string errorOff = "no error";
//errorOff = "";
+ //if user provided an order file containing the order the shared file should be in read it
+ if (globaldata->getOrderGroupFile() != "") { readOrderFile(); }
+
//read in listfile
read = new ReadOTUFile(globaldata->inputFileName);
read->read(&*globaldata);
void SharedCommand::printSharedData(vector<SharedRAbundVector*> thislookup) {
try {
- sort(thislookup.begin(), thislookup.end(), compareSharedRabunds);
-
- //initialize bin values
- for (int i = 0; i < thislookup.size(); i++) {
-//cout << "in printData " << thislookup[i]->getLabel() << '\t' << thislookup[i]->getGroup() << endl;
- out << thislookup[i]->getLabel() << '\t' << thislookup[i]->getGroup() << '\t';
- thislookup[i]->print(out);
+ if (order.size() == 0) { //user has not specified an order so do aplabetically
+ sort(thislookup.begin(), thislookup.end(), compareSharedRabunds);
+
+ //initialize bin values
+ for (int i = 0; i < thislookup.size(); i++) {
+ out << thislookup[i]->getLabel() << '\t' << thislookup[i]->getGroup() << '\t';
+ thislookup[i]->print(out);
+
+ RAbundVector rav = thislookup[i]->getRAbundVector();
+ openOutputFileAppend(fileroot + thislookup[i]->getGroup() + ".rabund", *(filehandles[thislookup[i]->getGroup()]));
+ rav.print(*(filehandles[thislookup[i]->getGroup()]));
+ (*(filehandles[thislookup[i]->getGroup()])).close();
+ }
+ }else{
+ //create a map from groupName to each sharedrabund
+ map<string, SharedRAbundVector*> myMap;
+ map<string, SharedRAbundVector*>::iterator myIt;
+
+ for (int i = 0; i < thislookup.size(); i++) {
+ myMap[thislookup[i]->getGroup()] = thislookup[i];
+ }
+
- RAbundVector rav = thislookup[i]->getRAbundVector();
- openOutputFileAppend(fileroot + thislookup[i]->getGroup() + ".rabund", *(filehandles[thislookup[i]->getGroup()]));
- rav.print(*(filehandles[thislookup[i]->getGroup()]));
- (*(filehandles[thislookup[i]->getGroup()])).close();
+ //loop through ordered list and print the rabund
+ for (int i = 0; i < order.size(); i++) {
+ myIt = myMap.find(order[i]);
+
+ if(myIt != myMap.end()) { //we found it
+ out << (myIt->second)->getLabel() << '\t' << (myIt->second)->getGroup() << '\t';
+ (myIt->second)->print(out);
+
+ RAbundVector rav = (myIt->second)->getRAbundVector();
+ openOutputFileAppend(fileroot + (myIt->second)->getGroup() + ".rabund", *(filehandles[(myIt->second)->getGroup()]));
+ rav.print(*(filehandles[(myIt->second)->getGroup()]));
+ (*(filehandles[(myIt->second)->getGroup()])).close();
+ }else{
+ m->mothurOut("Can't find shared info for " + order[i] + ", skipping."); m->mothurOutEndLine();
+ }
+ }
+
}
}
}
-
+//**********************************************************************************************************************
+int SharedCommand::readOrderFile() {
+ try {
+ //remove old names
+ order.clear();
+
+ ifstream in;
+ openInputFile(globaldata->getOrderGroupFile(), in);
+ string thisGroup;
+
+ while(!in.eof()){
+ in >> thisGroup; gobble(in);
+
+ order.push_back(thisGroup);
+
+ if (m->control_pressed) { order.clear(); break; }
+ }
+ in.close();
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SharedCommand", "readOrderFile");
+ exit(1);
+ }
+}
//**********************************************************************************************************************
bool SharedCommand::isValidGroup(string groupname, vector<string> groups) {