Package org.cipres.treebase.domain.matrix

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


    // String itemName = continuousData.getItemName(j);
    // itemDefNameSet.add(itemName);
    // }

    // populate itemDefNameToIDMap based on continuousMatrix.itemDefinitions
    ContinuousMatrix matrix = (ContinuousMatrix) getCharacterMatrix();

    for (ItemDefinition anItemDef : matrix.getItemDefinitions()) {

      mItemDefNameToIDMap.put(anItemDef.getDescription(), anItemDef.getId());
    }

    // The following code is used to populate itemDefNameToIDMap based on
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   */
  @Override
  protected MatrixJDBC createMatrix(CharacterData pMesqMatrix) {

    ContinuousData continuousData = (ContinuousData) pMesqMatrix;
    ContinuousMatrix m = new ContinuousMatrix();
   
    ContinuousMatrixJDBC matrixJDBC = new ContinuousMatrixJDBC(m, continuousData, this);

    int numChars = continuousData.getNumChars();
    int numItems = continuousData.getNumItems();

    mItemDefinitions = new Double2DArray[numItems];
    mItemDefinitionNames = new String[numItems];
   
    Set<ItemDefinition> itemDefs = new HashSet<ItemDefinition>();

    List<MatrixColumnJDBC> columnJDBCs = new ArrayList<MatrixColumnJDBC>();
    List<ItemDefinitionJDBC> itemDefJDBCs = new ArrayList<ItemDefinitionJDBC>();
   
    // add Item definitions if there are any:
    for (int j = 0; j < numItems; j++) {
      Double2DArray anItem = continuousData.getItem(j);

      String itemName = continuousData.getItemName(j);
      mItemDefinitionNames[j] = itemName;
      mItemDefinitions[j] = anItem;
       
      // This can be null, means the default definition 'AVG' is used.
      ItemDefinition definition = getItemDefinition(itemName);
      //ItemDefinitionJDBC itemDefJDBC = new ItemDefinitionJDBC();
      //itemDefJDBC.setColumnIndex(pNewColumnIndex);
      //itemDefJDBC.setItemDefinitionDesc(itemName);
     
      if (definition != null) {
        itemDefs.add(definition);
        getItemDefMap().put(anItem, definition);
      }
    }
   
    if (!itemDefs.isEmpty()) {
      m.setItemDefinitions(itemDefs);
    }

    // add character/column:
    for (int i = 0; i < numChars; i++) {

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   *
   * @param xmlMatrix
   * @return
   */
  private Matrix fromXmlToTreeBase(org.nexml.model.ContinuousMatrix xmlMatrix) {   
    ContinuousMatrix tbMatrix = new ContinuousMatrix();   
    ContinuousMatrixJDBC matrixJDBC = new ContinuousMatrixJDBC(tbMatrix, xmlMatrix, this);   
    List<MatrixColumnJDBC> columnJDBCs = new ArrayList<MatrixColumnJDBC>();
    long[] colIds = matrixJDBC.getColIDs();
    long[] rowIds = matrixJDBC.getRowIDs();
    List<ContinuousMatrixElementJDBC> elements = new ArrayList<ContinuousMatrixElementJDBC>();
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