org.biojava.nbio.structure.gui

Class JMatrixPanel

java.lang.Object

java.awt.Component

java.awt.Container

javax.swing.JComponent

javax.swing.JPanel

org.biojava.nbio.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

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 and Description
JMatrixPanel()

Method Summary

Modifier and Type	Method and Description
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, 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, getPeer, 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, 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