/** {@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());
}
}
/**
* 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));
}