diff --git a/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/AbstractAlgorithmRunner.java b/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/AbstractAlgorithmRunner.java
index 2610b8f52a..817bf7d4bc 100644
--- a/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/AbstractAlgorithmRunner.java
+++ b/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/AbstractAlgorithmRunner.java
@@ -493,6 +493,18 @@ private void transferVarNamesToParams(List<String> names) {
         getParams().set("varNames", names);
     }
 
+    /**
+     * Writes the object to the specified ObjectOutputStream.
+     *
+     * @param out The ObjectOutputStream to write the object to.
+     * @throws IOException If an I/O error occurs.
+     */
+    /**
+     * Writes the object to the specified ObjectOutputStream.
+     *
+     * @param out The ObjectOutputStream to write the object to.
+     * @throws IOException If an I/O error occurs.
+     */
     @Serial
     private void writeObject(ObjectOutputStream out) throws IOException {
         try {
@@ -504,6 +516,14 @@ private void writeObject(ObjectOutputStream out) throws IOException {
         }
     }
 
+    /**
+     * Reads the object from the specified ObjectInputStream. This method is used during deserialization
+     * to restore the state of the object.
+     *
+     * @param in The ObjectInputStream to read the object from.
+     * @throws IOException            If an I/O error occurs.
+     * @throws ClassNotFoundException If the class of the serialized object cannot be found.
+     */
     @Serial
     private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
         try {
diff --git a/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/AbstractMBSearchRunner.java b/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/AbstractMBSearchRunner.java
index c33d5dbf8e..fab4781393 100644
--- a/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/AbstractMBSearchRunner.java
+++ b/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/AbstractMBSearchRunner.java
@@ -217,6 +217,18 @@ IndependenceTest getIndependenceTest() {
         throw new IllegalStateException("Cannot find Independence for Data source.");
     }
 
+    /**
+     * Writes the object to the specified ObjectOutputStream.
+     *
+     * @param out The ObjectOutputStream to write the object to.
+     * @throws IOException If an I/O error occurs.
+     */
+    /**
+     * Writes the object to the specified ObjectOutputStream.
+     *
+     * @param out The ObjectOutputStream to write the object to.
+     * @throws IOException If an I/O error occurs.
+     */
     @Serial
     private void writeObject(ObjectOutputStream out) throws IOException {
         try {
@@ -228,6 +240,14 @@ private void writeObject(ObjectOutputStream out) throws IOException {
         }
     }
 
+    /**
+     * Reads the object from the specified ObjectInputStream. This method is used during deserialization
+     * to restore the state of the object.
+     *
+     * @param in The ObjectInputStream to read the object from.
+     * @throws IOException            If an I/O error occurs.
+     * @throws ClassNotFoundException If the class of the serialized object cannot be found.
+     */
     @Serial
     private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
         try {
diff --git a/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/ApproximateUpdaterWrapper.java b/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/ApproximateUpdaterWrapper.java
index df6837b0dc..c980c63252 100755
--- a/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/ApproximateUpdaterWrapper.java
+++ b/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/ApproximateUpdaterWrapper.java
@@ -212,6 +212,18 @@ private DiscreteVariable discreteVariable(Evidence evidence, String nodeName) {
     }
 
 
+    /**
+     * Writes the object to the specified ObjectOutputStream.
+     *
+     * @param out The ObjectOutputStream to write the object to.
+     * @throws IOException If an I/O error occurs.
+     */
+    /**
+     * Writes the object to the specified ObjectOutputStream.
+     *
+     * @param out The ObjectOutputStream to write the object to.
+     * @throws IOException If an I/O error occurs.
+     */
     @Serial
     private void writeObject(ObjectOutputStream out) throws IOException {
         try {
@@ -224,6 +236,14 @@ private void writeObject(ObjectOutputStream out) throws IOException {
     }
 
 
+    /**
+     * Reads the object from the specified ObjectInputStream. This method is used during deserialization
+     * to restore the state of the object.
+     *
+     * @param in The ObjectInputStream to read the object from.
+     * @throws IOException            If an I/O error occurs.
+     * @throws ClassNotFoundException If the class of the serialized object cannot be found.
+     */
     @Serial
     private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
         try {
diff --git a/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/BayesEstimatorWrapper.java b/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/BayesEstimatorWrapper.java
index 788ccc3f44..3fb5d6ea73 100644
--- a/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/BayesEstimatorWrapper.java
+++ b/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/BayesEstimatorWrapper.java
@@ -276,6 +276,18 @@ public void setModelIndex(int modelIndex) {
 
     //======================== Private Methods ======================//
 
+    /**
+     * Writes the object to the specified ObjectOutputStream.
+     *
+     * @param out The ObjectOutputStream to write the object to.
+     * @throws IOException If an I/O error occurs.
+     */
+    /**
+     * Writes the object to the specified ObjectOutputStream.
+     *
+     * @param out The ObjectOutputStream to write the object to.
+     * @throws IOException If an I/O error occurs.
+     */
     @Serial
     private void writeObject(ObjectOutputStream out) throws IOException {
         try {
@@ -287,6 +299,14 @@ private void writeObject(ObjectOutputStream out) throws IOException {
         }
     }
 
+    /**
+     * Reads the object from the specified ObjectInputStream. This method is used during deserialization
+     * to restore the state of the object.
+     *
+     * @param in The ObjectInputStream to read the object from.
+     * @throws IOException            If an I/O error occurs.
+     * @throws ClassNotFoundException If the class of the serialized object cannot be found.
+     */
     @Serial
     private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
         try {
diff --git a/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/BayesImWrapper.java b/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/BayesImWrapper.java
index fe26a6535c..a2a23f043a 100644
--- a/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/BayesImWrapper.java
+++ b/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/BayesImWrapper.java
@@ -368,6 +368,18 @@ private void setBayesIm(BayesPm bayesPm, BayesIm oldBayesIm, MlBayesIm.Initializ
         this.bayesIms.add(new MlBayesIm(bayesPm, oldBayesIm, initializationMethod));
     }
 
+    /**
+     * Writes the object to the specified ObjectOutputStream.
+     *
+     * @param out The ObjectOutputStream to write the object to.
+     * @throws IOException If an I/O error occurs.
+     */
+    /**
+     * Writes the object to the specified ObjectOutputStream.
+     *
+     * @param out The ObjectOutputStream to write the object to.
+     * @throws IOException If an I/O error occurs.
+     */
     @Serial
     private void writeObject(ObjectOutputStream out) throws IOException {
         try {
@@ -379,6 +391,14 @@ private void writeObject(ObjectOutputStream out) throws IOException {
         }
     }
 
+    /**
+     * Reads the object from the specified ObjectInputStream. This method is used during deserialization
+     * to restore the state of the object.
+     *
+     * @param in The ObjectInputStream to read the object from.
+     * @throws IOException            If an I/O error occurs.
+     * @throws ClassNotFoundException If the class of the serialized object cannot be found.
+     */
     @Serial
     private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
         try {
diff --git a/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/BayesImWrapperObs.java b/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/BayesImWrapperObs.java
index 9e18d1587b..73a6e0d793 100644
--- a/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/BayesImWrapperObs.java
+++ b/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/BayesImWrapperObs.java
@@ -165,6 +165,14 @@ private void log(BayesIm im) {
         TetradLogger.getInstance().log(message);
     }
 
+    /**
+     * Reads the object from the specified ObjectInputStream. This method is used during deserialization
+     * to restore the state of the object.
+     *
+     * @param in The ObjectInputStream to read the object from.
+     * @throws IOException            If an I/O error occurs.
+     * @throws ClassNotFoundException If the class of the serialized object cannot be found.
+     */
     @Serial
     private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
         try {
diff --git a/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/BayesPmWrapper.java b/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/BayesPmWrapper.java
index a7545a1618..590f85b661 100644
--- a/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/BayesPmWrapper.java
+++ b/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/BayesPmWrapper.java
@@ -511,6 +511,18 @@ private void setBayesPm(BayesPm b) {
         this.bayesPms.add(b);
     }
 
+    /**
+     * Writes the object to the specified ObjectOutputStream.
+     *
+     * @param out The ObjectOutputStream to write the object to.
+     * @throws IOException If an I/O error occurs.
+     */
+    /**
+     * Writes the object to the specified ObjectOutputStream.
+     *
+     * @param out The ObjectOutputStream to write the object to.
+     * @throws IOException If an I/O error occurs.
+     */
     @Serial
     private void writeObject(ObjectOutputStream out) throws IOException {
         try {
@@ -522,6 +534,14 @@ private void writeObject(ObjectOutputStream out) throws IOException {
         }
     }
 
+    /**
+     * Reads the object from the specified ObjectInputStream. This method is used during deserialization
+     * to restore the state of the object.
+     *
+     * @param in The ObjectInputStream to read the object from.
+     * @throws IOException            If an I/O error occurs.
+     * @throws ClassNotFoundException If the class of the serialized object cannot be found.
+     */
     @Serial
     private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
         try {
diff --git a/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/BayesUpdaterClassifierWrapper.java b/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/BayesUpdaterClassifierWrapper.java
index 8387d3d676..0dda984b6e 100644
--- a/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/BayesUpdaterClassifierWrapper.java
+++ b/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/BayesUpdaterClassifierWrapper.java
@@ -122,6 +122,18 @@ public ClassifierBayesUpdaterDiscrete getClassifier() {
         return this.classifier;
     }
 
+    /**
+     * Writes the object to the specified ObjectOutputStream.
+     *
+     * @param out The ObjectOutputStream to write the object to.
+     * @throws IOException If an I/O error occurs.
+     */
+    /**
+     * Writes the object to the specified ObjectOutputStream.
+     *
+     * @param out The ObjectOutputStream to write the object to.
+     * @throws IOException If an I/O error occurs.
+     */
     @Serial
     private void writeObject(ObjectOutputStream out) throws IOException {
         try {
@@ -133,6 +145,14 @@ private void writeObject(ObjectOutputStream out) throws IOException {
         }
     }
 
+    /**
+     * Reads the object from the specified ObjectInputStream. This method is used during deserialization
+     * to restore the state of the object.
+     *
+     * @param in The ObjectInputStream to read the object from.
+     * @throws IOException            If an I/O error occurs.
+     * @throws ClassNotFoundException If the class of the serialized object cannot be found.
+     */
     @Serial
     private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
         try {
diff --git a/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/BooleanGlassGeneIm.java b/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/BooleanGlassGeneIm.java
index 2aaf946aca..d8e582c82a 100644
--- a/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/BooleanGlassGeneIm.java
+++ b/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/BooleanGlassGeneIm.java
@@ -399,6 +399,12 @@ public Distribution getErrorDistribution(int factor) {
         return getBooleanGlassFunction().getErrorDistribution(factor);
     }
 
+    /**
+     * Writes the object to the specified ObjectOutputStream.
+     *
+     * @param out The ObjectOutputStream to write the object to.
+     * @throws IOException If an I/O error occurs.
+     */
     @Serial
     private void writeObject(ObjectOutputStream out) throws IOException {
         try {
@@ -410,6 +416,14 @@ private void writeObject(ObjectOutputStream out) throws IOException {
         }
     }
 
+    /**
+     * Reads the object from the specified ObjectInputStream. This method is used during deserialization
+     * to restore the state of the object.
+     *
+     * @param in The ObjectInputStream to read the object from.
+     * @throws IOException            If an I/O error occurs.
+     * @throws ClassNotFoundException If the class of the serialized object cannot be found.
+     */
     @Serial
     private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
         try {
diff --git a/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/BootstrapSamplerWrapper.java b/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/BootstrapSamplerWrapper.java
index aad9b8f771..0d5eccbc47 100644
--- a/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/BootstrapSamplerWrapper.java
+++ b/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/BootstrapSamplerWrapper.java
@@ -110,6 +110,18 @@ public DataSet getOutputDataset() {
         return this.outputDataSet;
     }
 
+    /**
+     * Writes the object to the specified ObjectOutputStream.
+     *
+     * @param out The ObjectOutputStream to write the object to.
+     * @throws IOException If an I/O error occurs.
+     */
+    /**
+     * Writes the object to the specified ObjectOutputStream.
+     *
+     * @param out The ObjectOutputStream to write the object to.
+     * @throws IOException If an I/O error occurs.
+     */
     @Serial
     private void writeObject(ObjectOutputStream out) throws IOException {
         try {
@@ -121,6 +133,14 @@ private void writeObject(ObjectOutputStream out) throws IOException {
         }
     }
 
+    /**
+     * Reads the object from the specified ObjectInputStream. This method is used during deserialization
+     * to restore the state of the object.
+     *
+     * @param in The ObjectInputStream to read the object from.
+     * @throws IOException            If an I/O error occurs.
+     * @throws ClassNotFoundException If the class of the serialized object cannot be found.
+     */
     @Serial
     private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
         try {
diff --git a/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/CPDAGFitModel.java b/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/CPDAGFitModel.java
index 96a991a1c5..b1028bc9df 100644
--- a/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/CPDAGFitModel.java
+++ b/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/CPDAGFitModel.java
@@ -260,6 +260,12 @@ public BayesIm getBayesIm(int i) {
         return this.bayesIms.get(i);
     }
 
+    /**
+     * Writes the object to the specified ObjectOutputStream.
+     *
+     * @param out The ObjectOutputStream to write the object to.
+     * @throws IOException If an I/O error occurs.
+     */
     @Serial
     private void writeObject(ObjectOutputStream out) throws IOException {
         try {
@@ -271,6 +277,14 @@ private void writeObject(ObjectOutputStream out) throws IOException {
         }
     }
 
+    /**
+     * Reads the object from the specified ObjectInputStream. This method is used during deserialization
+     * to restore the state of the object.
+     *
+     * @param in The ObjectInputStream to read the object from.
+     * @throws IOException            If an I/O error occurs.
+     * @throws ClassNotFoundException If the class of the serialized object cannot be found.
+     */
     @Serial
     private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
         try {
diff --git a/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/CalculatorWrapper.java b/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/CalculatorWrapper.java
index 47cb8e351c..bbb46a063a 100644
--- a/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/CalculatorWrapper.java
+++ b/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/CalculatorWrapper.java
@@ -127,6 +127,12 @@ private static DataSet copy(DataSet data) {
         return copy;
     }
 
+    /**
+     * Writes the object to the specified ObjectOutputStream.
+     *
+     * @param out The ObjectOutputStream to write the object to.
+     * @throws IOException If an I/O error occurs.
+     */
     @Serial
     private void writeObject(ObjectOutputStream out) throws IOException {
         try {
@@ -138,6 +144,14 @@ private void writeObject(ObjectOutputStream out) throws IOException {
         }
     }
 
+    /**
+     * Reads the object from the specified ObjectInputStream. This method is used during deserialization
+     * to restore the state of the object.
+     *
+     * @param in The ObjectInputStream to read the object from.
+     * @throws IOException            If an I/O error occurs.
+     * @throws ClassNotFoundException If the class of the serialized object cannot be found.
+     */
     @Serial
     private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
         try {
diff --git a/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/CheckKnowledgeModel.java b/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/CheckKnowledgeModel.java
index 591334d384..29aabb1eb4 100644
--- a/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/CheckKnowledgeModel.java
+++ b/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/CheckKnowledgeModel.java
@@ -139,6 +139,12 @@ public String getComparisonString() {
         return sb.toString();
     }
 
+    /**
+     * Writes the object to the specified ObjectOutputStream.
+     *
+     * @param out The ObjectOutputStream to write the object to.
+     * @throws IOException If an I/O error occurs.
+     */
     @Serial
     private void writeObject(ObjectOutputStream out) throws IOException {
         try {
@@ -150,6 +156,14 @@ private void writeObject(ObjectOutputStream out) throws IOException {
         }
     }
 
+    /**
+     * Reads the object from the specified ObjectInputStream. This method is used during deserialization
+     * to restore the state of the object.
+     *
+     * @param in The ObjectInputStream to read the object from.
+     * @throws IOException            If an I/O error occurs.
+     * @throws ClassNotFoundException If the class of the serialized object cannot be found.
+     */
     @Serial
     private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
         try {
diff --git a/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/CptInvariantUpdaterWrapper.java b/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/CptInvariantUpdaterWrapper.java
index 5d76971e59..27386362ac 100755
--- a/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/CptInvariantUpdaterWrapper.java
+++ b/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/CptInvariantUpdaterWrapper.java
@@ -193,6 +193,12 @@ private DiscreteVariable discreteVariable(Evidence evidence, String nodeName) {
         return evidence.getVariable(nodeName);
     }
 
+    /**
+     * Writes the object to the specified ObjectOutputStream.
+     *
+     * @param out The ObjectOutputStream to write the object to.
+     * @throws IOException If an I/O error occurs.
+     */
     @Serial
     private void writeObject(ObjectOutputStream out) throws IOException {
         try {
@@ -204,6 +210,14 @@ private void writeObject(ObjectOutputStream out) throws IOException {
         }
     }
 
+    /**
+     * Reads the object from the specified ObjectInputStream. This method is used during deserialization
+     * to restore the state of the object.
+     *
+     * @param in The ObjectInputStream to read the object from.
+     * @throws IOException            If an I/O error occurs.
+     * @throws ClassNotFoundException If the class of the serialized object cannot be found.
+     */
     @Serial
     private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
         try {
diff --git a/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/DagWrapper.java b/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/DagWrapper.java
index e89dd97081..de61791eed 100644
--- a/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/DagWrapper.java
+++ b/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/DagWrapper.java
@@ -292,6 +292,12 @@ private void log() {
         TetradLogger.getInstance().log(message);
     }
 
+    /**
+     * Writes the object to the specified ObjectOutputStream.
+     *
+     * @param out The ObjectOutputStream to write the object to.
+     * @throws IOException If an I/O error occurs.
+     */
     @Serial
     private void writeObject(ObjectOutputStream out) throws IOException {
         try {
@@ -303,6 +309,14 @@ private void writeObject(ObjectOutputStream out) throws IOException {
         }
     }
 
+    /**
+     * Reads the object from the specified ObjectInputStream. This method is used during deserialization
+     * to restore the state of the object.
+     *
+     * @param in The ObjectInputStream to read the object from.
+     * @throws IOException            If an I/O error occurs.
+     * @throws ClassNotFoundException If the class of the serialized object cannot be found.
+     */
     @Serial
     private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
         try {
diff --git a/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/DataWrapper.java b/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/DataWrapper.java
index ad8f57f407..496352c606 100644
--- a/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/DataWrapper.java
+++ b/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/DataWrapper.java
@@ -489,6 +489,12 @@ public List<Node> getVariables() {
         return this.getSelectedDataModel().getVariables();
     }
 
+    /**
+     * Writes the object to the specified ObjectOutputStream.
+     *
+     * @param out The ObjectOutputStream to write the object to.
+     * @throws IOException If an I/O error occurs.
+     */
     @Serial
     private void writeObject(ObjectOutputStream out) throws IOException {
         try {
@@ -500,6 +506,14 @@ private void writeObject(ObjectOutputStream out) throws IOException {
         }
     }
 
+    /**
+     * Reads the object from the specified ObjectInputStream. This method is used during deserialization
+     * to restore the state of the object.
+     *
+     * @param in The ObjectInputStream to read the object from.
+     * @throws IOException            If an I/O error occurs.
+     * @throws ClassNotFoundException If the class of the serialized object cannot be found.
+     */
     @Serial
     private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
         try {
diff --git a/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/DirichletBayesImWrapper.java b/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/DirichletBayesImWrapper.java
index 3cce5c40bd..92c7048a77 100644
--- a/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/DirichletBayesImWrapper.java
+++ b/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/DirichletBayesImWrapper.java
@@ -133,6 +133,12 @@ public DirichletBayesIm getDirichletBayesIm() {
         return this.dirichletBayesIm;
     }
 
+    /**
+     * Writes the object to the specified ObjectOutputStream.
+     *
+     * @param out The ObjectOutputStream to write the object to.
+     * @throws IOException If an I/O error occurs.
+     */
     @Serial
     private void writeObject(ObjectOutputStream out) throws IOException {
         try {
@@ -144,6 +150,14 @@ private void writeObject(ObjectOutputStream out) throws IOException {
         }
     }
 
+    /**
+     * Reads the object from the specified ObjectInputStream. This method is used during deserialization
+     * to restore the state of the object.
+     *
+     * @param in The ObjectInputStream to read the object from.
+     * @throws IOException            If an I/O error occurs.
+     * @throws ClassNotFoundException If the class of the serialized object cannot be found.
+     */
     @Serial
     private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
         try {
diff --git a/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/DirichletEstimatorWrapper.java b/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/DirichletEstimatorWrapper.java
index f2853211bc..1d59cc3ecc 100644
--- a/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/DirichletEstimatorWrapper.java
+++ b/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/DirichletEstimatorWrapper.java
@@ -164,6 +164,12 @@ public DirichletBayesIm getEstimatedBayesIm() {
         return this.dirichletBayesIm;
     }
 
+    /**
+     * Writes the object to the specified ObjectOutputStream.
+     *
+     * @param out The ObjectOutputStream to write the object to.
+     * @throws IOException If an I/O error occurs.
+     */
     @Serial
     private void writeObject(ObjectOutputStream out) throws IOException {
         try {
@@ -175,6 +181,14 @@ private void writeObject(ObjectOutputStream out) throws IOException {
         }
     }
 
+    /**
+     * Reads the object from the specified ObjectInputStream. This method is used during deserialization
+     * to restore the state of the object.
+     *
+     * @param in The ObjectInputStream to read the object from.
+     * @throws IOException            If an I/O error occurs.
+     * @throws ClassNotFoundException If the class of the serialized object cannot be found.
+     */
     @Serial
     private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
         try {
diff --git a/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/EdgewiseComparisonModel.java b/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/EdgewiseComparisonModel.java
index 3b9fb2a6e6..5d74bbdac1 100644
--- a/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/EdgewiseComparisonModel.java
+++ b/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/EdgewiseComparisonModel.java
@@ -179,6 +179,12 @@ public String getComparisonString() {
                 targetName, this.targetGraph);
     }
 
+    /**
+     * Writes the object to the specified ObjectOutputStream.
+     *
+     * @param out The ObjectOutputStream to write the object to.
+     * @throws IOException If an I/O error occurs.
+     */
     @Serial
     private void writeObject(ObjectOutputStream out) throws IOException {
         try {
@@ -190,6 +196,14 @@ private void writeObject(ObjectOutputStream out) throws IOException {
         }
     }
 
