jchempaintpanel.java

化学图形处理软件

	/**
	 *  Sets the lastSavedFile attribute of the JChemPaintPanel object
	 *
	 *@param  lsf  The new lastSavedFile value
	 */
	public void setLastSavedFile(File lsf) {
		this.lastSavedFile = lsf;
	}

//	private void setupWorkingDirectory() {
//		try {
//			if (System.getProperty("user.dir") != null) {
//				setCurrentWorkDirectory(new File(System.getProperty("user.dir")));
//			}
//		} catch (Exception exc) {
//			logger.error("Could not read a system property. I might be in a sandbox.");
//		}
//	}


	/**
	 *  Sets the jChemPaintModel attribute of the JChemPaintPanel object
	 *
	 *@param  model  The new jChemPaintModel value
	 */
	public void setJChemPaintModel(JChemPaintModel model, Dimension panelDimension) {
		lastUsedJCPP = this;
		if (model != null && jchemPaintModel != null && model.getChemModel().getMoleculeSet() != null) {
			model.getRendererModel().setBackgroundDimension(jchemPaintModel.getRendererModel().getBackgroundDimension());
			IAtomContainer acc = model.getChemModel().getBuilder().newAtomContainer();
			Iterator containers = ChemModelManipulator.getAllAtomContainers(model.getChemModel()).iterator();
			while (containers.hasNext()) acc.add((IAtomContainer)containers.next()); 
			Dimension molDim = GeometryTools.get2DDimension(acc,model.getRendererModel().getRenderingCoordinates());
//			Dimension molDim = GeometryTools.get2DDimension(model.getChemModel().getMoleculeSet().getAtomContainer(0));
			
			if (isViewerOnly) {
				Dimension viewerDim = null;
				//for some reason an EditorPanel opened by a ViewerPanel gets thet isViewerOnly flag set to true -- to be solved!!
				try {
					viewerDim = getViewerDimension();
				}
				catch (ClassCastException cce) {}
				if (viewerDim != null) {
					//sets BackgroundDim to default dim if using ViewerOnlyPanel
					model.getRendererModel().setBackgroundDimension(viewerDim);
				}
			}
			Dimension backDim = model.getRendererModel().getBackgroundDimension();
			int height = (int) backDim.getHeight();
			int width = (int) backDim.getWidth();
			if (molDim.getHeight() >= backDim.getHeight()) {
				height = (int) molDim.getHeight() + 10;
			}
			else if (molDim.getWidth() >= backDim.getWidth()) {
				width = (int) molDim.getWidth() + 10;
			}
			model.getRendererModel().setBackgroundDimension(new Dimension(width, height));
		}
		else if (model.getChemModel().getMoleculeSet() == null && isViewerOnly) {
			Dimension viewerDim = null;
			try {
				viewerDim = getViewerDimension();
			}
			catch (ClassCastException cce) {}
			if (viewerDim != null) {
				//sets BackgroundDim to default dim if using ViewerOnlyPanel
				model.getRendererModel().setBackgroundDimension(viewerDim);
				}
		}
		if(jchemPaintModel!=null && jchemPaintModel.getControllerModel()!=null)
			model.getControllerModel().setAutoUpdateImplicitHydrogens(jchemPaintModel.getControllerModel().getAutoUpdateImplicitHydrogens());
		if(jchemPaintModel!=null && jchemPaintModel.getRendererModel()!=null){
			model.getRendererModel().setUseAntiAliasing(jchemPaintModel.getRendererModel().getUseAntiAliasing());
			model.getRendererModel().setShowImplicitHydrogens(jchemPaintModel.getRendererModel().getShowImplicitHydrogens());
			model.getRendererModel().setShowEndCarbons(jchemPaintModel.getRendererModel().getShowEndCarbons());
			model.getRendererModel().setShowAromaticityInCDKStyle(jchemPaintModel.getRendererModel().getShowAromaticityInCDKStyle());
			model.getRendererModel().setDrawNumbers(jchemPaintModel.getRendererModel().getDrawNumbers());
			model.getRendererModel().setShowAtomAtomMapping(jchemPaintModel.getRendererModel().getShowAtomAtomMapping());
			model.getRendererModel().setKekuleStructure(jchemPaintModel.getRendererModel().getKekuleStructure());
			model.getRendererModel().setColorAtomsByType(jchemPaintModel.getRendererModel().getColorAtomsByType());
			model.getRendererModel().setShowTooltip(jchemPaintModel.getRendererModel().getShowTooltip());
			model.getRendererModel().setShowReactionBoxes(jchemPaintModel.getRendererModel().getShowReactionBoxes());
		}
		this.jchemPaintModel = model;
		jchemPaintModel.addChangeListener(this);
		org.openscience.cdk.interfaces.IChemModel chemModel = model.getChemModel();
		scaleAndCenterMolecule(chemModel,panelDimension);
		drawingPanel.setJChemPaintModel(model);
	}


