net.maizegenetics.dna.tag

Interface TagsByTaxa

All Superinterfaces:

Tags

All Known Implementing Classes:

AbstractTagsByTaxa, TagsByTaxaByte, TagsByTaxaByteFileMap, TagsByTaxaByteFileMapSeq, TagsByTaxaByteHDF5TagGroups, TagsByTaxaByteHDF5TaxaGroups, TagsByTaxaShort

public TagsByTaxa
extends Tags

Tags by Taxa is the interface for tracking the distribution of tags across taxa. It can be thought of as a matrix of nTaxa by nTags. Taxa names are also maintained by this interface.

Method Detail

addReadsToTagTaxon

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

Method for incrementing the read depth for the specified tag and taxon.

Parameters:

tagIndex -

taxaIndex -

addValue - value to add to the current value

getIndexOfTaxaName

int getIndexOfTaxaName(java.lang.String taxon)

Get the index of a taxon based on its name

Parameters:

taxon - name of the taxon (sample)

Returns:

org.jetbrains.dokka.NodeRenderContent@124aba86: taxon index

getReadCountForTagTaxon

int getReadCountForTagTaxon(int tagIndex,
                            int taxaIndex)

Returns the read count for a specified tag and taxon

Parameters:

tagIndex -

taxaIndex -

Returns:

org.jetbrains.dokka.NodeRenderContent@71f52300: read depth

getTaxaReadCountsForTag

kotlin.Array[] getTaxaReadCountsForTag(int tagIndex)

Returns all read counts for a specified tag index.

Parameters:

tagIndex - index of the tag

Returns:

org.jetbrains.dokka.NodeRenderContent@790c50ff: array of read depths in order of taxa

truncateTaxonNames

void truncateTaxonNames()

Deprecated.

TODO: Jeff annotate this

setMethodByRows

void setMethodByRows(boolean rowSetMethod)

Parameters:

rowSetMethod -

getTaxaReadBitsForTag

OpenBitSet getTaxaReadBitsForTag(int tagIndex)

The presence/absence of the taxa in a bitSet format (1=present, 0=absent)

Parameters:

tagIndex - the index of the tag

Returns:

org.jetbrains.dokka.NodeRenderContent@1f5a7382: BitSet representing distribution of taxa

getTaxaCount

int getTaxaCount()

Returns the number of taxa (samples)

Returns:

org.jetbrains.dokka.NodeRenderContent@58036465:

getNumberOfTaxaWithTag

int getNumberOfTaxaWithTag(int readIndex)

Get the number of taxa with a given tag It is count of the taxa with readCount>0

Parameters:

readIndex -

Returns:

org.jetbrains.dokka.NodeRenderContent@b6b146: number of taxa with a read

getTaxaName

java.lang.String getTaxaName(int taxaIndex)

Returns the name of a taxon

Parameters:

taxaIndex - the index of the taxon

Returns:

org.jetbrains.dokka.NodeRenderContent@1ba68207: taxon name

getTaxaNames

java.lang.String[] getTaxaNames()

Returns an array of taxa names

getTaxaList

TaxaList getTaxaList()

Return taxa list of this alignment.

Returns:

org.jetbrains.dokka.NodeRenderContent@57ac2492: taxa list.

setReadCountForTagTaxon

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

Set the read depth for a specific tag and taxon. Overwrite the depth that was previously there.

Parameters:

tagIndex - index of the tag

taxaIndex - index of the taxon

value - read depth

writeDistFile

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

Write the TagsByTaxa object to a file in one of the FilePacking formats. MinCount is useful for excluding the low depth tags (many of these are sequencing errors).

Parameters:

outFile - File for saving this object

fileType - Determine how to output the depth

minCount - Only tags greater than minCount are output

initMatrices

void initMatrices(int taxaNum,
                  int tagNum)

Initializes the storage matrices for reading (unclear why in interface)

addTaxa

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

Add taxa to the TagsByTaxa matrix, they will all be set to distribution value of zero.

Parameters:

addTaxaNames -

getFileReadyForClosing

void getFileReadyForClosing()

In implementations that use a RandomAccessFile for storage, this clears the RAM buffer of any remaining data, writes it to the file on disk, and closes the file.