net.maizegenetics.dna.map

Class TagsOnGeneticMap

AbstractTags

net.maizegenetics.dna.map.TagsOnGeneticMap

All Implemented Interfaces:

Tags

public class TagsOnGeneticMap
extends AbstractTags

Class that hold genetic position of tags, genetic positions are the position of markers associated with tags

Field Detail

gChr

protected kotlin.Array[] gChr

gPos

protected kotlin.Array[] gPos

ifPAV

protected kotlin.Array[] ifPAV

prediction

protected kotlin.Array[] prediction

Constructor Detail

TagsOnGeneticMap

public TagsOnGeneticMap(java.lang.String infileS,
                        net.maizegenetics.dna.tag.TagsByTaxa.FilePacking format)

Construct TOGM from a file

Parameters:

infileS - File name of input TagsOnGeneticMap file

format - FilePacking format

Method Detail

mergeTOGM

public void mergeTOGM(TagsOnGeneticMap another)

getGChr

public int getGChr(int index)

Return chromosome of genetic position

Parameters:

index -

Returns:

org.jetbrains.dokka.NodeRenderContent@7eccd711: Chromosome of genetic position

getGPos

public int getGPos(int index)

Return site of genetic position

Parameters:

index -

Returns:

org.jetbrains.dokka.NodeRenderContent@396ad322: Genetic position

getIfPAV

public byte getIfPAV(int index)

Return if this tag is PAV

Parameters:

index -

Returns:

org.jetbrains.dokka.NodeRenderContent@1cf5455:

isPAV

public boolean isPAV(int index)

Return if this tag is a PAV

Parameters:

index -

Returns:

org.jetbrains.dokka.NodeRenderContent@17722b76:

getPrediction

public float getPrediction(int index)

Return prediction value from model

Parameters:

index -

Returns:

org.jetbrains.dokka.NodeRenderContent@f9e12d6:

setIfPAV

public void setIfPAV(int index,
                     int value)

Set PAV value of tag

Parameters:

index -

value -

readDistFile

public void readDistFile(java.lang.String infileS,
                         net.maizegenetics.dna.tag.TagsByTaxa.FilePacking format)

Read tagsOnGeneticMap file

Parameters:

infileS -

format -

iniMatrix

protected void iniMatrix(int tagLengthInLong,
                         int tagNum)

Initialize the matrix of TOGM

Parameters:

tagLengthInLong - Tag length in Long primitive data type

tagNum - Total tag number

writeDistFile

public void writeDistFile(java.lang.String outfileS,
                          net.maizegenetics.dna.tag.TagsByTaxa.FilePacking format)

Write TagsOnGeneticMap file

Parameters:

outfileS - File name of output file

format - FilePacking format

writeDistFile

public void writeDistFile(java.lang.String outfileS,
                          kotlin.Array[] ifOut,
                          net.maizegenetics.dna.tag.TagsByTaxa.FilePacking format)

Write TagsOnGeneticMap file

Parameters:

outfileS -

ifOut -

format -

writeFastA

public void writeFastA(java.lang.String outfileS)

Output FASTA file of TOGM

Parameters:

outfileS -

writeFastQ

public void writeFastQ(java.lang.String outfileS)

Output FASTQ file of TOGM

Parameters:

outfileS -

swap

public void swap(int index1,
                 int index2)

sortByPosition

public void sortByPosition()

Sort TOGM by genetic position