	/**
	 *  Partitions a given String into separate words and writes them into an
	 *  array.
	 *
	 *@param  input  String The String to be cutted into pieces
	 *@return        String[] The array containing the separate words
	 */
	public String[] tokenize(String input) {
		Vector v = new Vector();
		StringTokenizer t = new StringTokenizer(input);
		String cmd[];
		while (t.hasMoreTokens()) {
			v.addElement(t.nextToken());
		}
		cmd = new String[v.size()];
		for (int i = 0; i < cmd.length; i++) {
			cmd[i] = (String) v.elementAt(i);
		}
		return cmd;
	}

	public void showChemFile(Reader file) {
		IChemObjectReader cor = null;

		/*
		 *  Have the ReaderFactory determine the file format
		 */
		try {
			cor = getChemObjectReader(file);
		} catch (IOException ioExc) {
			logger.warn("IOException while determining file format.");
			logger.debug(ioExc);
		} catch (Exception exc) {
			logger.warn("Exception while determining file format.");
			logger.debug(exc);
		}

		if (cor == null) {
			JOptionPane.showMessageDialog(this, "Could not determine file format.");
			return;
		}

		String error = null;
		ChemFile chemFile = null;
		ChemModel chemModel = null;
		if (cor.accepts(ChemFile.class)) {
			// try to read a ChemFile
			try {
				chemFile = (ChemFile) cor.read(new ChemFile());
				if (chemFile != null) {
					processChemFile(chemFile);
					return;
				} else {
					logger.warn("The object chemFile was empty unexpectedly!");
				}
			} catch (Exception exception) {
				error = "Error while reading file: " + exception.getMessage();
				logger.warn(error);
				logger.debug(exception);
			}
		}
		if (error != null) {
			JOptionPane.showMessageDialog(this, error);
			return;
		}
		if (cor.accepts(ChemModel.class)) {
			// try to read a ChemModel
			try {
				chemModel = (ChemModel) cor.read((ChemObject) new ChemModel());
				if (chemModel != null) {
					processChemModel(chemModel);
					return;
				} else {
					logger.warn("The object chemModel was empty unexpectedly!");
				}
				error = null;
				// overwrite previous problems, it worked now
			} catch (Exception exception) {
				error = "Error while reading file: " + exception.getMessage();
				logger.error(error);
				logger.debug(exception);
			}
		}
		if (error != null) {
			JOptionPane.showMessageDialog(this, error);
		}
	}


	/**
	 *  Gets the jChemPaintModel attribute of the JChemPaintPanel object
	 *
	 *@return    The jChemPaintModel value
	 */
	public JChemPaintModel getJChemPaintModel() {
		return jchemPaintModel;
	}

	public int showWarning() {
		if (jchemPaintModel.isModified() && !getIsOpenedByViewer() && !guiString.equals("applet")) {
			int answer = JOptionPane.showConfirmDialog(this, jchemPaintModel.getTitle() + " " + JCPLocalizationHandler.getInstance().getString("warning"), JCPLocalizationHandler.getInstance().getString("warningheader"), JOptionPane.YES_NO_CANCEL_OPTION, JOptionPane.WARNING_MESSAGE);
			if (answer == JOptionPane.YES_OPTION) {
				new SaveAction(this, false).actionPerformed(new ActionEvent(this, 12, ""));
			}
			return answer;
		} else if(guiString.equals("applet")){
			//In case of the applet we do not ask for save but put the clear into the undo stack
			ClearAllEdit coa = null;
			try {
				coa = new ClearAllEdit(this.getChemModel(),(IMoleculeSet)this.getChemModel().getMoleculeSet().clone(),this.getChemModel().getReactionSet());
				this.jchemPaintModel.getControllerModel().getUndoSupport().postEdit(coa);
			} catch (Exception e) {
				logger.error("Clone of IMoleculeSet failed: ", e.getMessage());
            	logger.debug(e);
			}
			return JOptionPane.YES_OPTION;
		} else {
			return JOptionPane.YES_OPTION;
		}
	}

	public void processChemFile(org.openscience.cdk.interfaces.IChemFile chemFile) {
		logger.info("Information read from file:");

		int chemSequenceCount = chemFile.getChemSequenceCount();
		logger.info("  # sequences: ", chemSequenceCount);

		for (int i = 0; i < chemSequenceCount; i++) {
			org.openscience.cdk.interfaces.IChemSequence chemSequence = chemFile.getChemSequence(i);

			int chemModelCount = chemSequence.getChemModelCount();
			logger.info("  # model in seq(" + i + "): ", chemModelCount);

			for (int j = 0; j < chemModelCount; j++) {
				org.openscience.cdk.interfaces.IChemModel chemModel = chemSequence.getChemModel(j);
				processChemModel(chemModel);
			}
		}
	}


