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

Example 36 with Constant

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

the class MatlabOdeFileCoder method write_V6_MFile.

/**
 * Insert the method's description here.
 * Creation date: (3/8/00 10:31:52 PM)
 */
public void write_V6_MFile(java.io.PrintWriter pw, String functionName) throws MathException, ExpressionException {
    MathDescription mathDesc = simulation.getMathDescription();
    if (!mathDesc.isValid()) {
        throw new MathException("invalid math description\n" + mathDesc.getWarning());
    }
    if (mathDesc.isSpatial()) {
        throw new MathException("spatial math description, cannot create ode file");
    }
    if (mathDesc.hasFastSystems()) {
        throw new MathException("math description contains algebraic constraints, cannot create .m file");
    }
    // 
    // print function declaration
    // 
    pw.println("function [T,Y,yinit,param, allNames, allValues] = " + functionName + "(argTimeSpan,argYinit,argParam)");
    pw.println("% [T,Y,yinit,param] = " + functionName + "(argTimeSpan,argYinit,argParam)");
    pw.println("%");
    pw.println("% input:");
    pw.println("%     argTimeSpan is a vector of start and stop times (e.g. timeSpan = [0 10.0])");
    pw.println("%     argYinit is a vector of initial conditions for the state variables (optional)");
    pw.println("%     argParam is a vector of values for the parameters (optional)");
    pw.println("%");
    pw.println("% output:");
    pw.println("%     T is the vector of times");
    pw.println("%     Y is the vector of state variables");
    pw.println("%     yinit is the initial conditions that were used");
    pw.println("%     param is the parameter vector that was used");
    pw.println("%     allNames is the output solution variable names");
    pw.println("%     allValues is the output solution variable values corresponding to the names");
    pw.println("%");
    pw.println("%     example of running this file: [T,Y,yinit,param,allNames,allValues] = myMatlabFunc; <-(your main function name)");
    pw.println("%");
    VariableHash varHash = new VariableHash();
    for (Variable var : simulationSymbolTable.getVariables()) {
        varHash.addVariable(var);
    }
    Variable[] variables = varHash.getTopologicallyReorderedVariables();
    CompartmentSubDomain subDomain = (CompartmentSubDomain) mathDesc.getSubDomains().nextElement();
    // 
    // collect "true" constants (Constants without identifiers)
    // 
    // 
    // collect "variables" (VolVariables only)
    // 
    // 
    // collect "functions" (Functions and Constants with identifiers)
    // 
    Vector<Constant> constantList = new Vector<Constant>();
    Vector<VolVariable> volVarList = new Vector<VolVariable>();
    Vector<Variable> functionList = new Vector<Variable>();
    for (int i = 0; i < variables.length; i++) {
        if (variables[i] instanceof Constant) {
            Constant constant = (Constant) variables[i];
            String[] symbols = constant.getExpression().getSymbols();
            if (symbols == null || symbols.length == 0) {
                constantList.addElement(constant);
            } else {
                functionList.add(constant);
            }
        } else if (variables[i] instanceof VolVariable) {
            volVarList.addElement((VolVariable) variables[i]);
        } else if (variables[i] instanceof Function) {
            functionList.addElement(variables[i]);
        }
    }
    Constant[] constants = (Constant[]) BeanUtils.getArray(constantList, Constant.class);
    VolVariable[] volVars = (VolVariable[]) BeanUtils.getArray(volVarList, VolVariable.class);
    Variable[] functions = (Variable[]) BeanUtils.getArray(functionList, Variable.class);
    int numVars = volVarList.size() + functionList.size();
    String varNamesForStringArray = "";
    String varNamesForValueArray = "";
    for (Variable var : volVarList) {
        varNamesForStringArray = varNamesForStringArray + "'" + var.getName() + "';";
        varNamesForValueArray = varNamesForValueArray + var.getName() + " ";
    }
    for (Variable func : functionList) {
        varNamesForStringArray = varNamesForStringArray + "'" + func.getName() + "';";
        varNamesForValueArray = varNamesForValueArray + func.getName() + " ";
    }
    pw.println("");
    pw.println("%");
    pw.println("% Default time span");
    pw.println("%");
    double beginTime = 0.0;
    double endTime = simulation.getSolverTaskDescription().getTimeBounds().getEndingTime();
    pw.println("timeSpan = [" + beginTime + " " + endTime + "];");
    pw.println("");
    pw.println("% output variable lengh and names");
    pw.println("numVars = " + numVars + ";");
    pw.println("allNames = {" + varNamesForStringArray + "};");
    pw.println("");
    pw.println("if nargin >= 1");
    pw.println("\tif length(argTimeSpan) > 0");
    pw.println("\t\t%");
    pw.println("\t\t% TimeSpan overridden by function arguments");
    pw.println("\t\t%");
    pw.println("\t\ttimeSpan = argTimeSpan;");
    pw.println("\tend");
    pw.println("end");
    pw.println("%");
    pw.println("% Default Initial Conditions");
    pw.println("%");
    pw.println("yinit = [");
    for (int j = 0; j < volVars.length; j++) {
        Expression initial = subDomain.getEquation(volVars[j]).getInitialExpression();
