X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=rarefact.cpp;h=67662496618d427c12363ea5ec120f21578e3f12;hb=a6c698b20eda3671d22466ab6b98b36331a30804;hp=e776393b47318e8a7f9b79016433f75a8ba049d9;hpb=8c548985e92f5be0bde10eddea89a6ae888b73da;p=mothur.git

diff --git a/rarefact.cpp b/rarefact.cpp
index e776393..6766249 100644
--- a/rarefact.cpp
+++ b/rarefact.cpp
@@ -8,7 +8,7 @@
  */
 
 #include "rarefact.h"
-#include "ordervector.hpp"
+//#include "ordervector.hpp"
 
 /***********************************************************************/
 
@@ -52,11 +52,15 @@ void Rarefact::getCurve(int increment = 1, int nIters = 1000){
 			for(int i=0;i<displays.size();i++){
 				displays[i]->reset();
 			}
+			
+			delete lookup;
+			delete rank;
 		}
 
 		for(int i=0;i<displays.size();i++){
 			displays[i]->close();
 		}
+		delete rcd;
 	}
 	catch(exception& e) {
 		cout << "Standard Error: " << e.what() << " has occurred in the Rarefact class Function getCurve. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
@@ -72,65 +76,56 @@ void Rarefact::getCurve(int increment = 1, int nIters = 1000){
 
 void Rarefact::getSharedCurve(int increment = 1, int nIters = 1000){
 try {
-		globaldata = GlobalData::getInstance();
 		SharedRarefactionCurveData* rcd = new SharedRarefactionCurveData();
 		
+		label = lookup[0]->getLabel();
+		
 		//register the displays
 		for(int i=0;i<displays.size();i++){
 			rcd->registerDisplay(displays[i]);
 		}
-
+		
 		for(int iter=0;iter<nIters;iter++){
-			//clear out old values for new iter
-			lookup.clear();
 		
-			//create and initialize vector of sharedvectors, one for each group
-			for (int i = 0; i < globaldata->gGroupmap->getNumGroups(); i++) { 
-				SharedRAbundVector* temp = new SharedRAbundVector(sharedorder->getNumBins());
-				temp->setLabel(sharedorder->getLabel());
-				temp->setGroup(globaldata->gGroupmap->namesOfGroups[i]);
-				lookup.push_back(temp);
-			}
-			
 			for(int i=0;i<displays.size();i++){
 				displays[i]->init(label);		  
 			}
-		
-			//sample all the members
-			for(int i=0;i<numSeqs;i++){
-				//get first sample
-				individual chosen = sharedorder->get(i);
-				int abundance; 
-					
-				//set info for sharedvector in chosens group
-				for (int j = 0; j < lookup.size(); j++) { 
-					if (chosen.group == lookup[j]->getGroup()) {
-						abundance = lookup[j]->getAbundance(chosen.bin);
-						lookup[j]->set(chosen.bin, (abundance + 1), chosen.group);
-						break;
-					}
-				}
-			}
-			
+
 			//randomize the groups
 			random_shuffle(lookup.begin(), lookup.end());
-		
+			
+			//make merge the size of lookup[0]
+			SharedRAbundVector* merge = new SharedRAbundVector(lookup[0]->size());
+			
+			//make copy of lookup zero
+			for(int i = 0; i<lookup[0]->size(); i++) {
+				merge->set(i, lookup[0]->getAbundance(i), "merge");
+			}
+			
+			vector<SharedRAbundVector*> subset;
 			//send each group one at a time
 			for (int k = 0; k < lookup.size(); k++) { 
-				rcd->updateSharedData(lookup[0], lookup[k], k+1, numGroupComb);
-				mergeVectors(lookup[0], lookup[k]);
+				subset.clear(); //clears out old pair of sharedrabunds
+				//add in new pair of sharedrabunds
+				subset.push_back(merge); subset.push_back(lookup[k]);
+				
+				rcd->updateSharedData(subset, k+1, numGroupComb);
+				mergeVectors(merge, lookup[k]);
 			}
 
 			//resets output files
 			for(int i=0;i<displays.size();i++){
 				displays[i]->reset();
 			}
+			
+			delete merge;
 		}
 		
 		for(int i=0;i<displays.size();i++){
 			displays[i]->close();
 		}
-
+		
+		delete rcd;
 	}
 	catch(exception& e) {
 		cout << "Standard Error: " << e.what() << " has occurred in the Rarefact class Function getSharedCurve. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
@@ -148,9 +143,7 @@ void Rarefact::mergeVectors(SharedRAbundVector* shared1, SharedRAbundVector* sha
 	try{
 		for (int k = 0; k < shared1->size(); k++) {
 			//merge new species into shared1
-			if ((shared1->getAbundance(k) == 0) && (shared2->getAbundance(k) != 0)) {
-				shared1->set(k, shared2->getAbundance(k), "combo");  //set to 'combo' since this vector now contains multiple groups
-			}
+			shared1->set(k, (shared1->getAbundance(k) + shared2->getAbundance(k)), "combo");  //set to 'combo' since this vector now contains multiple groups
 		}
 	}
 	catch(exception& e) {