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[Cdk-commits] SF.net SVN: cdk:[15072] jchempaint/trunk
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From: <sh...@us...> - 2009-11-20 11:35:26
|
Revision: 15072
http://cdk.svn.sourceforge.net/cdk/?rev=15072&view=rev
Author: shk3
Date: 2009-11-20 11:35:18 +0000 (Fri, 20 Nov 2009)
Log Message:
-----------
Reworked controllerhub to properly work on chemmodel, readded reaction to menus etc
Modified Paths:
--------------
jchempaint/trunk/META-INF/applet-core.files
jchempaint/trunk/META-INF/applet-editor.files
jchempaint/trunk/src/main/org/openscience/jchempaint/JCPMenuTextMaker.java
jchempaint/trunk/src/main/org/openscience/jchempaint/JChemPaintPanel.java
jchempaint/trunk/src/main/org/openscience/jchempaint/action/CopyPasteAction.java
jchempaint/trunk/src/main/org/openscience/jchempaint/application/JChemPaint.java
jchempaint/trunk/src/main/org/openscience/jchempaint/controller/ControllerHub.java
jchempaint/trunk/src/main/org/openscience/jchempaint/controller/IAtomBondEdits.java
jchempaint/trunk/src/main/org/openscience/jchempaint/resources/JCPGUI_applet.properties
jchempaint/trunk/src/main/org/openscience/jchempaint/resources/JCPGUI_stable.properties
jchempaint/trunk/src/main/org/openscience/jchempaint/resources/JChemPaintResources.properties
Added Paths:
-----------
jchempaint/trunk/src/main/org/openscience/jchempaint/action/CreateReactionAction.java
Modified: jchempaint/trunk/META-INF/applet-core.files
===================================================================
--- jchempaint/trunk/META-INF/applet-core.files 2009-11-19 16:47:09 UTC (rev 15071)
+++ jchempaint/trunk/META-INF/applet-core.files 2009-11-20 11:35:18 UTC (rev 15072)
@@ -12,7 +12,6 @@
javax/vecmath/Vector2f.class
javax/vecmath/Vector3d.class
org/_3pq/jgrapht/alg/ConnectivityInspector.class
-org/_3pq/jgrapht/alg/ConnectivityInspector$1.class
org/_3pq/jgrapht/alg/ConnectivityInspector$MyTraversalListener.class
org/_3pq/jgrapht/DirectedGraph.class
org/_3pq/jgrapht/Edge.class
@@ -32,7 +31,6 @@
org/_3pq/jgrapht/event/VertexTraversalEvent.class
org/_3pq/jgrapht/graph/AbstractBaseGraph$ArrayListFactory.class
org/_3pq/jgrapht/graph/AbstractBaseGraph.class
-org/_3pq/jgrapht/graph/AbstractBaseGraph$1.class
org/_3pq/jgrapht/graph/AbstractBaseGraph$DirectedEdgeContainer.class
org/_3pq/jgrapht/graph/AbstractBaseGraph$DirectedSpecifics.class
org/_3pq/jgrapht/graph/AbstractBaseGraph$Specifics.class
@@ -99,41 +97,23 @@
org/openscience/cdk/AtomContainerSet$AtomContainerIterator.class
org/openscience/cdk/AtomContainerSet.class
org/openscience/cdk/AtomContainer$SingleElectronIterator.class
+org/openscience/cdk/atomtype/CDKAtomTypeMatcher.class
org/openscience/cdk/AtomType.class
+org/openscience/cdk/atomtype/IAtomTypeMatcher.class
org/openscience/cdk/Bond$1.class
org/openscience/cdk/Bond$AtomsIterator.class
org/openscience/cdk/Bond.class
org/openscience/cdk/CDKConstants.class
org/openscience/cdk/ChemModel.class
org/openscience/cdk/ChemObject.class
-org/openscience/cdk/controller/AddBondDragModule.class
-org/openscience/cdk/controller/AddRingModule.class
-org/openscience/cdk/controller/AtomAtomMappingModule.class
-org/openscience/cdk/controller/ControllerHub.class
-org/openscience/cdk/controller/ControllerModel.class
-org/openscience/cdk/controller/ControllerModuleAdapter.class
-org/openscience/cdk/controller/ControllerParameters.class
-org/openscience/cdk/controller/HighlightModule.class
-org/openscience/cdk/controller/IChangeModeListener.class
-org/openscience/cdk/controller/IChemModelEventRelayHandler.class
-org/openscience/cdk/controller/IChemModelRelay.class
-org/openscience/cdk/controller/IControllerModel.class
-org/openscience/cdk/controller/IControllerModule.class
-org/openscience/cdk/controller/IMouseEventRelay.class
-org/openscience/cdk/controller/IViewEventRelay.class
-org/openscience/cdk/controller/MoveModule.class
-org/openscience/cdk/controller/PhantomBondGenerator.class
-org/openscience/cdk/controller/RemoveModule.class
-org/openscience/cdk/controller/RotateModule.class
-org/openscience/cdk/controller/SelectLassoModule.class
-org/openscience/cdk/controller/SelectSquareModule.class
-org/openscience/cdk/controller/SwingMouseEventRelay.class
-org/openscience/cdk/controller/undoredo/AddAtomsAndBondsEdit.class
-org/openscience/cdk/controller/undoredo/IUndoListener.class
-org/openscience/cdk/controller/undoredo/IUndoRedoable.class
-org/openscience/cdk/controller/undoredo/IUndoRedoFactory.class
-org/openscience/cdk/controller/undoredo/UndoRedoHandler.class
-org/openscience/cdk/controller/ZoomModule.class
+org/openscience/cdk/config/AtomTypeFactory.class
+org/openscience/cdk/config/atomtypes/OWLAtomTypeHandler.class
+org/openscience/cdk/config/atomtypes/OWLAtomTypeReader.class
+org/openscience/cdk/config/IAtomTypeConfigurator.class
+org/openscience/cdk/config/IsotopeFactory.class
+org/openscience/cdk/config/isotopes/IsotopeHandler.class
+org/openscience/cdk/config/isotopes/IsotopeReader.class
+org/openscience/cdk/config/OWLBasedAtomTypeConfigurator.class
org/openscience/cdk/DefaultChemObjectBuilder.class
org/openscience/cdk/ElectronContainer.class
org/openscience/cdk/Element.class
@@ -142,7 +122,6 @@
org/openscience/cdk/exception/CDKException.class
org/openscience/cdk/exception/NoSuchAtomException.class
org/openscience/cdk/exception/NoSuchAtomTypeException.class
-org/openscience/cdk/formula/MolecularFormula.class
org/openscience/cdk/geometry/GeometryTools.class
org/openscience/cdk/graph/BFSShortestPath.class
org/openscience/cdk/graph/BFSShortestPath$MyBreadthFirstIterator.class
@@ -151,7 +130,6 @@
org/openscience/cdk/graph/MoleculeGraphs.class
org/openscience/cdk/graph/PathTools.class
org/openscience/cdk/graph/SpanningTree.class
-org/openscience/cdk/inchi/InChIGenerator.class
org/openscience/cdk/interfaces/IAdductFormula.class
org/openscience/cdk/interfaces/IAminoAcid.class
org/openscience/cdk/interfaces/IAtom.class
@@ -163,6 +141,7 @@
org/openscience/cdk/interfaces/IBioPolymer.class
org/openscience/cdk/interfaces/IBond.class
org/openscience/cdk/interfaces/IBond$Order.class
+org/openscience/cdk/interfaces/IBond$Stereo.class
org/openscience/cdk/interfaces/IChemFile.class
org/openscience/cdk/interfaces/IChemModel.class
org/openscience/cdk/interfaces/IChemObjectBuilder.class
@@ -195,7 +174,6 @@
org/openscience/cdk/interfaces/IRingSet.class
org/openscience/cdk/interfaces/ISingleElectron.class
org/openscience/cdk/interfaces/IStrand.class
-org/openscience/cdk/io/CMLReader.class
org/openscience/cdk/io/DefaultChemObjectReader.class
org/openscience/cdk/io/FormatFactory.class
org/openscience/cdk/io/formats/ABINITFormat.class
@@ -297,6 +275,8 @@
org/openscience/cdk/io/ISimpleChemObjectReader.class
org/openscience/cdk/io/MDLV2000Reader.class
org/openscience/cdk/io/ReaderFactory.class
+org/openscience/cdk/io/setting/BooleanIOSetting.class
+org/openscience/cdk/io/setting/IOSetting.class
org/openscience/cdk/io/SMILESReader.class
org/openscience/cdk/Isotope.class
org/openscience/cdk/layout/AtomPlacer$1.class
@@ -304,65 +284,6 @@
org/openscience/cdk/layout/RingPlacer.class
org/openscience/cdk/Molecule.class
org/openscience/cdk/MoleculeSet.class
-org/openscience/cdk/renderer/AtomContainerRenderer.class
-org/openscience/cdk/renderer/BoundsCalculator.class
