1.23.0

[mothur.git] / shhhseqscommand.cpp

diff --git a/shhhseqscommand.cpp b/shhhseqscommand.cpp
index 8ef4c8c24f6d7a6398631591f0e7a2a34d7965c1..6a339b880eb54eedaa7be7af3c297ed0089beb10 100644 (file)
--- a/shhhseqscommand.cpp
+++ b/shhhseqscommand.cpp
@@ -37,7 +37,7 @@ string ShhhSeqsCommand::getHelpString(){
                string helpString = "";
                helpString += "The shhh.seqs command reads a fasta and name file and ....\n";
                helpString += "The shhh.seqs command parameters are fasta, name, group, sigma and processors.\n";
-               helpString += "The fasta parameter allows you to enter the fasta file containing your potentially sequences, and is required, unless you have a valid current fasta file. \n";
+               helpString += "The fasta parameter allows you to enter the fasta file containing your sequences, and is required, unless you have a valid current fasta file. \n";
                helpString += "The name parameter allows you to provide a name file associated with your fasta file. It is required. \n";
                helpString += "The group parameter allows you to provide a group file.  When checking sequences, only sequences from the same group as the query sequence will be used as the reference. \n";
                helpString += "The processors parameter allows you to specify how many processors you would like to use.  The default is 1. \n";
@@ -160,11 +160,11 @@ ShhhSeqsCommand::ShhhSeqsCommand(string option) {
                        else {   m->setGroupFile(groupfile);  }
                        
                        string temp     = validParameter.validFile(parameters, "sigma", false);         if(temp == "not found"){        temp = "0.01"; }
-                       convert(temp, sigma); 
+                       m->mothurConvert(temp, sigma); 
                        
                        temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){       temp = m->getProcessors();      }
                        m->setProcessors(temp);
-                       convert(temp, processors);
+                       m->mothurConvert(temp, processors);
                }
        }
        catch(exception& e) {