Examples with BioEvent cbit.vcell.mapping.BioEvent used on opensource projects

Example 16 with BioEvent

use of cbit.vcell.mapping.BioEvent 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 AssignmentRule) {
            AssignmentRule ar = (AssignmentRule) object;
            SimulationContext sc = ar.getSimulationContext();
            followHyperlink(new ActiveView(sc, DocumentEditorTreeFolderClass.PROTOCOLS_NODE, ActiveViewID.assignmentRules), new Object[] { ar });
        } else if (object instanceof RateRule) {
            RateRule rr = (RateRule) object;
            SimulationContext sc = rr.getSimulationContext();
            followHyperlink(new ActiveView(sc, DocumentEditorTreeFolderClass.PROTOCOLS_NODE, ActiveViewID.rateRules), new Object[] { rr });
        } 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, nc.getMaxMoleculesPerSpecies() + "", NetworkTransformer.defaultMaxMoleculesPerSpecies + "");
                        followHyperlink(new ActiveView(sc, DocumentEditorTreeFolderClass.SPECIFICATIONS_NODE, ActiveViewID.network_setting), new Object[] { nce });
                    } else {
                        NetworkConstraintsEntity nce = new NetworkConstraintsEntity(NetworkConstraintsTableModel.sMaxIterationName, nc.getMaxIteration() + "", NetworkTransformer.defaultMaxIteration + "");
                        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 17 with BioEvent

use of cbit.vcell.mapping.BioEvent in project vcell by virtualcell.

the class AssignmentRulesSummaryTableModel method updateSubdomainComboBox.

private void updateSubdomainComboBox() {
    if (steComboBox == null) {
        steComboBox = new JComboBox<>();
    }
    if (simulationContext == null) {
        return;
    }
    SpeciesContext[] scs = simulationContext.getModel().getSpeciesContexts();
    ModelParameter[] mps = simulationContext.getModel().getModelParameters();
    DefaultComboBoxModel<String> aModel = new DefaultComboBoxModel<>();
    for (SpeciesContext sc : scs) {
        aModel.addElement(sc.getName());
    }
    for (ModelParameter mp : mps) {
        aModel.addElement(mp.getName());
    }
    steComboBox.addFocusListener(new java.awt.event.FocusAdapter() {

        @Override
        public void focusGained(java.awt.event.FocusEvent evt) {
            DefaultComboBoxModel<String> aModel = (DefaultComboBoxModel<String>) steComboBox.getModel();
            SpeciesContext[] scs = simulationContext.getModel().getSpeciesContexts();
            ModelParameter[] mps = simulationContext.getModel().getModelParameters();
            for (SpeciesContext sc : scs) {
                int position = aModel.getIndexOf(sc.getName());
                if (position == -1) {
                    // element is missing, add it
                    aModel.addElement(sc.getName());
                }
            }
            for (ModelParameter mp : mps) {
                int position = aModel.getIndexOf(mp.getName());
                if (position == -1) {
                    aModel.addElement(mp.getName());
                }
            }
            Set<String> elementsToRemove = new HashSet<>();
            for (int i = 0; i < aModel.getSize(); i++) {
                String candidate = aModel.getElementAt(i);
                SpeciesContext sc = simulationContext.getModel().getSpeciesContext(candidate);
                ModelParameter mp = simulationContext.getModel().getModelParameter(candidate);
                if (sc == null && mp == null) {
                    elementsToRemove.add(candidate);
                }
                if (sc != null && simulationContext.getRateRule(sc) != null) {
                    elementsToRemove.add(candidate);
                    continue;
                }
                if (mp != null && simulationContext.getRateRule(mp) != null) {
                    elementsToRemove.add(candidate);
                    continue;
                }
                if (simulationContext.getBioEvents() == null) {
                    continue;
                }
                boolean found = false;
                for (BioEvent event : simulationContext.getBioEvents()) {
                    ArrayList<EventAssignment> eas = event.getEventAssignments();
                    if (eas == null) {
                        continue;
                    }
                    for (EventAssignment ea : eas) {
                        if (ea.getTarget() != null && candidate.contentEquals(ea.getTarget().getName())) {
                            found = true;
                            break;
                        }
                    }
                    if (found) {
                        break;
                    }
                }
                if (found) {
                    elementsToRemove.add(candidate);
                    continue;
                }
            }
            for (String candidate : elementsToRemove) {
                aModel.removeElement(candidate);
            }
        }
    });
    steComboBox.setRenderer(new DefaultListCellRenderer() {

        @Override
        public Component getListCellRendererComponent(JList<?> list, Object value, int index, boolean isSelected, boolean cellHasFocus) {
            super.getListCellRendererComponent(list, value, index, isSelected, cellHasFocus);
            setHorizontalTextPosition(SwingConstants.LEFT);
            if (value == null) {
                setText("");
            } else if (value instanceof String) {
                setText((String) value);
            } else {
                setText(value.toString());
                System.out.println("not String");
            }
            return this;
        }
    });
    steComboBox.setModel(aModel);
    ownerTable.getColumnModel().getColumn(COLUMN_ASSIGNMENTRULE_VAR).setCellEditor(new DefaultCellEditor(steComboBox));
}

Example 18 with BioEvent

use of cbit.vcell.mapping.BioEvent in project vcell by virtualcell.

the class EventsSummaryTableModel method propertyChange.

