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

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.Form
                          extended by edu.harvard.mgh.purcell.gPLINK2.forms.Clustering
All Implemented Interfaces:
java.awt.image.ImageObserver, java.awt.MenuContainer, java.io.Serializable, javax.accessibility.Accessible, javax.swing.RootPaneContainer, javax.swing.WindowConstants

public class Clustering
extends Form

Form for the clustering command --cluster

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 ccButton
           
private  javax.swing.JCheckBox ibmButton
           
private  javax.swing.JTextField ibmText
           
private  javax.swing.JCheckBox kButton
           
private  javax.swing.JTextField kText
           
private  Form.BrowseButton matchBrowse
           
private  javax.swing.JCheckBox matchButton
           
private  Form.BrowseButton matchTBrowse
           
private  javax.swing.JCheckBox matchTButton
           
private  javax.swing.JTextField matchText
           
private  javax.swing.JTextField matchTText
           
private  javax.swing.JCheckBox mcButton
           
private  javax.swing.JTextField mcc1Text
           
private  javax.swing.JTextField mcc2Text
           
private  javax.swing.JCheckBox mccButton
           
private  javax.swing.JTextField mcText
           
static java.lang.String name
           
(package private) static java.lang.Double PCC_DEFAULT
           
(package private) static java.lang.Double PIBS_G_DEFAULT
           
private  javax.swing.JTextField pibsGText
           
private  javax.swing.JCheckBox ppcButton
           
private  javax.swing.JTextField ppcText
           
private  Form.BrowseButton qmatchBrowse
           
private  javax.swing.JCheckBox qmatchButton
           
private  Form.BrowseButton qmatchQTBrowse
           
private  javax.swing.JTextField qmatchText
           
private  javax.swing.JTextField qtText
           
private  Form.BrowseButton readGBrowse
           
private  javax.swing.JTextField readGText
           
 
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
Clustering(GPLINK mf)
          create a show a new Clustering Form
 
Method Summary
protected  javax.swing.JPanel createBody()
          create the body of the form
protected  void isBodyValid()
          Check to see if the body is correctly filled out.
protected  java.lang.String processBody()
          process the body of the form to generate the plink command
 
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

ppcButton

private javax.swing.JCheckBox ppcButton

ccButton

private javax.swing.JCheckBox ccButton

kButton

private javax.swing.JCheckBox kButton

ibmButton

private javax.swing.JCheckBox ibmButton

matchButton

private javax.swing.JCheckBox matchButton

matchTButton

private javax.swing.JCheckBox matchTButton

qmatchButton

private javax.swing.JCheckBox qmatchButton

mcButton

private javax.swing.JCheckBox mcButton

mccButton

private javax.swing.JCheckBox mccButton

readGText

private javax.swing.JTextField readGText

ppcText

private javax.swing.JTextField ppcText

pibsGText

private javax.swing.JTextField pibsGText

mcText

private javax.swing.JTextField mcText

mcc1Text

private javax.swing.JTextField mcc1Text

mcc2Text

private javax.swing.JTextField mcc2Text

kText

private javax.swing.JTextField kText

ibmText

private javax.swing.JTextField ibmText

matchText

private javax.swing.JTextField matchText

matchTText

private javax.swing.JTextField matchTText

qmatchText

private javax.swing.JTextField qmatchText

qtText

private javax.swing.JTextField qtText

readGBrowse

private Form.BrowseButton readGBrowse

matchBrowse

private Form.BrowseButton matchBrowse

matchTBrowse

private Form.BrowseButton matchTBrowse

qmatchBrowse

private Form.BrowseButton qmatchBrowse

qmatchQTBrowse

private Form.BrowseButton qmatchQTBrowse

PIBS_G_DEFAULT

static java.lang.Double PIBS_G_DEFAULT

PCC_DEFAULT

static java.lang.Double PCC_DEFAULT
Constructor Detail

Clustering

public Clustering(GPLINK mf)
create a show a new Clustering Form

Parameters:
mf - MainFrame this form is attached to
Method Detail

createBody

protected javax.swing.JPanel createBody()
create the body of the form

Specified by:
createBody in class Form
Returns:
A JPanel that holds the body of this form.

isBodyValid

protected void isBodyValid()
Description copied from class: Form
Check to see if the body is correctly filled out. If it is then the forms validBody boolean flag is set to true, otherwise it is set to false.

Specified by:
isBodyValid in class Form

processBody

protected java.lang.String processBody()
process the body of the form to generate the plink command

Specified by:
processBody in class Form
Returns:
the command generated by this form