else {
m->splitAtDash(groups, Groups);
}
- m->Groups = Groups;
+ m->setGroups(Groups);
string temp;
temp = validParameter.validFile(parameters, "freq", false); if (temp == "not found") { temp = "100"; }
- convert(temp, freq);
+ m->mothurConvert(temp, freq);
temp = validParameter.validFile(parameters, "iters", false); if (temp == "not found") { temp = "1000"; }
- convert(temp, nIters);
+ m->mothurConvert(temp, nIters);
temp = validParameter.validFile(parameters, "jumble", false); if (temp == "not found") { temp = "T"; }
if (m->isTrue(temp)) { jumble = true; }
string lastLabel = lookup[0]->getLabel();
if (m->control_pressed) {
- m->Groups.clear();
+ m->clearGroups();
delete input;
for(int i=0;i<rDisplays.size();i++){ delete rDisplays[i]; }
for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); }
//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) {
- m->Groups.clear();
+ m->clearGroups();
delete input;
for(int i=0;i<rDisplays.size();i++){ delete rDisplays[i]; }
for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); }
}
if (m->control_pressed) {
- m->Groups.clear();
+ m->clearGroups();
delete input;
for(int i=0;i<rDisplays.size();i++){ delete rDisplays[i]; }
for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); }
}
if (m->control_pressed) {
- m->Groups.clear();
+ m->clearGroups();
delete input;
for(int i=0;i<rDisplays.size();i++){ delete rDisplays[i]; }
for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); }
}
for(int i=0;i<rDisplays.size();i++){ delete rDisplays[i]; }
- m->Groups.clear();
+ m->clearGroups();
delete input;
if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }