move to beastclassic namespace

BEAST2-Dev · Aug 3, 2022 · b1d8986 · b1d8986
1 parent b1e8eab
commit b1d8986
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Showing 67 changed files with 127 additions and 130 deletions.
diff --git a/...p/beauti/BeautiDiscreteTraitProvider.java → ...p/beauti/BeautiDiscreteTraitProvider.java b/...p/beauti/BeautiDiscreteTraitProvider.java → ...p/beauti/BeautiDiscreteTraitProvider.java
@@ -1,4 +1,4 @@
-package beast.app.beauti;
+package beastclassic.app.beauti;
 
 import java.awt.Frame;
 import java.util.ArrayList;
@@ -19,10 +19,10 @@
 import beast.base.parser.PartitionContext;
 import beast.base.evolution.alignment.Alignment;
 import beast.base.evolution.datatype.UserDataType;
-import beast.evolution.alignment.AlignmentFromTrait;
-import beast.evolution.likelihood.AncestralStateTreeLikelihood;
+import beastclassic.evolution.alignment.AlignmentFromTrait;
+import beastclassic.evolution.likelihood.AncestralStateTreeLikelihood;
+import beastclassic.evolution.substitutionmodel.SVSGeneralSubstitutionModel;
 import beast.base.evolution.sitemodel.SiteModel;
-import beast.evolution.substitutionmodel.SVSGeneralSubstitutionModel;
 import beast.base.evolution.tree.Tree;
 import beast.base.inference.distribution.ParametricDistribution;
 import beast.base.inference.distribution.Poisson;

diff --git a/...p/beauti/BeautiLocationTraitProvider.java → ...p/beauti/BeautiLocationTraitProvider.java b/...p/beauti/BeautiLocationTraitProvider.java → ...p/beauti/BeautiLocationTraitProvider.java
@@ -1,4 +1,4 @@
-package beast.app.beauti;
+package beastclassic.app.beauti;
 
 import java.awt.Frame;
 import java.util.ArrayList;
@@ -11,7 +11,7 @@
 import beastfx.app.inputeditor.BeautiAlignmentProvider;
 import beastfx.app.inputeditor.BeautiDoc;
 import beast.base.parser.PartitionContext;
-import beast.continuous.SampledMultivariateTraitLikelihood;
+import beastclassic.continuous.SampledMultivariateTraitLikelihood;
 import beast.base.core.BEASTInterface;
 import beast.base.core.Description;
 import beast.base.inference.State;
@@ -56,7 +56,7 @@ public List<BEASTInterface> getAlignments(BeautiDoc doc) {
 	@Override
 	public int matches(Alignment alignment) {
 		for (BEASTInterface output : alignment.getOutputs()) {
-			if (output instanceof beast.continuous.SampledMultivariateTraitLikelihood) {
+			if (output instanceof beastclassic.continuous.SampledMultivariateTraitLikelihood) {
 				return 10;
 			}
 		}

diff --git a/...beast/app/beauti/LocationInputEditor.java → ...assic/app/beauti/LocationInputEditor.java b/...beast/app/beauti/LocationInputEditor.java → ...assic/app/beauti/LocationInputEditor.java
@@ -1,4 +1,4 @@
-package beast.app.beauti;
+package beastclassic.app.beauti;
 
 
 import java.awt.Color;
@@ -28,9 +28,9 @@
 import beastfx.app.inputeditor.GuessPatternDialog;
 import beastfx.app.inputeditor.ListInputEditor;
 import beastfx.app.inputeditor.SmallLabel;
-import beast.continuous.SampledMultivariateTraitLikelihood;
-import beast.evolution.alignment.AlignmentFromTraitMap;
-import beast.evolution.tree.TreeTraitMap;
+import beastclassic.evolution.tree.TreeTraitMap;
+import beastclassic.continuous.SampledMultivariateTraitLikelihood;
+import beastclassic.evolution.alignment.AlignmentFromTraitMap;
 import beast.base.core.BEASTInterface;
 import beast.base.core.BEASTObject;
 import beast.base.core.Input;

diff --git a/src/beast/app/beauti/TraitDialog.java → src/beastclassic/app/beauti/TraitDialog.java b/src/beast/app/beauti/TraitDialog.java → src/beastclassic/app/beauti/TraitDialog.java
@@ -1,4 +1,4 @@
-package beast.app.beauti;
+package beastclassic.app.beauti;
 
 import javax.swing.JDialog;
 

diff --git a/src/beast/app/beauti/TraitInputEditor.java → ...tclassic/app/beauti/TraitInputEditor.java b/src/beast/app/beauti/TraitInputEditor.java → ...tclassic/app/beauti/TraitInputEditor.java
@@ -1,4 +1,4 @@
-package beast.app.beauti;
+package beastclassic.app.beauti;
 
 import java.awt.Color;
 import java.awt.Component;
@@ -36,8 +36,8 @@
 import beast.base.evolution.alignment.Alignment;
 import beast.base.evolution.alignment.TaxonSet;
 import beast.base.evolution.datatype.UserDataType;
-import beast.evolution.alignment.AlignmentFromTrait;
-import beast.evolution.likelihood.AncestralStateTreeLikelihood;
+import beastclassic.evolution.alignment.AlignmentFromTrait;
+import beastclassic.evolution.likelihood.AncestralStateTreeLikelihood;
 import beast.base.evolution.tree.TraitSet;
 import beast.base.evolution.tree.Tree;
 import beast.base.evolution.tree.TreeInterface;

diff --git a/.../AbstractMultivariateTraitLikelihood.java → .../AbstractMultivariateTraitLikelihood.java b/.../AbstractMultivariateTraitLikelihood.java → .../AbstractMultivariateTraitLikelihood.java
@@ -1,4 +1,4 @@
-package beast.continuous;
+package beastclassic.continuous;
 
 
 
@@ -16,13 +16,13 @@
 import beast.base.core.Input.Validate;
 import beast.base.inference.parameter.RealParameter;
 import beast.base.evolution.branchratemodel.BranchRateModel;
-import beast.evolution.alignment.AlignmentFromTraitMap;
-import beast.evolution.datatype.ContinuousDataType;
 import beast.base.evolution.likelihood.GenericTreeLikelihood;
 import beast.base.evolution.sitemodel.SiteModel;
-import beast.evolution.substitutionmodel.ContinuousSubstitutionModel;
-import beast.evolution.tree.TreeTrait;
-import beast.evolution.tree.TreeTraitMap;
+import beastclassic.evolution.tree.TreeTrait;
+import beastclassic.evolution.tree.TreeTraitMap;
+import beastclassic.evolution.alignment.AlignmentFromTraitMap;
+import beastclassic.evolution.datatype.ContinuousDataType;
+import beastclassic.evolution.substitutionmodel.ContinuousSubstitutionModel;
 import beast.base.evolution.tree.Node;
 import beast.base.evolution.tree.TreeInterface;
 

diff --git a/...ConjugateMultivariateTraitLikelihood.java → ...ConjugateMultivariateTraitLikelihood.java b/...ConjugateMultivariateTraitLikelihood.java → ...ConjugateMultivariateTraitLikelihood.java
@@ -23,15 +23,15 @@
  * Boston, MA  02110-1301  USA
  */
 
-package beast.continuous;
+package beastclassic.continuous;
 
 import beast.base.core.Description;
-import dr.math.distributions.MultivariateNormalDistribution;
-import dr.math.distributions.WishartSufficientStatistics;
 
 import java.util.List;
 
 import beast.base.inference.parameter.RealParameter;
+import beastclassic.dr.math.distributions.MultivariateNormalDistribution;
+import beastclassic.dr.math.distributions.WishartSufficientStatistics;
 import beast.base.evolution.branchratemodel.BranchRateModel;
 import beast.base.evolution.tree.Node;
 import beast.base.evolution.tree.TreeInterface;

diff --git a/...ntegratedMultivariateTraitLikelihood.java → ...ntegratedMultivariateTraitLikelihood.java b/...ntegratedMultivariateTraitLikelihood.java → ...ntegratedMultivariateTraitLikelihood.java
@@ -23,21 +23,21 @@
  * Boston, MA  02110-1301  USA
  */
 
-package beast.continuous;
+package beastclassic.continuous;
 
 
 import java.util.Arrays;
 import java.util.List;
 
 import beast.base.core.Description;
-import dr.evomodel.continuous.MissingTraits;
-import dr.math.distributions.WishartSufficientStatistics;
 import beast.base.core.Input;
 import beast.base.inference.parameter.RealParameter;
 import beast.base.evolution.branchratemodel.BranchRateModel;
 import beast.base.evolution.tree.Node;
 import beast.base.evolution.tree.TreeInterface;
 import beast.base.math.matrixalgebra.SymmetricMatrix;
+import beastclassic.dr.evolmodel.continuous.MissingTraits;
+import beastclassic.dr.math.distributions.WishartSufficientStatistics;
 
 /**
  * A multivariate trait likelihood that analytically integrates out the unobserved trait values at all internal
@@ -941,7 +941,7 @@ private void preOrderTraverseSample(/*MultivariateTraitTree*/ TreeInterface tree
                 double[][] variance = computeMarginalRootMeanAndVariance(rootMean, treePrecision, treeVariance,
                         rootPrecision);
 
-                double[] draw = dr.math.distributions.MultivariateNormalDistribution.nextMultivariateNormalVariance(rootMean, variance);
+                double[] draw = beastclassic.dr.math.distributions.MultivariateNormalDistribution.nextMultivariateNormalVariance(rootMean, variance);
 
                 if (DEBUG_PREORDER) {
                     Arrays.fill(draw, 1.0);
@@ -1004,7 +1004,7 @@ private void preOrderTraverseSample(/*MultivariateTraitTree*/ TreeInterface tree
                             var[i][j] = treeVariance[i][j] / totalPrecision;
                         }
                     }
-                    double[] draw = dr.math.distributions.MultivariateNormalDistribution.nextMultivariateNormalVariance(mean, var);
+                    double[] draw = beastclassic.dr.math.distributions.MultivariateNormalDistribution.nextMultivariateNormalVariance(mean, var);
                     System.arraycopy(draw, 0, drawnStates, thisOffset, dimTrait);
 
 //                    if (DEBUG) {

diff --git a/...ontinuous/MultivariateDiffusionModel.java → ...ontinuous/MultivariateDiffusionModel.java b/...ontinuous/MultivariateDiffusionModel.java → ...ontinuous/MultivariateDiffusionModel.java
@@ -1,12 +1,12 @@
-package beast.continuous;
+package beastclassic.continuous;
 
 import beast.base.core.Description;
 import beast.base.core.Input;
 import beast.base.core.Input.Validate;
 import beast.base.inference.parameter.RealParameter;
-import beast.evolution.substitutionmodel.*;
+import beastclassic.dr.math.distributions.MultivariateNormalDistribution;
+import beastclassic.evolution.substitutionmodel.ContinuousSubstitutionModel;
 import beast.base.evolution.tree.Tree;
-import dr.math.distributions.MultivariateNormalDistribution;
 
 
 

diff --git a/...s/SampledMultivariateTraitLikelihood.java → ...s/SampledMultivariateTraitLikelihood.java b/...s/SampledMultivariateTraitLikelihood.java → ...s/SampledMultivariateTraitLikelihood.java
@@ -1,4 +1,4 @@
-package beast.continuous;
+package beastclassic.continuous;
 
 //import dr.evolution.tree.NodeRef;
 //import dr.evolution.tree.Tree;

diff --git a/src/dr/math/GammaFunction.java → src/beastclassic/dr/GammaFunction.java b/src/dr/math/GammaFunction.java → src/beastclassic/dr/GammaFunction.java
@@ -23,7 +23,7 @@
  * Boston, MA  02110-1301  USA
  */
 
-package dr.math;
+package beastclassic.dr;
 
 import beast.base.core.Description;
 

diff --git a/...dr/evomodel/continuous/MissingTraits.java → ...r/evolmodel/continuous/MissingTraits.java b/...dr/evomodel/continuous/MissingTraits.java → ...r/evolmodel/continuous/MissingTraits.java
@@ -23,15 +23,15 @@
  * Boston, MA  02110-1301  USA
  */
 
-package dr.evomodel.continuous;
+package beastclassic.dr.evolmodel.continuous;
 
 
 import java.util.Arrays;
 import java.util.List;
 import java.util.logging.Logger;
 
-import beast.continuous.IntegratedMultivariateTraitLikelihood;
 import beast.base.evolution.tree.TreeInterface;
+import beastclassic.continuous.IntegratedMultivariateTraitLikelihood;
 
 /**
  * @author Marc A. Suchard

diff --git a/...stributions/MultivariateDistribution.java → ...stributions/MultivariateDistribution.java b/...stributions/MultivariateDistribution.java → ...stributions/MultivariateDistribution.java
@@ -1,4 +1,4 @@
-package dr.math.distributions;
+package beastclassic.dr.math.distributions;
 
 /**
  * @author Marc A. Suchard

diff --git a/...tions/MultivariateNormalDistribution.java → ...tions/MultivariateNormalDistribution.java b/...tions/MultivariateNormalDistribution.java → ...tions/MultivariateNormalDistribution.java
@@ -1,4 +1,4 @@
-package dr.math.distributions;
+package beastclassic.dr.math.distributions;
 
 
 import beast.base.core.Description;

diff --git a/...th/distributions/WishartDistribution.java → ...th/distributions/WishartDistribution.java b/...th/distributions/WishartDistribution.java → ...th/distributions/WishartDistribution.java
@@ -1,4 +1,4 @@
-package dr.math.distributions;
+package beastclassic.dr.math.distributions;
 
 
 import org.apache.commons.math.distribution.GammaDistribution;
@@ -9,10 +9,7 @@
 import beast.base.math.matrixalgebra.IllegalDimension;
 import beast.base.math.matrixalgebra.Matrix;
 import beast.base.util.Randomizer;
-
-
-
-import dr.math.GammaFunction;
+import beastclassic.dr.GammaFunction;
 
 /**
  * @author Marc Suchard

diff --git a/...ibutions/WishartSufficientStatistics.java → ...ibutions/WishartSufficientStatistics.java b/...ibutions/WishartSufficientStatistics.java → ...ibutions/WishartSufficientStatistics.java
@@ -1,4 +1,4 @@
-package dr.math.distributions;
+package beastclassic.dr.math.distributions;
 
 import java.util.Arrays;
 

diff --git a/src/dr/math/util/ArcCos.java → src/beastclassic/dr/util/ArcCos.java b/src/dr/math/util/ArcCos.java → src/beastclassic/dr/util/ArcCos.java
@@ -1,4 +1,4 @@
-package dr.math.util;
+package beastclassic.dr.util;
 
 import static java.lang.Math.sqrt;
 

diff --git a/...olution/alignment/AlignmentFromTrait.java → ...olution/alignment/AlignmentFromTrait.java b/...olution/alignment/AlignmentFromTrait.java → ...olution/alignment/AlignmentFromTrait.java
@@ -1,4 +1,4 @@
-package beast.evolution.alignment;
+package beastclassic.evolution.alignment;
 
 import java.util.ArrayList;
 import java.util.Arrays;

diff --git a/...tion/alignment/AlignmentFromTraitMap.java → ...tion/alignment/AlignmentFromTraitMap.java b/...tion/alignment/AlignmentFromTraitMap.java → ...tion/alignment/AlignmentFromTraitMap.java
@@ -1,4 +1,4 @@
-package beast.evolution.alignment;
+package beastclassic.evolution.alignment;
 
 
 import java.util.ArrayList;
@@ -8,8 +8,8 @@
 import beast.base.core.Input;
 import beast.base.core.Input.Validate;
 import beast.base.evolution.alignment.Alignment;
-import beast.evolution.datatype.ContinuousDataType;
-import beast.evolution.tree.TreeTraitMap;
+import beastclassic.evolution.tree.TreeTraitMap;
+import beastclassic.evolution.datatype.ContinuousDataType;
 
 
 

diff --git a/...volution/datatype/ContinuousDataType.java → ...volution/datatype/ContinuousDataType.java b/...volution/datatype/ContinuousDataType.java → ...volution/datatype/ContinuousDataType.java
@@ -1,4 +1,4 @@
-package beast.evolution.datatype;
+package beastclassic.evolution.datatype;
 
 import java.util.List;
 

diff --git a/.../evolution/datatype/LocationDataType.java → .../evolution/datatype/LocationDataType.java b/.../evolution/datatype/LocationDataType.java → .../evolution/datatype/LocationDataType.java
@@ -1,4 +1,4 @@
-package beast.evolution.datatype;
+package beastclassic.evolution.datatype;
 
 import beast.base.core.Description;
 

diff --git a/...n/likelihood/AncestralSequenceLogger.java → ...n/likelihood/AncestralSequenceLogger.java b/...n/likelihood/AncestralSequenceLogger.java → ...n/likelihood/AncestralSequenceLogger.java
@@ -1,4 +1,4 @@
-package beast.evolution.likelihood;
+package beastclassic.evolution.likelihood;
 
 import java.io.PrintStream;
 

diff --git a/...elihood/AncestralStateTreeLikelihood.java → ...elihood/AncestralStateTreeLikelihood.java b/...elihood/AncestralStateTreeLikelihood.java → ...elihood/AncestralStateTreeLikelihood.java
@@ -1,4 +1,4 @@
-package beast.evolution.likelihood;
+package beastclassic.evolution.likelihood;
 
