reworked amova / homova / anosim

[mothur.git] / makegroupcommand.cpp

diff --git a/makegroupcommand.cpp b/makegroupcommand.cpp
index c427db5b385c166176f3f3a5272df2f72c3400b8..1c04fecb477d09e0e6de73b1307a3878fcc8e4b3 100644 (file)
--- a/makegroupcommand.cpp
+++ b/makegroupcommand.cpp
@@ -13,7 +13,7 @@
 //**********************************************************************************************************************
 vector<string> MakeGroupCommand::getValidParameters(){ 
        try {
-               string Array[] =  {"fasta", "groups","outputdir","inputdir"};
+               string Array[] =  {"fasta", "output","groups","outputdir","inputdir"};
                vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
                return myArray;
        }
@@ -25,8 +25,7 @@ vector<string> MakeGroupCommand::getValidParameters(){
 //**********************************************************************************************************************
 MakeGroupCommand::MakeGroupCommand(){  
        try {
-               abort = true;
-               //initialize outputTypes
+               abort = true; calledHelp = true; 
                vector<string> tempOutNames;
                outputTypes["group"] = tempOutNames;
        }
@@ -63,15 +62,15 @@ vector<string> MakeGroupCommand::getRequiredFiles(){
 MakeGroupCommand::MakeGroupCommand(string option)  {
        try {
                
-               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
-                       string AlignArray[] =  {"fasta","groups","outputdir","inputdir"};
+                       string AlignArray[] =  {"fasta","groups","output","outputdir","inputdir"};
                        vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
                        
                        OptionParser parser(option);
@@ -92,8 +91,6 @@ MakeGroupCommand::MakeGroupCommand(string option)  {
                        //if the user changes the input directory command factory will send this info to us in the output parameter 
                        string inputDir = validParameter.validFile(parameters, "inputdir", false);              
                        if (inputDir == "not found"){   inputDir = "";          }
-                       
-                       filename = outputDir;
 
                        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;  }
@@ -155,13 +152,17 @@ MakeGroupCommand::MakeGroupCommand(string option)  {
                        //if the user changes the output directory command factory will send this info to us in the output parameter 
                        outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = "";         }
                        
+                       output = validParameter.validFile(parameters, "output", false);                 
+                       if (output == "not found") { output = "";  }
+                       else{ filename = output; }
+                       
                        groups = validParameter.validFile(parameters, "groups", false);                 
                        if (groups == "not found") { m->mothurOut("groups is a required parameter for the make.group command."); m->mothurOutEndLine(); abort = true;  }
                        else { m->splitAtDash(groups, groupsNames);     }
 
                        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");
@@ -178,9 +179,10 @@ 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 and groups, both are required.\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("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");
        }
@@ -195,10 +197,10 @@ void MakeGroupCommand::help(){
 
 int MakeGroupCommand::execute(){
        try {
-               if (abort == true) {    return 0;       }
+               if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
                
                if (outputDir == "") { outputDir = m->hasPath(fastaFileNames[0]); }
-               
+                       
                filename = outputDir + filename;
                
                ofstream out;