abstractcontroller2d.java

化学图形处理软件

		double bondLength;
		int pointerMarkX;
		int pointerMarkY;

		double ringRadius;

		double angle;

		double xDiff;

		double yDiff;

		double distance1 = 0;

		double distance2 = 0;
		IAtom firstAtom;
		IAtom secondAtom;
		IAtom spiroAtom;
		Point2d conAtomsCenter = null;
		Point2d newPoint1;
		Point2d newPoint2;

		RingPlacer ringPlacer = new RingPlacer();
		int ringSize = c2dm.getRingSize();
		String symbol = c2dm.getDrawElement();
		IAtomContainer sharedAtoms = getHighlighted();

		if (sharedAtoms.getAtomCount() == 0)
		{
			sharedAtoms = sharedAtoms.getBuilder().newAtomContainer();
			newRing = sharedAtoms.getBuilder().newRing(ringSize, symbol);
			if (c2dm.getDrawMode() == Controller2DModel.BENZENERING)
			{
				// make newRing a benzene ring
				newRing.getBond(0).setOrder(2.0);
				newRing.getBond(2).setOrder(2.0);
				newRing.getBond(4).setOrder(2.0);
				makeRingAromatic(newRing);
			}
			bondLength = r2dm.getBondLength();
			ringRadius = (bondLength / 2) / Math.sin(Math.PI / c2dm.getRingSize());
			sharedAtomsCenter = new Point2d(mouseX, mouseY - ringRadius);
			firstAtom = newRing.getAtom(0);
			firstAtom.setPoint2d(sharedAtomsCenter);
			sharedAtoms.addAtom(firstAtom);
			ringCenterVector = new Vector2d(new Point2d(mouseX, mouseY));
			ringCenterVector.sub(sharedAtomsCenter);
			ringPlacer.placeSpiroRing(newRing, sharedAtoms, sharedAtomsCenter, ringCenterVector, bondLength);
			IAtomContainer atomCon = ChemModelManipulator.createNewMolecule(chemModel);
			atomCon.add(newRing);
			undoRedoContainer.add(newRing);
		} else if (sharedAtoms.getAtomCount() == 1)	{
			spiroAtom = sharedAtoms.getAtom(0);
			sharedAtomsCenter = GeometryTools.get2DCenter(sharedAtoms,r2dm.getRenderingCoordinates());
			newRing = createAttachRing(sharedAtoms, ringSize, symbol);
			if (c2dm.getDrawMode() == Controller2DModel.BENZENERING)
			{
				// make newRing a benzene ring
				newRing.getBond(0).setOrder(2.0);
				newRing.getBond(2).setOrder(2.0);
				newRing.getBond(4).setOrder(2.0);
				makeRingAromatic(newRing);
			}
			bondLength = r2dm.getBondLength();
			conAtomsCenter = getConnectedAtomsCenter(sharedAtoms);
			if (conAtomsCenter.equals(((Point2d)r2dm.getRenderingCoordinate(spiroAtom))))
			{
				ringCenterVector = new Vector2d(0, 1);
			} else
			{
				ringCenterVector = new Vector2d(sharedAtomsCenter);
				ringCenterVector.sub(conAtomsCenter);
			}
			ringPlacer.placeSpiroRing(newRing, sharedAtoms, sharedAtomsCenter, ringCenterVector, bondLength);
			// removes the highlighed atom from the ring to add only the new placed
			// atoms to the AtomContainer.
			try
			{
				newRing.removeAtom(spiroAtom);
			} catch (Exception exc)
			{
				logger.error("Could not remove atom from ring");
				logger.debug(exc);
			}
			IAtomContainer atomCon = ChemModelManipulator.getRelevantAtomContainer(chemModel, spiroAtom);
			atomCon.add(newRing);
			undoRedoContainer.add(newRing);
		} else if (sharedAtoms.getAtomCount() == 2)	{
			sharedAtomsCenter = GeometryTools.get2DCenter(sharedAtoms,r2dm.getRenderingCoordinates());

