added list parameter to get.seqs and remove.seqs and added readline library for inter...

[mothur.git] / maligner.cpp

diff --git a/maligner.cpp b/maligner.cpp
index 824a2cc0ce19d3d2a7556c8e58776ea4b2cc9895..26ac563032bd93c8f46810d84b1c1a1ceb16c231 100644 (file)
--- a/maligner.cpp
+++ b/maligner.cpp
@@ -16,6 +16,8 @@ Maligner::Maligner(vector<Sequence*> temp, int num, int match, int misMatch, flo
 string Maligner::getResults(Sequence* q) {
        try {
                
+               outputResults.clear();
+               
                //make copy so trimming doesn't destroy query from calling class - remember to deallocate
                query = new Sequence(q->getName(), q->getAligned());
                
@@ -25,13 +27,7 @@ string Maligner::getResults(Sequence* q) {
                
                //find closest seqs to query in template - returns copies of seqs so trim does not destroy - remember to deallocate
                refSeqs = decalc->findClosest(query, db, numWanted);
-               
-               ofstream out;
-               string outFile = "parentsOf" + query->getName();
-               openOutputFile(outFile, out);
-               for (int i = 0; i < refSeqs.size(); i++) {   refSeqs[i]->printSequence(out);    }
-               out.close();
-               
+       
                refSeqs = minCoverageFilter(refSeqs);
                
                if (refSeqs.size() < 2)  {