X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=collectcommand.cpp;h=b892a91bee89e9b6d01ac7bda8e40833fd4db3b0;hp=7b8364b9b25d07e457508dbe5fe0153a4cc3a27f;hb=cf9987b67aa49777a4c91c2d21f96e58bf17aa82;hpb=8f7f4fc08b8c70d9ef0f79607813dba4e926e102

diff --git a/collectcommand.cpp b/collectcommand.cpp
index 7b8364b..b892a91 100644
--- a/collectcommand.cpp
+++ b/collectcommand.cpp
@@ -38,17 +38,17 @@
 //**********************************************************************************************************************
 vector<string> CollectCommand::setParameters(){	
 	try {
-		CommandParameter plist("list", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(plist);
-		CommandParameter prabund("rabund", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(prabund);
-		CommandParameter psabund("sabund", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(psabund);
-		CommandParameter pshared("shared", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(pshared);
-		CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
-		CommandParameter pfreq("freq", "Number", "", "100", "", "", "",false,false); parameters.push_back(pfreq);
-		CommandParameter pcalc("calc", "Multiple", "sobs-chao-nseqs-coverage-ace-jack-shannon-shannoneven-np_shannon-heip-smithwilson-simpson-simpsoneven-invsimpson-bootstrap-geometric-qstat-logseries-bergerparker-bstick-goodscoverage-efron-boneh-solow-shen", "sobs-chao-ace-jack-shannon-npshannon-simpson", "", "", "",true,false); parameters.push_back(pcalc);
-		CommandParameter pabund("abund", "Number", "", "10", "", "", "",false,false); parameters.push_back(pabund);
-		CommandParameter psize("size", "Number", "", "0", "", "", "",false,false); parameters.push_back(psize);
-		CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
-		CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+		CommandParameter plist("list", "InputTypes", "", "", "LRSS", "LRSS", "none","",false,false,true); parameters.push_back(plist);
+		CommandParameter prabund("rabund", "InputTypes", "", "", "LRSS", "LRSS", "none","",false,false,true); parameters.push_back(prabund);
+		CommandParameter psabund("sabund", "InputTypes", "", "", "LRSS", "LRSS", "none","",false,false,true); parameters.push_back(psabund);
+		CommandParameter pshared("shared", "InputTypes", "", "", "LRSS", "LRSS", "none","",false,false,true); parameters.push_back(pshared);
+		CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
+		CommandParameter pfreq("freq", "Number", "", "100", "", "", "","",false,false); parameters.push_back(pfreq);
+		CommandParameter pcalc("calc", "Multiple", "sobs-chao-nseqs-coverage-ace-jack-shannon-shannoneven-npshannon-heip-smithwilson-simpson-simpsoneven-invsimpson-bootstrap-geometric-qstat-logseries-bergerparker-bstick-goodscoverage-efron-boneh-solow-shen", "sobs-chao-ace-jack-shannon-npshannon-simpson", "", "", "","",true,false,true); parameters.push_back(pcalc);
+		CommandParameter pabund("abund", "Number", "", "10", "", "", "","",false,false); parameters.push_back(pabund);
+		CommandParameter psize("size", "Number", "", "0", "", "", "","",false,false); parameters.push_back(psize);
+		CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+		CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
 		