-org/openscience/cdk/renderer/color/CDK2DAtomColors.class
-org/openscience/cdk/renderer/color/IAtomColorer.class
-org/openscience/cdk/renderer/elements/ArrowElement.class
-org/openscience/cdk/renderer/elements/ElementGroup.class
-org/openscience/cdk/renderer/elements/IRenderingElement.class
-org/openscience/cdk/renderer/elements/IRenderingVisitor.class
-org/openscience/cdk/renderer/elements/LineElement.class
-org/openscience/cdk/renderer/elements/OvalElement.class
-org/openscience/cdk/renderer/elements/RectangleElement.class
-org/openscience/cdk/renderer/elements/TextElement.class
-org/openscience/cdk/renderer/elements/TextGroupElement$Child.class
-org/openscience/cdk/renderer/elements/TextGroupElement.class
-org/openscience/cdk/renderer/elements/TextGroupElement$Position.class
-org/openscience/cdk/renderer/elements/WedgeLineElement.class
-org/openscience/cdk/renderer/elements/WigglyLineElement.class
-org/openscience/cdk/renderer/font/AbstractFontManager.class
-org/openscience/cdk/renderer/font/AWTFontManager.class
-org/openscience/cdk/renderer/font/IFontManager.class
-org/openscience/cdk/renderer/font/IFontManager$FontStyle.class
-org/openscience/cdk/renderer/generators/BasicAtomGenerator.class
-org/openscience/cdk/renderer/generators/BasicBondGenerator$1.class
-org/openscience/cdk/renderer/generators/BasicBondGenerator.class
-org/openscience/cdk/renderer/generators/ExtendedAtomGenerator.class
-org/openscience/cdk/renderer/generators/ExternalHighlightGenerator.class
-org/openscience/cdk/renderer/generators/HighlightAtomGenerator.class
-org/openscience/cdk/renderer/generators/HighlightBondGenerator.class
-org/openscience/cdk/renderer/generators/IGenerator.class
-org/openscience/cdk/renderer/generators/IReactionGenerator.class
-org/openscience/cdk/renderer/generators/LonePairGenerator.class
-org/openscience/cdk/renderer/generators/MappingGenerator.class
-org/openscience/cdk/renderer/generators/MergeAtomsGenerator.class
-org/openscience/cdk/renderer/generators/ProductsBoxGenerator.class
-org/openscience/cdk/renderer/generators/RadicalGenerator.class
-org/openscience/cdk/renderer/generators/ReactantsBoxGenerator.class
-org/openscience/cdk/renderer/generators/ReactionArrowGenerator.class
-org/openscience/cdk/renderer/generators/ReactionBoxGenerator.class
-org/openscience/cdk/renderer/generators/ReactionPlusGenerator.class
-org/openscience/cdk/renderer/generators/RingGenerator.class
-org/openscience/cdk/renderer/generators/SelectAtomGenerator.class
-org/openscience/cdk/renderer/generators/SelectAtomGenerator$1.class
-org/openscience/cdk/renderer/generators/SelectBondGenerator.class
-org/openscience/cdk/renderer/elements/AtomSymbolElement.class
-org/openscience/cdk/renderer/IRenderer.class
-org/openscience/cdk/renderer/Renderer.class
-org/openscience/cdk/renderer/RendererModel.class
-org/openscience/cdk/renderer/RenderingParameters$AtomShape.class
-org/openscience/cdk/renderer/RenderingParameters.class
-org/openscience/cdk/renderer/selection/IChemObjectSelection.class
-org/openscience/cdk/renderer/selection/IncrementalSelection.class
-org/openscience/cdk/renderer/selection/LogicalSelection.class
-org/openscience/cdk/renderer/selection/LogicalSelection$Type.class
-org/openscience/cdk/renderer/selection/SingleSelection.class
-org/openscience/cdk/renderer/visitor/AbstractAWTDrawVisitor.class
-org/openscience/cdk/renderer/visitor/AWTDrawVisitor$1.class
-org/openscience/cdk/renderer/visitor/AWTDrawVisitor$2.class
-org/openscience/cdk/renderer/visitor/AWTDrawVisitor.class
-org/openscience/cdk/renderer/visitor/IDrawVisitor.class
org/openscience/cdk/Ring.class
org/openscience/cdk/ringsearch/cyclebasis/CycleBasis.class
org/openscience/cdk/ringsearch/cyclebasis/SimpleCycleBasis$AuxiliaryGraph.class
@@ -372,12 +293,13 @@
org/openscience/cdk/RingSet.class
org/openscience/cdk/smiles/SmilesParser.class
org/openscience/cdk/tools/CDKHydrogenAdder.class
+org/openscience/cdk/tools/ILoggingTool.class
org/openscience/cdk/tools/LoggingTool.class
-org/openscience/cdk/tools/manipulator/AtomContainerManipulator.class
+org/openscience/cdk/tools/LoggingToolFactory.class
+org/openscience/cdk/tools/manipulator/AtomContainerComparatorBy2DCenter.class
org/openscience/cdk/tools/manipulator/AtomContainerSetManipulator.class
org/openscience/cdk/tools/manipulator/ChemModelManipulator.class
org/openscience/cdk/tools/manipulator/MoleculeSetManipulator.class
-org/openscience/cdk/tools/manipulator/MolecularFormulaManipulator.class
org/openscience/cdk/tools/manipulator/RingSetManipulator.class
org/openscience/cdk/validate/ProblemMarker.class
org/openscience/jchempaint/AbstractJChemPaintPanel.class
@@ -386,41 +308,85 @@
org/openscience/jchempaint/applet/JChemPaintAbstractApplet.class
org/openscience/jchempaint/applet/JChemPaintViewerApplet.class
org/openscience/jchempaint/application/JChemPaint.class
-org/openscience/jchempaint/JChemPaintPanel$1.class
+org/openscience/jchempaint/controller/ControllerHub.class
+org/openscience/jchempaint/controller/ControllerModel.class
+org/openscience/jchempaint/controller/ControllerModuleAdapter.class
+org/openscience/jchempaint/controller/ControllerParameters.class
+org/openscience/jchempaint/controller/HighlightModule.class
+org/openscience/jchempaint/controller/IAtomBondEdits.class
+org/openscience/jchempaint/controller/IChangeModeListener.class
+org/openscience/jchempaint/controller/IChemModelEventRelayHandler.class
+org/openscience/jchempaint/controller/IChemModelRelay.class
+org/openscience/jchempaint/controller/IControllerModel.class
+org/openscience/jchempaint/controller/IControllerModule.class
+org/openscience/jchempaint/controller/IMouseEventRelay.class
+org/openscience/jchempaint/controller/IViewEventRelay.class
+org/openscience/jchempaint/controller/PhantomBondGenerator.class
+org/openscience/jchempaint/controller/SwingMouseEventRelay.class
+org/openscience/jchempaint/controller/undoredo/IUndoListener.class
+org/openscience/jchempaint/controller/undoredo/IUndoRedoable.class
+org/openscience/jchempaint/controller/undoredo/IUndoRedoFactory.class
+org/openscience/jchempaint/controller/undoredo/UndoRedoHandler.class
+org/openscience/jchempaint/controller/ZoomModule.class
org/openscience/jchempaint/JChemPaintPanel.class
org/openscience/jchempaint/JChemPaintViewerPanel.class
org/openscience/jchempaint/JCPPropertyHandler.class
org/openscience/jchempaint/JExternalFrame.class
+org/openscience/jchempaint/renderer/AtomContainerRenderer.class
+org/openscience/jchempaint/renderer/BoundsCalculator.class
+org/openscience/jchempaint/renderer/color/CDK2DAtomColors.class
+org/openscience/jchempaint/renderer/color/IAtomColorer.class
+org/openscience/jchempaint/renderer/elements/ArrowElement.class
+org/openscience/jchempaint/renderer/elements/ElementGroup.class
+org/openscience/jchempaint/renderer/elements/IRenderingElement.class
+org/openscience/jchempaint/renderer/elements/IRenderingVisitor.class
+org/openscience/jchempaint/renderer/elements/LineElement.class
+org/openscience/jchempaint/renderer/elements/OvalElement.class
+org/openscience/jchempaint/renderer/elements/path/Type.class
+org/openscience/jchempaint/renderer/elements/RectangleElement.class
+org/openscience/jchempaint/renderer/elements/TextElement.class
