Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
 PREV CLASS   NEXT CLASS FRAMES    NO FRAMES    
SUMMARY: NESTED | FIELD | CONSTR | METHOD DETAIL: FIELD | CONSTR | METHOD

de.jstacs.scoringFunctions.mix.motifSearch
Class HiddenMotifsMixture

java.lang.Object
  extended by de.jstacs.scoringFunctions.AbstractNormalizableScoringFunction
      extended by de.jstacs.scoringFunctions.mix.AbstractMixtureScoringFunction
          extended by de.jstacs.scoringFunctions.mix.motifSearch.HiddenMotifsMixture
All Implemented Interfaces:
MotifDiscoverer, MutableMotifDiscoverer, NormalizableScoringFunction, ScoringFunction, Storable, Cloneable
public class HiddenMotifsMixture
extends AbstractMixtureScoringFunction
implements MutableMotifDiscoverer

This class handles mixtures with at least one hidden motif.

Author:
Jens Keilwagen

Nested Class Summary
 
Nested classes/interfaces inherited from interface de.jstacs.motifDiscovery.MotifDiscoverer
MotifDiscoverer.KindOfProfile
 
Field Summary
static boolean CONTAINS_ALWAYS_A_MOTIF
          This constant indicates that in each sequence has one binding site of a motif instance (similar to OOPS).
static boolean CONTAINS_SOMETIMES_A_MOTIF
          This constant indicates that a sequence possibly has one binding site of a motif instance (similar to ZOOPS).
 
Fields inherited from class de.jstacs.scoringFunctions.mix.AbstractMixtureScoringFunction
componentScore, dList, freeParams, function, hiddenParameter, hiddenPotential, iList, logGammaSum, logHiddenNorm, logHiddenPotential, norm, optimizeHidden, paramRef, partNorm
 
Fields inherited from class de.jstacs.scoringFunctions.AbstractNormalizableScoringFunction
alphabets, length, r
 
Fields inherited from interface de.jstacs.scoringFunctions.ScoringFunction
UNKNOWN
 
Constructor Summary
HiddenMotifsMixture(boolean type, int length, int starts, boolean plugIn, HomogeneousScoringFunction bg, NormalizableScoringFunction[] motif, DurationScoringFunction[] posPrior, boolean plugInBg)
          This constructor creates an instance of HiddenMotifsMixture that allows to have one site of the specified motifs in a Sequence.
HiddenMotifsMixture(boolean type, int length, int starts, boolean plugIn, HomogeneousScoringFunction bg, NormalizableScoringFunction motif, DurationScoringFunction posPrior, boolean plugInBg)
          This constructor creates an instance of HiddenMotifsMixture that is either an OOPS or a ZOOPS model depending on the chosen type.
HiddenMotifsMixture(StringBuffer source)
          This is the constructor for the interface Storable.
 
Method Summary
 void adjustHiddenParameters(int classIndex, Sample[] data, double[][] dataWeights)
          Adjusts all hidden parameters including duration and mixture parameters according to the current values of the remaining parameters.
 HiddenMotifsMixture clone()
          Creates a clone (deep copy) of the current ScoringFunction instance.
protected  void extractFurtherInformation(StringBuffer xml)
          This method is the opposite of AbstractMixtureScoringFunction.getFurtherInformation().
protected  int fillComponentScoreOf(int i, Sequence seq, int start)
          This method fills an internal array with the partial scores.
protected  void fillComponentScores(Sequence seq, int start)
          Fills the internal array AbstractMixtureScoringFunction.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.
protected  StringBuffer getFurtherInformation()
          This method is used to append further information of the instance to the XML representation.
 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()
          Returns a short instance name.
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 getLogScore(Sequence seq, int start)
          Returns the logarithmic score for the Sequence seq beginning at position start in the Sequence.
 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 dist)
          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 initializeFunctionRandomly(boolean freeParams)
          This method initializes the ScoringFunction randomly.
 void initializeMotif(int motif, Sample 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 ScoringFunction.initializeFunctionRandomly(boolean).
protected  void initializeUsingPlugIn(int index, boolean freeParams, Sample[] data, double[][] weights)
          This method initializes the functions using the data in some way.
 boolean modifyMotif(int motif, int offsetLeft, int offsetRight)
          Manually modifies the motif model with index motifIndex.
 String toString()
           
