jchempainteditorpanel.java

化学图形处理软件

		if (jchemPaintModel != null)
		{
			return jchemPaintModel.getRendererModel().getBackColor();
		} else
		{
			return Color.WHITE;
		}
	}


	/**
	 *  Gets the toolBar attribute of the JChemPaintPanel object
	 *
	 *@return    The toolBar value
	 */
	public JToolBar getToolBar()
	{
		return toolBar;
	}

	/**
	 *  Gets the menu attribute of the JChemPaintPanel object
	 *
	 *@return    The menu value
	 */
	public JChemPaintMenuBar getMenu()
	{
		return menu;
	}
	

	/**
	 *  Creates a new JFrame that owns a new JChemPaintModel and returns it.
	 *
	 *@return    The new JFrame containing the JChemPaintEditorPanel
	 */
	public static JFrame getEmptyFrameWithModel()
	{
		JChemPaintModel model = new JChemPaintModel();
		model.setTitle(getNewFrameName());
		model.setAuthor(JCPPropertyHandler.getInstance().getJCPProperties().getProperty("General.UserName"));
		Package self = Package.getPackage("org.openscience.cdk.applications.jchempaint");
		String version = self.getImplementationVersion();
		model.setSoftware("JChemPaint " + version);
		model.setGendate((Calendar.getInstance()).getTime().toString());
		JFrame jcpf = getNewFrame(model);
		return jcpf;
	}
	/**
	 *  Creates a new JFrame that owns a new JChemPaintModel and returns it which contains
	 *  a model.
	 *
	 *@param  mod    The JChemPaintModel
	 *@return        The new JFrame containing the JChemPaintEditorPanel
	 */
	public static JFrame getFrameWithModel(IChemModel mod)
	{
		JChemPaintModel model = new JChemPaintModel(mod);
		model.setTitle(mod.getID());
		model.setAuthor(JCPPropertyHandler.getInstance().getJCPProperties().getProperty("General.UserName"));
		Package self = Package.getPackage("org.openscience.cdk.applications.jchempaint");
		String version = self.getImplementationVersion();
		model.setSoftware("JChemPaint " + version);
		model.setGendate((Calendar.getInstance()).getTime().toString());
		JFrame jcpf = getNewFrame(model);
		return jcpf;
	}

	/**
	 *  Creates a new JChemPaintEditorPanel and assigns a given Model to it.
	 *
	 *@param  model  The model to be assigned to the new frame.
	 *@return       The new JChemPaintFrame with its new JChemPaintModel
	 */
	public static JFrame getNewFrame(JChemPaintModel model)
	{
		JFrame frame = new JFrame();
		frame.addWindowListener(new JChemPaintPanel.AppCloser());
		frame.setDefaultCloseOperation(JFrame.DO_NOTHING_ON_CLOSE);
		JChemPaintEditorPanel jcpep = new JChemPaintEditorPanel();
		frame.getContentPane().add(jcpep);
		jcpep.registerModel(model);
		jcpep.setJChemPaintModel(model,null);
		frame.setTitle(model.getTitle());
		//This ensures that the drawingpanel is never smaller than the application
		frame.addComponentListener(new ComponentAdapter(){
			public void componentResized(ComponentEvent e) {
				if(((JChemPaintEditorPanel)((JFrame)e.getSource()).getContentPane().getComponent(0)).getJChemPaintModel().getRendererModel().getBackgroundDimension().width<((JFrame)e.getSource()).getWidth()-30)
					((JChemPaintEditorPanel)((JFrame)e.getSource()).getContentPane().getComponent(0)).getJChemPaintModel().getRendererModel().setBackgroundDimension(new Dimension(((JFrame)e.getSource()).getWidth()-30,((JChemPaintEditorPanel)((JFrame)e.getSource()).getContentPane().getComponent(0)).getJChemPaintModel().getRendererModel().getBackgroundDimension().height));
				if(((JChemPaintEditorPanel)((JFrame)e.getSource()).getContentPane().getComponent(0)).getJChemPaintModel().getRendererModel().getBackgroundDimension().height<((JFrame)e.getSource()).getHeight()-30)
					((JChemPaintEditorPanel)((JFrame)e.getSource()).getContentPane().getComponent(0)).getJChemPaintModel().getRendererModel().setBackgroundDimension(new Dimension(((JChemPaintEditorPanel)((JFrame)e.getSource()).getContentPane().getComponent(0)).getJChemPaintModel().getRendererModel().getBackgroundDimension().width,((JFrame)e.getSource()).getHeight()-30));
			}
		});
		model.getControllerModel().setAutoUpdateImplicitHydrogens(true);
		model.getRendererModel().setShowEndCarbons(true);
		return frame;
	}