        double defaultInitialCondition = 0;
        try {
            initial.bindExpression(mathDesc);
            defaultInitialCondition = initial.evaluateConstant();
            pw.println("\t" + defaultInitialCondition + ";\t\t% yinit(" + (j + 1) + ") is the initial condition for '" + cbit.vcell.parser.SymbolUtils.getEscapedTokenMatlab(volVars[j].getName()) + "'");
        } catch (ExpressionException e) {
            e.printStackTrace(System.out);
            pw.println("\t" + initial.infix_Matlab() + ";\t\t% yinit(" + (j + 1) + ") is the initial condition for '" + cbit.vcell.parser.SymbolUtils.getEscapedTokenMatlab(volVars[j].getName()) + "'");
        // throw new RuntimeException("error evaluating initial condition for variable "+volVars[j].getName());
        }
    }
    pw.println("];");
    pw.println("if nargin >= 2");
    pw.println("\tif length(argYinit) > 0");
    pw.println("\t\t%");
    pw.println("\t\t% initial conditions overridden by function arguments");
    pw.println("\t\t%");
    pw.println("\t\tyinit = argYinit;");
    pw.println("\tend");
    pw.println("end");
    pw.println("%");
    pw.println("% Default Parameters");
    pw.println("%   constants are only those \"Constants\" from the Math Description that are just floating point numbers (no identifiers)");
    pw.println("%   note: constants of the form \"A_init\" are really initial conditions and are treated in \"yinit\"");
    pw.println("%");
    pw.println("param = [");
    int paramIndex = 0;
    for (int i = 0; i < constants.length; i++) {
        pw.println("\t" + constants[i].getExpression().infix_Matlab() + ";\t\t% param(" + (paramIndex + 1) + ") is '" + cbit.vcell.parser.SymbolUtils.getEscapedTokenMatlab(constants[i].getName()) + "'");
        paramIndex++;
    }
    pw.println("];");
    pw.println("if nargin >= 3");
    pw.println("\tif length(argParam) > 0");
    pw.println("\t\t%");
    pw.println("\t\t% parameter values overridden by function arguments");
    pw.println("\t\t%");
    pw.println("\t\tparam = argParam;");
    pw.println("\tend");
    pw.println("end");
    pw.println("%");
    pw.println("% invoke the integrator");
    pw.println("%");
    pw.println("[T,Y] = ode15s(@f,timeSpan,yinit,odeset('OutputFcn',@odeplot),param,yinit);");
    pw.println("");
    pw.println("% get the solution");
    pw.println("all = zeros(size(T), numVars);");
    pw.println("for i = 1:size(T)");
    pw.println("\tall(i,:) = getRow(T(i), Y(i,:), yinit, param);");
    pw.println("end");
    pw.println("");
    pw.println("allValues = all;");
    pw.println("end");
    // get row data for solution
    pw.println("");
    pw.println("% -------------------------------------------------------");
    pw.println("% get row data");
    pw.println("function rowValue = getRow(t,y,y0,p)");
    // 
    // print volVariables (in order and assign to var vector)
    // 
    pw.println("\t% State Variables");
    for (int i = 0; i < volVars.length; i++) {
        pw.println("\t" + cbit.vcell.parser.SymbolUtils.getEscapedTokenMatlab(volVars[i].getName()) + " = y(" + (i + 1) + ");");
    }
    // 
    // print constants
    // 
    pw.println("\t% Constants");
    paramIndex = 0;
    for (int i = 0; i < constants.length; i++) {
        pw.println("\t" + cbit.vcell.parser.SymbolUtils.getEscapedTokenMatlab(constants[i].getName()) + " = p(" + (paramIndex + 1) + ");");
        paramIndex++;
    }
    // 
    // print variables
    // 
    pw.println("\t% Functions");
    for (int i = 0; i < functions.length; i++) {
        pw.println("\t" + cbit.vcell.parser.SymbolUtils.getEscapedTokenMatlab(functions[i].getName()) + " = " + functions[i].getExpression().infix_Matlab() + ";");
    }
    pw.println("");
    pw.println("\trowValue = [" + varNamesForValueArray + "];");
    pw.println("end");
    // 
    // print ode-rate
    // 
    pw.println("");
    pw.println("% -------------------------------------------------------");
    pw.println("% ode rate");
    pw.println("function dydt = f(t,y,p,y0)");
    // 
    // print volVariables (in order and assign to var vector)
    // 
    pw.println("\t% State Variables");
    for (int i = 0; i < volVars.length; i++) {
        pw.println("\t" + cbit.vcell.parser.SymbolUtils.getEscapedTokenMatlab(volVars[i].getName()) + " = y(" + (i + 1) + ");");
    }
    // 
    // print constants
    // 
    pw.println("\t% Constants");
    paramIndex = 0;
    for (int i = 0; i < constants.length; i++) {
        pw.println("\t" + cbit.vcell.parser.SymbolUtils.getEscapedTokenMatlab(constants[i].getName()) + " = p(" + (paramIndex + 1) + ");");
        paramIndex++;
    }
    // 
    // print variables
    // 
    pw.println("\t% Functions");
    for (int i = 0; i < functions.length; i++) {
        pw.println("\t" + cbit.vcell.parser.SymbolUtils.getEscapedTokenMatlab(functions[i].getName()) + " = " + functions[i].getExpression().infix_Matlab() + ";");
    }
    pw.println("\t% Rates");
    pw.println("\tdydt = [");
    for (int i = 0; i < volVars.length; i++) {
        pw.println("\t\t" + subDomain.getEquation(volVars[i]).getRateExpression().infix_Matlab() + ";    % rate for " + cbit.vcell.parser.SymbolUtils.getEscapedTokenMatlab(volVars[i].getName()));
    }
    pw.println("\t];");
    pw.println("end");
}

