public class MarkovMaxOrderScorer extends Scorer
E(M) = [N(m_1m_2m_3...m_n-1)*N(m_2m_3m_4...m_n)] / N(m_2m_3...m_n-1) Where N(M) counts the number of times M occurs.A LAPLACE correction of 1 is added to guard against zero counts.
Scorer.ScoreSoftValueHashMap
Modifier and Type | Field and Description |
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static int |
LAPLACE
The a pseuodo count that is added to all counts in the ratio calculations.
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lookupCount, mf, motifScoreCache2, usePrior
Constructor and Description |
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MarkovMaxOrderScorer(MotifFinder finder,
boolean discardOverlaps)
Sets the motif finder to be hte denominatorFinder and the group motif finder to be the numeratorFinder and tells them whether or not to
discard overlaps.
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Modifier and Type | Method and Description |
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double |
calculateScore(Motif m)
Returns the score of m and increments the lookupCount.
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double |
calculateScore(MotifList ml)
Not implemented.
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baseEntropy, computePhi, computePhi, computePhi, computePrior, computePrior, getDiscardOverlaps, getLookupCount, getMotifFinder, getUsePrior, setDiscardOverlaps, setMotifFinder, setScore, setScore, setScores, setScores, setUsePrior
public static final int LAPLACE
public MarkovMaxOrderScorer(MotifFinder finder, boolean discardOverlaps)
public double calculateScore(Motif m)
Scorer
calculateScore
in class Scorer
public double calculateScore(MotifList ml)
calculateScore
in class Scorer
java.lang.IllegalArgumentException
- because this method has not been implemented.