current datset selection fix

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
 

system/navigator.py

@@ -3,13 +3,17 @@ import gtk
 import gobject
 import plots
 import logger
+import dataset
+import project
 
 class NavigatorView (gtk.TreeView):
-    def __init__(self, nav, app):
+    def __init__(self, project, app):
-        gtk.TreeView.__init__(self, nav)
+        self.project = project
-        self.navigator = nav
+        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.data_tree.get_iter(path)
-        iter = self.navigator.get_iter(path)
+        obj = self.data_tree.get_value(iter, 2)
-        object = self.navigator.get_value(iter, 2)
+        if isinstance(obj, plots.Plot):
-        logger.log('notice', 'Button pressed')
+            logger.log('debug', 'Activating plot')
-        self.app.change_plot(object)
+            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)

system/project.py

@@ -87,3 +87,5 @@ class Project:
             object.show()
         return object
 
+    def set_current_data(self, obj):
+        self.current_data = obj

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)
+        d,sample_names = read_mootha()
-        x,gene_ids = data_dict_to_matrix(d)
+        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]