X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=collectsharedcommand.cpp;h=56e60d88bc88200a1b21d82d70b4a9c1f22ebdef;hp=b9b3606cd9318dd1fe1f3d32834dfc9c29e451f6;hb=a2cde58c1e72199498a2142983ef040dce36da10;hpb=e150b0b0664caec517485ee6d69dcdade6dcae77

diff --git a/collectsharedcommand.cpp b/collectsharedcommand.cpp
index b9b3606..56e60d8 100644
--- a/collectsharedcommand.cpp
+++ b/collectsharedcommand.cpp
@@ -49,19 +49,20 @@
 #include "memchord.h"
 #include "memeuclidean.h"
 #include "mempearson.h"
+#include "sharedjsd.h"
 
 
 //**********************************************************************************************************************
 vector<string> CollectSharedCommand::setParameters(){	
 	try {
-		CommandParameter pshared("shared", "InputTypes", "", "", "none", "none", "none",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", "sharedchao-sharedsobs-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan-kstest-whittaker-sharednseqs-ochiai-anderberg-skulczynski-kulczynskicody-lennon-morisitahorn-braycurtis-odum-canberra-structeuclidean-structchord-hellinger-manhattan-structpearson-soergel-spearman-structkulczynski-speciesprofile-structchi2-hamming-gower-memchi2-memchord-memeuclidean-mempearson", "sharedsobs-sharedchao-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan", "", "", "",true,false); parameters.push_back(pcalc);
-		CommandParameter pall("all", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pall);
-		CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
-		CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
-		CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+		CommandParameter pshared("shared", "InputTypes", "", "", "none", "none", "none","",false,true,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", "sharedchao-sharedsobs-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan-kstest-whittaker-sharednseqs-ochiai-anderberg-kulczynski-kulczynskicody-lennon-morisitahorn-braycurtis-odum-canberra-structeuclidean-structchord-hellinger-manhattan-structpearson-soergel-spearman-structkulczynski-speciesprofile-structchi2-hamming-gower-memchi2-memchord-memeuclidean-mempearson-jsd", "sharedsobs-sharedchao-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan", "", "", "","",true,false,true); parameters.push_back(pcalc);
+		CommandParameter pall("all", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pall);
+		CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups);
+		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);		}
@@ -89,7 +90,7 @@ string CollectSharedCommand::getHelpString(){
 		helpString += "The all parameter is used to specify if you want the estimate of all your groups together.  This estimate can only be made for sharedsobs and sharedchao calculators. The default is false.\n";
 		helpString += "If you use sharedchao and run into memory issues, set all to false. \n";
 		helpString += "The groups parameter allows you to specify which of the groups in your groupfile you would like analyzed.  You must enter at least 2 valid groups.\n";
-		helpString += "Note: No spaces between parameter labels (i.e. list), '=' and parameters (i.e.yourListfile).\n";
+		helpString += "Note: No spaces between parameter labels (i.e. shared), '=' and parameters (i.e.yourSharedfile).\n";
 		return helpString;
 	}
 	catch(exception& e) {
@@ -97,6 +98,61 @@ string CollectSharedCommand::getHelpString(){
 		exit(1);
 	}
 }
+//**********************************************************************************************************************
+string CollectSharedCommand::getOutputPattern(string type) {
+    try {
+        string pattern = "";
+        
+        if (type == "sharedchao")               {  pattern =  "[filename],shared.chao";     }
+        else if (type == "sharedsobs")          {  pattern =  "[filename],shared.sobs";     }
+        else if (type == "sharedace")           {  pattern =  "[filename],shared.ace";      }
+        else if (type == "jabund")              {  pattern =  "[filename],jabund";          }
+        else if (type == "sorabund")            {  pattern =  "[filename],sorabund";        }
+        else if (type == "jclass")              {  pattern =  "[filename],jclass";          }
+        else if (type == "sorclass")            {  pattern =  "[filename],sorclass";        }
+        else if (type == "jest")                {  pattern =  "[filename],jest";            }
+        else if (type == "sorest")              {  pattern =  "[filename],sorest";          }
+        else if (type == "thetayc")             {  pattern =  "[filename],thetayc";         }
+        else if (type == "thetan")              {  pattern =  "[filename],thetan";          }
+        else if (type == "kstest")              {  pattern =  "[filename],kstest";          }
+        else if (type == "whittaker")           {  pattern =  "[filename],whittaker";       }
+        else if (type == "sharednseqs")         {  pattern =  "[filename],shared.nseqs";    }
+        else if (type == "ochiai")              {  pattern =  "[filename],ochiai";          }
+        else if (type == "anderberg")           {  pattern =  "[filename],anderberg";       }
+        else if (type == "kulczynski")          {  pattern =  "[filename],kulczynski";      }
+        else if (type == "kulczynskicody")      {  pattern =  "[filename],kulczynskicody";  }
+        else if (type == "lennon")              {  pattern =  "[filename],lennon";          }
+        else if (type == "morisitahorn")        {  pattern =  "[filename],morisitahorn";    }
+        else if (type == "braycurtis")          {  pattern =  "[filename],braycurtis";      }
+        else if (type == "odum")                {  pattern =  "[filename],odum";            }
+        else if (type == "canberra")            {  pattern =  "[filename],canberra";        }
+        else if (type == "structeuclidean")     {  pattern =  "[filename],structeuclidean"; }
+        else if (type == "structchord")         {  pattern =  "[filename],structchord";     }
+        else if (type == "hellinger")           {  pattern =  "[filename],hellinger";       }
+        else if (type == "manhattan")           {  pattern =  "[filename],manhattan";       }
+        else if (type == "structpearson")       {  pattern =  "[filename],structpearson";   }
+        else if (type == "soergel")             {  pattern =  "[filename],soergel";         }
+        else if (type == "spearman")            {  pattern =  "[filename],spearman";        }
+        else if (type == "structkulczynski")    {  pattern =  "[filename],structkulczynski";}
+        else if (type == "structchi2")          {  pattern =  "[filename],structchi2";      }
+        else if (type == "speciesprofile")      {  pattern =  "[filename],speciesprofile";  }
+        else if (type == "hamming")             {  pattern =  "[filename],hamming";         }
+        else if (type == "gower")               {  pattern =  "[filename],gower";           }
+        else if (type == "memchi2")             {  pattern =  "[filename],memchi2";         }
+        else if (type == "memchord")            {  pattern =  "[filename],memchord";        }
+        else if (type == "memeuclidean")        {  pattern =  "[filename],memeuclidean";    }
+        else if (type == "mempearson")          {  pattern =  "[filename],mempearson";      }
+        else if (type == "jsd")                 {  pattern =  "[filename],jsd";             }
+        else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true;  }
+        
+        return pattern;
+    }
+    catch(exception& e) {
+        m->errorOut(e, "CollectSharedCommand", "getOutputPattern");
+        exit(1);
+    }
+}
+
 //**********************************************************************************************************************
 CollectSharedCommand::CollectSharedCommand(){	
 	try {
@@ -119,7 +175,7 @@ CollectSharedCommand::CollectSharedCommand(){
 		outputTypes["sharednseqs"] = tempOutNames;
 		outputTypes["ochiai"] = tempOutNames;
 		outputTypes["anderberg"] = tempOutNames;
-		outputTypes["skulczynski"] = tempOutNames;
+		outputTypes["kulczynski"] = tempOutNames;
 		outputTypes["kulczynskicody"] = tempOutNames;
 		outputTypes["lennon"] = tempOutNames;
 		outputTypes["morisitahorn"] = tempOutNames;
@@ -142,6 +198,7 @@ CollectSharedCommand::CollectSharedCommand(){
 		outputTypes["memchord"] = tempOutNames;
 		outputTypes["memeuclidean"] = tempOutNames;
 		outputTypes["mempearson"] = tempOutNames;
+        outputTypes["jsd"] = tempOutNames;
 		
