Package org.biojava.nbio.structure.align.gui.aligpanel

Class AligPanel

  • All Implemented Interfaces:
    java.awt.event.ActionListener, java.awt.event.WindowListener, java.awt.image.ImageObserver, java.awt.MenuContainer, java.awt.print.Printable, java.io.Serializable, java.util.EventListener, javax.accessibility.Accessible, AlignmentPositionListener
    public class AligPanel
extends JPrintPanel
implements AlignmentPositionListener, java.awt.event.WindowListener
    A JPanel that can display an AFPChain in a nice way and interact with Jmol.
    Author:
    Andreas Prlic
    See Also:
    Serialized Form

    • Nested Class Summary

      • Nested classes/interfaces inherited from class javax.swing.JPanel

        javax.swing.JPanel.AccessibleJPanel

      • Nested classes/interfaces inherited from class javax.swing.JComponent

        javax.swing.JComponent.AccessibleJComponent

      • 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.BaselineResizeBehavior, java.awt.Component.BltBufferStrategy, java.awt.Component.FlipBufferStrategy

    • Field Summary

      • Fields inherited from class javax.swing.JComponent

        listenerList, TOOL_TIP_TEXT_KEY, ui, UNDEFINED_CONDITION, WHEN_ANCESTOR_OF_FOCUSED_COMPONENT, WHEN_FOCUSED, WHEN_IN_FOCUSED_WINDOW

      • Fields inherited from class java.awt.Component

        accessibleContext, 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

      • Fields inherited from interface java.awt.print.Printable

        NO_SUCH_PAGE, PAGE_EXISTS

    • Constructor Summary

      Constructors 
      Constructor Description
      AligPanel()  

    • Method Summary

      All Methods Static Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      void actionPerformed​(java.awt.event.ActionEvent e)  
      void addAlignmentPositionListener​(AlignmentPositionListener li)  
      void destroy()  
      AFPChain getAFPChain()  
      Atom[] getCa1()  
      Atom[] getCa2()  
      AFPChainCoordManager getCoordManager()  
      static void main​(java.lang.String[] args)  
      void mouseOverPosition​(AlignedPosition p)  
      void paintComponent​(java.awt.Graphics g)  
      void positionSelected​(AlignedPosition p)  
      void rangeSelected​(AlignedPosition start, AlignedPosition end)  
      void selectionLocked()  
      void selectionUnlocked()  
      void setAFPChain​(AFPChain afpChain)  
      void setAlignmentJmol​(AbstractAlignmentJmol jmol)  
      void setCa1​(Atom[] ca1)  
      void setCa2​(Atom[] ca2)  
      void toggleSelection​(AlignedPosition p)  
      void windowActivated​(java.awt.event.WindowEvent e)  
      void windowClosed​(java.awt.event.WindowEvent e)  
      void windowClosing​(java.awt.event.WindowEvent e)  
      void windowDeactivated​(java.awt.event.WindowEvent e)  
      void windowDeiconified​(java.awt.event.WindowEvent e)  
      void windowIconified​(java.awt.event.WindowEvent e)  
      void windowOpened​(java.awt.event.WindowEvent e)  

      • Methods inherited from class org.biojava.nbio.structure.align.gui.JPrintPanel

        print

      • Methods inherited from class javax.swing.JPanel

        getAccessibleContext, getUI, getUIClassID, paramString, setUI, updateUI

      • Methods inherited from class javax.swing.JComponent

        addAncestorListener, addNotify, addVetoableChangeListener, computeVisibleRect, contains, createToolTip, disable, enable, firePropertyChange, firePropertyChange, firePropertyChange, fireVetoableChange, getActionForKeyStroke, getActionMap, getAlignmentX, getAlignmentY, getAncestorListeners, getAutoscrolls, getBaseline, getBaselineResizeBehavior, getBorder, getBounds, getClientProperty, getComponentGraphics, getComponentPopupMenu, getConditionForKeyStroke, getDebugGraphicsOptions, getDefaultLocale, getFontMetrics, getGraphics, getHeight, getInheritsPopupMenu, getInputMap, getInputMap, getInputVerifier, getInsets, getInsets, getListeners, getLocation, getMaximumSize, getMinimumSize, getNextFocusableComponent, getPopupLocation, getPreferredSize, getRegisteredKeyStrokes, getRootPane, getSize, getToolTipLocation, getToolTipText, getToolTipText, getTopLevelAncestor, getTransferHandler, getVerifyInputWhenFocusTarget, getVetoableChangeListeners, getVisibleRect, getWidth, getX, getY, grabFocus, hide, isDoubleBuffered, isLightweightComponent, isManagingFocus, isOpaque, isOptimizedDrawingEnabled, isPaintingForPrint, isPaintingOrigin, isPaintingTile, isRequestFocusEnabled, isValidateRoot, paint, paintBorder, paintChildren, paintImmediately, paintImmediately, print, printAll, printBorder, printChildren, printComponent, processComponentKeyEvent, processKeyBinding, processKeyEvent, processMouseEvent, processMouseMotionEvent, putClientProperty, registerKeyboardAction, registerKeyboardAction, removeAncestorListener, removeNotify, removeVetoableChangeListener, repaint, repaint, requestDefaultFocus, requestFocus, requestFocus, requestFocusInWindow, requestFocusInWindow, resetKeyboardActions, reshape, revalidate, scrollRectToVisible, setActionMap, setAlignmentX, setAlignmentY, setAutoscrolls, setBackground, setBorder, setComponentPopupMenu, setDebugGraphicsOptions, setDefaultLocale, setDoubleBuffered, setEnabled, setFocusTraversalKeys, setFont, setForeground, setInheritsPopupMenu, setInputMap, setInputVerifier, setMaximumSize, setMinimumSize, setNextFocusableComponent, setOpaque, setPreferredSize, setRequestFocusEnabled, setToolTipText, setTransferHandler, setUI, setVerifyInputWhenFocusTarget, setVisible, unregisterKeyboardAction, update

