net.maizegenetics.analysis.data

Class MergeRenameDeleteTaxaPlugin

AbstractPlugin

net.maizegenetics.analysis.data.MergeRenameDeleteTaxaPlugin

All Implemented Interfaces:

Plugin, PluginListener, ProgressListener

public class MergeRenameDeleteTaxaPlugin
extends AbstractPlugin

Constructor Detail

MergeRenameDeleteTaxaPlugin

public MergeRenameDeleteTaxaPlugin()

MergeRenameDeleteTaxaPlugin

public MergeRenameDeleteTaxaPlugin(java.awt.Frame parentFrame,
                                   boolean isInteractive)

Method Detail

pluginDescription

public java.lang.String pluginDescription()

preProcessParameters

protected void preProcessParameters(DataSet input)

processData

public DataSet processData(DataSet input)

getIcon

public javax.swing.ImageIcon getIcon()

getButtonName

public java.lang.String getButtonName()

getToolTipText

public java.lang.String getToolTipText()

runPlugin

public void runPlugin(GenotypeTable inputGenos)

Convenience method to run plugin with input and output GenotypeTable objects (rather than DataSets)

Parameters:

inputGenos - Input GenotypeTable.

runPlugin

public void runPlugin(DataSet input)

Convenience method to run plugin.

taxaRenameKey

public java.lang.String taxaRenameKey()

Tab-delimited file with original and new taxa names. Taxa with the same new name will be merged. Taxa with the new name "delete" will be removed. Any other columns (and the header line) are ignored.

Returns:

org.jetbrains.dokka.NodeRenderContent@75d4e930: Taxa Rename Key

taxaRenameKey

public MergeRenameDeleteTaxaPlugin taxaRenameKey(java.lang.String value)

Set Taxa Rename Key. Tab-delimited file with original and new taxa names. Taxa with the same new name will be merged. Taxa with the new name "delete" will be removed. Any other columns (and the header line) are ignored.

Parameters:

value - Taxa Rename Key

Returns:

org.jetbrains.dokka.NodeRenderContent@744e59b4: this plugin

outputHDF5Genotypes

public java.lang.String outputHDF5Genotypes()

Output genotypes file

Returns:

org.jetbrains.dokka.NodeRenderContent@4235b199: Output Genotypes

outputHDF5Genotypes

public MergeRenameDeleteTaxaPlugin outputHDF5Genotypes(java.lang.String value)

Set Output Genotypes. Output genotypes file

Parameters:

value - Output Genotypes

Returns:

org.jetbrains.dokka.NodeRenderContent@6d7c102e: this plugin

avgSeqErrorRate

public java.lang.Double avgSeqErrorRate()

Average sequencing error rate per base (used to decide between heterozygous and homozygous calls when merging taxa)

Returns:

org.jetbrains.dokka.NodeRenderContent@3fb3f9d8: Avg Seq Error Rate

avgSeqErrorRate

public MergeRenameDeleteTaxaPlugin avgSeqErrorRate(java.lang.Double value)

Set Avg Seq Error Rate. Average sequencing error rate per base (used to decide between heterozygous and homozygous calls when merging taxa)

Parameters:

value - Avg Seq Error Rate

Returns:

org.jetbrains.dokka.NodeRenderContent@39369463: this plugin

noDepthOutput

public java.lang.Boolean noDepthOutput()

No depth output: do not write depths to the output genotypes file (applies only to hdf5 or VCF)

Returns:

org.jetbrains.dokka.NodeRenderContent@56e043a5: No Depth Output

noDepthOutput

public MergeRenameDeleteTaxaPlugin noDepthOutput(java.lang.Boolean value)

Set No Depth Output. No depth output: do not write depths to the output genotypes file (applies only to hdf5 or VCF)

Parameters:

value - No Depth Output

Returns:

org.jetbrains.dokka.NodeRenderContent@5b10c437: this plugin

dataSetName

public java.lang.String dataSetName()

(Optional) Short data set name to be added as an root level annotation under "/DataSetName"

Returns:

org.jetbrains.dokka.NodeRenderContent@7b4d9bb4: Data set name

dataSetName

public MergeRenameDeleteTaxaPlugin dataSetName(java.lang.String value)

Set Data set name. (Optional) Short data set name to be added as an root level annotation under "dataSetName"

Parameters:

value - Data set name

Returns:

org.jetbrains.dokka.NodeRenderContent@76d59d32: this plugin

dataSetDescription

public java.lang.String dataSetDescription()

(Optional) Short data set description to be added as an root level annotation under "dataSetDescription"

Returns:

org.jetbrains.dokka.NodeRenderContent@22fc1526: Data set description

dataSetDescription

public MergeRenameDeleteTaxaPlugin dataSetDescription(java.lang.String value)

Set Data set description. (Optional) Short data set description to be added as an root level annotation under "/DataSetDescription"

Parameters:

value - Data set description

Returns:

org.jetbrains.dokka.NodeRenderContent@7f905c32: this plugin