Added a singleton project in the project module, so that the current project is

easily accessible from anywhere in the code. As there is only one project at
any given time this should not be a problem.

The Gene Ontology browser needed this to be able to set the selection without
passing the current project through several constructors. 

Added a context menu in the GO browser that allows the user to select all GO
terms in the subgraph that starts on the current node.

fluents/fluents.py

@@ -197,12 +197,13 @@ class FluentApp:
         tb = ViewFrameToolButton()
         self['toolbar'].add(tb)
 
-    def set_project(self, project):
+    def set_project(self, proj):
         logger.log('notice', 'Creating a new project')
-        self.project = project
+        self.project = proj
-        self.workflow.add_project(self.project)
+        project.project = proj
-        self.navigator_view.add_project(self.project)
+        self.workflow.add_project(proj)
-        self.dimlistcontroller.set_project(project)
+        self.navigator_view.add_project(proj)
+        self.dimlistcontroller.set_project(proj)
 
     def set_workflow(self, workflow):
         self.workflow = workflow

fluents/project.py

@@ -135,3 +135,8 @@ class Project:
     def set_current_data(self, obj):
         self.current_data = obj
 
+
+## Singleton project.
+## This is the current and only project in the application.
+project = None
+

workflows/go_workflow.py

@@ -1,5 +1,5 @@
 import gtk
-from fluents import dataset, logger, plots, workflow, fluents
+from fluents import dataset, logger, plots, workflow, fluents, project
 from fluents.lib import blmfuncs
 import geneontology
 #import gostat
@@ -77,6 +77,11 @@ class GeneOntologyTree (gtk.HPaned):
         self._treemodel = treemodel
         self._tree_view = gtk.TreeView(treemodel)
 
+        # Set up context menu
+        self._context_menu = GoTermContextMenu(treemodel, self._tree_view)
+        self._tree_view.connect('popup_menu', self._popup_menu)
+        self._tree_view.connect('button_press_event', self._on_button_press)
+
         renderer = gtk.CellRendererText()
         go_column = gtk.TreeViewColumn('GO ID', renderer, text=0)
         self._tree_view.insert_column(go_column, 0)
@@ -102,6 +107,54 @@ class GeneOntologyTree (gtk.HPaned):
         self._desc_view.set_go_term(term)        
         
 
+    ##
+    ## GTK Callback functions
+    ##
+    def _popup_menu(self, *rest):
+        self.menu.popup(None, None, None, 0, 0)
+
+    def _on_button_press(self, widget, event):
+        path = widget.get_path_at_pos(int(event.x), int(event.y))
+        iter = None
+
+        if path:
+            iter = self._treemodel.get_iter(path[0])
+            obj = self._treemodel.get_value(iter, 2)
+        else:
+            obj = None
+
+        self._context_menu.set_current_term(obj)
+
+        if event.button == 3:
+            self._context_menu.popup(None, None, None, event.button, event.time)
+
+
+class GoTermContextMenu (gtk.Menu):
+    """Context menu for GO terms in the gene ontology browser"""
+
+    def __init__(self, treemodel, treeview):
+        self._treemodel = treemodel
+        self._treeview = treeview
+        self._current_term = None
+
+        gtk.Menu.__init__(self)
+
+        # Popuplate tree
+        self._select_subtree_item = i = gtk.MenuItem('Select subtree')
+        i.connect('activate', self._on_select_subtree, treemodel, treeview)
+        self.append(i)
+        i.show()
+
+    def set_current_term(self, term):
+        self._current_term = term
+
+    def _on_select_subtree(self, item, treemodel, treeview):
+        logger.log('notice', 'Selecting subtree from GO id: %s (%s)' %
+                   (self._current_term['id'], self._current_term['name']))
+        ids = [x['id'] for x in networkx.bfs(go, self._current_term)]
+        project.project.set_selection('go-terms', set(ids))
+
+
 class GoWorkflow (workflow.Workflow):
 
     name = 'Gene Ontology'