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

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

Classes
class	Processor

Public Member Functions
	ScanStatisticScore (AlignmentModel model, Annotation annotation)

	ScanStatisticScore (AlignmentModel model, Annotation annotation, boolean fullyContained)

	ScanStatisticScore (AlignmentModel model, Annotation annotation, ScanStatisticScore previousScore, double newScore)

	ScanStatisticScore (MultiScore other)

	ScanStatisticScore (AlignmentModel model, Annotation annotation, double regionTotal, double regionLength)

	ScanStatisticScore (AlignmentModel model, Annotation annotation, double regionTotal, double regionLength, boolean fullyContained)

	ScanStatisticScore (AlignmentModel model, Annotation annotation, double regionTotal, double regionLength, double globalTotal, double globalLength, boolean fullyContained)

CoordinateSpace	getCoordinateSpace ()

void	refreshScanPvalue (AlignmentModel model)

double	getAverageCoverage (AlignmentModel data)

double	getEnrichment (AlignmentModel data)

double	getLocalLambda ()

void	setGlobalLength (double d)

double	getGlobalLambda ()

double	getGlobalLength ()

void	setRegionLength (double regionLength)

double	getRegionLength ()

void	setScanPvalue (double scanPvalue)

void	setPvalue (double scanPvalue)

double	getScanPvalue ()

double	getPvalue ()

void	setFullyContainedNumberOfReads (double fullyContainedNumberOfReads)

double	getFullyContainedNumberOfReads ()

double[]	getScores ()

void	getDebugInfo (String prefix)

String	toString ()

boolean	equals (Object o)

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 ()

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

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

Constructor & Destructor Documentation

umms.core.model.score.ScanStatisticScore.ScanStatisticScore	(	AlignmentModel	model,
		Annotation	annotation
	)

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umms.core.model.score.ScanStatisticScore.ScanStatisticScore	(	AlignmentModel	model,
		Annotation	annotation,
		boolean	fullyContained
	)

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umms.core.model.score.ScanStatisticScore.ScanStatisticScore	(	AlignmentModel	model,
		Annotation	annotation,
		ScanStatisticScore	previousScore,
		double	newScore
	)

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umms.core.model.score.ScanStatisticScore.ScanStatisticScore ( MultiScore other )

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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
	)

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umms.core.model.score.ScanStatisticScore.ScanStatisticScore	(	AlignmentModel	model,
		Annotation	annotation,
		double	regionTotal,
		double	regionLength,
		double	globalTotal,
		double	globalLength,
		boolean	fullyContained
	)

Control region length and total, global length and total Scan P value depends on global stats

Parameters

model	Alignment data
annotation	Annotation
regionTotal	Total number of fragments mapping to local region
regionLength	Total length of local region
globalTotal	Global number of fragments
globalLength	Global length

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Member Function Documentation

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

True iff scan P value and annotation are equal

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double umms.core.model.score.ScanStatisticScore.getAverageCoverage ( AlignmentModel data )

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CoordinateSpace umms.core.model.score.ScanStatisticScore.getCoordinateSpace ( )

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

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double umms.core.model.score.ScanStatisticScore.getEnrichment ( AlignmentModel data )

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double umms.core.model.score.ScanStatisticScore.getFullyContainedNumberOfReads ( )

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

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

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double umms.core.model.score.ScanStatisticScore.getLocalLambda ( )

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

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

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double umms.core.model.score.ScanStatisticScore.getScanPvalue ( )

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double [] umms.core.model.score.ScanStatisticScore.getScores ( )

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void umms.core.model.score.ScanStatisticScore.refreshScanPvalue ( AlignmentModel model )

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void umms.core.model.score.ScanStatisticScore.setFullyContainedNumberOfReads ( double fullyContainedNumberOfReads )

void umms.core.model.score.ScanStatisticScore.setGlobalLength ( double d )

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void umms.core.model.score.ScanStatisticScore.setPvalue ( double scanPvalue )

void umms.core.model.score.ScanStatisticScore.setRegionLength ( double regionLength )

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void umms.core.model.score.ScanStatisticScore.setScanPvalue ( double scanPvalue )

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String umms.core.model.score.ScanStatisticScore.toString ( )

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

java/umms/core/model/score/ScanStatisticScore.java

Classes

Public Member Functions

Additional Inherited Members

Constructor & Destructor Documentation

Member Function Documentation