broad.pda.seq.segmentation.AlignmentDataModel Interface Reference

Inheritance diagram for broad.pda.seq.segmentation.AlignmentDataModel:

Public Member Functions
CloseableIterator< Alignment >	getAnnotationOverlappingRegion (Annotation align) throws IOException
Map< String, Integer >	getChromosomeLengths ()
int	getChromosomeLength (String chr)
double	getCounts (String chr) throws IOException
double	getCountsPerAlignment (Annotation first, int EF) throws IOException
double	getCountsPerAlignment (Annotation align, IntervalTree< Alignment > tree, int EF)
double	getCountsPerAlignment (Gene gene, IntervalTree< Alignment > tree, int EF)
double	getCountsPerAnnotationtranded (Gene gene, IntervalTree< Alignment > tree, int EF, String orientation)
double	getCountsPerAlignment (Annotation[] Annotation, IntervalTree< Alignment > tree, int EF)
double	getCountsPerAlignmentFullyContained (Gene gene, IntervalTree< Alignment > tree, int EF)
double	getCountsPerAlignment (Annotation[] Annotation, int EF) throws IOException
double	getCountsPerAlignment (Annotation align, Map< String, IntervalTree< Annotation >> goodExonTree, IntervalTree< Alignment > tree, int extensionFactor)
int	getCountsWithinExons (Annotation align, Iterator< Alignment > iter, int EF)
int	getCountsWithinExons (Annotation align, IntervalTree< Alignment > tree, int EF)
double	getCountsOfUniqueOverlappers (Annotation target, Annotation exclude, IntervalTree< Alignment > tree, int EF)
double	getCountsOfUniqueOverlappers (Annotation target, Gene exclude, IntervalTree< Alignment > tree, int EF)
double	getCountsOnBase (String chr, int index) throws IOException
int	getBasesCovered (Annotation record, int EF) throws IOException
double	getNumberOfSplicedReads (Annotation align) throws IOException
GeneCounts	getGeneCounts (Gene gene, int extensionFactor) throws IOException
double	getBasesCoveredPerAlignment (Gene gene, IntervalTree< Alignment > tree, int EF)
Iterator< Annotation >	getExonAnnotationOverlappingRegion (Annotation align) throws IOException
Gene	getPeak (Gene gene, Gene startCodon, IntervalTree< Alignment > tree, int EF)
Collection< Annotation >	getOverlappingRegions (String chr) throws IOException
IntervalTree< Alignment >	getIntervalTree (String chr, int start, int end) throws IOException
IntervalTree< Alignment >	getIntervalTreeCached (String chr, int start, int end) throws IOException
Gene	updateGeneByFirstCounts (Gene gene, IntervalTree< Alignment > tree, int EF)
Map< Annotation, Integer >	getSplicedReads (Annotation align, int minIntronSize, int maxIntronSize) throws IOException
Map< Annotation, Integer >	getSplicedReads (Annotation region, Collection< Predicate< Annotation >> filters) throws IOException
Map< Annotation, Integer >	getSplicedReads (Annotation region) throws IOException
Map< Annotation, Integer >	getSplicedReads (Annotation align, final int minIntronSize, final int maxIntronSize, int minNumIntrons, Sequence chrSeq) throws IOException
Map< Annotation, Integer >	getSplicedReads (Annotation region, Collection< Predicate< Annotation >> filters, int minNumIntrons) throws IOException
Map< Annotation, Integer >	getSplicedReads (Annotation region, Collection< Predicate< Annotation >> filters, int minNumIntrons, Sequence chrSeq) throws IOException
Map< Annotation, Integer >	getSplicedReads (Annotation region, Predicate< Annotation > filter) throws IOException
Map< Annotation, Integer >	getSplicedReads (int minIntronSize, int maxIntronSize) throws IOException
double	getSpliceWeightFactor ()
Collection<?extends Annotation >	getSplicedReadExons (String chr) throws IOException
CloseableIterator< Alignment >	getReadIterator ()
CloseableIterator< Alignment >	getReadIterator (Annotation region) throws IOException
CloseableIterator< Alignment >	getChromosomeReadIterator (String chromosome) throws IOException
double	getTotalNumberOfStrandedReads ()
double	getScorePerAlignmentFromCache (Gene window, IntervalTree< Alignment > chunkAlignmentTree, int extensionFactor)
void	resetTreeCache ()
int	getChunkStart ()
int	getChunkEnd ()
IntervalTree< Alignment >	getIntervalTreeTruncatedCached (String chromosome, int start, int end) throws IOException
IntervalTree< Annotation >	getFullIntervalTreeAsAnnotation (String chr) throws IOException
double	getMinimumMappingQuality ()
void	setChunkSize (int chunkSize)
void	setNegativeStranded ()
void	setPositiveStranded ()
void	setSecondRead ()
void	setFirstRead ()
void	setNormalizationStrategy (ReadCountNormalizer normalizer)
void	setMinimumMappingQuality (double minimumMapQuality)
boolean	passes (Gene gene, IntervalTree< Alignment > tree, int EF, double cutoff)
long	passesCutoff (Annotation align, IntervalTree< Alignment > tree, int EF, double threshold)
boolean	hasNextExon (String chr) throws IOException
void	restartIterator ()
void	resetTreeCache (String chr)
void	clearFullIntervalTreeAsAlignmentsCached (String chr)
boolean	isStranded ()
void	unsetStranded ()
boolean	isPositiveStranded ()
boolean	isNegativeStranded ()
String	getModelFilePath ()
void	setExtensionFactor (int factor)

