rewrote metastats command in c++, added mothurRemove function to handle ~ error....

[mothur.git] / homovacommand.cpp

diff --git a/homovacommand.cpp b/homovacommand.cpp
index 9f7483057220568d27752d5c6d2b68238d274629..22fd1bff1b0af5ac23532423f7b42471e1b6b3b3 100644 (file)
--- a/homovacommand.cpp
+++ b/homovacommand.cpp
@@ -41,7 +41,7 @@ string HomovaCommand::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 homova command should be in the following format: homova(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) {
@@ -72,6 +72,7 @@ HomovaCommand::HomovaCommand(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 @@ HomovaCommand::HomovaCommand(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);
@@ -134,7 +135,7 @@ HomovaCommand::HomovaCommand(string option) {
                                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"; }