Added main.py that now contains the One & Only Singleton instance of these classes:

- Navigator
 - Aplication
 - Workflow
 - Project
 - Options
Corresponding changes have been added in lots of other files to account for this, but
the access to these objects should now be a lot easier.

workflows/geneontology.py

@@ -164,17 +164,12 @@ def read_gene_ontology(fd):
             section = s
             if s == 'Term':
                 term = GOTerm()
-#                print "[Term]"
             else:
                 term = None
-                #print "ignoring: %s" %s
+                print "ignoring: %s" %s
         else:
             if term:
                 _add_term_attribute(term, k, v, c)
-#                print "    %s: %s" % (k, v)
-#            else:
-#                print "no term: ignoring: %s" %line
-#        print '.',
         line = fd.readline()
 
     if term:
@@ -182,6 +177,18 @@ def read_gene_ontology(fd):
 
     return go            
 
+
+def pickle_gene_ontology(go, fn):
+    fd = open(fn, 'wb')
+    pickle.dump(go, fd)
+    fd.close()
+
+def load_pickled_ontology(fn):
+    fd = open(fn, 'rb')
+    go = pickle.load(fd)
+    fd.close()
+    return go
+
 def read_default_go():
     f = open("/usr/share/gene-ontology/gene_ontology.obo")
     go = read_gene_ontology(f)

workflows/gobrowser.py

@@ -37,7 +37,7 @@ class GoTermView (gtk.Frame):
 
     def __init__(self):
         gtk.Frame.__init__(self)
-        tab = gtk.Table(2, 2, False)
+        tab = gtk.Table(2, 3, False)
         self._table = tab
         
         self._name = gtk.Label('')
@@ -48,6 +48,11 @@ class GoTermView (gtk.Frame):
         tab.attach(name_label, 0, 1, 0, 1, gtk.FILL, gtk.FILL, 5, 5)
         tab.attach(self._name, 1, 2, 0, 1, gtk.FILL|gtk.EXPAND, gtk.FILL, 5, 5)
         
+        self._isa_parents = gtk.HBox()
+        isa_parents_label = gtk.Label('Is a:')
+        tab.attach(isa_parents_label, 0, 1, 1, 2, gtk.FILL, gtk.FILL, 5, 5)
+        tab.attach(self._isa_parents, 1, 2, 1, 2, gtk.FILL, gtk.FILL, 5, 5)
+        
         self._def = gtk.TextBuffer()
         textview = gtk.TextView(self._def)
         textview.set_wrap_mode(gtk.WRAP_WORD)
@@ -55,9 +60,10 @@ class GoTermView (gtk.Frame):
         scrolled_window.add(textview)
         def_label = gtk.Label('Def:')
         def_label.set_alignment(0.0, 0.0)
-        tab.attach(def_label, 0, 1, 1, 2, gtk.FILL, gtk.FILL, 5, 5)
-        tab.attach(scrolled_window, 1, 2, 1, 2, gtk.FILL|gtk.EXPAND, gtk.FILL|gtk.EXPAND, 5, 5)
+        tab.attach(def_label, 0, 1, 2, 3, gtk.FILL, gtk.FILL, 5, 5)
+        tab.attach(scrolled_window, 1, 2, 2, 3, gtk.FILL|gtk.EXPAND, gtk.FILL|gtk.EXPAND, 5, 5)
         
+        self._tab = tab
         self.add(tab)
         self.set_go_term(None)
 
@@ -66,16 +72,28 @@ class GoTermView (gtk.Frame):
             self.set_label(term['id'])
             self._name.set_text(term['name'])
             self._def.set_text(term['def'])
+            self._tab.remove(self._isa_parents)
+            self._isa_parents = gtk.HBox()
+            for p in term['is_a']:
+                btn = gtk.Button(p)
+                btn.show()
+                self._isa_parents.add(btn)
+            self._isa_parents.show()
+            self._tab.attach(self._isa_parents, 1, 2, 1, 2, gtk.FILL, gtk.FILL, 5, 5)
         else:
             self.set_label('GO Term')
             self._name.set_text('')
             self._def.set_text('')
-
+            self._tab.remove(self._isa_parents)
+            self._isa_parents = gtk.HBox()
+            self._tab.attach(self._isa_parents, 1, 2, 1, 2, gtk.FILL, gtk.FILL, 5, 5)
         
+
 class GeneOntologyTree (gtk.HPaned):
     
     def __init__(self, network):
         gtk.HPaned.__init__(self)
+        self.set_position(400)
     
         treemodel = geneontology.get_go_treestore(network)
         self._treemodel = treemodel

workflows/smokers.py

@@ -13,8 +13,8 @@ class SmallTestWorkflow(workflow.Workflow):
     ident = 'smokers'
     description = 'A small test workflow for gene expression analysis.'
 
-    def __init__(self, app):
-        workflow.Workflow.__init__(self, app)        
+    def __init__(self):
+        workflow.Workflow.__init__(self)        
 
         # DATA IMPORT
         load = workflow.Stage('load', 'Data')