Example 37 with Constant

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

the class MathDescPanel method refreshEquations.

/**
 * This method was created by a SmartGuide.
 */
private void refreshEquations() throws ExpressionException {
    TreePath selectionPath = getselectionModel1().getSelectionPath();
    if (selectionPath != null) {
        BioModelNode node = (BioModelNode) selectionPath.getLastPathComponent();
        Object[] objectPath = node.getUserObjectPath();
        Object lastPathObject = objectPath[objectPath.length - 1];
        // for non-stochastic
        Expression[] expArray = null;
        // for stochastic
        String[] expString = null;
        getExpressionCanvas1().setStrings(null);
        getExpressionCanvas1().setExpressions(null);
        if (lastPathObject instanceof Function) {
            Function function = (Function) lastPathObject;
            Expression exp = function.getExpression();
            if (getJRadioButtonValue().isSelected()) {
                exp.bindExpression(getMathDescription());
            } else {
                exp.bindExpression(null);
            }
            exp = exp.flatten();
            // stochastic variable initial value must be an int, therefore we must make it here.
            if (getMathDescription().isNonSpatialStoch() && function.getName().startsWith(DiffEquMathMapping.MATH_FUNC_SUFFIX_SPECIES_INIT_CONC_UNIT_PREFIX)) {
                try {
                    double value = exp.evaluateConstant();
                    expString = new String[] { function.getName() + " = " + Math.round(value) };
                    getExpressionCanvas1().setStrings(expString);
                } catch (Exception e) {
                    expArray = new Expression[] { Expression.assign(new Expression(function.getName()), exp) };
                    getExpressionCanvas1().setExpressions(expArray);
                }
            } else {
                expArray = new Expression[] { Expression.assign(new Expression(function.getName()), exp) };
                getExpressionCanvas1().setExpressions(expArray);
            }
        } else if (lastPathObject instanceof Constant) {
            Constant constant = (Constant) lastPathObject;
            Expression exp = constant.getExpression();
            if (getJRadioButtonValue().isSelected()) {
                exp.bindExpression(getMathDescription());
            } else {
                exp.bindExpression(null);
            }
            exp = exp.flatten();
            // stochastic variable initial value must be an int, therefore we must make it here.
            if (getMathDescription().isNonSpatialStoch() && constant.getName().startsWith(DiffEquMathMapping.MATH_FUNC_SUFFIX_SPECIES_INIT_CONC_UNIT_PREFIX)) {
                try {
                    double value = exp.evaluateConstant();
                    expString = new String[] { constant.getName() + " = " + Math.round(value) };
                    getExpressionCanvas1().setStrings(expString);
                } catch (Exception e) {
                    expArray = new Expression[] { Expression.assign(new Expression(constant.getName()), exp) };
                    getExpressionCanvas1().setExpressions(expArray);
                }
            } else {
                expArray = new Expression[] { Expression.assign(new Expression(constant.getName()), exp) };
                getExpressionCanvas1().setExpressions(expArray);
            }
        } else if (lastPathObject instanceof Equation) {
            Equation equ = (Equation) lastPathObject;
            Enumeration<Expression> enum_equ = equ.getTotalExpressions();
            Vector<Expression> expList = new Vector<Expression>();
            while (enum_equ.hasMoreElements()) {
                Expression exp = new Expression(enum_equ.nextElement());
