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

[mothur.git] / setcurrentcommand.cpp

diff --git a/setcurrentcommand.cpp b/setcurrentcommand.cpp
index a4f5c5c1f7ac756c1803bb25dfd7a95133477580..16685b24c7c706d0c6cf5aa9d15da2e08e863112 100644 (file)
--- a/setcurrentcommand.cpp
+++ b/setcurrentcommand.cpp
@@ -10,47 +10,67 @@
 #include "setcurrentcommand.h"
 
 //**********************************************************************************************************************
-vector<string> SetCurrentCommand::getValidParameters(){        
+vector<string> SetCurrentCommand::setParameters(){     
        try {
-               string Array[] =  {"outputdir","inputdir","clear", "phylip", "column", "list","rabund","sabund","name","group",
-                       "design","order","tree","shared","ordergroup","relabund","fasta","qfile","sff","oligos","accnos","taxonomy"};
-               vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+                       
+               CommandParameter pphylip("phylip", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pphylip);
+               CommandParameter pcolumn("column", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pcolumn);
+               CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pfasta);
+               CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pname);
+               CommandParameter pgroup("group", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pgroup);
+               CommandParameter plist("list", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(plist);
+               CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(ptaxonomy);
+               CommandParameter pqfile("qfile", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pqfile);
+               CommandParameter paccnos("accnos", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(paccnos);            
+               CommandParameter prabund("rabund", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(prabund);
+               CommandParameter psabund("sabund", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(psabund);
+               CommandParameter pdesign("design", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pdesign);
+               CommandParameter porder("order", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(porder);
+               CommandParameter ptree("tree", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(ptree);
+               CommandParameter pshared("shared", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pshared);
+               CommandParameter pordergroup("ordergroup", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pordergroup);
+               CommandParameter prelabund("relabund", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(prelabund);
+               CommandParameter psff("sff", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(psff);
+               CommandParameter poligos("oligos", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(poligos);
+               CommandParameter pclear("clear", "String", "", "", "", "", "",false,false); parameters.push_back(pclear);
+               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, "SetCurrentCommand", "getValidParameters");
-               exit(1);
-       }
-}
-//**********************************************************************************************************************
-SetCurrentCommand::SetCurrentCommand(){        
-       try {
-               abort = true; calledHelp = true; 
-       }
-       catch(exception& e) {
-               m->errorOut(e, "SetCurrentCommand", "SetCurrentCommand");
+               m->errorOut(e, "SetCurrentCommand", "setParameters");
                exit(1);
        }
 }
 //**********************************************************************************************************************
-vector<string> SetCurrentCommand::getRequiredParameters(){     
+string SetCurrentCommand::getHelpString(){     
        try {
-               vector<string> myArray;
-               return myArray;
+               string helpString = "";
+               helpString += "The set.current command allows you to set the current files saved by mothur.\n";
+               helpString += "The set.current command parameters are: clear, phylip, column, list, rabund, sabund, name, group, design, order, tree, shared, ordergroup, relabund, fasta, qfile, sff, oligos, accnos, taxonomy.\n";
+               helpString += "The clear paramter is used to indicate which file types you would like to clear values for, multiple types can be separated by dashes.\n";
+               helpString += "The set.current command should be in the following format: \n";
+               helpString += "set.current(fasta=yourFastaFile) or set.current(fasta=amazon.fasta, clear=name-accnos)\n";
+               return helpString;
        }
        catch(exception& e) {
-               m->errorOut(e, "SetCurrentCommand", "getRequiredParameters");
+               m->errorOut(e, "SetCurrentCommand", "getHelpString");
                exit(1);
        }
 }
+
+
 //**********************************************************************************************************************
-vector<string> SetCurrentCommand::getRequiredFiles(){  
+SetCurrentCommand::SetCurrentCommand(){        
        try {
-               vector<string> myArray;
-               return myArray;
+               abort = true; calledHelp = true;
+               setParameters();
        }
        catch(exception& e) {
-               m->errorOut(e, "SetCurrentCommand", "getRequiredFiles");
+               m->errorOut(e, "SetCurrentCommand", "SetCurrentCommand");
                exit(1);
        }
 }
@@ -64,9 +84,7 @@ SetCurrentCommand::SetCurrentCommand(string option)  {
                
                else {
                        //valid paramters for this command
-                       string Array[] =  {"outputdir","inputdir","clear", "phylip", "column", "list","rabund","sabund","name","group",
-                               "design","order","tree","shared","ordergroup","relabund","fasta","qfile","sff","oligos","accnos","taxonomy"};
-                       vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+                       vector<string> myArray = setParameters();
                        
                        OptionParser parser(option);
                        map<string,string> parameters = parser.getParameters();
@@ -354,25 +372,6 @@ SetCurrentCommand::SetCurrentCommand(string option)  {
 }
 //**********************************************************************************************************************
 
-void SetCurrentCommand::help(){
-       try {
-               m->mothurOut("The set.current command allows you to set the current files saved by mothur.\n");
-               m->mothurOut("The set.current command parameters are: clear, phylip, column, list, rabund, sabund, name, group, design, order, tree, shared, ordergroup, relabund, fasta, qfile, sff, oligos, accnos, taxonomy.\n");
-               m->mothurOut("The clear paramter is used to indicate which file types you would like to clear values for, multiple types can be separated by dashes.\n");
-               m->mothurOut("The set.current command should be in the following format: \n");
-               m->mothurOut("set.current(fasta=yourFastaFile) or set.current(fasta=amazon.fasta, clear=name-accnos)\n");
-               
-       }
-       catch(exception& e) {
-               m->errorOut(e, "SetCurrentCommand", "help");
-               exit(1);
-       }
-}
-
-//**********************************************************************************************************************
-SetCurrentCommand::~SetCurrentCommand(){}
-//**********************************************************************************************************************
-
 int SetCurrentCommand::execute(){
        try {