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Example 6 with CommentStringTokenizer

use of org.vcell.util.CommentStringTokenizer in project vcell by virtualcell.

the class OutputTimeSpec method readVCML.

/**
 * Insert the method's description here.
 * Creation date: (9/7/2005 9:10:09 AM)
 * @return cbit.vcell.solver.OutputTimeSpec
 */
public static OutputTimeSpec readVCML(CommentStringTokenizer tokens) throws DataAccessException {
    // 
    // read format as follows:
    // 
    // OutputOptions {
    // KeepEvery 1
    // KeepAtMost	1000
    // }
    // 
    // OR
    // OutputOptions {
    // OutputTimes 0.1,0.3,0.4,... (no spaces or line feeds between numbers)
    // }
    // 
    // OR
    // OutputOptions {
    // OutputTimeStep 10
    // }
    // 
    OutputTimeSpec ots = null;
    try {
        String token = tokens.nextToken();
        if (token.equalsIgnoreCase(VCML.OutputOptions)) {
            token = tokens.nextToken();
        }
        if (!token.equalsIgnoreCase(VCML.BeginBlock)) {
            throw new DataAccessException("unexpected token " + token + " expecting " + VCML.BeginBlock);
        }
        while (tokens.hasMoreTokens()) {
            token = tokens.nextToken();
            if (token.equalsIgnoreCase(VCML.EndBlock)) {
                break;
            }
            if (token.equalsIgnoreCase(VCML.KeepEvery)) {
                token = tokens.nextToken();
                int keepEvery = Integer.parseInt(token);
                token = tokens.nextToken();
                if (!token.equalsIgnoreCase(VCML.KeepAtMost)) {
                    throw new DataAccessException("unexpected identifier " + token);
                }
                token = tokens.nextToken();
                int keepAtMost = Integer.parseInt(token);
                ots = new DefaultOutputTimeSpec(keepEvery, keepAtMost);
                continue;
            } else if (token.equalsIgnoreCase(VCML.OutputTimeStep)) {
                token = tokens.nextToken();
                double outputTimeStep = Double.parseDouble(token);
                ots = new UniformOutputTimeSpec(outputTimeStep);
                continue;
            } else if (token.equalsIgnoreCase(VCML.OutputTimes)) {
                token = tokens.nextToken();
                java.util.StringTokenizer st = new java.util.StringTokenizer(token, ",");
                double[] times = new double[st.countTokens()];
                int count = 0;
                while (st.hasMoreTokens()) {
                    token = st.nextToken();
                    times[count++] = Double.parseDouble(token);
                }
                ots = new ExplicitOutputTimeSpec(times);
                continue;
            }
            throw new DataAccessException("unexpected identifier " + token);
        }
    } catch (Throwable e) {
        throw new DataAccessException("line #" + (tokens.lineIndex() + 1) + " Exception: " + e.getMessage());
    }
    return ots;
}
Also used : CommentStringTokenizer(org.vcell.util.CommentStringTokenizer) DataAccessException(org.vcell.util.DataAccessException)

Example 7 with CommentStringTokenizer

use of org.vcell.util.CommentStringTokenizer in project vcell by virtualcell.

the class ParticleDataBlock method readParticleData.

private void readParticleData(List<String> lines) throws DataAccessException {
    String lastSpecies = null;
    List<Coordinate> working = null;
    for (String line : lines) {
        try {
            CommentStringTokenizer st = new CommentStringTokenizer(line);
            String sp = st.nextToken();
            if (!sp.equals(lastSpecies)) {
                lastSpecies = sp;
                working = fetch(sp);
            }
            double x = Double.parseDouble(st.nextToken());
            double y = Double.parseDouble(st.nextToken());
            double z = Double.parseDouble(st.nextToken());
            Coordinate c = new Coordinate(x, y, z);
            working.add(c);
        } catch (Exception exc) {
            throw new DataAccessException("Particle data file invalid. " + exc.getMessage());
        }
    }
}
Also used : Coordinate(org.vcell.util.Coordinate) CommentStringTokenizer(org.vcell.util.CommentStringTokenizer) IOException(java.io.IOException) DataAccessException(org.vcell.util.DataAccessException) DataAccessException(org.vcell.util.DataAccessException)

