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The models added by --madd cannot be skipped. #42

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Merged
bqminh merged 1 commit into from
May 23, 2025
Merged

The models added by --madd cannot be skipped. #42

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8 changes: 4 additions & 4 deletions main/phylotesting.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -1655,7 +1655,7 @@ int CandidateModelSet::generate(Params &params, Alignment *aln, bool separate_ra
StrVector extra_model_names;
convert_string_vec(params.model_extra_set, extra_model_names);
for (auto s : extra_model_names)
push_back(CandidateModel(s, "", aln));
push_back(CandidateModel(s, "", aln, MF_CANNOT_BE_IGNORED));
}
return max_cats;
}
Expand Down Expand Up @@ -2832,7 +2832,7 @@ void CandidateModelSet::filterRates(int finished_model) {
ok_rates.insert(rate_name);
}
for (model = finished_model+1; model < size(); model++)
if (ok_rates.find(at(model).orig_rate_name) == ok_rates.end())
if (ok_rates.find(at(model).orig_rate_name) == ok_rates.end() && !at(model).hasFlag(MF_CANNOT_BE_IGNORED))
at(model).setFlag(MF_IGNORED);
}

Expand All @@ -2854,11 +2854,11 @@ void CandidateModelSet::filterSubst(int finished_model) {
if (at(model).getScore() <= ok_score) {
string subst_name = at(model).orig_subst_name;
ok_model.insert(subst_name);
} else
} else if (!at(model).hasFlag(MF_CANNOT_BE_IGNORED))
at(model).setFlag(MF_IGNORED);
}
for (model = finished_model+1; model < size(); model++)
if (ok_model.find(at(model).orig_subst_name) == ok_model.end())
if (ok_model.find(at(model).orig_subst_name) == ok_model.end() && !at(model).hasFlag(MF_CANNOT_BE_IGNORED))
at(model).setFlag(MF_IGNORED);
}

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1 change: 1 addition & 0 deletions main/phylotesting.h
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Original file line number Diff line number Diff line change
Expand Up @@ -31,6 +31,7 @@ const int MF_IGNORED = 2;
const int MF_RUNNING = 4;
const int MF_WAITING = 8;
const int MF_DONE = 16;
const int MF_CANNOT_BE_IGNORED = 32; // those models added by -madd cannot be filtered out

enum MixtureAction {MA_NONE, MA_FIND_RATE, MA_NUMBER_CLASS, MA_FIND_CLASS, MA_ADD_CLASS};

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