 		vector<string> myArray;
 		for (int i = 0; i < parameters.size(); i++) {	myArray.push_back(parameters[i].name);		}
@@ -67,8 +67,8 @@ string CollectCommand::getHelpString(){
 		helpString += "The collect.single command parameters are list, sabund, rabund, shared, label, freq, calc and abund.  list, sabund, rabund or shared is required unless you have a valid current file. \n";
 		helpString += "The collect.single command should be in the following format: \n";
 		helpString += "The freq parameter is used indicate when to output your data, by default it is set to 100. But you can set it to a percentage of the number of sequence. For example freq=0.10, means 10%. \n";
-		helpString += "collect.single(label=yourLabel, iters=yourIters, freq=yourFreq, calc=yourEstimators).\n";
-		helpString += "Example collect(label=unique-.01-.03, iters=10000, freq=10, calc=sobs-chao-ace-jack).\n";
+		helpString += "collect.single(label=yourLabel, freq=yourFreq, calc=yourEstimators).\n";
+		helpString += "Example collect(label=unique-.01-.03, freq=10, calc=sobs-chao-ace-jack).\n";
 		helpString += "The default values for freq is 100, and calc are sobs-chao-ace-jack-shannon-npshannon-simpson.\n";
 		helpString += validCalculator.printCalc("single");
 		helpString += "The label parameter is used to analyze specific labels in your input.\n";
@@ -81,6 +81,45 @@ string CollectCommand::getHelpString(){
 	}
 }
 //**********************************************************************************************************************
+string CollectCommand::getOutputPattern(string type) {
+    try {
+        string pattern = "";
+        
+        if (type == "sobs")             {  pattern =  "[filename],sobs";            }
+        else if (type == "chao")        {  pattern =  "[filename],chao";            }
+        else if (type == "nseqs")       {  pattern =  "[filename],nseqs";           }
+        else if (type == "coverage")    {  pattern =  "[filename],coverage";        }
+        else if (type == "ace")         {  pattern =  "[filename],ace";             }
+        else if (type == "jack")        {  pattern =  "[filename],jack";            }
+        else if (type == "shannon")     {  pattern =  "[filename],shannon";         }
+        else if (type == "shannoneven") {  pattern =  "[filename],shannoneven";     }
+        else if (type == "npshannon")   {  pattern =  "[filename],npshannon";       }
+        else if (type == "heip")        {  pattern =  "[filename],heip";            }
+        else if (type == "smithwilson") {  pattern =  "[filename],smithwilson";     }
+        else if (type == "simpson")     {  pattern =  "[filename],simpson";         }
+        else if (type == "simpsoneven") {  pattern =  "[filename],simpsoneven";     }
+        else if (type == "invsimpson")  {  pattern =  "[filename],invsimpson";      }
+        else if (type == "bootstrap")   {  pattern =  "[filename],bootstrap";       }
+        else if (type == "geometric")   {  pattern =  "[filename],geometric";       }
+        else if (type == "qstat")       {  pattern =  "[filename],qstat";           }
+        else if (type == "logseries")   {  pattern =  "[filename],logseries";       }
+        else if (type == "bergerparker") {  pattern =  "[filename],bergerparker";   }
+        else if (type == "bstick")      {  pattern =  "[filename],bstick";          }
+        else if (type == "goodscoverage") {  pattern =  "[filename],goodscoverage"; }
+        else if (type == "efron")       {  pattern =  "[filename],efron";           }
+        else if (type == "boneh")       {  pattern =  "[filename],boneh";           }
+        else if (type == "solow")       {  pattern =  "[filename],solow";           }
+        else if (type == "shen")        {  pattern =  "[filename],shen";            }
+        else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true;  }
+        
+        return pattern;
+    }
+    catch(exception& e) {
+        m->errorOut(e, "CollectCommand", "getOutputPattern");
+        exit(1);
+    }
+}
+//**********************************************************************************************************************
 CollectCommand::CollectCommand(){	
 	try {
 		abort = true; calledHelp = true; 
@@ -94,7 +133,7 @@ CollectCommand::CollectCommand(){
 		outputTypes["jack"] = tempOutNames;
 		outputTypes["shannon"] = tempOutNames;
 		outputTypes["shannoneven"] = tempOutNames;
-		outputTypes["np_shannon"] = tempOutNames;
+		outputTypes["npshannon"] = tempOutNames;
 		outputTypes["heip"] = tempOutNames;
 		outputTypes["smithwilson"] = tempOutNames;
 		outputTypes["simpson"] = tempOutNames;
@@ -151,7 +190,7 @@ CollectCommand::CollectCommand(string option)  {
 			outputTypes["jack"] = tempOutNames;
 			outputTypes["shannon"] = tempOutNames;
 			outputTypes["shannoneven"] = tempOutNames;
-			outputTypes["np_shannon"] = tempOutNames;
+			outputTypes["npshannon"] = tempOutNames;
 			outputTypes["heip"] = tempOutNames;
 			outputTypes["smithwilson"] = tempOutNames;
 			outputTypes["simpson"] = tempOutNames;
@@ -211,22 +250,22 @@ CollectCommand::CollectCommand(string option)  {
 			listfile = validParameter.validFile(parameters, "list", true);
 			if (listfile == "not open") { listfile = ""; abort = true; }
 			else if (listfile == "not found") { listfile = ""; }
-			else {  format = "list"; inputfile = listfile; }
+			else {  format = "list"; inputfile = listfile; m->setListFile(listfile); }
 			
