broad.pda.feature.genome.Chromosome Class Reference

Collaboration diagram for broad.pda.feature.genome.Chromosome:

Classes
class	AgpEntry
class	AgpEntryFactory

Public Member Functions
	Chromosome (final String name)
	Chromosome (String name, String agpFile) throws Exception
boolean	isSexChromosome ()
Annotation	getShortArm ()
boolean	isAutosome ()
String	getName ()
String	getSymbol ()
String	getChromosomeNumber ()
int	compareTo (Object o)
long	getUngappedSize ()
void	setSequenceFile (File file)
int	length ()
List< AgpEntry >	gaps ()
SequenceRegion	drawRandomRegion (int size)
List<?extends GenomicAnnotation >	shuffle (GenomicAnnotation toShuffle, List<?extends GenomicAnnotation > toAvoid)
List<?extends Annotation >	shuffleWithinValid (Annotation toShuffle, List<?extends Annotation > valid)
List<?extends GenomicAnnotation >	shuffle (List<?extends GenomicAnnotation > toShuffle, List<?extends GenomicAnnotation > toAvoid)
List<?extends GenomicAnnotation >	shuffleWithinValid (List<?extends Annotation > toShuffle, List<?extends Annotation > valid)
void	getRegion (SequenceRegion region)
void	getRegion (SequenceRegion region, boolean softmask)
void	getRegion (SequenceRegion region, boolean softmask, Map< String, IntervalTree< Alignments >> okRepeats)
List< SequenceRegion >	getRegions (List<?extends GenomicAnnotation > annotations, int padding) throws IOException
void	extractRegions (List<?extends SequenceRegion > regions) throws IOException
void	extractRegion (SequenceRegion region) throws IOException
void	loadSequence () throws IOException
void	unloadSequence ()
Sequence	getSequence ()
void	insert (SequenceRegion region, LightweightGenomicAnnotation insertPoint)
void	delete (SequenceRegion region)
void	invert (SequenceRegion region)

Static Public Member Functions
static boolean	isSexChromosome (String name)
static boolean	isAutosome (String name)
static String	getChromosomeNumber (String name)
static int	compareNames (String name1, String name2)

Detailed Description

Represents a chromosome in a genome

Author

engreitz

Constructor & Destructor Documentation

broad.pda.feature.genome.Chromosome.Chromosome

(

final String

name

)

Parameters

The	name of the chromosome e.g. "chr12"

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broad.pda.feature.genome.Chromosome.Chromosome	(	String	name,
		String	agpFile
	)		throws Exception

Parameters

The	name of the chromosome e.g. "chr12"
An	AGP file describing the chromosome assembly

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Member Function Documentation

static int broad.pda.feature.genome.Chromosome.compareNames ( String  name1, String  name2  )

static

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int broad.pda.feature.genome.Chromosome.compareTo

(

Object

o

)

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void broad.pda.feature.genome.Chromosome.delete

(

SequenceRegion

region

)

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SequenceRegion broad.pda.feature.genome.Chromosome.drawRandomRegion

(

int

size

)

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void broad.pda.feature.genome.Chromosome.extractRegion

(

SequenceRegion

region

)

throws IOException

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void broad.pda.feature.genome.Chromosome.extractRegions

(

List<?extends SequenceRegion >

regions

)

throws IOException

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List<AgpEntry> broad.pda.feature.genome.Chromosome.gaps

(

)

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String broad.pda.feature.genome.Chromosome.getChromosomeNumber

(

)

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static String broad.pda.feature.genome.Chromosome.getChromosomeNumber ( String  name )

static

String broad.pda.feature.genome.Chromosome.getName

(

)

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void broad.pda.feature.genome.Chromosome.getRegion

(

SequenceRegion

region

)

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void broad.pda.feature.genome.Chromosome.getRegion	(	SequenceRegion	region,
		boolean	softmask
	)

void broad.pda.feature.genome.Chromosome.getRegion	(	SequenceRegion	region,
		boolean	softmask,
		Map< String, IntervalTree< Alignments >>	okRepeats
	)

List<SequenceRegion> broad.pda.feature.genome.Chromosome.getRegions	(	List<?extends GenomicAnnotation >	annotations,
		int	padding
	)		throws IOException

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Sequence broad.pda.feature.genome.Chromosome.getSequence

(

)

Annotation broad.pda.feature.genome.Chromosome.getShortArm

(

)

String broad.pda.feature.genome.Chromosome.getSymbol

(

)

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long broad.pda.feature.genome.Chromosome.getUngappedSize

(

)

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void broad.pda.feature.genome.Chromosome.insert	(	SequenceRegion	region,
		LightweightGenomicAnnotation	insertPoint
	)

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void broad.pda.feature.genome.Chromosome.invert

(

SequenceRegion

region

)

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boolean broad.pda.feature.genome.Chromosome.isAutosome

(

)

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static boolean broad.pda.feature.genome.Chromosome.isAutosome ( String  name )

static

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boolean broad.pda.feature.genome.Chromosome.isSexChromosome

(

)

static boolean broad.pda.feature.genome.Chromosome.isSexChromosome ( String  name )

static

int broad.pda.feature.genome.Chromosome.length

(

)

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void broad.pda.feature.genome.Chromosome.loadSequence

(

)

throws IOException

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void broad.pda.feature.genome.Chromosome.setSequenceFile

(

File

file

)

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List<? extends GenomicAnnotation> broad.pda.feature.genome.Chromosome.shuffle	(	GenomicAnnotation	toShuffle,
		List<?extends GenomicAnnotation >	toAvoid
	)

List<? extends GenomicAnnotation> broad.pda.feature.genome.Chromosome.shuffle	(	List<?extends GenomicAnnotation >	toShuffle,
		List<?extends GenomicAnnotation >	toAvoid
	)

Randomizes (using a quasi uniform distribution) a list of genomic annotations

Parameters

toShuffle	List of genomic annotations to shuffle
toAvoid	regions to avoid placing a shuffled annotation.

Returns

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List<? extends Annotation> broad.pda.feature.genome.Chromosome.shuffleWithinValid	(	Annotation	toShuffle,
		List<?extends Annotation >	valid
	)

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List<? extends GenomicAnnotation> broad.pda.feature.genome.Chromosome.shuffleWithinValid	(	List<?extends Annotation >	toShuffle,
		List<?extends Annotation >	valid
	)

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void broad.pda.feature.genome.Chromosome.unloadSequence

(

)

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

• java/broad/pda/feature/genome/Chromosome.java