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

Example 61 with SymbolTableEntry

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

the class ElectricalStimulusPanel method getProtocolParameterExprPreview.

public static Expression getProtocolParameterExprPreview(Expression expr, SymbolTable symbolTable, ReservedSymbol timeSymbol) throws Exception {
    Expression protocolParameterExp = new Expression(expr);
    protocolParameterExp = MathUtilities.substituteModelParameters(protocolParameterExp, symbolTable);
    String[] symbols = protocolParameterExp.getSymbols();
    for (int i = 0; symbols != null && i < symbols.length; i++) {
        SymbolTableEntry ste = protocolParameterExp.getSymbolBinding(symbols[i]);
        if (!ste.equals(timeSymbol) && !(ste instanceof LocalProxyParameter && ((LocalProxyParameter) ste).getTarget().equals(timeSymbol))) {
            throw new ExpressionException("Expression symbol '" + ste.getName() + "' doesn't match timeSymbol " + timeSymbol.getName());
        }
    }
    return protocolParameterExp;
}

Example 62 with SymbolTableEntry

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

the class InitialConditionsPanel method jMenuItemCopy_ActionPerformed.

/**
 * Comment
 */
private void jMenuItemCopy_ActionPerformed(java.awt.event.ActionEvent actionEvent) {
    if (actionEvent.getSource() == getJMenuItemCopy() || actionEvent.getSource() == getJMenuItemCopyAll()) {
        try {
            // 
            // Copy Symbols and Values Init Conditions
            // 
            int[] rows = null;
            if (actionEvent.getSource() == getJMenuItemCopyAll()) {
                rows = new int[getScrollPaneTable().getRowCount()];
                for (int i = 0; i < rows.length; i += 1) {
                    rows[i] = i;
                }
            } else {
                rows = getScrollPaneTable().getSelectedRows();
            }
            MathSymbolMapping msm = null;
            try {
                msm = getSimulationContext().createNewMathMapping().getMathSymbolMapping();
            } catch (Exception e) {
                e.printStackTrace(System.out);
                DialogUtils.showWarningDialog(this, "current math not valid, some paste operations will be limited\n\nreason: " + e.getMessage());
            }
            StringBuffer sb = new StringBuffer();
            sb.append("initial Conditions Parameters for (BioModel)" + getSimulationContext().getBioModel().getName() + " (App)" + getSimulationContext().getName() + "\n");
            java.util.Vector<SymbolTableEntry> primarySymbolTableEntriesV = new java.util.Vector<SymbolTableEntry>();
            java.util.Vector<SymbolTableEntry> alternateSymbolTableEntriesV = new java.util.Vector<SymbolTableEntry>();
            java.util.Vector<Expression> resolvedValuesV = new java.util.Vector<Expression>();
            for (int i = 0; i < rows.length; i += 1) {
                SpeciesContextSpec scs = tableModel.getValueAt(rows[i]);
                if (scs.isConstant()) {
                    // need to change
                    primarySymbolTableEntriesV.add(scs.getInitialConditionParameter());
                    if (msm != null) {
                        alternateSymbolTableEntriesV.add(msm.getVariable(scs.getSpeciesContext()));
                    } else {
                        alternateSymbolTableEntriesV.add(null);
                    }
                    resolvedValuesV.add(new Expression(scs.getInitialConditionParameter().getExpression()));
                    sb.append(scs.getSpeciesContext().getName() + "\t" + scs.getInitialConditionParameter().getName() + "\t" + scs.getInitialConditionParameter().getExpression().infix() + "\n");
                } else {
                    for (int j = 0; j < scs.getParameters().length; j += 1) {
                        SpeciesContextSpec.SpeciesContextSpecParameter scsp = (SpeciesContextSpec.SpeciesContextSpecParameter) scs.getParameters()[j];
                        if (VCellCopyPasteHelper.isSCSRoleForDimension(scsp.getRole(), getSimulationContext().getGeometry().getDimension())) {
                            Expression scspExpression = scsp.getExpression();
                            sb.append(scs.getSpeciesContext().getName() + "\t" + scsp.getName() + "\t" + (scspExpression != null ? scspExpression.infix() : "") + "\n");
                            if (scspExpression != null) {
                                // "Default" boundary conditions can't be copied
                                primarySymbolTableEntriesV.add(scsp);
                                if (msm != null) {
                                    alternateSymbolTableEntriesV.add(msm.getVariable(scsp));
                                } else {
                                    alternateSymbolTableEntriesV.add(null);
                                }
                                resolvedValuesV.add(new Expression(scspExpression));
                            }
                        }
                    }
                }
            }
            // 
            // Send to clipboard
            // 
            VCellTransferable.ResolvedValuesSelection rvs = new VCellTransferable.ResolvedValuesSelection((SymbolTableEntry[]) BeanUtils.getArray(primarySymbolTableEntriesV, SymbolTableEntry.class), (SymbolTableEntry[]) BeanUtils.getArray(alternateSymbolTableEntriesV, SymbolTableEntry.class), (Expression[]) BeanUtils.getArray(resolvedValuesV, Expression.class), sb.toString());
            VCellTransferable.sendToClipboard(rvs);
        } catch (Throwable e) {
            PopupGenerator.showErrorDialog(InitialConditionsPanel.this, "InitialConditionsPanel Copy failed.  " + e.getMessage(), e);
        }
    }
}

