net.maizegenetics.dna.tag

Class TagsByTaxaByteHDF5TaxaGroups

AbstractTags

AbstractTagsByTaxa

net.maizegenetics.dna.tag.TagsByTaxaByteHDF5TaxaGroups

All Implemented Interfaces:

Tags, TagsByTaxa

public class TagsByTaxaByteHDF5TaxaGroups
extends AbstractTagsByTaxa

Tags by Taxa file based on the HDF5 data structure. This version is optimized for rapid access of tags within taxa (ie it buffers the tag counts within one taxon). It is good for adding, removing, and combining taxa

Constructor Detail

TagsByTaxaByteHDF5TaxaGroups

public TagsByTaxaByteHDF5TaxaGroups(Tags inTags,
                                    java.lang.String newHDF5file)

TagsByTaxaByteHDF5TaxaGroups

public TagsByTaxaByteHDF5TaxaGroups(java.lang.String infile)

Method Detail

addTaxon

public boolean addTaxon(java.lang.String taxonName,
                        kotlin.Array[] values)

addTaxon

public boolean addTaxon(java.lang.String taxonName)

deleteTaxon

public boolean deleteTaxon(java.lang.String taxonName)

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)

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)

getReadCountDistributionForTaxon

public kotlin.Array[] getReadCountDistributionForTaxon(int taxaIndex)

getNumberOfChunks

public int getNumberOfChunks()

getNumberOfTagsPerChunk

public int getNumberOfTagsPerChunk()

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()

getTaxaCount

public int getTaxaCount()

getTaxaName

public java.lang.String getTaxaName(int taxaIndex)

getTaxaNames

public java.lang.String[] getTaxaNames()

convertToTBTByte

public TagsByTaxaByte convertToTBTByte()