use getExcludedGenerator first #136

LinguaPhylo · Apr 16, 2024 · 5a3b303 · 5a3b303
1 parent 502a991
commit 5a3b303
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diff --git a/lphybeast/src/main/java/lphybeast/spi/LPhyBEASTExt.java b/lphybeast/src/main/java/lphybeast/spi/LPhyBEASTExt.java
@@ -3,34 +3,12 @@
 import beast.base.evolution.datatype.DataType;
 import jebl.evolution.sequences.SequenceType;
 import lphy.base.distribution.DiscretizedGamma;
-import lphy.base.distribution.RandomComposition;
-import lphy.base.distribution.Sample;
-import lphy.base.distribution.WeightedDirichlet;
 import lphy.base.evolution.Taxa;
 import lphy.base.evolution.alignment.Alignment;
 import lphy.base.evolution.tree.TimeTree;
-import lphy.base.function.*;
-import lphy.base.function.alignment.*;
-import lphy.base.function.datatype.BinaryDatatypeFunction;
-import lphy.base.function.datatype.NucleotidesFunction;
-import lphy.base.function.datatype.StandardDatatypeFunction;
-import lphy.base.function.io.WriteFasta;
-import lphy.base.function.taxa.*;
-import lphy.base.function.tree.ExtantTree;
-import lphy.base.function.tree.MigrationCount;
-import lphy.base.function.tree.NodeCount;
-import lphy.core.model.ExpressionNode;
 import lphy.core.model.Generator;
 import lphy.core.model.Value;
-import lphy.core.parser.function.ExpressionNodeWrapper;
-import lphy.core.parser.function.MapFunction;
-import lphy.core.parser.function.MethodCall;
-import lphy.core.simulator.Simulate;
 import lphy.core.vectorization.IID;
-import lphy.core.vectorization.array.ArrayFunction;
-import lphy.core.vectorization.operation.ElementsAt;
-import lphy.core.vectorization.operation.Range;
-import lphy.core.vectorization.operation.RangeList;
 import lphybeast.GeneratorToBEAST;
 import lphybeast.ValueToBEAST;
 import lphybeast.tobeast.operators.DefaultTreeOperatorStrategy;
@@ -77,6 +55,7 @@ default TreeOperatorStrategy getTreeOperatorStrategy() {
      * For a complex logic, or arrays.
      * @param val  Value
      * @return     if the value type is excluded.
+     * @see LPhyBEASTExtImpl#getExcludedValueType()
      */
     static boolean isExcludedValue(Value<?> val) {
         Object ob = val.value();
@@ -86,33 +65,16 @@ static boolean isExcludedValue(Value<?> val) {
                 ob instanceof TimeTree[];
     }
 
+    /**
+     * For a complex logic, or arrays.
+     * @param generator   Generator
+     * @return     if the Generator is excluded.
+     * @see LPhyBEASTExtImpl#getExcludedGenerator()
+     */
     static boolean isExcludedGenerator(Generator generator) {
 
-        return generator instanceof WeightedDirichlet || generator instanceof ArrayFunction ||
-                generator instanceof ExpressionNode || generator instanceof RandomComposition ||
-                generator instanceof NTaxaFunction || generator instanceof NCharFunction ||
-                generator instanceof TaxaFunction || generator instanceof NodeCount ||
-                generator instanceof CreateTaxa || generator instanceof SpeciesTaxa ||
-                generator instanceof TaxaAgesFromFunction || generator instanceof Get<?> ||
-                generator instanceof MissingSites || generator instanceof SelectSitesByMissingFraction ||
-                generator instanceof InvariableSites || generator instanceof VariableSites ||
-                generator instanceof CopySites || generator instanceof Sample<?> ||
-                generator instanceof Simulate || generator instanceof WriteFasta ||
-//                generator instanceof ReadNexus || generator instanceof ReadFasta ||
-                generator instanceof ExtractTrait || generator instanceof Unique ||
-                generator instanceof Intersect || generator instanceof RepArray ||
-                generator instanceof Sort<?> || generator instanceof ConcatArray ||
-                generator instanceof ARange || generator instanceof Range ||
-                generator instanceof MapFunction || generator instanceof MethodCall ||
-                generator instanceof RangeList || generator instanceof ElementsAt || generator instanceof Rep ||
-                generator instanceof MigrationMatrix || generator instanceof MigrationCount ||
-                generator instanceof Length || generator instanceof Select || generator instanceof SumBoolean ||
-                generator instanceof DiscretizedGamma || generator instanceof ExtantTree ||
-                // ignore all data types
-                generator instanceof NucleotidesFunction || generator instanceof StandardDatatypeFunction ||
-                generator instanceof BinaryDatatypeFunction || //generator instanceof PhasedGenotypeFunction ||
-                (generator instanceof IID && ((IID<?>) generator).getBaseDistribution() instanceof DiscretizedGamma) ||
-                generator instanceof ExpressionNodeWrapper;
+        return (generator instanceof IID && ((IID<?>) generator).getBaseDistribution() instanceof DiscretizedGamma);
+// use || to add more ...
     }
 
