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

Example 6 with AssignmentRule

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

the class IssueTableModel method getSourceObjectPathDescription.

private String getSourceObjectPathDescription(VCDocument vcDocument, Issue issue) {
    VCAssert.assertValid(issue);
    Object source = issue.getSource();
    {
        IssueOrigin io = BeanUtils.downcast(IssueOrigin.class, source);
        if (io != null) {
            return io.getDescription();
        }
    }
    if (vcDocument instanceof BioModel) {
        BioModel bioModel = (BioModel) vcDocument;
        String description = "";
        if (source instanceof SymbolTableEntry) {
            if (source instanceof SpeciesContext) {
                description = "Model / Species";
            } else if (source instanceof RbmObservable) {
                description = "Model / Observables";
            } else {
                description = ((SymbolTableEntry) source).getNameScope().getPathDescription();
            }
        } else if (source instanceof MolecularType) {
            description = "Model / Molecules";
        } else if (source instanceof ReactionStep) {
            ReactionStep reactionStep = (ReactionStep) source;
            description = ((ReactionNameScope) reactionStep.getNameScope()).getPathDescription();
        } else if (source instanceof ReactionRule) {
            ReactionRule reactionRule = (ReactionRule) source;
            description = ((ReactionRuleNameScope) reactionRule.getNameScope()).getPathDescription();
        } else if (source instanceof SpeciesPattern) {
            // if (issue.getIssueContext().hasContextType(ContextType.SpeciesContext)){
            // description = "Model / Species";
            // }else if(issue.getIssueContext().hasContextType(ContextType.ReactionRule)) {
            // ReactionRule thing = (ReactionRule)issue.getIssueContext().getContextObject(ContextType.ReactionRule);
            // description = ((ReactionRuleNameScope)thing.getNameScope()).getPathDescription();
            // }else if(issue.getIssueContext().hasContextType(ContextType.RbmObservable)) {
            // description = "Model / Observables";
            // } else {
            System.err.println("Bad issue context for " + ((SpeciesPattern) source).toString());
            description = ((SpeciesPattern) source).toString();
        // }
        } else if (source instanceof Structure) {
            Structure structure = (Structure) source;
            description = "Model / " + structure.getTypeName() + "(" + structure.getName() + ")";
        } else if (source instanceof StructureMapping) {
            StructureMapping structureMapping = (StructureMapping) source;
            description = ((StructureMappingNameScope) structureMapping.getNameScope()).getPathDescription();
        } else if (source instanceof OutputFunctionIssueSource) {
            SimulationContext simulationContext = (SimulationContext) ((OutputFunctionIssueSource) source).getOutputFunctionContext().getSimulationOwner();
            description = "App(" + simulationContext.getName() + ") / " + "Simulations" + " / " + "Output Functions";
        } else if (source instanceof RateRule) {
            SimulationContext simulationContext = ((RateRule) source).getSimulationContext();
            description = "App(" + simulationContext.getName() + ") / " + "Protocols / " + RateRule.typeName;
        } else if (source instanceof AssignmentRule) {
            SimulationContext simulationContext = ((AssignmentRule) source).getSimulationContext();
            description = "App(" + simulationContext.getName() + ") / " + "Protocols / " + AssignmentRule.typeName;
        } else if (source instanceof Simulation) {
            Simulation simulation = (Simulation) source;
            try {
                SimulationContext simulationContext = bioModel.getSimulationContext(simulation);
                description = "App(" + simulationContext.getName() + ") / Simulations";
            } catch (ObjectNotFoundException e) {
                e.printStackTrace();
