abstractcontroller2d.java

化学图形处理软件

			// update atoms
			updateAtom(atomCon, newAtom1);
			chemModel.getMoleculeSet().addAtomContainer(atomCon);
			//FIXME undoredo
			IAtomContainer undoRedoContainer= chemModel.getBuilder().newAtomContainer();
			undoRedoContainer.addAtom(newAtom1);
			UndoableEdit  edit = new AddAtomsAndBondsEdit(chemModel, undoRedoContainer, "Add Atom",c2dm);
			undoRedoHandler.postEdit(edit);
			this.updateMoleculeCoordinates();
			r2dm.fireChange();
			fireChange();
		}
	}

	private void changeSymbol() {
		IAtom atomInRange = r2dm.getHighlightedAtom();
		if (atomInRange != null)
		{
			if (currentCommonElement.get(atomInRange) == null)
			{
				currentCommonElement.put(atomInRange, new Integer(1));
			}
			int oldCommonElement = ((Integer) currentCommonElement.get(atomInRange)).intValue();
			String symbol = (String) commonElements.elementAt(oldCommonElement);
			if (!(atomInRange.getSymbol().equals(symbol)))
			{
				// only change symbol if needed
                String formerSymbol = atomInRange.getSymbol();
				atomInRange.setSymbol(symbol);
				// configure the atom, so that the atomic number matches the symbol
				try
				{
					IsotopeFactory.getInstance(atomInRange.getBuilder()).configure(atomInRange);
				} catch (Exception exception)
				{
					logger.error("Error while configuring atom");
					logger.debug(exception);
				}
				// update atom
				IAtomContainer container = ChemModelManipulator.getRelevantAtomContainer(chemModel, atomInRange);
				updateAtom(container, atomInRange);

				/*
				 *  PRESERVE THIS. This notifies the
				 *  the listener responsible for
				 *  undo and redo storage that it
				 *  should store this change of an atom symbol
				 */
				isUndoableChange = true;
				/*
				 *  ---
				 */
                UndoableEdit  edit = new ChangeAtomSymbolEdit(atomInRange, formerSymbol, symbol);
                undoRedoHandler.postEdit(edit);
				r2dm.fireChange();
				fireChange();
			}
			oldCommonElement++;
			if (oldCommonElement == commonElements.size())
			{
				oldCommonElement = 0;
			}
			currentCommonElement.put(atomInRange, new Integer(oldCommonElement));
		}
	}

	/**
	 *  Makes a ring aromatic
	 *
	 *@param  ring  The ring to be made aromatic
	 */
	private void makeRingAromatic(IRing ring)
	{
		Iterator atoms = ring.atoms();
		while (atoms.hasNext()) {
			((IAtom)atoms.next()).setFlag(CDKConstants.ISAROMATIC, true);
		}
		Iterator bonds = ring.bonds();
		while (bonds.hasNext()) {
			((IBond)bonds.next()).setFlag(CDKConstants.ISAROMATIC, true);
		}
	}


	/**
	 *  manages all actions that will be invoked when a mouse button is clicked
	 *
	 *@param  e  MouseEvent object
	 */
	public void mouseClicked(MouseEvent e)
	{
		// logger.debug("Mouse clicked");
	}


	/**
	 *  manages all actions that will be invoked when a mouse enters a component
	 *
	 *@param  e  MouseEvent object
	 */
	public void mouseEntered(MouseEvent e)
	{
		// logger.debug("Mouse entered");
	}


	/**
	 *  manages all actions that will be invoked when a mouse exits a component
	 *
	 *@param  e  MouseEvent object
	 */
	public void mouseExited(MouseEvent e)
	{
		// logger.debug("Mouse exited");
	}


	/**
	 *  manages all actions that will be invoked when a key is released
	 *
	 *@param  e  MouseEvent object
	 */
	public void keyReleased(KeyEvent e)
	{
		logger.debug("Key released");
	}


