net.maizegenetics.pangenome.io

Class PHGtoGFAv1Plugin

net.maizegenetics.pangenome.io.PHGtoGFAv1Plugin

public class PHGtoGFAv1Plugin

This plugin exports a PHG Graph to GFAv1 format. PHG Paths can also be included if "Walk Lines" are wanted in the file. http://gfa-spec.github.io/GFA-spec/GFA1.html

Constructor Detail

PHGtoGFAv1Plugin

public PHGtoGFAv1Plugin(@Nullable
                        java.awt.Frame parentFrame,
                        boolean isInteractive)

This plugin exports a PHG Graph to GFAv1 format. PHG Paths can also be included if "Walk Lines" are wanted in the file. http://gfa-spec.github.io/GFA-spec/GFA1.html

PHGtoGFAv1Plugin

public PHGtoGFAv1Plugin()

This plugin exports a PHG Graph to GFAv1 format. PHG Paths can also be included if "Walk Lines" are wanted in the file. http://gfa-spec.github.io/GFA-spec/GFA1.html

Method Detail

preProcessParameters

protected void preProcessParameters(@NotNull
                                    net.maizegenetics.plugindef.DataSet input)

processData

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

outputFile

@NotNull
public java.lang.String outputFile()

Output filename

Returns:

Output File

outputFile

@NotNull
public PHGtoGFAv1Plugin outputFile(@NotNull
                                            java.lang.String value)

Set Output File. Output filename

Parameters:

value - Output File

Returns:

this plugin

fullyConnected

public boolean fullyConnected()

Set to true to have adjacent reference ranges fully connected

Returns:

Fully Connected

fullyConnected

@NotNull
public PHGtoGFAv1Plugin fullyConnected(boolean value)

Set Fully Connected. Set to true to have adjacent reference ranges fully connected

Parameters:

value - Fully Connected

Returns:

this plugin

getIcon

@Nullable
public javax.swing.ImageIcon getIcon()

getButtonName

@NotNull
public java.lang.String getButtonName()

getToolTipText

@NotNull
public java.lang.String getToolTipText()