+    /**
+     * Reads the object from the specified ObjectInputStream. This method is used during deserialization
+     * to restore the state of the object.
+     *
+     * @param in The ObjectInputStream to read the object from.
+     * @throws IOException            If an I/O error occurs.
+     * @throws ClassNotFoundException If the class of the serialized object cannot be found.
+     */
     @Serial
     private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
         try {
diff --git a/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/EmBayesEstimatorWrapper.java b/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/EmBayesEstimatorWrapper.java
index e9649b572f..7ea9204545 100644
--- a/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/EmBayesEstimatorWrapper.java
+++ b/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/EmBayesEstimatorWrapper.java
@@ -156,6 +156,12 @@ private void estimate(DataSet dataSet, BayesPm bayesPm, double thresh) {
     public DataSet getDataSet() {
         return this.dataSet;
     }
+    /**
+     * Writes the object to the specified ObjectOutputStream.
+     *
+     * @param out The ObjectOutputStream to write the object to.
+     * @throws IOException If an I/O error occurs.
+     */
     @Serial
     private void writeObject(ObjectOutputStream out) throws IOException {
         try {
@@ -167,6 +173,14 @@ private void writeObject(ObjectOutputStream out) throws IOException {
         }
     }
 
+    /**
+     * Reads the object from the specified ObjectInputStream. This method is used during deserialization
+     * to restore the state of the object.
+     *
+     * @param in The ObjectInputStream to read the object from.
+     * @throws IOException            If an I/O error occurs.
+     * @throws ClassNotFoundException If the class of the serialized object cannot be found.
+     */
     @Serial
     private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
         try {
diff --git a/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/GeneralAlgorithmRunner.java b/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/GeneralAlgorithmRunner.java
index 3bf8a69663..17f4641f49 100644
--- a/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/GeneralAlgorithmRunner.java
+++ b/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/GeneralAlgorithmRunner.java
@@ -709,6 +709,12 @@ private void transferVarNamesToParams(List<String> names) {
         getParameters().set("varNames", names);
     }
 
+    /**
+     * Writes the object to the specified ObjectOutputStream.
+     *
+     * @param out The ObjectOutputStream to write the object to.
+     * @throws IOException If an I/O error occurs.
+     */
     @Serial
     private void writeObject(ObjectOutputStream out) throws IOException {
         try {
@@ -720,6 +726,14 @@ private void writeObject(ObjectOutputStream out) throws IOException {
         }
     }
 
+    /**
+     * Reads the object from the specified ObjectInputStream. This method is used during deserialization
+     * to restore the state of the object.
+     *
+     * @param in The ObjectInputStream to read the object from.
+     * @throws IOException            If an I/O error occurs.
+     * @throws ClassNotFoundException If the class of the serialized object cannot be found.
+     */
     @Serial
     private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
         try {
diff --git a/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/GeneralizedSemEstimatorWrapper.java b/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/GeneralizedSemEstimatorWrapper.java
index c995c78119..9f38df41fb 100644
--- a/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/GeneralizedSemEstimatorWrapper.java
+++ b/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/GeneralizedSemEstimatorWrapper.java
@@ -131,6 +131,12 @@ public GeneralizedSemIm getSemIm() {
         return this.estIm;
     }
 
+    /**
+     * Writes the object to the specified ObjectOutputStream.
+     *
+     * @param out The ObjectOutputStream to write the object to.
+     * @throws IOException If an I/O error occurs.
+     */
     @Serial
     private void writeObject(ObjectOutputStream out) throws IOException {
         try {
@@ -142,6 +148,14 @@ private void writeObject(ObjectOutputStream out) throws IOException {
         }
     }
 
+    /**
+     * Reads the object from the specified ObjectInputStream. This method is used during deserialization
+     * to restore the state of the object.
+     *
+     * @param in The ObjectInputStream to read the object from.
+     * @throws IOException            If an I/O error occurs.
+     * @throws ClassNotFoundException If the class of the serialized object cannot be found.
+     */
     @Serial
     private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
         try {
diff --git a/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/GeneralizedSemImWrapper.java b/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/GeneralizedSemImWrapper.java
index 09d2a3afea..7668f129ac 100644
--- a/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/GeneralizedSemImWrapper.java
+++ b/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/GeneralizedSemImWrapper.java
@@ -146,6 +146,12 @@ public List<GeneralizedSemIm> getSemIms() {
         return this.semIms;
     }
 
+    /**
+     * Writes the object to the specified ObjectOutputStream.
+     *
+     * @param out The ObjectOutputStream to write the object to.
+     * @throws IOException If an I/O error occurs.
+     */
     @Serial
     private void writeObject(ObjectOutputStream out) throws IOException {
         try {
@@ -157,6 +163,14 @@ private void writeObject(ObjectOutputStream out) throws IOException {
         }
     }
 
+    /**
+     * Reads the object from the specified ObjectInputStream. This method is used during deserialization
+     * to restore the state of the object.
+     *
+     * @param in The ObjectInputStream to read the object from.
+     * @throws IOException            If an I/O error occurs.
+     * @throws ClassNotFoundException If the class of the serialized object cannot be found.
+     */
     @Serial
     private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
         try {
diff --git a/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/GeneralizedSemPmWrapper.java b/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/GeneralizedSemPmWrapper.java
index 3167c04cdb..6cada1ae41 100644
--- a/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/GeneralizedSemPmWrapper.java
+++ b/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/GeneralizedSemPmWrapper.java
@@ -393,6 +393,12 @@ public GeneralizedSemPm getSemPm() {
         return this.semPm;
     }
 
+    /**
+     * Writes the object to the specified ObjectOutputStream.
+     *
+     * @param out The ObjectOutputStream to write the object to.
+     * @throws IOException If an I/O error occurs.
+     */
     @Serial
     private void writeObject(ObjectOutputStream out) throws IOException {
         try {
@@ -404,6 +410,14 @@ private void writeObject(ObjectOutputStream out) throws IOException {
         }
     }
 
+    /**
+     * Reads the object from the specified ObjectInputStream. This method is used during deserialization
+     * to restore the state of the object.
+     *
+     * @param in The ObjectInputStream to read the object from.
+     * @throws IOException            If an I/O error occurs.
+     * @throws ClassNotFoundException If the class of the serialized object cannot be found.
+     */
     @Serial
     private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
         try {
diff --git a/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/GraphComparisonParams.java b/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/GraphComparisonParams.java
index 940a037a41..a2e85451cf 100644
--- a/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/GraphComparisonParams.java
+++ b/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/GraphComparisonParams.java
@@ -225,6 +225,12 @@ public void setReferenceGraphName(String name) {
         this.referenceGraphName = name;
     }
 
+    /**
+     * Writes the object to the specified ObjectOutputStream.
+     *
+     * @param out The ObjectOutputStream to write the object to.
+     * @throws IOException If an I/O error occurs.
+     */
     @Serial
     private void writeObject(ObjectOutputStream out) throws IOException {
         try {
@@ -236,6 +242,14 @@ private void writeObject(ObjectOutputStream out) throws IOException {
         }
     }
 
+    /**
+     * Reads the object from the specified ObjectInputStream. This method is used during deserialization
+     * to restore the state of the object.
+     *
+     * @param in The ObjectInputStream to read the object from.
+     * @throws IOException            If an I/O error occurs.
+     * @throws ClassNotFoundException If the class of the serialized object cannot be found.
+     */
     @Serial
     private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
         try {
diff --git a/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/GraphSelectionWrapper.java b/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/GraphSelectionWrapper.java
index 0379c3ae8c..8fd3d40263 100644
--- a/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/GraphSelectionWrapper.java
+++ b/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/GraphSelectionWrapper.java
@@ -981,6 +981,12 @@ private Set<Edge> getEdgesFromPath(List<Node> path, Graph graph) {
         return edges;
     }
 
+    /**
+     * Writes the object to the specified ObjectOutputStream.
+     *
+     * @param out The ObjectOutputStream to write the object to.
+     * @throws IOException If an I/O error occurs.
+     */
     @Serial
     private void writeObject(ObjectOutputStream out) throws IOException {
         try {
@@ -992,6 +998,14 @@ private void writeObject(ObjectOutputStream out) throws IOException {
         }
     }
 
+    /**
+     * Reads the object from the specified ObjectInputStream. This method is used during deserialization
+     * to restore the state of the object.
+     *
+     * @param in The ObjectInputStream to read the object from.
+     * @throws IOException            If an I/O error occurs.
+     * @throws ClassNotFoundException If the class of the serialized object cannot be found.
+     */
     @Serial
     private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
         try {
diff --git a/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/GraphWrapper.java b/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/GraphWrapper.java
index 1e7b616e4d..acc7f242eb 100644
--- a/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/GraphWrapper.java
+++ b/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/GraphWrapper.java
@@ -425,6 +425,12 @@ public Parameters getParameters() {
 //        TetradLogger.getInstance().log("graph", "" + getGraph());
 //    }
 
+    /**
+     * Writes the object to the specified ObjectOutputStream.
+     *
+     * @param out The ObjectOutputStream to write the object to.
+     * @throws IOException If an I/O error occurs.
+     */
     @Serial
     private void writeObject(ObjectOutputStream out) throws IOException {
         try {
@@ -436,6 +442,14 @@ private void writeObject(ObjectOutputStream out) throws IOException {
         }
     }
 
+    /**
+     * Reads the object from the specified ObjectInputStream. This method is used during deserialization
+     * to restore the state of the object.
+     *
+     * @param in The ObjectInputStream to read the object from.
+     * @throws IOException            If an I/O error occurs.
+     * @throws ClassNotFoundException If the class of the serialized object cannot be found.
+     */
     @Serial
     private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
         try {
diff --git a/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/GridSearchModel.java b/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/GridSearchModel.java
index f2077c7548..bad4c1b66e 100644
--- a/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/GridSearchModel.java
+++ b/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/GridSearchModel.java
@@ -1052,6 +1052,12 @@ public void setLastVerboseOutputText(String lastVerboseOutputText) {
         this.lastVerboseOutputText = lastVerboseOutputText;
     }
 
+    /**
+     * Writes the object to the specified ObjectOutputStream.
+     *
+     * @param out The ObjectOutputStream to write the object to.
+     * @throws IOException If an I/O error occurs.
+     */
     @Serial
     private void writeObject(ObjectOutputStream out) throws IOException {
         try {
@@ -1063,6 +1069,14 @@ private void writeObject(ObjectOutputStream out) throws IOException {
         }
     }
 
+    /**
+     * Reads the object from the specified ObjectInputStream. This method is used during deserialization
+     * to restore the state of the object.
+     *
+     * @param in The ObjectInputStream to read the object from.
+     * @throws IOException            If an I/O error occurs.
+     * @throws ClassNotFoundException If the class of the serialized object cannot be found.
+     */
     @Serial
     private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
         try {
diff --git a/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/IdentifiabilityWrapper.java b/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/IdentifiabilityWrapper.java
index 342c37e5d5..52fa8c16e3 100755
--- a/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/IdentifiabilityWrapper.java
+++ b/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/IdentifiabilityWrapper.java
@@ -176,6 +176,12 @@ private DiscreteVariable discreteVariable(Evidence evidence, String nodeName) {
         return evidence.getVariable(nodeName);
     }
 
+    /**
+     * Writes the object to the specified ObjectOutputStream.
+     *
+     * @param out The ObjectOutputStream to write the object to.
+     * @throws IOException If an I/O error occurs.
+     */
     @Serial
     private void writeObject(ObjectOutputStream out) throws IOException {
         try {
@@ -187,6 +193,14 @@ private void writeObject(ObjectOutputStream out) throws IOException {
         }
     }
 
+    /**
+     * Reads the object from the specified ObjectInputStream. This method is used during deserialization
+     * to restore the state of the object.
+     *
+     * @param in The ObjectInputStream to read the object from.
+     * @throws IOException            If an I/O error occurs.
+     * @throws ClassNotFoundException If the class of the serialized object cannot be found.
+     */
     @Serial
     private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
         try {
diff --git a/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/IndependenceResultIndFacts.java b/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/IndependenceResultIndFacts.java
index 286e899a7f..6988c5fb40 100644
--- a/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/IndependenceResultIndFacts.java
+++ b/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/IndependenceResultIndFacts.java
@@ -151,6 +151,12 @@ public enum Type {
         UNDETERMINED
     }
 
+    /**
+     * Writes the object to the specified ObjectOutputStream.
+     *
+     * @param out The ObjectOutputStream to write the object to.
+     * @throws IOException If an I/O error occurs.
+     */
     @Serial
     private void writeObject(ObjectOutputStream out) throws IOException {
         try {
@@ -162,6 +168,14 @@ private void writeObject(ObjectOutputStream out) throws IOException {
         }
     }
 
+    /**
+     * Reads the object from the specified ObjectInputStream. This method is used during deserialization
+     * to restore the state of the object.
+     *
+     * @param in The ObjectInputStream to read the object from.
+     * @throws IOException            If an I/O error occurs.
+     * @throws ClassNotFoundException If the class of the serialized object cannot be found.
+     */
     @Serial
     private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
         try {
diff --git a/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/LogisticRegressionRunner.java b/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/LogisticRegressionRunner.java
index bb00556825..ce583c77a0 100644
--- a/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/LogisticRegressionRunner.java
+++ b/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/LogisticRegressionRunner.java
@@ -407,6 +407,12 @@ public void setTargetName(String target) {
         this.targetName = target;
     }
 
+    /**
+     * Writes the object to the specified ObjectOutputStream.
+     *
+     * @param out The ObjectOutputStream to write the object to.
+     * @throws IOException If an I/O error occurs.
+     */
     @Serial
     private void writeObject(ObjectOutputStream out) throws IOException {
         try {
@@ -418,6 +424,14 @@ private void writeObject(ObjectOutputStream out) throws IOException {
         }
     }
 
+    /**
+     * Reads the object from the specified ObjectInputStream. This method is used during deserialization
+     * to restore the state of the object.
+     *
+     * @param in The ObjectInputStream to read the object from.
+     * @throws IOException            If an I/O error occurs.
+     * @throws ClassNotFoundException If the class of the serialized object cannot be found.
+     */
     @Serial
     private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
         try {
diff --git a/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/MeasurementModelWrapper.java b/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/MeasurementModelWrapper.java
index 063a12398e..9f08f2583b 100644
--- a/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/MeasurementModelWrapper.java
+++ b/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/MeasurementModelWrapper.java
@@ -176,6 +176,12 @@ public void setName(String name) {
         this.name = name;
     }
 
+    /**
+     * Writes the object to the specified ObjectOutputStream.
+     *
+     * @param out The ObjectOutputStream to write the object to.
+     * @throws IOException If an I/O error occurs.
+     */
     @Serial
     private void writeObject(ObjectOutputStream out) throws IOException {
         try {
@@ -187,6 +193,14 @@ private void writeObject(ObjectOutputStream out) throws IOException {
         }
     }
 
+    /**
+     * Reads the object from the specified ObjectInputStream. This method is used during deserialization
+     * to restore the state of the object.
+     *
+     * @param in The ObjectInputStream to read the object from.
+     * @throws IOException            If an I/O error occurs.
+     * @throws ClassNotFoundException If the class of the serialized object cannot be found.
+     */
     @Serial
     private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
         try {
diff --git a/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/Misclassifications.java b/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/Misclassifications.java
index 9f6668195d..1173eeb0eb 100644
--- a/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/Misclassifications.java
+++ b/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/Misclassifications.java
@@ -181,6 +181,12 @@ public String getComparisonString() {
                "\n\n\n" + table;
     }
 
+    /**
+     * Writes the object to the specified ObjectOutputStream.
+     *
+     * @param out The ObjectOutputStream to write the object to.
+     * @throws IOException If an I/O error occurs.
+     */
     @Serial
     private void writeObject(ObjectOutputStream out) throws IOException {
         try {
@@ -192,6 +198,14 @@ private void writeObject(ObjectOutputStream out) throws IOException {
         }
     }
 
+    /**
+     * Reads the object from the specified ObjectInputStream. This method is used during deserialization
+     * to restore the state of the object.
+     *
+     * @param in The ObjectInputStream to read the object from.
+     * @throws IOException            If an I/O error occurs.
+     * @throws ClassNotFoundException If the class of the serialized object cannot be found.
+     */
     @Serial
     private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
         try {
diff --git a/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/MissingDataInjectorWrapper.java b/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/MissingDataInjectorWrapper.java
index 01a2218849..c1f2f501a7 100755
--- a/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/MissingDataInjectorWrapper.java
+++ b/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/MissingDataInjectorWrapper.java
@@ -98,6 +98,12 @@ public DataSet getOutputDataset() {
         return this.outputDataSet;
     }
 
+    /**
+     * Writes the object to the specified ObjectOutputStream.
+     *
+     * @param out The ObjectOutputStream to write the object to.
+     * @throws IOException If an I/O error occurs.
+     */
     @Serial
     private void writeObject(ObjectOutputStream out) throws IOException {
         try {
@@ -109,6 +115,14 @@ private void writeObject(ObjectOutputStream out) throws IOException {
         }
     }
 
+    /**
+     * Reads the object from the specified ObjectInputStream. This method is used during deserialization
+     * to restore the state of the object.
+     *
+     * @param in The ObjectInputStream to read the object from.
+     * @throws IOException            If an I/O error occurs.
+     * @throws ClassNotFoundException If the class of the serialized object cannot be found.
+     */
     @Serial
     private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
         try {
diff --git a/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/PValueImproverWrapper.java b/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/PValueImproverWrapper.java
index bb94da8959..e6fb390b89 100644
--- a/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/PValueImproverWrapper.java
+++ b/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/PValueImproverWrapper.java
@@ -530,6 +530,12 @@ public DataSet simulateDataCholesky(int sampleSize, Matrix covar, List<Node> var
         return DataTransforms.restrictToMeasured(fullDataSet);
     }
 
+    /**
+     * Writes the object to the specified ObjectOutputStream.
+     *
+     * @param out The ObjectOutputStream to write the object to.
+     * @throws IOException If an I/O error occurs.
+     */
     @Serial
     private void writeObject(ObjectOutputStream out) throws IOException {
         try {
@@ -541,6 +547,14 @@ private void writeObject(ObjectOutputStream out) throws IOException {
         }
     }
 
+    /**
+     * Reads the object from the specified ObjectInputStream. This method is used during deserialization
+     * to restore the state of the object.
+     *
+     * @param in The ObjectInputStream to read the object from.
+     * @throws IOException            If an I/O error occurs.
+     * @throws ClassNotFoundException If the class of the serialized object cannot be found.
+     */
     @Serial
     private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
         try {
diff --git a/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/RegressionRunner.java b/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/RegressionRunner.java
index 1df8a5b776..a5c4a252dd 100755
--- a/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/RegressionRunner.java
+++ b/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/RegressionRunner.java
@@ -394,6 +394,12 @@ public void setTargetName(String target) {
         this.targetName = target;
     }
 
+    /**
+     * Writes the object to the specified ObjectOutputStream.
+     *
+     * @param out The ObjectOutputStream to write the object to.
+     * @throws IOException If an I/O error occurs.
+     */
     @Serial
     private void writeObject(ObjectOutputStream out) throws IOException {
         try {
@@ -405,6 +411,14 @@ private void writeObject(ObjectOutputStream out) throws IOException {
         }
     }
 
+    /**
+     * Reads the object from the specified ObjectInputStream. This method is used during deserialization
+     * to restore the state of the object.
+     *
+     * @param in The ObjectInputStream to read the object from.
+     * @throws IOException            If an I/O error occurs.
+     * @throws ClassNotFoundException If the class of the serialized object cannot be found.
+     */
     @Serial
     private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
         try {
diff --git a/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/ReplaceMissingWithRandomWrapper.java b/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/ReplaceMissingWithRandomWrapper.java
index c0fc8fa47c..1f0a9a87ac 100755
--- a/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/ReplaceMissingWithRandomWrapper.java
+++ b/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/ReplaceMissingWithRandomWrapper.java
@@ -79,6 +79,12 @@ public static PcRunner serializableInstance() {
 
     //==========================PUBLIC METHODS============================//
 
+    /**
+     * Writes the object to the specified ObjectOutputStream.
+     *
+     * @param out The ObjectOutputStream to write the object to.
+     * @throws IOException If an I/O error occurs.
+     */
     @Serial
     private void writeObject(ObjectOutputStream out) throws IOException {
         try {
@@ -90,6 +96,14 @@ private void writeObject(ObjectOutputStream out) throws IOException {
         }
     }
 
+    /**
+     * Reads the object from the specified ObjectInputStream. This method is used during deserialization
+     * to restore the state of the object.
+     *
+     * @param in The ObjectInputStream to read the object from.
+     * @throws IOException            If an I/O error occurs.
+     * @throws ClassNotFoundException If the class of the serialized object cannot be found.
+     */
     @Serial
     private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
         try {
diff --git a/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/RowSummingExactWrapper.java b/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/RowSummingExactWrapper.java
index 258d160986..22aa121d64 100755
--- a/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/RowSummingExactWrapper.java
+++ b/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/RowSummingExactWrapper.java
@@ -228,6 +228,12 @@ private DiscreteVariable discreteVariable(Evidence evidence, String nodeName) {
         return evidence.getVariable(nodeName);
     }
 
+    /**
+     * Writes the object to the specified ObjectOutputStream.
+     *
+     * @param out The ObjectOutputStream to write the object to.
+     * @throws IOException If an I/O error occurs.
+     */
     @Serial
     private void writeObject(ObjectOutputStream out) throws IOException {
         try {
@@ -239,6 +245,14 @@ private void writeObject(ObjectOutputStream out) throws IOException {
         }
     }
 
+    /**
+     * Reads the object from the specified ObjectInputStream. This method is used during deserialization
+     * to restore the state of the object.
+     *
+     * @param in The ObjectInputStream to read the object from.
+     * @throws IOException            If an I/O error occurs.
+     * @throws ClassNotFoundException If the class of the serialized object cannot be found.
+     */
     @Serial
     private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
         try {
diff --git a/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/ScoredGraphsWrapper.java b/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/ScoredGraphsWrapper.java
index 1220eadf02..cd2f93dbcd 100644
--- a/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/ScoredGraphsWrapper.java
+++ b/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/ScoredGraphsWrapper.java
@@ -212,6 +212,12 @@ private void log() {
     }
 
 
+    /**
+     * Writes the object to the specified ObjectOutputStream.
+     *
+     * @param out The ObjectOutputStream to write the object to.
+     * @throws IOException If an I/O error occurs.
+     */
     @Serial
     private void writeObject(ObjectOutputStream out) throws IOException {
         try {
@@ -223,6 +229,14 @@ private void writeObject(ObjectOutputStream out) throws IOException {
         }
     }
 
+    /**
+     * Reads the object from the specified ObjectInputStream. This method is used during deserialization
+     * to restore the state of the object.
+     *
+     * @param in The ObjectInputStream to read the object from.
+     * @throws IOException            If an I/O error occurs.
+     * @throws ClassNotFoundException If the class of the serialized object cannot be found.
+     */
     @Serial
     private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
         try {
diff --git a/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/SemEstimatorWrapper.java b/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/SemEstimatorWrapper.java
index 1e41b6a6f5..33cb91e80a 100644
--- a/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/SemEstimatorWrapper.java
+++ b/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/SemEstimatorWrapper.java
@@ -259,6 +259,12 @@ private void log() {
         TetradLogger.getInstance().log(message);
     }
 
+    /**
+     * Writes the object to the specified ObjectOutputStream.
+     *
+     * @param out The ObjectOutputStream to write the object to.
+     * @throws IOException If an I/O error occurs.
+     */
     @Serial
     private void writeObject(ObjectOutputStream out) throws IOException {
         try {
@@ -270,6 +276,14 @@ private void writeObject(ObjectOutputStream out) throws IOException {
         }
     }
 
+    /**
+     * Reads the object from the specified ObjectInputStream. This method is used during deserialization
+     * to restore the state of the object.
+     *
+     * @param in The ObjectInputStream to read the object from.
+     * @throws IOException            If an I/O error occurs.
+     * @throws ClassNotFoundException If the class of the serialized object cannot be found.
+     */
     @Serial
     private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
         try {
diff --git a/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/SemGraphWrapper.java b/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/SemGraphWrapper.java
index 8bc9300910..b46cb60c11 100644
--- a/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/SemGraphWrapper.java
+++ b/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/SemGraphWrapper.java
@@ -377,6 +377,12 @@ private void log() {
         TetradLogger.getInstance().log(message);
     }
 
+    /**
+     * Writes the object to the specified ObjectOutputStream.
+     *
+     * @param out The ObjectOutputStream to write the object to.
+     * @throws IOException If an I/O error occurs.
+     */
     @Serial
     private void writeObject(ObjectOutputStream out) throws IOException {
         try {
@@ -388,6 +394,14 @@ private void writeObject(ObjectOutputStream out) throws IOException {
         }
     }
 
+    /**
+     * Reads the object from the specified ObjectInputStream. This method is used during deserialization
+     * to restore the state of the object.
+     *
+     * @param in The ObjectInputStream to read the object from.
+     * @throws IOException            If an I/O error occurs.
+     * @throws ClassNotFoundException If the class of the serialized object cannot be found.
+     */
     @Serial
     private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
         try {
diff --git a/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/SemImWrapper.java b/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/SemImWrapper.java
index 2f1b4a1789..99a183c3d8 100644
--- a/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/SemImWrapper.java
+++ b/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/SemImWrapper.java
@@ -248,6 +248,12 @@ private void log(int i, SemIm pm) {
         TetradLogger.getInstance().log(message);
     }
 
+    /**
+     * Writes the object to the specified ObjectOutputStream.
+     *
+     * @param out The ObjectOutputStream to write the object to.
+     * @throws IOException If an I/O error occurs.
+     */
     @Serial
     private void writeObject(ObjectOutputStream out) throws IOException {
         try {
@@ -259,6 +265,14 @@ private void writeObject(ObjectOutputStream out) throws IOException {
         }
     }
 
+    /**
+     * Reads the object from the specified ObjectInputStream. This method is used during deserialization
+     * to restore the state of the object.
+     *
+     * @param in The ObjectInputStream to read the object from.
+     * @throws IOException            If an I/O error occurs.
+     * @throws ClassNotFoundException If the class of the serialized object cannot be found.
+     */
     @Serial
     private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
         try {
diff --git a/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/SemPmWrapper.java b/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/SemPmWrapper.java
index 524164db08..57b3a19dfe 100644
--- a/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/SemPmWrapper.java
+++ b/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/SemPmWrapper.java
@@ -285,6 +285,12 @@ private void setSemPm(SemPm oldSemPm) {
         }
     }
 
+    /**
+     * Writes the object to the specified ObjectOutputStream.
+     *
+     * @param out The ObjectOutputStream to write the object to.
+     * @throws IOException If an I/O error occurs.
+     */
     @Serial
     private void writeObject(ObjectOutputStream out) throws IOException {
         try {
@@ -296,6 +302,14 @@ private void writeObject(ObjectOutputStream out) throws IOException {
         }
     }
 
+    /**
+     * Reads the object from the specified ObjectInputStream. This method is used during deserialization
+     * to restore the state of the object.
+     *
+     * @param in The ObjectInputStream to read the object from.
+     * @throws IOException            If an I/O error occurs.
+     * @throws ClassNotFoundException If the class of the serialized object cannot be found.
+     */
     @Serial
     private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
         try {
diff --git a/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/SemUpdaterWrapper.java b/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/SemUpdaterWrapper.java
index ef1da8581a..1c27615d73 100644
--- a/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/SemUpdaterWrapper.java
+++ b/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/SemUpdaterWrapper.java
@@ -100,6 +100,12 @@ public SemUpdater getSemUpdater() {
         return this.semUpdater;
     }
 
+    /**
+     * Writes the object to the specified ObjectOutputStream.
+     *
+     * @param out The ObjectOutputStream to write the object to.
+     * @throws IOException If an I/O error occurs.
+     */
     @Serial
     private void writeObject(ObjectOutputStream out) throws IOException {
         try {
@@ -111,6 +117,14 @@ private void writeObject(ObjectOutputStream out) throws IOException {
         }
     }
 
+    /**
+     * Reads the object from the specified ObjectInputStream. This method is used during deserialization
+     * to restore the state of the object.
+     *
+     * @param in The ObjectInputStream to read the object from.
+     * @throws IOException            If an I/O error occurs.
+     * @throws ClassNotFoundException If the class of the serialized object cannot be found.
+     */
     @Serial
     private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
         try {
diff --git a/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/SessionNodeWrapper.java b/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/SessionNodeWrapper.java
index 979e124a29..be52dfcd4c 100644
--- a/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/SessionNodeWrapper.java
+++ b/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/SessionNodeWrapper.java
@@ -195,6 +195,12 @@ public String toString() {
                getSessionName() + ")";
     }
 
+    /**
+     * Writes the object to the specified ObjectOutputStream.
+     *
+     * @param out The ObjectOutputStream to write the object to.
+     * @throws IOException If an I/O error occurs.
+     */
     @Serial
     private void writeObject(ObjectOutputStream out) throws IOException {
         try {
@@ -206,6 +212,14 @@ private void writeObject(ObjectOutputStream out) throws IOException {
         }
     }
 
+    /**
+     * Reads the object from the specified ObjectInputStream. This method is used during deserialization
+     * to restore the state of the object.
+     *
+     * @param in The ObjectInputStream to read the object from.
+     * @throws IOException            If an I/O error occurs.
+     * @throws ClassNotFoundException If the class of the serialized object cannot be found.
+     */
     @Serial
     private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
         try {
diff --git a/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/SessionWrapper.java b/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/SessionWrapper.java
index 31bbbe9e3b..a07d348955 100644
--- a/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/SessionWrapper.java
+++ b/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/SessionWrapper.java
@@ -737,6 +737,12 @@ public void setNewSession(boolean newSession) {
         this.session.setNewSession(newSession);
     }
 
+    /**
+     * Writes the object to the specified ObjectOutputStream.
+     *
+     * @param out The ObjectOutputStream to write the object to.
+     * @throws IOException If an I/O error occurs.
+     */
     @Serial
     private void writeObject(ObjectOutputStream out) throws IOException {
         try {
@@ -748,6 +754,14 @@ private void writeObject(ObjectOutputStream out) throws IOException {
         }
     }
 
+    /**
+     * Reads the object from the specified ObjectInputStream. This method is used during deserialization
+     * to restore the state of the object.
+     *
+     * @param in The ObjectInputStream to read the object from.
+     * @throws IOException            If an I/O error occurs.
+     * @throws ClassNotFoundException If the class of the serialized object cannot be found.
+     */
     @Serial
     private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
         try {
diff --git a/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/StandardizedSemImWrapper.java b/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/StandardizedSemImWrapper.java
index 188dab4b67..7ee60128b4 100644
--- a/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/StandardizedSemImWrapper.java
+++ b/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/StandardizedSemImWrapper.java
@@ -156,6 +156,12 @@ public void setShowErrors(boolean showErrors) {
 
     //======================== Private methods =======================//
 
+    /**
+     * Writes the object to the specified ObjectOutputStream.
+     *
+     * @param out The ObjectOutputStream to write the object to.
+     * @throws IOException If an I/O error occurs.
+     */
     @Serial
     private void writeObject(ObjectOutputStream out) throws IOException {
         try {
@@ -167,6 +173,14 @@ private void writeObject(ObjectOutputStream out) throws IOException {
         }
     }
 
+    /**
+     * Reads the object from the specified ObjectInputStream. This method is used during deserialization
+     * to restore the state of the object.
+     *
+     * @param in The ObjectInputStream to read the object from.
+     * @throws IOException            If an I/O error occurs.
+     * @throws ClassNotFoundException If the class of the serialized object cannot be found.
+     */
     @Serial
     private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
         try {
diff --git a/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/StructEmBayesSearchRunner.java b/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/StructEmBayesSearchRunner.java
index 0a3273c1b5..a0c7d38781 100644
--- a/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/StructEmBayesSearchRunner.java
+++ b/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/StructEmBayesSearchRunner.java
@@ -222,6 +222,12 @@ public DataSet getDataSet() {
         return this.dataSet;
     }
 
+    /**
+     * Writes the object to the specified ObjectOutputStream.
+     *
+     * @param out The ObjectOutputStream to write the object to.
+     * @throws IOException If an I/O error occurs.
+     */
     @Serial
     private void writeObject(ObjectOutputStream out) throws IOException {
         try {
@@ -233,6 +239,14 @@ private void writeObject(ObjectOutputStream out) throws IOException {
         }
     }
 
+    /**
+     * Reads the object from the specified ObjectInputStream. This method is used during deserialization
+     * to restore the state of the object.
+     *
+     * @param in The ObjectInputStream to read the object from.
+     * @throws IOException            If an I/O error occurs.
+     * @throws ClassNotFoundException If the class of the serialized object cannot be found.
+     */
     @Serial
     private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
         try {
diff --git a/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/TabularComparison.java b/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/TabularComparison.java
index 90fc5a7fef..4ae775e94e 100644
--- a/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/TabularComparison.java
+++ b/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/TabularComparison.java
@@ -227,6 +227,12 @@ public void setName(String name) {
 
     //============================PRIVATE METHODS=========================//
 
+    /**
+     * Writes the object to the specified ObjectOutputStream.
+     *
+     * @param out The ObjectOutputStream to write the object to.
+     * @throws IOException If an I/O error occurs.
+     */
     @Serial
     private void writeObject(ObjectOutputStream out) throws IOException {
         try {
@@ -238,6 +244,14 @@ private void writeObject(ObjectOutputStream out) throws IOException {
         }
     }
 
+    /**
+     * Reads the object from the specified ObjectInputStream. This method is used during deserialization
+     * to restore the state of the object.
+     *
+     * @param in The ObjectInputStream to read the object from.
+     * @throws IOException            If an I/O error occurs.
+     * @throws ClassNotFoundException If the class of the serialized object cannot be found.
+     */
     @Serial
     private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
         try {
diff --git a/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/TetradMetadata.java b/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/TetradMetadata.java
index 28f8adfc78..a04a2b0f14 100644
--- a/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/TetradMetadata.java
+++ b/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/TetradMetadata.java
@@ -107,6 +107,12 @@ public Date getDate() {
 
     //============================PRIVATE METHODS=======================//
 
+    /**
+     * Writes the object to the specified ObjectOutputStream.
+     *
+     * @param out The ObjectOutputStream to write the object to.
+     * @throws IOException If an I/O error occurs.
+     */
     @Serial
     private void writeObject(ObjectOutputStream out) throws IOException {
         try {
@@ -118,6 +124,14 @@ private void writeObject(ObjectOutputStream out) throws IOException {
         }
     }
 
+    /**
+     * Reads the object from the specified ObjectInputStream. This method is used during deserialization
+     * to restore the state of the object.
+     *
+     * @param in The ObjectInputStream to read the object from.
+     * @throws IOException            If an I/O error occurs.
+     * @throws ClassNotFoundException If the class of the serialized object cannot be found.
+     */
     @Serial
     private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
         try {
diff --git a/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/TimeLagGraphWrapper.java b/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/TimeLagGraphWrapper.java
index 4d3668ab8c..96f14cabdc 100644
--- a/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/TimeLagGraphWrapper.java
+++ b/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/TimeLagGraphWrapper.java
@@ -186,6 +186,12 @@ private void log() {
         TetradLogger.getInstance().log(this.graph + "");
     }
 
+    /**
+     * Writes the object to the specified ObjectOutputStream.
+     *
+     * @param out The ObjectOutputStream to write the object to.
+     * @throws IOException If an I/O error occurs.
+     */
     @Serial
     private void writeObject(ObjectOutputStream out) throws IOException {
         try {
@@ -197,6 +203,14 @@ private void writeObject(ObjectOutputStream out) throws IOException {
         }
     }
 
+    /**
+     * Reads the object from the specified ObjectInputStream. This method is used during deserialization
+     * to restore the state of the object.
+     *
+     * @param in The ObjectInputStream to read the object from.
+     * @throws IOException            If an I/O error occurs.
+     * @throws ClassNotFoundException If the class of the serialized object cannot be found.
+     */
     @Serial
     private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
         try {
diff --git a/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/datamanip/DeterminismWraper.java b/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/datamanip/DeterminismWraper.java
index 8f3c908afb..eb678376a5 100644
--- a/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/datamanip/DeterminismWraper.java
+++ b/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/datamanip/DeterminismWraper.java
@@ -65,6 +65,12 @@ public static PcRunner serializableInstance() {
         return PcRunner.serializableInstance();
     }
 
+    /**
+     * Writes the object to the specified ObjectOutputStream.
+     *
+     * @param out The ObjectOutputStream to write the object to.
+     * @throws IOException If an I/O error occurs.
+     */
     @Serial
     private void writeObject(ObjectOutputStream out) throws IOException {
         try {
@@ -76,6 +82,14 @@ private void writeObject(ObjectOutputStream out) throws IOException {
         }
     }
 
+    /**
+     * Reads the object from the specified ObjectInputStream. This method is used during deserialization
+     * to restore the state of the object.
+     *
+     * @param in The ObjectInputStream to read the object from.
+     * @throws IOException            If an I/O error occurs.
+     * @throws ClassNotFoundException If the class of the serialized object cannot be found.
+     */
     @Serial
     private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
         try {
diff --git a/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/datamanip/DiscretizationWrapper.java b/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/datamanip/DiscretizationWrapper.java
index bb63c74793..4eed9cb0f3 100644
--- a/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/datamanip/DiscretizationWrapper.java
+++ b/tetrad-gui/src/main/java/edu/cmu/tetradapp/model/datamanip/DiscretizationWrapper.java
@@ -96,6 +96,12 @@ public static PcRunner serializableInstance() {
         return PcRunner.serializableInstance();
     }
 
+    /**
+     * Writes the object to the specified ObjectOutputStream.
+     *
+     * @param out The ObjectOutputStream to write the object to.
+     * @throws IOException If an I/O error occurs.
+     */
     @Serial
     private void writeObject(ObjectOutputStream out) throws IOException {
         try {
@@ -107,6 +113,14 @@ private void writeObject(ObjectOutputStream out) throws IOException {
         }
     }
 
+    /**
+     * Reads the object from the specified ObjectInputStream. This method is used during deserialization
+     * to restore the state of the object.
+     *
+     * @param in The ObjectInputStream to read the object from.
+     * @throws IOException            If an I/O error occurs.
+     * @throws ClassNotFoundException If the class of the serialized object cannot be found.
+     */
     @Serial
     private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
         try {
diff --git a/tetrad-gui/src/main/java/edu/cmu/tetradapp/workbench/AbstractWorkbench.java b/tetrad-gui/src/main/java/edu/cmu/tetradapp/workbench/AbstractWorkbench.java
index 7325f95a10..308e685c3b 100644
--- a/tetrad-gui/src/main/java/edu/cmu/tetradapp/workbench/AbstractWorkbench.java
+++ b/tetrad-gui/src/main/java/edu/cmu/tetradapp/workbench/AbstractWorkbench.java
@@ -2985,6 +2985,12 @@ public void propertyChange(PropertyChangeEvent e) {
         }
     }
 
+    /**
+     * Writes the object to the specified ObjectOutputStream.
+     *
+     * @param out The ObjectOutputStream to write the object to.
+     * @throws IOException If an I/O error occurs.
+     */
     @Serial
     private void writeObject(ObjectOutputStream out) throws IOException {
         try {
@@ -2996,6 +3002,14 @@ private void writeObject(ObjectOutputStream out) throws IOException {
         }
     }
 
+    /**
+     * Reads the object from the specified ObjectInputStream. This method is used during deserialization
+     * to restore the state of the object.
+     *
+     * @param in The ObjectInputStream to read the object from.
+     * @throws IOException            If an I/O error occurs.
+     * @throws ClassNotFoundException If the class of the serialized object cannot be found.
+     */
     @Serial
     private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
         try {
diff --git a/tetrad-gui/src/main/java/edu/cmu/tetradapp/workbench/GraphNodeError.java b/tetrad-gui/src/main/java/edu/cmu/tetradapp/workbench/GraphNodeError.java
index 3c708cef35..fdc273507a 100644
--- a/tetrad-gui/src/main/java/edu/cmu/tetradapp/workbench/GraphNodeError.java
+++ b/tetrad-gui/src/main/java/edu/cmu/tetradapp/workbench/GraphNodeError.java
@@ -155,6 +155,12 @@ else if (nodes != null) {
         return newName;
     }
 
+    /**
+     * Writes the object to the specified ObjectOutputStream.
+     *
+     * @param out The ObjectOutputStream to write the object to.
+     * @throws IOException If an I/O error occurs.
+     */
     @Serial
     private void writeObject(ObjectOutputStream out) throws IOException {
         try {
@@ -166,6 +172,14 @@ private void writeObject(ObjectOutputStream out) throws IOException {
         }
     }
 
+    /**
+     * Reads the object from the specified ObjectInputStream. This method is used during deserialization
+     * to restore the state of the object.
+     *
+     * @param in The ObjectInputStream to read the object from.
+     * @throws IOException            If an I/O error occurs.
+     * @throws ClassNotFoundException If the class of the serialized object cannot be found.
+     */
     @Serial
     private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
         try {
diff --git a/tetrad-gui/src/main/java/edu/cmu/tetradapp/workbench/GraphNodeLatent.java b/tetrad-gui/src/main/java/edu/cmu/tetradapp/workbench/GraphNodeLatent.java
index befd2d0d0b..9ff54f7b6c 100644
--- a/tetrad-gui/src/main/java/edu/cmu/tetradapp/workbench/GraphNodeLatent.java
+++ b/tetrad-gui/src/main/java/edu/cmu/tetradapp/workbench/GraphNodeLatent.java
@@ -167,6 +167,12 @@ public void doDoubleClickAction() {
         doDoubleClickAction(new EdgeListGraph());
     }
 
+    /**
+     * Writes the object to the specified ObjectOutputStream.
+     *
+     * @param out The ObjectOutputStream to write the object to.
+     * @throws IOException If an I/O error occurs.
+     */
     @Serial
     private void writeObject(ObjectOutputStream out) throws IOException {
         try {
@@ -178,6 +184,14 @@ private void writeObject(ObjectOutputStream out) throws IOException {
         }
     }
 
+    /**
+     * Reads the object from the specified ObjectInputStream. This method is used during deserialization
+     * to restore the state of the object.
+     *
+     * @param in The ObjectInputStream to read the object from.
+     * @throws IOException            If an I/O error occurs.
+     * @throws ClassNotFoundException If the class of the serialized object cannot be found.
+     */
     @Serial
     private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
         try {
diff --git a/tetrad-gui/src/main/java/edu/cmu/tetradapp/workbench/GraphNodeLocked.java b/tetrad-gui/src/main/java/edu/cmu/tetradapp/workbench/GraphNodeLocked.java
index aa345ab50f..e550cbb00e 100644
--- a/tetrad-gui/src/main/java/edu/cmu/tetradapp/workbench/GraphNodeLocked.java
+++ b/tetrad-gui/src/main/java/edu/cmu/tetradapp/workbench/GraphNodeLocked.java
@@ -166,6 +166,12 @@ public void doDoubleClickAction() {
         doDoubleClickAction(new EdgeListGraph());
     }
 
+    /**
+     * Writes the object to the specified ObjectOutputStream.
+     *
+     * @param out The ObjectOutputStream to write the object to.
+     * @throws IOException If an I/O error occurs.
+     */
     @Serial
     private void writeObject(ObjectOutputStream out) throws IOException {
         try {
@@ -177,6 +183,14 @@ private void writeObject(ObjectOutputStream out) throws IOException {
         }
     }
 
+    /**
+     * Reads the object from the specified ObjectInputStream. This method is used during deserialization
+     * to restore the state of the object.
+     *
+     * @param in The ObjectInputStream to read the object from.
+     * @throws IOException            If an I/O error occurs.
+     * @throws ClassNotFoundException If the class of the serialized object cannot be found.
+     */
     @Serial
     private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
         try {
diff --git a/tetrad-gui/src/main/java/edu/cmu/tetradapp/workbench/GraphNodeMeasured.java b/tetrad-gui/src/main/java/edu/cmu/tetradapp/workbench/GraphNodeMeasured.java
index c0a80f4c5a..3975fa1ab1 100644
--- a/tetrad-gui/src/main/java/edu/cmu/tetradapp/workbench/GraphNodeMeasured.java
+++ b/tetrad-gui/src/main/java/edu/cmu/tetradapp/workbench/GraphNodeMeasured.java
@@ -209,6 +209,12 @@ public void setEditExitingMeasuredVarsAllowed(boolean editExitingMeasuredVarsAll
         this.editExitingMeasuredVarsAllowed = editExitingMeasuredVarsAllowed;
     }
 
