X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=collectcommand.cpp;h=88be43b9a283b3313eacb6093ffe4f496c6bc452;hb=8ab46c171b45ae3782d839539792d049017a361b;hp=9bf2c9a88c49f49f27d8a641aabc4d9f8d2ab3fe;hpb=182db2b6f1747bc1e0b8cd3eceec8751abdd31d5;p=mothur.git

diff --git a/collectcommand.cpp b/collectcommand.cpp
index 9bf2c9a..88be43b 100644
--- a/collectcommand.cpp
+++ b/collectcommand.cpp
@@ -110,6 +110,7 @@ void CollectCommand::help(){
 		m->mothurOut("The collect.single command can be executed after a successful cluster command.  It will use the .list file from the output of the cluster.\n");
 		m->mothurOut("The collect.single command parameters are label, freq, calc and abund.  No parameters are required. \n");
 		m->mothurOut("The collect.single command should be in the following format: \n");
+		m->mothurOut("The freq parameter is used indicate when to output your data, by default it is set to 100. But you can set it to a percentage of the number of sequence. For example freq=0.10, means 10%. \n");
 		m->mothurOut("collect.single(label=yourLabel, iters=yourIters, freq=yourFreq, calc=yourEstimators).\n");
 		m->mothurOut("Example collect(label=unique-.01-.03, iters=10000, freq=10, calc=sobs-chao-ace-jack).\n");
 		m->mothurOut("The default values for freq is 100, and calc are sobs-chao-ace-jack-shannon-npshannon-simpson.\n");
@@ -234,8 +235,8 @@ int CollectCommand::execute(){
 			set<string> userLabels = labels;
 			
 			if (m->control_pressed) {  
-				for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str()); 	}  
 				for(int i=0;i<cDisplays.size();i++){	delete cDisplays[i];	}
+				for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str()); 	}
 				delete input;  globaldata->ginput = NULL;
 				delete read;
 				delete order; globaldata->gorder = NULL;
@@ -246,25 +247,26 @@ int CollectCommand::execute(){
 
 
 			while((order != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
+			
+				if (m->control_pressed) { 
+					for(int i=0;i<cDisplays.size();i++){	delete cDisplays[i];	}
+					for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str()); 	}
+					delete input;  globaldata->ginput = NULL;
+					delete read;
+					delete order; globaldata->gorder = NULL;
+					delete validCalculator;
+					globaldata->Groups.clear();
+					return 0;
+				}
+
 				
 				if(allLines == 1 || labels.count(order->getLabel()) == 1){
-					
+				
+					m->mothurOut(order->getLabel()); m->mothurOutEndLine();
 					cCurve = new Collect(order, cDisplays);
-					int error = cCurve->getCurve(freq);
+					cCurve->getCurve(freq);
 					delete cCurve;
 					
-					if (error == 1) {
-						for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str()); 	}  
-						for(int i=0;i<cDisplays.size();i++){	delete cDisplays[i];	}
-						delete input;  globaldata->ginput = NULL;
-						delete read;
-						delete order; globaldata->gorder = NULL;
-						delete validCalculator;
-						globaldata->Groups.clear();
-						return 0;
-					}
-					
-					m->mothurOut(order->getLabel()); m->mothurOutEndLine();
 					processedLabels.insert(order->getLabel());
 					userLabels.erase(order->getLabel());
 					
@@ -277,22 +279,12 @@ int CollectCommand::execute(){
 					delete order;
 					order = (input->getOrderVector(lastLabel));
 					
+					m->mothurOut(order->getLabel()); m->mothurOutEndLine();
 					cCurve = new Collect(order, cDisplays);
-					int error = cCurve->getCurve(freq);
+					cCurve->getCurve(freq);
 					delete cCurve;
 					
-					if (error == 1) {
-						for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str()); 	}  
-						for(int i=0;i<cDisplays.size();i++){	delete cDisplays[i];	}
-						delete input;  globaldata->ginput = NULL;
-						delete read;
-						delete order; globaldata->gorder = NULL;
-						delete validCalculator;
-						globaldata->Groups.clear();
-						return 0;
-					}
 					
-					m->mothurOut(order->getLabel()); m->mothurOutEndLine();
 					processedLabels.insert(order->getLabel());
 					userLabels.erase(order->getLabel());
 					
@@ -306,6 +298,17 @@ int CollectCommand::execute(){
 				order = (input->getOrderVector());
 			}
 			
+			
+			if (m->control_pressed) { 
+					for(int i=0;i<cDisplays.size();i++){	delete cDisplays[i];	}
+					for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str()); 	}
+					delete input;  globaldata->ginput = NULL;
+					delete read;
+					delete validCalculator;
+					globaldata->Groups.clear();
+					return 0;
+			}
+				
 			//output error messages about any remaining user labels
 			set<string>::iterator it;
 			bool needToRun = false;
@@ -327,12 +330,12 @@ int CollectCommand::execute(){
 				m->mothurOut(order->getLabel()); m->mothurOutEndLine();
 				
 				cCurve = new Collect(order, cDisplays);
-				int error = cCurve->getCurve(freq);
+				cCurve->getCurve(freq);
 				delete cCurve;
 				
-				if (error == 1) {
-					for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str()); 	}  
+				if (m->control_pressed) { 
 					for(int i=0;i<cDisplays.size();i++){	delete cDisplays[i];	}
+					for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str()); 	}
 					delete input;  globaldata->ginput = NULL;
 					delete read;
 					delete order; globaldata->gorder = NULL;
@@ -351,6 +354,8 @@ int CollectCommand::execute(){
 			delete validCalculator;
 		}
 		
+		if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str()); 	} return 0; }
+
 		m->mothurOutEndLine();
 		m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 		for (int i = 0; i < outputNames.size(); i++) {	m->mothurOut(outputNames[i]); m->mothurOutEndLine();	}