incorporation of nast-ier code

[mothur.git] / chimeraslayer.cpp

diff --git a/chimeraslayer.cpp b/chimeraslayer.cpp
index 1f7160aa0d91e8f049fbca4c8b5a85c0bed349d9..59b2fea4fa895a10ffe6ff9f462c448c7fa88014 100644 (file)
--- a/chimeraslayer.cpp
+++ b/chimeraslayer.cpp
@@ -763,22 +763,18 @@ int ChimeraSlayer::getChimeras(Sequence* query) {
                for (int i = 0; i < refSeqs.size(); i++) {  delete refSeqs[i];  }
                
                if (chimeraFlag == "yes") {
-               
+
                        if (realign) {
-                               vector<Sequence*> parents;
+                               vector<string> parents;
                                for (int i = 0; i < Results.size(); i++) {
-cout << Results[i].parent  << '\t' << Results[i].nastRegionStart << '\t' << Results[i].nastRegionEnd  << endl;
-                                       Sequence* parent = new Sequence(Results[i].parent, Results[i].parentAligned);
-                                       
-                                       parents.push_back(parent);
+                                       parents.push_back(Results[i].parentAligned);
                                }
                                
-                               ChimeraReAligner realigner;
-                               //realigner.reAlign(query, parents);
-                               
-                               for (int i = 0; i < parents.size(); i++) { delete parents[i]; }
+                               ChimeraReAligner realigner;             
+                               realigner.reAlign(query, parents);
+
                        }
-       //query->printSequence(cout);
+
                        //get sequence that were given from maligner results
                        vector<SeqDist> seqs;
                        map<string, float> removeDups;