Examples with SymbolTableEntry cbit.vcell.parser.SymbolTableEntry used on opensource projects

Example 56 with SymbolTableEntry

use of cbit.vcell.parser.SymbolTableEntry in project vcell by virtualcell.

the class ReactionStep method getAutoCompleteSymbolFilter.

public AutoCompleteSymbolFilter getAutoCompleteSymbolFilter() {
    AutoCompleteSymbolFilter stef = new AutoCompleteSymbolFilter() {

        public boolean accept(SymbolTableEntry ste) {
            if (ste instanceof StructureSize) {
                if (((StructureSize) ste).getStructure() != structure) {
                    return false;
                }
            } else {
                if (structure instanceof Membrane) {
                    Membrane membrane = (Membrane) structure;
                    StructureTopology structTopology = getModel().getStructureTopology();
                    if (ste instanceof SpeciesContext) {
                        Structure entryStructure = ((SpeciesContext) ste).getStructure();
                        if (entryStructure != membrane && entryStructure != structTopology.getInsideFeature(membrane) && entryStructure != structTopology.getOutsideFeature(membrane)) {
                            return false;
                        }
                    } else if (ste instanceof MembraneVoltage) {
                        if (((MembraneVoltage) ste).getMembrane() != membrane) {
                            return false;
                        }
                    }
                } else {
                    if (ste instanceof SpeciesContext) {
                        Structure entryStructure = ((SpeciesContext) ste).getStructure();
                        if (entryStructure != structure) {
                            return false;
                        }
                    } else if (ste instanceof MembraneVoltage) {
                        return false;
                    }
                }
            }
            return true;
        }

        public boolean acceptFunction(String funcName) {
            return true;
        }
    };
    return stef;
}

Example 57 with SymbolTableEntry

use of cbit.vcell.parser.SymbolTableEntry in project vcell by virtualcell.

the class ReactionStep method getLocalEntry.

public SymbolTableEntry getLocalEntry(String identifier) {
    // 
    // if resolved parameter exists, then return it
    // 
    SymbolTableEntry ste = getKinetics().getKineticsParameter(identifier);
    if (ste != null) {
        return ste;
    }
    // 
    // if unnresolved parameter exists, then return it
    // 
    ste = getKinetics().getUnresolvedParameter(identifier);
    if (ste != null) {
        return ste;
    }
    // 
    // if proxy parameter exists, then return it
    // 
    ste = getKinetics().getProxyParameter(identifier);
    if (ste != null) {
        return ste;
    }
    return null;
}

Example 58 with SymbolTableEntry

use of cbit.vcell.parser.SymbolTableEntry in project vcell by virtualcell.

the class ModelOptimizationMapping method getRemappedReferenceData.

/**
 * Gets the constraintData property (cbit.vcell.opt.ConstraintData) value.
 * @return The constraintData property value.
 * @see #setConstraintData
 */
private ReferenceData getRemappedReferenceData(MathMapping mathMapping) throws MappingException {
    if (modelOptimizationSpec.getReferenceData() == null) {
        return null;
    }
    // 
    // make sure time is mapped
    // 
    ReferenceData refData = modelOptimizationSpec.getReferenceData();
    ReferenceDataMappingSpec[] refDataMappingSpecs = modelOptimizationSpec.getReferenceDataMappingSpecs();
    RowColumnResultSet rowColResultSet = new RowColumnResultSet();
    Vector<SymbolTableEntry> modelObjectList = new Vector<SymbolTableEntry>();
    Vector<double[]> dataList = new Vector<double[]>();
    // 
    // find bound columns, (time is always mapped to the first column)
    // 
    int mappedColumnCount = 0;
    for (int i = 0; i < refDataMappingSpecs.length; i++) {
        SymbolTableEntry modelObject = refDataMappingSpecs[i].getModelObject();
        if (modelObject != null) {
            int mappedColumnIndex = mappedColumnCount;
            if (modelObject instanceof Model.ReservedSymbol && ((ReservedSymbol) modelObject).isTime()) {
                mappedColumnIndex = 0;
            }
            String origRefDataColumnName = refDataMappingSpecs[i].getReferenceDataColumnName();
            int origRefDataColumnIndex = refData.findColumn(origRefDataColumnName);
            if (origRefDataColumnIndex < 0) {
                throw new RuntimeException("reference data column named '" + origRefDataColumnName + "' not found");
            }
            double[] columnData = refData.getDataByColumn(origRefDataColumnIndex);
            if (modelObjectList.contains(modelObject)) {
                throw new RuntimeException("multiple reference data columns mapped to same model object '" + modelObject.getName() + "'");
            }
            modelObjectList.insertElementAt(modelObject, mappedColumnIndex);
            dataList.insertElementAt(columnData, mappedColumnIndex);
            mappedColumnCount++;
        }
    }
    // 
    if (modelObjectList.size() == 0) {
        throw new RuntimeException("reference data was not associated with model");
    }
    if (modelObjectList.size() == 1) {
        throw new RuntimeException("reference data was not associated with model, must map time and at least one other column");
    }
    boolean bFoundTimeVar = false;
    for (SymbolTableEntry ste : modelObjectList) {
        if (ste instanceof Model.ReservedSymbol && ((ReservedSymbol) ste).isTime()) {
            bFoundTimeVar = true;
            break;
        }
    }
    if (!bFoundTimeVar) {
        throw new RuntimeException("must map time column of reference data to model");
    }
    // 
    for (int i = 0; i < modelObjectList.size(); i++) {
        SymbolTableEntry modelObject = (SymbolTableEntry) modelObjectList.elementAt(i);
        try {
            // Find by name because MathSybolMapping has different 'objects' than refDataMapping 'objects'
            Variable variable = mathMapping.getMathSymbolMapping().findVariableByName(modelObject.getName());
            if (variable != null) {
                String symbol = variable.getName();
                rowColResultSet.addDataColumn(new ODESolverResultSetColumnDescription(symbol));
            } else if (modelObject instanceof Model.ReservedSymbol && ((Model.ReservedSymbol) modelObject).isTime()) {
                Model.ReservedSymbol time = (Model.ReservedSymbol) modelObject;
                String symbol = time.getName();
                rowColResultSet.addDataColumn(new ODESolverResultSetColumnDescription(symbol));
            }
        } catch (MathException | MatrixException | ExpressionException | ModelException e) {
            e.printStackTrace();
            throw new MappingException(e.getMessage(), e);
        }
    }
    // 
    // populate data columns (time and rest)
    // 
    double[] weights = new double[rowColResultSet.getColumnDescriptionsCount()];
    weights[0] = 1.0;
    int numRows = ((double[]) dataList.elementAt(0)).length;
    int numColumns = modelObjectList.size();
    for (int j = 0; j < numRows; j++) {
        double[] row = new double[numColumns];
        for (int i = 0; i < numColumns; i++) {
            row[i] = ((double[]) dataList.elementAt(i))[j];
            if (i > 0) {
                weights[i] += row[i] * row[i];
            }
        }
        rowColResultSet.addRow(row);
    }
    for (int i = 0; i < numColumns; i++) {
        if (weights[i] == 0) {
            weights[i] = 1;
        } else {
            weights[i] = 1 / weights[i];
        }
    }
    SimpleReferenceData remappedRefData = new SimpleReferenceData(rowColResultSet, weights);
    return remappedRefData;
}

