//**********************************************************************************************************************
vector<seqData> ChimeraPerseusCommand::loadSequences(SequenceParser& parser, string group){
try {
vector<Sequence> thisGroupsSeqs = parser.getSeqs(group);
map<string, string> nameMap = parser.getNameMap(group);
map<string, string>::iterator it;
vector<seqData> sequences;
bool error = false;
for (int i = 0; i < thisGroupsSeqs.size(); i++) {
if (m->control_pressed) { return sequences; }
it = nameMap.find(thisGroupsSeqs[i].getName());
if (it == nameMap.end()) { error = true; m->mothurOut("[ERROR]: " + thisGroupsSeqs[i].getName() + " is in your fasta file and not in your namefile, please correct."); m->mothurOutEndLine(); }
else {
int num = m->getNumNames(it->second);
sequences.push_back(seqData(thisGroupsSeqs[i].getName(), thisGroupsSeqs[i].getUnaligned(), num));
}
}
if (error) { m->control_pressed = true; }
//sort by frequency
sort(sequences.rbegin(), sequences.rend());
return sequences;
}
catch(exception& e) {
m->errorOut(e, "ChimeraPerseusCommand", "loadSequences");
exit(1);
}
}
//**********************************************************************************************************************
int SplitGroupCommand::runNameGroup(){
try {
SequenceParser* parser;
if (namefile == "") { parser = new SequenceParser(groupfile, fastafile); }
else { parser = new SequenceParser(groupfile, fastafile, namefile); }
if (m->control_pressed) { delete parser; return 0; }
vector<string> namesGroups = parser->getNamesOfGroups();
SharedUtil util; util.setGroups(Groups, namesGroups);
string fastafileRoot = outputDir + m->getRootName(m->getSimpleName(fastafile));
string namefileRoot = outputDir + m->getRootName(m->getSimpleName(namefile));
m->mothurOutEndLine();
for (int i = 0; i < Groups.size(); i++) {
m->mothurOut("Processing group: " + Groups[i]); m->mothurOutEndLine();
map<string, string> variables;
variables["[filename]"] = fastafileRoot;
variables["[group]"] = Groups[i];
string newFasta = getOutputFileName("fasta",variables);
variables["[filename]"] = namefileRoot;
string newName = getOutputFileName("name",variables);
parser->getSeqs(Groups[i], newFasta, "/ab=", "/", false);
outputNames.push_back(newFasta); outputTypes["fasta"].push_back(newFasta);
if (m->control_pressed) { delete parser; for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
if (namefile != "") {
parser->getNameMap(Groups[i], newName);
outputNames.push_back(newName); outputTypes["name"].push_back(newName);
}
if (m->control_pressed) { delete parser; for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
}
delete parser;
return 0;
}
catch(exception& e) {
m->errorOut(e, "SplitGroupCommand", "runNameGroup");
exit(1);
}
}