mainly overhaul of observers, and removal of project singleton

fluent

@@ -14,10 +14,12 @@ import gnome.ui
 import pango
 import project
 import workflow
+import dataset
 import logger
 import plots
 import navigator
 import go_workflow
+import scipy
 
 PROGRAM_NAME = 'fluent'
 VERSION = '0.1.0'
@@ -29,11 +31,22 @@ class FluentApp:
 
     def __init__(self):
         # Application variables
-        self.navigator = navigator.NavigatorStore()
-        self.current_data = None
-
         self.project = project.Project()
 
+        # add test data ##################
+        x = scipy.rand(200,3)
+        def_list = [ ['samples',[]], ['genes',['a','b','c']] ]
+        test_data1 = dataset.Dataset(x,def_list)
+        self.project.add_dataset(test_data1)
+        #y = scipy.rand(200,2)
+        #def_list = [ ['samples',[]], ['yclasses',['C','N']] ]
+        #test_data2 = dataset.Dataset(y,def_list)
+
+        ####################
+
+        
+        self.navigator = navigator.NavigatorStore(self.project)
+        self.current_data = None
         gtk.glade.set_custom_handler(self.custom_object_factory)
         self.widget_tree = gtk.glade.XML(GLADEFILENAME, 'appwindow')
         self.workflow = go_workflow.EinarsWorkflow(self)
@@ -59,7 +72,7 @@ class FluentApp:
         self.small_view.show()
         return self.small_view
 
-    def create_large_view(self, str1, str2, int1, int2):
+    def create_large_view(self, str1, str2, int1, int2,project):
         self.large_view = plots.LargeView()
         self.large_view.show()
         return self.large_view

system/dataset.py

@@ -22,9 +22,10 @@ class Dataset:
             raise ValueError,"array dims and identifyer mismatch"
         for axis,(dim_name,ids) in enumerate(def_list):
             enum_ids = {}
-            if dim_name not in project.c_p.dim_names:
+            #if dim_name not in project.c_p.dim_names:
-                dim_name = project.c_p.suggest_dim_name(dim_name)
+            #    dim_name = project.c_p.suggest_dim_name(dim_name)
             if not ids:
+                logger.log('debug','Creating identifiers along: '+dim_name)
                 ids = self._create_identifiers(axis)
             for num,name in enumerate(ids):
                 enum_ids[name] = num
@@ -70,6 +71,7 @@ class Dataset:
         dim_ids = self.ids[dim_name]
         if type(index)==int:
             index = [index]
+            
         return set([id for id,ind in dim_ids.items() if ind in index])
 
     def extract_index_from_id(self,dim_name,id):

system/navigator.py

@@ -5,22 +5,20 @@ import plots
 import logger
 
 class NavigatorStore (gtk.TreeStore):
-    def __init__(self):
+    def __init__(self,project):
         gtk.TreeStore.__init__(self, gobject.TYPE_STRING, plots.Plot)
-
+        self.project = project
         iter = self.append(None)
         self.set_value(iter, 0, ('Sine Plot'))
-        self.set_value(iter, 1, (plots.SinePlot()))
+        self.set_value(iter, 1, (plots.SinePlot(project)))
 
         iter = self.append(None)
         self.set_value(iter, 0, ('Scatter Plot'))
-        self.set_value(iter, 1, (plots.ScatterPlot()))
+        self.set_value(iter, 1, (plots.ScatterPlot(project)))
 
         iter = self.append(None)
         self.set_value(iter, 0, ('Scatter Plot 2'))
-        self.set_value(iter, 1, (plots.ScatterPlot()))
+        self.set_value(iter, 1, (plots.ScatterPlot(project)))
-
-        
 
     def plot_at(self, path):
         iter = self.get_iter(path)

system/plots.py

@@ -163,12 +163,14 @@ class LargeView (gtk.Frame):
 
 class Plot (gtk.Frame):
 
-    def __init__(self):
+    def __init__(self,project):
         gtk.Frame.__init__(self)
+        self.project = project
         self.mark_active(False)
         self.connect('button_press_event', self.on_button_press)
         self.sel_obj = None
-        project.c_p.attach(self)
+        if project!=None: #its not an Emptyview
+            project.attach(self,'selection_update')
         
     def on_button_press(self, *rest):
         logger.log('debug', 'button pressed in plot')
@@ -183,12 +185,12 @@ class Plot (gtk.Frame):
         else:
             self.set_shadow_type(gtk.SHADOW_OUT)
 