			// calculate two points that are perpendicular to the highlighted bond
			// and have a certain distance from the bondcenter
			firstAtom = sharedAtoms.getAtom(0);
			secondAtom = sharedAtoms.getAtom(1);
			xDiff = ((Point2d)r2dm.getRenderingCoordinate(secondAtom)).x - ((Point2d)r2dm.getRenderingCoordinate(firstAtom)).x;
			yDiff = ((Point2d)r2dm.getRenderingCoordinate(secondAtom)).y - ((Point2d)r2dm.getRenderingCoordinate(firstAtom)).y;
			bondLength = Math.sqrt(Math.pow(xDiff, 2) + Math.pow(yDiff, 2));
			angle = GeometryTools.getAngle(xDiff, yDiff);
			newPoint1 = new Point2d((Math.cos(angle + (Math.PI / 2)) * bondLength / 4) + sharedAtomsCenter.x, (Math.sin(angle + (Math.PI / 2)) * bondLength / 4) + sharedAtomsCenter.y);
			newPoint2 = new Point2d((Math.cos(angle - (Math.PI / 2)) * bondLength / 4) + sharedAtomsCenter.x, (Math.sin(angle - (Math.PI / 2)) * bondLength / 4) + sharedAtomsCenter.y);

			if (wasDragged)
			{
				// check which one of the two points is nearest to the endpoint of the pointer
				// vector that was dragged to make the ringCenterVector point into the right direction.
				pointerMarkX = r2dm.getPointerVectorEnd().x;
				pointerMarkY = r2dm.getPointerVectorEnd().y;
				distance1 = -1 * (Math.sqrt(Math.pow(newPoint1.x - pointerMarkX, 2) + Math.pow(newPoint1.y - pointerMarkY, 2)));
				distance2 = -1 * (Math.sqrt(Math.pow(newPoint2.x - pointerMarkX, 2) + Math.pow(newPoint2.y - pointerMarkY, 2)));
				r2dm.setPointerVectorStart(null);
				r2dm.setPointerVectorEnd(null);
			} else {
				// check which one of the two points is nearest to the center of the
				// connected atoms to make the ringCenterVector point into the right direction.
				conAtomsCenter = getConnectedAtomsCenter(sharedAtoms);
				distance1 = Math.sqrt(Math.pow(newPoint1.x - conAtomsCenter.x, 2) + Math.pow(newPoint1.y - conAtomsCenter.y, 2));
				distance2 = Math.sqrt(Math.pow(newPoint2.x - conAtomsCenter.x, 2) + Math.pow(newPoint2.y - conAtomsCenter.y, 2));
			}
			ringCenterVector = new Vector2d(sharedAtomsCenter);
			// no ring is attached if the two ditances are equal
			//shk3: I removed this condition since it leads to npe and I cannot see why it is necessary.
			//the npe is if you draw a single bond and want to attach a ring to it. Now the ring is in an arbitrary direction, but this is ok
			/*if (distance1 == distance2)
			{
				logger.warn("don't know where to draw the new Ring");
			} else*/
			{
				if (distance1 < distance2)
				{
					ringCenterVector.sub(newPoint1);
				} else if (distance2 < distance1)
				{
					ringCenterVector.sub(newPoint2);
				} else{
					ringCenterVector.sub(newPoint2);
				}

				IAtomContainer atomCon = ChemModelManipulator.getRelevantAtomContainer(chemModel, firstAtom);

				// construct a new Ring that contains the highlighted bond an its two atoms
				newRing = createAttachRing(sharedAtoms, ringSize, symbol);
				if (c2dm.getDrawMode() == Controller2DModel.BENZENERING)
				{
					// make newRing a benzene ring
					IBond existingBond = atomCon.getBond(firstAtom, secondAtom);
					if (existingBond.getOrder() == 1.0)
					{
						if (existingBond.getFlag(CDKConstants.ISAROMATIC))
						{
							newRing.getBond(2).setOrder(2.0);
							newRing.getBond(4).setOrder(2.0);
						} else
						{
							newRing.getBond(1).setOrder(2.0);
							newRing.getBond(3).setOrder(2.0);
							newRing.getBond(5).setOrder(2.0);
						}
					} else
					{
						newRing.getBond(2).setOrder(2.0);
						newRing.getBond(4).setOrder(2.0);
					}
					makeRingAromatic(newRing);
				}

				// place the new atoms of the new ring to the right position
				ringPlacer.placeFusedRing(newRing, sharedAtoms, sharedAtomsCenter, ringCenterVector, bondLength);

