X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=clusterdoturcommand.cpp;h=5bcfe03416f90700a02a4ff3d58ad312f788bb96;hb=348de0f8b17d84ede77081dcf67bd6ef43496677;hp=21840e482d4ccadcd138f35f4ef9fda1e0f7881c;hpb=26b30b0881a37665b18746d2851607c494e8ccc0;p=mothur.git

diff --git a/clusterdoturcommand.cpp b/clusterdoturcommand.cpp
index 21840e4..5bcfe03 100644
--- a/clusterdoturcommand.cpp
+++ b/clusterdoturcommand.cpp
@@ -25,8 +25,7 @@ vector<string> ClusterDoturCommand::getValidParameters(){
 //**********************************************************************************************************************
 ClusterDoturCommand::ClusterDoturCommand(){	
 	try {
-		abort = true;
-		//initialize outputTypes
+		abort = true; calledHelp = true; 
 		vector<string> tempOutNames;
 		outputTypes["list"] = tempOutNames;
 		outputTypes["rabund"] = tempOutNames;
@@ -65,10 +64,10 @@ vector<string> ClusterDoturCommand::getRequiredFiles(){
 ClusterDoturCommand::ClusterDoturCommand(string option)  {
 	try{
 		
-		abort = false;
+		abort = false; calledHelp = false;   
 		
 		//allow user to run help
-		if(option == "help") { help(); abort = true; }
+		if(option == "help") { help(); abort = true; calledHelp = true; }
 		
 		else {
 			//valid paramters for this command
@@ -189,7 +188,7 @@ ClusterDoturCommand::~ClusterDoturCommand(){}
 int ClusterDoturCommand::execute(){
 	try {
 	
-		if (abort == true) {	return 0;	}
+		if (abort == true) { if (calledHelp) { return 0; }  return 2;	}
 		
 		if(namefile != ""){	
 			nameMap = new NameAssignment(namefile);
@@ -223,11 +222,11 @@ int ClusterDoturCommand::execute(){
 		oldRAbund = *rabund;
 		oldList = *list;
 
-		double saveCutoff = cutoff;
+		//double saveCutoff = cutoff;
 		
 		int estart = time(NULL);
 	
-		while ((cluster->getSmallDist() < cutoff) && (cluster->getNSeqs() > 0)){
+		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;  }
 		
 			cluster->update(cutoff);
@@ -266,10 +265,29 @@ int ClusterDoturCommand::execute(){
 		
 		delete cluster; delete nameMap; delete list; delete rabund;
 	
-		if (saveCutoff != cutoff) { 
-			if (hard)	{  saveCutoff = m->ceilDist(saveCutoff, precision);	}
-			else		{	saveCutoff = m->roundDist(saveCutoff, precision);  }
-			m->mothurOut("changed cutoff to " + toString(cutoff)); m->mothurOutEndLine(); 
+		//if (saveCutoff != cutoff) { 
+		//	if (hard)	{  saveCutoff = m->ceilDist(saveCutoff, precision);	}
+		//	else		{	saveCutoff = m->roundDist(saveCutoff, precision);  }
+		//	m->mothurOut("changed cutoff to " + toString(cutoff)); m->mothurOutEndLine(); 
+		//}
+		
+		//set list file as new current listfile
+		string current = "";
+		itTypes = outputTypes.find("list");
+		if (itTypes != outputTypes.end()) {
+			if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setListFile(current); }
+		}
+		
+		//set rabund file as new current rabundfile
+		itTypes = outputTypes.find("rabund");
+		if (itTypes != outputTypes.end()) {
+			if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setRabundFile(current); }
+		}
+		
+		//set sabund file as new current sabundfile
+		itTypes = outputTypes.find("sabund");
+		if (itTypes != outputTypes.end()) {
+			if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setSabundFile(current); }
 		}
 		
 		m->mothurOutEndLine();