Examples with CopasiOptimizationMethod cbit.vcell.opt.CopasiOptimizationMethod used on opensource projects

Example 1 with CopasiOptimizationMethod

use of cbit.vcell.opt.CopasiOptimizationMethod in project vcell by virtualcell.

the class ParameterEstimationRunTaskPanel method solve.

private void solve() throws NumberFormatException {
    CopasiOptimizationMethod com = optimizationMethodParameterTableModel.copasiOptimizationMethod;
    OptimizationSolverSpec optSolverSpec = new OptimizationSolverSpec(com);
    // get num runs for stochstic opt mehtods before starting solving...
    if (com.getType().isStochasticMethod()) {
        int numRuns = Integer.parseInt(((String) numberOfRunComboBox.getSelectedItem()));
        optSolverSpec.setNumOfRuns(numRuns);
    }
    parameterEstimationTask.setOptimizationSolverSpec(optSolverSpec);
    parameterEstimationTask.getModelOptimizationSpec().setComputeProfileDistributions(computeProfileDistributionsCheckBox.isSelected());
    optSolverCallbacks.reset();
    Double endValue = com.getEndValue();
    optSolverCallbacks.setEvaluation(0, Double.POSITIVE_INFINITY, 0, endValue, 0);
    // (endValue != null);
    getRunStatusDialog().showProgressBar(com);
    Collection<AsynchClientTask> taskList = ClientRequestManager.updateMath(this, parameterEstimationTask.getSimulationContext(), false, NetworkGenerationRequirements.ComputeFullStandardTimeout);
    AsynchClientTask task1 = new AsynchClientTask("checking issues", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            StringBuffer issueText = new StringBuffer();
            java.util.Vector<Issue> issueList = new java.util.Vector<Issue>();
            IssueContext issueContext = new IssueContext();
            parameterEstimationTask.gatherIssues(issueContext, issueList);
            boolean bFailed = false;
            for (int i = 0; i < issueList.size(); i++) {
                Issue issue = (Issue) issueList.elementAt(i);
                issueText.append(issue.getMessage() + "\n");
                if (issue.getSeverity() == Issue.SEVERITY_ERROR) {
                    bFailed = true;
                    break;
                }
            }
            if (bFailed) {
                throw new OptimizationException(issueText.toString());
            }
            parameterEstimationTask.refreshMappings();
        }
    };
    taskList.add(task1);
    AsynchClientTask task2 = new AsynchClientTask("solving", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            MathMappingCallback mathMappingCallback = new MathMappingCallbackTaskAdapter(getClientTaskStatusSupport());
            // OptimizationResultSet optResultSet = CopasiOptimizationSolver.solveLocalPython(new ParameterEstimationTaskSimulatorIDA(),parameterEstimationTask,optSolverCallbacks,mathMappingCallback);
            OptimizationResultSet optResultSet = CopasiOptimizationSolver.solveRemoteApi(new ParameterEstimationTaskSimulatorIDA(), parameterEstimationTask, optSolverCallbacks, mathMappingCallback);
            hashTable.put(ORS_KEY, optResultSet);
        }
    };
    taskList.add(task2);
    AsynchClientTask setResultTask = new AsynchClientTask("set results", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            OptimizationResultSet optResultSet = (OptimizationResultSet) hashTable.get(ORS_KEY);
            parameterEstimationTask.setOptimizationResultSet(optResultSet);
        }
    };
    taskList.add(setResultTask);
    ClientTaskDispatcher.dispatch(this, new Hashtable<String, Object>(), taskList.toArray(new AsynchClientTask[taskList.size()]), getRunStatusDialog(), true, true, true, null, false);
}

Example 2 with CopasiOptimizationMethod

use of cbit.vcell.opt.CopasiOptimizationMethod in project vcell by virtualcell.

the class ParameterEstimationTaskXMLPersistence method getParameterEstimationTask.

