net.maizegenetics.dna.map

Interface PositionList

public PositionList

List of positions in the genome. This type is used by every interface GenotypeTable, but it can also be used list of GWAS results and other genomic annotations.

See Also:

interface GenotypeTable

Method Detail

allele

byte allele(WHICH_ALLELE alleleType,
            int site)

Return the (haploid) reference allele at given site.

Parameters:

site - site

Returns:

org.jetbrains.dokka.NodeRenderContent@7f2bb3da: byte from 0-15

alleles

kotlin.Array[] alleles(WHICH_ALLELE alleleType,
                       int startSite,
                       int endSite)

Returns reference sequence alleles in specified range. End site not included. One haploid allele for each site.

Parameters:

startSite - start site

endSite - end site (not included in result)

Returns:

org.jetbrains.dokka.NodeRenderContent@6265a1fa: reference sequence of haploid allele values.

alleleForAllSites

kotlin.Array[] alleleForAllSites(WHICH_ALLELE alleleType)

Returns sequence alleles. One haploid allele for each site.

Returns:

org.jetbrains.dokka.NodeRenderContent@2d7bf4ba: reference sequence of haploid allele values.

hasReference

boolean hasReference()

Return whether this alignment has defined reference sequence.

Returns:

org.jetbrains.dokka.NodeRenderContent@23603687: true if this alignment has reference sequence.

siteName

java.lang.String siteName(int site)

Get SNP ID for specified site.

Parameters:

site - site

Returns:

org.jetbrains.dokka.NodeRenderContent@177e452: site name

numberOfSites

int numberOfSites()

Returns total number of sites of this alignment.

Returns:

org.jetbrains.dokka.NodeRenderContent@4e52eff7: number of sites

chromosomeSiteCount

int chromosomeSiteCount(Chromosome chromosome)

Return number of sites for given Chromosome

Parameters:

chromosome -

Returns:

org.jetbrains.dokka.NodeRenderContent@3c7e0ca3: number of sites

startAndEndOfChromosome

kotlin.Array[] startAndEndOfChromosome(Chromosome chromosome)

Get the first (inclusive) and last (inclusive) site of the specified chromosome in this alignment.

Parameters:

chromosome - chromosome

Returns:

org.jetbrains.dokka.NodeRenderContent@1e88d1a5: first and last site

chromosomalPosition

int chromosomalPosition(int site)

Returns the physical position at given site.

Parameters:

site - site

Returns:

org.jetbrains.dokka.NodeRenderContent@20e3f352: physical position

siteOfPhysicalPosition

int siteOfPhysicalPosition(int physicalPosition,
                           Chromosome chromosome)

Return site of given physical position in chromosome. If the physical position doesn't exist, (-(insertion point) - 1) is returned. If chromosome is not found, an exception is thrown.

Parameters:

physicalPosition - physical position

chromosome - chromosome. if null, the first chromosome is used.

Returns:

org.jetbrains.dokka.NodeRenderContent@79978dee: index

siteOfPhysicalPosition

int siteOfPhysicalPosition(int physicalPosition,
                           Chromosome chromosome,
                           java.lang.String snpName)

Return site of given physical position / SNP ID in chromosome. If the physical position doesn't exist, (-(insertion point) - 1) is returned. If chromosome is not found, an exception is thrown. This is to support multiple sites with the same physical position but different SNP IDs.

Parameters:

physicalPosition - physical position

chromosome - chromosome. if null, the first chromosome is used.

snpName - SNP ID

Returns:

org.jetbrains.dokka.NodeRenderContent@35408d6b: index

physicalPositions

kotlin.Array[] physicalPositions()

Returns all physical positions.

Returns:

org.jetbrains.dokka.NodeRenderContent@6d1d679f: physical positions.

chromosomeName

java.lang.String chromosomeName(int site)

Return Chromosome Name for given site.

Parameters:

site - site

Returns:

org.jetbrains.dokka.NodeRenderContent@525b600d: Chromosome Name

chromosome

Chromosome chromosome(int site)

Return Chromosome for given site.

Parameters:

site - site

Returns:

org.jetbrains.dokka.NodeRenderContent@17667f55: Chromosome

chromosome

Chromosome chromosome(java.lang.String name)

Return Chromosome with matching name. First to match will be returned.

Parameters:

name - name

Returns:

org.jetbrains.dokka.NodeRenderContent@26fc8307: Chromosome

chromosomes

Chromosome[] chromosomes()

Return all chromosomes.

Returns:

org.jetbrains.dokka.NodeRenderContent@20db29d8: chromosomes

numChromosomes

int numChromosomes()

Return number of chromosomes.

Returns:

org.jetbrains.dokka.NodeRenderContent@29896ec6: number of chromosomes

chromosomesOffsets

kotlin.Array[] chromosomesOffsets()

Returns starting site for each chromosome.

Returns:

org.jetbrains.dokka.NodeRenderContent@d313075: starting site for each chromosome.

indelSize

int indelSize(int site)

Return size of indel at given site.

Parameters:

site - site

Returns:

org.jetbrains.dokka.NodeRenderContent@4f977e6f: indel size

isIndel

boolean isIndel(int site)

Returns whether give site is an indel.

Parameters:

site - site

Returns:

org.jetbrains.dokka.NodeRenderContent@367b1bac: true if indel

genomeVersion

java.lang.String genomeVersion()

Gets the Genome Assembly.

Returns:

org.jetbrains.dokka.NodeRenderContent@5466acfb: the genome assembly.

isPositiveStrand

boolean isPositiveStrand(int site)

Return whether is positive strand at given site.

Parameters:

site - site

Returns:

org.jetbrains.dokka.NodeRenderContent@50d08c9a: whether is positive strand.

collectValidateOrder

static java.util.stream.Collector<net.maizegenetics.dna.map.Position,?,net.maizegenetics.dna.map.PositionList> collectValidateOrder()

Returns PositionList Collector that validates order of Positions.

Returns:

org.jetbrains.dokka.NodeRenderContent@24c0e4e9: collector

collectReorder

static java.util.stream.Collector<net.maizegenetics.dna.map.Position,?,net.maizegenetics.dna.map.PositionList> collectReorder()

Returns PositionList Collector that reorders position if necessary.

Returns:

org.jetbrains.dokka.NodeRenderContent@4a083da6: collector