EmpiricalSubstitutionModel: normalize empirical frequencies#75
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Empirical amino-acid models published in the literature (e.g. FLU, LG, WAG) report stationary frequencies rounded to a fixed number of decimal places, so the values do not sum to exactly 1.0 (typical delta ~1e-7). The Simplex isValid() check uses a 1e-10 tolerance, which rejects them as invalid. Normalize the values before constructing the SimplexParam so the empirical frequencies pass Simplex validation. The normalization is a no-op when the values already sum to within 1e-10 of 1.0. Surfaced while migrating obama where every OBAMA_<aa> empirical model hits this on initialisation.
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Summary
Simplex.isValid()uses a 1e-10 tolerance; the rounding error is ~1e-7, so every empirical model fails initialisation when its frequencies are wrapped into aSimplexParam.SimplexParam. No-op when the values already sum to within 1e-10 of 1.0.Arose while migrating obama where all 16
OBAMA_<aa>empirical models hit this.Test plan
examples/testOBAMA.xmlon the obama beast3-migration branch) and confirm it parses pastEmpiricalSubstitutionModel.getEmpericalFrequencieValues().[0.25, 0.25, 0.25, 0.25]) are unchanged.