X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=summarysharedcommand.cpp;h=4363eaa9523570cd56146a75805b9dfc8e65e3d7;hb=4de093e3b92bdab1579565cb2873553412f6671e;hp=13a77ed31b19ae8b87006ea36ba5a53839365ebe;hpb=1d898dc6edaf9e9f287fab53bf1f21fb29757a17;p=mothur.git

diff --git a/summarysharedcommand.cpp b/summarysharedcommand.cpp
index 13a77ed..4363eaa 100644
--- a/summarysharedcommand.cpp
+++ b/summarysharedcommand.cpp
@@ -56,7 +56,7 @@ vector<string> SummarySharedCommand::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 pdistance("distance", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pdistance);
-		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 pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
 		CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
@@ -119,6 +119,7 @@ SummarySharedCommand::SummarySharedCommand(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();
@@ -183,6 +184,11 @@ SummarySharedCommand::SummarySharedCommand(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 = ""; }
@@ -574,7 +580,7 @@ int SummarySharedCommand::process(vector<SharedRAbundVector*> thisLookup, string
 							ifstream intemp;
 							m->openInputFile(tempdistFileName, intemp);
 							
-							for (int i = 0; i < calcDists.size(); i++) {
+							for (int k = 0; k < calcDists.size(); k++) {
 								int size = 0;
 								intemp >> size; m->gobble(intemp);
 									
@@ -586,7 +592,7 @@ int SummarySharedCommand::process(vector<SharedRAbundVector*> thisLookup, string
 									intemp >> seq1 >> seq2 >> dist;   m->gobble(intemp);
 									
 									seqDist tempDist(seq1, seq2, dist);
-									calcDists[i].push_back(tempDist);
+									calcDists[k].push_back(tempDist);
 								}
 							}
 							intemp.close();