broad.core.annotation.AnnotationReader< T extends GenomicAnnotation > Class Reference

Classes
class	AnnotationSet< T extends LightweightGenomicAnnotation >
class	trivialFilter

Public Member Functions
	AnnotationReader ()
void	init ()
	AnnotationReader (Collection< T > annotations)
void	clear ()
void	load (File source, AnnotationFactory<?extends T > factory) throws IOException, ParseException
void	load (BufferedReader br, AnnotationFactory<?extends T > factory) throws IOException, ParseException
void	load (File source, AnnotationFactory<?extends T > factory, GenomicAnnotationFilter< T > filter) throws IOException, ParseException
void	load (BufferedReader br, AnnotationFactory<?extends T > factory, GenomicAnnotationFilter< T > filter) throws IOException, ParseException
abstract int	parse (String file, GenomicAnnotationFilter< T > filter, AnnotationHandler handler) throws ParseException, IOException
abstract int	parse (BufferedReader br, GenomicAnnotationFilter< T > filter, AnnotationHandler handler) throws ParseException, IOException
Map< String, List< T > >	getChromosomeAnnotationMap ()
Iterator< String >	getChromosomeIterator ()
ShortBEDReader	cloneRegions ()
Map< String, List< T > >	getChromosomeAnnotationMap (int i)
int	getBaseCoverage (List< T > annotations)
int	numberCovered (List<?extends GenomicAnnotation > annotations)
void	intersect (AnnotationReader< T > other)
void	intersect (List<?extends GenomicAnnotation > annotations)
Collection< T >	takeIntersection (List<?extends GenomicAnnotation > annotations)
T	findClosest (final LightweightGenomicAnnotation annotation)
T	findClosestNonOverlapping (final LightweightGenomicAnnotation annotation)
T	findClosest (final LightweightGenomicAnnotation annotation, boolean nonOverlapping)
Map< T, LightweightGenomicAnnotation >	findClosestForAll (final AnnotationReader<?extends GenomicAnnotation > otherReader, boolean nonOverlapping)
Map< T, LightweightGenomicAnnotation >	findClosestForAll (final AnnotationReader<?extends GenomicAnnotation > otherReader)
Map< T, LightweightGenomicAnnotation >	findClosestNonoverlappingForAll (final AnnotationReader<?extends GenomicAnnotation > otherReader)
int	getDistanceToClosest (final LightweightGenomicAnnotation annotation)
Map< T, Integer >	getDistancesToClosest (final AnnotationReader<?extends GenomicAnnotation > otherReader)
void	permuteAnnotationsOnChromosome (final Map< String, Integer > sizes)
BasicAnnotationReader	takeComplement (List<?extends Annotation > annotations)
List< Annotation >	getOverlappers (Annotation a)
void	minus (List<?extends GenomicAnnotation > annotations)
void	filterByOverlap (List<?extends Annotation > annotations)
void	filterByOverlap (List<?extends Annotation > annotations, int extensionFactor)
void	filterByOverlapOfLastExonOrAfterLastExon (List<?extends GenomicAnnotation > annotations, int extensionFactor)
void	filterByOverlapOfLastExon (List<?extends GenomicAnnotation > annotations, int extensionFactor)
void	filterByOverlapAndOrientation (List<?extends GenomicAnnotation > annotations)
void	IncrementScoreIfOverlap (AnnotationReader<?extends GenomicAnnotation > annotReader, int setNumber, Boolean setToZero)
int	getBaseCoverage ()
abstract T	createAnnotation (GenomicAnnotation a)
void	shift (int amountToShift)
void	merge ()
List< Annotation >	getOverlappers (List<?extends Annotation > annotationList)
List< Annotation >	getOverlappers (List<?extends Annotation > annotationList, boolean fullyContained)
List< Annotation >	getOverlappers (AnnotationReader<?extends GenomicAnnotation > other)
int	getBasesCovered (Annotation region)
int	getBasesCovered (Annotation region, boolean fullyContained)
int	getBasesCovered (Annotation region, int fudgeFactor)
int	getBasesCovered (Annotation region, int fudgeFactor, boolean fullyContained)
List< T >	getOverlappers (LightweightGenomicAnnotation annotation)
double	getScoreSum (LightweightGenomicAnnotation region)
double	getAverageScore (LightweightGenomicAnnotation region)
void	merge (int setNumber)
void	concatAnnotationSet (int setNumber, List<?extends GenomicAnnotation > list)
void	addAnnotation (T annotation, int track)
void	addAnnotation (T annotation)
void	addAnnotationToLastTrack (T annotation)
List< T >	getAnnotationsForSequence (String sequenceName)
List< T >	getAnnotationsForSequence (String sequenceName, int setNumber)
Map< String, List< T > >	getSequenceAnnotationMap ()
Map< String, List< T > >	getSequenceAnnotationMap (int setNumber)
void	addBrowserLine (String line)
void	startTrack (String line)
void	startTrack (String line, int trackNum)
IntervalTree< T >	getChromosomeTree (String chr, int i)
IntervalTree< T >	getChromosomeTree (String chr)
Map< String, IntervalTree< T > >	getChromosomeTreeMap (int i)
Map< String, IntervalTree< T > >	getChromosomeTreeMap ()
String	getTrackInfo (int i)
List< T >	getChromosomeBEDs (String chr)
List< T >	getChromosomeBEDs (String chr, int i)
List< T >	getAnnotationList (int setNumber)
T	getAnnotation (int setNumber, String name)
boolean	containsAnnotation (int setNumber, String name)
T	getAnnotation (String name)
boolean	containsAnnotation (String name)
void	shuffleScores (String chr, int setNum)
void	shuffleScores (String chr)
List< T >	getAnnotationList ()
int	numOfAnnotation (int setNum)
int	size ()
String	toStringForWriting ()
void	write (BufferedWriter bw) throws IOException
void	write (String outputFile) throws IOException
void	filterByScore (double set1FilterScore)
void	addFilter (Predicate< T > filter)
void	addFilters (Collection< Predicate< T >> filters)

