X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=clusterdoturcommand.cpp;h=56fbd5c0d6c2b8e9380959bd6ba97435b28fcd70;hb=995238e9aa4455e3b59053e3dfe497b89caed79e;hp=1c0c78d274359b7156506f6697e0aa039754a38d;hpb=6cf9539162b0fb0b5c0b99673e999df3cd717c55;p=mothur.git

diff --git a/clusterdoturcommand.cpp b/clusterdoturcommand.cpp
index 1c0c78d..56fbd5c 100644
--- a/clusterdoturcommand.cpp
+++ b/clusterdoturcommand.cpp
@@ -13,7 +13,7 @@
 //**********************************************************************************************************************
 vector<string> ClusterDoturCommand::getValidParameters(){	
 	try {
-		string AlignArray[] =  {"phylip","cutoff","precision","method","outputdir","inputdir"};
+		string AlignArray[] =  {"phylip","name","hard","cutoff","precision","method","outputdir","inputdir"};
 		vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
 		return myArray;
 	}
@@ -72,7 +72,7 @@ ClusterDoturCommand::ClusterDoturCommand(string option)  {
 		
 		else {
 			//valid paramters for this command
-			string Array[] =  {"phylip","cutoff","precision","method","outputdir","inputdir"};
+			string Array[] =  {"phylip","name","cutoff","hard","precision","method","outputdir","inputdir"};
 			vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
 			
 			OptionParser parser(option);
@@ -223,12 +223,11 @@ 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);
@@ -267,11 +266,11 @@ 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(); 
+		//}
 		
 		m->mothurOutEndLine();
 		m->mothurOut("Output File Names: "); m->mothurOutEndLine();