pal.gui
Class LinkageDisequilibriumComponent

java.lang.Object
  extended by java.awt.Component
      extended by 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
static int DPRIME
           
static int P_VALUE
           
static int RSQUARE
           
 
Fields inherited from class java.awt.Component
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
 
Constructor Summary
LinkageDisequilibriumComponent(LinkageDisequilibrium theLD, boolean includeBlockSchematic, boolean chromosomalScale)
           
 
Method Summary
 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, 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