Collaboration diagram for umms.core.utils.AnnotationUtils:

Static Public Member Functions
static Map< String, Collection < Gene > >	collapseOverlappers (Map< String, Collection< Gene >> genes, boolean ignoreStrand)

static boolean	pairwiseNonoverlappingIgnoreStrand (Collection< Annotation > regions)

static Collection< Annotation >	mergeOverlappingBlocks (TreeSet<?extends Annotation > windows)

static< TextendsAnnotation > Collection< Annotation >	mergeOverlappingBlocksSingleOrientation (Collection< T > regions, boolean enforceSameOrientation)

static< TextendsAnnotation > T	getLargestParent (T child, Map< String, Collection< T >> parents)

static< TextendsAnnotation > Map< T, T >	mapChildToLargestParent (Map< String, Collection< T >> children, Map< String, Collection< T >> parents)

static< TextendsAnnotation > Collection< T >	getParents (T child, Map< String, Collection< T >> parents)

static< TextendsAnnotation > Collection< T >	getChildren (T parent, Map< String, Collection< T >> children)

static< TextendsAnnotation > Map< T, Collection< T > >	mapParentsToChildren (Map< String, Collection< T >> children, Map< String, Collection< T >> parents)

static< TextendsAnnotation > Map< T, Collection< T > >	mapChildToParents (Map< String, Collection< T >> children, Map< String, Collection< T >> parents)

static Map< String, Collection < Annotation > >	loadAnnotations (String bedFile) throws IOException

static int	getMidpoint (Annotation annot)

static int	getSubAnnotationMidpointWithinAnnotation (Annotation annot, Annotation subAnnot)

Static Public Attributes
static Logger	logger = Logger.getLogger(AnnotationUtils.class.getName())

Detailed Description

Author: prussell

Member Function Documentation

static Map<String, Collection<Gene> > umms.core.utils.AnnotationUtils.collapseOverlappers	(	Map< String, Collection< Gene >>	genes,
		boolean	ignoreStrand
	)

static

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static <TextendsAnnotation> Collection<T> umms.core.utils.AnnotationUtils.getChildren	(	T	parent,
		Map< String, Collection< T >>	children
	)

static

Get children of parent annotation

Parameters

parent	Parent
children	Potential children by chromosome

Returns: Set of children contained in parent or empty set if none

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static <TextendsAnnotation> T umms.core.utils.AnnotationUtils.getLargestParent	(	T	child,
		Map< String, Collection< T >>	parents
	)

static

Get largest parent

Parameters

child	Child annotation
parents	Possible parent annotations by chromosome

Returns: Largest parent (annotation containing child on same strand) or null if none exists

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static int umms.core.utils.AnnotationUtils.getMidpoint ( Annotation annot )

static

Get midpoint along mature transcript of a spliced annotation

Parameters

annot Annotation

Returns: Genome coordinate of mature transcript midpoint

static <TextendsAnnotation> Collection<T> umms.core.utils.AnnotationUtils.getParents	(	T	child,
		Map< String, Collection< T >>	parents
	)

static

Get parents of child annotation

Parameters

child	Child
parents	Parents by chromosome

Returns: Set of parents containing child or empty set if none

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static int umms.core.utils.AnnotationUtils.getSubAnnotationMidpointWithinAnnotation	(	Annotation	annot,
		Annotation	subAnnot
	)

static

Get midpoint of a sub annotation with respect to a possibly spliced parent annotation Ignores blocks of sub annotation and only considers blocks of parent annotation

Parameters

annot	Parent annotation
subAnnot	Sub annotation contained in parent annotation

Returns: Midpoint of sub annotation span considering blocks of parent annotation

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static Map<String, Collection<Annotation> > umms.core.utils.AnnotationUtils.loadAnnotations ( String bedFile ) throws IOException

static

Load annotations in the bed file as annotation objects

Parameters

bedFile Bed file

Returns: Map of chromosome to collection of annotations

Exceptions

IOException

static <TextendsAnnotation> Map<T, T> umms.core.utils.AnnotationUtils.mapChildToLargestParent	(	Map< String, Collection< T >>	children,
		Map< String, Collection< T >>	parents
	)

static

Map each child annotation to its largest parent defined as annotations overlapping and containing child

Parameters

children	Child annotations by chromosome
parents	Parent annotations by chromosome

Returns: Map of child to largest parent. Does not include children with no parents.

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static <TextendsAnnotation> Map<T, Collection<T> > umms.core.utils.AnnotationUtils.mapChildToParents	(	Map< String, Collection< T >>	children,
		Map< String, Collection< T >>	parents
	)

static

Map each child annotation to its set of parents defined as annotations overlapping and containing child

Parameters

<T>
children	Child annotations by chromosome
parents	Parent annotations by chromosome

Returns: Map of child to set of parents. Does not include children with no parents.

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static <TextendsAnnotation> Map<T, Collection<T> > umms.core.utils.AnnotationUtils.mapParentsToChildren	(	Map< String, Collection< T >>	children,
		Map< String, Collection< T >>	parents
	)

static

Map each parent annotation to its set of contained children

Parameters

<T>
children	Child annotations by chromosome
parents	Parent annotations by chromosome

Returns: Map of parent to set of children. Annotations with no children map to empty set.

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static Collection<Annotation> umms.core.utils.AnnotationUtils.mergeOverlappingBlocks ( TreeSet<?extends Annotation > windows )

static

Merge annotations that overlap in the same orientation as each other, and leave singleton windows the same

Parameters

windows Annotation set

Returns: New set of merged windows

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static <TextendsAnnotation> Collection<Annotation> umms.core.utils.AnnotationUtils.mergeOverlappingBlocksSingleOrientation	(	Collection< T >	regions,
		boolean	enforceSameOrientation
	)

static

Merge annotations that overlap, and leave singleton windows the same All returned annotations will have the same orientation: unknown if not enforcing same orientation, or the common orientation of all input regions if enforcing

Parameters