Examples of MatrixDataType

org.cipres.treebase.domain.matrix.MatrixDataType
MatrixDataType.java Created on Mar 21, 2006 @author Jin Ruan

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

    StandardMatrix matrix = new StandardMatrix();
    matrix.setAligned(true);
    matrix.setTitle(newName);
    matrix.setNexusFileName("None");


    MatrixDataType dnaType = getMatrixDataTypeHome().findByDescription(
      MatrixDataType.MATRIX_DATATYPE_DNA);
    matrix.setDataType(dnaType);


    // add two columns:
    DiscreteChar dnaChar = (DiscreteChar) dnaType.getDefaultCharacter();
    assertTrue("Failed to load dna character", dnaChar != null);


    MatrixColumn c1 = new MatrixColumn();
    c1.setCharacter(dnaChar);
    matrix.addColumn(c1);

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

    // get symbols as one String. need to do conversion:
    buildSymbols(categoricalData, m);


    // first consider the default char based on matrix data type.
    // For standard matrix, we know it has to be discrete char:
    MatrixDataType dataType = getMatrixDataType();
    DiscreteChar defaultChar = (DiscreteChar) dataType.getDefaultCharacter();
    if (defaultChar != null) {
      matrixJDBC.setDefaultCharID(defaultChar.getId());
    }


    List<MatrixColumnJDBC> columnJDBCs = new ArrayList<MatrixColumnJDBC>();

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


    MesquiteMatrixConverter converter = null;
    if (mesqDataType == MESQUITE_DNA_TYPE) {
      converter = new MesquiteStandardMatrixConverter();


      MatrixDataType dataType = pDataTypeHome
        .findByDescription(MatrixDataType.MATRIX_DATATYPE_DNA);
      converter.setMatrixDataType(dataType);
    } else if (mesqDataType == MESQUITE_RNA_TYPE) {
      converter = new MesquiteStandardMatrixConverter();


      MatrixDataType dataType = pDataTypeHome
        .findByDescription(MatrixDataType.MATRIX_DATATYPE_RNA);
      converter.setMatrixDataType(dataType);
    } else if (mesqDataType == MESQUITE_PROTEIN_TYPE) {
      converter = new MesquiteStandardMatrixConverter();


      MatrixDataType dataType = pDataTypeHome
        .findByDescription(MatrixDataType.MATRIX_DATATYPE_PROTEIN);
      converter.setMatrixDataType(dataType);
      // } else if (mesqDataType == DiscreteDatatypes._CODON_DATATYPE) {
      // converter = new MesquiteStandardMatrixConverter();
      //
      // // TODO: per Mark H. CODON should be depreciated in NCL.
      // MatrixDataType dataType = pDataTypeHome
      // .findByDescription(MatrixDataType.MATRIX_DATATYPE_DNA);
      // converter.setMatrixDataType(dataType);
    } else if (mesqDataType == MESQUITE_CATEGORICAL_TYPE) {
      converter = new MesquiteStandardMatrixConverter();


      MatrixDataType dataType = pDataTypeHome
        .findByDescription(MatrixDataType.MATRIX_DATATYPE_STANDARD);
      converter.setMatrixDataType(dataType);
    } else if (mesqDataType == MESQUITE_CONTINUOUS_TYPE) {
      MesquiteContinuousMatrixConverter continousConverter = new MesquiteContinuousMatrixConverter();
      continousConverter.setItemDefinitionHome(pItemDefHome);


      converter = continousConverter;
      MatrixDataType dataType = pDataTypeHome
        .findByDescription(MatrixDataType.MATRIX_DATATYPE_CONTINUOUS);
      converter.setMatrixDataType(dataType);
    } else {
      // TODO: other types: nucleotide, distance, ...


      // a missing datatype means use standard type:
      converter = new MesquiteStandardMatrixConverter();


      MatrixDataType dataType = pDataTypeHome
        .findByDescription(MatrixDataType.MATRIX_DATATYPE_STANDARD);
      converter.setMatrixDataType(dataType);
    }


    return converter;

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

  /**
   * 
   * @see org.cipres.treebase.domain.matrix.MatrixDataTypeHome#findByDescription(java.lang.String)
   */
  public MatrixDataType findByDescription(String pDescription) {
    MatrixDataType returnVal = null;


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


    returnVal = (MatrixDataType) c.uniqueResult();

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

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


    String desc = MatrixDataType.MATRIX_DATATYPE_DNA;
    MatrixDataType result = getFixture().findByDescription(desc);


    // verify
    assertTrue(result != null);
    assertTrue(result.getDefaultCharacter() != null);
    assertTrue(result.getDescription().equals(desc));


    if (logger.isInfoEnabled()) {
      logger.info(testName + " verified type:" + desc);
    }
  }

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