int GetRelAbundCommand::execute(){
try {
if (abort) { if (calledHelp) { return 0; } return 2; }
map<string, string> variables;
variables["[filename]"] = outputDir + util.getRootName(util.getSimpleName(sharedfile));
string outputFileName = getOutputFileName("relabund", variables);
ofstream out;
util.openOutputFile(outputFileName, out);
out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
InputData input(sharedfile, "sharedfile", Groups);
lookup = input.getSharedRAbundVectors();
Groups = lookup->getNamesGroups();
string lastLabel = lookup->getLabel();
vector<string> binLabels = lookup->getOTUNames();
out << "label\tGroup\tnumOtus";
for (int i = 0; i < binLabels.size(); i++) { out << '\t' << binLabels[i]; } out << endl;
//if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
set<string> processedLabels;
set<string> userLabels = labels;
//as long as you are not at the end of the file or done wih the lines you want
while((lookup != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
if (m->getControl_pressed()) { outputTypes.clear(); delete lookup; out.close(); util.mothurRemove(outputFileName); return 0; }
if(allLines == 1 || labels.count(lookup->getLabel()) == 1){
m->mothurOut(lookup->getLabel()+"\n");
getRelAbundance(lookup, out);
processedLabels.insert(lookup->getLabel()); userLabels.erase(lookup->getLabel());
}
if ((util.anyLabelsToProcess(lookup->getLabel(), userLabels, "") ) && (processedLabels.count(lastLabel) != 1)) {
string saveLabel = lookup->getLabel();
delete lookup;
lookup = input.getSharedRAbundVectors(lastLabel);
m->mothurOut(lookup->getLabel()+"\n");
getRelAbundance(lookup, out);
processedLabels.insert(lookup->getLabel()); userLabels.erase(lookup->getLabel());
//restore real lastlabel to save below
lookup->setLabels(saveLabel);
}
lastLabel = lookup->getLabel();
//prevent memory leak
delete lookup;
if (m->getControl_pressed()) { outputTypes.clear(); out.close(); util.mothurRemove(outputFileName); return 0; }
//get next line to process
lookup = input.getSharedRAbundVectors();
}
if (m->getControl_pressed()) { outputTypes.clear(); out.close(); util.mothurRemove(outputFileName); return 0; }
//output error messages about any remaining user labels
bool needToRun = false;
for (set<string>::iterator 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 + ".\n"); needToRun = true; }
else { m->mothurOut(". Please refer to " + lastLabel + ".\n"); }
}
//run last label if you need to
if (needToRun ) {
delete lookup;
lookup = input.getSharedRAbundVectors(lastLabel);
m->mothurOut(lookup->getLabel()+"\n");
getRelAbundance(lookup, out);
delete lookup;
}
out.close();
if (m->getControl_pressed()) { outputTypes.clear(); util.mothurRemove(outputFileName); return 0; }
m->mothurOut("\nOutput File Names: \n");
m->mothurOut(outputFileName); m->mothurOutEndLine(); outputNames.push_back(outputFileName); outputTypes["relabund"].push_back(outputFileName);
m->mothurOutEndLine();
//set relabund file as new current relabundfile
string currentName = "";
itTypes = outputTypes.find("relabund");
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { currentName = (itTypes->second)[0]; current->setRelAbundFile(currentName); }
}
return 0;
}
catch(exception& e) {
m->errorOut(e, "GetRelAbundCommand", "execute");
exit(1);
}
}
int GetRelAbundCommand::execute(){
try {
if (abort == true) { if (calledHelp) { return 0; } return 2; }
string outputFileName = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + "relabund";
ofstream out;
m->openOutputFile(outputFileName, out);
out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
input = new InputData(sharedfile, "sharedfile");
lookup = input->getSharedRAbundVectors();
string lastLabel = lookup[0]->getLabel();
//if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
set<string> processedLabels;
set<string> userLabels = labels;
//as long as you are not at the end of the file or done wih the lines you want
while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
if (m->control_pressed) { outputTypes.clear(); for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } m->clearGroups(); delete input; out.close(); m->mothurRemove(outputFileName); return 0; }
if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){
m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
if (!m->printedHeaders) { lookup[0]->printHeaders(out); }
getRelAbundance(lookup, out);
processedLabels.insert(lookup[0]->getLabel());
userLabels.erase(lookup[0]->getLabel());
}
if ((m->anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
string saveLabel = lookup[0]->getLabel();
for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
lookup = input->getSharedRAbundVectors(lastLabel);
m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
if (!m->printedHeaders) { lookup[0]->printHeaders(out); }
getRelAbundance(lookup, out);
processedLabels.insert(lookup[0]->getLabel());
userLabels.erase(lookup[0]->getLabel());
//restore real lastlabel to save below
lookup[0]->setLabel(saveLabel);
}
lastLabel = lookup[0]->getLabel();
//prevent memory leak
for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; lookup[i] = NULL; }
if (m->control_pressed) { outputTypes.clear(); m->clearGroups(); delete input; out.close(); m->mothurRemove(outputFileName); return 0; }
//get next line to process
lookup = input->getSharedRAbundVectors();
}
if (m->control_pressed) { outputTypes.clear(); m->clearGroups(); delete input; out.close(); m->mothurRemove(outputFileName); 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) {
for (int i = 0; i < lookup.size(); i++) { if (lookup[i] != NULL) { delete lookup[i]; } }
lookup = input->getSharedRAbundVectors(lastLabel);
m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
if (!m->printedHeaders) { lookup[0]->printHeaders(out); }
getRelAbundance(lookup, out);
for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
}
//reset groups parameter
m->clearGroups();
delete input;
out.close();
if (m->control_pressed) { outputTypes.clear(); m->mothurRemove(outputFileName); return 0;}
m->mothurOutEndLine();
m->mothurOut("Output File Names: "); m->mothurOutEndLine();
m->mothurOut(outputFileName); m->mothurOutEndLine(); outputNames.push_back(outputFileName); outputTypes["relabund"].push_back(outputFileName);
m->mothurOutEndLine();
//set relabund file as new current relabundfile
string current = "";
itTypes = outputTypes.find("relabund");
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setRelAbundFile(current); }
}
return 0;
}
catch(exception& e) {
m->errorOut(e, "GetRelAbundCommand", "execute");
exit(1);
}
}