/**
 * Insert the method's description here.
 * Creation date: (5/5/2006 4:50:36 PM)
 * @return cbit.vcell.modelopt.ParameterEstimationTask
 * @param element org.jdom.Element
 * @param simContext cbit.vcell.mapping.SimulationContext
 */
public static ParameterEstimationTask getParameterEstimationTask(Element parameterEstimationTaskElement, SimulationContext simContext) throws ExpressionException, MappingException, MathException, java.beans.PropertyVetoException {
    Namespace ns = parameterEstimationTaskElement.getNamespace();
    ParameterEstimationTask parameterEstimationTask = new ParameterEstimationTask(simContext);
    String name = parameterEstimationTaskElement.getAttributeValue(NameAttribute);
    parameterEstimationTask.setName(name);
    Element annotationElement = parameterEstimationTaskElement.getChild(AnnotationTag, ns);
    if (annotationElement != null) {
        String annotationText = annotationElement.getText();
        parameterEstimationTask.setAnnotation(annotationText);
    }
    // 
    // read ParameterMappingSpecs
    // 
    Element parameterMappingSpecListElement = parameterEstimationTaskElement.getChild(ParameterMappingSpecListTag, ns);
    if (parameterMappingSpecListElement != null) {
        List<Element> parameterMappingSpecElementList = parameterMappingSpecListElement.getChildren(ParameterMappingSpecTag, ns);
        for (Element parameterMappingSpecElement : parameterMappingSpecElementList) {
            String parameterName = parameterMappingSpecElement.getAttributeValue(ParameterReferenceAttribute);
            SymbolTableEntry ste = getSymbolTableEntry(simContext, parameterName);
            if (ste instanceof Parameter) {
                Parameter parameter = (Parameter) ste;
                ParameterMappingSpec parameterMappingSpec = parameterEstimationTask.getModelOptimizationSpec().getParameterMappingSpec(parameter);
                if (parameterMappingSpec != null) {
                    String lowLimitString = parameterMappingSpecElement.getAttributeValue(LowLimitAttribute);
                    if (lowLimitString != null) {
                        parameterMappingSpec.setLow(parseDouble(lowLimitString));
                    }
                    String highLimitString = parameterMappingSpecElement.getAttributeValue(HighLimitAttribute);
                    if (highLimitString != null) {
                        parameterMappingSpec.setHigh(parseDouble(highLimitString));
                    }
                    String currentValueString = parameterMappingSpecElement.getAttributeValue(CurrentValueAttribute);
                    if (currentValueString != null) {
                        parameterMappingSpec.setCurrent(Double.parseDouble(currentValueString));
                    }
                    String selectedString = parameterMappingSpecElement.getAttributeValue(SelectedAttribute);
                    if (selectedString != null) {
                        parameterMappingSpec.setSelected(Boolean.valueOf(selectedString).booleanValue());
                    }
                }
            } else {
                System.out.println("couldn't read parameterMappingSpec '" + parameterName + "', ste=" + ste);
            }
        }
    }
    // 
    // read ReferenceData
    // 
    Element referenceDataElement = parameterEstimationTaskElement.getChild(ReferenceDataTag, ns);
    if (referenceDataElement != null) {
        String numRowsText = referenceDataElement.getAttributeValue(NumRowsAttribute);
        String numColsText = referenceDataElement.getAttributeValue(NumColumnsAttribute);
        // int numRows = Integer.parseInt(numRowsText);
        int numCols = Integer.parseInt(numColsText);
        // 
        // read columns
        // 
        String[] columnNames = new String[numCols];
        double[] columnWeights = new double[numCols];
        int columnCounter = 0;
        Element dataColumnListElement = referenceDataElement.getChild(DataColumnListTag, ns);
        List<Element> dataColumnList = dataColumnListElement.getChildren(DataColumnTag, ns);
        for (Element dataColumnElement : dataColumnList) {
            columnNames[columnCounter] = dataColumnElement.getAttributeValue(NameAttribute);
            columnWeights[columnCounter] = Double.parseDouble(dataColumnElement.getAttributeValue(WeightAttribute));
            columnCounter++;
        }
        // 
        // read rows
        // 
        Vector<double[]> rowDataVector = new Vector<double[]>();
        Element dataRowListElement = referenceDataElement.getChild(DataRowListTag, ns);
        List<Element> dataRowList = dataRowListElement.getChildren(DataRowTag, ns);
        for (Element dataRowElement : dataRowList) {
            String rowText = dataRowElement.getText();
            CommentStringTokenizer tokens = new CommentStringTokenizer(rowText);
            double[] rowData = new double[numCols];
            for (int j = 0; j < numCols; j++) {
                if (tokens.hasMoreTokens()) {
                    String token = tokens.nextToken();
                    rowData[j] = Double.parseDouble(token);
                } else {
                    throw new RuntimeException("failed to read row data for ReferenceData");
                }
            }
            rowDataVector.add(rowData);
        }
        ReferenceData referenceData = new SimpleReferenceData(columnNames, columnWeights, rowDataVector);
        parameterEstimationTask.getModelOptimizationSpec().setReferenceData(referenceData);
    }
    // 
    // read ReferenceDataMappingSpecs
    // 
    Element referenceDataMappingSpecListElement = parameterEstimationTaskElement.getChild(ReferenceDataMappingSpecListTag, ns);
    if (referenceDataMappingSpecListElement != null) {
        List<Element> referenceDataMappingSpecList = referenceDataMappingSpecListElement.getChildren(ReferenceDataMappingSpecTag, ns);
        for (Element referenceDataMappingSpecElement : referenceDataMappingSpecList) {
            String referenceDataColumnName = referenceDataMappingSpecElement.getAttributeValue(ReferenceDataColumnNameAttribute);
            String referenceDataModelSymbolName = referenceDataMappingSpecElement.getAttributeValue(ReferenceDataModelSymbolAttribute);
            ReferenceDataMappingSpec referenceDataMappingSpec = parameterEstimationTask.getModelOptimizationSpec().getReferenceDataMappingSpec(referenceDataColumnName);
