Examples with CompoundInfo cbit.vcell.dictionary.CompoundInfo used on opensource projects

Example 6 with CompoundInfo

use of cbit.vcell.dictionary.CompoundInfo in project vcell by virtualcell.

the class EnzymeReactionTable method getReactions.

/**
 * returns a Compound object from the ResultSet
 * @return cbit.vcell.dictionary.Compound
 * @param rset java.sql.ResultSet
 */
public ReactionDescription[] getReactions(java.sql.ResultSet rset) throws java.sql.SQLException {
    Vector reactions = new Vector();
    String currentReactionID = null;
    String currentEnzymeFID = null;
    ReactionDescription current_dbfr = null;
    while (rset.next()) {
        String reactionID = null;
        String enzymeFID = null;
        if (!rset.isAfterLast()) {
            reactionID = rset.getString(EnzymeReactionTable.table.reactionId.toString());
            enzymeFID = rset.getString(RXQ_ENZYMEFID_ALIAS);
        }
        if (!reactionID.equals(currentReactionID) || !org.vcell.util.Compare.isEqualOrNull(enzymeFID, currentEnzymeFID)) {
            java.math.BigDecimal enzymeID = rset.getBigDecimal(RXQ_ENZYMEID_ALIAS);
            if (enzymeID != null) {
                String enzymeName = rset.getString(RXQ_ENZYMENAME_ALIAS);
                current_dbfr = new ReactionDescription(reactionID);
                current_dbfr.addReactionElement(new FormalEnzyme(new KeyValue(enzymeID), new EnzymeInfo(enzymeFID, new String[] { enzymeName }, null, null, null)), 0, ReactionDescription.RX_ELEMENT_CATALYST);
            } else if (enzymeFID != null) {
                current_dbfr = new ReactionDescription(reactionID);
                current_dbfr.addReactionElement(new DBNonFormalUnboundSpecies(enzymeFID), /*FormalUnknown(enzymeFID,null)*/
                0, ReactionDescription.RX_ELEMENT_CATALYST);
            } else {
                current_dbfr = new ReactionDescription(reactionID);
            }
            reactions.add(current_dbfr);
        }
        currentReactionID = reactionID;
        currentEnzymeFID = enzymeFID;
        // 
        FormalCompound formalCompound = new FormalCompound(new KeyValue(rset.getBigDecimal(RXQ_CMPNDID_ALIAS)), new CompoundInfo(rset.getString(CompoundTable.table.keggID.toString()), new String[] { rset.getString(RXQ_CMPDNDNAME_ALIAS) }, null, null, null));
        current_dbfr.addReactionElement(formalCompound, rset.getInt(EnzymeReactionTable.table.stoich.toString()), rset.getString(EnzymeReactionTable.table.type.toString()).charAt(0));
    }
    ReactionDescription[] reactionsArr = null;
    if (reactions.size() > 0) {
        reactionsArr = new ReactionDescription[reactions.size()];
        reactions.copyInto(reactionsArr);
    }
    return reactionsArr;
}