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103 changes: 49 additions & 54 deletions
103
phylonco-lphybeast/src/main/java/phylonco/lphybeast/tobeast/generators/GompertzToBEAST.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,54 +1,49 @@ | ||
| package phylonco.lphybeast.tobeast.generators; | ||
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| import beast.base.core.BEASTInterface; | ||
| import beast.base.evolution.tree.coalescent.PopulationFunction; | ||
| import beast.base.inference.parameter.RealParameter; | ||
| import lphy.core.model.Generator; | ||
| import lphybeast.BEASTContext; | ||
| import lphybeast.GeneratorToBEAST; | ||
| import phylonco.beast.evolution.populationmodel.GompertzGrowth; | ||
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| public class GompertzToBEAST implements GeneratorToBEAST<GompertzGrowth, phylonco.beast.evolution.populationmodel.GompertzGrowth> { | ||
| // <populationModel id="gompertzPopulationModel" spec="phylonco.beast.evolution.populationmodel.GompertzGrowth"> | ||
| // <parameter name="f0" idref="f0"/> | ||
| // <parameter name="NInfinity" idref="NInfinity"/> | ||
| // <parameter name="b" idref="b"/> | ||
| // </populationModel> | ||
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| @Override | ||
| public phylonco.beast.evolution.populationmodel.GompertzGrowth generatorToBEAST(GompertzGrowth gompertzGrowth, BEASTInterface value, BEASTContext context) { | ||
| phylonco.beast.evolution.populationmodel.GompertzGrowth beastGompertzGrowth = new phylonco.beast.evolution.populationmodel.GompertzGrowth(); | ||
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| double f0 = gompertzGrowth.getF0(); | ||
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| double b = gompertzGrowth.getGrowthRateB(); | ||
| double NInfinity = gompertzGrowth.getNInfinity(); | ||
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| RealParameter f0Param = new RealParameter(Double.toString(f0)); | ||
| RealParameter bParam = new RealParameter(Double.toString(b)); | ||
| RealParameter NInfinityParam = new RealParameter(Double.toString(NInfinity)); | ||
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| beastGompertzGrowth.setInputValue("f0", f0Param); | ||
| beastGompertzGrowth.setInputValue("b", bParam); | ||
| beastGompertzGrowth.setInputValue("NInfinity", NInfinityParam); | ||
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| beastGompertzGrowth.initAndValidate(); | ||
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| return beastGompertzGrowth; | ||
| } | ||
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| @Override | ||
| public Class<GompertzGrowth> getGeneratorClass() { | ||
| return GompertzGrowth.class; | ||
| } | ||
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| @Override | ||
| public Class<phylonco.beast.evolution.populationmodel.GompertzGrowth> getBEASTClass() { | ||
| return phylonco.beast.evolution.populationmodel.GompertzGrowth.class; | ||
| } | ||
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| } | ||
| //package phylonco.lphybeast.tobeast.generators; | ||
| // | ||
| //import beast.base.core.BEASTInterface; | ||
| //import beast.base.core.Function; | ||
| //import beast.base.evolution.tree.coalescent.PopulationFunction; | ||
| //import beast.base.inference.parameter.RealParameter; | ||
| //import lphy.base.evolution.coalescent.populationmodel.GompertzPopulation; | ||
| //import lphy.base.evolution.coalescent.populationmodel.GompertzPopulationFunction; | ||
| //import lphy.core.model.Generator; | ||
| //import lphy.core.model.ValueUtils; | ||
| //import lphybeast.BEASTContext; | ||
| //import lphybeast.GeneratorToBEAST; | ||
| //import phylonco.beast.evolution.populationmodel.GompertzGrowth; | ||
| //import phylonco.lphy.evolution.substitutionmodel.GT16; | ||
| // | ||
| //import java.util.List; | ||
| // | ||
| //public class GompertzToBEAST implements GeneratorToBEAST<GompertzPopulationFunction, GompertzGrowth> { | ||
| //// <populationModel id="gompertzPopulationModel" spec="phylonco.beast.evolution.populationmodel.GompertzGrowth"> | ||
| //// <parameter name="f0" idref="f0"/> | ||
| //// <parameter name="NInfinity" idref="NInfinity"/> | ||
| //// <parameter name="b" idref="b"/> | ||
| //// </populationModel> | ||
| // | ||
| // @Override | ||
| // public GompertzGrowth generatorToBEAST(GompertzPopulationFunction gompertzPopulationFunction, BEASTInterface beastInterface, BEASTContext beastContext) { | ||
| // | ||
| // GompertzGrowth beastGompertzGrowth = new GompertzGrowth(); | ||
| // | ||
| // RealParameter f0Param = beastContext.getAsRealParameter(gompertzPopulationFunction.getF0()); | ||
| // RealParameter bParam = beastContext.getAsRealParameter(gompertzPopulationFunction.getB()); | ||
| // RealParameter NInfinityParam = beastContext.getAsRealParameter(gompertzPopulationFunction.getNInfinity()); | ||
| // | ||
| // beastGompertzGrowth.setInputValue("f0", f0Param); | ||
| // beastGompertzGrowth.setInputValue("b", bParam); | ||
| // beastGompertzGrowth.setInputValue("NInfinity", NInfinityParam); | ||
| // beastGompertzGrowth.initAndValidate(); | ||
| // | ||
| // return beastGompertzGrowth; | ||
| // } | ||
| // | ||
| // @Override | ||
| // public Class<GompertzPopulationFunction> getGeneratorClass() { return GompertzPopulationFunction.class; } | ||
| // | ||
| // @Override | ||
| // public Class<GompertzGrowth> getBEASTClass() { | ||
| // return GompertzGrowth.class; | ||
| // } | ||
| //} |
58 changes: 58 additions & 0 deletions
58
...hybeast/src/main/java/phylonco/lphybeast/tobeast/generators/PopFuncCoalescentToBEAST.java
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,58 @@ | ||
| package phylonco.lphybeast.tobeast.generators; | ||
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| import beast.base.core.BEASTInterface; | ||
| import beast.base.evolution.tree.TreeIntervals; | ||
| import beast.base.evolution.tree.coalescent.ConstantPopulation; | ||
