Class SequencePanel

  • All Implemented Interfaces:
    java.awt.image.ImageObserver, java.awt.MenuContainer, java.io.Serializable, javax.swing.SwingConstants, SequenceRenderContext, Changeable

    public class SequencePanel
    extends javax.swing.JComponent
    implements javax.swing.SwingConstants, SequenceRenderContext, Changeable
    A panel that displays a Sequence.

    A SequencePanel can either display the sequence from left-to-right (HORIZONTAL) or from top-to-bottom (VERTICAL). It has an associated scale which is the number of pixels per symbol. It also has a lines property that controls how to wrap the sequence off one end and onto the other.

    Each line in the SequencePanel is broken down into a list of strips, each rendered by an individual SequenceRenderer object. You could add a SequenceRenderer that draws on genes, another that draws repeats and another that prints out the DNA sequence. They are responsible for rendering their view of the sequence in the place that the SequencePanel positions them.

    Author:
    Thomas Down, Matthew Pocock, David Huen
    See Also:
    Serialized Form
    • Nested Class Summary

      Nested Classes 
      Modifier and Type Class Description
      class  SequencePanel.Border  
      • 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 
      Modifier and Type Field Description
      static ChangeType RENDERER  
      • 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 javax.swing.SwingConstants

        BOTTOM, CENTER, EAST, HORIZONTAL, LEADING, LEFT, NEXT, NORTH, NORTH_EAST, NORTH_WEST, PREVIOUS, RIGHT, SOUTH, SOUTH_EAST, SOUTH_WEST, TOP, TRAILING, VERTICAL, WEST
    • Constructor Summary

      Constructors 
      Constructor Description
      SequencePanel()
      Create a new SequencePanel.
    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      protected void _setRenderer​(SequenceRenderer r)  
      void addChangeListener​(ChangeListener cl)
      Add a listener that will be informed of all changes.
      void addChangeListener​(ChangeListener cl, ChangeType ct)
      Add a listener that will be informed of changes of a given type.
      void addSequenceViewerListener​(SequenceViewerListener svl)  
      void addSequenceViewerMotionListener​(SequenceViewerMotionListener svml)  
      protected int[] calcDist()  
      boolean equals​(java.lang.Object o)  
      protected ChangeSupport getChangeSupport​(ChangeType ct)  
      int getDirection()
      Retrieve the current rendering direction.
      FeatureHolder getFeatures()
      The features to render.
      SequenceRenderContext.Border getLeadingBorder()
      Retrieve the object that encapsulates the leading border area - the space before sequence information is rendered.
      RangeLocation getRange()
      The range of the SymbolList to render.
      java.awt.RenderingHints getRenderingHints()  
      double getScale()
      Retrieve the current scale.
      SymbolList getSequence()  
      SymbolList getSymbols()
      Retrieve the currently rendered SymbolList
      SequenceRenderContext.Border getTrailingBorder()
      Retrieve the object that encapsulates the trailing border area - the space after sequence information is rendered.
      int graphicsToSequence​(double gPos)
      Converts a graphical position into a sequence coordinate.
      int graphicsToSequence​(java.awt.geom.Point2D point)
      Converts a graphical position into a sequence coordinate.
      protected boolean hasChangeListeners()  
      int hashCode()  
      protected boolean hasListeners()  
      protected boolean isActive()  
      boolean isUnchanging​(ChangeType ct)
      A particular ChangeType can never be raised by this Changeable.
      void paintComponent​(java.awt.Graphics g)
      Paint this component.
      void removeChangeListener​(ChangeListener cl)
      Remove a listener that was interested in all types of changes.
      void removeChangeListener​(ChangeListener cl, ChangeType ct)
      Remove a listener that was interested in a specific types of changes.
      void removeSequenceViewerListener​(SequenceViewerListener svl)  
      void removeSequenceViewerMotionListener​(SequenceViewerMotionListener svml)  
      void resizeAndValidate()  
      double sequenceToGraphics​(int seqPos)
      Converts a sequence index into a graphical coordinate.
      void setDirection​(int dir)
      Set the direction that this SequencePanel renders in.
      void setRange​(RangeLocation range)  
      void setRenderer​(SequenceRenderer r)  
      void setRenderingHints​(java.awt.RenderingHints hints)
      Use this to switch on effects like Anti-aliasing etc
      void setScale​(double scale)
      Set the scale.
      void setSequence​(SymbolList s)
      Set the SymboList to be rendered.
      • 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, getUI, getUIClassID, getVerifyInputWhenFocusTarget, getVetoableChangeListeners, getVisibleRect, getWidth, getX, getY, grabFocus, hide, isDoubleBuffered, isLightweightComponent, isManagingFocus, isOpaque, isOptimizedDrawingEnabled, isPaintingForPrint, isPaintingOrigin, isPaintingTile, isRequestFocusEnabled, isValidateRoot, paint, paintBorder, paintChildren, paintImmediately, paintImmediately, paramString, 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, updateUI
      • 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, getAccessibleContext, 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, finalize, getClass, notify, notifyAll, wait, wait, wait
    • Field Detail