Example 8 with CommentStringTokenizer

use of org.vcell.util.CommentStringTokenizer 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;
}
Also used : OptimizationResultSet(cbit.vcell.opt.OptimizationResultSet) Element(org.jdom.Element) ArrayList(java.util.ArrayList) OptSolverResultSet(cbit.vcell.opt.OptSolverResultSet) SymbolTableEntry(cbit.vcell.parser.SymbolTableEntry) CopasiOptimizationMethod(cbit.vcell.opt.CopasiOptimizationMethod) CopasiOptimizationParameter(cbit.vcell.opt.CopasiOptimizationParameter) OptimizationSolverSpec(cbit.vcell.opt.OptimizationSolverSpec) Vector(java.util.Vector) Namespace(org.jdom.Namespace) SimpleReferenceData(cbit.vcell.opt.SimpleReferenceData) SimpleReferenceData(cbit.vcell.opt.SimpleReferenceData) ReferenceData(cbit.vcell.opt.ReferenceData) Parameter(cbit.vcell.model.Parameter) CopasiOptimizationParameter(cbit.vcell.opt.CopasiOptimizationParameter) CommentStringTokenizer(org.vcell.util.CommentStringTokenizer) OptRunResultSet(cbit.vcell.opt.OptSolverResultSet.OptRunResultSet)

Example 9 with CommentStringTokenizer

use of org.vcell.util.CommentStringTokenizer in project vcell by virtualcell.

the class BioCartoonTool method pasteReactionSteps0.

