Examples of org.cipres.treebase.domain.matrix.MatrixKind

Package org.cipres.treebase.domain.matrix

Examples of org.cipres.treebase.domain.matrix.MatrixKind

org.cipres.treebase.domain.matrix.MatrixKind
Another matrix property: describing the "kind" of the matrix. Please also see the "Matrix Data Type", which is defined in Nexus. It's very important to realize that the matrix kind is not the same thing as the matrix DATATYPE. For example, a Nucleotide dataset can be stored in a NEXUS format in which DATATYPE=STANDARD -- it does not have to be stored in DATATYPE=DNA. Also, the choices for Matrix kind is much more specific than the broad categories of DATATYPE in NEXUS. @author Jin Ruan

        warn("  Fixing matrix " + m.getId());
          
        // Map matrixDataType -> matrixKind
        {
          Collection<MatrixKind> mks = matrixService.findSomethingByString(MatrixKind.class, "description", matrixDataType);
          MatrixKind mk = null;
          if (mks.isEmpty()) {
            warn("Unknown MatrixKind '" + matrixDataType + "'; skipping it");
/*            // Or you can manufacture a fresh one here, which is not normally allowed
 *                      // Note that mk.setDescription is private, so you will have to make it public to use this code
 *                      // 20090320 MJD

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  public MatrixKind findKindByDescription(String pDescription) {
    if (TreebaseUtil.isEmpty(pDescription)) {
      return null;
    }


    MatrixKind returnVal = null;


    Criteria c = getSession().createCriteria(MatrixKind.class).add(
      org.hibernate.criterion.Expression.eq("description", pDescription));


    returnVal = (MatrixKind) c.uniqueResult();

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    if (logger.isInfoEnabled()) {
      logger.info("\n\t\tRunning Test: " + testName);
    }


    String desc = MatrixKind.KIND_AA;
    MatrixKind result = getFixture().findKindByDescription(desc);
    
    //verify
    assertTrue(result != null);
    assertTrue(result.getDescription().equals(desc));    


    if (logger.isInfoEnabled()) {
      logger.info(testName + " - end "); //$NON-NLS-1$
    }
  }

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        testList.remove(0);
        request.setAttribute("errors", testList);
        return showForm(request, response, myerrors);
      } else {
        for (Matrix matrix : matrices) {
          MatrixKind kind = getMatrixHome().findKindByDescription(matrix.getKindDescription());
          matrix.setMatrixKind(kind);
        }
        getMatrixService().updateCollection(matrices);
      }
    }

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org.cipres.treebase.auxdata.AddMetaDataAction

org.cipres.treebase.dao.matrix.MatrixDAO

org.cipres.treebase.dao.matrix.MatrixDAOTest

org.cipres.treebase.web.controllers.ListMatrixController

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