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java.lang.Object de.jstacs.sequenceScores.statisticalModels.trainable.discrete.ConstraintManager
public class ConstraintManager
The class manipulate some constraints.
Nested Class Summary | |
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static class |
ConstraintManager.Decomposition
This enum defines the different possible types of decomposition of a model. |
Method Summary | |
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static void |
computeFreqs(double ess,
Constraint... constr)
This method computes the (smoothed) relative frequencies. |
static double |
countInhomogeneous(AlphabetContainer alphabets,
int length,
DataSet data,
double[] weights,
boolean reset,
Constraint... constr)
Fills the (inhomogeneous) constr with the weighted absolute frequency of the DataSet
data and computes the frequencies will not be computed. |
static MEMConstraint[] |
createConstraints(AbstractList<int[]> list,
int[] alphabetLength)
Creates the constraints of a model |
static MEMConstraint[] |
createConstraints(AbstractList<int[]> list,
int[] alphabetLength,
int[] indices)
Creates the constraints for a part of a model |
static MEM[] |
disconnect(AbstractList<int[]> list,
int[] alphabetLength,
ConstraintManager.Decomposition decomposition)
This method tries to disconnect the constraints and create the models. |
static void |
drawFreqs(double ess,
InhCondProb... constr)
This method draws relative frequencies. |
static ArrayList<int[]> |
extract(int length,
String encoded)
Extracts the constraint of a String and returns an ArrayList of int[]. |
static double |
getEntropy(Constraint c)
Tries to compute the entropy as exact as possible. |
static double |
getLogGammaSum(Constraint c,
double ess)
Computes the sum of differences of the logarithmic values of the prior knowledge and all counts. |
static void |
reduce(AbstractList<int[]> list)
This method tries to find and remove subconstraints that are already fulfilled by a bigger one. |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Method Detail |
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public static void computeFreqs(double ess, Constraint... constr) throws IllegalArgumentException
ess=0
no smoothing is done.
ess
- the ESS, if ESS is zero than MLE otherwise MAPEconstr
- the constraints, should be fill with absolute frequencies
IllegalArgumentException
- if the ess is negativepublic static double countInhomogeneous(AlphabetContainer alphabets, int length, DataSet data, double[] weights, boolean reset, Constraint... constr) throws WrongAlphabetException, IllegalArgumentException
constr
with the weighted absolute frequency of the DataSet
data
and computes the frequencies will not be computed.
alphabets
- the alphabets over which the constraints are definedlength
- the length for which the constraints are defineddata
- the sequencesweights
- the weights for the sequences,
weights==null
or
weights.length = data.getNumberOfElements()
, for all i:weights[i]>=0
reset
- whether the constraints should be resetedconstr
- constraints to fill
WrongAlphabetException
- if the alphabet of the data is not correct
IllegalArgumentException
- if the weights array has wrong dimension or the element length of the data is not correctpublic static void drawFreqs(double ess, InhCondProb... constr) throws IllegalArgumentException
ess
- the ESS (additional pseudocount)constr
- the constraints (can be fill with absolute frequencies)
IllegalArgumentException
- if the ess is negativepublic static ArrayList<int[]> extract(int length, String encoded) throws IllegalArgumentException
length
- the sequence respectively the model lengthencoded
- constraints encoded in a String
IllegalArgumentException
- if the constraints can not be parsed correctlypublic static double getEntropy(Constraint c)
c
- the constraint
public static double getLogGammaSum(Constraint c, double ess)
\sum_i [\ln \Gamma(\alpha_i) - \ln \Gamma(\alpha_i + N_i)]
c
- the constraintess
- the ESS
public static void reduce(AbstractList<int[]> list)
list
- the list of all constraintspublic static MEMConstraint[] createConstraints(AbstractList<int[]> list, int[] alphabetLength, int[] indices)
list
- the list of all cliques, each clique is used for one constraintalphabetLength
- the array of alpahebtLength for each positionindices
- the positions used in this part of the model
public static MEMConstraint[] createConstraints(AbstractList<int[]> list, int[] alphabetLength)
list
- the list of all cliques, each clique is used for one constraintalphabetLength
- the array of alpahebtLength for each position
public static MEM[] disconnect(AbstractList<int[]> list, int[] alphabetLength, ConstraintManager.Decomposition decomposition)
list
- the list of all constraintsalphabetLength
- the length of the alphabets at the specific positionsdecomposition
- the choice how to disconnect the constraints
MEM
ConstraintManager.Decomposition.DECOMPOSE_LESS_CONNECTED
,
ConstraintManager.Decomposition.DECOMPOSE_UNCONNECTED
,
ConstraintManager.Decomposition.DECOMPOSE_NOTHING
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