 }
diff --git a/lphybeast/src/main/java/lphybeast/spi/LPhyBEASTExtImpl.java b/lphybeast/src/main/java/lphybeast/spi/LPhyBEASTExtImpl.java
@@ -2,16 +2,40 @@
 
 import beast.base.evolution.datatype.DataType;
 import jebl.evolution.sequences.SequenceType;
+import lphy.base.distribution.DiscretizedGamma;
+import lphy.base.distribution.RandomComposition;
+import lphy.base.distribution.Sample;
+import lphy.base.distribution.WeightedDirichlet;
 import lphy.base.evolution.datatype.Binary;
 import lphy.base.evolution.datatype.Continuous;
+import lphy.base.function.*;
+import lphy.base.function.alignment.*;
+import lphy.base.function.datatype.BinaryDatatypeFunction;
+import lphy.base.function.datatype.NucleotidesFunction;
+import lphy.base.function.datatype.StandardDatatypeFunction;
 import lphy.base.function.io.ReadFasta;
 import lphy.base.function.io.ReadNexus;
+import lphy.base.function.io.WriteFasta;
+import lphy.base.function.taxa.*;
+import lphy.base.function.tree.ExtantTree;
+import lphy.base.function.tree.MigrationCount;
+import lphy.base.function.tree.NodeCount;
+import lphy.core.model.ExpressionNode;
 import lphy.core.model.Generator;
+import lphy.core.parser.function.ExpressionNodeWrapper;
+import lphy.core.parser.function.MapFunction;
+import lphy.core.parser.function.MethodCall;
+import lphy.core.simulator.Simulate;
+import lphy.core.vectorization.array.ArrayFunction;
+import lphy.core.vectorization.operation.ElementsAt;
+import lphy.core.vectorization.operation.Range;
+import lphy.core.vectorization.operation.RangeList;
 import lphybeast.GeneratorToBEAST;
 import lphybeast.ValueToBEAST;
 import lphybeast.tobeast.generators.*;
 import lphybeast.tobeast.values.*;
 
+import java.util.Map;
 import java.util.*;
 import java.util.concurrent.ConcurrentHashMap;
 
@@ -99,7 +123,28 @@ public Map<SequenceType, DataType> getDataTypeMap() {
     @Override
     public List<Class<? extends Generator>> getExcludedGenerator() {
         return List.of(
-                ReadNexus.class, ReadFasta.class
+                ReadNexus.class, ReadFasta.class, WriteFasta.class, // IO
+                // Taxa and sites
+                NTaxaFunction.class, NCharFunction.class, TaxaFunction.class, CreateTaxa.class,
+                SpeciesTaxa.class, TaxaAgesFromFunction.class,
+                CopySites.class, MissingSites.class, SelectSitesByMissingFraction.class, InvariableSites.class,
+                VariableSites.class,
+                DiscretizedGamma.class,
+                // Tree
+                NodeCount.class, ExtractTrait.class, ExtantTree.class,
+                MigrationMatrix.class, MigrationCount.class,
+                // distribution
+                WeightedDirichlet.class,
+                // utils
+                MapFunction.class, ConcatArray.class, ARange.class, Range.class, RangeList.class,
+                ElementsAt.class, Rep.class, RepArray.class, Sort.class, Unique.class,
+                Get.class, Length.class, Select.class, Intersect.class,
+                RandomComposition.class, SumBoolean.class,
+                // sequence typs
+                NucleotidesFunction.class, StandardDatatypeFunction.class, BinaryDatatypeFunction.class,
+                // lphy
+                MethodCall.class, Simulate.class, Sample.class, ArrayFunction.class,
+                ExpressionNode.class, ExpressionNodeWrapper.class
         );
     }