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Checking some of my desktop apps, when I use the Append geoprocessing tool, I use FeatureLayer objects as inputs and targets.
public FeatureLayer getLayerByName(String layerName, com.esri.arcgis.carto.Map map) { FeatureLayer layer = null; try { for (int i = 0; i < map.getLayerCount(); i++) { if (map.getLayer(i).getName().equalsIgnoreCase(layerName)) { layer = (FeatureLayer) map.getLayer(i); break; } } } catch (AutomationException ae) { ae.printStackTrace(); } catch (IOException e) { e.printStackTrace(); } return layer; }