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

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

Classes
class	Processor

Public Member Functions
	BasicScanStatisticScore (AlignmentModel model, Annotation annotation, double score, boolean global, double regionLength, double regionScore)

	BasicScanStatisticScore (AlignmentModel model, Annotation annotation, double regionTotal, double regionLength2, boolean fullyContainedReads)

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

double	calculateGlobalPvalue (AlignmentModel model)

double	calculateLocalPvalue ()

double	getAverageCoverage ()

double	getWindowLength ()

void	setWindowLength (double length)

double	getGlobalEnrichment ()

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 ()

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.BasicScanStatisticScore.BasicScanStatisticScore	(	AlignmentModel	model,
		Annotation	annotation,
		double	score,
		boolean	global,
		double	regionLength,
		double	regionScore
	)

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umms.core.model.score.BasicScanStatisticScore.BasicScanStatisticScore	(	AlignmentModel	model,
		Annotation	annotation,
		double	regionTotal,
		double	regionLength2,
		boolean	fullyContainedReads
	)

BAD constructor

Parameters

model
annotation
regionTotal
regionLength2
fullyContainedReads

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

BAD CONSTRUCTOR

Parameters

model
annotation
previousScore
newScore

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Member Function Documentation

double umms.core.model.score.BasicScanStatisticScore.calculateGlobalPvalue ( AlignmentModel model )

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double umms.core.model.score.BasicScanStatisticScore.calculateLocalPvalue ( )

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

True iff scan P value and annotation are equal

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double umms.core.model.score.BasicScanStatisticScore.getAverageCoverage ( )

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

double umms.core.model.score.BasicScanStatisticScore.getGlobalEnrichment ( )

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

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

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

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

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

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

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

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double umms.core.model.score.BasicScanStatisticScore.getWindowLength ( )

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

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

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

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

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

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void umms.core.model.score.BasicScanStatisticScore.setWindowLength ( double length )

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

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

java/umms/core/model/score/BasicScanStatisticScore.java

Classes

Public Member Functions

Additional Inherited Members

Constructor & Destructor Documentation

Member Function Documentation