X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=rarefact.cpp;h=f5e7952688cdbb1dd182ca44df9c152ef46879d9;hb=aa9238c0a9e6e7aa0ed8b8b606b08ad4fd7dcfe3;hp=ba0c02e2a474545474e4cf13efbdc633bfbbb3a3;hpb=526a868606faa50caf86e7399f7554c0335b39e5;p=mothur.git

diff --git a/rarefact.cpp b/rarefact.cpp
index ba0c02e..f5e7952 100644
--- a/rarefact.cpp
+++ b/rarefact.cpp
@@ -12,7 +12,7 @@
 
 /***********************************************************************/
 
-void Rarefact::getCurve(int increment = 1, int nIters = 1000){
+int Rarefact::getCurve(int increment = 1, int nIters = 1000){
 	try {
 		RarefactionCurveData* rcd = new RarefactionCurveData();
 		for(int i=0;i<displays.size();i++){
@@ -31,6 +31,8 @@ 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);
 			
@@ -61,20 +63,17 @@ 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(int increment = 1, int nIters = 1000){
 try {
 		SharedRarefactionCurveData* rcd = new SharedRarefactionCurveData();
 		
@@ -85,14 +84,19 @@ try {
 			rcd->registerDisplay(displays[i]);
 		}
 		
+		//if jumble is false all iters will be the same
+		if (globaldata->jumble == false)  {  nIters = 1;  }
+		
 		for(int iter=0;iter<nIters;iter++){
 		
 			for(int i=0;i<displays.size();i++){
 				displays[i]->init(label);		  
 			}
-
-			//randomize the groups
-			random_shuffle(lookup.begin(), lookup.end());
+			
+			if (globaldata->jumble == true)  {
+				//randomize the groups
+				random_shuffle(lookup.begin(), lookup.end());
+			}
 			
 			//make merge the size of lookup[0]
 			SharedRAbundVector* merge = new SharedRAbundVector(lookup[0]->size());
@@ -105,6 +109,8 @@ try {
 			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(merge); subset.push_back(lookup[k]);
@@ -118,6 +124,7 @@ try {
 				displays[i]->reset();
 			}
 			
+			delete merge;
 		}
 		
 		for(int i=0;i<displays.size();i++){
@@ -125,16 +132,12 @@ 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);
 	}
-
 }
 
 /**************************************************************************************/
@@ -146,12 +149,8 @@ void Rarefact::mergeVectors(SharedRAbundVector* shared1, SharedRAbundVector* sha
 		}
 	}
 	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);
-	}	
 }