Plot largest features only

ediacara/Comparator.py

@@ -76,38 +76,34 @@ class CustomTranslator(dna_features_viewer.BiopythonTranslator):
 
     def compute_filtered_features(self, features):
         """Display only selected features."""
-        has_dnacauldron_annotation = False
+        n = 10  # max number of features that fit on the plot
+        if len(features) <= n:
+            return features  # plot all, no need for calculations
+
         filtered_features = []
         for feature in features:
-            # DNA Cauldron annotations:
+            # DNA Cauldron annotations have priority:
             try:
                 if "From " in str(feature.qualifiers.get("note", "")):
                     filtered_features += [feature]
             except:
                 pass
 
-        if len(filtered_features) == 0:  # no DNA Cauldron annotations
-            # Keep up to n longest features:
-            n = 10
-            if len(features) > n:
-                feature_lengths = []
-                for feature in features:
-                    feature_lengths += [len(feature.location)]
-                feature_lengths.sort(reverse=True)
-                max_length = feature_lengths[n]
-                for feature in features:
-                    if len(feature.location) > max_length:
-                        filtered_features += [feature]
-            else:
-                filtered_features = features
-        else:
-            # add 4-letter overhang annotations:
-            for feature in features:
-                try:  # may not have a 'label'
-                    if len(feature.qualifiers.get("label", "")[0]) == 4:
-                        filtered_features += [feature]
-                except:
-                    pass
+        # Fill remaining spaces:
+        n_remains = n - len(filtered_features)
+        feature_lengths = []
+        for feature in features:
+            try:
+                if "From " in str(feature.qualifiers.get("note", "")):
+                    continue  # already added above
+            except:
+                pass
+            feature_lengths += [len(feature.location)]
+        feature_lengths.sort(reverse=True)
+        max_length = feature_lengths[n_remains]
+        for feature in features:
+            if len(feature.location) > max_length:
+                filtered_features += [feature]
 
         return filtered_features