Adds numOtus to opti output

source/commands/clustercommand.cpp

@@ -886,18 +886,17 @@ int ClusterCommand::runOptiCluster(){
         
         cluster.initialize(listVectorMetric, true, initialize);
         
-        ListVector* list = cluster.getList();
+        long long numBins = cluster.getNumBins();
         m->mothurOut("\n\niter\ttime\tlabel\tnum_otus\tcutoff\ttp\ttn\tfp\tfn\tsensitivity\tspecificity\tppv\tnpv\tfdr\taccuracy\tmcc\tf1score\n");
         outStep << "iter\ttime\tlabel\tnum_otus\tcutoff\ttp\ttn\tfp\tfn\tsensitivity\tspecificity\tppv\tnpv\tfdr\taccuracy\tmcc\tf1score\n";
          long long tp, tn, fp, fn;
         vector<double> results = cluster.getStats(tp, tn, fp, fn);
-        m->mothurOut("0\t0\t" + toString(cutoff) + "\t" + toString(list->getNumBins()) + "\t"+ toString(cutoff) + "\t" + toString(tp) + "\t" + toString(tn) + "\t" + toString(fp) + "\t" + toString(fn) + "\t");
-        outStep << "0\t0\t" + toString(cutoff) + "\t" + toString(list->getNumBins()) + "\t" + toString(cutoff) + "\t" << tp << '\t' << tn << '\t' << fp << '\t' << fn << '\t';
+        m->mothurOut("0\t0\t" + toString(cutoff) + "\t" + toString(numBins) + "\t"+ toString(cutoff) + "\t" + toString(tp) + "\t" + toString(tn) + "\t" + toString(fp) + "\t" + toString(fn) + "\t");
+        outStep << "0\t0\t" + toString(cutoff) + "\t" + toString(numBins) + "\t" + toString(cutoff) + "\t" << tp << '\t' << tn << '\t' << fp << '\t' << fn << '\t';
         for (int i = 0; i < results.size(); i++) { m->mothurOut(toString(results[i]) + "\t"); outStep << results[i] << "\t"; }
         m->mothurOutEndLine();
         outStep << endl;
-        delete list;
-    
+        
         while ((delta > stableMetric) && (iters < maxIters)) {
             
             int start = time(NULL);
@@ -911,18 +910,17 @@ int ClusterCommand::runOptiCluster(){
             iters++;
             
             results = cluster.getStats(tp, tn, fp, fn);
-            list = cluster.getList();
+            numBins = cluster.getNumBins();
             
-            m->mothurOut(toString(iters) + "\t" + toString(time(NULL) - start) + "\t" + toString(cutoff) + "\t" + toString(list->getNumBins()) + "\t" + toString(cutoff) + "\t"+ toString(tp) + "\t" + toString(tn) + "\t" + toString(fp) + "\t" + toString(fn) + "\t");
-            outStep << (toString(iters) + "\t" + toString(time(NULL) - start) + "\t" + toString(cutoff) + "\t" + toString(list->getNumBins()) + "\t" + toString(cutoff) + "\t") << tp << '\t' << tn << '\t' << fp << '\t' << fn << '\t';
+            m->mothurOut(toString(iters) + "\t" + toString(time(NULL) - start) + "\t" + toString(cutoff) + "\t" + toString(numBins) + "\t" + toString(cutoff) + "\t"+ toString(tp) + "\t" + toString(tn) + "\t" + toString(fp) + "\t" + toString(fn) + "\t");
+            outStep << (toString(iters) + "\t" + toString(time(NULL) - start) + "\t" + toString(cutoff) + "\t" + toString(numBins) + "\t" + toString(cutoff) + "\t") << tp << '\t' << tn << '\t' << fp << '\t' << fn << '\t';
             for (int i = 0; i < results.size(); i++) { m->mothurOut(toString(results[i]) + "\t"); outStep << results[i] << "\t"; }
             m->mothurOutEndLine();
             outStep << endl;
-            delete list;
         }
         m->mothurOutEndLine(); m->mothurOutEndLine();
         
-        list = cluster.getList();
+        ListVector* list = cluster.getList();
         list->setLabel(toString(cutoff));
         if (!m->printedListHeaders) { m->listBinLabelsInFile.clear(); list->printHeaders(listFile); }
         if(countfile != "") { list->print(listFile, counts); }

source/opticluster.cpp

@@ -562,8 +562,8 @@ double OptiCluster::calcFDR( long long tp,  long long tn,  long long fp,  long l
 /***********************************************************************/
 vector<double> OptiCluster::getStats( long long& tp,  long long& tn,  long long& fp,  long long& fn) {
     try {
-         long long singletn = matrix->getNumSingletons() + numSingletons;
-         long long tempnumSeqs = numSeqs + singletn;
+        long long singletn = matrix->getNumSingletons() + numSingletons;
+        long long tempnumSeqs = numSeqs + singletn;
         
         tp = truePositives;
         fp = falsePositives;
@@ -640,6 +640,25 @@ ListVector* OptiCluster::getList() {
     }
 }
 /***********************************************************************/
+long long OptiCluster::getNumBins() {
+    try {
+        long long singletn = matrix->getNumSingletons();
+        
+        for (int i = 0; i < bins.size(); i++) {
+            if (bins[i].size() != 0) {
+                singletn++;
+            }
+        }
+        
+        return singletn;
+    }
+    catch(exception& e) {
+        m->errorOut(e, "OptiCluster", "getNumBins");
+        exit(1);
+    }
+}
+
+/***********************************************************************/
 int OptiCluster::findInsert() {
     try {
         

source/opticluster.h

@@ -29,6 +29,7 @@ class OptiCluster : public Cluster {
     ~OptiCluster() {}
     bool updateDistance(PDistCell& colCell, PDistCell& rowCell) { return false; } //inheritance compliant
     string getTag() { string tag = "opti_" + metric; return tag; }
+    long long getNumBins();
     int initialize(double&, bool, string);  //randomize and place in "best" OTUs
     bool update(double&); //returns whether list changed and MCC
     vector<double> getStats( long long&,  long long&,  long long&,  long long&);