Package org.biojava.nbio.structure.gui
Class JMatrixPanel
- java.lang.Object
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- java.awt.Component
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- java.awt.Container
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- javax.swing.JComponent
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- javax.swing.JPanel
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- org.biojava.nbio.structure.gui.JMatrixPanel
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- 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 alignmentNote: This panel displays the transpose of its underlying matrix. Thus its width will be the same as
Matrix.getRowDimension()
and its height the same asMatrix.getColumnDimension()
. This stems from the unfortunate ordering ofMatrix.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
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Nested Class Summary
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Nested classes/interfaces inherited from class javax.swing.JPanel
JPanel.AccessibleJPanel
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Nested classes/interfaces inherited from class javax.swing.JComponent
JComponent.AccessibleJComponent
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Nested classes/interfaces inherited from class java.awt.Container
Container.AccessibleAWTContainer
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Nested classes/interfaces inherited from class java.awt.Component
Component.AccessibleAWTComponent, Component.BaselineResizeBehavior, Component.BltBufferStrategy, Component.FlipBufferStrategy
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Field Summary
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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
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Fields inherited from class java.awt.Component
accessibleContext, BOTTOM_ALIGNMENT, CENTER_ALIGNMENT, LEFT_ALIGNMENT, RIGHT_ALIGNMENT, TOP_ALIGNMENT
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Fields inherited from interface java.awt.image.ImageObserver
ABORT, ALLBITS, ERROR, FRAMEBITS, HEIGHT, PROPERTIES, SOMEBITS, WIDTH
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Constructor Summary
Constructors Constructor Description JMatrixPanel()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
drawBoxes(Graphics g)
draw high scoring fragments that are used for the initial alignment seed selectionvoid
drawDistances(Graphics g1)
For each element in matrix, draw it as a colored square or pixel.void
drawPairs(Graphics g)
draw alternative alignmentsAlternativeAlignment[]
getAlternativeAligs()
ContinuousColorMapper
getCellColor()
FragmentPair[]
getFragmentPairs()
Matrix
getMatrix()
float
getScale()
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 displayedvoid
setPreferredSize()
void
setScale(float scale)
void
setSelectedAlignmentPos(int selectedAlignmentPos)
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Methods inherited from class javax.swing.JPanel
getAccessibleContext, getUI, getUIClassID, paramString, setUI, updateUI
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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
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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
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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
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Constructor Detail
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JMatrixPanel
public JMatrixPanel()
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Method Detail
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getSelectedAlignmentPos
public int getSelectedAlignmentPos()
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setSelectedAlignmentPos
public void setSelectedAlignmentPos(int selectedAlignmentPos)
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getAlternativeAligs
public AlternativeAlignment[] getAlternativeAligs()
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setAlternativeAligs
public void setAlternativeAligs(AlternativeAlignment[] aligs)
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getFragmentPairs
public FragmentPair[] getFragmentPairs()
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setFragmentPairs
public void setFragmentPairs(FragmentPair[] fragmentPairs)
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getScale
public float getScale()
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setPreferredSize
public void setPreferredSize()
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setScale
public void setScale(float scale)
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setMatrix
public void setMatrix(Matrix matrix)
sets the distance matrix to be displayed- Parameters:
matrix
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paintComponent
public void paintComponent(Graphics g)
- Overrides:
paintComponent
in classJComponent
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drawBoxes
public void drawBoxes(Graphics g)
draw high scoring fragments that are used for the initial alignment seed selection- Parameters:
g
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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
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getCellColor
public ContinuousColorMapper getCellColor()
- Returns:
- the color mapping of the JMatrixPanel
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setCellColor
public void setCellColor(ContinuousColorMapper cellColor)
- Parameters:
cellColor
- the color mapping of the JMatrixPanel to set
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