Package pal.gui

Class 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 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.image.ImageObserver

        ABORT, ALLBITS, ERROR, FRAMEBITS, HEIGHT, PROPERTIES, SOMEBITS, WIDTH

      • Fields inherited from interface java.awt.print.Printable

        NO_SUCH_PAGE, PAGE_EXISTS

    • 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 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, 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

      • Methods inherited from class java.lang.Object

        clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

    • 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