 	}
 	catch(exception& e) {
@@ -191,7 +248,7 @@ CollectSharedCommand::CollectSharedCommand(string option)  {
 			outputTypes["sharednseqs"] = tempOutNames;
 			outputTypes["ochiai"] = tempOutNames;
 			outputTypes["anderberg"] = tempOutNames;
-			outputTypes["skulczynski"] = tempOutNames;
+			outputTypes["kulczynski"] = tempOutNames;
 			outputTypes["kulczynskicody"] = tempOutNames;
 			outputTypes["lennon"] = tempOutNames;
 			outputTypes["morisitahorn"] = tempOutNames;
@@ -214,6 +271,7 @@ CollectSharedCommand::CollectSharedCommand(string option)  {
 			outputTypes["memchord"] = tempOutNames;
 			outputTypes["memeuclidean"] = tempOutNames;
 			outputTypes["mempearson"] = tempOutNames;
+            outputTypes["jsd"] = tempOutNames;
 			
 			
 			//if the user changes the input directory command factory will send this info to us in the output parameter 
@@ -238,7 +296,7 @@ CollectSharedCommand::CollectSharedCommand(string option)  {
 				sharedfile = m->getSharedFile(); 
 				if (sharedfile != "") { m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
 				else { 	m->mothurOut("You have no current sharedfile and the shared parameter is required."); m->mothurOutEndLine(); abort = true; }
-			}
+			}else { m->setSharedFile(sharedfile); }
 			