            SymbolTableEntry modelSymbolTableEntry = null;
            if (referenceDataModelSymbolName != null) {
                modelSymbolTableEntry = getSymbolTableEntry(simContext, referenceDataModelSymbolName);
                if (referenceDataMappingSpec != null && modelSymbolTableEntry != null) {
                    referenceDataMappingSpec.setModelObject(modelSymbolTableEntry);
                }
            }
        }
    }
    // 
    // read OptimizationSolverSpec
    // 
    Element optimizationSolverSpecElement = parameterEstimationTaskElement.getChild(OptimizationSolverSpecTag, ns);
    if (optimizationSolverSpecElement != null) {
        OptimizationSolverSpec optSolverSpec = null;
        String optimizationSolverTypeName = optimizationSolverSpecElement.getAttributeValue(OptimizationSolverTypeAttribute);
        // getting parameters
        Element optimizationSolverParameterList = optimizationSolverSpecElement.getChild(OptimizationListOfParametersTag, ns);
        if (optimizationSolverParameterList != null) {
            List<Element> listOfSolverParams = optimizationSolverParameterList.getChildren(OptimizationParameterTag, ns);
            CopasiOptimizationMethod copasiOptMethod = null;
            if (listOfSolverParams != null && listOfSolverParams.size() > 0) {
                List<CopasiOptimizationParameter> copasiSolverParams = new ArrayList<CopasiOptimizationParameter>();
                for (Element solverParam : listOfSolverParams) {
                    String paramName = solverParam.getAttributeValue(OptimizationParameterNameAttribute);
                    double paramValue = Double.parseDouble(solverParam.getAttributeValue(OptimizationParameterValueAttribute));
                    CopasiOptimizationParameter copasiParam = new CopasiOptimizationParameter(getCopasiOptimizationParameterTypeByName(paramName), paramValue);
                    copasiSolverParams.add(copasiParam);
                }
                copasiOptMethod = new CopasiOptimizationMethod(getCopasiOptimizationMethodTypeByName(optimizationSolverTypeName), copasiSolverParams.toArray(new CopasiOptimizationParameter[copasiSolverParams.size()]));
            } else // no parameters
            {
                copasiOptMethod = new CopasiOptimizationMethod(getCopasiOptimizationMethodTypeByName(optimizationSolverTypeName), new CopasiOptimizationParameter[0]);
            }
            optSolverSpec = new OptimizationSolverSpec(copasiOptMethod);
            // add number of runs attribute
            String numOfRunsStr = optimizationSolverSpecElement.getAttributeValue(OptimizationSolverNumOfRunsAttribute);
            if (numOfRunsStr != null) {
                int numOfRuns = Integer.parseInt(numOfRunsStr);
                optSolverSpec.setNumOfRuns(numOfRuns);
            }
        }
        parameterEstimationTask.setOptimizationSolverSpec(optSolverSpec);
    }
    if (// optimization solver spec is null create a default copasi evolutionary programming
    optimizationSolverSpecElement == null || parameterEstimationTask.getOptimizationSolverSpec() == null) {
        OptimizationSolverSpec optSolverSpec = new OptimizationSolverSpec(new CopasiOptimizationMethod(CopasiOptimizationMethodType.EvolutionaryProgram));
        parameterEstimationTask.setOptimizationSolverSpec(optSolverSpec);
    }
    // read optimization solver result set
    Element optimizationResultSetElement = parameterEstimationTaskElement.getChild(OptXmlTags.OptimizationResultSet_Tag, ns);
    if (optimizationResultSetElement != null) {
        OptimizationResultSet optResultSet = null;
        // read optsolverResultSet
        if (optimizationResultSetElement.getChild(OptXmlTags.bestOptRunResultSet_Tag, ns) != null) {
            Element optSolverResultSetElement = optimizationResultSetElement.getChild(OptXmlTags.bestOptRunResultSet_Tag, ns);
            OptSolverResultSet optSolverResultSet = null;
            // get best parameters, best func value, number of evaluations and construct an optRunResultSet
            Element paramListElement = optSolverResultSetElement.getChild(OptimizationListOfParametersTag, ns);
            OptRunResultSet optRunResultSet = null;
            List<String> paramNames = new ArrayList<String>();
            List<Double> paramValues = new ArrayList<Double>();
            if (paramListElement != null && !paramListElement.getChildren().isEmpty()) {
                List<Element> paramElements = paramListElement.getChildren(OptimizationParameterTag, ns);
                if (paramElements != null) {
                    for (Element paramElement : paramElements) {
                        String paramName = paramElement.getAttributeValue(OptimizationParameterNameAttribute);
                        double paramValue = Double.parseDouble(paramElement.getAttributeValue(OptimizationParameterValueAttribute));
                        paramNames.add(paramName);
                        paramValues.add(paramValue);
                    }
                }
            }
            Element bestFuncValueElement = optSolverResultSetElement.getChild(OptXmlTags.ObjectiveFunction_Tag, ns);
            double bestFuncValue = Double.parseDouble(bestFuncValueElement.getAttributeValue(OptimizationParameterValueAttribute));
            Element numEvaluationsElement = optSolverResultSetElement.getChild(OptXmlTags.OptSolverResultSetFunctionEvaluations_Tag, ns);
            long numEvaluations = Long.parseLong(numEvaluationsElement.getAttributeValue(OptimizationParameterValueAttribute));
            // change List<Double> to double[]
            double[] values = new double[paramValues.size()];
            int index = 0;
            for (Double value : paramValues) {
                values[index++] = value;
            }
            optRunResultSet = new OptRunResultSet(values, bestFuncValue, numEvaluations, null);
            // create optSolverResultSet
            optSolverResultSet = new OptSolverResultSet(paramNames.toArray(new String[paramNames.size()]), optRunResultSet);
            // create optimization result set
            optResultSet = new OptimizationResultSet(optSolverResultSet, null);
        }
        parameterEstimationTask.setOptimizationResultSet(optResultSet);
    }
    return parameterEstimationTask;
}