 
Methods inherited from class de.jstacs.scoringFunctions.mix.AbstractMixtureScoringFunction
addGradientOfLogPriorTerm, cloneFunctions, computeHiddenParameter, computeLogGammaSum, determineIsNormalized, fromXML, getCurrentParameterValues, getFunction, getFunctions, getIndexOfMaximalComponentFor, getIndices, getLogNormalizationConstant, getLogPriorTerm, getNumberOfComponents, getNumberOfParameters, getNumberOfRecommendedStarts, getProbsForComponent, getScoringFunctions, getSizeOfEventSpaceForRandomVariablesOfParameter, getXMLTag, init, initializeFunction, initializeHiddenPotentialRandomly, initializeHiddenUniformly, initWithLength, isInitialized, isNormalized, precomputeNorm, setHiddenParameters, setParameters, setParametersForFunction, toXML
 
Methods inherited from class de.jstacs.scoringFunctions.AbstractNormalizableScoringFunction
getAlphabetContainer, getInitialClassParam, getLength, getLogScore, getLogScoreAndPartialDerivation, getNumberOfStarts, isNormalized
 
Methods inherited from class java.lang.Object
equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
 
Methods inherited from interface de.jstacs.motifDiscovery.MotifDiscoverer
getNumberOfComponents
 
Methods inherited from interface de.jstacs.Storable
toXML
 

Field Detail

CONTAINS_ALWAYS_A_MOTIF

public static final boolean CONTAINS_ALWAYS_A_MOTIF
This constant indicates that in each sequence has one binding site of a motif instance (similar to OOPS).

See Also:
Constant Field Values

CONTAINS_SOMETIMES_A_MOTIF

public static final boolean CONTAINS_SOMETIMES_A_MOTIF
This constant indicates that a sequence possibly has one binding site of a motif instance (similar to ZOOPS).

See Also:
Constant Field Values
Constructor Detail

HiddenMotifsMixture

public HiddenMotifsMixture(boolean type,
                           int length,
                           int starts,
                           boolean plugIn,
                           HomogeneousScoringFunction bg,
                           NormalizableScoringFunction motif,
                           DurationScoringFunction posPrior,
                           boolean plugInBg)
                    throws Exception
This constructor creates an instance of HiddenMotifsMixture that is either an OOPS or a ZOOPS model depending on the chosen type.

Parameters:
type - the type of hidden motifs, either CONTAINS_ALWAYS_A_MOTIF or CONTAINS_SOMETIMES_A_MOTIF
length - the length of the modeled sequences (e.g. 500)
starts - the number of recommended starts
plugIn - a switch whether to use plug-in or randomly chosen parameter when using ScoringFunction.initializeFunction(int, boolean, Sample[], double[][])
bg - the ScoringFunction for the overall background (i.e. flanking sequence that does not contain a motif)
motif - the ScoringFunction for the motif
posPrior - the ScoringFunction for the position
plugInBg - a switch whether to plug in the (old = last) parameters of the background model, if false the background model is initialized again
Throws:
Exception - if something went wrong (e.g. the AlphabetContainer is not simple, ...)

HiddenMotifsMixture

public HiddenMotifsMixture(boolean type,
                           int length,
                           int starts,
                           boolean plugIn,
                           HomogeneousScoringFunction bg,
                           NormalizableScoringFunction[] motif,
                           DurationScoringFunction[] posPrior,
                           boolean plugInBg)
                    throws Exception
This constructor creates an instance of HiddenMotifsMixture that allows to have one site of the specified motifs in a Sequence.

Parameters:
type - the type of hidden motifs, either CONTAINS_ALWAYS_A_MOTIF or CONTAINS_SOMETIMES_A_MOTIF
length - the length of the modeled sequences (e.g. 500)
starts - the number of recommended starts
plugIn - a switch whether to use plug-in or randomly chosen parameter when using ScoringFunction.initializeFunction(int, boolean, Sample[], double[][])
bg - the ScoringFunction for the overall background (i.e. flanking sequence that does not contain a motif)
motif - the ScoringFunctions for the sequence motif
posPrior - the ScoringFunctions for the position of the the sequence motifs
plugInBg - a switch whether to plug in the parameters of the background model in some way, if false the background model is initialized uniformly
Throws:
Exception - if something went wrong (e.g. the AlphabetContainer is not simple, ...)

