vector<string> setParameters();
string getCommandName() { return "classify.seqs"; }
string getCommandCategory() { return "Phylotype Analysis"; }
- string getOutputFileNameTag(string, string);
+
string getHelpString();
+ string getOutputPattern(string);
string getCitation() { return "Wang Q, Garrity GM, Tiedje JM, Cole JR (2007). Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol 73: 5261-7. [ for Bayesian classifier ] \nAltschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997). Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25: 3389-402. [ for BLAST ] \nDeSantis TZ, Hugenholtz P, Larsen N, Rojas M, Brodie EL, Keller K, Huber T, Dalevi D, Hu P, Andersen GL (2006). Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol 72: 5069-72. [ for kmer ] \nhttp://www.mothur.org/wiki/Classify.seqs"; }
string getDescription() { return "classify sequences"; }
inFASTA.seekg(pDataArray->start-1); pDataArray->m->gobble(inFASTA);
}
- pDataArray->count = pDataArray->end;
-
//make classify
Classify* myclassify;
string outputMethodTag = pDataArray->method + ".";
if (pDataArray->m->control_pressed) { delete myclassify; return 0; }
- int count = 0;
+ pDataArray->count = 0;
for(int i = 0; i < pDataArray->end; i++){ //end is the number of sequences to process
if (pDataArray->m->control_pressed) { delete myclassify; return 0; }
if (myclassify->getFlipped()) { outAcc << candidateSeq->getName() << endl; }
- count++;
+ pDataArray->count++;
}
delete candidateSeq;
//report progress
- if((count) % 100 == 0){ pDataArray->m->mothurOut("Processing sequence: " + toString(count)); pDataArray->m->mothurOutEndLine(); }
+ if((pDataArray->count) % 100 == 0){ pDataArray->m->mothurOutJustToScreen("Processing sequence: " + toString(pDataArray->count)+"\n"); }
}
//report progress
- if((count) % 100 != 0){ pDataArray->m->mothurOut("Processing sequence: " + toString(count)); pDataArray->m->mothurOutEndLine(); }
+ if((pDataArray->count) % 100 != 0){ pDataArray->m->mothurOutJustToScreen("Processing sequence: " + toString(pDataArray->count)+"\n"); }
delete myclassify;
inFASTA.close();