Example 3 with CopasiOptimizationMethod

use of cbit.vcell.opt.CopasiOptimizationMethod in project vcell by virtualcell.

the class ParameterEstimationTaskXMLPersistence method getXML.

/**
 * Insert the method's description here.
 * Creation date: (5/5/2006 9:02:39 AM)
 * @return java.lang.String
 * @param parameterEstimationTask cbit.vcell.modelopt.ParameterEstimationTask
 */
public static Element getXML(ParameterEstimationTask parameterEstimationTask) {
    Element parameterEstimationTaskElement = new Element(XMLTags.ParameterEstimationTaskTag);
    // name attribute
    parameterEstimationTaskElement.setAttribute(NameAttribute, mangle(parameterEstimationTask.getName()));
    // annotation content (optional)
    String annotation = parameterEstimationTask.getAnnotation();
    if (annotation != null && annotation.length() > 0) {
        org.jdom.Element annotationElement = new org.jdom.Element(AnnotationTag);
        annotationElement.setText(mangle(annotation));
        parameterEstimationTaskElement.addContent(annotationElement);
    }
    // 
    // add ParameterMappingSpecs
    // 
    ParameterMappingSpec[] parameterMappingSpecs = parameterEstimationTask.getModelOptimizationSpec().getParameterMappingSpecs();
    if (parameterMappingSpecs != null && parameterMappingSpecs.length > 0) {
        Element parameterMappingSpecListElement = new Element(ParameterMappingSpecListTag);
        for (int i = 0; i < parameterMappingSpecs.length; i++) {
            Element parameterMappingSpecElement = new Element(ParameterMappingSpecTag);
            Parameter parameter = parameterMappingSpecs[i].getModelParameter();
            parameterMappingSpecElement.setAttribute(ParameterReferenceAttribute, parameter.getNameScope().getAbsoluteScopePrefix() + parameter.getName());
            parameterMappingSpecElement.setAttribute(LowLimitAttribute, Double.toString(parameterMappingSpecs[i].getLow()));
            parameterMappingSpecElement.setAttribute(HighLimitAttribute, Double.toString(parameterMappingSpecs[i].getHigh()));
            parameterMappingSpecElement.setAttribute(CurrentValueAttribute, Double.toString(parameterMappingSpecs[i].getCurrent()));
            parameterMappingSpecElement.setAttribute(SelectedAttribute, String.valueOf(parameterMappingSpecs[i].isSelected()));
            parameterMappingSpecListElement.addContent(parameterMappingSpecElement);
        }
        parameterEstimationTaskElement.addContent(parameterMappingSpecListElement);
    }
    // 
    // add ReferenceData
    // 
    ReferenceData referenceData = parameterEstimationTask.getModelOptimizationSpec().getReferenceData();
    if (referenceData != null && referenceData.getNumDataColumns() > 0) {
        Element referenceDataElement = new Element(ReferenceDataTag);
        referenceDataElement.setAttribute(NumRowsAttribute, Integer.toString(referenceData.getNumDataRows()));
        referenceDataElement.setAttribute(NumColumnsAttribute, Integer.toString(referenceData.getNumDataColumns()));
        Element dataColumnListElement = new Element(DataColumnListTag);
        for (int i = 0; i < referenceData.getColumnNames().length; i++) {
            Element dataColumnElement = new Element(DataColumnTag);
            dataColumnElement.setAttribute(NameAttribute, referenceData.getColumnNames()[i]);
            dataColumnElement.setAttribute(WeightAttribute, Double.toString(referenceData.getColumnWeights()[i]));
            dataColumnListElement.addContent(dataColumnElement);
        }
        referenceDataElement.addContent(dataColumnListElement);
        Element dataRowListElement = new Element(DataRowListTag);
        for (int i = 0; i < referenceData.getNumDataRows(); i++) {
            Element dataRowElement = new Element(DataRowTag);
            String rowText = "";
            for (int j = 0; j < referenceData.getNumDataColumns(); j++) {
                if (j > 0) {
                    rowText += " ";
                }
                rowText += referenceData.getDataByRow(i)[j];
            }
            dataRowElement.addContent(rowText);
            dataRowListElement.addContent(dataRowElement);
        }
        referenceDataElement.addContent(dataRowListElement);
        parameterEstimationTaskElement.addContent(referenceDataElement);
    }
    // 
    // add ReferenceDataMappingSpecs
    // 
    ReferenceDataMappingSpec[] referenceDataMappingSpecs = parameterEstimationTask.getModelOptimizationSpec().getReferenceDataMappingSpecs();
    if (referenceDataMappingSpecs != null && referenceDataMappingSpecs.length > 0) {
        Element referenceDataMappingSpecListElement = new Element(ReferenceDataMappingSpecListTag);
        for (int i = 0; i < referenceDataMappingSpecs.length; i++) {
            SymbolTableEntry modelSymbol = referenceDataMappingSpecs[i].getModelObject();
