1.19.0

[mothur.git] / maligner.cpp

diff --git a/maligner.cpp b/maligner.cpp
index 0cd8336c6de865d85d0fea9d607199599f10ab9e..f4c4a9821350c38a9bde8ca7a4fcd6ae01d6b3c3 100644 (file)
--- a/maligner.cpp
+++ b/maligner.cpp
@@ -42,7 +42,7 @@ string Maligner::getResults(Sequence* q, DeCalculator* decalc) {
                }
                
                int chimeraPenalty = computeChimeraPenalty();
-               
+       
                //fills outputResults
                chimera = chimeraMaligner(chimeraPenalty, decalc);
                
@@ -95,7 +95,7 @@ string Maligner::chimeraMaligner(int chimeraPenalty, DeCalculator* decalc) {
                if (m->control_pressed) { return chimera;  }
                
                vector<trace_struct> trace = mapTraceRegionsToAlignment(path, refSeqs);
-                       
+                               
                if (trace.size() > 1) {         chimera = "yes";        }
                else { chimera = "no";  return chimera; }
                
@@ -161,7 +161,7 @@ string Maligner::chimeraMaligner(int chimeraPenalty, DeCalculator* decalc) {
                        
                        temp.queryToParentLocal = computePercentID(queryInRegion, parentInRegion);
                        
-//                     cout << query->getName() << '\t' << temp.parent << '\t' << "NAST:" << temp.nastRegionStart << '-' << temp.nastRegionEnd << " G:" << temp.queryToParent << " L:" << temp.queryToParentLocal << ", " <<  temp.divR << endl;
+                       //cout << query->getName() << '\t' << temp.parent << '\t' << "NAST:" << temp.nastRegionStart << '-' << temp.nastRegionEnd << " G:" << temp.queryToParent << " L:" << temp.queryToParentLocal << ", " <<  temp.divR << endl;
 
                        outputResults.push_back(temp);
                }
@@ -490,7 +490,7 @@ vector<trace_struct> Maligner::mapTraceRegionsToAlignment(vector<score_struct> p
                for (int i = 1; i < path.size(); i++) {
                        
                        int next_region_index = path[i].row;
-//                     cout << i << '\t' << next_region_index << endl;
+                       //cout << i << '\t' << next_region_index << endl;
 
                        if (next_region_index != region_index) {