net.maizegenetics.dna.map

Interface Position

All Known Implementing Classes:

GeneralPosition

public Position

Defines a genomic positions and its known variants. Includes attributes of chromosome, position, sub-position, strand, name (or SNP ID), whether this position is a nucleotide, or includes an indel.

Field Detail

STRAND_PLUS

static byte STRAND_PLUS

See Also:

Constant Field Values

STRAND_MINUS

static byte STRAND_MINUS

See Also:

Constant Field Values

STRAND_UNKNOWN

static byte STRAND_UNKNOWN

See Also:

Constant Field Values

STRAND_PLUS_STR

static java.lang.String STRAND_PLUS_STR

See Also:

Constant Field Values

STRAND_MINUS_STR

static java.lang.String STRAND_MINUS_STR

See Also:

Constant Field Values

STRAND_UNKNOWN_STR

static java.lang.String STRAND_UNKNOWN_STR

See Also:

Constant Field Values

Method Detail

of

static Position of(int chromosomeNumber,
                   int positionWithinChromosome)

Create Position given chromosome number and position.

Parameters:

chromosomeNumber - chromosome number

positionWithinChromosome - physical position

Returns:

org.jetbrains.dokka.NodeRenderContent@15c38d8c: Position

of

static Position of(java.lang.String chromosomeName,
                   int positionWithinChromosome)

Create Position given chromosome name and position.

Parameters:

chromosomeName - chromosome name

positionWithinChromosome - physical position

Returns:

org.jetbrains.dokka.NodeRenderContent@4cd38fe7: Position

of

static Position of(Chromosome chromosome,
                   int positionWithinChromosome)

Create Position given chromosome and position.

Parameters:

chromosome - chromosome

positionWithinChromosome - physical position

Returns:

org.jetbrains.dokka.NodeRenderContent@5016a4c1: Position

builder

static net.maizegenetics.dna.map.GeneralPosition.Builder builder(int chromosomeNumber,
                                                                 int positionWithinChromosome)

Create Position Builder given chromosome number and position.

Parameters:

chromosomeNumber - chromosome number

positionWithinChromosome - physical position

Returns:

org.jetbrains.dokka.NodeRenderContent@5b7fa7ce: Position Builder

builder

static net.maizegenetics.dna.map.GeneralPosition.Builder builder(java.lang.String chromosomeName,
                                                                 int positionWithinChromosome)

Create Position Builder given chromosome name and position.

Parameters:

chromosomeName - chromosome name

positionWithinChromosome - physical position

Returns:

org.jetbrains.dokka.NodeRenderContent@5259fec0: Position Builder

getStrand

static java.lang.String getStrand(byte value)

getStrand

static byte getStrand(java.lang.String value)

getChromosome

Chromosome getChromosome()

Return the locus (generally a chromosome) of a site

getPosition

int getPosition()

Return the physical position of a site

getInsertionPosition

short getInsertionPosition()

Return the insertion-position of a site. This will be zero for the main physical position and sequentially numbered (1, 2, 3,...) for any (if any) sites with the same net.maizegenetics.dna.map.Position$getPosition(). This will mostly be used for insertions relative to the reference.

See Also:

net.maizegenetics.dna.map.Position$getPosition()

getStrand

byte getStrand()

Return the strand for a site definition

getStrandStr

java.lang.String getStrandStr()

getSNPID

java.lang.String getSNPID()

Return the ID (name) for a site

getActualSNPID

java.lang.String getActualSNPID()

Returns SNP ID only if assigned. getSNPID() returns a default if not assigned.

Returns:

org.jetbrains.dokka.NodeRenderContent@2a5efdb: SNP ID

isNucleotide

boolean isNucleotide()

Whether the position is a nucleotide position or another marker type (SSR, AFLP, RAPD, CNV, which are recoded with text states)

isIndel

boolean isIndel()

Whether the position includes indels, which would be defined in the variants

getKnownVariants

java.lang.String[] getKnownVariants()

Returns the nature of the polymorphism {"ACTAT","-"} or {"A","C","G"} or {"100","103","106"}

getGlobalMAF

float getGlobalMAF()

Return the minor allele frequency in a global scope

getGlobalSiteCoverage

float getGlobalSiteCoverage()

Returns the proportion of genotypes scored at a given site

getAllele

byte getAllele(WHICH_ALLELE alleleType)

Return the allele specified by alleleType, if unknown Alignment.Unknown is return

getAnnotation

GeneralAnnotation getAnnotation()