public abstract class GroupScorer extends Scorer
public double calculateScore(Motif m) public double calculateScore(MotifList ml)
Scorer.ScoreSoftValueHashMap
Modifier and Type | Field and Description |
---|---|
protected MotifFinder |
groupMF |
protected boolean |
separateMotifFinders |
lookupCount, mf, motifScoreCache2, usePrior
Modifier | Constructor and Description |
---|---|
protected |
GroupScorer(MotifFinder finder,
MotifFinder groupFinder,
boolean discardOverlaps,
int wildcardOptimizationCutoff)
Sets the motif finder and group motif finder and tells them whether or not to discard overlaps and what wildcard optimization cutoff to
use.
|
Modifier and Type | Method and Description |
---|---|
double |
computePhi(MotifList m1,
MotifList m2)
Calculates a phi score for a pair of motifs.
|
double |
computePhi(Motif m1,
Motif m2)
Calculates a phi score for a pair of motifs.
|
double |
computePhi(Motif m1,
MotifList m2)
Calculates a phi score for a pair of motifs.
|
MotifFinder |
getGenomicMotifFinder()
Returns the genomic MotifFinder.
|
int |
getGroupCount(Motif m)
Changed 6/10/04: Now returns the number of distinct genes m occurs in the group.
|
int |
getGroupSize()
Returns the number of genes in the group
|
MotifFinder |
getMotifFinder()
Overrides Scorer's method to return the groupMF instead of the genomic MF.
|
void |
setDiscardOverlaps(boolean b)
Sets the discard overlaps variable appropriately for the internal motif finders.
|
void |
setMotifFinder(MotifFinder mf)
Overrides Scorer's method to set the groupMF instead of the genomic MF.
|
void |
setSeparateMotifFinders(boolean b)
If true, will cause the background probabilities to be computed from both the genomic mf and the groupMF.
|
baseEntropy, calculateScore, calculateScore, computePrior, computePrior, getDiscardOverlaps, getLookupCount, getUsePrior, setScore, setScore, setScores, setScores, setUsePrior
protected MotifFinder groupMF
protected boolean separateMotifFinders
protected GroupScorer(MotifFinder finder, MotifFinder groupFinder, boolean discardOverlaps, int wildcardOptimizationCutoff)
public double computePhi(Motif m1, Motif m2)
computePhi
in class Scorer
public double computePhi(Motif m1, MotifList m2)
computePhi
in class Scorer
public double computePhi(MotifList m1, MotifList m2)
computePhi
in class Scorer
public MotifFinder getGenomicMotifFinder()
public final int getGroupCount(Motif m)
public final int getGroupSize()
public MotifFinder getMotifFinder()
getMotifFinder
in class Scorer
public void setDiscardOverlaps(boolean b)
setDiscardOverlaps
in class Scorer
public void setMotifFinder(MotifFinder mf)
setMotifFinder
in class Scorer
public void setSeparateMotifFinders(boolean b)