public class AffinityEvaluator
extends java.lang.Object
Modifier and Type | Field and Description |
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private static boolean |
DEBUGGING |
private static java.lang.String |
ROC_ROOT |
Constructor and Description |
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AffinityEvaluator() |
Modifier and Type | Method and Description |
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static StatBox |
computeROC(CREModel cre,
MotifList truePositives,
MotifList trueNegatives,
boolean plotCurve,
java.lang.String source) |
private static StatBox |
computeSensSpec(MotifList matches,
MotifList truePositives,
int testSetSize)
Returns a FPFNStatBox that includes the TP FP FN and FP rates when matches is compared against the truePositives.
|
static StatBox |
getFPFNStats(CREModel cre,
MotifList truePositives,
MotifList trueNegatives,
int numToEval) |
static StatBox |
getLinCorStats(CREModel cre,
MotifList testSet) |
static double |
getOverlap(CREModel cre,
MotifList truePositives,
MotifList trueNegatives)
Essentially computes the phi score between the scores of the truePositives and teh true negatives.
|
static StatBox |
getOverlapStats(CREModel cre,
MotifList truePositives,
MotifList trueNegatives) |
static StatBox |
getRankLinCorStats(CREModel cre,
MotifList testSet) |
static java.util.HashSet<Motif> |
motifListToHashSet(MotifList ml)
Creates a new HashSet consisting of each motif in ml.
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private static java.lang.String |
motifListToString(MotifList ml)
Returns a string of the form m1#m2#...mN#, where mi is the sequence of the ith motif in the given MotifList.
|
static void |
plotROC(CREModel cre,
Motif[] posArr,
Motif[] negArr,
java.lang.String source) |
private static int |
sequenceSearch(Motif[] arr,
Motif m)
Returns the rank of m in arr, assuming arr is already sorted.
|
static MotifList |
setToMotifList(java.util.Set<Motif> set)
Returns a MotifList backed by the given set of Motifs.
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private static MotifList |
subMotifList(MotifList ml,
int start,
int stop)
Returns a new motif list that is the given motif list in the ranges [start ..
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private static final boolean DEBUGGING
private static java.lang.String ROC_ROOT
public static StatBox computeROC(CREModel cre, MotifList truePositives, MotifList trueNegatives, boolean plotCurve, java.lang.String source)
private static StatBox computeSensSpec(MotifList matches, MotifList truePositives, int testSetSize)
public static StatBox getFPFNStats(CREModel cre, MotifList truePositives, MotifList trueNegatives, int numToEval)
public static double getOverlap(CREModel cre, MotifList truePositives, MotifList trueNegatives)
public static StatBox getOverlapStats(CREModel cre, MotifList truePositives, MotifList trueNegatives)
public static java.util.HashSet<Motif> motifListToHashSet(MotifList ml)
private static java.lang.String motifListToString(MotifList ml)
public static void plotROC(CREModel cre, Motif[] posArr, Motif[] negArr, java.lang.String source)
private static int sequenceSearch(Motif[] arr, Motif m)
public static MotifList setToMotifList(java.util.Set<Motif> set)