added sequence name to error string in fastq.info. Changed np_shannon to npshannon.

[mothur.git] / summarycommand.cpp

diff --git a/summarycommand.cpp b/summarycommand.cpp
index 629750bbccb5ed027edf5ef53dbba3686ddb4bba..83ea8c9b4b5ab077283454089b35d9de13908003 100644 (file)
--- 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);