+    /**
+     * Writes the object to the specified ObjectOutputStream.
+     *
+     * @param out The ObjectOutputStream to write the object to.
+     * @throws IOException If an I/O error occurs.
+     */
     @Serial
     private void writeObject(ObjectOutputStream out) throws IOException {
         try {
@@ -220,6 +226,14 @@ private void writeObject(ObjectOutputStream out) throws IOException {
         }
     }
 
+    /**
+     * Reads the object from the specified ObjectInputStream. This method is used during deserialization
+     * to restore the state of the object.
+     *
+     * @param in The ObjectInputStream to read the object from.
+     * @throws IOException            If an I/O error occurs.
+     * @throws ClassNotFoundException If the class of the serialized object cannot be found.
+     */
     @Serial
     private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
         try {
diff --git a/tetrad-gui/src/main/java/edu/cmu/tetradapp/workbench/GraphNodeRandomized.java b/tetrad-gui/src/main/java/edu/cmu/tetradapp/workbench/GraphNodeRandomized.java
index 844f53992a..f49b2605ae 100644
--- a/tetrad-gui/src/main/java/edu/cmu/tetradapp/workbench/GraphNodeRandomized.java
+++ b/tetrad-gui/src/main/java/edu/cmu/tetradapp/workbench/GraphNodeRandomized.java
@@ -166,6 +166,12 @@ public void doDoubleClickAction() {
         doDoubleClickAction(new EdgeListGraph());
     }
 
+    /**
+     * Writes the object to the specified ObjectOutputStream.
+     *
+     * @param out The ObjectOutputStream to write the object to.
+     * @throws IOException If an I/O error occurs.
+     */
     @Serial
     private void writeObject(ObjectOutputStream out) throws IOException {
         try {
@@ -177,6 +183,14 @@ private void writeObject(ObjectOutputStream out) throws IOException {
         }
     }
 
+    /**
+     * Reads the object from the specified ObjectInputStream. This method is used during deserialization
+     * to restore the state of the object.
+     *
+     * @param in The ObjectInputStream to read the object from.
+     * @throws IOException            If an I/O error occurs.
+     * @throws ClassNotFoundException If the class of the serialized object cannot be found.
+     */
     @Serial
     private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
         try {
diff --git a/tetrad-lib/src/main/java/edu/cmu/tetrad/algcomparison/algorithm/Algorithms.java b/tetrad-lib/src/main/java/edu/cmu/tetrad/algcomparison/algorithm/Algorithms.java
index 3e8ddb7511..394c8b4182 100644
--- a/tetrad-lib/src/main/java/edu/cmu/tetrad/algcomparison/algorithm/Algorithms.java
+++ b/tetrad-lib/src/main/java/edu/cmu/tetrad/algcomparison/algorithm/Algorithms.java
@@ -51,6 +51,12 @@ public List<Algorithm> getAlgorithms() {
         return new ArrayList<>(this.algorithms);
     }
 
+    /**
+     * Writes the object to the specified ObjectOutputStream.
+     *
+     * @param out The ObjectOutputStream to write the object to.
+     * @throws IOException If an I/O error occurs.
+     */
     @Serial
     private void writeObject(ObjectOutputStream out) throws IOException {
         try {
@@ -62,6 +68,14 @@ private void writeObject(ObjectOutputStream out) throws IOException {
         }
     }
 
+    /**
+     * Reads the object from the specified ObjectInputStream. This method is used during deserialization
+     * to restore the state of the object.
+     *
+     * @param in The ObjectInputStream to read the object from.
+     * @throws IOException            If an I/O error occurs.
+     * @throws ClassNotFoundException If the class of the serialized object cannot be found.
+     */
     @Serial
     private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
         try {
diff --git a/tetrad-lib/src/main/java/edu/cmu/tetrad/algcomparison/simulation/Simulations.java b/tetrad-lib/src/main/java/edu/cmu/tetrad/algcomparison/simulation/Simulations.java
index 5a2794e05d..d2b117591c 100644
--- a/tetrad-lib/src/main/java/edu/cmu/tetrad/algcomparison/simulation/Simulations.java
+++ b/tetrad-lib/src/main/java/edu/cmu/tetrad/algcomparison/simulation/Simulations.java
@@ -49,6 +49,12 @@ public List<Simulation> getSimulations() {
         return new ArrayList<>(this.simulations);
     }
 
+    /**
+     * Writes the object to the specified ObjectOutputStream.
+     *
+     * @param out The ObjectOutputStream to write the object to.
+     * @throws IOException If an I/O error occurs.
+     */
     @Serial
     private void writeObject(ObjectOutputStream out) throws IOException {
         try {
@@ -60,6 +66,14 @@ private void writeObject(ObjectOutputStream out) throws IOException {
         }
     }
 
+    /**
+     * Reads the object from the specified ObjectInputStream. This method is used during deserialization
+     * to restore the state of the object.
+     *
+     * @param in The ObjectInputStream to read the object from.
+     * @throws IOException            If an I/O error occurs.
+     * @throws ClassNotFoundException If the class of the serialized object cannot be found.
+     */
     @Serial
     private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
         try {
diff --git a/tetrad-lib/src/main/java/edu/cmu/tetrad/algcomparison/statistic/LocalGraphPrecision.java b/tetrad-lib/src/main/java/edu/cmu/tetrad/algcomparison/statistic/LocalGraphPrecision.java
index cdc2c3b57c..79df272a45 100644
--- a/tetrad-lib/src/main/java/edu/cmu/tetrad/algcomparison/statistic/LocalGraphPrecision.java
+++ b/tetrad-lib/src/main/java/edu/cmu/tetrad/algcomparison/statistic/LocalGraphPrecision.java
@@ -4,17 +4,41 @@
 import edu.cmu.tetrad.data.DataModel;
 import edu.cmu.tetrad.graph.Graph;
 
+/**
+ * The LocalGraphPrecision class implements the Statistic interface and represents the Local Graph Precision statistic.
+ * It calculates the precision between the true graph and the estimated graph locally.
+ */
 public class LocalGraphPrecision implements Statistic {
+
+    /**
+     * This method returns the abbreviation for the statistic.
+     *
+     * @return The abbreviation for the statistic.
+     */
     @Override
     public String getAbbreviation() {
         return "LGP";
     }
 
+    /**
+     * Returns a short one-line description of this statistic.
+     *
+     * @return The description of the statistic.
+     */
     @Override
     public String getDescription() {
         return "Local Graph Precision";
     }
 
+    /**
+     * This method calculates the Local Graph Precision.
+     * It calculates the precision between the true graph and the estimated graph locally.
+     *
+     * @param trueGraph The true graph.
+     * @param estGraph The estimated graph.
+     * @param dataModel The data model.
+     * @return The local graph precision.
+     */
     @Override
     public double getValue(Graph trueGraph, Graph estGraph, DataModel dataModel) {
         LocalGraphConfusion lgConfusion = new LocalGraphConfusion(trueGraph, estGraph);
@@ -23,6 +47,12 @@ public double getValue(Graph trueGraph, Graph estGraph, DataModel dataModel) {
         return lgTp / (double) (lgTp + lgFp);
     }
 
+    /**
+     * This method returns the normalized value of a given statistic.
+     *
+     * @param value The value of the statistic.
+     * @return The normalized value of the statistic.
+     */
     @Override
     public double getNormValue(double value) {
         return value;
diff --git a/tetrad-lib/src/main/java/edu/cmu/tetrad/algcomparison/statistic/LocalGraphRecall.java b/tetrad-lib/src/main/java/edu/cmu/tetrad/algcomparison/statistic/LocalGraphRecall.java
index 94b893d248..5fed2647e0 100644
--- a/tetrad-lib/src/main/java/edu/cmu/tetrad/algcomparison/statistic/LocalGraphRecall.java
+++ b/tetrad-lib/src/main/java/edu/cmu/tetrad/algcomparison/statistic/LocalGraphRecall.java
@@ -4,6 +4,11 @@
 import edu.cmu.tetrad.data.DataModel;
 import edu.cmu.tetrad.graph.Graph;
 
+/**
+ * LocalGraphRecall implements the Statistic interface and represents the local graph recall statistic.
+ * It calculates the recall of the estimated graph with respect to the true graph. The recall is defined as the ratio
+ * of true positives (TP) to the sum of true positives and false negatives (TP + FN).
+ */
 public class LocalGraphRecall implements Statistic {
     @Override
     public String getAbbreviation() {
diff --git a/tetrad-lib/src/main/java/edu/cmu/tetrad/algcomparison/statistic/Statistics.java b/tetrad-lib/src/main/java/edu/cmu/tetrad/algcomparison/statistic/Statistics.java
index 5b32a76dca..f9df70d026 100644
--- a/tetrad-lib/src/main/java/edu/cmu/tetrad/algcomparison/statistic/Statistics.java
+++ b/tetrad-lib/src/main/java/edu/cmu/tetrad/algcomparison/statistic/Statistics.java
@@ -100,6 +100,12 @@ public int size() {
         return this.statistics.size();
     }
 
+    /**
+     * Writes the object to the specified ObjectOutputStream.
+     *
+     * @param out The ObjectOutputStream to write the object to.
+     * @throws IOException If an I/O error occurs.
+     */
     @Serial
     private void writeObject(ObjectOutputStream out) throws IOException {
         try {
@@ -111,6 +117,14 @@ private void writeObject(ObjectOutputStream out) throws IOException {
         }
     }
 
+    /**
+     * Reads the object from the specified ObjectInputStream. This method is used during deserialization
+     * to restore the state of the object.
+     *
+     * @param in The ObjectInputStream to read the object from.
+     * @throws IOException            If an I/O error occurs.
+     * @throws ClassNotFoundException If the class of the serialized object cannot be found.
+     */
     @Serial
     private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
         try {
diff --git a/tetrad-lib/src/main/java/edu/cmu/tetrad/algcomparison/statistic/utils/LocalGraphConfusion.java b/tetrad-lib/src/main/java/edu/cmu/tetrad/algcomparison/statistic/utils/LocalGraphConfusion.java
index c10e7c2da4..e7eab67d0c 100644
--- a/tetrad-lib/src/main/java/edu/cmu/tetrad/algcomparison/statistic/utils/LocalGraphConfusion.java
+++ b/tetrad-lib/src/main/java/edu/cmu/tetrad/algcomparison/statistic/utils/LocalGraphConfusion.java
@@ -206,18 +206,38 @@ public LocalGraphConfusion(Graph trueGraph, Graph estGraph) {
         }
     }
 
+    /**
+     * Returns the true positives (TP) value of the LocalGraphConfusion object.
+     *
+     * @return The true positives (TP) value.
+     */
     public int getTp() {
         return tp;
     }
 
+    /**
+     * Retrieves the value of true negatives (TN) from the LocalGraphConfusion object.
+     *
+     * @return The true negatives (TN) value.
+     */
     public int getTn() {
         return tn;
     }
 
+    /**
+     * Retrieves the value of false positives (FP) from the LocalGraphConfusion object.
+     *
+     * @return The false positives (FP) value.
+     */
     public int getFp() {
         return fp;
     }
 
+    /**
+     * Returns the false negatives (FN) value of the LocalGraphConfusion object.
+     *
+     * @return The false negatives (FN) value.
+     */
     public int getFn() {
         return fn;
     }
diff --git a/tetrad-lib/src/main/java/edu/cmu/tetrad/bayes/ApproximateUpdater.java b/tetrad-lib/src/main/java/edu/cmu/tetrad/bayes/ApproximateUpdater.java
index 2d19b7d17d..1a23b11ef8 100755
--- a/tetrad-lib/src/main/java/edu/cmu/tetrad/bayes/ApproximateUpdater.java
+++ b/tetrad-lib/src/main/java/edu/cmu/tetrad/bayes/ApproximateUpdater.java
@@ -372,6 +372,12 @@ private Dag createManipulatedGraph(Graph graph) {
         return updatedGraph;
     }
 
+    /**
+     * Writes the object to the specified ObjectOutputStream.
+     *
+     * @param out The ObjectOutputStream to write the object to.
+     * @throws IOException If an I/O error occurs.
+     */
     @Serial
     private void writeObject(ObjectOutputStream out) throws IOException {
         try {
@@ -383,6 +389,14 @@ private void writeObject(ObjectOutputStream out) throws IOException {
         }
     }
 
+    /**
+     * Reads the object from the specified ObjectInputStream. This method is used during deserialization
+     * to restore the state of the object.
+     *
+     * @param in The ObjectInputStream to read the object from.
+     * @throws IOException            If an I/O error occurs.
+     * @throws ClassNotFoundException If the class of the serialized object cannot be found.
+     */
     @Serial
     private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
         try {
diff --git a/tetrad-lib/src/main/java/edu/cmu/tetrad/bayes/BayesImProbs.java b/tetrad-lib/src/main/java/edu/cmu/tetrad/bayes/BayesImProbs.java
index 2ce649fa99..2d94e0ff99 100755
--- a/tetrad-lib/src/main/java/edu/cmu/tetrad/bayes/BayesImProbs.java
+++ b/tetrad-lib/src/main/java/edu/cmu/tetrad/bayes/BayesImProbs.java
@@ -285,6 +285,12 @@ public List<Node> getVariables() {
         return this.variables;
     }
 
+    /**
+     * Writes the object to the specified ObjectOutputStream.
+     *
+     * @param out The ObjectOutputStream to write the object to.
+     * @throws IOException If an I/O error occurs.
+     */
     @Serial
     private void writeObject(ObjectOutputStream out) throws IOException {
         try {
@@ -296,6 +302,14 @@ private void writeObject(ObjectOutputStream out) throws IOException {
         }
     }
 
+    /**
+     * Reads the object from the specified ObjectInputStream. This method is used during deserialization
+     * to restore the state of the object.
+     *
+     * @param in The ObjectInputStream to read the object from.
+     * @throws IOException            If an I/O error occurs.
+     * @throws ClassNotFoundException If the class of the serialized object cannot be found.
+     */
     @Serial
     private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
         try {
diff --git a/tetrad-lib/src/main/java/edu/cmu/tetrad/bayes/BayesPm.java b/tetrad-lib/src/main/java/edu/cmu/tetrad/bayes/BayesPm.java
index b21b35cdae..7cb084b8e9 100644
--- a/tetrad-lib/src/main/java/edu/cmu/tetrad/bayes/BayesPm.java
+++ b/tetrad-lib/src/main/java/edu/cmu/tetrad/bayes/BayesPm.java
@@ -576,6 +576,12 @@ private void initializeValues(int lowerBound, int upperBound) {
         }
     }
 
+    /**
+     * Writes the object to the specified ObjectOutputStream.
+     *
+     * @param out The ObjectOutputStream to write the object to.
+     * @throws IOException If an I/O error occurs.
+     */
     @Serial
     private void writeObject(ObjectOutputStream out) throws IOException {
         try {
@@ -587,6 +593,14 @@ private void writeObject(ObjectOutputStream out) throws IOException {
         }
     }
 
+    /**
+     * Reads the object from the specified ObjectInputStream. This method is used during deserialization
+     * to restore the state of the object.
+     *
+     * @param in The ObjectInputStream to read the object from.
+     * @throws IOException            If an I/O error occurs.
+     * @throws ClassNotFoundException If the class of the serialized object cannot be found.
+     */
     @Serial
     private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
         try {
diff --git a/tetrad-lib/src/main/java/edu/cmu/tetrad/bayes/CptInvariantMarginalCalculator.java b/tetrad-lib/src/main/java/edu/cmu/tetrad/bayes/CptInvariantMarginalCalculator.java
index f4df08d42b..0f18ccd164 100644
--- a/tetrad-lib/src/main/java/edu/cmu/tetrad/bayes/CptInvariantMarginalCalculator.java
+++ b/tetrad-lib/src/main/java/edu/cmu/tetrad/bayes/CptInvariantMarginalCalculator.java
@@ -215,6 +215,12 @@ private boolean noModifiedCpts(int[] parents, int i) {
         return intersection.isEmpty();
     }
 
+    /**
+     * Writes the object to the specified ObjectOutputStream.
+     *
+     * @param out The ObjectOutputStream to write the object to.
+     * @throws IOException If an I/O error occurs.
+     */
     @Serial
     private void writeObject(ObjectOutputStream out) throws IOException {
         try {
@@ -226,6 +232,14 @@ private void writeObject(ObjectOutputStream out) throws IOException {
         }
     }
 
+    /**
+     * Reads the object from the specified ObjectInputStream. This method is used during deserialization
+     * to restore the state of the object.
+     *
+     * @param in The ObjectInputStream to read the object from.
+     * @throws IOException            If an I/O error occurs.
+     * @throws ClassNotFoundException If the class of the serialized object cannot be found.
+     */
     @Serial
     private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
         try {
diff --git a/tetrad-lib/src/main/java/edu/cmu/tetrad/bayes/CptInvariantUpdater.java b/tetrad-lib/src/main/java/edu/cmu/tetrad/bayes/CptInvariantUpdater.java
index e558efd37b..2a0bde7dba 100755
--- a/tetrad-lib/src/main/java/edu/cmu/tetrad/bayes/CptInvariantUpdater.java
+++ b/tetrad-lib/src/main/java/edu/cmu/tetrad/bayes/CptInvariantUpdater.java
@@ -293,6 +293,12 @@ private Dag createManipulatedGraph(Graph graph) {
         return updatedGraph;
     }
 
+    /**
+     * Writes the object to the specified ObjectOutputStream.
+     *
+     * @param out The ObjectOutputStream to write the object to.
+     * @throws IOException If an I/O error occurs.
+     */
     @Serial
     private void writeObject(ObjectOutputStream out) throws IOException {
         try {
@@ -304,6 +310,14 @@ private void writeObject(ObjectOutputStream out) throws IOException {
         }
     }
 
+    /**
+     * Reads the object from the specified ObjectInputStream. This method is used during deserialization
+     * to restore the state of the object.
+     *
+     * @param in The ObjectInputStream to read the object from.
+     * @throws IOException            If an I/O error occurs.
+     * @throws ClassNotFoundException If the class of the serialized object cannot be found.
+     */
     @Serial
     private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
         try {
diff --git a/tetrad-lib/src/main/java/edu/cmu/tetrad/bayes/DirichletBayesIm.java b/tetrad-lib/src/main/java/edu/cmu/tetrad/bayes/DirichletBayesIm.java
index 6b441d612a..5ebe897e2a 100644
--- a/tetrad-lib/src/main/java/edu/cmu/tetrad/bayes/DirichletBayesIm.java
+++ b/tetrad-lib/src/main/java/edu/cmu/tetrad/bayes/DirichletBayesIm.java
@@ -1173,6 +1173,12 @@ private int getUniqueCompatibleOldRow(int nodeIndex, int rowIndex,
         return oldBayesIm.getRowIndex(oldNodeIndex, oldParentValues);
     }
 
+    /**
+     * Writes the object to the specified ObjectOutputStream.
+     *
+     * @param out The ObjectOutputStream to write the object to.
+     * @throws IOException If an I/O error occurs.
+     */
     @Serial
     private void writeObject(ObjectOutputStream out) throws IOException {
         try {
@@ -1184,6 +1190,14 @@ private void writeObject(ObjectOutputStream out) throws IOException {
         }
     }
 
+    /**
+     * Reads the object from the specified ObjectInputStream. This method is used during deserialization
+     * to restore the state of the object.
+     *
+     * @param in The ObjectInputStream to read the object from.
+     * @throws IOException            If an I/O error occurs.
+     * @throws ClassNotFoundException If the class of the serialized object cannot be found.
+     */
     @Serial
     private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
         try {
diff --git a/tetrad-lib/src/main/java/edu/cmu/tetrad/bayes/Evidence.java b/tetrad-lib/src/main/java/edu/cmu/tetrad/bayes/Evidence.java
index dccc670de7..5b16ea8ecd 100755
--- a/tetrad-lib/src/main/java/edu/cmu/tetrad/bayes/Evidence.java
+++ b/tetrad-lib/src/main/java/edu/cmu/tetrad/bayes/Evidence.java
@@ -340,6 +340,12 @@ public int hashCode() {
         return hashCode;
     }
 
+    /**
+     * Writes the object to the specified ObjectOutputStream.
+     *
+     * @param out The ObjectOutputStream to write the object to.
+     * @throws IOException If an I/O error occurs.
+     */
     @Serial
     private void writeObject(ObjectOutputStream out) throws IOException {
         try {
@@ -351,6 +357,14 @@ private void writeObject(ObjectOutputStream out) throws IOException {
         }
     }
 
+    /**
+     * Reads the object from the specified ObjectInputStream. This method is used during deserialization
+     * to restore the state of the object.
+     *
+     * @param in The ObjectInputStream to read the object from.
+     * @throws IOException            If an I/O error occurs.
+     * @throws ClassNotFoundException If the class of the serialized object cannot be found.
+     */
     @Serial
     private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
         try {
diff --git a/tetrad-lib/src/main/java/edu/cmu/tetrad/bayes/Identifiability.java b/tetrad-lib/src/main/java/edu/cmu/tetrad/bayes/Identifiability.java
index 1f1704a25d..03303bce8d 100644
--- a/tetrad-lib/src/main/java/edu/cmu/tetrad/bayes/Identifiability.java
+++ b/tetrad-lib/src/main/java/edu/cmu/tetrad/bayes/Identifiability.java
@@ -996,6 +996,12 @@ private Dag createManipulatedGraph(Graph graph) {
 
     /////////////////////////////////////////////////////////////////
 
+    /**
+     * Writes the object to the specified ObjectOutputStream.
+     *
+     * @param out The ObjectOutputStream to write the object to.
+     * @throws IOException If an I/O error occurs.
+     */
     @Serial
     private void writeObject(ObjectOutputStream out) throws IOException {
         try {
@@ -1007,6 +1013,14 @@ private void writeObject(ObjectOutputStream out) throws IOException {
         }
     }
 
