//allow user to run help
if(option == "help") { help(); abort = true; calledHelp = true; }
+ else if(option == "citation") { citation(); abort = true; calledHelp = true;}
else {
vector<string> myArray = setParameters();
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); }
sabundfile = validParameter.validFile(parameters, "sabund", true);
if (sabundfile == "not open") { sabundfile = ""; abort = true; }
else if (sabundfile == "not found") { sabundfile = ""; }
- else { format = "sabund"; inputfile = sabundfile; }
+ else { format = "sabund"; inputfile = sabundfile; m->setSabundFile(sabundfile); }
//check for optional parameter and set defaults
set<string> processedLabels;
set<string> userLabels = labels;
- if (m->control_pressed) { outputTypes.clear(); out.close(); remove(filename.c_str()); delete rabund; delete input; return 0; }
+ if (m->control_pressed) { outputTypes.clear(); out.close(); m->mothurRemove(filename); delete rabund; delete input; return 0; }
while((rabund != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
if(allLines == 1 || labels.count(rabund->getLabel()) == 1){
m->mothurOut(rabund->getLabel()); m->mothurOutEndLine();
- if (m->control_pressed) { outputTypes.clear(); out.close(); remove(filename.c_str()); delete input; delete rabund; return 0; }
+ if (m->control_pressed) { outputTypes.clear(); out.close(); m->mothurRemove(filename); delete input; delete rabund; return 0; }
if(sorted) { rabund->print(out); }
else { rabund->nonSortedPrint(out); }
-
- delete rabund;
processedLabels.insert(rabund->getLabel());
userLabels.erase(rabund->getLabel());
m->mothurOut(rabund->getLabel()); m->mothurOutEndLine();
- if (m->control_pressed) { outputTypes.clear(); out.close(); remove(filename.c_str()); delete input; delete rabund; return 0; }
+ if (m->control_pressed) { outputTypes.clear(); out.close(); m->mothurRemove(filename); delete input; delete rabund; return 0; }
if(sorted) { rabund->print(out); }
else { rabund->nonSortedPrint(out); }
- delete rabund;
-
processedLabels.insert(rabund->getLabel());
userLabels.erase(rabund->getLabel());
m->mothurOut(rabund->getLabel()); m->mothurOutEndLine();
- if (m->control_pressed) { outputTypes.clear(); out.close(); remove(filename.c_str()); delete input; delete rabund; return 0; }
+ if (m->control_pressed) { outputTypes.clear(); out.close(); m->mothurRemove(filename); delete input; delete rabund; return 0; }
if(sorted) { rabund->print(out); }
else { rabund->nonSortedPrint(out); }