 			
 			//if the user changes the output directory command factory will send this info to us in the output parameter 
@@ -259,17 +317,22 @@ CollectSharedCommand::CollectSharedCommand(string option)  {
 				 if (calc == "default")  {  calc = "sharedsobs-sharedchao-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan";  }
 			}
 			m->splitAtDash(calc, Estimators);
+			if (m->inUsersGroups("citation", Estimators)) { 
+				ValidCalculators validCalc; validCalc.printCitations(Estimators); 
+				//remove citation from list of calcs
+				for (int i = 0; i < Estimators.size(); i++) { if (Estimators[i] == "citation") {  Estimators.erase(Estimators.begin()+i); break; } }
+			}
 			
 			groups = validParameter.validFile(parameters, "groups", false);			
 			if (groups == "not found") { groups = ""; }
 			else { 
 				m->splitAtDash(groups, Groups);
 			}
-			m->Groups = Groups;
+			m->setGroups(Groups);
 			
 			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, "all", false);				if (temp == "not found") { temp = "false"; }
 			all = m->isTrue(temp);
@@ -277,128 +340,133 @@ CollectSharedCommand::CollectSharedCommand(string option)  {
 			if (abort == false) {
 				
 				string fileNameRoot = outputDir + m->getRootName(m->getSimpleName(sharedfile));
-				
+				map<string, string> variables; 
+                variables["[filename]"] = fileNameRoot;
+                
 				ValidCalculators validCalculator;
 				
