X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=summarysharedcommand.cpp;h=59c12a03dae958f4bb199a6aad94056264c0426a;hp=d93fb6e775392b5436b6dadbb99c88761e862de8;hb=b206f634aae1b4ce13978d203247fb64757d5482;hpb=70491a12902e89b85cfa6b44a7b7fbe066ee2ac1

diff --git a/summarysharedcommand.cpp b/summarysharedcommand.cpp
index d93fb6e..59c12a0 100644
--- a/summarysharedcommand.cpp
+++ b/summarysharedcommand.cpp
@@ -17,7 +17,7 @@ vector<string> SummarySharedCommand::setParameters(){
 		CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
         CommandParameter psubsample("subsample", "String", "", "", "", "", "","phylip",false,false); parameters.push_back(psubsample);
 		CommandParameter pdistance("distance", "Boolean", "", "F", "", "", "","phylip",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-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,true); 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-jsd-rjsd", "sharedsobs-sharedchao-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan", "", "", "","",true,false,true); parameters.push_back(pcalc);
         CommandParameter poutput("output", "Multiple", "lt-square", "lt", "", "", "","",false,false); parameters.push_back(poutput);
 		CommandParameter pall("all", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pall);
         CommandParameter piters("iters", "Number", "", "1000", "", "", "","",false,false); parameters.push_back(piters);
@@ -184,9 +184,6 @@ SummarySharedCommand::SummarySharedCommand(string option)  {
 			string temp = validParameter.validFile(parameters, "all", false);				if (temp == "not found") { temp = "false"; }
 			all = m->isTrue(temp);
 			
-			temp = validParameter.validFile(parameters, "distance", false);					if (temp == "not found") { temp = "false"; }
-			createPhylip = m->isTrue(temp);
-			
             temp = validParameter.validFile(parameters, "iters", false);			if (temp == "not found") { temp = "1000"; }
 			m->mothurConvert(temp, iters); 
             
@@ -204,6 +201,10 @@ SummarySharedCommand::SummarySharedCommand(string option)  {
             
             if (subsample == false) { iters = 0; }
             
+            temp = validParameter.validFile(parameters, "distance", false);					if (temp == "not found") { temp = "false"; }
+			createPhylip = m->isTrue(temp);
+            if (subsample) { createPhylip = true; }
+            
 			temp = validParameter.validFile(parameters, "processors", false);	if (temp == "not found"){	temp = m->getProcessors();	}
 			m->setProcessors(temp);
 			m->mothurConvert(temp, processors); 
@@ -293,6 +294,10 @@ SummarySharedCommand::SummarySharedCommand(string option)  {
 							sumCalculators.push_back(new MemEuclidean());
 						}else if (Estimators[i] == "mempearson") { 
 							sumCalculators.push_back(new MemPearson());
+						}else if (Estimators[i] == "jsd") {
+							sumCalculators.push_back(new JSD());
+						}else if (Estimators[i] == "rjsd") {
+							sumCalculators.push_back(new RJSD());
 						}
 					}
 				}