vector<string> setParameters();
string getCommandName() { return "pairwise.seqs"; }
string getCommandCategory() { return "Sequence Processing"; }
+
string getHelpString();
+ string getOutputPattern(string);
string getCitation() { return "Needleman SB, Wunsch CD (1970). A general method applicable to the search for similarities in the amino acid sequence of two proteins. J Mol Biol 48: 443-53. [ for needleman ]\nGotoh O (1982). An improved algorithm for matching biological sequences. J Mol Biol 162: 705-8. [ for gotoh ] \nhttp://www.mothur.org/wiki/Pairwise.seqs"; }
string getDescription() { return "calculates pairwise distances from an unaligned fasta file"; }
outFile.setf(ios::fixed, ios::showpoint);
outFile << setprecision(4);
- pDataArray->count = pDataArray->end;
+ pDataArray->count = 0;
int startTime = time(NULL);
if(pDataArray->start == 0){ outFile << pDataArray->alignDB.getNumSeqs() << endl; }
for(int i=pDataArray->start;i<pDataArray->end;i++){
+ pDataArray->count++;
string name = pDataArray->alignDB.get(i).getName();
//pad with spaces to make compatible
}
}
- pDataArray->m->mothurOut(toString(pDataArray->end-1) + "\t" + toString(time(NULL) - startTime)); pDataArray->m->mothurOutEndLine();
+ pDataArray->m->mothurOut(toString(pDataArray->count) + "\t" + toString(time(NULL) - startTime)); pDataArray->m->mothurOutEndLine();
outFile.close();
delete alignment;