 				for (int i=0; i<Estimators.size(); i++) {
 					if (validCalculator.isValidCalculator("shared", Estimators[i]) == true) { 
 						if (Estimators[i] == "sharedchao") { 
-							cDisplays.push_back(new CollectDisplay(new SharedChao1(), new SharedOneColumnFile(fileNameRoot+"shared.chao")));
-							outputNames.push_back(fileNameRoot+"shared.chao"); outputTypes["sharedchao"].push_back(fileNameRoot+"shared.chao");
+							cDisplays.push_back(new CollectDisplay(new SharedChao1(), new SharedOneColumnFile(getOutputFileName("sharedchao", variables))));
+							outputNames.push_back(getOutputFileName("sharedchao", variables)); outputTypes["sharedchao"].push_back(getOutputFileName("sharedchao", variables));
 						}else if (Estimators[i] == "sharedsobs") { 
-							cDisplays.push_back(new CollectDisplay(new SharedSobsCS(), new SharedOneColumnFile(fileNameRoot+"shared.sobs")));
-							outputNames.push_back(fileNameRoot+"shared.sobs"); outputTypes["sharedsobs"].push_back(fileNameRoot+"shared.sobs");
+							cDisplays.push_back(new CollectDisplay(new SharedSobsCS(), new SharedOneColumnFile(getOutputFileName("sharedsobs", variables))));
+							outputNames.push_back(getOutputFileName("sharedsobs", variables)); outputTypes["sharedsobs"].push_back(getOutputFileName("sharedsobs", variables));
 						}else if (Estimators[i] == "sharedace") { 
-							cDisplays.push_back(new CollectDisplay(new SharedAce(), new SharedOneColumnFile(fileNameRoot+"shared.ace")));
-							outputNames.push_back(fileNameRoot+"shared.ace"); outputTypes["sharedace"].push_back(fileNameRoot+"shared.ace");
+							cDisplays.push_back(new CollectDisplay(new SharedAce(), new SharedOneColumnFile(getOutputFileName("sharedace", variables))));
+							outputNames.push_back(getOutputFileName("sharedace", variables)); outputTypes["sharedace"].push_back(getOutputFileName("sharedace", variables));
 						}else if (Estimators[i] == "jabund") { 	
-							cDisplays.push_back(new CollectDisplay(new JAbund(), new SharedOneColumnFile(fileNameRoot+"jabund")));
-							outputNames.push_back(fileNameRoot+"jabund"); outputTypes["jabund"].push_back(fileNameRoot+"jabund");
+							cDisplays.push_back(new CollectDisplay(new JAbund(), new SharedOneColumnFile(getOutputFileName("jabund", variables))));
+							outputNames.push_back(getOutputFileName("jabund", variables)); outputTypes["jabund"].push_back(getOutputFileName("jabund", variables));
 						}else if (Estimators[i] == "sorabund") { 
-							cDisplays.push_back(new CollectDisplay(new SorAbund(), new SharedOneColumnFile(fileNameRoot+"sorabund")));
-							outputNames.push_back(fileNameRoot+"sorabund"); outputTypes["sorabund"].push_back(fileNameRoot+"sorabund");
+							cDisplays.push_back(new CollectDisplay(new SorAbund(), new SharedOneColumnFile(getOutputFileName("sorabund", variables))));
+							outputNames.push_back(getOutputFileName("sorabund", variables)); outputTypes["sorabund"].push_back(getOutputFileName("sorabund", variables));
 						}else if (Estimators[i] == "jclass") { 
-							cDisplays.push_back(new CollectDisplay(new Jclass(), new SharedOneColumnFile(fileNameRoot+"jclass")));
-							outputNames.push_back(fileNameRoot+"jclass"); outputTypes["jclass"].push_back(fileNameRoot+"jclass");
+							cDisplays.push_back(new CollectDisplay(new Jclass(), new SharedOneColumnFile(getOutputFileName("jclass", variables))));
+							outputNames.push_back(getOutputFileName("jclass", variables)); outputTypes["jclass"].push_back(getOutputFileName("jclass", variables));
 						}else if (Estimators[i] == "sorclass") { 
-							cDisplays.push_back(new CollectDisplay(new SorClass(), new SharedOneColumnFile(fileNameRoot+"sorclass")));
-							outputNames.push_back(fileNameRoot+"sorclass"); outputTypes["sorclass"].push_back(fileNameRoot+"sorclass");
+							cDisplays.push_back(new CollectDisplay(new SorClass(), new SharedOneColumnFile(getOutputFileName("sorclass", variables))));
+							outputNames.push_back(getOutputFileName("sorclass", variables)); outputTypes["sorclass"].push_back(getOutputFileName("sorclass", variables));
 						}else if (Estimators[i] == "jest") { 
-							cDisplays.push_back(new CollectDisplay(new Jest(), new SharedOneColumnFile(fileNameRoot+"jest")));
-							outputNames.push_back(fileNameRoot+"jest"); outputTypes["jest"].push_back(fileNameRoot+"jest");
+							cDisplays.push_back(new CollectDisplay(new Jest(), new SharedOneColumnFile(getOutputFileName("jest", variables))));
+							outputNames.push_back(getOutputFileName("jest", variables)); outputTypes["jest"].push_back(getOutputFileName("jest", variables));
 						}else if (Estimators[i] == "sorest") { 
-							cDisplays.push_back(new CollectDisplay(new SorEst(), new SharedOneColumnFile(fileNameRoot+"sorest")));
-							outputNames.push_back(fileNameRoot+"sorest"); outputTypes["sorest"].push_back(fileNameRoot+"sorest");
+							cDisplays.push_back(new CollectDisplay(new SorEst(), new SharedOneColumnFile(getOutputFileName("sorest", variables))));
+							outputNames.push_back(getOutputFileName("sorest", variables)); outputTypes["sorest"].push_back(getOutputFileName("sorest", variables));
 						}else if (Estimators[i] == "thetayc") { 
-							cDisplays.push_back(new CollectDisplay(new ThetaYC(), new SharedOneColumnFile(fileNameRoot+"thetayc")));
-							outputNames.push_back(fileNameRoot+"thetayc"); outputTypes["thetayc"].push_back(fileNameRoot+"thetayc");
+							cDisplays.push_back(new CollectDisplay(new ThetaYC(), new SharedOneColumnFile(getOutputFileName("thetayc", variables))));
+							outputNames.push_back(getOutputFileName("thetayc", variables)); outputTypes["thetayc"].push_back(getOutputFileName("thetayc", variables));
