public class MergeRenameDeleteTaxaPlugin
extends AbstractPlugin
public MergeRenameDeleteTaxaPlugin()
public MergeRenameDeleteTaxaPlugin(java.awt.Frame parentFrame,
boolean isInteractive)
public java.lang.String pluginDescription()
protected void preProcessParameters(DataSet input)
public javax.swing.ImageIcon getIcon()
public java.lang.String getButtonName()
public java.lang.String getToolTipText()
public void runPlugin(GenotypeTable inputGenos)
Convenience method to run plugin with input and output GenotypeTable objects (rather than DataSets)
inputGenos - Input GenotypeTable.public void runPlugin(DataSet input)
Convenience method to run plugin.
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.
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.
value - Taxa Rename Keypublic java.lang.String outputHDF5Genotypes()
Output genotypes file
public MergeRenameDeleteTaxaPlugin outputHDF5Genotypes(java.lang.String value)
Set Output Genotypes. Output genotypes file
value - Output Genotypespublic java.lang.Double avgSeqErrorRate()
Average sequencing error rate per base (used to decide between heterozygous and homozygous calls when merging taxa)
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)
value - Avg Seq Error Ratepublic java.lang.Boolean noDepthOutput()
No depth output: do not write depths to the output genotypes file (applies only to hdf5 or VCF)
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)
value - No Depth Outputpublic java.lang.String dataSetName()
(Optional) Short data set name to be added as an root level annotation under "/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"
value - Data set namepublic java.lang.String dataSetDescription()
(Optional) Short data set description to be added as an root level annotation under "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"
value - Data set description