sharedfile = m->getSharedFile();
if (sharedfile != "") { m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
else { m->mothurOut("You have no current sharedfile and the shared parameter is required."); m->mothurOutEndLine(); abort = true; }
- }
+ }else { m->setSharedFile(sharedfile); }
//if the user changes the output directory command factory will send this info to us in the output parameter
ifstream intemp;
m->openInputFile(tempdistFileName, intemp);
- for (int i = 0; i < calcDists.size(); i++) {
+ for (int k = 0; k < calcDists.size(); k++) {
int size = 0;
intemp >> size; m->gobble(intemp);
intemp >> seq1 >> seq2 >> dist; m->gobble(intemp);
seqDist tempDist(seq1, seq2, dist);
- calcDists[i].push_back(tempDist);
+ calcDists[k].push_back(tempDist);
}
}
intemp.close();
outputFileHandle << '\t';
sumCalculators[i]->print(outputFileHandle);
- seqDist temp(l, k, (1.0 - tempdata[0]));
+ seqDist temp(l, k, tempdata[0]);
calcDists[i].push_back(temp);
}
outputFileHandle << endl;