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'STRAP:multiple sequence alignments ' | ||||||||
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java.lang.Object java.awt.Component java.awt.Container javax.swing.JComponent javax.swing.JPanel charite.christo.ChPanel charite.christo.strap.AbstractDialogJPanel charite.christo.strap.DialogHighlightPattern
public class DialogHighlightPattern
HELP
This dialog is used to underline all occurrences of sequence
patterns.
The search patterns are entered into the table.
Several search patterns can be entered in one single table row and must be separated
by white space.
A search pattern may match an amino acid sequence zero, once or several times.
The hits are underlined. They are CLASS_REF:ResidueSelectionresidue selection objects which have a context menu.
The table contains three check-boxes to toggle visualization on and
off for the sequence alignment window, the horizontal scrollbar, and
the 3D-views.
A 4th check-box indicates whether the search string is applied to
the amino acid sequence or nucleotide sequence
and is only applicable if the amino acid sequence is
translated from nucleotide sequence.
The search string may be a simple string of letters or a complex WIKI:Regular_expression.
The syntax of is explained in the following:
Nested Class Summary |
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Nested classes/interfaces inherited from class javax.swing.JComponent |
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javax.swing.JComponent.AccessibleJComponent |
Nested classes/interfaces inherited from class java.awt.Component |
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java.awt.Component.BaselineResizeBehavior |
Field Summary |
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Fields inherited from class charite.christo.ChPanel |
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KEY_REPRESENT_COMPONENT |
Fields inherited from class javax.swing.JComponent |
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TOOL_TIP_TEXT_KEY, UNDEFINED_CONDITION, WHEN_ANCESTOR_OF_FOCUSED_COMPONENT, WHEN_FOCUSED, WHEN_IN_FOCUSED_WINDOW |
Fields inherited from class java.awt.Component |
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BOTTOM_ALIGNMENT, CENTER_ALIGNMENT, LEFT_ALIGNMENT, RIGHT_ALIGNMENT, TOP_ALIGNMENT |
Fields inherited from interface charite.christo.Disposable |
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NONE |
Fields inherited from interface java.awt.image.ImageObserver |
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ABORT, ALLBITS, ERROR, FRAMEBITS, HEIGHT, PROPERTIES, SOMEBITS, WIDTH |
Constructor Summary | |
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DialogHighlightPattern()
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Method Summary | |
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void |
actionPerformed(java.awt.event.ActionEvent ev)
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void |
addTableModelListener(javax.swing.event.TableModelListener li)
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void |
dispose()
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java.lang.Class |
getColumnClass(int col)
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int |
getColumnCount()
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java.lang.String |
getColumnName(int col)
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int |
getRowCount()
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java.lang.Object |
getValueAt(int row,
int col)
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void |
handleEvent(StrapEvent ev)
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boolean |
isCellEditable(int row,
int col)
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void |
removeTableModelListener(javax.swing.event.TableModelListener li)
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void |
run()
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void |
setValueAt(java.lang.Object o,
int row,
int col)
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Methods inherited from class charite.christo.strap.AbstractDialogJPanel |
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isDisposed, pTop |
Methods inherited from class javax.swing.JPanel |
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getAccessibleContext, getUI, getUIClassID, setUI, updateUI |
Methods inherited from class javax.swing.JComponent |
