public class MultipleAligPanel extends JPrintPanel implements AlignmentPositionListener, java.awt.event.WindowListener
MultipleAlignment
in a
nice way and interact with Jmol by selecting the aligned atoms of the sequence selection.
Coloring options include: sequence similarity, by Block or by Structure. Colors are connected with the JmolPanel.
The positions can be selected individually or in ranges and they will be translated to jmol commands.
javax.swing.JPanel.AccessibleJPanel
javax.swing.JComponent.AccessibleJComponent
accessibleContext, listenerList, TOOL_TIP_TEXT_KEY, ui, UNDEFINED_CONDITION, WHEN_ANCESTOR_OF_FOCUSED_COMPONENT, WHEN_FOCUSED, WHEN_IN_FOCUSED_WINDOW
Constructor and Description |
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MultipleAligPanel()
Default constructor.
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MultipleAligPanel(AFPChain afpChain,
Atom[] ca1,
Atom[] ca2,
AbstractAlignmentJmol jmol)
Constructor using an afpChain and the atom arrays for pairwise alignments.
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MultipleAligPanel(MultipleAlignment multAln,
AbstractAlignmentJmol jmol)
Constructor using a MultipleAlignment.
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Modifier and Type | Method and Description |
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void |
actionPerformed(java.awt.event.ActionEvent e) |
void |
addAlignmentPositionListener(AlignmentPositionListener li) |
void |
destroy() |
java.util.List<java.lang.String> |
getAlnSequences() |
java.util.List<Atom[]> |
getAtomArrays() |
MultipleAlignmentCoordManager |
getCoordManager() |
java.util.List<java.lang.Integer> |
getMapSeqToStruct() |
MultipleAlignment |
getMultipleAlignment() |
void |
mouseOverPosition(AlignedPosition p) |
void |
paintComponent(java.awt.Graphics g) |
void |
positionSelected(AlignedPosition p) |
void |
rangeSelected(AlignedPosition start,
AlignedPosition end) |
void |
selectionLocked() |
void |
selectionUnlocked() |
void |
setStructureAlignmentJmol(AbstractAlignmentJmol jmol) |
void |
toggleSelection(AlignedPosition p) |
void |
windowActivated(java.awt.event.WindowEvent e) |
void |
windowClosed(java.awt.event.WindowEvent e) |
void |
windowClosing(java.awt.event.WindowEvent e) |
void |
windowDeactivated(java.awt.event.WindowEvent e) |
void |
windowDeiconified(java.awt.event.WindowEvent e) |
void |
windowIconified(java.awt.event.WindowEvent e) |
void |
windowOpened(java.awt.event.WindowEvent e) |
print
getAccessibleContext, getUI, getUIClassID, paramString, setUI, updateUI
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
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
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
public MultipleAligPanel()
public MultipleAligPanel(AFPChain afpChain, Atom[] ca1, Atom[] ca2, AbstractAlignmentJmol jmol) throws StructureException
afpChain
- ca1
- ca2
- StructureException
public MultipleAligPanel(MultipleAlignment multAln, AbstractAlignmentJmol jmol)
multAln
- colors
- public MultipleAlignmentCoordManager getCoordManager()
public void addAlignmentPositionListener(AlignmentPositionListener li)
public void destroy()
public void paintComponent(java.awt.Graphics g)
paintComponent
in class javax.swing.JComponent
public void mouseOverPosition(AlignedPosition p)
mouseOverPosition
in interface AlignmentPositionListener
public void positionSelected(AlignedPosition p)
positionSelected
in interface AlignmentPositionListener
public void rangeSelected(AlignedPosition start, AlignedPosition end)
rangeSelected
in interface AlignmentPositionListener
public void selectionLocked()
selectionLocked
in interface AlignmentPositionListener
public void selectionUnlocked()
selectionUnlocked
in interface AlignmentPositionListener
public void toggleSelection(AlignedPosition p)
toggleSelection
in interface AlignmentPositionListener
public void setStructureAlignmentJmol(AbstractAlignmentJmol jmol)
public void windowActivated(java.awt.event.WindowEvent e)
windowActivated
in interface java.awt.event.WindowListener
public void windowClosed(java.awt.event.WindowEvent e)
windowClosed
in interface java.awt.event.WindowListener
public void windowClosing(java.awt.event.WindowEvent e)
windowClosing
in interface java.awt.event.WindowListener
public void windowDeactivated(java.awt.event.WindowEvent e)
windowDeactivated
in interface java.awt.event.WindowListener
public void windowDeiconified(java.awt.event.WindowEvent e)
windowDeiconified
in interface java.awt.event.WindowListener
public void windowIconified(java.awt.event.WindowEvent e)
windowIconified
in interface java.awt.event.WindowListener
public void windowOpened(java.awt.event.WindowEvent e)
windowOpened
in interface java.awt.event.WindowListener
public void actionPerformed(java.awt.event.ActionEvent e)
actionPerformed
in interface java.awt.event.ActionListener
actionPerformed
in class JPrintPanel
public java.util.List<Atom[]> getAtomArrays()
public MultipleAlignment getMultipleAlignment()
public java.util.List<java.lang.String> getAlnSequences()
public java.util.List<java.lang.Integer> getMapSeqToStruct()