removed read.dist, read.otu, read.tree and globaldata. added current to defaults...

[mothur.git] / mergefilecommand.cpp

diff --git a/mergefilecommand.cpp b/mergefilecommand.cpp
index 2b34a00b8c3961d581032dcf6b6929404428a3b4..cb241c6b301396e7c7d0482d98be861a926b8a64 100644 (file)
--- a/mergefilecommand.cpp
+++ b/mergefilecommand.cpp
@@ -10,49 +10,48 @@
 #include "mergefilecommand.h"
 
 //**********************************************************************************************************************
-vector<string> MergeFileCommand::getValidParameters(){ 
+vector<string> MergeFileCommand::setParameters(){      
        try {
-               string Array[] =  {"input", "output","outputdir","inputdir"};
-               vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+               CommandParameter pinput("input", "String", "", "", "", "", "",false,true); parameters.push_back(pinput);
+               CommandParameter poutput("output", "String", "", "", "", "", "",false,true); parameters.push_back(poutput);
+               CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
+               CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+               
+               vector<string> myArray;
+               for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
                return myArray;
        }
        catch(exception& e) {
-               m->errorOut(e, "MergeFileCommand", "getValidParameters");
+               m->errorOut(e, "MergeFileCommand", "setParameters");
                exit(1);
        }
 }
 //**********************************************************************************************************************
-MergeFileCommand::MergeFileCommand(){  
+string MergeFileCommand::getHelpString(){      
        try {
-               abort = true; calledHelp = true; 
-               vector<string> tempOutNames;
-               outputTypes["merge"] = tempOutNames;
+               string helpString = "";
+               helpString += "The merge.file command takes a list of files separated by dashes and merges them into one file."; 
+               helpString += "The merge.file command parameters are input and output."; 
+               helpString += "Example merge.file(input=small.fasta-large.fasta, output=all.fasta).";
+               helpString += "Note: No spaces between parameter labels (i.e. output), '=' and parameters (i.e.yourOutputFileName).\n\n";
+               return helpString;
        }
        catch(exception& e) {
-               m->errorOut(e, "MergeFileCommand", "MergeFileCommand");
-               exit(1);
-       }
-}
-//**********************************************************************************************************************
-vector<string> MergeFileCommand::getRequiredParameters(){      
-       try {
-               string Array[] =  {"input","output"};
-               vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
-               return myArray;
-       }
-       catch(exception& e) {
-               m->errorOut(e, "MergeFileCommand", "getRequiredParameters");
+               m->errorOut(e, "MergeFileCommand", "getHelpString");
                exit(1);
        }
 }
+
 //**********************************************************************************************************************
-vector<string> MergeFileCommand::getRequiredFiles(){   
+MergeFileCommand::MergeFileCommand(){  
        try {
-               vector<string> myArray;
-               return myArray;
+               abort = true; calledHelp = true; 
+               setParameters();
+               vector<string> tempOutNames;
+               outputTypes["merge"] = tempOutNames;
        }
        catch(exception& e) {
-               m->errorOut(e, "MergeFileCommand", "getRequiredFiles");
+               m->errorOut(e, "MergeFileCommand", "MergeFileCommand");
                exit(1);
        }
 }
@@ -67,9 +66,7 @@ MergeFileCommand::MergeFileCommand(string option)  {
                        abort = true; calledHelp = true;
                }
                else {
-                       //valid paramters for this command
-                       string Array[] =  {"input", "output","outputdir","inputdir"};
-                       vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+                       vector<string> myArray = setParameters();
                        
                        OptionParser parser(option);
                        map<string,string> parameters = parser.getParameters();
@@ -127,11 +124,6 @@ MergeFileCommand::MergeFileCommand(string option)  {
                exit(1);
        }
 }
-
-//**********************************************************************************************************************
-
-MergeFileCommand::~MergeFileCommand()  {       /*      do nothing      */      }
-
 //**********************************************************************************************************************
 
 int MergeFileCommand::execute(){
@@ -174,17 +166,4 @@ int MergeFileCommand::execute(){
                exit(1);
        }
 }
-
-//**********************************************************************************************************************
-
-void MergeFileCommand::help(){
-       try {
-               m->mothurOut("The merge.file command..."); m->mothurOutEndLine();
-       }
-       catch(exception& e) {
-               m->errorOut(e, "MergeFileCommand", "help");
-               exit(1);
-       }
-}
-
 //**********************************************************************************************************************