Member Function Documentation

void broad.pda.seq.segmentation.AlignmentDataModel.clearFullIntervalTreeAsAlignmentsCached

(

String

chr

)

Implemented in broad.pda.seq.segmentation.GenericAlignmentDataModel.

CloseableIterator<Alignment> broad.pda.seq.segmentation.AlignmentDataModel.getAnnotationOverlappingRegion

(

Annotation

align

)

throws IOException

Implemented in broad.pda.seq.segmentation.GenericAlignmentDataModel.

int broad.pda.seq.segmentation.AlignmentDataModel.getBasesCovered	(	Annotation	record,
		int	EF
	)		throws IOException

Implemented in broad.pda.seq.segmentation.GenericAlignmentDataModel.

double broad.pda.seq.segmentation.AlignmentDataModel.getBasesCoveredPerAlignment	(	Gene	gene,
		IntervalTree< Alignment >	tree,
		int	EF
	)

Implemented in broad.pda.seq.segmentation.GenericAlignmentDataModel.

int broad.pda.seq.segmentation.AlignmentDataModel.getChromosomeLength

(

String

chr

)

Get length of a chromosome

Parameters

chr

Returns

Implemented in broad.pda.seq.segmentation.GenericAlignmentDataModel.

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Map<String, Integer> broad.pda.seq.segmentation.AlignmentDataModel.getChromosomeLengths

(

)

Implemented in broad.pda.seq.segmentation.GenericAlignmentDataModel.

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CloseableIterator<Alignment> broad.pda.seq.segmentation.AlignmentDataModel.getChromosomeReadIterator

(

String

chromosome

)

throws IOException

Parameters

the	chromosome over which to iterate

Returns

CloseableIterator over all reads mapped to the given Chromosome

Implemented in broad.pda.seq.segmentation.GenericAlignmentDataModel.

int broad.pda.seq.segmentation.AlignmentDataModel.getChunkEnd

(

)

Implemented in broad.pda.seq.segmentation.GenericAlignmentDataModel.

int broad.pda.seq.segmentation.AlignmentDataModel.getChunkStart

(

)

Implemented in broad.pda.seq.segmentation.GenericAlignmentDataModel.

double broad.pda.seq.segmentation.AlignmentDataModel.getCounts

(

String

chr

)

throws IOException

Counts the number of reads for the specified chromosome

Returns

Exceptions

IOException

Implemented in broad.pda.seq.segmentation.GenericAlignmentDataModel.

double broad.pda.seq.segmentation.AlignmentDataModel.getCountsOfUniqueOverlappers	(	Annotation	target,
		Annotation	exclude,
		IntervalTree< Alignment >	tree,
		int	EF
	)

Implemented in broad.pda.seq.segmentation.GenericAlignmentDataModel.

double broad.pda.seq.segmentation.AlignmentDataModel.getCountsOfUniqueOverlappers	(	Annotation	target,
		Gene	exclude,
		IntervalTree< Alignment >	tree,
		int	EF
	)

Implemented in broad.pda.seq.segmentation.GenericAlignmentDataModel.

double broad.pda.seq.segmentation.AlignmentDataModel.getCountsOnBase	(	String	chr,
		int	index
	)		throws IOException

Implemented in broad.pda.seq.segmentation.GenericAlignmentDataModel.

double broad.pda.seq.segmentation.AlignmentDataModel.getCountsPerAlignment	(	Annotation	first,
		int	EF
	)		throws IOException

Implemented in broad.pda.seq.segmentation.GenericAlignmentDataModel.

