Examples with ReservedVariable cbit.vcell.math.ReservedVariable used on opensource projects

Example 1 with ReservedVariable

use of cbit.vcell.math.ReservedVariable in project vcell by virtualcell.

the class ParameterEstimationPanel method initialize.

@Override
protected void initialize() {
    super.initialize();
    setName("Parameter Estimation");
    setLayout(new java.awt.BorderLayout());
    referenceDataPanel = new ReferenceDataPanel();
    runTaskPanel = new ParameterEstimationRunTaskPanel();
    getparameterMappingPanel().setBorder(GuiConstants.TAB_PANEL_BORDER);
    referenceDataPanel.setBorder(GuiConstants.TAB_PANEL_BORDER);
    getDataMappingPanel().setBorder(GuiConstants.TAB_PANEL_BORDER);
    runTaskPanel.setBorder(GuiConstants.TAB_PANEL_BORDER);
    tabbedPane.addTab(ParameterEstimationPanelTabID.parameters.title, getparameterMappingPanel());
    tabbedPane.addTab(ParameterEstimationPanelTabID.experimental_data_import.title, referenceDataPanel);
    tabbedPane.addTab(ParameterEstimationPanelTabID.experimental_data_mapping.title, getDataMappingPanel());
    tabbedPane.addTab(ParameterEstimationPanelTabID.run_task.title, runTaskPanel);
    add(tabbedPane, BorderLayout.CENTER);
    add(getButtonPanel(), BorderLayout.NORTH);
    getNewAnalysisTaskButton().addActionListener(eventHandler);
    getDeleteAnalysisTaskButton().addActionListener(eventHandler);
    getCopyButton().addActionListener(eventHandler);
    getAnalysisTaskComboBox().addActionListener(eventHandler);
    getMapButton().addActionListener(eventHandler);
    getEvaluateConfidenceIntervalButton().addActionListener(eventHandler);
    getDataModelMappingTable().getSelectionModel().addListSelectionListener(eventHandler);
    dataModelMappingTable.addMouseListener(eventHandler);
    getDataModelMappingTable().setDefaultRenderer(SymbolTableEntry.class, new DefaultScrollTableCellRenderer() {

        public java.awt.Component getTableCellRendererComponent(javax.swing.JTable table, Object value, boolean isSelected, boolean hasFocus, int row, int column) {
            super.getTableCellRendererComponent(table, value, isSelected, hasFocus, row, column);
            if (value == null) {
                setText("unmapped");
                return this;
            }
            SymbolTableEntry ste = (SymbolTableEntry) value;
            if (ste instanceof Model.ReservedSymbol) {
                setText(ste.getName());
            } else if (ste instanceof SpeciesContext) {
                setText("[" + ste.getName() + "]");
            } else if (ste instanceof KineticsParameter) {
                setText(ste.getNameScope().getName() + ":" + ste.getName());
            } else if (ste instanceof ModelParameter) {
                setText(ste.getName());
            } else if (ste instanceof ReservedVariable) {
                setText(ste.getName());
            } else {
                setText(ste.getNameScope().getAbsoluteScopePrefix() + ste.getName());
            }
            return this;
        }
    });
    getDataModelMappingTable().setModel(getreferenceDataMappingSpecTableModel());
    getDataModelMappingTable().createDefaultColumnsFromModel();
}

Example 2 with ReservedVariable

use of cbit.vcell.math.ReservedVariable in project vcell by virtualcell.

the class SimulationSymbolTable method hasTimeVaryingDiffusionOrAdvection.

public boolean hasTimeVaryingDiffusionOrAdvection(Variable variable) throws MathException, ExpressionException {
    Enumeration<SubDomain> enum1 = simulation.getMathDescription().getSubDomains();
    while (enum1.hasMoreElements()) {
        SubDomain subDomain = enum1.nextElement();
        Equation equation = subDomain.getEquation(variable);
        // 
        if (equation instanceof PdeEquation) {
            Vector<Expression> spatialExpressionList = new Vector<Expression>();
            spatialExpressionList.add(((PdeEquation) equation).getDiffusionExpression());
            if (((PdeEquation) equation).getVelocityX() != null) {
                spatialExpressionList.add(((PdeEquation) equation).getVelocityX());
            }
            if (((PdeEquation) equation).getVelocityY() != null) {
                spatialExpressionList.add(((PdeEquation) equation).getVelocityY());
            }
            if (((PdeEquation) equation).getVelocityZ() != null) {
                spatialExpressionList.add(((PdeEquation) equation).getVelocityZ());
            }
            for (int i = 0; i < spatialExpressionList.size(); i++) {
                Expression spatialExp = spatialExpressionList.elementAt(i);
                spatialExp = substituteFunctions(spatialExp);
                String[] symbols = spatialExp.getSymbols();
                if (symbols != null) {
                    for (int j = 0; j < symbols.length; j++) {
                        SymbolTableEntry entry = spatialExp.getSymbolBinding(symbols[j]);
                        if (entry instanceof ReservedVariable) {
                            if (((ReservedVariable) entry).isTIME()) {
                                return true;
                            }
                        }
                        if (entry instanceof VolVariable) {
                            return true;
                        }
                        if (entry instanceof VolumeRegionVariable) {
                            return true;
                        }
                        if (entry instanceof MemVariable || entry instanceof MembraneRegionVariable) {
                            return true;
                        }
                    }
                }
            }
        }
    }
    return false;
}