HiddenMotifsMixture

public HiddenMotifsMixture(StringBuffer source)
                    throws NonParsableException
This is the constructor for the interface Storable. Recreates a new HiddenMotifsMixture out of a StringBuffer as returned by AbstractMixtureScoringFunction.toXML().

Parameters:
source - the XML representation as StringBuffer
Throws:
NonParsableException - if the representation could not be parsed
Method Detail

clone

public HiddenMotifsMixture clone()
                          throws CloneNotSupportedException
Description copied from interface: ScoringFunction
Creates a clone (deep copy) of the current ScoringFunction instance.

Specified by:
clone in interface MotifDiscoverer
Specified by:
clone in interface ScoringFunction
Overrides:
clone in class AbstractMixtureScoringFunction
Returns:
the cloned instance of the current ScoringFunction
Throws:
CloneNotSupportedException - if something went wrong while cloning the ScoringFunction
See Also:
Cloneable

getHyperparameterForHiddenParameter

public double getHyperparameterForHiddenParameter(int index)
Description copied from class: AbstractMixtureScoringFunction
This method returns the hyperparameter for the hidden parameter with index index.

Specified by:
getHyperparameterForHiddenParameter in class AbstractMixtureScoringFunction
Parameters:
index - the index of the hidden parameter
Returns:
the hyperparameter for the hidden parameter

getLogNormalizationConstantForComponent

protected double getLogNormalizationConstantForComponent(int i)
Description copied from class: AbstractMixtureScoringFunction
Computes the logarithm of the normalization constant for the component i.

Specified by:
getLogNormalizationConstantForComponent in class AbstractMixtureScoringFunction
Parameters:
i - the index of the component
Returns:
the logarithm of the normalization constant of the component

getLogPartialNormalizationConstant

public double getLogPartialNormalizationConstant(int parameterIndex)
                                          throws Exception
Description copied from interface: NormalizableScoringFunction
Returns the logarithm of the partial normalization constant for the parameter with index parameterIndex. This is the logarithm of the partial derivation of the normalization constant for the parameter with index parameterIndex,
\[\log \frac{\partial Z(\underline{\lambda})}{\partial \lambda_{parameterindex}}\]
.

Specified by:
getLogPartialNormalizationConstant in interface NormalizableScoringFunction
Parameters:
parameterIndex - the index of the parameter
Returns:
the logarithm of the partial normalization constant
Throws:
Exception - if something went wrong with the normalization
See Also:
NormalizableScoringFunction.getLogNormalizationConstant()

getEss

public double getEss()
Description copied from interface: NormalizableScoringFunction
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.

Specified by:
getEss in interface NormalizableScoringFunction
Returns:
the equivalent sample size.

initializeFunctionRandomly

public void initializeFunctionRandomly(boolean freeParams)
                                throws Exception
Description copied from interface: ScoringFunction
This method initializes the ScoringFunction randomly. It has to create the underlying structure of the ScoringFunction.

Specified by:
initializeFunctionRandomly in interface ScoringFunction
Overrides:
initializeFunctionRandomly in class AbstractMixtureScoringFunction
Parameters:
freeParams - indicates whether the (reduced) parameterization is used
Throws:
Exception - if something went wrong

getInstanceName

public String getInstanceName()
Description copied from interface: ScoringFunction
Returns a short instance name.

Specified by:
getInstanceName in interface ScoringFunction
Returns:
a short instance name

fillComponentScoreOf

protected int fillComponentScoreOf(int i,
                                   Sequence seq,
                                   int start)
This method fills an internal array with the partial scores.

Parameters:
i - the index of the component
seq - the Sequence
start - the start position
Returns:
the number of computed partial scores

fillComponentScores

protected void fillComponentScores(Sequence seq,
                                   int start)
Description copied from class: AbstractMixtureScoringFunction
Fills the internal array AbstractMixtureScoringFunction.componentScore with the logarithmic scores of the components given a Sequence.

Specified by:
fillComponentScores in class AbstractMixtureScoringFunction
Parameters:
seq - the sequence
start - the start position in seq

getLogScore

public double getLogScore(Sequence seq,
                          int start)
Description copied from interface: ScoringFunction
Returns the logarithmic score for the Sequence seq beginning at position start in the Sequence.

