Added text-input for contrast-matrix creator for affymetrics workflow.

workflows/affy_workflow.py

@@ -1,5 +1,5 @@
 import gtk
-from system import dataset, logger, plots, workflow
+from system import dataset, logger, plots, workflow, dialogs
 from scipy import randn, array, transpose, zeros
 import cPickle
 
@@ -17,6 +17,7 @@ class AffyWorkflow (workflow.Workflow):
         load.add_function(PhenotypeImportFunction())
         load.add_function(TestDataFunction())
         load.add_function(DatasetLoadFunction())
+        load.add_function(ContrastMatrixGenerateFunction())
         self.add_stage(load)
 
         explore = workflow.Stage('explore', 'Explorative analysis')
@@ -103,7 +104,20 @@ class DatasetSaveFunction(workflow.Function):
                 logger.log("notice", "Saved data to %r." % chooser.get_filename())
         finally:
             chooser.destroy()
-                
+
+
+class ContrastMatrixGenerateFunction(workflow.Function):
+    def __init__(self):
+        workflow.Function.__init__(self, 'contrast_create', 'Create contrast matrix')
+
+    def run(self, data):
+        response = dialogs.get_text('Enter contrasts...', """\
+Enter comma-separated list of contrasts.
+Available categories: %s
+
+Example: Y-N, M-F""" % ", ".join(data.get_categories()))
+        logger.log("notice", "contrasts selected: %s" % response)
+
 
 class CelFileImportFunction(workflow.Function):
     """Loads Affymetrics .CEL-files into matrix."""