	public void setupPopupMenus(PopupController2D inputAdapter)
	{
    if (inputAdapter.getPopupMenu(Atom.class) == null)
		{
			inputAdapter.setPopupMenu(Atom.class, new JChemPaintPopupMenu(this, "atom"));
		}
		if (inputAdapter.getPopupMenu(PseudoAtom.class) == null)
		{
			inputAdapter.setPopupMenu(PseudoAtom.class, new JChemPaintPopupMenu(this, "pseudo"));
		}
		if (inputAdapter.getPopupMenu(Bond.class) == null)
		{
			inputAdapter.setPopupMenu(Bond.class, new JChemPaintPopupMenu(this, "bond"));
		}
		if (inputAdapter.getPopupMenu(ChemModel.class) == null)
		{
			inputAdapter.setPopupMenu(ChemModel.class, new JChemPaintPopupMenu(this, "chemmodel"));
		}
		if (inputAdapter.getPopupMenu(Reaction.class) == null)
		{
			inputAdapter.setPopupMenu(Reaction.class, new JChemPaintPopupMenu(this, "reaction"));
		}
	}

	public Image takeSnapshot()
	{
		Image snapImage = null;
		try
		{
			logger.info("Making snapshot... ");

            Renderer2D r2d = new Renderer2D(jchemPaintModel.getRendererModel());
            r2d.setRenderer2DModel(jchemPaintModel.getRendererModel());
            IChemModel model = null;
            try {
            	model = (IChemModel) jchemPaintModel.getChemModel().clone();
            } catch (CloneNotSupportedException exception) {
            	logger.error("Clone of IChemModel failed: ", exception.getMessage());
            	logger.debug(exception);
            	return null;
            }
    		IAtomContainer ac = model.getBuilder().newAtomContainer();
    		Iterator containers = MoleculeSetManipulator.getAllAtomContainers(model.getMoleculeSet()).iterator();
    		while (containers.hasNext()) ac.add((IAtomContainer)containers.next());
            HashMap oldrenderingcoordinates=new HashMap();
            Iterator it=jchemPaintModel.getRendererModel().getRenderingCoordinates().keySet().iterator();
            while(it.hasNext()){
            	Object key=it.next();
            	oldrenderingcoordinates.put(key,new Point2d(((Point2d)jchemPaintModel.getRendererModel().getRenderingCoordinates().get(key)).x,((Point2d)jchemPaintModel.getRendererModel().getRenderingCoordinates().get(key)).y));
            }
            Dimension dim = GeometryTools.get2DDimension(ac,jchemPaintModel.getRendererModel().getRenderingCoordinates());
            GeometryTools.translateAllPositive(ac,jchemPaintModel.getRendererModel().getRenderingCoordinates());
            GeometryTools.translate2D(ac, new Vector2d(40,40),jchemPaintModel.getRendererModel().getRenderingCoordinates());
            it=jchemPaintModel.getRendererModel().getRenderingCoordinates().keySet().iterator();
            while(it.hasNext()){
            	Point2d point =(Point2d)jchemPaintModel.getRendererModel().getRenderingCoordinates().get(it.next());
            	point.y=(int)dim.getHeight()+80-point.y;
            }
            snapImage = createImage((int)dim.getWidth()+80, (int)dim.getHeight()+80);
            Graphics2D snapGraphics = (Graphics2D) snapImage.getGraphics();
            snapGraphics.setBackground(Color.WHITE);
            snapGraphics.clearRect(0,0,(int)dim.getWidth()+80, (int)dim.getHeight()+80);
            r2d.getRenderer2DModel().setRenderingCoordinates(jchemPaintModel.getRendererModel().getRenderingCoordinates());
            r2d.useScreenSize=false;
            r2d.paintMolecule(ac, (Graphics2D) snapGraphics,false,true);
            r2d.useScreenSize=true;
            jchemPaintModel.getRendererModel().setRenderingCoordinates(oldrenderingcoordinates);
            logger.info("created...");


			logger.debug("painting succeeded.");
		} catch (NullPointerException e)
		{
            snapImage = null;
		}
		return snapImage;
	}


