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

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

Classes
class	Factory

class	Processor

Public Member Functions
	CountScore (Annotation a)

	CountScore (CountScore other)

	CountScore (CountScore other, Annotation newAnnotation, double newCount)

	CountScore (AnnotationCollection<?extends Annotation > model, Annotation annotation)

	CountScore (AnnotationCollection<?extends Annotation > model, Annotation annotation, double regionTotal)

	CountScore (AnnotationCollection<?extends Annotation > model, Annotation annotation, boolean fullyContained)

	CountScore (AnnotationCollection<?extends Annotation > model, Annotation annotation, double regionTotal, boolean fullyContained)

	CountScore (Annotation annotation, double count, double regionTotal, double total)

double	getCount ()

double	getScore ()

double	getTotal ()

double	getRegionTotal ()

double	getRPKM ()

double	getRPK ()

void	setCount (double count)

void	setTotal (double total)

void	setRegionTotal (double regionTotal)

String	toString ()

boolean	equals (Object o)

int	compareTo (CountScore o)

int	hashCode ()

void	refreshPvalue ()

double	getPvalue ()

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

Annotation	getAnnotation ()

Static Public Member Functions
static double	asRPKM (double count, double total, int windowSize)

Static Public Attributes
static double	DEFAULT_REGION_TOTAL = -1.0

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

Detailed Description

Author: engreitz This class represents a simple count scoring function for the DataAlignmentModel.

Constructor & Destructor Documentation

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

umms.core.model.score.CountScore.CountScore ( CountScore other )

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umms.core.model.score.CountScore.CountScore	(	CountScore	other,
		Annotation	newAnnotation,
		double	newCount
	)

umms.core.model.score.CountScore.CountScore	(	AnnotationCollection<?extends Annotation >	model,
		Annotation	annotation
	)

Parameters

model	Alignment data
annotation	Region

umms.core.model.score.CountScore.CountScore	(	AnnotationCollection<?extends Annotation >	model,
		Annotation	annotation,
		double	regionTotal
	)

Parameters

model	Alignment data
annotation	Region
regionTotal	Override region total

umms.core.model.score.CountScore.CountScore	(	AnnotationCollection<?extends Annotation >	model,
		Annotation	annotation,
		boolean	fullyContained
	)

Parameters

model	Alignment data
annotation	Region
fullyContained	Only count fully contained reads

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umms.core.model.score.CountScore.CountScore	(	AnnotationCollection<?extends Annotation >	model,
		Annotation	annotation,
		double	regionTotal,
		boolean	fullyContained
	)

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umms.core.model.score.CountScore.CountScore	(	Annotation	annotation,
		double	count,
		double	regionTotal,
		double	total
	)

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Member Function Documentation

static double umms.core.model.score.CountScore.asRPKM	(	double	count,
		double	total,
		int	windowSize
	)

static

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int umms.core.model.score.CountScore.compareTo ( CountScore o )

First compare counts Then compare annotations

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boolean umms.core.model.score.CountScore.equals ( Object o )

True iff count and annotation are equal

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double umms.core.model.score.CountScore.getCount ( )

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double umms.core.model.score.CountScore.getPvalue ( )

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double umms.core.model.score.CountScore.getRegionTotal ( )

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double umms.core.model.score.CountScore.getRPK ( )

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double umms.core.model.score.CountScore.getRPKM ( )

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double umms.core.model.score.CountScore.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.)

Implements umms.core.model.score.WindowScore.

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