                if (getJRadioButtonValue().isSelected()) {
                    exp.bindExpression(getMathDescription());
                } else {
                    exp.bindExpression(null);
                }
                expList.addElement(exp.flatten());
            }
            expArray = new Expression[expList.size()];
            expList.copyInto(expArray);
            getExpressionCanvas1().setExpressions(expArray);
        } else if (// added Sept 29, 2006
        lastPathObject instanceof VarIniCondition) {
            VarIniCondition varIni = (VarIniCondition) lastPathObject;
            expString = new String[] { varIni.toString() };
            getExpressionCanvas1().setStrings(expString);
        } else if (// added Sept 29, 2006
        lastPathObject instanceof Action) {
            Action action = (Action) lastPathObject;
            expString = new String[] { action.toString() };
            getExpressionCanvas1().setStrings(expString);
        } else if (// added Sept 29, 2006
        lastPathObject instanceof String) {
            // to check if the string is the probability string
            int index1 = ((String) lastPathObject).indexOf("probability_rate");
            int index2 = ((String) lastPathObject).indexOf("=");
            if (// has probability eqution,but don't calculate prob string, since it is not a constant value.
            (index1 == 0) && ((index2 + 2) < ((String) lastPathObject).length())) {
                expString = new String[] { (String) lastPathObject };
                getExpressionCanvas1().setStrings(expString);
            }
        }
    } else {
        getExpressionCanvas1().setExpressions(null);
        getExpressionCanvas1().setStrings(null);
        getExpressionCanvas1().repaint();
    }
// Variable var = getMathDescription().getVariable(varName);
// SubDomain subDomain = getMathDescription().getSubDomain(subDomainName);
// Equation equ = null;
// if (var != null && subDomain != null){
// equ = subDomain.getEquation(var);
// }
// if (equ == null){
// if (subDomain instanceof MembraneSubDomain && var instanceof VolVariable){
// equ = ((MembraneSubDomain)subDomain).getJumpCondition((VolVariable)var);
// }
// }
// if (equ == null){
// Expression exp = null;
// String title = "hello";
// if (var instanceof Constant || var instanceof Function){
// exp = var.getExpression();
// title = "Expression for "+var.getName();
// }
// if (getJRadioButtonValue().isSelected()){
// exp.bindExpression(getMathDescription());
// }else{
// exp.bindExpression(null);
// }
// getExpressionCanvas1().setExpression(exp.flatten());
// getEquationTitleLabel().setText(title);
// }else{
// Enumeration enum_equ = equ.getTotalExpressions();
// Vector expList = new Vector();
// while (enum_equ.hasMoreElements()){
// Expression exp = new Expression((Expression)enum_equ.nextElement());
// if (getJRadioButtonValue().isSelected()){
// exp.bindExpression(getMathDescription());
// }else{
// exp.bindExpression(null);
// }
// expList.addElement(exp.flatten());
// }
// Expression expArray[] = new Expression[expList.size()];
// expList.copyInto(expArray);
// getExpressionCanvas1().setExpressions(expArray);
// getEquationTitleLabel().setText("Equations for "+var.getName()+" within "+subDomain.getName());
// }
// } catch (java.lang.Throwable ivjExc) {
// handleException(ivjExc);
// getEquationTitleLabel().setText("Equations for "+varName+" within "+subDomainName+" *** "+ivjExc.getMessage());
// }
// }
// }else{
// getEquationTitleLabel().setText("no variable selected");
// getExpressionCanvas1().setExpression((Expression)null);
// }
}

Example 38 with Constant

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

the class MathDescriptionCellRenderer method getTreeCellRendererComponent.