 						}else if (Estimators[i] == "thetan") { 
-							cDisplays.push_back(new CollectDisplay(new ThetaN(), new SharedOneColumnFile(fileNameRoot+"thetan")));
-							outputNames.push_back(fileNameRoot+"thetan"); outputTypes["thetan"].push_back(fileNameRoot+"thetan");
+							cDisplays.push_back(new CollectDisplay(new ThetaN(), new SharedOneColumnFile(getOutputFileName("thetan", variables))));
+							outputNames.push_back(getOutputFileName("thetan", variables)); outputTypes["thetan"].push_back(getOutputFileName("thetan", variables));
 						}else if (Estimators[i] == "kstest") { 
-							cDisplays.push_back(new CollectDisplay(new KSTest(), new SharedOneColumnFile(fileNameRoot+"kstest")));
-							outputNames.push_back(fileNameRoot+"kstest"); outputTypes["kstest"].push_back(fileNameRoot+"kstest");
+							cDisplays.push_back(new CollectDisplay(new KSTest(), new SharedOneColumnFile(getOutputFileName("kstest", variables))));
+							outputNames.push_back(getOutputFileName("kstest", variables)); outputTypes["kstest"].push_back(getOutputFileName("kstest", variables));
 						}else if (Estimators[i] == "whittaker") { 
-							cDisplays.push_back(new CollectDisplay(new Whittaker(), new SharedOneColumnFile(fileNameRoot+"whittaker")));
-							outputNames.push_back(fileNameRoot+"whittaker"); outputTypes["whittaker"].push_back(fileNameRoot+"whittaker");
+							cDisplays.push_back(new CollectDisplay(new Whittaker(), new SharedOneColumnFile(getOutputFileName("whittaker", variables))));
+							outputNames.push_back(getOutputFileName("whittaker", variables)); outputTypes["whittaker"].push_back(getOutputFileName("whittaker", variables));
 						}else if (Estimators[i] == "sharednseqs") { 
-							cDisplays.push_back(new CollectDisplay(new SharedNSeqs(), new SharedOneColumnFile(fileNameRoot+"shared.nseqs")));
-							outputNames.push_back(fileNameRoot+"shared.nseqs"); outputTypes["shared.nseqs"].push_back(fileNameRoot+"shared.nseqs");
+							cDisplays.push_back(new CollectDisplay(new SharedNSeqs(), new SharedOneColumnFile(getOutputFileName("sharednseqs", variables))));
+							outputNames.push_back(getOutputFileName("sharednseqs", variables)); outputTypes["shared.nseqs"].push_back(getOutputFileName("sharednseqs", variables));
 						}else if (Estimators[i] == "ochiai") { 
-							cDisplays.push_back(new CollectDisplay(new Ochiai(), new SharedOneColumnFile(fileNameRoot+"ochiai")));
-							outputNames.push_back(fileNameRoot+"ochiai"); outputTypes["ochiai"].push_back(fileNameRoot+"ochiai");
+							cDisplays.push_back(new CollectDisplay(new Ochiai(), new SharedOneColumnFile(getOutputFileName("ochiai", variables))));
+							outputNames.push_back(getOutputFileName("ochiai", variables)); outputTypes["ochiai"].push_back(getOutputFileName("ochiai", variables));
 						}else if (Estimators[i] == "anderberg") { 
-							cDisplays.push_back(new CollectDisplay(new Anderberg(), new SharedOneColumnFile(fileNameRoot+"anderberg")));
-							outputNames.push_back(fileNameRoot+"anderberg"); outputTypes["anderberg"].push_back(fileNameRoot+"anderberg");
-						}else if (Estimators[i] == "skulczynski") { 
-							cDisplays.push_back(new CollectDisplay(new Kulczynski(), new SharedOneColumnFile(fileNameRoot+"kulczynski")));
-							outputNames.push_back(fileNameRoot+"kulczynski"); outputTypes["kulczynski"].push_back(fileNameRoot+"kulczynski");
+							cDisplays.push_back(new CollectDisplay(new Anderberg(), new SharedOneColumnFile(getOutputFileName("anderberg", variables))));
+							outputNames.push_back(getOutputFileName("anderberg", variables)); outputTypes["anderberg"].push_back(getOutputFileName("anderberg", variables));
+						}else if (Estimators[i] == "kulczynski") { 
+							cDisplays.push_back(new CollectDisplay(new Kulczynski(), new SharedOneColumnFile(getOutputFileName("kulczynski", variables))));
+							outputNames.push_back(getOutputFileName("kulczynski", variables)); outputTypes["kulczynski"].push_back(getOutputFileName("kulczynski", variables));
 						}else if (Estimators[i] == "kulczynskicody") { 
-							cDisplays.push_back(new CollectDisplay(new KulczynskiCody(), new SharedOneColumnFile(fileNameRoot+"kulczynskicody")));
-							outputNames.push_back(fileNameRoot+"kulczynskicody"); outputTypes["kulczynskicody"].push_back(fileNameRoot+"kulczynskicody");
+							cDisplays.push_back(new CollectDisplay(new KulczynskiCody(), new SharedOneColumnFile(getOutputFileName("kulczynskicody", variables))));
+							outputNames.push_back(getOutputFileName("kulczynskicody", variables)); outputTypes["kulczynskicody"].push_back(getOutputFileName("kulczynskicody", variables));
 						}else if (Estimators[i] == "lennon") { 
-							cDisplays.push_back(new CollectDisplay(new Lennon(), new SharedOneColumnFile(fileNameRoot+"lennon")));
-							outputNames.push_back(fileNameRoot+"lennon"); outputTypes["lennon"].push_back(fileNameRoot+"lennon");
+							cDisplays.push_back(new CollectDisplay(new Lennon(), new SharedOneColumnFile(getOutputFileName("lennon", variables))));
+							outputNames.push_back(getOutputFileName("lennon", variables)); outputTypes["lennon"].push_back(getOutputFileName("lennon", variables));
 						}else if (Estimators[i] == "morisitahorn") { 
-							cDisplays.push_back(new CollectDisplay(new MorHorn(), new SharedOneColumnFile(fileNameRoot+"morisitahorn")));
-							outputNames.push_back(fileNameRoot+"morisitahorn"); outputTypes["morisitahorn"].push_back(fileNameRoot+"morisitahorn");
+							cDisplays.push_back(new CollectDisplay(new MorHorn(), new SharedOneColumnFile(getOutputFileName("morisitahorn", variables))));
+							outputNames.push_back(getOutputFileName("morisitahorn", variables)); outputTypes["morisitahorn"].push_back(getOutputFileName("morisitahorn", variables));
