chimeras

[mothur.git] / chimeraslayer.cpp

diff --git a/chimeraslayer.cpp b/chimeraslayer.cpp
index 2cbd5d8343f8b96614020d2be5f04250089b73ee..8a0cbd067cc6cbfb8ced9fbb3a3cb89ea6fdc62b 100644 (file)
--- a/chimeraslayer.cpp
+++ b/chimeraslayer.cpp
@@ -11,7 +11,7 @@
 #include "chimerarealigner.h"
 
 //***************************************************************************************************************
-ChimeraSlayer::ChimeraSlayer(string mode) : searchMethod(mode) {       decalc = new DeCalculator();      }
+ChimeraSlayer::ChimeraSlayer(string mode, bool r) : searchMethod(mode), realign(r) {   decalc = new DeCalculator();      }
 //***************************************************************************************************************
 ChimeraSlayer::~ChimeraSlayer() {      delete decalc;   }
 //***************************************************************************************************************
@@ -63,10 +63,12 @@ int ChimeraSlayer::getChimeras(Sequence* query) {
                string chimeraFlag = maligner->getResults(query, decalc);
                vector<results> Results = maligner->getOutput();
 
-               //realign query to parents to improve slayers detection rate
-               ChimeraReAligner realigner(templateSeqs, match, misMatch);
-               realigner.reAlign(query, Results);
-cout << query->getName() << '\n' << query->getAligned() << endl;
+               //realign query to parents to improve slayers detection rate???
+               if (realign) {
+                       ChimeraReAligner realigner(templateSeqs, match, misMatch);
+                       realigner.reAlign(query, Results);
+               }
+
                        //if (chimeraFlag == "yes") {
                        
                //get sequence that were given from maligner results