New data structures for nodes

alignment/seqregions.cpp

@@ -644,6 +644,13 @@ void SeqRegions::mergeUpperLower(SeqRegions* &merged_regions,
             {
                 merge_RACGT_ORACGT(*seq1_region, *seq2_region, total_blength_1, total_blength_2, upper_plength, end_pos, threshold_prob, model, aln, *merged_regions);
             }
+
+            // NHANLT: LOGS FOR DEBUGGING
+            /*if (merged_regions->at(merged_regions->size()-1).type == TYPE_O)
+            {
+                SeqRegion::LHType lh =  *merged_regions->at(merged_regions->size()-1).likelihood;
+                std::cout << "mergeUpLow " << pos << " " << std::setprecision(20) << lh[0] << " " << lh[1] << " " << lh[2] << " " << lh[3] << " " << std::endl;
+            }*/
         }
 
         // update pos
@@ -1011,6 +1018,13 @@ RealNumType SeqRegions::mergeTwoLowers(SeqRegions* &merged_regions, RealNumType
         {
             if (!merge_notN_notN_TwoLowers(*seq1_region, *seq2_region, plength1, plength2, end_pos, pos, aln, model, threshold_prob, log_lh, merged_regions, return_log_lh)) return MIN_NEGATIVE;
         }
+
+        // NHANLT: LOGS FOR DEBUGGING
+        /*if (merged_regions->at(merged_regions->size()-1).type == TYPE_O)
+        {
+            SeqRegion::LHType lh =  *merged_regions->at(merged_regions->size()-1).likelihood;
+            std::cout << "merge2Low " << pos << " " << std::setprecision(20) << lh[0] << " " << lh[1] << " " << lh[2] << " " << lh[3] << " " << std::endl;
+        }*/
         // update pos
         pos = end_pos + 1;
     }

maple/cmaple.cpp

@@ -295,14 +295,14 @@ void test()
     std::cout << " Update partial_lh " << std::endl;
     std::unique_ptr<SeqRegions> new_partial_lh = std::make_unique<SeqRegions>(SeqRegions());
     new_partial_lh->emplace_back(0, 100);
-    phylonode1.setPartialLh(mini_index, std::move(new_partial_lh));
+    phylonode1.setPartialLh(mini_index, new_partial_lh);
     std::cout << "- (size of) partial_lh: " << phylonode1.getPartialLh(mini_index)->size() << std::endl;
 
     std::cout << " Update partial_lh 2nd time" << std::endl;
     std::unique_ptr<SeqRegions> new_partial_lh2 = std::make_unique<SeqRegions>(SeqRegions());
     new_partial_lh2->emplace_back(1, 200);
     new_partial_lh2->emplace_back(2, 300);
-    phylonode1.setPartialLh(mini_index, std::move(new_partial_lh2));
+    phylonode1.setPartialLh(mini_index, new_partial_lh2);
     std::cout << "- (size of) partial_lh: " << phylonode1.getPartialLh(mini_index)->size() << std::endl;
 
     // test phylonode is an internal node
@@ -322,7 +322,7 @@ void test()
     std::unique_ptr<SeqRegions> new_partial_lh1 = std::make_unique<SeqRegions>(SeqRegions());
     new_partial_lh1->emplace_back(0, 100);
     new_partial_lh1->emplace_back(1, 200);
-    phylonode2.setPartialLh(mini_index2, std::move(new_partial_lh1));
+    phylonode2.setPartialLh(mini_index2, new_partial_lh1);
     std::cout << "- (size of) partial_lh at the left mininode: " << phylonode2.getPartialLh(mini_index2)->size() << std::endl;
 
     // create a phylonode as an internal node

tree/node.cpp

@@ -88,7 +88,7 @@ std::unique_ptr<SeqRegions>& PhyloNode::getPartialLh(const MiniIndex mini_index)
     return data_.leaf.partial_lh_;
 }
 
-void PhyloNode::setPartialLh(const MiniIndex mini_index, std::unique_ptr<SeqRegions>&& partial_lh)
+void PhyloNode::setPartialLh(const MiniIndex mini_index, std::unique_ptr<SeqRegions>& partial_lh)
 {
     // if it's an internal node
     if (is_internal_)

tree/node.h

@@ -288,7 +288,7 @@ class PhyloNode
     /**
         Set partial_lh
      */
-    void setPartialLh(const MiniIndex mini_index, std::unique_ptr<SeqRegions>&& partial_lh);
+    void setPartialLh(const MiniIndex mini_index, std::unique_ptr<SeqRegions>& partial_lh);
 
     /**
         Get the index of the neighbor node

tree/tree.cpp

@@ -1715,6 +1715,10 @@ void Tree::connectNewSample2Branch(SeqRegions* const sample, const std::string &
         next_node_1->getPartialLhAtNode(aln, model, threshold_prob)->mergeUpperLower(new_sample_node->mid_branch_lh, half_branch_length, *sample, half_branch_length, aln, model, threshold_prob);
     }
 
+    // NHANLT: LOGS FOR DEBUGGING
+    /*cout << "2Branch " << seq_name << " " << (best_blength > 0?new_sample_node->total_lh->size():0)<< " " << (best_blength > 0?new_sample_node->mid_branch_lh->size():0)<< " " << new_sample_node->partial_lh->size()<< " " << new_internal_node->total_lh->size()<< " " << new_internal_node->mid_branch_lh->size()<< " " << new_internal_node->partial_lh->size() << " " << next_node_1->partial_lh->size() << " " << next_node_2->partial_lh->size() << std::endl;
+    cout << std::setprecision(20) << new_internal_node->length << " " << sibling_node->length << " " << new_sample_node->length << std::endl;*/
+
     // update pseudo_count
     model.updatePesudoCount(aln, *next_node_1->getPartialLhAtNode(aln, model, threshold_prob), *sample);
 
@@ -1957,6 +1961,10 @@ void Tree::connectNewSample2Root(SeqRegions* const sample, const std::string &se
             createFurtherMidNodes(new_root.children[1],new_root.probVectUpLeft)*/
     }
 
+    // NHANLT: LOGS FOR DEBUGGING
+    /*cout << "2Root " << seq_name << " " << (best_length2 > 0 ?new_sample_node->total_lh->size():0)<< " " << (best_length2 > 0?new_sample_node->mid_branch_lh->size():0)<< " " << new_sample_node->partial_lh->size()<< " " << new_root->total_lh->size()<< " " << new_root->partial_lh->size() << " " << next_node_1->partial_lh->size() << " " << next_node_2->partial_lh->size() << std::endl;
+    cout << std::setprecision(20) << sibling_node->length << " " << new_sample_node->length << std::endl;*/
+
     // update tree->root;
     root = new_root;