public class ConservationRatioScorer extends Scorer
Scorer.ScoreSoftValueHashMap
Modifier and Type | Field and Description |
---|---|
protected int |
HD
The hamming space around which to expand each motif.
|
static int |
WOC
The wildcard optimization cutoff used for the motif finders.
|
lookupCount, mf, motifScoreCache2, usePrior
Constructor and Description |
---|
ConservationRatioScorer(MotifFinder finder,
boolean discardOverlaps,
int hammingDistance)
Sets the motif finder and discardOverlaps parameters of the motif finder appropriately; hammingDistance determines the space into which
we will expand each motif.
|
Modifier and Type | Method and Description |
---|---|
double |
calculateScore(Motif m)
The conservation of this motif as measured by the ratio of the number of occurrences of m to the the number of occurrences of m and all
it's
HD neighbors. |
double |
calculateScore(MotifList ml)
This method has not been implemented.
|
baseEntropy, computePhi, computePhi, computePhi, computePrior, computePrior, getDiscardOverlaps, getLookupCount, getMotifFinder, getUsePrior, setDiscardOverlaps, setMotifFinder, setScore, setScore, setScores, setScores, setUsePrior
public static final int WOC
protected int HD
public ConservationRatioScorer(MotifFinder finder, boolean discardOverlaps, int hammingDistance)
public double calculateScore(Motif m)
HD
neighbors.calculateScore
in class Scorer
public double calculateScore(MotifList ml)
calculateScore
in class Scorer
java.lang.IllegalArgumentException
- since this method has not been implemented.