net.maizegenetics.dna.tag

Class TagsByTaxaByteFileMapSeq

AbstractTags

AbstractTagsByTaxa

net.maizegenetics.dna.tag.TagsByTaxaByteFileMapSeq

All Implemented Interfaces:

Tags, TagsByTaxa

public class TagsByTaxaByteFileMapSeq
extends AbstractTagsByTaxa

A bit implementation of TagByTaxa, so only presence or absence of a tags is known. 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

TagsByTaxaByteFileMapSeq

public TagsByTaxaByteFileMapSeq(java.lang.String infile)

Method Detail

readDistFile

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

getReadCountForTagTaxon

public int getReadCountForTagTaxon(int tagIndex,
                                   int taxaIndex)

advanceToTagDist

public kotlin.Array[] advanceToTagDist(kotlin.Array[] tag)

initMatrices

public void initMatrices(int taxaNum,
                         int tagNum)

addTaxa

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

setMethodByRows

public void setMethodByRows(boolean rowSetMethod)

setReadCountForTagTaxon

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

getFileReadyForClosing

public void getFileReadyForClosing()