Examples of NexusDataSetJDBC


      NexusDataSet dataSet = null;
      try {
        // first start a transaction, use Hibernate to add and persist most of the data
        dataSet = addNexusFile(pSubmission, file);
        NexusDataSetJDBC dataJDBC = dataSet.getDataJDBC();


        // Next use direct JDBC to batch insert data, for performance reason.
        // getDomainHome().refreshAll(dataJDBC.getAllMatrices());


        // TODO: create a new method:
        Connection conn = getSubmissionHome().getConnection();
        for (MatrixJDBC matrixJDBC : dataJDBC.getMatrixJDBCList()) {
          matrixJDBC.batchInsertColumn(conn);
          matrixJDBC.prepElementBatchInsert(conn);
          matrixJDBC.processMatrixElements(conn);
          // MesquiteMatrixConverter converter = matrixJDBC.getMesqMatrixConverter();
          // converter.processMatrixElements(matrixJDBC, conn);

Examples of org.cipres.treebase.dao.jdbc.NexusDataSetJDBC

    Submission sub = update(pSubmission);


    Study study = sub.getStudy();


    NexusDataSet data = getNexusService().parseNexus(study, pNexusFiles, pListener);
    NexusDataSetJDBC dataJDBC = null;


    if (data != null) {


      long timeStart = System.currentTimeMillis();

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