Examples with MolecularType org.vcell.model.rbm.MolecularType used on opensource projects

Example 61 with MolecularType

use of org.vcell.model.rbm.MolecularType in project vcell by virtualcell.

the class ReactionRulePropertiesTreeModel method createMolecularTypePatternNode.

private BioModelNode createMolecularTypePatternNode(MolecularTypePattern molecularTypePattern) {
    MolecularType molecularType = molecularTypePattern.getMolecularType();
    BioModelNode node = new BioModelNode(molecularTypePattern, true);
    if (molecularTypePattern.hasExplicitParticipantMatch()) {
        ParticipantMatchLabelLocal pmll = new ParticipantMatchLabelLocal(molecularTypePattern.getParticipantMatchLabel());
        BioModelNode nm = new BioModelNode(pmll, true);
        node.add(nm);
    }
    for (MolecularComponent mc : molecularType.getComponentList()) {
        // dead code, we don't show state and bond
        if (bShowDetails || molecularTypePattern.getMolecularComponentPattern(mc).isbVisible()) {
            BioModelNode n = createMolecularComponentPatternNode(molecularTypePattern.getMolecularComponentPattern(mc));
            if (n != null) {
                node.add(n);
            }
        }
    }
    return node;
}

Example 62 with MolecularType

use of org.vcell.model.rbm.MolecularType in project vcell by virtualcell.

the class IssuePanel method invokeHyperlink.