	/**
	 *  manages all actions that will be invoked when a key is typed
	 *
	 *@param  e  MouseEvent object
	 */
	public void keyTyped(KeyEvent e)
	{
		try{
			logger.debug("Key typed");
			if(r2dm.getHighlightedAtom()!=null){
				IsotopeFactory ifa=IsotopeFactory.getInstance(r2dm.getHighlightedAtom().getBuilder());
				IIsotope iso=ifa.getMajorIsotope(e.getKeyChar());
				if(iso!=null)
					r2dm.getHighlightedAtom().setSymbol(e.getKeyChar()+"");
			}
		}catch(Exception ex){
			logger.debug("Exception "+ex.getMessage()+" in keyPressed in AbstractController");
		}
	}


	/**
	 *  manages all actions that will be invoked when a key is pressed
	 *
	 *@param  e  MouseEvent object
	 */
	public void keyPressed(KeyEvent e)
	{
		logger.debug("Key pressed");
	}


	/*
	 *  Start of private methods
	 */
	/**
	 *  Updates an array of atoms with respect to its hydrogen count
	 *
	 *@param  container  The AtomContainer to work on
	 *@param  atoms       The Atoms to update
	 */
	private void updateAtoms(IAtomContainer container, java.util.Iterator atoms)
	{
		while (atoms.hasNext())
		{
			updateAtom(container, (IAtom)atoms.next());
		}
	}


	/**
	 *  Updates an atom with respect to its hydrogen count
	 *
	 *@param  container  The AtomContainer to work on
	 *@param  atom       The Atom to update
	 */
	public void updateAtom(IAtomContainer container, IAtom atom)
	{
		if (c2dm.getAutoUpdateImplicitHydrogens())
		{
			atom.setHydrogenCount(0);
			try
			{
				hydrogenAdder.addImplicitHydrogensToSatisfyValency(container, atom);
			} catch (Exception exception)
			{
				logger.error(exception.getMessage());
				logger.debug(exception);
			}
		}
	}


	/**
	 *  No idea what this does
	 *
	 *@param  angle  Some kind of angle
	 *@return        Don't know what
	 */
	private double snapAngle(double angle)
	{
		double div = (Math.PI / 180) * c2dm.getSnapAngle();
		return (Math.rint(angle / div)) * div;
	}


	/**
	 *  Gets the chemObjectInRange attribute of the Controller2D object
	 *
	 *@param  X  Current mouse x
	 *@param  Y  Current mouse x
	 *@return    The chemObjectInRange value
	 */
	public IChemObject getChemObjectInRange(int X, int Y)
	{
		IChemObject objectInRange = getAtomInRange(X, Y);
		if (objectInRange != null)
		{
			// logger.debug("Returning nearest Atom: " + objectInRange);
			return objectInRange;
		}
		objectInRange = getBondInRange(X, Y);
		if (objectInRange != null)
		{
			// logger.debug("Returning nearest Bond: " + objectInRange);
			return objectInRange;
		}
		objectInRange = getReactionInRange(X, Y);
		if (objectInRange != null)
		{
			// logger.debug("Returning nearest Reaction: " + objectInRange);
			return objectInRange;
		}
		/*
		 *  chemModel covers whole of editing window, and if nothing
		 *  more interesting is near, then them model is in range.
		 */
		// logger.debug("Returning nearest ChemModel: " + chemModel);
		return chemModel;
	}


	/**
	 *  Returns an Atom if it is in a certain range of the given point. Used to
	 *  highlight an atom that is near the cursor. <p>
	 *
	 *  <b>Important: the coordinates must be given in world coordinates and not in
	 *  screen coordinates!
	 *
	 *@param  X  The x world coordinate of the point
	 *@param  Y  The y world coordinate of the point
	 *@return    An Atom if it is in a certain range of the given point
	 */
	private IAtom getAtomInRange(int X, int Y)
	{
		return getAtomInRange(X,Y,null);
	}
	
