Examples with BioModel cbit.vcell.biomodel.BioModel used on opensource projects

Example 26 with BioModel

use of cbit.vcell.biomodel.BioModel 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 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 27 with BioModel

use of cbit.vcell.biomodel.BioModel 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 {
            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 28 with BioModel

use of cbit.vcell.biomodel.BioModel in project vcell by virtualcell.

the class MolecularTypeTableModel method bioModelChange.

@Override
protected void bioModelChange(PropertyChangeEvent evt) {
    super.bioModelChange(evt);
    BioModel oldValue = (BioModel) evt.getOldValue();
    if (oldValue != null) {
        RbmModelContainer rbmModelContainer = (RbmModelContainer) (oldValue.getModel().getRbmModelContainer());
        // rbmModelContainer.removePropertyChangeListener(this);
        for (MolecularType molecularType : rbmModelContainer.getMolecularTypeList()) {
            RbmUtils.removePropertyChangeListener(molecularType, this);
        }
    }
    BioModel newValue = (BioModel) evt.getNewValue();
    if (newValue != null) {
        RbmModelContainer rbmModelContainer = newValue.getModel().getRbmModelContainer();
        // rbmModelContainer.addPropertyChangeListener(this);
        for (MolecularType molecularType : rbmModelContainer.getMolecularTypeList()) {
            RbmUtils.addPropertyChangeListener(molecularType, this);
        }
    }
}

Example 29 with BioModel

use of cbit.vcell.biomodel.BioModel in project vcell by virtualcell.

the class PathwayModelTableModel method setBioModel.

public void setBioModel(BioModel newValue) {
    if (this.bioModel == newValue) {
        return;
    }
    BioModel oldValue = bioModel;
    if (oldValue != null) {
        oldValue.getPathwayModel().removePathwayListener(this);
    }
    if (newValue != null) {
        newValue.getPathwayModel().addPathwayListener(this);
    }
    bioModel = newValue;
    refreshData();
}

Example 30 with BioModel

use of cbit.vcell.biomodel.BioModel in project vcell by virtualcell.

the class PathwayTableModel method setBioModel.

public void setBioModel(BioModel newValue) {
    BioModel oldValue = bioModel;
    this.bioModel = newValue;
    if (oldValue != null) {
        oldValue.getPathwayModel().removePathwayListener(this);
    }
    if (newValue != null) {
        newValue.getPathwayModel().addPathwayListener(this);
    }
}