net.maizegenetics.dna.tag

Class TagsByTaxaByte

AbstractTags

AbstractTagsByTaxa

net.maizegenetics.dna.tag.TagsByTaxaByte

All Implemented Interfaces:

Tags, TagsByTaxa

public class TagsByTaxaByte
extends AbstractTagsByTaxa

A bit implementation of TagByTaxa, so only counts as high as 127 can be maintained.

Constructor Detail

TagsByTaxaByte

public TagsByTaxaByte()

TagsByTaxaByte

public TagsByTaxaByte(java.lang.String infile,
                      net.maizegenetics.dna.tag.TagsByTaxa.FilePacking binary)

TagsByTaxaByte

public TagsByTaxaByte(java.lang.String[] taxaNames,
                      Tags theDistinctReads)

TagsByTaxaByte

public TagsByTaxaByte(kotlin.Array[] tags,
                      kotlin.Array[] tagLength,
                      kotlin.Array[] tagDist,
                      java.lang.String[] namesForTaxa)

TagsByTaxaByte

public TagsByTaxaByte(kotlin.Array[] reads,
                      kotlin.Array[] readDist,
                      java.lang.String[] namesForTaxa)

Method Detail

setReadCountForTagTaxon

public void setReadCountForTagTaxon(int tagIndex,
                                    int taxaIndex,
                                    int value)

getReadCountForTagTaxon

public int getReadCountForTagTaxon(int tagIndex,
                                   int taxaIndex)

initMatrices

public void initMatrices(int taxaNum,
                         int tagNum)

addTaxa

public void addTaxa(java.lang.String[] addTaxaNames)

setMethodByRows

public void setMethodByRows(boolean rowSetMethod)

getFileReadyForClosing

public void getFileReadyForClosing()