string GlobalData::getNameFile() { return namefile; }
string GlobalData::getGroupFile() { return groupfile; }
string GlobalData::getOrderFile() { return orderfile; }
+string GlobalData::getOrderGroupFile() { return ordergroup; }
string GlobalData::getTreeFile() { return treefile; }
string GlobalData::getSharedFile() { return sharedfile; }
string GlobalData::getFormat() { return format; }
void GlobalData::setSharedFile(string file) { sharedfile = file; inputFileName = file; }
void GlobalData::setNameFile(string file) { namefile = file; }
void GlobalData::setOrderFile(string file) { orderfile = file; }
+void GlobalData::setOrderGroupFile(string file) { ordergroup = file; }
void GlobalData::setFormat(string Format) { format = Format; }
/******************************************************/
GlobalData::GlobalData() {
+ m = MothurOut::getInstance();
//option definitions should go here...
clear();
gListVector = NULL;
namefile = ""; //do we need this?
groupfile = ""; //do we need this?
orderfile = "";
+ ordergroup = "";
// fastafile = ""; //do we need this?
treefile = "";
sharedfile = "";
+ format = "";
}
labels.clear(); Groups.clear();
allLines = 1;
runParse = true;
+ names.clear();
}
catch(exception& e) {
- errorOut(e, "GlobalData", "newRead");
+ m->errorOut(e, "GlobalData", "newRead");
exit(1);
}
}
if (nameMap != NULL) { delete nameMap; nameMap = NULL; }
}
catch(exception& e) {
- errorOut(e, "GlobalData", "~GlobalData");
+ m->errorOut(e, "GlobalData", "~GlobalData");
exit(1);
}
}