edu.harvard.mgh.purcell.gPLINK2.baseForm
Class ThresholdDialog

java.lang.Object
  extended by java.awt.Component
      extended by java.awt.Container
          extended by java.awt.Window
              extended by java.awt.Dialog
                  extended by javax.swing.JDialog
                      extended by edu.harvard.mgh.purcell.gPLINK2.baseForm.ThresholdDialog
All Implemented Interfaces:
java.awt.image.ImageObserver, java.awt.MenuContainer, java.io.Serializable, javax.accessibility.Accessible, javax.swing.RootPaneContainer, javax.swing.WindowConstants

public class ThresholdDialog
extends javax.swing.JDialog

An extention of JDialog to modify thresholds in the plink command.

Author:
Kathe Todd-Brown
See Also:
Serialized Form

Nested Class Summary
 
Nested classes/interfaces inherited from class javax.swing.JDialog
javax.swing.JDialog.AccessibleJDialog
 
Nested classes/interfaces inherited from class java.awt.Dialog
java.awt.Dialog.AccessibleAWTDialog
 
Nested classes/interfaces inherited from class java.awt.Window
java.awt.Window.AccessibleAWTWindow
 
Nested classes/interfaces inherited from class java.awt.Container
java.awt.Container.AccessibleAWTContainer
 
Nested classes/interfaces inherited from class java.awt.Component
java.awt.Component.AccessibleAWTComponent, java.awt.Component.BltBufferStrategy, java.awt.Component.FlipBufferStrategy
 
Field Summary
(package private)  java.awt.event.ActionListener cancel
          Cancel the dailog and throw it away without changing things
private  javax.swing.JButton cancelButton
          Buttons to operate this dialog
private  javax.swing.JTextField geno
          Fields for user entered thresholds
private static java.lang.Double GENO_DEFAULT
          The default maximum per-SNP missing
private  javax.swing.JCheckBox genoButton
          Buttons to flag user specified thresholds
private  javax.swing.JTextField hwe
          Fields for user entered thresholds
private  javax.swing.JCheckBox hweButton
          Buttons to flag user specified thresholds
private  javax.swing.JTextField maf
          Fields for user entered thresholds
private static java.lang.Double MAF_DEFAULT
          The default minor allelic frequency
private  javax.swing.JCheckBox mafButton
          Buttons to flag user specified thresholds
private  javax.swing.JTextField maxMaf
          Fields for user entered thresholds
private static java.lang.Double MAXMAF_DEFAULT
          The default maximum minor allelic frequency
private  javax.swing.JCheckBox maxMafButton
          Buttons to flag user specified thresholds
private  javax.swing.JTextField mendell
          Fields for user entered thresholds
private  javax.swing.JTextField mendell2
          Fields for user entered thresholds
private  javax.swing.JCheckBox mendellButton
          Buttons to flag user specified thresholds
private  javax.swing.JTextField mind
          Fields for user entered thresholds
private static java.lang.Double MIND_DEFAULT
          The default maximum per-person missing
private  javax.swing.JCheckBox mindButton
          Buttons to flag user specified thresholds
private  javax.swing.JButton okButton
          Buttons to operate this dialog
private  Form parent
          The form that this dialog is attached to
(package private)  java.awt.event.ActionListener process
          Process the dialog to command line.
private  java.awt.event.WindowListener properClosing
           
(package private)  java.awt.event.ActionListener reset
          Reset all the defaults
private  javax.swing.JButton resetButton
          Buttons to operate this dialog
 
Fields inherited from class javax.swing.JDialog
accessibleContext, rootPane, rootPaneCheckingEnabled
 
Fields inherited from class java.awt.Component
BOTTOM_ALIGNMENT, CENTER_ALIGNMENT, LEFT_ALIGNMENT, RIGHT_ALIGNMENT, TOP_ALIGNMENT
 
Fields inherited from interface javax.swing.WindowConstants
DISPOSE_ON_CLOSE, DO_NOTHING_ON_CLOSE, EXIT_ON_CLOSE, HIDE_ON_CLOSE
 
Fields inherited from interface java.awt.image.ImageObserver
ABORT, ALLBITS, ERROR, FRAMEBITS, HEIGHT, PROPERTIES, SOMEBITS, WIDTH
 
Constructor Summary
ThresholdDialog(Form givenParent)
          Create a dialog to allow the user to specify threshold values
 
Method Summary
private  void initalize()
          Initalize all the variables and fields.
 
