Uses of Class
org.snpeff.interval.Genome

Packages that use Genome

Package	Description
org.snpeff
org.snpeff.binseq
org.snpeff.codons
org.snpeff.fileIterator
org.snpeff.fileIterator.microCosm
org.snpeff.interval
org.snpeff.interval.tree
org.snpeff.probablility
org.snpeff.serializer
org.snpeff.snpEffect
org.snpeff.snpEffect.testCases.integration
org.snpeff.snpEffect.testCases.unity
org.snpeff.spliceSites
org.snpeff.stats

Uses of Genome in org.snpeff

Fields in org.snpeff declared as Genome

Modifier and Type	Field	Description
protected Genome	SnpEff.genome

Uses of Genome in org.snpeff.binseq

Constructors in org.snpeff.binseq with parameters of type Genome

Constructor	Description
GenomicSequences(Genome genome)

Uses of Genome in org.snpeff.codons

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

Modifier and Type	Method	Description
java.lang.String	CodonTables.aa(java.lang.String codon, Genome genome, java.lang.String chromosome)	Translate a codon into an amino acid for a given genome+chromosome
java.util.List<java.lang.String>	CodonTables.codon(java.lang.String aa, Genome genome, java.lang.String chromosome)	Translate an amino acid into a codon for a given genome+chromosome
CodonTable	CodonTables.getTable(Genome genome)	Get default genome-wide codon table
CodonTable	CodonTables.getTable(Genome genome, java.lang.String chromosome)	Get a codon table WARNING: It will return the standard codon table if nothing if found
void	CodonTables.set(Genome genome, CodonTable codonTable)	Set a codon table for a all chromosomes in a genome I.e.: Default genome-wide chromosome table
void	CodonTables.set(Genome genome, Chromosome chr, CodonTable codonTable)	Set a codon table for a given genome & chromosome

Constructors in org.snpeff.codons with parameters of type Genome

Constructor	Description
FindRareAaIntervals(Genome genome)

Uses of Genome in org.snpeff.fileIterator

Fields in org.snpeff.fileIterator declared as Genome

Modifier and Type	Field	Description
protected Genome	MarkerFileIterator.genome
protected Genome	VcfHapMapFileIterator.genome

Methods in org.snpeff.fileIterator that return Genome

Modifier and Type	Method	Description
Genome	MarkerFileIterator.getGenome()

Constructors in org.snpeff.fileIterator with parameters of type Genome

Constructor	Description
BedFileIterator(java.lang.String fileName, Genome genome)
Gff3FileIterator(java.lang.String fileName, Genome genome)
Gff3FileIterator(java.lang.String fileName, Genome genome, int inOffset)
MarkerFileIterator(java.lang.String fileName, Genome genome, int inOffset)
MotifFileIterator(java.lang.String fileName, Genome genome, Jaspar jaspar)
RegulationBedFileIterator(java.lang.String fileName, Genome genome, java.lang.String name, java.lang.String cellType)
RegulationFileIterator(java.lang.String fileName, Genome genome, int inOffset)
RegulationGffFileIterator(java.lang.String fileName, Genome genome)
VariantFileIterator(java.lang.String fileName, Genome genome)
VariantTxtFileIterator(java.lang.String fileName, Genome genome)
VcfFileIterator(java.lang.String fileName, Genome genome)
VcfHapMapFileIterator(java.lang.String hapMapFileName, java.lang.String fatsaFileName, Genome genome)

Uses of Genome in org.snpeff.fileIterator.microCosm

Methods in org.snpeff.fileIterator.microCosm with parameters of type Genome

Modifier and Type	Method	Description
MicroRnaBindingSite	MicroCosmEntry.getMarker(Genome genome)	Create a MicroRnaBindingSite marker

Uses of Genome in org.snpeff.interval

Methods in org.snpeff.interval that return Genome

Modifier and Type	Method	Description
static Genome	Genome.createFromFaidx(java.lang.String genomeName, java.lang.String faidxFile)	Create a genome from a faidx file.
Genome	Interval.getGenome()	Find genome

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

Modifier and Type	Method	Description
void	Markers.load(java.lang.String fileName, Genome genome)
protected void	GffMarker.parse(Genome genome, java.lang.String line)	Parse an entry (line) from a GFF file
void	Marker.readTxt(java.lang.String line, int lineNum, Genome genome, int positionBase)	Parse a line (form a file) Format: "chromosome \t start \t end \t id \n"
static Markers	MarkerUtil.readTxt(java.lang.String fileName, Genome genome, int positionBase)	Read intervals from a file using a simplt TXT format Format: chr \t start \t end \t id Note: Zero-based positions

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

Constructor	Description
Chromosome(Genome parent, int start, int end, java.lang.String id)
CytoBands(Genome genome)
ExonSpliceCharacterizer(Genome genome)
Genes(Genome genome)
GffMarker(Genome genome, java.lang.String line)
Gtf2Marker(Genome genome, java.lang.String line)

Uses of Genome in org.snpeff.interval.tree

Methods in org.snpeff.interval.tree with parameters of type Genome

Modifier and Type	Method	Description
void	IntervalTree.load(java.lang.String fileName, Genome genome)
void	IntervalTreeArray.load(java.lang.String fileName, Genome genome)
void	IntervalTreeOri.load(java.lang.String fileName, Genome genome)
void	Itree.load(java.lang.String fileName, Genome genome)	Load intervals from file

Uses of Genome in org.snpeff.probablility

Constructors in org.snpeff.probablility with parameters of type Genome

Constructor	Description
RandMarker(Genome genome)
RandMarker(Genome genome, int seed)

Uses of Genome in org.snpeff.serializer

Constructors in org.snpeff.serializer with parameters of type Genome

Constructor	Description
MarkerSerializer(Genome genome)

Uses of Genome in org.snpeff.snpEffect

Fields in org.snpeff.snpEffect declared as Genome

Modifier and Type	Field	Description
protected Genome	Hgvs.genome

Methods in org.snpeff.snpEffect that return Genome

Modifier and Type	Method	Description
Genome	Config.getGenome()
Genome	Config.getGenome(java.lang.String genomeId)
Genome	SnpEffectPredictor.getGenome()

Constructors in org.snpeff.snpEffect with parameters of type Genome

Constructor	Description
Config(Genome genome)	This constructor is used in test cases
SnpEffectPredictor(Genome genome)

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

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

Modifier and Type	Field	Description
protected Genome	TestCasesHgvsBase.genome

Methods in org.snpeff.snpEffect.testCases.integration with parameters of type Genome

Modifier and Type	Method	Description
java.lang.String	TestCasesIntegrationBase.showTranscripts(Genome genome)
java.lang.String	TestCasesIntegrationBase.showTranscripts(Genome genome, boolean hideProtein)	Show a genome in a 'standard' way

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

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

Modifier and Type	Field	Description
protected Genome	TestCasesBase.genome
protected Genome	TestCasesIntervalTree.genome
protected Genome	TestCasesVariantDecompose.genome
Genome	TestGenome.genome

Uses of Genome in org.snpeff.spliceSites

Constructors in org.snpeff.spliceSites with parameters of type Genome

Constructor	Description
TranscriptSet(Genome genome)

Uses of Genome in org.snpeff.stats

Constructors in org.snpeff.stats with parameters of type Genome

Constructor	Description
VariantEffectStats(Genome genome)
VariantStats(Genome genome)