org.biojava.bio.structure.gui
Class JMatrixPanel

java.lang.Object
  extended by java.awt.Component
      extended by java.awt.Container
          extended by javax.swing.JComponent
              extended by javax.swing.JPanel
                  extended by org.biojava.bio.structure.gui.JMatrixPanel
All Implemented Interfaces:
ImageObserver, MenuContainer, Serializable, Accessible

public class JMatrixPanel
extends 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
JPanel.AccessibleJPanel
 
Nested classes/interfaces inherited from class javax.swing.JComponent
JComponent.AccessibleJComponent
 
Nested classes/interfaces inherited from class java.awt.Container
Container.AccessibleAWTContainer
 
Nested classes/interfaces inherited from class java.awt.Component
Component.AccessibleAWTComponent, Component.BaselineResizeBehavior, Component.BltBufferStrategy, Component.FlipBufferStrategy
 
Field Summary
 
Fields inherited from class javax.swing.JComponent
accessibleContext, 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
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
JMatrixPanel()
           
 
Method Summary
 void drawBoxes(Graphics g)
          draw high scoring fragments that are used for the initial alignment seed selection
 void drawDistances(Graphics g1)
          For each element in matrix, draw it as a colored square or pixel.
 void drawPairs(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(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, isDoubleBuffered, isLightweightComponent, isManagingFocus, isOpaque, isOptimizedDrawingEnabled, isPaintingForPrint, 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, getPeer, getPropertyChangeListeners, getPropertyChangeListeners, getSize, getToolkit, getTreeLock, gotFocus, handleEvent, hasFocus, hide, 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, resize, resize, setBounds, setBounds, setComponentOrientation, setCursor, setDropTarget, setFocusable, setFocusTraversalKeysEnabled, setIgnoreRepaint, setLocale, setLocation, setLocation, 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)

getAlternativeAligs

public AlternativeAlignment[] getAlternativeAligs()

setAlternativeAligs

public void setAlternativeAligs(AlternativeAlignment[] aligs)

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(Graphics g)
Overrides:
paintComponent in class JComponent

drawPairs

public void drawPairs(Graphics g)
draw alternative alignments

Parameters:
g -

drawBoxes

public void drawBoxes(Graphics g)
draw high scoring fragments that are used for the initial alignment seed selection

Parameters:
g -

drawDistances

public void drawDistances(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