Uses of Class
org.snpeff.interval.Chromosome

Packages that use Chromosome

Package	Description
org.snpeff.codons
org.snpeff.fileIterator
org.snpeff.gsa
org.snpeff.interval
org.snpeff.snpEffect.factory
org.snpeff.snpEffect.testCases.integration
org.snpeff.snpEffect.testCases.unity

Uses of Chromosome in org.snpeff.codons

Methods in org.snpeff.codons with parameters of type Chromosome

Modifier and Type	Method	Description
void	CodonTables.set(Genome genome, Chromosome chr, CodonTable codonTable)	Set a codon table for a given genome & chromosome

Uses of Chromosome in org.snpeff.fileIterator

Methods in org.snpeff.fileIterator that return Chromosome

Modifier and Type	Method	Description
Chromosome	MarkerFileIterator.getChromosome(java.lang.String chromoName)	Find chromosome 'chromoName'.

Methods in org.snpeff.fileIterator with parameters of type Chromosome

Modifier and Type	Method	Description
void	MarkerFileIterator.sanityCheckChromo(java.lang.String chromoName, Chromosome chromo)	Sanity check

Uses of Chromosome in org.snpeff.gsa

Methods in org.snpeff.gsa that return Chromosome

Modifier and Type	Method	Description
Chromosome	ChrPosScoreList.getChromosome(int index)

Methods in org.snpeff.gsa with parameters of type Chromosome

Modifier and Type	Method	Description
void	ChrPosScoreList.add(Chromosome chr, int start, int end, double score)

Uses of Chromosome in org.snpeff.interval

Methods in org.snpeff.interval that return Chromosome

Modifier and Type	Method	Description
Chromosome	Chromosome.cloneShallow()
Chromosome	Genome.getChromosome(java.lang.String chromoName)	Find chromosome 'chromoName'
Chromosome	Interval.getChromosome()
Chromosome	Genome.getOrCreateChromosome(java.lang.String chromoName)	Get or create a chromosome

Methods in org.snpeff.interval that return types with arguments of type Chromosome

Modifier and Type	Method	Description
java.util.Collection<Chromosome>	Genome.getChromosomes()
java.util.List<Chromosome>	Genome.getChromosomesSortedSize()	Return chromosomes sorted by size (largest chromosomes first)
java.util.Iterator<Chromosome>	Genome.iterator()

Methods in org.snpeff.interval with parameters of type Chromosome

Modifier and Type	Method	Description
void	Genome.add(Chromosome chromo)	Add a chromosome
static java.util.List<Variant>	Variant.factory(Chromosome chromo, int start, java.lang.String ref, java.lang.String altStr, java.lang.String id, boolean expand)	Create variants from ALT (which can be multiple values)
void	Genome.remove(Chromosome chromo)	Remove a chromosome WARINIG: Doesn't check any dependencies!

Constructors in org.snpeff.interval with parameters of type Chromosome

Constructor	Description
Intergenic(Chromosome parent, int start, int end, boolean strandMinus, java.lang.String id, java.lang.String name)
IntergenicConserved(Chromosome parent, int start, int end, boolean strandMinus, java.lang.String id)
VariantBnd(Marker parent, int start, java.lang.String ref, java.lang.String alt, Chromosome chrTr, int startTr, boolean left, boolean before)

Uses of Chromosome in org.snpeff.snpEffect.factory

Methods in org.snpeff.snpEffect.factory that return Chromosome

Modifier and Type	Method	Description
Chromosome	SnpEffPredictorFactoryRand.getChromo()
protected Chromosome	SnpEffPredictorFactory.getOrCreateChromosome(java.lang.String chromoName)	Get a chromosome.

Methods in org.snpeff.snpEffect.factory with parameters of type Chromosome

Modifier and Type	Method	Description
protected void	SnpEffPredictorFactory.add(Chromosome chromo)
void	SnpEffPredictorFactoryRand.setChromo(Chromosome chromo)

Uses of Chromosome in org.snpeff.snpEffect.testCases.integration

Fields in org.snpeff.snpEffect.testCases.integration declared as Chromosome

Modifier and Type	Field	Description
protected Chromosome	TestCasesHgvsBase.chromosome

Uses of Chromosome in org.snpeff.snpEffect.testCases.unity

Fields in org.snpeff.snpEffect.testCases.unity declared as Chromosome

Modifier and Type	Field	Description
protected Chromosome	TestCasesVariantDecompose.chr
Chromosome	TestGenome.chr
protected Chromosome	TestCasesBase.chromosome
protected Chromosome	TestCasesIntervalTree.chromosome

Methods in org.snpeff.snpEffect.testCases.unity with parameters of type Chromosome

Modifier and Type	Method	Description
protected Markers	TestCasesIntervalTree.createRandomLargeMarkers(Chromosome chr, int num)
protected Markers	TestCasesIntervalTree.createRandomSmallMarkers(Chromosome chr, int num)