Class MultipleAligPanel

  • 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 MultipleAligPanel
    extends JPrintPanel
    implements AlignmentPositionListener, java.awt.event.WindowListener
    A JPanel that can display the sequence alignment of a MultipleAlignment in a nice way and interact with Jmol by selecting the aligned atoms of the sequence selection.

    Coloring options include: sequence similarity, by Block or by Structure. Colors are connected with the JmolPanel using the same pattelete.

    The positions can be selected individually or in ranges and they will be translated to jmol commands.

    Since:
    4.1.0
    Author:
    Aleix Lafita
    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
    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      void actionPerformed​(java.awt.event.ActionEvent e)  
      void addAlignmentPositionListener​(AlignmentPositionListener li)  
      void destroy()  
      java.util.List<java.lang.String> getAlnSequences()  
      java.util.List<Atom[]> getAtomArrays()  
      MultipleAlignmentCoordManager getCoordManager()  
      java.util.List<java.lang.Integer> getMapSeqToStruct()  
      MultipleAlignment getMultipleAlignment()  
      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 setStructureAlignmentJmol​(AbstractAlignmentJmol jmol)  
      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

      • MultipleAligPanel

        public MultipleAligPanel()
        Default constructor. Empty MultipleAligPanel instance.
    • Method Detail

      • destroy

        public void destroy()
      • 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
      • getAtomArrays

        public java.util.List<Atom[]> getAtomArrays()
      • getAlnSequences

        public java.util.List<java.lang.String> getAlnSequences()
      • getMapSeqToStruct

        public java.util.List<java.lang.Integer> getMapSeqToStruct()