                description = "App(" + "unknown" + ") / Simulations";
            }
        } else if (source instanceof UnmappedGeometryClass) {
            UnmappedGeometryClass unmappedGC = (UnmappedGeometryClass) source;
            description = "App(" + unmappedGC.getSimulationContext().getName() + ") / Subdomain(" + unmappedGC.getGeometryClass().getName() + ")";
        } else if (source instanceof GeometryContext) {
            description = "App(" + ((GeometryContext) source).getSimulationContext().getName() + ")";
        } else if (source instanceof ModelOptimizationSpec) {
            description = "App(" + ((ModelOptimizationSpec) source).getSimulationContext().getName() + ") / Parameter Estimation";
        } else if (source instanceof MicroscopeMeasurement) {
            description = "App(" + ((MicroscopeMeasurement) source).getSimulationContext().getName() + ") / Microscope Measurements";
        } else if (source instanceof SpatialObject) {
            description = "App(" + ((SpatialObject) source).getSimulationContext().getName() + ") / Spatial Objects";
        } else if (source instanceof SpatialProcess) {
            description = "App(" + ((SpatialProcess) source).getSimulationContext().getName() + ") / Spatial Processes";
        } else if (source instanceof SpeciesContextSpec) {
            SpeciesContextSpec scs = (SpeciesContextSpec) source;
            description = "App(" + scs.getSimulationContext().getName() + ") / Specifications / Species";
        } else if (source instanceof ReactionCombo) {
            ReactionCombo rc = (ReactionCombo) source;
            description = "App(" + rc.getReactionContext().getSimulationContext().getName() + ") / Specifications / Reactions";
        } else if (source instanceof RbmModelContainer) {
            IssueCategory ic = issue.getCategory();
            switch(ic) {
                case RbmMolecularTypesTableBad:
                    description = "Model / " + MolecularType.typeName + "s";
                    break;
                case RbmReactionRulesTableBad:
                    description = "Model / Reactions";
                    break;
                case RbmObservablesTableBad:
                    description = "Model / Observables";
                    break;
                case RbmNetworkConstraintsBad:
                    description = "Network Constrains";
                    break;
                default:
                    description = "Model";
                    break;
            }
        } else if (source instanceof SimulationContext) {
            SimulationContext sc = (SimulationContext) source;
            IssueCategory ic = issue.getCategory();
            switch(ic) {
                case RbmNetworkConstraintsBad:
                    description = "Specifications / Network";
                    break;
                default:
                    description = "Application";
                    break;
            }
        } else if (source instanceof Model) {
            description = "Model";
        } else if (source instanceof BioEvent) {
            return "Protocols / Events";
        } else if (source instanceof MathDescription) {
            return "Math Description";
        } else {
            System.err.println("unknown source type in IssueTableModel.getSourceObjectPathDescription(): " + source.getClass());
        }
        return description;
    } else if (vcDocument instanceof MathModel) {
        if (source instanceof Geometry) {
            return GuiConstants.DOCUMENT_EDITOR_FOLDERNAME_MATH_GEOMETRY;
        } else if (source instanceof OutputFunctionIssueSource) {
            return GuiConstants.DOCUMENT_EDITOR_FOLDERNAME_MATH_OUTPUTFUNCTIONS;
        } else if (source instanceof Simulation) {
            return "Simulation(" + ((Simulation) source).getName() + ")";
        } else {
            return GuiConstants.DOCUMENT_EDITOR_FOLDERNAME_MATH_VCML;
        }
    } else {
        System.err.println("unknown document type in IssueTableModel.getSourceObjectPathDescription()");
        return "";
    }
}