	/**
	 *  Method to notify this CDKChangeListener if something has changed in another
	 *  object
	 *
	 *@param  e  The EventObject containing information on the nature and source of
	 *      the event
	 */
	public void stateChanged(EventObject e)
	{
		//FIXME was dependant on ReallyPaintPanel.drawingnow
		drawingPanel.repaint();
	}


	/**
	 *  Enlarges the 'one molecule' dimension to fit a set of reactions or
	 *  molecules.
	 *
	 *@param  baseDim  Description of the Parameter
	 *@param  model    Description of the Parameter
	 *@return          Description of the Return Value
	 */
	private Dimension makeChemModelFit(Dimension baseDim, IChemModel model)
	{
		Dimension newDim = new Dimension(baseDim);
		// a bit ugly, but assume moleculeSet *or* reactionSet
		IMoleculeSet moleculeSet = model.getMoleculeSet();
		if (moleculeSet != null)
		{
			newDim.height = newDim.height * (moleculeSet.getMoleculeCount());
			return newDim;
		}
		org.openscience.cdk.interfaces.IReactionSet reactionSet = model.getReactionSet();
		if (reactionSet != null)
		{
			newDim.height = newDim.height * (reactionSet.getReactionCount());
		}
		return newDim;
	}


	/**
	 *  Lays out the molecules in a MoleculeSet, or reaction in a ReactionSet
	 *  in a one column table.
	 *
	 *@param  baseDim  Description of the Parameter
	 *@param  model    Description of the Parameter
	 */
	private void layoutInTable(Dimension baseDim, IChemModel model, Renderer2DModel rm)
	{
		// a bit ugly, but assume moleculeSet *or* reactionSet
		IMoleculeSet moleculeSet = model.getMoleculeSet();
		if (moleculeSet != null)
		{
			for (int i = 0; i < moleculeSet.getAtomContainerCount(); i++)
			{
				GeometryTools.center(moleculeSet.getAtomContainer(i), baseDim,rm.getRenderingCoordinates());
				GeometryTools.translate2D(moleculeSet.getAtomContainer(i), 0, baseDim.height * i,rm.getRenderingCoordinates());
			}
			return;
		}
		org.openscience.cdk.interfaces.IReactionSet reactionSet = model.getReactionSet();
		if (reactionSet != null)
		{
			
			for (int i = 1; i <= reactionSet.getReactionCount(); i++)
			{
				IAtomContainer ac = reactionSet.getBuilder().newAtomContainer();
				Iterator containers = ReactionManipulator.getAllAtomContainers(reactionSet.getReaction(i - 1)).iterator();
				while (containers.hasNext()) ac.add((IAtomContainer)containers.next());
				GeometryTools.center(ac, baseDim,rm.getRenderingCoordinates());
				GeometryTools.translate2D(ac, 0, baseDim.height * (reactionSet.getReactionCount() - i),rm.getRenderingCoordinates());
			}
		}
	}


	/**
	 *  Gets the validatorEngine attribute of the JChemPaintEditorPanel class
	 *
	 *@return    The validatorEngine value
	 */
	public static ValidatorEngine getValidatorEngine()
	{
		if (engine == null)
		{
			engine = new ValidatorEngine();
			// default validators
			engine.addValidator(new BasicValidator());
			engine.addValidator(new ValencyValidator());
			engine.addValidator(new CDKValidator());
			engine.addValidator(new DictionaryValidator(dictdb));
			engine.addValidator(new PDBValidator());
		}
		return engine;
	}


