chimeracode

[mothur.git] / maligner.cpp

diff --git a/maligner.cpp b/maligner.cpp
index de6004d7e387d0e241dfbc205695d359dbcf6dda..b393194bbc3a4c89fd2ae8ea3f7f7ba67f84b927 100644 (file)
--- a/maligner.cpp
+++ b/maligner.cpp
@@ -32,28 +32,8 @@ string Maligner::getResults(Sequence* q, DeCalculator* decalc) {
                        refSeqs = getBlastSeqs(query, numWanted);
                }
                
-//ofstream out;
-//string name = toString(numi+1); 
-//cout << name << endl;
-//name = name.substr(name.find_first_of("|")+1);
-//cout << name << endl;
-//name = name.substr(name.find_first_of("|")+1);
-//cout << name << endl;
-//name = name.substr(0, name.find_last_of("|"));
-//cout << name << endl;
-//string filename = name + ".seqsformaligner";
-//openOutputFile(filename, out);       
-//for (int u = 0; u < refSeqs.size(); u++) {  refSeqs[u]->printSequence(out);  }
-//out.close();
-//filename = name + ".fasta";
-//openOutputFile(filename, out);       
-//query->printSequence(out);
-//out.close();
-
-//for (int i = 0; i < refSeqs.size(); i++)  { cout << refSeqs[i]->getName() << endl;  }        
-//cout << "before = " << refSeqs.size() << endl;
                refSeqs = minCoverageFilter(refSeqs);
-//cout << "after = " << refSeqs.size() << endl;                
+               
                if (refSeqs.size() < 2)  { 
                        for (int i = 0; i < refSeqs.size(); i++) {  delete refSeqs[i];  }
                        percentIdenticalQueryChimera = 0.0;
@@ -61,7 +41,7 @@ string Maligner::getResults(Sequence* q, DeCalculator* decalc) {
                }
                
                int chimeraPenalty = computeChimeraPenalty();
-//cout << chimeraPenalty << endl;              
+       
                //fills outputResults
                chimera = chimeraMaligner(chimeraPenalty, decalc);
                
@@ -500,8 +480,7 @@ float Maligner::computePercentID(string queryAlign, string chimera) {
 }
 //***************************************************************************************************************
 vector<Sequence*> Maligner::getBlastSeqs(Sequence* q, int num) {
-       try {
-cout << q->getName() << endl;  
+       try {   
                //generate blastdb
                Database* database = new BlastDB(-2.0, -1.0, matchScore, misMatchPenalty);
                for (int i = 0; i < db.size(); i++) {   database->addSequence(*db[i]);  }
@@ -509,55 +488,42 @@ cout << q->getName() << endl;
                database->setNumSeqs(db.size());
                
                //get parts of query
-               string queryAligned = q->getAligned();
-               string leftQuery = queryAligned.substr(0, (queryAligned.length() / 3)); //first 1/3 of the sequence
-               string rightQuery = queryAligned.substr(((queryAligned.length() / 3)*2)); //last 1/3 of the sequence
-               
+               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);
                
-               map<int, float> tempIndexesRight = database->findClosest(queryRight, num);
-               map<int, float> tempIndexesLeft = database->findClosest(queryLeft, num);
-               
-               //merge results
-               vector<rank> mergedResults;
+               vector<int> tempIndexesRight = database->findClosestMegaBlast(queryRight, num+1);
+               vector<int> tempIndexesLeft = database->findClosestMegaBlast(queryLeft, num+1);
                
-               map<int, float>::iterator it;
-               map<int, float>::iterator it2;
+               //merge results         
+               map<int, int> seen;
+               map<int, int>::iterator it;
                
-               //add in right guys merging common finds
-               for (it = tempIndexesRight.begin(); it != tempIndexesRight.end(); it++) {
-                       it2 = tempIndexesLeft.find(it->first);
-                       
-                       if (it2 == tempIndexesLeft.end()) {  //result only present in right
-                               rank temp(it->first, it->second);
-                               mergedResults.push_back(temp); 
+               vector<int> mergedResults;
+               for (int i = 0; i < tempIndexesLeft.size(); i++) {
+                       //add left if you havent already
+                       it = seen.find(tempIndexesLeft[i]);
+                       if (it == seen.end()) {  
+                               mergedResults.push_back(tempIndexesLeft[i]);
+                               seen[tempIndexesLeft[i]] = tempIndexesLeft[i];
+                       }
 
-                       }else { //result present in both save best score
-                               float bestscore;
-                               if (it->second > it2->second)   {  bestscore = it->second;  }
-                               else                                                    {  bestscore = it2->second; }
-                               
-                               rank temp(it->first, bestscore);
-                               mergedResults.push_back(temp);
-                               
-                               tempIndexesLeft.erase(it2);
+                       //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];
                        }
                }
                
-               //add in unique left guys
-               for (it = tempIndexesLeft.begin(); it != tempIndexesLeft.end(); it++) {
-                       rank temp(it->first, it->second);
-                       mergedResults.push_back(temp); 
-               }
-               
-               sort(mergedResults.begin(), mergedResults.end(), compareMembers);
                
                vector<Sequence*> refResults;
                for (int i = 0; i < numWanted; i++) {
-                       Sequence* temp = new Sequence(db[mergedResults[i].num]->getName(), db[mergedResults[i].num]->getAligned());
+                       Sequence* temp = new Sequence(db[mergedResults[i]]->getName(), db[mergedResults[i]]->getAligned());
                        refResults.push_back(temp);
-cout << db[mergedResults[i].num]->getName() << endl;
                }
                
                delete queryRight;