Example 63 with SymbolTableEntry

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

the class ReactionCartoonTool method detailsDeleteSpecies.

private static DeleteSpeciesInfo detailsDeleteSpecies(Component requester, SpeciesContext[] speciesContextArr, ReactionStep[] toBeDeletedReactStepArr, ReactionCartoon rxCartoon) throws Exception, UserCancelException {
    if (speciesContextArr == null || speciesContextArr.length == 0) {
        return null;
    }
    // Warn user that there may be some BioModel components that reference speciesContext to be removed
    // Get ReactionParticipant list
    Collection<Shape> rxPartColl = rxCartoon.getShapes();
    HashMap<SpeciesContext, HashSet<ReactionParticipant>> rxPartHashMap = new HashMap<SpeciesContext, HashSet<ReactionParticipant>>();
    for (Shape objShape : rxPartColl) {
        if (objShape instanceof ReactionParticipantShape) {
            ReactionParticipant objReactionParticipant = ((ReactionParticipantShape) objShape).getReactionParticipant();
            if (Arrays.asList(speciesContextArr).contains(objReactionParticipant.getSpeciesContext())) {
                if (!rxPartHashMap.containsKey(objReactionParticipant.getSpeciesContext())) {
                    rxPartHashMap.put(objReactionParticipant.getSpeciesContext(), new HashSet<ReactionParticipant>());
                }
                if (!rxPartHashMap.get(objReactionParticipant.getSpeciesContext()).contains(objReactionParticipant)) {
                    rxPartHashMap.get(objReactionParticipant.getSpeciesContext()).add(objReactionParticipant);
                }
            }
        }
    }
    int reactionParticipantCount = 0;
    for (HashSet<ReactionParticipant> objReactPart : rxPartHashMap.values()) {
        reactionParticipantCount += objReactPart.size();
    }
    // find bioModel and get SymbolTable references to SpeciesContext
    BioModelEditor bioModelEditor = (BioModelEditor) BeanUtils.findTypeParentOfComponent(requester, BioModelEditor.class);
    if (bioModelEditor == null) {
        throw new Exception("Error deleting Speciescontext, Can't find BiomodelEditor");
    }
    BioModel bioModel = bioModelEditor.getBioModelWindowManager().getVCDocument();
    HashMap<SpeciesContext, HashSet<SymbolTableEntry>> referencingSymbolsHashMap = new HashMap<SpeciesContext, HashSet<SymbolTableEntry>>();
    for (int i = 0; i < speciesContextArr.length; i++) {
        List<SymbolTableEntry> referencingSymbolsList = bioModel.findReferences(speciesContextArr[i]);
        if (referencingSymbolsList != null && referencingSymbolsList.size() > 0) {
            if (!referencingSymbolsHashMap.containsKey(speciesContextArr[i])) {
                referencingSymbolsHashMap.put(speciesContextArr[i], new HashSet<SymbolTableEntry>());
            }
            referencingSymbolsHashMap.get(speciesContextArr[i]).addAll(referencingSymbolsList);
        }
    }
    int referencingSymbolsCount = 0;
    for (HashSet<SymbolTableEntry> objSimTableEntry : referencingSymbolsHashMap.values()) {
        referencingSymbolsCount += objSimTableEntry.size();
    }
    // Warn user about delete
    HashMap<SpeciesContext, Boolean> bUnresolvableHashMap = new HashMap<SpeciesContext, Boolean>();
    for (int i = 0; i < speciesContextArr.length; i++) {
        bUnresolvableHashMap.put(speciesContextArr[i], Boolean.FALSE);
    }
    String[][] rowData = null;
    if (rxPartHashMap.size() == 0 && referencingSymbolsHashMap.size() == 0) {
        rowData = new String[speciesContextArr.length][4];
        for (int i = 0; i < speciesContextArr.length; i++) {
            rowData[i][0] = speciesContextArr[i].getName();
            rowData[i][1] = "";
            rowData[i][2] = "";
            rowData[i][3] = "";
        }
        Arrays.sort(rowData, new Comparator<String[]>() {

