Added categorygetter for PhenotypeDataset.

workflows/affy_workflow.py

@@ -231,6 +231,7 @@ class PhenotypeDataset(dataset.Dataset):
         col_names = rows[0][1:]
         phenotypes = []
         categories = {}
+        self._categories = set()
 
         for col_name, column in zip(col_names, columns[1:]):
             try:
@@ -247,8 +248,8 @@ class PhenotypeDataset(dataset.Dataset):
 
                     entries[entry].append(i)
                     
-
                 for key in keys:
+                    self._categories.add(key)
                     z = zeros(len(column))
                     for i in entries[key]:
                         z[i] = 1
@@ -269,6 +270,14 @@ class PhenotypeDataset(dataset.Dataset):
                                                        ('phenotypes', phenotypes)],
                                  shape=(len(cel_names),len(phenotypes)), name="Phenotype Data")
             
-
     def get_phenotype_table(self):
+        """Get string based table of phenotypes as read from file."""
         return self._table
+
+    def get_categories(self):
+        """Get categories of factors.
+
+        If factor 'sick' had possibilites Y/N, and 'sex' M/F, the
+        categories would be Y, N, M and F.
+        """
+        return self._categories