net.maizegenetics.pangenome.hapCalling

Class SplitKeyFilePlugin

net.maizegenetics.pangenome.hapCalling.SplitKeyFilePlugin

public class SplitKeyFilePlugin

Constructor Detail

SplitKeyFilePlugin

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

SplitKeyFilePlugin

public SplitKeyFilePlugin()

Method Detail

processData

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

getIcon

@Nullable
public javax.swing.ImageIcon getIcon()

getButtonName

@NotNull
public java.lang.String getButtonName()

getToolTipText

@NotNull
public java.lang.String getToolTipText()

inputKeyFile

@NotNull
public java.lang.String inputKeyFile()

Name of the inputKeyFile file to process.

Returns:

Input Key File

inputKeyFile

@NotNull
public SplitKeyFilePlugin inputKeyFile(@NotNull
                                                java.lang.String value)

Set Input Key File. Name of the inputKeyFile file to process.

Parameters:

value - Input Key File

Returns:

this plugin

outputKeyFile

@NotNull
public java.lang.String outputKeyFile()

Name of the output file to process.

Returns:

Output KeyFile

outputKeyFile

@NotNull
public SplitKeyFilePlugin outputKeyFile(@NotNull
                                                 java.lang.String value)

Set Output KeyFile. Name of the output file to process.

Parameters:

value - Output KeyFile

Returns:

this plugin

fileName

@NotNull
public java.lang.String fileName()

Name from the SAM or Fastq file to know which key file record to output. This will look at the filename column

Returns:

File Name

fileName

@NotNull
public SplitKeyFilePlugin fileName(@NotNull
                                            java.lang.String value)

Set File Name. Name from the SAM or Fastq file to know which key file record to output. This will look at the filename column

Parameters:

value - File Name

Returns:

this plugin

outputFiltered

public boolean outputFiltered()

If set to true, output the filtered name expected by the snakemake script.

Returns:

Output Filtered File Name

outputFiltered

@NotNull
public SplitKeyFilePlugin outputFiltered(boolean value)

Set Output Filtered File Name. If set to true, output the filtered name expected by the snakemake script.

Parameters:

value - Output Filtered File Name

Returns:

this plugin

removeLastToken

public boolean removeLastToken()

If set to true, this will remove the last token from the file names.

Returns:

Remove Last Token From FileName

removeLastToken

@NotNull
public SplitKeyFilePlugin removeLastToken(boolean value)

Set Remove Last Token From FileName. If set to true, this will remove the last token from the file names.

Parameters:

value - Remove Last Token From FileName

Returns:

this plugin