chimeras, fix to sabundvector and sharedsabundvector that caused getRabundVector...

[mothur.git] / ccode.cpp

diff --git a/ccode.cpp b/ccode.cpp
index bfcd44d8239a30f8ad18db73f0c06268dc0e7474..326af7cec61a88eb6ab859f203098c0ded3a9cfb 100644 (file)
--- a/ccode.cpp
+++ b/ccode.cpp
@@ -48,13 +48,10 @@ void Ccode::print(ostream& out) {
                        out2 << it->first << '\t' << it->second << endl;
                }
                out2.close();
-               
-               out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
-               
                out << querySeq->getName() << endl << endl << "Reference sequences used and distance to query:" << endl;
                        
                for (int j = 0; j < closest.size(); j++) {
-                       out << setprecision(3) << closest[j].seq->getName() << '\t' << closest[j].dist << endl;
+                       out << closest[j].seq->getName() << '\t' << closest[j].dist << endl;
                }
                out << endl << endl;
                
@@ -72,14 +69,12 @@ void Ccode::print(ostream& out) {
                        
                out << endl << "Window\tStartPos\tEndPos" << endl;
                it = trim.begin();
-                       
                for (int k = 0; k < windows.size()-1; k++) {
                        out << k+1 << '\t' << spotMap[windows[k]-it->first] << '\t' << spotMap[windows[k]-it->first+windowSizes] << endl;
                }
                        
                out << windows.size() << '\t' << spotMap[windows[windows.size()-1]-it->first] << '\t' << spotMap[it->second-it->first-1] << endl;
                out << endl;
-                       
                out << "Window\tAvgQ\t(sdQ)\tAvgR\t(sdR)\tRatio\tAnova" << endl;
                for (int k = 0; k < windows.size(); k++) {
                        float ds = averageQuery[k] / averageRef[k]; 
@@ -94,7 +89,7 @@ void Ccode::print(ostream& out) {
                //float fs = varQuery[query] / varRef[query];   /* F-Snedecor, test for differences of variances */
                        
                bool results = false;   
-                                               
+                                       
                //confidence limit, t - Student, anova
                out << "Window\tConfidenceLimit\tt-Student\tAnova" << endl;
                        
@@ -118,6 +113,10 @@ void Ccode::print(ostream& out) {
                if (results) {
                        mothurOut(querySeq->getName() + " was found have at least one chimeric window."); mothurOutEndLine();
                }
+
+               //free memory
+               for (int i = 0; i < closest.size(); i++) {  delete closest[i].seq;  }
+
                
        }
        catch(exception& e) {
@@ -176,7 +175,7 @@ int Ccode::getChimeras(Sequence* query) {
                        for (int i = 0; i < closest.size(); i++) { temp.push_back(closest[i].seq);  }
                        temp.push_back(query);  
                        
-                       createFilter(temp);
+                       createFilter(temp, 0.5);
                
                        for (int i = 0; i < temp.size(); i++) { runFilter(temp[i]);  }
                        
@@ -221,9 +220,6 @@ int Ccode::getChimeras(Sequence* query) {
                                        
                determineChimeras();  //fills anova, isChimericConfidence, isChimericTStudent and isChimericANOVA. 
                
-               //free memory
-               for (int i = 0; i < closest.size(); i++) {  delete closest[i].seq;  }
-               
                return 0;
        }
        catch(exception& e) {
@@ -525,6 +521,10 @@ vector<SeqDist>  Ccode::findClosest(Sequence* q, int numWanted) {
                }
                        
                sort(topMatches.begin(), topMatches.end(), compareSeqDist);
+               
+               for (int i = numWanted; i < topMatches.size(); i++) {  delete topMatches[i].seq;  }
+               
+               topMatches.resize(numWanted);
                        
                return topMatches;