//allow user to run help
if(option == "help") { help(); abort = true; calledHelp = true; }
+ else if(option == "citation") { citation(); abort = true; calledHelp = true;}
else {
vector<string> myArray = setParameters();
phylipfile = validParameter.validFile(parameters, "phylip", true);
if (phylipfile == "not open") { abort = true; }
else if (phylipfile == "not found") { phylipfile = ""; }
- else { format = "phylip"; inputfile = phylipfile; if (outputDir == "") { outputDir += m->hasPath(phylipfile); } }
+ else { format = "phylip"; inputfile = phylipfile; m-> setPhylipFile(phylipfile); if (outputDir == "") { outputDir += m->hasPath(phylipfile); } }
columnfile = validParameter.validFile(parameters, "column", true);
if (columnfile == "not open") { abort = true; }
else if (columnfile == "not found") { columnfile = ""; }
- else { format = "column"; inputfile = columnfile; if (outputDir == "") { outputDir += m->hasPath(columnfile); } }
+ else { format = "column"; inputfile = columnfile; m->setColumnFile(columnfile); if (outputDir == "") { outputDir += m->hasPath(columnfile); } }
sharedfile = validParameter.validFile(parameters, "shared", true);
if (sharedfile == "not open") { abort = true; }
else if (sharedfile == "not found") { sharedfile = ""; }
- else { format = "shared"; inputfile = sharedfile; if (outputDir == "") { outputDir += m->hasPath(sharedfile); } }
+ else { format = "shared"; inputfile = sharedfile; m->setSharedFile(sharedfile); if (outputDir == "") { outputDir += m->hasPath(sharedfile); } }
namefile = validParameter.validFile(parameters, "name", true);
if (namefile == "not open") { abort = true; }
else if (namefile == "not found") { namefile = ""; }
+ else { m->setNameFile(namefile); }
//error checking on files
if (calc == "default") { calc = "jest-thetayc"; }
}
m->splitAtDash(calc, Estimators);
+ if (m->inUsersGroups("citation", Estimators)) {
+ ValidCalculators validCalc; validCalc.printCitations(Estimators);
+ //remove citation from list of calcs
+ for (int i = 0; i < Estimators.size(); i++) { if (Estimators[i] == "citation") { Estimators.erase(Estimators.begin()+i); break; } }
+ }
groups = validParameter.validFile(parameters, "groups", false);
if (groups == "not found") { groups = ""; }
else {
m->splitAtDash(groups, Groups);
- m->Groups = Groups;
+ m->setGroups(Groups);
}
delete heatmap;
- if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } outputTypes.clear(); return 0; }
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear(); return 0; }
m->mothurOutEndLine();
m->mothurOut("Output File Names: "); m->mothurOutEndLine();
set<string> processedLabels;
set<string> userLabels = labels;
- if (m->control_pressed) { delete input; for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } m->Groups.clear(); return 0; }
+ if (m->control_pressed) { delete input; for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } m->clearGroups(); return 0; }
//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) { delete input; for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } m->Groups.clear(); return 0; }
+ if (m->control_pressed) { delete input; for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } m->clearGroups(); return 0; }
if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){
}
- if (m->control_pressed) { delete input; m->Groups.clear(); return 0; }
+ if (m->control_pressed) { delete input; m->clearGroups(); return 0; }
//output error messages about any remaining user labels
set<string>::iterator it;
}
}
- if (m->control_pressed) { delete input; m->Groups.clear(); return 0; }
+ if (m->control_pressed) { delete input; m->clearGroups(); return 0; }
//run last label if you need to
if (needToRun == true) {
for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
}
- if (m->control_pressed) { delete input; m->Groups.clear(); return 0; }
+ if (m->control_pressed) { delete input; m->clearGroups(); return 0; }
//reset groups parameter
- m->Groups.clear();
+ m->clearGroups();
delete input;