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

Example 41 with RbmObservable

use of cbit.vcell.model.RbmObservable 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 42 with RbmObservable

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

the class ObservablePropertiesPanel method setObservable.

private void setObservable(RbmObservable newValue) {
    if (observable == newValue) {
        return;
    }
    RbmObservable oldValue = observable;
    if (oldValue != null) {
        oldValue.removePropertyChangeListener(eventHandler);
    }
    if (newValue != null) {
        newValue.addPropertyChangeListener(eventHandler);
    }
    observable = newValue;
    observableTreeModel.setObservable(observable);
    if (observable != null) {
        shapePanel.setHighlightedRecursively(observable, LargeShapePanel.Highlight.off);
    }
    updateInterface();
    // scroll to top to show the first species pattern of the observable
    scrollPane.getViewport().setViewPosition(new Point(0, 0));
}

Example 43 with RbmObservable

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

the class ObservableTableModel method isCellEditable.

public boolean isCellEditable(int row, int columnIndex) {
    Column col = Column.values()[columnIndex];
    if (col == Column.name) {
        return true;
    }
    RbmObservable o = getValueAt(row);
    if (o == null) {
        return false;
    }
    if (col == Column.structure) {
        return false;
    }
    if (col == Column.type) {
        return true;
    }
    if (col == Column.depiction) {
        return false;
    }
    final List<SpeciesPattern> spList = o.getSpeciesPatternList();
    for (SpeciesPattern sp : spList) {
        final List<MolecularTypePattern> mtpList = sp.getMolecularTypePatterns();
        for (MolecularTypePattern mtp : mtpList) {
            MolecularType mt = mtp.getMolecularType();
            if (mt.getComponentList().size() != 0) {
                return false;
            }
        }
    }
    return true;
}

Example 44 with RbmObservable

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

the class ObservableTableModel method propertyChange.

@Override
public void propertyChange(PropertyChangeEvent evt) {
    super.propertyChange(evt);
    Object source = evt.getSource();
    // if (source == getModel().getRbmModelContainer()) {
    if (source == getModel()) {
        if (evt.getPropertyName().equals(RbmModelContainer.PROPERTY_NAME_OBSERVABLE_LIST)) {
            refreshData();
            List<RbmObservable> oldValue = (List<RbmObservable>) evt.getOldValue();
            if (oldValue != null) {
                for (RbmObservable observable : oldValue) {
                    observable.removePropertyChangeListener(this);
                    SpeciesPattern speciesPattern = observable.getSpeciesPattern(0);
                    RbmUtils.removePropertyChangeListener(speciesPattern, this);
                }
            }
            List<RbmObservable> newValue = (List<RbmObservable>) evt.getNewValue();
            if (newValue != null) {
                for (RbmObservable observable : newValue) {
                    observable.addPropertyChangeListener(this);
                    SpeciesPattern speciesPattern = observable.getSpeciesPattern(0);
                    RbmUtils.addPropertyChangeListener(speciesPattern, this);
                }
            }
        } else if (evt.getPropertyName().equals(RbmModelContainer.PROPERTY_NAME_MOLECULAR_TYPE_LIST)) {
            // we need this?
            refreshData();
        }
    } else if (source instanceof RbmObservable) {
        RbmObservable mt = (RbmObservable) source;
        int changeRow = getRowIndex(mt);
        if (changeRow >= 0) {
            fireTableRowsUpdated(changeRow, changeRow);
        }
    // if (evt.getPropertyName().equals(RbmObservable.PROPERTY_NAME_SPECIES_PATTERN_LIST)) {
    // SpeciesPattern oldValue = (SpeciesPattern) evt.getOldValue();
    // if (oldValue != null) {
    // RbmUtils.removePropertyChangeListener(oldValue, this);
    // }
    // SpeciesPattern newValue = (SpeciesPattern) evt.getNewValue();
    // if (newValue != null) {
    // RbmUtils.addPropertyChangeListener(newValue, this);
    // }
    // }
    } else if (source instanceof SpeciesPattern) {
        fireTableRowsUpdated(0, getRowCount() - 1);
        if (evt.getPropertyName().equals(SpeciesPattern.PROPERTY_NAME_MOLECULAR_TYPE_PATTERNS)) {
            List<MolecularTypePattern> oldValue = (List<MolecularTypePattern>) evt.getOldValue();
            if (oldValue != null) {
                for (MolecularTypePattern mtp : oldValue) {
                    RbmUtils.removePropertyChangeListener(mtp, this);
                }
            }
            List<MolecularTypePattern> newValue = (List<MolecularTypePattern>) evt.getNewValue();
            if (newValue != null) {
                for (MolecularTypePattern mtp : newValue) {
                    RbmUtils.addPropertyChangeListener(mtp, this);
                }
            }
        }
    } else if (source instanceof MolecularTypePattern) {
        fireTableRowsUpdated(0, getRowCount() - 1);
        if (evt.getPropertyName().equals(MolecularTypePattern.PROPERTY_NAME_COMPONENT_PATTERN_LIST)) {
            List<MolecularComponentPattern> oldValue = (List<MolecularComponentPattern>) evt.getOldValue();
            if (oldValue != null) {
                for (MolecularComponentPattern mcp : oldValue) {
                    RbmUtils.removePropertyChangeListener(mcp, this);
                }
            }
            List<MolecularComponentPattern> newValue = (List<MolecularComponentPattern>) evt.getNewValue();
            if (newValue != null) {
                for (MolecularComponentPattern mcp : newValue) {
                    RbmUtils.addPropertyChangeListener(mcp, this);
                }
            }
        }
    } else if (source instanceof MolecularComponentPattern) {
        fireTableRowsUpdated(0, getRowCount() - 1);
        if (source.equals(MolecularComponentPattern.PROPERTY_NAME_COMPONENT_STATE)) {
            ComponentStateDefinition oldValue = (ComponentStateDefinition) evt.getOldValue();
            if (oldValue != null) {
                oldValue.removePropertyChangeListener(this);
            }
            ComponentStateDefinition newValue = (ComponentStateDefinition) evt.getNewValue();
            if (newValue != null) {
                newValue.addPropertyChangeListener(this);
            }
        }
    } else if (evt.getSource() instanceof MolecularComponent) {
        fireTableRowsUpdated(0, getRowCount() - 1);
    } else if (evt.getSource() instanceof ComponentStateDefinition) {
        fireTableRowsUpdated(0, getRowCount() - 1);
    }
// updateStructureComboBox();
}

Example 45 with RbmObservable

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

the class ObservableTableModel method getValueAt.

public Object getValueAt(int rowIndex, int columnIndex) {
    RbmObservable observable = getValueAt(rowIndex);
    Column col = Column.values()[columnIndex];
    if (observable == null) {
        if (col == Column.name) {
            return ADD_NEW_HERE_TEXT;
        }
    } else {
        switch(col) {
            case name:
                return observable.getName();
            case species_pattern:
                if (!observable.getSpeciesPatternList().isEmpty()) {
                    String speciesPatterns = "";
                    for (SpeciesPattern sp : observable.getSpeciesPatternList()) {
                        speciesPatterns += sp.toString() + " ";
                    }
                    return speciesPatterns;
                } else {
                    return ("");
                }
            case type:
                return observable.getType();
            case structure:
                return observable.getStructure();
        }
    }
    return null;
}