Inheritance diagram for umms.core.model.score.SumScore:

Collaboration diagram for umms.core.model.score.SumScore:

Public Member Functions
	SumScore (Annotation a)

	SumScore (AnnotationCollection<?extends Annotation > model, Annotation region)

double	getScore ()

Public Member Functions inherited from umms.core.model.score.AbstractListScore
	AbstractListScore (Annotation a)

void	setScores (List< Double > scores)

double	getScore ()

double	getCount ()

double	getSum ()

double	getMedian ()

double	getMean ()

double	getStandardDeviation ()

double[]	getScores ()

String	toString ()

Public Member Functions inherited from umms.core.model.score.WindowScore.AbstractWindowScore
	AbstractWindowScore (Annotation t)

Annotation	getAnnotation ()

Additional Inherited Members
Static Public Attributes inherited from umms.core.model.score.AbstractListScore
static double	DEFAULT_VALUE = -1.0

Protected Attributes inherited from umms.core.model.score.WindowScore.AbstractWindowScore
Annotation	annotation

Detailed Description

Author: engreitz This class calculates statistics (sum, average, stddev, median, etc.) on the scores of annotations in the given region, in addition to counting the number of annotations.

Constructor & Destructor Documentation

umms.core.model.score.SumScore.SumScore ( Annotation a )

umms.core.model.score.SumScore.SumScore	(	AnnotationCollection<?extends Annotation >	model,
		Annotation	region
	)

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double umms.core.model.score.SumScore.getScore ( )

Returns the number of reads overlapping this region

Returns: number of reds overlapping this window Returns the "score" as defined by each subclass (e.g. count, ratio, sum of annotation scores, etc.)

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The documentation for this class was generated from the following file: