minor mods to seq.error

[mothur.git] / phylotypecommand.cpp

diff --git a/phylotypecommand.cpp b/phylotypecommand.cpp
index e7d12969a73a1a2d6576593fc36ec8eb5a9b1d2a..ef23375df9425f11816acbf8594f46e613e9e148 100644 (file)
--- a/phylotypecommand.cpp
+++ b/phylotypecommand.cpp
@@ -45,7 +45,7 @@ string PhylotypeCommand::getHelpString(){
                helpString += "For the label parameter, levels count down from the root to keep the output similiar to mothur's other commands which report information from finer resolution to coarser resolutions.\n";
                helpString += "The phylotype command should be in the following format: \n";
                helpString += "phylotype(taxonomy=yourTaxonomyFile, cutoff=yourCutoff, label=yourLabels) \n";
-               helpString += "Eaxample: phylotype(taxonomy=amazon.taxonomy, cutoff=5, label=1-3-5).\n\n";
+               helpString += "Eaxample: phylotype(taxonomy=amazon.taxonomy, cutoff=5, label=1-3-5).\n";
                return helpString;
        }
        catch(exception& e) {
@@ -76,6 +76,7 @@ PhylotypeCommand::PhylotypeCommand(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();
@@ -128,11 +129,12 @@ PhylotypeCommand::PhylotypeCommand(string option)  {
                                        abort = true; 
                                }
                        }else if (taxonomyFileName == "not open") { abort = true; }     
+                       else { m->setTaxonomyFile(taxonomyFileName); }
                        
                        namefile = validParameter.validFile(parameters, "name", true);
                        if (namefile == "not open") { abort = true; }
                        else if (namefile == "not found") { namefile = ""; }
-                       else { readNamesFile(); }       
+                       else { readNamesFile(); m->setNameFile(namefile); }     
                        
                        //if the user changes the output directory command factory will send this info to us in the output parameter 
                        outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){