/**
 * Insert the method's description here.
 * Creation date: (7/27/2000 6:41:57 PM)
 * @return java.awt.Component
 */
public java.awt.Component getTreeCellRendererComponent(JTree tree, Object value, boolean sel, boolean expanded, boolean leaf, int row, boolean hasFocus) {
    JLabel component = (JLabel) super.getTreeCellRendererComponent(tree, value, sel, expanded, leaf, row, hasFocus);
    boolean bLoaded = false;
    // 
    try {
        if (value instanceof BioModelNode) {
            BioModelNode node = (BioModelNode) value;
            if (node.getUserObject() instanceof PdeEquation) {
                PdeEquation pdeEquation = (PdeEquation) node.getUserObject();
                Variable var = pdeEquation.getVariable();
                component.setToolTipText("PDE Equation");
                // \u2207 = nabla ... del operator
                // \u2219 = dot
                String DEL = "\u2207";
                // "\u2202";     //  '\u2202' is partial differentiation    'd' is regular diff
                String PARTIAL_DIFF = "d";
                String Super2 = "\u00b2";
                String DOT = "\u2219";
                // String diffusionTerm = DEL+" "+DOT+" "+"("+pdeEquation.getDiffusionExpression()+" "+DEL+" "+var.getName()+")";
                String diffusionTerm = "";
                if (pdeEquation.getVelocityX() != null || pdeEquation.getVelocityY() != null || pdeEquation.getVelocityZ() != null) {
                    if (pdeEquation.getDiffusionExpression().isZero()) {
                        // reaction/advection
                        diffusionTerm = "- " + DEL + " " + DOT + "( velocity " + var.getName() + " )";
                    } else {
                        // reaction/diffusion/advection
                        diffusionTerm = DEL + " " + DOT + " (" + pdeEquation.getDiffusionExpression().infix() + " " + DEL + "  " + var.getName() + "   -   velocity " + var.getName() + ")";
                    }
                } else {
                    diffusionTerm = "(" + pdeEquation.getDiffusionExpression().infix() + ") " + DEL + Super2 + " " + var.getName();
                }
                String gradTerm = "";
                if (pdeEquation.getGradientX() != null && !pdeEquation.getGradientX().isZero()) {
                    gradTerm += " + " + PARTIAL_DIFF + "[" + pdeEquation.getGradientX().infix() + "]/" + PARTIAL_DIFF + "x";
                }
                if (pdeEquation.getGradientY() != null && !pdeEquation.getGradientY().isZero()) {
                    gradTerm += " + " + PARTIAL_DIFF + "[" + pdeEquation.getGradientY().infix() + "]/" + PARTIAL_DIFF + "y";
                }
                if (pdeEquation.getGradientZ() != null && !pdeEquation.getGradientZ().isZero()) {
                    gradTerm += " + " + PARTIAL_DIFF + "[" + pdeEquation.getGradientZ().infix() + "]/" + PARTIAL_DIFF + "z";
                }
                String sourceTerm = pdeEquation.getRateExpression().infix();
                if (!sourceTerm.equals("0.0")) {
                    component.setText(PARTIAL_DIFF + "[" + var.getName() + "]/" + PARTIAL_DIFF + "t = " + diffusionTerm + gradTerm + " + " + sourceTerm);
                } else {
                    component.setText(PARTIAL_DIFF + "[" + var.getName() + "]/" + PARTIAL_DIFF + "t = " + diffusionTerm + gradTerm);
                }
            } else if (node.getUserObject() instanceof OdeEquation) {
                OdeEquation odeEquation = (OdeEquation) node.getUserObject();
                Variable var = odeEquation.getVariable();
                component.setToolTipText("ODE Equation");
                component.setText("d[" + var.getName() + "]/dt = " + odeEquation.getRateExpression().infix());
            } else if (node.getUserObject() instanceof MembraneRegionEquation) {
                MembraneRegionEquation membraneRegionEquation = (MembraneRegionEquation) node.getUserObject();
                Variable var = membraneRegionEquation.getVariable();
                component.setToolTipText("Membrane Region Equation");
                component.setText("Membrane Region Equation for " + var.getName());
            } else if (node.getUserObject() instanceof JumpCondition) {
                JumpCondition jumpCondition = (JumpCondition) node.getUserObject();
                Variable var = jumpCondition.getVariable();
                component.setToolTipText("Jump Condition");
                component.setText("Flux for " + var.getName());
            } else if (node.getUserObject() instanceof Constant) {
                Constant constant = (Constant) node.getUserObject();
                component.setToolTipText("Constant");
                component.setText(constant.getName() + " = " + constant.getExpression().infix());
            } else if (node.getUserObject() instanceof Function) {
                Function function = (Function) node.getUserObject();
                component.setToolTipText("Function");
                component.setText(function.getName() + " = " + function.getExpression().infix());
            } else if (node.getUserObject() instanceof SubDomain) {
                SubDomain subDomain = (SubDomain) node.getUserObject();
                component.setToolTipText("SubDomain");
                component.setText(subDomain.getName());
            } else if (node.getUserObject() instanceof FastSystem) {
                component.setToolTipText("Fast System");
                component.setText("Fast System");
            } else if (node.getUserObject() instanceof FastInvariant) {
                FastInvariant fi = (FastInvariant) node.getUserObject();
                component.setToolTipText("Fast Invariant");
                component.setText("fast invariant: " + fi.getFunction().infix());
            } else if (node.getUserObject() instanceof FastRate) {
                FastRate fr = (FastRate) node.getUserObject();
                component.setToolTipText("Fast Rate");
                component.setText("fast rate: " + fr.getFunction().infix());
            } else if (node.getUserObject() instanceof Annotation) {
                Annotation annotation = (Annotation) node.getUserObject();
                component.setToolTipText("Annotation");
                component.setText("\"" + annotation + "\"");
            } else {
            }
            if (selectedFont == null && component.getFont() != null) {
                selectedFont = component.getFont().deriveFont(Font.BOLD);
            }
            if (unselectedFont == null && component.getFont() != null) {
                unselectedFont = component.getFont().deriveFont(Font.PLAIN);
            }
            if (bLoaded) {
                component.setFont(selectedFont);
            } else {
                component.setFont(unselectedFont);
            }
        }
    } catch (Throwable e) {
        e.printStackTrace(System.out);
    }
    // 
    return component;
}

