//**********************************************************************************************************************
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;
}
//**********************************************************************************************************************
MakeGroupCommand::MakeGroupCommand(){
try {
- abort = true;
- //initialize outputTypes
+ abort = true; calledHelp = true;
vector<string> tempOutNames;
outputTypes["group"] = tempOutNames;
}
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);
//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; }
//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");
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");
}
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;
m->mothurOutEndLine();
m->mothurOut("Output File Name: " + filename); m->mothurOutEndLine(); outputNames.push_back(filename); outputTypes["group"].push_back(filename);
m->mothurOutEndLine();
-
+
+ //set group file as new current groupfile
+ string current = "";
+ itTypes = outputTypes.find("group");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setGroupFile(current); }
+ }
+
return 0;
}
catch(exception& e) {