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double broad.pda.seq.segmentation.AlignmentDataModel.getCountsPerAlignment	(	Annotation	align,
		IntervalTree< Alignment >	tree,
		int	EF
	)

Implemented in broad.pda.seq.segmentation.GenericAlignmentDataModel.

double broad.pda.seq.segmentation.AlignmentDataModel.getCountsPerAlignment	(	Gene	gene,
		IntervalTree< Alignment >	tree,
		int	EF
	)

Implemented in broad.pda.seq.segmentation.GenericAlignmentDataModel.

double broad.pda.seq.segmentation.AlignmentDataModel.getCountsPerAlignment	(	Annotation[]	Annotation,
		IntervalTree< Alignment >	tree,
		int	EF
	)

Implemented in broad.pda.seq.segmentation.GenericAlignmentDataModel.

double broad.pda.seq.segmentation.AlignmentDataModel.getCountsPerAlignment	(	Annotation[]	Annotation,
		int	EF
	)		throws IOException

Similar to

See also

getCountsPerAlignment(Annotation[] Annotation, IntervalTree<Alignment> tree, int EF) but delegates the management of the alignment interval tree to the implementing class rather than the caller

Parameters

Annotation
EF

Returns

Exceptions

IOException

Implemented in broad.pda.seq.segmentation.GenericAlignmentDataModel.

double broad.pda.seq.segmentation.AlignmentDataModel.getCountsPerAlignment	(	Annotation	align,
		Map< String, IntervalTree< Annotation >>	goodExonTree,
		IntervalTree< Alignment >	tree,
		int	extensionFactor
	)

Implemented in broad.pda.seq.segmentation.GenericAlignmentDataModel.

double broad.pda.seq.segmentation.AlignmentDataModel.getCountsPerAlignmentFullyContained	(	Gene	gene,
		IntervalTree< Alignment >	tree,
		int	EF
	)

Implemented in broad.pda.seq.segmentation.GenericAlignmentDataModel.

double broad.pda.seq.segmentation.AlignmentDataModel.getCountsPerAnnotationtranded	(	Gene	gene,
		IntervalTree< Alignment >	tree,
		int	EF,
		String	orientation
	)

Implemented in broad.pda.seq.segmentation.GenericAlignmentDataModel.

int broad.pda.seq.segmentation.AlignmentDataModel.getCountsWithinExons	(	Annotation	align,
		Iterator< Alignment >	iter,
		int	EF
	)

Implemented in broad.pda.seq.segmentation.GenericAlignmentDataModel.

int broad.pda.seq.segmentation.AlignmentDataModel.getCountsWithinExons	(	Annotation	align,
		IntervalTree< Alignment >	tree,
		int	EF
	)

Implemented in broad.pda.seq.segmentation.GenericAlignmentDataModel.

Iterator<Annotation> broad.pda.seq.segmentation.AlignmentDataModel.getExonAnnotationOverlappingRegion

(

Annotation

align

)

throws IOException

Implemented in broad.pda.seq.segmentation.GenericAlignmentDataModel.

IntervalTree<Annotation> broad.pda.seq.segmentation.AlignmentDataModel.getFullIntervalTreeAsAnnotation

(

String

chr

)

throws IOException

Implemented in broad.pda.seq.segmentation.GenericAlignmentDataModel.

GeneCounts broad.pda.seq.segmentation.AlignmentDataModel.getGeneCounts	(	Gene	gene,
		int	extensionFactor
	)		throws IOException

Implemented in broad.pda.seq.segmentation.GenericAlignmentDataModel.

IntervalTree<Alignment> broad.pda.seq.segmentation.AlignmentDataModel.getIntervalTree	(	String	chr,
		int	start,
		int	end
	)		throws IOException

Implemented in broad.pda.seq.segmentation.GenericAlignmentDataModel.

IntervalTree<Alignment> broad.pda.seq.segmentation.AlignmentDataModel.getIntervalTreeCached	(	String	chr,
		int	start,
		int	end
	)		throws IOException

Implemented in broad.pda.seq.segmentation.GenericAlignmentDataModel.

