net.maizegenetics.dna.tag

Class TagsByTaxaShort

AbstractTags

AbstractTagsByTaxa

net.maizegenetics.dna.tag.TagsByTaxaShort

All Implemented Interfaces:

Tags, TagsByTaxa

public class TagsByTaxaShort
extends AbstractTagsByTaxa

Tags by taxa that supports depths captured by a short (max 32767)

Constructor Detail

TagsByTaxaShort

public TagsByTaxaShort()

TagsByTaxaShort

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

TagsByTaxaShort

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

TagsByTaxaShort

public TagsByTaxaShort(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()