, DifferentiableStatisticalModel... component) throws CloneNotSupportedException
MixtureDiffSM
. The first component determines the length of the sequences that can be modeled.
starts
- the number of starts that should be done in an optimizationplugIn
- indicates whether the initial parameters for an optimization
should be related to the data or randomly drawncomponent
- the DifferentiableStatisticalModel
s
CloneNotSupportedException
- if an element of component
could not be clonedpublic MixtureDiffSM(StringBuffer xml) throws NonParsableException
Storable
.
Creates a new MixtureDiffSM
out of a
StringBuffer
.
xml
- the XML representation as StringBuffer
NonParsableException
- if the XML representation could not be parsedMethod Detail |
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public MixtureDiffSM clone() throws CloneNotSupportedException
DifferentiableSequenceScore
DifferentiableSequenceScore
instance.
clone
in interface MotifDiscoverer
clone
in interface DifferentiableSequenceScore
clone
in interface SequenceScore
clone
in class AbstractMixtureDiffSM
DifferentiableSequenceScore
CloneNotSupportedException
- if something went wrong while cloning the
DifferentiableSequenceScore
Cloneable
protected double getLogNormalizationConstantForComponent(int i)
AbstractMixtureDiffSM
i
.
getLogNormalizationConstantForComponent
in class AbstractMixtureDiffSM
i
- the index of the component
public double getLogPartialNormalizationConstant(int parameterIndex) throws Exception
DifferentiableStatisticalModel
parameterIndex
. This is the logarithm of the partial derivation of the
normalization constant for the parameter with index
parameterIndex
,
getLogPartialNormalizationConstant
in interface DifferentiableStatisticalModel
parameterIndex
- the index of the parameter
Exception
- if something went wrong with the normalizationDifferentiableStatisticalModel.getLogNormalizationConstant()
public double getHyperparameterForHiddenParameter(int index)
AbstractMixtureDiffSM
index
.
getHyperparameterForHiddenParameter
in class AbstractMixtureDiffSM
index
- the index of the hidden parameter
public double getESS()
DifferentiableStatisticalModel
getESS
in interface DifferentiableStatisticalModel
protected void initializeUsingPlugIn(int index, boolean freeParams, DataSet[] data, double[][] weights) throws Exception
AbstractMixtureDiffSM
initializeUsingPlugIn
in class AbstractMixtureDiffSM
index
- the class indexfreeParams
- if true, the (reduced) parameterization is used
data
- the data
weights
- the weights for the data
Throws:
Exception
- if the initialization could not be done
See Also:
DifferentiableSequenceScore.initializeFunction(int,
boolean, DataSet[], double[][])
adjustHiddenParameters
public void adjustHiddenParameters(int index,
DataSet[] data,
double[][] weights)
throws Exception
- Adjusts all hidden parameters including duration and mixture parameters according to the current values of the remaining parameters.
- Specified by:
adjustHiddenParameters
in interface MutableMotifDiscoverer
- Parameters:
index
- the index of the class of this instancedata
- the array of data for all classesweights
- the weights for all sequences in data
- Throws:
Exception
- thrown if the hidden parameters could not be adjusted
getInstanceName
public String getInstanceName()
- Description copied from interface:
SequenceScore
- Should return a short instance name such as iMM(0), BN(2), ...
- Specified by:
getInstanceName
in interface SequenceScore
- Returns:
- a short instance name
fillComponentScores
protected void fillComponentScores(Sequence seq,
int start)
- Description copied from class:
AbstractMixtureDiffSM
- Fills the internal array
AbstractMixtureDiffSM.componentScore
with the logarithmic
scores of the components given a Sequence
.
- Specified by:
fillComponentScores
in class AbstractMixtureDiffSM
- Parameters:
seq
- the sequencestart
- the start position in seq
getLogScoreAndPartialDerivation
public double getLogScoreAndPartialDerivation(Sequence seq,
int start,
IntList indices,
DoubleList partialDer)
- Description copied from interface:
DifferentiableSequenceScore
- Returns the logarithmic score for a
Sequence
beginning at
position start
in the Sequence
and fills lists with
the indices and the partial derivations.
- Specified by:
getLogScoreAndPartialDerivation
in interface DifferentiableSequenceScore
- Parameters:
seq
- the Sequence
start
- the start position in the Sequence
indices
- an IntList
of indices, after method invocation the
list should contain the indices i where
is not zeropartialDer
- a DoubleList
of partial derivations, after method
invocation the list should contain the corresponding
that are not zero
- Returns:
- the logarithmic score for the
Sequence
toString
public String toString()
- Overrides:
toString
in class Object
initializeMotif
public void initializeMotif(int motifIndex,
DataSet data,
double[] weights)
throws Exception
- Description copied from interface:
MutableMotifDiscoverer
- This method allows to initialize the model of a motif manually using a weighted sample.
- Specified by:
initializeMotif
in interface MutableMotifDiscoverer
- Parameters:
motifIndex
- the index of the motif in the motif discovererdata
- the sample of sequencesweights
- either null
or an array of length data.getNumberofElements()
with non-negative weights.