Example 3 with ReservedVariable

use of cbit.vcell.math.ReservedVariable in project vcell by virtualcell.

the class OutputFunctionContext method getAutoCompleteSymbolFilter.

public AutoCompleteSymbolFilter getAutoCompleteSymbolFilter(final Domain functionDomain) {
    AutoCompleteSymbolFilter stef = new AutoCompleteSymbolFilter() {

        public boolean accept(SymbolTableEntry ste) {
            if (simulationOwner.getGeometry().getDimension() > 0) {
                if (functionDomain == null) {
                    return true;
                }
                if (ste.getName().endsWith(InsideVariable.INSIDE_VARIABLE_SUFFIX) || ste.getName().endsWith(OutsideVariable.OUTSIDE_VARIABLE_SUFFIX)) {
                    return false;
                }
                if (ste instanceof ReservedVariable) {
                    return true;
                }
                if (ste instanceof AnnotatedFunction) {
                    return functionDomain.compareEqual(((AnnotatedFunction) ste).getDomain());
                }
                if (ste instanceof Variable) {
                    Variable var = (Variable) ste;
                    if (var.getDomain() == null) {
                        return true;
                    }
                    GeometryClass gc = simulationOwner.getGeometry().getGeometryClass(functionDomain.getName());
                    GeometryClass vargc = simulationOwner.getGeometry().getGeometryClass(var.getDomain().getName());
                    if (gc instanceof SurfaceClass && vargc instanceof SubVolume) {
                        if (((SurfaceClass) gc).isAdjacentTo((SubVolume) vargc)) {
                            return true;
                        } else {
                            return false;
                        }
                    } else {
                        return var.getDomain().compareEqual(functionDomain);
                    }
                }
            }
            return true;
        }

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

Example 4 with ReservedVariable

use of cbit.vcell.math.ReservedVariable in project vcell by virtualcell.

the class SymbolTableEntryTableCellRenderer method getTableCellRendererComponent.

public java.awt.Component getTableCellRendererComponent(javax.swing.JTable table, Object value, boolean isSelected, boolean hasFocus, int row, int column) {
    super.getTableCellRendererComponent(table, value, isSelected, hasFocus, row, column);
    if (value == null) {
        setText("unmapped");
        return this;
    }
    SymbolTableEntry ste = (SymbolTableEntry) value;
    if (ste instanceof Model.ReservedSymbol) {
        setText(ste.getName());
    } else if (ste instanceof SpeciesContext) {
        setText("[" + ste.getName() + "]");
    } else if (ste instanceof KineticsParameter) {
        setText(ste.getNameScope().getName() + ":" + ste.getName());
    } else if (ste instanceof ModelParameter) {
        setText(ste.getName());
    } else if (ste instanceof ReservedVariable) {
        setText(ste.getName());
    } else {
        setText(ste.getNameScope().getAbsoluteScopePrefix() + ste.getName());
    }
    // setToolTipText("Kinetic parameter \""+ste.getName()+"\" in reaction "+);
    return this;
}

Example 5 with ReservedVariable

use of cbit.vcell.math.ReservedVariable in project vcell by virtualcell.

the class DataSetControllerImpl method identifyDataDependencies.

private Vector<DataSetIdentifier> identifyDataDependencies(AnnotatedFunction function) {
    // 
    // identify data dependencies
    // 
    Expression exp = function.getExpression();
    String[] dependentIDs = exp.getSymbols();
    Vector<DataSetIdentifier> dependencyList = new Vector<DataSetIdentifier>();
    // 
    // get Dependents
    // variables are indexed by a number, t=0, x=1, y=2, z=3, a(i) = 4+i where a's are other variables
    // 
    int varIndex = TXYZ_OFFSET;
    for (int i = 0; dependentIDs != null && i < dependentIDs.length; i++) {
        SymbolTableEntry ste = exp.getSymbolBinding(dependentIDs[i]);
        if (ste instanceof DataSetIdentifier) {
            DataSetIdentifier dsi = (DataSetIdentifier) ste;
            dependencyList.addElement(dsi);
            dsi.setIndex(varIndex++);
        } else if (ste instanceof ReservedVariable) {
            ReservedVariable rv = (ReservedVariable) ste;
            if (rv.isTIME()) {
                rv.setIndex(0);
            } else if (rv.isX()) {
                rv.setIndex(1);
            } else if (rv.isY()) {
                rv.setIndex(2);
            } else if (rv.isZ()) {
                rv.setIndex(3);
            }
        }
    }
    return dependencyList;
}