net.maizegenetics.analysis.popgen

Class LinkageDisequilibriumComponent

net.maizegenetics.analysis.popgen.LinkageDisequilibriumComponent

public class LinkageDisequilibriumComponent

An AWT Component for displaying information on linkage disequilibrium. Nice schematics are produced if an annotation alignment is used to construct LinkageDisequilibrium. It can portray things both on the gene and chromosomal scale.

Field Detail

P_VALUE

public static int P_VALUE

See Also:

Constant Field Values

DPRIME

public static int DPRIME

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Constant Field Values

RSQUARE

public static int RSQUARE

See Also:

Constant Field Values

Constructor Detail

LinkageDisequilibriumComponent

public LinkageDisequilibriumComponent(LinkageDisequilibrium theLD,
                                      boolean includeBlockSchematic,
                                      boolean chromosomalScale,
                                      int windowSize,
                                      int windowX,
                                      int windowY)

Method Detail

setXStart

public void setXStart()

This sets the X start and end positions

setYStart

public void setYStart()

This sets the Y start and end positions

setWindowSize

public void setWindowSize(int newSize,
                          int newX,
                          int newY,
                          int ldMeasureLower,
                          int ldMeasureUpper)

This sets a new viewable size

setWindowX

public void setWindowX(int newX,
                       int ldMeasureLower,
                       int ldMeasureUpper)

This sets a new X position

setWindowY

public void setWindowY(int newY,
                       int ldMeasureLower,
                       int ldMeasureUpper)

This sets a new Y position

setLowerCorner

public void setLowerCorner(int ldMeasure)

This determines what is displayed in the lower left corner. Options are: P_VALUE, DPRIME, and RSQUARE

setUpperCorner

public void setUpperCorner(int ldMeasure)

This determines what is displayed in the upper right corner. Options are: P_VALUE, DPRIME, and RSQUARE

setScaleOfView

public void setScaleOfView(boolean chromosomalScale)

This sets the scale of the LD view, either sites are organized by chromosomes if chromosomalScale is true, otherwise they are organized by genes

setShowSchematic

public void setShowSchematic(boolean includeBlockSchematic)

This sets whether a schematic is displayed. If true a schematic of genes or chromosomes is displayed, otherwise no schematic is displayed

setShowLabels

public void setShowLabels(boolean includeLabels)

paintComponent

protected void paintComponent(java.awt.Graphics g)

paint

public void paint(java.awt.Graphics g)

getToolTipText

public java.lang.String getToolTipText(java.awt.event.MouseEvent e)

setGraphSize

public void setGraphSize(int graphX,
                         int graphY)