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

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

Classes
class	Processor

Public Member Functions
	MultiScore (AlignmentModel sample, AlignmentModel ctrl, Annotation a, double regionLength, boolean fullyContained)

	MultiScore (AlignmentModel sample, AlignmentModel ctrl, Annotation a, boolean fullyContained)

	MultiScore (AlignmentModel sample, AlignmentModel ctrl, Annotation a, double regionLength)

	MultiScore (AlignmentModel sample, AlignmentModel ctrl, Annotation a)

	MultiScore (AlignmentModel sample, AlignmentModel ctrl, Annotation a, Gene gene, boolean fullyContained)

	MultiScore (AlignmentModel sample, AlignmentModel ctrl, Annotation a, Gene gene)

	MultiScore (AlignmentModel sample, Annotation a, boolean fullyContained)

	MultiScore (AlignmentModel sample, AlignmentModel ctrl, Annotation a, double sampleRegCount, double ctrlRegCount)

	MultiScore (AlignmentModel sample, AlignmentModel ctrl, Annotation a, double sampleRegCount, double ctrlRegCount, double regionLength)

	MultiScore (AlignmentModel sample, AlignmentModel ctrl, Annotation a, double sampleRegCount, double ctrlRegCount, double regionLength, boolean fullyContained)

	MultiScore (AlignmentModel sample, AlignmentModel ctrl, Annotation annotation, MultiScore previousScore, double newSampleCount, double newCtrlCount)

void	updateScores ()

void	updateScores (String scoreName)

double	getEnrichmentOverControl ()

double	getAverageCoverage (AlignmentModel model)

void	getDebugInfo (String prefix)

double	getPvalue (String scoreName)

void	setSampleCount (double d)

void	setCtrlCount (double d)

void	setSampleRegionCount (double d)

void	setCtrlRegionCount (double d)

double	getSampleCount ()

double	getCtrlCount ()

double	getCtrlRegionCount ()

double	getSampleRegionCount ()

void	setRegionLength (double d)

double	getRegionLength ()

void	setGene (Gene g)

Gene	getGene ()

CoordinateSpace	getSampleCoordSpace ()

void	setSampleCoordSpace (CoordinateSpace sampleCoordSpace)

CoordinateSpace	getCtrlCoordSpace ()

void	setCtrlCoordSpace (CoordinateSpace sampleCoordSpace)

double	getGlobalLength ()

double	getGlobalLambda ()

Public Member Functions inherited from umms.core.model.score.CountScore
	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 ()

Protected Attributes
AlignmentModel	sampleModel

AlignmentModel	ctrlModel

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

Additional Inherited Members
Static Public Member Functions inherited from umms.core.model.score.CountScore
static double	asRPKM (double count, double total, int windowSize)

Static Public Attributes inherited from umms.core.model.score.CountScore
static double	DEFAULT_REGION_TOTAL = -1.0

Detailed Description

Author: shari Stores scores from multiple tests To use additional scores, add score class to scores hash p-values are stored in the other score classes included here "Region" refers to an arbitrary region being scanned, like a gene, or a chromosome, or some subset of the whole coordinate space

Constructor & Destructor Documentation

umms.core.model.score.MultiScore.MultiScore	(	AlignmentModel	sample,
		AlignmentModel	ctrl,
		Annotation	a,
		double	regionLength,
		boolean	fullyContained
	)

Constructs score without region/gene info

Parameters

sample	sample alignment data
ctrl	control alignment data
a	annotation window/gene/etc being scored
regionLength	length of gene
fullyContained	only count reads fully contained in window

