1.21.0

[mothur.git] / amovacommand.cpp

diff --git a/amovacommand.cpp b/amovacommand.cpp
index f1e5f61197475b43d52d7dac46dab04cc7f657c2..141673375fb8bb1a37e67980df9708fe6d2da126 100644 (file)
--- a/amovacommand.cpp
+++ b/amovacommand.cpp
@@ -50,7 +50,6 @@ string AmovaCommand::getHelpString(){
                exit(1);
        }
 }
-
 //**********************************************************************************************************************
 AmovaCommand::AmovaCommand(){  
        try {
@@ -71,6 +70,7 @@ AmovaCommand::AmovaCommand(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();
@@ -122,17 +122,17 @@ AmovaCommand::AmovaCommand(string option) {
                                phylipFileName = m->getPhylipFile(); 
                                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"; }