Example 39 with Constant

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

the class MathDescriptionTreeModel method createBaseTree.

/**
 * Insert the method's description here.
 * Creation date: (11/28/00 1:06:51 PM)
 * @return cbit.vcell.desktop.BioModelNode
 * @param docManager cbit.vcell.clientdb.DocumentManager
 */
private BioModelNode createBaseTree() {
    if (getMathDescription() == null) {
        return new BioModelNode(" ", false);
    }
    // 
    // make root node
    // 
    BioModelNode rootNode = new BioModelNode("math description", true);
    // 
    // create subTree of Constants
    // 
    BioModelNode constantRootNode = new BioModelNode("constants", true);
    Enumeration<Constant> enum1 = getMathDescription().getConstants();
    while (enum1.hasMoreElements()) {
        Constant constant = enum1.nextElement();
        BioModelNode constantNode = new BioModelNode(constant, false);
        constantRootNode.add(constantNode);
    }
    if (constantRootNode.getChildCount() > 0) {
        rootNode.add(constantRootNode);
    }
    // 
    // create subTree of Functions
    // 
    BioModelNode functionRootNode = new BioModelNode("functions", true);
    Enumeration<Function> enum2 = getMathDescription().getFunctions();
    while (enum2.hasMoreElements()) {
        Function function = enum2.nextElement();
        BioModelNode functionNode = new BioModelNode(function, false);
        functionRootNode.add(functionNode);
    }
    if (functionRootNode.getChildCount() > 0) {
        rootNode.add(functionRootNode);
    }
    // 
    // create subTree of VolumeSubDomains and MembraneSubDomains
    // 
    BioModelNode volumeRootNode = new BioModelNode("volume domains", true);
    BioModelNode membraneRootNode = new BioModelNode("membrane domains", true);
    Enumeration<SubDomain> enum3 = getMathDescription().getSubDomains();
    while (enum3.hasMoreElements()) {
        SubDomain subDomain = enum3.nextElement();
        if (subDomain instanceof cbit.vcell.math.CompartmentSubDomain) {
            CompartmentSubDomain volumeSubDomain = (CompartmentSubDomain) subDomain;
            BioModelNode volumeSubDomainNode = new BioModelNode(volumeSubDomain, true);
            if (// stochastic subtree
            getMathDescription().isNonSpatialStoch()) {
                // add stoch variable initial conditions
                BioModelNode varIniConditionNode = new BioModelNode("variable_initial_conditions", true);
                for (VarIniCondition varIni : volumeSubDomain.getVarIniConditions()) {
                    BioModelNode varIniNode = new BioModelNode(varIni, false);
                    varIniConditionNode.add(varIniNode);
                }
                volumeSubDomainNode.add(varIniConditionNode);
                // add jump processes
                for (JumpProcess jp : volumeSubDomain.getJumpProcesses()) {
                    BioModelNode jpNode = new BioModelNode(jp, true);
                    // add probability rate.
                    String probRate = "P_" + jp.getName();
                    BioModelNode prNode = new BioModelNode("probability_rate = " + probRate, false);
                    jpNode.add(prNode);
                    // add Actions
                    Enumeration<Action> actions = Collections.enumeration(jp.getActions());
                    while (actions.hasMoreElements()) {
                        Action action = actions.nextElement();
                        BioModelNode actionNode = new BioModelNode(action, false);
                        jpNode.add(actionNode);
                    }
                    volumeSubDomainNode.add(jpNode);
                }
            } else // non-stochastic subtree
            {
                // 
