}
}
//**********************************************************************************************************************
+string MergeGroupsCommand::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 == "shared") { outputFileName = "merge" + m->getExtension(inputName); }
+ else if (type == "group") { outputFileName = "merge" + m->getExtension(inputName); }
+ 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, "MergeGroupsCommand", "getOutputFileNameTag");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
MergeGroupsCommand::MergeGroupsCommand(){
try {
abort = true; calledHelp = true;
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(sharedfile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(sharedfile)) + "merge" + m->getExtension(sharedfile);
- outputTypes["shared"].push_back(outputFileName); outputNames.push_back(outputFileName);
+ string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(sharedfile)) + getOutputFileNameTag("shared", sharedfile);
+ outputTypes["shared"].push_back(outputFileName); outputNames.push_back(outputFileName);
ofstream out;
m->openOutputFile(outputFileName, out);
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(groupfile); }
- string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(groupfile)) + "merge" + m->getExtension(groupfile);
+ string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(groupfile)) + getOutputFileNameTag("group", groupfile);
outputTypes["group"].push_back(outputFileName); outputNames.push_back(outputFileName);
ofstream out;