//cout << "a = " << a[i] << " t = " << t[i] << " g = " << g[i] << " c = " << c[i] << endl;
}
- mothurOut("Filter removed " + toString(numColRemoved) + " columns."); mothurOutEndLine();
+ m->mothurOut("Filter removed " + toString(numColRemoved) + " columns."); m->mothurOutEndLine();
return filterString;
}
catch(exception& e) {
- errorOut(e, "Chimera", "createFilter");
+ m->errorOut(e, "Chimera", "createFilter");
exit(1);
}
}
return maskMap;
}
catch(exception& e) {
- errorOut(e, "Chimera", "runFilter");
+ m->errorOut(e, "Chimera", "runFilter");
exit(1);
}
}
vector<Sequence*> Chimera::readSeqs(string file) {
try {
- mothurOut("Reading sequences... "); cout.flush();
+ m->mothurOut("Reading sequences... "); cout.flush();
ifstream in;
openInputFile(file, in);
+
vector<Sequence*> container;
int count = 0;
length = 0;
}
in.close();
- mothurOut("Done."); mothurOutEndLine();
+ m->mothurOut("Done."); m->mothurOutEndLine();
return container;
}
catch(exception& e) {
- errorOut(e, "Chimera", "readSeqs");
+ m->errorOut(e, "Chimera", "readSeqs");
exit(1);
}
}
}
}
catch(exception& e) {
- errorOut(e, "Chimera", "setMask");
+ m->errorOut(e, "Chimera", "setMask");
exit(1);
}
}
}
catch(exception& e) {
- errorOut(e, "Chimera", "readQuantiles");
+ m->errorOut(e, "Chimera", "readQuantiles");
exit(1);
}
}
}
}
- if(spot == -1) { mothurOut("Error: Could not find sequence."); mothurOutEndLine(); return NULL; }
+ if(spot == -1) { m->mothurOut("Error: Could not find sequence."); m->mothurOutEndLine(); return NULL; }
temp = new Sequence(templateSeqs[spot]->getName(), templateSeqs[spot]->getAligned());
return temp;
}
catch(exception& e) {
- errorOut(e, "Chimera", "getSequence");
+ m->errorOut(e, "Chimera", "getSequence");
exit(1);
}
}