	/**
	 *  Scales and centers the structure in the dimensions of the DrawingPanel.
	 *
	 *@param  chemModel  The cheModel of the structure to be scaled and centered.
	 */
	public void scaleAndCenterMolecule(org.openscience.cdk.interfaces.IChemModel chemModel) {
    scaleAndCenterMolecule(chemModel, null);
  }

	public void scaleAndCenterMolecule(org.openscience.cdk.interfaces.IChemModel chemModel, Dimension dim) {
		IAtomContainer ac = chemModel.getBuilder().newAtomContainer();
		Iterator containers = ChemModelManipulator.getAllAtomContainers(chemModel).iterator();
		while (containers.hasNext()) ac.add((IAtomContainer)containers.next());
		scaleAndCenterMolecule(ac,dim);
	}
	
	/**
	 *  Scales and centers the structure in the dimensions of the DrawingPanel.
	 *
	 *@param  ac  The IAtomContainer of the structure to be scaled and centered.
	 */
	public void scaleAndCenterMolecule(IAtomContainer ac, Dimension dim){
	    if(showscrollbars){
			((JViewport) drawingPanel.getParent()).setViewPosition(new Point((drawingPanel.getWidth()-getWidth())/2>0 ? (drawingPanel.getWidth()-getWidth())/2 : 0 ,(drawingPanel.getHeight()-getHeight())/2>0 ? (drawingPanel.getHeight()-getHeight())/2 : 0));
		}
	    JChemPaintModel jcpm = getJChemPaintModel();
	    Renderer2DModel rendererModel = jcpm.getRendererModel();
	    
	    double scaleFactor = GeometryTools.getScaleFactor(ac, rendererModel.getBondLength(),jchemPaintModel.getRendererModel().getRenderingCoordinates());
	    GeometryTools.scaleMolecule(ac, scaleFactor, jchemPaintModel.getRendererModel().getRenderingCoordinates());
	    if(!showscrollbars && dim!=null){
	    	Dimension moldims=GeometryTools.get2DDimension(ac, rendererModel.getRenderingCoordinates());
	    	scaleFactor=1;
	    	if(moldims.width>dim.width){
	    		scaleFactor=((float)dim.width-100)/(float)moldims.width;
	    	}
	    	if(moldims.height>dim.height && dim.height/moldims.height<scaleFactor){
	    		scaleFactor=((float)dim.height-100)/(float)moldims.height;
	    	}
	        GeometryTools.scaleMolecule(ac, scaleFactor, jchemPaintModel.getRendererModel().getRenderingCoordinates());
	    }
	    
	    Rectangle view;
	    if(showscrollbars){
	    	view = ((JViewport) drawingPanel.getParent()).getViewRect();
	    }else{
	    	view = new Rectangle(drawingPanel.getSize());
	    }
	    Renderer2DModel model = jchemPaintModel.getRendererModel();
	    double x = view.getX() + view.getWidth();
	    double y = view.getY() + view.getHeight();
	    double relocatedY = model.getBackgroundDimension().getSize().getHeight() - (y + view.getY() / 2);
	    double relocatedX = view.getX() / 2;
	    Dimension viewablePart = new Dimension((int) x, (int) y);
	   //GeometryTools.center(ac, viewablePart);
	    //to be fixed - check if molDim is reaching over viewablePart borders...
	    if (this instanceof JChemPaintViewerOnlyPanel) {
	    	GeometryTools.center(ac, model.getBackgroundDimension(),jchemPaintModel.getRendererModel().getRenderingCoordinates());
	        relocatedX=0;
	        relocatedY=0;
	    } else {
	        if(dim==null){
	            if(viewablePart.getWidth()==0 && viewablePart.getHeight()==0){
	                relocatedX=0;
	                relocatedY=0;
	                GeometryTools.center(ac, model.getBackgroundDimension(),jchemPaintModel.getRendererModel().getRenderingCoordinates());
	            }else{
	            	GeometryTools.center(ac, viewablePart,jchemPaintModel.getRendererModel().getRenderingCoordinates());
	            }
	        }else{
	            relocatedY = model.getBackgroundDimension().getSize().getHeight() - (dim.getHeight());
	            relocatedX = 0;
	            GeometryTools.center(ac, dim,jchemPaintModel.getRendererModel().getRenderingCoordinates());
	        }
	    }
	    //fixing the coords regarding the position of the viewablePart
	    java.util.Iterator atoms = ac.atoms();
	    while (atoms.hasNext()) {
	    	IAtom atom = (IAtom)atoms.next();
	        if (jchemPaintModel.getRendererModel().getRenderingCoordinate(atom) != null) {
	        	jchemPaintModel.getRendererModel().setRenderingCoordinate(atom,new Point2d(((Point2d)jchemPaintModel.getRendererModel().getRenderingCoordinate(atom)).x + relocatedX,((Point2d)jchemPaintModel.getRendererModel().getRenderingCoordinate(atom)).y + relocatedY));
	        }
	    }
	}