 
 
@@ -23,8 +23,8 @@
 import beast.base.evolution.tree.Tree;
 import beast.base.evolution.tree.TreeInterface;
 import beast.base.util.Randomizer;
-import beast.evolution.tree.TreeTrait;
-import beast.evolution.tree.TreeTraitProvider;
+import beastclassic.evolution.tree.TreeTrait;
+import beastclassic.evolution.tree.TreeTraitProvider;
 
 /**
  * @author Marc A. Suchard

diff --git a/...beast/evolution/likelihood/LeafTrait.java → ...assic/evolution/likelihood/LeafTrait.java b/...beast/evolution/likelihood/LeafTrait.java → ...assic/evolution/likelihood/LeafTrait.java
@@ -1,4 +1,4 @@
-package beast.evolution.likelihood;
+package beastclassic.evolution.likelihood;
 
 import beast.base.inference.CalculationNode;
 import beast.base.core.Description;

diff --git a/...ution/operators/BitFlipBSSVSOperator.java → ...ution/operators/BitFlipBSSVSOperator.java b/...ution/operators/BitFlipBSSVSOperator.java → ...ution/operators/BitFlipBSSVSOperator.java
@@ -1,4 +1,4 @@
-package beast.evolution.operators;
+package beastclassic.evolution.operators;
 
 import beast.base.core.Description;
 import beast.base.core.Input;

diff --git a/...MultilocusSkyrideBlockUpdateOperator.java → ...MultilocusSkyrideBlockUpdateOperator.java b/...MultilocusSkyrideBlockUpdateOperator.java → ...MultilocusSkyrideBlockUpdateOperator.java
@@ -23,7 +23,7 @@
  * Boston, MA  02110-1301  USA
  */
 
-package beast.evolution.operators;
+package beastclassic.evolution.operators;
 
 import no.uib.cipr.matrix.*;
 
@@ -39,8 +39,8 @@
 import beast.base.inference.Operator;
 import beast.base.inference.StateNode;
 import beast.base.inference.parameter.RealParameter;
-import beast.evolution.tree.coalescent.GMRFMultilocusSkyrideLikelihood;
 import beast.base.util.Randomizer;
+import beastclassic.evolution.tree.coalescent.GMRFMultilocusSkyrideLikelihood;
 
 /* A Metropolis-Hastings operator to update the log population sizes and precision parameter jointly under a Gaussian Markov random field prior
  *

diff --git a/...ators/GMRFSkyrideBlockUpdateOperator.java → ...ators/GMRFSkyrideBlockUpdateOperator.java b/...ators/GMRFSkyrideBlockUpdateOperator.java → ...ators/GMRFSkyrideBlockUpdateOperator.java
@@ -1,4 +1,4 @@
-package beast.evolution.operators;
+package beastclassic.evolution.operators;
 
 
 import no.uib.cipr.matrix.*;
@@ -14,8 +14,8 @@
 import beast.base.inference.StateNode;
 import beast.base.core.Input.Validate;
 import beast.base.inference.parameter.RealParameter;
-import beast.evolution.tree.coalescent.GMRFSkyrideLikelihood;
 import beast.base.util.Randomizer;
+import beastclassic.evolution.tree.coalescent.GMRFSkyrideLikelihood;
 
 
 

diff --git a/...ion/operators/GeneralIntegerOperator.java → ...ion/operators/GeneralIntegerOperator.java b/...ion/operators/GeneralIntegerOperator.java → ...ion/operators/GeneralIntegerOperator.java
@@ -1,4 +1,4 @@
-package beast.evolution.operators;
+package beastclassic.evolution.operators;
 
 import java.util.Arrays;
 

diff --git a/...tion/operators/PickIndicatorOperator.java → ...tion/operators/PickIndicatorOperator.java b/...tion/operators/PickIndicatorOperator.java → ...tion/operators/PickIndicatorOperator.java
@@ -1,4 +1,4 @@
-package beast.evolution.operators;
+package beastclassic.evolution.operators;
 
 
 import java.util.HashSet;