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


    for (int i = 0; i < pSetVector.size(); i++) {
      SpecsSet ss = (SpecsSet) pSetVector.elementAt(i);
      if (ss instanceof CharSelectionSet) {
        CharSelectionSet charSet = (CharSelectionSet) ss;
        UserDefinedCharSet tbCharSet = createCharSet(pMesqMatrix, charSet, pMatrix);


        pMatrix.getCharSets().add(tbCharSet);
      }
    }

  private UserDefinedCharSet createCharSet(
    CharacterData pMesqMatrix,
    CharSelectionSet pCharSet,
    CharacterMatrix pMatrix) {


    UserDefinedCharSet tbCharSet = new UserDefinedCharSet();
    tbCharSet.setTitle(pCharSet.getName());
    tbCharSet.setMatrix(pMatrix);


    int numChars = pMesqMatrix.getNumChars();
    // Set<CharWeight> tbWeights = new HashSet<CharWeight>();


    // create one char weight for each columnRangeConvertHelper
    ColumnRangeConvertHelper colRangeHelper = decodeBitsSpecsSet(pCharSet, numChars);
    tbCharSet.setColumns(colRangeHelper.getColRanges());


    if (LOGGER.isDebugEnabled()) {
      StringBuilder sb = new StringBuilder();
      sb.append(tbCharSet.getTitle()).append(" = ");
      for (ColumnRange aRange : tbCharSet.getColumns()) {
        aRange.appendRange(sb).append(" ");
      }
      LOGGER.debug(sb.toString());
    }

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

Related Classes of org.cipres.treebase.domain.matrix.UserDefinedCharSet