1.21.0

[mothur.git] / anosimcommand.cpp

diff --git a/anosimcommand.cpp b/anosimcommand.cpp
index 623b4333948a8996ab5122389a67bac2cb21bc6f..c5cb4d60c751d6614b82cd961c29d9e645fcbaa8 100644 (file)
--- a/anosimcommand.cpp
+++ b/anosimcommand.cpp
@@ -41,7 +41,7 @@ string AnosimCommand::getHelpString(){
                helpString += "The design file looks like the group file.  It is a 2 column tab delimited file, where the first column is the sample name and the second column is the group the sample belongs to.\n";
                helpString += "The iters parameter allows you to set number of randomization for the P value.  The default is 1000. \n";
                helpString += "The anosim command should be in the following format: anosim(phylip=file.dist, design=file.design).\n";
-               helpString += "Note: No spaces between parameter labels (i.e. iters), '=' and parameters (i.e. 1000).\n\n";
+               helpString += "Note: No spaces between parameter labels (i.e. iters), '=' and parameters (i.e. 1000).\n";
                return helpString;
        }
        catch(exception& e) {
@@ -71,6 +71,7 @@ AnosimCommand::AnosimCommand(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();
@@ -123,17 +124,17 @@ AnosimCommand::AnosimCommand(string option) {
                                if (phylipFileName != "") { m->mothurOut("Using " + phylipFileName + " as input file for the phylip parameter."); m->mothurOutEndLine(); }
                                else {  m->mothurOut("You have no current phylip file and the phylip parameter is required."); m->mothurOutEndLine(); abort = true; }
                                
-                       }       
+                       }else { m->setPhylipFile(phylipFileName); }     
                        
                        //check for required parameters
                        designFileName = validParameter.validFile(parameters, "design", true);
-                       if (designFileName == "not open") { abort = true; }
+                       if (designFileName == "not open") { designFileName = ""; abort = true; }
                        else if (designFileName == "not found") {
                                //if there is a current design file, use it
                                designFileName = m->getDesignFile(); 
                                if (designFileName != "") { m->mothurOut("Using " + designFileName + " as input file for the design parameter."); m->mothurOutEndLine(); }
                                else {  m->mothurOut("You have no current design file and the design parameter is required."); m->mothurOutEndLine(); abort = true; }                                                           
-                       }       
+                       }else { m->setDesignFile(designFileName); }     
                        
                        string temp = validParameter.validFile(parameters, "iters", false);
                        if (temp == "not found") { temp = "1000"; }