Adding warning to UIs re clean_data

Author: Jon Hill

stk/stk

@@ -371,7 +371,7 @@ def main():
 
     # Clean data
     parser_cm = subparsers.add_parser('clean_data',
-            help='Remove errant taxa, uninformative trees and empty sources.'
+            help='Renames all sources and trees sensibly. Removes errant taxa, uninformative trees and empty sources.'
             )
     parser_cm.add_argument('input', 
             help='The input phyml file')

stk/supertree_toolkit.py

@@ -3132,9 +3132,11 @@ def clean_data(XML):
     # check trees are informative
     XML = _check_informative_trees(XML,delete=True)
 
+    
     # check sources
     XML = _check_sources(XML,delete=True)
-
+    XML = all_sourcenames(XML)
+    
     # fix tree names
     XML = set_unique_names(XML)
     XML = set_all_tree_names(XML,overwrite=True)

stk_gui/stk_gui/interface.py

@@ -2429,8 +2429,13 @@ def on_clean_data(self, widget = None):
      self.tree.write(f)
      XML = f.getvalue() 
      try:
-        XML = stk.clean_data(XML) 
-        XML = stk.all_sourcenames(XML)
+        prompt_response = dialogs.prompt(self.main_window, 
+                "This function will remove data and rename sources and trees. Sure you want to go ahead?", gtk.MESSAGE_WARNING, True)
+        if (prompt_response == gtk.RESPONSE_CANCEL or
+           prompt_response == gtk.RESPONSE_NO):
+            return
+        elif prompt_response == gtk.RESPONSE_YES:
+            XML = stk.clean_data(XML) 
      except NoAuthors as detail:
         dialogs.error(self.main_window,detail.msg)
         return