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

[mothur.git] / makegroupcommand.cpp

diff --git a/makegroupcommand.cpp b/makegroupcommand.cpp
index 8adfe09f7db893f6f8366f7cbecd18639b72f42c..6f640eb0732274bf6970c346dc9d6b9de553b1b4 100644 (file)
--- a/makegroupcommand.cpp
+++ b/makegroupcommand.cpp
@@ -10,53 +10,56 @@
 #include "makegroupcommand.h"
 #include "sequence.hpp"
 
+
 //**********************************************************************************************************************
-vector<string> MakeGroupCommand::getValidParameters(){ 
+vector<string> MakeGroupCommand::setParameters(){      
        try {
-               string Array[] =  {"fasta", "output","groups","outputdir","inputdir"};
-               vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+               CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta);
+               CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
+               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, "MakeGroupCommand", "getValidParameters");
-               exit(1);
-       }
-}
-//**********************************************************************************************************************
-MakeGroupCommand::MakeGroupCommand(){  
-       try {
-               abort = true; calledHelp = true; 
-               vector<string> tempOutNames;
-               outputTypes["group"] = tempOutNames;
-       }
-       catch(exception& e) {
-               m->errorOut(e, "MakeGroupCommand", "MakeGroupCommand");
+               m->errorOut(e, "MakeGroupCommand", "setParameters");
                exit(1);
        }
 }
 //**********************************************************************************************************************
-vector<string> MakeGroupCommand::getRequiredParameters(){      
+string MakeGroupCommand::getHelpString(){      
        try {
-               string Array[] =  {"fasta","groups"};
-               vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
-               return myArray;
+               string helpString = "";
+               helpString += "The make.group command reads a fasta file or series of fasta files and creates a groupfile.\n";
+               helpString += "The make.group command parameters are fasta, groups and output. Fasta and group are required.\n";
+               helpString += "The output parameter allows you to specify the name of groupfile created. \n";
+               helpString += "The make.group command should be in the following format: \n";
+               helpString += "make.group(fasta=yourFastaFiles, groups=yourGroups). \n";
+               helpString += "Example make.group(fasta=seqs1.fasta-seq2.fasta-seqs3.fasta, groups=A-B-C)\n";
+               helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFiles).\n\n";
+               return helpString;
        }
        catch(exception& e) {
-               m->errorOut(e, "MakeGroupCommand", "getRequiredParameters");
+               m->errorOut(e, "MakeGroupCommand", "getHelpString");
                exit(1);
        }
 }
 //**********************************************************************************************************************
-vector<string> MakeGroupCommand::getRequiredFiles(){   
+MakeGroupCommand::MakeGroupCommand(){  
        try {
-               vector<string> myArray;
-               return myArray;
+               abort = true; calledHelp = true; 
+               setParameters();
+               vector<string> tempOutNames;
+               outputTypes["group"] = tempOutNames;
        }
        catch(exception& e) {
-               m->errorOut(e, "MakeGroupCommand", "getRequiredFiles");
+               m->errorOut(e, "MakeGroupCommand", "MakeGroupCommand");
                exit(1);
        }
 }
+
 //**********************************************************************************************************************
 
 MakeGroupCommand::MakeGroupCommand(string option)  {
@@ -68,10 +71,7 @@ MakeGroupCommand::MakeGroupCommand(string option)  {
                if(option == "help") { help(); abort = true; calledHelp = true; }
                
                else {
-                       
-                       //valid paramters for this command
-                       string AlignArray[] =  {"fasta","groups","output","outputdir","inputdir"};
-                       vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
+                       vector<string> myArray = setParameters();
                        
                        OptionParser parser(option);
                        map<string, string> parameters = parser.getParameters(); 
@@ -93,8 +93,11 @@ MakeGroupCommand::MakeGroupCommand(string option)  {
                        if (inputDir == "not found"){   inputDir = "";          }
 
                        fastaFileName = validParameter.validFile(parameters, "fasta", false);
-                       if (fastaFileName == "not found") { m->mothurOut("fasta is a required parameter for the make.group command."); m->mothurOutEndLine(); abort = true;  }
-                       else { 
+                       if (fastaFileName == "not found") {                             //if there is a current fasta file, use it
+                               string filename = m->getFastaFile(); 
+                               if (filename != "") { fastaFileNames.push_back(filename); m->mothurOut("Using " + filename + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
+                               else {  m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
+                       }else { 
                                m->splitAtDash(fastaFileName, fastaFileNames);
                                
                                //go through files and make sure they are good, if not, then disregard them
@@ -162,37 +165,12 @@ MakeGroupCommand::MakeGroupCommand(string option)  {
 
                        if (groupsNames.size() != fastaFileNames.size()) { m->mothurOut("You do not have the same number of valid fastfile files as groups.  This could be because we could not open a fastafile."); m->mothurOutEndLine(); abort = true;  }
                }
-               cout << "here" << endl;
        }
        catch(exception& e) {
                m->errorOut(e, "MakeGroupCommand", "MakeGroupCommand");
                exit(1);
        }
 }
-
-//**********************************************************************************************************************
-
-MakeGroupCommand::~MakeGroupCommand(){ }
-
-//**********************************************************************************************************************
-
-void MakeGroupCommand::help(){
-       try {
-               m->mothurOut("The make.group command reads a fasta file or series of fasta files and creates a groupfile.\n");
-               m->mothurOut("The make.group command parameters are fasta, groups and output. Fasta and group are required.\n");
-               m->mothurOut("The output parameter allows you to specify the name of groupfile created. \n");
-               m->mothurOut("The make.group command should be in the following format: \n");
-               m->mothurOut("make.group(fasta=yourFastaFiles, groups=yourGroups). \n");
-               m->mothurOut("Example make.group(fasta=seqs1.fasta-seq2.fasta-seqs3.fasta, groups=A-B-C)\n");
-               m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFiles).\n\n");
-       }
-       catch(exception& e) {
-               m->errorOut(e, "MakeGroupCommand", "help");
-               exit(1);
-       }
-}
-
-
 //**********************************************************************************************************************
 
 int MakeGroupCommand::execute(){