 						}else if (Estimators[i] == "braycurtis") { 
-							cDisplays.push_back(new CollectDisplay(new BrayCurtis(), new SharedOneColumnFile(fileNameRoot+"braycurtis")));
-							outputNames.push_back(fileNameRoot+"braycurtis"); outputTypes["braycurtis"].push_back(fileNameRoot+"braycurtis");
+							cDisplays.push_back(new CollectDisplay(new BrayCurtis(), new SharedOneColumnFile(getOutputFileName("braycurtis", variables))));
+							outputNames.push_back(getOutputFileName("braycurtis", variables)); outputTypes["braycurtis"].push_back(getOutputFileName("braycurtis", variables));
 						}else if (Estimators[i] == "odum") { 
-							cDisplays.push_back(new CollectDisplay(new Odum(), new SharedOneColumnFile(fileNameRoot+"odum")));
-							outputNames.push_back(fileNameRoot+"odum"); outputTypes["odum"].push_back(fileNameRoot+"odum");
+							cDisplays.push_back(new CollectDisplay(new Odum(), new SharedOneColumnFile(getOutputFileName("odum", variables))));
+							outputNames.push_back(getOutputFileName("odum", variables)); outputTypes["odum"].push_back(getOutputFileName("odum", variables));
 						}else if (Estimators[i] == "canberra") { 
-							cDisplays.push_back(new CollectDisplay(new Canberra(), new SharedOneColumnFile(fileNameRoot+"canberra")));
-							outputNames.push_back(fileNameRoot+"canberra"); outputTypes["canberra"].push_back(fileNameRoot+"canberra");
+							cDisplays.push_back(new CollectDisplay(new Canberra(), new SharedOneColumnFile(getOutputFileName("canberra", variables))));
+							outputNames.push_back(getOutputFileName("canberra", variables)); outputTypes["canberra"].push_back(getOutputFileName("canberra", variables));
 						}else if (Estimators[i] == "structeuclidean") { 
-							cDisplays.push_back(new CollectDisplay(new StructEuclidean(), new SharedOneColumnFile(fileNameRoot+"structeuclidean")));
-							outputNames.push_back(fileNameRoot+"structeuclidean"); outputTypes["structeuclidean"].push_back(fileNameRoot+"structeuclidean");
+							cDisplays.push_back(new CollectDisplay(new StructEuclidean(), new SharedOneColumnFile(getOutputFileName("structeuclidean", variables))));
+							outputNames.push_back(getOutputFileName("structeuclidean", variables)); outputTypes["structeuclidean"].push_back(getOutputFileName("structeuclidean", variables));
 						}else if (Estimators[i] == "structchord") { 
-							cDisplays.push_back(new CollectDisplay(new StructChord(), new SharedOneColumnFile(fileNameRoot+"structchord")));
-							outputNames.push_back(fileNameRoot+"structchord"); outputTypes["structchord"].push_back(fileNameRoot+"structchord");
+							cDisplays.push_back(new CollectDisplay(new StructChord(), new SharedOneColumnFile(getOutputFileName("structchord", variables))));
+							outputNames.push_back(getOutputFileName("structchord", variables)); outputTypes["structchord"].push_back(getOutputFileName("structchord", variables));
 						}else if (Estimators[i] == "hellinger") { 
-							cDisplays.push_back(new CollectDisplay(new Hellinger(), new SharedOneColumnFile(fileNameRoot+"hellinger")));
-							outputNames.push_back(fileNameRoot+"hellinger"); outputTypes["hellinger"].push_back(fileNameRoot+"hellinger");
+							cDisplays.push_back(new CollectDisplay(new Hellinger(), new SharedOneColumnFile(getOutputFileName("hellinger", variables))));
+							outputNames.push_back(getOutputFileName("hellinger", variables)); outputTypes["hellinger"].push_back(getOutputFileName("hellinger", variables));
 						}else if (Estimators[i] == "manhattan") { 
-							cDisplays.push_back(new CollectDisplay(new Manhattan(), new SharedOneColumnFile(fileNameRoot+"manhattan")));
-							outputNames.push_back(fileNameRoot+"manhattan"); outputTypes["manhattan"].push_back(fileNameRoot+"manhattan");
+							cDisplays.push_back(new CollectDisplay(new Manhattan(), new SharedOneColumnFile(getOutputFileName("manhattan", variables))));
+							outputNames.push_back(getOutputFileName("manhattan", variables)); outputTypes["manhattan"].push_back(getOutputFileName("manhattan", variables));
 						}else if (Estimators[i] == "structpearson") { 
-							cDisplays.push_back(new CollectDisplay(new StructPearson(), new SharedOneColumnFile(fileNameRoot+"structpearson")));
-							outputNames.push_back(fileNameRoot+"structpearson"); outputTypes["structpearson"].push_back(fileNameRoot+"structpearson");
+							cDisplays.push_back(new CollectDisplay(new StructPearson(), new SharedOneColumnFile(getOutputFileName("structpearson", variables))));
+							outputNames.push_back(getOutputFileName("structpearson", variables)); outputTypes["structpearson"].push_back(getOutputFileName("structpearson", variables));
 						}else if (Estimators[i] == "soergel") { 
-							cDisplays.push_back(new CollectDisplay(new Soergel(), new SharedOneColumnFile(fileNameRoot+"soergel")));
-							outputNames.push_back(fileNameRoot+"soergel"); outputTypes["soergel"].push_back(fileNameRoot+"soergel");
+							cDisplays.push_back(new CollectDisplay(new Soergel(), new SharedOneColumnFile(getOutputFileName("soergel", variables))));
+							outputNames.push_back(getOutputFileName("soergel", variables)); outputTypes["soergel"].push_back(getOutputFileName("soergel", variables));
 						}else if (Estimators[i] == "spearman") { 
-							cDisplays.push_back(new CollectDisplay(new Spearman(), new SharedOneColumnFile(fileNameRoot+"spearman")));
-							outputNames.push_back(fileNameRoot+"spearman"); outputTypes["spearman"].push_back(fileNameRoot+"spearman");
+							cDisplays.push_back(new CollectDisplay(new Spearman(), new SharedOneColumnFile(getOutputFileName("spearman", variables))));
