int KruskalWallisCommand::execute(){
try {
if (abort == true) { if (calledHelp) { return 0; } return 2; }
DesignMap designMap(designfile);
//if user set classes set groups=those classes
if (classes != "") {
map<string, vector<string> > thisClasses = m->parseClasses(classes);
vector<string> groups = designMap.getNamesUnique(thisClasses);
if (groups.size() != 0) { m->setGroups(groups); }
else { m->mothurOut("[ERROR]: no groups meet your classes requirement, quitting.\n"); return 0; }
}
//if user did not select class use first column
if (mclass == "") { mclass = designMap.getDefaultClass(); m->mothurOut("\nYou did not provide a class, using " + mclass +".\n\n"); }
InputData input(sharedfile, "sharedfile");
vector<SharedRAbundVector*> 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) { for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } return 0; }
if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){
m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
process(lookup, designMap);
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();
process(lookup, designMap);
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) { return 0; }
//get next line to process
lookup = input.getSharedRAbundVectors();
}
if (m->control_pressed) { 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();
process(lookup, designMap);
for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
}
//output files created by command
m->mothurOutEndLine();
m->mothurOut("Output File Names: "); m->mothurOutEndLine();
for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
m->mothurOutEndLine();
return 0;
}
catch(exception& e) {
m->errorOut(e, "KruskalWallisCommand", "execute");
exit(1);
}
}
int KruskalWallisCommand::execute(){
try {
if (abort) { if (calledHelp) { return 0; } return 2; }
DesignMap designMap(designfile);
//if user did not select class use first column
if (mclass == "") { mclass = designMap.getDefaultClass(); m->mothurOut("\nYou did not provide a class, using " + mclass +".\n\n"); }
InputData input(sharedfile, "sharedfile", nullVector);
SharedRAbundVectors* lookup = input.getSharedRAbundVectors();
string lastLabel = lookup->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;
vector<string> currentLabels = lookup->getOTUNames();
//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()) { delete lookup; return 0; }
if(allLines == 1 || labels.count(lookup->getLabel()) == 1){
m->mothurOut(lookup->getLabel()+"\n");
vector<SharedRAbundVector*> data = lookup->getSharedRAbundVectors();
process(data, designMap, currentLabels);
for (int i = 0; i < data.size(); i++) { delete data[i]; } data.clear();
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");
vector<SharedRAbundVector*> data = lookup->getSharedRAbundVectors();
process(data, designMap, currentLabels);
for (int i = 0; i < data.size(); i++) { delete data[i]; } data.clear();
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()) { return 0; }
//get next line to process
lookup = input.getSharedRAbundVectors();
}
if (m->getControl_pressed()) { 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 ) {
delete lookup;
lookup = input.getSharedRAbundVectors(lastLabel);
m->mothurOut(lookup->getLabel()+"\n");
vector<SharedRAbundVector*> data = lookup->getSharedRAbundVectors();
process(data, designMap, currentLabels);
for (int i = 0; i < data.size(); i++) { delete data[i]; } data.clear();
delete lookup;
}
//output files created by command
m->mothurOut("\nOutput File Names: \n");
for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i] +"\n"); } m->mothurOutEndLine();
return 0;
}
catch(exception& e) {
m->errorOut(e, "KruskalWallisCommand", "execute");
exit(1);
}
}