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

Example 1 with FormalEnzyme

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

the class DictionaryDBTopLevel method getEnzymeFromECNumber.

/**
 * 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.
 */
FormalEnzyme getEnzymeFromECNumber(String dbID, boolean bEnableRetry) throws java.sql.SQLException {
    Object lock = new Object();
    Connection con = conFactory.getConnection(lock);
    try {
        FormalEnzyme result = dictionaryDB.getEnzymeFromECNumber(con, dbID);
        return result;
    } catch (Throwable e) {
        lg.error(e.getMessage(), e);
        if (bEnableRetry && isBadConnection(con)) {
            conFactory.failed(con, lock);
            return getEnzymeFromECNumber(dbID, false);
        } else {
            handle_SQLException(e);
            // never gets here;
            return null;
        }
    } finally {
        conFactory.release(con, lock);
    }
}

Example 2 with FormalEnzyme

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

the class XmlReader method getDBFormalSpecies.

/**
 * This method returns a DBFormalSpecies from a XML representation.
 * Creation date: (6/3/2003 8:46:44 PM)
 * @return cbit.vcell.dictionary.DBFormalSpecies
 * @param formalSpeciesElement org.jdom.Element
 */
private DBFormalSpecies getDBFormalSpecies(Element formalSpeciesElement) throws XmlParseException {
    // read key
    String keystring = formalSpeciesElement.getAttributeValue(XMLTags.KeyValueAttrTag);
    KeyValue key = new KeyValue(keystring);
    // read type
    String typestring = formalSpeciesElement.getAttributeValue(XMLTags.TypeAttrTag);
    // read the FormalSpeciesInfo
    Element speciesInfoElement = formalSpeciesElement.getChild(XMLTags.FormalSpeciesInfoTag, vcNamespace);
    // create the DBFormalSpecies upon the type
    DBFormalSpecies formalSpecies = null;
    if (typestring.equalsIgnoreCase(XMLTags.CompoundTypeTag)) {
        formalSpecies = new FormalCompound(key, (CompoundInfo) getFormalSpeciesInfo(speciesInfoElement));
    } else if (typestring.equalsIgnoreCase(XMLTags.EnzymeTypeTag)) {
        formalSpecies = new FormalEnzyme(key, (EnzymeInfo) getFormalSpeciesInfo(speciesInfoElement));
    } else if (typestring.equalsIgnoreCase(XMLTags.ProteinTypeTag)) {
        formalSpecies = new FormalProtein(key, (ProteinInfo) getFormalSpeciesInfo(speciesInfoElement));
    } else {
        throw new XmlParseException("DBFormalSpecies type:" + typestring + ", not supported yet!");
    }
    return formalSpecies;
}

Example 3 with FormalEnzyme

use of cbit.vcell.dictionary.FormalEnzyme 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 4 with FormalEnzyme

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

the class EnzymeTable method getEnzymes.

/**
 * returns a enzyme object from the ResultSet
 * @return cbit.vcell.dictionary.enzyme
 * @param rset java.sql.ResultSet
 */
public DBFormalSpecies[] getEnzymes(java.sql.ResultSet rset, boolean createBound) throws java.sql.SQLException {
    Vector enzymes = new Vector();
    Vector aliasNames = new Vector();
    String currentAliasName = null;
    String currentECNumber = null;
    String currentSysname = null;
    String currentReaction = null;
    String currentPreferred = null;
    String currentCasID = null;
    org.vcell.util.document.KeyValue currentEnzymeID = null;
    org.vcell.util.document.KeyValue currentDBSpeciesID = null;
    while (rset.next() || rset.isAfterLast()) {
        KeyValue enzymeID = null;
        if (!rset.isAfterLast()) {
            enzymeID = new KeyValue(rset.getBigDecimal(EnzymeTable.table.id.toString()));
        }
        if (!rset.isFirst() && (!currentEnzymeID.equals(enzymeID))) {
            if (currentEnzymeID != null) {
                if (aliasNames.size() > 0) {
                    String[] aliasNamesArr = new String[aliasNames.size()];
                    aliasNames.copyInto(aliasNamesArr);
                    EnzymeInfo enzymeInfo = new EnzymeInfo(currentECNumber, aliasNamesArr, currentReaction, currentSysname, currentCasID);
                    FormalEnzyme formalEnzyme = new FormalEnzyme(currentEnzymeID, enzymeInfo);
                    Object enzyme = formalEnzyme;
                    if (createBound) {
                        BoundEnzyme boundEnzyme = new BoundEnzyme(currentDBSpeciesID, formalEnzyme);
                        enzyme = boundEnzyme;
                    }
                    enzymes.add(enzyme);
                }
            }
            aliasNames.clear();
            if (rset.isAfterLast()) {
                break;
            }
        }
        if (aliasNames.size() == 0) {
            currentEnzymeID = enzymeID;
            currentECNumber = rset.getString(EnzymeTable.table.ecNumber.toString());
            currentSysname = rset.getString(EnzymeTable.table.sysname.toString());
            currentSysname = (currentSysname != null ? org.vcell.util.TokenMangler.getSQLRestoredString(currentSysname) : null);
            currentReaction = rset.getString(EnzymeTable.table.reaction.toString());
            currentReaction = (currentReaction != null ? org.vcell.util.TokenMangler.getSQLRestoredString(currentReaction) : null);
            currentCasID = rset.getString(EnzymeTable.table.casID.toString());
            currentCasID = (currentCasID != null ? org.vcell.util.TokenMangler.getSQLRestoredString(currentCasID) : null);
            if (createBound) {
                currentDBSpeciesID = new KeyValue(rset.getBigDecimal("dbspecies_id"));
            }
        }
        currentPreferred = rset.getString(EnzymeAliasTable.table.preferred.toString());
        currentAliasName = org.vcell.util.TokenMangler.getSQLRestoredString(rset.getString(EnzymeAliasTable.table.name.toString()));
        if (currentPreferred.compareToIgnoreCase("T") == 0) {
            aliasNames.add(0, currentAliasName);
        } else {
            aliasNames.add(currentAliasName);
        }
    }
    DBFormalSpecies[] enzymesArr = null;
    if (enzymes.size() > 0) {
        if (createBound) {
            BoundEnzyme[] boundEnzymesArr = null;
            boundEnzymesArr = new BoundEnzyme[enzymes.size()];
            enzymes.copyInto(boundEnzymesArr);
            enzymesArr = boundEnzymesArr;
        } else {
            FormalEnzyme[] formalEnzymesArr = null;
            formalEnzymesArr = new FormalEnzyme[enzymes.size()];
            enzymes.copyInto(formalEnzymesArr);
            enzymesArr = formalEnzymesArr;
        }
    }
    return enzymesArr;
}

Example 5 with FormalEnzyme

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

the class DictionaryDbDriver method getEnzymeFromECNumber.

/**
 * Returns the enzyme referenced by the given ECNumber
 * @return Enzyme
 * @param con Connection
 * @param ecNumber String
 */
public FormalEnzyme getEnzymeFromECNumber(Connection con, String ecNumber) throws SQLException {
    FormalEnzyme result = null;
    DBFormalSpecies[] dbfsArr = getDatabaseSpecies(con, null, ecNumber, false, FormalSpeciesType.enzyme, FormalSpeciesType.ENZYME_ECNUMBER, -1, false);
    if (dbfsArr != null && dbfsArr.length > 0) {
        result = (FormalEnzyme) dbfsArr[0];
    } else {
        throw new RuntimeException("Expecting only 1 result");
    }
    return result;
}