Example 59 with SymbolTableEntry

use of cbit.vcell.parser.SymbolTableEntry in project vcell by virtualcell.

the class ReactionRulePropertiesTableModel method isCellEditable.

/**
 * Insert the method's description here.
 * Creation date: (2/24/01 12:27:46 AM)
 * @return boolean
 * @param rowIndex int
 * @param columnIndex int
 */
public boolean isCellEditable(int rowIndex, int columnIndex) {
    if (!bEditable) {
        return false;
    }
    Object o = getValueAt(rowIndex);
    if (!(o instanceof Parameter)) {
        return false;
    }
    Parameter parameter = (Parameter) o;
    if (reactionRule != null && reactionRule.getKineticLaw().getLocalParameter(RbmKineticLawParameterType.MassActionReverseRate) == parameter) {
        if (!reactionRule.isReversible()) {
            // disable Kr if rule is not reversible
            return false;
        }
    }
    switch(columnIndex) {
        case COLUMN_NAME:
            return parameter.isNameEditable();
        case COLUMN_DESCRIPTION:
            return false;
        case COLUMN_IS_GLOBAL:
            // if the parameter is reaction rate param or a ReservedSymbol in the model, it should not be editable
            if ((parameter instanceof LocalParameter) && (((LocalParameter) parameter).getRole() != RbmKineticLaw.RbmKineticLawParameterType.UserDefined)) {
                return false;
            }
            if (parameter instanceof UnresolvedParameter) {
                return false;
            }
            if (parameter instanceof LocalProxyParameter) {
                LocalProxyParameter kpp = (LocalProxyParameter) parameter;
                SymbolTableEntry ste = kpp.getTarget();
                if ((ste instanceof Model.ReservedSymbol) || (ste instanceof SpeciesContext) || (ste instanceof ModelQuantity)) {
                    return false;
                }
            }
            return true;
        case COLUMN_VALUE:
            return parameter.isExpressionEditable();
        case COLUMN_UNITS:
            return parameter.isUnitEditable();
    }
    return false;
}

Example 60 with SymbolTableEntry

use of cbit.vcell.parser.SymbolTableEntry in project vcell by virtualcell.

the class GeometrySubVolumeTableModel method setGeometry.

/**
 * Sets the geometry property (cbit.vcell.geometry.Geometry) value.
 * @param geometry The new value for the property.
 * @see #getGeometry
 */
public void setGeometry(Geometry geometry) {
    if (fieldGeometry == geometry) {
        return;
    }
    Geometry oldValue = fieldGeometry;
    if (oldValue != null) {
        oldValue.getGeometrySpec().removePropertyChangeListener(this);
        for (SubVolume sv : oldValue.getGeometrySpec().getSubVolumes()) {
            sv.removePropertyChangeListener(this);
        }
    }
    fieldGeometry = geometry;
    if (fieldGeometry != null) {
        fieldGeometry.getGeometrySpec().addPropertyChangeListener(this);
        for (SubVolume sv : fieldGeometry.getGeometrySpec().getSubVolumes()) {
            sv.addPropertyChangeListener(this);
        }
        autoCompleteSymbolFilter = new AutoCompleteSymbolFilter() {

            public boolean accept(SymbolTableEntry ste) {
                int dimension = fieldGeometry.getDimension();
                if (ste.equals(ReservedVariable.X) || dimension > 1 && ste.equals(ReservedVariable.Y) || dimension > 2 && ste.equals(ReservedVariable.Z)) {
                    return true;
                }
                return false;
            }

            public boolean acceptFunction(String funcName) {
                return true;
            }
        };
    }
    firePropertyChange("geometry", oldValue, fieldGeometry);
}