exit(1);
}
}
-
+//**********************************************************************************************************************
+string GetSAbundCommand::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 == "sabund") { outputFileName = "sabund"; }
+ 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, "GetSAbundCommand", "getOutputFileNameTag");
+ exit(1);
+ }
+}
//**********************************************************************************************************************
GetSAbundCommand::GetSAbundCommand(){
try {
listfile = validParameter.validFile(parameters, "list", true);
if (listfile == "not open") { listfile = ""; abort = true; }
else if (listfile == "not found") { listfile = ""; }
- else { format = "list"; inputfile = listfile; }
+ else { format = "list"; inputfile = listfile; m->setListFile(listfile); }
rabundfile = validParameter.validFile(parameters, "rabund", true);
if (rabundfile == "not open") { rabundfile = ""; abort = true; }
else if (rabundfile == "not found") { rabundfile = ""; }
- else { format = "rabund"; inputfile = rabundfile; }
+ else { format = "rabund"; inputfile = rabundfile; m->setRabundFile(rabundfile); }
//check for optional parameter and set defaults
try {
if (abort == true) { if (calledHelp) { return 0; } return 2; }
- filename = outputDir + m->getRootName(m->getSimpleName(inputfile)) + "sabund";
+ filename = outputDir + m->getRootName(m->getSimpleName(inputfile)) + getOutputFileNameTag("sabund");
m->openOutputFile(filename, out);
input = new InputData(inputfile, format);
set<string> processedLabels;
set<string> userLabels = labels;
- if (m->control_pressed) { outputTypes.clear(); out.close(); remove(filename.c_str()); delete sabund; delete input; return 0; }
+ if (m->control_pressed) { outputTypes.clear(); out.close(); m->mothurRemove(filename); delete sabund; delete input; return 0; }
while((sabund != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
sabund->print(out);
- if (m->control_pressed) { outputTypes.clear(); out.close(); remove(filename.c_str()); delete sabund; delete input; return 0; }
+ if (m->control_pressed) { outputTypes.clear(); out.close(); m->mothurRemove(filename); delete sabund; delete input; return 0; }
processedLabels.insert(sabund->getLabel());
userLabels.erase(sabund->getLabel());
m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
sabund->print(out);
- if (m->control_pressed) { outputTypes.clear(); out.close(); remove(filename.c_str()); delete sabund; delete input; return 0; }
+ if (m->control_pressed) { outputTypes.clear(); out.close(); m->mothurRemove(filename); delete sabund; delete input; return 0; }
processedLabels.insert(sabund->getLabel());
userLabels.erase(sabund->getLabel());
sabund->print(out);
delete sabund;
- if (m->control_pressed) { outputTypes.clear(); out.close(); remove(filename.c_str()); delete input; return 0; }
+ if (m->control_pressed) { outputTypes.clear(); out.close(); m->mothurRemove(filename); delete input; return 0; }
}