/**
 * pasteReactionSteps0 : does the actual pasting. First called with a cloned model, to track issues. If user still wants to proceed, the paste
 * is performed on the original model.
 *
 * Insert the method's description here.
 * Creation date: (5/10/2003 3:55:25 PM)
 * @param pasteToModel cbit.vcell.model.Model
 * @param pasteToStructure cbit.vcell.model.Structure
 * @param bNew boolean
 */
private static final PasteHelper pasteReactionSteps0(HashMap<String, HashMap<ReactionParticipant, Structure>> rxPartMapStructure, Component parent, IssueContext issueContext, ReactionStep[] copyFromRxSteps, Model pasteToModel, Structure pasteToStructure, boolean bNew, /*boolean bUseDBSpecies,*/
UserResolvedRxElements userResolvedRxElements) throws Exception {
    HashMap<BioModelEntityObject, BioModelEntityObject> reactionsAndSpeciesContexts = new HashMap<>();
    if (copyFromRxSteps == null || copyFromRxSteps.length == 0 || pasteToModel == null || pasteToStructure == null) {
        throw new IllegalArgumentException("CartoonTool.pasteReactionSteps Error " + (copyFromRxSteps == null || copyFromRxSteps.length == 0 ? "reactionStepsArr empty " : "") + (pasteToModel == null ? "model is null " : "") + (pasteToStructure == null ? "struct is null " : ""));
    }
    if (!pasteToModel.contains(pasteToStructure)) {
        throw new IllegalArgumentException("CartoonTool.pasteReactionSteps model " + pasteToModel.getName() + " does not contain structure " + pasteToStructure.getName());
    }
    // Check PasteToModel has preferred targets if set
    if (userResolvedRxElements != null) {
        for (int i = 0; i < userResolvedRxElements.toSpeciesArr.length; i++) {
            if (userResolvedRxElements.toSpeciesArr[i] != null) {
                if (!pasteToModel.contains(userResolvedRxElements.toSpeciesArr[i])) {
                    throw new RuntimeException("PasteToModel does not contain preferred Species " + userResolvedRxElements.toSpeciesArr[i]);
                }
            }
            if (userResolvedRxElements.toStructureArr[i] != null) {
                if (!pasteToModel.contains(userResolvedRxElements.toStructureArr[i])) {
                    throw new RuntimeException("PasteToModel does not contain preferred Structure " + userResolvedRxElements.toStructureArr[i]);
                }
            }
        }
    }
    int counter = 0;
    Structure currentStruct = pasteToStructure;
    String copiedStructName = copyFromRxSteps[counter].getStructure().getName();
    StructureTopology structTopology = (copyFromRxSteps[counter].getModel() == null ? pasteToModel.getStructureTopology() : copyFromRxSteps[counter].getModel().getStructureTopology());
    IdentityHashMap<Species, Species> speciesHash = new IdentityHashMap<Species, Species>();
    IdentityHashMap<SpeciesContext, SpeciesContext> speciesContextHash = new IdentityHashMap<SpeciesContext, SpeciesContext>();
    Vector<Issue> issueVector = new Vector<Issue>();
    do {
        // create a new reaction, instead of cloning the old one; set struc
        ReactionStep copyFromReactionStep = copyFromRxSteps[counter];
        String newName = copyFromReactionStep.getName();
        while (pasteToModel.getReactionStep(newName) != null) {
            newName = org.vcell.util.TokenMangler.getNextEnumeratedToken(newName);
        }
        ReactionStep newReactionStep = null;
        if (copyFromReactionStep instanceof SimpleReaction) {
            newReactionStep = new SimpleReaction(pasteToModel, currentStruct, newName, copyFromReactionStep.isReversible());
        } else if (copyFromReactionStep instanceof FluxReaction && currentStruct instanceof Membrane) {
            newReactionStep = new FluxReaction(pasteToModel, (Membrane) currentStruct, null, newName, copyFromReactionStep.isReversible());
        }
        pasteToModel.addReactionStep(newReactionStep);
        reactionsAndSpeciesContexts.put(newReactionStep, copyFromReactionStep);
        Structure toRxnStruct = newReactionStep.getStructure();
        Structure fromRxnStruct = copyFromReactionStep.getStructure();
        if (!fromRxnStruct.getClass().equals(pasteToStructure.getClass())) {
            throw new Exception("Cannot copy reaction from " + fromRxnStruct.getTypeName() + " to " + pasteToStructure.getTypeName() + ".");
        }
        // add appropriate reactionParticipants to newReactionStep.
        StructureTopology toStructureTopology = pasteToModel.getStructureTopology();
        ReactionParticipant[] copyFromRxParticipantArr = copyFromReactionStep.getReactionParticipants();
        if (rxPartMapStructure == null) {
            // null during 'issues' trial
            rxPartMapStructure = new HashMap<String, HashMap<ReactionParticipant, Structure>>();