@Override
public void propertyChange(java.beans.PropertyChangeEvent evt) {
    super.propertyChange(evt);
    // } else
    if (evt.getPropertyName().equals("trigger") || evt.getPropertyName().equals("delay") || evt.getPropertyName().equals("eventAssignments")) {
        fireTableRowsUpdated(0, getRowCount() - 1);
    } else {
        if (evt.getPropertyName().equals("bioevents")) {
            BioEvent[] oldValue = (BioEvent[]) evt.getOldValue();
            if (oldValue != null) {
                for (BioEvent be : oldValue) {
                    be.removePropertyChangeListener(this);
                }
            }
            BioEvent[] newValue = (BioEvent[]) evt.getNewValue();
            if (newValue != null) {
                for (BioEvent be : newValue) {
                    be.addPropertyChangeListener(this);
                }
            }
        }
        refreshData();
    }
}

Example 19 with BioEvent

use of cbit.vcell.mapping.BioEvent in project vcell by virtualcell.

the class EventsSummaryTableModel method computeData.

protected List<BioEvent> computeData() {
    if (simulationContext == null || simulationContext.getBioEvents() == null) {
        return null;
    }
    List<BioEvent> bioEventList = new ArrayList<BioEvent>();
    for (BioEvent bioEvent : simulationContext.getBioEvents()) {
        if (searchText == null || searchText.length() == 0) {
            bioEventList.add(bioEvent);
        } else {
            String lowerCaseSearchText = searchText.toLowerCase();
            try {
                Expression delayExp = bioEvent.getParameter(BioEventParameterType.TriggerDelay).getExpression();
                Expression generatedTriggerExp = bioEvent.generateTriggerExpression();
                if (bioEvent.getName().toLowerCase().contains(lowerCaseSearchText) || generatedTriggerExp.infix().toLowerCase().contains(lowerCaseSearchText) || delayExp != null && delayExp.infix().toLowerCase().contains(lowerCaseSearchText)) {
                    bioEventList.add(bioEvent);
                }
            } catch (ExpressionException e) {
                e.printStackTrace();
                throw new RuntimeException(this.getClass().getSimpleName() + ".computeData() error: " + e.getMessage(), e);
            }
        }
    }
    return bioEventList;
}

Example 20 with BioEvent

use of cbit.vcell.mapping.BioEvent in project vcell by virtualcell.

the class Xmlproducer method getXML.

// For events in SimulationContext - XML is very similar to math events
public Element getXML(BioEvent[] bioEvents) throws XmlParseException {
    Element bioEventsElement = new Element(XMLTags.BioEventsTag);
    for (int i = 0; i < bioEvents.length; i++) {
        Element eventElement = new Element(XMLTags.BioEventTag);
        eventElement.setAttribute(XMLTags.NameAttrTag, mangle(bioEvents[i].getName()));
        String triggerType = bioEvents[i].getTriggerType().getXmlName();
        // Add atributes
        eventElement.setAttribute(XMLTags.BioEventTriggerTypeAttrTag, triggerType);
        eventElement.setAttribute(XMLTags.UseValuesFromTriggerTimeAttrTag, Boolean.toString(bioEvents[i].getUseValuesFromTriggerTime()));
        // Add BioEvent Parameters
        LocalParameter[] parameters = bioEvents[i].getEventParameters();
        for (LocalParameter parm : parameters) {
            if (parm.getExpression() != null) {
                Element tempparameter = new Element(XMLTags.ParameterTag);
                // Get parameter attributes
                tempparameter.setAttribute(XMLTags.NameAttrTag, mangle(parm.getName()));
                tempparameter.setAttribute(XMLTags.ParamRoleAttrTag, bioEvents[i].getParameterType(parm).getRoleXmlName());
                VCUnitDefinition unit = parm.getUnitDefinition();
                if (unit != null) {
                    tempparameter.setAttribute(XMLTags.VCUnitDefinitionAttrTag, unit.getSymbol());
                }
                tempparameter.addContent(mangleExpression(parm.getExpression()));
                // Add the parameter to the general kinetics object
                eventElement.addContent(tempparameter);
            }
        }
        ArrayList<BioEvent.EventAssignment> eventAssignmentsList = bioEvents[i].getEventAssignments();
        if (eventAssignmentsList != null) {
            for (BioEvent.EventAssignment eventAssignment : eventAssignmentsList) {
                Element eventAssignmentElement = new Element(XMLTags.EventAssignmentTag);
                eventAssignmentElement.setAttribute(XMLTags.EventAssignmentVariableAttrTag, eventAssignment.getTarget().getName());
                eventAssignmentElement.addContent(mangleExpression(eventAssignment.getAssignmentExpression()));
                eventElement.addContent(eventAssignmentElement);
            }
        }
        bioEventsElement.addContent(eventElement);
    }
    System.out.println(XmlUtil.xmlToString(bioEventsElement));
    return bioEventsElement;
}