net.maizegenetics.dna.tag

Class ReadsByTaxa

net.maizegenetics.dna.tag.ReadsByTaxa

All Implemented Interfaces:

Reads

public class ReadsByTaxa
implements Reads

Field Detail

haplotype

public kotlin.Array[] haplotype

hapDist

public kotlin.Array[] hapDist

taxaNum

public int taxaNum

haplotypeNum

public int haplotypeNum

taxaNames

public java.lang.String[] taxaNames

tagLengthInLong

public int tagLengthInLong

tagLength

public kotlin.Array[] tagLength

Constructor Detail

ReadsByTaxa

public ReadsByTaxa()

ReadsByTaxa

public ReadsByTaxa(java.lang.String infile,
                   boolean binary)

ReadsByTaxa

public ReadsByTaxa(java.lang.String[] taxaNames,
                   Reads theDistinctReads)

ReadsByTaxa

public ReadsByTaxa(kotlin.Array[] reads,
                   kotlin.Array[] readDist,
                   java.lang.String[] namesForTaxa)

Method Detail

getTaxaCount

public int getTaxaCount()

getTaxaName

public java.lang.String getTaxaName(int taxaIndex)

getTaxaNames

public java.lang.String[] getTaxaNames()

getIndexOfTaxaName

public int getIndexOfTaxaName(java.lang.String taxon)

getReadCountForTaxa

public int getReadCountForTaxa(int readIndex,
                               int taxaIndex)

setReadCountForTaxa

public void setReadCountForTaxa(int readIndex,
                                int taxaIndex,
                                int value)

addToReadCountForTaxa

public void addToReadCountForTaxa(int readIndex,
                                  int taxaIndex,
                                  int addValue)

getReadCountsForTaxa

public kotlin.Array[] getReadCountsForTaxa(int readIndex)

getTaxaCountForRead

public int getTaxaCountForRead(int readIndex)

getRead

public kotlin.Array[] getRead(int i)

getReadIndex

public int getReadIndex(kotlin.Array[] read)

Gets the first index of a read (the only one if a unique list). If the read is not found then it return a negative value indicating its insertion point.

Parameters:

read - as a compressed long array

Returns:

org.jetbrains.dokka.NodeRenderContent@47975430: the index of the read in the array

readTBTFile

public void readTBTFile(java.io.File inFile)

Converts a TBT Bit file to a ReadsByTaxa object (for compatibility only).

writeDistFile

public void writeDistFile(java.io.File outFile,
                          boolean binary,
                          int minCount)

filterForListOfReads

public void filterForListOfReads(java.io.File readsToKeepFile,
                                 java.io.File outFile,
                                 boolean binary)

writeReadCountFile

protected void writeReadCountFile(java.io.File outFile,
                                  boolean binary,
                                  int minCount)

getReadCount

public int getReadCount(int index)

getReadIndexSet

public kotlin.Array[] getReadIndexSet(kotlin.Array[] read)

areReadsUnique

public boolean areReadsUnique()

getReadTotal

public int getReadTotal()