        }
        if (rxPartMapStructure.get(copyFromReactionStep.getName()) == null) {
            // Ask user to assign species to compartments for each reaction to be pasted
            rxPartMapStructure.put(copyFromReactionStep.getName(), askUserResolveMembraneConnections(parent, pasteToModel.getStructures(), currentStruct, fromRxnStruct, toRxnStruct, copyFromRxParticipantArr, toStructureTopology, structTopology));
        }
        for (int i = 0; i < copyFromRxParticipantArr.length; i += 1) {
            Structure pasteToStruct = currentStruct;
            // if(toRxnStruct instanceof Membrane){
            pasteToStruct = rxPartMapStructure.get(copyFromReactionStep.getName()).get(copyFromRxParticipantArr[i]);
            // if(pasteToStruct == null){
            // for(ReactionParticipant myRXPart:rxPartMapStructure.get(copyFromReactionStep.getName()).keySet()){
            // if(myRXPart.getSpeciesContext().getName().equals(copyFromRxParticipantArr[i].getSpeciesContext().getName())){
            // pasteToStruct = rxPartMapStructure.get(copyFromReactionStep.getName()).get(myRXPart);
            // break;
            // }
            // }
            // }
            // }
            // this adds the speciesContexts and species (if any) to the model)
            String rootSC = ReactionCartoonTool.speciesContextRootFinder(copyFromRxParticipantArr[i].getSpeciesContext());
            SpeciesContext newSc = null;
            SpeciesContext[] matchSC = pasteToModel.getSpeciesContexts();
            for (int j = 0; matchSC != null && j < matchSC.length; j++) {
                String matchRoot = ReactionCartoonTool.speciesContextRootFinder(matchSC[j]);
                if (matchRoot != null && matchRoot.equals(rootSC) && matchSC[j].getStructure().getName().equals(pasteToStruct.getName())) {
                    newSc = matchSC[j];
                    reactionsAndSpeciesContexts.put(newSc, matchSC[j]);
                    break;
                }
            }
            if (newSc == null) {
                newSc = pasteSpecies(parent, copyFromRxParticipantArr[i].getSpecies(), rootSC, pasteToModel, pasteToStruct, bNew, /*bUseDBSpecies,*/
                speciesHash, UserResolvedRxElements.getPreferredReactionElement(userResolvedRxElements, copyFromRxParticipantArr[i]));
                reactionsAndSpeciesContexts.put(newSc, copyFromRxParticipantArr[i].getSpeciesContext());
            }
            // record the old-new speciesContexts (reactionparticipants) in the IdHashMap, this is useful, esp for 'Paste new', while replacing proxyparams.
            SpeciesContext oldSc = copyFromRxParticipantArr[i].getSpeciesContext();
            if (speciesContextHash.get(oldSc) == null) {
                speciesContextHash.put(oldSc, newSc);
            }
            if (copyFromRxParticipantArr[i] instanceof Reactant) {
                newReactionStep.addReactionParticipant(new Reactant(null, newReactionStep, newSc, copyFromRxParticipantArr[i].getStoichiometry()));
            } else if (copyFromRxParticipantArr[i] instanceof Product) {
                newReactionStep.addReactionParticipant(new Product(null, newReactionStep, newSc, copyFromRxParticipantArr[i].getStoichiometry()));
            } else if (copyFromRxParticipantArr[i] instanceof Catalyst) {
                newReactionStep.addCatalyst(newSc);
            }
        }
        // // If 'newReactionStep' is a fluxRxn, set its fluxCarrier
        // if (newReactionStep instanceof FluxReaction) {
        // if (fluxCarrierSp != null) {
        // ((FluxReaction)newReactionStep).setFluxCarrier(fluxCarrierSp, pasteToModel);
        // } else {
        // throw new RuntimeException("Could not set FluxCarrier species for the flux reaction to be pasted");
        // }
        // }
        // For each kinetic parameter expression for new kinetics, replace the proxyParams from old kinetics with proxyParams in new kinetics
        // i.e., if the proxyParams are speciesContexts, replace with corresponding speciesContext in newReactionStep;
        // if the proxyParams are structureSizes or MembraneVoltages, replace with corresponding structure quantity in newReactionStep
        Kinetics oldKinetics = copyFromReactionStep.getKinetics();
        KineticsParameter[] oldKps = oldKinetics.getKineticsParameters();
        KineticsProxyParameter[] oldKprps = oldKinetics.getProxyParameters();
        Hashtable<String, Expression> paramExprHash = new Hashtable<String, Expression>();
        for (int i = 0; oldKps != null && i < oldKps.length; i++) {
            Expression newExpression = new Expression(oldKps[i].getExpression());
            for (int j = 0; oldKprps != null && j < oldKprps.length; j++) {