 			sabundfile = validParameter.validFile(parameters, "sabund", true);
 			if (sabundfile == "not open") { sabundfile = ""; abort = true; }	
 			else if (sabundfile == "not found") { sabundfile = ""; }
-			else {  format = "sabund"; inputfile = sabundfile; }
+			else {  format = "sabund"; inputfile = sabundfile; m->setSabundFile(sabundfile); }
 			
 			rabundfile = validParameter.validFile(parameters, "rabund", true);
 			if (rabundfile == "not open") { rabundfile = ""; abort = true; }	
 			else if (rabundfile == "not found") { rabundfile = ""; }
-			else {  format = "rabund"; inputfile = rabundfile; }
+			else {  format = "rabund"; inputfile = rabundfile; m->setRabundFile(rabundfile); }
 			
 			sharedfile = validParameter.validFile(parameters, "shared", true);
 			if (sharedfile == "not open") { sharedfile = ""; abort = true; }	
 			else if (sharedfile == "not found") { sharedfile = ""; }
-			else {  format = "sharedfile"; inputfile = sharedfile; }
+			else {  format = "sharedfile"; inputfile = sharedfile; m->setSharedFile(sharedfile); }
 			
 			
 			//if the user changes the output directory command factory will send this info to us in the output parameter 
@@ -280,13 +319,13 @@ CollectCommand::CollectCommand(string option)  {
 
 			string temp;
 			temp = validParameter.validFile(parameters, "freq", false);			if (temp == "not found") { temp = "100"; }
-			convert(temp, freq); 
+			m->mothurConvert(temp, freq); 
 			
 			temp = validParameter.validFile(parameters, "abund", false);		if (temp == "not found") { temp = "10"; }
-			convert(temp, abund); 
+			m->mothurConvert(temp, abund); 
 			
 			temp = validParameter.validFile(parameters, "size", false);			if (temp == "not found") { temp = "0"; }
-			convert(temp, size); 
+			m->mothurConvert(temp, size); 
 		}
 		
 	}
@@ -307,10 +346,12 @@ int CollectCommand::execute(){
 	
 		for (int p = 0; p < inputFileNames.size(); p++) {
 			
-			if (m->control_pressed) {  outputTypes.clear(); for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str()); 	}  m->Groups.clear();  return 0; }
+			if (m->control_pressed) {  outputTypes.clear(); for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]); 	}  m->clearGroups();  return 0; }
 			
 			if (outputDir == "") { outputDir += m->hasPath(inputFileNames[p]); }
 			string fileNameRoot = outputDir + m->getRootName(m->getSimpleName(inputFileNames[p]));
+            map<string, string> variables; 
+            variables["[filename]"] = fileNameRoot;
 			//globaldata->inputFileName = inputFileNames[p];
 		
