edu.harvard.mgh.purcell.gPLINK2
Class PLINK_Import

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

public class PLINK_Import
extends javax.swing.JDialog

An extention of JDialog that imports a new command into OpView from a log file.

Author:
Kathe Todd-Brown
See Also:
Serialized Form

Nested Class Summary
private static class PLINK_Import.ExitStatus
          A boolean flag that is true if the operation is done and false otherwise.
 
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 allBox
          A JCheckBox that flags selection of all the non-included roots.
private  Project data
          The Project that the operation is added to.
private  PLINK_Import.ExitStatus done
           
private  java.util.Vector<java.lang.String> finalLogRoots
          A Vector that holds all non-included roots
private  StartFrame frame
          The StartFrame that this dialog is attached to.
private  org.apache.log4j.Logger logger
          A logger for this class
private  javax.swing.JComboBox nonincludedRoots
          A combo box that contains all the log file roots that are not already in the operation tree.
 
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
PLINK_Import(StartFrame mf, Project d)
          Create a JDialog that will allow the user to input plink operations from log files in their home directory.
 
Method Summary
private  javax.swing.JPanel createButtons()
          Create the JButtons for this form.
private  javax.swing.JPanel createRoots()
          Create a JPanel that contains the JComboBox with the appropreate file root options.
private  java.lang.String getCommandline(java.lang.String outputRoot)
          Get the command line based on the log file.
private  java.util.Vector<java.lang.String[]> getInput(java.lang.String cline)
          Pulls an array of strings identifing the input files
private  void process()
          Take the options selected on the form and add an appropreate operation.
 
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 org.apache.log4j.Logger logger
A logger for this class


frame

private StartFrame frame
The StartFrame that this dialog is attached to.


data

private Project data
The Project that the operation is added to.


nonincludedRoots

private javax.swing.JComboBox nonincludedRoots
A combo box that contains all the log file roots that are not already in the operation tree.


allBox

private javax.swing.JCheckBox allBox
A JCheckBox that flags selection of all the non-included roots.


finalLogRoots

private java.util.Vector<java.lang.String> finalLogRoots
A Vector that holds all non-included roots


done

private PLINK_Import.ExitStatus done
Constructor Detail

PLINK_Import

public PLINK_Import(StartFrame mf,
                    Project d)
Create a JDialog that will allow the user to input plink operations from log files in their home directory.

Parameters:
mf - a StartFrame this dialog is attached to and unloads/downloads with.
d - a Project that the imported operations are added to.
Method Detail

getInput

private java.util.Vector<java.lang.String[]> getInput(java.lang.String cline)
Pulls an array of strings identifing the input files

Parameters:
cline - a command line string. Any file names with spaces must be quoted.
Returns:
an array of strings identifying the input files

getCommandline

private java.lang.String getCommandline(java.lang.String outputRoot)
Get the command line based on the log file.

Parameters:
outputRoot - A String that is the file root for our log file.
Returns:
A String that is a command line in this log file.

process

private void process()
Take the options selected on the form and add an appropreate operation.


createRoots

private javax.swing.JPanel createRoots()
Create a JPanel that contains the JComboBox with the appropreate file root options.

Returns:
A JPanel that gives the user the option of selecting a specific file root to import.

createButtons

private javax.swing.JPanel createButtons()
Create the JButtons for this form.

Returns:
A JPanel that contains the ok and cancel JButtons.