                // check if kinetic proxy parameter is in kinetic parameter expression
                if (newExpression.hasSymbol(oldKprps[j].getName())) {
                    SymbolTableEntry ste = oldKprps[j].getTarget();
                    Model pasteFromModel = copyFromReactionStep.getModel();
                    if (ste instanceof SpeciesContext) {
                        // if newRxnStruct is a feature/membrane, get matching spContexts from old reaction and replace them in new rate expr.
                        SpeciesContext oldSC = (SpeciesContext) ste;
                        SpeciesContext newSC = speciesContextHash.get(oldSC);
                        if (newSC == null) {
                            // check if oldSc is present in paste-model; if not, add it.
                            if (!pasteToModel.equals(pasteFromModel)) {
                                if (pasteToModel.getSpeciesContext(oldSC.getName()) == null) {
                                    // if paste-model has oldSc struct, paste it there,
                                    Structure newSCStruct = pasteToModel.getStructure(oldSC.getStructure().getName());
                                    if (newSCStruct != null) {
                                        newSC = pasteSpecies(parent, oldSC.getSpecies(), null, pasteToModel, newSCStruct, bNew, /*bUseDBSpecies,*/
                                        speciesHash, UserResolvedRxElements.getPreferredReactionElement(userResolvedRxElements, oldSC));
                                        speciesContextHash.put(oldSC, newSC);
                                    } else {
                                        // oldStruct wasn't found in paste-model, paste it in newRxnStruct and add warning to issues list
                                        newSC = pasteSpecies(parent, oldSC.getSpecies(), null, pasteToModel, toRxnStruct, bNew, /*bUseDBSpecies,*/
                                        speciesHash, UserResolvedRxElements.getPreferredReactionElement(userResolvedRxElements, oldSC));
                                        speciesContextHash.put(oldSC, newSC);
                                        Issue issue = new Issue(oldSC, issueContext, IssueCategory.CopyPaste, "SpeciesContext '" + oldSC.getSpecies().getCommonName() + "' was not found in compartment '" + oldSC.getStructure().getName() + "' in the model; the species was added to the compartment '" + toRxnStruct.getName() + "' where the reaction was pasted.", Issue.SEVERITY_WARNING);
                                        issueVector.add(issue);
                                    }
                                }
                            }
                        // if models are the same and newSc is null, then oldSc is not a rxnParticipant. Leave it as is in the expr.
                        }
                        if (newSC != null) {
                            reactionsAndSpeciesContexts.put(newSC, oldSC);
                            newExpression.substituteInPlace(new Expression(ste.getName()), new Expression(newSC.getName()));
                        }
                    // SpeciesContext sc = null;
                    // Species newSp = model.getSpecies(oldSc.getSpecies().getCommonName());
                    // if  (oldSc.getStructure() == (oldRxnStruct)) {
                    // sc = model.getSpeciesContext(newSp, newRxnStruct);
                    // } else {
                    // if (newRxnStruct instanceof Membrane) {
                    // // for a membrane, we need to make sure that inside-outside spContexts used are appropriately replaced.
                    // if (oldSc.getStructure() == ((Membrane)oldRxnStruct).getOutsideFeature()) {
                    // // old speciesContext is outside (old) membrane, new spContext should be outside new membrane
                    // sc = model.getSpeciesContext(newSp, ((Membrane)newRxnStruct).getOutsideFeature());
                    // } else if (oldSc.getStructure() == ((Membrane)oldRxnStruct).getInsideFeature()) {
                    // // old speciesContext is inside (old) membrane, new spContext should be inside new membrane
                    // sc = model.getSpeciesContext(newSp, ((Membrane)newRxnStruct).getInsideFeature());
                    // }
                    // }
                    // }
                    // if (sc != null) {
                    // newExpression.substituteInPlace(new Expression(ste.getName()), new Expression(sc.getName()));
                    // }
                    } else if (ste instanceof StructureSize) {
                        Structure str = ((StructureSize) ste).getStructure();
                        // if the structure size used is same as the structure in which the reaction is present, change the structSize to appropriate new struct
                        if (str.compareEqual(fromRxnStruct)) {
                            newExpression.substituteInPlace(new Expression(ste.getName()), new Expression(toRxnStruct.getStructureSize().getName()));
                        } else {
                            if (fromRxnStruct instanceof Membrane) {
                                if (str.equals(structTopology.getOutsideFeature((Membrane) fromRxnStruct))) {
                                    newExpression.substituteInPlace(new Expression(ste.getName()), new Expression(structTopology.getOutsideFeature((Membrane) toRxnStruct).getStructureSize().getName()));
                                } else if (str.equals(structTopology.getInsideFeature((Membrane) fromRxnStruct))) {
                                    newExpression.substituteInPlace(new Expression(ste.getName()), new Expression(structTopology.getInsideFeature((Membrane) toRxnStruct).getStructureSize().getName()));
                                }
                            }
                        }
                    } else if (ste instanceof MembraneVoltage) {
                        Membrane membr = ((MembraneVoltage) ste).getMembrane();
                        // if the MembraneVoltage used is same as that of the membrane in which the reaction is present, change the MemVoltage
                        if ((fromRxnStruct instanceof Membrane) && (membr.compareEqual(fromRxnStruct))) {
                            newExpression.substituteInPlace(new Expression(ste.getName()), new Expression(((Membrane) toRxnStruct).getMembraneVoltage().getName()));
                        }
                    } else if (ste instanceof ModelParameter) {
                        // see if model has this global parameter (if rxn is being pasted into another model, it won't)
                        if (!pasteToModel.equals(pasteFromModel)) {
                            ModelParameter oldMp = (ModelParameter) ste;
                            ModelParameter mp = pasteToModel.getModelParameter(oldMp.getName());
                            boolean bNonNumeric = false;
                            String newMpName = oldMp.getName();
                            if (mp != null) {
                                // new model has a model parameter with same name - are they the same param?
                                if (!mp.getExpression().equals(oldMp.getExpression())) {
                                    // no, they are not the same param, so mangle the 'ste' name and add as global in the other model
                                    while (pasteToModel.getModelParameter(newMpName) != null) {
                                        newMpName = TokenMangler.getNextEnumeratedToken(newMpName);
                                    }
                                    // if expression if numeric, add it as such. If not, set it to 0.0 and add it as global
                                    Expression exp = oldMp.getExpression();
                                    if (!exp.flatten().isNumeric()) {
                                        exp = new Expression(0.0);
                                        bNonNumeric = true;
                                    }
                                    ModelParameter newMp = pasteToModel.new ModelParameter(newMpName, exp, Model.ROLE_UserDefined, oldMp.getUnitDefinition());
                                    String annotation = "Copied from model : " + pasteFromModel.getNameScope();
                                    newMp.setModelParameterAnnotation(annotation);
                                    pasteToModel.addModelParameter(newMp);
                                    // if global param name had to be changed, make sure newExpr is updated as well.
                                    if (!newMpName.equals(oldMp.getName())) {
                                        newExpression.substituteInPlace(new Expression(oldMp.getName()), new Expression(newMpName));
                                    }
                                }
                            } else {
                                // no global param with same name was found in other model, so add it to other model.
                                // if expression if numeric, add it as such. If not, set it to 0.0 and add it as global
                                Expression exp = oldMp.getExpression();
                                if (!exp.flatten().isNumeric()) {
                                    exp = new Expression(0.0);
                                    bNonNumeric = true;
                                }
