Package | Description |
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de.jstacs.sequenceScores.statisticalModels.trainable.discrete | |
de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous |
This package contains various inhomogeneous models.
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Modifier and Type | Method and Description |
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static MEMConstraint[] |
ConstraintManager.createConstraints(AbstractList<int[]> list,
int[] alphabetLength)
Creates the constraints of a model
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static MEMConstraint[] |
ConstraintManager.createConstraints(AbstractList<int[]> list,
int[] alphabetLength,
int[] indices)
Creates the constraints for a part of a model
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Modifier and Type | Field and Description |
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protected MEMConstraint[] |
MEM.constraints
The specific constraints of this MEM.
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Modifier and Type | Method and Description |
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MEMConstraint |
MEMConstraint.clone() |
Modifier and Type | Method and Description |
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void |
MEMConstraint.addParameters(int offset,
IntList list,
MEMConstraint[] constraint,
double[] params,
int[] start)
This method implements a heuristic to modify a constraint if a number of constraints should be delete.
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int |
MEMConstraint.comparePosition(int offset,
MEMConstraint constr)
This method computes the number of overlapping positions between the current and the given constraints.
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static double |
MEMTools.getExpPartOfProb(MEMConstraint[] constraints,
int[] fulfilled,
SequenceIterator sequence)
This method computes the exponential part of the probability, i.e., everything except the normalization constant.
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static void |
MEMTools.setParametersToValue(MEMConstraint[] constraint,
double val)
This method is a convenience method that sets the same value for all parameter of the constraints
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static double |
MEMTools.train(MEMConstraint[] constraints,
int[][] cond,
SequenceIterator sequence,
byte algorithm,
TerminationCondition condition,
OutputStream stream,
int[] alphLen)
This method approximates the distribution either analytically or numerically.
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Constructor and Description |
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MEMTools.DualFunction(SequenceIterator it,
MEMConstraint[] constraints)
The constructor of a dual function.
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