private void invokeHyperlink(Issue issue) {
    if (selectionManager != null) {
        // followHyperlink is no-op if selectionManger null, so no point in proceeding if it is
        IssueContext issueContext = issue.getIssueContext();
        IssueSource object = issue.getSource();
        if (object instanceof DecoratedIssueSource) {
            DecoratedIssueSource dis = (DecoratedIssueSource) object;
            dis.activateView(selectionManager);
        } else if (object instanceof Parameter) {
            followHyperlink(new ActiveView(null, DocumentEditorTreeFolderClass.BIOMODEL_PARAMETERS_NODE, ActiveViewID.parameters_functions), new Object[] { object });
        } else if (object instanceof StructureMapping) {
            StructureMapping structureMapping = (StructureMapping) object;
            StructureMappingNameScope structureMappingNameScope = (StructureMappingNameScope) structureMapping.getNameScope();
            SimulationContext simulationContext = ((SimulationContextNameScope) (structureMappingNameScope.getParent())).getSimulationContext();
            followHyperlink(new ActiveView(simulationContext, DocumentEditorTreeFolderClass.GEOMETRY_NODE, ActiveViewID.structure_mapping), new Object[] { object });
        } else if (object instanceof SpatialObject) {
            SpatialObject spatialObject = (SpatialObject) object;
            SimulationContext simulationContext = spatialObject.getSimulationContext();
            followHyperlink(new ActiveView(simulationContext, DocumentEditorTreeFolderClass.GEOMETRY_NODE, ActiveViewID.spatial_objects), new Object[] { object });
        } else if (object instanceof SpatialProcess) {
            SpatialProcess spatialProcess = (SpatialProcess) object;
            SimulationContext simulationContext = spatialProcess.getSimulationContext();
            followHyperlink(new ActiveView(simulationContext, DocumentEditorTreeFolderClass.GEOMETRY_NODE, ActiveViewID.spatial_processes), new Object[] { object });
        } else if (object instanceof GeometryContext.UnmappedGeometryClass) {
            UnmappedGeometryClass unmappedGeometryClass = (UnmappedGeometryClass) object;
            SimulationContext simulationContext = unmappedGeometryClass.getSimulationContext();
            followHyperlink(new ActiveView(simulationContext, DocumentEditorTreeFolderClass.GEOMETRY_NODE, ActiveViewID.structure_mapping), new Object[] { object });
        } else if (object instanceof MicroscopeMeasurement) {
            SimulationContext simulationContext = ((MicroscopeMeasurement) object).getSimulationContext();
            followHyperlink(new ActiveView(simulationContext, DocumentEditorTreeFolderClass.PROTOCOLS_NODE, ActiveViewID.microscope_measuremments), new Object[] { object });
        } else if (object instanceof BioEvent) {
            BioEvent be = (BioEvent) object;
            SimulationContext simulationContext = be.getSimulationContext();
            followHyperlink(new ActiveView(simulationContext, DocumentEditorTreeFolderClass.PROTOCOLS_NODE, ActiveViewID.events), new Object[] { object });
        } else if (object instanceof OutputFunctionIssueSource) {
            SimulationOwner simulationOwner = ((OutputFunctionIssueSource) object).getOutputFunctionContext().getSimulationOwner();
            if (simulationOwner instanceof SimulationContext) {
                SimulationContext simulationContext = (SimulationContext) simulationOwner;
                followHyperlink(new ActiveView(simulationContext, DocumentEditorTreeFolderClass.SIMULATIONS_NODE, ActiveViewID.output_functions), new Object[] { ((OutputFunctionIssueSource) object).getAnnotatedFunction() });
            } else if (simulationOwner instanceof MathModel) {
                followHyperlink(new ActiveView(null, DocumentEditorTreeFolderClass.MATH_OUTPUT_FUNCTIONS_NODE, ActiveViewID.math_output_functions), new Object[] { ((OutputFunctionIssueSource) object).getAnnotatedFunction() });
            }
        } else if (object instanceof Simulation) {
            Simulation simulation = (Simulation) object;
            SimulationOwner simulationOwner = simulation.getSimulationOwner();
            if (simulationOwner instanceof SimulationContext) {
                SimulationContext simulationContext = (SimulationContext) simulationOwner;
                followHyperlink(new ActiveView(simulationContext, DocumentEditorTreeFolderClass.SIMULATIONS_NODE, ActiveViewID.simulations), new Object[] { simulation });
            } else if (simulationOwner instanceof MathModel) {
                followHyperlink(new ActiveView(null, DocumentEditorTreeFolderClass.MATH_SIMULATIONS_NODE, ActiveViewID.math_simulations), new Object[] { simulation });
            }
        } else if (object instanceof GeometryContext) {
            setActiveView(new ActiveView(((GeometryContext) object).getSimulationContext(), DocumentEditorTreeFolderClass.GEOMETRY_NODE, ActiveViewID.geometry_definition));
        } else if (object instanceof Structure) {
            followHyperlink(new ActiveView(null, DocumentEditorTreeFolderClass.STRUCTURES_NODE, ActiveViewID.structures), new Object[] { object });
        } else if (object instanceof MolecularType) {
            followHyperlink(new ActiveView(null, DocumentEditorTreeFolderClass.MOLECULAR_TYPES_NODE, ActiveViewID.structures), new Object[] { object });
        } else if (object instanceof ReactionStep) {
            followHyperlink(new ActiveView(null, DocumentEditorTreeFolderClass.REACTIONS_NODE, ActiveViewID.reactions), new Object[] { object });