| import lphy.base.evolution.coalescent.PopulationFunction; | ||
| import lphy.base.evolution.coalescent.PopulationFunctionCoalescent; | ||
| import lphy.base.evolution.coalescent.populationmodel.GompertzPopulation; | ||
| import lphy.core.model.Value; | ||
| import lphybeast.BEASTContext; | ||
| import lphybeast.GeneratorToBEAST; | ||
| import phylonco.beast.evolution.populationmodel.GompertzGrowth; | ||
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| public class PopFuncCoalescentToBEAST implements | ||
| GeneratorToBEAST<PopulationFunctionCoalescent, beast.base.evolution.tree.coalescent.Coalescent> { | ||
| @Override | ||
| public beast.base.evolution.tree.coalescent.Coalescent generatorToBEAST(PopulationFunctionCoalescent coalescent, BEASTInterface value, BEASTContext context) { | ||
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| beast.base.evolution.tree.coalescent.Coalescent beastCoalescent = new beast.base.evolution.tree.coalescent.Coalescent(); | ||
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| TreeIntervals treeIntervals = new TreeIntervals(); | ||
| treeIntervals.setInputValue("tree", value); | ||
| treeIntervals.initAndValidate(); | ||
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| beastCoalescent.setInputValue("treeIntervals", treeIntervals); | ||
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| beast.base.evolution.tree.coalescent.PopulationFunction.Abstract populationFunction; | ||
| //TODO why private ? | ||
| Value<PopulationFunction> lphyPF = coalescent.getParams().get("popFunc"); | ||
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| if (lphyPF.getType().isAssignableFrom(GompertzPopulation.class)) { | ||
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| populationFunction = (GompertzGrowth) context.getBEASTObject(lphyPF); | ||
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| } else { | ||
| // TODO other pop function types | ||
| populationFunction = new ConstantPopulation(); | ||
| populationFunction.setInputValue("popSize", context.getBEASTObject("TODO")); | ||
| populationFunction.initAndValidate(); | ||
| } | ||
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| beastCoalescent.setInputValue("populationModel", populationFunction); | ||
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| beastCoalescent.initAndValidate(); | ||
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| return beastCoalescent; | ||
| } | ||
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| @Override | ||
| public Class<PopulationFunctionCoalescent> getGeneratorClass() { | ||
| return PopulationFunctionCoalescent.class; | ||
| } | ||
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| @Override | ||
| public Class<beast.base.evolution.tree.coalescent.Coalescent> getBEASTClass() { | ||
| return beast.base.evolution.tree.coalescent.Coalescent.class; | ||
| } | ||
| } |
49 changes: 49 additions & 0 deletions
49
...-lphybeast/src/main/java/phylonco/lphybeast/tobeast/values/PopulationFunctionToBEAST.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,49 @@ | ||
| package phylonco.lphybeast.tobeast.values; | ||
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| import beast.base.inference.parameter.RealParameter; | ||
| import lphy.base.evolution.coalescent.PopulationFunction; | ||
| import lphy.base.evolution.coalescent.populationmodel.GompertzPopulation; | ||
| import lphy.base.evolution.coalescent.populationmodel.GompertzPopulationFunction; | ||
| import lphy.core.model.Value; | ||
| import lphybeast.BEASTContext; | ||
| import lphybeast.ValueToBEAST; | ||
| import lphybeast.tobeast.values.ValueToParameter; | ||
| import phylonco.beast.evolution.populationmodel.GompertzGrowth; | ||
| //TODO exclude | ||
| public class PopulationFunctionToBEAST implements ValueToBEAST<PopulationFunction, beast.base.evolution.tree.coalescent.PopulationFunction.Abstract> { | ||
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| public beast.base.evolution.tree.coalescent.PopulationFunction.Abstract valueToBEAST(Value<PopulationFunction> lphyPopFuncVal, BEASTContext context) { | ||
| beast.base.evolution.tree.coalescent.PopulationFunction.Abstract beastPopFunc; | ||
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| if (lphyPopFuncVal.getType().isAssignableFrom(GompertzPopulation.class)) { | ||
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| GompertzPopulationFunction gen = (GompertzPopulationFunction) lphyPopFuncVal.getGenerator(); | ||
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| RealParameter f0Param = context.getAsRealParameter(gen.getF0()); | ||
| RealParameter bParam = context.getAsRealParameter(gen.getB()); | ||
| RealParameter NInfinityParam = context.getAsRealParameter(gen.getNInfinity()); | ||
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| beastPopFunc = new GompertzGrowth(); | ||
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| beastPopFunc.setInputValue("f0", f0Param); | ||
| beastPopFunc.setInputValue("b", bParam); | ||
| beastPopFunc.setInputValue("NInfinity", NInfinityParam); | ||
| beastPopFunc.initAndValidate(); | ||
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| ValueToParameter.setID(beastPopFunc, lphyPopFuncVal); | ||
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| return beastPopFunc; | ||
| } | ||
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| throw new UnsupportedOperationException("TODO"); | ||
| } | ||
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| public Class getValueClass() { | ||
| return PopulationFunction.class; | ||
| } | ||
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| public Class<beast.base.evolution.tree.coalescent.PopulationFunction.Abstract> getBEASTClass() { | ||
| return beast.base.evolution.tree.coalescent.PopulationFunction.Abstract.class; | ||
| } | ||
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| } |
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