net.maizegenetics.pangenome.pipeline

Class MakeDefaultDirectoryPlugin

net.maizegenetics.pangenome.pipeline.MakeDefaultDirectoryPlugin

public class MakeDefaultDirectoryPlugin

Constructor Detail

MakeDefaultDirectoryPlugin

public MakeDefaultDirectoryPlugin(@Nullable
                                  java.awt.Frame parentFrame,
                                  boolean isInteractive)

MakeDefaultDirectoryPlugin

public MakeDefaultDirectoryPlugin()

Method Detail

getPluginsToGetParams

@NotNull
public NonExistentClass getPluginsToGetParams()

processData

@Nullable
public net.maizegenetics.plugindef.DataSet processData(@Nullable
                                                                 net.maizegenetics.plugindef.DataSet input)

exportReadMe

public void exportReadMe(@NotNull
                         java.lang.String file)

Function to export a readme file denoting which things need to be changed before pipeline is run.

exportConfigFile

public void exportConfigFile(@NotNull
                             java.lang.String file)

Function to export a default config file.

exportASMKeyFile

public void exportASMKeyFile(@NotNull
                             java.lang.String file)

Function to export the ASM keyFile Template

exportWGSKeyFile

public void exportWGSKeyFile(@NotNull
                             java.lang.String file)

Function to export the WGS keyFile Template

exportReadMappingKeyFile

public void exportReadMappingKeyFile(@NotNull
                                     java.lang.String file)

Function to export the ReadMapping KeyFile

exportLoadDataFile

public void exportLoadDataFile(@NotNull
                               java.lang.String file)

Function to create a load_data_file

getIcon

@Nullable
public javax.swing.ImageIcon getIcon()

getButtonName

@NotNull
public java.lang.String getButtonName()

getToolTipText

@NotNull
public java.lang.String getToolTipText()

workingDir

@NotNull
public java.lang.String workingDir()

Root directory to write out directory structure.

Returns:

Working Dir

workingDir

@NotNull
public MakeDefaultDirectoryPlugin workingDir(@NotNull
                                                      java.lang.String value)

Set Working Dir. Root directory to write out directory structure.

Parameters:

value - Working Dir

Returns:

this plugin

jarFiles

@NotNull
public java.lang.String jarFiles()

Jar files to pull plugin parameters from.

Returns:

Jars

jarFiles

@NotNull
public MakeDefaultDirectoryPlugin jarFiles(@NotNull
                                                    java.lang.String value)

Set Jars. Jar files to pull plugin parameters from.

Parameters:

value - Jars

Returns:

this plugin