Static Public Member Functions
static Map< Annotation, Integer >	getLastExons (List<?extends Annotation > annotations)

Protected Member Functions
int	parse (String file, AnnotationFactory<?extends T > factory, GenomicAnnotationFilter< T > filter, AnnotationHandler handler) throws ParseException, IOException
int	parse (BufferedReader br, AnnotationFactory<?extends T > factory, GenomicAnnotationFilter< T > filter, AnnotationHandler handler) throws ParseException
void	addAnnotationSet (AnnotationSet< T > track)

Constructor & Destructor Documentation

broad.core.annotation.AnnotationReader< T extends GenomicAnnotation >.AnnotationReader

(

)

broad.core.annotation.AnnotationReader< T extends GenomicAnnotation >.AnnotationReader

(

Collection< T >

annotations

)

Jesse Engreitz September 26, 2012 Allow for creating a reader from a collection of annotations

Parameters

annotations

Member Function Documentation

void broad.core.annotation.AnnotationReader< T extends GenomicAnnotation >.addAnnotation	(	T	annotation,
		int	track
	)

void broad.core.annotation.AnnotationReader< T extends GenomicAnnotation >.addAnnotation

(

T

annotation

)

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void broad.core.annotation.AnnotationReader< T extends GenomicAnnotation >.addAnnotationSet ( AnnotationSet< T >  track )

protected

void broad.core.annotation.AnnotationReader< T extends GenomicAnnotation >.addAnnotationToLastTrack

(

T

annotation

)

void broad.core.annotation.AnnotationReader< T extends GenomicAnnotation >.addBrowserLine

(

String

line

)

void broad.core.annotation.AnnotationReader< T extends GenomicAnnotation >.addFilter

(

Predicate< T >

filter

)

void broad.core.annotation.AnnotationReader< T extends GenomicAnnotation >.addFilters

(

Collection< Predicate< T >>

filters

)

void broad.core.annotation.AnnotationReader< T extends GenomicAnnotation >.clear

(

)

