LinkageDisequilibriumComponent

java.lang.Object
- java.awt.Component
- - pal.gui.LinkageDisequilibriumComponent

All Implemented Interfaces:

java.awt.image.ImageObserver, java.awt.MenuContainer, java.awt.print.Printable, java.io.Serializable
```
public class LinkageDisequilibriumComponent
extends java.awt.Component
implements java.awt.print.Printable
```
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.

Version:

$Id: LinkageDisequilibriumComponent.java

Author:

Ed Buckler

See Also:

Serialized Form

Nested Class Summary
- Nested classes/interfaces inherited from class java.awt.Component
  java.awt.Component.AccessibleAWTComponent, java.awt.Component.BaselineResizeBehavior, java.awt.Component.BltBufferStrategy, java.awt.Component.FlipBufferStrategy

Field Summary

Fields
Modifier and Type Field and Description

static int DPRIME

static int P_VALUE

static int RSQUARE
- Fields inherited from class java.awt.Component
  accessibleContext, BOTTOM_ALIGNMENT, CENTER_ALIGNMENT, LEFT_ALIGNMENT, RIGHT_ALIGNMENT, TOP_ALIGNMENT
- Fields inherited from interface java.awt.print.Printable
  NO_SUCH_PAGE, PAGE_EXISTS
- Fields inherited from interface java.awt.image.ImageObserver
  ABORT, ALLBITS, ERROR, FRAMEBITS, HEIGHT, PROPERTIES, SOMEBITS, WIDTH

Fields
Modifier and Type	Field and Description
`static int`	`DPRIME`
`static int`	`P_VALUE`
`static int`	`RSQUARE`

Constructor Summary

Constructors
Constructor and Description
`LinkageDisequilibriumComponent(LinkageDisequilibrium theLD, boolean includeBlockSchematic, boolean chromosomalScale)`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`void`	`paint(java.awt.Graphics g)`
`protected void`	`paintComponent(java.awt.Graphics g)`
`int`	`print(java.awt.Graphics g, java.awt.print.PageFormat pf, int pageIndex)`
`void`	`setLowerCorner(int ldMeasure)` This determines what is displayed in the lower left corner.
`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
`void`	`setShowSchematic(boolean includeBlockSchematic)` This sets whether a schematic is displayed.
`void`	`setUpperCorner(int ldMeasure)` This determines what is displayed in the upper right corner.

Methods inherited from class java.awt.Component
action, add, addComponentListener, addFocusListener, addHierarchyBoundsListener, addHierarchyListener, addInputMethodListener, addKeyListener, addMouseListener, addMouseMotionListener, addMouseWheelListener, addNotify, addPropertyChangeListener, addPropertyChangeListener, applyComponentOrientation, areFocusTraversalKeysSet, bounds, checkImage, checkImage, coalesceEvents, contains, contains, createImage, createImage, createVolatileImage, createVolatileImage, deliverEvent, disable, disableEvents, dispatchEvent, doLayout, enable, enable, enableEvents, enableInputMethods, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, getAccessibleContext, getAlignmentX, getAlignmentY, getBackground, getBaseline, getBaselineResizeBehavior, getBounds, getBounds, getColorModel, getComponentAt, getComponentAt, getComponentListeners, getComponentOrientation, getCursor, getDropTarget, getFocusCycleRootAncestor, getFocusListeners, getFocusTraversalKeys, getFocusTraversalKeysEnabled, getFont, getFontMetrics, getForeground, getGraphics, getGraphicsConfiguration, getHeight, getHierarchyBoundsListeners, getHierarchyListeners, getIgnoreRepaint, getInputContext, getInputMethodListeners, getInputMethodRequests, getKeyListeners, getListeners, getLocale, getLocation, getLocation, getLocationOnScreen, getMaximumSize, getMinimumSize, getMouseListeners, getMouseMotionListeners, getMousePosition, getMouseWheelListeners, getName, getParent, getPeer, getPreferredSize, getPropertyChangeListeners, getPropertyChangeListeners, getSize, getSize, getToolkit, getTreeLock, getWidth, getX, getY, gotFocus, handleEvent, hasFocus, hide, imageUpdate, inside, invalidate, isBackgroundSet, isCursorSet, isDisplayable, isDoubleBuffered, isEnabled, isFocusable, isFocusCycleRoot, isFocusOwner, isFocusTraversable, isFontSet, isForegroundSet, isLightweight, isMaximumSizeSet, isMinimumSizeSet, isOpaque, isPreferredSizeSet, isShowing, isValid, isVisible, keyDown, keyUp, layout, list, list, list, list, list, locate, location, lostFocus, minimumSize, mouseDown, mouseDrag, mouseEnter, mouseExit, mouseMove, mouseUp, move, nextFocus, paintAll, paramString, postEvent, preferredSize, prepareImage, prepareImage, print, printAll, processComponentEvent, processEvent, processFocusEvent, processHierarchyBoundsEvent, processHierarchyEvent, processInputMethodEvent, processKeyEvent, processMouseEvent, processMouseMotionEvent, processMouseWheelEvent, remove, removeComponentListener, removeFocusListener, removeHierarchyBoundsListener, removeHierarchyListener, removeInputMethodListener, removeKeyListener, removeMouseListener, removeMouseMotionListener, removeMouseWheelListener, removeNotify, removePropertyChangeListener, removePropertyChangeListener, repaint, repaint, repaint, repaint, requestFocus, requestFocus, requestFocusInWindow, requestFocusInWindow, reshape, resize, resize, revalidate, setBackground, setBounds, setBounds, setComponentOrientation, setCursor, setDropTarget, setEnabled, setFocusable, setFocusTraversalKeys, setFocusTraversalKeysEnabled, setFont, setForeground, setIgnoreRepaint, setLocale, setLocation, setLocation, setMaximumSize, setMinimumSize, setName, setPreferredSize, setSize, setSize, setVisible, show, show, size, toString, transferFocus, transferFocusBackward, transferFocusUpCycle, update, validate

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

- Field Detail
  - P_VALUE
```
public static final int P_VALUE
```
    See Also:
    
    Constant Field Values
  - DPRIME
```
public static final int DPRIME
```
    See Also:
    
    Constant Field Values
  - RSQUARE
```
public static final int RSQUARE
```
    See Also:
    
    Constant Field Values
- Constructor Detail
  - LinkageDisequilibriumComponent
```
public LinkageDisequilibriumComponent(LinkageDisequilibrium theLD,
                                      boolean includeBlockSchematic,
                                      boolean chromosomalScale)
```
- Method Detail
  - 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
  - paintComponent
```
protected void paintComponent(java.awt.Graphics g)
```
  - paint
```
public void paint(java.awt.Graphics g)
```
    Overrides:
    
    paint in class java.awt.Component
  - print
```
public int print(java.awt.Graphics g,
                 java.awt.print.PageFormat pf,
                 int pageIndex)
```
    Specified by:
    
    print in interface java.awt.print.Printable

Class LinkageDisequilibriumComponent

Nested Class Summary

Nested classes/interfaces inherited from class java.awt.Component

Field Summary

Fields inherited from class java.awt.Component

Fields inherited from interface java.awt.print.Printable

Fields inherited from interface java.awt.image.ImageObserver

Constructor Summary

Method Summary

Methods inherited from class java.awt.Component

Methods inherited from class java.lang.Object

Field Detail

P_VALUE

DPRIME

RSQUARE

Constructor Detail

LinkageDisequilibriumComponent

Method Detail

setLowerCorner

setUpperCorner

setScaleOfView

setShowSchematic

paintComponent

paint

print