before extract vectorMatch #294 #364

LinguaPhylo · May 31, 2023 · c4572bb · c4572bb
1 parent eab6653
commit c4572bb
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diff --git a/lphy-base/src/main/java/lphy/base/distributions/BernoulliMulti.java b/lphy-base/src/main/java/lphy/base/distributions/BernoulliMulti.java
@@ -2,7 +2,7 @@
 
 import lphy.core.graphicalmodel.components.*;
 import lphy.core.graphicalmodel.types.IntegerValue;
-import lphy.core.graphicalmodel.vectorization.IID;
+import lphy.core.vectorization.IID;
 import org.apache.commons.math3.distribution.BinomialDistribution;
 import org.apache.commons.math3.random.RandomGenerator;
 

diff --git a/lphy-base/src/main/java/lphy/base/distributions/CompoundDistribution.java b/lphy-base/src/main/java/lphy/base/distributions/CompoundDistribution.java
@@ -3,7 +3,7 @@
 import lphy.core.graphicalmodel.components.GenerativeDistribution;
 import lphy.core.graphicalmodel.components.RandomVariable;
 import lphy.core.graphicalmodel.components.Value;
-import lphy.core.graphicalmodel.vectorization.RangeElement;
+import lphy.core.vectorization.RangeElement;
 
 import java.util.Map;
 

diff --git a/lphy-base/src/main/java/lphy/base/evolution/coalescent/StructuredCoalescent.java b/lphy-base/src/main/java/lphy/base/evolution/coalescent/StructuredCoalescent.java
@@ -6,7 +6,7 @@
 import lphy.base.evolution.tree.TimeTreeNode;
 import lphy.core.graphicalmodel.components.*;
 import lphy.core.graphicalmodel.types.DoubleArray2DValue;
-import lphy.core.graphicalmodel.vectorization.VectorUtils;
+import lphy.core.vectorization.VectorUtils;
 import org.apache.commons.math3.util.CombinatoricsUtils;
 
 import java.util.*;

diff --git a/lphy-base/src/main/java/lphy/base/functions/Unique.java b/lphy-base/src/main/java/lphy/base/functions/Unique.java
@@ -4,7 +4,7 @@
 import lphy.core.graphicalmodel.components.GeneratorInfo;
 import lphy.core.graphicalmodel.components.ParameterInfo;
 import lphy.core.graphicalmodel.components.Value;
-import lphy.core.graphicalmodel.vectorization.CompoundVectorValue;
+import lphy.core.vectorization.CompoundVectorValue;
 
 import java.util.*;
 

diff --git a/lphy-base/src/main/java/lphy/base/logger/TreeFileLogger.java b/lphy-base/src/main/java/lphy/base/logger/TreeFileLogger.java
@@ -3,9 +3,9 @@
 import lphy.base.evolution.tree.TimeTree;
 import lphy.base.parser.nexus.NexusWriter;
 import lphy.core.graphicalmodel.components.Value;
-import lphy.core.graphicalmodel.vectorization.VectorUtils;
 import lphy.core.logger.RandomValueLogger;
 import lphy.core.util.Symbols;
+import lphy.core.vectorization.VectorUtils;
 
 import java.io.File;
 import java.io.PrintStream;

diff --git a/lphy-studio/src/main/java/lphystudio/app/graphicalmodelpanel/GraphicalModelPanel.java b/lphy-studio/src/main/java/lphystudio/app/graphicalmodelpanel/GraphicalModelPanel.java
@@ -10,13 +10,13 @@
 import lphy.core.graphicalmodel.components.GenerativeDistribution;
 import lphy.core.graphicalmodel.components.Generator;
 import lphy.core.graphicalmodel.components.Value;
-import lphy.core.graphicalmodel.vectorization.VectorizedFunction;
 import lphy.core.layeredgraph.Layering;
 import lphy.core.logger.RandomValueLogger;
 import lphy.core.parser.GraphicalLPhyParser;
 import lphy.core.parser.LPhyMetaParser;
 import lphy.core.parser.REPL;
 import lphy.core.util.LoggerUtils;
+import lphy.core.vectorization.VectorizedFunction;
 import lphystudio.app.alignmentcomponent.AlignmentComponent;
 import lphystudio.app.alignmentcomponent.SequenceTypePanel;
 import lphystudio.app.graphicalmodelcomponent.GraphicalModelComponent;

diff --git a/lphy-studio/src/main/java/lphystudio/app/graphicalmodelpanel/VectorComponent.java b/lphy-studio/src/main/java/lphystudio/app/graphicalmodelpanel/VectorComponent.java
@@ -2,7 +2,7 @@
 
 import lphy.core.graphicalmodel.components.Value;
 import lphy.core.graphicalmodel.types.Vector;
-import lphy.core.graphicalmodel.vectorization.CompoundVectorValue;
+import lphy.core.vectorization.CompoundVectorValue;
 
 import javax.swing.*;
 import java.awt.*;

diff --git a/...main/java/lphystudio/app/graphicalmodelpanel/viewer/ContinuousCharacterDataComponent.java b/...main/java/lphystudio/app/graphicalmodelpanel/viewer/ContinuousCharacterDataComponent.java
@@ -5,7 +5,7 @@
 
 import javax.swing.*;
 
-import static lphy.core.graphicalmodel.vectorization.VectorUtils.INDEX_SEPARATOR;
+import static lphy.core.vectorization.VectorUtils.INDEX_SEPARATOR;
 
 public class ContinuousCharacterDataComponent extends JLabel {
 

diff --git a/lphy-studio/src/main/java/lphystudio/app/narrative/HTMLNarrative.java b/lphy-studio/src/main/java/lphystudio/app/narrative/HTMLNarrative.java
@@ -24,8 +24,8 @@
 import java.util.List;
 import java.util.prefs.Preferences;
 
-import static lphy.core.graphicalmodel.vectorization.VectorUtils.INDEX_SEPARATOR;
 import static lphy.core.narrative.NarrativeUtils.getURL;
+import static lphy.core.vectorization.VectorUtils.INDEX_SEPARATOR;
 
 public class HTMLNarrative implements Narrative {
 

diff --git a/lphy-studio/src/main/java/lphystudio/app/narrative/LaTeXNarrative.java b/lphy-studio/src/main/java/lphystudio/app/narrative/LaTeXNarrative.java
@@ -6,16 +6,16 @@
 import lphy.core.graphicalmodel.components.Generator;
 import lphy.core.graphicalmodel.components.RandomVariable;
 import lphy.core.graphicalmodel.components.Value;
-import lphy.core.graphicalmodel.vectorization.IID;
-import lphy.core.graphicalmodel.vectorization.VectorizedDistribution;
-import lphy.core.graphicalmodel.vectorization.VectorizedFunction;
 import lphy.core.layeredgraph.LatticePoint;
 import lphy.core.layeredgraph.LayeredNode;
 import lphy.core.layeredgraph.NodeWrapper;
 import lphy.core.layeredgraph.ProperLayeredGraph;
 import lphy.core.narrative.Narrative;
 import lphy.core.parser.LPhyMetaParser;
 import lphy.core.util.Symbols;
+import lphy.core.vectorization.IID;
+import lphy.core.vectorization.VectorizedDistribution;
+import lphy.core.vectorization.VectorizedFunction;
 import lphystudio.core.layeredgraph.LayeredGNode;
 import lphystudio.core.theme.ThemeColours;
 

diff --git a/lphy-studio/src/main/java/lphystudio/app/narrative/LaTeXUtils.java b/lphy-studio/src/main/java/lphystudio/app/narrative/LaTeXUtils.java
@@ -7,7 +7,7 @@
 
 import java.util.List;
 
-import static lphy.core.graphicalmodel.vectorization.VectorUtils.INDEX_SEPARATOR;
+import static lphy.core.vectorization.VectorUtils.INDEX_SEPARATOR;
 
 public class LaTeXUtils {
 

diff --git a/lphy-studio/src/main/java/lphystudio/core/layeredgraph/NodePaintUtils.java b/lphy-studio/src/main/java/lphystudio/core/layeredgraph/NodePaintUtils.java
@@ -4,12 +4,12 @@
 import lphy.core.graphicalmodel.components.RandomVariable;
 import lphy.core.graphicalmodel.components.Value;
 import lphy.core.graphicalmodel.components.ValueUtils;
-import lphy.core.graphicalmodel.vectorization.IID;
-import lphy.core.graphicalmodel.vectorization.VectorizedDistribution;
-import lphy.core.graphicalmodel.vectorization.VectorizedFunction;
 import lphy.core.layeredgraph.LayeredNode;
 import lphy.core.layeredgraph.NodeWrapper;
 import lphy.core.parser.LPhyMetaParser;
+import lphy.core.vectorization.IID;
+import lphy.core.vectorization.VectorizedDistribution;
+import lphy.core.vectorization.VectorizedFunction;
 import lphystudio.core.theme.ThemeColours;
 
 import javax.swing.*;

diff --git a/lphy/src/main/java/lphy/core/graphicalmodel/types/BooleanArrayValue.java b/lphy/src/main/java/lphy/core/graphicalmodel/types/BooleanArrayValue.java
@@ -1,7 +1,7 @@
 package lphy.core.graphicalmodel.types;
 
 import lphy.core.graphicalmodel.components.DeterministicFunction;
-import lphy.core.graphicalmodel.vectorization.VectorValue;
+import lphy.core.vectorization.VectorValue;
 
 public class BooleanArrayValue extends VectorValue<Boolean> {
 

diff --git a/lphy/src/main/java/lphy/core/graphicalmodel/types/DoubleArrayValue.java b/lphy/src/main/java/lphy/core/graphicalmodel/types/DoubleArrayValue.java
@@ -1,7 +1,7 @@
 package lphy.core.graphicalmodel.types;
 
 import lphy.core.graphicalmodel.components.DeterministicFunction;
-import lphy.core.graphicalmodel.vectorization.VectorValue;
+import lphy.core.vectorization.VectorValue;
 
 public class DoubleArrayValue extends VectorValue<Double> {
 

diff --git a/lphy/src/main/java/lphy/core/graphicalmodel/types/IntegerArrayValue.java b/lphy/src/main/java/lphy/core/graphicalmodel/types/IntegerArrayValue.java
@@ -1,8 +1,8 @@
 package lphy.core.graphicalmodel.types;
 
 import lphy.core.graphicalmodel.components.DeterministicFunction;
-import lphy.core.graphicalmodel.vectorization.RangeElement;
-import lphy.core.graphicalmodel.vectorization.VectorValue;
+import lphy.core.vectorization.RangeElement;
+import lphy.core.vectorization.VectorValue;
 
 import java.util.Arrays;
 public class IntegerArrayValue extends VectorValue<Integer> implements RangeElement {

diff --git a/lphy/src/main/java/lphy/core/graphicalmodel/types/IntegerValue.java b/lphy/src/main/java/lphy/core/graphicalmodel/types/IntegerValue.java
@@ -1,7 +1,7 @@
 package lphy.core.graphicalmodel.types;
 
 import lphy.core.graphicalmodel.components.DeterministicFunction;
-import lphy.core.graphicalmodel.vectorization.RangeElement;
+import lphy.core.vectorization.RangeElement;
 
 public class IntegerValue extends NumberValue<Integer> implements RangeElement {
 

diff --git a/lphy/src/main/java/lphy/core/graphicalmodel/types/NumberArrayValue.java b/lphy/src/main/java/lphy/core/graphicalmodel/types/NumberArrayValue.java
@@ -1,7 +1,7 @@
 package lphy.core.graphicalmodel.types;
 
 import lphy.core.graphicalmodel.components.DeterministicFunction;
-import lphy.core.graphicalmodel.vectorization.VectorValue;
+import lphy.core.vectorization.VectorValue;
 
 public class NumberArrayValue extends VectorValue<Number> {
 

diff --git a/lphy/src/main/java/lphy/core/graphicalmodel/types/StringArrayValue.java b/lphy/src/main/java/lphy/core/graphicalmodel/types/StringArrayValue.java
@@ -1,7 +1,7 @@
 package lphy.core.graphicalmodel.types;
 
 import lphy.core.graphicalmodel.components.DeterministicFunction;
-import lphy.core.graphicalmodel.vectorization.VectorValue;
+import lphy.core.vectorization.VectorValue;
 
 import static lphy.core.graphicalmodel.components.ValueUtils.quotedString;
 

diff --git a/lphy/src/main/java/lphy/core/logger/VarFileLogger.java b/lphy/src/main/java/lphy/core/logger/VarFileLogger.java
@@ -2,8 +2,8 @@
 
 import lphy.core.graphicalmodel.components.RandomVariable;
 import lphy.core.graphicalmodel.components.Value;
-import lphy.core.graphicalmodel.vectorization.VectorUtils;
 import lphy.core.util.Symbols;
+import lphy.core.vectorization.VectorUtils;
 
 import java.io.File;
 import java.io.FileWriter;

diff --git a/lphy/src/main/java/lphy/core/parser/ParserLoader.java b/lphy/src/main/java/lphy/core/parser/ParserLoader.java
@@ -1,17 +1,17 @@
 package lphy.core.parser;
 
 import lphy.core.graphicalmodel.components.*;
-import lphy.core.graphicalmodel.vectorization.IID;
-import lphy.core.graphicalmodel.vectorization.VectorizedDistribution;
-import lphy.core.graphicalmodel.vectorization.VectorizedFunction;
 import lphy.core.spi.LPhyLoader;
 import lphy.core.util.LoggerUtils;
+import lphy.core.vectorization.IID;
+import lphy.core.vectorization.VectorizedDistribution;
+import lphy.core.vectorization.VectorizedFunction;
 
 import java.lang.reflect.Constructor;
 import java.lang.reflect.InvocationTargetException;
 import java.util.*;
 
-import static lphy.core.graphicalmodel.vectorization.IID.REPLICATES_PARAM_NAME;
+import static lphy.core.vectorization.IID.REPLICATES_PARAM_NAME;
 
 public class ParserLoader {
 

diff --git a/lphy/src/main/java/lphy/core/parser/functions/MethodCall.java b/lphy/src/main/java/lphy/core/parser/functions/MethodCall.java
@@ -2,10 +2,10 @@
 
 import lphy.core.graphicalmodel.components.*;
 import lphy.core.graphicalmodel.types.Vector;
-import lphy.core.graphicalmodel.vectorization.CompoundVectorValue;
-import lphy.core.graphicalmodel.vectorization.VectorizedFunction;
 import lphy.core.narrative.Narrative;
 import lphy.core.narrative.NarrativeUtils;
+import lphy.core.vectorization.CompoundVectorValue;
+import lphy.core.vectorization.VectorizedFunction;
 
 import java.lang.reflect.Array;
 import java.lang.reflect.InvocationTargetException;

diff --git a/lphy/src/main/java/lphy/core/parser/functions/Range.java b/lphy/src/main/java/lphy/core/parser/functions/Range.java
@@ -4,7 +4,7 @@
 import lphy.core.graphicalmodel.components.GeneratorInfo;
 import lphy.core.graphicalmodel.components.ParameterInfo;
 import lphy.core.graphicalmodel.components.Value;
-import lphy.core.graphicalmodel.vectorization.RangeElement;
+import lphy.core.vectorization.RangeElement;
 
 public class Range extends DeterministicFunction<Integer[]> implements RangeElement {
 

diff --git a/...almodel/vectorization/CompoundVector.java → ...hy/core/vectorization/CompoundVector.java b/...almodel/vectorization/CompoundVector.java → ...hy/core/vectorization/CompoundVector.java
@@ -1,4 +1,4 @@
-package lphy.core.graphicalmodel.vectorization;
+package lphy.core.vectorization;
 
 import lphy.core.graphicalmodel.components.Value;
 import lphy.core.graphicalmodel.types.Vector;

diff --git a/...el/vectorization/CompoundVectorValue.java → ...re/vectorization/CompoundVectorValue.java b/...el/vectorization/CompoundVectorValue.java → ...re/vectorization/CompoundVectorValue.java
@@ -1,4 +1,4 @@
-package lphy.core.graphicalmodel.vectorization;
+package lphy.core.vectorization;
 
 import lphy.core.graphicalmodel.components.DeterministicFunction;
 import lphy.core.graphicalmodel.components.Value;

diff --git a/...ore/graphicalmodel/vectorization/IID.java → ...ain/java/lphy/core/vectorization/IID.java b/...ore/graphicalmodel/vectorization/IID.java → ...ain/java/lphy/core/vectorization/IID.java
@@ -1,4 +1,4 @@
-package lphy.core.graphicalmodel.vectorization;
+package lphy.core.vectorization;
 
