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Merge pull request #644 from sjspielman/2.3.4
Binary model, JC69 nucleotide model, and minor cleanups to relative_nucleotide_rates.bf
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,71 @@ | ||
| LoadFunctionLibrary("../DNA.bf"); | ||
| LoadFunctionLibrary("../parameters.bf"); | ||
| LoadFunctionLibrary("../frequencies.bf"); | ||
| LoadFunctionLibrary("../../UtilityFunctions.bf"); | ||
| LoadFunctionLibrary ("libv3/all-terms.bf"); | ||
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| /** @module models.DNA.JC69 */ | ||
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| /** | ||
| * @name models.DNA.JC69.ModelDescription | ||
| * @param {String} type | ||
| */ | ||
| lfunction models.DNA.JC69.ModelDescription(type) { | ||
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| return { | ||
| utility.getGlobalValue("terms.alphabet"): utility.getGlobalValue("models.DNA.alphabet"), | ||
| utility.getGlobalValue("terms.description"): "The JC69 equal-rates model of nucleotide substitution", | ||
| utility.getGlobalValue("terms.model.canonical"): 1, // is of the r_ij \times \pi_j form | ||
| utility.getGlobalValue("terms.model.reversible"): 1, | ||
| utility.getGlobalValue("terms.model.efv_estimate_name"): utility.getGlobalValue("terms.frequencies.equal"), | ||
| utility.getGlobalValue("terms.parameters"): { | ||
| utility.getGlobalValue("terms.global"): {}, | ||
| utility.getGlobalValue("terms.local"): {}, | ||
| utility.getGlobalValue("terms.model.empirical"): 0 | ||
| }, | ||
| utility.getGlobalValue("terms.model.type"): type, | ||
| utility.getGlobalValue("terms.model.get_branch_length"): "", | ||
| utility.getGlobalValue("terms.model.set_branch_length"): "models.generic.SetBranchLength", | ||
| utility.getGlobalValue("terms.model.constrain_branch_length"): "models.generic.constrain_branch_length", | ||
| utility.getGlobalValue("terms.model.frequency_estimator"): "frequencies.equal", | ||
| utility.getGlobalValue("terms.model.q_ij"): "models.DNA.JC69._generateRate", | ||
| utility.getGlobalValue("terms.model.time"): "models.DNA.generic.Time", | ||
| utility.getGlobalValue("terms.model.defineQ"): "models.DNA.JC69._defineQ", | ||
| utility.getGlobalValue("terms.model.post_definition"): "models.generic.post.definition" | ||
| }; | ||
| } | ||
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| /** | ||
| * @name models.DNA.JC69._generateRate | ||
| * @param {Number} fromChar | ||
| * @param {Number} toChar | ||
| * @param {String} namespace | ||
| * @param {String} model_type | ||
| * @returns models.DNA.JC69._generateRate.p | ||
| */ | ||
| function models.DNA.JC69._generateRate(fromChar, toChar, namespace, model_type) { | ||
| models.DNA.JC69._generateRate.p = {}; | ||
| models.DNA.JC69._generateRate.p[model_type] = {}; | ||
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| models.DNA.JC69.parameter_name = "theta"; | ||
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| if (model_type == terms.global) { | ||
| models.DNA.JC69.parameter_name = parameters.ApplyNameSpace(models.DNA.JC69.parameter_name, namespace); | ||
| } | ||
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| (models.DNA.JC69._generateRate.p[model_type])[terms.nucleotideRate(fromChar, toChar)] = models.DNA.JC69.parameter_name; | ||
| models.DNA.JC69._generateRate.p[terms.model.rate_entry] = models.DNA.JC69.parameter_name; | ||
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| return models.DNA.JC69._generateRate.p; | ||
| } | ||
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| /** | ||
| * @name models.DNA.JC69._defineQ | ||
| * @param {Dictionary} jc69 | ||
| * @param {String} namespace | ||
| */ | ||
| function models.DNA.JC69._defineQ(jc69, namespace) { | ||
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| models.DNA.generic.DefineQMatrix(jc69, namespace); | ||
| return jc69; | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,109 @@ | ||
| LoadFunctionLibrary ("../all-terms.bf"); | ||
| LoadFunctionLibrary ("frequencies.bf"); | ||
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| /** @module models.binary */ | ||
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| /* Alphabet */ | ||
| models.binary.alphabet = {{"0","1"}}; | ||
| models.binary.dimensions = 2; | ||
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| /** | ||
| * @name models.binary.generic.DefineQMatrix | ||
| * @param {Dictionary} modelSpec | ||
| * @param {String} namespace | ||
| */ | ||
| function models.binary.generic.DefineQMatrix (modelSpec, namespace) { | ||
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| __alphabet = modelSpec [terms.alphabet]; | ||
| assert (Type (__alphabet) == "Matrix" && Columns (__alphabet) == models.binary.dimensions, "Unsupported or missing alphabet '" + __alphabet + "'"); | ||
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| __modelType = modelSpec[terms.model.type]; | ||
| if (Type (__modelType) == "None" || Type (__modelType) == "Number") { | ||
| __modelType = terms.global; | ||
| } | ||
| modelSpec[terms.model.type] = __modelType; | ||
| assert (__modelType == terms.local || __modelType == terms.global, "Unsupported or missing model type '" + __modelType + "'"); | ||
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| __rate_function = modelSpec [terms.model.q_ij]; | ||
| assert (utility.IsFunction (__rate_function), "Missing q_ij callback in model specification"); | ||
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| __time_function = modelSpec [terms.model.time]; | ||
| assert (utility.IsFunction (__time_function), "Missing time callback in model specification"); | ||
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| __rate_matrix = {models.binary.dimensions, models.binary.dimensions}; | ||
| __rate_matrix [0][0] = ""; | ||
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| __rate_variation = model.generic.get_rate_variation (modelSpec); | ||
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| __global_cache = {}; | ||
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| if (None != __rate_variation) { | ||
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| __rp = Call (__rate_variation[terms.rate_variation.distribution], __rate_variation[terms.rate_variation.options], namespace); | ||
| __rate_variation [terms.id] = (__rp[terms.category])[terms.id]; | ||
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| parameters.DeclareCategory (__rp[terms.category]); | ||
| parameters.helper.copy_definitions (modelSpec[terms.parameters], __rp); | ||
| } | ||
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| for (_rowChar = 0; _rowChar < models.binary.dimensions; _rowChar +=1 ){ | ||
| __rate_matrix [_rowChar][_rowChar] = ""; | ||
| for (_colChar = _rowChar + 1; _colChar < models.binary.dimensions; _colChar += 1) { | ||
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| __rp = Call (__rate_function, __alphabet[_rowChar], | ||
| __alphabet[_colChar], | ||
| namespace, | ||
| __modelType); | ||
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| if (None != __rate_variation) { | ||
| __rp = Call (__rate_variation[terms.rate_variation.rate_modifier], | ||
| __rp, | ||
| __alphabet[_rowChar], | ||
| __alphabet[_colChar], | ||
| namespace, | ||
| __rate_variation [terms.id]); | ||
| } | ||
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| if (Abs (__rp[terms.model.rate_entry])) { | ||
| parameters.DeclareGlobal (__rp[terms.global], __global_cache); | ||
| parameters.helper.copy_definitions (modelSpec[terms.parameters], __rp); | ||
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| __rate_matrix [_rowChar][_colChar] = __rp[terms.model.rate_entry]; | ||
| __rate_matrix [_colChar][_rowChar] = __rp[terms.model.rate_entry]; | ||
| continue; | ||
| } | ||
| __rate_matrix [_rowChar][_colChar] = ""; | ||
| } | ||
| } | ||
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| __rp = Call (__time_function, __modelType); | ||
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| if (Abs (__rp)) { | ||
| ((modelSpec[terms.parameters])[terms.local])[terms.timeParameter ()] = __rp; | ||
| modelSpec [terms.model.rate_matrix] = parameters.AddMultiplicativeTerm (__rate_matrix, __rp, 0); | ||
| } else { | ||
| modelSpec [terms.model.rate_matrix] = __rate_matrix; | ||
| } | ||
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| } | ||
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| /** | ||
| * @name models.binary.generic.Time | ||
| * @param option - does nothing | ||
| * @returns default time | ||
| */ | ||
| function models.binary.generic.Time (option) { | ||
| return terms.parameters.default_time; | ||
| } | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,76 @@ | ||