	public void processChemModel(org.openscience.cdk.interfaces.IChemModel chemModel) {
		// check for bonds
		if (ChemModelManipulator.getBondCount(chemModel) == 0) {
			String error = "Model does not have bonds. Cannot depict contents.";
			logger.warn(error);
			JOptionPane.showMessageDialog(this, error);
			return;
		}

		// check for coordinates
		if ((GeometryTools.has2DCoordinatesNew(chemModel)==0)) {
			String error = "Model does not have 2D coordinates. Cannot open file.";
			logger.warn(error);
			JOptionPane.showMessageDialog(this, error);
			CreateCoordinatesForFileDialog frame = new CreateCoordinatesForFileDialog(chemModel, jchemPaintModel.getRendererModel().getRenderingCoordinates());
			frame.pack();
			frame.show();
			return;
		} else if ((GeometryTools.has2DCoordinatesNew(chemModel)==1)) {
			int result=JOptionPane.showConfirmDialog(this,"Model has some 2d coordinates. Do you want to show only the atoms with 2d coordiantes?","Only some 2d cooridantes",JOptionPane.YES_NO_OPTION);
			if(result>1){
				CreateCoordinatesForFileDialog frame = new CreateCoordinatesForFileDialog(chemModel, jchemPaintModel.getRendererModel().getRenderingCoordinates());
				frame.pack();
				frame.show();
				return;
			}else{
				for(int i=0;i<chemModel.getMoleculeSet().getAtomContainerCount();i++){
					for(int k=0;i<chemModel.getMoleculeSet().getAtomContainer(i).getAtomCount();k++){
						if(chemModel.getMoleculeSet().getAtomContainer(i).getAtom(k).getPoint2d()==null)
							chemModel.getMoleculeSet().getAtomContainer(i).removeAtomAndConnectedElectronContainers(chemModel.getMoleculeSet().getAtomContainer(i).getAtom(k));
					}						
				}
			}
		}

		JChemPaintModel jcpm = new JChemPaintModel(chemModel);
		lastUsedJCPP = this;
		if (isEmbedded()) {
			if (showWarning() != JOptionPane.CANCEL_OPTION) {
				registerModel(jcpm);
				setJChemPaintModel(jcpm,null);
				repaint();
			}
		}else if (getJChemPaintModel().getChemModel().getMoleculeSet() == null ||
				getJChemPaintModel().getChemModel().getReactionSet() == null /*|| 
				getJChemPaintModel().getChemModel().getMoleculeSet().getMolecule(0).getAtoms().length == 0*/) {
			    registerModel(jcpm);
				setJChemPaintModel(jcpm,null);
				repaint();
		} else {
			JFrame jcpf = JChemPaintEditorPanel.getNewFrame(jcpm);
			jcpf.setVisible(true);
			scaleAndCenterMolecule(chemModel);
			jcpf.pack();
			lastUsedJCPP = (JChemPaintPanel) jcpf.getContentPane().getComponents()[0];
		}
	}


	/**
	 *  Gets the chemObjectReader attribute of the JChemPaintPanel object
	 *
	 *@param  reader           Description of the Parameter
	 *@return                  The chemObjectReader value
	 *@exception  IOException  Description of the Exception
	 */
	public IChemObjectReader getChemObjectReader(Reader reader) throws IOException {
		ReaderFactory factory = new ReaderFactory();
		IChemObjectReader coReader = factory.createReader(reader);
		if (coReader != null) {
			coReader.addChemObjectIOListener(new SwingGUIListener(this, 4));
		}
		return coReader;
	}