int MergeGroupsCommand::execute(){
try {
if (abort) { if (calledHelp) { return 0; } return 2; }
designMap = new DesignMap(designfile);
if (method != "sum") {
string defaultClass = designMap->getDefaultClass();
vector<string> treatments = designMap->getCategory(defaultClass);
set<int> numGroupsPerTreatment;
for (int i = 0; i < treatments.size(); i++) {
if (m->getControl_pressed()) { break; }
map<string, vector<string> > checkTreatments;
vector<string> temp; temp.push_back(treatments[i]);
checkTreatments[defaultClass] = temp;
numGroupsPerTreatment.insert(designMap->getNumUnique(checkTreatments));
}
if (numGroupsPerTreatment.size() > 1) { m->mothurOut("[ERROR]: The median and average methods require you to have the same number of sequences in each treatment, quitting.\n"); delete designMap; return 0; }
}
if (groupfile != "") { processGroupFile(designMap); }
if (sharedfile != "") { processSharedFile(designMap); }
if (countfile != "") { processCountFile(designMap); }
//reset groups parameter
delete designMap;
if (m->getControl_pressed()) { for (int i = 0; i < outputNames.size(); i++) { util.mothurRemove(outputNames[i]); } return 0;}
//set shared file as new current sharedfile
string currentName = "";
itTypes = outputTypes.find("shared");
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { currentName = (itTypes->second)[0]; current->setSharedFile(currentName); }
}
itTypes = outputTypes.find("group");
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { currentName = (itTypes->second)[0]; current->setGroupFile(currentName); }
}
itTypes = outputTypes.find("count");
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { currentName = (itTypes->second)[0]; current->setCountFile(currentName); }
}
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, "MergeGroupsCommand", "execute");
exit(1);
}
}
int MergeGroupsCommand::execute(){
try {
if (abort == true) { if (calledHelp) { return 0; } return 2; }
designMap = new GroupMap(designfile);
designMap->readDesignMap();
if (groupfile != "") { processGroupFile(designMap); }
if (sharedfile != "") { processSharedFile(designMap); }
//reset groups parameter
m->clearGroups();
delete designMap;
if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0;}
//set shared file as new current sharedfile
string current = "";
itTypes = outputTypes.find("shared");
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setSharedFile(current); }
}
itTypes = outputTypes.find("group");
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setGroupFile(current); }
}
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, "MergeGroupsCommand", "execute");
exit(1);
}
}
