fastafile = m->getFastaFile();
if (fastafile != "") { m->mothurOut("Using " + fastafile + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
else { m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
- }
+ }else { m->setFastaFile(fastafile); }
namefile = validParameter.validFile(parameters, "name", true);
if (namefile == "not open") { namefile = ""; abort = true; }
else if (namefile == "not found") { namefile = ""; }
+ else { m->setNameFile(namefile); }
//if the user changes the output directory command factory will send this info to us in the output parameter
outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){
int count = 0;
while(!in.eof()){
- if (m->control_pressed) { in.close(); out.close(); remove(outfile.c_str()); return 0; }
+ if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outfile); return 0; }
Sequence seq(in); m->gobble(in);
if (seq.getName() != "") {
in.close();
out.close();
- if (m->control_pressed) { remove(outfile.c_str()); return 0; }
+ if (m->control_pressed) { m->mothurRemove(outfile); return 0; }
sort(pound.begin(), pound.end());
sort(dash.begin(), dash.end());
int ptile97_5 = int(size * 0.975);
int ptile100 = size - 1;
- if (m->control_pressed) { remove(outfile.c_str()); return 0; }
+ if (m->control_pressed) { m->mothurRemove(outfile); return 0; }
m->mothurOutEndLine();
m->mothurOut("\t\tPound\tDash\tPlus\tEqual\tLoop\tTilde\tTotal"); m->mothurOutEndLine();