        } else if (object instanceof ReactionRule) {
            followHyperlink(new ActiveView(null, DocumentEditorTreeFolderClass.REACTIONS_NODE, ActiveViewID.reactions), new Object[] { object });
        } else if (object instanceof SpeciesContextSpec) {
            SpeciesContextSpec scs = (SpeciesContextSpec) object;
            ActiveView av = new ActiveView(scs.getSimulationContext(), DocumentEditorTreeFolderClass.SPECIFICATIONS_NODE, ActiveViewID.species_settings);
            followHyperlink(av, new Object[] { object });
        } else if (object instanceof ReactionCombo) {
            ReactionCombo rc = (ReactionCombo) object;
            followHyperlink(new ActiveView(rc.getReactionContext().getSimulationContext(), DocumentEditorTreeFolderClass.SPECIFICATIONS_NODE, ActiveViewID.reaction_setting), new Object[] { ((ReactionCombo) object).getReactionSpec() });
        } else if (object instanceof SpeciesContext) {
            followHyperlink(new ActiveView(null, DocumentEditorTreeFolderClass.SPECIES_NODE, ActiveViewID.species), new Object[] { object });
        } else if (object instanceof RbmObservable) {
            followHyperlink(new ActiveView(null, DocumentEditorTreeFolderClass.OBSERVABLES_NODE, ActiveViewID.observables), new Object[] { object });
        } else if (object instanceof MathDescription) {
            // followHyperlink(new ActiveView(null, DocumentEditorTreeFolderClass.MATH_SIMULATIONS_NODE, ActiveViewID.generated_math), new Object[] {object});
            followHyperlink(new ActiveView(null, DocumentEditorTreeFolderClass.GEOMETRY_NODE, ActiveViewID.structure_mapping), new Object[] { object });
        } else if (object instanceof SpeciesPattern) {
            // if (issue.getIssueContext().hasContextType(ContextType.SpeciesContext)){
            // SpeciesContext thing = (SpeciesContext)issue.getIssueContext().getContextObject(ContextType.SpeciesContext);
            // followHyperlink(new ActiveView(null, DocumentEditorTreeFolderClass.SPECIES_NODE, ActiveViewID.species), new Object[] {thing});
            // }else if(issue.getIssueContext().hasContextType(ContextType.ReactionRule)) {
            // ReactionRule thing = (ReactionRule)issue.getIssueContext().getContextObject(ContextType.ReactionRule);
            // followHyperlink(new ActiveView(null, DocumentEditorTreeFolderClass.REACTIONS_NODE, ActiveViewID.reactions), new Object[] {thing});
            // }else if(issue.getIssueContext().hasContextType(ContextType.RbmObservable)) {
            // RbmObservable thing = (RbmObservable)issue.getIssueContext().getContextObject(ContextType.RbmObservable);
            // followHyperlink(new ActiveView(null, DocumentEditorTreeFolderClass.OBSERVABLES_NODE, ActiveViewID.observables), new Object[] {thing});
            // } else {
            System.err.println("SpeciesPattern object missing a proper issue context.");
        // }
        } else if (object instanceof SimulationContext) {
            SimulationContext sc = (SimulationContext) object;
            IssueCategory ic = issue.getCategory();
            switch(ic) {
                case RbmNetworkConstraintsBad:
                    NetworkConstraints nc = sc.getNetworkConstraints();
                    if (issue.getMessage() == SimulationContext.IssueInsufficientMolecules) {
                        NetworkConstraintsEntity nce = new NetworkConstraintsEntity(NetworkConstraintsTableModel.sMaxMoleculesName, NetworkConstraintsTableModel.sValueType, nc.getMaxMoleculesPerSpecies() + "");
                        followHyperlink(new ActiveView(sc, DocumentEditorTreeFolderClass.SPECIFICATIONS_NODE, ActiveViewID.network_setting), new Object[] { nce });
                    } else {
                        NetworkConstraintsEntity nce = new NetworkConstraintsEntity(NetworkConstraintsTableModel.sMaxIterationName, NetworkConstraintsTableModel.sValueType, nc.getMaxIteration() + "");
                        followHyperlink(new ActiveView(sc, DocumentEditorTreeFolderClass.SPECIFICATIONS_NODE, ActiveViewID.network_setting), new Object[] { nce });
                    }
                    break;
                default:
                    followHyperlink(new ActiveView(sc, DocumentEditorTreeFolderClass.SPECIFICATIONS_NODE, ActiveViewID.network_setting), new Object[] { object });
                    break;
            }
        } else if (object instanceof Geometry) {
            if (issueContext.hasContextType(ContextType.SimContext)) {
                SimulationContext simContext = (SimulationContext) issueContext.getContextObject(ContextType.SimContext);
                followHyperlink(new ActiveView(simContext, DocumentEditorTreeFolderClass.GEOMETRY_NODE, ActiveViewID.geometry_definition), new Object[] { object });
            } else if (issueContext.hasContextType(ContextType.MathModel)) {
                followHyperlink(new ActiveView(null, DocumentEditorTreeFolderClass.MATH_GEOMETRY_NODE, ActiveViewID.math_geometry), new Object[] { object });
            } else if (issueContext.hasContextType(ContextType.MathDescription)) {
                followHyperlink(new ActiveView(null, DocumentEditorTreeFolderClass.GEOMETRY_NODE, ActiveViewID.geometry_definition), new Object[] { object });
            }
        } else {
            System.err.println("unknown object type in IssuePanel.invokeHyperlink(): " + object.getClass() + ", context type: " + issueContext.getContextType());
        }
    }
}

