Example usage for java.sql Clob length

List of usage examples for java.sql Clob length

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Introduction

In this page you can find the example usage for java.sql Clob length.

Prototype

long length() throws SQLException;

Source Link

Document

Retrieves the number of characters in the CLOB value designated by this Clob object.

Usage

From source file:uk.ac.ebi.orchem.search.SimilaritySearch.java

/**
 * Similarity score calculation between one database compound and a user's query compound.
 * @param userQuery  query structure in SMILES or MOL
 * @param queryType  MOL or SMILES//from   www.  j  ava  2s  .  c o  m
 * @param compoundId ID of database compound to calculate similarity with
 * @return tanimoto similarity score
 * @throws Exception
 */
public static float singleCompoundSimilarity(Clob userQuery, String queryType, String compoundId)
        throws Exception {

    OracleConnection conn = null;
    PreparedStatement pstmtFp = null;
    ResultSet resFp = null;
    float tanimotoCoeff = 0;

    try {
        //User query
        int clobLen = new Long(userQuery.length()).intValue();
        String query = (userQuery.getSubString(1, clobLen));
        IAtomContainer molecule = null;
        if (queryType.equals(Utils.QUERY_TYPE_MOL)) {
            molecule = MoleculeCreator.getMoleculeFromMolfile(query);
        } else if (queryType.equals(Utils.QUERY_TYPE_SMILES)) {
            SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
            molecule = sp.parseSmiles(query);
        } else
            throw new RuntimeException("Query type not recognized");
        BitSet queryFp = FingerPrinterAgent.FP.getExtendedFingerPrinter().getFingerprint(molecule);
        float queryBitCount = queryFp.cardinality();
        byte[] queryBytes = Utils.toByteArray(queryFp, extFpSize);

        //Database comound
        conn = (OracleConnection) new OracleDriver().defaultConnection();
        String compoundQuery = "select bit_count, fp from orchem_fingprint_simsearch s where id=?";
        pstmtFp = conn.prepareStatement(compoundQuery);
        pstmtFp.setFetchSize(1);
        pstmtFp.setString(1, compoundId);
        resFp = pstmtFp.executeQuery();

        if (resFp.next()) {
            byte[] dbByteArray = resFp.getBytes("fp");
            float compoundBitCount = resFp.getFloat("bit_count");
            tanimotoCoeff = calcTanimoto(queryBytes, queryBytes.length, dbByteArray, queryBitCount,
                    compoundBitCount);
        } else
            throw new RuntimeException("Compound " + compoundId + " not found in similarity table");

    } catch (Exception e) {
        e.printStackTrace();
        throw e;
    } finally {
        if (resFp != null)
            resFp.close();
        if (pstmtFp != null)
            pstmtFp.close();
        if (conn != null)
            conn.close();
    }
    return tanimotoCoeff;
}