Package org.biojava.bio.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.bio.structure.gui.JMatrixPanel
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- 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- 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
javax.swing.JPanel.AccessibleJPanel
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Nested classes/interfaces inherited from class javax.swing.JComponent
javax.swing.JComponent.AccessibleJComponent
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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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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(java.awt.Graphics g)
draw high scoring fragments that are used for the initial alignment seed selectionvoid
drawDistances(java.awt.Graphics g1)
void
drawPairs(java.awt.Graphics g)
draw alternative alignmentsAlternativeAlignment[]
getAlternativeAligs()
FragmentPair[]
getFragmentPairs()
Matrix
getMatrix()
float
getSaturation()
float
getScale()
float
getScalevalue()
int
getSelectedAlignmentPos()
void
paintComponent(java.awt.Graphics g)
void
setAlternativeAligs(AlternativeAlignment[] aligs)
void
setFragmentPairs(FragmentPair[] fragmentPairs)
void
setMatrix(Matrix matrix)
sets the distance matrix to be displayedvoid
setPreferredSize()
void
setSaturation(float saturation)
void
setScale(float scale)
void
setScalevalue(float scalevalue)
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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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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getMatrix
public Matrix getMatrix()
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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(java.awt.Graphics g)
- Overrides:
paintComponent
in classjavax.swing.JComponent
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drawPairs
public void drawPairs(java.awt.Graphics g)
draw alternative alignments- Parameters:
g
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drawBoxes
public void drawBoxes(java.awt.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(java.awt.Graphics g1)
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getSaturation
public float getSaturation()
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setSaturation
public void setSaturation(float saturation)
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getScalevalue
public float getScalevalue()
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setScalevalue
public void setScalevalue(float scalevalue)
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