            Element referenceDataMappingSpecElement = new Element(ReferenceDataMappingSpecTag);
            referenceDataMappingSpecElement.setAttribute(ReferenceDataColumnNameAttribute, referenceDataMappingSpecs[i].getReferenceDataColumnName());
            if (modelSymbol != null) {
                referenceDataMappingSpecElement.setAttribute(ReferenceDataModelSymbolAttribute, modelSymbol.getName());
            }
            referenceDataMappingSpecListElement.addContent(referenceDataMappingSpecElement);
        }
        parameterEstimationTaskElement.addContent(referenceDataMappingSpecListElement);
    }
    // 
    if (parameterEstimationTask.getOptimizationSolverSpec() != null) {
        OptimizationSolverSpec solverSpec = parameterEstimationTask.getOptimizationSolverSpec();
        if (solverSpec.getCopasiOptimizationMethod() != null) {
            CopasiOptimizationMethod copasiOptMethod = solverSpec.getCopasiOptimizationMethod();
            Element optimizationSolverSpecElement = new Element(OptimizationSolverSpecTag);
            optimizationSolverSpecElement.setAttribute(OptimizationSolverTypeAttribute, copasiOptMethod.getType().getName());
            optimizationSolverSpecElement.setAttribute(OptimizationSolverNumOfRunsAttribute, solverSpec.getNumOfRuns() + "");
            // adding solve parameter list to optimization solver spec
            CopasiOptimizationParameter[] solverParams = copasiOptMethod.getParameters();
            if (solverParams != null && solverParams.length > 0) {
                Element listOfSolverParams = new Element(OptimizationListOfParametersTag);
                for (CopasiOptimizationParameter solverParam : solverParams) {
                    Element optSolverParam = new Element(OptimizationParameterTag);
                    optSolverParam.setAttribute(OptimizationParameterNameAttribute, solverParam.getType().getDisplayName());
                    optSolverParam.setAttribute(OptimizationParameterValueAttribute, solverParam.getValue() + "");
                    listOfSolverParams.addContent(optSolverParam);
                }
                optimizationSolverSpecElement.addContent(listOfSolverParams);
            }
            parameterEstimationTaskElement.addContent(optimizationSolverSpecElement);
        }
    }
    // add optimization solver result set
    if (parameterEstimationTask.getOptimizationResultSet() != null) {
        OptimizationResultSet optResultSet = parameterEstimationTask.getOptimizationResultSet();
        Element optimizationResultSetElement = new Element(OptXmlTags.OptimizationResultSet_Tag);
        if (optResultSet.getOptSolverResultSet() != null) {
            OptSolverResultSet optSolverResultSet = optResultSet.getOptSolverResultSet();
            Element optSolverResultSetElement = new Element(OptXmlTags.bestOptRunResultSet_Tag);
            // write best parameters
            String[] paramNames = optSolverResultSet.getParameterNames();
            double[] bestValues = optSolverResultSet.getBestEstimates();
            if (paramNames != null && paramNames.length > 0 && bestValues != null && bestValues.length > 0 && paramNames.length == bestValues.length) {
                Element listOfBestParams = new Element(OptimizationListOfParametersTag);
                for (int i = 0; i < paramNames.length; i++) {
                    Element resultParam = new Element(OptimizationParameterTag);
                    resultParam.setAttribute(OptimizationParameterNameAttribute, paramNames[i]);
                    resultParam.setAttribute(OptimizationParameterValueAttribute, bestValues[i] + "");
                    listOfBestParams.addContent(resultParam);
                }
                optSolverResultSetElement.addContent(listOfBestParams);
            }
            // write objective function value
            double objectiveFuncValue = optSolverResultSet.getLeastObjectiveFunctionValue();
            Element objFuncElement = new Element(OptXmlTags.ObjectiveFunction_Tag);
            objFuncElement.setAttribute(OptimizationParameterValueAttribute, objectiveFuncValue + "");
            optSolverResultSetElement.addContent(objFuncElement);
            // write num function evaluations
            long numFuncEvaluations = optSolverResultSet.getObjFunctionEvaluations();
            Element numFuncEvaluationsElement = new Element(OptXmlTags.OptSolverResultSetFunctionEvaluations_Tag);
            numFuncEvaluationsElement.setAttribute(OptimizationParameterValueAttribute, numFuncEvaluations + "");
            optSolverResultSetElement.addContent(numFuncEvaluationsElement);
            optimizationResultSetElement.addContent(optSolverResultSetElement);
        }
        parameterEstimationTaskElement.addContent(optimizationResultSetElement);
    }
    return parameterEstimationTaskElement;
}

