try {
CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta);
CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
+ CommandParameter poutput("output", "String", "", "", "", "", "",false,false); parameters.push_back(poutput);
CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
}
}
//**********************************************************************************************************************
+string MakeGroupCommand::getOutputFileNameTag(string type, string inputName=""){
+ try {
+ string outputFileName = "";
+ map<string, vector<string> >::iterator it;
+
+ //is this a type this command creates
+ it = outputTypes.find(type);
+ if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
+ else {
+ if (type == "group") { outputFileName = "groups"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
+ }
+ return outputFileName;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "MakeGroupCommand", "getOutputFileNameTag");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
MakeGroupCommand::MakeGroupCommand(){
try {
abort = true; calledHelp = true;
//erase from file list
fastaFileNames.erase(fastaFileNames.begin()+i);
i--;
- }else{ filename += m->getRootName(m->getSimpleName(fastaFileNames[i])); }
+ }else{ filename += m->getRootName(m->getSimpleName(fastaFileNames[i])); m->setFastaFile(fastaFileNames[i]); }
}
}
//prevent giantic file name
- if (fastaFileNames.size() > 3) { filename = outputDir + "merge.groups"; }
- else { filename += "groups"; }
+ if (fastaFileNames.size() > 3) { filename = outputDir + "merge." + getOutputFileNameTag("group"); }
+ else { filename += getOutputFileNameTag("group"); }
//make sure there is at least one valid file left
if (fastaFileNames.size() == 0) { m->mothurOut("no valid files."); m->mothurOutEndLine(); abort = true; }
for (int i = 0; i < fastaFileNames.size(); i++) {
- if (m->control_pressed) { outputTypes.clear(); out.close(); remove(filename.c_str()); return 0; }
+ if (m->control_pressed) { outputTypes.clear(); out.close(); m->mothurRemove(filename); return 0; }
ifstream in;
m->openInputFile(fastaFileNames[i], in);
Sequence seq(in, "no align"); m->gobble(in);
- if (m->control_pressed) { outputTypes.clear(); in.close(); out.close(); remove(filename.c_str()); return 0; }
+ if (m->control_pressed) { outputTypes.clear(); in.close(); out.close(); m->mothurRemove(filename); return 0; }
if (seq.getName() != "") { out << seq.getName() << '\t' << groupsNames[i] << endl; }
}