      • RENDERER

        public static final ChangeType RENDERER
    • Constructor Detail

      • SequencePanel

        public SequencePanel()
        Create a new SequencePanel.
    • Method Detail

      • setRenderingHints

        public void setRenderingHints​(java.awt.RenderingHints hints)
        Use this to switch on effects like Anti-aliasing etc
        Parameters:
        hints - the desired rendering properties
      • getRenderingHints

        public java.awt.RenderingHints getRenderingHints()
        Returns:
        the current rendering properties
      • hasChangeListeners

        protected boolean hasChangeListeners()
      • hasListeners

        protected boolean hasListeners()
      • addChangeListener

        public void addChangeListener​(ChangeListener cl)
        Description copied from interface: Changeable
        Add a listener that will be informed of all changes.
        Specified by:
        addChangeListener in interface Changeable
        Parameters:
        cl - the ChangeListener to add
      • addChangeListener

        public void addChangeListener​(ChangeListener cl,
                                      ChangeType ct)
        Description copied from interface: Changeable
        Add a listener that will be informed of changes of a given type.
        Specified by:
        addChangeListener in interface Changeable
        Parameters:
        cl - the ChangeListener
        ct - the ChangeType it is to be informed of
      • removeChangeListener

        public void removeChangeListener​(ChangeListener cl)
        Description copied from interface: Changeable
        Remove a listener that was interested in all types of changes.
        Specified by:
        removeChangeListener in interface Changeable
        Parameters:
        cl - a ChangeListener to remove
      • removeChangeListener

        public void removeChangeListener​(ChangeListener cl,
                                         ChangeType ct)
        Description copied from interface: Changeable
        Remove a listener that was interested in a specific types of changes.
        Specified by:
        removeChangeListener in interface Changeable
        Parameters:
        cl - a ChangeListener to remove
        ct - the ChangeType that it was interested in
      • isUnchanging

        public boolean isUnchanging​(ChangeType ct)
        Description copied from interface: Changeable

        A particular ChangeType can never be raised by this Changeable.

        If this returns true, then it is guaranteed that change events of this type (and all child types) can never under any circumstances be fired by this Changeable instance. If it returns false, that does not mean that this type of event will or even can be raised, but that it is worth registering listeners incase.

        Specified by:
        isUnchanging in interface Changeable
        Parameters:
        ct - the ChangeType to check
        Returns:
        true if ChangeEvents of this type are guaranteed to never be fired
      • setSequence

        public void setSequence​(SymbolList s)
        Set the SymboList to be rendered. This symbol list will be passed onto the SequenceRenderer instances registered with this SequencePanel.
        Parameters:
        s - the SymboList to render
      • setDirection

        public void setDirection​(int dir)
                          throws java.lang.IllegalArgumentException
        Set the direction that this SequencePanel renders in. The direction can be one of HORIZONTAL or VERTICAL. Once the direction is set, the display will redraw. HORIZONTAL represents left-to-right rendering. VERTICAL represents AceDB-style vertical rendering.
        Parameters:
        dir - the new rendering direction
        Throws:
        java.lang.IllegalArgumentException
      • getDirection

        public int getDirection()
        Retrieve the current rendering direction.
        Specified by:
        getDirection in interface SequenceRenderContext
        Returns:
        the rendering direction (one of HORIZONTAL and VERTICAL)
      • setScale

        public void setScale​(double scale)
        Set the scale.

        The scale parameter is interpreted as the number of pixels per symbol. This may take on a wide range of values - for example, to render the symbols as text, you will need a scale of > 8, where as to render chromosome 1 you will want a scale < 0.00000001

        Parameters:
        scale - the new pixels-per-symbol ratio
      • getScale

        public double getScale()
        Retrieve the current scale.
        Specified by:
        getScale in interface SequenceRenderContext
        Returns:
        the number of pixels used to render one symbol
      • paintComponent

        public void paintComponent​(java.awt.Graphics g)
        Paint this component.

        This calls the paint method of the currently registered SequenceRenderer after setting up the graphics appropriately.

        Overrides:
        paintComponent in class javax.swing.JComponent
      • sequenceToGraphics

        public double sequenceToGraphics​(int seqPos)
        Description copied from interface: SequenceRenderContext
        Converts a sequence index into a graphical coordinate. You will need to use this in conjunction with getDirection to correctly lay graphics out.
        Specified by:
        sequenceToGraphics in interface SequenceRenderContext
        Parameters:
        seqPos - Index within the sequence
        Returns:
        Equivalent graphical position in pixels
      • graphicsToSequence

        public int graphicsToSequence​(double gPos)
        Description copied from interface: SequenceRenderContext
        Converts a graphical position into a sequence coordinate. You will need to have used getDirection to decide whether to use the x or y coordinate.
        Specified by:
        graphicsToSequence in interface SequenceRenderContext
        Parameters:
        gPos - A pixel position
        Returns:
        The corresponding sequence index
      • graphicsToSequence

        public int graphicsToSequence​(java.awt.geom.Point2D point)
        Description copied from interface: SequenceRenderContext
        Converts a graphical position into a sequence coordinate. This will use getDirection to decide whether to use the x or y coordinate.
        Specified by:
        graphicsToSequence in interface SequenceRenderContext
        Parameters:
        point - a point representing the position
        Returns:
        the corresponding sequence index
      • resizeAndValidate

        public void resizeAndValidate()
      • calcDist

        protected int[] calcDist()
      • isActive

        protected boolean isActive()
      • equals

        public boolean equals​(java.lang.Object o)
        Overrides:
        equals in class java.lang.Object
      • hashCode

        public int hashCode()
        Overrides:
        hashCode in class java.lang.Object