net.maizegenetics.dna.tag

Class AbstractTagsByTaxa

AbstractTags

net.maizegenetics.dna.tag.AbstractTagsByTaxa

All Implemented Interfaces:

Tags, TagsByTaxa

Direct Known Subclasses:

TagsByTaxaByte, TagsByTaxaByteFileMap, TagsByTaxaByteFileMapSeq, TagsByTaxaByteHDF5TagGroups, TagsByTaxaByteHDF5TaxaGroups, TagsByTaxaShort

public class AbstractTagsByTaxa
extends AbstractTags
implements TagsByTaxa

Basic method implementation of Tags by Taxa, including methods for reading and writing files

Field Detail

taxaNum

protected int taxaNum

taxaNames

protected java.lang.String[] taxaNames

Deprecated.

taxaList

protected TaxaList taxaList

Method Detail

getTaxaCount

public int getTaxaCount()

getTaxaName

public java.lang.String getTaxaName(int taxaIndex)

getTaxaNames

public java.lang.String[] getTaxaNames()

getTaxaList

public TaxaList getTaxaList()

getIndexOfTaxaName

public int getIndexOfTaxaName(java.lang.String taxon)

truncateTaxonNames

public void truncateTaxonNames()

Truncates each taxon name to everything up to the first colon, and converts all letters to lower case. This causes tag counts from taxa with identical names to be merged.

addReadsToTagTaxon

public void addReadsToTagTaxon(int tagIndex,
                               int taxaIndex,
                               int addValue)

getTaxaReadCountsForTag

public kotlin.Array[] getTaxaReadCountsForTag(int tagIndex)

getTaxaReadBitsForTag

public OpenBitSet getTaxaReadBitsForTag(int tagIndex)

Parameters:

tagIndex - Number of organisms/bits that must be stored in the bitset.

Returns:

org.jetbrains.dokka.NodeRenderContent@5d8f94b8: r A new OpenBitSet object containing the tag distribution of its parent TagsByTaxa object.

getNumberOfTaxaWithTag

public int getNumberOfTaxaWithTag(int readIndex)

readDistFile

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

readChannel

public void readChannel(java.io.File inFile)

writeDistFile

public void writeDistFile(java.io.File outFile,
                          net.maizegenetics.dna.tag.TagsByTaxa.FilePacking numberType,
                          int minCount)

writeReadCountFile

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

Writes a tag count file in binary (true) or text (false) format, containing the tag sequences from this TBT file.

getReadCount

public int getReadCount(int tagIndex)

areTagsUnique

public boolean areTagsUnique()