fix nodegraph containment

sourmash-bio · Apr 18, 2021 · 9531a23 · 9531a23
1 parent 556b101
commit 9531a23
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Showing 2 changed files with 4 additions and 11 deletions.
diff --git a/src/core/src/sketch/nodegraph.rs b/src/core/src/sketch/nodegraph.rs
@@ -364,7 +364,7 @@ impl Comparable<Nodegraph> for Nodegraph {
             .zip(&other.bs)
             .map(|(bs, bs_other)| bs.intersection(bs_other).count())
             .sum();
-        let size: usize = self.bs.iter().map(|bs| bs.len()).sum();
+        let size: usize = self.bs.iter().map(|bs| bs.ones().count()).sum();
         result as f64 / size as f64
     }
 }

diff --git a/src/sourmash/sbtmh.py b/src/sourmash/sbtmh.py
@@ -89,11 +89,6 @@ def _max_jaccard_underneath_internal_node(node, query):
         # J(A, B) = |A intersection B| / |A union B|
         # If we use only |A| as denominator, it is the containment
         # Because |A| <= |A union B|, it is also an upper bound on the max jaccard
-
-        # count the maximum number of hash matches beneath this node
-        #matches = node.data.matches(mh)
-        #max_score = float(matches) / len(mh)
-
         max_score = query_bf.containment(node.data)
 
     return max_score
@@ -151,7 +146,6 @@ def search_minhashes_containment(node, sig, threshold, results=None, downsample=
     else:  # Node or Leaf, Nodegraph by minhash comparison
         bf = _get_bf(node, sig)
         matches = bf.containment(node.data) * len(mh)
-        #matches = node.data.matches(mh)
 
     if len(mh) and float(matches) / len(mh) >= threshold:
         return 1
@@ -166,14 +160,14 @@ def search_minhashes_max_containment(node, sig, threshold, results=None,
 
     if isinstance(node, SigLeaf):
         node_mh = node.data.minhash
+
         matches = node_mh.count_common(mh, downsample)
         node_size = len(node_mh)
     else:  # Node or Leaf, Nodegraph by minhash comparison
-        bf = _get_bf(node, sig)
-        matches = bf.containment(node.data) * len(mh)
         node_size = len(mh) # FIXME
 
-        #matches = node.data.matches(mh)
+        bf = _get_bf(node, sig)
+        matches = bf.containment(node.data) * len(mh)
 
     denom = min((len(mh), node_size))
 
@@ -199,7 +193,6 @@ def search(self, node, query, threshold, results=None):
         else:  # Nodegraph by minhash comparison
             bf = _get_bf(node, query)
             matches = bf.containment(node.data) * len(mh)
-            #matches = node.data.matches(mh)
 
         if not matches:
             return 0