                                ModelParameter newMp = pasteToModel.new ModelParameter(newMpName, exp, Model.ROLE_UserDefined, oldMp.getUnitDefinition());
                                String annotation = "Copied from model : " + pasteFromModel.getNameScope();
                                newMp.setModelParameterAnnotation(annotation);
                                pasteToModel.addModelParameter(newMp);
                            }
                            // if a non-numeric parameter was encountered in the old model, it was added as a numeric (0.0), warn user of change.
                            if (bNonNumeric) {
                                Issue issue = new Issue(oldMp, issueContext, IssueCategory.CopyPaste, "Global parameter '" + oldMp.getName() + "' was non-numeric; it has been added " + "as global parameter '" + newMpName + "' in the new model with value = 0.0. " + "Please update its value, if required, before using it.", Issue.SEVERITY_WARNING);
                                issueVector.add(issue);
                            }
                        }
                    }
                }
            // end - if newExpr.hasSymbol(ProxyParam)
            }
            // now if store <param names, new expression> in hashTable
            if (paramExprHash.get(oldKps[i].getName()) == null) {
                paramExprHash.put(oldKps[i].getName(), newExpression);
            }
        }
        // end for - oldKps (old kinetic parameters)
        // use this new expression to generate 'vcml' for the (new) kinetics (easier way to transfer all kinetic parameters)
        String newKineticsStr = oldKinetics.writeTokensWithReplacingProxyParams(paramExprHash);
        // convert the kinetics 'vcml' to tokens.
        CommentStringTokenizer kineticsTokens = new CommentStringTokenizer(newKineticsStr);
        // skip the first token;
        kineticsTokens.nextToken();
        // second token is the kinetic type; use this to create a dummy kinetics
        String kineticType = kineticsTokens.nextToken();
        Kinetics newkinetics = KineticsDescription.fromVCMLKineticsName(kineticType).createKinetics(newReactionStep);
        // use the remaining tokens to construct the new kinetics
        newkinetics.fromTokens(newKineticsStr);
        // bind newkinetics to newReactionStep and add it to newReactionStep
        newkinetics.bind(newReactionStep);
        newReactionStep.setKinetics(newkinetics);
        counter += 1;
        if (counter == copyFromRxSteps.length) {
            break;
        }
        if (!copiedStructName.equals(fromRxnStruct.getName())) {
            if (currentStruct instanceof Feature) {
                currentStruct = structTopology.getMembrane((Feature) currentStruct);
            } else if (currentStruct instanceof Membrane) {
                currentStruct = structTopology.getInsideFeature((Membrane) currentStruct);
            }
        }
        copiedStructName = fromRxnStruct.getName();
    } while (true);
    return new PasteHelper(issueVector, rxPartMapStructure, reactionsAndSpeciesContexts);
}
Also used : Issue(org.vcell.util.Issue) IdentityHashMap(java.util.IdentityHashMap) HashMap(java.util.HashMap) LinkedHashMap(java.util.LinkedHashMap) IdentityHashMap(java.util.IdentityHashMap) Product(cbit.vcell.model.Product) FluxReaction(cbit.vcell.model.FluxReaction) SpeciesContext(cbit.vcell.model.SpeciesContext) Reactant(cbit.vcell.model.Reactant) Feature(cbit.vcell.model.Feature) SymbolTableEntry(cbit.vcell.parser.SymbolTableEntry) KineticsParameter(cbit.vcell.model.Kinetics.KineticsParameter) Membrane(cbit.vcell.model.Membrane) Structure(cbit.vcell.model.Structure) Species(cbit.vcell.model.Species) Vector(java.util.Vector) SimpleReaction(cbit.vcell.model.SimpleReaction) KineticsProxyParameter(cbit.vcell.model.Kinetics.KineticsProxyParameter) StructureTopology(cbit.vcell.model.Model.StructureTopology) Hashtable(java.util.Hashtable) BioModelEntityObject(cbit.vcell.model.BioModelEntityObject) StructureSize(cbit.vcell.model.Structure.StructureSize) PropertyVetoException(java.beans.PropertyVetoException) ExpressionBindingException(cbit.vcell.parser.ExpressionBindingException) ModelException(cbit.vcell.model.ModelException) UserCancelException(org.vcell.util.UserCancelException) ModelParameter(cbit.vcell.model.Model.ModelParameter) Expression(cbit.vcell.parser.Expression) MembraneVoltage(cbit.vcell.model.Membrane.MembraneVoltage) ReactionStep(cbit.vcell.model.ReactionStep) Model(cbit.vcell.model.Model) CommentStringTokenizer(org.vcell.util.CommentStringTokenizer) Kinetics(cbit.vcell.model.Kinetics) ReactionParticipant(cbit.vcell.model.ReactionParticipant) Catalyst(cbit.vcell.model.Catalyst)