                // add equation children
                // 
                Enumeration<Equation> eqnEnum = volumeSubDomain.getEquations();
                while (eqnEnum.hasMoreElements()) {
                    Equation equation = eqnEnum.nextElement();
                    BioModelNode equationNode = new BioModelNode(equation, false);
                    volumeSubDomainNode.add(equationNode);
                }
                // 
                // add fast system
                // 
                FastSystem fastSystem = volumeSubDomain.getFastSystem();
                if (fastSystem != null) {
                    BioModelNode fsNode = new BioModelNode(fastSystem, true);
                    Enumeration<FastInvariant> enumFI = fastSystem.getFastInvariants();
                    while (enumFI.hasMoreElements()) {
                        FastInvariant fi = enumFI.nextElement();
                        fsNode.add(new BioModelNode(fi, false));
                    }
                    Enumeration<FastRate> enumFR = fastSystem.getFastRates();
                    while (enumFR.hasMoreElements()) {
                        FastRate fr = enumFR.nextElement();
                        fsNode.add(new BioModelNode(fr, false));
                    }
                    volumeSubDomainNode.add(fsNode);
                }
            }
            volumeRootNode.add(volumeSubDomainNode);
        } else if (subDomain instanceof MembraneSubDomain) {
            MembraneSubDomain membraneSubDomain = (MembraneSubDomain) subDomain;
            BioModelNode membraneSubDomainNode = new BioModelNode(membraneSubDomain, true);
            // 
            // add equation children
            // 
            Enumeration<Equation> eqnEnum = membraneSubDomain.getEquations();
            while (eqnEnum.hasMoreElements()) {
                Equation equation = eqnEnum.nextElement();
                BioModelNode equationNode = new BioModelNode(equation, false);
                membraneSubDomainNode.add(equationNode);
            }
            // 
            // add jump condition children
            // 
            Enumeration<JumpCondition> jcEnum = membraneSubDomain.getJumpConditions();
            while (jcEnum.hasMoreElements()) {
                JumpCondition jumpCondition = jcEnum.nextElement();
                BioModelNode jcNode = new BioModelNode(jumpCondition, false);
                membraneSubDomainNode.add(jcNode);
            }
            // 
            // add fast system
            // 
            FastSystem fastSystem = membraneSubDomain.getFastSystem();
            if (fastSystem != null) {
                BioModelNode fsNode = new BioModelNode(fastSystem, true);
                Enumeration<FastInvariant> enumFI = fastSystem.getFastInvariants();
                while (enumFI.hasMoreElements()) {
                    FastInvariant fi = enumFI.nextElement();
                    fsNode.add(new BioModelNode(fi, false));
                }
                Enumeration<FastRate> enumFR = fastSystem.getFastRates();
                while (enumFR.hasMoreElements()) {
                    FastRate fr = enumFR.nextElement();
                    fsNode.add(new BioModelNode(fr, false));
                }
                membraneSubDomainNode.add(fsNode);
            }
            membraneRootNode.add(membraneSubDomainNode);
        }
    }
    if (volumeRootNode.getChildCount() > 0) {
        rootNode.add(volumeRootNode);
    }
    if (membraneRootNode.getChildCount() > 0) {
        rootNode.add(membraneRootNode);
    }
    return rootNode;
}

Example 40 with Constant

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

the class MathOverridesPanel method jMenuItemPaste_ActionPerformed.

