net.maizegenetics.analysis.data

Class ProjectPcsAndRunModelSelectionPlugin

AbstractPlugin

net.maizegenetics.analysis.data.ProjectPcsAndRunModelSelectionPlugin

All Implemented Interfaces:

Plugin, PluginListener, ProgressListener

public class ProjectPcsAndRunModelSelectionPlugin
extends AbstractPlugin

Constructor Detail

ProjectPcsAndRunModelSelectionPlugin

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

Creates a new instance of ProjectPcsAndRunModelSelectionLPlugin

Method Detail

preProcessParameters

protected void preProcessParameters(DataSet input)

processData

public DataSet processData(DataSet input)

runPlugin

public GenotypeTable runPlugin(DataSet input)

Convenience method to run plugin with one return object.

recombinationBreakpoints

public java.lang.String recombinationBreakpoints()

Recombination Breakpoints

Returns:

org.jetbrains.dokka.NodeRenderContent@66087314: Recombination Breakpoints

recombinationBreakpoints

public ProjectPcsAndRunModelSelectionPlugin recombinationBreakpoints(java.lang.String value)

Set Recombination Breakpoints. Recombination Breakpoints

Parameters:

value - Recombination Breakpoints

Returns:

org.jetbrains.dokka.NodeRenderContent@5f422259: this plugin

getIcon

public javax.swing.ImageIcon getIcon()

Icon for this plugin to be used in buttons, etc.

Returns:

org.jetbrains.dokka.NodeRenderContent@373f18c3: ImageIcon

getButtonName

public java.lang.String getButtonName()

Button name for this plugin to be used in buttons, etc.

Returns:

org.jetbrains.dokka.NodeRenderContent@141712a0: String

getToolTipText

public java.lang.String getToolTipText()

Tool Tip Text for this plugin

Returns:

org.jetbrains.dokka.NodeRenderContent@31a253e5: String

loadFile

public DataSet loadFile(java.lang.String theRecombinationBreakpoints,
                        GenotypeTable theHighDensityMarkers)

calculatePCsAcrossNAMFounders

public DoubleMatrix calculatePCsAcrossNAMFounders(Chromosome[] chr,
                                                  GenotypeTable theGenotypesForCalculatingPCs,
                                                  java.util.ArrayList<java.lang.String> chrVector,
                                                  java.util.ArrayList<java.lang.Double> posVector,
                                                  java.util.ArrayList<java.lang.Double> startPosVector,
                                                  java.util.ArrayList<java.lang.Double> endPosVector,
                                                  int increment,
                                                  kotlin.Array[] selectedColumns)

projectPCsOntoNAMFounders

public DoubleMatrix projectPCsOntoNAMFounders(GenotypeTable theAlignmentForGenotype,
                                              DoubleMatrix PCResults,
                                              java.util.ArrayList<java.lang.String> chrVector,
                                              java.util.ArrayList<java.lang.Double> posVector,
                                              GenotypeTable theGenotypesForCalculatingPCs,
                                              Chromosome[] chr)

displayProjectedPCsOnTASSELGUI

public DataSet displayProjectedPCsOnTASSELGUI(DoubleMatrix ProjectedPCs,
                                              java.util.ArrayList<java.lang.String> chrVector,
                                              java.util.ArrayList<java.lang.Double> posVector,
                                              java.util.ArrayList<java.lang.Double> startPosVector,
                                              java.util.ArrayList<java.lang.Double> endPosVector,
                                              GenotypeTable theAlignmentForGenotype)

displayNamPCsOnTASSELGUI

public DataSet displayNamPCsOnTASSELGUI(DoubleMatrix PCResults,
                                        java.util.ArrayList<java.lang.String> chrVector,
                                        java.util.ArrayList<java.lang.Double> posVector,
                                        java.util.ArrayList<java.lang.Double> startPosVector,
                                        java.util.ArrayList<java.lang.Double> endPosVector,
                                        GenotypeTable theGenotypesForCalculatingPCs)

identifySitesOfFlankingMarkers

public kotlin.Array[] identifySitesOfFlankingMarkers(int site,
                                                     java.util.ArrayList<java.lang.String> chrVector,
                                                     java.util.ArrayList<java.lang.Double> posVector,
                                                     GenotypeTable theGenotypesForCalculatingPCs,
                                                     ProjectionGenotypeCallTable pg,
                                                     Chromosome[] chr)