net.maizegenetics.analysis.data

Class BuildUnfinishedHDF5GenotypesPlugin

AbstractPlugin

net.maizegenetics.analysis.data.BuildUnfinishedHDF5GenotypesPlugin

All Implemented Interfaces:

Plugin, PluginListener, ProgressListener

public class BuildUnfinishedHDF5GenotypesPlugin
extends AbstractPlugin

Opens an "unfinished" HDF5 genotypes file, on which .closeUnfinished() was called rather than .build() and finalizes it by calling .build(). If an output file name is provided, then the input file is first copied to that, and then build() is called on that copy. If provided, root level annotations DataSetName and DataSetDescription are also added. "__DATE__" in the provided dataSet name is replaced a current date stamp ("_yyyyMMdd"). "__SNPS__" and "__TAXA__" in the dataSetDescription are replaced with the number of sites and taxa, respectively.

Constructor Detail

BuildUnfinishedHDF5GenotypesPlugin

public BuildUnfinishedHDF5GenotypesPlugin()

BuildUnfinishedHDF5GenotypesPlugin

public BuildUnfinishedHDF5GenotypesPlugin(java.awt.Frame parentFrame,
                                          boolean isInteractive)

Method Detail

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()

inputFile

public java.lang.String inputFile()

Input, unfinished HDF5 genotype (*.h5) file to be fininalized

Returns:

org.jetbrains.dokka.NodeRenderContent@7c26637d: Input file

inputFile

public BuildUnfinishedHDF5GenotypesPlugin inputFile(java.lang.String value)

Set Input file. Input, unfinished HDF5 genotype (*.h5) file to be fininalized

Parameters:

value - Input file

Returns:

org.jetbrains.dokka.NodeRenderContent@5740eecc: this plugin

outputFile

public java.lang.String outputFile()

Output, finished HDF5 genotype (*.h5) file which can be opened with the TASSEL5 GUI

Returns:

org.jetbrains.dokka.NodeRenderContent@46b9e3c5: Output file

outputFile

public BuildUnfinishedHDF5GenotypesPlugin outputFile(java.lang.String value)

Set Output file. Output, finished HDF5 genotype (*.h5) file which can be opened with the TASSEL5 GUI

Parameters:

value - Output file

Returns:

org.jetbrains.dokka.NodeRenderContent@450e7e92: 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@afcd0c5: Data set name

dataSetName

public BuildUnfinishedHDF5GenotypesPlugin 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@5a1a69d8: 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@53341e95: Data set description

dataSetDescription

public BuildUnfinishedHDF5GenotypesPlugin 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@6578008f: this plugin