X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;ds=sidebyside;f=collectsharedcommand.cpp;h=d72dd7139735f16b8fcd8b02aa39058a5f4a3110;hb=75962c819c16814e5c2340d99af1aa62e564dc20;hp=3a2875afb62b882e9e8654eecb19e2caab5c9673;hpb=1d898dc6edaf9e9f287fab53bf1f21fb29757a17;p=mothur.git

diff --git a/collectsharedcommand.cpp b/collectsharedcommand.cpp
index 3a2875a..d72dd71 100644
--- a/collectsharedcommand.cpp
+++ b/collectsharedcommand.cpp
@@ -57,7 +57,7 @@ vector<string> CollectSharedCommand::setParameters(){
 		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 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", "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);
@@ -119,7 +119,7 @@ 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;
@@ -157,6 +157,7 @@ CollectSharedCommand::CollectSharedCommand(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();
@@ -190,7 +191,7 @@ 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;
@@ -258,6 +259,11 @@ 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 = ""; }
@@ -329,7 +335,7 @@ CollectSharedCommand::CollectSharedCommand(string option)  {
 						}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") { 
+						}else if (Estimators[i] == "kulczynski") { 
 							cDisplays.push_back(new CollectDisplay(new Kulczynski(), new SharedOneColumnFile(fileNameRoot+"kulczynski")));
 							outputNames.push_back(fileNameRoot+"kulczynski"); outputTypes["kulczynski"].push_back(fileNameRoot+"kulczynski");
 						}else if (Estimators[i] == "kulczynskicody") {