Class JMatrixPanel

  • All Implemented Interfaces:
    java.awt.image.ImageObserver, java.awt.MenuContainer, java.io.Serializable, javax.accessibility.Accessible

    public class JMatrixPanel
    extends javax.swing.JPanel
    a JPanel that can display a difference of distance matrix and paths that have been taken for the alignment

    Note: This panel displays the transpose of its underlying matrix. Thus its width will be the same as Matrix.getRowDimension() and its height the same as Matrix.getColumnDimension(). This stems from the unfortunate ordering of Matrix.get(int, int) parameters as (row, col), which is opposite from the normal (x,y) order used when displaying graphics.

    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
    • Constructor Summary

      Constructors 
      Constructor Description
      JMatrixPanel()  
    • Method Summary

      All Methods Instance Methods Concrete Methods Deprecated Methods 
      Modifier and Type Method Description
      void drawBoxes​(java.awt.Graphics g)
      draw high scoring fragments that are used for the initial alignment seed selection
      void drawDistances​(java.awt.Graphics g1)
      For each element in matrix, draw it as a colored square or pixel.
      void drawPairs​(java.awt.Graphics g)
      draw alternative alignments
      AlternativeAlignment[] getAlternativeAligs()  
      ContinuousColorMapper getCellColor()  
      FragmentPair[] getFragmentPairs()  
      Matrix getMatrix()  
      float getSaturation()
      Deprecated.
      float getScale()  
      float getScalevalue()
      Deprecated.
      int getSelectedAlignmentPos()  
      void paintComponent​(java.awt.Graphics g)  
      void setAlternativeAligs​(AlternativeAlignment[] aligs)  
      void setCellColor​(ContinuousColorMapper cellColor)  
      void setFragmentPairs​(FragmentPair[] fragmentPairs)  
      void setMatrix​(Matrix matrix)
      sets the distance matrix to be displayed
      void setPreferredSize()  
      void setSaturation​(float saturation)
      Deprecated.
      void setScale​(float scale)  
      void setScalevalue​(float scalevalue)
      Deprecated.
      void setSelectedAlignmentPos​(int selectedAlignmentPos)  
      • 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

      • JMatrixPanel

        public JMatrixPanel()
    • Method Detail

      • getSelectedAlignmentPos

        public int getSelectedAlignmentPos()
      • setSelectedAlignmentPos

        public void setSelectedAlignmentPos​(int selectedAlignmentPos)
      • getFragmentPairs

        public FragmentPair[] getFragmentPairs()
      • setFragmentPairs

        public void setFragmentPairs​(FragmentPair[] fragmentPairs)
      • getScale

        public float getScale()
      • setPreferredSize

        public void setPreferredSize()
      • setScale

        public void setScale​(float scale)
      • getMatrix

        public Matrix getMatrix()
      • setMatrix

        public void setMatrix​(Matrix matrix)
        sets the distance matrix to be displayed
        Parameters:
        matrix -
      • paintComponent

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

        public void drawPairs​(java.awt.Graphics g)
        draw alternative alignments
        Parameters:
        g -
      • drawBoxes

        public void drawBoxes​(java.awt.Graphics g)
        draw high scoring fragments that are used for the initial alignment seed selection
        Parameters:
        g -
      • drawDistances

        public void drawDistances​(java.awt.Graphics g1)
        For each element in matrix, draw it as a colored square or pixel. The color of a matrix element with value x is specified as - H: 1-x/scalevalue - S: saturation - B: 1-x/scalevalue
        Parameters:
        g1 -
      • getSaturation

        @Deprecated
        public float getSaturation()
        Deprecated.
      • setSaturation

        @Deprecated
        public void setSaturation​(float saturation)
        Deprecated.
      • getScalevalue

        @Deprecated
        public float getScalevalue()
        Deprecated.
      • setScalevalue

        @Deprecated
        public void setScalevalue​(float scalevalue)
        Deprecated.
      • getCellColor

        public ContinuousColorMapper getCellColor()
        Returns:
        the color mapping of the JMatrixPanel
      • setCellColor

        public void setCellColor​(ContinuousColorMapper cellColor)
        Parameters:
        cellColor - the color mapping of the JMatrixPanel to set