            @Override
            public int compare(String[] o1, String[] o2) {
                return o1[0].compareToIgnoreCase(o2[0]);
            }
        });
    } else {
        // find SpeciesContext that had no reference warnings
        Vector<SpeciesContext> speciesContextNoReferences = new Vector<SpeciesContext>();
        for (int i = 0; i < speciesContextArr.length; i++) {
            if (!rxPartHashMap.containsKey(speciesContextArr[i]) && !referencingSymbolsHashMap.containsKey(speciesContextArr[i])) {
                speciesContextNoReferences.add(speciesContextArr[i]);
            }
        }
        rowData = new String[reactionParticipantCount + referencingSymbolsCount + speciesContextNoReferences.size()][4];
        int count = 0;
        for (SpeciesContext objSpeciesContext : speciesContextNoReferences) {
            rowData[count][0] = objSpeciesContext.getName();
            rowData[count][1] = "";
            rowData[count][2] = "";
            rowData[count][3] = "";
            count++;
        }
        for (SpeciesContext objSpeciesContext : rxPartHashMap.keySet()) {
            Iterator<ReactionParticipant> iterRxPart = rxPartHashMap.get(objSpeciesContext).iterator();
            while (iterRxPart.hasNext()) {
                rowData[count][0] = objSpeciesContext.getName();
                rowData[count][1] = "";
                rowData[count][2] = "Reaction Diagram stoichiometry '" + iterRxPart.next().getReactionStep().getName() + "'";
                rowData[count][3] = "";
                count++;
            }
        }
        for (SpeciesContext objSpeciesContext : referencingSymbolsHashMap.keySet()) {
            Iterator<SymbolTableEntry> iterSymbolTableEntry = referencingSymbolsHashMap.get(objSpeciesContext).iterator();
            while (iterSymbolTableEntry.hasNext()) {
                rowData[count][0] = objSpeciesContext.getName();
                rowData[count][1] = "";
                SymbolTableEntry objSymbolTableEntry = iterSymbolTableEntry.next();
                boolean bKineticsParameter = objSymbolTableEntry instanceof KineticsParameter;
                if (bKineticsParameter) {
                    KineticsParameter kp = (KineticsParameter) objSymbolTableEntry;
                    boolean isOK = kp.isRegenerated();
                    for (int i = 0; toBeDeletedReactStepArr != null && i < toBeDeletedReactStepArr.length; i++) {
                        if (toBeDeletedReactStepArr[i] == kp.getKinetics().getReactionStep()) {
                            // OK to delete this Speciescontext if were deleting the reaction that contained the reference
                            isOK = true;
                        }
                    }
                    rowData[count][1] = (isOK ? "" : RXSPECIES_ERROR);
                    bUnresolvableHashMap.put(objSpeciesContext, bUnresolvableHashMap.get(objSpeciesContext) || !isOK);
                }
                boolean bReaction = objSymbolTableEntry.getNameScope() instanceof ReactionNameScope;
                rowData[count][2] = (bReaction ? "Reaction" : objSymbolTableEntry.getNameScope().getClass().getName()) + "( " + objSymbolTableEntry.getNameScope().getName() + " )";
                rowData[count][3] = (bKineticsParameter ? "Parameter" : objSymbolTableEntry.getClass().getName()) + "( " + objSymbolTableEntry.getName() + " )";
                count++;
            }
        }
        // for (SymbolTableEntry referencingSTE : referencingSymbols) {
        // System.out.println("REFERENCE   "+referencingSTE.getClass().getName()+"("+referencingSTE.getName()+") nameScope "+referencingSTE.getNameScope().getClass().getName()+"("+referencingSTE.getNameScope().getName()+")");
        // }
        Arrays.sort(rowData, new Comparator<String[]>() {

            @Override
            public int compare(String[] o1, String[] o2) {
                return o1[0].compareToIgnoreCase(o2[0]);
            }
        });
    }
    if (rowData == null || rowData.length == 0) {
        return null;
    }
    return new DeleteSpeciesInfo(rxPartHashMap, bUnresolvableHashMap, rowData);
}

Example 64 with SymbolTableEntry

use of cbit.vcell.parser.SymbolTableEntry 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);
}

Example 65 with SymbolTableEntry

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

the class InitialConditionsPanel method jMenuItemPaste_ActionPerformed.

/**
 * Comment
 */
private void jMenuItemPaste_ActionPerformed(final java.awt.event.ActionEvent actionEvent) {
    final Vector<String> pasteDescriptionsV = new Vector<String>();
    final Vector<Expression> newExpressionsV = new Vector<Expression>();
    final Vector<SpeciesContextSpec.SpeciesContextSpecParameter> changedParametersV = new Vector<SpeciesContextSpec.SpeciesContextSpecParameter>();
    AsynchClientTask task1 = new AsynchClientTask("validating", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            if (actionEvent.getSource() == getJMenuItemPaste() || actionEvent.getSource() == getJMenuItemPasteAll()) {
                Object pasteThis = VCellTransferable.getFromClipboard(VCellTransferable.OBJECT_FLAVOR);
                MathSymbolMapping msm = null;
                Exception mathMappingException = null;
                try {
                    MathMapping mm = null;
                    mm = getSimulationContext().createNewMathMapping();
                    msm = mm.getMathSymbolMapping();
                } catch (Exception e) {
                    mathMappingException = e;
                    e.printStackTrace(System.out);
                }
                int[] rows = null;
                if (actionEvent.getSource() == getJMenuItemPasteAll()) {
                    rows = new int[getScrollPaneTable().getRowCount()];
                    for (int i = 0; i < rows.length; i += 1) {
                        rows[i] = i;
                    }
                } else {
                    rows = getScrollPaneTable().getSelectedRows();
                }
                // 
                // Check paste
                // 
                StringBuffer errors = null;
                for (int i = 0; i < rows.length; i += 1) {
                    SpeciesContextSpec scs = tableModel.getValueAt(rows[i]);
                    try {
                        if (pasteThis instanceof VCellTransferable.ResolvedValuesSelection) {
                            VCellTransferable.ResolvedValuesSelection rvs = (VCellTransferable.ResolvedValuesSelection) pasteThis;
                            for (int j = 0; j < rvs.getPrimarySymbolTableEntries().length; j += 1) {
                                SpeciesContextSpec.SpeciesContextSpecParameter pasteDestination = null;
                                SpeciesContextSpec.SpeciesContextSpecParameter clipboardBiologicalParameter = null;
                                if (rvs.getPrimarySymbolTableEntries()[j] instanceof SpeciesContextSpec.SpeciesContextSpecParameter) {
                                    clipboardBiologicalParameter = (SpeciesContextSpec.SpeciesContextSpecParameter) rvs.getPrimarySymbolTableEntries()[j];
                                } else if (rvs.getAlternateSymbolTableEntries() != null && rvs.getAlternateSymbolTableEntries()[j] instanceof SpeciesContextSpec.SpeciesContextSpecParameter) {
                                    clipboardBiologicalParameter = (SpeciesContextSpec.SpeciesContextSpecParameter) rvs.getAlternateSymbolTableEntries()[j];
                                }
                                if (clipboardBiologicalParameter == null) {
                                    Variable pastedMathVariable = null;
                                    if (rvs.getPrimarySymbolTableEntries()[j] instanceof Variable) {
                                        pastedMathVariable = (Variable) rvs.getPrimarySymbolTableEntries()[j];
                                    } else if (rvs.getAlternateSymbolTableEntries() != null && rvs.getAlternateSymbolTableEntries()[j] instanceof Variable) {
                                        pastedMathVariable = (Variable) rvs.getAlternateSymbolTableEntries()[j];
                                    }
                                    if (pastedMathVariable != null) {
                                        if (msm == null) {
                                            throw mathMappingException;
                                        }
                                        Variable localMathVariable = msm.findVariableByName(pastedMathVariable.getName());
                                        if (localMathVariable == null) {
                                            // try if localMathVariable is a speciesContext init parameter
