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();
}
public void setNotation(String notation) {
if (null == notation || notation.length() == 0) {
notFiringOnChange = true;
sequenceTextArea.setText("");
connectionTableModel.setupEmptyData(CONNECTION_TABLE_ROW_COUNT);
annotationTableModel.setupEmptyData(ANNOTATION_TABLE_ROW_COUNT);
notFiringOnChange = false;
return;
}
notFiringOnChange = true;
try {
ComplexProtein cp = ComplexProtein.convert(notation);
List<String> sequences = cp.getSequences();
if (null != sequences && !sequences.isEmpty()) {
StringBuilder sb = new StringBuilder();
for (String seq : sequences) {
if (sb.length() > 0) {
sb.append(ComplexProtein.SEQUENCE_SEPARATOR_SYMBOL);
sb.append("\n");
}
sb.append(toBlockedSequence(seq));
sb.append("\n");
}
sequenceTextArea.setText(sb.toString());
List<PeptideConnection> conList = cp.getConnections();
if (null != conList && !conList.isEmpty()) {
if (conList.size() >= CONNECTION_TABLE_ROW_COUNT) {
connectionTableModel.setData(conList);
} else {
List<PeptideConnection> l = new ArrayList<PeptideConnection>();
l.addAll(conList);
for (int i = 0; i < CONNECTION_TABLE_ROW_COUNT - conList.size(); i++) {
l.add(new PeptideConnection());
}
connectionTableModel.setData(l);
}
} else {
connectionTableModel.setupEmptyData(CONNECTION_TABLE_ROW_COUNT);
}
List<SequenceAnnotation> annList = cp.getAnnotations();
if (null != annList && !annList.isEmpty()) {
if (annList.size() >= ANNOTATION_TABLE_ROW_COUNT) {
annotationTableModel.setData(annList);
} else {
List<SequenceAnnotation> l = new ArrayList<SequenceAnnotation>();
l.addAll(annList);
for (int i = 0; i < ANNOTATION_TABLE_ROW_COUNT - annList.size(); i++) {
l.add(new SequenceAnnotation());
}
annotationTableModel.setData(l);
}
} else {
annotationTableModel.setupEmptyData(ANNOTATION_TABLE_ROW_COUNT);
}
} else {
sequenceTextArea.setText("");
connectionTableModel.setupEmptyData(CONNECTION_TABLE_ROW_COUNT);
annotationTableModel.setupEmptyData(ANNOTATION_TABLE_ROW_COUNT);
}
} catch (Exception ex) {
Logger.getLogger(ProteinEditor.class.getName()).log(Level.SEVERE, null, ex);
ExceptionHandler.handleException(ex);
}
notFiringOnChange = false;
}