From e5cd8a80777702d8f0b04eb76b33c40764ef1df1 Mon Sep 17 00:00:00 2001
From: einarr <einarr@pvv.ntnu.no>
Date: Fri, 22 Jun 2007 15:37:22 +0000
Subject: [PATCH] Started on a function to enhance gene lists by using GO
 similarities. Not in a usable state.

---
 workflows/gobrowser.py | 122 +++++++++++++++++++++++++++++++++++++++++
 1 file changed, 122 insertions(+)

diff --git a/workflows/gobrowser.py b/workflows/gobrowser.py
index aca0872..a3abe38 100644
--- a/workflows/gobrowser.py
+++ b/workflows/gobrowser.py
@@ -222,3 +222,125 @@ class LoadGOFunction(workflow.Function):
         label.set_use_underline(True)
         fluents.app['bottom_notebook'].append_page(browser, label)
 
+class LoadAnnotationsFunction(workflow.Function):
+
+    def __init__(self):
+        workflow.Function.__init__(self, 'load-go-ann', 'Load Annotations')
+        self.annotations = None
+    
+    def run(self):
+        global evidence
+        f = open(GO_DATA_DIR + '/goa-condensed')
+        ev_codes = f.readline().split()
+        go_terms = []
+    
+        lines = f.readlines()
+        m = zeros((len(lines), len(ev_codes)))
+
+        for i, l in enumerate(lines):
+            values = l.split()
+            go_terms.append(values[0])
+            for j, v in enumerate(values[1:]):
+                m[i,j] = float(v.strip())
+        
+        d = dataset.Dataset(m, 
+                            [['go-terms', go_terms], ['evidence', ev_codes]],
+                            name='GO evidence')
+
+        evidence = d
+        return [d]
+            
+
+class GOWeightDialog(gtk.Dialog):
+    def __init__(self):
+        gtk.Dialog.__init__(self, 'GO Gene List Influence',
+                            None,
+                            gtk.DIALOG_MODAL | gtk.DIALOG_DESTROY_WITH_PARENT,
+                            (gtk.STOCK_OK, gtk.RESPONSE_OK,
+                             gtk.STOCK_CANCEL, gtk.RESPONSE_CANCEL))
+
+        table = gtk.Table(2, 2)
+        
+        sim_lbl = gtk.Label('Similarity threshold: ')
+        table.attach(sim_lbl, 0, 1, 0, 1)
+        adjustment = gtk.Adjustment(0, 0, 10, 0.1, 1.0, 1.0)
+        sim_spin = gtk.SpinButton(adjustment, 0.0, 2)
+        table.attach(sim_spin, 1, 2, 0, 1)
+
+        rank_lbl = gtk.Label('Rank threshold: ')
+        table.attach(rank_lbl, 0, 1, 1, 2)
+        rank_adj = gtk.Adjustment(0, 0, 10, 0.1, 1.0, 1.0)
+        rank_spin = gtk.SpinButton(rank_adj, 0.0, 2)
+        table.attach(rank_spin, 1, 2, 1, 2)
+        
+        sim_lbl.show()
+        sim_spin.show()
+        rank_lbl.show()
+        rank_spin.show()
+        
+        table.show()
+        self.vbox.add(table)
+        self._sim_spin = sim_spin
+        self._rank_spin = rank_spin
+
+    def set_options(self, options):
+        self._sim_spin.set_value(options['similarity_threshold'])
+        self._rank_spin.set_value(options['rank_threshold'])
+
+    def set_editable(self, editable):
+        self._sim_spin.set_sensitive(editable)
+        self._rank_spin.set_sensitive(editable)
+
+    def update_options(self, options):
+        options['similarity_threshold'] = self._sim_spin.get_value()
+        options['rank_threshold'] = self._rank_spin.get_value()
+        
+
+class GOWeightFunction(workflow.Function):
+    def __init__(self):
+        workflow.Function.__init__(self, 'load-go-ann', 'GO Influence')
+        self.options = GOWeightOptions()
+    
+    def run(self, genelist, similarity):
+        ## Show dialog box
+        self.show_gui(self.options)
+
+        ## assure that data is "correct", i.e., that we can perform
+        ## the desired operations.
+        common_dims = genelist.common_dims(similarity)
+        if len(common_dims) == 0:
+            logger.log('error', 'No common dimension in the selected datasets.')
+        elif len(common_dims) > 1:
+            logger.log('error', "More than one common dimension in the " +
+                       "selected datasets. Don't know what to do.")
+        gene_dim = common_dims[0]
+        logger.log('debug', 'Assuming genes are in dimension: %s' % gene_dim)
+
+        ## Do the calculations.
+        d = {}
+        
+        
+    def show_gui(self, options, edit=True):
+        dialog = GOWeightDialog()
+        dialog.set_options(self.options)
+        dialog.show_all()
+        dialog.set_editable(edit)
+        response = dialog.run()
+        dialog.hide()
+        if response == gtk.RESPONSE_OK:
+            return dialog.update_options(self.options)
+        else:
+            return options
+
+
+class Options(dict):
+    def __init__(self):
+        dict.__init__(self)
+
+
+class GOWeightOptions(Options):
+    def __init__(self):
+        Options.__init__(self)
+        self['similarity_threshold'] = 0.0
+        self['rank_threshold'] = 0.0
+