ShortBEDReader broad.core.annotation.AnnotationReader< T extends GenomicAnnotation >.cloneRegions

(

)

void broad.core.annotation.AnnotationReader< T extends GenomicAnnotation >.concatAnnotationSet	(	int	setNumber,
		List<?extends GenomicAnnotation >	list
	)

Moran, Feb22 2010 concat an annotation set to an exciting one (without merging) WARNING: assumes that same types are concatenated- uses casting to current objets annotation type

boolean broad.core.annotation.AnnotationReader< T extends GenomicAnnotation >.containsAnnotation	(	int	setNumber,
		String	name
	)

boolean broad.core.annotation.AnnotationReader< T extends GenomicAnnotation >.containsAnnotation

(

String

name

)

abstract T broad.core.annotation.AnnotationReader< T extends GenomicAnnotation >.createAnnotation ( GenomicAnnotation  a )

abstract

void broad.core.annotation.AnnotationReader< T extends GenomicAnnotation >.filterByOverlap

(

List<?extends Annotation >

annotations

)

Filters this reader by removing all elements that do not overlap the given list of annotations

Parameters

annotations

a list of Annotations to filter

void broad.core.annotation.AnnotationReader< T extends GenomicAnnotation >.filterByOverlap	(	List<?extends Annotation >	annotations,
		int	extensionFactor
	)

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void broad.core.annotation.AnnotationReader< T extends GenomicAnnotation >.filterByOverlapAndOrientation

(

List<?extends GenomicAnnotation >

annotations

)

ADDED BY MORAN Feb 8th 2010 Filters this reader by removing all elements that do not overlap AND HAVE THE SAME ORIENTATION as the given list of annotations

Parameters

annotations

a list of Annotations to filter

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void broad.core.annotation.AnnotationReader< T extends GenomicAnnotation >.filterByOverlapOfLastExon	(	List<?extends GenomicAnnotation >	annotations,
		int	extensionFactor
	)

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void broad.core.annotation.AnnotationReader< T extends GenomicAnnotation >.filterByOverlapOfLastExonOrAfterLastExon	(	List<?extends GenomicAnnotation >	annotations,
		int	extensionFactor
	)

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void broad.core.annotation.AnnotationReader< T extends GenomicAnnotation >.filterByScore

(

double

set1FilterScore

)

T broad.core.annotation.AnnotationReader< T extends GenomicAnnotation >.findClosest

(

final LightweightGenomicAnnotation

annotation

)

T broad.core.annotation.AnnotationReader< T extends GenomicAnnotation >.findClosest	(	final LightweightGenomicAnnotation	annotation,
		boolean	nonOverlapping
	)

Added "nonOverlapping" option June 13, 2012

Parameters

nonOverlapping

Set to true to get the closest non-overlapping annotation

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Map<T,LightweightGenomicAnnotation> broad.core.annotation.AnnotationReader< T extends GenomicAnnotation >.findClosestForAll	(	final AnnotationReader<?extends GenomicAnnotation >	otherReader,
		boolean	nonOverlapping
	)

Jesse Engreitz June 24, 2012 Return a map of elements in this reader to the closest elements in another reader

Parameters

otherReader	second set of annotations
nonOverlapping	set to true to get the closest non-overlapping elements

Returns

Map<T,LightweightGenomicAnnotation> broad.core.annotation.AnnotationReader< T extends GenomicAnnotation >.findClosestForAll

(

final AnnotationReader<?extends GenomicAnnotation >

otherReader

)

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T broad.core.annotation.AnnotationReader< T extends GenomicAnnotation >.findClosestNonOverlapping

(

final LightweightGenomicAnnotation

annotation

)

Map<T,LightweightGenomicAnnotation> broad.core.annotation.AnnotationReader< T extends GenomicAnnotation >.findClosestNonoverlappingForAll

(

final AnnotationReader<?extends GenomicAnnotation >

otherReader

)

T broad.core.annotation.AnnotationReader< T extends GenomicAnnotation >.getAnnotation	(	int	setNumber,
		String	name
	)

T broad.core.annotation.AnnotationReader< T extends GenomicAnnotation >.getAnnotation

