net.maizegenetics.analysis.distance

Class VCAPScanPlugin

AbstractPlugin

net.maizegenetics.analysis.distance.VCAPScanPlugin

All Implemented Interfaces:

Plugin, PluginListener, ProgressListener

public class VCAPScanPlugin
extends AbstractPlugin

Constructor Detail

VCAPScanPlugin

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

Method Detail

preProcessParameters

protected void preProcessParameters(DataSet input)

postProcessParameters

protected void postProcessParameters()

processData

public DataSet processData(DataSet input)

method

public net.maizegenetics.analysis.distance.VCAPScanPlugin.SCAN_METHOD method()

Scan method

Returns:

org.jetbrains.dokka.NodeRenderContent@72d43aa2: Scan method

method

public VCAPScanPlugin method(net.maizegenetics.analysis.distance.VCAPScanPlugin.SCAN_METHOD value)

Set Scan method. Scan method

Parameters:

value - Scan method

Returns:

org.jetbrains.dokka.NodeRenderContent@51d9ca00: this plugin

blockingWindowSize

public java.lang.Integer blockingWindowSize()

Blocking window size

Returns:

org.jetbrains.dokka.NodeRenderContent@64df62a7: Blocking Window Size

blockingWindowSize

public VCAPScanPlugin blockingWindowSize(java.lang.Integer value)

Set Blocking Window Size. Blocking window size

Parameters:

value - Blocking Window Size

Returns:

org.jetbrains.dokka.NodeRenderContent@39c04f9f: this plugin

numSitesPerBlock

public java.lang.Integer numSitesPerBlock()

Num Sites Per Block

Returns:

org.jetbrains.dokka.NodeRenderContent@6a92732f: Num Sites Per Block

numSitesPerBlock

public VCAPScanPlugin numSitesPerBlock(java.lang.Integer value)

Set Num Sites Per Block. Num Sites Per Block

Parameters:

value - Num Sites Per Block

Returns:

org.jetbrains.dokka.NodeRenderContent@75042db7: this plugin

stepSize

public java.lang.Integer stepSize()

Step Size

Returns:

org.jetbrains.dokka.NodeRenderContent@6a51a3ea: Step Size

stepSize

public VCAPScanPlugin stepSize(java.lang.Integer value)

Set Step Size. Step Size

Parameters:

value - Step Size

Returns:

org.jetbrains.dokka.NodeRenderContent@5156a588: this plugin

dirOfFiles

public java.lang.String dirOfFiles()

Directory contains files for sub-matrices. Can be text (.txt) containing chromosome / positions, Bed (.bed), or Position List (.json or .json.gz)

Returns:

org.jetbrains.dokka.NodeRenderContent@2824bf86: Dir Of Files

dirOfFiles

public VCAPScanPlugin dirOfFiles(java.lang.String value)

Set Dir Of Files. Directory contains files for sub-matrices. Can be text (.txt) containing chromosome / positions, Bed (.bed), or Position List (.json or .json.gz)

Parameters:

value - Dir Of Files

Returns:

org.jetbrains.dokka.NodeRenderContent@7c9956a0: this plugin

bedFile

public java.lang.String bedFile()

Bed File

Returns:

org.jetbrains.dokka.NodeRenderContent@1b30e42a: Bed File

bedFile

public VCAPScanPlugin bedFile(java.lang.String value)

Set Bed File. Bed File

Parameters:

value - Bed File

Returns:

org.jetbrains.dokka.NodeRenderContent@7f2e6821: this plugin

blockingBedFile

public java.lang.String blockingBedFile()

For Bed_File method, this specifies optional bed file to define blocking window for each block in the main bed file.

Returns:

org.jetbrains.dokka.NodeRenderContent@727b20cd: Blocking Bed File

blockingBedFile

public VCAPScanPlugin blockingBedFile(java.lang.String value)

Set Blocking Bed File. For Bed_File method, this specifies optional bed file to define blocking window for each block in the main bed file.

Parameters:

value - Blocking Bed File

Returns:

org.jetbrains.dokka.NodeRenderContent@44e15474: this plugin

phenotypeFile

public java.lang.String phenotypeFile()

Phenotype File

Returns:

org.jetbrains.dokka.NodeRenderContent@58ece976: Phenotype File

phenotypeFile

public VCAPScanPlugin phenotypeFile(java.lang.String value)

Set Phenotype File. Phenotype File

Parameters:

value - Phenotype File

Returns:

org.jetbrains.dokka.NodeRenderContent@540ffd2a: this plugin

ldakCommand

public java.lang.String ldakCommand()

Ldak Command

Returns:

org.jetbrains.dokka.NodeRenderContent@7fd9c22e: Ldak Command

ldakCommand

public VCAPScanPlugin ldakCommand(java.lang.String value)

Set Ldak Command. Ldak Command

Parameters:

value - Ldak Command

Returns:

org.jetbrains.dokka.NodeRenderContent@31556b55: this plugin

outputDir

public java.lang.String outputDir()

Output Dir

Returns:

org.jetbrains.dokka.NodeRenderContent@e4d9350: Output Dir

outputDir

public VCAPScanPlugin outputDir(java.lang.String value)

Set Output Dir. Output Dir

Parameters:

value - Output Dir

Returns:

org.jetbrains.dokka.NodeRenderContent@2580c91e: this plugin

wholeMatrix

public java.lang.String wholeMatrix()

Whole Matrix

Returns:

org.jetbrains.dokka.NodeRenderContent@1479a732: Whole Matrix

wholeMatrix

public VCAPScanPlugin wholeMatrix(java.lang.String value)

Set Whole Matrix. Whole Matrix

Parameters:

value - Whole Matrix

Returns:

org.jetbrains.dokka.NodeRenderContent@eec792b: this plugin

getIcon

public javax.swing.ImageIcon getIcon()

getButtonName

public java.lang.String getButtonName()

getToolTipText

public java.lang.String getToolTipText()

pluginUserManualURL

public java.lang.String pluginUserManualURL()