public class CoverageScorer extends GroupScorer
Scorer.ScoreSoftValueHashMap
groupMF, separateMotifFinders
lookupCount, mf, motifScoreCache2, usePrior
Constructor and Description |
---|
CoverageScorer(MotifFinder genomicFinder,
MotifFinder groupFinder,
boolean discardOverlaps)
Sets the motif finder and group motif finder and tells them whether or not to discard overlaps.
|
Modifier and Type | Method and Description |
---|---|
protected double |
calculateScore(int groupCount,
int totalCount,
double prior)
Computes the score based on the groupCount, total count and a prior to use.
|
double |
calculateScore(Motif m)
Returns the score of m.
|
double |
calculateScore(MotifList ml)
Calculates the score of ml using the sum of the group counts and total counts of all motifs in ml and using the average prior and motif
length.
|
computePhi, computePhi, computePhi, getGenomicMotifFinder, getGroupCount, getGroupSize, getMotifFinder, setDiscardOverlaps, setMotifFinder, setSeparateMotifFinders
baseEntropy, computePrior, computePrior, getDiscardOverlaps, getLookupCount, getUsePrior, setScore, setScore, setScores, setScores, setUsePrior
public CoverageScorer(MotifFinder genomicFinder, MotifFinder groupFinder, boolean discardOverlaps)
protected double calculateScore(int groupCount, int totalCount, double prior)
public double calculateScore(Motif m)
calculateScore
in class Scorer
public double calculateScore(MotifList ml)
calculateScore
in class Scorer