 			if (inputFileNames.size() > 1) {
@@ -322,80 +363,80 @@ int CollectCommand::execute(){
 			for (int i=0; i<Estimators.size(); i++) {
 				if (validCalculator.isValidCalculator("single", Estimators[i]) == true) { 
 					if (Estimators[i] == "sobs") { 
-						cDisplays.push_back(new CollectDisplay(new Sobs(), new OneColumnFile(fileNameRoot+"sobs")));
-						outputNames.push_back(fileNameRoot+"sobs"); outputTypes["sobs"].push_back(fileNameRoot+"sobs");
+						cDisplays.push_back(new CollectDisplay(new Sobs(), new OneColumnFile(getOutputFileName("sobs", variables))));
+						outputNames.push_back(getOutputFileName("sobs", variables)); outputTypes["sobs"].push_back(getOutputFileName("sobs", variables));
 					}else if (Estimators[i] == "chao") { 
-						cDisplays.push_back(new CollectDisplay(new Chao1(), new ThreeColumnFile(fileNameRoot+"chao")));
-						outputNames.push_back(fileNameRoot+"chao"); outputTypes["chao"].push_back(fileNameRoot+"chao");
+						cDisplays.push_back(new CollectDisplay(new Chao1(), new ThreeColumnFile(getOutputFileName("chao", variables))));
+						outputNames.push_back(getOutputFileName("chao", variables)); outputTypes["chao"].push_back(getOutputFileName("chao", variables));
 					}else if (Estimators[i] == "nseqs") { 
-						cDisplays.push_back(new CollectDisplay(new NSeqs(), new OneColumnFile(fileNameRoot+"nseqs")));
-						outputNames.push_back(fileNameRoot+"nseqs"); outputTypes["nseqs"].push_back(fileNameRoot+"nseqs");
+						cDisplays.push_back(new CollectDisplay(new NSeqs(), new OneColumnFile(getOutputFileName("nseqs", variables))));
+						outputNames.push_back(getOutputFileName("nseqs", variables)); outputTypes["nseqs"].push_back(getOutputFileName("nseqs", variables));
 					}else if (Estimators[i] == "coverage") { 
-						cDisplays.push_back(new CollectDisplay(new Coverage(), new OneColumnFile(fileNameRoot+"coverage")));
-						outputNames.push_back(fileNameRoot+"coverage"); outputTypes["coverage"].push_back(fileNameRoot+"coverage");
+						cDisplays.push_back(new CollectDisplay(new Coverage(), new OneColumnFile(getOutputFileName("coverage", variables))));
+						outputNames.push_back(getOutputFileName("coverage", variables)); outputTypes["coverage"].push_back(getOutputFileName("coverage", variables));
 					}else if (Estimators[i] == "ace") { 
-						cDisplays.push_back(new CollectDisplay(new Ace(abund), new ThreeColumnFile(fileNameRoot+"ace")));
-						outputNames.push_back(fileNameRoot+"ace"); outputTypes["ace"].push_back(fileNameRoot+"ace");
+						cDisplays.push_back(new CollectDisplay(new Ace(abund), new ThreeColumnFile(getOutputFileName("ace", variables))));
+						outputNames.push_back(getOutputFileName("ace", variables)); outputTypes["ace"].push_back(getOutputFileName("ace", variables));
 					}else if (Estimators[i] == "jack") { 
-						cDisplays.push_back(new CollectDisplay(new Jackknife(), new ThreeColumnFile(fileNameRoot+"jack")));
-						outputNames.push_back(fileNameRoot+"jack"); outputTypes["jack"].push_back(fileNameRoot+"jack");
+						cDisplays.push_back(new CollectDisplay(new Jackknife(), new ThreeColumnFile(getOutputFileName("jack", variables))));
+						outputNames.push_back(getOutputFileName("jack", variables)); outputTypes["jack"].push_back(getOutputFileName("jack", variables));
 					}else if (Estimators[i] == "shannon") { 
-						cDisplays.push_back(new CollectDisplay(new Shannon(), new ThreeColumnFile(fileNameRoot+"shannon")));
-						outputNames.push_back(fileNameRoot+"shannon"); outputTypes["shannon"].push_back(fileNameRoot+"shannon");
+						cDisplays.push_back(new CollectDisplay(new Shannon(), new ThreeColumnFile(getOutputFileName("shannon", variables))));
+						outputNames.push_back(getOutputFileName("shannon", variables)); outputTypes["shannon"].push_back(getOutputFileName("shannon", variables));
 					}else if (Estimators[i] == "shannoneven") { 
-						cDisplays.push_back(new CollectDisplay(new ShannonEven(), new OneColumnFile(fileNameRoot+"shannoneven")));
-						outputNames.push_back(fileNameRoot+"shannoneven"); outputTypes["shannoneven"].push_back(fileNameRoot+"shannoneven");
+						cDisplays.push_back(new CollectDisplay(new ShannonEven(), new OneColumnFile(getOutputFileName("shannoneven", variables))));
+						outputNames.push_back(getOutputFileName("shannoneven", variables)); outputTypes["shannoneven"].push_back(getOutputFileName("shannoneven", variables));
 					}else if (Estimators[i] == "npshannon") { 
-						cDisplays.push_back(new CollectDisplay(new NPShannon(), new OneColumnFile(fileNameRoot+"np_shannon")));
-						outputNames.push_back(fileNameRoot+"np_shannon"); outputTypes["np_shannon"].push_back(fileNameRoot+"np_shannon");
+						cDisplays.push_back(new CollectDisplay(new NPShannon(), new OneColumnFile(getOutputFileName("npshannon", variables))));
+						outputNames.push_back(getOutputFileName("npshannon", variables)); outputTypes["npshannon"].push_back(getOutputFileName("npshannon", variables));
 					}else if (Estimators[i] == "heip") { 
-						cDisplays.push_back(new CollectDisplay(new Heip(), new OneColumnFile(fileNameRoot+"heip")));
-						outputNames.push_back(fileNameRoot+"heip"); outputTypes["heip"].push_back(fileNameRoot+"heip");
+						cDisplays.push_back(new CollectDisplay(new Heip(), new OneColumnFile(getOutputFileName("heip", variables))));
+						outputNames.push_back(getOutputFileName("heip", variables)); outputTypes["heip"].push_back(getOutputFileName("heip", variables));
 					}else if (Estimators[i] == "smithwilson") { 
-						cDisplays.push_back(new CollectDisplay(new SmithWilson(), new OneColumnFile(fileNameRoot+"smithwilson")));
-						outputNames.push_back(fileNameRoot+"smithwilson"); outputTypes["smithwilson"].push_back(fileNameRoot+"smithwilson");
+						cDisplays.push_back(new CollectDisplay(new SmithWilson(), new OneColumnFile(getOutputFileName("smithwilson", variables))));
+						outputNames.push_back(getOutputFileName("smithwilson", variables)); outputTypes["smithwilson"].push_back(getOutputFileName("smithwilson", variables));
 					}else if (Estimators[i] == "simpson") { 
-						cDisplays.push_back(new CollectDisplay(new Simpson(), new ThreeColumnFile(fileNameRoot+"simpson")));
-						outputNames.push_back(fileNameRoot+"simpson"); outputTypes["simpson"].push_back(fileNameRoot+"simpson");
+						cDisplays.push_back(new CollectDisplay(new Simpson(), new ThreeColumnFile(getOutputFileName("simpson", variables))));
+						outputNames.push_back(getOutputFileName("simpson", variables)); outputTypes["simpson"].push_back(getOutputFileName("simpson", variables));
 					}else if (Estimators[i] == "simpsoneven") { 
-						cDisplays.push_back(new CollectDisplay(new SimpsonEven(), new OneColumnFile(fileNameRoot+"simpsoneven")));
-						outputNames.push_back(fileNameRoot+"simpsoneven"); outputTypes["simpsoneven"].push_back(fileNameRoot+"simpsoneven");
+						cDisplays.push_back(new CollectDisplay(new SimpsonEven(), new OneColumnFile(getOutputFileName("simpsoneven", variables))));
+						outputNames.push_back(getOutputFileName("simpsoneven", variables)); outputTypes["simpsoneven"].push_back(getOutputFileName("simpsoneven", variables));
 					}else if (Estimators[i] == "invsimpson") { 
-						cDisplays.push_back(new CollectDisplay(new InvSimpson(), new ThreeColumnFile(fileNameRoot+"invsimpson")));
-						outputNames.push_back(fileNameRoot+"invsimpson"); outputTypes["invsimpson"].push_back(fileNameRoot+"invsimpson");
+						cDisplays.push_back(new CollectDisplay(new InvSimpson(), new ThreeColumnFile(getOutputFileName("invsimpson", variables))));
+						outputNames.push_back(getOutputFileName("invsimpson", variables)); outputTypes["invsimpson"].push_back(getOutputFileName("invsimpson", variables));
 					}else if (Estimators[i] == "bootstrap") { 
-						cDisplays.push_back(new CollectDisplay(new Bootstrap(), new OneColumnFile(fileNameRoot+"bootstrap")));
-						outputNames.push_back(fileNameRoot+"bootstrap"); outputTypes["bootstrap"].push_back(fileNameRoot+"bootstrap");
+						cDisplays.push_back(new CollectDisplay(new Bootstrap(), new OneColumnFile(getOutputFileName("bootstrap", variables))));
+						outputNames.push_back(getOutputFileName("bootstrap", variables)); outputTypes["bootstrap"].push_back(getOutputFileName("bootstrap", variables));
 					}else if (Estimators[i] == "geometric") { 
-						cDisplays.push_back(new CollectDisplay(new Geom(), new OneColumnFile(fileNameRoot+"geometric")));
-						outputNames.push_back(fileNameRoot+"geometric"); outputTypes["geometric"].push_back(fileNameRoot+"geometric");
+						cDisplays.push_back(new CollectDisplay(new Geom(), new OneColumnFile(getOutputFileName("geometric", variables))));
+						outputNames.push_back(getOutputFileName("geometric", variables)); outputTypes["geometric"].push_back(getOutputFileName("geometric", variables));
 					}else if (Estimators[i] == "qstat") { 
-						cDisplays.push_back(new CollectDisplay(new QStat(), new OneColumnFile(fileNameRoot+"qstat")));
-						outputNames.push_back(fileNameRoot+"qstat"); outputTypes["qstat"].push_back(fileNameRoot+"qstat");
+						cDisplays.push_back(new CollectDisplay(new QStat(), new OneColumnFile(getOutputFileName("qstat", variables))));
+						outputNames.push_back(getOutputFileName("qstat", variables)); outputTypes["qstat"].push_back(getOutputFileName("qstat", variables));
 					}else if (Estimators[i] == "logseries") { 
-						cDisplays.push_back(new CollectDisplay(new LogSD(), new OneColumnFile(fileNameRoot+"logseries")));
-						outputNames.push_back(fileNameRoot+"logseries"); outputTypes["logseries"].push_back(fileNameRoot+"logseries");
+						cDisplays.push_back(new CollectDisplay(new LogSD(), new OneColumnFile(getOutputFileName("logseries", variables))));
+						outputNames.push_back(getOutputFileName("logseries", variables)); outputTypes["logseries"].push_back(getOutputFileName("logseries", variables));
 					}else if (Estimators[i] == "bergerparker") { 
-						cDisplays.push_back(new CollectDisplay(new BergerParker(), new OneColumnFile(fileNameRoot+"bergerparker")));
-						outputNames.push_back(fileNameRoot+"bergerparker"); outputTypes["bergerparker"].push_back(fileNameRoot+"bergerparker");
+						cDisplays.push_back(new CollectDisplay(new BergerParker(), new OneColumnFile(getOutputFileName("bergerparker", variables))));
+						outputNames.push_back(getOutputFileName("bergerparker", variables)); outputTypes["bergerparker"].push_back(getOutputFileName("bergerparker", variables));
 					}else if (Estimators[i] == "bstick") { 
-						cDisplays.push_back(new CollectDisplay(new BStick(), new ThreeColumnFile(fileNameRoot+"bstick")));
-						outputNames.push_back(fileNameRoot+"bstick"); outputTypes["bstick"].push_back(fileNameRoot+"bstick");
+						cDisplays.push_back(new CollectDisplay(new BStick(), new ThreeColumnFile(getOutputFileName("bstick", variables))));
+						outputNames.push_back(getOutputFileName("bstick", variables)); outputTypes["bstick"].push_back(getOutputFileName("bstick", variables));
 					}else if (Estimators[i] == "goodscoverage") { 
-						cDisplays.push_back(new CollectDisplay(new GoodsCoverage(), new OneColumnFile(fileNameRoot+"goodscoverage")));
-						outputNames.push_back(fileNameRoot+"goodscoverage"); outputTypes["goodscoverage"].push_back(fileNameRoot+"goodscoverage");
+						cDisplays.push_back(new CollectDisplay(new GoodsCoverage(), new OneColumnFile(getOutputFileName("goodscoverage", variables))));
+						outputNames.push_back(getOutputFileName("goodscoverage", variables)); outputTypes["goodscoverage"].push_back(getOutputFileName("goodscoverage", variables));
 					}else if (Estimators[i] == "efron") {
-						cDisplays.push_back(new CollectDisplay(new Efron(size), new OneColumnFile(fileNameRoot+"efron")));
-						outputNames.push_back(fileNameRoot+"efron"); outputTypes["efron"].push_back(fileNameRoot+"efron");
+						cDisplays.push_back(new CollectDisplay(new Efron(size), new OneColumnFile(getOutputFileName("efron", variables))));
+						outputNames.push_back(getOutputFileName("efron", variables)); outputTypes["efron"].push_back(getOutputFileName("efron", variables));
 					}else if (Estimators[i] == "boneh") {
-						cDisplays.push_back(new CollectDisplay(new Boneh(size), new OneColumnFile(fileNameRoot+"boneh")));
-						outputNames.push_back(fileNameRoot+"boneh"); outputTypes["boneh"].push_back(fileNameRoot+"boneh");
+						cDisplays.push_back(new CollectDisplay(new Boneh(size), new OneColumnFile(getOutputFileName("boneh", variables))));
+						outputNames.push_back(getOutputFileName("boneh", variables)); outputTypes["boneh"].push_back(getOutputFileName("boneh", variables));
 					}else if (Estimators[i] == "solow") {
-						cDisplays.push_back(new CollectDisplay(new Solow(size), new OneColumnFile(fileNameRoot+"solow")));
-						outputNames.push_back(fileNameRoot+"solow"); outputTypes["solow"].push_back(fileNameRoot+"solow");
+						cDisplays.push_back(new CollectDisplay(new Solow(size), new OneColumnFile(getOutputFileName("solow", variables))));
+						outputNames.push_back(getOutputFileName("solow", variables)); outputTypes["solow"].push_back(getOutputFileName("solow", variables));
 					}else if (Estimators[i] == "shen") {
-						cDisplays.push_back(new CollectDisplay(new Shen(size, abund), new OneColumnFile(fileNameRoot+"shen")));
-						outputNames.push_back(fileNameRoot+"shen"); outputTypes["shen"].push_back(fileNameRoot+"shen");
+						cDisplays.push_back(new CollectDisplay(new Shen(size, abund), new OneColumnFile(getOutputFileName("shen", variables))));
+						outputNames.push_back(getOutputFileName("shen", variables)); outputTypes["shen"].push_back(getOutputFileName("shen", variables));
 					}
 				}
 			}
@@ -413,10 +454,10 @@ int CollectCommand::execute(){
 			
