public class OccurrenceKSScorer extends GroupScorer
Scorer.ScoreSoftValueHashMap
Modifier and Type | Field and Description |
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protected CombinedScorer |
scorer |
groupMF, separateMotifFinders
lookupCount, mf, motifScoreCache2, usePrior
Constructor and Description |
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OccurrenceKSScorer(MotifFinder genomicFinder,
MotifFinder groupFinder,
boolean discardOverlaps)
Sets the scores, and takes the motif finders from s1.
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Modifier and Type | Method and Description |
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double |
calculateScore(Motif m)
Returns the some of the scores from s1 and s2, minus the prior.
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double |
calculateScore(MotifList ml)
Returns the some of the scores from s1 and s2, minus the prior.
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void |
setMotifFinder(MotifFinder newMF)
Calls setMotifFinder on all the scorers, including this one.
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void |
setSeparateMotifFinders(boolean b)
If true, will cause the background probabilities to be computed from both the genomic mf and the groupMF.
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void |
setUsePrior(boolean b)
Sets whether or not Bayesian priors are used.
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computePhi, computePhi, computePhi, getGenomicMotifFinder, getGroupCount, getGroupSize, getMotifFinder, setDiscardOverlaps
baseEntropy, computePrior, computePrior, getDiscardOverlaps, getLookupCount, getUsePrior, setScore, setScore, setScores, setScores
protected CombinedScorer scorer
public OccurrenceKSScorer(MotifFinder genomicFinder, MotifFinder groupFinder, boolean discardOverlaps)
public double calculateScore(Motif m)
calculateScore
in class Scorer
public double calculateScore(MotifList ml)
calculateScore
in class Scorer
public void setMotifFinder(MotifFinder newMF)
setMotifFinder
in class GroupScorer
public void setSeparateMotifFinders(boolean b)
GroupScorer
setSeparateMotifFinders
in class GroupScorer
public void setUsePrior(boolean b)
Scorer
setUsePrior
in class Scorer