IntervalTree<Alignment> broad.pda.seq.segmentation.AlignmentDataModel.getIntervalTreeTruncatedCached	(	String	chromosome,
		int	start,
		int	end
	)		throws IOException

Implemented in broad.pda.seq.segmentation.GenericAlignmentDataModel.

double broad.pda.seq.segmentation.AlignmentDataModel.getMinimumMappingQuality

(

)

Implemented in broad.pda.seq.segmentation.GenericAlignmentDataModel.

String broad.pda.seq.segmentation.AlignmentDataModel.getModelFilePath

(

)

Implemented in broad.pda.seq.segmentation.GenericAlignmentDataModel.

double broad.pda.seq.segmentation.AlignmentDataModel.getNumberOfSplicedReads

(

Annotation

align

)

throws IOException

Implemented in broad.pda.seq.segmentation.GenericAlignmentDataModel.

Collection<Annotation> broad.pda.seq.segmentation.AlignmentDataModel.getOverlappingRegions

(

String

chr

)

throws IOException

Implemented in broad.pda.seq.segmentation.GenericAlignmentDataModel.

Gene broad.pda.seq.segmentation.AlignmentDataModel.getPeak	(	Gene	gene,
		Gene	startCodon,
		IntervalTree< Alignment >	tree,
		int	EF
	)

Implemented in broad.pda.seq.segmentation.GenericAlignmentDataModel.

CloseableIterator<Alignment> broad.pda.seq.segmentation.AlignmentDataModel.getReadIterator

(

)

Implemented in broad.pda.seq.segmentation.GenericAlignmentDataModel.

CloseableIterator<Alignment> broad.pda.seq.segmentation.AlignmentDataModel.getReadIterator

(

Annotation

region

)

throws IOException

Implemented in broad.pda.seq.segmentation.GenericAlignmentDataModel.

double broad.pda.seq.segmentation.AlignmentDataModel.getScorePerAlignmentFromCache	(	Gene	window,
		IntervalTree< Alignment >	chunkAlignmentTree,
		int	extensionFactor
	)

Implemented in broad.pda.seq.segmentation.GenericAlignmentDataModel.

Collection<? extends Annotation> broad.pda.seq.segmentation.AlignmentDataModel.getSplicedReadExons

(

String

chr

)

throws IOException

Implemented in broad.pda.seq.segmentation.GenericAlignmentDataModel.

Map<Annotation, Integer> broad.pda.seq.segmentation.AlignmentDataModel.getSplicedReads	(	Annotation	align,
		int	minIntronSize,
		int	maxIntronSize
	)		throws IOException

Map<Annotation, Integer> broad.pda.seq.segmentation.AlignmentDataModel.getSplicedReads	(	Annotation	region,
		Collection< Predicate< Annotation >>	filters
	)		throws IOException

Implemented in broad.pda.seq.segmentation.GenericAlignmentDataModel.

Map<Annotation, Integer> broad.pda.seq.segmentation.AlignmentDataModel.getSplicedReads

(

Annotation

region

)

throws IOException

Implemented in broad.pda.seq.segmentation.GenericAlignmentDataModel.

Map<Annotation, Integer> broad.pda.seq.segmentation.AlignmentDataModel.getSplicedReads	(	Annotation	align,
		final int	minIntronSize,
		final int	maxIntronSize,
		int	minNumIntrons,
		Sequence	chrSeq
	)		throws IOException

Implemented in broad.pda.seq.segmentation.GenericAlignmentDataModel.

Map<Annotation, Integer> broad.pda.seq.segmentation.AlignmentDataModel.getSplicedReads	(	Annotation	region,
		Collection< Predicate< Annotation >>	filters,
		int	minNumIntrons
	)		throws IOException

Implemented in broad.pda.seq.segmentation.GenericAlignmentDataModel.

Map<Annotation, Integer> broad.pda.seq.segmentation.AlignmentDataModel.getSplicedReads	(	Annotation	region,
		Collection< Predicate< Annotation >>	filters,
		int	minNumIntrons,
		Sequence	chrSeq
	)		throws IOException

Implemented in broad.pda.seq.segmentation.GenericAlignmentDataModel.

Map<Annotation, Integer> broad.pda.seq.segmentation.AlignmentDataModel.getSplicedReads	(	Annotation	region,
		Predicate< Annotation >	filter
	)		throws IOException

Implemented in broad.pda.seq.segmentation.GenericAlignmentDataModel.

