public String getNotation() throws NotationException, IOException, MonomerException, JDOMException { ComplexProtein cp = new ComplexProtein(); cp.setSequences(getSequences()); if (annotationTable.getCellEditor() != null) { annotationTable.getCellEditor().stopCellEditing(); } cp.setAnnotations(annotationTableModel.getPopulatedSeqeuenceAnnotations()); if (connectionTable.getCellEditor() != null) { connectionTable.getCellEditor().stopCellEditing(); } cp.setConnections(connectionTableModel.getPopulatedConnections()); return cp.getNotation(); }