X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=hclustercommand.cpp;h=47136938a19e6c5d4b8dd2b8110849249ac50b06;hb=b86361f726a0d1dfc9f2e91b795e402d97c46f9d;hp=12f1f9e0b33904639cca446f0b0d698e9f64f625;hpb=e51cb7e261265800fa2d2831b6516e33ebc7d78b;p=mothur.git

diff --git a/hclustercommand.cpp b/hclustercommand.cpp
index 12f1f9e..4713693 100644
--- a/hclustercommand.cpp
+++ b/hclustercommand.cpp
@@ -74,6 +74,7 @@ HClusterCommand::HClusterCommand(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();
@@ -134,16 +135,17 @@ HClusterCommand::HClusterCommand(string option)  {
 			phylipfile = validParameter.validFile(parameters, "phylip", true);
 			if (phylipfile == "not open") { abort = true; }
 			else if (phylipfile == "not found") { phylipfile = ""; }	
-			else {  distfile = phylipfile;  format = "phylip"; 	}
+			else {  distfile = phylipfile;  format = "phylip"; 	m->setPhylipFile(phylipfile); }
 			
 			columnfile = validParameter.validFile(parameters, "column", true);
 			if (columnfile == "not open") { abort = true; }	
 			else if (columnfile == "not found") { columnfile = ""; }
-			else {  distfile = columnfile; format = "column";	}
+			else {  distfile = columnfile; format = "column";	m->setColumnFile(columnfile); }
 			
 			namefile = validParameter.validFile(parameters, "name", true);
 			if (namefile == "not open") { abort = true; }	
 			else if (namefile == "not found") { namefile = ""; }
+			else { m->setNameFile(namefile); }
 			
 			if ((phylipfile == "") && (columnfile == "")) { 
 				//is there are current file available for either of these?
@@ -180,14 +182,14 @@ HClusterCommand::HClusterCommand(string option)  {
 			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, "hard", false);			if (temp == "not found") { temp = "T"; }
 			hard = m->isTrue(temp);
 			
 			temp = validParameter.validFile(parameters, "cutoff", false);
 			if (temp == "not found") { temp = "10"; }
-			convert(temp, cutoff); 
+			m->mothurConvert(temp, cutoff); 
 			cutoff += (5 / (precision * 10.0)); 
 			
 			method = validParameter.validFile(parameters, "method", false);
@@ -258,7 +260,7 @@ int HClusterCommand::execute(){
 				sabundFile.close();
 				rabundFile.close();
 				listFile.close();
-				for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str());  } outputTypes.clear();
+				for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]);  } outputTypes.clear();
 				return 0;  
 			}
 			
@@ -274,7 +276,7 @@ int HClusterCommand::execute(){
 			sabundFile.close();
 			rabundFile.close();
 			listFile.close();
-			for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str());  } outputTypes.clear();
+			for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]);  } outputTypes.clear();
 			return 0;  
 		}
 
@@ -304,35 +306,41 @@ int HClusterCommand::execute(){
 				sabundFile.close();
 				rabundFile.close();
 				listFile.close();
-				for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str());  } outputTypes.clear();
+				for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]);  } outputTypes.clear();
 				return 0;  
 		}
 
+		float saveCutoff = cutoff;
 		
 		while (seqs.size() != 0){
 		
 			seqs = cluster->getSeqs();
 			
+			//to account for cutoff change in average neighbor
+			if (seqs.size() != 0) {
+				if (seqs[0].dist > cutoff) { break; }
+			}
+			
 			if (m->control_pressed) {  
 				delete cluster;
 				sabundFile.close();
 				rabundFile.close();
 				listFile.close();
-				for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str());  } outputTypes.clear();
+				for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]);  } outputTypes.clear();
 				return 0;  
 			}
 
 			for (int i = 0; i < seqs.size(); i++) {  //-1 means skip me
 				
 				if (seqs[i].seq1 != seqs[i].seq2) {
-					cluster->update(seqs[i].seq1, seqs[i].seq2, seqs[i].dist);
+					cutoff = cluster->update(seqs[i].seq1, seqs[i].seq2, seqs[i].dist);
 					
 					if (m->control_pressed) {  
 						delete cluster;
 						sabundFile.close();
 						rabundFile.close();
 						listFile.close();
-						for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str());  } outputTypes.clear();
+						for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]);  } outputTypes.clear();
 						return 0;  
 					}
 
@@ -365,7 +373,7 @@ int HClusterCommand::execute(){
 			sabundFile.close();
 			rabundFile.close();
 			listFile.close();
-			for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str());  } outputTypes.clear();
+			for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]);  } outputTypes.clear();
 			return 0;  
 		}
 					
@@ -382,10 +390,18 @@ int HClusterCommand::execute(){
 		delete cluster;
 		
 		if (m->control_pressed) {  
-			for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str());  } outputTypes.clear();
+			for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]);  } outputTypes.clear();
 			return 0;  
 		}
 		
+		
+		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");