      • Methods inherited from class java.awt.Container

        add, add, add, add, add, addContainerListener, addImpl, addPropertyChangeListener, addPropertyChangeListener, applyComponentOrientation, areFocusTraversalKeysSet, countComponents, deliverEvent, doLayout, findComponentAt, findComponentAt, getComponent, getComponentAt, getComponentAt, getComponentCount, getComponents, getComponentZOrder, getContainerListeners, getFocusTraversalKeys, getFocusTraversalPolicy, getLayout, getMousePosition, insets, invalidate, isAncestorOf, isFocusCycleRoot, isFocusCycleRoot, isFocusTraversalPolicyProvider, isFocusTraversalPolicySet, layout, list, list, locate, minimumSize, paintComponents, preferredSize, printComponents, processContainerEvent, processEvent, remove, remove, removeAll, removeContainerListener, setComponentZOrder, setFocusCycleRoot, setFocusTraversalPolicy, setFocusTraversalPolicyProvider, setLayout, 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, createImage, createImage, createVolatileImage, createVolatileImage, disableEvents, dispatchEvent, enable, enableEvents, enableInputMethods, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, getBackground, getBounds, getColorModel, getComponentListeners, getComponentOrientation, getCursor, getDropTarget, getFocusCycleRootAncestor, getFocusListeners, getFocusTraversalKeysEnabled, getFont, getForeground, getGraphicsConfiguration, getHierarchyBoundsListeners, getHierarchyListeners, getIgnoreRepaint, getInputContext, getInputMethodListeners, getInputMethodRequests, getKeyListeners, getLocale, getLocation, getLocationOnScreen, getMouseListeners, getMouseMotionListeners, getMousePosition, getMouseWheelListeners, getName, getParent, getPropertyChangeListeners, getPropertyChangeListeners, getSize, getToolkit, getTreeLock, gotFocus, handleEvent, hasFocus, imageUpdate, inside, isBackgroundSet, isCursorSet, isDisplayable, isEnabled, isFocusable, isFocusOwner, isFocusTraversable, isFontSet, isForegroundSet, isLightweight, isMaximumSizeSet, isMinimumSizeSet, isPreferredSizeSet, isShowing, isValid, isVisible, keyDown, keyUp, list, list, list, location, lostFocus, mouseDown, mouseDrag, mouseEnter, mouseExit, mouseMove, mouseUp, move, nextFocus, paintAll, postEvent, prepareImage, prepareImage, processComponentEvent, processFocusEvent, processHierarchyBoundsEvent, processHierarchyEvent, processInputMethodEvent, processMouseWheelEvent, remove, removeComponentListener, removeFocusListener, removeHierarchyBoundsListener, removeHierarchyListener, removeInputMethodListener, removeKeyListener, removeMouseListener, removeMouseMotionListener, removeMouseWheelListener, removePropertyChangeListener, removePropertyChangeListener, repaint, repaint, repaint, requestFocus, requestFocus, requestFocusInWindow, resize, resize, setBounds, setBounds, setComponentOrientation, setCursor, setDropTarget, setFocusable, setFocusTraversalKeysEnabled, setIgnoreRepaint, setLocale, setLocation, setLocation, setMixingCutoutShape, setName, setSize, setSize, show, show, size, toString, transferFocus, transferFocusBackward, transferFocusUpCycle

      • Methods inherited from class java.lang.Object

        clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

    • Constructor Detail

      • AligPanel

        public AligPanel()

    • Method Detail

      • main

        public static void main​(java.lang.String[] args)

      • destroy

        public void destroy()

      • getAFPChain

        public AFPChain getAFPChain()

      • setAFPChain

        public void setAFPChain​(AFPChain afpChain)

      • paintComponent

        public void paintComponent​(java.awt.Graphics g)
        Overrides:
        paintComponent in class javax.swing.JComponent

      • windowActivated

        public void windowActivated​(java.awt.event.WindowEvent e)
        Specified by:
        windowActivated in interface java.awt.event.WindowListener

      • windowClosed

        public void windowClosed​(java.awt.event.WindowEvent e)
        Specified by:
        windowClosed in interface java.awt.event.WindowListener

      • windowClosing

        public void windowClosing​(java.awt.event.WindowEvent e)
        Specified by:
        windowClosing in interface java.awt.event.WindowListener

      • windowDeactivated

        public void windowDeactivated​(java.awt.event.WindowEvent e)
        Specified by:
        windowDeactivated in interface java.awt.event.WindowListener

      • windowDeiconified

        public void windowDeiconified​(java.awt.event.WindowEvent e)
        Specified by:
        windowDeiconified in interface java.awt.event.WindowListener

      • windowIconified

        public void windowIconified​(java.awt.event.WindowEvent e)
        Specified by:
        windowIconified in interface java.awt.event.WindowListener

      • windowOpened

        public void windowOpened​(java.awt.event.WindowEvent e)
        Specified by:
        windowOpened in interface java.awt.event.WindowListener

      • actionPerformed

        public void actionPerformed​(java.awt.event.ActionEvent e)
        Specified by:
        actionPerformed in interface java.awt.event.ActionListener
        Overrides:
        actionPerformed in class JPrintPanel

      • getCa1

        public Atom[] getCa1()

      • setCa1

        public void setCa1​(Atom[] ca1)

      • getCa2

        public Atom[] getCa2()

      • setCa2

        public void setCa2​(Atom[] ca2)