namefile = m->getNameFile();
if (namefile != "") { m->mothurOut("Using " + namefile + " as input file for the name parameter."); m->mothurOutEndLine(); }
else { m->mothurOut("You have no current namefile and the name parameter is required."); m->mothurOutEndLine(); abort = true; }
- }
+ }else { m->setNameFile(namefile); }
groupfile = validParameter.validFile(parameters, "group", true);
if (groupfile == "not open") { abort = true; }
else if (groupfile == "not found") { groupfile = ""; }
+ else { m->setGroupFile(groupfile); }
groups = validParameter.validFile(parameters, "groups", false);
if (groups == "not found") { groups = "all"; }
if (abort == true) { if (calledHelp) { return 0; } return 2; }
ofstream out;
- string outputFileName = outputDir + m->getRootName(m->getSimpleName(namefile)) + ".seq.count";
+ string outputFileName = outputDir + m->getRootName(m->getSimpleName(namefile)) + "seq.count";
m->openOutputFile(outputFileName, out); outputTypes["summary"].push_back(outputFileName);
- out << "Representative Sequence\t total\t";
+ out << "Representative_Sequence\ttotal\t";
GroupMap* groupMap;
if (groupfile != "") {
//make sure groups are valid. takes care of user setting groupNames that are invalid or setting groups=all
SharedUtil* util = new SharedUtil();
- util->setGroups(Groups, groupMap->namesOfGroups);
+ vector<string> nameGroups = groupMap->getNamesOfGroups();
+ util->setGroups(Groups, nameGroups);
delete util;
//sort groupNames so that the group title match the counts below, this is needed because the map object automatically sorts
if (groupfile != "") { delete groupMap; }
- if (m->control_pressed) { remove(outputFileName.c_str()); return 0; }
+ if (m->control_pressed) { m->mothurRemove(outputFileName); return 0; }
m->mothurOutEndLine();
m->mothurOut("Output File Name: "); m->mothurOutEndLine();