Example 63 with MolecularType

use of org.vcell.model.rbm.MolecularType in project vcell by virtualcell.

the class MolecularTypePropertiesPanel method setMolecularType.

private void setMolecularType(MolecularType newValue) {
    if (molecularType == newValue) {
        return;
    }
    MolecularType oldValue = molecularType;
    if (oldValue != null) {
        oldValue.removePropertyChangeListener(eventHandler);
        oldValue.removePropertyChangeListener(molecularTypeTreeModel);
    }
    if (newValue != null) {
        newValue.addPropertyChangeListener(eventHandler);
        newValue.addPropertyChangeListener(molecularTypeTreeModel);
    }
    molecularType = newValue;
    molecularTypeTreeModel.setMolecularType(molecularType);
    updateInterface();
}

Example 64 with MolecularType

use of org.vcell.model.rbm.MolecularType in project vcell by virtualcell.

the class MolecularTypePropertiesPanel method deleteFromTree.

public void deleteFromTree() {
    Object obj = molecularTypeTree.getLastSelectedPathComponent();
    if (obj == null || !(obj instanceof BioModelNode)) {
        return;
    }
    BioModelNode selectedNode = (BioModelNode) obj;
    TreeNode parent = selectedNode.getParent();
    if (!(parent instanceof BioModelNode)) {
        return;
    }
    BioModelNode parentNode = (BioModelNode) parent;
    Object selectedUserObject = selectedNode.getUserObject();
    if (selectedUserObject instanceof MolecularComponent) {
        MolecularComponent mc = (MolecularComponent) selectedUserObject;
        Object userObject = parentNode.getUserObject();
        if (userObject instanceof MolecularType) {
            MolecularType mt = (MolecularType) userObject;
            // detailed verifications will be done there, to see if they are being used in reactions, species, observables
            if (!mc.getComponentStateDefinitions().isEmpty()) {
                String[] options = { "OK" };
                String errMsg = mc.getDisplayType() + " '<b>" + mc.getDisplayName() + "</b>' cannot be deleted because it contains explicit States.";
                errMsg += "<br>Please delete each individual State first.";
                errMsg += "<br><br>Detailed usage information will be provided at that time to help you decide.";
                errMsg = "<html>" + errMsg + "</html>";
                JOptionPane.showOptionDialog(this.getParent().getParent(), errMsg, "Delete " + mc.getDisplayType(), JOptionPane.NO_OPTION, JOptionPane.WARNING_MESSAGE, null, options, options[0]);
                return;
            }
            // we find and display component usage information to help the user decide
            Map<String, Pair<Displayable, SpeciesPattern>> usedHere = new LinkedHashMap<String, Pair<Displayable, SpeciesPattern>>();
            bioModel.getModel().getRbmModelContainer().findComponentUsage(mt, mc, usedHere);
            if (!usedHere.isEmpty()) {
                String errMsg = mc.dependenciesToHtml(usedHere);
                errMsg += "<br><br>Delete anyway?";
                errMsg = "<html>" + errMsg + "</html>";
                int dialogButton = JOptionPane.YES_NO_OPTION;
                int returnCode = JOptionPane.showConfirmDialog(this.getParent().getParent(), errMsg, "Delete " + mc.getDisplayType(), dialogButton);
                if (returnCode == JOptionPane.YES_OPTION) {
                    // keep this code in sync with MolecularTypeTableModel.setValueAt
                    if (bioModel.getModel().getRbmModelContainer().delete(mt, mc) == true) {
                        mt.removeMolecularComponent(mc);
                    }
                } else {
                    return;
                }
            } else {
                if (bioModel.getModel().getRbmModelContainer().delete(mt, mc) == true) {
                    mt.removeMolecularComponent(mc);
