From fc4e62f799adf109fda33f87fe7a9065f03694a3 Mon Sep 17 00:00:00 2001
From: flatberg <flatberg@pvv.ntnu.no>
Date: Fri, 21 Apr 2006 09:23:05 +0000
Subject: [PATCH] current datset selection fix

---
 fluent                    |  2 +-
 system/navigator.py       | 26 ++++++++++++++++++--------
 system/project.py         |  2 ++
 workflows/pca_workflow.py | 21 +++++++++++++++------
 4 files changed, 36 insertions(+), 15 deletions(-)

diff --git a/fluent b/fluent
index 1753c2f..f233911 100755
--- a/fluent
+++ b/fluent
@@ -77,7 +77,7 @@ class FluentApp:
 
     def create_navigator_view(self, str1, str2, int1, int2):
         tree = self.project.data_tree
-        self.navigator_view = navigator.NavigatorView(tree, self)
+        self.navigator_view = navigator.NavigatorView(self.project, self)
         self.navigator_view.show()
         return self.navigator_view
 
diff --git a/system/navigator.py b/system/navigator.py
index b26163d..e268916 100644
--- a/system/navigator.py
+++ b/system/navigator.py
@@ -3,12 +3,16 @@ import gtk
 import gobject
 import plots
 import logger
+import dataset
+import project
 
 class NavigatorView (gtk.TreeView):
-    def __init__(self, nav, app):
-        gtk.TreeView.__init__(self, nav)
-        self.navigator = nav
+    def __init__(self, project, app):
+        self.project = project
+        self.data_tree = project.data_tree
         self.app = app
+        
+        gtk.TreeView.__init__(self, self.data_tree)
 
         self.set_headers_visible(False)
         self.connect('row-activated', self.row_activated_handler)
@@ -20,8 +24,14 @@ class NavigatorView (gtk.TreeView):
         logger.log('debug', 'Initializing naviagor window')
 
     def row_activated_handler(self, widget, path, column):
-            
-        iter = self.navigator.get_iter(path)
-        object = self.navigator.get_value(iter, 2)
-        logger.log('notice', 'Button pressed')
-        self.app.change_plot(object)
+        iter = self.data_tree.get_iter(path)
+        obj = self.data_tree.get_value(iter, 2)
+        if isinstance(obj, plots.Plot):
+            logger.log('debug', 'Activating plot')
+            self.app.change_plot(obj)
+        elif isinstance(obj, dataset.Dataset):
+            logger.log('debug', 'Selecting dataset')
+            self.project.set_current_data(obj)
+        else:
+            t = type(obj)
+            logger.log('debug', 'Datatype was %s. Don\'t know what to do.' % t)
diff --git a/system/project.py b/system/project.py
index 0b834c1..0ac43a9 100644
--- a/system/project.py
+++ b/system/project.py
@@ -87,3 +87,5 @@ class Project:
             object.show()
         return object
 
+    def set_current_data(self, obj):
+        self.current_data = obj
diff --git a/workflows/pca_workflow.py b/workflows/pca_workflow.py
index d61c056..9033bf9 100644
--- a/workflows/pca_workflow.py
+++ b/workflows/pca_workflow.py
@@ -1,9 +1,10 @@
 import gtk
 import logger
 from workflow import *
-from scipy import array
+from scipy import array,zeros
 from data import read_affy_annot,read_mootha,data_dict_to_matrix
 import plots
+import dataset
 
 class PCAWorkflow(Workflow):
 
@@ -12,7 +13,7 @@ class PCAWorkflow(Workflow):
         self.name = 'PCAs Workflow'
 
         load = Stage('load', 'Load Data')
-        load.add_function(Function('load_mootha', 'Load'))
+        load.add_function(LoadMoothaData())
         self.add_stage(load)
 
         preproc = Stage('preprocess', 'Preprocessing')
@@ -113,6 +114,7 @@ class LoadMoothaData(Function):
         f = open(filename)
         logger.log('notice', 'Loading expression file: %s' % filename)
         self.file = f
+        self.filename = filename
         
     def on_response(self, dialog, response):
         if response == gtk.RESPONSE_OK:
@@ -122,16 +124,23 @@ class LoadMoothaData(Function):
     def run(self, data):
         btns = ('Open', gtk.RESPONSE_OK, \
                 'Cancel', gtk.RESPONSE_CANCEL)
-        dialog = gtk.FileChooserDialog('Open Affy Annotation File',
+        dialog = gtk.FileChooserDialog('Open diabetes expression File',
                                        buttons=btns)
         dialog.connect('response', self.on_response)
         dialog.run()
         dialog.destroy()
 
         ### Reading and parsing here
-        d,sample_names = read_mootha(self.file)
-        x,gene_ids = data_dict_to_matrix(d)
+        d,sample_names = read_mootha()
+        n_samps = len(sample_names)
+        n_genes = len(d.keys())
+        typecode = 'f'
+        x = zeros((n_samps,n_genes),typecode)
+        gene_ids = []
+        for i,(id,desc) in enumerate(d.items()):
+            gene_ids.append(id)
+            x[:,i] = desc[0].astype(typecode)
         gene_def = ['genes',gene_ids]
         sample_def = ['samples', sample_names]
         X = dataset.Dataset(x,[sample_def,gene_def]) # samples x genes
-        return X
+        return [X]