 			if (m->control_pressed) {  
 				for(int i=0;i<cDisplays.size();i++){	delete cDisplays[i];	}
-				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(); 
 				delete input;  
 				delete order; 
-				m->Groups.clear();
+				m->clearGroups();
 				return 0;
 			}
 
@@ -425,10 +466,10 @@ int CollectCommand::execute(){
 			
 				if (m->control_pressed) { 
 					for(int i=0;i<cDisplays.size();i++){	delete cDisplays[i];	}
-					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(); 
 					delete input;  
 					delete order; 
-					m->Groups.clear();
+					m->clearGroups();
 					return 0;
 				}
 
@@ -474,9 +515,9 @@ int CollectCommand::execute(){
 			
 			if (m->control_pressed) { 
 					for(int i=0;i<cDisplays.size();i++){	delete cDisplays[i];	}
-					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(); 
 					delete input;  
-					m->Groups.clear();
+					m->clearGroups();
 					return 0;
 			}
 				
@@ -506,10 +547,10 @@ int CollectCommand::execute(){
 				
 				if (m->control_pressed) { 
 					for(int i=0;i<cDisplays.size();i++){	delete cDisplays[i];	}
-					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(); 
 					delete input;  
 					delete order;
-					m->Groups.clear();
+					m->clearGroups();
 					return 0;
 				}
 				delete order;
@@ -520,7 +561,7 @@ int CollectCommand::execute(){
 			delete input;  
 		}
 		
-		if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str()); 	} return 0; }
+		if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]); 	} return 0; }
 				
 		m->mothurOutEndLine();
 		m->mothurOut("Output File Names: "); m->mothurOutEndLine();
@@ -551,7 +592,7 @@ vector<string> CollectCommand::parseSharedFile(string filename) {
 		
 		//clears file before we start to write to it below
 		for (int i=0; i<lookup.size(); i++) {
-			remove((sharedFileRoot + lookup[i]->getGroup() + ".rabund").c_str());
+			m->mothurRemove((sharedFileRoot + lookup[i]->getGroup() + ".rabund"));
 			filenames.push_back((sharedFileRoot + lookup[i]->getGroup() + ".rabund"));
 		}