+							outputNames.push_back(getOutputFileName("spearman", variables)); outputTypes["spearman"].push_back(getOutputFileName("spearman", variables));
 						}else if (Estimators[i] == "structkulczynski") { 
-							cDisplays.push_back(new CollectDisplay(new StructKulczynski(), new SharedOneColumnFile(fileNameRoot+"structkulczynski")));
-							outputNames.push_back(fileNameRoot+"structkulczynski"); outputTypes["structkulczynski"].push_back(fileNameRoot+"structkulczynski");
+							cDisplays.push_back(new CollectDisplay(new StructKulczynski(), new SharedOneColumnFile(getOutputFileName("structkulczynski", variables))));
+							outputNames.push_back(getOutputFileName("structkulczynski", variables)); outputTypes["structkulczynski"].push_back(getOutputFileName("structkulczynski", variables));
 						}else if (Estimators[i] == "speciesprofile") { 
-							cDisplays.push_back(new CollectDisplay(new SpeciesProfile(), new SharedOneColumnFile(fileNameRoot+"speciesprofile")));
-							outputNames.push_back(fileNameRoot+"speciesprofile"); outputTypes["speciesprofile"].push_back(fileNameRoot+"speciesprofile");
+							cDisplays.push_back(new CollectDisplay(new SpeciesProfile(), new SharedOneColumnFile(getOutputFileName("speciesprofile", variables))));
+							outputNames.push_back(getOutputFileName("speciesprofile", variables)); outputTypes["speciesprofile"].push_back(getOutputFileName("speciesprofile", variables));
 						}else if (Estimators[i] == "hamming") { 
-							cDisplays.push_back(new CollectDisplay(new Hamming(), new SharedOneColumnFile(fileNameRoot+"hamming")));
-							outputNames.push_back(fileNameRoot+"hamming"); outputTypes["hamming"].push_back(fileNameRoot+"hamming");
+							cDisplays.push_back(new CollectDisplay(new Hamming(), new SharedOneColumnFile(getOutputFileName("hamming", variables))));
+							outputNames.push_back(getOutputFileName("hamming", variables)); outputTypes["hamming"].push_back(getOutputFileName("hamming", variables));
 						}else if (Estimators[i] == "structchi2") { 
-							cDisplays.push_back(new CollectDisplay(new StructChi2(), new SharedOneColumnFile(fileNameRoot+"structchi2")));
-							outputNames.push_back(fileNameRoot+"structchi2"); outputTypes["structchi2"].push_back(fileNameRoot+"structchi2");
+							cDisplays.push_back(new CollectDisplay(new StructChi2(), new SharedOneColumnFile(getOutputFileName("structchi2", variables))));
+							outputNames.push_back(getOutputFileName("structchi2", variables)); outputTypes["structchi2"].push_back(getOutputFileName("structchi2", variables));
 						}else if (Estimators[i] == "gower") { 
-							cDisplays.push_back(new CollectDisplay(new Gower(), new SharedOneColumnFile(fileNameRoot+"gower")));
-							outputNames.push_back(fileNameRoot+"gower"); outputTypes["gower"].push_back(fileNameRoot+"gower");
+							cDisplays.push_back(new CollectDisplay(new Gower(), new SharedOneColumnFile(getOutputFileName("gower", variables))));
+							outputNames.push_back(getOutputFileName("gower", variables)); outputTypes["gower"].push_back(getOutputFileName("gower", variables));
 						}else if (Estimators[i] == "memchi2") { 
-							cDisplays.push_back(new CollectDisplay(new MemChi2(), new SharedOneColumnFile(fileNameRoot+"memchi2")));
-							outputNames.push_back(fileNameRoot+"memchi2"); outputTypes["memchi2"].push_back(fileNameRoot+"memchi2");
+							cDisplays.push_back(new CollectDisplay(new MemChi2(), new SharedOneColumnFile(getOutputFileName("memchi2", variables))));
+							outputNames.push_back(getOutputFileName("memchi2", variables)); outputTypes["memchi2"].push_back(getOutputFileName("memchi2", variables));
 						}else if (Estimators[i] == "memchord") { 
-							cDisplays.push_back(new CollectDisplay(new MemChord(), new SharedOneColumnFile(fileNameRoot+"memchord")));
-							outputNames.push_back(fileNameRoot+"memchord"); outputTypes["memchord"].push_back(fileNameRoot+"memchord");
+							cDisplays.push_back(new CollectDisplay(new MemChord(), new SharedOneColumnFile(getOutputFileName("memchord", variables))));
+							outputNames.push_back(getOutputFileName("memchord", variables)); outputTypes["memchord"].push_back(getOutputFileName("memchord", variables));
 						}else if (Estimators[i] == "memeuclidean") { 
-							cDisplays.push_back(new CollectDisplay(new MemEuclidean(), new SharedOneColumnFile(fileNameRoot+"memeuclidean")));
-							outputNames.push_back(fileNameRoot+"memeuclidean"); outputTypes["memeuclidean"].push_back(fileNameRoot+"memeuclidean");
+							cDisplays.push_back(new CollectDisplay(new MemEuclidean(), new SharedOneColumnFile(getOutputFileName("memeuclidean", variables))));
+							outputNames.push_back(getOutputFileName("memeuclidean", variables)); outputTypes["memeuclidean"].push_back(getOutputFileName("memeuclidean", variables));
 						}else if (Estimators[i] == "mempearson") { 
-							cDisplays.push_back(new CollectDisplay(new MemPearson(), new SharedOneColumnFile(fileNameRoot+"mempearson")));
-							outputNames.push_back(fileNameRoot+"mempearson"); outputTypes["mempearson"].push_back(fileNameRoot+"mempearson");
+							cDisplays.push_back(new CollectDisplay(new MemPearson(), new SharedOneColumnFile(getOutputFileName("mempearson", variables))));
+							outputNames.push_back(getOutputFileName("mempearson", variables)); outputTypes["mempearson"].push_back(getOutputFileName("mempearson", variables));
+						}else if (Estimators[i] == "jsd") {
+							cDisplays.push_back(new CollectDisplay(new JSD(), new SharedOneColumnFile(getOutputFileName("jsd", variables))));
+							outputNames.push_back(getOutputFileName("jsd", variables)); outputTypes["jsd"].push_back(getOutputFileName("jsd", variables));
 						}
 						
