X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=rarefactsharedcommand.cpp;h=d0179be91a5b2eac505632797a8ebb3f74232282;hp=66ef6ddf24d6132bd355663c3dbdd24d5662c18c;hb=cd37904452dc95b183ff313ff05720c562902487;hpb=0470f6d037aacb3563c3f7010708120a4a67d4e6

diff --git a/rarefactsharedcommand.cpp b/rarefactsharedcommand.cpp
index 66ef6dd..d0179be 100644
--- a/rarefactsharedcommand.cpp
+++ b/rarefactsharedcommand.cpp
@@ -30,14 +30,14 @@ RareFactSharedCommand::RareFactSharedCommand(string option){
 			string Array[] =  {"iters","line","label","calc","groups"};
 			vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
 			
-			parser = new OptionParser();
-			parser->parse(option, parameters);  delete parser;
+			OptionParser parser(option);
+			map<string,string> parameters = parser.getParameters();
+			
+			ValidParameters validParameter;
 			
-			ValidParameters* validParameter = new ValidParameters();
-		
 			//check to make sure all parameters are valid for command
-			for (it = parameters.begin(); it != parameters.end(); it++) { 
-				if (validParameter->isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
+			for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) { 
+				if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 			}
 			
 			//make sure the user has already run the read.otu command
@@ -49,14 +49,14 @@ RareFactSharedCommand::RareFactSharedCommand(string option){
 			
 			//check for optional parameter and set defaults
 			// ...at some point should added some additional type checking...
-			line = validParameter->validFile(parameters, "line", false);				
+			line = validParameter.validFile(parameters, "line", false);				
 			if (line == "not found") { line = "";  }
 			else { 
 				if(line != "all") {  splitAtDash(line, lines);  allLines = 0;  }
 				else { allLines = 1;  }
 			}
 			
-			label = validParameter->validFile(parameters, "label", false);			
+			label = validParameter.validFile(parameters, "label", false);			
 			if (label == "not found") { label = ""; }
 			else { 
 				if(label != "all") {  splitAtDash(label, labels);  allLines = 0;  }
@@ -72,14 +72,14 @@ RareFactSharedCommand::RareFactSharedCommand(string option){
 				lines = globaldata->lines;
 			}
 				
-			calc = validParameter->validFile(parameters, "calc", false);			
+			calc = validParameter.validFile(parameters, "calc", false);			
 			if (calc == "not found") { calc = "sharedobserved";  }
 			else { 
 				 if (calc == "default")  {  calc = "sharedobserved";  }
 			}
 			splitAtDash(calc, Estimators);
 			
-			groups = validParameter->validFile(parameters, "groups", false);			
+			groups = validParameter.validFile(parameters, "groups", false);			
 			if (groups == "not found") { groups = ""; }
 			else { 
 				splitAtDash(groups, Groups);
@@ -87,20 +87,18 @@ RareFactSharedCommand::RareFactSharedCommand(string option){
 			}
 			
 			string temp;
-			temp = validParameter->validFile(parameters, "iters", false);			if (temp == "not found") { temp = "1000"; }
+			temp = validParameter.validFile(parameters, "iters", false);			if (temp == "not found") { temp = "1000"; }
 			convert(temp, nIters); 
 			
-			delete validParameter;
-			
 			if (abort == false) {
 			
 				string fileNameRoot = getRootName(globaldata->inputFileName);
-				format = globaldata->getFormat();
-				int i;
+//				format = globaldata->getFormat();
+
 				
 				validCalculator = new ValidCalculators();
 				
-				for (i=0; i<Estimators.size(); i++) {
+				for (int i=0; i<Estimators.size(); i++) {
 					if (validCalculator->isValidCalculator("sharedrarefaction", Estimators[i]) == true) { 
 						if (Estimators[i] == "sharedobserved") { 
 							rDisplays.push_back(new RareDisplay(new SharedSobs(), new SharedThreeColumnFile(fileNameRoot+"shared.rarefaction", "")));