| 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.ScanStatisticScore | |
| getAnnotation() | umms.core.model.score.WindowScore.AbstractWindowScore | |
| getAverageCoverage(AlignmentModel data) | umms.core.model.score.ScanStatisticScore | |
| getCoordinateSpace() | umms.core.model.score.ScanStatisticScore | |
| getCount() | umms.core.model.score.CountScore | |
| getDebugInfo(String prefix) | umms.core.model.score.ScanStatisticScore | |
| getEnrichment(AlignmentModel data) | umms.core.model.score.ScanStatisticScore | |
| getFullyContainedNumberOfReads() | umms.core.model.score.ScanStatisticScore | |
| getGlobalLambda() | umms.core.model.score.ScanStatisticScore | |
| getGlobalLength() | umms.core.model.score.ScanStatisticScore | |
| getLocalLambda() | umms.core.model.score.ScanStatisticScore | |
| getPvalue() | umms.core.model.score.ScanStatisticScore | |
| getRegionLength() | umms.core.model.score.ScanStatisticScore | |
| getRegionTotal() | umms.core.model.score.CountScore | |
| getRPK() | umms.core.model.score.CountScore | |
| getRPKM() | umms.core.model.score.CountScore | |
| getScanPvalue() | umms.core.model.score.ScanStatisticScore | |
| getScore() | umms.core.model.score.CountScore | |
| getScores() | umms.core.model.score.ScanStatisticScore | |
| getTotal() | umms.core.model.score.CountScore | |
| hashCode() | umms.core.model.score.CountScore | |
| refreshPvalue() | umms.core.model.score.CountScore | |
| refreshScanPvalue(AlignmentModel model) | umms.core.model.score.ScanStatisticScore | |
| ScanStatisticScore(AlignmentModel model, Annotation annotation) | umms.core.model.score.ScanStatisticScore | |
| ScanStatisticScore(AlignmentModel model, Annotation annotation, boolean fullyContained) | umms.core.model.score.ScanStatisticScore | |
| ScanStatisticScore(AlignmentModel model, Annotation annotation, ScanStatisticScore previousScore, double newScore) | umms.core.model.score.ScanStatisticScore | |
| ScanStatisticScore(MultiScore other) | umms.core.model.score.ScanStatisticScore | |
| ScanStatisticScore(AlignmentModel model, Annotation annotation, double regionTotal, double regionLength) | umms.core.model.score.ScanStatisticScore | |
| ScanStatisticScore(AlignmentModel model, Annotation annotation, double regionTotal, double regionLength, boolean fullyContained) | umms.core.model.score.ScanStatisticScore | |
| ScanStatisticScore(AlignmentModel model, Annotation annotation, double regionTotal, double regionLength, double globalTotal, double globalLength, boolean fullyContained) | umms.core.model.score.ScanStatisticScore | |
| setCount(double count) | umms.core.model.score.CountScore | |
| setFullyContainedNumberOfReads(double fullyContainedNumberOfReads) | umms.core.model.score.ScanStatisticScore | |
| setGlobalLength(double d) | umms.core.model.score.ScanStatisticScore | |
| setPvalue(double scanPvalue) | umms.core.model.score.ScanStatisticScore | |
| setRegionLength(double regionLength) | umms.core.model.score.ScanStatisticScore | |
| setRegionTotal(double regionTotal) | umms.core.model.score.CountScore | |
| setScanPvalue(double scanPvalue) | umms.core.model.score.ScanStatisticScore | |
| setTotal(double total) | umms.core.model.score.CountScore | |
| toString() | umms.core.model.score.ScanStatisticScore | |
1.8.7
