net.maizegenetics.dna.tag

Class PETagCounts

AbstractPETags

net.maizegenetics.dna.tag.PETagCounts

All Implemented Interfaces:

PETags

public class PETagCounts
extends AbstractPETags

Hold PE tags and their counts, also including contigs

Constructor Detail

PETagCounts

public PETagCounts(java.lang.String inFile,
                   net.maizegenetics.dna.tag.TagsByTaxa.FilePacking format)

Construct PETagCounts from a file

Parameters:

inFile - Filename of PETagCounts

format - FilePacking format

PETagCounts

public PETagCounts(int tagLengthInLong,
                   int tagNum)

Initialize PETagCounts with empty matrix

Parameters:

tagLengthInLong - Tag length In Long primitive data type

tagNum - Tag number

Method Detail

getCollapsedPETagCounts

public PETagCounts getCollapsedPETagCounts()

Collapse the PETagCounts and return a new collapsed PETagCounts object

Returns:

org.jetbrains.dokka.NodeRenderContent@58999b28: Collapsed PETagCounts object

collapseCounts

public int collapseCounts()

Collapse PETagCounts, the tag count of collapsed tags is set to 0

Returns:

org.jetbrains.dokka.NodeRenderContent@593db937: total read count of collapsed PE tags

getMergedPETagCounts

public PETagCounts getMergedPETagCounts(PETagCounts another,
                                        boolean ifCollapsed)

Merge two PETagCounts objects

Parameters:

another - Another PETagCounts object

ifCollapsed - Boolean value of another PETagCounts object (If it is collapsed). Both objects should be collapsed first

Returns:

org.jetbrains.dokka.NodeRenderContent@6b9b6fd4:

getTotalReadCount

public int getTotalReadCount()

Return total read count of PE tags

Returns:

org.jetbrains.dokka.NodeRenderContent@1860dbd5: Total read count of this PETagCounts object

getReadCount

public int getReadCount(int index)

Return read count of a PE tag

Parameters:

index -

Returns:

org.jetbrains.dokka.NodeRenderContent@cb4532a: Read count of a PE tag

readDistFile

public void readDistFile(java.lang.String infileS,
                         net.maizegenetics.dna.tag.TagsByTaxa.FilePacking format)

Read PETagCounts file

Parameters:

infileS - File name of PETagCounts file

format - FilePacking format

writeDistFile

public void writeDistFile(java.lang.String outfileS,
                          net.maizegenetics.dna.tag.TagsByTaxa.FilePacking format,
                          int minCount)

Write PETagCounts file

Parameters:

outfileS - File name of output PETagCounts file

format - FilePakcing format

minCount - Minimum count of PE Tag in the output

iniMatrix

protected void iniMatrix(int tagLengthInLong,
                         int tagNum)

swap

public void swap(int index1,
                 int index2)