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

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.Merge
All Implemented Interfaces:
java.awt.image.ImageObserver, java.awt.MenuContainer, java.io.Serializable, javax.accessibility.Accessible, javax.swing.RootPaneContainer, javax.swing.WindowConstants

public class Merge
extends Form

Merge two file sets.

Author:
Kathe Todd-Brown
See Also:
Serialized Form

Nested Class Summary
private  class Merge.BinSelectPanel
           
private  class Merge.ListSelectPanel
           
private  class Merge.TextSelectPanel
           
 
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.JRadioButton makeBin
           
private  javax.swing.JTabbedPane mergeInputs
           
static java.lang.String name
          The name of the form
private  javax.swing.JRadioButton op1
           
private  javax.swing.JRadioButton op2
           
private  javax.swing.JRadioButton op3
           
private  javax.swing.JRadioButton op4
           
private  javax.swing.JRadioButton op5
           
private  javax.swing.JRadioButton op6
           
private  javax.swing.JRadioButton op7
           
private  javax.swing.JPanel optional
           
private  javax.swing.JRadioButton recode
           
private  javax.swing.JRadioButton recode12
           
private  javax.swing.JRadioButton recodeAD
           
private  javax.swing.JRadioButton recodeHV
           
private  javax.swing.JPanel recodeOp
           
private  Merge.BinSelectPanel targetBin
           
private  Merge.TextSelectPanel targetText
           
private  Merge.ListSelectPanel targetTXT
           
 
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
Merge(GPLINK mf)
           
 
Method Summary
private  javax.swing.JPanel bundle(javax.swing.JLabel label, javax.swing.JTextField field, Form.BrowseButton browse)
          Create a JPanel that contains a lable, textfield and browse button.
protected  javax.swing.JPanel createBody()
          Create the body for this form.
(package private)  void createMergeTarget()
           
(package private)  void createOptions()
           
(package private)  void createRecodeOps()
           
protected  void initalize()
           
protected  void isBodyValid()
          Check to see if the body is correctly filled out.
protected  java.lang.String processBody()
          Create the commandline based on the fields of 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


targetText

private Merge.TextSelectPanel targetText

targetBin

private Merge.BinSelectPanel targetBin

targetTXT

private Merge.ListSelectPanel targetTXT

mergeInputs

private javax.swing.JTabbedPane mergeInputs

recode

private javax.swing.JRadioButton recode

recodeAD

private javax.swing.JRadioButton recodeAD

recode12

private javax.swing.JRadioButton recode12

recodeHV

private javax.swing.JRadioButton recodeHV

makeBin

private javax.swing.JRadioButton makeBin

recodeOp

private javax.swing.JPanel recodeOp

op1

private javax.swing.JRadioButton op1

op2

private javax.swing.JRadioButton op2

op3

private javax.swing.JRadioButton op3

op4

private javax.swing.JRadioButton op4

op5

private javax.swing.JRadioButton op5

op6

private javax.swing.JRadioButton op6

op7

private javax.swing.JRadioButton op7

optional

private javax.swing.JPanel optional
Constructor Detail

Merge

public Merge(GPLINK mf)
Method Detail

initalize

protected void initalize()

createMergeTarget

void createMergeTarget()

createRecodeOps

void createRecodeOps()

createOptions

void createOptions()

createBody

protected javax.swing.JPanel createBody()
Description copied from class: Form
Create the body for this form.

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

processBody

protected java.lang.String processBody()
Description copied from class: Form
Create the commandline based on the fields of 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()
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

bundle

private javax.swing.JPanel bundle(javax.swing.JLabel label,
                                  javax.swing.JTextField field,
                                  Form.BrowseButton browse)
Create a JPanel that contains a lable, textfield and browse button. This allows us to bundle these more effectively

Parameters:
label - A JLabel that discribes this panel.
field - A JTextField that holds the file name.
browse - A BrowseButton that selectes the file name.
Returns:
A JPanel that contains the given label, field and browse button.