create lphy.core.model.component.argument and refactor vector args #294

#364
LinguaPhylo · Jun 5, 2023 · 3cd83dd · 3cd83dd
1 parent 0225e54
commit 3cd83dd
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diff --git a/lphy-base/src/main/java/lphy/base/bmodeltest/BModelSetFunction.java b/lphy-base/src/main/java/lphy/base/bmodeltest/BModelSetFunction.java
@@ -1,10 +1,10 @@
 package lphy.base.bmodeltest;
 
 import lphy.core.model.annotation.GeneratorInfo;
-import lphy.core.model.annotation.ParameterInfo;
 import lphy.core.model.component.DeterministicFunction;
 import lphy.core.model.component.GeneratorCategory;
 import lphy.core.model.component.Value;
+import lphy.core.model.component.argument.ParameterInfo;
 
 public class BModelSetFunction extends DeterministicFunction<BModelSet> {
 

diff --git a/lphy-base/src/main/java/lphy/base/bmodeltest/NucleotideModel.java b/lphy-base/src/main/java/lphy/base/bmodeltest/NucleotideModel.java
@@ -3,9 +3,9 @@
 import lphy.base.evolution.substitutionmodel.RateMatrix;
 import lphy.core.model.annotation.Citation;
 import lphy.core.model.annotation.GeneratorInfo;
-import lphy.core.model.annotation.ParameterInfo;
 import lphy.core.model.component.GeneratorCategory;
 import lphy.core.model.component.Value;
+import lphy.core.model.component.argument.ParameterInfo;
 import lphy.core.model.datatype.DoubleArray2DValue;
 
 import java.util.Map;

diff --git a/lphy-base/src/main/java/lphy/base/bmodeltest/bSiteModelFunction.java b/lphy-base/src/main/java/lphy/base/bmodeltest/bSiteModelFunction.java
@@ -3,10 +3,10 @@
 import lphy.base.evolution.sitemodel.SiteModel;
 import lphy.core.model.annotation.Citation;
 import lphy.core.model.annotation.GeneratorInfo;
-import lphy.core.model.annotation.ParameterInfo;
 import lphy.core.model.component.DeterministicFunction;
 import lphy.core.model.component.GeneratorCategory;
 import lphy.core.model.component.Value;
+import lphy.core.model.component.argument.ParameterInfo;
 
 import java.util.Map;
 

diff --git a/lphy-base/src/main/java/lphy/base/bmodeltest/bSiteRates.java b/lphy-base/src/main/java/lphy/base/bmodeltest/bSiteRates.java
@@ -3,11 +3,11 @@
 import lphy.base.distribution.DiscretizedGamma;
 import lphy.base.math.RandomUtils;
 import lphy.core.model.annotation.GeneratorInfo;
-import lphy.core.model.annotation.ParameterInfo;
 import lphy.core.model.component.GenerativeDistribution;
 import lphy.core.model.component.GeneratorCategory;
 import lphy.core.model.component.RandomVariable;
 import lphy.core.model.component.Value;
+import lphy.core.model.component.argument.ParameterInfo;
 import org.apache.commons.math3.random.RandomGenerator;
 
 import java.util.Arrays;

diff --git a/lphy-base/src/main/java/lphy/base/distribution/Bernoulli.java b/lphy-base/src/main/java/lphy/base/distribution/Bernoulli.java
@@ -1,11 +1,11 @@
 package lphy.base.distribution;
 
 import lphy.core.model.annotation.GeneratorInfo;
-import lphy.core.model.annotation.ParameterInfo;
 import lphy.core.model.component.GeneratorCategory;
 import lphy.core.model.component.RandomVariable;
 import lphy.core.model.component.Value;
 import lphy.core.model.component.ValueUtils;
+import lphy.core.model.component.argument.ParameterInfo;
 import org.apache.commons.math3.random.RandomGenerator;
 
 import java.util.Collections;

diff --git a/lphy-base/src/main/java/lphy/base/distribution/BernoulliMulti.java b/lphy-base/src/main/java/lphy/base/distribution/BernoulliMulti.java
@@ -1,10 +1,10 @@
 package lphy.base.distribution;
 
 import lphy.core.model.annotation.GeneratorInfo;
-import lphy.core.model.annotation.ParameterInfo;
 import lphy.core.model.component.GeneratorCategory;
 import lphy.core.model.component.RandomVariable;
 import lphy.core.model.component.Value;
+import lphy.core.model.component.argument.ParameterInfo;
 import lphy.core.model.datatype.IntegerValue;
 import lphy.core.vectorization.IID;
 import org.apache.commons.math3.distribution.BinomialDistribution;

diff --git a/lphy-base/src/main/java/lphy/base/distribution/Beta.java b/lphy-base/src/main/java/lphy/base/distribution/Beta.java
@@ -1,8 +1,8 @@
 package lphy.base.distribution;
 
 import lphy.core.model.annotation.GeneratorInfo;
-import lphy.core.model.annotation.ParameterInfo;
 import lphy.core.model.component.*;
+import lphy.core.model.component.argument.ParameterInfo;
 import org.apache.commons.math3.distribution.BetaDistribution;
 import org.apache.commons.math3.random.RandomGenerator;
 

diff --git a/lphy-base/src/main/java/lphy/base/distribution/Binomial.java b/lphy-base/src/main/java/lphy/base/distribution/Binomial.java
@@ -1,10 +1,10 @@
 package lphy.base.distribution;
 
 import lphy.core.model.annotation.GeneratorInfo;
-import lphy.core.model.annotation.ParameterInfo;
 import lphy.core.model.component.GenerativeDistribution1D;
 import lphy.core.model.component.RandomVariable;
 import lphy.core.model.component.Value;
+import lphy.core.model.component.argument.ParameterInfo;
 import org.apache.commons.math3.distribution.BinomialDistribution;
 import org.apache.commons.math3.random.RandomGenerator;
 

diff --git a/lphy-base/src/main/java/lphy/base/distribution/Categorical.java b/lphy-base/src/main/java/lphy/base/distribution/Categorical.java
@@ -1,8 +1,8 @@
 package lphy.base.distribution;
 
-import lphy.core.model.annotation.ParameterInfo;
 import lphy.core.model.component.RandomVariable;
 import lphy.core.model.component.Value;
+import lphy.core.model.component.argument.ParameterInfo;
 import org.apache.commons.math3.random.RandomGenerator;
 
 import java.util.Collections;

diff --git a/lphy-base/src/main/java/lphy/base/distribution/Cauchy.java b/lphy-base/src/main/java/lphy/base/distribution/Cauchy.java
@@ -1,11 +1,11 @@
 package lphy.base.distribution;
 
 import lphy.core.model.annotation.GeneratorInfo;
-import lphy.core.model.annotation.ParameterInfo;
 import lphy.core.model.component.GeneratorCategory;
 import lphy.core.model.component.RandomVariable;
 import lphy.core.model.component.Value;
 import lphy.core.model.component.ValueUtils;
+import lphy.core.model.component.argument.ParameterInfo;
 import org.apache.commons.math3.distribution.CauchyDistribution;
 import org.apache.commons.math3.random.RandomGenerator;
 

diff --git a/lphy-base/src/main/java/lphy/base/distribution/Dirichlet.java b/lphy-base/src/main/java/lphy/base/distribution/Dirichlet.java
@@ -2,10 +2,10 @@
 
 import lphy.base.math.MathUtils;
 import lphy.core.model.annotation.GeneratorInfo;
-import lphy.core.model.annotation.ParameterInfo;
 import lphy.core.model.component.GeneratorCategory;
 import lphy.core.model.component.RandomVariable;
 import lphy.core.model.component.Value;
+import lphy.core.model.component.argument.ParameterInfo;
 import org.apache.commons.math3.random.RandomGenerator;
 
 import java.util.Collections;

diff --git a/lphy-base/src/main/java/lphy/base/distribution/DiscretizedGamma.java b/lphy-base/src/main/java/lphy/base/distribution/DiscretizedGamma.java
@@ -1,11 +1,11 @@
 package lphy.base.distribution;
 
 import lphy.core.model.annotation.GeneratorInfo;
-import lphy.core.model.annotation.ParameterInfo;
 import lphy.core.model.component.GeneratorCategory;
 import lphy.core.model.component.RandomVariable;
 import lphy.core.model.component.Value;
 import lphy.core.model.component.ValueUtils;
+import lphy.core.model.component.argument.ParameterInfo;
 import org.apache.commons.math3.distribution.GammaDistribution;
 import org.apache.commons.math3.random.RandomGenerator;
 

diff --git a/lphy-base/src/main/java/lphy/base/distribution/Exp.java b/lphy-base/src/main/java/lphy/base/distribution/Exp.java
@@ -1,8 +1,8 @@
 package lphy.base.distribution;
 
 import lphy.core.model.annotation.GeneratorInfo;
-import lphy.core.model.annotation.ParameterInfo;
 import lphy.core.model.component.*;
+import lphy.core.model.component.argument.ParameterInfo;
 import org.apache.commons.math3.distribution.ExponentialDistribution;
 import org.apache.commons.math3.random.RandomGenerator;
 

diff --git a/lphy-base/src/main/java/lphy/base/distribution/ExpMarkovChain.java b/lphy-base/src/main/java/lphy/base/distribution/ExpMarkovChain.java
@@ -1,11 +1,11 @@
 package lphy.base.distribution;
 
 import lphy.core.model.annotation.GeneratorInfo;
-import lphy.core.model.annotation.ParameterInfo;
 import lphy.core.model.component.GenerativeDistribution1D;
 import lphy.core.model.component.GeneratorCategory;
 import lphy.core.model.component.RandomVariable;
 import lphy.core.model.component.Value;
+import lphy.core.model.component.argument.ParameterInfo;
 import org.apache.commons.math3.distribution.ExponentialDistribution;
 import org.apache.commons.math3.random.RandomGenerator;
 

diff --git a/lphy-base/src/main/java/lphy/base/distribution/ExpMulti.java b/lphy-base/src/main/java/lphy/base/distribution/ExpMulti.java
@@ -2,10 +2,10 @@
 
 import lphy.base.math.RandomUtils;
 import lphy.core.model.annotation.GeneratorInfo;
-import lphy.core.model.annotation.ParameterInfo;
 import lphy.core.model.component.GenerativeDistribution;
 import lphy.core.model.component.RandomVariable;
 import lphy.core.model.component.Value;
+import lphy.core.model.component.argument.ParameterInfo;
 import org.apache.commons.math3.distribution.ExponentialDistribution;
 import org.apache.commons.math3.random.RandomGenerator;
 

diff --git a/lphy-base/src/main/java/lphy/base/distribution/Gamma.java b/lphy-base/src/main/java/lphy/base/distribution/Gamma.java
@@ -1,8 +1,8 @@
 package lphy.base.distribution;
 
 import lphy.core.model.annotation.GeneratorInfo;
-import lphy.core.model.annotation.ParameterInfo;
 import lphy.core.model.component.*;
+import lphy.core.model.component.argument.ParameterInfo;
 import org.apache.commons.math3.distribution.GammaDistribution;
 import org.apache.commons.math3.random.RandomGenerator;
 

diff --git a/lphy-base/src/main/java/lphy/base/distribution/GeneralLinearModel.java b/lphy-base/src/main/java/lphy/base/distribution/GeneralLinearModel.java
@@ -2,11 +2,11 @@
 
 import lphy.base.function.GeneralLinearFunction;
 import lphy.core.model.annotation.GeneratorInfo;
-import lphy.core.model.annotation.ParameterInfo;
 import lphy.core.model.component.GeneratorCategory;
 import lphy.core.model.component.RandomVariable;
 import lphy.core.model.component.Value;
 import lphy.core.model.component.ValueUtils;
+import lphy.core.model.component.argument.ParameterInfo;
 import org.apache.commons.math3.distribution.NormalDistribution;
 import org.apache.commons.math3.random.RandomGenerator;
 

diff --git a/lphy-base/src/main/java/lphy/base/distribution/Geometric.java b/lphy-base/src/main/java/lphy/base/distribution/Geometric.java
@@ -1,11 +1,11 @@
 package lphy.base.distribution;
 
 import lphy.core.model.annotation.GeneratorInfo;
-import lphy.core.model.annotation.ParameterInfo;
 import lphy.core.model.component.GenerativeDistribution1D;
 import lphy.core.model.component.GeneratorCategory;
 import lphy.core.model.component.RandomVariable;
 import lphy.core.model.component.Value;
+import lphy.core.model.component.argument.ParameterInfo;
 import org.apache.commons.math3.distribution.GeometricDistribution;
 import org.apache.commons.math3.random.RandomGenerator;
 

diff --git a/lphy-base/src/main/java/lphy/base/distribution/InverseGamma.java b/lphy-base/src/main/java/lphy/base/distribution/InverseGamma.java
@@ -1,8 +1,8 @@
 package lphy.base.distribution;
 
 import lphy.core.model.annotation.GeneratorInfo;
-import lphy.core.model.annotation.ParameterInfo;
 import lphy.core.model.component.*;
+import lphy.core.model.component.argument.ParameterInfo;
 import org.apache.commons.math3.distribution.GammaDistribution;
 import org.apache.commons.math3.random.RandomGenerator;
 

diff --git a/lphy-base/src/main/java/lphy/base/distribution/LogNormal.java b/lphy-base/src/main/java/lphy/base/distribution/LogNormal.java
@@ -1,8 +1,8 @@
 package lphy.base.distribution;
 
 import lphy.core.model.annotation.GeneratorInfo;
-import lphy.core.model.annotation.ParameterInfo;
 import lphy.core.model.component.*;
+import lphy.core.model.component.argument.ParameterInfo;
 import org.apache.commons.math3.distribution.LogNormalDistribution;
 import org.apache.commons.math3.random.RandomGenerator;
 

diff --git a/lphy-base/src/main/java/lphy/base/distribution/LogNormalMulti.java b/lphy-base/src/main/java/lphy/base/distribution/LogNormalMulti.java
@@ -1,11 +1,11 @@
 package lphy.base.distribution;
 
 import lphy.core.model.annotation.GeneratorInfo;
-import lphy.core.model.annotation.ParameterInfo;
 import lphy.core.model.component.GenerativeDistribution;
 import lphy.core.model.component.RandomVariable;
 import lphy.core.model.component.Value;
 import lphy.core.model.component.ValueUtils;
+import lphy.core.model.component.argument.ParameterInfo;
 import org.apache.commons.math3.distribution.LogNormalDistribution;
 
 import java.util.Map;

diff --git a/lphy-base/src/main/java/lphy/base/distribution/MVN.java b/lphy-base/src/main/java/lphy/base/distribution/MVN.java
@@ -1,9 +1,9 @@
 package lphy.base.distribution;
 
 import lphy.core.model.annotation.GeneratorInfo;
-import lphy.core.model.annotation.ParameterInfo;
 import lphy.core.model.component.RandomVariable;
 import lphy.core.model.component.Value;
+import lphy.core.model.component.argument.ParameterInfo;
 import org.apache.commons.math3.distribution.MultivariateNormalDistribution;
 import org.apache.commons.math3.random.RandomGenerator;
 

diff --git a/lphy-base/src/main/java/lphy/base/distribution/NegativeBinomial.java b/lphy-base/src/main/java/lphy/base/distribution/NegativeBinomial.java
@@ -1,11 +1,11 @@
 package lphy.base.distribution;
 
