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| Original file line number | Diff line number | Diff line change |
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| RequireVersion ("2.5.60"); | ||
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| LoadFunctionLibrary("../codon.bf"); | ||
| LoadFunctionLibrary("../DNA.bf"); | ||
| LoadFunctionLibrary("../parameters.bf"); | ||
| LoadFunctionLibrary("../frequencies.bf"); | ||
| LoadFunctionLibrary("../../UtilityFunctions.bf"); | ||
| LoadFunctionLibrary("MG_REV.bf"); | ||
| LoadFunctionLibrary("../protein.bf"); | ||
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| /** @module models.codon.GTR */ | ||
| //---------------------------------------------------------------------------------------------------------------- | ||
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| lfunction model.codon.MG_GTR.prompt_and_define (type, code) { | ||
| console.log (type); | ||
| return models.codon.MG_GTR.ModelDescription(type, code); | ||
| } | ||
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| lfunction models.codon.MG_GTR.ModelDescription(type, code) { | ||
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| io.CheckAssertion ("`&type` == '`^'terms.global'`'", "MG_GTR only supports `^'terms.global'` type"); | ||
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| // piggyback on the standard MG_REV model for most of the code | ||
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| mg_base = models.codon.MG_REV.ModelDescription (type, code); | ||
| mg_base[utility.getGlobalValue("terms.description")] = "The Muse-Gaut 94 codon-substitution model coupled with the general time reversible (GTR) model of nucleotide substitution, which defines a separate dN/dS ratio for each pair of amino-acids"; | ||
| mg_base[utility.getGlobalValue("terms.model.q_ij")] = "models.codon.MG_GTR._GenerateRate"; | ||
| mg_base[utility.getGlobalValue("terms.model.post_definition")] = "models.codon.MG_GTR.post_definition"; | ||
| return mg_base; | ||
| } | ||
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| lfunction models.codon.MG_GTR._GenerateRate(fromChar, toChar, namespace, model_type, model) { | ||
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| return models.codon.MG_GTR._GenerateRate_generic (fromChar, toChar, namespace, model_type, | ||
| model[utility.getGlobalValue("terms.translation_table")], | ||
| "alpha", utility.getGlobalValue("terms.parameters.synonymous_rate"), | ||
| "omega", utility.getGlobalValue("terms.parameters.omega_ratio"), | ||
| ); | ||
| } | ||
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| /** | ||
| * @name models.codon.MG_GTR._GenerateRate | ||
| * @param {Number} fromChar | ||
| * @param {Number} toChar | ||
| * @param {String} namespace | ||
| * @param {String} model_type | ||
| * @param {Matrix} _tt - translation table | ||
| */ | ||
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| lfunction models.codon.MG_GTR._GenerateRate_generic (fromChar, toChar, namespace, model_type, _tt, alpha, alpha_term, omega, omega_term) { | ||
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| _GenerateRate.p = {}; | ||
| _GenerateRate.diff = models.codon.diff.complete(fromChar, toChar); | ||
| diff_count = utility.Array1D (_GenerateRate.diff); | ||
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| if (diff_count == 1) { | ||
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| _GenerateRate.p[model_type] = {}; | ||
| _GenerateRate.p[utility.getGlobalValue("terms.global")] = {}; | ||
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| nuc_rate = ""; | ||
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| for (i = 0; i < diff_count; i += 1) { | ||
| if ((_GenerateRate.diff[i])[utility.getGlobalValue("terms.diff.from")] > (_GenerateRate.diff[i])[utility.getGlobalValue("terms.diff.to")]) { | ||
| nuc_p = "theta_" + (_GenerateRate.diff[i])[utility.getGlobalValue("terms.diff.to")] + (_GenerateRate.diff[i])[utility.getGlobalValue("terms.diff.from")]; | ||
| } else { | ||
| nuc_p = "theta_" + (_GenerateRate.diff[i])[utility.getGlobalValue("terms.diff.from")] +(_GenerateRate.diff[i])[utility.getGlobalValue("terms.diff.to")]; | ||
| } | ||
| nuc_p = parameters.ApplyNameSpace(nuc_p, namespace); | ||
| (_GenerateRate.p[utility.getGlobalValue("terms.global")])[terms.nucleotideRateReversible((_GenerateRate.diff[i])[utility.getGlobalValue("terms.diff.from")], (_GenerateRate.diff[i])[utility.getGlobalValue("terms.diff.to")])] = nuc_p; | ||
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| nuc_rate = parameters.AppendMultiplicativeTerm (nuc_rate, nuc_p); | ||
| } | ||
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| rate_entry = nuc_rate; | ||
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| if (_tt[fromChar] != _tt[toChar]) { | ||
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| if (_tt[fromChar] < _tt[toChar]) { | ||
| aa_pair = _tt[fromChar] + " and " + _tt[toChar]; | ||
| aa_tag = "_" + _tt[fromChar] + _tt[toChar]; | ||
| } else { | ||
| aa_pair = _tt[toChar] + " and " + _tt[fromChar]; | ||
| aa_tag = "_" + _tt[toChar] + _tt[fromChar]; | ||
| } | ||
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| omega_p = parameters.ApplyNameSpace (omega + aa_tag , namespace); | ||
| (_GenerateRate.p[model_type]) [^"terms.parameters.omega_ratio" + " for " + aa_pair] = omega_p; | ||
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| rate_entry = parameters.AppendMultiplicativeTerm (rate_entry, omega_p); | ||
| } else { | ||
| _GenerateRate.p[utility.getGlobalValue("terms.model.rate_entry")] = nuc_rate; | ||
| } | ||
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| _GenerateRate.p[utility.getGlobalValue("terms.model.rate_entry")] = rate_entry; | ||
| } | ||
| return _GenerateRate.p; | ||
| } | ||
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| lfunction models.codon.MG_GTR.post_definition (model) { | ||
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| for (id; in ; model.GetParameters_RegExp (model, ^"terms.parameters.omega_ratio")) { | ||
| parameters.SetValue(id, 0.25); | ||
| } | ||
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| models.generic.post.definition (model); | ||
| } | ||
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| lfunction models.codon.MG_GTR.set_branch_length(model, value, parameter) { | ||
| return models.codon.MG_REV.set_branch_length(model,value,parameter); | ||
| } |
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