Methods inherited from class javax.swing.JDialog
addImpl, createRootPane, dialogInit, getAccessibleContext, getContentPane, getDefaultCloseOperation, getGlassPane, getJMenuBar, getLayeredPane, getRootPane, isDefaultLookAndFeelDecorated, isRootPaneCheckingEnabled, paramString, processWindowEvent, remove, setContentPane, setDefaultCloseOperation, setDefaultLookAndFeelDecorated, setGlassPane, setJMenuBar, setLayeredPane, setLayout, setRootPane, setRootPaneCheckingEnabled, update
 
Methods inherited from class java.awt.Dialog
addNotify, getTitle, hide, isModal, isResizable, isUndecorated, setModal, setResizable, setTitle, setUndecorated, show
 
Methods inherited from class java.awt.Window
addPropertyChangeListener, addPropertyChangeListener, addWindowFocusListener, addWindowListener, addWindowStateListener, applyResourceBundle, applyResourceBundle, createBufferStrategy, createBufferStrategy, dispose, finalize, getBufferStrategy, getFocusableWindowState, getFocusCycleRootAncestor, getFocusOwner, getFocusTraversalKeys, getGraphicsConfiguration, getInputContext, getListeners, getLocale, getMostRecentFocusOwner, getOwnedWindows, getOwner, getToolkit, getWarningString, getWindowFocusListeners, getWindowListeners, getWindowStateListeners, isActive, isAlwaysOnTop, isFocusableWindow, isFocusCycleRoot, isFocused, isLocationByPlatform, isShowing, pack, postEvent, processEvent, processWindowFocusEvent, processWindowStateEvent, removeWindowFocusListener, removeWindowListener, removeWindowStateListener, setAlwaysOnTop, setBounds, setCursor, setFocusableWindowState, setFocusCycleRoot, setLocationByPlatform, setLocationRelativeTo, toBack, toFront
 
Methods inherited from class java.awt.Container
add, add, add, add, add, addContainerListener, applyComponentOrientation, areFocusTraversalKeysSet, countComponents, deliverEvent, doLayout, findComponentAt, findComponentAt, getAlignmentX, getAlignmentY, getComponent, getComponentAt, getComponentAt, getComponentCount, getComponents, getComponentZOrder, getContainerListeners, getFocusTraversalPolicy, getInsets, getLayout, getMaximumSize, getMinimumSize, getMousePosition, getPreferredSize, insets, invalidate, isAncestorOf, isFocusCycleRoot, isFocusTraversalPolicyProvider, isFocusTraversalPolicySet, layout, list, list, locate, minimumSize, paint, paintComponents, preferredSize, print, printComponents, processContainerEvent, remove, removeAll, removeContainerListener, removeNotify, setComponentZOrder, setFocusTraversalKeys, setFocusTraversalPolicy, setFocusTraversalPolicyProvider, setFont, transferFocusBackward, transferFocusDownCycle, validate, validateTree
 
