//**********************************************************************************************************************
int GetOtusCommand::readListGroup(){
try {
InputData* input = new InputData(listfile, "list");
ListVector* list = input->getListVector();
string lastLabel = list->getLabel();
//using first label seen if none is provided
if (label == "") { label = lastLabel; }
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(listfile); }
map<string, string> variables;
variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(listfile));
variables["[tag]"] = label;
variables["[extension]"] = m->getExtension(listfile);
string outputFileName = getOutputFileName("list", variables);
ofstream out;
m->openOutputFile(outputFileName, out);
string GroupOutputDir = outputDir;
if (outputDir == "") { GroupOutputDir += m->hasPath(groupfile); }
variables["[filename]"] = GroupOutputDir + m->getRootName(m->getSimpleName(groupfile));
variables["[extension]"] = m->getExtension(groupfile);
string outputGroupFileName = getOutputFileName("group", variables);
ofstream outGroup;
m->openOutputFile(outputGroupFileName, outGroup);
//if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
set<string> labels; labels.insert(label);
set<string> processedLabels;
set<string> userLabels = labels;
bool wroteSomething = false;
//as long as you are not at the end of the file or done wih the lines you want
while((list != NULL) && (userLabels.size() != 0)) {
if (m->control_pressed) { delete list; delete input; out.close(); outGroup.close(); m->mothurRemove(outputFileName); m->mothurRemove(outputGroupFileName);return 0; }
if(labels.count(list->getLabel()) == 1){
processList(list, groupMap, out, outGroup, wroteSomething);
processedLabels.insert(list->getLabel());
userLabels.erase(list->getLabel());
}
if ((m->anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
string saveLabel = list->getLabel();
delete list;
list = input->getListVector(lastLabel);
processList(list, groupMap, out, outGroup, wroteSomething);
processedLabels.insert(list->getLabel());
userLabels.erase(list->getLabel());
//restore real lastlabel to save below
list->setLabel(saveLabel);
}
lastLabel = list->getLabel();
delete list; list = NULL;
//get next line to process
list = input->getListVector();
}
if (m->control_pressed) { if (list != NULL) { delete list; } delete input; out.close(); outGroup.close(); m->mothurRemove(outputFileName); m->mothurRemove(outputGroupFileName); return 0; }
//output error messages about any remaining user labels
set<string>::iterator it;
bool needToRun = false;
for (it = userLabels.begin(); it != userLabels.end(); it++) {
m->mothurOut("Your file does not include the label " + *it);
if (processedLabels.count(lastLabel) != 1) {
m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
needToRun = true;
}else {
m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
}
}
//run last label if you need to
if (needToRun == true) {
if (list != NULL) { delete list; }
list = input->getListVector(lastLabel);
processList(list, groupMap, out, outGroup, wroteSomething);
delete list; list = NULL;
}
out.close();
outGroup.close();
if (wroteSomething == false) { m->mothurOut("At distance " + label + " your file does NOT contain any otus containing sequences from the groups you wish to get."); m->mothurOutEndLine(); }
outputTypes["list"].push_back(outputFileName); outputNames.push_back(outputFileName);
outputTypes["group"].push_back(outputGroupFileName); outputNames.push_back(outputGroupFileName);
return 0;
}
catch(exception& e) {
m->errorOut(e, "GetOtusCommand", "readList");
exit(1);
}
}
