edu.harvard.mgh.purcell.gPLINK2.forms
Class AlleleAssoc

java.lang.Object
  java.awt.Component
      java.awt.Container
          java.awt.Window
              java.awt.Dialog
                  javax.swing.JDialog
                      edu.harvard.mgh.purcell.gPLINK2.baseForm.Form
                          edu.harvard.mgh.purcell.gPLINK2.forms.AlleleAssoc

All Implemented Interfaces:

java.awt.image.ImageObserver, java.awt.MenuContainer, java.io.Serializable, javax.accessibility.Accessible, javax.swing.RootPaneContainer, javax.swing.WindowConstants

public class AlleleAssoc
extends Form

Creates a form that does a basic --assoc test

Author:

Kathe Todd-Brown

See Also:

Serialized Form

Nested Class Summary

Nested classes/interfaces inherited from class edu.harvard.mgh.purcell.gPLINK2.baseForm.Form

Form.BrowseButton

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

private javax.swing.JCheckBox	adjustButton Flag the --adjust button
private static java.lang.Double	CI_DEFAULT The default ci parameter is 0.95
private javax.swing.JCheckBox	ciButton Flag the ci option
private javax.swing.JTextField	ciText Allow the user to set the --ci parameter
private static java.lang.Integer	MPERM_DEFAULT The default mperm perameter is 1000
private javax.swing.JCheckBox	mpermButton Flag the --mperm option
private javax.swing.JTextField	mpermText Allow the user to set the --mperm perameter
static java.lang.String	name The name of the form
private javax.swing.JCheckBox	permButton Flag the --perm option

Fields inherited from class edu.harvard.mgh.purcell.gPLINK2.baseForm.Form

filterButton, input, output, parent, thresholdButton, validateBodyAL, validateBodyDL, validBody

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

AlleleAssoc(GPLINK mf)
Create and show an allelic assocation test form.

Method Summary

protected javax.swing.JPanel	createBody() create the body specific to this form.
protected void	isBodyValid() Return true.
protected java.lang.String	processBody() Pull the commandline from this form

Methods inherited from class edu.harvard.mgh.purcell.gPLINK2.baseForm.Form

addFilter, addThreshold, bundel, bundel, bundel, bundel, bundel, closeButtons, okForm, openButtons, resetFilter, resetThreshold

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

name

public static java.lang.String name

The name of the form

permButton

private javax.swing.JCheckBox permButton

Flag the --perm option

mpermButton

private javax.swing.JCheckBox mpermButton

Flag the --mperm option

ciButton

private javax.swing.JCheckBox ciButton

Flag the ci option

adjustButton

private javax.swing.JCheckBox adjustButton

Flag the --adjust button

ciText

private javax.swing.JTextField ciText

Allow the user to set the --ci parameter

mpermText

private javax.swing.JTextField mpermText

Allow the user to set the --mperm perameter

CI_DEFAULT

private static java.lang.Double CI_DEFAULT

The default ci parameter is 0.95

MPERM_DEFAULT

private static java.lang.Integer MPERM_DEFAULT

The default mperm perameter is 1000

Constructor Detail

AlleleAssoc

public AlleleAssoc(GPLINK mf)

Create and show an allelic assocation test form.

Parameters:

mf - MainFrame that this form is aassociation with

Method Detail

createBody

protected javax.swing.JPanel createBody()

create the body specific to this form.

Specified by:

createBody in class Form

Returns:

A JPanel that holds the body of this form.

processBody

protected java.lang.String processBody()

Pull the commandline from this form

Specified by:

processBody in class Form

Returns:

A String that is the PLINK command for this from. Note that this includes the any noted plink prefixes and the plink path.

isBodyValid

protected void isBodyValid()

Return true. --assoc is a vaild command by itself.

Specified by:

isBodyValid in class Form