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

Example 1 with IllegalMappingException

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

the class StructureMappingTableModel method setValueAt.

public void setValueAt(Object aValue, int rowIndex, int columnIndex) {
    if (rowIndex < 0 || rowIndex >= getRowCount()) {
        throw new RuntimeException("StructureMappingTableModel.setValueAt(), row = " + rowIndex + " out of range [" + 0 + "," + (getRowCount() - 1) + "]");
    }
    if (columnIndex < 0 || columnIndex >= getColumnCount()) {
        throw new RuntimeException("StructureMappingTableModel.setValueAt(), column = " + columnIndex + " out of range [" + 0 + "," + (getColumnCount() - 1) + "]");
    }
    StructureMapping structureMapping = getValueAt(rowIndex);
    Structure structure = structureMapping.getStructure();
    if (bNonSpatial) {
        switch(columnIndex) {
            case NONSPATIAL_COLUMN_SIZE:
                {
                    try {
                        Expression exp = null;
                        if (aValue instanceof String) {
                            exp = new Expression((String) aValue);
                        } else if (aValue instanceof Double) {
                            exp = new Expression(((Double) aValue).doubleValue());
                        }
                        // if the input volumn is null, leave it as it was.
                        if (exp != null) {
                            // for old ode model, once one size is input, solve the rest.                                                                                                          if it is unnamed compartment(the only one), we don't need to solve anything
                            if (!getGeometryContext().getSimulationContext().isStoch() && getGeometryContext().isAllSizeSpecifiedNull() && getGeometryContext().isAllVolFracAndSurfVolSpecified() && getGeometryContext().getStructureMappings().length > 1) {
                                structureMapping.getSizeParameter().setExpression(exp);
                                double size;
                                try {
                                    size = exp.evaluateConstant();
                                    VCUnitDefinition volumeUnit = getGeometryContext().getSimulationContext().getModel().getUnitSystem().getVolumeUnit();
                                    StructureSizeSolver.updateAbsoluteStructureSizes(getGeometryContext().getSimulationContext(), structure, size, volumeUnit);
                                    fireTableRowsUpdated(0, getRowCount());
                                } catch (ExpressionException ex) {
                                    ex.printStackTrace(System.out);
                                    PopupGenerator.showErrorDialog(ownerTable, "Size of Feature " + structure.getName() + " can not be solved as constant!");
                                } catch (Exception ex) {
                                    ex.printStackTrace(System.out);
                                    PopupGenerator.showErrorDialog(ownerTable, ex.getMessage());
                                }
                            } else {
                                structureMapping.getSizeParameter().setExpression(exp);
                                // set fraction in stoch math description, because these might be used when copy from stoch app to ode app.
                                if (getGeometryContext().isAllSizeSpecifiedPositive()) /*&& !getGeometryContext().getSimulationContext().isStoch()*/
                                {
                                    try {
                                        StructureSizeSolver.updateRelativeStructureSizes(getGeometryContext().getSimulationContext());
                                    } catch (Exception ex) {
                                        ex.printStackTrace(System.out);
                                        PopupGenerator.showErrorDialog(ownerTable, ex.getMessage());
                                    }
                                }
                            }
                        }
                    } catch (ExpressionException e) {
                        e.printStackTrace(System.out);
                        PopupGenerator.showErrorDialog(ownerTable, "expression error\n" + e.getMessage());
                    }
                    break;
                }
        }
    } else {
        switch(columnIndex) {
            case SPATIAL_COLUMN_SUBDOMAIN:
                {
                    GeometryClass geometryClass = null;
                    if (aValue instanceof String) {
                        String svname = (String) aValue;
                        geometryClass = getGeometryContext().getGeometry().getGeometryClass(svname);
                    } else if (aValue instanceof GeometryClass) {
                        geometryClass = (GeometryClass) aValue;
                    }
                    if (geometryClass != null) {
                        try {
                            getGeometryContext().assignStructure(structure, geometryClass);
                        } catch (PropertyVetoException e) {
                            e.printStackTrace(System.out);
                            PopupGenerator.showErrorDialog(ownerTable, e.getMessage());
                        } catch (IllegalMappingException e) {
                            e.printStackTrace(System.out);
                            PopupGenerator.showErrorDialog(ownerTable, e.getMessage());
                        } catch (MappingException e) {
                            e.printStackTrace(System.out);
                            PopupGenerator.showErrorDialog(ownerTable, e.getMessage());
                        }
                    }
                    break;
                }
            case SPATIAL_COLUMN_SIZERATIO:
                try {
                    Expression exp = null;
                    if (aValue instanceof String) {
                        exp = new Expression((String) aValue);
                    } else if (aValue instanceof Double) {
                        exp = new Expression(((Double) aValue).doubleValue());
                    }
                    if (exp != null) {
                        structureMapping.getUnitSizeParameter().setExpression(exp);
                        StructureSizeSolver.updateUnitStructureSizes(getGeometryContext().getSimulationContext(), structureMapping.getGeometryClass());
                    }
                } catch (ExpressionException e) {
                    e.printStackTrace(System.out);
                    PopupGenerator.showErrorDialog(ownerTable, "expression error\n" + e.getMessage());
                }
                break;
            case SPATIAL_COLUMN_X_MINUS:
                {
                    if (aValue != null) {
                        structureMapping.setBoundaryConditionTypeXm(new BoundaryConditionType((String) aValue));
                    }
                    break;
                }
            case SPATIAL_COLUMN_X_PLUS:
                {
                    if (aValue != null) {
                        structureMapping.setBoundaryConditionTypeXp(new BoundaryConditionType((String) aValue));
                    }
                    break;
                }
            case SPATIAL_COLUMN_Y_MINUS:
                {
                    if (aValue != null) {
                        structureMapping.setBoundaryConditionTypeYm(new BoundaryConditionType((String) aValue));
                    }
                    break;
                }
            case SPATIAL_COLUMN_Y_PLUS:
                {
                    if (aValue != null) {
                        structureMapping.setBoundaryConditionTypeYp(new BoundaryConditionType((String) aValue));
                    }
                    break;
                }
            case SPATIAL_COLUMN_Z_MINUS:
                {
                    if (aValue != null) {
                        structureMapping.setBoundaryConditionTypeZm(new BoundaryConditionType((String) aValue));
                    }
                    break;
                }
            case SPATIAL_COLUMN_Z_PLUS:
                {
                    if (aValue != null) {
                        structureMapping.setBoundaryConditionTypeZp(new BoundaryConditionType((String) aValue));
                    }
                    break;
                }
        }
    }
}

