X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=clustercommand.cpp;h=4db95b45d00e3857513606383f05810f31a30ecd;hb=753dc84cf289b1d5dc0ca5b0c043640927aa951a;hp=36fff2242ee65d3cdb1e72868d173c69ed5bc3ff;hpb=0470f6d037aacb3563c3f7010708120a4a67d4e6;p=mothur.git

diff --git a/clustercommand.cpp b/clustercommand.cpp
index 36fff22..4db95b4 100644
--- a/clustercommand.cpp
+++ b/clustercommand.cpp
@@ -24,14 +24,14 @@ ClusterCommand::ClusterCommand(string option){
 			string Array[] =  {"cutoff","precision","method"};
 			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 = new ValidParameters();
+			ValidParameters validParameter;
 		
 			//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;  }
 			}
 			
 			//error checking to make sure they read a distance file
@@ -43,18 +43,17 @@ ClusterCommand::ClusterCommand(string option){
 			// ...at some point should added some additional type checking...
 			//get user cutoff and precision or use defaults
 			string temp;
-			temp = validParameter->validFile(parameters, "precision", false);		if (temp == "not found") { temp = "100"; }
+			temp = validParameter.validFile(parameters, "precision", false);		if (temp == "not found") { temp = "100"; }
 			//saves precision legnth for formatting below
 			length = temp.length();
 			convert(temp, precision); 
 			
-			temp = validParameter->validFile(parameters, "cutoff", false);			if (temp == "not found") { temp = "10"; }
+			temp = validParameter.validFile(parameters, "cutoff", false);			if (temp == "not found") { temp = "10"; }
 			convert(temp, cutoff); 
 			cutoff += (5 / (precision * 10.0));
 			
-			method = validParameter->validFile(parameters, "method", false);			if (method == "not found") { method = "furthest"; }
+			method = validParameter.validFile(parameters, "method", false);			if (method == "not found") { method = "furthest"; }
 
-			delete validParameter;
 			
 			if ((method == "furthest") || (method == "nearest") || (method == "average")) { }
 			else {cout << "Not a valid clustering method.  Valid clustering algorithms are furthest, nearest or average." << endl; abort = true; }
@@ -63,10 +62,10 @@ ClusterCommand::ClusterCommand(string option){
 			if (abort == false) {
 			
 				//get matrix, list and rabund for execute
-				if(globaldata->gSparseMatrix != NULL)	{	matrix = new SparseMatrix(*globaldata->gSparseMatrix);		}
+				if(globaldata->gSparseMatrix != NULL)	{	matrix = globaldata->gSparseMatrix;		}
 			
 				if(globaldata->gListVector != NULL){
-					list = new ListVector(*globaldata->gListVector);
+					list = globaldata->gListVector;
 					rabund = new RAbundVector(list->getRAbundVector());
 				}
 				
@@ -122,8 +121,6 @@ void ClusterCommand::help(){
 
 ClusterCommand::~ClusterCommand(){
 	delete cluster;
-	delete matrix;
-	delete list;
 	delete rabund;
 }