@Override
protected PortObject[] execute(final PortObject[] inObjects, final ExecutionContext exec)
throws Exception {
// Initialising
exec.setMessage("initialising");
final ClusterTreeModel model = (ClusterTreeModel) inObjects[0];
final BufferedDataTable data = (BufferedDataTable) inObjects[1];
final int distanceColumnIdx =
data.getDataTableSpec().findColumnIndex(distanceColumnModel.getColumnName());
final Map<RowKey, DistanceVectorDataValue> distanceMatrix =
new HashMap<RowKey, DistanceVectorDataValue>();
for (final DataRow dataRow : data) {
final DistanceVectorDataValue distanceVector =
(DistanceVectorDataValue) dataRow.getCell(distanceColumnIdx);
distanceMatrix.put(dataRow.getKey(), distanceVector);
}
exec.setMessage("computing");
final DendrogramNode origRoot = model.getRoot();
final Map<Triple<DendrogramNode, RowKey, RowKey>, Number> m =
visit(
origRoot,
new HashMap<Triple<DendrogramNode, RowKey, RowKey>, Number>(),
distanceMatrix,
model.getClusterDistances().length + 1,
exec.createSilentSubExecutionContext(.9));
final Map<RowKey, Pair<DataRow, Integer>> rows = new HashMap<RowKey, Pair<DataRow, Integer>>();
int idx = 0;
for (final DataRow dataRow : data) {
rows.put(dataRow.getKey(), Pair.create(dataRow, Integer.valueOf(idx++)));
}
exec.setMessage("creating final tree");
final ClusterViewNode tree = buildNewTree(convertM(m), origRoot, rows, exec).getO1();
final ArrayList<DistanceVectorDataValue>
origList = new ArrayList<DistanceVectorDataValue>(model.getClusterDistances().length + 1),
newList = new ArrayList<DistanceVectorDataValue>(model.getClusterDistances().length + 1);
flatten(origRoot, origList, distanceMatrix);
exec.checkCanceled();
flatten(tree, newList, distanceMatrix);
logger.info("Before: " + sumDistance(origList));
logger.info("After: " + sumDistance(newList));
final ClusterTreeModel clusterTreeModel =
new ClusterTreeModel(
(DataTableSpec) model.getSpec(),
tree,
model.getClusterDistances(),
model.getClusterDistances().length + 1) {
@Override
public String getSummary() {
return "Before: " + sumDistance(origList) + "\nAfter: " + sumDistance(newList);
}
};
return new PortObject[] {clusterTreeModel};
}
/** {@inheritDoc} */
@Override
protected void loadValidatedSettingsFrom(final NodeSettingsRO settings)
throws InvalidSettingsException {
distanceColumnModel.loadSettingsFrom(settings);
}
/** {@inheritDoc} */
@Override
protected void validateSettings(final NodeSettingsRO settings) throws InvalidSettingsException {
distanceColumnModel.validateSettings(settings);
}
/** {@inheritDoc} */
@Override
protected void saveSettingsTo(final NodeSettingsWO settings) {
distanceColumnModel.saveSettingsTo(settings);
}
