abstractcontroller2d.java

化学图形处理软件

			 */
			UndoableEdit  edit = new AdjustBondOrdersEdit(changedBonds);
			undoRedoHandler.postEdit(edit);
			updateAtoms(container, bondInRange.atoms());
		} else
		{
			IAtomContainer undoRedoContainer = chemModel.getBuilder().newAtomContainer();
			if (atomInRange != null)
			{
				logger.debug("We had an atom in range");
				newAtom1 = atomInRange;
			} else if (!wasDragged)
			{
				// create a new molecule
				logger.debug("We make a new molecule");
				newAtom1 = undoRedoContainer.getBuilder().newAtom(c2dm.getDrawElement(), new Point2d(startX, startY));
				IAtomContainer atomCon = ChemModelManipulator.createNewMolecule(chemModel);
				atomCon.addAtom(newAtom1);
				r2dm.setRenderingCoordinate(newAtom1,new Point2d(startX, startY));
				// update atoms
				updateAtom(atomCon, newAtom1);
				undoRedoContainer.add(atomCon);
			}

			if (wasDragged)
			{
				if (dragMode == DRAG_DRAWING_PROPOSED_BOND)
				{
					int endX = r2dm.getPointerVectorEnd().x;
					int endY = r2dm.getPointerVectorEnd().y;
					atomInRange = getAtomInRange(endX, endY);
					// OK, there is some repartitioning done on atomCon later, so put everything in the first AC
					IAtomContainer atomCon = null;
					Iterator atomCons = ChemModelManipulator.getAllAtomContainers(chemModel).iterator();
					while (atomCons.hasNext()) {
						if (atomCon == null) { 
							atomCon = (IAtomContainer)atomCons.next();
						} else {
							atomCon.add((IAtomContainer)atomCons.next());							
						}
					}
					if (atomCon == null) atomCon = chemModel.getBuilder().newAtomContainer();
					if (atomInRange != null)
					{
						logger.debug("*** atom in range");

						newAtom2 = atomInRange;
						logger.debug("atomCon.getAtomCount() " + atomCon.getAtomCount());
					} else
					{
						logger.debug("*** new atom");
						newAtom2 = atomCon.getBuilder().newAtom(c2dm.getDrawElement(), new Point2d(endX, endY));
						atomCon.addAtom(newAtom2);
						r2dm.setRenderingCoordinate(newAtom2,new Point2d(endX, endY));
						undoRedoContainer.addAtom(newAtom2);
					}
					newAtom1 = lastAtomInRange;
					if (newAtom1 == null)
					{
						newAtom1 = atomCon.getBuilder().newAtom(c2dm.getDrawElement(), new Point2d(r2dm.getPointerVectorStart().x, r2dm.getPointerVectorStart().y));
						undoRedoContainer.addAtom(newAtom1);
					}
					if (newAtom1 != newAtom2)
					{
						newBond = atomCon.getBuilder().newBond(newAtom1, newAtom2, 1);
						if(c2dm.getDrawMode() == Controller2DModel.UP_BOND)
							newBond.setStereo(CDKConstants.STEREO_BOND_UP);
						if(c2dm.getDrawMode() == Controller2DModel.DOWN_BOND)
							newBond.setStereo(CDKConstants.STEREO_BOND_DOWN);
						logger.debug(newAtom1 + " - " + newAtom2);
						atomCon.addBond(newBond);
						undoRedoContainer.addBond(newBond);
					}

					try
					{
						IMoleculeSet setOfMolecules = ConnectivityChecker.partitionIntoMolecules(atomCon);
						chemModel.setMoleculeSet(setOfMolecules);
						logger.debug("We have " + setOfMolecules.getAtomContainerCount() + " molecules on screen");
					} catch (Exception exception)
					{
						logger.warn("Could not partition molecule: ", exception.getMessage());
						logger.debug(exception);
						return;
					}

					// update atoms
					updateAtom(atomCon, newAtom2);

					/*
					 *  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;
					/*
					 *  ---
					 */
				}
			} else if (atomInRange != null)
			{
				// add a new atom to the current atom in some random
				// direction
				IAtomContainer atomCon = ChemModelManipulator.getRelevantAtomContainer(chemModel, atomInRange);
				newAtom2 = atomCon.getBuilder().newAtom(c2dm.getDrawElement(), ((Point2d)r2dm.getRenderingCoordinate(atomInRange)));

