Examples with ParseException org.vcell.model.bngl.ParseException used on opensource projects

Example 6 with ParseException

use of org.vcell.model.bngl.ParseException in project vcell by virtualcell.

the class ViewObservablesMapPanel method updateShapeSpecies.

public void updateShapeSpecies(int selectedRow) {
    GeneratedSpeciesTableRow speciesTableRow = speciesTableModel.getValueAt(selectedRow);
    String inputString = speciesTableRow.getExpression();
    // System.out.println(selectedRows[0] + ": " + inputString);
    Model tempModel = null;
    try {
        tempModel = new Model("MyTempModel");
        tempModel.addFeature("c0");
    } catch (ModelException | PropertyVetoException e1) {
        e1.printStackTrace();
    }
    if (owner != null && owner.getSimulationContext() != null) {
        List<MolecularType> mtList = owner.getSimulationContext().getModel().getRbmModelContainer().getMolecularTypeList();
        try {
            tempModel.getRbmModelContainer().setMolecularTypeList(mtList);
        } catch (PropertyVetoException e1) {
            e1.printStackTrace();
            throw new RuntimeException("Unexpected exception setting " + MolecularType.typeName + " list: " + e1.getMessage(), e1);
        }
    } else {
        System.out.println("something is wrong, we just do nothing rather than crash");
        return;
    }
    try {
        String strStructure = null;
        if (inputString.contains(RbmUtils.SiteStruct)) {
            // we are in the mode where we emulate compartments by adding the compartment name as a fake site
            Pair<List<String>, String> p = RbmUtils.extractCompartment(inputString);
            // we'll just assume there's only one, may want to throw exception if more
            strStructure = p.one.get(0);
            inputString = p.two;
        } else {
            // should be the normal @comp:expression format - if it's not it will return null
            strStructure = RbmUtils.parseCompartment(inputString, tempModel);
        }
        Structure structure;
        if (strStructure != null) {
            if (tempModel.getStructure(strStructure) == null) {
                if (owner.getSimulationContext().getModel().getStructure(strStructure).getTypeName().equals(Structure.TYPE_NAME_MEMBRANE)) {
                    tempModel.addMembrane(strStructure);
                } else {
                    tempModel.addFeature(strStructure);
                }
            }
            structure = tempModel.getStructure(strStructure);
        } else {
            structure = tempModel.getStructure(0);
        }
        SpeciesPattern sp = (SpeciesPattern) RbmUtils.parseSpeciesPattern(inputString, tempModel);
        sp.resolveBonds();
        SpeciesContext sc = new SpeciesContext(new Species("a", ""), structure, sp);
        spls = new SpeciesPatternLargeShape(20, 20, -1, sp, shapePanelSpecies, sc, issueManager);
    } catch (ParseException | PropertyVetoException | ModelException e1) {
        e1.printStackTrace();
        // error (red circle)
        spls = new SpeciesPatternLargeShape(20, 20, -1, shapePanelSpecies, true, issueManager);
        shapePanelSpecies.repaint();
    }
    int xOffset = spls.getRightEnd() + 45;
    Dimension preferredSize = new Dimension(xOffset + 90, 50);
    shapePanelSpecies.setPreferredSize(preferredSize);
    shapePanelSpecies.repaint();
}

Example 7 with ParseException

use of org.vcell.model.bngl.ParseException in project vcell by virtualcell.

the class RbmUtils method parseReactionRule.

public static ReactionRule parseReactionRule(String inputString, String name, Structure structure, BioModel bioModel) throws ParseException {
    try {
        String label = name;
        // int labelIndex = inputString.indexOf(':');		// TODO: the way we edit reaction rules now, we have no labels here
        // String label = "";
        // if(labelIndex>=0) {
        // label = inputString.substring(0, labelIndex);
        // inputString = inputString.substring(labelIndex+1);
        // }
        // if(label.isEmpty() || (reactionRuleNames.indexOf(label) != -1)) {
        // do {	// no label or label in use, we generate new label
        // label = generateReactionRuleName();
        // } while(reactionRuleNames.indexOf(label) != -1);
        // reactionRuleNames.add(label);
        // } else {
        // reactionRuleNames.add(label);
        // }
        int arrowIndex = inputString.indexOf("<->");
        boolean bReversible = true;
        if (arrowIndex < 0) {
            arrowIndex = inputString.indexOf("->");
            bReversible = false;
        }
        String left = inputString.substring(0, arrowIndex).trim();
        String right = inputString.substring(arrowIndex + (bReversible ? 3 : 2)).trim();
        if (left.length() == 0 && right.length() == 0) {
            return null;
        }
        // note that the constructor will try to honor the label from the editor but will generate a new one if already in use
        ReactionRule reactionRule = bioModel.getModel().getRbmModelContainer().createReactionRule(label, structure, bReversible);
        String regex = "[^!]\\+";
        String[] patterns = left.split(regex);
        for (String sp : patterns) {
            SpeciesPattern speciesPattern = parseSpeciesPattern(sp, bioModel.getModel());
            reactionRule.addReactant(new ReactantPattern(speciesPattern, reactionRule.getStructure()));
        }
        patterns = right.split(regex);
        for (String sp : patterns) {
            SpeciesPattern speciesPattern = parseSpeciesPattern(sp, bioModel.getModel());
            reactionRule.addProduct(new ProductPattern(speciesPattern, reactionRule.getStructure()));
        }
        return reactionRule;
    } catch (Throwable ex) {
        ex.printStackTrace();
        throw new ParseException(ex.getMessage());
    }
}

Example 8 with ParseException

use of org.vcell.model.bngl.ParseException in project vcell by virtualcell.

the class RbmUtils method parseSpeciesPattern.

public static SpeciesPattern parseSpeciesPattern(String originalInputString, Model model) throws ParseException {
    String inputString = new String(originalInputString);
    try {
        if (inputString.startsWith("@") && inputString.contains(":")) {
            // throw new ParseException("RbmUtils: Unable to parse SpeciesPattern with compartment information.");
            // clean up the compartment information and parse the pure sp expression
            inputString = inputString.substring(inputString.lastIndexOf(":") + 1);
        }
        BNGLParser parser = new BNGLParser(new StringReader(inputString));
        ASTSpeciesPattern astSpeciesPattern = parser.SpeciesPattern();
        BnglObjectConstructionVisitor constructionVisitor = new BnglObjectConstructionVisitor(model, null, true);
        SpeciesPattern speciesPattern = (SpeciesPattern) astSpeciesPattern.jjtAccept(constructionVisitor, null);
        return speciesPattern;
    } catch (Throwable ex) {
        ex.printStackTrace();
        throw new ParseException(ex.getMessage());
    }
}

Example 9 with ParseException

use of org.vcell.model.bngl.ParseException in project vcell by virtualcell.

the class SpeciesContext method parseSpeciesPatternString.

public void parseSpeciesPatternString(Model model) {
    if (speciesPatternString.equalsIgnoreCase("null")) {
        System.out.println("Species Pattern String is 'NULL'.");
        return;
    }
    if (speciesPatternString != null) {
        try {
            if (speciesPattern != null) {
                System.out.println("Species pattern already exists: " + speciesPattern.toString());
                return;
            }
            SpeciesPattern sp = RbmUtils.parseSpeciesPattern(speciesPatternString, model);
            setSpeciesPattern(sp);
        } catch (ParseException e) {
            e.printStackTrace();
            throw new RuntimeException("Bad format for repository species pattern string: " + e.getMessage());
        }
    }
}