From f45c9c6bf7cb9af73d19ebf8b26b4f7dd68bdc33 Mon Sep 17 00:00:00 2001
From: einarr <einarr@pvv.ntnu.no>
Date: Wed, 19 Apr 2006 19:59:55 +0000
Subject: [PATCH]  * fluent: General cleanup.

---
 fluent                   | 31 ++++++++++---------------------
 system/project.py        |  2 +-
 system/workflow.py       | 11 ++++++++---
 workflows/go_workflow.py | 24 +++++++++++++++++++++++-
 4 files changed, 42 insertions(+), 26 deletions(-)

diff --git a/fluent b/fluent
index 63d4d60..234b5b7 100755
--- a/fluent
+++ b/fluent
@@ -12,6 +12,7 @@ import gtk.glade
 import gnome
 import gnome.ui
 import pango
+import project
 import workflow
 import logger
 import plots
@@ -21,7 +22,6 @@ import go_workflow
 PROGRAM_NAME = 'fluent'
 VERSION = '0.1.0'
 GLADEFILENAME = 'system/fluent.glade'
-APP = 'appwindow'
 WF_BOX = 'workflow_vbox'
 DATA_BOX = 'data_vbox'
 
@@ -32,8 +32,10 @@ class FluentApp:
         self.navigator = navigator.NavigatorStore()
         self.current_data = None
 
+        self.project = project.Project()
+
         gtk.glade.set_custom_handler(self.custom_object_factory)
-        self.widget_tree = gtk.glade.XML(GLADEFILENAME, APP)
+        self.widget_tree = gtk.glade.XML(GLADEFILENAME, 'appwindow')
         self.workflow = go_workflow.EinarsWorkflow(self)
 
     def custom_object_factory(self, glade, function_name, widget_name,\
@@ -71,31 +73,15 @@ class FluentApp:
         self.init_gui()
 
     def init_gui(self):
-        self.app = self.widget_tree.get_widget(APP)
-        self.app.set_size_request(800, 600)
+        self['appwindow'].set_size_request(800, 600)
 
         # Set up workflow
-        wf_box = self.widget_tree.get_widget(WF_BOX)
         wf_menu = workflow.WorkflowView(self.workflow)
         wf_menu.show()
-        wf_box.pack_end(wf_menu)
+        self['workflow_vbox'].pack_end(wf_menu)
 
-        # Set up plots
-        pt = self.widget_tree.get_widget('small_view')
-        plot = plots.SinePlot()
-        plot.show()
-        plot.mark_active(True)
-
-        plot2 = plots.ScatterPlot()
-        plot2.show()
-
-        plot3 = plots.ScatterPlot()
-        plot3.show()
-
-        #        pt.set_child(plot, 0, 1)
         # Set up plot toolbar
-        dock = self.widget_tree.get_widget('plot_toolbar_dock')
-        dock.add(plot.get_toolbar(self.app))
+#        self['plot_toolbar_dock'].add(plot.get_toolbar(self.app))
 
         # Connect signals
         signals = {'on_quit1_activate' : (gtk.main_quit),
@@ -128,6 +114,9 @@ class FluentApp:
         nb = self.widget_tree.get_widget('main_view')
         nb.goto_small()
 
+    def __getitem__(self, key):
+        return self.widget_tree.get_widget(key)
+
 if __name__ == '__main__':
     gnome.program_init(PROGRAM_NAME, VERSION)
     app = FluentApp()
diff --git a/system/project.py b/system/project.py
index 6d840eb..36e454b 100644
--- a/system/project.py
+++ b/system/project.py
@@ -6,7 +6,7 @@ class Project:
         self.name = name
         self.dim_names = []
         self._selection_observers = []
-        self.current_data=[]
+        self.current_data=None
         self.datasets=[]
         self.sel_obj = dataset.Selection()
         
diff --git a/system/workflow.py b/system/workflow.py
index 6a980e0..85b7baa 100644
--- a/system/workflow.py
+++ b/system/workflow.py
@@ -87,9 +87,14 @@ class WorkflowView (gtk.VBox):
             exp.show()
             self.pack_start(exp, expand=False, fill=False)
 
-    def button_click_handler(self, button):
-        function = button.function
+    def run_function(self, function):
         logger.log('debug', 'Starting function: %s' % function.name)
-        function.run(self.workflow.app.current_data)
+        project = self.workflow.app.project
+        new_data = function.run(project.current_data)
+        if new_data != None:
+            project.current_data = new_data
         logger.log('debug', 'Function ended: %s' % function.name)
+        
+    def button_click_handler(self, button):
+        self.run_function(function = button.function)
 
diff --git a/workflows/go_workflow.py b/workflows/go_workflow.py
index 0808202..2bbf023 100644
--- a/workflows/go_workflow.py
+++ b/workflows/go_workflow.py
@@ -2,6 +2,9 @@ import gtk
 import logger
 from annotations import Annotations
 from workflow import *
+import geneontology
+import gostat
+from scipy import array
 
 class EinarsWorkflow (Workflow):
 
@@ -19,7 +22,7 @@ class EinarsWorkflow (Workflow):
 
         go = Stage('go', 'Gene Ontology Data')
         go.add_function(LoadAnnotationsFunction())
-        go.add_function(Function('godist', 'GO Distances'))
+        go.add_function(GODistanceFunction())
         self.add_stage(go)
 
         regression = Stage('regression', 'Regression')
@@ -37,6 +40,7 @@ class LoadAnnotationsFunction(Function):
     def load_file(self, filename):
         f = open(filename)
         self.annotations = Annotations('genes', 'go-terms')
+        logger.log('notice', 'Loading annotation file: %s' % filename)
 
         for line in f.readlines():
             val = line.split(' \t')
@@ -61,3 +65,21 @@ class LoadAnnotationsFunction(Function):
         dialog.destroy()
         return [self.annotations]
 
+class GODistanceFunction(Function):
+
+    def __init__(self):
+        Function.__init__(self, 'go_diatance', 'GO Distances')
+        self.output = None
+
+    def run(self, data):
+        logger.log('debug', 'datatype: %s' % type(data))
+        if not type(data) == Annotations:
+            return None
+
+        logger.log('debug', 'dimensions: %s' % data.dimensions)
+        
+        genes = data.get_ids('genes')
+        gene_distances = array((len(genes), len(genes)))
+
+        return gene_distances
+