/** {@inheritDoc} */
  @Override
  protected void loadInternals(final File internDir, final ExecutionMonitor exec)
      throws IOException, CanceledExecutionException {

    File file = new File(internDir, "muscle-internals.xml");
    FileInputStream fis = new FileInputStream(file);
    ModelContentRO modelContent = ModelContent.loadFromXML(fis);
    try {
      String[] keys = modelContent.getStringArray("internal-muscle-map-keys");
      m_muscle_map.clear();
      ModelContentRO subkey = modelContent.getModelContent("internal-muscle-map");
      for (String key : keys) {
        DataCell dc = subkey.getDataCell(key);
        if (dc instanceof MultiAlignmentCell) {
          m_muscle_map.put(key, (MultiAlignmentCell) dc);
        }
      }
      fis.close();
    } catch (InvalidSettingsException e) {
      throw new IOException(e.getMessage());
    }
  }
Exemple #2
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 /**
  * Loads the contained row IDs.
  *
  * @param modelContent to read contained RowKeys from.
  * @throws InvalidSettingsException if the settings are invalid
  */
 public void loadFrom(final ModelContentRO modelContent) throws InvalidSettingsException {
   RowKey[] rkArray = modelContent.getRowKeyArray(CFG_KEY_CELLS);
   m_containedRowIds.addAll(Arrays.asList(rkArray));
 }