last changes before move

[mothur.git] / pintail.cpp

diff --git a/pintail.cpp b/pintail.cpp
index 53bdd9e63f396ec44c608398e54bd649dca31073..f46e0e290f0c99f344bb9e809c7c5b20989e9da0 100644 (file)
--- a/pintail.cpp
+++ b/pintail.cpp
@@ -10,6 +10,11 @@
 #include "pintail.h"
 #include "ignoregaps.h"
 
+//********************************************************************************************************************
+//sorts lowest to highest
+inline bool compareQuanMembers(quanMember left, quanMember right){
+       return (left.score < right.score);      
+} 
 //***************************************************************************************************************
 
 Pintail::Pintail(string filename, string temp) {  fastafile = filename;  templateFile = temp;  }
@@ -89,7 +94,6 @@ void Pintail::getChimeras() {
                h.resize(numSeqs);
                quantiles.resize(100);  //one for every percent mismatch
                quantilesMembers.resize(100);  //one for every percent mismatch
-               makeCompliant.resize(templateSeqs.size(), 0.0);
                
                //break up file if needed
                int linesPerProcess = numSeqs / processors ;
@@ -242,10 +246,12 @@ void Pintail::getChimeras() {
                        
                        mothurOut("Calculating quantiles for your template.  This can take a while...  I will output the quantiles to a .quan file that you can input them using the quantiles parameter next time you run this command.  Providing the .quan file will dramatically improve speed.    "); cout.flush();
                        if (processors == 1) { 
-                               quantilesMembers = decalc->getQuantiles(templateSeqs, windowSizesTemplate, window, probabilityProfile, increment, 0, templateSeqs.size(), makeCompliant);
+                               quantilesMembers = decalc->getQuantiles(templateSeqs, windowSizesTemplate, window, probabilityProfile, increment, 0, templateSeqs.size());
                        }else {         createProcessesQuan();          }
                        
+                       
                                                
+                       
                        //decided against this because we were having trouble setting the sensitivity... may want to revisit this...
                        //quantiles = decalc->removeObviousOutliers(quantilesMembers, templateSeqs.size());
                        
@@ -257,30 +263,30 @@ void Pintail::getChimeras() {
                        openOutputFile(o, out4);
                        
                        //adjust quantiles
-                       for (int i = 0; i < quantiles.size(); i++) {
+                       for (int i = 0; i < quantilesMembers.size(); i++) {
                                vector<float> temp;
                                
-                               if (quantiles[i].size() == 0) {
+                               if (quantilesMembers[i].size() == 0) {
                                        //in case this is not a distance found in your template files
                                        for (int g = 0; g < 6; g++) {
                                                temp.push_back(0.0);
                                        }
                                }else{
                                        
-                                       sort(quantiles[i].begin(), quantiles[i].end());
+                                       sort(quantilesMembers[i].begin(), quantilesMembers[i].end(), compareQuanMembers);
                                        
                                        //save 10%
-                                       temp.push_back(quantiles[i][int(quantiles[i].size() * 0.10)]);
+                                       temp.push_back(quantilesMembers[i][int(quantilesMembers[i].size() * 0.10)].score);
                                        //save 25%
-                                       temp.push_back(quantiles[i][int(quantiles[i].size() * 0.25)]);
+                                       temp.push_back(quantilesMembers[i][int(quantilesMembers[i].size() * 0.25)].score);
                                        //save 50%
-                                       temp.push_back(quantiles[i][int(quantiles[i].size() * 0.5)]);
+                                       temp.push_back(quantilesMembers[i][int(quantilesMembers[i].size() * 0.5)].score);
                                        //save 75%
-                                       temp.push_back(quantiles[i][int(quantiles[i].size() * 0.75)]);
+                                       temp.push_back(quantilesMembers[i][int(quantilesMembers[i].size() * 0.75)].score);
                                        //save 95%
-                                       temp.push_back(quantiles[i][int(quantiles[i].size() * 0.95)]);
+                                       temp.push_back(quantilesMembers[i][int(quantilesMembers[i].size() * 0.95)].score);
                                        //save 99%
-                                       temp.push_back(quantiles[i][int(quantiles[i].size() * 0.99)]);
+                                       temp.push_back(quantilesMembers[i][int(quantilesMembers[i].size() * 0.99)].score);
                                        
                                }
                                
@@ -900,7 +906,7 @@ void Pintail::createProcessesQuan() {
                                process++;
                        }else if (pid == 0){
                                
-                               quantilesMembers = decalc->getQuantiles(templateSeqs, windowSizesTemplate, window, probabilityProfile, increment, templateLines[process]->start, templateLines[process]->end, makeCompliant);
+                               quantilesMembers = decalc->getQuantiles(templateSeqs, windowSizesTemplate, window, probabilityProfile, increment, templateLines[process]->start, templateLines[process]->end);
                                
                                //write out data to file so parent can read it
                                ofstream out;
@@ -971,7 +977,7 @@ void Pintail::createProcessesQuan() {
                }
                
 #else
-               quantilesMembers = decalc->getQuantiles(templateSeqs, windowSizesTemplate, window, probabilityProfile, increment, 0, templateSeqs.size(), makeCompliant);
+               quantilesMembers = decalc->getQuantiles(templateSeqs, windowSizesTemplate, window, probabilityProfile, increment, 0, templateSeqs.size());
 #endif         
        }
        catch(exception& e) {