+org/openscience/jchempaint/renderer/elements/TextGroupElement$Child.class
+org/openscience/jchempaint/renderer/elements/TextGroupElement.class
+org/openscience/jchempaint/renderer/elements/TextGroupElement$Position.class
+org/openscience/jchempaint/renderer/elements/WedgeLineElement.class
+org/openscience/jchempaint/renderer/elements/WigglyLineElement.class
+org/openscience/jchempaint/renderer/font/AbstractFontManager.class
+org/openscience/jchempaint/renderer/font/AWTFontManager.class
+org/openscience/jchempaint/renderer/font/IFontManager.class
+org/openscience/jchempaint/renderer/font/IFontManager$FontStyle.class
+org/openscience/jchempaint/renderer/generators/BasicAtomGenerator.class
+org/openscience/jchempaint/renderer/generators/BasicBondGenerator$1.class
+org/openscience/jchempaint/renderer/generators/BasicBondGenerator.class
+org/openscience/jchempaint/renderer/generators/ExtendedAtomGenerator.class
+org/openscience/jchempaint/renderer/generators/ExternalHighlightGenerator.class
+org/openscience/jchempaint/renderer/generators/HighlightAtomGenerator.class
+org/openscience/jchempaint/renderer/generators/HighlightBondGenerator.class
+org/openscience/jchempaint/renderer/generators/IGenerator.class
+org/openscience/jchempaint/renderer/generators/IReactionGenerator.class
+org/openscience/jchempaint/renderer/generators/LonePairGenerator.class
+org/openscience/jchempaint/renderer/generators/MappingGenerator.class
+org/openscience/jchempaint/renderer/generators/MergeAtomsGenerator.class
+org/openscience/jchempaint/renderer/generators/ProductsBoxGenerator.class
+org/openscience/jchempaint/renderer/generators/RadicalGenerator.class
+org/openscience/jchempaint/renderer/generators/ReactantsBoxGenerator.class
+org/openscience/jchempaint/renderer/generators/ReactionArrowGenerator.class
+org/openscience/jchempaint/renderer/generators/ReactionBoxGenerator.class
+org/openscience/jchempaint/renderer/generators/ReactionPlusGenerator.class
+org/openscience/jchempaint/renderer/generators/RingGenerator.class
+org/openscience/jchempaint/renderer/generators/SelectAtomGenerator.class
+org/openscience/jchempaint/renderer/generators/SelectBondGenerator.class
+org/openscience/jchempaint/renderer/IRenderer.class
+org/openscience/jchempaint/renderer/Renderer.class
+org/openscience/jchempaint/renderer/RendererModel.class
+org/openscience/jchempaint/renderer/RenderingParameters$AtomShape.class
+org/openscience/jchempaint/renderer/RenderingParameters.class
+org/openscience/jchempaint/renderer/selection/IChemObjectSelection.class
+org/openscience/jchempaint/renderer/selection/IncrementalSelection.class
+org/openscience/jchempaint/renderer/selection/LogicalSelection.class
+org/openscience/jchempaint/renderer/selection/LogicalSelection$Type.class
+org/openscience/jchempaint/renderer/visitor/AbstractAWTDrawVisitor.class
+org/openscience/jchempaint/renderer/visitor/AWTDrawVisitor$2.class
+org/openscience/jchempaint/renderer/visitor/AWTDrawVisitor.class
+org/openscience/jchempaint/renderer/visitor/IDrawVisitor.class
org/openscience/jchempaint/RenderPanel.class
-io-formats.set
-org/openscience/jchempaint/undoredo/SwingUndoRedoFactory$EditOperationWrapper.class
org/openscience/jchempaint/undoredo/SwingUndoRedoFactory.class
-org/openscience/jchempaint/InsertTextPanel.class
-org/openscience/jchempaint/JCPMenuTextMaker.class
-org/openscience/cdk/controller/undoredo/AdjustBondOrdersEdit.class
-org/openscience/jchempaint/undoredo/SwingAdjustBondOrdersEdit.class
-org/openscience/cdk/controller/IChemModelRelay$Direction.class
-org/openscience/cdk/renderer/elements/WedgeLineElement$Direction.class
-org/openscience/cdk/controller/AddAtomModule.class
-org/openscience/cdk/controller/undoredo/ChangeAtomSymbolEdit.class
-org/openscience/jchempaint/undoredo/SwingChangeAtomSymbolEdit.class
-org/openscience/cdk/interfaces/IBond$Stereo.class
-org/openscience/cdk/renderer/elements/path/Close.class
-org/openscience/cdk/renderer/elements/path/CubicTo.class
-org/openscience/cdk/renderer/elements/path/LineTo.class
-org/openscience/cdk/renderer/elements/path/MoveTo.class
-org/openscience/cdk/renderer/elements/path/PathBuilder.class
-org/openscience/cdk/renderer/elements/path/PathElement.class
-org/openscience/cdk/renderer/elements/path/QuadTo.class
-org/openscience/cdk/renderer/elements/path/Type.class
-org/openscience/cdk/controller/IAtomBondEdits.class
-org/openscience/cdk/renderer/elements/AtomMassSymbolElement.class
-org/openscience/cdk/renderer/elements/GeneralPath.class
-org/openscience/cdk/renderer/elements/LineElement$LineType.class
-org/openscience/cdk/renderer/elements/PathElement.class
-org/openscience/cdk/renderer/elements/RingElement.class
-org/openscience/cdk/renderer/selection/MultiSelection.class
-org/openscience/cdk/tools/manipulator/BondManipulator.class
-org/openscience/cdk/tools/manipulator/AtomContainerComparatorBy2DCenter.class
-org/openscience/cdk/io/MDLReader.class
-org/openscience/jchempaint/dialog/TemplateBrowser.class
Modified: jchempaint/trunk/META-INF/applet-editor.files
===================================================================
--- jchempaint/trunk/META-INF/applet-editor.files 2009-11-19 16:47:09 UTC (rev 15071)
+++ jchempaint/trunk/META-INF/applet-editor.files 2009-11-20 11:35:18 UTC (rev 15072)
@@ -1,3 +1,4 @@
+io-formats.set
javax/vecmath/Point2d.class
javax/vecmath/Point2f.class
javax/vecmath/Point3d.class
@@ -88,32 +89,20 @@
org/openscience/cdk/AtomContainerSet$AtomContainerIterator.class
org/openscience/cdk/AtomContainerSet.class
org/openscience/cdk/AtomContainer$SingleElectronIterator.class
+org/openscience/cdk/atomtype/CDKAtomTypeMatcher.class
org/openscience/cdk/AtomType.class
+org/openscience/cdk/atomtype/IAtomTypeMatcher.class
org/openscience/cdk/Bond$1.class
org/openscience/cdk/Bond$AtomsIterator.class
org/openscience/cdk/Bond.class
org/openscience/cdk/CDKConstants.class
org/openscience/cdk/ChemModel.class
org/openscience/cdk/ChemObject.class
-org/openscience/cdk/controller/ControllerHub.class
-org/openscience/cdk/controller/ControllerModel.class
-org/openscience/cdk/controller/ControllerModuleAdapter.class
-org/openscience/cdk/controller/ControllerParameters.class
-org/openscience/cdk/controller/HighlightModule.class
-org/openscience/cdk/controller/IChangeModeListener.class
-org/openscience/cdk/controller/IChemModelEventRelayHandler.class
-org/openscience/cdk/controller/IChemModelRelay.class
-org/openscience/cdk/controller/IControllerModel.class
-org/openscience/cdk/controller/IControllerModule.class
-org/openscience/cdk/controller/IMouseEventRelay.class
-org/openscience/cdk/controller/IViewEventRelay.class
-org/openscience/cdk/controller/PhantomBondGenerator.class
-org/openscience/cdk/controller/SwingMouseEventRelay.class
-org/openscience/cdk/controller/undoredo/IUndoListener.class
-org/openscience/cdk/controller/undoredo/IUndoRedoable.class
-org/openscience/cdk/controller/undoredo/IUndoRedoFactory.class
-org/openscience/cdk/controller/undoredo/UndoRedoHandler.class
-org/openscience/cdk/controller/ZoomModule.class
+org/openscience/cdk/config/AtomTypeFactory.class
+org/openscience/cdk/config/atomtypes/OWLAtomTypeHandler.class
+org/openscience/cdk/config/atomtypes/OWLAtomTypeReader.class
+org/openscience/cdk/config/IAtomTypeConfigurator.class
+org/openscience/cdk/config/OWLBasedAtomTypeConfigurator.class
org/openscience/cdk/DefaultChemObjectBuilder.class
org/openscience/cdk/ElectronContainer.class
org/openscience/cdk/Element.class
@@ -123,6 +112,7 @@
org/openscience/cdk/exception/InvalidSmilesException.class
org/openscience/cdk/exception/NoSuchAtomException.class
org/openscience/cdk/exception/NoSuchAtomTypeException.class
+org/openscience/cdk/formula/MolecularFormula.class
org/openscience/cdk/geometry/GeometryTools.class
org/openscience/cdk/graph/BFSShortestPath.class
org/openscience/cdk/graph/BFSShortestPath$MyBreadthFirstIterator.class
@@ -141,6 +131,7 @@
org/openscience/cdk/interfaces/IBioPolymer.class
org/openscience/cdk/interfaces/IBond.class
org/openscience/cdk/interfaces/IBond$Order.class
+org/openscience/cdk/interfaces/IBond$Stereo.class
org/openscience/cdk/interfaces/IChemFile.class
org/openscience/cdk/interfaces/IChemModel.class
org/openscience/cdk/interfaces/IChemObjectBuilder.class
@@ -179,7 +170,7 @@
org/openscience/cdk/io/IChemObjectWriter.class
org/openscience/cdk/io/ISimpleChemObjectReader.class
org/openscience/cdk/io/listener/IChemObjectIOListener.class
-org/openscience/cdk/io/MDLV2000Reader.class
+org/openscience/cdk/io/MDLReader.class
org/openscience/cdk/Isotope.class
org/openscience/cdk/layout/AtomPlacer$1.class
org/openscience/cdk/layout/AtomPlacer.class
@@ -187,63 +178,7 @@
org/openscience/cdk/Molecule.class
org/openscience/cdk/MoleculeSet.class
org/openscience/cdk/PseudoAtom.class
-org/openscience/cdk/renderer/AtomContainerRenderer.class
-org/openscience/cdk/renderer/color/CDK2DAtomColors.class
-org/openscience/cdk/renderer/color/IAtomColorer.class
-org/openscience/cdk/renderer/elements/ArrowElement.class
-org/openscience/cdk/renderer/elements/ElementGroup.class
-org/openscience/cdk/renderer/elements/IRenderingElement.class
-org/openscience/cdk/renderer/elements/IRenderingVisitor.class
-org/openscience/cdk/renderer/elements/LineElement.class
-org/openscience/cdk/renderer/elements/OvalElement.class
-org/openscience/cdk/renderer/elements/RectangleElement.class
-org/openscience/cdk/renderer/elements/TextElement.class
-org/openscience/cdk/renderer/elements/TextGroupElement$Child.class
-org/openscience/cdk/renderer/elements/TextGroupElement.class
-org/openscience/cdk/renderer/elements/TextGroupElement$Position.class
-org/openscience/cdk/renderer/elements/WedgeLineElement.class
-org/openscience/cdk/renderer/elements/WigglyLineElement.class
-org/openscience/cdk/renderer/font/AbstractFontManager.class
-org/openscience/cdk/renderer/font/AWTFontManager.class
-org/openscience/cdk/renderer/font/IFontManager.class
-org/openscience/cdk/renderer/font/IFontManager$FontStyle.class
-org/openscience/cdk/renderer/generators/BasicAtomGenerator.class
-org/openscience/cdk/renderer/generators/BasicBondGenerator.class
-org/openscience/cdk/renderer/generators/ExtendedAtomGenerator.class
-org/openscience/cdk/renderer/generators/ExternalHighlightGenerator.class
-org/openscience/cdk/renderer/generators/HighlightAtomGenerator.class
-org/openscience/cdk/renderer/generators/HighlightBondGenerator.class
-org/openscience/cdk/renderer/generators/IGenerator.class
-org/openscience/cdk/renderer/generators/IReactionGenerator.class
-org/openscience/cdk/renderer/generators/LonePairGenerator.class
-org/openscience/cdk/renderer/generators/MappingGenerator.class
-org/openscience/cdk/renderer/generators/MergeAtomsGenerator.class
-org/openscience/cdk/renderer/generators/ProductsBoxGenerator.class
-org/openscience/cdk/renderer/generators/RadicalGenerator.class
-org/openscience/cdk/renderer/generators/ReactantsBoxGenerator.class
-org/openscience/cdk/renderer/generators/ReactionArrowGenerator.class
-org/openscience/cdk/renderer/generators/ReactionBoxGenerator.class
-org/openscience/cdk/renderer/generators/ReactionPlusGenerator.class
-org/openscience/cdk/renderer/generators/RingGenerator.class
-org/openscience/cdk/renderer/generators/SelectAtomGenerator.class
-org/openscience/cdk/renderer/generators/SelectBondGenerator.class
-org/openscience/cdk/renderer/IRenderer.class
-org/openscience/cdk/renderer/Renderer.class
-org/openscience/cdk/renderer/RendererModel.class
-org/openscience/cdk/renderer/RenderingParameters$AtomShape.class
-org/openscience/cdk/renderer/RenderingParameters.class
-org/openscience/cdk/renderer/selection/AbstractSelection$1.class
-org/openscience/cdk/renderer/selection/AbstractSelection.class
-org/openscience/cdk/renderer/selection/IChemObjectSelection.class
-org/openscience/cdk/renderer/selection/IncrementalSelection.class
-org/openscience/cdk/renderer/selection/LogicalSelection.class
-org/openscience/cdk/renderer/selection/LogicalSelection$Type.class
-org/openscience/cdk/renderer/selection/RectangleSelection.class
-org/openscience/cdk/renderer/selection/ShapeSelection.class
-org/openscience/cdk/renderer/visitor/AbstractAWTDrawVisitor.class
-org/openscience/cdk/renderer/visitor/AWTDrawVisitor$1.class
-org/openscience/cdk/renderer/visitor/AWTDrawVisitor.class
-org/openscience/cdk/renderer/visitor/IDrawVisitor.class
+org/openscience/cdk/Reaction.class
org/openscience/cdk/Ring.class
org/openscience/cdk/ringsearch/cyclebasis/CycleBasis.class
org/openscience/cdk/ringsearch/cyclebasis/SimpleCycleBasis$AuxiliaryGraph.class
@@ -252,28 +187,33 @@
org/openscience/cdk/ringsearch/SSSRFinder.class
org/openscience/cdk/RingSet.class
org/openscience/cdk/smiles/SmilesParser.class
+org/openscience/cdk/tools/CDKHydrogenAdder.class
+org/openscience/cdk/tools/ILoggingTool.class
org/openscience/cdk/tools/LoggingTool.class
+org/openscience/cdk/tools/LoggingToolFactory.class
+org/openscience/cdk/tools/manipulator/AtomContainerComparatorBy2DCenter.class
+org/openscience/cdk/tools/manipulator/AtomContainerManipulator.class
org/openscience/cdk/tools/manipulator/AtomContainerSetManipulator.class
org/openscience/cdk/tools/manipulator/ChemModelManipulator.class
+org/openscience/cdk/tools/manipulator/MolecularFormulaManipulator.class
org/openscience/cdk/tools/manipulator/MoleculeSetManipulator.class
org/openscience/cdk/tools/manipulator/RingSetManipulator.class
org/openscience/cdk/validate/ProblemMarker.class
org/openscience/jchempaint/AbstractJChemPaintPanel.class
org/openscience/jchempaint/action/AboutAction.class
org/openscience/jchempaint/action/AddHydrogenAction.class
-org/openscience/jchempaint/action/AdjustBondOrdersAction.class
org/openscience/jchempaint/action/ChangeAtomSymbolAction.class
org/openscience/jchempaint/action/ChangeBondAction.class
org/openscience/jchempaint/action/ChangeIsotopeAction.class
org/openscience/jchempaint/action/ChangeModeAction.class
+org/openscience/jchempaint/action/ChangeSingleElectronAction.class
org/openscience/jchempaint/action/ChangeValenceAction.class
org/openscience/jchempaint/action/ChargeAction.class
org/openscience/jchempaint/action/CleanupAction.class
org/openscience/jchempaint/action/ConvertToPseudoAtomAction.class
-org/openscience/jchempaint/action/ConvertToRadicalAction.class
org/openscience/jchempaint/action/CopyPasteAction.class
org/openscience/jchempaint/action/CopyPasteAction$JcpSelection.class
-org/openscience/jchempaint/action/CreateInChIAction.class
+org/openscience/jchempaint/action/CreateReactionAction.class
org/openscience/jchempaint/action/CreateSmilesAction.class
org/openscience/jchempaint/action/EditAtomContainerPropsAction.class
org/openscience/jchempaint/action/EditChemObjectPropsAction.class
@@ -293,6 +233,35 @@
org/openscience/jchempaint/action/ZoomAction.class
org/openscience/jchempaint/applet/JChemPaintAbstractApplet.class
org/openscience/jchempaint/applet/JChemPaintEditorApplet.class
+org/openscience/jchempaint/controller/AbstractSelectModule.class
+org/openscience/jchempaint/controller/AddBondDragModule.class
+org/openscience/jchempaint/controller/AddRingModule.class
+org/openscience/jchempaint/controller/AtomAtomMappingModule.class
+org/openscience/jchempaint/controller/ControllerHub.class
+org/openscience/jchempaint/controller/ControllerModel.class
+org/openscience/jchempaint/controller/ControllerModuleAdapter.class
+org/openscience/jchempaint/controller/ControllerParameters.class
+org/openscience/jchempaint/controller/HighlightModule.class
+org/openscience/jchempaint/controller/IAtomBondEdits.class
+org/openscience/jchempaint/controller/IChangeModeListener.class
+org/openscience/jchempaint/controller/IChemModelEventRelayHandler.class
+org/openscience/jchempaint/controller/IChemModelRelay.class
+org/openscience/jchempaint/controller/IControllerModel.class
+org/openscience/jchempaint/controller/IControllerModule.class
+org/openscience/jchempaint/controller/IMouseEventRelay.class
+org/openscience/jchempaint/controller/IViewEventRelay.class
+org/openscience/jchempaint/controller/MoveModule.class
+org/openscience/jchempaint/controller/PhantomBondGenerator.class
+org/openscience/jchempaint/controller/RotateModule.class
+org/openscience/jchempaint/controller/SelectLassoModule.class
+org/openscience/jchempaint/controller/SelectSquareModule.class
+org/openscience/jchempaint/controller/SwingMouseEventRelay.class
+org/openscience/jchempaint/controller/undoredo/AddAtomsAndBondsEdit.class
+org/openscience/jchempaint/controller/undoredo/IUndoListener.class
+org/openscience/jchempaint/controller/undoredo/IUndoRedoable.class
+org/openscience/jchempaint/controller/undoredo/IUndoRedoFactory.class
+org/openscience/jchempaint/controller/undoredo/UndoRedoHandler.class
+org/openscience/jchempaint/controller/ZoomModule.class
org/openscience/jchempaint/dialog/editor/AtomContainerEditor.class
org/openscience/jchempaint/dialog/editor/AtomEditor.class
org/openscience/jchempaint/dialog/editor/BondEditor.class
@@ -302,29 +271,92 @@
org/openscience/jchempaint/dialog/FieldTablePanel.class
org/openscience/jchempaint/GT.class
org/openscience/jchempaint/GT$Language.class
+org/openscience/jchempaint/InsertTextPanel.class
org/openscience/jchempaint/io/JCPFileView.class
org/openscience/jchempaint/JChemPaintMenuBar.class
org/openscience/jchempaint/JChemPaintMenuHelper$1.class
org/openscience/jchempaint/JChemPaintMenuHelper.class
+org/openscience/jchempaint/JChemPaintPanel$1.class
org/openscience/jchempaint/JChemPaintPanel.class
org/openscience/jchempaint/JChemPaintPopupMenu.class
+org/openscience/jchempaint/JCPMenuTextMaker.class
org/openscience/jchempaint/JCPPropertyHandler.class
org/openscience/jchempaint/JCPStatusBar.class
org/openscience/jchempaint/JCPToolBar$1.class
org/openscience/jchempaint/JCPToolBar.class
org/openscience/jchempaint/JExternalFrame.class
+org/openscience/jchempaint/renderer/AtomContainerRenderer.class
+org/openscience/jchempaint/renderer/color/CDK2DAtomColors.class
+org/openscience/jchempaint/renderer/color/IAtomColorer.class
+org/openscience/jchempaint/renderer/elements/ArrowElement.class
+org/openscience/jchempaint/renderer/elements/AtomSymbolElement.class
+org/openscience/jchempaint/renderer/elements/ElementGroup.class
+org/openscience/jchempaint/renderer/elements/GeneralPath.class
+org/openscience/jchempaint/renderer/elements/IRenderingElement.class
+org/openscience/jchempaint/renderer/elements/IRenderingVisitor.class
+org/openscience/jchempaint/renderer/elements/LineElement.class
+org/openscience/jchempaint/renderer/elements/OvalElement.class
+org/openscience/jchempaint/renderer/elements/path/Close.class
+org/openscience/jchempaint/renderer/elements/path/CubicTo.class
+org/openscience/jchempaint/renderer/elements/PathElement.class
+org/openscience/jchempaint/renderer/elements/path/LineTo.class
+org/openscience/jchempaint/renderer/elements/path/MoveTo.class
+org/openscience/jchempaint/renderer/elements/path/PathBuilder.class
+org/openscience/jchempaint/renderer/elements/path/PathElement.class
+org/openscience/jchempaint/renderer/elements/path/QuadTo.class
+org/openscience/jchempaint/renderer/elements/path/Type.class
+org/openscience/jchempaint/renderer/elements/RectangleElement.class
+org/openscience/jchempaint/renderer/elements/TextElement.class
+org/openscience/jchempaint/renderer/elements/TextGroupElement$Child.class
+org/openscience/jchempaint/renderer/elements/TextGroupElement.class
+org/openscience/jchempaint/renderer/elements/TextGroupElement$Position.class
+org/openscience/jchempaint/renderer/elements/WedgeLineElement.class
+org/openscience/jchempaint/renderer/elements/WigglyLineElement.class
+org/openscience/jchempaint/renderer/font/AbstractFontManager.class
+org/openscience/jchempaint/renderer/font/AWTFontManager.class
+org/openscience/jchempaint/renderer/font/IFontManager.class
+org/openscience/jchempaint/renderer/font/IFontManager$FontStyle.class
+org/openscience/jchempaint/renderer/generators/BasicAtomGenerator.class
+org/openscience/jchempaint/renderer/generators/BasicBondGenerator.class
+org/openscience/jchempaint/renderer/generators/ExtendedAtomGenerator.class
+org/openscience/jchempaint/renderer/generators/ExternalHighlightGenerator.class
+org/openscience/jchempaint/renderer/generators/HighlightAtomGenerator.class
+org/openscience/jchempaint/renderer/generators/HighlightBondGenerator.class
+org/openscience/jchempaint/renderer/generators/IGenerator.class
+org/openscience/jchempaint/renderer/generators/IReactionGenerator.class
+org/openscience/jchempaint/renderer/generators/LonePairGenerator.class
+org/openscience/jchempaint/renderer/generators/MappingGenerator.class
+org/openscience/jchempaint/renderer/generators/MergeAtomsGenerator.class
+org/openscience/jchempaint/renderer/generators/ProductsBoxGenerator.class
+org/openscience/jchempaint/renderer/generators/RadicalGenerator.class
+org/openscience/jchempaint/renderer/generators/ReactantsBoxGenerator.class
+org/openscience/jchempaint/renderer/generators/ReactionArrowGenerator.class
+org/openscience/jchempaint/renderer/generators/ReactionBoxGenerator.class
+org/openscience/jchempaint/renderer/generators/ReactionPlusGenerator.class
+org/openscience/jchempaint/renderer/generators/RingGenerator.class
+org/openscience/jchempaint/renderer/generators/SelectAtomGenerator.class
+org/openscience/jchempaint/renderer/generators/SelectBondGenerator.class
+org/openscience/jchempaint/renderer/IRenderer.class
+org/openscience/jchempaint/renderer/Renderer.class
+org/openscience/jchempaint/renderer/RendererModel.class
+org/openscience/jchempaint/renderer/RenderingParameters$AtomShape.class
+org/openscience/jchempaint/renderer/RenderingParameters.class
+org/openscience/jchempaint/renderer/selection/AbstractSelection$1.class
+org/openscience/jchempaint/renderer/selection/AbstractSelection.class
+org/openscience/jchempaint/renderer/selection/IChemObjectSelection.class
+org/openscience/jchempaint/renderer/selection/IncrementalSelection.class
+org/openscience/jchempaint/renderer/selection/LogicalSelection.class
+org/openscience/jchempaint/renderer/selection/LogicalSelection$Type.class
+org/openscience/jchempaint/renderer/selection/RectangleSelection.class
+org/openscience/jchempaint/renderer/selection/ShapeSelection.class
+org/openscience/jchempaint/renderer/selection/SingleSelection.class
+org/openscience/jchempaint/renderer/visitor/AbstractAWTDrawVisitor.class
+org/openscience/jchempaint/renderer/visitor/AWTDrawVisitor$1.class
+org/openscience/jchempaint/renderer/visitor/AWTDrawVisitor$2.class
+org/openscience/jchempaint/renderer/visitor/AWTDrawVisitor.class
+org/openscience/jchempaint/renderer/visitor/IDrawVisitor.class
org/openscience/jchempaint/RenderPanel.class
org/openscience/jchempaint/StringHelper.class
org/openscience/jchempaint/SwingPopupModule.class
org/openscience/jchempaint/undoredo/SwingAddAtomsAndBondsEdit.class
org/openscience/jchempaint/undoredo/SwingUndoRedoFactory.class
-org/openscience/cdk/atomtype/CDKAtomTypeMatcher.class
-org/openscience/cdk/atomtype/IAtomTypeMatcher.class
-org/openscience/cdk/config/AtomTypeFactory.class
-org/openscience/cdk/config/atomtypes/OWLAtomTypeHandler.class
-org/openscience/cdk/config/atomtypes/OWLAtomTypeReader.class
-org/openscience/cdk/config/IAtomTypeConfigurator.class
-org/openscience/cdk/config/OWLBasedAtomTypeConfigurator.class
-org/openscience/cdk/dict/data/cdk-atom-types.owl
-org/openscience/jchempaint/action/ChangeSingleElectronAction.class
-org/openscience/cdk/controller/AbstractSelectModule.class
Modified: jchempaint/trunk/src/main/org/openscience/jchempaint/JCPMenuTextMaker.java
===================================================================
--- jchempaint/trunk/src/main/org/openscience/jchempaint/JCPMenuTextMaker.java 2009-11-19 16:47:09 UTC (rev 15071)
+++ jchempaint/trunk/src/main/org/openscience/jchempaint/JCPMenuTextMaker.java 2009-11-20 11:35:18 UTC (rev 15072)
@@ -295,8 +295,15 @@
entries.put("ClTooltip", GT._("Change drawing symbol to Cl"));
entries.put("BrTooltip", GT._("Change drawing symbol to Br"));
entries.put("ITooltip", GT._("Change drawing symbol to I"));
-
-}
+ entries.put("reaction", GT._("Reaction"));
+ entries.put("addReactantToNewReaction", GT._("Make Reactant in New Reaction"));
+ entries.put("addReactantToExistingReaction", GT._("Make Reactant in Existing Reaction"));
+ entries.put("addProductToNewReaction", GT._("Make Product in New Reaction"));
+ entries.put("addProductToExistingReaction", GT._("Make Product in Existing Reaction"));
+ entries.put("selectReactants", GT._("Select Reactants"));
+ entries.put("selectProducts", GT._("Select Products"));
+ entries.put("reactionMenuTitle", GT._("Reaction Popup Menu"));
+ }
/**
* Gives the text for an item.
Modified: jchempaint/trunk/src/main/org/openscience/jchempaint/JChemPaintPanel.java
===================================================================
--- jchempaint/trunk/src/main/org/openscience/jchempaint/JChemPaintPanel.java 2009-11-19 16:47:09 UTC (rev 15071)
+++ jchempaint/trunk/src/main/org/openscience/jchempaint/JChemPaintPanel.java 2009-11-20 11:35:18 UTC (rev 15072)
@@ -67,6 +67,7 @@
import org.openscience.cdk.CDKConstants;
import org.openscience.cdk.ChemModel;
import org.openscience.cdk.PseudoAtom;
+import org.openscience.cdk.Reaction;
import org.openscience.cdk.config.IsotopeFactory;
import org.openscience.cdk.event.ICDKChangeListener;
import org.openscience.cdk.interfaces.IAtom;
@@ -198,6 +199,10 @@
inputAdapter.setPopupMenu(ChemModel.class, new JChemPaintPopupMenu(
this, "chemmodel", this.guistring));
}
+ if (inputAdapter.getPopupMenu(Reaction.class) == null) {
+ inputAdapter.setPopupMenu(Reaction.class, new JChemPaintPopupMenu(
+ this, "reaction", this.guistring));
+ }
}
/**
Modified: jchempaint/trunk/src/main/org/openscience/jchempaint/action/CopyPasteAction.java
===================================================================
--- jchempaint/trunk/src/main/org/openscience/jchempaint/action/CopyPasteAction.java 2009-11-19 16:47:09 UTC (rev 15071)
+++ jchempaint/trunk/src/main/org/openscience/jchempaint/action/CopyPasteAction.java 2009-11-20 11:35:18 UTC (rev 15072)
@@ -75,6 +75,7 @@
import org.openscience.cdk.tools.manipulator.AtomContainerManipulator;
import org.openscience.cdk.tools.manipulator.ChemFileManipulator;
import org.openscience.cdk.tools.manipulator.ChemModelManipulator;
+import org.openscience.cdk.tools.manipulator.MoleculeSetManipulator;
import org.openscience.cdk.tools.manipulator.ReactionManipulator;
import org.openscience.jchempaint.GT;
import org.openscience.jchempaint.JChemPaintPanel;
@@ -433,6 +434,52 @@
else {
logger.warn("Cannot select everything in : ", object);
}
+ } else if (type.equals("selectReactionReactants")) {
+ IChemObject object = getSource(e);
+ if (object instanceof IReaction) {
+ IReaction reaction = (IReaction) object;
+ IAtomContainer wholeModel =
+ jcpPanel.getChemModel().getBuilder().newAtomContainer();
+ for (IAtomContainer container :
+ MoleculeSetManipulator.getAllAtomContainers(
+ reaction.getReactants())) {
+ wholeModel.add(container);
+ }
+ ShapeSelection container = new RectangleSelection();
+ for (IAtom atom : wholeModel.atoms()) {
+ container.atoms.add(atom);
+ }
+ for (IBond bond : wholeModel.bonds()) {
+ container.bonds.add(bond);
+ }
+ renderModel.setSelection(container);
+ }
+ else {
+ logger.warn("Cannot select reactants from : ", object);
+ }
+ } else if (type.equals("selectReactionProducts")) {
+ IChemObject object = getSource(e);
+ if (object instanceof IReaction) {
+ IReaction reaction = (IReaction) object;
+ IAtomContainer wholeModel =
+ jcpPanel.getChemModel().getBuilder().newAtomContainer();
+ for (IAtomContainer container :
+ MoleculeSetManipulator.getAllAtomContainers(
+ reaction.getProducts())) {
+ wholeModel.add(container);
+ }
+ ShapeSelection container = new RectangleSelection();
+ for (IAtom atom : wholeModel.atoms()) {
+ container.atoms.add(atom);
+ }
+ for (IBond bond : wholeModel.bonds()) {
+ container.bonds.add(bond);
+ }
+ renderModel.setSelection(container);
+ }
+ else {
+ logger.warn("Cannot select reactants from : ", object);
+ }
}
jcpPanel.get2DHub().updateView();
jcpPanel.updateStatusBar();
Added: jchempaint/trunk/src/main/org/openscience/jchempaint/action/CreateReactionAction.java
===================================================================
--- jchempaint/trunk/src/main/org/openscience/jchempaint/action/CreateReactionAction.java (rev 0)
+++ jchempaint/trunk/src/main/org/openscience/jchempaint/action/CreateReactionAction.java 2009-11-20 11:35:18 UTC (rev 15072)
@@ -0,0 +1,205 @@
+/*
+ * $RCSfile$
+ * $Author: egonw $
+ * $Date: 2007-01-04 17:26:00 +0000 (Thu, 04 Jan 2007) $
+ * $Revision: 7634 $
+ *
+ * Copyright (C) 1997-2008 Christoph Steinbeck, Stefan Kuhn
+ *
+ * Contact: cdk...@li...
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ * All we ask is that proper credit is given for our work, which includes
+ * - but is not limited to - adding the above copyright notice to the beginning
+ * of your source code files, and to any copyright notice that you may distribute
+ * with programs based on this work.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA.
+ */
+package org.openscience.jchempaint.action;
+
+import java.awt.event.ActionEvent;
+
+import javax.swing.JOptionPane;
+
+import org.openscience.cdk.interfaces.IAtom;
+import org.openscience.cdk.interfaces.IAtomContainer;
+import org.openscience.cdk.interfaces.IBond;
+import org.openscience.cdk.interfaces.IChemModel;
+import org.openscience.cdk.interfaces.IChemObject;
+import org.openscience.cdk.interfaces.IReactionSet;
+import org.openscience.cdk.tools.manipulator.ChemModelManipulator;
+import org.openscience.jchempaint.GT;
+import org.openscience.jchempaint.controller.ControllerHub;
+import org.openscience.jchempaint.controller.IChemModelRelay;
+import org.openscience.jchempaint.controller.ReactionHub;
+
+
+/**
+ * Creates a reaction object
+ *
+ */
+public class CreateReactionAction extends JCPAction
+{
+
+ private static final long serialVersionUID = -7625810885316702776L;
+
+ public void actionPerformed(ActionEvent event)
+ {
+ IChemObject object = getSource(event);
+
+ logger.debug("CreateReaction action");
+ IChemModel model = jcpPanel.getChemModel();
+ IReactionSet reactionSet = model.getReactionSet();
+ if (reactionSet == null)
+ {
+ reactionSet = model.getBuilder().newReactionSet();
+ }
+ IAtomContainer container = null;
+ if (object instanceof IAtom)
+ {
+ container = ChemModelManipulator.getRelevantAtomContainer(model, (IAtom) object);
+ } else if(object instanceof IBond)
+ {
+ container = ChemModelManipulator.getRelevantAtomContainer(model, (IBond) object);
+ } else
+ {
+ logger.error("Cannot add to reaction object of type: " + object.getClass().getName());
+ }
+ if (container == null)
+ {
+ logger.error("Cannot find container to add object to!");
+ } else
+ {
+ IChemModelRelay hub = jcpPanel.get2DHub();
+ IAtomContainer newContainer;
+ try {
+ newContainer = (IAtomContainer) container.clone();
+ if(container.getID()!=null)
+ newContainer.setID(container.getID());
+ else
+ newContainer.setID("ac"+System.currentTimeMillis());
+ } catch (CloneNotSupportedException e) {
+ logger.error("Could not clone IAtomContainer: ", e.getMessage());
+ logger.debug(e);
+ return;
+ }
+
+ logger.debug("type: ", type);
+ if ("addReactantToNew".equals(type))
+ {
+ ReactionHub.makeReactantInNewReaction((ControllerHub)hub, newContainer, container);
+ //TODO this.jcpPanel.atomAtomMappingButton.setEnabled(true);
+ } else if ("addReactantToExisting".equals(type))
+ {
+ if (reactionSet.getReactionCount() == 0)
+ {
+ logger.warn("Cannot add to reaction if no one exists");
+ JOptionPane.showMessageDialog(jcpPanel, GT._("No reaction existing. Cannot add therefore to something!"), GT._("No existing reactions"), JOptionPane.WARNING_MESSAGE);
+ return;
+ } else
+ {
+ Object[] ids = getReactionIDs(reactionSet);
+
+ String s = (String)ids[0];
+ if(ids.length>1){
+ s = (String) JOptionPane.showInputDialog(
+ null,
+ "Reaction Chooser",
+ "Choose reaction to add reaction to",
+ JOptionPane.PLAIN_MESSAGE,
+ null,
+ ids,
+ ids[0]
+ );
+ }
+ if ((s != null) && (s.length() > 0))
+ {
+ ReactionHub.makeReactantInExistingReaction((ControllerHub)hub, s, newContainer, container);
+ //TODO this.jcpPanel.atomAtomMappingButton.setEnabled(true);
+ } else
+ {
+ logger.error("No reaction selected");
+ }
+ }
+ } else if ("addProductToNew".equals(type))
+ {
+ ReactionHub.makeProductInNewReaction((ControllerHub)hub, newContainer, container);
+ //this.jcpPanel.atomAtomMappingButton.setEnabled(true);
+ } else if ("addProductToExisting".equals(type))
+ {
+ if (reactionSet.getReactionCount() == 0)
+ {
+ logger.warn("Cannot add to reaction if no one exists");
+ JOptionPane.showMessageDialog(jcpPanel, GT._("No reaction existing. Cannot add therefore to something!"), GT._("No existing reactions"), JOptionPane.WARNING_MESSAGE);
+ return;
+ } else
+ {
+ Object[] ids = getReactionIDs(reactionSet);
+ String s = (String)ids[0];
+ if(ids.length>1){
+ s = (String) JOptionPane.showInputDialog(
+ null,
+ "Reaction Chooser",
+ "Choose reaction to add reaction to",
+ JOptionPane.PLAIN_MESSAGE,
+ null,
+ ids,
+ ids[0]
+ );
+ }
+
+ if ((s != null) && (s.length() > 0))
+ {
+ ReactionHub.makeProductInExistingReaction((ControllerHub)hub, s, newContainer, container);
+ //TODO this.jcpPanel.atomAtomMappingButton.setEnabled(true);
+ } else
+ {
+ logger.error("No reaction selected");
+ }
+ }
+ } else
+ {
+ logger.warn("Don't know about this action type: " + type);
+ return;
+ }
+ }
+ logger.debug("Deleted atom from old container...");
+ jcpPanel.get2DHub().updateView();
+ }
+
+
+ /**
+ * Gets the reactionIDs attribute of the CreateReactionAction object
+ *
+ *@param reactionSet Description of the Parameter
+ *@return The reactionIDs value
+ */
+ private Object[] getReactionIDs(IReactionSet reactionSet)
+ {
+ if (reactionSet != null)
+ {
+
+ String[] ids = new String[reactionSet.getReactionCount()];
+ for (int i = 0; i < reactionSet.getReactionCount(); i++)
+ {
+ ids[i] = reactionSet.getReaction(i).getID();
+ }
+ return ids;
+ } else
+ {
+ return new String[0];
+ }
+ }
+}
+
Property changes on: jchempaint/trunk/src/main/org/openscience/jchempaint/action/CreateReactionAction.java
___________________________________________________________________
Added: svn:executable
+ *
Modified: jchempaint/trunk/src/main/org/openscience/jchempaint/application/JChemPaint.java
===================================================================
--- jchempaint/trunk/src/main/org/openscience/jchempaint/application/JChemPaint.java 2009-11-19 16:47:09 UTC (rev 15071)
+++ jchempaint/trunk/src/main/org/openscience/jchempaint/application/JChemPaint.java 2009-11-20 11:35:18 UTC (rev 15072)
@@ -254,8 +254,7 @@
throws CDKException {
JChemPaint.setReactionIDs(chemModel);
JChemPaint.replaceReferencesWithClones(chemModel);
- //if we want to have reactions, we need this
- //JChemPaint.removeDuplicateMolecules(chemModel);
+ JChemPaint.removeDuplicateMolecules(chemModel);
// check for bonds
if (ChemModelManipulator.getBondCount(chemModel) == 0) {
Modified: jchempaint/trunk/src/main/org/openscience/jchempaint/controller/ControllerHub.java
===================================================================
--- jchempaint/trunk/src/main/org/openscience/jchempaint/controller/ControllerHub.java 2009-11-19 16:47:09 UTC (rev 15071)
+++ jchempaint/trunk/src/main/org/openscience/jchempaint/controller/ControllerHub.java 2009-11-20 11:35:18 UTC (rev 15072)
@@ -157,7 +157,6 @@
public void setChemModel(IChemModel model) {
this.chemModel = model;
- //updateAtoms(ring, ring.atoms());
structureChanged();
}
@@ -334,6 +333,7 @@
changeModeListeners.get(i).modeChanged(activeDrawModule);
}
+ //OK
public IAtom getClosestAtom(Point2d worldCoord) {
IAtom closestAtom = null;
double closestDistanceSQ = Double.MAX_VALUE;
@@ -356,6 +356,7 @@
return closestAtom;
}
+ //OK
public IBond getClosestBond(Point2d worldCoord) {
IBond closestBond = null;
double closestDistanceSQ = Double.MAX_VALUE;
@@ -380,17 +381,14 @@
return closestBond;
}
-
+ //OK
public IAtomContainer removeAtomWithoutUndo(IAtom atom) {
IAtomContainer ac = atom.getBuilder().newAtomContainer();
ac.addAtom(atom);
Iterator<IBond> connbonds = ChemModelManipulator.getRelevantAtomContainer(chemModel, atom).getConnectedBondsList(atom).iterator();
while(connbonds.hasNext())
ac.addBond(connbonds.next());
- //FIXME: This assumes the only-one-atom-container architecture. The old method
- //split up the atom container, which we don't want right now.
- chemModel.getMoleculeSet().getAtomContainer(0).removeAtomAndConnectedElectronContainers(atom);
- //ChemModelManipulator.removeAtomAndConnectedElectronContainers(chemModel, atom);
+ ChemModelManipulator.removeAtomAndConnectedElectronContainers(chemModel, atom);
for(IBond bond : ac.bonds()){
if(bond.getAtom(0)==atom)
updateAtom(bond.getAtom(1));
@@ -401,6 +399,7 @@
return ac;
}
+ //OK TODO this could do with less partitioning
public IAtomContainer removeAtom(IAtom atom) {
IAtomContainer ac = removeAtomWithoutUndo(atom);
if(getUndoRedoFactory()!=null && getUndoRedoHandler()!=null){
@@ -410,6 +409,7 @@
return ac;
}
+ //OK
/* (non-Javadoc)
* @see org.openscience.cdk.controller.IChemModelRelay#addAtom(java.lang.String, javax.vecmath.Point2d)
*/
@@ -417,6 +417,7 @@
return addAtom(atomType, 0, worldCoord);
}
+ //OK
/* (non-Javadoc)
* @see org.openscience.cdk.controller.IChemModelRelay#addAtom(java.lang.String, int, javax.vecmath.Point2d)
*/
@@ -430,6 +431,7 @@
return undoRedoContainer.getAtom(0);
}
+ //OK
/* (non-Javadoc)
* @see org.openscience.cdk.controller.IChemModelRelay#addAtomWithoutUndo(java.lang.String, javax.vecmath.Point2d)
*/
@@ -437,6 +439,7 @@
return addAtomWithoutUndo(atomType, 0, worldCoord);
}
+ //OK
/* (non-Javadoc)
* @see org.openscience.cdk.controller.IChemModelRelay#addAtomWithoutUndo(java.lang.String, int, javax.vecmath.Point2d)
*/
@@ -453,10 +456,10 @@
ac.addAtom(newAtom);
molSet.addMolecule(ac);
chemModel.setMoleculeSet(molSet);
- } else {
- // FIXME : always add to the first container?
- molSet.getMolecule(0).addAtom(newAtom);
}
+ IAtomContainer newAtomContainer = chemModel.getBuilder().newAtomContainer();
+ newAtomContainer.addAtom(newAtom);
+ molSet.addAtomContainer(newAtomContainer);
updateAtom(newAtom);
RendererModel model = this.getRenderer().getRenderer2DModel();
double nudgeDistance = model.getHighlightDistance() / model.getScale();
@@ -466,6 +469,7 @@
return newAtom;
}
+ //OK
public IAtom addAtom(String atomType, IAtom atom) {
IAtomContainer undoRedoContainer = atom.getBuilder().newAtomContainer();
undoRedoContainer.addAtom(addAtomWithoutUndo(atomType, atom));
@@ -481,6 +485,7 @@
return undoRedoContainer.getAtom(0);
}
+ //OK
/* (non-Javadoc)
* @see org.openscience.cdk.controller.IChemModelRelay#addAtomWithoutUndo(java.lang.String, org.openscience.cdk.interfaces.IAtom)
*/
@@ -488,6 +493,7 @@
return addAtomWithoutUndo(atomType, atom, IBond.Stereo.NONE);
}
+ //OK
/* (non-Javadoc)
* @see org.openscience.cdk.controller.IChemModelRelay#addAtomWithoutUndo(java.lang.String, org.openscience.cdk.interfaces.IAtom, int)
*/
@@ -563,6 +569,7 @@
return newAtom;
}
+ //OK
public void addNewBond(Point2d worldCoordinate) {
IAtomContainer undoRedoContainer =
getIChemModel().getBuilder().newAtomContainer();
@@ -592,6 +599,7 @@
}
}
+ //OK
public void cycleBondValence(IBond bond) {
IBond.Order[] orders=new IBond.Order[2];
IBond.Stereo[] stereos=new IBond.Stereo[2];
@@ -627,6 +635,7 @@
}
}
+ //OK
public IBond makeNewStereoBond(IAtom atom, Direction desiredDirection) {
String atomType = getController2DModel().getDrawElement();
IAtom newAtom = addAtomWithoutUndo(atomType, atom);
@@ -656,6 +665,7 @@
return newBond;
}
+ //OK
public void moveToWithoutUndo( IAtom atom, Point2d worldCoords ) {
if ( atom != null ) {
Point2d atomCoord = new Point2d( worldCoords );
@@ -664,6 +674,7 @@
coordinatesChanged();
}
+ //OK
public void moveTo( IAtom atom, Point2d worldCoords ) {
if ( atom != null ) {
if(getUndoRedoFactory()!=null && getUndoRedoHandler()!=null){
@@ -678,6 +689,7 @@
}
}
+ //OK
public void moveToWithoutUndo( IBond bond, Point2d point ) {
if (bond != null) {
Point2d center = bond.get2DCenter();
@@ -693,6 +705,7 @@
coordinatesChanged();
}
+ //OK
public void moveTo( IBond bond, Point2d point ) {
if (bond != null) {
if(getUndoRedoFactory()!=null && getUndoRedoHandler()!=null){
@@ -708,20 +721,28 @@
}
}
-
+ //OK
/* (non-Javadoc)
* @see org.openscience.cdk.controller.IChemModelRelay#addBond(org.openscience.cdk.interfaces.IAtom, org.openscience.cdk.interfaces.IAtom, int)
*/
public IBond addBond(IAtom fromAtom, IAtom toAtom, IBond.Stereo stereo) {
IBond newBond = chemModel.getBuilder().newBond(fromAtom, toAtom,
CDKConstants.BONDORDER_SINGLE, stereo);
- chemModel.getMoleculeSet().getAtomContainer(0).addBond(newBond);
+ IAtomContainer fromContainer = ChemModelManipulator.getRelevantAtomContainer(chemModel, fromAtom);
+ IAtomContainer toContainer = ChemModelManipulator.getRelevantAtomContainer(chemModel, toAtom);
+ //we need to check if this merges two atomconainers or not
+ if(fromContainer!=toContainer){
+ fromContainer.add(toContainer);
+ chemModel.getMoleculeSet().removeAtomContainer(toContainer);
+ }
+ fromContainer.addBond(newBond);
updateAtom(newBond.getAtom(0));
updateAtom(newBond.getAtom(1));
structureChanged();
return newBond;
}
+ //OK
/* (non-Javadoc)
* @see org.openscience.cdk.controller.IChemModelRelay#addBond(org.openscience.cdk.interfaces.IAtom, org.openscience.cdk.interfaces.IAtom)
*/
@@ -729,6 +750,7 @@
return addBond(fromAtom, toAtom, IBond.Stereo.NONE);
}
+ //OK
public void setCharge(IAtom atom, int charge) {
if(getUndoRedoFactory()!=null && getUndoRedoHandler()!=null){
IUndoRedoable undoredo = getUndoRedoFactory().getChangeChargeEdit(atom,atom.getFormalCharge(),charge, "Change charge to "+charge,this);
@@ -739,6 +761,7 @@
structurePropertiesChanged();
}
+ //OK
public void setMassNumber(IAtom atom, int massNumber) {
if(getUndoRedoFactory()!=null && getUndoRedoHandler()!=null){
IUndoRedoable undoredo = getUndoRedoFactory().getChangeIsotopeEdit(atom, atom.getMassNumber(), massNumber, "Change Atomic Mass to "+massNumber);
@@ -748,6 +771,7 @@
structurePropertiesChanged();
}
+ //OK
public void setOrder(IBond bond, Order order) {
Map<IBond, IBond.Order[]> changedBonds= new HashMap<IBond, IBond.Order[]>();
changedBonds.put(bond,new Order[]{order,bond.getOrder()});
@@ -766,6 +790,7 @@
}
}
+ //OK
public void setSymbol(IAtom atom, String symbol) {
if(getUndoRedoFactory()!=null && getUndoRedoHandler()!=null){
IUndoRedoable undoredo = getUndoRedoFactory().getChangeAtomSymbolEdit(atom,atom.getSymbol(),symbol,"Change Atom Symbol to "+symbol,this);
@@ -789,11 +814,7 @@
structurePropertiesChanged();
}
- public void setWedgeType(IBond bond, IBond.Stereo type) {
- bond.setStereo(type);
- structurePropertiesChanged();
- }
-
+ //OK
public void updateImplicitHydr...
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