speed up rarefaction.shared

[mothur.git] / sharedordervector.cpp

diff --git a/sharedordervector.cpp b/sharedordervector.cpp
index 973f69553a476c4e67f72c4b9f10cecae0bc32b6..08692de4ca3fec388ff31407aeee1c0a4d04dd61 100644 (file)
--- a/sharedordervector.cpp
+++ b/sharedordervector.cpp
@@ -149,7 +149,7 @@ individual SharedOrderVector::get(int index){
 
 
 /***********************************************************************/
-
+//commented updateStats out to improve speed, but whoever calls this must remember to update when they are done with all the pushbacks they are doing 
 void SharedOrderVector::push_back(int binNumber, int abund, string groupName){
        individual newGuy;
        newGuy.group = groupName;
@@ -159,7 +159,8 @@ void SharedOrderVector::push_back(int binNumber, int abund, string groupName){
        //numSeqs++;
        //numBins++;
        //if (abund > maxRank) { maxRank = abund; }
-       updateStats();
+       
+       //updateStats();
 }
 
 /***********************************************************************/
@@ -354,25 +355,18 @@ void SharedOrderVector::updateStats(){
                numBins = 0;
                maxRank = 0;
        
-               for(int i=0;i<data.size();i++){
-
-                       if(data[i].bin != -1){
-                               numSeqs++;
-                       }
-               }
-               //vector<individual> hold(numSeqs, 0);
-       
-               //for(int i=0;i<numSeqs;i++){
-                       //if(data[i].bin != -1){
-                               //hold[data[i].bin].bin = hold[data[i].bin].bin+1;
-                       //}
-               //}     
-
+               numSeqs = data.size();
+                               
+               vector<int> hold(numSeqs, 0);
                for(int i=0;i<numSeqs;i++){
-                       if(data[i].bin > numBins) { numBins = data[i].bin;      } 
-                       if(data[i].abundance > maxRank) {       maxRank = data[i].abundance;    }
+                       hold[data[i].bin] = hold[data[i].bin]+1;
+               }       
+               
+               for(int i=0;i<numSeqs;i++){
+                       if(hold[i] > 0)                         {       numBins++;                              }
+                       if(hold[i] > maxRank)           {       maxRank = hold[i];              }
                }
-               numBins++; //if you have 10 bins largest .bin is 9 since we start at 0.
+               
        }
        catch(exception& e) {
                cout << "Standard Error: " << e.what() << " has occurred in the SharedOrderVector class Function updateStats. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";