makeDistTree quality computation (no -noqual) uses threads

ncbi · Mar 23, 2021 · 1331f7d · 1331f7d
1 parent c25b4a9
commit 1331f7d
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Showing 3 changed files with 62 additions and 15 deletions.
diff --git a/phylogeny/distTree.cpp b/phylogeny/distTree.cpp
@@ -8012,6 +8012,26 @@ Real DistTree::getUnoptimizable () const
 
 
 
+namespace
+{
+
+void setErrorDensity_array (size_t from,
+                            size_t to,
+                            Notype /*&res*/,
+                            const VectorPtr<DiGraph::Node> &nodeVec,
+                            Real c)
+{
+  FOR_START (size_t, i, from, to)
+  {
+    DTNode* dtNode = const_static_cast <DTNode*> (nodeVec [i]);
+    dtNode->setErrorDensity (c);
+  }
+}
+
+}
+
+
+
 void DistTree::setErrorDensities () 
 {
   ASSERT (optimizable ());
@@ -8024,11 +8044,14 @@ void DistTree::setErrorDensities ()
 
   const Real c = absCriterion / (Real) n;
   ASSERT (c >= 0.0);
-  for (DiGraph::Node* node : nodes)  // --> Threads ??
-  {
-    DTNode* dtNode = static_cast <DTNode*> (node);
-    dtNode->setErrorDensity (c);
-  }
+
+  VectorPtr<DiGraph::Node> nodeVec;  nodeVec. reserve (nodes. size ());
+  for (DiGraph::Node* node : nodes)  
+    nodeVec << node;
+  nodeVec. randomOrder ();
+
+  vector<Notype> notypes;
+  arrayThreads (false, setErrorDensity_array, nodeVec. size (), notypes, cref (nodeVec), c);
 }
 
 
@@ -8068,25 +8091,47 @@ void DistTree::setLeafNormCriterion ()
 
 
 
-void DistTree::setNodeMaxDeformationDissimNum ()
+namespace
 {
- ASSERT (optimizable ());
-
-  for (DiGraph::Node* node : nodes)  // --> Threads ??
+
+void setNodeMaxDeformationDissimNum_array (size_t from,
+                                           size_t to,
+                                           Notype /*&res*/,
+                                           const VectorPtr<DiGraph::Node> &nodeVec,
+                                           const DistTree &tree)
+{
+  FOR_START (size_t, i, from, to)
   {
-    DTNode* dtNode = static_cast <DTNode*> (node);
+    DTNode* dtNode = const_static_cast <DTNode*> (nodeVec [i]);
     dtNode->maxDeformationDissimNum = dissims_max;
     Real target = 0.0;
     for (const uint dissimNum : dtNode->pathDissimNums)
     {
-      const Dissim& dissim = dissims [dissimNum];
+      const Dissim& dissim = tree. dissims [dissimNum];
       if (dissim. validMult ())
         if (maximize (target, dissim. getDeformation ()))
           dtNode->maxDeformationDissimNum = dissimNum;
     }
   }
 }
 
+}
+
+
+
+void DistTree::setNodeMaxDeformationDissimNum ()
+{
+  ASSERT (optimizable ());
+
+  VectorPtr<DiGraph::Node> nodeVec;  nodeVec. reserve (nodes. size ());
+  for (DiGraph::Node* node : nodes)  
+    nodeVec << node;
+  nodeVec. randomOrder ();
+
+  vector<Notype> notypes;
+  arrayThreads (false, setNodeMaxDeformationDissimNum_array, nodeVec. size (), notypes, cref (nodeVec), cref (*this));
+}
+
 
 
 Real DistTree::getDeformation_mean () const

diff --git a/phylogeny/distTree.hpp b/phylogeny/distTree.hpp
@@ -485,6 +485,9 @@ struct DTNode : Tree::TreeNode
     // Deterministic <=> (bool)seed
     // Invokes: getDistTree().rand
     // Time: O(log(n))
+  void setErrorDensity (Real absCriterion_ave);
+    // Output: errorDensity
+    // Time: O(|pathDissimNums|)
 private:
   void saveFeatureTree (ostream &os,
                         bool withTime,
@@ -506,9 +509,6 @@ struct DTNode : Tree::TreeNode
   Vector<uint/*dissimNum*/> getLcaDissimNums ();
     // Return: dissimNum's s.t. getDistTree().dissims[dissimNum].lca = this
     // Invokes: DTNode::pathDissimNums.sort()
-  void setErrorDensity (Real absCriterion_ave);
-    // Output: errorDensity
-    // Time: O(|pathDissimNums|)
   VectorPtr<Leaf> getSparseLeafMatches (const string &targetName,
                                         size_t depth_max,
                                         bool subtractDissims,

diff --git a/version.inc b/version.inc
@@ -1,6 +1,8 @@
-#define VERSION "1.5.6"
+#define VERSION "1.5.8"
 
 
+// 1.5.8  03/22/2021  makeDistTree: quality calculation uses threads
+// 1.5.7  03/21/2021  FeatureTree::globalSingletonsSize bug
 // 1.5.6  03/17/2021  feature tree: only-optional features are removed; 
 //                                  Genome::coreNonSingletons does not include optionalCore[]  
 //                                  oneFeatureInTree => Genome::coreSet has no optional nominal attributes