org.strbio.app
Class JThread

java.lang.Object
  extended by java.awt.Component
      extended by java.awt.Container
          extended by java.awt.Window
              extended by java.awt.Frame
                  extended by javax.swing.JFrame
                      extended by org.strbio.util.ui.GUIApp
                          extended by org.strbio.util.ui.ProfileGUIApp
                              extended by org.strbio.app.JThread
All Implemented Interfaces:
java.awt.image.ImageObserver, java.awt.MenuContainer, java.io.Serializable, javax.accessibility.Accessible, javax.swing.RootPaneContainer, javax.swing.WindowConstants

public class JThread
extends ProfileGUIApp

Thread one or more proteins. Combined GUI and CLI version.

  Version 1.2, 3/17/00 - more detailed output
  Version 1.1, 2/22/00 - added new threading method
  Version 1.0, 7/12/99 - original version
  

Version:
1.2, 3/17/00
Author:
JMC
See Also:
Serialized Form

Nested Class Summary
 
Nested classes/interfaces inherited from class org.strbio.util.ui.ProfileGUIApp
ProfileGUIApp.LoadFormats, ProfileGUIApp.LoadProgressDialog
 
Nested classes/interfaces inherited from class javax.swing.JFrame
javax.swing.JFrame.AccessibleJFrame
 
Nested classes/interfaces inherited from class java.awt.Frame
java.awt.Frame.AccessibleAWTFrame
 
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
 
Fields inherited from class org.strbio.util.ui.ProfileGUIApp
loadDir, loadFile, loadPD, loadProteins, loadThread, logText, p
 
Fields inherited from class org.strbio.util.ui.GUIApp
aboutDialog, fontSize, helpFrame, helpFrameLoc, helpFrameSize, mainFrame, mainFrameLoc, mainFrameSize, statusLine
 
Fields inherited from class javax.swing.JFrame
accessibleContext, EXIT_ON_CLOSE, rootPane, rootPaneCheckingEnabled
 
Fields inherited from class java.awt.Frame
CROSSHAIR_CURSOR, DEFAULT_CURSOR, E_RESIZE_CURSOR, HAND_CURSOR, ICONIFIED, MAXIMIZED_BOTH, MAXIMIZED_HORIZ, MAXIMIZED_VERT, MOVE_CURSOR, N_RESIZE_CURSOR, NE_RESIZE_CURSOR, NORMAL, NW_RESIZE_CURSOR, S_RESIZE_CURSOR, SE_RESIZE_CURSOR, SW_RESIZE_CURSOR, TEXT_CURSOR, W_RESIZE_CURSOR, WAIT_CURSOR
 
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, HIDE_ON_CLOSE
 
Fields inherited from interface java.awt.image.ImageObserver
ABORT, ALLBITS, ERROR, FRAMEBITS, HEIGHT, PROPERTIES, SOMEBITS, WIDTH
 
Constructor Summary
JThread()
           
JThread(java.lang.String[] argv)
           
 
Method Summary
 void adjustSplitPane(boolean newShow)
           
protected  java.lang.String appDataPath()
          where is data for this app stored, relative to the app itself?
protected  void disableActions()
          disable all actions
protected  void enableActions()
          enable options, depending on whether there are proteins.
protected  void enableWithoutProteins()
          enable various actions when there are no proteins
protected  void enableWithProteins()
          enable various actions when proteins are there.
static void main(java.lang.String[] argv)
           
protected  ProfileSet newProfileSet()
          Return a new profile set of whatever subclass is wanted.
protected  void setProteins(ProfilePSISet set)
           
protected  void setShownAl(int n)
          called when row N in the table is clicked.
protected  void setShownProtein(int n)
           
protected  void setupActions()
          set up what each Action is supposed to do.
 void showAboutDialog()
          show the "about" dialog.
protected  void showProteins()
           
protected  java.lang.String version()
          what's the version?
 
