added forward and reverse barcodes to trim.seqs to process illumina seqs

[mothur.git] / mantelcommand.cpp

diff --git a/mantelcommand.cpp b/mantelcommand.cpp
index c41cde34e92374d4c21a57f51636d2729d464d13..409eae414779acb412abec7aa295b61e82cd0e16 100644 (file)
--- a/mantelcommand.cpp
+++ b/mantelcommand.cpp
@@ -41,7 +41,7 @@ string MantelCommand::getHelpString(){
                helpString += "The iters parameter allows you to set number of randomization for the P value.  The default is 1000. \n";
                helpString += "The mantel command should be in the following format: mantel(phylip1=veg.dist, phylip2=env.dist).\n";
                helpString += "The mantel command outputs a .mantel file.\n";
-               helpString += "Note: No spaces between parameter labels (i.e. phylip1), '=' and parameters (i.e. veg.dist).\n\n";
+               helpString += "Note: No spaces between parameter labels (i.e. phylip1), '=' and parameters (i.e. veg.dist).\n";
                return helpString;
        }
        catch(exception& e) {
@@ -69,6 +69,7 @@ MantelCommand::MantelCommand(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();
@@ -124,7 +125,7 @@ MantelCommand::MantelCommand(string option)  {
                        method = validParameter.validFile(parameters, "method", false);         if (method == "not found"){     method = "pearson";             }
                        
                        string temp = validParameter.validFile(parameters, "iters", false);                     if (temp == "not found") { temp = "1000"; }
-                       convert(temp, iters);
+                       m->mothurConvert(temp, iters);
                        
                        if ((method != "pearson") && (method != "spearman") && (method != "kendall")) { m->mothurOut(method + " is not a valid method. Valid methods are pearson, spearman, and kendall."); m->mothurOutEndLine(); abort = true; }
                }