globaldata = GlobalData::getInstance();
filename = globaldata->inputFileName;
read = new ReadPhilFile(filename);
+ if (globaldata->getFormat() == "shared") {
+ //read in group map info.
+ groupMap = new GroupMap(globaldata->getGroupFile());
+ }
}
catch(exception& e) {
cout << "Standard Error: " << e.what() << " has occurred in the ReadOtuCommand class Function ReadOtuCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
int ReadOtuCommand::execute(){
try {
read->read(&*globaldata);
+ if (globaldata->getFormat() == "shared") {
+ groupMap->readMap();
+ globaldata->gGroupmap = groupMap;
+
+ shared = new SharedCommand();
+ shared->execute();
+ parselist = new ParseListCommand();
+ parselist->execute();
+ }
return 0;
}
catch(exception& e) {
exit(1);
}
}
-//**********************************************************************************************************************
\ No newline at end of file
+//**********************************************************************************************************************