net.maizegenetics.dna.tag

Class TagsByTaxaByteFileMap

AbstractTags

AbstractTagsByTaxa

net.maizegenetics.dna.tag.TagsByTaxaByteFileMap

All Implemented Interfaces:

Tags, TagsByTaxa

public class TagsByTaxaByteFileMap
extends AbstractTagsByTaxa

A byte implementation of TagByTaxa, maximum depth of tags is 127. This version works directly from a RandomAccessFile, which is slow but can work with very large files. It will need to be transitioned nio2, when Java 7 comes out. If possible, it holds the current row cached in memory, so try to work with the files sequentially.

Constructor Detail

TagsByTaxaByteFileMap

public TagsByTaxaByteFileMap(java.lang.String infile)

TagsByTaxaByteFileMap

public TagsByTaxaByteFileMap(java.lang.String outFile,
                             java.lang.String[] taxaNames,
                             Tags theTags)

Creates an empty Byte File Map

Parameters:

outFile -

taxaNames -

theTags -

Method Detail

readDistFile

public void readDistFile(java.io.File inFile,
                         net.maizegenetics.dna.tag.TagsByTaxa.FilePacking binary)

setReadCountForTagTaxon

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

setFastPointReadCountForTagTaxon

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

setFastReadCountForAdjacentTagTaxonSet

public void setFastReadCountForAdjacentTagTaxonSet(int tagIndex,
                                                   int firstTaxaIndex,
                                                   kotlin.Array[] values)

setMethodByRows

public void setMethodByRows(boolean rowSetMethod)

getFileReadyForClosing

public void getFileReadyForClosing()

getReadCountForTagTaxon

public int getReadCountForTagTaxon(int tagIndex,
                                   int taxaIndex)

initMatrices

public void initMatrices(int taxaNum,
                         int tagNum)

addTaxa

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

main

public static void main(java.lang.String[] args)