(

String

name

)

List<T> broad.core.annotation.AnnotationReader< T extends GenomicAnnotation >.getAnnotationList

(

int

setNumber

)

List<T> broad.core.annotation.AnnotationReader< T extends GenomicAnnotation >.getAnnotationList

(

)

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List<T> broad.core.annotation.AnnotationReader< T extends GenomicAnnotation >.getAnnotationsForSequence

(

String

sequenceName

)

List<T> broad.core.annotation.AnnotationReader< T extends GenomicAnnotation >.getAnnotationsForSequence	(	String	sequenceName,
		int	setNumber
	)

double broad.core.annotation.AnnotationReader< T extends GenomicAnnotation >.getAverageScore

(

LightweightGenomicAnnotation

region

)

int broad.core.annotation.AnnotationReader< T extends GenomicAnnotation >.getBaseCoverage

(

List< T >

annotations

)

int broad.core.annotation.AnnotationReader< T extends GenomicAnnotation >.getBaseCoverage

(

)

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int broad.core.annotation.AnnotationReader< T extends GenomicAnnotation >.getBasesCovered

(

Annotation

region

)

Adds a 0 fudge fact

Parameters

region

Returns

Exceptions

IOException

int broad.core.annotation.AnnotationReader< T extends GenomicAnnotation >.getBasesCovered	(	Annotation	region,
		boolean	fullyContained
	)

int broad.core.annotation.AnnotationReader< T extends GenomicAnnotation >.getBasesCovered	(	Annotation	region,
		int	fudgeFactor
	)

int broad.core.annotation.AnnotationReader< T extends GenomicAnnotation >.getBasesCovered	(	Annotation	region,
		int	fudgeFactor,
		boolean	fullyContained
	)

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Map<String, List<T> > broad.core.annotation.AnnotationReader< T extends GenomicAnnotation >.getChromosomeAnnotationMap

(

)

Map<String, List<T> > broad.core.annotation.AnnotationReader< T extends GenomicAnnotation >.getChromosomeAnnotationMap

(

int

i

)

List<T> broad.core.annotation.AnnotationReader< T extends GenomicAnnotation >.getChromosomeBEDs

(

String

chr

)

List<T> broad.core.annotation.AnnotationReader< T extends GenomicAnnotation >.getChromosomeBEDs	(	String	chr,
		int	i
	)

Iterator<String> broad.core.annotation.AnnotationReader< T extends GenomicAnnotation >.getChromosomeIterator

(

)

IntervalTree<T> broad.core.annotation.AnnotationReader< T extends GenomicAnnotation >.getChromosomeTree	(	String	chr,
		int	i
	)

IntervalTree<T> broad.core.annotation.AnnotationReader< T extends GenomicAnnotation >.getChromosomeTree

(

String

chr

)

Map<String,IntervalTree<T> > broad.core.annotation.AnnotationReader< T extends GenomicAnnotation >.getChromosomeTreeMap

(

int

i

)

Map<String,IntervalTree<T> > broad.core.annotation.AnnotationReader< T extends GenomicAnnotation >.getChromosomeTreeMap

(

)

Map<T, Integer> broad.core.annotation.AnnotationReader< T extends GenomicAnnotation >.getDistancesToClosest

(

final AnnotationReader<?extends GenomicAnnotation >

otherReader

)

int broad.core.annotation.AnnotationReader< T extends GenomicAnnotation >.getDistanceToClosest

(

final LightweightGenomicAnnotation

annotation

)

Jesse - June 13, 2012

Parameters

annotation

Returns

static Map<Annotation, Integer> broad.core.annotation.AnnotationReader< T extends GenomicAnnotation >.getLastExons ( List<?extends Annotation >  annotations )

static

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List<Annotation> broad.core.annotation.AnnotationReader< T extends GenomicAnnotation >.getOverlappers

(

Annotation

a

)

List<Annotation> broad.core.annotation.AnnotationReader< T extends GenomicAnnotation >.getOverlappers

(

List<?extends Annotation >

annotationList

)