Methods inherited from class org.strbio.util.ui.ProfileGUIApp
setProteins
 
Methods inherited from class org.strbio.util.ui.GUIApp
getImageIcon, printStatus, setFontSize, setupFontSizeMenu, showHelp, warnUser
 
Methods inherited from class javax.swing.JFrame
addImpl, createRootPane, frameInit, getAccessibleContext, getContentPane, getDefaultCloseOperation, getGlassPane, getJMenuBar, getLayeredPane, getRootPane, isDefaultLookAndFeelDecorated, isRootPaneCheckingEnabled, paramString, processWindowEvent, remove, setContentPane, setDefaultCloseOperation, setDefaultLookAndFeelDecorated, setGlassPane, setIconImage, setJMenuBar, setLayeredPane, setLayout, setRootPane, setRootPaneCheckingEnabled, update
 
Methods inherited from class java.awt.Frame
addNotify, finalize, getCursorType, getExtendedState, getFrames, getIconImage, getMaximizedBounds, getMenuBar, getState, getTitle, isResizable, isUndecorated, remove, removeNotify, setCursor, setExtendedState, setMaximizedBounds, setMenuBar, setResizable, setState, setTitle, setUndecorated
 
Methods inherited from class java.awt.Window
addPropertyChangeListener, addPropertyChangeListener, addWindowFocusListener, addWindowListener, addWindowStateListener, applyResourceBundle, applyResourceBundle, createBufferStrategy, createBufferStrategy, dispose, getBufferStrategy, getFocusableWindowState, getFocusCycleRootAncestor, getFocusOwner, getFocusTraversalKeys, getGraphicsConfiguration, getInputContext, getListeners, getLocale, getMostRecentFocusOwner, getOwnedWindows, getOwner, getToolkit, getWarningString, getWindowFocusListeners, getWindowListeners, getWindowStateListeners, hide, isActive, isAlwaysOnTop, isFocusableWindow, isFocusCycleRoot, isFocused, isLocationByPlatform, isShowing, pack, postEvent, processEvent, processWindowFocusEvent, processWindowStateEvent, removeWindowFocusListener, removeWindowListener, removeWindowStateListener, setAlwaysOnTop, setBounds, setCursor, setFocusableWindowState, setFocusCycleRoot, setLocationByPlatform, setLocationRelativeTo, show, 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, 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, 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
 
Methods inherited from interface java.awt.MenuContainer
getFont, postEvent
 

Constructor Detail

JThread

public JThread()

JThread

public JThread(java.lang.String[] argv)
Method Detail

enableWithProteins

protected void enableWithProteins()
enable various actions when proteins are there.


enableWithoutProteins

protected void enableWithoutProteins()
enable various actions when there are no proteins


enableActions

protected void enableActions()
enable options, depending on whether there are proteins.

Overrides:
enableActions in class ProfileGUIApp

disableActions

protected void disableActions()
disable all actions

Overrides:
disableActions in class ProfileGUIApp

showProteins

protected void showProteins()
Overrides:
showProteins in class ProfileGUIApp

setShownProtein

protected void setShownProtein(int n)

setShownAl

protected void setShownAl(int n)
called when row N in the table is clicked.


newProfileSet

protected ProfileSet newProfileSet()
Description copied from class: ProfileGUIApp
Return a new profile set of whatever subclass is wanted.

Overrides:
newProfileSet in class ProfileGUIApp

setProteins

protected void setProteins(ProfilePSISet set)

appDataPath

protected java.lang.String appDataPath()
where is data for this app stored, relative to the app itself?

Overrides:
appDataPath in class GUIApp

version

protected java.lang.String version()
what's the version?

Overrides:
version in class GUIApp

setupActions

protected void setupActions()
Description copied from class: ProfileGUIApp
set up what each Action is supposed to do.

Overrides:
setupActions in class ProfileGUIApp

showAboutDialog

public void showAboutDialog()
show the "about" dialog.


adjustSplitPane

public void adjustSplitPane(boolean newShow)

main

public static final void main(java.lang.String[] argv)