X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=clusterdoturcommand.cpp;h=9bfb52b9d92b0222af2e4b1acff37c82f968349f;hb=ccae9eef0b44f2d63fdf4a707d0d40243aa1b990;hp=a9d3214b1d7ffb793d8a7813a55f26b7824795a0;hpb=ca9ac1d80c62f57270b0dcd49410ebe08a8aecd6;p=mothur.git

diff --git a/clusterdoturcommand.cpp b/clusterdoturcommand.cpp
index a9d3214..9bfb52b 100644
--- a/clusterdoturcommand.cpp
+++ b/clusterdoturcommand.cpp
@@ -17,8 +17,8 @@ vector<string> ClusterDoturCommand::setParameters(){
 		CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pname);
 		CommandParameter pcutoff("cutoff", "Number", "", "10", "", "", "",false,false); parameters.push_back(pcutoff);
 		CommandParameter pprecision("precision", "Number", "", "100", "", "", "",false,false); parameters.push_back(pprecision);
-		CommandParameter pmethod("method", "Multiple", "furthest-nearest-average-weighted", "furthest", "", "", "",false,false); parameters.push_back(pmethod);
-		CommandParameter phard("hard", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(phard);
+		CommandParameter pmethod("method", "Multiple", "furthest-nearest-average-weighted", "average", "", "", "",false,false); parameters.push_back(pmethod);
+		CommandParameter phard("hard", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(phard);
 		CommandParameter psim("sim", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(psim);
 		CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
 		CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
@@ -40,7 +40,7 @@ string ClusterDoturCommand::getHelpString(){
 		helpString += "The cluster.classic command parameter options are phylip, name, method, cuttoff, hard, sim, precision. Phylip is required, unless you have a valid current file.\n";
 		helpString += "The cluster.classic command should be in the following format: \n";
 		helpString += "cluster.classic(phylip=yourDistanceMatrix, method=yourMethod, cutoff=yourCutoff, precision=yourPrecision) \n";
-		helpString += "The acceptable cluster methods are furthest, nearest, weighted and average.  If no method is provided then furthest is assumed.\n\n";	
+		helpString += "The acceptable cluster methods are furthest, nearest, weighted and average.  If no method is provided then average is assumed.\n";	
 		return helpString;
 	}
 	catch(exception& e) {
@@ -49,6 +49,28 @@ string ClusterDoturCommand::getHelpString(){
 	}
 }
 //**********************************************************************************************************************
+string ClusterDoturCommand::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, "ClusterDoturCommand", "getOutputFileNameTag");
+		exit(1);
+	}
+}
+//**********************************************************************************************************************
 ClusterDoturCommand::ClusterDoturCommand(){	
 	try {
 		abort = true; calledHelp = true;
@@ -72,6 +94,7 @@ 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();
@@ -131,34 +154,35 @@ 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 = "F"; }
+			temp = validParameter.validFile(parameters, "hard", false);			if (temp == "not found") { temp = "T"; }
 			hard = m->isTrue(temp);
 			
 			temp = validParameter.validFile(parameters, "sim", false);				if (temp == "not found") { temp = "F"; }
 			sim = m->isTrue(temp); 
 			
 			method = validParameter.validFile(parameters, "method", false);
-			if (method == "not found") { method = "furthest"; }
+			if (method == "not found") { method = "average"; }
 			
 			if ((method == "furthest") || (method == "nearest") || (method == "average") || (method == "weighted")) { 
 				if (method == "furthest") { tag = "fn"; }
@@ -199,13 +223,17 @@ int ClusterDoturCommand::execute(){
 		if (outputDir == "") { outputDir += m->hasPath(phylipfile); }
 		fileroot = outputDir + m->getRootName(m->getSimpleName(phylipfile));
 			
-		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);
 		
 		float previousDist = 0.00000;
 		float rndPreviousDist = 0.00000;
@@ -217,7 +245,7 @@ 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);