X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=hclustercommand.cpp;h=cf35cd9d6fa4c2a8fe1349b63399eb60007a4217;hb=c7e8c2d15bd7cedcfdf18675cb0ea1a0dcd0e3c0;hp=d98f5c69926f795cb75510853184197676647ab9;hpb=7bf9a81bba76538ecaf351ae208de3da4bf1b6dd;p=mothur.git

diff --git a/hclustercommand.cpp b/hclustercommand.cpp
index d98f5c6..cf35cd9 100644
--- a/hclustercommand.cpp
+++ b/hclustercommand.cpp
@@ -52,6 +52,28 @@ string HClusterCommand::getHelpString(){
 	}
 }
 //**********************************************************************************************************************
+string HClusterCommand::getOutputFileNameTag(string type, string inputName=""){	
+	try {
+        string outputFileName = "";
+		map<string, vector<string> >::iterator it;
+        
+        //is this a type this command creates
+        it = outputTypes.find(type);
+        if (it == outputTypes.end()) {  m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
+        else {
+            if (type == "list") {  outputFileName =  "list"; }
+            else if (type == "rabund") {  outputFileName =  "rabund"; }
+            else if (type == "sabund") {  outputFileName =  "sabund"; }
+            else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true;  }
+        }
+        return outputFileName;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "HClusterCommand", "getOutputFileNameTag");
+		exit(1);
+	}
+}
+//**********************************************************************************************************************
 HClusterCommand::HClusterCommand(){	
 	try {
 		abort = true; calledHelp = true; 
@@ -182,14 +204,14 @@ 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);
@@ -219,13 +241,17 @@ HClusterCommand::HClusterCommand(string option)  {
 				else if (method == "weighted")	{ tag = "wn";  }
 				else							{ tag = "an";  }
 			
-				m->openOutputFile(fileroot+ tag + ".sabund",	sabundFile);
-				m->openOutputFile(fileroot+ tag + ".rabund",	rabundFile);
-				m->openOutputFile(fileroot+ tag + ".list",		listFile);
-				
-				outputNames.push_back(fileroot+ tag + ".sabund"); outputTypes["sabund"].push_back(fileroot+ tag + ".sabund");
-				outputNames.push_back(fileroot+ tag + ".rabund"); outputTypes["rabund"].push_back(fileroot+ tag + ".rabund");
-				outputNames.push_back(fileroot+ tag + ".list"); outputTypes["list"].push_back(fileroot+ tag + ".list");
+				string sabundFileName = fileroot+ tag + "." + getOutputFileNameTag("sabund");
+                string rabundFileName = fileroot+ tag + "." + getOutputFileNameTag("rabund");
+                string listFileName = fileroot+ tag + "." + getOutputFileNameTag("list");
+                
+                m->openOutputFile(sabundFileName,	sabundFile);
+                m->openOutputFile(rabundFileName,	rabundFile);
+                m->openOutputFile(listFileName,	listFile);
+                
+                outputNames.push_back(sabundFileName); outputTypes["sabund"].push_back(sabundFileName);
+                outputNames.push_back(rabundFileName); outputTypes["rabund"].push_back(rabundFileName);
+                outputNames.push_back(listFileName); outputTypes["list"].push_back(listFileName);
 			}
 		}
 	}
@@ -260,7 +286,7 @@ 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;  
 			}
 			
@@ -276,7 +302,7 @@ 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;  
 		}
 
@@ -306,35 +332,41 @@ 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;  
 					}
 
@@ -367,7 +399,7 @@ 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;  
 		}
 					
@@ -384,10 +416,18 @@ 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");