Example 7 with AssignmentRule

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

the class InitialConditionsPanel method initialize.

/**
 * Initialize the class.
 */
/* WARNING: THIS METHOD WILL BE REGENERATED. */
private void initialize() {
    try {
        // user code begin {1}
        // user code end
        setName("InitialConditionsPanel");
        setLayout(new BorderLayout());
        add(getRadioButtonAndCheckboxPanel(), BorderLayout.NORTH);
        add(getScrollPaneTable().getEnclosingScrollPane(), BorderLayout.CENTER);
        getScrollPaneTable().getSelectionModel().addListSelectionListener(ivjEventHandler);
        getJMenuItemPaste().addActionListener(ivjEventHandler);
        getJMenuItemCopy().addActionListener(ivjEventHandler);
        getJMenuItemCopyAll().addActionListener(ivjEventHandler);
        getJMenuItemPasteAll().addActionListener(ivjEventHandler);
        getAmountRadioButton().addActionListener(ivjEventHandler);
        getConcentrationRadioButton().addActionListener(ivjEventHandler);
        getRandomizeInitCondnCheckbox().addActionListener(ivjEventHandler);
        DefaultTableCellRenderer renderer = new DefaultScrollTableCellRenderer() {

            public Component getTableCellRendererComponent(JTable table, Object value, boolean isSelected, boolean hasFocus, int row, int column) {
                super.getTableCellRendererComponent(table, value, isSelected, hasFocus, row, column);
                setIcon(null);
                defaultToolTipText = null;
                if (value instanceof Species) {
                    setText(((Species) value).getCommonName());
                    defaultToolTipText = getText();
                    setToolTipText(defaultToolTipText);
                } else if (value instanceof SpeciesContext) {
                    setText(((SpeciesContext) value).getName());
                    defaultToolTipText = getText();
                    setToolTipText(defaultToolTipText);
                } else if (value instanceof Structure) {
                    setText(((Structure) value).getName());
                    defaultToolTipText = getText();
                    setToolTipText(defaultToolTipText);
                } else if (value instanceof ScopedExpression) {
                    SpeciesContextSpec scSpec = tableModel.getValueAt(row);
                    VCUnitDefinition unit = null;
                    if (table.getColumnName(column).equals(SpeciesContextSpecsTableModel.ColumnType.COLUMN_INITIAL.label)) {
                        SpeciesContextSpecParameter initialConditionParameter = scSpec.getInitialConditionParameter();
                        unit = initialConditionParameter.getUnitDefinition();
                    } else if (table.getColumnName(column).equals(SpeciesContextSpecsTableModel.ColumnType.COLUMN_DIFFUSION.label)) {
                        SpeciesContextSpecParameter diffusionParameter = scSpec.getDiffusionParameter();
                        unit = diffusionParameter.getUnitDefinition();
                    }
                    if (unit != null) {
                        setHorizontalTextPosition(JLabel.LEFT);
                        setIcon(new TextIcon("[" + unit.getSymbolUnicode() + "]", DefaultScrollTableCellRenderer.uneditableForeground));
                    }
                    int rgb = 0x00ffffff & DefaultScrollTableCellRenderer.uneditableForeground.getRGB();
                    defaultToolTipText = "<html>" + StringEscapeUtils.escapeHtml4(getText()) + " <font color=#" + Integer.toHexString(rgb) + "> [" + unit.getSymbolUnicode() + "] </font></html>";
                    setToolTipText(defaultToolTipText);
                    if (unit != null) {
                        setText(defaultToolTipText);
                    }
                }
                TableModel tableModel = table.getModel();
                if (tableModel instanceof SortTableModel) {
                    DefaultScrollTableCellRenderer.issueRenderer(this, defaultToolTipText, table, row, column, (SortTableModel) tableModel);
                    setHorizontalTextPosition(JLabel.TRAILING);
                }
                return this;
            }
        };
        DefaultTableCellRenderer rbmSpeciesShapeDepictionCellRenderer = new DefaultScrollTableCellRenderer() {

            SpeciesPatternSmallShape spss = null;

            @Override
            public Component getTableCellRendererComponent(JTable table, Object value, boolean isSelected, boolean hasFocus, int row, int column) {
                super.getTableCellRendererComponent(table, value, isSelected, hasFocus, row, column);
                if (table.getModel() instanceof VCellSortTableModel<?>) {
                    Object selectedObject = null;
                    if (table.getModel() == tableModel) {
                        selectedObject = tableModel.getValueAt(row);
                    }
                    if (selectedObject != null) {
                        if (selectedObject instanceof SpeciesContextSpec) {
                            SpeciesContextSpec scs = (SpeciesContextSpec) selectedObject;
                            SpeciesContext sc = scs.getSpeciesContext();
                            // sp may be null for "plain" species contexts
                            SpeciesPattern sp = sc.getSpeciesPattern();
                            Graphics panelContext = table.getGraphics();
                            spss = new SpeciesPatternSmallShape(4, 2, sp, shapeManager, panelContext, sc, isSelected, issueManager);
                        }
                    } else {
                        spss = null;
                    }
                }
                setText("");
                return this;
            }

