org.strbio.app
Class Pred2ary

java.lang.Object
  java.awt.Component
      java.awt.Container
          java.awt.Window
              java.awt.Frame
                  javax.swing.JFrame
                      org.strbio.app.Pred2ary

All Implemented Interfaces:

java.awt.image.ImageObserver, java.awt.MenuContainer, java.io.Serializable, javax.accessibility.Accessible, javax.swing.RootPaneContainer, javax.swing.WindowConstants

public class Pred2ary
extends javax.swing.JFrame

Predict secondary structure/class, using profiles. Designed using Swing classes for extra GUI-ness. Run with no options for interactive version, or use -help to get command line options. Command line options for this class make org.strbio.app.Pred2aryJury obsolete.

  Version 1.33, 4/6/00 - remembers loadDir
  Version 1.32, 2/10/00 - fixed bug with null protein sets, reads more
    bogus MSF files.
  Version 1.31, 6/9/99 - improved memory use when many proteins are
    being predicted, moved some code to general use classes
  Version 1.3, 3/30/99 - added more BLAST types, online help, improved
    speed
  Version 1.23, 1/21/99 - reads native BLAST files, can take 1
    file on command line to load
  Version 1.221, 12/21/98 - fixed bug in BLAST thread
  Version 1.22, 12/10/98 - shows correct secondary structure if known
  Version 1.211, 12/4/98 - fixed bug with nameless MSF files.
  Version 1.21, 11/30/98 - proper multithreading
  Version 1.2, 11/18/98 - can do BLAST
  Version 1.171, 10/26/96 - can load lower case FASTA and MSF files
  Version 1.17, 9/4/98 - fixed bug triggered by choosing sequence
    and repredicting
  Version 1.16, 8/31/98 - added key to graph
  Version 1.15, 8/30/98 - added pointer to online help
  Version 1.14, 8/18/98 - can use new FileChooser class if present.
  Version 1.13, 8/13/98 - saves window positions, fixed minor
    graphics bug in prediction graphs
  Version 1.12, 7/15/98 - added new About dialog, remembers settings.
  Version 1.11, 7/14/98 - added more menu items
  Version 1.1, 7/9/98 - can print the prediction, sort out 1 particular
    sequence.
  Version 1.0, 6/18/98 - adapted from Pred2aryJury 1.1 (5/20/98)
  

Version:

1.33, 4/6/00

Author:

JMC

See Also:

Serialized Form

Nested Class Summary

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 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

Pred2ary()
This handles the interactive, GUI version of the program.

Pred2ary(java.lang.String[] argv)
This constructor handles the non-interactive text version of the program.

Method Summary

static void	main(java.lang.String[] argv)
void	showHelp(java.lang.String filename) shows help, located under lib/Pred2ary/, or the index if null filename given.
void	warnUser(java.lang.String message)

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

Pred2ary

public Pred2ary()

This handles the interactive, GUI version of the program.

Pred2ary

public Pred2ary(java.lang.String[] argv)

This constructor handles the non-interactive text version of the program.

Method Detail

warnUser

public void warnUser(java.lang.String message)

showHelp

public void showHelp(java.lang.String filename)

shows help, located under lib/Pred2ary/, or the index if null filename given.

main

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