X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=summarycommand.cpp;h=83ea8c9b4b5ab077283454089b35d9de13908003;hb=46626aa16c99fcdf2e3c76a61b80a5d4b0c3b898;hp=629750bbccb5ed027edf5ef53dbba3686ddb4bba;hpb=19fcbbdba99658f5eca244803280f9ee7f9f6607;p=mothur.git

diff --git a/summarycommand.cpp b/summarycommand.cpp
index 629750b..83ea8c9 100644
--- a/summarycommand.cpp
+++ b/summarycommand.cpp
@@ -42,7 +42,7 @@ vector<string> SummaryCommand::setParameters(){
 		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 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 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); 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 pgroupmode("groupmode", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pgroupmode);
@@ -231,10 +231,10 @@ SummaryCommand::SummaryCommand(string option)  {
 
 			string temp;
 			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); 
 			
 			temp = validParameter.validFile(parameters, "groupmode", false);		if (temp == "not found") { temp = "T"; }
 			groupMode = m->isTrue(temp);