            @Override
            public void paintComponent(Graphics g) {
                super.paintComponent(g);
                if (spss != null) {
                    spss.paintSelf(g);
                }
            }
        };
        DefaultScrollTableCellRenderer rulesTableCellRenderer = new DefaultScrollTableCellRenderer() {

            final Color lightBlueBackground = new Color(214, 234, 248);

            @Override
            public Component getTableCellRendererComponent(JTable table, Object value, boolean isSelected, boolean hasFocus, int row, int column) {
                super.getTableCellRendererComponent(table, value, isSelected, hasFocus, row, column);
                if (table.getModel() instanceof SpeciesContextSpecsTableModel) {
                    Icon icon = VCellIcons.issueGoodIcon;
                    Object selectedObject = null;
                    if (table.getModel() == tableModel) {
                        selectedObject = tableModel.getValueAt(row);
                    }
                    if (selectedObject != null) {
                        if (isSelected) {
                            setBackground(lightBlueBackground);
                        }
                        if (selectedObject instanceof SpeciesContextSpec) {
                            SpeciesContextSpec scs = (SpeciesContextSpec) selectedObject;
                            SpeciesContext sc = scs.getSpeciesContext();
                            boolean foundRuleMatch = false;
                            if (fieldSimulationContext.getRateRules() != null && fieldSimulationContext.getRateRules().length > 0) {
                                for (RateRule rr : fieldSimulationContext.getRateRules()) {
                                    if (rr.getRateRuleVar() == null) {
                                        continue;
                                    }
                                    if (sc.getName().equals(rr.getRateRuleVar().getName())) {
                                        foundRuleMatch = true;
                                        icon = VCellIcons.ruleRateIcon;
                                        break;
                                    }
                                }
                            }
                            if (!foundRuleMatch && fieldSimulationContext.getAssignmentRules() != null && fieldSimulationContext.getAssignmentRules().length > 0) {
                                for (AssignmentRule rr : fieldSimulationContext.getAssignmentRules()) {
                                    if (rr.getAssignmentRuleVar() == null) {
                                        continue;
                                    }
                                    if (sc.getName().equals(rr.getAssignmentRuleVar().getName())) {
                                        icon = VCellIcons.ruleAssignIcon;
                                        break;
                                    }
                                }
                            }
                        }
                    }
                    setIcon(icon);
                }
                return this;
            }
        };
        getScrollPaneTable().setDefaultRenderer(SpeciesContext.class, renderer);
        getScrollPaneTable().setDefaultRenderer(Structure.class, renderer);
        // depiction icons
        getScrollPaneTable().setDefaultRenderer(SpeciesPattern.class, rbmSpeciesShapeDepictionCellRenderer);
        getScrollPaneTable().setDefaultRenderer(Species.class, renderer);
        getScrollPaneTable().setDefaultRenderer(ScopedExpression.class, renderer);
        getScrollPaneTable().setDefaultRenderer(Boolean.class, new ScrollTableBooleanCellRenderer());
        // rules icons
        getScrollPaneTable().setDefaultRenderer(SpeciesContextSpecsTableModel.RulesProvenance.class, rulesTableCellRenderer);
    // TODO: find out why the code below is not working properly
    // int ordinal = SpeciesContextSpecsTableModel.ColumnType.COLUMN_RULES.ordinal();
    // getScrollPaneTable().getColumnModel().getColumn(ordinal).setCellRenderer(rulesTableCellRenderer);
    // final int rulesWidth = 50;		// fixed max size, there's no point to enlarge some columns
    // int index = SpeciesContextSpecsTableModel.ColumnType.COLUMN_RULES.ordinal();
    // getScrollPaneTable().getColumnModel().getColumn(index).setPreferredWidth(rulesWidth);
    // getScrollPaneTable().getColumnModel().getColumn(index).setMaxWidth(rulesWidth);
    } catch (java.lang.Throwable ivjExc) {
        handleException(ivjExc);
    }
}

Example 8 with AssignmentRule

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

the class IssueTableModel method getSourceObjectDescription.

