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java.lang.Objectde.jstacs.sequenceScores.statisticalModels.trainable.discrete.ConstraintManager
public class ConstraintManager
This class manipulates and manages some constraints.
Method Summary | |
---|---|
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) Constraint constr with the
weighted absolute frequencies of the DataSet data . |
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 void |
drawFreqs(double ess,
InhCondProb... constr)
This method draws relative frequencies for the constraints in constr . |
static ArrayList<int[]> |
extract(int length,
String encoded)
Extracts the constraints of a String and returns an
ArrayList of int[] . |
static double |
getEntropy(Constraint c)
Tries to compute the entropy of a Constraint as exact as
possible. |
static double |
getLogGammaSum(Constraint c,
double ess)
Computes the sum of the differences between the logarithmic values of the prior knowledge and all counts of a Constraint c . |
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 |
---|
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
- the ess (equivalent sample size), if the
ess is zero then MLE (maximum likelihood
estimation) otherwise MAPE (maximum a
posteriori estimation)constr
- the constraints, should be filled 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
Constraint
constr
with the
weighted absolute frequencies of the DataSet
data
.
The relative frequencies will not be computed, for this task use
computeFreqs(double, Constraint...)
alphabets
- the alphabets over which the constraints are definedlength
- the length for which the constraints are defineddata
- the DataSet
weights
- the weights for the Sequence
s in the DataSet
:
weights == null
or
weights.length = data.getNumberOfElements()
,
for all i
: weights[i] >= 0
reset
- indicates whether the constraints should be resetedconstr
- the (inhomogeneous) constraints to be filled
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
constr
.
ess
- the ess (equivalent sample size,
additional pseudocount)constr
- the constraints (can be filled with absolute frequencies)
IllegalArgumentException
- if the ess is negativeInhCondProb.drawParameters(double)
public static ArrayList<int[]> extract(int length, String encoded) throws IllegalArgumentException
String
and returns an
ArrayList
of int[]
. This can be used to create
constraints.
length
- the sequence/model lengthencoded
- constraints encoded in a String
ArrayList
of int[]
IllegalArgumentException
- if something is wrong with the length
or the
encoded String
public static double getEntropy(Constraint c)
Constraint
as exact as
possible.
c
- the constraint
public static double getLogGammaSum(Constraint c, double ess)
Constraint
c
.
c
- the constraintess
- the ess (equivalent sample size)
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 alphabet lengths for each positionindices
- the positions used in this part of the model
extract(int, String)
,
createConstraints(AbstractList, int[])
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 alphabet lengths for each position
extract(int, String)
,
createConstraints(AbstractList, int[], int[])
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