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umms.core.model.score.MultiScore.MultiScore	(	AlignmentModel	sample,
		AlignmentModel	ctrl,
		Annotation	a,
		boolean	fullyContained
	)

umms.core.model.score.MultiScore.MultiScore	(	AlignmentModel	sample,
		AlignmentModel	ctrl,
		Annotation	a,
		double	regionLength
	)

umms.core.model.score.MultiScore.MultiScore	(	AlignmentModel	sample,
		AlignmentModel	ctrl,
		Annotation	a
	)

umms.core.model.score.MultiScore.MultiScore	(	AlignmentModel	sample,
		AlignmentModel	ctrl,
		Annotation	a,
		Gene	gene,
		boolean	fullyContained
	)

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umms.core.model.score.MultiScore.MultiScore	(	AlignmentModel	sample,
		AlignmentModel	ctrl,
		Annotation	a,
		Gene	gene
	)

umms.core.model.score.MultiScore.MultiScore	(	AlignmentModel	sample,
		Annotation	a,
		boolean	fullyContained
	)

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umms.core.model.score.MultiScore.MultiScore	(	AlignmentModel	sample,
		AlignmentModel	ctrl,
		Annotation	a,
		double	sampleRegCount,
		double	ctrlRegCount
	)

umms.core.model.score.MultiScore.MultiScore	(	AlignmentModel	sample,
		AlignmentModel	ctrl,
		Annotation	a,
		double	sampleRegCount,
		double	ctrlRegCount,
		double	regionLength
	)

umms.core.model.score.MultiScore.MultiScore	(	AlignmentModel	sample,
		AlignmentModel	ctrl,
		Annotation	a,
		double	sampleRegCount,
		double	ctrlRegCount,
		double	regionLength,
		boolean	fullyContained
	)

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umms.core.model.score.MultiScore.MultiScore	(	AlignmentModel	sample,
		AlignmentModel	ctrl,
		Annotation	annotation,
		MultiScore	previousScore,
		double	newSampleCount,
		double	newCtrlCount
	)

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Member Function Documentation

double umms.core.model.score.MultiScore.getAverageCoverage ( AlignmentModel model )

CoordinateSpace umms.core.model.score.MultiScore.getCtrlCoordSpace ( )

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double umms.core.model.score.MultiScore.getCtrlCount ( )

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double umms.core.model.score.MultiScore.getCtrlRegionCount ( )

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void umms.core.model.score.MultiScore.getDebugInfo ( String prefix )

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double umms.core.model.score.MultiScore.getEnrichmentOverControl ( )

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Gene umms.core.model.score.MultiScore.getGene ( )

double umms.core.model.score.MultiScore.getGlobalLambda ( )

double umms.core.model.score.MultiScore.getGlobalLength ( )

double umms.core.model.score.MultiScore.getPvalue ( String scoreName )

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double umms.core.model.score.MultiScore.getRegionLength ( )

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CoordinateSpace umms.core.model.score.MultiScore.getSampleCoordSpace ( )

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double umms.core.model.score.MultiScore.getSampleCount ( )

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double umms.core.model.score.MultiScore.getSampleRegionCount ( )

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void umms.core.model.score.MultiScore.setCtrlCoordSpace ( CoordinateSpace sampleCoordSpace )

void umms.core.model.score.MultiScore.setCtrlCount ( double d )

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void umms.core.model.score.MultiScore.setCtrlRegionCount ( double d )

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void umms.core.model.score.MultiScore.setGene ( Gene g )

void umms.core.model.score.MultiScore.setRegionLength ( double d )

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void umms.core.model.score.MultiScore.setSampleCoordSpace ( CoordinateSpace sampleCoordSpace )

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void umms.core.model.score.MultiScore.setSampleCount ( double d )

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void umms.core.model.score.MultiScore.setSampleRegionCount ( double d )

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void umms.core.model.score.MultiScore.updateScores ( )

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void umms.core.model.score.MultiScore.updateScores ( String scoreName )

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Member Data Documentation

AlignmentModel umms.core.model.score.MultiScore.ctrlModel

protected

AlignmentModel umms.core.model.score.MultiScore.sampleModel

protected

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

java/umms/core/model/score/MultiScore.java

Classes

Public Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation