Examples with ReactionSpeciesCopy cbit.vcell.model.ReactionSpeciesCopy used on opensource projects

Example 1 with ReactionSpeciesCopy

use of cbit.vcell.model.ReactionSpeciesCopy in project vcell by virtualcell.

the class ReactionCartoonTool method shapeHasMenuActionEnabled.

@Override
public boolean shapeHasMenuActionEnabled(Shape shape, String menuAction) {
    if (menuAction.equals(CartoonToolMiscActions.Properties.MENU_ACTION)) {
        if (shape instanceof CatalystShape) {
            return false;
        }
    }
    if (menuAction.equals(CartoonToolMiscActions.SearchReactions.MENU_ACTION)) {
        if (!(shape instanceof ReactionContainerShape) || !getReactionCartoon().getStructureSuite().getStructures().contains(shape.getModelObject())) {
            return false;
        }
    }
    GraphViewAction paintingAction = ActionUtil.getAction(paintingActions, menuAction);
    if (paintingAction != null) {
        return paintingAction.isEnabledForShape(shape);
    }
    GraphViewAction groupAction = ActionUtil.getAction(groupActions, menuAction);
    if (groupAction != null) {
        return groupAction.isEnabledForShape(shape);
    }
    if (shape instanceof ReactionContainerShape) {
        if (menuAction.equals(CartoonToolEditActions.PasteNew.MENU_ACTION)) {
            ReactionSpeciesCopy reactionSpeciesCopy = (ReactionSpeciesCopy) VCellTransferable.getFromClipboard(VCellTransferable.REACTION_SPECIES_ARRAY_FLAVOR);
            if (reactionSpeciesCopy != null) {
                Structure targetStructure = ((ReactionContainerShape) shape).getStructure();
                if (reactionSpeciesCopy.getReactStepArr() != null) {
                    for (int i = 0; i < reactionSpeciesCopy.getReactStepArr().length; i++) {
                        if (!reactionSpeciesCopy.getReactStepArr()[i].getStructure().getClass().equals(targetStructure.getClass())) {
                            return false;
                        }
                    }
                }
                return true;
            } else {
                return false;
            }
        } else if (menuAction.equals(CartoonToolEditActions.Delete.MENU_ACTION)) {
            if (((ReactionContainerShape) shape).getStructureSuite().getStructures().size() == 1) {
                return false;
            }
        }
    }
    return true;
}

Example 2 with ReactionSpeciesCopy

use of cbit.vcell.model.ReactionSpeciesCopy in project vcell by virtualcell.

the class ReactionCartoonTool method pasteReactionsAndSpecies.

private void pasteReactionsAndSpecies(Component requester, Structure pasteToStructure) {
    final String RXSPECIES_PASTERX = "Reactions";
    final String RXSPECIES_SPECIES = "Species";
    ReactionSpeciesCopy reactionSpeciesCopy = (ReactionSpeciesCopy) SimpleTransferable.getFromClipboard(VCellTransferable.REACTION_SPECIES_ARRAY_FLAVOR);
    if (reactionSpeciesCopy != null) {
        // TODO: here we may want to warn the user about compartment number / type / name mismatch
        // between the source and the destination
        String response = null;
        if ((reactionSpeciesCopy.getReactStepArr() != null || reactionSpeciesCopy.getReactionRuleArr() != null) && reactionSpeciesCopy.getSpeciesContextArr() != null) {
            String msg = "There are ";
            msg += reactionSpeciesCopy.getSpeciesContextArr().length + " Species and ";
            int rlen = 0;
            if (reactionSpeciesCopy.getReactStepArr() != null)
                rlen += reactionSpeciesCopy.getReactStepArr().length;
            if (reactionSpeciesCopy.getReactionRuleArr() != null)
                rlen += reactionSpeciesCopy.getReactionRuleArr().length;
            msg += rlen + " Reactions / Rules on the clipboard, choose which set to paste.";
            response = DialogUtils.showWarningDialog(getGraphPane(), "Choose Species or Reactions to paste", msg, new String[] { RXSPECIES_SPECIES, RXSPECIES_PASTERX, RXSPECIES_CANCEL }, RXSPECIES_CANCEL);
            if (response == null || response.equals(RXSPECIES_CANCEL)) {
                return;
            }
        }
        if (reactionSpeciesCopy.getSpeciesContextArr() != null && (response == null || response.equals(RXSPECIES_SPECIES))) {
            IdentityHashMap<Species, Species> speciesHash = new IdentityHashMap<Species, Species>();
            Vector<BioModelEntityObject> pastedSpeciesContextV = new Vector<BioModelEntityObject>();
            for (int i = 0; i < reactionSpeciesCopy.getSpeciesContextArr().length; i++) {
                String rootSC = speciesContextRootFinder(reactionSpeciesCopy.getSpeciesContextArr()[i]);
                pastedSpeciesContextV.add(pasteSpecies(getGraphPane(), reactionSpeciesCopy.getSpeciesContextArr()[i].getSpecies(), rootSC, getModel(), pasteToStructure, true, speciesHash, null));
                copyRelativePosition(getGraphModel(), reactionSpeciesCopy.getSpeciesContextArr()[i], pastedSpeciesContextV.lastElement());
            }
            ReactionCartoonTool.selectAndSaveDiagram(ReactionCartoonTool.this, pastedSpeciesContextV);
        }
        if (reactionSpeciesCopy.getReactStepArr() != null && reactionSpeciesCopy.getReactionRuleArr() == null && (response == null || response.equals(RXSPECIES_PASTERX))) {
            BioModel bioModel = null;
            try {
                bioModel = findBioModel(requester);
            } catch (Exception e) {
                // TODO Auto-generated catch block
                e.printStackTrace();
                DialogUtils.showErrorDialog(requester, e.getMessage());
                return;
            }
            ReactionDescription reactionDescription = DBReactionWizardPanel.createReactionDescription(reactionSpeciesCopy.getReactStepArr()[0], null, reactionSpeciesCopy.getFromStructure().getKey());
            RXParticipantResolverPanel rxParticipantResolverPanel = new RXParticipantResolverPanel();
            // rxParticipantResolverPanel.setPasteToModel(getModel());
            rxParticipantResolverPanel.setupRX(reactionDescription, getModel(), pasteToStructure);
            // JDialog j = new JDialog();
            // j.setModal(true);
            // j.setAlwaysOnTop(true);
            // j.getContentPane().add(rxParticipantResolverPanel);
            // j.pack();
            // j.setVisible(true);
            // int result = DialogUtils.showComponentOKCancelDialog(getGraphPane(), rxParticipantResolverPanel, "Assign Reaction elements");
            // if(result != JOptionPane.OK_OPTION) {
            // return;
            // }
            BioCartoonTool.AssignmentHelper assignmentHelper = new BioCartoonTool.AssignmentHelper() {

                @Override
                public JComboBox[] getStructureAssignmentJCB() {
                    return rxParticipantResolverPanel.getStructureAssignmentJCB();
                }

                @Override
                public JComboBox[] getSpeciesAssignmentJCB() {
                    return rxParticipantResolverPanel.getSpeciesAssignmentJCB();
                }

                @Override
                public ArrayList<JTextField> getFinalNames() {
                    // TODO Auto-generated method stub
                    return rxParticipantResolverPanel.getFinalNamesJTF();
                }

                @Override
                public Component getParent() {
                    return getGraphPane();
                }

                @Override
                public Component getAssignmentInterface() {
                    return rxParticipantResolverPanel;
                }

                @Override
                public void close() {
                // Do Nothing
                }
            };
            BioCartoonTool.pasteReactionSteps(requester, ReactionCartoonTool.this, reactionDescription, reactionSpeciesCopy.getReactStepArr()[0].getModel(), reactionSpeciesCopy.getFromStructure(), reactionSpeciesCopy.getReactStepArr()[0], bioModel.getModel(), pasteToStructure, assignmentHelper);
        // pasteReactionSteps(getGraphPane(),reactionSpeciesCopy.getReactStepArr(), getModel(),structure,true, null,ReactionCartoonTool.this);
        } else if (reactionSpeciesCopy.getReactionRuleArr() != null && (response == null || response.equals(RXSPECIES_PASTERX))) {
            pasteReactionsAndRules(getGraphPane(), reactionSpeciesCopy, getModel(), pasteToStructure, ReactionCartoonTool.this);
        }
    // try {
    // for(MolecularType mtOurs : mtNewList) {
    // rbmmcOurs.addMolecularType(mtOurs, false);
    // }
    // } catch (ModelException | PropertyVetoException e) {
    // e.printStackTrace();
    // }
    // 
    // // ReactionRules
    // if(reactionSpeciesCopy.getReactionRuleArr() != null) {
    // for(ReactionRule rrTheirs : reactionSpeciesCopy.getReactionRuleArr()) {
    // 
    // }
    // }
    }
}

Example 3 with ReactionSpeciesCopy

use of cbit.vcell.model.ReactionSpeciesCopy in project vcell by virtualcell.

the class ReactionCartoonTool method menuAction.

@Override
protected void menuAction(Shape shape, String menuAction) {
    if (shape == null) {
        return;
    }
    if (menuAction.equals(CartoonToolMiscActions.Properties.MENU_ACTION)) {
        if (shape instanceof FluxReactionShape) {
        // showFluxReactionPropertiesDialog((FluxReactionShape) shape);
        } else if (shape instanceof SimpleReactionShape) {
        // showSimpleReactionPropertiesDialog((SimpleReactionShape) shape);
        } else if (shape instanceof ReactantShape) {
        // Point locationOnScreen = shape.getSpaceManager().getAbsLoc();
        // Point graphPaneLocation = getGraphPane().getLocationOnScreen();
        // locationOnScreen.translate(graphPaneLocation.x,
        // graphPaneLocation.y);
        // showReactantPropertiesDialog((ReactantShape) shape,
        // locationOnScreen);
        } else if (shape instanceof ProductShape) {
        // Point locationOnScreen = shape.getSpaceManager().getAbsLoc();
        // Point graphPaneLocation = getGraphPane().getLocationOnScreen();
        // locationOnScreen.translate(graphPaneLocation.x,
        // graphPaneLocation.y);
        // showProductPropertiesDialog((ProductShape) shape,
        // locationOnScreen);
        } else if (shape instanceof SpeciesContextShape) {
        // showEditSpeciesDialog(getGraphPane(), getReactionCartoon()
        // .getModel(), ((SpeciesContextShape) shape)
        // .getSpeciesContext());
        } else if (shape instanceof ReactionContainerShape) {
        // ReactionContainerShape rcs = (ReactionContainerShape) shape;
        // if (rcs.getStructure() instanceof Feature) {
        // //
        // // showFeaturePropertyDialog is invoked in two modes:
        // //
        // // 1) parent!=null and child==null
        // // upon ok, it adds a new feature to the supplied parent.
        // //
        // // 2) parent==null and child!=null
        // // upon ok, edits the feature name
        // //
        // showFeaturePropertiesDialog(getGraphPane(),
        // (getReactionCartoon().getModel() == null ? null
        // : getReactionCartoon().getModel()), null,
        // (Feature) rcs.getStructure());
        // } else if (rcs.getStructure() instanceof Membrane) {
        // showMembranePropertiesDialog(getGraphPane(), (Membrane) rcs
        // .getStructure());
        // }
        }
    } else if (menuAction.equals(CartoonToolMiscActions.AddSpecies.MENU_ACTION)) {
        if (shape instanceof ReactionContainerShape) {
            getGraphModel().deselectShape(shape);
            // showCreateSpeciesContextDialog(getGraphPane(),
            // getReactionCartoon().getModel(),
            // ((ReactionContainerShape) shape).getStructure(), null);
            SpeciesContext speciesContext = getReactionCartoon().getModel().createSpeciesContext(((ReactionContainerShape) shape).getStructure());
            getGraphModel().select(speciesContext);
        }
    } else if (menuAction.equals(CartoonToolEditActions.Copy.MENU_ACTION)) {
        if (shape instanceof SpeciesContextShape || shape instanceof ReactionStepShape || // rule participants whose rule is not selected won't
        shape instanceof RuleParticipantSignatureDiagramShape || // be copied since standalone they are meaningless
        shape instanceof ReactionRuleDiagramShape) {
            SpeciesContext[] spArray = getSelectedSpeciesContextArray();
            ReactionStep[] rsArray = getSelectedReactionStepArray();
            ReactionRule[] rrArray = getSelectedReactionRuleArray();
            MolecularType[] mtArray = getSelectedMolecularTypeArray(rrArray, rsArray, spArray);
            Structure[] structArray = getSelectedStructuresArray(rrArray, rsArray, spArray, mtArray);
            Structure fromStruct = null;
            ReactionContainerShape rcs = null;
            Shape parentShape = shape.getParent();
            if (parentShape instanceof ReactionContainerShape) {
                rcs = (ReactionContainerShape) parentShape;
                fromStruct = rcs.getStructure();
            }
            ReactionSpeciesCopy reactionSpeciesCopy = new ReactionSpeciesCopy(spArray, rsArray, rrArray, mtArray, fromStruct, structArray);
            VCellTransferable.sendToClipboard(reactionSpeciesCopy);
        }
    } else if (/*menuAction.equals(CartoonToolEditActions.Paste.MENU_ACTION)
				|| */
    menuAction.equals(CartoonToolEditActions.PasteNew.MENU_ACTION)) {
        if (shape instanceof ReactionContainerShape) {
            pasteReactionsAndSpecies(getGraphPane().getRootPane(), ((ReactionContainerShape) shape).getStructure());
        }
    } else if (menuAction.equals(CartoonToolEditActions.Delete.MENU_ACTION)) {
        try {
            if (getGraphModel().getSelectedShape() instanceof ReactionContainerShape && menuAction.equals(CartoonToolEditActions.Delete.MENU_ACTION)) {
                getModel().removeStructure(((ReactionContainerShape) getGraphModel().getSelectedShape()).getStructure());
                return;
            }
            if (getSelectedReactionStepArray() != null || getSelectedSpeciesContextArray() != null) {
                deleteReactionsAndSpecies(getGraphPane(), getSelectedReactionStepArray(), getSelectedSpeciesContextArray());
            }
            if (getSelectedReactionParticipantArray() != null && menuAction.equals(CartoonToolEditActions.Delete.MENU_ACTION)) {
                ReactionParticipant[] reactionParticipantArr = getSelectedReactionParticipantArray();
                if (ReactionCartoonTool.checkAllCatalyst(reactionParticipantArr)) {
                    DialogUtils.showWarningDialog(getGraphPane(), "Catalysts are determined automatically from the reaction kinetic expression.");
                    return;
                }
                String response = DialogUtils.showWarningDialog(getGraphPane(), "Delete " + reactionParticipantArr.length + " Reaction Stoichiometries", new String[] { RXSPECIES_DELETE, RXSPECIES_CANCEL }, RXSPECIES_CANCEL);
                if (response != null && response.equals(RXSPECIES_DELETE)) {
                    for (int i = 0; i < reactionParticipantArr.length; i++) {
                        if (reactionParticipantArr[i] instanceof Catalyst) {
                            // Catalysts may only be deleted by editing kynetic / proxy parameters
                            continue;
                        }
                        ReactionStep reactionStep = reactionParticipantArr[i].getReactionStep();
                        reactionStep.removeReactionParticipant(reactionParticipantArr[i]);
                    }
                }
            }
        } catch (UserCancelException uce) {
            return;
        } catch (PropertyVetoException e) {
            DialogUtils.showErrorDialog(getGraphPane(), e.getMessage());
        } catch (Exception e) {
            DialogUtils.showErrorDialog(getGraphPane(), e.getMessage(), e);
        }
    } else if (menuAction.equals(CartoonToolMiscActions.SearchReactions.MENU_ACTION)) {
        try {
            if (shape instanceof ReactionContainerShape) {
                showReactionBrowserDialog(((ReactionContainerShape) shape).getStructure(), null);
            }
        } catch (Exception e) {
            DialogUtils.showErrorDialog(getGraphPane(), e.getMessage(), e);
        }
    } else if (menuAction.equals(CartoonToolSaveAsImageActions.MenuAction.MENU_ACTION)) {
        try {
            String resType = null;
            if (shape instanceof ReactionContainerShape) {
                showSaveReactionImageDialog();
            }
        } catch (Exception e) {
            e.printStackTrace();
            DialogUtils.showErrorDialog(getGraphPane(), e.getMessage(), e);
        }
    } else if (menuAction.equals(CartoonToolMiscActions.Annotate.MENU_ACTION)) {
        if (shape instanceof ReactionStepShape) {
            // MIRIAMHelper.showMIRIAMAnnotationDialog(((SimpleReactionShape)shape).getReactionStep());
            // System.out.println("Menu action annotate activated...");
            ReactionStep rs = ((ReactionStepShape) shape).getReactionStep();
            VCMetaData vcMetaData = rs.getModel().getVcMetaData();
            try {
                String newAnnotation = DialogUtils.showAnnotationDialog(getGraphPane(), vcMetaData.getFreeTextAnnotation(rs));
                vcMetaData.setFreeTextAnnotation(rs, newAnnotation);
            } catch (UtilCancelException e) {
            // Do Nothing
            } catch (Throwable exc) {
                exc.printStackTrace(System.out);
                DialogUtils.showErrorDialog(getGraphPane(), "Failed to edit annotation!\n" + exc.getMessage(), exc);
            }
        }
    } else {
    // default action is to ignore
    }
}

Example 4 with ReactionSpeciesCopy

use of cbit.vcell.model.ReactionSpeciesCopy in project vcell by virtualcell.

the class ReactionCartoonTool method pasteReactionsAndSpecies.

private void pasteReactionsAndSpecies(Structure structure) {
    final String RXSPECIES_PASTERX = "Reactions";
    final String RXSPECIES_SPECIES = "Species";
    ReactionSpeciesCopy reactionSpeciesCopy = (ReactionSpeciesCopy) SimpleTransferable.getFromClipboard(VCellTransferable.REACTION_SPECIES_ARRAY_FLAVOR);
    if (reactionSpeciesCopy != null) {
        // TODO: here we may want to warn the user about compartment number / type / name mismatch
        // between the source and the destination
        String response = null;
        if ((reactionSpeciesCopy.getReactStepArr() != null || reactionSpeciesCopy.getReactionRuleArr() != null) && reactionSpeciesCopy.getSpeciesContextArr() != null) {
            String msg = "There are ";
            msg += reactionSpeciesCopy.getSpeciesContextArr().length + " Species and ";
            int rlen = 0;
            if (reactionSpeciesCopy.getReactStepArr() != null)
                rlen += reactionSpeciesCopy.getReactStepArr().length;
            if (reactionSpeciesCopy.getReactionRuleArr() != null)
                rlen += reactionSpeciesCopy.getReactionRuleArr().length;
            msg += rlen + " Reactions / Rules on the clipboard, choose which set to paste.";
            response = DialogUtils.showWarningDialog(getGraphPane(), "Choose Species or Reactions to paste", msg, new String[] { RXSPECIES_SPECIES, RXSPECIES_PASTERX, RXSPECIES_CANCEL }, RXSPECIES_CANCEL);
            if (response == null || response.equals(RXSPECIES_CANCEL)) {
                return;
            }
        }
        if (reactionSpeciesCopy.getSpeciesContextArr() != null && (response == null || response.equals(RXSPECIES_SPECIES))) {
            IdentityHashMap<Species, Species> speciesHash = new IdentityHashMap<Species, Species>();
            Vector<BioModelEntityObject> pastedSpeciesContextV = new Vector<BioModelEntityObject>();
            for (int i = 0; i < reactionSpeciesCopy.getSpeciesContextArr().length; i++) {
                String rootSC = speciesContextRootFinder(reactionSpeciesCopy.getSpeciesContextArr()[i]);
                pastedSpeciesContextV.add(pasteSpecies(getGraphPane(), reactionSpeciesCopy.getSpeciesContextArr()[i].getSpecies(), rootSC, getModel(), structure, true, speciesHash, null));
                copyRelativePosition(getGraphModel(), reactionSpeciesCopy.getSpeciesContextArr()[i], pastedSpeciesContextV.lastElement());
            }
            ReactionCartoonTool.selectAndSaveDiagram(ReactionCartoonTool.this, pastedSpeciesContextV);
        }
        if (reactionSpeciesCopy.getReactStepArr() != null && reactionSpeciesCopy.getReactionRuleArr() == null && (response == null || response.equals(RXSPECIES_PASTERX))) {
            pasteReactionSteps(getGraphPane(), reactionSpeciesCopy.getReactStepArr(), getModel(), structure, true, null, ReactionCartoonTool.this);
        } else if (reactionSpeciesCopy.getReactionRuleArr() != null && (response == null || response.equals(RXSPECIES_PASTERX))) {
            pasteReactionsAndRules(getGraphPane(), reactionSpeciesCopy, getModel(), structure, ReactionCartoonTool.this);
        }
    // try {
    // for(MolecularType mtOurs : mtNewList) {
    // rbmmcOurs.addMolecularType(mtOurs, false);
    // }
    // } catch (ModelException | PropertyVetoException e) {
    // e.printStackTrace();
    // }
    // 
    // // ReactionRules
    // if(reactionSpeciesCopy.getReactionRuleArr() != null) {
    // for(ReactionRule rrTheirs : reactionSpeciesCopy.getReactionRuleArr()) {
    // 
    // }
    // }
    }
}