                }
            }
        }
    } else if (selectedUserObject instanceof ComponentStateDefinition) {
        ComponentStateDefinition csd = (ComponentStateDefinition) selectedUserObject;
        Object userObject = parentNode.getUserObject();
        if (!(userObject instanceof MolecularComponent)) {
            System.out.println("Unexpected parent in tree hierarchy for " + ComponentStateDefinition.typeName + " " + csd.getDisplayName() + "!");
            return;
        }
        MolecularComponent mc = (MolecularComponent) userObject;
        TreeNode grandParent = parentNode.getParent();
        BioModelNode grandParentNode = (BioModelNode) grandParent;
        userObject = grandParentNode.getUserObject();
        if (!(userObject instanceof MolecularType)) {
            System.out.println("Unexpected parent in tree hierarchy for " + mc.getDisplayType() + " " + mc.getDisplayName() + "!");
            return;
        }
        MolecularType mt = (MolecularType) userObject;
        Map<String, Pair<Displayable, SpeciesPattern>> usedHere = new LinkedHashMap<String, Pair<Displayable, SpeciesPattern>>();
        bioModel.getModel().getRbmModelContainer().findStateUsage(mt, mc, csd, usedHere);
        if (!usedHere.isEmpty()) {
            String errMsg = csd.dependenciesToHtml(usedHere);
            errMsg += "<br><br>Delete anyway?";
            errMsg = "<html>" + errMsg + "</html>";
            int dialogButton = JOptionPane.YES_NO_OPTION;
            int returnCode = JOptionPane.showConfirmDialog(this.getParent().getParent(), errMsg, "Delete " + ComponentStateDefinition.typeName, dialogButton);
            if (returnCode == JOptionPane.YES_OPTION) {
                // keep this code in sync with MolecularTypeTableModel.setValueAt
                if (bioModel.getModel().getRbmModelContainer().delete(mt, mc, csd) == true) {
                    // this stays
                    mc.deleteComponentStateDefinition(csd);
                }
            } else {
                return;
            }
        } else {
            if (bioModel.getModel().getRbmModelContainer().delete(mt, mc, csd) == true) {
                // this stays
                mc.deleteComponentStateDefinition(csd);
            }
        }
    // mc.deleteComponentStateDefinition(csd);
    }
}

Example 65 with MolecularType

use of org.vcell.model.rbm.MolecularType in project vcell by virtualcell.

the class MolecularTypeTableModel method computeData.

@Override
protected List<MolecularType> computeData() {
    if (getModel() == null) {
        return new ArrayList<MolecularType>();
    }
    List<MolecularType> mtList;
    if (searchText == null || searchText.length() == 0) {
        mtList = new ArrayList<MolecularType>(getModel().getRbmModelContainer().getMolecularTypeList());
    } else {
        mtList = new ArrayList<MolecularType>();
        String lowerCaseSearchText = searchText.toLowerCase();
        for (MolecularType mt : getModel().getRbmModelContainer().getMolecularTypeList()) {
            boolean bMatchRelationshipObj = false;
            HashSet<RelationshipObject> relObjsHash = bioModel.getRelationshipModel().getRelationshipObjects(mt);
            for (RelationshipObject relObj : relObjsHash) {
                if (relObj.getBioPaxObject() instanceof Entity) {
                    if (((Entity) relObj.getBioPaxObject()).getName().get(0).toLowerCase().contains(lowerCaseSearchText)) {
                        bMatchRelationshipObj = true;
                        break;
                    }
                }
            }
            String expression = pattern(mt);
            if (expression != null && expression.toLowerCase().contains(lowerCaseSearchText)) {
                mtList.add(mt);
            }
        }
    }
    return mtList;
}