net.maizegenetics.analysis.gbs

Class Barcode

net.maizegenetics.analysis.gbs.Barcode

public class Barcode

Container class for storing information on GBS barcodes.

Constructor Detail

Barcode

public Barcode(java.lang.String barcodeS,
               java.lang.String[] overhangSunsort,
               java.lang.String taxa,
               int globalTaxaIndex,
               java.lang.String flowcell,
               java.lang.String lane)

Constructor creating a barcode

Parameters:

barcodeS - barcode sequence

overhangSunsort - overhang sequence array unsorted (array size is 1 for non-degerate restriction enzymes, degenerate enzymes >1)

taxa - name of taxon (sample)

flowcell - name of the flowcell

lane - name of the lane

Barcode

public Barcode(java.lang.String barcodeS,
               java.lang.String[] overhangSunsort,
               java.lang.String taxa,
               int globalTaxaIndex,
               java.lang.String tissue,
               int globalTissueIndex,
               java.lang.String flowcell,
               java.lang.String lane)

Constructor creating a barcode

Parameters:

barcodeS - barcode sequence

overhangSunsort - overhang sequence array unsorted (array size is 1 for non-degerate restriction enzymes, degenerate enzymes >1)

taxa - name of taxon (sample)

tissue - name identifying the tissue

flowcell - name of the flowcell

lane - name of the lane

Method Detail

compareSequence

public int compareSequence(long queryLong,
                           int maxDivCheck)

Return the minimum sequence divergence between a query sequence and barcode with its overhang

Parameters:

queryLong - query sequence encoded in 2-bit long

maxDivCheck - maximum divergence to search upto

Returns:

org.jetbrains.dokka.NodeRenderContent@47d09b6e: minimum divergence between barcode and query

compareTo

public int compareTo(Barcode anotherBarcode)

getTaxaName

public java.lang.String getTaxaName()

getBarcodeString

public java.lang.String getBarcodeString()

getBarWOverHangLong

public kotlin.Array[] getBarWOverHangLong()

getBarWOverHang

public java.lang.String[] getBarWOverHang()

getBarWithOverHangLength

public int getBarWithOverHangLength()

getBarLength

public int getBarLength()

getTaxaIndex

public int getTaxaIndex()

getTissueIndex

public int getTissueIndex()

getTaxon

public Taxon getTaxon()

toString

public java.lang.String toString()