 import lphy.core.model.annotation.GeneratorInfo;
-import lphy.core.model.annotation.ParameterInfo;
 import lphy.core.model.component.GenerativeDistribution1D;
 import lphy.core.model.component.GeneratorCategory;
 import lphy.core.model.component.RandomVariable;
 import lphy.core.model.component.Value;
+import lphy.core.model.component.argument.ParameterInfo;
 import org.apache.commons.math3.random.RandomGenerator;
 
 import java.util.Map;

diff --git a/lphy-base/src/main/java/lphy/base/distribution/Normal.java b/lphy-base/src/main/java/lphy/base/distribution/Normal.java
@@ -2,8 +2,8 @@
 
 import lphy.base.math.RandomUtils;
 import lphy.core.model.annotation.GeneratorInfo;
-import lphy.core.model.annotation.ParameterInfo;
 import lphy.core.model.component.*;
+import lphy.core.model.component.argument.ParameterInfo;
 import org.apache.commons.math3.distribution.NormalDistribution;
 import org.apache.commons.math3.random.RandomGenerator;
 

diff --git a/lphy-base/src/main/java/lphy/base/distribution/NormalGamma.java b/lphy-base/src/main/java/lphy/base/distribution/NormalGamma.java
@@ -1,11 +1,11 @@
 package lphy.base.distribution;
 
 import lphy.core.model.annotation.GeneratorInfo;
-import lphy.core.model.annotation.ParameterInfo;
 import lphy.core.model.component.GeneratorCategory;
 import lphy.core.model.component.RandomVariable;
 import lphy.core.model.component.Value;
 import lphy.core.model.component.ValueUtils;
+import lphy.core.model.component.argument.ParameterInfo;
 import org.apache.commons.math3.distribution.GammaDistribution;
 import org.apache.commons.math3.distribution.NormalDistribution;
 import org.apache.commons.math3.random.RandomGenerator;

diff --git a/lphy-base/src/main/java/lphy/base/distribution/OrnsteinUhlenbeck.java b/lphy-base/src/main/java/lphy/base/distribution/OrnsteinUhlenbeck.java
@@ -1,8 +1,8 @@
 package lphy.base.distribution;
 
-import lphy.core.model.annotation.ParameterInfo;
 import lphy.core.model.component.RandomVariable;
 import lphy.core.model.component.Value;
+import lphy.core.model.component.argument.ParameterInfo;
 import org.apache.commons.math3.distribution.NormalDistribution;
 import org.apache.commons.math3.random.RandomGenerator;
 

diff --git a/lphy-base/src/main/java/lphy/base/distribution/Poisson.java b/lphy-base/src/main/java/lphy/base/distribution/Poisson.java
@@ -2,8 +2,8 @@
 
 import lphy.base.math.RandomUtils;
 import lphy.core.model.annotation.GeneratorInfo;
-import lphy.core.model.annotation.ParameterInfo;
 import lphy.core.model.component.*;
+import lphy.core.model.component.argument.ParameterInfo;
 import org.apache.commons.math3.distribution.PoissonDistribution;
 import org.apache.commons.math3.random.RandomGenerator;
 

diff --git a/lphy-base/src/main/java/lphy/base/distribution/RandomBooleanArray.java b/lphy-base/src/main/java/lphy/base/distribution/RandomBooleanArray.java
@@ -2,11 +2,11 @@
 
 import lphy.base.math.RandomUtils;
 import lphy.core.model.annotation.GeneratorInfo;
-import lphy.core.model.annotation.ParameterInfo;
 import lphy.core.model.component.GenerativeDistribution;
 import lphy.core.model.component.GeneratorCategory;
 import lphy.core.model.component.RandomVariable;
 import lphy.core.model.component.Value;
+import lphy.core.model.component.argument.ParameterInfo;
 
 import java.util.*;
 