Example 4 with CopasiOptimizationMethod

use of cbit.vcell.opt.CopasiOptimizationMethod in project vcell by virtualcell.

the class ParameterEstimationRunTaskPanel method optimizationMethodComboBox_ActionPerformed.

/**
 * Comment
 */
private void optimizationMethodComboBox_ActionPerformed() {
    CopasiOptimizationMethodType methodType = (CopasiOptimizationMethodType) getOptimizationMethodComboBox().getSelectedItem();
    CopasiOptimizationMethod com = new CopasiOptimizationMethod(methodType);
    if (parameterEstimationTask != null && parameterEstimationTask.getOptimizationSolverSpec() != null) {
        if (parameterEstimationTask.getOptimizationSolverSpec().getCopasiOptimizationMethod() == null || !parameterEstimationTask.getOptimizationSolverSpec().getCopasiOptimizationMethod().getType().getDisplayName().equals(methodType.getDisplayName())) {
            parameterEstimationTask.getOptimizationSolverSpec().setCopasiOptimizationMethod(com);
        }
    }
    optimizationMethodParameterTableModel.setCopasiOptimizationMethod(com);
    if (methodType.isStochasticMethod()) {
        numberOfRunComboBox.setVisible(true);
        numberOfRunLabel.setVisible(true);
    } else {
        numberOfRunComboBox.setVisible(false);
        numberOfRunLabel.setVisible(false);
    }
}