 import lphy.core.graphicalmodel.components.*;
 import lphy.core.narrative.Narrative;

diff --git a/.../vectorization/IndexedRandomVariable.java → .../vectorization/IndexedRandomVariable.java b/.../vectorization/IndexedRandomVariable.java → .../vectorization/IndexedRandomVariable.java
@@ -1,4 +1,4 @@
-package lphy.core.graphicalmodel.vectorization;
+package lphy.core.vectorization;
 
 import lphy.core.graphicalmodel.components.GenerativeDistribution;
 import lphy.core.graphicalmodel.components.GraphicalModelNode;

diff --git a/...icalmodel/vectorization/RangeElement.java → ...lphy/core/vectorization/RangeElement.java b/...icalmodel/vectorization/RangeElement.java → ...lphy/core/vectorization/RangeElement.java
@@ -1,4 +1,4 @@
-package lphy.core.graphicalmodel.vectorization;
+package lphy.core.vectorization;
 
 public interface RangeElement {
 

diff --git a/...phicalmodel/vectorization/SliceValue.java → ...a/lphy/core/vectorization/SliceValue.java b/...phicalmodel/vectorization/SliceValue.java → ...a/lphy/core/vectorization/SliceValue.java
@@ -1,4 +1,4 @@
-package lphy.core.graphicalmodel.vectorization;
+package lphy.core.vectorization;
 
 import lphy.core.graphicalmodel.components.Value;
 

diff --git a/...hicalmodel/vectorization/VectorUtils.java → .../lphy/core/vectorization/VectorUtils.java b/...hicalmodel/vectorization/VectorUtils.java → .../lphy/core/vectorization/VectorUtils.java
@@ -1,4 +1,4 @@
-package lphy.core.graphicalmodel.vectorization;
+package lphy.core.vectorization;
 
 import lphy.core.graphicalmodel.components.Argument;
 import lphy.core.graphicalmodel.components.Generator;

diff --git a/...hicalmodel/vectorization/VectorValue.java → .../lphy/core/vectorization/VectorValue.java b/...hicalmodel/vectorization/VectorValue.java → .../lphy/core/vectorization/VectorValue.java
@@ -1,4 +1,4 @@
-package lphy.core.graphicalmodel.vectorization;
+package lphy.core.vectorization;
 
 import lphy.core.graphicalmodel.components.DeterministicFunction;
 import lphy.core.graphicalmodel.components.Value;

diff --git a/...vectorization/VectorizedDistribution.java → ...vectorization/VectorizedDistribution.java b/...vectorization/VectorizedDistribution.java → ...vectorization/VectorizedDistribution.java
@@ -1,4 +1,4 @@
-package lphy.core.graphicalmodel.vectorization;
+package lphy.core.vectorization;
 
 import lphy.core.graphicalmodel.components.*;
 import lphy.core.narrative.Narrative;

diff --git a/...del/vectorization/VectorizedFunction.java → ...ore/vectorization/VectorizedFunction.java b/...del/vectorization/VectorizedFunction.java → ...ore/vectorization/VectorizedFunction.java
@@ -1,4 +1,4 @@
-package lphy.core.graphicalmodel.vectorization;
+package lphy.core.vectorization;
 
 import lphy.core.graphicalmodel.components.*;
 import lphy.core.narrative.Narrative;

diff --git a/...ctorization/VectorizedRandomVariable.java → ...ctorization/VectorizedRandomVariable.java b/...ctorization/VectorizedRandomVariable.java → ...ctorization/VectorizedRandomVariable.java
@@ -1,4 +1,4 @@
-package lphy.core.graphicalmodel.vectorization;
+package lphy.core.vectorization;
 
 import lphy.core.graphicalmodel.components.GenerativeDistribution;
 import lphy.core.graphicalmodel.components.RandomVariable;

diff --git a/lphy/src/main/java/module-info.java b/lphy/src/main/java/module-info.java
@@ -24,7 +24,7 @@
     exports lphy.core.codebuilder;
     exports lphy.core.graphicalmodel.components;
     exports lphy.core.graphicalmodel.types;
-    exports lphy.core.graphicalmodel.vectorization;
+    exports lphy.core.vectorization;
     exports lphy.core.layeredgraph;
 
     // parser