edu.harvard.mgh.purcell.gPLINK2
Class PLINK_Import

java.lang.Object
  java.awt.Component
      java.awt.Container
          java.awt.Window
              java.awt.Dialog
                  javax.swing.JDialog
                      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.