Example 2 with IllegalMappingException

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

the class SimulationContextDbDriver method getSimulationContextSQL.

/**
 * getModel method comment.
 */
private SimulationContext getSimulationContextSQL(QueryHashtable dbc, Connection con, User user, KeyValue simContextKey) throws /*, ReactStepDbDriver reactStepDB*/
SQLException, DataAccessException, IllegalMappingException, PropertyVetoException {
    SimulationContext simContext = null;
    String sql;
    Field[] f = { new cbit.sql.StarField(simContextTable), userTable.userid };
    Table[] t = { simContextTable, userTable };
    String condition = simContextTable.id.getQualifiedColName() + " = " + simContextKey + " AND " + simContextTable.ownerRef.getQualifiedColName() + " = " + userTable.id.getQualifiedColName();
    sql = DatabasePolicySQL.enforceOwnershipSelect(user, f, t, (OuterJoin) null, condition, null, dbSyntax);
    // System.out.println(sql);
    Statement stmt = con.createStatement();
    try {
        ResultSet rset = stmt.executeQuery(sql);
        if (rset.next()) {
            simContext = simContextTable.getSimContext(dbc, con, user, rset, geomDB, modelDB, mathDescDB);
        } else {
            throw new ObjectNotFoundException("SimulationContext id=" + simContextKey + " not found for user '" + user + "'");
        }
    } finally {
        stmt.close();
    }
    DataSymbolTable.table.populateDataSymbols(con, simContextKey, simContext.getDataContext(), user, simContext.getModel().getUnitSystem());
    ArrayList<AnnotatedFunction> outputFunctionList = ApplicationMathTable.table.getOutputFunctionsSimcontext(con, simContextKey, dbSyntax);
    if (outputFunctionList != null) {
        OutputFunctionContext outputFnContext = simContext.getOutputFunctionContext();
        outputFnContext.setOutputFunctions(outputFunctionList);
    }
    SimContextTable.table.readAppComponents(con, simContext, dbSyntax);
    assignStimuliSQL(con, simContextKey, simContext);
    assignStructureMappingsSQL(dbc, con, simContextKey, simContext);
    assignSpeciesContextSpecsSQL(con, simContextKey, simContext);
    assignReactionSpecsSQL(con, simContextKey, simContext);
    for (GeometryClass gc : simContext.getGeometry().getGeometryClasses()) {
        try {
            StructureSizeSolver.updateUnitStructureSizes(simContext, gc);
        } catch (Exception e) {
            e.printStackTrace(System.out);
        }
    }
    simContext.getGeometryContext().enforceHierarchicalBoundaryConditions(simContext.getModel().getStructureTopology());
    simContext.getModel().refreshDependencies();
    assignAnalysisTasksSQL(con, simContextKey, simContext);
    // really needed to calculate MembraneMapping parameters that are not stored (inside/outside flux correction factors).
    simContext.refreshDependencies();
    return simContext;
}

Example 3 with IllegalMappingException

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

the class StructureMappingCartoonTool method menuAction.

protected void menuAction(Shape shape, String menuAction) {
    // 
    if (shape == null) {
        return;
    }
    // 
    if (menuAction.equals(CartoonToolEditActions.Delete.MENU_ACTION)) {
        if (shape instanceof StructureMappingShape) {
            try {
                StructureMapping sm = (StructureMapping) ((StructureMappingShape) shape).getModelObject();
                getStructureMappingCartoon().getGeometryContext().assignStructure(sm.getStructure(), null);
                getStructureMappingCartoon().refreshAll();
            } catch (IllegalMappingException e) {
                e.printStackTrace(System.out);
                PopupGenerator.showErrorDialog(getGraphPane(), e.getMessage());
            } catch (java.beans.PropertyVetoException e) {
                e.printStackTrace(System.out);
                PopupGenerator.showErrorDialog(getGraphPane(), e.getMessage());
            } catch (MappingException e) {
                e.printStackTrace(System.out);
                PopupGenerator.showErrorDialog(getGraphPane(), e.getMessage());
            }
        }
    } else {
        // default action is to ignore
        System.out.println("unsupported menu action '" + menuAction + "' on shape '" + shape + "'");
    }
}