				// removes the highlighed bond and its atoms from the ring to add only
				// the new placed atoms to the AtomContainer.
				try
				{
					newRing.remove(sharedAtoms);
				} catch (Exception exc)
				{
					logger.error("Could not remove atom from ring");
					logger.debug(exc);
				}
				atomCon.add(newRing);
			}
		}
		double highlightRadius = r2dm.getHighlightRadius();
		for (int i = 0; i < newRing.getAtomCount(); i++)
		{
			IAtom atom=newRing.getAtom(i);
			r2dm.setRenderingCoordinate(atom,new Point2d(atom.getPoint2d()));
		}
		for (int i = 0; i < newRing.getAtomCount(); i++)
		{
			IAtom atom=newRing.getAtom(i);
			r2dm.setRenderingCoordinate(atom,new Point2d(atom.getPoint2d()));
			centerAtom(atom,chemModel);
			//We make sure atoms don't overlap
			//Solution is a bit crude, we would need to find an unoccupied place (and even the bond display should be optimized)
			IAtom inrange=getAtomInRange((int)((Point2d)r2dm.getRenderingCoordinate(atom)).x, (int)((Point2d)r2dm.getRenderingCoordinate(atom)).y, atom);
			if(inrange!=null && Math.sqrt(Math.pow(((Point2d)r2dm.getRenderingCoordinate(inrange)).x - ((Point2d)r2dm.getRenderingCoordinate(atom)).x, 2) + Math.pow(((Point2d)r2dm.getRenderingCoordinate(inrange)).y - ((Point2d)r2dm.getRenderingCoordinate(atom)).y, 2)) < highlightRadius/4){
				((Point2d)r2dm.getRenderingCoordinate(atom)).x-=highlightRadius/4;
				((Point2d)r2dm.getRenderingCoordinate(atom)).y-=highlightRadius/4;
			}
		}
		this.updateMoleculeCoordinates();
		this.updateAtoms(ChemModelManipulator.getRelevantAtomContainer(chemModel, newRing.getAtom(0)), sharedAtoms.atoms());
		this.updateAtoms(ChemModelManipulator.getRelevantAtomContainer(chemModel, newRing.getAtom(0)), newRing.atoms());
		undoRedoContainer.add(newRing);
		UndoableEdit  edit = new AddAtomsAndBondsEdit(chemModel, undoRedoContainer, "Added Ring",c2dm);
		undoRedoHandler.postEdit(edit);
		r2dm.fireChange();
		fireChange();
	}

	private void eraseSelection() {
		IAtomContainer undoRedoContainer = chemModel.getBuilder().newAtomContainer();
		String type = null;
		IAtom highlightedAtom = r2dm.getHighlightedAtom();
		IBond highlightedBond = r2dm.getHighlightedBond();
		if (highlightedAtom != null && (r2dm.getSelectedPart()==null || !r2dm.getSelectedPart().contains(highlightedAtom)))
		{
			logger.info("User asks to delete an Atom");
			IAtomContainer container = ChemModelManipulator.getRelevantAtomContainer(chemModel, highlightedAtom);
			IElectronContainer[] eContainer = AtomContainerManipulator.getElectronContainerArray(container.getConnectedElectronContainersList(highlightedAtom));
			for (int i=0; i<eContainer.length; i++) {
				undoRedoContainer.addBond((IBond) eContainer[i]);
			}
			logger.debug("Atoms before delete: ", container.getAtomCount());
			Iterator atoms = container.getConnectedAtomsList(highlightedAtom).iterator();
			ChemModelManipulator.removeAtomAndConnectedElectronContainers(chemModel, highlightedAtom);
			updateAtoms(container, atoms);
			undoRedoContainer.addAtom(highlightedAtom);
			if (type == null) {
				type = "Remove Atom";
			}
			else {
				type = "Remove Substructure";
			}
			logger.debug("Atoms before delete: ", container.getAtomCount());
		} else if (highlightedBond != null && (r2dm.getSelectedPart()==null || !r2dm.getSelectedPart().contains(highlightedBond))){
			logger.info("User asks to delete a Bond");
			ChemModelManipulator.removeElectronContainer(chemModel, highlightedBond);
			undoRedoContainer.addBond(highlightedBond);
			if (type == null) {
				type = "Remove Bond";
			}
			else {
				type = "Remove Substructure";
			}
			// update atoms
			java.util.Iterator atoms = highlightedBond.atoms();
			IAtomContainer container = ChemModelManipulator.getRelevantAtomContainer(chemModel, highlightedBond.getAtom(0));
			updateAtoms(container, atoms);
		} else if(r2dm.getSelectedPart()!=null && (r2dm.getSelectedPart().getAtomCount()>0 || r2dm.getSelectedPart().getBondCount()>0)){
			logger.info("User asks to delete selected part");
			IAtomContainer containerToUpdate = ChemModelManipulator.getRelevantAtomContainer(chemModel, r2dm.getSelectedPart().getAtom(0));
			for(int i=0;i<r2dm.getSelectedPart().getAtomCount();i++){
				undoRedoContainer.addAtom(r2dm.getSelectedPart().getAtom(i));
				for(int k=0;k<ChemModelManipulator.getRelevantAtomContainer(chemModel,r2dm.getSelectedPart().getAtom(i)).getConnectedBondsCount(r2dm.getSelectedPart().getAtom(i));k++){
					undoRedoContainer.addBond((IBond)ChemModelManipulator.getRelevantAtomContainer(chemModel,r2dm.getSelectedPart().getAtom(i)).getConnectedBondsList(r2dm.getSelectedPart().getAtom(i)).get(k));
				}
				ChemModelManipulator.removeAtomAndConnectedElectronContainers(chemModel,r2dm.getSelectedPart().getAtom(i));
			}
			type = "Remove Substructure";
			// update atoms
			updateAtoms(containerToUpdate, containerToUpdate.atoms());
		}else{
			logger.warn("Cannot deleted if nothing is highlighted");
			return;
		}
		/*
		 *  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 RemoveAtomsAndBondsEdit(chemModel, undoRedoContainer, type);
		undoRedoHandler.postEdit(edit);
		r2dm.fireChange();
		fireChange();
	}

