names.push_back(temp.getName());
database->addSequence(temp);
}
- database->generateDB();
+ if ((method == "kmer") && (!shortcuts)) {;} //don't print
+ else {database->generateDB(); }
}else if ((method == "kmer") && (!needToGenerate)) {
ifstream kmerFileTest(kmerDBName.c_str());
database->readKmerDB(kmerFileTest);
}
fastaFile.close();
- database->generateDB();
+ if ((method == "kmer") && (!shortcuts)) {;} //don't print
+ else {database->generateDB(); }
}else if ((method == "kmer") && (!needToGenerate)) {
ifstream kmerFileTest(kmerDBName.c_str());
m->mothurOutEndLine();
m->mothurOut("Reading in the " + file + " taxonomy...\t"); cout.flush();
-
+ if (m->debug) { m->mothurOut("[DEBUG]: Taxonomies read in...\n"); }
+
#ifdef USE_MPI
int pid, num, processors;
vector<unsigned long long> positions;
MPI_File inMPI;
MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
MPI_Comm_size(MPI_COMM_WORLD, &processors);
-
- //char* inFileName = new char[file.length()];
- //memcpy(inFileName, file.c_str(), file.length());
char inFileName[1024];
strcpy(inFileName, file.c_str());
istringstream iss (tempBuf,istringstream::in);
iss >> name; m->gobble(iss);
iss >> taxInfo;
+ if (m->debug) { m->mothurOut("[DEBUG]: name = " + name + " tax = " + taxInfo + "\n"); }
taxonomy[name] = taxInfo;
phyloTree->addSeqToTree(name, taxInfo);
}
MPI_File_close(&inMPI);
MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
-#else
- ifstream inTax;
- m->openInputFile(file, inTax);
-
- //read template seqs and save
- while (!inTax.eof()) {
- inTax >> name; m->gobble(inTax);
- inTax >> taxInfo;
-
- taxonomy[name] = taxInfo;
-
- phyloTree->addSeqToTree(name, taxInfo);
-
- m->gobble(inTax);
- }
- inTax.close();
+#else
+
+ taxonomy.clear();
+ m->readTax(file, taxonomy);
+ for (map<string, string>::iterator itTax = taxonomy.begin(); itTax != taxonomy.end(); itTax++) { phyloTree->addSeqToTree(itTax->first, itTax->second); }
#endif
-
phyloTree->assignHeirarchyIDs(0);
phyloTree->setUp(file);