+    /**
+     * Reads the object from the specified ObjectInputStream. This method is used during deserialization
+     * to restore the state of the object.
+     *
+     * @param in The ObjectInputStream to read the object from.
+     * @throws IOException            If an I/O error occurs.
+     * @throws ClassNotFoundException If the class of the serialized object cannot be found.
+     */
     @Serial
     private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
         try {
diff --git a/tetrad-lib/src/main/java/edu/cmu/tetrad/bayes/JunctionTreeAlgorithm.java b/tetrad-lib/src/main/java/edu/cmu/tetrad/bayes/JunctionTreeAlgorithm.java
index afdf665eaf..dfec59cca1 100644
--- a/tetrad-lib/src/main/java/edu/cmu/tetrad/bayes/JunctionTreeAlgorithm.java
+++ b/tetrad-lib/src/main/java/edu/cmu/tetrad/bayes/JunctionTreeAlgorithm.java
@@ -996,6 +996,12 @@ public String toString() {
 
     }
 
+    /**
+     * Writes the object to the specified ObjectOutputStream.
+     *
+     * @param out The ObjectOutputStream to write the object to.
+     * @throws IOException If an I/O error occurs.
+     */
     @Serial
     private void writeObject(ObjectOutputStream out) throws IOException {
         try {
@@ -1007,6 +1013,14 @@ private void writeObject(ObjectOutputStream out) throws IOException {
         }
     }
 
+    /**
+     * Reads the object from the specified ObjectInputStream. This method is used during deserialization
+     * to restore the state of the object.
+     *
+     * @param in The ObjectInputStream to read the object from.
+     * @throws IOException            If an I/O error occurs.
+     * @throws ClassNotFoundException If the class of the serialized object cannot be found.
+     */
     @Serial
     private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
         try {
diff --git a/tetrad-lib/src/main/java/edu/cmu/tetrad/bayes/JunctionTreeUpdater.java b/tetrad-lib/src/main/java/edu/cmu/tetrad/bayes/JunctionTreeUpdater.java
index 97bca6bc8f..8b35c47a1b 100644
--- a/tetrad-lib/src/main/java/edu/cmu/tetrad/bayes/JunctionTreeUpdater.java
+++ b/tetrad-lib/src/main/java/edu/cmu/tetrad/bayes/JunctionTreeUpdater.java
@@ -327,6 +327,12 @@ private Dag createManipulatedGraph(Graph graph) {
         return updatedGraph;
     }
 
+    /**
+     * Writes the object to the specified ObjectOutputStream.
+     *
+     * @param out The ObjectOutputStream to write the object to.
+     * @throws IOException If an I/O error occurs.
+     */
     @Serial
     private void writeObject(ObjectOutputStream out) throws IOException {
         try {
@@ -338,6 +344,14 @@ private void writeObject(ObjectOutputStream out) throws IOException {
         }
     }
 
+    /**
+     * Reads the object from the specified ObjectInputStream. This method is used during deserialization
+     * to restore the state of the object.
+     *
+     * @param in The ObjectInputStream to read the object from.
+     * @throws IOException            If an I/O error occurs.
+     * @throws ClassNotFoundException If the class of the serialized object cannot be found.
+     */
     @Serial
     private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
         try {
diff --git a/tetrad-lib/src/main/java/edu/cmu/tetrad/bayes/Manipulation.java b/tetrad-lib/src/main/java/edu/cmu/tetrad/bayes/Manipulation.java
index c2292c82af..e440745e2a 100755
--- a/tetrad-lib/src/main/java/edu/cmu/tetrad/bayes/Manipulation.java
+++ b/tetrad-lib/src/main/java/edu/cmu/tetrad/bayes/Manipulation.java
@@ -185,6 +185,12 @@ public boolean isManipulated(int nodeIndex) {
         return this.manipulated[nodeIndex];
     }
 
+    /**
+     * Writes the object to the specified ObjectOutputStream.
+     *
+     * @param out The ObjectOutputStream to write the object to.
+     * @throws IOException If an I/O error occurs.
+     */
     @Serial
     private void writeObject(ObjectOutputStream out) throws IOException {
         try {
@@ -196,6 +202,14 @@ private void writeObject(ObjectOutputStream out) throws IOException {
         }
     }
 
+    /**
+     * Reads the object from the specified ObjectInputStream. This method is used during deserialization
+     * to restore the state of the object.
+     *
+     * @param in The ObjectInputStream to read the object from.
+     * @throws IOException            If an I/O error occurs.
+     * @throws ClassNotFoundException If the class of the serialized object cannot be found.
+     */
     @Serial
     private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
         try {
diff --git a/tetrad-lib/src/main/java/edu/cmu/tetrad/bayes/MlBayesIm.java b/tetrad-lib/src/main/java/edu/cmu/tetrad/bayes/MlBayesIm.java
index 9f5ceaadb6..4d2a6be550 100644
--- a/tetrad-lib/src/main/java/edu/cmu/tetrad/bayes/MlBayesIm.java
+++ b/tetrad-lib/src/main/java/edu/cmu/tetrad/bayes/MlBayesIm.java
@@ -1398,6 +1398,12 @@ private void copyValuesFromOldToNew(int oldNodeIndex, int oldRowIndex,
         }
     }
 
+    /**
+     * Writes the object to the specified ObjectOutputStream.
+     *
+     * @param out The ObjectOutputStream to write the object to.
+     * @throws IOException If an I/O error occurs.
+     */
     @Serial
     private void writeObject(ObjectOutputStream out) throws IOException {
         try {
@@ -1409,6 +1415,14 @@ private void writeObject(ObjectOutputStream out) throws IOException {
         }
     }
 
+    /**
+     * Reads the object from the specified ObjectInputStream. This method is used during deserialization
+     * to restore the state of the object.
+     *
+     * @param in The ObjectInputStream to read the object from.
+     * @throws IOException            If an I/O error occurs.
+     * @throws ClassNotFoundException If the class of the serialized object cannot be found.
+     */
     @Serial
     private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
         try {
diff --git a/tetrad-lib/src/main/java/edu/cmu/tetrad/bayes/MlBayesImObs.java b/tetrad-lib/src/main/java/edu/cmu/tetrad/bayes/MlBayesImObs.java
index 3126f1a29b..664d1b9ae0 100644
--- a/tetrad-lib/src/main/java/edu/cmu/tetrad/bayes/MlBayesImObs.java
+++ b/tetrad-lib/src/main/java/edu/cmu/tetrad/bayes/MlBayesImObs.java
@@ -1196,6 +1196,12 @@ private void initializeNode(int nodeIndex) {
 
     }
 
+    /**
+     * Writes the object to the specified ObjectOutputStream.
+     *
+     * @param out The ObjectOutputStream to write the object to.
+     * @throws IOException If an I/O error occurs.
+     */
     @Serial
     private void writeObject(ObjectOutputStream out) throws IOException {
         try {
@@ -1207,6 +1213,14 @@ private void writeObject(ObjectOutputStream out) throws IOException {
         }
     }
 
+    /**
+     * Reads the object from the specified ObjectInputStream. This method is used during deserialization
+     * to restore the state of the object.
+     *
+     * @param in The ObjectInputStream to read the object from.
+     * @throws IOException            If an I/O error occurs.
+     * @throws ClassNotFoundException If the class of the serialized object cannot be found.
+     */
     @Serial
     private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
         try {
diff --git a/tetrad-lib/src/main/java/edu/cmu/tetrad/bayes/Proposition.java b/tetrad-lib/src/main/java/edu/cmu/tetrad/bayes/Proposition.java
index 3e35240487..51c57fc54c 100755
--- a/tetrad-lib/src/main/java/edu/cmu/tetrad/bayes/Proposition.java
+++ b/tetrad-lib/src/main/java/edu/cmu/tetrad/bayes/Proposition.java
@@ -535,6 +535,12 @@ private int getMaxNumCategories() {
         return max;
     }
 
+    /**
+     * Writes the object to the specified ObjectOutputStream.
+     *
+     * @param out The ObjectOutputStream to write the object to.
+     * @throws IOException If an I/O error occurs.
+     */
     @Serial
     private void writeObject(ObjectOutputStream out) throws IOException {
         try {
@@ -546,6 +552,14 @@ private void writeObject(ObjectOutputStream out) throws IOException {
         }
     }
 
+    /**
+     * Reads the object from the specified ObjectInputStream. This method is used during deserialization
+     * to restore the state of the object.
+     *
+     * @param in The ObjectInputStream to read the object from.
+     * @throws IOException            If an I/O error occurs.
+     * @throws ClassNotFoundException If the class of the serialized object cannot be found.
+     */
     @Serial
     private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
         try {
diff --git a/tetrad-lib/src/main/java/edu/cmu/tetrad/bayes/StoredCellProbs.java b/tetrad-lib/src/main/java/edu/cmu/tetrad/bayes/StoredCellProbs.java
index 3f340492b0..3575057cd9 100755
--- a/tetrad-lib/src/main/java/edu/cmu/tetrad/bayes/StoredCellProbs.java
+++ b/tetrad-lib/src/main/java/edu/cmu/tetrad/bayes/StoredCellProbs.java
@@ -407,6 +407,12 @@ private void setCellProbability(int[] variableValues, double probability) {
         this.probs[getOffset(variableValues)] = probability;
     }
 
+    /**
+     * Writes the object to the specified ObjectOutputStream.
+     *
+     * @param out The ObjectOutputStream to write the object to.
+     * @throws IOException If an I/O error occurs.
+     */
     @Serial
     private void writeObject(ObjectOutputStream out) throws IOException {
         try {
@@ -418,6 +424,14 @@ private void writeObject(ObjectOutputStream out) throws IOException {
         }
     }
 
+    /**
+     * Reads the object from the specified ObjectInputStream. This method is used during deserialization
+     * to restore the state of the object.
+     *
+     * @param in The ObjectInputStream to read the object from.
+     * @throws IOException            If an I/O error occurs.
+     * @throws ClassNotFoundException If the class of the serialized object cannot be found.
+     */
     @Serial
     private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
         try {
diff --git a/tetrad-lib/src/main/java/edu/cmu/tetrad/data/BoxDataSet.java b/tetrad-lib/src/main/java/edu/cmu/tetrad/data/BoxDataSet.java
index ac017bed50..13d280404b 100644
--- a/tetrad-lib/src/main/java/edu/cmu/tetrad/data/BoxDataSet.java
+++ b/tetrad-lib/src/main/java/edu/cmu/tetrad/data/BoxDataSet.java
@@ -166,6 +166,12 @@ public static BoxDataSet serializableInstance() {
         return new BoxDataSet(new ShortDataBox(4, 4), vars);
     }
 
+    /**
+     * Writes the object to the specified ObjectOutputStream.
+     *
+     * @param out The ObjectOutputStream to write the object to.
+     * @throws IOException If an I/O error occurs.
+     */
     @Serial
     private void writeObject(ObjectOutputStream out) throws IOException {
         try {
@@ -177,6 +183,14 @@ private void writeObject(ObjectOutputStream out) throws IOException {
         }
     }
 
+    /**
+     * Reads the object from the specified ObjectInputStream. This method is used during deserialization
+     * to restore the state of the object.
+     *
+     * @param in The ObjectInputStream to read the object from.
+     * @throws IOException            If an I/O error occurs.
+     * @throws ClassNotFoundException If the class of the serialized object cannot be found.
+     */
     @Serial
     private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
         try {
diff --git a/tetrad-lib/src/main/java/edu/cmu/tetrad/data/Clusters.java b/tetrad-lib/src/main/java/edu/cmu/tetrad/data/Clusters.java
index 29a1af20e7..9155ba5916 100644
--- a/tetrad-lib/src/main/java/edu/cmu/tetrad/data/Clusters.java
+++ b/tetrad-lib/src/main/java/edu/cmu/tetrad/data/Clusters.java
@@ -323,6 +323,12 @@ private int numClustersStored() {
         return max;
     }
 
+    /**
+     * Writes the object to the specified ObjectOutputStream.
+     *
+     * @param out The ObjectOutputStream to write the object to.
+     * @throws IOException If an I/O error occurs.
+     */
     @Serial
     private void writeObject(ObjectOutputStream out) throws IOException {
         try {
@@ -334,6 +340,14 @@ private void writeObject(ObjectOutputStream out) throws IOException {
         }
     }
 
+    /**
+     * Reads the object from the specified ObjectInputStream. This method is used during deserialization
+     * to restore the state of the object.
+     *
+     * @param in The ObjectInputStream to read the object from.
+     * @throws IOException            If an I/O error occurs.
+     * @throws ClassNotFoundException If the class of the serialized object cannot be found.
+     */
     @Serial
     private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
         try {
diff --git a/tetrad-lib/src/main/java/edu/cmu/tetrad/data/ContinuousDiscretizationSpec.java b/tetrad-lib/src/main/java/edu/cmu/tetrad/data/ContinuousDiscretizationSpec.java
index 7ae03427ff..23ecb5c162 100644
--- a/tetrad-lib/src/main/java/edu/cmu/tetrad/data/ContinuousDiscretizationSpec.java
+++ b/tetrad-lib/src/main/java/edu/cmu/tetrad/data/ContinuousDiscretizationSpec.java
@@ -154,6 +154,12 @@ public double[] getBreakpoints() {
         return this.breakpoints;
     }
 
+    /**
+     * Writes the object to the specified ObjectOutputStream.
+     *
+     * @param out The ObjectOutputStream to write the object to.
+     * @throws IOException If an I/O error occurs.
+     */
     @Serial
     private void writeObject(ObjectOutputStream out) throws IOException {
         try {
@@ -165,6 +171,14 @@ private void writeObject(ObjectOutputStream out) throws IOException {
         }
     }
 
+    /**
+     * Reads the object from the specified ObjectInputStream. This method is used during deserialization
+     * to restore the state of the object.
+     *
+     * @param in The ObjectInputStream to read the object from.
+     * @throws IOException            If an I/O error occurs.
+     * @throws ClassNotFoundException If the class of the serialized object cannot be found.
+     */
     @Serial
     private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
         try {
diff --git a/tetrad-lib/src/main/java/edu/cmu/tetrad/data/ContinuousVariable.java b/tetrad-lib/src/main/java/edu/cmu/tetrad/data/ContinuousVariable.java
index 313d49f5a6..e94af1b0a3 100644
--- a/tetrad-lib/src/main/java/edu/cmu/tetrad/data/ContinuousVariable.java
+++ b/tetrad-lib/src/main/java/edu/cmu/tetrad/data/ContinuousVariable.java
@@ -286,6 +286,12 @@ private PropertyChangeSupport getPcs() {
         return this.pcs;
     }
 
+    /**
+     * Writes the object to the specified ObjectOutputStream.
+     *
+     * @param out The ObjectOutputStream to write the object to.
+     * @throws IOException If an I/O error occurs.
+     */
     @Serial
     private void writeObject(ObjectOutputStream out) throws IOException {
         try {
@@ -297,6 +303,14 @@ private void writeObject(ObjectOutputStream out) throws IOException {
         }
     }
 
+    /**
+     * Reads the object from the specified ObjectInputStream. This method is used during deserialization
+     * to restore the state of the object.
+     *
+     * @param in The ObjectInputStream to read the object from.
+     * @throws IOException            If an I/O error occurs.
+     * @throws ClassNotFoundException If the class of the serialized object cannot be found.
+     */
     @Serial
     private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
         try {
diff --git a/tetrad-lib/src/main/java/edu/cmu/tetrad/data/CorrelationMatrixOnTheFly.java b/tetrad-lib/src/main/java/edu/cmu/tetrad/data/CorrelationMatrixOnTheFly.java
index b794ca75a1..eb6152efdb 100644
--- a/tetrad-lib/src/main/java/edu/cmu/tetrad/data/CorrelationMatrixOnTheFly.java
+++ b/tetrad-lib/src/main/java/edu/cmu/tetrad/data/CorrelationMatrixOnTheFly.java
@@ -442,6 +442,12 @@ public void removeVariables(List<String> remaining) {
         this.cov.removeVariables(remaining);
     }
 
+    /**
+     * Writes the object to the specified ObjectOutputStream.
+     *
+     * @param out The ObjectOutputStream to write the object to.
+     * @throws IOException If an I/O error occurs.
+     */
     @Serial
     private void writeObject(ObjectOutputStream out) throws IOException {
         try {
@@ -453,6 +459,14 @@ private void writeObject(ObjectOutputStream out) throws IOException {
         }
     }
 
+    /**
+     * Reads the object from the specified ObjectInputStream. This method is used during deserialization
+     * to restore the state of the object.
+     *
+     * @param in The ObjectInputStream to read the object from.
+     * @throws IOException            If an I/O error occurs.
+     * @throws ClassNotFoundException If the class of the serialized object cannot be found.
+     */
     @Serial
     private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
         try {
diff --git a/tetrad-lib/src/main/java/edu/cmu/tetrad/data/CovarianceMatrix.java b/tetrad-lib/src/main/java/edu/cmu/tetrad/data/CovarianceMatrix.java
index 85788530c4..bae830f798 100644
--- a/tetrad-lib/src/main/java/edu/cmu/tetrad/data/CovarianceMatrix.java
+++ b/tetrad-lib/src/main/java/edu/cmu/tetrad/data/CovarianceMatrix.java
@@ -560,6 +560,12 @@ private Set<Node> getSelectedVariables() {
         return this.selectedVariables;
     }
 
+    /**
+     * Writes the object to the specified ObjectOutputStream.
+     *
+     * @param out The ObjectOutputStream to write the object to.
+     * @throws IOException If an I/O error occurs.
+     */
     @Serial
     private void writeObject(ObjectOutputStream out) throws IOException {
         try {
@@ -571,6 +577,14 @@ private void writeObject(ObjectOutputStream out) throws IOException {
         }
     }
 
+    /**
+     * Reads the object from the specified ObjectInputStream. This method is used during deserialization
+     * to restore the state of the object.
+     *
+     * @param in The ObjectInputStream to read the object from.
+     * @throws IOException            If an I/O error occurs.
+     * @throws ClassNotFoundException If the class of the serialized object cannot be found.
+     */
     @Serial
     private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
         try {
diff --git a/tetrad-lib/src/main/java/edu/cmu/tetrad/data/CovarianceMatrixOnTheFly.java b/tetrad-lib/src/main/java/edu/cmu/tetrad/data/CovarianceMatrixOnTheFly.java
index 4d1fd07a7d..67753e8c81 100644
--- a/tetrad-lib/src/main/java/edu/cmu/tetrad/data/CovarianceMatrixOnTheFly.java
+++ b/tetrad-lib/src/main/java/edu/cmu/tetrad/data/CovarianceMatrixOnTheFly.java
@@ -859,6 +859,12 @@ private void checkMatrix() {
         }
     }
 
+    /**
+     * Writes the object to the specified ObjectOutputStream.
+     *
+     * @param out The ObjectOutputStream to write the object to.
+     * @throws IOException If an I/O error occurs.
+     */
     @Serial
     private void writeObject(ObjectOutputStream out) throws IOException {
         try {
@@ -870,6 +876,14 @@ private void writeObject(ObjectOutputStream out) throws IOException {
         }
     }
 
+    /**
+     * Reads the object from the specified ObjectInputStream. This method is used during deserialization
+     * to restore the state of the object.
+     *
+     * @param in The ObjectInputStream to read the object from.
+     * @throws IOException            If an I/O error occurs.
+     * @throws ClassNotFoundException If the class of the serialized object cannot be found.
+     */
     @Serial
     private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
         try {
diff --git a/tetrad-lib/src/main/java/edu/cmu/tetrad/data/DataModelList.java b/tetrad-lib/src/main/java/edu/cmu/tetrad/data/DataModelList.java
index 0720eb8908..b7e46f98c3 100644
--- a/tetrad-lib/src/main/java/edu/cmu/tetrad/data/DataModelList.java
+++ b/tetrad-lib/src/main/java/edu/cmu/tetrad/data/DataModelList.java
@@ -347,6 +347,12 @@ public boolean equals(Object o) {
 
     }
 
+    /**
+     * Writes the object to the specified ObjectOutputStream.
+     *
+     * @param out The ObjectOutputStream to write the object to.
+     * @throws IOException If an I/O error occurs.
+     */
     @Serial
     private void writeObject(ObjectOutputStream out) throws IOException {
         try {
@@ -358,6 +364,14 @@ private void writeObject(ObjectOutputStream out) throws IOException {
         }
     }
 
+    /**
+     * Reads the object from the specified ObjectInputStream. This method is used during deserialization
+     * to restore the state of the object.
+     *
+     * @param in The ObjectInputStream to read the object from.
+     * @throws IOException            If an I/O error occurs.
+     * @throws ClassNotFoundException If the class of the serialized object cannot be found.
+     */
     @Serial
     private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
         try {
diff --git a/tetrad-lib/src/main/java/edu/cmu/tetrad/data/DelimiterType.java b/tetrad-lib/src/main/java/edu/cmu/tetrad/data/DelimiterType.java
index ff07ae7501..b57c2c29aa 100644
--- a/tetrad-lib/src/main/java/edu/cmu/tetrad/data/DelimiterType.java
+++ b/tetrad-lib/src/main/java/edu/cmu/tetrad/data/DelimiterType.java
@@ -119,6 +119,12 @@ Object readResolve() throws ObjectStreamException {
         return DelimiterType.TYPES[this.ordinal]; // Canonicalize.
     }
 
+    /**
+     * Writes the object to the specified ObjectOutputStream.
+     *
+     * @param out The ObjectOutputStream to write the object to.
+     * @throws IOException If an I/O error occurs.
+     */
     @Serial
     private void writeObject(ObjectOutputStream out) throws IOException {
         try {
@@ -130,6 +136,14 @@ private void writeObject(ObjectOutputStream out) throws IOException {
         }
     }
 
+    /**
+     * Reads the object from the specified ObjectInputStream. This method is used during deserialization
+     * to restore the state of the object.
+     *
+     * @param in The ObjectInputStream to read the object from.
+     * @throws IOException            If an I/O error occurs.
+     * @throws ClassNotFoundException If the class of the serialized object cannot be found.
+     */
     @Serial
     private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
         try {
diff --git a/tetrad-lib/src/main/java/edu/cmu/tetrad/data/DiscreteDiscretizationSpec.java b/tetrad-lib/src/main/java/edu/cmu/tetrad/data/DiscreteDiscretizationSpec.java
index 6d2a516bba..311b178251 100644
--- a/tetrad-lib/src/main/java/edu/cmu/tetrad/data/DiscreteDiscretizationSpec.java
+++ b/tetrad-lib/src/main/java/edu/cmu/tetrad/data/DiscreteDiscretizationSpec.java
@@ -101,6 +101,12 @@ public int[] getRemap() {
         return this.remap;
     }
 
