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

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
All Implemented Interfaces:
java.awt.image.ImageObserver, java.awt.MenuContainer, java.io.Serializable, javax.accessibility.Accessible, javax.swing.RootPaneContainer, javax.swing.WindowConstants
Direct Known Subclasses:
AlleleAssoc, AlleleFreq, Basic, CCAssoc, Clustering, FamAssoc, GenFileSet, HapCCAssoc, HaploFreq, HaploPhase, HapTDTAssoc, HardyWinEq, HomozRuns, IBSdist, IndHetz, MendelErr, Merge, Missing, NearNeigh, QuantTrtInt, Regression, SetAssoc, StratAnaly, Validate

public abstract class Form
extends javax.swing.JDialog

See Also:
Serialized Form

Nested Class Summary
 class 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.JButton cancel
           
private  java.lang.String filter
           
protected  javax.swing.JButton filterButton
           
 InputPane input
          The InputPane for this form.
private static org.apache.log4j.Logger logger
          Optionally log messages.
private  javax.swing.JButton ok
          The ok button on the form, this is a class variable because it is en/disabled in okForm()
protected  OutputPane output
          The OutputPane for this form.
 GPLINK parent
          The GPLINK instance that this form is attached to.
private  java.lang.String threshold
           
protected  javax.swing.JButton thresholdButton
           
protected  java.awt.event.ActionListener validateBodyAL
           
protected  javax.swing.event.DocumentListener validateBodyDL
           
protected  boolean validBody
          Flag if the body of the form is filled out correctly.
 
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
Form(GPLINK p, java.lang.String name)
           
 
Method Summary
 void addFilter(java.lang.String newParam)
           
 void addThreshold(java.lang.String newParam)
           
static javax.swing.JPanel bundel(javax.swing.JTextField text, javax.swing.JButton button)
           
static javax.swing.JPanel bundel(javax.swing.JToggleButton toggle, javax.swing.JTextField text)
           
static void bundel(javax.swing.JToggleButton toggle, javax.swing.JTextField[] texts)
           
static void bundel(javax.swing.JToggleButton toggle, javax.swing.JTextField[] texts, Form.BrowseButton[] buttons)
           
static javax.swing.JPanel bundel(javax.swing.JToggleButton toggle, javax.swing.JTextField text, javax.swing.JButton button)
           
 void closeButtons()
           
protected abstract  javax.swing.JPanel createBody()
          Create the body for this form.
private  javax.swing.JPanel createButtonPane()
          Create a JPanel that holds the ok/cancel buttons for this form.
protected abstract  void isBodyValid()
          Check to see if the body is correctly filled out.
protected  void okForm()
          Enable and disable the ok button to reflect if the form is correctly or incorrectly filled out.
 void openButtons()
           
private  java.lang.String process()
          Process forms in general.
protected abstract  java.lang.String processBody()
          Create the commandline based on the fields of this form.
 void resetFilter()
           
 void 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

logger

private static org.apache.log4j.Logger logger
Optionally log messages.


parent

public GPLINK parent
The GPLINK instance that this form is attached to.


input

public InputPane input
The InputPane for this form. This is made public so that the merge form can access certain functions.


output

protected OutputPane output
The OutputPane for this form.


filter

private java.lang.String filter

threshold

private java.lang.String threshold

validBody

protected boolean validBody
Flag if the body of the form is filled out correctly.


ok

private javax.swing.JButton ok
The ok button on the form, this is a class variable because it is en/disabled in okForm()


cancel

private javax.swing.JButton cancel

filterButton

protected javax.swing.JButton filterButton

thresholdButton

protected javax.swing.JButton thresholdButton

validateBodyAL

protected java.awt.event.ActionListener validateBodyAL

validateBodyDL

protected javax.swing.event.DocumentListener validateBodyDL
Constructor Detail

Form

public Form(GPLINK p,
            java.lang.String name)
Parameters:
p -
name -
Method Detail

resetFilter

public void resetFilter()

addFilter

public void addFilter(java.lang.String newParam)

resetThreshold

public void resetThreshold()

addThreshold

public void addThreshold(java.lang.String newParam)

createBody

protected abstract javax.swing.JPanel createBody()
Create the body for this form.

Returns:
A JPanel that holds the body of this form.

processBody

protected abstract java.lang.String processBody()
Create the commandline based on the fields of this 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 abstract void isBodyValid()
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.


okForm

protected void okForm()
Enable and disable the ok button to reflect if the form is correctly or incorrectly filled out.


closeButtons

public void closeButtons()

openButtons

public void openButtons()

createButtonPane

private javax.swing.JPanel createButtonPane()
Create a JPanel that holds the ok/cancel buttons for this form.

Returns:
A JPanel that has the ok/cancel/threshold/filter buttons that will be located at the end of the form.

process

private java.lang.String process()
Process forms in general.

Returns:
A String that is the command line to be run.

bundel

public static javax.swing.JPanel bundel(javax.swing.JToggleButton toggle,
                                        javax.swing.JTextField text,
                                        javax.swing.JButton button)

bundel

public static javax.swing.JPanel bundel(javax.swing.JToggleButton toggle,
                                        javax.swing.JTextField text)

bundel

public static void bundel(javax.swing.JToggleButton toggle,
                          javax.swing.JTextField[] texts,
                          Form.BrowseButton[] buttons)

bundel

public static void bundel(javax.swing.JToggleButton toggle,
                          javax.swing.JTextField[] texts)

bundel

public static javax.swing.JPanel bundel(javax.swing.JTextField text,
                                        javax.swing.JButton button)