Gets a list of overlapping annotations

List<Annotation> broad.core.annotation.AnnotationReader< T extends GenomicAnnotation >.getOverlappers	(	List<?extends Annotation >	annotationList,
		boolean	fullyContained
	)

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List<Annotation> broad.core.annotation.AnnotationReader< T extends GenomicAnnotation >.getOverlappers

(

AnnotationReader<?extends GenomicAnnotation >

other

)

List<T> broad.core.annotation.AnnotationReader< T extends GenomicAnnotation >.getOverlappers

(

LightweightGenomicAnnotation

annotation

)

Gets a list of overlapping annotations

public Collection<T> getOverlappers(AnnotationReader<T> other) { Set<T> overlappers = new TreeSet<T>(); Iterator<String> chrIt = other.getChromosomeIterator(); while(chrIt.hasNext()) { String chr = chrIt.next(); Iterator<T> annotationIt = other.getChromosomeTree(chr).valueIterator(); IntervalTree<T> tree = getChromosomeTree(chr); if(tree == null) { continue; } while(annotationIt.hasNext()) { LightweightGenomicAnnotation annot = annotationIt.next(); Iterator<T> overlapperIt = new IntervalTree.ValuesIterator<T>(tree.overlappers(annot.getStart(), annot.getEnd())); while(overlapperIt.hasNext()) { T overlapper = overlapperIt.next(); overlappers.add(overlapper); } } } return overlappers; }

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double broad.core.annotation.AnnotationReader< T extends GenomicAnnotation >.getScoreSum

(

LightweightGenomicAnnotation

region

)

Map<String, List<T> > broad.core.annotation.AnnotationReader< T extends GenomicAnnotation >.getSequenceAnnotationMap

(

)

Map<String, List<T> > broad.core.annotation.AnnotationReader< T extends GenomicAnnotation >.getSequenceAnnotationMap

(

int

setNumber

)

String broad.core.annotation.AnnotationReader< T extends GenomicAnnotation >.getTrackInfo

(

int

i

)

void broad.core.annotation.AnnotationReader< T extends GenomicAnnotation >.IncrementScoreIfOverlap	(	AnnotationReader<?extends GenomicAnnotation >	annotReader,
		int	setNumber,
		Boolean	setToZero
	)

Moran FEB23 2010 Increments by one the score of the annotations in the current object if they overlap the input set. Set to zero flag will first initialize all scores to zero

Returns

void broad.core.annotation.AnnotationReader< T extends GenomicAnnotation >.init

(

)

void broad.core.annotation.AnnotationReader< T extends GenomicAnnotation >.intersect

(

AnnotationReader< T >

other

)

void broad.core.annotation.AnnotationReader< T extends GenomicAnnotation >.intersect

(

List<?extends GenomicAnnotation >

annotations

)

void broad.core.annotation.AnnotationReader< T extends GenomicAnnotation >.load	(	File	source,
		AnnotationFactory<?extends T >	factory
	)		throws IOException, ParseException

void broad.core.annotation.AnnotationReader< T extends GenomicAnnotation >.load	(	BufferedReader	br,
		AnnotationFactory<?extends T >	factory
	)		throws IOException, ParseException

void broad.core.annotation.AnnotationReader< T extends GenomicAnnotation >.load	(	File	source,
		AnnotationFactory<?extends T >	factory,
		GenomicAnnotationFilter< T >	filter
	)		throws IOException, ParseException

void broad.core.annotation.AnnotationReader< T extends GenomicAnnotation >.load	(	BufferedReader	br,
		AnnotationFactory<?extends T >	factory,
		GenomicAnnotationFilter< T >	filter
	)		throws IOException, ParseException

void broad.core.annotation.AnnotationReader< T extends GenomicAnnotation >.merge

(

)

Merge list of annotations by combining overlapping annotations into one.

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void broad.core.annotation.AnnotationReader< T extends GenomicAnnotation >.merge

(

int

setNumber

)

Merge list of annotations by combining overlapping annotations into one.

void broad.core.annotation.AnnotationReader< T extends GenomicAnnotation >.minus

(

List<?extends GenomicAnnotation >

annotations

)

Removes from this reader all elements that overlap the given list.