+    /**
+     * Writes the object to the specified ObjectOutputStream.
+     *
+     * @param out The ObjectOutputStream to write the object to.
+     * @throws IOException If an I/O error occurs.
+     */
     @Serial
     private void writeObject(ObjectOutputStream out) throws IOException {
         try {
@@ -112,6 +118,14 @@ private void writeObject(ObjectOutputStream out) throws IOException {
         }
     }
 
+    /**
+     * Reads the object from the specified ObjectInputStream. This method is used during deserialization
+     * to restore the state of the object.
+     *
+     * @param in The ObjectInputStream to read the object from.
+     * @throws IOException            If an I/O error occurs.
+     * @throws ClassNotFoundException If the class of the serialized object cannot be found.
+     */
     @Serial
     private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
         try {
diff --git a/tetrad-lib/src/main/java/edu/cmu/tetrad/data/DiscreteVariable.java b/tetrad-lib/src/main/java/edu/cmu/tetrad/data/DiscreteVariable.java
index a44f180bcf..5c7040bec0 100644
--- a/tetrad-lib/src/main/java/edu/cmu/tetrad/data/DiscreteVariable.java
+++ b/tetrad-lib/src/main/java/edu/cmu/tetrad/data/DiscreteVariable.java
@@ -504,6 +504,12 @@ private PropertyChangeSupport getPcs() {
         return this.pcs;
     }
 
+    /**
+     * Writes the object to the specified ObjectOutputStream.
+     *
+     * @param out The ObjectOutputStream to write the object to.
+     * @throws IOException If an I/O error occurs.
+     */
     @Serial
     private void writeObject(ObjectOutputStream out) throws IOException {
         try {
@@ -515,6 +521,14 @@ private void writeObject(ObjectOutputStream out) throws IOException {
         }
     }
 
+    /**
+     * Reads the object from the specified ObjectInputStream. This method is used during deserialization
+     * to restore the state of the object.
+     *
+     * @param in The ObjectInputStream to read the object from.
+     * @throws IOException            If an I/O error occurs.
+     * @throws ClassNotFoundException If the class of the serialized object cannot be found.
+     */
     @Serial
     private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
         try {
diff --git a/tetrad-lib/src/main/java/edu/cmu/tetrad/data/DiscreteVariableType.java b/tetrad-lib/src/main/java/edu/cmu/tetrad/data/DiscreteVariableType.java
index 9d83f4adf3..6d8f4bf892 100755
--- a/tetrad-lib/src/main/java/edu/cmu/tetrad/data/DiscreteVariableType.java
+++ b/tetrad-lib/src/main/java/edu/cmu/tetrad/data/DiscreteVariableType.java
@@ -102,6 +102,12 @@ Object readResolve() throws ObjectStreamException {
         return DiscreteVariableType.TYPES[this.ordinal]; // Canonicalize.
     }
 
+    /**
+     * Writes the object to the specified ObjectOutputStream.
+     *
+     * @param out The ObjectOutputStream to write the object to.
+     * @throws IOException If an I/O error occurs.
+     */
     @Serial
     private void writeObject(ObjectOutputStream out) throws IOException {
         try {
@@ -113,6 +119,14 @@ private void writeObject(ObjectOutputStream out) throws IOException {
         }
     }
 
+    /**
+     * Reads the object from the specified ObjectInputStream. This method is used during deserialization
+     * to restore the state of the object.
+     *
+     * @param in The ObjectInputStream to read the object from.
+     * @throws IOException            If an I/O error occurs.
+     * @throws ClassNotFoundException If the class of the serialized object cannot be found.
+     */
     @Serial
     private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
         try {
diff --git a/tetrad-lib/src/main/java/edu/cmu/tetrad/data/KnowledgeEdge.java b/tetrad-lib/src/main/java/edu/cmu/tetrad/data/KnowledgeEdge.java
index 29ea7b7469..8bf9585914 100644
--- a/tetrad-lib/src/main/java/edu/cmu/tetrad/data/KnowledgeEdge.java
+++ b/tetrad-lib/src/main/java/edu/cmu/tetrad/data/KnowledgeEdge.java
@@ -127,6 +127,12 @@ public String toString() {
         return this.from + "-->" + this.to;
     }
 
+    /**
+     * Writes the object to the specified ObjectOutputStream.
+     *
+     * @param out The ObjectOutputStream to write the object to.
+     * @throws IOException If an I/O error occurs.
+     */
     @Serial
     private void writeObject(ObjectOutputStream out) throws IOException {
         try {
@@ -138,6 +144,14 @@ private void writeObject(ObjectOutputStream out) throws IOException {
         }
     }
 
+    /**
+     * Reads the object from the specified ObjectInputStream. This method is used during deserialization
+     * to restore the state of the object.
+     *
+     * @param in The ObjectInputStream to read the object from.
+     * @throws IOException            If an I/O error occurs.
+     * @throws ClassNotFoundException If the class of the serialized object cannot be found.
+     */
     @Serial
     private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
         try {
diff --git a/tetrad-lib/src/main/java/edu/cmu/tetrad/data/KnowledgeGroup.java b/tetrad-lib/src/main/java/edu/cmu/tetrad/data/KnowledgeGroup.java
index 2618bae63b..8dbe5c6d4d 100644
--- a/tetrad-lib/src/main/java/edu/cmu/tetrad/data/KnowledgeGroup.java
+++ b/tetrad-lib/src/main/java/edu/cmu/tetrad/data/KnowledgeGroup.java
@@ -223,6 +223,12 @@ public boolean equals(Object o) {
 
     }
 
+    /**
+     * Writes the object to the specified ObjectOutputStream.
+     *
+     * @param out The ObjectOutputStream to write the object to.
+     * @throws IOException If an I/O error occurs.
+     */
     @Serial
     private void writeObject(ObjectOutputStream out) throws IOException {
         try {
@@ -234,6 +240,14 @@ private void writeObject(ObjectOutputStream out) throws IOException {
         }
     }
 
+    /**
+     * Reads the object from the specified ObjectInputStream. This method is used during deserialization
+     * to restore the state of the object.
+     *
+     * @param in The ObjectInputStream to read the object from.
+     * @throws IOException            If an I/O error occurs.
+     * @throws ClassNotFoundException If the class of the serialized object cannot be found.
+     */
     @Serial
     private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
         try {
diff --git a/tetrad-lib/src/main/java/edu/cmu/tetrad/data/NumberObjectDataSet.java b/tetrad-lib/src/main/java/edu/cmu/tetrad/data/NumberObjectDataSet.java
index f75055fdce..2091a61fc5 100644
--- a/tetrad-lib/src/main/java/edu/cmu/tetrad/data/NumberObjectDataSet.java
+++ b/tetrad-lib/src/main/java/edu/cmu/tetrad/data/NumberObjectDataSet.java
@@ -182,6 +182,12 @@ public static NumberObjectDataSet serializableInstance() {
         return new NumberObjectDataSet(0, new LinkedList<>());
     }
 
+    /**
+     * Writes the object to the specified ObjectOutputStream.
+     *
+     * @param out The ObjectOutputStream to write the object to.
+     * @throws IOException If an I/O error occurs.
+     */
     @Serial
     private void writeObject(ObjectOutputStream out) throws IOException {
         try {
@@ -193,6 +199,14 @@ private void writeObject(ObjectOutputStream out) throws IOException {
         }
     }
 
+    /**
+     * Reads the object from the specified ObjectInputStream. This method is used during deserialization
+     * to restore the state of the object.
+     *
+     * @param in The ObjectInputStream to read the object from.
+     * @throws IOException            If an I/O error occurs.
+     * @throws ClassNotFoundException If the class of the serialized object cannot be found.
+     */
     @Serial
     private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
         try {
diff --git a/tetrad-lib/src/main/java/edu/cmu/tetrad/data/SplitCasesSpec.java b/tetrad-lib/src/main/java/edu/cmu/tetrad/data/SplitCasesSpec.java
index f5d810bc81..f8f4fc78d7 100644
--- a/tetrad-lib/src/main/java/edu/cmu/tetrad/data/SplitCasesSpec.java
+++ b/tetrad-lib/src/main/java/edu/cmu/tetrad/data/SplitCasesSpec.java
@@ -100,6 +100,12 @@ public int[] getBreakpoints() {
         return this.breakpoints;
     }
 
+    /**
+     * Writes the object to the specified ObjectOutputStream.
+     *
+     * @param out The ObjectOutputStream to write the object to.
+     * @throws IOException If an I/O error occurs.
+     */
     @Serial
     private void writeObject(ObjectOutputStream out) throws IOException {
         try {
@@ -111,6 +117,14 @@ private void writeObject(ObjectOutputStream out) throws IOException {
         }
     }
 
+    /**
+     * Reads the object from the specified ObjectInputStream. This method is used during deserialization
+     * to restore the state of the object.
+     *
+     * @param in The ObjectInputStream to read the object from.
+     * @throws IOException            If an I/O error occurs.
+     * @throws ClassNotFoundException If the class of the serialized object cannot be found.
+     */
     @Serial
     private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
         try {
diff --git a/tetrad-lib/src/main/java/edu/cmu/tetrad/data/TimeSeriesData.java b/tetrad-lib/src/main/java/edu/cmu/tetrad/data/TimeSeriesData.java
index 2f2fc01cf8..b675dc43a5 100644
--- a/tetrad-lib/src/main/java/edu/cmu/tetrad/data/TimeSeriesData.java
+++ b/tetrad-lib/src/main/java/edu/cmu/tetrad/data/TimeSeriesData.java
@@ -248,6 +248,12 @@ public double getDatum(int row, int col) {
         return this.data2.get(row, col);
     }
 
+    /**
+     * Writes the object to the specified ObjectOutputStream.
+     *
+     * @param out The ObjectOutputStream to write the object to.
+     * @throws IOException If an I/O error occurs.
+     */
     @Serial
     private void writeObject(ObjectOutputStream out) throws IOException {
         try {
@@ -259,6 +265,14 @@ private void writeObject(ObjectOutputStream out) throws IOException {
         }
     }
 
+    /**
+     * Reads the object from the specified ObjectInputStream. This method is used during deserialization
+     * to restore the state of the object.
+     *
+     * @param in The ObjectInputStream to read the object from.
+     * @throws IOException            If an I/O error occurs.
+     * @throws ClassNotFoundException If the class of the serialized object cannot be found.
+     */
     @Serial
     private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
         try {
diff --git a/tetrad-lib/src/main/java/edu/cmu/tetrad/graph/Edge.java b/tetrad-lib/src/main/java/edu/cmu/tetrad/graph/Edge.java
index 732bd4d4a8..75d793d5f3 100644
--- a/tetrad-lib/src/main/java/edu/cmu/tetrad/graph/Edge.java
+++ b/tetrad-lib/src/main/java/edu/cmu/tetrad/graph/Edge.java
@@ -457,6 +457,12 @@ private boolean pointingLeft(Endpoint endpoint1, Endpoint endpoint2) {
 
     // ===========================PRIVATE METHODS===========================//
 
+    /**
+     * Writes the object to the specified ObjectOutputStream.
+     *
+     * @param out The ObjectOutputStream to write the object to.
+     * @throws IOException If an I/O error occurs.
+     */
     @Serial
     private void writeObject(ObjectOutputStream out) throws IOException {
         try {
@@ -468,6 +474,14 @@ private void writeObject(ObjectOutputStream out) throws IOException {
         }
     }
 
+    /**
+     * Reads the object from the specified ObjectInputStream. This method is used during deserialization
+     * to restore the state of the object.
+     *
+     * @param in The ObjectInputStream to read the object from.
+     * @throws IOException            If an I/O error occurs.
+     * @throws ClassNotFoundException If the class of the serialized object cannot be found.
+     */
     @Serial
     private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
         try {
diff --git a/tetrad-lib/src/main/java/edu/cmu/tetrad/graph/EdgeTypeProbability.java b/tetrad-lib/src/main/java/edu/cmu/tetrad/graph/EdgeTypeProbability.java
index 5dd7515568..467e1e99c5 100644
--- a/tetrad-lib/src/main/java/edu/cmu/tetrad/graph/EdgeTypeProbability.java
+++ b/tetrad-lib/src/main/java/edu/cmu/tetrad/graph/EdgeTypeProbability.java
@@ -178,6 +178,12 @@ public enum EdgeType {
         tt
     }
 
+    /**
+     * Writes the object to the specified ObjectOutputStream.
+     *
+     * @param out The ObjectOutputStream to write the object to.
+     * @throws IOException If an I/O error occurs.
+     */
     @Serial
     private void writeObject(ObjectOutputStream out) throws IOException {
         try {
@@ -189,6 +195,14 @@ private void writeObject(ObjectOutputStream out) throws IOException {
         }
     }
 
+    /**
+     * Reads the object from the specified ObjectInputStream. This method is used during deserialization
+     * to restore the state of the object.
+     *
+     * @param in The ObjectInputStream to read the object from.
+     * @throws IOException            If an I/O error occurs.
+     * @throws ClassNotFoundException If the class of the serialized object cannot be found.
+     */
     @Serial
     private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
         try {
diff --git a/tetrad-lib/src/main/java/edu/cmu/tetrad/graph/Endpoint.java b/tetrad-lib/src/main/java/edu/cmu/tetrad/graph/Endpoint.java
index ab1703fdf6..2ebb92026d 100644
--- a/tetrad-lib/src/main/java/edu/cmu/tetrad/graph/Endpoint.java
+++ b/tetrad-lib/src/main/java/edu/cmu/tetrad/graph/Endpoint.java
@@ -67,6 +67,12 @@ public enum Endpoint implements TetradSerializable {
      */
     private static final long serialVersionUID = 23L;
 
+    /**
+     * Writes the object to the specified ObjectOutputStream.
+     *
+     * @param out The ObjectOutputStream to write the object to.
+     * @throws IOException If an I/O error occurs.
+     */
     @Serial
     private void writeObject(ObjectOutputStream out) throws IOException {
         try {
@@ -78,6 +84,14 @@ private void writeObject(ObjectOutputStream out) throws IOException {
         }
     }
 
+    /**
+     * Reads the object from the specified ObjectInputStream. This method is used during deserialization
+     * to restore the state of the object.
+     *
+     * @param in The ObjectInputStream to read the object from.
+     * @throws IOException            If an I/O error occurs.
+     * @throws ClassNotFoundException If the class of the serialized object cannot be found.
+     */
     @Serial
     private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
         try {
diff --git a/tetrad-lib/src/main/java/edu/cmu/tetrad/graph/IndependenceFact.java b/tetrad-lib/src/main/java/edu/cmu/tetrad/graph/IndependenceFact.java
index 440e6b0d6c..f0ece5871c 100644
--- a/tetrad-lib/src/main/java/edu/cmu/tetrad/graph/IndependenceFact.java
+++ b/tetrad-lib/src/main/java/edu/cmu/tetrad/graph/IndependenceFact.java
@@ -253,6 +253,12 @@ public int compareTo(IndependenceFact fact) {
         return 0;
     }
 
+    /**
+     * Writes the object to the specified ObjectOutputStream.
+     *
+     * @param out The ObjectOutputStream to write the object to.
+     * @throws IOException If an I/O error occurs.
+     */
     @Serial
     private void writeObject(ObjectOutputStream out) throws IOException {
         try {
@@ -264,6 +270,14 @@ private void writeObject(ObjectOutputStream out) throws IOException {
         }
     }
 
+    /**
+     * Reads the object from the specified ObjectInputStream. This method is used during deserialization
+     * to restore the state of the object.
+     *
+     * @param in The ObjectInputStream to read the object from.
+     * @throws IOException            If an I/O error occurs.
+     * @throws ClassNotFoundException If the class of the serialized object cannot be found.
+     */
     @Serial
     private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
         try {
diff --git a/tetrad-lib/src/main/java/edu/cmu/tetrad/graph/OrderedPair.java b/tetrad-lib/src/main/java/edu/cmu/tetrad/graph/OrderedPair.java
index 4e1e3ddc80..bc7ef87d6a 100644
--- a/tetrad-lib/src/main/java/edu/cmu/tetrad/graph/OrderedPair.java
+++ b/tetrad-lib/src/main/java/edu/cmu/tetrad/graph/OrderedPair.java
@@ -116,6 +116,12 @@ public String toString() {
         return "<" + this.first + ", " + this.second + ">";
     }
 
+    /**
+     * Writes the object to the specified ObjectOutputStream.
+     *
+     * @param out The ObjectOutputStream to write the object to.
+     * @throws IOException If an I/O error occurs.
+     */
     @Serial
     private void writeObject(ObjectOutputStream out) throws IOException {
         try {
@@ -127,6 +133,14 @@ private void writeObject(ObjectOutputStream out) throws IOException {
         }
     }
 
+    /**
+     * Reads the object from the specified ObjectInputStream. This method is used during deserialization
+     * to restore the state of the object.
+     *
+     * @param in The ObjectInputStream to read the object from.
+     * @throws IOException            If an I/O error occurs.
+     * @throws ClassNotFoundException If the class of the serialized object cannot be found.
+     */
     @Serial
     private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
         try {
diff --git a/tetrad-lib/src/main/java/edu/cmu/tetrad/graph/Paths.java b/tetrad-lib/src/main/java/edu/cmu/tetrad/graph/Paths.java
index 347a6327d4..098f9c2297 100644
--- a/tetrad-lib/src/main/java/edu/cmu/tetrad/graph/Paths.java
+++ b/tetrad-lib/src/main/java/edu/cmu/tetrad/graph/Paths.java
@@ -2605,6 +2605,12 @@ private static Set<Integer> union(Set<Integer> set, int element) {
         }
     }
 
+    /**
+     * Writes the object to the specified ObjectOutputStream.
+     *
+     * @param out The ObjectOutputStream to write the object to.
+     * @throws IOException If an I/O error occurs.
+     */
     @Serial
     private void writeObject(ObjectOutputStream out) throws IOException {
         try {
@@ -2616,6 +2622,14 @@ private void writeObject(ObjectOutputStream out) throws IOException {
         }
     }
 
+    /**
+     * Reads the object from the specified ObjectInputStream. This method is used during deserialization
+     * to restore the state of the object.
+     *
+     * @param in The ObjectInputStream to read the object from.
+     * @throws IOException            If an I/O error occurs.
+     * @throws ClassNotFoundException If the class of the serialized object cannot be found.
+     */
     @Serial
     private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
         try {
diff --git a/tetrad-lib/src/main/java/edu/cmu/tetrad/graph/Triple.java b/tetrad-lib/src/main/java/edu/cmu/tetrad/graph/Triple.java
index ed70040453..bf483f8b54 100644
--- a/tetrad-lib/src/main/java/edu/cmu/tetrad/graph/Triple.java
+++ b/tetrad-lib/src/main/java/edu/cmu/tetrad/graph/Triple.java
@@ -175,6 +175,12 @@ public boolean alongPathIn(Graph graph) {
         return graph.isAdjacentTo(this.x, this.y) && graph.isAdjacentTo(this.y, this.z) && this.x != this.z;
     }
 
+    /**
+     * Writes the object to the specified ObjectOutputStream.
+     *
+     * @param out The ObjectOutputStream to write the object to.
+     * @throws IOException If an I/O error occurs.
+     */
     @Serial
     private void writeObject(ObjectOutputStream out) throws IOException {
         try {
@@ -186,6 +192,14 @@ private void writeObject(ObjectOutputStream out) throws IOException {
         }
     }
 
+    /**
+     * Reads the object from the specified ObjectInputStream. This method is used during deserialization
+     * to restore the state of the object.
+     *
+     * @param in The ObjectInputStream to read the object from.
+     * @throws IOException            If an I/O error occurs.
+     * @throws ClassNotFoundException If the class of the serialized object cannot be found.
+     */
     @Serial
     private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
         try {
diff --git a/tetrad-lib/src/main/java/edu/cmu/tetrad/regression/RegressionResult.java b/tetrad-lib/src/main/java/edu/cmu/tetrad/regression/RegressionResult.java
index 2591f7eeab..99107c80b8 100644
--- a/tetrad-lib/src/main/java/edu/cmu/tetrad/regression/RegressionResult.java
+++ b/tetrad-lib/src/main/java/edu/cmu/tetrad/regression/RegressionResult.java
@@ -358,6 +358,12 @@ public Vector getResiduals() {
         return this.res;
     }
 
+    /**
+     * Writes the object to the specified ObjectOutputStream.
+     *
+     * @param out The ObjectOutputStream to write the object to.
+     * @throws IOException If an I/O error occurs.
+     */
     @Serial
     private void writeObject(ObjectOutputStream out) throws IOException {
         try {
@@ -369,6 +375,14 @@ private void writeObject(ObjectOutputStream out) throws IOException {
         }
     }
 
+    /**
+     * Reads the object from the specified ObjectInputStream. This method is used during deserialization
+     * to restore the state of the object.
+     *
+     * @param in The ObjectInputStream to read the object from.
+     * @throws IOException            If an I/O error occurs.
+     * @throws ClassNotFoundException If the class of the serialized object cannot be found.
+     */
     @Serial
     private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
         try {
diff --git a/tetrad-lib/src/main/java/edu/cmu/tetrad/search/BFci.java b/tetrad-lib/src/main/java/edu/cmu/tetrad/search/BFci.java
index 782701621e..48705cc112 100644
--- a/tetrad-lib/src/main/java/edu/cmu/tetrad/search/BFci.java
+++ b/tetrad-lib/src/main/java/edu/cmu/tetrad/search/BFci.java
@@ -281,6 +281,8 @@ public void setDoDiscriminatingPathTailRule(boolean doDiscriminatingPathTailRule
 
     /**
      * Sets whether the discriminating path collider rule should be used.
+     *
+     * @param doDiscriminatingPathColliderRule True if the discriminating path collider rule should be used, false.
      */
     public void setDoDiscriminatingPathColliderRule(boolean doDiscriminatingPathColliderRule) {
         this.doDiscriminatingPathColliderRule = doDiscriminatingPathColliderRule;
diff --git a/tetrad-lib/src/main/java/edu/cmu/tetrad/search/Cstar.java b/tetrad-lib/src/main/java/edu/cmu/tetrad/search/Cstar.java
index d4a3d8e2b0..bcc0ff5b42 100644
--- a/tetrad-lib/src/main/java/edu/cmu/tetrad/search/Cstar.java
+++ b/tetrad-lib/src/main/java/edu/cmu/tetrad/search/Cstar.java
@@ -1038,6 +1038,12 @@ public double getMinBeta() {
         }
     }
 