private String getSourceObjectDescription(VCDocument vcDocument, Issue issue) {
    if (vcDocument instanceof BioModel) {
        Object object = issue.getSource();
        {
            DecoratedIssueSource dis = BeanUtils.downcast(DecoratedIssueSource.class, object);
            if (dis != null) {
                return dis.getSourcePath();
            }
        }
        String description = "";
        if (object instanceof SymbolTableEntry) {
            description = ((SymbolTableEntry) object).getName();
        } else if (object instanceof ReactionStep) {
            description = ((ReactionStep) object).getName();
        } else if (object instanceof ReactionRule) {
            description = ((ReactionRule) object).getName();
        } else if (object instanceof SpeciesPattern) {
            // Object parent = issue.getIssueContext().getContextObject();
            // if (parent instanceof SpeciesContext){
            // description = ((SpeciesContext)parent).getName();
            // }
            // if (issue.getIssueContext().hasContextType(ContextType.SpeciesContext)){
            // SpeciesContext thing = (SpeciesContext)issue.getIssueContext().getContextObject(ContextType.SpeciesContext);
            // description = thing.getName();
            // }else if(issue.getIssueContext().hasContextType(ContextType.ReactionRule)) {
            // ReactionRule thing = (ReactionRule)issue.getIssueContext().getContextObject(ContextType.ReactionRule);
            // description = thing.getName();
            // }else if(issue.getIssueContext().hasContextType(ContextType.RbmObservable)) {
            // RbmObservable thing = (RbmObservable)issue.getIssueContext().getContextObject(ContextType.RbmObservable);
            // description = thing.getName();
            // } else {
            System.err.println("Bad issue context for " + ((SpeciesPattern) object).toString());
            description = ((SpeciesPattern) object).toString();
        // }
        } else if (object instanceof MolecularType) {
            description = ((MolecularType) object).getName();
        } else if (object instanceof MolecularComponent) {
            description = ((MolecularComponent) object).getName();
        } else if (object instanceof ComponentStateDefinition) {
            description = ((ComponentStateDefinition) object).getName();
        } else if (object instanceof Structure) {
            description = ((Structure) object).getName();
        } else if (object instanceof SubDomain) {
            description = ((SubDomain) object).getName();
        } else if (object instanceof Geometry) {
            description = ((Geometry) object).getName();
        } else if (object instanceof StructureMapping) {
            description = ((StructureMapping) object).getStructure().getName();
        } else if (object instanceof OutputFunctionIssueSource) {
            description = ((OutputFunctionIssueSource) object).getAnnotatedFunction().getName();
        } else if (object instanceof UnmappedGeometryClass) {
            description = ((UnmappedGeometryClass) object).getGeometryClass().getName();
        } else if (object instanceof MicroscopeMeasurement) {
            description = ((MicroscopeMeasurement) object).getName();
        } else if (object instanceof SpatialObject) {
            description = ((SpatialObject) object).getName();
        } else if (object instanceof SpatialProcess) {
            description = ((SpatialProcess) object).getName();
        } else if (object instanceof GeometryContext) {
            description = "Geometry";
        } else if (object instanceof ModelOptimizationSpec) {
            description = ((ModelOptimizationSpec) object).getParameterEstimationTask().getName();
        } else if (object instanceof Simulation) {
            description = ((Simulation) object).getName();
        } else if (object instanceof SpeciesContextSpec) {
            SpeciesContextSpec scs = (SpeciesContextSpec) object;
            description = scs.getSpeciesContext().getName();
        } else if (object instanceof ReactionCombo) {
            ReactionSpec rs = ((ReactionCombo) object).getReactionSpec();
            description = rs.getReactionStep().getName();
        } else if (object instanceof RbmModelContainer) {
            // RbmModelContainer mc = (RbmModelContainer)object;
            description = "Rules validator";
        } else if (object instanceof SimulationContext) {
            SimulationContext sc = (SimulationContext) object;
            description = sc.getName();
        } else if (object instanceof Model) {
            Model m = (Model) object;
            description = m.getName();
        } else if (object instanceof BioEvent) {
            return ((BioEvent) object).getName() + "";
        } else if (object instanceof MathDescription) {
            return ((MathDescription) object).getName() + "";
        } else if (object instanceof AssignmentRule) {
            return ((AssignmentRule) object).getDisplayName() + "";
        } else if (object instanceof RateRule) {
            return ((RateRule) object).getDisplayName() + "";
        } else {
            System.err.println("unknown object type in IssueTableModel.getSourceObjectDescription(): " + object.getClass());
        }
        return description;
    } else if (vcDocument instanceof MathModel) {
        Object object = issue.getSource();
        String description = "";
        if (object instanceof Variable) {
            description = ((Variable) object).getName();
        } else if (object instanceof SubDomain) {
            description = ((SubDomain) object).getName();
        } else if (object instanceof Geometry) {
            description = "Geometry";
        } else if (object instanceof OutputFunctionIssueSource) {
            description = ((OutputFunctionIssueSource) object).getAnnotatedFunction().getName();
        } else if (object instanceof MathDescription) {
            return "math";
        } else if (object instanceof Simulation) {
            return "Simulation " + ((Simulation) object).getName() + "";
        }
        return description;
    } else {
        System.err.println("unknown document type in IssueTableModel.getSourceObjectDescription()");
        return "";
    }
}

