public class KSScorer extends Scorer
KS.computeOneSampleKS(int[], CDF)
. The data pumped into the KS is the positions relative to genes if the genes are of the
same length, or the straight hits from the motif finder otherwise.Scorer.ScoreSoftValueHashMap
Modifier and Type | Field and Description |
---|---|
protected CDF |
cdf |
protected int |
geneLength |
static int |
WOC
The Wilcard Optimization Cutoff; note that this is different from OccurrenceScorer because KSScorer must call find() on every search,
which may change the optimization.
|
lookupCount, mf, motifScoreCache2, usePrior
Constructor and Description |
---|
KSScorer(MotifFinder finder,
boolean discardOverlaps)
Sets the motif finder and discardOverlaps parameters of the motif finder appropriately and defaults the cdf for the uniform cdf with a
range [0..averageGeneLength] (if finder has uniform gene lengths) or [0..sequenceLength] (if finder has variable length genes).
|
KSScorer(MotifFinder finder,
boolean discardOverlaps,
CDF cdf)
Sets the motif finder and discardOverlaps parameters of the motif finder appropriately and sets the cdf to the given cdf.
|
Modifier and Type | Method and Description |
---|---|
protected double |
calculateScore(FindResults hits,
double prior,
double motifLength) |
protected double |
calculateScore(int[] hits,
double prior,
double motifLength)
Returns the -log likelihood that hits came from the CDF given in the constructor.
|
double |
calculateScore(Motif m)
Returns the -log probability that this motif is drawn from the CDF supplied in the constructor.
|
double |
calculateScore(MotifList ml)
Returns the -log probability that this motif is drawn from the CDF supplied in the constructor.
|
baseEntropy, computePhi, computePhi, computePhi, computePrior, computePrior, getDiscardOverlaps, getLookupCount, getMotifFinder, getUsePrior, setDiscardOverlaps, setMotifFinder, setScore, setScore, setScores, setScores, setUsePrior
public static final int WOC
protected CDF cdf
protected int geneLength
public KSScorer(MotifFinder finder, boolean discardOverlaps)
public KSScorer(MotifFinder finder, boolean discardOverlaps, CDF cdf)
protected double calculateScore(FindResults hits, double prior, double motifLength)
protected double calculateScore(int[] hits, double prior, double motifLength)
public double calculateScore(Motif m)
calculateScore
in class Scorer
CDF
,
KS.computeOneSampleKS(int[], CDF)
,
calculateScore(int[], double, double)
public double calculateScore(MotifList ml)
calculateScore
in class Scorer
CDF
,
KS.computeOneSampleKS(int[], CDF)
,
calculateScore(int[], double, double)