broad.pda.feature.genome.DirectoryInstalledGenomeAssembly Class Reference

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Public Member Functions
	DirectoryInstalledGenomeAssembly (File sequenceDirectory) throws Exception
List< Chromosome >	getAllNonRandomChromosomes ()
List< Chromosome >	getAllChromosomes ()
Chromosome	getX ()
void	writeSizes (String outFile) throws IOException
long	getNonRandomTotalSize ()
List< Chromosome >	getAutosomes ()
int	getAutosomeNumber ()
Chromosome	getChromosome (String chr)
List< Chromosome >	getUn ()
long	getGenomeSize ()
long	getAutosomeGenomeSize ()
Chromosome	drawChromosome ()
SequenceRegion	drawRandomRegion (int size)
Chromosome	drawAutosome ()
SequenceRegion	drawRandomAutosomeRegion (int size)
File	getSequenceDir ()
File	getRepeatFile (String chrSymbol)
File	getAnnotationDirectory ()
List< GenomicAnnotation >	getReducedRepresentation (int totalSize, List< GenomicAnnotation > toAvoid)
void	delete (SequenceRegion region)
void	invert (SequenceRegion region)
void	insert (SequenceRegion region, GenomicAnnotation insertionPoint)
void	translocate (SequenceRegion region1, SequenceRegion region2)

Protected Member Functions
boolean	areRepeatsInDeepDirHierarchy ()
boolean	useMergedUn ()
boolean	doRepeatListNeedsCleanup ()

Protected Attributes
File	sequenceDirectory

Detailed Description

Represents a Genome Assembly were each directory is in its own directory which includes the AGP file It is a convenient way to access genomic data when it is stored in this standard way.

Author

mgarber

Constructor & Destructor Documentation

broad.pda.feature.genome.DirectoryInstalledGenomeAssembly.DirectoryInstalledGenomeAssembly

(

File

sequenceDirectory

)

throws Exception

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Member Function Documentation

boolean broad.pda.feature.genome.DirectoryInstalledGenomeAssembly.areRepeatsInDeepDirHierarchy ( )

protected

to be overrided if repeats are in directories

Returns

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void broad.pda.feature.genome.DirectoryInstalledGenomeAssembly.delete

(

SequenceRegion

region

)

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boolean broad.pda.feature.genome.DirectoryInstalledGenomeAssembly.doRepeatListNeedsCleanup ( )

protected

subclasses should override if the repeats contain overlapping segments (i.e. are merged with trf)

Returns

Chromosome broad.pda.feature.genome.DirectoryInstalledGenomeAssembly.drawAutosome

(

)

Uses pseudo random number generation to draw a (non random) autosome with chance proportional to the autosome size

Returns

Chromosome draw by random.

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Chromosome broad.pda.feature.genome.DirectoryInstalledGenomeAssembly.drawChromosome

(

)

Uses pseudo random number generation to draw a (non random) chromosome with chance proportional to the chromosome size

Returns

Chromosome draw by random.

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SequenceRegion broad.pda.feature.genome.DirectoryInstalledGenomeAssembly.drawRandomAutosomeRegion

(

int

size

)

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SequenceRegion broad.pda.feature.genome.DirectoryInstalledGenomeAssembly.drawRandomRegion

(

int

size

)

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List<Chromosome> broad.pda.feature.genome.DirectoryInstalledGenomeAssembly.getAllChromosomes

(

)

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List<Chromosome> broad.pda.feature.genome.DirectoryInstalledGenomeAssembly.getAllNonRandomChromosomes

(

)

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File broad.pda.feature.genome.DirectoryInstalledGenomeAssembly.getAnnotationDirectory

(

)

long broad.pda.feature.genome.DirectoryInstalledGenomeAssembly.getAutosomeGenomeSize

(

)

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int broad.pda.feature.genome.DirectoryInstalledGenomeAssembly.getAutosomeNumber

(

)

List<Chromosome> broad.pda.feature.genome.DirectoryInstalledGenomeAssembly.getAutosomes

(

)

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Chromosome broad.pda.feature.genome.DirectoryInstalledGenomeAssembly.getChromosome

(

String

chr

)

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long broad.pda.feature.genome.DirectoryInstalledGenomeAssembly.getGenomeSize

(

)

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long broad.pda.feature.genome.DirectoryInstalledGenomeAssembly.getNonRandomTotalSize

(

)

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List<GenomicAnnotation> broad.pda.feature.genome.DirectoryInstalledGenomeAssembly.getReducedRepresentation	(	int	totalSize,
		List< GenomicAnnotation >	toAvoid
	)

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File broad.pda.feature.genome.DirectoryInstalledGenomeAssembly.getRepeatFile

(

String

chrSymbol

)

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File broad.pda.feature.genome.DirectoryInstalledGenomeAssembly.getSequenceDir

(

)

List<Chromosome> broad.pda.feature.genome.DirectoryInstalledGenomeAssembly.getUn

(

)

Chromosome broad.pda.feature.genome.DirectoryInstalledGenomeAssembly.getX

(

)

void broad.pda.feature.genome.DirectoryInstalledGenomeAssembly.insert	(	SequenceRegion	region,
		GenomicAnnotation	insertionPoint
	)

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void broad.pda.feature.genome.DirectoryInstalledGenomeAssembly.invert

(

SequenceRegion

region

)

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void broad.pda.feature.genome.DirectoryInstalledGenomeAssembly.translocate	(	SequenceRegion	region1,
		SequenceRegion	region2
	)

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boolean broad.pda.feature.genome.DirectoryInstalledGenomeAssembly.useMergedUn ( )

protected

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void broad.pda.feature.genome.DirectoryInstalledGenomeAssembly.writeSizes

(

String

outFile

)

throws IOException

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Member Data Documentation

File broad.pda.feature.genome.DirectoryInstalledGenomeAssembly.sequenceDirectory

protected

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

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