Map<Annotation, Integer> broad.pda.seq.segmentation.AlignmentDataModel.getSplicedReads	(	int	minIntronSize,
		int	maxIntronSize
	)		throws IOException

Implemented in broad.pda.seq.segmentation.GenericAlignmentDataModel.

double broad.pda.seq.segmentation.AlignmentDataModel.getSpliceWeightFactor

(

)

Implemented in broad.pda.seq.segmentation.GenericAlignmentDataModel.

double broad.pda.seq.segmentation.AlignmentDataModel.getTotalNumberOfStrandedReads

(

)

Implemented in broad.pda.seq.segmentation.GenericAlignmentDataModel.

boolean broad.pda.seq.segmentation.AlignmentDataModel.hasNextExon

(

String

chr

)

throws IOException

Implemented in broad.pda.seq.segmentation.GenericAlignmentDataModel.

boolean broad.pda.seq.segmentation.AlignmentDataModel.isNegativeStranded

(

)

Implemented in broad.pda.seq.segmentation.GenericAlignmentDataModel.

boolean broad.pda.seq.segmentation.AlignmentDataModel.isPositiveStranded

(

)

Implemented in broad.pda.seq.segmentation.GenericAlignmentDataModel.

boolean broad.pda.seq.segmentation.AlignmentDataModel.isStranded

(

)

Implemented in broad.pda.seq.segmentation.GenericAlignmentDataModel.

boolean broad.pda.seq.segmentation.AlignmentDataModel.passes	(	Gene	gene,
		IntervalTree< Alignment >	tree,
		int	EF,
		double	cutoff
	)

Implemented in broad.pda.seq.segmentation.GenericAlignmentDataModel.

long broad.pda.seq.segmentation.AlignmentDataModel.passesCutoff	(	Annotation	align,
		IntervalTree< Alignment >	tree,
		int	EF,
		double	threshold
	)

Implemented in broad.pda.seq.segmentation.GenericAlignmentDataModel.

void broad.pda.seq.segmentation.AlignmentDataModel.resetTreeCache

(

)

Implemented in broad.pda.seq.segmentation.GenericAlignmentDataModel.

void broad.pda.seq.segmentation.AlignmentDataModel.resetTreeCache

(

String

chr

)

Implemented in broad.pda.seq.segmentation.GenericAlignmentDataModel.

void broad.pda.seq.segmentation.AlignmentDataModel.restartIterator

(

)

Implemented in broad.pda.seq.segmentation.GenericAlignmentDataModel.

void broad.pda.seq.segmentation.AlignmentDataModel.setChunkSize

(

int

chunkSize

)

Implemented in broad.pda.seq.segmentation.GenericAlignmentDataModel.

void broad.pda.seq.segmentation.AlignmentDataModel.setExtensionFactor

(

int

factor

)

Implemented in broad.pda.seq.segmentation.GenericAlignmentDataModel.

void broad.pda.seq.segmentation.AlignmentDataModel.setFirstRead

(

)

Implemented in broad.pda.seq.segmentation.GenericAlignmentDataModel.

void broad.pda.seq.segmentation.AlignmentDataModel.setMinimumMappingQuality

(

double

minimumMapQuality

)

Implemented in broad.pda.seq.segmentation.GenericAlignmentDataModel.

void broad.pda.seq.segmentation.AlignmentDataModel.setNegativeStranded

(

)

Implemented in broad.pda.seq.segmentation.GenericAlignmentDataModel.

void broad.pda.seq.segmentation.AlignmentDataModel.setNormalizationStrategy

(

ReadCountNormalizer

normalizer

)

Implemented in broad.pda.seq.segmentation.GenericAlignmentDataModel.

void broad.pda.seq.segmentation.AlignmentDataModel.setPositiveStranded

(

)

Implemented in broad.pda.seq.segmentation.GenericAlignmentDataModel.

void broad.pda.seq.segmentation.AlignmentDataModel.setSecondRead

(

)

Implemented in broad.pda.seq.segmentation.GenericAlignmentDataModel.

void broad.pda.seq.segmentation.AlignmentDataModel.unsetStranded

(

)

Implemented in broad.pda.seq.segmentation.GenericAlignmentDataModel.

Gene broad.pda.seq.segmentation.AlignmentDataModel.updateGeneByFirstCounts	(	Gene	gene,
		IntervalTree< Alignment >	tree,
		int	EF
	)

Implemented in broad.pda.seq.segmentation.GenericAlignmentDataModel.

---

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

• java/broad/pda/seq/segmentation/AlignmentDataModel.java