				// now create 2D coords for new atom
				double bondLength = r2dm.getBondLength();
				java.util.List connectedAtoms = atomCon.getConnectedAtomsList(atomInRange);
				logger.debug("connectedAtoms.length: " + connectedAtoms.size());
				IAtomContainer placedAtoms = atomCon.getBuilder().newAtomContainer();
				//placedAtoms.addAtom(atomInRange);
				for (int i = 0; i < connectedAtoms.size(); i++)
				{
					placedAtoms.addAtom((IAtom)connectedAtoms.get(i));
				}
				IAtomContainer unplacedAtoms = atomCon.getBuilder().newAtomContainer();
				unplacedAtoms.addAtom(newAtom2);
				AtomPlacer atomPlacer = new AtomPlacer();
				atomPlacer.setMolecule(atomCon.getBuilder().newMolecule(atomCon));
				Point2d center2D = GeometryTools.get2DCenter(placedAtoms,r2dm.getRenderingCoordinates());
				logger.debug("placedAtoms.getAtomCount(): " + placedAtoms.getAtomCount());
				logger.debug("unplacedAtoms.getAtomCount(): " + unplacedAtoms.getAtomCount());
				if (placedAtoms.getAtomCount() == 1)
				{
					Vector2d bondVector = atomPlacer.getNextBondVector(
							atomInRange, placedAtoms.getAtom(0), 
							GeometryTools.get2DCenter(atomCon.getBuilder().newMolecule(atomCon),r2dm.getRenderingCoordinates()),
							true // FIXME: is this correct? (see SF bug #1367002)
					);
					Point2d atomPoint = new Point2d(((Point2d)r2dm.getRenderingCoordinate(atomInRange)));
					bondVector.normalize();
					bondVector.scale(bondLength);
					atomPoint.add(bondVector);
					newAtom2.setPoint2d(atomPoint);
					r2dm.setRenderingCoordinate(newAtom2,atomPoint);

				} else
				{
					atomPlacer.distributePartners(atomInRange, placedAtoms, center2D,
							unplacedAtoms, bondLength);
				}

				// now add the new atom
				atomCon.addAtom(newAtom2);
				undoRedoContainer.addAtom(newAtom2);
				r2dm.setRenderingCoordinate(newAtom2,new Point2d(newAtom2.getPoint2d()));
				newBond= undoRedoContainer.getBuilder().newBond(atomInRange, newAtom2, 1.0);
				atomCon.addBond(newBond);
				undoRedoContainer.addBond(newBond);
				if(c2dm.getDrawMode() == Controller2DModel.UP_BOND)
					newBond.setStereo(CDKConstants.STEREO_BOND_UP);
				if(c2dm.getDrawMode() == Controller2DModel.DOWN_BOND)
					newBond.setStereo(CDKConstants.STEREO_BOND_DOWN);
				// update atoms
				updateAtom(atomCon, atomInRange);
				updateAtom(atomCon, newAtom2);
			}
			UndoableEdit  edit = new AddAtomsAndBondsEdit(chemModel, undoRedoContainer, "Add Bond",c2dm);
			undoRedoHandler.postEdit(edit);
		}
		r2dm.fireChange();
		fireChange();
		if(newAtom1!=null && r2dm.getRenderingCoordinate(newAtom1)==null)
			r2dm.setRenderingCoordinate(newAtom1,new Point2d(newAtom1.getPoint2d()));
		if(newAtom2!=null)
			r2dm.setRenderingCoordinate(newAtom2,new Point2d(newAtom2.getPoint2d()));
		centerAtom(newAtom1,chemModel);
		centerAtom(newAtom2,chemModel);
		this.updateMoleculeCoordinates();
	}

	private void decreaseCharge() {
		IAtom atomInRange = r2dm.getHighlightedAtom();
		if (atomInRange != null)
		{
			int formerCharge = atomInRange.getFormalCharge();
			atomInRange.setFormalCharge(atomInRange.getFormalCharge() - 1);
			// update atom
			IAtomContainer container = ChemModelManipulator.getRelevantAtomContainer(chemModel, atomInRange);
			updateAtom(container, atomInRange);
			//undoredo support
            UndoableEdit  edit = new ChangeChargeEdit(atomInRange, formerCharge, atomInRange.getFormalCharge());
			undoRedoHandler.postEdit(edit);
			r2dm.fireChange();
			fireChange();
		}
	}