diff --git a/lphy-base/src/main/java/lphy/base/distribution/RandomComposition.java b/lphy-base/src/main/java/lphy/base/distribution/RandomComposition.java
@@ -1,10 +1,10 @@
 package lphy.base.distribution;
 
 import lphy.core.model.annotation.GeneratorInfo;
-import lphy.core.model.annotation.ParameterInfo;
 import lphy.core.model.component.GeneratorCategory;
 import lphy.core.model.component.RandomVariable;
 import lphy.core.model.component.Value;
+import lphy.core.model.component.argument.ParameterInfo;
 import org.apache.commons.math3.random.RandomGenerator;
 
 import java.util.*;

diff --git a/lphy-base/src/main/java/lphy/base/distribution/Sample.java b/lphy-base/src/main/java/lphy/base/distribution/Sample.java
@@ -3,11 +3,11 @@
 import lphy.base.ParameterNames;
 import lphy.base.math.RandomUtils;
 import lphy.core.model.annotation.GeneratorInfo;
-import lphy.core.model.annotation.ParameterInfo;
 import lphy.core.model.component.GenerativeDistribution;
 import lphy.core.model.component.RandomVariable;
 import lphy.core.model.component.Value;
 import lphy.core.model.component.VariableUtils;
+import lphy.core.model.component.argument.ParameterInfo;
 
 import java.util.*;
 

diff --git a/lphy-base/src/main/java/lphy/base/distribution/Uniform.java b/lphy-base/src/main/java/lphy/base/distribution/Uniform.java
@@ -1,8 +1,8 @@
 package lphy.base.distribution;
 
 import lphy.core.model.annotation.GeneratorInfo;
-import lphy.core.model.annotation.ParameterInfo;
 import lphy.core.model.component.*;
+import lphy.core.model.component.argument.ParameterInfo;
 import org.apache.commons.math3.random.RandomGenerator;
 
 import java.util.Map;

diff --git a/lphy-base/src/main/java/lphy/base/distribution/UniformDiscrete.java b/lphy-base/src/main/java/lphy/base/distribution/UniformDiscrete.java
@@ -1,10 +1,10 @@
 package lphy.base.distribution;
 
 import lphy.core.model.annotation.GeneratorInfo;
-import lphy.core.model.annotation.ParameterInfo;
 import lphy.core.model.component.GeneratorCategory;
 import lphy.core.model.component.RandomVariable;
 import lphy.core.model.component.Value;
+import lphy.core.model.component.argument.ParameterInfo;
 import org.apache.commons.math3.random.RandomGenerator;
 
 import java.util.Map;

diff --git a/lphy-base/src/main/java/lphy/base/distribution/Weibull.java b/lphy-base/src/main/java/lphy/base/distribution/Weibull.java
@@ -1,11 +1,11 @@
 package lphy.base.distribution;
 
 import lphy.core.model.annotation.GeneratorInfo;
-import lphy.core.model.annotation.ParameterInfo;
 import lphy.core.model.component.GeneratorCategory;
 import lphy.core.model.component.RandomVariable;
 import lphy.core.model.component.Value;
 import lphy.core.model.component.ValueUtils;
+import lphy.core.model.component.argument.ParameterInfo;
 import org.apache.commons.math3.distribution.WeibullDistribution;
 import org.apache.commons.math3.random.RandomGenerator;
 

diff --git a/lphy-base/src/main/java/lphy/base/distribution/WeightedDirichlet.java b/lphy-base/src/main/java/lphy/base/distribution/WeightedDirichlet.java
@@ -2,10 +2,10 @@
 
 import lphy.base.math.MathUtils;
 import lphy.core.model.annotation.GeneratorInfo;
-import lphy.core.model.annotation.ParameterInfo;
 import lphy.core.model.component.GeneratorCategory;
 import lphy.core.model.component.RandomVariable;
 import lphy.core.model.component.Value;
+import lphy.core.model.component.argument.ParameterInfo;
 import org.apache.commons.math3.random.RandomGenerator;
 
 import java.util.Map;