charite.christo.strap
Class DialogHighlightPattern

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

All Implemented Interfaces:

Disposable, StrapListener, java.awt.event.ActionListener, java.awt.image.ImageObserver, java.awt.MenuContainer, java.io.Serializable, java.lang.Runnable, java.util.EventListener, javax.accessibility.Accessible, javax.swing.Scrollable, javax.swing.table.TableModel

public class DialogHighlightPattern
extends AbstractDialogJPanel
implements Disposable, StrapListener, javax.swing.table.TableModel, java.awt.event.ActionListener, java.lang.Runnable

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:

• "FSP" is a simple search string identifying all occurrences of "FSP" in the amino acid sequence. Each position is highlighted in the specified color.
• "F.P" leaves the second residue undefined since dots match any character.
• "IFSP|TFSP" is equivalent to "[IT]FSP" or "(IF|TF)SP" or "IFSP TFSP" and highlights all occurrences of IFSP and TFSP. Vertical bars separate alternatives.
• "(.....)\1" selects all penta repeats. A backslash-number is a reference to a parenthesized group.
• "[FYW][FYW]" selects adjacent aromatic amino acids. Square brackets enclose groups of letters at one single sequence position.
• "CGT|CGC|CGA|CGG|AGA|AGG" highlights all codons for Arg. Searching the underlying nucleotide sequence requires the check-box "n" not to be checked
• "[ke]{3,99}"highlights all occurrences of 3 to 99 continuous positions containing either Lys or Glu.

SEE_CLASS:ResidueSelection

See Also:

Serialized Form

Nested Class Summary

Nested classes/interfaces inherited from class javax.swing.JComponent

javax.swing.JComponent.AccessibleJComponent

Nested classes/interfaces inherited from class java.awt.Component

java.awt.Component.BaselineResizeBehavior

Field Summary

Fields inherited from class charite.christo.ChPanel

KEY_REPRESENT_COMPONENT

Fields inherited from class javax.swing.JComponent

TOOL_TIP_TEXT_KEY, UNDEFINED_CONDITION, WHEN_ANCESTOR_OF_FOCUSED_COMPONENT, WHEN_FOCUSED, WHEN_IN_FOCUSED_WINDOW

Fields inherited from class java.awt.Component

BOTTOM_ALIGNMENT, CENTER_ALIGNMENT, LEFT_ALIGNMENT, RIGHT_ALIGNMENT, TOP_ALIGNMENT

Fields inherited from interface charite.christo.Disposable

NONE

Fields inherited from interface java.awt.image.ImageObserver

ABORT, ALLBITS, ERROR, FRAMEBITS, HEIGHT, PROPERTIES, SOMEBITS, WIDTH

Constructor Summary

DialogHighlightPattern()

Method Summary

void	actionPerformed(java.awt.event.ActionEvent ev)
void	addTableModelListener(javax.swing.event.TableModelListener li)
void	dispose()
java.lang.Class	getColumnClass(int col)
int	getColumnCount()
java.lang.String	getColumnName(int col)
int	getRowCount()
java.lang.Object	getValueAt(int row, int col)
void	handleEvent(StrapEvent ev)
boolean	isCellEditable(int row, int col)
void	removeTableModelListener(javax.swing.event.TableModelListener li)
void	run()
void	setValueAt(java.lang.Object o, int row, int col)

Methods inherited from class charite.christo.strap.AbstractDialogJPanel

isDisposed, pTop

Methods inherited from class charite.christo.ChPanel

cp, getDndDateien, getMaximumSize, getPreferredScrollableViewportSize, getPreferredSize, getScrollableBlockIncrement, getScrollableTracksViewportHeight, getScrollableTracksViewportWidth, getScrollableUnitIncrement, getToolTipLocation, getToolTipText, getWhenPainted, invalidate, isAlreadyPainted, isEnabled, isShowing, isValidateRoot, paint, paintChildren, paintComponent, processEvent, removeAll

Methods inherited from class javax.swing.JPanel

getAccessibleContext, getUI, getUIClassID, setUI, updateUI

Methods inherited from class javax.swing.JComponent

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

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

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

equals, getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Detail

DialogHighlightPattern

public DialogHighlightPattern()

Method Detail

dispose

public final void dispose()

Specified by:

dispose in interface Disposable

Overrides:

dispose in class AbstractDialogJPanel

actionPerformed

public void actionPerformed(java.awt.event.ActionEvent ev)

Specified by:

actionPerformed in interface java.awt.event.ActionListener

handleEvent

public final void handleEvent(StrapEvent ev)

Specified by:

handleEvent in interface StrapListener

getRowCount

public int getRowCount()

Specified by:

getRowCount in interface javax.swing.table.TableModel

getColumnCount

public int getColumnCount()

Specified by:

getColumnCount in interface javax.swing.table.TableModel

getColumnName

public java.lang.String getColumnName(int col)

Specified by:

getColumnName in interface javax.swing.table.TableModel

getColumnClass

public java.lang.Class getColumnClass(int col)

Specified by:

getColumnClass in interface javax.swing.table.TableModel

isCellEditable

public boolean isCellEditable(int row,
                              int col)

Specified by:

isCellEditable in interface javax.swing.table.TableModel

getValueAt

public java.lang.Object getValueAt(int row,
                                   int col)

Specified by:

getValueAt in interface javax.swing.table.TableModel

setValueAt

public final void setValueAt(java.lang.Object o,
                             int row,
                             int col)

Specified by:

setValueAt in interface javax.swing.table.TableModel

addTableModelListener

public final void addTableModelListener(javax.swing.event.TableModelListener li)

Specified by:

addTableModelListener in interface javax.swing.table.TableModel

removeTableModelListener

public final void removeTableModelListener(javax.swing.event.TableModelListener li)

Specified by:

removeTableModelListener in interface javax.swing.table.TableModel

run

public void run()

Specified by:

run in interface java.lang.Runnable