RAbundVector ListVector::getRAbundVector() {
try {
RAbundVector rav;
for(int i=0; i<data.size(); i++) {
int binSize = m->getNumNames(data[i]);
rav.push_back(binSize);
}
// This was here before to output data in a nice format, but it screws up the name mapping steps
// sort(rav.rbegin(), rav.rend());
//
// for(int i=data.size()-1;i>=0;i--){
// if(rav.get(i) == 0){ rav.pop_back(); }
// else{
// break;
// }
// }
rav.setLabel(label);
return rav;
}
catch(exception& e) {
m->errorOut(e, "ListVector", "getRAbundVector");
exit(1);
}
}
RAbundVector SAbundVector::getRAbundVector(){
try {
RAbundVector rav;
for(int i=1;i < data.size();i++){
for(int j=0;j<data[i];j++){
rav.push_back(i);
}
}
sort(rav.rbegin(), rav.rend());
rav.setLabel(label);
return rav;
}
catch(exception& e) {
m->errorOut(e, "SAbundVector", "getRAbundVector");
exit(1);
}
}
RAbundVector Geom::getRAbundVector(SAbundVector* rank){
vector <int> rData;
int mr = 1;
int nb = 0;
int ns = 0;
for(int i = rank->size()-1; i > 0; i--) {
int cur = rank->get(i);
if(mr == 1 && cur > 0)
mr = i;
nb += cur;
ns += i*cur;
for(int j = 0; j < cur; j++)
rData.push_back(i);
}
RAbundVector rav = RAbundVector(rData, mr, nb, ns);
rav.setLabel(rank->getLabel());
return rav;
}
int GetRAbundCommand::execute(){
try {
if (abort == true) { if (calledHelp) { return 0; } return 2; }
map<string, string> variables;
variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(inputfile));
filename = getOutputFileName("rabund", variables);
m->openOutputFile(filename, out);
if (countfile != "") {
processList(out);
}else {
InputData input(inputfile, format);
RAbundVector* rabund = input.getRAbundVector();
string lastLabel = rabund->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;
if (m->control_pressed) { outputTypes.clear(); out.close(); m->mothurRemove(filename); delete rabund; return 0; }
while((rabund != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
if(allLines == 1 || labels.count(rabund->getLabel()) == 1){
m->mothurOut(rabund->getLabel()); m->mothurOutEndLine();
if (m->control_pressed) { outputTypes.clear(); out.close(); m->mothurRemove(filename); delete rabund; return 0; }
if(sorted) { rabund->print(out); }
else { rabund->nonSortedPrint(out); }
processedLabels.insert(rabund->getLabel());
userLabels.erase(rabund->getLabel());
}
if ((m->anyLabelsToProcess(rabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
string saveLabel = rabund->getLabel();
delete rabund;
rabund = input.getRAbundVector(lastLabel);
m->mothurOut(rabund->getLabel()); m->mothurOutEndLine();
if (m->control_pressed) { outputTypes.clear(); out.close(); m->mothurRemove(filename); delete rabund; return 0; }
if(sorted) { rabund->print(out); }
else { rabund->nonSortedPrint(out); }
processedLabels.insert(rabund->getLabel());
userLabels.erase(rabund->getLabel());
//restore real lastlabel to save below
rabund->setLabel(saveLabel);
}
lastLabel = rabund->getLabel();
delete rabund;
rabund = input.getRAbundVector();
}
//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 (rabund != NULL) { delete rabund; }
rabund = input.getRAbundVector(lastLabel);
m->mothurOut(rabund->getLabel()); m->mothurOutEndLine();
if (m->control_pressed) { outputTypes.clear(); out.close(); m->mothurRemove(filename); delete rabund; return 0; }
if(sorted) { rabund->print(out); }
else { rabund->nonSortedPrint(out); }
delete rabund;
}
}
if (m->control_pressed) { outputTypes.clear(); out.close(); m->mothurRemove(filename); return 0; }
m->mothurOutEndLine();
m->mothurOut("Output File Names: "); m->mothurOutEndLine();
m->mothurOut(filename); m->mothurOutEndLine(); outputNames.push_back(filename); outputTypes["rabund"].push_back(filename);
m->mothurOutEndLine();
out.close();
//set rabund file as new current rabundfile
string current = "";
itTypes = outputTypes.find("rabund");
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setRabundFile(current); }
}
return 0;
}
catch(exception& e) {
m->errorOut(e, "GetRAbundCommand", "execute");
exit(1);
}
}
//**********************************************************************************************************************
int RemoveRareCommand::processRabund(){
try {
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(rabundfile); }
string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(rabundfile)) + "pick" + m->getExtension(rabundfile);
outputTypes["rabund"].push_back(outputFileName); outputNames.push_back(outputFileName);
ofstream out;
m->openOutputFile(outputFileName, out);
//if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
InputData input(rabundfile, "rabund");
RAbundVector* rabund = input.getRAbundVector();
string lastLabel = rabund->getLabel();
set<string> processedLabels;
set<string> userLabels = labels;
while((rabund != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
if (m->control_pressed) { delete rabund; out.close(); return 0; }
if(allLines == 1 || labels.count(rabund->getLabel()) == 1){
m->mothurOut(rabund->getLabel()); m->mothurOutEndLine();
processedLabels.insert(rabund->getLabel());
userLabels.erase(rabund->getLabel());
RAbundVector newRabund; newRabund.setLabel(rabund->getLabel());
for (int i = 0; i < rabund->getNumBins(); i++) {
if (rabund->get(i) > nseqs) {
newRabund.push_back(rabund->get(i));
}
}
if (newRabund.getNumBins() > 0) { newRabund.print(out); }
}
if ((m->anyLabelsToProcess(rabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
string saveLabel = rabund->getLabel();
delete rabund;
rabund = input.getRAbundVector(lastLabel);
m->mothurOut(rabund->getLabel()); m->mothurOutEndLine();
processedLabels.insert(rabund->getLabel());
userLabels.erase(rabund->getLabel());
RAbundVector newRabund; newRabund.setLabel(rabund->getLabel());
for (int i = 0; i < rabund->getNumBins(); i++) {
if (rabund->get(i) > nseqs) {
newRabund.push_back(rabund->get(i));
}
}
if (newRabund.getNumBins() > 0) { newRabund.print(out); }
//restore real lastlabel to save below
rabund->setLabel(saveLabel);
}
lastLabel = rabund->getLabel();
delete rabund;
rabund = input.getRAbundVector();
}
if (m->control_pressed) { out.close(); 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 (rabund != NULL) { delete rabund; }
rabund = input.getRAbundVector(lastLabel);
m->mothurOut(rabund->getLabel()); m->mothurOutEndLine();
RAbundVector newRabund; newRabund.setLabel(rabund->getLabel());
for (int i = 0; i < rabund->getNumBins(); i++) {
if (rabund->get(i) > nseqs) {
newRabund.push_back(rabund->get(i));
}
}
if (newRabund.getNumBins() > 0) { newRabund.print(out); }
delete rabund;
}
return 0;
}
catch(exception& e) {
m->errorOut(e, "RemoveRareCommand", "processRabund");
exit(1);
}
}