| 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 |
| 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 | |
| getDenominatorCount() | umms.core.model.score.WindowAllScore | |
| getDenominatorLambda() | umms.core.model.score.WindowAllScore | |
| getDenominatorRegionTotal() | umms.core.model.score.WindowAllScore | |
| getDenominatorRPKM() | umms.core.model.score.WindowAllScore | |
| getDenominatorScanPVal() | umms.core.model.score.WindowAllScore | |
| getDenominatorTotal() | umms.core.model.score.WindowAllScore | |
| getDepletionBinomialPValue() | umms.core.model.score.WindowAllScore | |
| getEnrichmentBinomialPValue() | umms.core.model.score.WindowAllScore | |
| getLog2Ratio() | umms.core.model.score.WindowAllScore | |
| getLog2RegionRatio() | umms.core.model.score.WindowAllScore | |
| getNumeratorCount() | umms.core.model.score.WindowAllScore | |
| getNumeratorLambda() | umms.core.model.score.WindowAllScore | |
| getNumeratorRegionTotal() | umms.core.model.score.WindowAllScore | |
| getNumeratorRPKM() | umms.core.model.score.WindowAllScore | |
| getNumeratorScanPVal() | umms.core.model.score.WindowAllScore | |
| getNumeratorTotal() | umms.core.model.score.WindowAllScore | |
| getPvalue() | umms.core.model.score.CountScore | |
| getRatio() | umms.core.model.score.WindowAllScore | |
| getRegionDenominatorRPKM() | umms.core.model.score.WindowAllScore | |
| getRegionNumeratorRPKM() | umms.core.model.score.WindowAllScore | |
| getRegionRatio() | umms.core.model.score.WindowAllScore | |
| getRegionTotal() | umms.core.model.score.CountScore | |
| getRPK() | umms.core.model.score.CountScore | |
| getRPKM() | umms.core.model.score.CountScore | |
| getScore() | umms.core.model.score.WindowAllScore | |
| getSkellamPValue() | umms.core.model.score.WindowAllScore | |
| getTotal() | umms.core.model.score.CountScore | |
| hashCode() | umms.core.model.score.CountScore | |
| refreshPvalue() | umms.core.model.score.CountScore | |
| RPKM_OFFSET | umms.core.model.score.WindowAllScore | static |
| setCount(double count) | umms.core.model.score.CountScore | |
| setDenominatorCount(double d) | umms.core.model.score.WindowAllScore | |
| setDenominatorRegionTotal(double d) | umms.core.model.score.WindowAllScore | |
| setDenominatorScanPVal(double pval) | umms.core.model.score.WindowAllScore | |
| setDenominatorTotal(double d) | umms.core.model.score.WindowAllScore | |
| setNumeratorCount(double d) | umms.core.model.score.WindowAllScore | |
| setNumeratorRegionTotal(double d) | umms.core.model.score.WindowAllScore | |
| setNumeratorScanPVal(double pval) | umms.core.model.score.WindowAllScore | |
| setNumeratorTotal(double d) | umms.core.model.score.WindowAllScore | |
| setRegionTotal(double regionTotal) | umms.core.model.score.CountScore | |
| setTotal(double total) | umms.core.model.score.CountScore | |
| toString() | umms.core.model.score.WindowAllScore | |
| WindowAllScore(Annotation a) | umms.core.model.score.WindowAllScore | |
| WindowAllScore(AlignmentModel numerator, AlignmentModel denominator, Annotation annotation) | umms.core.model.score.WindowAllScore | |
| WindowAllScore(AlignmentModel numerator, AlignmentModel denominator, Annotation annotation, double numeratorRegionTotal, double denominatorRegionTotal, double rapLambda, double backgroundLambda) | umms.core.model.score.WindowAllScore | |
1.8.7