-    def update_selection(self,project):
+    def update(self,project,key):
         pass
     
 class EmptyView (Plot):
     def __init__(self):
-        Plot.__init__(self)
+        Plot.__init__(self,None)
         
         label = gtk.Label('No view')
         ebox = gtk.EventBox()
@@ -212,8 +214,8 @@ class EmptyView (Plot):
         
 class SinePlot(Plot):
     
-    def __init__(self):
+    def __init__(self,project):
-        Plot.__init__(self)
+        Plot.__init__(self,project)
         fig = Figure(figsize=(5,4), dpi=72)
         ax = fig.add_subplot(111)
         t = arange(0.0,3.0,0.01)
@@ -229,14 +231,13 @@ class SinePlot (Plot):
         return self.toolbar
 
 class ScatterPlot(Plot):
-    def __init__(self):
+    def __init__(self,project):
-        Plot.__init__(self)
+        Plot.__init__(self,project)
         fig = Figure(figsize=(5,4), dpi=72)
         self.ax = ax = fig.add_subplot(111)
         
         # testing testing
-        self.c_p = project.c_p
+        self.x_dataset = project.datasets[0]
-        self.x_dataset = self.c_p.datasets[0]
         x = self.x_dataset._data
         self.xaxis_data = xaxis_data =  x[:,0] + scipy.randn(scipy.shape(x)[0])
         self.yaxis_data = yaxis_data = x[:,1]
@@ -286,15 +287,16 @@ class ScatterPlot (Plot):
             logger.log('debug','Selected:\n%s'%index)
             ids = self.x_dataset.extract_id_from_index('samples',index)
             #update selection object
-            self.c_p.set_selection(self.current_dim,ids)
+            self.project.set_selection(self.current_dim,ids)
             logger.log('debug','Selected identifiers:\n%s'%ids)
 
-    def update_selection(self,project):
+    def update(self,project,key):
         curr_sel = project.get_selection() # get selection object
         ids = curr_sel[self.current_dim] # current identifiers
         index = self.x_dataset.extract_index_from_id(self.current_dim,ids) #conversion to index
         xdata_new = scipy.take(self.xaxis_data,index) #take data
         ydata_new = scipy.take(self.yaxis_data,index)
+        self.ax.plot(self.xaxis_data,self.yaxis_data,'ob')
         self.ax.plot(xdata_new,ydata_new,'or')
         self.canvas.draw()
         

system/project.py

@@ -5,33 +5,35 @@ class Project:
     def __init__(self,name="Testing"):
         self.name = name
         self.dim_names = []
-        self._selection_observers = []
+        self._observers = {}
         self.current_data=None
         self.datasets=[]
         self.sel_obj = dataset.Selection()
         
-    def attach(self, observer):
+    def attach(self,observer,key):
         """Attach observer for selection updates"""
-        if not observer in self._selection_observers:
+        if not self._observers.has_key(key):
-            self._selection_observers.append(observer)
+            self._observers[key]=[]        
+        if not observer in self._observers[key]:
+            self._observers[key].append(observer)
 
-    def detach(self, observer):
+    def detach(self,observer,key):
         """Detach observer for selection updates"""
         try:
-            self.selection_observers.remove(observer)
+            self._observers[key].remove(observer)
         except ValueError:
             pass
 
-    def notify(self, modifier=None):
+    def notify(self,key,modifier=None):
-        """Notifies observers that selection is updated"""
+        """Notifies observers"""
-        for observer in self._selection_observers:
+        for observer in self._observers[key]:
             if modifier != observer:
-                observer.update_selection(self)
+                observer.update(self,key)
 
     def set_selection(self,dim_name,selection):
-        """Sets selection and notifies observers"""
+        """Sets a current selection and notify observers"""
         self.sel_obj.current_selection[dim_name] = set(selection)
-        self.notify()
+        self.notify('selection_update')
 
     def get_selection(self):
         """Returns the current selection object"""
@@ -50,18 +52,6 @@ class Project:
             dim_name = dim_name + "_t" 
         return dim_name
         
-# FIXME: Singleton project should be removed.
+
-c_p = Project()
-
-#add test data
-x = scipy.rand(2000,3)
-def_list = [ ['samples',[]], ['genes',['a','b','c']] ]
-test_data = dataset.Dataset(x,def_list)
-c_p.add_dataset(test_data)
-
-y = scipy.rand(2000,2)
-def_list = [ ['samples',[]], ['yclasses',['C','N']] ]
-test_data = dataset.Dataset(y,def_list)
-c_p.add_dataset(test_data)
 
 

workflows/go_workflow.py

@@ -2,8 +2,8 @@ import gtk
 import logger
 from annotations import Annotations
 from workflow import *
-import geneontology
+#import geneontology
-import gostat
+#import gostat
 from scipy import array
 
 class EinarsWorkflow (Workflow):