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'STRAP:multiple sequence alignments '
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charite.christo.strap
Class DialogPublishAlignment

java.lang.Object
  extended by java.awt.Component
      extended by java.awt.Container
          extended by javax.swing.JComponent
              extended by javax.swing.JPanel
                  extended by charite.christo.ChPanel
                      extended by charite.christo.strap.AbstractDialogJPanel
                          extended by charite.christo.strap.DialogPublishAlignment
All Implemented Interfaces:
Disposable, java.awt.event.ActionListener, java.awt.image.ImageObserver, java.awt.MenuContainer, java.io.Serializable, java.util.EventListener, javax.accessibility.Accessible, javax.swing.Scrollable
public class DialogPublishAlignment
extends AbstractDialogJPanel
implements java.awt.event.ActionListener

HELP

Figure: Generation of a Web link. The included information is specified with check-boxes and radio buttons. The link text appears in the text field from where it can be copied into the html source. A test button allows to quickly test the generated link.
JCOMPONENT:new DialogPublishAlignment("")
With this dialog a Web-Link can be formed which loads the proteins from the public databases into STRAP and displays an alignment. When the link is clicked on a computer with Java, the alignment will be displayed in STRAP. Depending on the purpose of the link and on how much information should be transfered two different types are available:
  1. A compact URL
  2. A Web form
In both types, proteins that are stored in protein databases are included by database reference. This has the advantage that always the most recent version of the protein file is loaded and the current state of sequence features and cross links are available.

Single URL

Since the URL contains the information in a compact form in a single line, not all information is stored. The advantage is that the WIKI:URL can not only be included in web-pages, but also in e-mails, Office-documents. The generation of the URL is conducted in two steps:
  1. BUTTON:DialogPublishAlignment#BUT_LAB_P The parameter String is written into the first text-field and can be modified by the user. The following table summarizes the "|"-separated fields.
    WIKI:Vertical_bar separated fields of protein entries
    NoDescriptionExample
    1URL of protein file or database colon ID EMBL:M57965
    2Protein name. Optionally with exclamation mark and residue subset. b_myosin_heavy_chain
    3Icon http://www.ebi.ac.uk/thornton.../duc_temp.gif
    4Residue selections. Supported 3D-styles: sticks, spheres and dots. #00FFFF,sticks,16-20,#FF00FF,spheres,40-50
    5Coding sequence of a nucleotide sequence reverse,40-100
    The 5th field is required only for nucleotide sequence files. It contains either the index of the CDS such as "#1" for the first or "#2" for the second CDS or the CDS expression directly.
  2. BUTTON:DialogPublishAlignment#BUT_LAB_U From the text in the first text-field the web-link will be generated using WIKI:Url_encoding and written into the 2nd text-field. The generated URL acts as a hyperlink and can be tested by clicking. A new STRAP session will be opened in web-mode and an alignment will be loaded with the specified information.

Web form

Since the web form has no size limitation, the entire information for the alignment can be included. The draw-back is that it can only be included in web-pages, but not in office documents or e-mails. A minimal html-page including the web link for the selected proteins is generated on pressing BUTTON:DialogPublishAlignment#BUT_LAB_F. For testing it is loaded into the web browser upon pressing BUTTON:DialogPublishAlignment#BUT_LAB_B. From this html code the text between the opening and closing and <body> tags can be used in any html-page. An overview of the STRAP scripting commands is given in http://3d-alignment.eu/web/strap_script.html.

The following commands are available:

STRING_ARRAY:StrapScriptInterpreter#allScriptCommands()

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
static java.lang.String BUT_LAB_B
           
static java.lang.String BUT_LAB_F
           
static java.lang.String BUT_LAB_P
           
static java.lang.String BUT_LAB_U
           
 
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
DialogPublishAlignment()
           
DialogPublishAlignment(java.lang.String isHtmlDocumentation)
           
 
Method Summary
 void actionPerformed(java.awt.event.ActionEvent ev)
           
 
Methods inherited from class charite.christo.strap.AbstractDialogJPanel
dispose, 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
 

Field Detail

BUT_LAB_B

public static final java.lang.String BUT_LAB_B
See Also:
Constant Field Values

BUT_LAB_F

public static final java.lang.String BUT_LAB_F
See Also:
Constant Field Values

BUT_LAB_P

public static final java.lang.String BUT_LAB_P
See Also:
Constant Field Values

BUT_LAB_U

public static final java.lang.String BUT_LAB_U
See Also:
Constant Field Values
Constructor Detail

DialogPublishAlignment

public DialogPublishAlignment()

DialogPublishAlignment

public DialogPublishAlignment(java.lang.String isHtmlDocumentation)
Method Detail

actionPerformed

public void actionPerformed(java.awt.event.ActionEvent ev)
Specified by:
actionPerformed in interface java.awt.event.ActionListener
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'STRAP:multiple sequence alignments '
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'The most important classes are StrapAlign, Protein and StrapEvent.'