net.maizegenetics.pangenome.io

Class PathsToFastaPlugin

net.maizegenetics.pangenome.io.PathsToFastaPlugin

public class PathsToFastaPlugin

This exports paths to a Fasta file(s).

The input to this plugin is Map>. The keys are taxon names. The values are lists of paths (list of nodes).

Each file contains one haploid path for a taxon. The filename will be the given output filename appended with taxon name and haplotype number. Each entry in the files will be a single chromosome.

Constructor Detail

PathsToFastaPlugin

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

This exports paths to a Fasta file(s).

The input to this plugin is Map>. The keys are taxon names. The values are lists of paths (list of nodes).

Each file contains one haploid path for a taxon. The filename will be the given output filename appended with taxon name and haplotype number. Each entry in the files will be a single chromosome.

PathsToFastaPlugin

public PathsToFastaPlugin()

This exports paths to a Fasta file(s).

The input to this plugin is Map>. The keys are taxon names. The values are lists of paths (list of nodes).

Each file contains one haploid path for a taxon. The filename will be the given output filename appended with taxon name and haplotype number. Each entry in the files will be a single chromosome.

Method Detail

processData

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

outputFile

@NotNull
public java.lang.String outputFile()

Output base file name

Returns:

Output Base VCF File Name

outputFile

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

Set Output Base VCF File Name. Output base file name

Parameters:

value - Output Base VCF File Name

Returns:

this plugin

getIcon

@Nullable
public javax.swing.ImageIcon getIcon()

getButtonName

@NotNull
public java.lang.String getButtonName()

getToolTipText

@NotNull
public java.lang.String getToolTipText()