added chimera.uchime

[mothur.git] / amovacommand.cpp

diff --git a/amovacommand.cpp b/amovacommand.cpp
index 8e3edd573b40706458c0b4c8a5803b6ed2265b14..ad5823b15e108396ee1b0e0977167c8e4f1fbb22 100644 (file)
--- a/amovacommand.cpp
+++ b/amovacommand.cpp
@@ -35,14 +35,14 @@ vector<string> AmovaCommand::setParameters(){
 string AmovaCommand::getHelpString(){  
        try {
                string helpString = "";
-               helpString += "Referenced: Anderson MJ (2001). A new method for non-parametric multivariate analysis of variance. Austral Ecol 26: 32-46.\n";
-               helpString += "The amova command outputs a .amova file. \n";
-               helpString += "The amova command parameters are phylip, iters, and alpha.  The phylip and design parameters are required, unless you have valid current files.\n";
-               helpString += "The design parameter allows you to assign your samples to groups when you are running amova. It is required. \n";
-               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 amova command should be in the following format: amova(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 += "Referenced: Anderson MJ (2001). A new method for non-parametric multivariate analysis of variance. Austral Ecol 26: 32-46.";
+               helpString += "The amova command outputs a .amova file.";
+               helpString += "The amova command parameters are phylip, iters, and alpha.  The phylip and design parameters are required, unless you have valid current files.";
+               helpString += "The design parameter allows you to assign your samples to groups when you are running amova. It is required.";
+               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.";
+               helpString += "The iters parameter allows you to set number of randomization for the P value.  The default is 1000.";
+               helpString += "The amova command should be in the following format: amova(phylip=file.dist, design=file.design).";
+               helpString += "Note: No spaces between parameter labels (i.e. iters), '=' and parameters (i.e. 1000).";
                return helpString;
        }
        catch(exception& e) {
@@ -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();