| AbstractWindowScore(Annotation t) | umms.core.model.score.WindowScore.AbstractWindowScore | |
| annotation | umms.core.model.score.WindowScore.AbstractWindowScore | protected |
| asRPKM(double count, double total, int windowSize) | umms.core.model.score.CountScore | static |
| BinomialEnrichmentScore(AlignmentModel sample, AlignmentModel ctrl, Annotation a, boolean fullyContained) | umms.core.model.score.BinomialEnrichmentScore | |
| BinomialEnrichmentScore(AlignmentModel sample, AlignmentModel ctrl, Annotation a, double regionLength, boolean fullyContained) | umms.core.model.score.BinomialEnrichmentScore | |
| BinomialEnrichmentScore(AlignmentModel sample, AlignmentModel ctrl, Annotation a, double regionLength) | umms.core.model.score.BinomialEnrichmentScore | |
| BinomialEnrichmentScore(AlignmentModel sample, Annotation a) | umms.core.model.score.BinomialEnrichmentScore | |
| BinomialEnrichmentScore(AlignmentModel sample, AlignmentModel ctrl, Annotation a) | umms.core.model.score.BinomialEnrichmentScore | |
| BinomialEnrichmentScore(AlignmentModel sample, AlignmentModel ctrl, Annotation a, double sampleRegCount, double ctrlRegCount) | umms.core.model.score.BinomialEnrichmentScore | |
| BinomialEnrichmentScore(AlignmentModel sample, AlignmentModel ctrl, Annotation a, double sampleRegCount, double ctrlRegCount, boolean fullyContained) | umms.core.model.score.BinomialEnrichmentScore | |
| BinomialEnrichmentScore(AlignmentModel sample, AlignmentModel ctrl, Annotation annotation, BinomialEnrichmentScore previousScore, double newSampleCount, double newCtrlCount) | umms.core.model.score.BinomialEnrichmentScore | |
| BinomialEnrichmentScore(MultiScore other) | umms.core.model.score.BinomialEnrichmentScore | |
| calculatePVal(double a, double b, double sampleRegionCounts, double ctrlRegionCounts) | umms.core.model.score.BinomialEnrichmentScore | |
| calculatePVal(double a, double b, double sampleRegionCounts, double ctrlRegionCounts, double regionLength, double windowSize) | umms.core.model.score.BinomialEnrichmentScore | |
| compareTo(CountScore o) | umms.core.model.score.CountScore | |
| CountScore(Annotation a) | umms.core.model.score.CountScore | |
| CountScore(CountScore other) | umms.core.model.score.CountScore | |
| CountScore(CountScore other, Annotation newAnnotation, double newCount) | umms.core.model.score.CountScore | |
| CountScore(AnnotationCollection<?extends Annotation > model, Annotation annotation) | umms.core.model.score.CountScore | |
| CountScore(AnnotationCollection<?extends Annotation > model, Annotation annotation, double regionTotal) | umms.core.model.score.CountScore | |
| CountScore(AnnotationCollection<?extends Annotation > model, Annotation annotation, boolean fullyContained) | umms.core.model.score.CountScore | |
| CountScore(AnnotationCollection<?extends Annotation > model, Annotation annotation, double regionTotal, boolean fullyContained) | umms.core.model.score.CountScore | |
| CountScore(Annotation annotation, double count, double regionTotal, double total) | umms.core.model.score.CountScore | |
| DEFAULT_REGION_TOTAL | umms.core.model.score.CountScore | static |
| equals(Object o) | umms.core.model.score.CountScore | |
| getAnnotation() | umms.core.model.score.WindowScore.AbstractWindowScore | |
| getCount() | umms.core.model.score.CountScore | |
| getCtrlCount() | umms.core.model.score.BinomialEnrichmentScore | |
| getCtrlRegionCount() | umms.core.model.score.BinomialEnrichmentScore | |
| getEnrichmentOverControl() | umms.core.model.score.BinomialEnrichmentScore | |
| getPvalue() | umms.core.model.score.BinomialEnrichmentScore | |
| getRegionLength() | umms.core.model.score.BinomialEnrichmentScore | |
| getRegionTotal() | umms.core.model.score.CountScore | |
| getRPK() | umms.core.model.score.CountScore | |
| getRPKM() | umms.core.model.score.CountScore | |
| getSampleCount() | umms.core.model.score.BinomialEnrichmentScore | |
| getSampleRegionCount() | umms.core.model.score.BinomialEnrichmentScore | |
| getScore() | umms.core.model.score.CountScore | |
| getTotal() | umms.core.model.score.CountScore | |
| hashCode() | umms.core.model.score.CountScore | |
| refreshPvalue() | umms.core.model.score.BinomialEnrichmentScore | |
| setCount(double count) | umms.core.model.score.CountScore | |
| setCtrlCount(double d) | umms.core.model.score.BinomialEnrichmentScore | |
| setCtrlRegionCount(double d) | umms.core.model.score.BinomialEnrichmentScore | |
| setPvalue(double scanPvalue) | umms.core.model.score.BinomialEnrichmentScore | |
| setRegionLength(double d) | umms.core.model.score.BinomialEnrichmentScore | |
| setRegionTotal(double regionTotal) | umms.core.model.score.CountScore | |
| setSampleCount(double d) | umms.core.model.score.BinomialEnrichmentScore | |
| setSampleRegionCount(double d) | umms.core.model.score.BinomialEnrichmentScore | |
| setTotal(double total) | umms.core.model.score.CountScore | |
| toString() | umms.core.model.score.CountScore | |
1.8.7