+    /**
+     * Writes the object to the specified ObjectOutputStream.
+     *
+     * @param out The ObjectOutputStream to write the object to.
+     * @throws IOException If an I/O error occurs.
+     */
     @Serial
     private void writeObject(ObjectOutputStream out) throws IOException {
         try {
@@ -1049,6 +1055,14 @@ private void writeObject(ObjectOutputStream out) throws IOException {
         }
     }
 
+    /**
+     * Reads the object from the specified ObjectInputStream. This method is used during deserialization
+     * to restore the state of the object.
+     *
+     * @param in The ObjectInputStream to read the object from.
+     * @throws IOException            If an I/O error occurs.
+     * @throws ClassNotFoundException If the class of the serialized object cannot be found.
+     */
     @Serial
     private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
         try {
diff --git a/tetrad-lib/src/main/java/edu/cmu/tetrad/search/FciMax.java b/tetrad-lib/src/main/java/edu/cmu/tetrad/search/FciMax.java
index 3f3bc474c5..de8ab640c0 100644
--- a/tetrad-lib/src/main/java/edu/cmu/tetrad/search/FciMax.java
+++ b/tetrad-lib/src/main/java/edu/cmu/tetrad/search/FciMax.java
@@ -481,6 +481,11 @@ private void doNode(Graph graph, Map<Triple, Double> scores, Node b) {
         }
     }
 
+    /**
+     * Sets whether the discriminating path collider rule should be applied during the search.
+     *
+     * @param doDiscriminatingPathColliderRule True, if the rule should be applied. False otherwise.
+     */
     public void setDoDiscriminatingPathColliderRule(boolean doDiscriminatingPathColliderRule) {
         this.doDiscriminatingPathColliderRule = doDiscriminatingPathColliderRule;
     }
diff --git a/tetrad-lib/src/main/java/edu/cmu/tetrad/search/LvLite.java b/tetrad-lib/src/main/java/edu/cmu/tetrad/search/LvLite.java
index de42e400e0..bdaa237aa2 100644
--- a/tetrad-lib/src/main/java/edu/cmu/tetrad/search/LvLite.java
+++ b/tetrad-lib/src/main/java/edu/cmu/tetrad/search/LvLite.java
@@ -129,15 +129,20 @@ public LvLite(Score score) {
      * algorithm, and the graph is modified in place. The call to this method may be repeated to account for the
      * possibility that the removal of an edge may allow for further removals or orientations.
      *
-     * @param pag               The original graph.
-     * @param fciOrient         The orientation rules to be applied.
-     * @param best              The list of best nodes.
-     * @param scorer            The scorer used to evaluate edge orientations.
-     * @param equalityThreshold The threshold for equality. (This is not used for Oracle scoring.)
+     * @param pag                 The original graph.
+     * @param fciOrient           The orientation rules to be applied.
+     * @param best                The list of best nodes.
+     * @param scorer              The scorer used to evaluate edge orientations.
+     * @param unshieldedColliders The set of unshielded colliders.
+     * @param cpdag               The CPDAG.
+     * @param knowledge           The knowledge object.
+     * @param allowTucks          A boolean value indicating whether tucks are allowed.
+     * @param equalityThreshold   The threshold for equality. (This is not used for Oracle scoring.)
+     * @param verbose             A boolean value indicating whether verbose output should be printed.
      */
     public static void orientCollidersAndRemoveEdges(Graph pag, FciOrient fciOrient, List<Node> best, TeyssierScorer scorer,
-                                                        Set<Triple> unshieldedColliders, Graph cpdag, Knowledge knowledge,
-                                                        boolean allowTucks, boolean verbose, double equalityThreshold) {
+                                                     Set<Triple> unshieldedColliders, Graph cpdag, Knowledge knowledge,
+                                                     boolean allowTucks, boolean verbose, double equalityThreshold) {
         reorientWithCircles(pag, verbose);
         recallUnshieldedTriples(pag, unshieldedColliders, verbose);
 
@@ -189,9 +194,19 @@ public static void orientCollidersAndRemoveEdges(Graph pag, FciOrient fciOrient,
     /**
      * Determines the final orientation of the graph using the given FciOrient object, Graph object, and scorer object.
      *
-     * @param fciOrient The FciOrient object used to determine the final orientation.
-     * @param pag       The Graph object for which the final orientation is determined.
-     * @param scorer    The scorer object used in the score-based discriminating path rule.
+     * @param fciOrient                        The FciOrient object used to determine the final orientation.
+     * @param pag                              The Graph object for which the final orientation is determined.
+     * @param scorer                           The scorer object used in the score-based discriminating path rule.
+     * @param doDiscriminatingPathTailRule     A boolean value indicating whether the discriminating path tail rule
+     *                                         should be applied. If set to true, the discriminating path tail rule will
+     *                                         be applied. If set to false, the discriminating path tail rule will not
+     *                                         be applied.
+     * @param doDiscriminatingPathColliderRule A boolean value indicating whether the discriminating path collider rule
+     *                                         should be applied. If set to true, the discriminating path collider rule
+     *                                         will be applied. If set to false, the discriminating path collider rule
+     *                                         will not be applied.
+     * @param completeRuleSetUsed              A boolean value indicating whether the complete rule set should be used.
+     * @param verbose                          A boolean value indicating whether verbose output should be printed.
      */
     public static void finalOrientation(FciOrient fciOrient, Graph pag, TeyssierScorer scorer, boolean completeRuleSetUsed,
                                         boolean doDiscriminatingPathTailRule, boolean doDiscriminatingPathColliderRule, boolean verbose) {
@@ -864,7 +879,17 @@ public void setEqualityThreshold(double equalityThreshold) {
         this.equalityThreshold = equalityThreshold;
     }
 
+    /**
+     * Enumeration representing different start options.
+     */
     public enum START_WITH {
-        BOSS, GRASP
+        /**
+         * Start with BOSS.
+         */
+        BOSS,
+        /**
+         * Start with GRaSP.
+         */
+        GRASP
     }
 }
diff --git a/tetrad-lib/src/main/java/edu/cmu/tetrad/search/LvLiteDsepFriendly.java b/tetrad-lib/src/main/java/edu/cmu/tetrad/search/LvLiteDsepFriendly.java
index 49d6483283..73bdd23ee6 100644
--- a/tetrad-lib/src/main/java/edu/cmu/tetrad/search/LvLiteDsepFriendly.java
+++ b/tetrad-lib/src/main/java/edu/cmu/tetrad/search/LvLiteDsepFriendly.java
@@ -30,7 +30,10 @@
 import edu.cmu.tetrad.util.TetradLogger;
 import org.jetbrains.annotations.NotNull;
 
-import java.util.*;
+import java.util.ArrayList;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Set;
 
 /**
  * The LV-Lite algorithm implements the IGraphSearch interface and represents a search algorithm for learning the
@@ -47,14 +50,14 @@ public final class LvLiteDsepFriendly implements IGraphSearch {
      * hence it cannot be modified or accessed from outside the class where it is declared.
      */
     private final ArrayList<Node> variables;
-    /**
-     * Indicates whether to use Raskutti Uhler feature.
-     */
-    private boolean useRaskuttiUhler;
     /**
      * The independence test.
      */
     private final IndependenceTest test;
+    /**
+     * Indicates whether to use Raskutti Uhler feature.
+     */
+    private boolean useRaskuttiUhler;
     /**
      * The score.
      */
@@ -121,8 +124,8 @@ public final class LvLiteDsepFriendly implements IGraphSearch {
      */
     private int maxPathLength = -1;
     /**
-     * The equality threshold, a fraction of abs(BIC) used to determine equality of scores.
-     * This is not used for MSEP tests.
+     * The equality threshold, a fraction of abs(BIC) used to determine equality of scores. This is not used for MSEP
+     * tests.
      */
     private double equalityThreshold;
 
@@ -366,13 +369,20 @@ public void setMaxPathLength(int maxPathLength) {
         this.maxPathLength = maxPathLength;
     }
 
+    /**
+     * Sets whether internal randomness is allowed in the search algorithm.
+     *
+     * @param allowInternalRandomness true to allow internal randomness, false otherwise
+     */
     public void setAllowInternalRandomness(boolean allowInternalRandomness) {
         this.allowInternalRandomness = allowInternalRandomness;
     }
 
     /**
-     * The equality threshold, a fraction of abs(BIC) used to determine equality of scores.
-     * This is not used for MSEP tests.
+     * The equality threshold, a fraction of abs(BIC) used to determine equality of scores. This is not used for MSEP
+     * tests.
+     *
+     * @param equalityThreshold the equality threshold
      */
     public void setEqualityThreshold(double equalityThreshold) {
         this.equalityThreshold = equalityThreshold;
diff --git a/tetrad-lib/src/main/java/edu/cmu/tetrad/search/MarkovCheck.java b/tetrad-lib/src/main/java/edu/cmu/tetrad/search/MarkovCheck.java
index 0cd85ec0ee..b64b561f11 100644
--- a/tetrad-lib/src/main/java/edu/cmu/tetrad/search/MarkovCheck.java
+++ b/tetrad-lib/src/main/java/edu/cmu/tetrad/search/MarkovCheck.java
@@ -203,7 +203,7 @@ public AllSubsetsIndependenceFacts getAllSubsetsIndependenceFacts() {
                     Set<Node> z = GraphUtils.asSet(list, _other);
 
                     if (!checkNodeIndependenceAndConditioning(x, y, z)) {
-                         continue;
+                        continue;
                     }
 
                     IndependenceFact fact = new IndependenceFact(x, y, z);
@@ -271,10 +271,10 @@ public List<Double> getLocalPValues(IndependenceTest independenceTest, List<Inde
     /**
      * Get Local P values with shuffle threshold provided.
      *
-     * @param independenceTest
-     * @param facts
-     * @param shuffleThreshold
-     * @return
+     * @param independenceTest The independence test used for calculating the p-values.
+     * @param facts            The list of independence facts.
+     * @param shuffleThreshold The threshold value for shuffling the data.
+     * @return The list of local p-values.
      */
     public List<List<Double>> getLocalPValues(IndependenceTest independenceTest, List<IndependenceFact> facts, Double shuffleThreshold) {
         // Shuffle to generate more data from the same graph.
@@ -319,6 +319,7 @@ public Double checkAgainstAndersonDarlingTest(List<Double> pValues) {
      * @param independenceTest The independence test to be used for calculating p-values.
      * @param graph            The graph containing the nodes for testing.
      * @param threshold        The threshold value for classifying nodes.
+     * @param shuffleThreshold The threshold value for shuffling the data.
      * @return A list containing two lists: the first list contains the accepted nodes and the second list contains the
      * rejected nodes.
      */
@@ -355,12 +356,12 @@ public List<List<Node>> getAndersonDarlingTestAcceptsRejectsNodesForAllNodes(Ind
      * Confusion statistics were calculated using Adjacency (AdjacencyPrecision, AdjacencyRecall) and Arrowhead
      * (ArrowheadPrecision, ArrowheadRecall)
      *
-     * @param independenceTest
-     * @param estimatedCpdag
-     * @param trueGraph
-     * @param threshold
-     * @param shuffleThreshold
-     * @return
+     * @param independenceTest The independence test to be used for calculating p-values.
+     * @param estimatedCpdag   The estimated CPDAG.
+     * @param trueGraph        The true graph.
+     * @param threshold        The threshold value for classifying nodes.
+     * @param shuffleThreshold The threshold value for shuffling the data.
+     * @return A list containing two lists: the first list contains the accepted nodes and the second list contains the
      */
     public List<List<Node>> getAndersonDarlingTestAcceptsRejectsNodesForAllNodesPlotData(IndependenceTest independenceTest, Graph estimatedCpdag, Graph trueGraph, Double threshold, Double shuffleThreshold) {
         // When calling, default reject null as <=0.05
@@ -508,12 +509,12 @@ public List<List<Node>> getAndersonDarlingTestAcceptsRejectsNodesForAllNodesPlot
      * Confusion statistics were calculated using Local Graph Precision and Recall (LocalGraphPrecision,
      * LocalGraphRecall).
      *
-     * @param independenceTest
-     * @param estimatedCpdag
-     * @param trueGraph
-     * @param threshold
-     * @param shuffleThreshold
-     * @return
+     * @param independenceTest The independence test to be used for calculating p-values.
+     * @param estimatedCpdag   The estimated CPDAG.
+     * @param trueGraph        The true graph.
+     * @param threshold        The threshold value for classifying nodes.
+     * @param shuffleThreshold The threshold value for shuffling the data.
+     * @return A list containing two lists: the first list contains the accepted nodes and the second list contains the
      */
     public List<List<Node>> getAndersonDarlingTestAcceptsRejectsNodesForAllNodesPlotData2(IndependenceTest independenceTest, Graph estimatedCpdag, Graph trueGraph, Double threshold, Double shuffleThreshold) {
         // When calling, default reject null as <=0.05
@@ -638,6 +639,15 @@ public void getPrecisionAndRecallOnMarkovBlanketGraph(Node x, Graph estimatedGra
                            " ArrowHeadPrecision = " + nf.format(ahp) + " ArrowHeadRecall = " + nf.format(ahr));
     }
 
+    /**
+     * Calculates the precision and recall on the markov blanket graph plot data.
+     *
+     * @param x              the target node
+     * @param estimatedGraph the estimated graph
+     * @param trueGraph      the true graph
+     * @return a list of doubles representing the precision and recall values: [adjacency precision, adjacency recall,
+     * arrowhead precision, arrowhead recall]
+     */
     public List<Double> getPrecisionAndRecallOnMarkovBlanketGraphPlotData(Node x, Graph estimatedGraph, Graph trueGraph) {
         // Lookup graph is the same structure as trueGraph's structure but node objects replaced by estimated graph nodes.
         Graph lookupGraph = GraphUtils.replaceNodes(trueGraph, estimatedGraph.getNodes());
@@ -677,6 +687,14 @@ public void getPrecisionAndRecallOnMarkovBlanketGraph2(Node x, Graph estimatedGr
                            " LocalGraphPrecision = " + nf.format(lgp) + " LocalGraphRecall = " + nf.format(lgr) + " \n");
     }
 
+    /**
+     * This method calculates the precision and recall of a target node's Markov Blanket in the given estimated graph.
+     *
+     * @param x              the target node for which the precision and recall are calculated
+     * @param estimatedGraph the estimated graph
+     * @param trueGraph      the true graph
+     * @return a list of two doubles representing the precision and recall, respectively
+     */
     public List<Double> getPrecisionAndRecallOnMarkovBlanketGraphPlotData2(Node x, Graph estimatedGraph, Graph trueGraph) {
         // Lookup graph is the same structure as trueGraph's structure but node objects replaced by estimated graph nodes.
         Graph lookupGraph = GraphUtils.replaceNodes(trueGraph, estimatedGraph.getNodes());
diff --git a/tetrad-lib/src/main/java/edu/cmu/tetrad/search/test/IndependenceResult.java b/tetrad-lib/src/main/java/edu/cmu/tetrad/search/test/IndependenceResult.java
index 077ba4865e..0c911758cb 100644
--- a/tetrad-lib/src/main/java/edu/cmu/tetrad/search/test/IndependenceResult.java
+++ b/tetrad-lib/src/main/java/edu/cmu/tetrad/search/test/IndependenceResult.java
@@ -167,6 +167,12 @@ public boolean isValid() {
         return isValid;
     }
 
+    /**
+     * Writes the object to the specified ObjectOutputStream.
+     *
+     * @param out The ObjectOutputStream to write the object to.
+     * @throws IOException If an I/O error occurs.
+     */
     @Serial
     private void writeObject(ObjectOutputStream out) throws IOException {
         try {
@@ -178,6 +184,14 @@ private void writeObject(ObjectOutputStream out) throws IOException {
         }
     }
 
+    /**
+     * Reads the object from the specified ObjectInputStream. This method is used during deserialization
+     * to restore the state of the object.
+     *
+     * @param in The ObjectInputStream to read the object from.
+     * @throws IOException            If an I/O error occurs.
+     * @throws ClassNotFoundException If the class of the serialized object cannot be found.
+     */
     @Serial
     private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
         try {
diff --git a/tetrad-lib/src/main/java/edu/cmu/tetrad/search/utils/BpcAlgorithmType.java b/tetrad-lib/src/main/java/edu/cmu/tetrad/search/utils/BpcAlgorithmType.java
index 4eb5e38ec5..4b00065bac 100644
--- a/tetrad-lib/src/main/java/edu/cmu/tetrad/search/utils/BpcAlgorithmType.java
+++ b/tetrad-lib/src/main/java/edu/cmu/tetrad/search/utils/BpcAlgorithmType.java
@@ -101,6 +101,12 @@ public static BpcAlgorithmType[] getAlgorithmDescriptions() {
         };
     }
 
+    /**
+     * Writes the object to the specified ObjectOutputStream.
+     *
+     * @param out The ObjectOutputStream to write the object to.
+     * @throws IOException If an I/O error occurs.
+     */
     @Serial
     private void writeObject(ObjectOutputStream out) throws IOException {
         try {
@@ -112,6 +118,14 @@ private void writeObject(ObjectOutputStream out) throws IOException {
         }
     }
 
+    /**
+     * Reads the object from the specified ObjectInputStream. This method is used during deserialization
+     * to restore the state of the object.
+     *
+     * @param in The ObjectInputStream to read the object from.
+     * @throws IOException            If an I/O error occurs.
+     * @throws ClassNotFoundException If the class of the serialized object cannot be found.
+     */
     @Serial
     private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
         try {
diff --git a/tetrad-lib/src/main/java/edu/cmu/tetrad/search/utils/BpcTestType.java b/tetrad-lib/src/main/java/edu/cmu/tetrad/search/utils/BpcTestType.java
index 528ceb31f0..d14e1226cf 100644
--- a/tetrad-lib/src/main/java/edu/cmu/tetrad/search/utils/BpcTestType.java
+++ b/tetrad-lib/src/main/java/edu/cmu/tetrad/search/utils/BpcTestType.java
@@ -179,6 +179,12 @@ public static BpcTestType[] getTestDescriptions() {
          */
     }
 
+    /**
+     * Writes the object to the specified ObjectOutputStream.
+     *
+     * @param out The ObjectOutputStream to write the object to.
+     * @throws IOException If an I/O error occurs.
+     */
     @Serial
     private void writeObject(ObjectOutputStream out) throws IOException {
         try {
@@ -190,6 +196,14 @@ private void writeObject(ObjectOutputStream out) throws IOException {
         }
     }
 
+    /**
+     * Reads the object from the specified ObjectInputStream. This method is used during deserialization
+     * to restore the state of the object.
+     *
+     * @param in The ObjectInputStream to read the object from.
+     * @throws IOException            If an I/O error occurs.
+     * @throws ClassNotFoundException If the class of the serialized object cannot be found.
+     */
     @Serial
     private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
         try {
diff --git a/tetrad-lib/src/main/java/edu/cmu/tetrad/search/utils/Sextad.java b/tetrad-lib/src/main/java/edu/cmu/tetrad/search/utils/Sextad.java
index 5573b2801d..ba5ba6e3a4 100644
--- a/tetrad-lib/src/main/java/edu/cmu/tetrad/search/utils/Sextad.java
+++ b/tetrad-lib/src/main/java/edu/cmu/tetrad/search/utils/Sextad.java
@@ -216,6 +216,12 @@ private void testDistinctness(int i, int j, int k, int l, int m, int n) {
         }
     }
 
+    /**
+     * Writes the object to the specified ObjectOutputStream.
+     *
+     * @param out The ObjectOutputStream to write the object to.
+     * @throws IOException If an I/O error occurs.
+     */
     @Serial
     private void writeObject(ObjectOutputStream out) throws IOException {
         try {
@@ -227,6 +233,14 @@ private void writeObject(ObjectOutputStream out) throws IOException {
         }
     }
 
+    /**
+     * Reads the object from the specified ObjectInputStream. This method is used during deserialization
+     * to restore the state of the object.
+     *
+     * @param in The ObjectInputStream to read the object from.
+     * @throws IOException            If an I/O error occurs.
+     * @throws ClassNotFoundException If the class of the serialized object cannot be found.
+     */
     @Serial
     private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
         try {
diff --git a/tetrad-lib/src/main/java/edu/cmu/tetrad/search/work_in_progress/Sextad.java b/tetrad-lib/src/main/java/edu/cmu/tetrad/search/work_in_progress/Sextad.java
index 0eb1023815..14e47b56bd 100644
--- a/tetrad-lib/src/main/java/edu/cmu/tetrad/search/work_in_progress/Sextad.java
+++ b/tetrad-lib/src/main/java/edu/cmu/tetrad/search/work_in_progress/Sextad.java
@@ -263,6 +263,12 @@ public List<Node> getNodes() {
         return nodes;
     }
 
+    /**
+     * Writes the object to the specified ObjectOutputStream.
+     *
+     * @param out The ObjectOutputStream to write the object to.
+     * @throws IOException If an I/O error occurs.
+     */
     @Serial
     private void writeObject(ObjectOutputStream out) throws IOException {
         try {
@@ -274,6 +280,14 @@ private void writeObject(ObjectOutputStream out) throws IOException {
         }
     }
 
+    /**
+     * Reads the object from the specified ObjectInputStream. This method is used during deserialization
+     * to restore the state of the object.
+     *
+     * @param in The ObjectInputStream to read the object from.
+     * @throws IOException            If an I/O error occurs.
+     * @throws ClassNotFoundException If the class of the serialized object cannot be found.
+     */
     @Serial
     private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
         try {
diff --git a/tetrad-lib/src/main/java/edu/cmu/tetrad/sem/DagScorer.java b/tetrad-lib/src/main/java/edu/cmu/tetrad/sem/DagScorer.java
index 5d1582b10d..d86c025550 100644
--- a/tetrad-lib/src/main/java/edu/cmu/tetrad/sem/DagScorer.java
+++ b/tetrad-lib/src/main/java/edu/cmu/tetrad/sem/DagScorer.java
@@ -330,6 +330,18 @@ public double getPValue() {
         return 1.0 - ProbUtils.chisqCdf(getChiSquare(), getDof());
     }
 
