}
catch(exception& e) {
- errorOut(e, "SharedListVector", "SharedListVector");
+ m->errorOut(e, "SharedListVector", "SharedListVector");
exit(1);
}
}
numSeqs += (nNames_new - nNames_old);
}
catch(exception& e) {
- errorOut(e, "SharedListVector", "set");
+ m->errorOut(e, "SharedListVector", "set");
exit(1);
}
}
numSeqs += nNames;
}
catch(exception& e) {
- errorOut(e, "SharedListVector", "push_back");
+ m->errorOut(e, "SharedListVector", "push_back");
exit(1);
}
}
output << endl;
}
catch(exception& e) {
- errorOut(e, "SharedListVector", "print");
+ m->errorOut(e, "SharedListVector", "print");
exit(1);
}
}
return rav;
}
catch(exception& e) {
- errorOut(e, "SharedListVector", "getRAbundVector");
+ m->errorOut(e, "SharedListVector", "getRAbundVector");
exit(1);
}
}
return sav;
}
catch(exception& e) {
- errorOut(e, "SharedListVector", "getSAbundVector");
+ m->errorOut(e, "SharedListVector", "getSAbundVector");
exit(1);
}
}
names = names.substr(names.find_first_of(',')+1, names.length());
groupName = groupmap->getGroup(name);
- if(groupName == "not found") { mothurOut("Error: Sequence '" + name + "' was not found in the group file, please correct."); mothurOutEndLine(); exit(1); }
+ if(groupName == "not found") { m->mothurOut("Error: Sequence '" + name + "' was not found in the group file, please correct."); m->mothurOutEndLine(); exit(1); }
order->push_back(i, binSize, groupName); //i represents what bin you are in
}
//get last name
groupName = groupmap->getGroup(names);
- if(groupName == "not found") { mothurOut("Error: Sequence '" + names + "' was not found in the group file, please correct."); mothurOutEndLine(); exit(1); }
+ if(groupName == "not found") { m->mothurOut("Error: Sequence '" + names + "' was not found in the group file, please correct."); m->mothurOutEndLine(); exit(1); }
order->push_back(i, binSize, groupName);
}
return order;
}
catch(exception& e) {
- errorOut(e, "SharedListVector", "getSharedOrderVector");
+ m->errorOut(e, "SharedListVector", "getSharedOrderVector");
exit(1);
}
}
name = names.substr(0,names.find_first_of(','));
names = names.substr(names.find_first_of(',')+1, names.length());
group = groupmap->getGroup(name);
- if(group == "not found") { mothurOut("Error: Sequence '" + name + "' was not found in the group file, please correct."); mothurOutEndLine(); exit(1); }
+ if(group == "not found") { m->mothurOut("Error: Sequence '" + name + "' was not found in the group file, please correct."); m->mothurOutEndLine(); exit(1); }
if (group == groupName) { //this name is in the group you want the vector for.
rav.set(i, rav.getAbundance(i) + 1, group); //i represents what bin you are in
}
//get last name
groupName = groupmap->getGroup(names);
- if(groupName == "not found") { mothurOut("Error: Sequence '" + names + "' was not found in the group file, please correct."); mothurOutEndLine(); exit(1); }
+ if(groupName == "not found") { m->mothurOut("Error: Sequence '" + names + "' was not found in the group file, please correct."); m->mothurOutEndLine(); exit(1); }
if (group == groupName) { //this name is in the group you want the vector for.
rav.set(i, rav.getAbundance(i) + 1, group); //i represents what bin you are in
}
}
catch(exception& e) {
- errorOut(e, "SharedListVector", "getSharedRAbundVector");
+ m->errorOut(e, "SharedListVector", "getSharedRAbundVector");
exit(1);
}
}
try {
SharedUtil* util;
util = new SharedUtil();
- vector<SharedRAbundVector*> lookup;
- map<string, SharedRAbundVector*> finder;
+ vector<SharedRAbundVector*> lookup; //contains just the groups the user selected
+ map<string, SharedRAbundVector*> finder; //contains all groups in groupmap
string group, names, name;
-
+
util->setGroups(globaldata->Groups, globaldata->gGroupmap->namesOfGroups);
-
delete util;
- for (int i = 0; i < globaldata->Groups.size(); i++) {
+ for (int i = 0; i < globaldata->gGroupmap->namesOfGroups.size(); i++) {
SharedRAbundVector* temp = new SharedRAbundVector(data.size());
- finder[globaldata->Groups[i]] = temp;
- finder[globaldata->Groups[i]]->setLabel(label);
- finder[globaldata->Groups[i]]->setGroup(globaldata->Groups[i]);
- //*temp = getSharedRAbundVector(globaldata->Groups[i]);
- lookup.push_back(finder[globaldata->Groups[i]]);
+ finder[globaldata->gGroupmap->namesOfGroups[i]] = temp;
+ finder[globaldata->gGroupmap->namesOfGroups[i]]->setLabel(label);
+ finder[globaldata->gGroupmap->namesOfGroups[i]]->setGroup(globaldata->gGroupmap->namesOfGroups[i]);
+ if (inVector(globaldata->gGroupmap->namesOfGroups[i], globaldata->Groups)) { //if this group is in user groups
+ lookup.push_back(finder[globaldata->gGroupmap->namesOfGroups[i]]);
+ }
}
-
+
//fill vectors
for(int i=0;i<numBins;i++){
names = get(i);
name = names.substr(0,names.find_first_of(','));
names = names.substr(names.find_first_of(',')+1, names.length());
group = groupmap->getGroup(name);
- if(group == "not found") { mothurOut("Error: Sequence '" + name + "' was not found in the group file, please correct."); mothurOutEndLine(); exit(1); }
+ if(group == "not found") { m->mothurOut("Error: Sequence '" + name + "' was not found in the group file, please correct."); m->mothurOutEndLine(); exit(1); }
finder[group]->set(i, finder[group]->getAbundance(i) + 1, group); //i represents what bin you are in
}
//get last name
group = groupmap->getGroup(names);
- if(group == "not found") { mothurOut("Error: Sequence '" + names + "' was not found in the group file, please correct."); mothurOutEndLine(); exit(1); }
+ if(group == "not found") { m->mothurOut("Error: Sequence '" + names + "' was not found in the group file, please correct."); m->mothurOutEndLine(); exit(1); }
finder[group]->set(i, finder[group]->getAbundance(i) + 1, group); //i represents what bin you are in
}
return lookup;
}
catch(exception& e) {
- errorOut(e, "SharedListVector", "getSharedRAbundVector");
+ m->errorOut(e, "SharedListVector", "getSharedRAbundVector");
exit(1);
}
}
return sav;
}
catch(exception& e) {
- errorOut(e, "SharedListVector", "getSharedSAbundVector");
+ m->errorOut(e, "SharedListVector", "getSharedSAbundVector");
exit(1);
}
}
}
else{
if(orderMap->count(seqName) == 0){
- mothurOut(seqName + " not found, check *.names file\n");
+ m->mothurOut(seqName + " not found, check *.names file\n");
exit(1);
}
}
if(orderMap->count(seqName) == 0){
- mothurOut(seqName + " not found, check *.names file\n");
+ m->mothurOut(seqName + " not found, check *.names file\n");
exit(1);
}
ov.set((*orderMap)[seqName], i);
}
}
catch(exception& e) {
- errorOut(e, "SharedListVector", "getOrderVector");
+ m->errorOut(e, "SharedListVector", "getOrderVector");
exit(1);
}
}