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

Example 6 with FormalCompound

use of cbit.vcell.dictionary.FormalCompound 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;
}

Example 7 with FormalCompound

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

the class DictionaryDBTopLevel method getCompoundFromKeggID.

/**
 * gets a Species from the DB based on the dbID given as a parameter
 * @return Species
 * @param dbID String
 * @param bVersion boolean
 * @exception java.sql.SQLException The exception description.
 */
FormalCompound getCompoundFromKeggID(String dbID, boolean bEnableRetry) throws java.sql.SQLException {
    Object lock = new Object();
    Connection con = conFactory.getConnection(lock);
    try {
        FormalCompound result = dictionaryDB.getCompoundFromKeggID(con, dbID);
        return result;
    } catch (Throwable e) {
        lg.error(e.getMessage(), e);
        if (bEnableRetry && isBadConnection(con)) {
            conFactory.failed(con, lock);
            return getCompoundFromKeggID(dbID, false);
        } else {
            handle_SQLException(e);
            // never gets here;
            return null;
        }
    } finally {
        conFactory.release(con, lock);
    }
}

Example 8 with FormalCompound

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

the class DictionaryDbDriver method getCompoundFromCasID.

/**
 * Returns the compound referenced by the casID
 * @return Compound
 * @param con Connection
 * @param casID String
 */
public FormalCompound getCompoundFromCasID(Connection con, String casID) throws SQLException {
    FormalCompound result = null;
    DBFormalSpecies[] dbfsArr = getDatabaseSpecies(con, null, casID, false, FormalSpeciesType.compound, FormalSpeciesType.COMPOUND_CASID, -1, false);
    if (dbfsArr != null && dbfsArr.length == 1) {
        result = (FormalCompound) dbfsArr[0];
    } else {
        throw new RuntimeException("Expecting only 1 result");
    }
    return result;
}