fixed id match

[mothur.git] / chimeraslayer.cpp

diff --git a/chimeraslayer.cpp b/chimeraslayer.cpp
index e62c2f047417f29658673493595a5ee1f01e8d29..1f7160aa0d91e8f049fbca4c8b5a85c0bed349d9 100644 (file)
--- a/chimeraslayer.cpp
+++ b/chimeraslayer.cpp
@@ -765,10 +765,20 @@ int ChimeraSlayer::getChimeras(Sequence* query) {
                if (chimeraFlag == "yes") {
                
                        if (realign) {
+                               vector<Sequence*> 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);
+                               }
+                               
                                ChimeraReAligner realigner;
-                               realigner.reAlign(query, Results);
+                               //realigner.reAlign(query, parents);
+                               
+                               for (int i = 0; i < parents.size(); i++) { delete parents[i]; }
                        }
-               
+       //query->printSequence(cout);
                        //get sequence that were given from maligner results
                        vector<SeqDist> seqs;
                        map<string, float> removeDups;
@@ -1037,7 +1047,7 @@ vector<Sequence*> ChimeraSlayer::getBlastSeqs(Sequence* q, vector<Sequence*>& db
                vector<int> mergedResults;
                for (int i = 0; i < smaller.size(); i++) {
                        if (m->control_pressed) { delete queryRight; delete queryLeft; return refResults; }
-                       
+       
                        //add left if you havent already
                        it = seen.find(smaller[i]);
                        if (it == seen.end()) {  
@@ -1065,7 +1075,7 @@ vector<Sequence*> ChimeraSlayer::getBlastSeqs(Sequence* q, vector<Sequence*>& db
                }
 
                for (int i = 0; i < mergedResults.size(); i++) {
-                       
+                       //cout << mergedResults[i]  << '\t' << db[mergedResults[i]]->getName() << endl; 
                        if (db[mergedResults[i]]->getName() != q->getName()) { 
                                Sequence* temp = new Sequence(db[mergedResults[i]]->getName(), db[mergedResults[i]]->getAligned());
                                refResults.push_back(temp);