/**
 * Comment
 */
private void jMenuItemPaste_ActionPerformed(java.awt.event.ActionEvent actionEvent) {
    java.util.Vector<String> pasteDescriptionsV = new java.util.Vector<String>();
    java.util.Vector<Expression> newConstantsV = new java.util.Vector<Expression>();
    java.util.Vector<String> changedParameterNamesV = new java.util.Vector<String>();
    try {
        if (actionEvent.getSource().equals(getJMenuItemPaste()) || actionEvent.getSource().equals(getJMenuItemPasteAll())) {
            int[] rows = null;
            if (actionEvent.getSource() == getJMenuItemPasteAll()) {
                rows = new int[getJTableFixed().getRowCount()];
                for (int i = 0; i < rows.length; i += 1) {
                    rows[i] = i;
                }
            } else {
                rows = getJTableFixed().getSelectedRows();
            }
            Object pasteThis = VCellTransferable.getFromClipboard(VCellTransferable.OBJECT_FLAVOR);
            for (int i = 0; i < rows.length; i += 1) {
                if (pasteThis instanceof VCellTransferable.ResolvedValuesSelection) {
                    VCellTransferable.ResolvedValuesSelection rvs = (VCellTransferable.ResolvedValuesSelection) pasteThis;
                    for (int j = 0; j < rvs.getPrimarySymbolTableEntries().length; j += 1) {
                        Constant pastedConstant = null;
                        if (rvs.getPrimarySymbolTableEntries()[j] instanceof Constant) {
                            pastedConstant = (Constant) rvs.getPrimarySymbolTableEntries()[j];
                        } else if (rvs.getAlternateSymbolTableEntries() != null && rvs.getAlternateSymbolTableEntries()[j] instanceof Constant) {
                            pastedConstant = (Constant) rvs.getAlternateSymbolTableEntries()[j];
                        }
                        // 
                        if (pastedConstant == null && (rvs.getPrimarySymbolTableEntries()[j] instanceof Function) || (rvs.getPrimarySymbolTableEntries()[j] instanceof VolVariable) || (rvs.getPrimarySymbolTableEntries()[j] instanceof VolumeRegionVariable) || (rvs.getPrimarySymbolTableEntries()[j] instanceof MemVariable) || (rvs.getPrimarySymbolTableEntries()[j] instanceof MembraneRegionVariable)) {
                            MathDescription mathDescription = getMathOverrides().getSimulation().getMathDescription();
                            Enumeration<Constant> constants = mathDescription.getConstants();
                            while (constants.hasMoreElements()) {
                                Constant constant = constants.nextElement();
                                if (constant.getName().startsWith(rvs.getPrimarySymbolTableEntries()[j].getName() + DiffEquMathMapping.MATH_FUNC_SUFFIX_SPECIES_INIT_CONC_UNIT_PREFIX)) {
                                    pastedConstant = new Constant(constant.getName(), rvs.getExpressionValues()[j]);
                                }
                            }
                        }
                        // 
                        // find row of math overrides table with the same name as the pastedConstant and propose to change that override to the pasted value
                        // 
                        String rowName = (String) getJTableFixed().getValueAt(rows[i], MathOverridesTableModel.COLUMN_PARAMETER);
                        if (pastedConstant != null && pastedConstant.getName().equals(rowName)) {
                            changedParameterNamesV.add(rowName);
                            newConstantsV.add(rvs.getExpressionValues()[j]);
                            String originalValueDescription = null;
                            if (getMathOverrides().getConstantArraySpec(rowName) != null) {
                                originalValueDescription = getMathOverrides().getConstantArraySpec(rowName).toString();
                            } else if (getMathOverrides().getActualExpression(rowName, 0) != null) {
                                originalValueDescription = getMathOverrides().getActualExpression(rowName, 0).infix();
                            } else {
                                throw new Exception("MathOverridesPanel can't find value for '" + rowName + "'");
                            }
                            pasteDescriptionsV.add(VCellCopyPasteHelper.formatPasteList(rowName, pastedConstant.getName(), originalValueDescription, rvs.getExpressionValues()[j].infix() + ""));
                        }
                    }
                }
            }
        }
    } catch (Throwable e) {
        PopupGenerator.showErrorDialog(this, "Paste failed during pre-check (no changes made).\n" + e.getClass().getName() + " " + e.getMessage(), e);
        return;
    }
    // Do paste
    try {
        if (pasteDescriptionsV.size() > 0) {
            String[] pasteDescriptionArr = new String[pasteDescriptionsV.size()];
            pasteDescriptionsV.copyInto(pasteDescriptionArr);
            String[] changedParameterNamesArr = new String[changedParameterNamesV.size()];
            changedParameterNamesV.copyInto(changedParameterNamesArr);
            VCellCopyPasteHelper.chooseApplyPaste(this, pasteDescriptionArr, getMathOverrides(), changedParameterNamesArr, newConstantsV);
        } else {
            PopupGenerator.showInfoDialog(this, "No paste items match the destination (no changes made).");
        }
    } catch (Throwable e) {
        PopupGenerator.showErrorDialog(this, "Paste Error\n" + e.getClass().getName() + " " + e.getMessage(), e);
    }
}