chimera.slayer debugging

[mothur.git] / chimeraslayer.cpp

diff --git a/chimeraslayer.cpp b/chimeraslayer.cpp
index 1d22bdfe36f74194d2609c01b956cf0ab8ba67c8..a182b846cc4f84288e029188f53c25dcf4ea93cc 100644 (file)
--- a/chimeraslayer.cpp
+++ b/chimeraslayer.cpp
@@ -545,6 +545,8 @@ Sequence* ChimeraSlayer::print(MPI_File& out, MPI_File& outAcc, data_results lef
                        
                        bool rightChimeric = false;
                        bool leftChimeric = false;
+
+                       cout << endl;
                        
                        if (chimeraFlag == "yes") {     
                                //which peice is chimeric or are both
@@ -552,7 +554,7 @@ Sequence* ChimeraSlayer::print(MPI_File& out, MPI_File& outAcc, data_results lef
                                if (leftPiece.flag == "yes") { if ((leftPiece.results[0].bsa >= minBS) || (leftPiece.results[0].bsb >= minBS))  { leftChimeric = true;  } }
                                
                                if (rightChimeric || leftChimeric) {
-//                                     cout << querySeq->getName() <<  "\tyes" << endl;
+                                       cout << querySeq->getName() <<  "\tyes" << endl;
                                        outAccString += querySeq->getName() + "\n";
                                        results = true;
                                        
@@ -1049,46 +1051,66 @@ vector<Sequence*> ChimeraSlayer::getBlastSeqs(Sequence* q, vector<Sequence*>& db
                
                vector<int> tempIndexesLeft = databaseLeft->findClosestMegaBlast(queryLeft, num+1, minSim);
                vector<int> tempIndexesRight = databaseLeft->findClosestMegaBlast(queryRight, num+1, minSim);
-               //cout << q->getName() << '\t' << leftQuery << '\t' << "leftMatches = " << tempIndexesLeft.size() << '\t' << rightQuery << " rightMatches = " << tempIndexesRight.size() << endl;
-               vector<int> smaller;
-               vector<int> larger;
+                               
                
-               if (tempIndexesRight.size() < tempIndexesLeft.size()) { smaller = tempIndexesRight;  larger = tempIndexesLeft;  }
-               else { smaller = tempIndexesLeft;  larger = tempIndexesRight;  } 
+               //cout << q->getName() << '\t' << leftQuery << '\t' << "leftMatches = " << tempIndexesLeft.size() << '\t' << rightQuery << " rightMatches = " << tempIndexesRight.size() << endl;
+//             vector<int> smaller;
+//             vector<int> larger;
+//             
+//             if (tempIndexesRight.size() < tempIndexesLeft.size()) { smaller = tempIndexesRight;  larger = tempIndexesLeft;  }
+//             else { smaller = tempIndexesLeft;  larger = tempIndexesRight;  } 
                
                //merge results         
                map<int, int> seen;
                map<int, int>::iterator it;
                vector<int> mergedResults;
-               for (int i = 0; i < smaller.size(); i++) {
+               
+               int index = 0;
+//             for (int i = 0; i < smaller.size(); i++) {
+               while(index < tempIndexesLeft.size() && index < tempIndexesRight.size()){
+                       
                        if (m->control_pressed) { delete queryRight; delete queryLeft; return refResults; }
        
                        //add left if you havent already
-                       it = seen.find(smaller[i]);
+                       it = seen.find(tempIndexesLeft[index]);
                        if (it == seen.end()) {  
-                               mergedResults.push_back(smaller[i]);
-                               seen[smaller[i]] = smaller[i];
+                               mergedResults.push_back(tempIndexesLeft[index]);
+                               seen[tempIndexesLeft[index]] = tempIndexesLeft[index];
                        }
                        
                        //add right if you havent already
-                       it = seen.find(larger[i]);
+                       it = seen.find(tempIndexesRight[index]);
                        if (it == seen.end()) {  
-                               mergedResults.push_back(larger[i]);
-                               seen[larger[i]] = larger[i];
+                               mergedResults.push_back(tempIndexesRight[index]);
+                               seen[tempIndexesRight[index]] = tempIndexesRight[index];
                        }
+                       index++;
                }
+
                
-               for (int i = smaller.size(); i < larger.size(); i++) {
+               for (int i = index; i < tempIndexesLeft.size(); i++) {
                        if (m->control_pressed) { delete queryRight; delete queryLeft; return refResults; }
                        
                        //add right if you havent already
-                       it = seen.find(larger[i]);
+                       it = seen.find(tempIndexesLeft[i]);
                        if (it == seen.end()) {  
-                               mergedResults.push_back(larger[i]);
-                               seen[larger[i]] = larger[i];
+                               mergedResults.push_back(tempIndexesLeft[i]);
+                               seen[tempIndexesLeft[i]] = tempIndexesLeft[i];
                        }
                }
 
+               for (int i = index; i < tempIndexesRight.size(); i++) {
+                       if (m->control_pressed) { delete queryRight; delete queryLeft; return refResults; }
+                       
+                       //add right if you havent already
+                       it = seen.find(tempIndexesRight[i]);
+                       if (it == seen.end()) {  
+                               mergedResults.push_back(tempIndexesRight[i]);
+                               seen[tempIndexesRight[i]] = tempIndexesRight[i];
+                       }
+               }
+               
+               
                for (int i = 0; i < mergedResults.size(); i++) {
                        //cout << mergedResults[i]  << '\t' << db[mergedResults[i]]->getName() << endl; 
                        if (db[mergedResults[i]]->getName() != q->getName()) { 
@@ -1098,11 +1120,7 @@ vector<Sequence*> ChimeraSlayer::getBlastSeqs(Sequence* q, vector<Sequence*>& db
                        }
                }
                
-               
-//             for(int i=0;i<refResults.size();i++){
-//                     cout << refResults[i]->getName() << endl;
-//             }
-                       
+
                delete queryRight;
                delete queryLeft;