added parse.fastaq command, added permute option to venn command, fixed bug with...

[mothur.git] / maligner.cpp

diff --git a/maligner.cpp b/maligner.cpp
index f06884fcad747a84e8c3d8ae673a5eabf839f2ec..1d5258964650cad8c2e90d39414022e7dc2f0455 100644 (file)
--- a/maligner.cpp
+++ b/maligner.cpp
@@ -496,24 +496,19 @@ vector<Sequence*> Maligner::getBlastSeqs(Sequence* q, int num) {
        try {   
                indexes.clear();
                vector<Sequence*> refResults;
-               //generate blastdb
-               Database* database = new BlastDB(-2.0, -1.0, matchScore, misMatchPenalty);
-               for (int i = 0; i < db.size(); i++) {   database->addSequence(*db[i]);  }
-               database->generateDB();
-               database->setNumSeqs(db.size());
-               
+                               
                //get parts of query
                string queryUnAligned = q->getUnaligned();
                string leftQuery = queryUnAligned.substr(0, int(queryUnAligned.length() * 0.33)); //first 1/3 of the sequence
                string rightQuery = queryUnAligned.substr(int(queryUnAligned.length() * 0.66)); //last 1/3 of the sequence
 
-               Sequence* queryLeft = new Sequence(q->getName(), leftQuery);
-               Sequence* queryRight = new Sequence(q->getName(), rightQuery);
+               Sequence* queryLeft = new Sequence(q->getName()+"left", leftQuery);
+               Sequence* queryRight = new Sequence(q->getName()+"right", rightQuery);
                
-               vector<int> tempIndexesRight = database->findClosestMegaBlast(queryRight, num+1);
-               vector<int> tempIndexesLeft = database->findClosestMegaBlast(queryLeft, num+1);
-               
-               //if ((tempIndexesRight.size() != (num+1)) || (tempIndexesLeft.size() != (num+1)))  {  m->mothurOut("megablast returned " + toString(tempIndexesRight.size()) + " results for the right end, and " + toString(tempIndexesLeft.size()) + " for the left end. Needed " + toString(num+1) + ". Unable to porcess sequence " + q->getName()); m->mothurOutEndLine(); return refResults; }
+               vector<int> tempIndexesRight = databaseLeft->findClosestMegaBlast(queryRight, num+1);
+               vector<int> tempIndexesLeft = databaseLeft->findClosestMegaBlast(queryLeft, num+1);
+                       
+               //if ((tempIndexesRight.size() == 0) && (tempIndexesLeft.size() == 0))  {  m->mothurOut("megablast returned " + toString(tempIndexesRight.size()) + " results for the right end, and " + toString(tempIndexesLeft.size()) + " for the left end. Needed " + toString(num+1) + ". Unable to process sequence " + q->getName()); m->mothurOutEndLine(); return refResults; }
                
                vector<int> smaller;
                vector<int> larger;
@@ -564,8 +559,7 @@ vector<Sequence*> Maligner::getBlastSeqs(Sequence* q, int num) {
 //cout << endl;                
                delete queryRight;
                delete queryLeft;
-               delete database;
-               
+                       
                return refResults;
        }
        catch(exception& e) {