	/**
	 *  Gets the dictionaryDatabase attribute of the JChemPaint object
	 *
	 *@return    The dictionaryDatabase value
	 */
	public static DictionaryDatabase getDictionaryDatabase()
	{
		if (dictdb == null)
		{
			dictdb = new DictionaryDatabase();
			try
			{
				File dictdir = new File(JCPPropertyHandler.getInstance().getJChemPaintDir(), "dicts");
				logger.info("User dict dir: ", dictdir);
				logger.debug("       exists: ", dictdir.exists());
				logger.debug("  isDirectory: ", dictdir.isDirectory());
				if (dictdir.exists() && dictdir.isDirectory())
				{
					File[] dicts = dictdir.listFiles();
					for (int i = 0; i < dicts.length; i++)
					{
						// loop over these files and load them
						try
						{
							FileReader reader = new FileReader(dicts[i]);
							String filename = dicts[i].getName();
							dictdb.readDictionary(reader, filename.substring(0, filename.indexOf('.')));
						} catch (IOException exception)
						{
							logger.error("Problem with reading macie dictionary...");
						}
					}
				}
				logger.info("Read these dictionaries: ");
				Enumeration dicts = dictdb.listDictionaries();
				while (dicts.hasMoreElements())
				{
					logger.info(" - ", dicts.nextElement().toString());
				}
			} catch (Exception exc)
			{
				logger.error("Could not handle dictionary initialization. Maybe I'm running in a sandbox.");
			}
		}
		return dictdb;
	}


	/*
	 *  Methods implementing the CDKEditBus interface
	 */
	/**
	 *  Gets the aPIVersion attribute of the JChemPaintEditorPanel object
	 *
	 *@return    The aPIVersion value
	 */
	public String getAPIVersion()
	{
		return "1.8";
	}


	public void runScript(String s1, String s2)
	{
		logger.info("runScript method currently not supported");
	}


	/**
    *  Mandatory because JChemPaint is a ChangeListener. Used by other classes to
    *  update the information in one of the three statusbar fields.
    *
    *@param  e  ChangeEvent
    */
   //As long there is nothing it it, it shouldn't overwrite the function of JChemPaintPanel
    public void stateChanged(ChangeEvent e)
   {
        if(e.getSource() instanceof JChemPaintPanel) {
            IChemModel editorModel = ((JChemPaintPanel)e.getSource()).getJChemPaintModel().getChemModel();
            JViewport viewPort =((JScrollPane) ((Container) this.getComponent(0)).getComponent(0)).getViewport();
            if (viewPort.getView() == null) {
                viewPort.add(this.getDrawingPanel());
            }
            this.getJChemPaintModel().setChemModel(editorModel);
            if (editorModel != null) {
                this.scaleAndCenterMolecule(this.getJChemPaintModel().getChemModel());
            }
        }
        super.stateChanged(e);

        if (jchemPaintModel != null) {
          for (int i = 0; i < 3; i++) {
            String status = jchemPaintModel.getStatus(i);
            statusBar.setStatus(i + 1, status);
          }
        } else {
          if (statusBar != null) {
            statusBar.setStatus(1, "no model");
          }
        }
   }



       /*
    *  Listener notification support methods START here
    */
   /**
    *  Adds a feature to the ChangeListener attribute of the SenecaDataset object
    *
    * @param  x  The feature to be added to the ChangeListener attribute
    */
   public void addChangeListener(ChangeListener x)
   {
       if (changeListeners == null) changeListeners = new EventListenerList();
       changeListeners.add(ChangeListener.class, x);
       // bring it up to date with current state
       x.stateChanged(new ChangeEvent(this));
   }


   public void removeChangeListener(ChangeListener x)
   {
       changeListeners.remove(ChangeListener.class, x);
   }

   protected void fireChange(String reason)
   {
       lastEventReason = reason;
       // Create the event:
       ChangeEvent c = new ChangeEvent(this);
       // Get the listener list
	   if (changeListeners != null) {
		   Object[] listeners = changeListeners.getListenerList();
		   // Process the listeners last to first
		   // List is in pairs, Class and instance
		   for (int i = listeners.length - 2; i >= 0; i -= 2)
		   {
			   if (listeners[i] == ChangeListener.class)
			   {
				   ChangeListener cl = (ChangeListener) listeners[i + 1];
				   cl.stateChanged(c);
			   }
		   }
	   }
   }

}