Example 9 with AssignmentRule

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

the class AssignmentRulesSummaryTableModel method propertyChange.

@Override
public void propertyChange(java.beans.PropertyChangeEvent evt) {
    super.propertyChange(evt);
    if (evt.getPropertyName().equals(SimulationContext.PROPERTY_NAME_ASSIGNMENTRULES)) {
        AssignmentRule[] oldValue = (AssignmentRule[]) evt.getOldValue();
        if (oldValue != null) {
            for (AssignmentRule rr : oldValue) {
                rr.removePropertyChangeListener(this);
            }
        }
        AssignmentRule[] newValue = (AssignmentRule[]) evt.getNewValue();
        if (newValue != null) {
            for (AssignmentRule rr : newValue) {
                rr.addPropertyChangeListener(this);
            }
        }
    }
    refreshData();
}

Example 10 with AssignmentRule

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

the class AssignmentRulesSummaryTableModel method setValueAt.

public void setValueAt(Object value, int row, int column) {
    try {
        AssignmentRule assignmentRule = getValueAt(row);
        if (assignmentRule == null) {
            assignmentRule = simulationContext.createAssignmentRule(null);
        } else {
            assignmentRule = getValueAt(row);
        }
        switch(column) {
            case COLUMN_ASSIGNMENTRULE_NAME:
                assignmentRule.setName((String) value);
                break;
            case COLUMN_ASSIGNMENTRULE_VAR:
                if (value instanceof String) {
                    String var = (String) value;
                    SymbolTableEntry newVar = simulationContext.getModel().getEntry(var);
                    SymbolTableEntry oldVar = assignmentRule.getAssignmentRuleVar();
                    // dummy rule, just for the var
                    AssignmentRule oldRule = new AssignmentRule(null, oldVar, null, simulationContext);
                    assignmentRule.setAssignmentRuleVar(newVar);
                    if (simulationContext != null && newVar != null) {
                        // broadcast the change
                        // the event generated by the simContext used to clamp the SpeciesContextSpec
                        simulationContext.fireAssignmentRuleChanged(oldRule, assignmentRule);
                    }
                }
                break;
            case COLUMN_ASSIGNMENTRULE_EXPR:
                SymbolTableEntry ste = null;
                if (assignmentRule.getAssignmentRuleVar() != null) {
                    ste = simulationContext.getModel().getEntry(assignmentRule.getAssignmentRuleVar().getName());
                }
                Expression exp = new Expression((String) value);
                assignmentRule.setAssignmentRuleExpression(exp);
                assignmentRule.bind();
                if (simulationContext != null && ste != null) {
                    // broadcast the change
                    // the event generated by the simContext used to clamp the SpeciesContextSpec
                    simulationContext.fireAssignmentRuleChanged(null, assignmentRule);
                }
                break;
            case COLUMN_ASSIGNMENTRULE_TYPE:
                return;
        }
    } catch (Exception e) {
        e.printStackTrace(System.out);
        DialogUtils.showErrorDialog(ownerTable, e.getMessage());
    }
}