 					}
@@ -435,15 +503,19 @@ int CollectSharedCommand::execute(){
 			
 		//set users groups
 		SharedUtil* util = new SharedUtil();
-		util->setGroups(m->Groups, m->namesOfGroups, "collect");
+		Groups = m->getGroups();
+		vector<string> allGroups = m->getAllGroups();
+		util->setGroups(Groups, allGroups, "collect");
+		m->setGroups(Groups);
+		m->setAllGroups(allGroups);
 		delete util;
 
 		while((order != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 			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();
 					for(int i=0;i<cDisplays.size();i++){	delete cDisplays[i];	}
 					delete order; delete input;
-					m->Groups.clear();
+					m->clearGroups();
 					return 0;
 			}
 
@@ -488,9 +560,9 @@ int CollectSharedCommand::execute(){
 		}
 		
 		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();
 					for(int i=0;i<cDisplays.size();i++){	delete cDisplays[i];	}
-					m->Groups.clear();
+					m->clearGroups();
 					delete input;
 					return 0;
 		}
@@ -519,11 +591,11 @@ int CollectSharedCommand::execute(){
 			delete cCurve;
 			
 			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();
 				for(int i=0;i<cDisplays.size();i++){	delete cDisplays[i];	}
 				delete order; 
 				delete input;
-				m->Groups.clear();
+				m->clearGroups();
 				return 0;
 			}
 
@@ -533,7 +605,7 @@ int CollectSharedCommand::execute(){
 		for(int i=0;i<cDisplays.size();i++){	delete cDisplays[i];	}	
 		
 		//reset groups parameter
-		m->Groups.clear(); 
+		m->clearGroups(); 
 		delete input;
 		
 		m->mothurOutEndLine();