//**********************************************************************************************************************
void MGClusterCommand::printData(ListVector* mergedList){
try {
mergedList->print(listFile);
mergedList->getRAbundVector().print(rabundFile);
SAbundVector sabund = mergedList->getSAbundVector();
sabund.print(cout);
sabund.print(sabundFile);
}
catch(exception& e) {
m->errorOut(e, "MGClusterCommand", "printData");
exit(1);
}
}
//**********************************************************************************************************************
vector<string> CatchAllCommand::parseSharedFile(string filename) {
try {
vector<string> filenames;
//read first line
InputData input(filename, "sharedfile");
vector<SharedRAbundVector*> lookup = input.getSharedRAbundVectors();
string sharedFileRoot = outputDir + m->getRootName(m->getSimpleName(filename));
//clears file before we start to write to it below
for (int i=0; i<lookup.size(); i++) {
m->mothurRemove((sharedFileRoot + lookup[i]->getGroup() + ".sabund"));
filenames.push_back((sharedFileRoot + lookup[i]->getGroup() + ".sabund"));
groups.push_back(lookup[i]->getGroup());
}
while(lookup[0] != NULL) {
for (int i = 0; i < lookup.size(); i++) {
SAbundVector sav = lookup[i]->getSAbundVector();
ofstream out;
m->openOutputFileAppend(sharedFileRoot + lookup[i]->getGroup() + ".sabund", out);
sav.print(out);
out.close();
}
for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
lookup = input.getSharedRAbundVectors();
}
return filenames;
}
catch(exception& e) {
m->errorOut(e, "CatchAllCommand", "parseSharedFile");
exit(1);
}
}
//**********************************************************************************************************************
int RemoveRareCommand::processSabund(){
try {
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(sabundfile); }
string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(sabundfile)) + "pick" + m->getExtension(sabundfile);
outputTypes["sabund"].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(sabundfile, "sabund");
SAbundVector* sabund = input.getSAbundVector();
string lastLabel = sabund->getLabel();
set<string> processedLabels;
set<string> userLabels = labels;
while((sabund != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
if (m->control_pressed) { delete sabund; out.close(); return 0; }
if(allLines == 1 || labels.count(sabund->getLabel()) == 1){
m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
processedLabels.insert(sabund->getLabel());
userLabels.erase(sabund->getLabel());
if (sabund->getMaxRank() > nseqs) {
for(int i = 1; i <=nseqs; i++) { sabund->set(i, 0); }
}else { sabund->clear(); }
if (sabund->getNumBins() > 0) { sabund->print(out); }
}
if ((m->anyLabelsToProcess(sabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
string saveLabel = sabund->getLabel();
delete sabund;
sabund = input.getSAbundVector(lastLabel);
m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
processedLabels.insert(sabund->getLabel());
userLabels.erase(sabund->getLabel());
if (sabund->getMaxRank() > nseqs) {
for(int i = 1; i <=nseqs; i++) { sabund->set(i, 0); }
}else { sabund->clear(); }
if (sabund->getNumBins() > 0) { sabund->print(out); }
//restore real lastlabel to save below
sabund->setLabel(saveLabel);
}
lastLabel = sabund->getLabel();
delete sabund;
sabund = input.getSAbundVector();
}
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 (sabund != NULL) { delete sabund; }
sabund = input.getSAbundVector(lastLabel);
m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
if (sabund->getMaxRank() > nseqs) {
for(int i = 1; i <=nseqs; i++) { sabund->set(i, 0); }
}else { sabund->clear(); }
if (sabund->getNumBins() > 0) { sabund->print(out); }
delete sabund;
}
return 0;
}
catch(exception& e) {
m->errorOut(e, "RemoveRareCommand", "processSabund");
exit(1);
}
}
//**********************************************************************************************************************
int GetSAbundCommand::processList(ofstream& out){
try {
CountTable ct;
ct.readTable(countfile, false);
InputData input(inputfile, format);
ListVector* list = input.getListVector();
string lastLabel = list->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) { delete list; return 0; }
while((list != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
if(allLines == 1 || labels.count(list->getLabel()) == 1){
m->mothurOut(list->getLabel()); m->mothurOutEndLine();
if (m->control_pressed) { delete list; return 0; }
RAbundVector* rabund = new RAbundVector();
createRabund(ct, list, rabund);
SAbundVector sabund = rabund->getSAbundVector();
sabund.print(out);
delete rabund;
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);
m->mothurOut(list->getLabel()); m->mothurOutEndLine();
if (m->control_pressed) { delete list; return 0; }
RAbundVector* rabund = new RAbundVector();
createRabund(ct, list, rabund);
SAbundVector sabund = rabund->getSAbundVector();
sabund.print(out);
delete rabund;
processedLabels.insert(list->getLabel());
userLabels.erase(list->getLabel());
//restore real lastlabel to save below
list->setLabel(saveLabel);
}
lastLabel = list->getLabel();
delete list;
list = input.getListVector();
}
//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);
m->mothurOut(list->getLabel()); m->mothurOutEndLine();
if (m->control_pressed) { delete list; return 0; }
RAbundVector* rabund = new RAbundVector();
createRabund(ct, list, rabund);
SAbundVector sabund = rabund->getSAbundVector();
sabund.print(out);
delete rabund;
delete list;
}
return 0;
}
catch(exception& e) {
m->errorOut(e, "GetSAbundCommand", "processList");
exit(1);
}
}
int GetSAbundCommand::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("sabund", variables);
m->openOutputFile(filename, out);
if (countfile != "") {
processList(out);
}else {
InputData input(inputfile, format);
SAbundVector* sabund = input.getSAbundVector();
string lastLabel = sabund->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 sabund; return 0; }
while((sabund != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
if(allLines == 1 || labels.count(sabund->getLabel()) == 1){
m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
sabund->print(out);
if (m->control_pressed) { outputTypes.clear(); out.close(); m->mothurRemove(filename); delete sabund; return 0; }
processedLabels.insert(sabund->getLabel());
userLabels.erase(sabund->getLabel());
}
if ((m->anyLabelsToProcess(sabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
string saveLabel = sabund->getLabel();
delete sabund;
sabund = (input.getSAbundVector(lastLabel));
m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
sabund->print(out);
if (m->control_pressed) { outputTypes.clear(); out.close(); m->mothurRemove(filename); delete sabund; return 0; }
processedLabels.insert(sabund->getLabel());
userLabels.erase(sabund->getLabel());
//restore real lastlabel to save below
sabund->setLabel(saveLabel);
}
lastLabel = sabund->getLabel();
delete sabund;
sabund = (input.getSAbundVector());
}
//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 (sabund != NULL) { delete sabund; }
sabund = (input.getSAbundVector(lastLabel));
m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
sabund->print(out);
delete sabund;
if (m->control_pressed) { outputTypes.clear(); out.close(); m->mothurRemove(filename); return 0; }
}
}
out.close();
if (m->control_pressed) { outputTypes.clear(); m->mothurRemove(filename); return 0; }
m->mothurOutEndLine();
m->mothurOut("Output File Names: "); m->mothurOutEndLine();
m->mothurOut(filename); m->mothurOutEndLine(); outputNames.push_back(filename); outputTypes["sabund"].push_back(filename);
m->mothurOutEndLine();
//set sabund file as new current sabundfile
string current = "";
itTypes = outputTypes.find("sabund");
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setSabundFile(current); }
}
return 0;
}
catch(exception& e) {
m->errorOut(e, "GetSAbundCommand", "execute");
exit(1);
}
}