Uses of Class
org.snpeff.interval.Chromosome
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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.unity -
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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)
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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 chromosomeMethods 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 chromosomestatic 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)
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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)
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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
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)
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