	
	/**
	 *  Returns an Atom if it is in a certain range of the given point. Used to
	 *  highlight an atom that is near the cursor. <p>
	 *
	 *  <b>Important: the coordinates must be given in world coordinates and not in
	 *  screen coordinates!
	 *
	 *@param  X  The x world coordinate of the point
	 *@param  Y  The y world coordinate of the point
	 *@return    An Atom if it is in a certain range of the given point
	 */
	private IAtom getAtomInRange(int X, int Y, IAtom ignore)
	{
		double highlightRadius = r2dm.getHighlightRadius();
		IAtom closestAtom = GeometryTools.getClosestAtom(X, Y, chemModel, ignore, r2dm.getRenderingCoordinates());
		if (closestAtom != null)
		{
			//logger.debug("getAtomInRange(): An atom is near");
			if (!(Math.sqrt(Math.pow(r2dm.getRenderingCoordinate(closestAtom).x - X, 2) +
					Math.pow(r2dm.getRenderingCoordinate(closestAtom).y - Y, 2)) < highlightRadius))
			{
				closestAtom = null;
			} else {
				// we got a winner!
				// set the associated AtomContainer, for use by JCP's Molecule Properties action
                // COMMENTED OUT: causes cloning trouble
/*				closestAtom.setProperty(
					SimpleController2D.MATCHING_ATOMCONTAINER,
					ChemModelManipulator.getRelevantAtomContainer(chemModel, closestAtom)
				);*/
			}
		}
		return closestAtom;
	}

	private IAtomContainer getBondInRangeTemporaryAtomContainer = null;

	/**
	 *  Returns a Bond if it is in a certain range of the given point. Used to
	 *  highlight a bond that is near the cursor. <p>
	 *
	 *  <b>Important: the coordinates must be given in world coordinates and not in
	 *  screen coordinates!
	 *
	 *@param  X  The x world coordinate of the point
	 *@param  Y  The y world coordinate of the point
	 *@return    An Atom if it is in a certain range of the given point
	 */
	private IBond getBondInRange(int X, int Y) {
		if (getBondInRangeTemporaryAtomContainer == null) {
			getBondInRangeTemporaryAtomContainer = chemModel.getBuilder().newAtomContainer();
		} else {
			getBondInRangeTemporaryAtomContainer.removeAllElements();
		}
        double highlightRadius = r2dm.getHighlightRadius();
		Iterator atomCons = ChemModelManipulator.getAllAtomContainers(chemModel).iterator();
		while (atomCons.hasNext()) {
			getBondInRangeTemporaryAtomContainer.add((IAtomContainer)atomCons.next());
		}
        if (getBondInRangeTemporaryAtomContainer.getBondCount() != 0) {
            IBond closestBond = GeometryTools.getClosestBond(X, Y, getBondInRangeTemporaryAtomContainer,r2dm.getRenderingCoordinates());
    		if (closestBond == null)
    		{
    			return null;
    		}
    		// logger.debug("closestBond  "+ closestBond);
    		int[] coords = GeometryTools.distanceCalculator(
    				GeometryTools.getBondCoordinates(closestBond, r2dm.getRenderingCoordinates()), highlightRadius);
    		int[] xCoords = {coords[0], coords[2], coords[4], coords[6]};
    		int[] yCoords = {coords[1], coords[3], coords[5], coords[7]};
    		if ((new Polygon(xCoords, yCoords, 4)).contains(new Point(X, Y)))
    		{
    			return closestBond;
    		}
        }
		return null;
	}

	abstract IReaction getReactionInRange(int X, int Y);

	/**
	 *  Returns an AtomContainer that contains the atom or the the bond with its
	 *  two atoms that are highlighted at the moment.
	 *
	 *@return    An AtomContainer containig the highlighted atom\atoms\bond
	 */
	 IAtomContainer getHighlighted()
	{
		IAtomContainer highlighted = chemModel.getBuilder().newAtomContainer();
		IAtom highlightedAtom = r2dm.getHighlightedAtom();
		IBond highlightedBond = r2dm.getHighlightedBond();
		if (highlightedAtom != null)
		{
			highlighted.addAtom(highlightedAtom);
		} else if (highlightedBond != null)
		{
			highlighted.addBond(highlightedBond);
			for (int i = 0; i < highlightedBond.getAtomCount(); i++)
			{
				highlighted.ad