Examples with Kinetics cbit.vcell.model.Kinetics used on opensource projects

Example 31 with Kinetics

use of cbit.vcell.model.Kinetics in project vcell by virtualcell.

the class ReactStepTable method getReactionStep.

/**
 * This method was created in VisualAge.
 * @return cbit.vcell.model.ReactionParticipant
 * @param rset java.sql.ResultSet
 */
public ReactionStep getReactionStep(Structure structure, Model model, KeyValue rsKey, java.sql.ResultSet rset, DatabaseSyntax dbSyntax) throws java.sql.SQLException, DataAccessException {
    KeyValue key = rsKey;
    if (rset.wasNull()) {
        key = null;
    }
    String reactType = rset.getString(ReactStepTable.table.reactType.toString());
    String reactionStepName = null;
    String nameString = rset.getString(ReactStepTable.table.name.toString());
    if (rset.wasNull()) {
        nameString = null;
    }
    if (nameString != null) {
        reactionStepName = TokenMangler.getSQLRestoredString(nameString);
    }
    ReactionStep rs = null;
    try {
        if (reactType.equals(ReactStepTable.REACTTYPE_FLUX_REVERSIBLE)) {
            rs = new FluxReaction(model, (Membrane) structure, key, reactionStepName, true);
        } else if (reactType.equals(ReactStepTable.REACTTYPE_FLUX_IRREVERSIBLE)) {
            rs = new FluxReaction(model, (Membrane) structure, key, reactionStepName, false);
        } else if (reactType.equals(ReactStepTable.REACTTYPE_SIMPLE_REVERSIBLE)) {
            rs = new SimpleReaction(model, structure, key, reactionStepName, true);
        } else if (reactType.equals(ReactStepTable.REACTTYPE_SIMPLE_IRREVERSIBLE)) {
            rs = new SimpleReaction(model, structure, key, reactionStepName, false);
        }
    } catch (java.beans.PropertyVetoException e) {
        e.printStackTrace(System.out);
        throw new DataAccessException(e.getMessage());
    }
    // 
    // if valence is stored as a 'null', it was an error (previous models were updated administratively).
    // 
    int valenceValue = rset.getInt(ReactStepTable.table.chargeValence.toString());
    if (rset.wasNull()) {
        throw new DataAccessException("unexpected null for chargeValence");
    }
    // 
    // New procedure for getting kinetics
    // 
    String kinetics_vcml = DbDriver.varchar2_CLOB_get(rset, ReactStepTable.table.kineticsSmall, ReactStepTable.table.kineticsLarge, dbSyntax);
    if (kinetics_vcml == null || kinetics_vcml.length() == 0) {
        throw new DataAccessException("no data stored for kinetics");
    }
    // This isn't needed?
    // if (kinetics_vcml.endsWith(";}\n")){
    // StringBuffer buffer = new StringBuffer(kinetics_vcml.substring(0,kinetics_vcml.length()-2));
    // buffer.append("\n}\n");
    // kinetics_vcml = buffer.toString();
    // }
    org.vcell.util.CommentStringTokenizer tokens = new org.vcell.util.CommentStringTokenizer(kinetics_vcml);
    Kinetics kinetics = null;
    try {
        String token = tokens.nextToken();
        if (!token.equalsIgnoreCase(VCMODL.Kinetics)) {
            throw new DataAccessException("expected " + VCMODL.Kinetics);
        }
        token = tokens.nextToken();
        KineticsDescription kineticsDescription = KineticsDescription.fromVCMLKineticsName(token);
        if (kineticsDescription != null) {
            kinetics = kineticsDescription.createKinetics(rs);
        } else {
            throw new DataAccessException("expected valid kinetics type, read '" + token + "'");
        }
        kinetics.fromTokens(kinetics_vcml);
        // 
        // for debug purposes only, remove when unresolvedParameters are ok ... when globals exist
        // 
        // if (kinetics.getUnresolvedParameters().length!=0){
        // System.out.println("<<<WARNING>>> ReactStepTable.getReactionStep(key="+rsKey+") has "+kinetics.getUnresolvedParameters().length+" UnresolvedParameters");
        // for (int i = 0; i < kinetics.getUnresolvedParameters().length; i++){
        // System.out.println(">>>>>>>>>>>>> UnresolvedParameter["+i+"] = "+kinetics.getUnresolvedParameters()[i].toString());
        // }
        // }
        KineticsParameter chargeValenceParameter = kinetics.getChargeValenceParameter();
        if (chargeValenceParameter != null) {
            chargeValenceParameter.setExpression(new cbit.vcell.parser.Expression(valenceValue));
        }
    } catch (Exception e) {
        lg.error(e.getMessage(), e);
        throw new DataAccessException(e.getMessage());
    }
    rs.setKinetics(kinetics);
    // 
    // if physicsOptions is stored as a 'null', it was an error (previous models were updated administratively).
    // 
    int physicsOptionsValue = rset.getInt(ReactStepTable.table.physicsOptions.toString());
    if (rset.wasNull()) {
        throw new DataAccessException("unexpected null for physicsOptions");
    }
    try {
        rs.setPhysicsOptions(physicsOptionsValue);
    } catch (java.beans.PropertyVetoException e) {
        e.printStackTrace(System.out);
    }
    String annot = rset.getString(ReactStepTable.table.annotation.getUnqualifiedColName());
    if (!rset.wasNull()) {
    // annot = TokenMangler.getSQLRestoredString(annot);
    // rs.setAnnotation(annot);
    }
    return rs;
}