added pipeline commands which involved change to command factory and command class...

[mothur.git] / readtreecommand.cpp

diff --git a/readtreecommand.cpp b/readtreecommand.cpp
index 89efc9abcf0057f68189ddad6975b5e1464fca09..edfdf3b77e0d85ff51afce83323d0204ab987a66 100644 (file)
--- a/readtreecommand.cpp
+++ b/readtreecommand.cpp
@@ -9,6 +9,41 @@
 
 #include "readtreecommand.h"
 
+//**********************************************************************************************************************
+vector<string> ReadTreeCommand::getValidParameters(){  
+       try {
+               string Array[] =  {"tree","group","name","outputdir","inputdir"};
+               vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "ReadTreeCommand", "getValidParameters");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+vector<string> ReadTreeCommand::getRequiredParameters(){       
+       try {
+               string Array[] =  {"tree"};
+               vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "ReadTreeCommand", "getRequiredParameters");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+vector<string> ReadTreeCommand::getRequiredFiles(){    
+       try {
+               vector<string> myArray;
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "ReadTreeCommand", "getRequiredFiles");
+               exit(1);
+       }
+}
 //**********************************************************************************************************************
 ReadTreeCommand::ReadTreeCommand(string option)  {
        try {
@@ -122,7 +157,7 @@ void ReadTreeCommand::help(){
                m->mothurOut("It also must be run before using the parsimony command, unless you are using the randomtree parameter.\n");
                m->mothurOut("The read.tree command parameters are tree, group and name.\n");
                m->mothurOut("The read.tree command should be in the following format: read.tree(tree=yourTreeFile, group=yourGroupFile).\n");
-               m->mothurOut("The tree and group parameters are both required.\n");
+               m->mothurOut("The tree and group parameters are both required, if no group file is given then one group is assumed.\n");
                m->mothurOut("The name parameter allows you to enter a namefile.\n");
                m->mothurOut("Note: No spaces between parameter labels (i.e. tree), '=' and parameters (i.e.yourTreefile).\n\n");
        }