X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=clusterdoturcommand.cpp;h=603bd73d680b485fb4df6ef6cf62e935af3f1ff5;hb=4c302368ef34f0d897afefc7853edf86fb45b9f3;hp=2b7b02b63a3a97d683d16a01b4514c5aa2671626;hpb=e51cb7e261265800fa2d2831b6516e33ebc7d78b;p=mothur.git

diff --git a/clusterdoturcommand.cpp b/clusterdoturcommand.cpp
index 2b7b02b..603bd73 100644
--- a/clusterdoturcommand.cpp
+++ b/clusterdoturcommand.cpp
@@ -72,6 +72,7 @@ ClusterDoturCommand::ClusterDoturCommand(string option)  {
 		
 		//allow user to run help
 		if(option == "help") { help(); abort = true; calledHelp = true; }
+		else if(option == "citation") { citation(); abort = true; calledHelp = true;}
 		
 		else {
 			vector<string> myArray = setParameters();
@@ -131,24 +132,25 @@ ClusterDoturCommand::ClusterDoturCommand(string option)  {
 					m->mothurOut("You need to provide a phylip file with the cluster.classic command."); m->mothurOutEndLine(); 
 					abort = true; 
 				}	
-			}	
+			}else { m->setPhylipFile(phylipfile); }	
 
 		
 			//check for optional parameter and set defaults
 			namefile = validParameter.validFile(parameters, "name", true);
 			if (namefile == "not open") { abort = true; }	
 			else if (namefile == "not found") { namefile = ""; }
+			else { m->setNameFile(namefile); }
 			
 			string temp;
 			temp = validParameter.validFile(parameters, "precision", false);
 			if (temp == "not found") { temp = "100"; }
 			//saves precision legnth for formatting below
 			length = temp.length();
-			convert(temp, precision); 
+			m->mothurConvert(temp, precision); 
 			
 			temp = validParameter.validFile(parameters, "cutoff", false);
 			if (temp == "not found") { temp = "10"; }
-			convert(temp, cutoff); 
+			m->mothurConvert(temp, cutoff); 
 			cutoff += (5 / (precision * 10.0));  
 			
 			temp = validParameter.validFile(parameters, "hard", false);			if (temp == "not found") { temp = "T"; }
@@ -217,7 +219,7 @@ int ClusterDoturCommand::execute(){
 		int estart = time(NULL);
 	
 		while ((cluster->getSmallDist() < cutoff) && (cluster->getNSeqs() > 1)){
-			if (m->control_pressed) { delete cluster; delete list; delete rabund; sabundFile.close();rabundFile.close();listFile.close();  for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str()); 	} outputTypes.clear();  return 0;  }
+			if (m->control_pressed) { delete cluster; delete list; delete rabund; sabundFile.close();rabundFile.close();listFile.close();  for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]); 	} outputTypes.clear();  return 0;  }
 		
 			cluster->update(cutoff);