	private void enterElement() {
		IAtom atomInRange = r2dm.getHighlightedAtom();
		if (atomInRange != null)
		{
			String[] funcGroupsKeys=new String[funcgroupsmap.keySet().size()+1];
	        Iterator it=funcgroupsmap.keySet().iterator();
	        int h=1;
	        funcGroupsKeys[0]="";
	        while(it.hasNext()){
	        	funcGroupsKeys[h]=(String)it.next();
	        	h++;
	        }
			String x=EnterElementOrGroupDialog.showDialog(null,null, "Enter an element symbol or choose/enter a functional group abbrivation:", "Enter element", funcGroupsKeys, "","");
			try{
				IAtomContainer ac=(IAtomContainer)funcgroupsmap.get(x.toLowerCase());
				//this means a functional group was entered
				//TODO undo-redo
				if(ac!=null && !x.equals("")){
					ac=(IAtomContainer)((IAtomContainer)funcgroupsmap.get(x)).clone();
					IAtomContainer container = ChemModelManipulator.getRelevantAtomContainer(chemModel, atomInRange);
					IAtom lastplaced=null;
					int counter=0;
					//this is the starting point for placing
					ac.getAtom(0).setPoint2d((Point2d)r2dm.getRenderingCoordinate(atomInRange));
					r2dm.setRenderingCoordinate(ac.getAtom(0), (Point2d)r2dm.getRenderingCoordinate(atomInRange));
					lastplaced=ac.getAtom(0);
					counter=1;
					container.add(ac);
					List connbonds=container.getConnectedBondsList(atomInRange);
					//this is needed for undo redo
					IAtomContainer undoredocontainer=ac.getBuilder().newAtomContainer();
					undoredocontainer.addAtom(atomInRange);
					for(int i=0;i<connbonds.size();i++){
						IBond bond=(IBond)connbonds.get(i);
						if(bond.getAtom(0)==atomInRange){
							bond.setAtom(ac.getAtom(0), 0);
							undoredocontainer.addBond(bond);
						}else{
							bond.setAtom(ac.getAtom(0), 1);
							undoredocontainer.addBond(bond);
						}
					}
					container.removeAtomAndConnectedElectronContainers(atomInRange);
					AtomPlacer ap=new AtomPlacer();
					while(lastplaced!=null){
						IAtomContainer placedNeighbours=container.getBuilder().newAtomContainer();
						IAtomContainer unplacedNeighbours=container.getBuilder().newAtomContainer();
						List l=container.getConnectedAtomsList(lastplaced);
						for(int i=0;i<l.size();i++){
							if(r2dm.getRenderingCoordinate((IAtom)l.get(i))!=null)
								placedNeighbours.addAtom((IAtom)l.get(i));
							else
								unplacedNeighbours.addAtom((IAtom)l.get(i));
						}
						ap.distributePartners(lastplaced, placedNeighbours, GeometryTools.get2DCenter(placedNeighbours,r2dm.getRenderingCoordinates()), unplacedNeighbours, r2dm.getBondLength(), r2dm.getRenderingCoordinates());
						lastplaced=ac.getAtom(counter);
						counter++;
						if(counter==ac.getAtomCount())
							lastplaced=null;
					}
					it=container.atoms();
					while(it.hasNext()){
						IAtom atom=(IAtom)it.next();
						if(r2dm.getRenderingCoordinate(atom)==null)
							r2dm.setRenderingCoordinate(atom, atom.getPoint2d());
					}
					/*
					 *  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;
					/*
					 *  ---
					 */
					// undoredo support
					UndoableEdit  edit = new AddFuncGroupEdit(chemModel, undoredocontainer ,ac, "add "+x);
					undoRedoHandler.postEdit(edit);
					//undoRedoHandler.postEdit(edit);
					r2dm.fireChange();
					fireChange();
				}else if(x!=null && x.length()>0){
					String formerSymbol="";
					if(Character.isLowerCase(x.toCharArray()[0]))
						x=Character.toUpperCase(x.charAt(0))+x.substring(1);
					IsotopeFactory ifa=IsotopeFactory.getInstance(r2dm.getHighlightedAtom().getBuilder());
					IIsotope iso=ifa.getMajorIsotope(x);
					formerSymbol=r2dm.getHighlightedAtom().getSymbol();
					if(iso!=null)
						r2dm.getHighlightedAtom().setSymbol(x);
					// 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;
					/*
					 *  ---
					 */
					// undoredo support
					UndoableEdit  edit = new ChangeAtomSymbolEdit(atomInRange, formerSymbol, x);
					undoRedoHandler.postEdit(edit);
					r2dm.fireChange();
					fireChange();
				}
			}catch(Exception ex){
				ex.printStackTrace();
				logger.debug(ex.getMessage()+" in SELECTELEMENT");
			}
		}
	}

	private void increaseCharge() {
		IAtom atomInRange = r2dm.getHighlightedAtom();
		if (atomInRange != null)
		{
			int formerCharge = atomInRange.getFormalCharge();
			atomInRange.setFormalCharge(atomInRange.getFormalCharge() + 1);

			// update atom
			IAtomContainer container = ChemModelManipulator.getRelevantAtomContainer(chemModel, atomInRange);
			updateAtom(container, atomInRange);
			//undoredo support
            UndoableEdit  edit = new ChangeChargeEdit(atomInRange, formerCharge, atomInRange.getFormalCharge());
			undoRedoHandler.postEdit(edit);
			r2dm.fireChange();
			fireChange();
		}
	}

	private void changeElement() {
		IAtom atomInRange = r2dm.getHighlightedAtom();
		if (atomInRange != null)
		{
			String symbol = c2dm.getDrawElement();
			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;
				/*
				 *  ---
				 */
				// undoredo support
				UndoableEdit  edit = new ChangeAtomSymbolEdit(atomInRange, formerSymbol, symbol);
				undoRedoHandler.postEdit(edit);
				r2dm.fireChange();
				fireChange();
			}
		}else{
			int startX = r2dm.getPointerVectorStart().x;
			int startY = r2dm.getPointerVectorStart().y;
			IAtom newAtom1 = chemModel.getBuilder().newAtom(c2dm.getDrawElement(), new Point2d(startX, startY));
			r2dm.setRenderingCoordinate(newAtom1,new Point2d(startX, startY));
			IAtomContainer atomCon = ChemModelManipulator.createNewMolecule(chemModel);
			atomCon.addAtom(newAtom1);