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)