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addAncestorListener, addNotify, addVetoableChangeListener, computeVisibleRect, contains, createToolTip, disable, enable, firePropertyChange, firePropertyChange, firePropertyChange, getActionForKeyStroke, getActionMap, getAlignmentX, getAlignmentY, getAncestorListeners, getAutoscrolls, getBaseline, getBaselineResizeBehavior, getBorder, getBounds, getClientProperty, getComponentPopupMenu, getConditionForKeyStroke, getDebugGraphicsOptions, getDefaultLocale, getFontMetrics, getGraphics, getHeight, getInheritsPopupMenu, getInputMap, getInputMap, getInputVerifier, getInsets, getInsets, getListeners, getLocation, getMinimumSize, getNextFocusableComponent, getPopupLocation, getRegisteredKeyStrokes, getRootPane, getSize, getToolTipText, getTopLevelAncestor, getTransferHandler, getVerifyInputWhenFocusTarget, getVetoableChangeListeners, getVisibleRect, getWidth, getX, getY, grabFocus, isDoubleBuffered, isLightweightComponent, isManagingFocus, isOpaque, isOptimizedDrawingEnabled, isPaintingForPrint, isPaintingTile, isRequestFocusEnabled, paintImmediately, paintImmediately, print, printAll, putClientProperty, registerKeyboardAction, registerKeyboardAction, removeAncestorListener, removeNotify, removeVetoableChangeListener, repaint, repaint, requestDefaultFocus, requestFocus, requestFocus, 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, setVerifyInputWhenFocusTarget, setVisible, unregisterKeyboardAction, update |
Methods inherited from class java.awt.Container |
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add, add, add, add, add, addContainerListener, addPropertyChangeListener, addPropertyChangeListener, applyComponentOrientation, areFocusTraversalKeysSet, countComponents, deliverEvent, doLayout, findComponentAt, findComponentAt, getComponent, getComponentAt, getComponentAt, getComponentCount, getComponents, getComponentZOrder, getContainerListeners, getFocusTraversalKeys, getFocusTraversalPolicy, getLayout, getMousePosition, insets, isAncestorOf, isFocusCycleRoot, isFocusCycleRoot, isFocusTraversalPolicyProvider, isFocusTraversalPolicySet, layout, list, list, locate, minimumSize, paintComponents, preferredSize, printComponents, remove, remove, removeContainerListener, setComponentZOrder, setFocusCycleRoot, setFocusTraversalPolicy, setFocusTraversalPolicyProvider, setLayout, transferFocusBackward, transferFocusDownCycle, validate |
Methods inherited from class java.awt.Component |
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action, add, addComponentListener, addFocusListener, addHierarchyBoundsListener, addHierarchyListener, addInputMethodListener, addKeyListener, addMouseListener, addMouseMotionListener, addMouseWheelListener, bounds, checkImage, checkImage, contains, createImage, createImage, createVolatileImage, createVolatileImage, dispatchEvent, enable, enableInputMethods, 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, isFocusable, isFocusOwner, isFocusTraversable, isFontSet, isForegroundSet, isLightweight, isMaximumSizeSet, isMinimumSizeSet, isPreferredSizeSet, isValid, isVisible, keyDown, keyUp, list, list, list, location, lostFocus, mouseDown, mouseDrag, mouseEnter, mouseExit, mouseMove, mouseUp, move, nextFocus, paintAll, postEvent, prepareImage, prepareImage, 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, transferFocusUpCycle |
Methods inherited from class java.lang.Object |
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equals, getClass, hashCode, notify, notifyAll, wait, wait, wait |
Constructor Detail |
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public DialogHighlightPattern()
Method Detail |
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public final void dispose()
dispose
in interface Disposable
dispose
in class AbstractDialogJPanel
public void actionPerformed(java.awt.event.ActionEvent ev)
actionPerformed
in interface java.awt.event.ActionListener
public final void handleEvent(StrapEvent ev)
handleEvent
in interface StrapListener
public int getRowCount()
getRowCount
in interface javax.swing.table.TableModel
public int getColumnCount()
getColumnCount
in interface javax.swing.table.TableModel
public java.lang.String getColumnName(int col)
getColumnName
in interface javax.swing.table.TableModel
public java.lang.Class getColumnClass(int col)
getColumnClass
in interface javax.swing.table.TableModel
public boolean isCellEditable(int row, int col)
isCellEditable
in interface javax.swing.table.TableModel
public java.lang.Object getValueAt(int row, int col)
getValueAt
in interface javax.swing.table.TableModel
public final void setValueAt(java.lang.Object o, int row, int col)
setValueAt
in interface javax.swing.table.TableModel
public final void addTableModelListener(javax.swing.event.TableModelListener li)
addTableModelListener
in interface javax.swing.table.TableModel
public final void removeTableModelListener(javax.swing.event.TableModelListener li)
removeTableModelListener
in interface javax.swing.table.TableModel
public void run()
run
in interface java.lang.Runnable
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