Parameters

annotations

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int broad.core.annotation.AnnotationReader< T extends GenomicAnnotation >.numberCovered

(

List<?extends GenomicAnnotation >

annotations

)

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int broad.core.annotation.AnnotationReader< T extends GenomicAnnotation >.numOfAnnotation

(

int

setNum

)

abstract int broad.core.annotation.AnnotationReader< T extends GenomicAnnotation >.parse ( String  file, GenomicAnnotationFilter< T >  filter, AnnotationHandler  handler  ) throws ParseException, IOException

abstract

int broad.core.annotation.AnnotationReader< T extends GenomicAnnotation >.parse ( String  file, AnnotationFactory<?extends T >  factory, GenomicAnnotationFilter< T >  filter, AnnotationHandler  handler  ) throws ParseException, IOException

protected

abstract int broad.core.annotation.AnnotationReader< T extends GenomicAnnotation >.parse ( BufferedReader  br, GenomicAnnotationFilter< T >  filter, AnnotationHandler  handler  ) throws ParseException, IOException

abstract

int broad.core.annotation.AnnotationReader< T extends GenomicAnnotation >.parse ( BufferedReader  br, AnnotationFactory<?extends T >  factory, GenomicAnnotationFilter< T >  filter, AnnotationHandler  handler  ) throws ParseException

protected

void broad.core.annotation.AnnotationReader< T extends GenomicAnnotation >.permuteAnnotationsOnChromosome

(

final Map< String, Integer >

sizes

)

Jesse Engreitz June 24, 2012 Takes the annotations in the reader and permutes them on their respective chromosomes. Note that this alters the positions of annotations in the reader, although not their sizes;

Parameters

sizes

map of chromosome sizes

void broad.core.annotation.AnnotationReader< T extends GenomicAnnotation >.shift

(

int

amountToShift

)

void broad.core.annotation.AnnotationReader< T extends GenomicAnnotation >.shuffleScores	(	String	chr,
		int	setNum
	)

void broad.core.annotation.AnnotationReader< T extends GenomicAnnotation >.shuffleScores

(

String

chr

)

int broad.core.annotation.AnnotationReader< T extends GenomicAnnotation >.size

(

)

Jesse June 23, 2012

Returns

total number of annotations

void broad.core.annotation.AnnotationReader< T extends GenomicAnnotation >.startTrack

(

String

line

)

void broad.core.annotation.AnnotationReader< T extends GenomicAnnotation >.startTrack	(	String	line,
		int	trackNum
	)

BasicAnnotationReader broad.core.annotation.AnnotationReader< T extends GenomicAnnotation >.takeComplement

(

List<?extends Annotation >

annotations

)

Takes the complement in the given list in this Reader. That is, if an annotation in the list reader does not overlap any in the this reader, the annotation is kept intact. If it is contained in any annotation in the reader then it is removed. If it incompletely overlapped, then the annotation resulting from taking out overlapping regions replaces the overlapped one.

Collection<T> broad.core.annotation.AnnotationReader< T extends GenomicAnnotation >.takeIntersection

(

List<?extends GenomicAnnotation >

annotations

)

String broad.core.annotation.AnnotationReader< T extends GenomicAnnotation >.toStringForWriting

(

)

Jesse June 23, 2012

Returns

string representation of all annotations, one per line

void broad.core.annotation.AnnotationReader< T extends GenomicAnnotation >.write

(

BufferedWriter

bw

)

throws IOException

Author

mgarber

Parameters

BufferedWriter

- buffer to write annotations to

Returns

writes all annotations to the provided BufferedWriter

Exceptions

IOException

void broad.core.annotation.AnnotationReader< T extends GenomicAnnotation >.write

(

String

outputFile

)

throws IOException

Author

mgarber

Parameters

BufferedWriter

- buffer to write annotations to

Returns

writes all annotations to the provided BufferedWriter

Exceptions

IOException

---

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

• java/broad/core/annotation/AnnotationReader.java