X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=rarefact.cpp;h=691d01708bab5b5bef4118ab38662819280b56de;hb=8ab46c171b45ae3782d839539792d049017a361b;hp=cb4bbbce9a4047ae08b5f37b807be3f78c255d89;hpb=599af78a6ea4916919d460a131e2d0dffa28d35e;p=mothur.git

diff --git a/rarefact.cpp b/rarefact.cpp
index cb4bbbc..691d017 100644
--- a/rarefact.cpp
+++ b/rarefact.cpp
@@ -12,13 +12,18 @@
 
 /***********************************************************************/
 
-void Rarefact::getCurve(int increment = 1, int nIters = 1000){
+int Rarefact::getCurve(float percentFreq = 0.01, int nIters = 1000){
 	try {
 		RarefactionCurveData* rcd = new RarefactionCurveData();
 		for(int i=0;i<displays.size();i++){
 			rcd->registerDisplay(displays[i]);
 		}
-	
+		
+		//convert freq percentage to number
+		int increment = 1;
+		if (percentFreq < 1.0) {  increment = numSeqs * percentFreq;  }
+		else { increment = percentFreq;  }	
+			
 		for(int iter=0;iter<nIters;iter++){
 		
 			for(int i=0;i<displays.size();i++){
@@ -31,6 +36,8 @@ void Rarefact::getCurve(int increment = 1, int nIters = 1000){
 		
 			for(int i=0;i<numSeqs;i++){
 			
+				if (m->control_pressed) { delete lookup; delete rank; delete rcd; return 0;  }
+			
 				int binNumber = order->get(i);
 				int abundance = lookup->get(binNumber);
 			
@@ -61,73 +68,65 @@ void Rarefact::getCurve(int increment = 1, int nIters = 1000){
 			displays[i]->close();
 		}
 		delete rcd;
+		return 0;
 	}
 	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";
-		exit(1);
-	}
-	catch(...) {
-		cout << "An unknown error has occurred in the Rarefact class function getCurve. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "Rarefact", "getCurve");
 		exit(1);
 	}
 }
 
 /***********************************************************************/
 
-void Rarefact::getSharedCurve(int increment = 1, int nIters = 1000){
+int Rarefact::getSharedCurve(float percentFreq = 0.01, 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]);
 		}
-
+		
+		//if jumble is false all iters will be the same
+		if (globaldata->jumble == false)  {  nIters = 1;  }
+		
+		//convert freq percentage to number
+		int increment = 1;
+		if (percentFreq < 1.0) {  increment = numSeqs * percentFreq;  }
+		else { increment = percentFreq;  }
+		
 		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->Groups.size(); i++) { 
-				SharedRAbundVector* temp = new SharedRAbundVector(sharedorder->getNumBins());
-				temp->setLabel(sharedorder->getLabel());
-				temp->setGroup(globaldata->Groups[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;
-					}
-				}
+			
+			if (globaldata->jumble == true)  {
+				//randomize the groups
+				random_shuffle(lookup.begin(), lookup.end());
 			}
 			
-			//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++) { 
+				if (m->control_pressed) {  delete merge; delete rcd; return 0;  }
+				
 				subset.clear(); //clears out old pair of sharedrabunds
 				//add in new pair of sharedrabunds
-				subset.push_back(lookup[0]); subset.push_back(lookup[k]);
+				subset.push_back(merge); subset.push_back(lookup[k]);
 				
 				rcd->updateSharedData(subset, k+1, numGroupComb);
-				mergeVectors(lookup[0], lookup[k]);
+				mergeVectors(merge, lookup[k]);
 			}
 
 			//resets output files
@@ -135,9 +134,7 @@ try {
 				displays[i]->reset();
 			}
 			
-			for (int i = 0; i < lookup.size(); i++) {
-				delete lookup[i];
-			}
+			delete merge;
 		}
 		
 		for(int i=0;i<displays.size();i++){
@@ -145,16 +142,12 @@ try {
 		}
 		
 		delete rcd;
+		return 0;
 	}
 	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";
-		exit(1);
-	}
-	catch(...) {
-		cout << "An unknown error has occurred in the Rarefact class function getSharedCurve. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "Rarefact", "getSharedCurve");
 		exit(1);
 	}
-
 }
 
 /**************************************************************************************/
@@ -162,18 +155,12 @@ 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) {
-		cout << "Standard Error: " << e.what() << " has occurred in the Rarefact class Function mergeVectors. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "Rarefact", "mergeVectors");
 		exit(1);
 	}
-	catch(...) {
-		cout << "An unknown error has occurred in the Rarefact class function mergeVectors. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}	
 }