	private void drawBond(int mouseX, int mouseY) {
		this.updateMoleculeCoordinates();
		logger.debug("mouseReleased->drawbond");
		IAtom atomInRange;
		IAtom newAtom1 = null;
		IAtom newAtom2 = null;
		IBond newBond = null;
		int startX = r2dm.getPointerVectorStart().x;
		int startY = r2dm.getPointerVectorStart().y;
		IBond bondInRange = r2dm.getHighlightedBond();
		

		
		//atomInRange = r2dm.getHighlightedAtom();
		//Bond bondInRange = getBondInRange(mouseX, mouseY);
		/*
		 *  IMPORTANT: I don't use getHighlighteAtom()
		 *  here because of the special case of
		 *  only one atom on the screen.
		 *  In this case, this atom will not detected
		 *  if the mouse hasn't moved after it's creation
		 */
		atomInRange = getAtomInRange(mouseX, mouseY);
		if (bondInRange != null)
		{
//			update atoms
			IAtomContainer container = ChemModelManipulator.getRelevantAtomContainer(chemModel, bondInRange.getAtom(0));
			updateAtoms(container, bondInRange.atoms());
			HashMap changedBonds = new HashMap();
			double formerBondOrder = bondInRange.getOrder();
			if (c2dm.getDrawMode() == Controller2DModel.DRAWBOND){
				if(bondInRange.getStereo()!=CDKConstants.STEREO_BOND_NONE){
					bondInRange.setStereo(CDKConstants.STEREO_BOND_NONE);
				}else{
					// increase Bond order
					double order = bondInRange.getOrder();
					if (order >= CDKConstants.BONDORDER_TRIPLE)
					{
						bondInRange.setOrder(CDKConstants.BONDORDER_SINGLE);
					} else {
						bondInRange.setOrder(order + 1.0);
						// this is tricky as it depends on the fact that the
						// constants are unidistant, i.e. {1.0, 2.0, 3.0}.
					}
				}
			}else if(c2dm.getDrawMode() == Controller2DModel.DOWN_BOND){
	            // toggle bond stereo
	            double stereo = bondInRange.getStereo();
	            if (stereo == CDKConstants.STEREO_BOND_DOWN)
	            {
	              bondInRange.setStereo(CDKConstants.STEREO_BOND_DOWN_INV);
	            } else if (stereo == CDKConstants.STEREO_BOND_DOWN_INV)
	            {
	              bondInRange.setStereo(CDKConstants.STEREO_BOND_NONE);
	            } else
	            {
	              bondInRange.setStereo(CDKConstants.STEREO_BOND_DOWN);
	            }
	            bondInRange.setOrder(1);
			}else{
	            // toggle bond stereo
	            double stereo = bondInRange.getStereo();
	            if (stereo == CDKConstants.STEREO_BOND_UP)
	            {
	              bondInRange.setStereo(CDKConstants.STEREO_BOND_UP_INV);
	            } else if (stereo == CDKConstants.STEREO_BOND_UP_INV)
	            {
	              bondInRange.setStereo(CDKConstants.STEREO_BOND_NONE);
	            } else
	            {
	              bondInRange.setStereo(CDKConstants.STEREO_BOND_UP);
	            }
	            bondInRange.setOrder(1);
			}           
			/*
			 *  PRESERVE THIS. This notifies the
			 *  the listener responsible for
			 *  undo and redo storage that it
			 *  should store this change of an atom symbol
			 */
			if (bondInRange.getOrder() != formerBondOrder) {
                double[] bondOrders = new double[2];
                bondOrders[0] = bondInRange.getOrder();
                bondOrders[1] = formerBondOrder;
                changedBonds.put(bondInRange, bondOrders);
            }
			isUndoableChange = true;
			/*
			 *  ---