Updated README and added t itself to argmax_clusters

niemasd · Apr 5, 2018 · 7ee995a · 7ee995a
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diff --git a/README.md b/README.md
@@ -75,6 +75,7 @@ optional arguments:
 
 ## Threshold-Free Approaches
 * **Argmax Clusters:** Choose the threshold that maximizes the number of non-singleton clusters over all thresholds from 0 to *t*
+    * Currently, for the sake of speed, only every 0.0001 threshold is tested (i.e., 0, 0.001, 0.002, ..., *t*)
 
 ## Requirements
 * [Biopython](http://biopython.org/)
diff --git a/TreeCluster.py b/TreeCluster.py
@@ -319,7 +319,7 @@ def argmax_clusters(method,tree,threshold,support):
     from copy import deepcopy
     assert threshold > 0, "Threshold must be positive"
     #thresholds = pairwise_dists_below_thresh(deepcopy(tree),threshold)
-    thresholds = [i*threshold/NUM_THRESH for i in range(NUM_THRESH)]
+    thresholds = [i*threshold/NUM_THRESH for i in range(NUM_THRESH+1)]
     best = None; best_num = -1; best_t = -1
     for i,t in enumerate(thresholds):
         print("%s%%"%str(i*100/len(thresholds)).rstrip('0'),end='\r',file=stderr)