worked on trim.seqs - added in the groupfiles for allfiles=t, cleaned up the outputNa...

[mothur.git] / readtreecommand.cpp

diff --git a/readtreecommand.cpp b/readtreecommand.cpp
index 89efc9abcf0057f68189ddad6975b5e1464fca09..05a65b736f93c376525b1cf64e2ed8275fc9c486 100644 (file)
--- a/readtreecommand.cpp
+++ b/readtreecommand.cpp
@@ -9,14 +9,49 @@
 
 #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 {
                globaldata = GlobalData::getInstance();
-               abort = false;
+               abort = false; calledHelp = false;   
                                
                //allow user to run help
-               if(option == "help") { help(); abort = true; }
+               if(option == "help") { help(); abort = true; calledHelp = true; }
                
                else {
                        //valid paramters for this command
@@ -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");
        }
@@ -143,7 +178,7 @@ ReadTreeCommand::~ReadTreeCommand(){
 int ReadTreeCommand::execute(){
        try {
        
-               if (abort == true) { return 0; }
+               if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
                
                int readOk;