Specified by:
getLogScore in interface ScoringFunction
Overrides:
getLogScore in class AbstractMixtureScoringFunction
Parameters:
seq - the Sequence
start - the start position in the Sequence
Returns:
the logarithmic score for the Sequence

getLogScoreAndPartialDerivation

public double getLogScoreAndPartialDerivation(Sequence seq,
                                              int start,
                                              IntList indices,
                                              DoubleList partialDer)
Description copied from interface: ScoringFunction
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 ScoringFunction
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 $\frac{\partial \log score(seq)}{\partial \lambda_i}$ is not zero
partialDer - a DoubleList of partial derivations, after method invocation the list should contain the corresponding $\frac{\partial \log score(seq)}{\partial \lambda_i}$ that are not zero
Returns:
the logarithmic score for the Sequence

toString

public String toString()
Overrides:
toString in class Object

getFurtherInformation

protected StringBuffer getFurtherInformation()
Description copied from class: AbstractMixtureScoringFunction
This method is used to append further information of the instance to the XML representation. This method is designed to allow subclasses to add information to the XML representation.

Overrides:
getFurtherInformation in class AbstractMixtureScoringFunction
Returns:
the further information as XML code in a StringBuffer
See Also:
AbstractMixtureScoringFunction.extractFurtherInformation(StringBuffer)

extractFurtherInformation

protected void extractFurtherInformation(StringBuffer xml)
                                  throws NonParsableException
Description copied from class: AbstractMixtureScoringFunction
This method is the opposite of AbstractMixtureScoringFunction.getFurtherInformation(). It extracts further information of the instance from a XML representation.

Overrides:
extractFurtherInformation in class AbstractMixtureScoringFunction
Parameters:
xml - the StringBuffer containing the information to be extracted as XML code
Throws:
NonParsableException - if the StringBuffer could not be parsed
See Also:
AbstractMixtureScoringFunction.getFurtherInformation()

modifyMotif

public boolean modifyMotif(int motif,
                           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:
motif - the index of the motif in the motif discoverer
offsetLeft - the offset on the left side
offsetRight - 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)

initializeMotif

public void initializeMotif(int motif,
                            Sample 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:
motif - the index of the motif in the motif discoverer
data - the sample of sequences
weights - 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 ScoringFunction.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 ScoringFunction.initializeFunctionRandomly(boolean)

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

getIndexOfMaximalComponentFor

public int getIndexOfMaximalComponentFor(Sequence sequence)
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

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 index
motif - the motif index in the component
Returns:
the global index of the motif in component

getProfileOfScoresFor

public double[] getProfileOfScoresFor(int component,
                                      int motif,
                                      Sequence sequence,
                                      int startpos,
                                      MotifDiscoverer.KindOfProfile dist)
                               throws WrongLengthException
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 index
motif - the index of the motif in the component
sequence - the given sequence
startpos - the start position in the sequence
dist - indicates the kind of profile
Returns:
the profile of scores
Throws:
WrongLengthException

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

adjustHiddenParameters

public void adjustHiddenParameters(int classIndex,
                                   Sample[] data,
                                   double[][] dataWeights)
                            throws Exception
Description copied from interface: MutableMotifDiscoverer
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:
classIndex - the index of the class of this MutableMotifDiscoverer
data - the array of data for all classes
dataWeights - the weights for all sequences in data
Throws:
Exception - thrown if the hidden parameters could not be adjusted

initializeUsingPlugIn

protected void initializeUsingPlugIn(int index,
                                     boolean freeParams,
                                     Sample[] data,
                                     double[][] weights)
                              throws Exception
Description copied from class: AbstractMixtureScoringFunction
This method initializes the functions using the data in some way.

Specified by:
initializeUsingPlugIn in class AbstractMixtureScoringFunction
Parameters:
index - the class index
freeParams - 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:
ScoringFunction.initializeFunction(int, boolean, Sample[], double[][])

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 index
motif - the index of the motif in the component
sequence - the given sequence
startpos - 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
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
 PREV CLASS   NEXT CLASS FRAMES    NO FRAMES    
SUMMARY: NESTED | FIELD | CONSTR | METHOD DETAIL: FIELD | CONSTR | METHOD