Methods inherited from class java.awt.Component
action, add, addComponentListener, addFocusListener, addHierarchyBoundsListener, addHierarchyListener, addInputMethodListener, addKeyListener, addMouseListener, addMouseMotionListener, addMouseWheelListener, bounds, checkImage, checkImage, coalesceEvents, contains, contains, createImage, createImage, createVolatileImage, createVolatileImage, disable, disableEvents, dispatchEvent, enable, enable, enableEvents, enableInputMethods, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, getBackground, getBounds, getBounds, getColorModel, getComponentListeners, getComponentOrientation, getCursor, getDropTarget, getFocusListeners, getFocusTraversalKeysEnabled, getFont, getFontMetrics, getForeground, getGraphics, getHeight, getHierarchyBoundsListeners, getHierarchyListeners, getIgnoreRepaint, getInputMethodListeners, getInputMethodRequests, getKeyListeners, getLocation, getLocation, getLocationOnScreen, getMouseListeners, getMouseMotionListeners, getMousePosition, getMouseWheelListeners, getName, getParent, getPeer, getPropertyChangeListeners, getPropertyChangeListeners, getSize, getSize, getTreeLock, getWidth, getX, getY, gotFocus, handleEvent, hasFocus, imageUpdate, inside, isBackgroundSet, isCursorSet, isDisplayable, isDoubleBuffered, isEnabled, isFocusable, isFocusOwner, isFocusTraversable, isFontSet, isForegroundSet, isLightweight, isMaximumSizeSet, isMinimumSizeSet, isOpaque, isPreferredSizeSet, isValid, isVisible, keyDown, keyUp, list, list, list, location, lostFocus, mouseDown, mouseDrag, mouseEnter, mouseExit, mouseMove, mouseUp, move, nextFocus, paintAll, prepareImage, prepareImage, printAll, processComponentEvent, processFocusEvent, processHierarchyBoundsEvent, processHierarchyEvent, processInputMethodEvent, processKeyEvent, processMouseEvent, processMouseMotionEvent, processMouseWheelEvent, remove, removeComponentListener, removeFocusListener, removeHierarchyBoundsListener, removeHierarchyListener, removeInputMethodListener, removeKeyListener, removeMouseListener, removeMouseMotionListener, removeMouseWheelListener, removePropertyChangeListener, removePropertyChangeListener, repaint, repaint, repaint, repaint, requestFocus, requestFocus, requestFocusInWindow, requestFocusInWindow, reshape, resize, resize, setBackground, setBounds, setComponentOrientation, setDropTarget, setEnabled, setFocusable, setFocusTraversalKeysEnabled, setForeground, setIgnoreRepaint, setLocale, setLocation, setLocation, setMaximumSize, setMinimumSize, setName, setPreferredSize, setSize, setSize, setVisible, show, size, toString, transferFocus, transferFocusUpCycle
 
Methods inherited from class java.lang.Object
clone, equals, getClass, hashCode, notify, notifyAll, wait, wait, wait
 

Field Detail

MAF_DEFAULT

private static java.lang.Double MAF_DEFAULT
The default minor allelic frequency


MAXMAF_DEFAULT

private static java.lang.Double MAXMAF_DEFAULT
The default maximum minor allelic frequency


GENO_DEFAULT

private static java.lang.Double GENO_DEFAULT
The default maximum per-SNP missing


MIND_DEFAULT

private static java.lang.Double MIND_DEFAULT
The default maximum per-person missing


parent

private Form parent
The form that this dialog is attached to


maf

private javax.swing.JTextField maf
Fields for user entered thresholds


maxMaf

private javax.swing.JTextField maxMaf
Fields for user entered thresholds


geno

private javax.swing.JTextField geno
Fields for user entered thresholds


mind

private javax.swing.JTextField mind
Fields for user entered thresholds


hwe

private javax.swing.JTextField hwe
Fields for user entered thresholds


mendell

private javax.swing.JTextField mendell
Fields for user entered thresholds


mendell2

private javax.swing.JTextField mendell2
Fields for user entered thresholds


mafButton

private javax.swing.JCheckBox mafButton
Buttons to flag user specified thresholds


maxMafButton

private javax.swing.JCheckBox maxMafButton
Buttons to flag user specified thresholds


genoButton

private javax.swing.JCheckBox genoButton
Buttons to flag user specified thresholds


hweButton

private javax.swing.JCheckBox hweButton
Buttons to flag user specified thresholds


mendellButton

private javax.swing.JCheckBox mendellButton
Buttons to flag user specified thresholds


mindButton

private javax.swing.JCheckBox mindButton
Buttons to flag user specified thresholds


okButton

private javax.swing.JButton okButton
Buttons to operate this dialog


resetButton

private javax.swing.JButton resetButton
Buttons to operate this dialog


cancelButton

private javax.swing.JButton cancelButton
Buttons to operate this dialog


properClosing

private java.awt.event.WindowListener properClosing

process

java.awt.event.ActionListener process
Process the dialog to command line.


reset

java.awt.event.ActionListener reset
Reset all the defaults


cancel

java.awt.event.ActionListener cancel
Cancel the dailog and throw it away without changing things

Constructor Detail

ThresholdDialog

public ThresholdDialog(Form givenParent)
Create a dialog to allow the user to specify threshold values

Parameters:
givenParent - form that this dialog is anchored to
Method Detail

initalize

private void initalize()
Initalize all the variables and fields.