net.maizegenetics.dna.tag

Class TagsByTaxaByteHDF5TagGroups

AbstractTags

AbstractTagsByTaxa

net.maizegenetics.dna.tag.TagsByTaxaByteHDF5TagGroups

All Implemented Interfaces:

Tags, TagsByTaxa

public class TagsByTaxaByteHDF5TagGroups
extends AbstractTagsByTaxa

Tags by Taxa file based on the HDF5 data structure. This version is optimized for rapid access of taxa within Tag (ie it buffers the taxa counts within one tag).

Constructor Detail

TagsByTaxaByteHDF5TagGroups

public TagsByTaxaByteHDF5TagGroups(Tags inTags,
                                   java.lang.String newHDF5file)

TagsByTaxaByteHDF5TagGroups

public TagsByTaxaByteHDF5TagGroups(java.lang.String infile)

Method Detail

writeDistFile

public void writeDistFile(java.lang.String newHDF5file,
                          kotlin.Array[] tagIndex)

createRandomDistribution

public static kotlin.Array[] createRandomDistribution(int arraySize,
                                                      double proportionToFill,
                                                      int maxValue)

encodeBySign

public static kotlin.Array[] encodeBySign(kotlin.Array[] source,
                                          int chunkSize)

encodeBySign

public static kotlin.Array[] encodeBySign(kotlin.Array[] source)

decodeBySign

public static kotlin.Array[] decodeBySign(kotlin.Array[] srcCompChunk)

decodeBySign

public static kotlin.Array[] decodeBySign(kotlin.Array[] source)

convertToTBTByte

public TagsByTaxaByte convertToTBTByte()

main

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

getIndexOfTaxaName

public int getIndexOfTaxaName(java.lang.String taxon)

getReadCountForTagTaxon

public int getReadCountForTagTaxon(int tagIndex,
                                   int taxaIndex)

setMethodByRows

public void setMethodByRows(boolean rowSetMethod)

setReadCountForTagTaxon

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

initMatrices

public void initMatrices(int taxaNum,
                         int tagNum)

addTaxa

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

getFileReadyForClosing

public void getFileReadyForClosing()