                                            String initSuffix = DiffEquMathMapping.MATH_FUNC_SUFFIX_SPECIES_INIT_CONC_UNIT_PREFIX + TokenMangler.fixTokenStrict(scs.getInitialConcentrationParameter().getUnitDefinition().getSymbol());
                                            localMathVariable = msm.findVariableByName(pastedMathVariable.getName() + initSuffix);
                                        }
                                        if (localMathVariable != null) {
                                            SymbolTableEntry[] localBiologicalSymbolArr = msm.getBiologicalSymbol(localMathVariable);
                                            for (int k = 0; k < localBiologicalSymbolArr.length; k += 1) {
                                                if (localBiologicalSymbolArr[k] instanceof SpeciesContext && scs.getSpeciesContext() == localBiologicalSymbolArr[k]) {
                                                    // need to change
                                                    pasteDestination = scs.getInitialConditionParameter();
                                                } else if (localBiologicalSymbolArr[k] instanceof SpeciesContextSpec.SpeciesContextSpecParameter) {
                                                    for (int l = 0; l < scs.getParameters().length; l += 1) {
                                                        if (scs.getParameters()[l] == localBiologicalSymbolArr[k]) {
                                                            pasteDestination = (SpeciesContextSpec.SpeciesContextSpecParameter) localBiologicalSymbolArr[k];
                                                            break;
                                                        }
                                                    }
                                                }
                                                if (pasteDestination != null) {
                                                    break;
                                                }
                                            }
                                        }
                                    }
                                } else {
                                    for (int k = 0; k < scs.getParameters().length; k += 1) {
                                        SpeciesContextSpec.SpeciesContextSpecParameter scsp = (SpeciesContextSpec.SpeciesContextSpecParameter) scs.getParameters()[k];
                                        if (scsp.getRole() == clipboardBiologicalParameter.getRole() && scs.getSpeciesContext().compareEqual(((SpeciesContextSpec) clipboardBiologicalParameter.getNameScope().getScopedSymbolTable()).getSpeciesContext())) {
                                            pasteDestination = (SpeciesContextSpec.SpeciesContextSpecParameter) scsp;
                                        }
                                    }
                                }
                                if (pasteDestination != null) {
                                    changedParametersV.add(pasteDestination);
                                    newExpressionsV.add(rvs.getExpressionValues()[j]);
                                    pasteDescriptionsV.add(VCellCopyPasteHelper.formatPasteList(scs.getSpeciesContext().getName(), pasteDestination.getName(), pasteDestination.getExpression().infix(), rvs.getExpressionValues()[j].infix()));
                                }
                            }
                        }
                    } catch (Throwable e) {
                        if (errors == null) {
                            errors = new StringBuffer();
                        }
                        errors.append(scs.getSpeciesContext().getName() + " (" + e.getClass().getName() + ") " + e.getMessage() + "\n\n");
                    }
                }
                if (errors != null) {
                    throw new Exception(errors.toString());
                }
            }
        }
    };
    AsynchClientTask task2 = new AsynchClientTask("pasting", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            // Do paste
            if (pasteDescriptionsV.size() > 0) {
                String[] pasteDescriptionArr = new String[pasteDescriptionsV.size()];
                pasteDescriptionsV.copyInto(pasteDescriptionArr);
                SpeciesContextSpec.SpeciesContextSpecParameter[] changedParametersArr = new SpeciesContextSpec.SpeciesContextSpecParameter[changedParametersV.size()];
                changedParametersV.copyInto(changedParametersArr);
                Expression[] newExpressionsArr = new Expression[newExpressionsV.size()];
                newExpressionsV.copyInto(newExpressionsArr);
                VCellCopyPasteHelper.chooseApplyPaste(InitialConditionsPanel.this, pasteDescriptionArr, changedParametersArr, newExpressionsArr);
            } else {
                PopupGenerator.showInfoDialog(InitialConditionsPanel.this, "No paste items match the destination (no changes made).");
            }
        }
    };
    ClientTaskDispatcher.dispatch(this, new Hashtable<String, Object>(), new AsynchClientTask[] { task1, task2 });
}