Package pal.gui
Class LinkageDisequilibriumComponent
- java.lang.Object
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- java.awt.Component
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- pal.gui.LinkageDisequilibriumComponent
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- 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
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Field Summary
Fields Modifier and Type Field Description static int
DPRIME
static int
P_VALUE
static int
RSQUARE
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Fields inherited from class java.awt.Component
accessibleContext, BOTTOM_ALIGNMENT, CENTER_ALIGNMENT, LEFT_ALIGNMENT, RIGHT_ALIGNMENT, TOP_ALIGNMENT
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Constructor Summary
Constructors Constructor Description LinkageDisequilibriumComponent(LinkageDisequilibrium theLD, boolean includeBlockSchematic, boolean chromosomalScale)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method 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 genesvoid
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, 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, requestFocus, requestFocus, requestFocusInWindow, requestFocusInWindow, requestFocusInWindow, reshape, resize, resize, revalidate, setBackground, setBounds, setBounds, setComponentOrientation, setCursor, setDropTarget, setEnabled, setFocusable, setFocusTraversalKeys, setFocusTraversalKeysEnabled, setFont, setForeground, setIgnoreRepaint, setLocale, setLocation, setLocation, setMaximumSize, setMinimumSize, setMixingCutoutShape, setName, setPreferredSize, setSize, setSize, setVisible, show, show, size, toString, transferFocus, transferFocusBackward, transferFocusUpCycle, update, validate
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Field Detail
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P_VALUE
public static final int P_VALUE
- See Also:
- Constant Field Values
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DPRIME
public static final int DPRIME
- See Also:
- Constant Field Values
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RSQUARE
public static final int RSQUARE
- See Also:
- Constant Field Values
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Constructor Detail
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LinkageDisequilibriumComponent
public LinkageDisequilibriumComponent(LinkageDisequilibrium theLD, boolean includeBlockSchematic, boolean chromosomalScale)
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Method Detail
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setLowerCorner
public void setLowerCorner(int ldMeasure)
This determines what is displayed in the lower left corner. Options are: P_VALUE, DPRIME, and RSQUARE
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setUpperCorner
public void setUpperCorner(int ldMeasure)
This determines what is displayed in the upper right corner. Options are: P_VALUE, DPRIME, and RSQUARE
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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
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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
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paintComponent
protected void paintComponent(java.awt.Graphics g)
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paint
public void paint(java.awt.Graphics g)
- Overrides:
paint
in classjava.awt.Component
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print
public int print(java.awt.Graphics g, java.awt.print.PageFormat pf, int pageIndex)
- Specified by:
print
in interfacejava.awt.print.Printable
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