Example 10 with CommentStringTokenizer

use of org.vcell.util.CommentStringTokenizer in project vcell by virtualcell.

the class SimulationTable method getSimulationRep.

public SimulationRep getSimulationRep(ResultSet rset, DatabaseSyntax dbSyntax) throws IllegalArgumentException, SQLException, DataAccessException {
    KeyValue scKey = new KeyValue(rset.getBigDecimal(table.id.toString()));
    String name = rset.getString(table.name.toString());
    BigDecimal branchID = rset.getBigDecimal(table.versionBranchID.toString());
    KeyValue ownerRef = new KeyValue(rset.getBigDecimal(table.ownerRef.toString()));
    String ownerName = rset.getString(UserTable.table.userid.toString());
    User owner = new User(ownerName, ownerRef);
    KeyValue mathKey = new KeyValue(rset.getBigDecimal(table.mathRef.toString()));
    String taskDesc = rset.getString(table.taskDescription.toString());
    SolverTaskDescription solverTaskDescription = null;
    try {
        solverTaskDescription = new SolverTaskDescription(new CommentStringTokenizer(taskDesc));
    } catch (DataAccessException e) {
        System.out.println("SimulationTable:getSimulationRep(): failed to parse solver task description, exception=[" + e.getMessage() + "]::\n[[[" + taskDesc + "]]]\n");
    // e.printStackTrace();
    }
    CommentStringTokenizer mathOverridesTokenizer = getMathOverridesTokenizer(rset, dbSyntax);
    List<Element> mathOverrideElements = MathOverrides.parseOverrideElementsFromVCML(mathOverridesTokenizer);
    return new SimulationRep(scKey, branchID, name, owner, mathKey, solverTaskDescription, mathOverrideElements.toArray(new MathOverrides.Element[0]));
}
Also used : KeyValue(org.vcell.util.document.KeyValue) User(org.vcell.util.document.User) Element(cbit.vcell.solver.MathOverrides.Element) CommentStringTokenizer(org.vcell.util.CommentStringTokenizer) SolverTaskDescription(cbit.vcell.solver.SolverTaskDescription) BigDecimal(java.math.BigDecimal) DataAccessException(org.vcell.util.DataAccessException)

Aggregations

CommentStringTokenizer (org.vcell.util.CommentStringTokenizer)19 DataAccessException (org.vcell.util.DataAccessException)8 MathDescription (cbit.vcell.math.MathDescription)4 Expression (cbit.vcell.parser.Expression)4 ArrayList (java.util.ArrayList)4 IOException (java.io.IOException)3 Vector (java.util.Vector)3 Element (org.jdom.Element)3 ImageException (cbit.image.ImageException)2 AsynchClientTask (cbit.vcell.client.task.AsynchClientTask)2 SetMathDescription (cbit.vcell.client.task.SetMathDescription)2 CSGObject (cbit.vcell.geometry.CSGObject)2 GeometryException (cbit.vcell.geometry.GeometryException)2 MathException (cbit.vcell.math.MathException)2 MathFormatException (cbit.vcell.math.MathFormatException)2 MathModel (cbit.vcell.mathmodel.MathModel)2 SimpleReferenceData (cbit.vcell.opt.SimpleReferenceData)2 SymbolTableEntry (cbit.vcell.parser.SymbolTableEntry)2 BufferedReader (java.io.BufferedReader)2 FileReader (java.io.FileReader)2