org.strbio.mol.lib.pred2ary
Class Pred2aryAppletFrame

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 org.strbio.mol.lib.pred2ary.Pred2aryAppletFrame
All Implemented Interfaces:
java.awt.image.ImageObserver, java.awt.MenuContainer, java.io.Serializable, javax.accessibility.Accessible

public class Pred2aryAppletFrame
extends java.awt.Frame

Predict secondary structure/class, using profiles. This is a java applet version. All 1.1 event handling has been reverted to 1.0, to please old versions of Netscape.

  Version 
  Version 1.06AP, 6/9/99 - moved to org.strbio.mol.lib.pred2ary, uses more
    functionality from generic classes
  Version 1.052AP, 12/10/98 - fixed bug with nameless MSF files
  Version 1.051AP, 10/26/98 - can load lower case FASTA and MSF files
  Version 1.05AP, 9/4/98 - fixed bug triggered by choosing sequence
    and repredicting
  Version 1.04AP, 8/31/98 - fixed loading bug, includes key.
  Version 1.03AP, 8/26/98 - more help buttons
  Version 1.02AP, 8/20/98 - prevents users from clicking Predict twice.
  Version 1.01AP, 8/18/98 - cosmetic changes
  Version 1.0AP, 8/5/98 - adapted from Pred2ary 1.12NS (8/4/98)
  

Version:
1.06AP, 6/9/99
Author:
JMC
See Also:
Serialized Form

Nested Class Summary
 class Pred2aryAppletFrame.AboutDialog
          This gets displayed if user wants to know about the program.
 class Pred2aryAppletFrame.AboutMessage
           
 class Pred2aryAppletFrame.LoadWindow
           
 class Pred2aryAppletFrame.ProgressDialog
           
 class Pred2aryAppletFrame.ProteinPane
           
 class Pred2aryAppletFrame.SaveWindow
           
 
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
 Pred2aryAppletFrame.AboutDialog aboutDialog
           
 Pred2aryApplet applet
           
 java.awt.Button chooseSequenceB
           
 AppletJury currentJury
           
 int fontSize
           
 Pred2aryAppletFrame frame
           
 java.awt.Button loadProteinsB
           
 java.awt.MenuItem loadProteinsMI
           
 Pred2aryAppletFrame.LoadWindow loadWindow
           
 OldBufferedPrintfTextArea logText
           
 java.awt.Label mainLabel
           
 java.awt.Label networkLabel
           
 char[] numBuffer
           
 PredictionSet p
           
 ProfileDisplayArea pda
           
 java.awt.Button predictProteinsB
           
 Pred2aryAppletFrame.ProgressDialog progressDialog
           
 Pred2aryAppletFrame.ProteinPane proteinPane
           
 java.awt.Button saveProteinsB
           
 java.awt.MenuItem saveProteinsMI
           
 Pred2aryAppletFrame.SaveWindow saveWindow
           
 JMCScrollPane scrollPanel
           
 java.awt.Panel tabbedPane
           
static java.lang.String VERSION
           
 
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 java.awt.image.ImageObserver
ABORT, ALLBITS, ERROR, FRAMEBITS, HEIGHT, PROPERTIES, SOMEBITS, WIDTH
 
Constructor Summary
Pred2aryAppletFrame(Pred2aryApplet ap)
          This handles the interactive, GUI version of the program.
 
Method Summary
 void chooseSequence()
           
 void clearLog()
           
 void disableEverything()
           
 void enableWithoutProteins()
           
 void enableWithProteins()
           
 boolean handleEvent(java.awt.Event e)
           
 void loadProteins()
          open up a new load window.
static void main(java.lang.String[] argv)
           
 void predictProteins()
           
 void saveProteins()
          open up a new save window and save in ea format to it.
 void setFontSize(int size)
           
 void setLabel(java.lang.String s)
          give user a short message.
 java.awt.Menu setupFontSizeMenu()
           
 java.awt.MenuItem setupFontSizeMenuItem(int size, java.awt.Menu menu)
           
 void showHelp(java.lang.String helpLoc)
           
 void showProteins()
           
 
Methods inherited from class java.awt.Frame
addNotify, finalize, getAccessibleContext, getCursorType, getExtendedState, getFrames, getIconImage, getMaximizedBounds, getMenuBar, getState, getTitle, isResizable, isUndecorated, paramString, remove, removeNotify, setCursor, setExtendedState, setIconImage, 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, processWindowEvent, 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, addImpl, 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, remove, removeAll, removeContainerListener, setComponentZOrder, setFocusTraversalKeys, setFocusTraversalPolicy, setFocusTraversalPolicyProvider, setFont, setLayout, transferFocusBackward, transferFocusDownCycle, update, 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, 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
 

Field Detail

VERSION

public static final java.lang.String VERSION
See Also:
Constant Field Values

applet

public Pred2aryApplet applet

frame

public Pred2aryAppletFrame frame

aboutDialog

public Pred2aryAppletFrame.AboutDialog aboutDialog

progressDialog

public Pred2aryAppletFrame.ProgressDialog progressDialog

saveWindow

public Pred2aryAppletFrame.SaveWindow saveWindow

loadWindow

public Pred2aryAppletFrame.LoadWindow loadWindow

logText

public OldBufferedPrintfTextArea logText

proteinPane

public Pred2aryAppletFrame.ProteinPane proteinPane

pda

public ProfileDisplayArea pda

scrollPanel

public JMCScrollPane scrollPanel

tabbedPane

public java.awt.Panel tabbedPane

mainLabel

public java.awt.Label mainLabel

p

public PredictionSet p

currentJury

public AppletJury currentJury

fontSize

public int fontSize

networkLabel

public java.awt.Label networkLabel

chooseSequenceB

public java.awt.Button chooseSequenceB

loadProteinsB

public java.awt.Button loadProteinsB

loadProteinsMI

public java.awt.MenuItem loadProteinsMI

saveProteinsB

public java.awt.Button saveProteinsB

predictProteinsB

public java.awt.Button predictProteinsB

saveProteinsMI

public java.awt.MenuItem saveProteinsMI

numBuffer

public final char[] numBuffer
Constructor Detail

Pred2aryAppletFrame

public Pred2aryAppletFrame(Pred2aryApplet ap)
This handles the interactive, GUI version of the program.

Method Detail

showHelp

public void showHelp(java.lang.String helpLoc)

disableEverything

public void disableEverything()

enableWithProteins

public void enableWithProteins()

enableWithoutProteins

public void enableWithoutProteins()

setLabel

public void setLabel(java.lang.String s)
give user a short message. can't be private due to bug in Java


loadProteins

public void loadProteins()
open up a new load window.


saveProteins

public void saveProteins()
open up a new save window and save in ea format to it.


clearLog

public void clearLog()

predictProteins

public void predictProteins()

chooseSequence

public void chooseSequence()

showProteins

public void showProteins()

setFontSize

public void setFontSize(int size)

setupFontSizeMenuItem

public java.awt.MenuItem setupFontSizeMenuItem(int size,
                                               java.awt.Menu menu)

setupFontSizeMenu

public java.awt.Menu setupFontSizeMenu()

handleEvent

public boolean handleEvent(java.awt.Event e)
Overrides:
handleEvent in class java.awt.Component

main

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