vector<string> Estimators;
MothurOut* m;
string output;
- int numNewFasta;
+ int numNewFasta, count;
string countends;
distanceData(){}
ofstream outFile(pDataArray->dFileName.c_str(), ios::trunc);
outFile.setf(ios::fixed, ios::showpoint);
outFile << setprecision(4);
-
+ pDataArray->count = 0;
if (pDataArray->output != "square") {
if((pDataArray->output == "lt") && (pDataArray->startLine == 0)){ outFile << pDataArray->alignDB.getNumSeqs() << endl; }
if (pDataArray->output == "lt") { outFile << endl; }
if(i % 100 == 0){
- pDataArray->m->mothurOut(toString(i) + "\t" + toString(time(NULL) - startTime)); pDataArray->m->mothurOutEndLine();
- }
-
+ pDataArray->m->mothurOutJustToScreen(toString(i) + "\t" + toString(time(NULL) - startTime)+"\n"); }
+ pDataArray->count++;
}
- pDataArray->m->mothurOut(toString(pDataArray->endLine-1) + "\t" + toString(time(NULL) - startTime)); pDataArray->m->mothurOutEndLine();
+ pDataArray->m->mothurOutJustToScreen(toString(pDataArray->count) + "\t" + toString(time(NULL) - startTime)+"\n");
}else{
if(pDataArray->startLine == 0){ outFile << pDataArray->alignDB.getNumSeqs() << endl; }
outFile << endl;
if(i % 100 == 0){
- pDataArray->m->mothurOut(toString(i) + "\t" + toString(time(NULL) - startTime)); pDataArray->m->mothurOutEndLine();
+ pDataArray->m->mothurOutJustToScreen(toString(i) + "\t" + toString(time(NULL) - startTime)+"\n");
}
-
+ pDataArray->count++;
}
- pDataArray->m->mothurOut(toString(pDataArray->endLine-1) + "\t" + toString(time(NULL) - startTime)); pDataArray->m->mothurOutEndLine();
+ pDataArray->m->mothurOutJustToScreen(toString(pDataArray->count) + "\t" + toString(time(NULL) - startTime)+"\n");
}
outFile.close();
vector<string> setParameters();
string getCommandName() { return "dist.seqs"; }
string getCommandCategory() { return "Sequence Processing"; }
+
string getHelpString();
+ string getOutputPattern(string);
string getCitation() { return "Schloss PD (2010). The effects of alignment quality, distance calculation method, sequence filtering, and region on the analysis of 16S rRNA gene-based studies. PLoS Comput Biol 6: e1000844. \nhttp://www.mothur.org/wiki/Dist.seqs"; }
string getDescription() { return "calculate the pairwaise distances between aligned sequences"; }