- Throws:
Exception
- if initialize was not possible
initializeMotifRandomly
public void initializeMotifRandomly(int motif)
throws Exception
- Description copied from interface:
MutableMotifDiscoverer
- This method initializes the motif with index
motif
randomly using for instance DifferentiableSequenceScore.initializeFunctionRandomly(boolean)
.
Furthermore, if available, it also initializes the positional distribution.
- Specified by:
initializeMotifRandomly
in interface MutableMotifDiscoverer
- Parameters:
motif
- the index of the motif
- Throws:
Exception
- either if the index is wrong or if it is thrown by the method DifferentiableSequenceScore.initializeFunctionRandomly(boolean)
modifyMotif
public boolean modifyMotif(int motifIndex,
int offsetLeft,
int offsetRight)
throws Exception
- Description copied from interface:
MutableMotifDiscoverer
- Manually modifies the motif model with index
motifIndex
. The two offsets offsetLeft
and offsetRight
define how many positions the left or right border positions shall be moved. Negative numbers indicate moves to the left while positive
numbers correspond to moves to the right. The distribution for sequences to the left and right side of the motif shall be computed internally.
- Specified by:
modifyMotif
in interface MutableMotifDiscoverer
- Parameters:
motifIndex
- the index of the motif in the motif discovereroffsetLeft
- the offset on the left sideoffsetRight
- the offset on the right side
- Returns:
true
if the motif model was modified otherwise false
- Throws:
Exception
- if some unexpected error occurred during the modification- See Also:
MutableMotifDiscoverer.modifyMotif(int, int, int)
,
Mutable.modify(int, int)
getGlobalIndexOfMotifInComponent
public int getGlobalIndexOfMotifInComponent(int component,
int motif)
- Description copied from interface:
MotifDiscoverer
- Returns the global index of the
motif
used in
component
. The index returned must be at least 0 and less
than MotifDiscoverer.getNumberOfMotifs()
.
- Specified by:
getGlobalIndexOfMotifInComponent
in interface MotifDiscoverer
- Parameters:
component
- the component indexmotif
- the motif index in the component
- Returns:
- the global index of the
motif in component
getIndexOfMaximalComponentFor
public int getIndexOfMaximalComponentFor(Sequence sequence)
throws Exception
- Description copied from interface:
MotifDiscoverer
- Returns the index of the component with the maximal score for the
sequence
sequence
.
- Specified by:
getIndexOfMaximalComponentFor
in interface MotifDiscoverer
- Parameters:
sequence
- the given sequence
- Returns:
- the index of the component with the maximal score for the given
sequence
- Throws:
Exception
- if the index could not be computed for any reasons
getMotifLength
public int getMotifLength(int motif)
- Description copied from interface:
MotifDiscoverer
- This method returns the length of the motif with index
motif
.
- Specified by:
getMotifLength
in interface MotifDiscoverer
- Parameters:
motif
- the index of the motif
- Returns:
- the length of the motif with index
motif
getNumberOfMotifs
public int getNumberOfMotifs()
- Description copied from interface:
MotifDiscoverer
- Returns the number of motifs for this
MotifDiscoverer
.
- Specified by:
getNumberOfMotifs
in interface MotifDiscoverer
- Returns:
- the number of motifs
getNumberOfMotifsInComponent
public int getNumberOfMotifsInComponent(int component)
- Description copied from interface:
MotifDiscoverer
- Returns the number of motifs that are used in the component
component
of this MotifDiscoverer
.
- Specified by:
getNumberOfMotifsInComponent
in interface MotifDiscoverer
- Parameters:
component
- the component of the MotifDiscoverer
- Returns:
- the number of motifs
getProfileOfScoresFor
public double[] getProfileOfScoresFor(int component,
int motif,
Sequence sequence,
int startpos,
MotifDiscoverer.KindOfProfile kind)
throws Exception
- Description copied from interface:
MotifDiscoverer
- 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
.
This array should be of length
sequence.length() - startpos - motifs[motif].length() + 1
.
A high score should encode for a probable start position.
- Specified by:
getProfileOfScoresFor
in interface MotifDiscoverer
- Parameters:
component
- the component indexmotif
- the index of the motif in the componentsequence
- the given sequencestartpos
- the start position in the sequencekind
- indicates the kind of profile
- Returns:
- the profile of scores
- Throws:
Exception
- if the score could not be computed for any reasons
getStrandProbabilitiesFor
public double[] getStrandProbabilitiesFor(int component,
int motif,
Sequence sequence,
int startpos)
throws Exception
- Description copied from interface:
MotifDiscoverer
- This method returns the probabilities of the strand orientations for a given subsequence if it is
considered as site of the motif model in a specific component.
- Specified by:
getStrandProbabilitiesFor
in interface MotifDiscoverer
- Parameters:
component
- the component indexmotif
- the index of the motif in the componentsequence
- the given sequencestartpos
- the start position in the sequence
- Returns:
- the probabilities of the strand orientations
- Throws:
Exception
- if the strand could not be computed for any reasons
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