| LoadFunctionLibrary("../binary.bf"); | ||
| LoadFunctionLibrary("../parameters.bf"); | ||
| LoadFunctionLibrary("../frequencies.bf"); | ||
| LoadFunctionLibrary("../../UtilityFunctions.bf"); | ||
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| /** @module models.protein.REV */ | ||
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| /** | ||
| * @name models.protein.REV.ModelDescription | ||
| * @param {String} type | ||
| */ | ||
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| lfunction models.binary.ModelDescription(type) { | ||
| return { | ||
| utility.getGlobalValue("terms.alphabet"): utility.getGlobalValue("models.binary.alphabet"), | ||
| utility.getGlobalValue("terms.description"): "General time reversible model for binary characters", | ||
| utility.getGlobalValue("terms.model.canonical"): 1, // is of the r_ij \times \pi_j form | ||
| utility.getGlobalValue("terms.model.reversible"): 1, | ||
| utility.getGlobalValue("terms.model.efv_estimate_name"): utility.getGlobalValue("terms.frequencies.binary"), | ||
| utility.getGlobalValue("terms.parameters"): { | ||
| utility.getGlobalValue("terms.global"): {}, | ||
| utility.getGlobalValue("terms.local"): {}, | ||
| utility.getGlobalValue("terms.model.empirical"): 1 | ||
| }, | ||
| utility.getGlobalValue("terms.model.type"): type, | ||
| utility.getGlobalValue("terms.model.get_branch_length"): "", | ||
| utility.getGlobalValue("terms.model.set_branch_length"): "models.generic.SetBranchLength", | ||
| utility.getGlobalValue("terms.model.constrain_branch_length"): "models.generic.constrain_branch_length", | ||
| utility.getGlobalValue("terms.model.frequency_estimator"): "frequencies.empirical.binary", | ||
| utility.getGlobalValue("terms.model.q_ij"): "models.binary._GenerateRate", | ||
| utility.getGlobalValue("terms.model.time"): "models.binary.generic.Time", | ||
| utility.getGlobalValue("terms.model.defineQ"): "models.binary._DefineQ", | ||
| utility.getGlobalValue("terms.model.post_definition"): "models.generic.post.definition" | ||
| }; | ||
| } | ||
|
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| lfunction models.binary._GenerateRate(fromChar, toChar, namespace, model_type) { | ||
| models.binary._generateRate.p = {}; | ||
| models.binary._generateRate.p[model_type] = {}; | ||
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| if (fromChar > toChar) { | ||
| models.binary.parameter_name = "mu_" + toChar + fromChar; | ||
| } else { | ||
| models.binary.parameter_name = "mu_" + fromChar + toChar; | ||
| } | ||
|
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| if (model_type == utility.getGlobalValue("terms.global")) { | ||
| models.binary.parameter_name = parameters.ApplyNameSpace(models.binary.parameter_name, namespace); | ||
| } | ||
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| (models.binary._generateRate.p[model_type])[terms.binaryRate(fromChar, toChar)] = models.binary.parameter_name; | ||
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| models.binary._generateRate.p[utility.getGlobalValue("terms.model.rate_entry")] = models.binary.parameter_name; | ||
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| return models.binary._generateRate.p; | ||
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| } | ||
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| /** | ||
| * @name models.protein.REV._DefineQ | ||
| * @param {Dictionary} model definition | ||
| * @param {String} namespace | ||
| */ | ||
| lfunction models.binary._DefineQ(model_dict, namespace) { | ||
| models.binary.generic.DefineQMatrix (model_dict, namespace); | ||
| /* | ||
| if (model_dict[utility.getGlobalValue("terms.model.type")] == utility.getGlobalValue("terms.global")) { | ||
| parameters.SetConstraint( ((model_dict[utility.getGlobalValue("terms.parameters")])[utility.getGlobalValue("terms.global")])[terms.binaryRate("0", "1")], "1", "" ); | ||
| } | ||
| if (model_dict[utility.getGlobalValue("terms.model.type")] == utility.getGlobalValue("terms.local")) { | ||
| parameters.SetConstraint(((model_dict[utility.getGlobalValue("terms.parameters")])[utility.getGlobalValue("terms.local")])[terms.binaryRate("0", "1")], "1", ""); | ||
| } | ||
| */ | ||
|
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| return model_dict; | ||
| } |
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