+    /**
+     * Writes the object to the specified ObjectOutputStream.
+     *
+     * @param out The ObjectOutputStream to write the object to.
+     * @throws IOException If an I/O error occurs.
+     */
+    /**
+     * Writes the object to the specified ObjectOutputStream.
+     *
+     * @param out The ObjectOutputStream to write the object to.
+     * @throws IOException If an I/O error occurs.
+     */
     @Serial
     private void writeObject(ObjectOutputStream out) throws IOException {
         try {
@@ -341,6 +353,22 @@ private void writeObject(ObjectOutputStream out) throws IOException {
         }
     }
 
+    /**
+     * Reads the object from the specified ObjectInputStream. This method is used during deserialization
+     * to restore the state of the object.
+     *
+     * @param in The ObjectInputStream to read the object from.
+     * @throws IOException            If an I/O error occurs.
+     * @throws ClassNotFoundException If the class of the serialized object cannot be found.
+     */
+    /**
+     * Reads the object from the specified ObjectInputStream. This method is used during deserialization
+     * to restore the state of the object.
+     *
+     * @param in The ObjectInputStream to read the object from.
+     * @throws IOException            If an I/O error occurs.
+     * @throws ClassNotFoundException If the class of the serialized object cannot be found.
+     */
     @Serial
     private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
         try {
diff --git a/tetrad-lib/src/main/java/edu/cmu/tetrad/sem/GeneralizedSemPm.java b/tetrad-lib/src/main/java/edu/cmu/tetrad/sem/GeneralizedSemPm.java
index 68656a5ec8..c62a73b9c6 100644
--- a/tetrad-lib/src/main/java/edu/cmu/tetrad/sem/GeneralizedSemPm.java
+++ b/tetrad-lib/src/main/java/edu/cmu/tetrad/sem/GeneralizedSemPm.java
@@ -1066,6 +1066,12 @@ private List<Node> putErrorNodesLast(List<Node> parents) {
         return sortedNodes;
     }
 
+    /**
+     * Writes the object to the specified ObjectOutputStream.
+     *
+     * @param out The ObjectOutputStream to write the object to.
+     * @throws IOException If an I/O error occurs.
+     */
     @Serial
     private void writeObject(ObjectOutputStream out) throws IOException {
         try {
@@ -1077,6 +1083,14 @@ private void writeObject(ObjectOutputStream out) throws IOException {
         }
     }
 
+    /**
+     * Reads the object from the specified ObjectInputStream. This method is used during deserialization
+     * to restore the state of the object.
+     *
+     * @param in The ObjectInputStream to read the object from.
+     * @throws IOException            If an I/O error occurs.
+     * @throws ClassNotFoundException If the class of the serialized object cannot be found.
+     */
     @Serial
     private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
         try {
diff --git a/tetrad-lib/src/main/java/edu/cmu/tetrad/sem/Mapping.java b/tetrad-lib/src/main/java/edu/cmu/tetrad/sem/Mapping.java
index 92c4a55ed5..34c3fe2a05 100644
--- a/tetrad-lib/src/main/java/edu/cmu/tetrad/sem/Mapping.java
+++ b/tetrad-lib/src/main/java/edu/cmu/tetrad/sem/Mapping.java
@@ -174,6 +174,12 @@ public String toString() {
                "[" + this.i + "][" + this.j + "]>";
     }
 
+    /**
+     * Writes the object to the specified ObjectOutputStream.
+     *
+     * @param out The ObjectOutputStream to write the object to.
+     * @throws IOException If an I/O error occurs.
+     */
     @Serial
     private void writeObject(ObjectOutputStream out) throws IOException {
         try {
@@ -185,6 +191,14 @@ private void writeObject(ObjectOutputStream out) throws IOException {
         }
     }
 
+    /**
+     * Reads the object from the specified ObjectInputStream. This method is used during deserialization
+     * to restore the state of the object.
+     *
+     * @param in The ObjectInputStream to read the object from.
+     * @throws IOException            If an I/O error occurs.
+     * @throws ClassNotFoundException If the class of the serialized object cannot be found.
+     */
     @Serial
     private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
         try {
diff --git a/tetrad-lib/src/main/java/edu/cmu/tetrad/sem/ParamComparison.java b/tetrad-lib/src/main/java/edu/cmu/tetrad/sem/ParamComparison.java
index 64b4ce196d..febe89c98e 100755
--- a/tetrad-lib/src/main/java/edu/cmu/tetrad/sem/ParamComparison.java
+++ b/tetrad-lib/src/main/java/edu/cmu/tetrad/sem/ParamComparison.java
@@ -25,9 +25,33 @@
  * An enum of the types of the various comparisons a parameter may have with respect to one another for SEM estimation.
  */
 public enum ParamComparison {
+    /**
+     * Represents the "Non-comparable" comparison type for a parameter in SEM estimation.
+     *
+     * This type of comparison indicates that the parameter is not comparable to any other parameter
+     * in the structural equation model.
+     */
     NC("NC"),
+    /**
+     * An enum representing the "EQ" comparison type for a parameter in SEM estimation.
+     *
+     * This type of comparison indicates that the parameter is equal to another parameter
+     * in the structural equation model.
+     */
     EQ("EQ"),
+    /**
+     * Represents the "LT" comparison type for a parameter in SEM estimation.
+     *
+     * This type of comparison indicates that the parameter is less than another parameter
+     * in the structural equation model.
+     */
     LT("LT"),
+    /**
+     * An enum value representing the "LE" comparison type for a parameter in SEM estimation.
+     *
+     * This type of comparison indicates that the parameter is less than or equal to another parameter
+     * in the structural equation model.
+     */
     LE("LE");
 
     private final String name;
diff --git a/tetrad-lib/src/main/java/edu/cmu/tetrad/sem/ParamConstraint.java b/tetrad-lib/src/main/java/edu/cmu/tetrad/sem/ParamConstraint.java
index 01802f374d..f1e5f4f7ff 100644
--- a/tetrad-lib/src/main/java/edu/cmu/tetrad/sem/ParamConstraint.java
+++ b/tetrad-lib/src/main/java/edu/cmu/tetrad/sem/ParamConstraint.java
@@ -147,6 +147,12 @@ public SemIm getSemIm() {
         return this.semIm;
     }
 
+    /**
+     * Writes the object to the specified ObjectOutputStream.
+     *
+     * @param out The ObjectOutputStream to write the object to.
+     * @throws IOException If an I/O error occurs.
+     */
     @Serial
     private void writeObject(ObjectOutputStream out) throws IOException {
         try {
@@ -158,6 +164,14 @@ private void writeObject(ObjectOutputStream out) throws IOException {
         }
     }
 
+    /**
+     * Reads the object from the specified ObjectInputStream. This method is used during deserialization
+     * to restore the state of the object.
+     *
+     * @param in The ObjectInputStream to read the object from.
+     * @throws IOException            If an I/O error occurs.
+     * @throws ClassNotFoundException If the class of the serialized object cannot be found.
+     */
     @Serial
     private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
         try {
diff --git a/tetrad-lib/src/main/java/edu/cmu/tetrad/sem/ParamConstraintType.java b/tetrad-lib/src/main/java/edu/cmu/tetrad/sem/ParamConstraintType.java
index 90cf90aad5..3772ef1e33 100644
--- a/tetrad-lib/src/main/java/edu/cmu/tetrad/sem/ParamConstraintType.java
+++ b/tetrad-lib/src/main/java/edu/cmu/tetrad/sem/ParamConstraintType.java
@@ -26,10 +26,31 @@
 
 import java.io.*;
 
+/**
+ * Enum for representing different types of parameter constraints.
+ */
 public enum ParamConstraintType {
+    /**
+     * Represents a parameter constraint type LT (less than).
+     */
     LT("LT"),
+    /**
+     * Represents a parameter constraint type GT (greater than).
+     */
     GT("GT"),
+    /**
+     * The EQ represents a parameter constraint type EQ (equal).
+     *
+     * This enum value is used to represent the equality constraint on a parameter. It indicates that the parameter value
+     * should be equal to a specific value.
+     */
     EQ("EQ"),
+    /**
+     * Represents a parameter constraint type NONE.
+     *
+     * This enum value is used to represent the absence of a constraint on a parameter. It indicates that there is no specific
+     * constraint on the parameter value.
+     */
     NONE("NONE");
 
     private final String name;
diff --git a/tetrad-lib/src/main/java/edu/cmu/tetrad/sem/ParamType.java b/tetrad-lib/src/main/java/edu/cmu/tetrad/sem/ParamType.java
index 2e01b4e8fe..83bffe409a 100644
--- a/tetrad-lib/src/main/java/edu/cmu/tetrad/sem/ParamType.java
+++ b/tetrad-lib/src/main/java/edu/cmu/tetrad/sem/ParamType.java
@@ -30,10 +30,33 @@
  * @version $Id: $Id
  */
 public enum ParamType {
+    /**
+     * Enum representing the free parameter type for structural equation modeling (SEM) models.
+     * COEF free parameters are edge coefficients in the linear SEM model.
+     */
     COEF("Linear Coefficient"),
+    /**
+     * Variable Mean parameter type for SEM models.
+     */
     MEAN("Variable Mean"),
+    /**
+     * Represents the error variance parameter in a structural equation modeling (SEM) model.
+     */
     VAR("Error Variance"),
+    /**
+     * Represents a free parameter type for structural equation modeling (SEM) models. Specifically, the COVAR free parameter type is used to represent non-variance covariances among
+     *  the error terms in the SEM model.
+     *
+     * This enum type is a part of the ParamType enum, which is used to categorize different types of free parameters for SEM models.
+     *
+     * The COVAR free parameter type is associated with the description "Error Covariance".
+     */
     COVAR("Error Covariance"),
+    /**
+     * Represents a free parameter type for structural equation modeling (SEM) models.
+     * Specifically, the DIST free parameter type is used to represent distribution parameters in the SEM model.
+     * It is associated with the description "Distribution Parameter".
+     */
     DIST("Distribution Parameter");
 
     private final String name;
diff --git a/tetrad-lib/src/main/java/edu/cmu/tetrad/sem/Parameter.java b/tetrad-lib/src/main/java/edu/cmu/tetrad/sem/Parameter.java
index ef7f54bc27..2a7bdcf41b 100644
--- a/tetrad-lib/src/main/java/edu/cmu/tetrad/sem/Parameter.java
+++ b/tetrad-lib/src/main/java/edu/cmu/tetrad/sem/Parameter.java
@@ -300,6 +300,12 @@ public void setInitializedRandomly(boolean initializedRandomly) {
         this.initializedRandomly = initializedRandomly;
     }
 
+    /**
+     * Writes the object to the specified ObjectOutputStream.
+     *
+     * @param out The ObjectOutputStream to write the object to.
+     * @throws IOException If an I/O error occurs.
+     */
     @Serial
     private void writeObject(ObjectOutputStream out) throws IOException {
         try {
@@ -311,6 +317,14 @@ private void writeObject(ObjectOutputStream out) throws IOException {
         }
     }
 
+    /**
+     * Reads the object from the specified ObjectInputStream. This method is used during deserialization
+     * to restore the state of the object.
+     *
+     * @param in The ObjectInputStream to read the object from.
+     * @throws IOException            If an I/O error occurs.
+     * @throws ClassNotFoundException If the class of the serialized object cannot be found.
+     */
     @Serial
     private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
         try {
diff --git a/tetrad-lib/src/main/java/edu/cmu/tetrad/sem/ParameterPair.java b/tetrad-lib/src/main/java/edu/cmu/tetrad/sem/ParameterPair.java
index a48d840100..19625540c5 100644
--- a/tetrad-lib/src/main/java/edu/cmu/tetrad/sem/ParameterPair.java
+++ b/tetrad-lib/src/main/java/edu/cmu/tetrad/sem/ParameterPair.java
@@ -139,6 +139,12 @@ private void setPair(Parameter a, Parameter b) {
         this.b = b;
     }
 
+    /**
+     * Writes the object to the specified ObjectOutputStream.
+     *
+     * @param out The ObjectOutputStream to write the object to.
+     * @throws IOException If an I/O error occurs.
+     */
     @Serial
     private void writeObject(ObjectOutputStream out) throws IOException {
         try {
@@ -150,6 +156,14 @@ private void writeObject(ObjectOutputStream out) throws IOException {
         }
     }
 
+    /**
+     * Reads the object from the specified ObjectInputStream. This method is used during deserialization
+     * to restore the state of the object.
+     *
+     * @param in The ObjectInputStream to read the object from.
+     * @throws IOException            If an I/O error occurs.
+     * @throws ClassNotFoundException If the class of the serialized object cannot be found.
+     */
     @Serial
     private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
         try {
diff --git a/tetrad-lib/src/main/java/edu/cmu/tetrad/sem/SemEstimator.java b/tetrad-lib/src/main/java/edu/cmu/tetrad/sem/SemEstimator.java
index 4b6ddd7454..edc15b480b 100644
--- a/tetrad-lib/src/main/java/edu/cmu/tetrad/sem/SemEstimator.java
+++ b/tetrad-lib/src/main/java/edu/cmu/tetrad/sem/SemEstimator.java
@@ -441,6 +441,12 @@ private void setMeans(SemIm semIm, DataSet dataSet) {
         }
     }
 
+    /**
+     * Writes the object to the specified ObjectOutputStream.
+     *
+     * @param out The ObjectOutputStream to write the object to.
+     * @throws IOException If an I/O error occurs.
+     */
     @Serial
     private void writeObject(ObjectOutputStream out) throws IOException {
         try {
@@ -452,6 +458,14 @@ private void writeObject(ObjectOutputStream out) throws IOException {
         }
     }
 
+    /**
+     * Reads the object from the specified ObjectInputStream. This method is used during deserialization
+     * to restore the state of the object.
+     *
+     * @param in The ObjectInputStream to read the object from.
+     * @throws IOException            If an I/O error occurs.
+     * @throws ClassNotFoundException If the class of the serialized object cannot be found.
+     */
     @Serial
     private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
         try {
diff --git a/tetrad-lib/src/main/java/edu/cmu/tetrad/sem/SemEstimatorGibbs.java b/tetrad-lib/src/main/java/edu/cmu/tetrad/sem/SemEstimatorGibbs.java
index 15839cb8ad..1087f7eed7 100644
--- a/tetrad-lib/src/main/java/edu/cmu/tetrad/sem/SemEstimatorGibbs.java
+++ b/tetrad-lib/src/main/java/edu/cmu/tetrad/sem/SemEstimatorGibbs.java
@@ -532,6 +532,12 @@ public Matrix getDataSet() {
         return this.dataSet;
     }
 
+    /**
+     * Writes the object to the specified ObjectOutputStream.
+     *
+     * @param out The ObjectOutputStream to write the object to.
+     * @throws IOException If an I/O error occurs.
+     */
     @Serial
     private void writeObject(ObjectOutputStream out) throws IOException {
         try {
@@ -543,6 +549,14 @@ private void writeObject(ObjectOutputStream out) throws IOException {
         }
     }
 
+    /**
+     * Reads the object from the specified ObjectInputStream. This method is used during deserialization
+     * to restore the state of the object.
+     *
+     * @param in The ObjectInputStream to read the object from.
+     * @throws IOException            If an I/O error occurs.
+     * @throws ClassNotFoundException If the class of the serialized object cannot be found.
+     */
     @Serial
     private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
         try {
diff --git a/tetrad-lib/src/main/java/edu/cmu/tetrad/sem/SemEstimatorGibbsParams.java b/tetrad-lib/src/main/java/edu/cmu/tetrad/sem/SemEstimatorGibbsParams.java
index 01fbd0b929..d91f223d48 100644
--- a/tetrad-lib/src/main/java/edu/cmu/tetrad/sem/SemEstimatorGibbsParams.java
+++ b/tetrad-lib/src/main/java/edu/cmu/tetrad/sem/SemEstimatorGibbsParams.java
@@ -174,6 +174,12 @@ public void setFlatPrior(boolean flatPrior) {
         this.flatPrior = flatPrior;
     }
 
+    /**
+     * Writes the object to the specified ObjectOutputStream.
+     *
+     * @param out The ObjectOutputStream to write the object to.
+     * @throws IOException If an I/O error occurs.
+     */
     @Serial
     private void writeObject(ObjectOutputStream out) throws IOException {
         try {
@@ -185,6 +191,14 @@ private void writeObject(ObjectOutputStream out) throws IOException {
         }
     }
 
+    /**
+     * Reads the object from the specified ObjectInputStream. This method is used during deserialization
+     * to restore the state of the object.
+     *
+     * @param in The ObjectInputStream to read the object from.
+     * @throws IOException            If an I/O error occurs.
+     * @throws ClassNotFoundException If the class of the serialized object cannot be found.
+     */
     @Serial
     private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
         try {
diff --git a/tetrad-lib/src/main/java/edu/cmu/tetrad/sem/SemEvidence.java b/tetrad-lib/src/main/java/edu/cmu/tetrad/sem/SemEvidence.java
index 52701e9f13..0ab18f3c95 100644
--- a/tetrad-lib/src/main/java/edu/cmu/tetrad/sem/SemEvidence.java
+++ b/tetrad-lib/src/main/java/edu/cmu/tetrad/sem/SemEvidence.java
@@ -270,6 +270,12 @@ public int hashCode() {
         return hashCode;
     }
 
+    /**
+     * Writes the object to the specified ObjectOutputStream.
+     *
+     * @param out The ObjectOutputStream to write the object to.
+     * @throws IOException If an I/O error occurs.
+     */
     @Serial
     private void writeObject(ObjectOutputStream out) throws IOException {
         try {
@@ -281,6 +287,14 @@ private void writeObject(ObjectOutputStream out) throws IOException {
         }
     }
 
+    /**
+     * Reads the object from the specified ObjectInputStream. This method is used during deserialization
+     * to restore the state of the object.
+     *
+     * @param in The ObjectInputStream to read the object from.
+     * @throws IOException            If an I/O error occurs.
+     * @throws ClassNotFoundException If the class of the serialized object cannot be found.
+     */
     @Serial
     private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
         try {
diff --git a/tetrad-lib/src/main/java/edu/cmu/tetrad/sem/SemIm.java b/tetrad-lib/src/main/java/edu/cmu/tetrad/sem/SemIm.java
index 155a20df50..41c924b7cb 100644
--- a/tetrad-lib/src/main/java/edu/cmu/tetrad/sem/SemIm.java
+++ b/tetrad-lib/src/main/java/edu/cmu/tetrad/sem/SemIm.java
@@ -2308,6 +2308,12 @@ private double[] standardErrors() {
         return this.standardErrors;
     }
 
+    /**
+     * Writes the object to the specified ObjectOutputStream.
+     *
+     * @param out The ObjectOutputStream to write the object to.
+     * @throws IOException If an I/O error occurs.
+     */
     @Serial
     private void writeObject(ObjectOutputStream out) throws IOException {
         try {
@@ -2319,6 +2325,14 @@ private void writeObject(ObjectOutputStream out) throws IOException {
         }
     }
 
+    /**
+     * Reads the object from the specified ObjectInputStream. This method is used during deserialization
+     * to restore the state of the object.
+     *
+     * @param in The ObjectInputStream to read the object from.
+     * @throws IOException            If an I/O error occurs.
+     * @throws ClassNotFoundException If the class of the serialized object cannot be found.
+     */
     @Serial
     private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
         try {
diff --git a/tetrad-lib/src/main/java/edu/cmu/tetrad/sem/SemManipulation.java b/tetrad-lib/src/main/java/edu/cmu/tetrad/sem/SemManipulation.java
index 5ab0be2925..3c1b214207 100644
--- a/tetrad-lib/src/main/java/edu/cmu/tetrad/sem/SemManipulation.java
+++ b/tetrad-lib/src/main/java/edu/cmu/tetrad/sem/SemManipulation.java
@@ -203,6 +203,12 @@ public int hashCode() {
         return hashCode;
     }
 
+    /**
+     * Writes the object to the specified ObjectOutputStream.
+     *
+     * @param out The ObjectOutputStream to write the object to.
+     * @throws IOException If an I/O error occurs.
+     */
     @Serial
     private void writeObject(ObjectOutputStream out) throws IOException {
         try {
@@ -214,6 +220,14 @@ private void writeObject(ObjectOutputStream out) throws IOException {
         }
     }
 
+    /**
+     * Reads the object from the specified ObjectInputStream. This method is used during deserialization
+     * to restore the state of the object.
+     *
+     * @param in The ObjectInputStream to read the object from.
+     * @throws IOException            If an I/O error occurs.
+     * @throws ClassNotFoundException If the class of the serialized object cannot be found.
+     */
     @Serial
     private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
         try {
diff --git a/tetrad-lib/src/main/java/edu/cmu/tetrad/sem/SemPm.java b/tetrad-lib/src/main/java/edu/cmu/tetrad/sem/SemPm.java
index 7699ad3380..a7e76cd2b8 100644
--- a/tetrad-lib/src/main/java/edu/cmu/tetrad/sem/SemPm.java
+++ b/tetrad-lib/src/main/java/edu/cmu/tetrad/sem/SemPm.java
@@ -667,6 +667,12 @@ private String newBName() {
         return "B" + (++this.bIndex);
     }
 
+    /**
+     * Writes the object to the specified ObjectOutputStream.
+     *
+     * @param out The ObjectOutputStream to write the object to.
+     * @throws IOException If an I/O error occurs.
+     */
     @Serial
     private void writeObject(ObjectOutputStream out) throws IOException {
         try {
@@ -678,6 +684,14 @@ private void writeObject(ObjectOutputStream out) throws IOException {
         }
     }
 
+    /**
+     * Reads the object from the specified ObjectInputStream. This method is used during deserialization
+     * to restore the state of the object.
+     *
+     * @param in The ObjectInputStream to read the object from.
+     * @throws IOException            If an I/O error occurs.
+     * @throws ClassNotFoundException If the class of the serialized object cannot be found.
+     */
     @Serial
     private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
         try {
diff --git a/tetrad-lib/src/main/java/edu/cmu/tetrad/sem/SemProposition.java b/tetrad-lib/src/main/java/edu/cmu/tetrad/sem/SemProposition.java
index b36707a959..2d47604076 100644
--- a/tetrad-lib/src/main/java/edu/cmu/tetrad/sem/SemProposition.java
+++ b/tetrad-lib/src/main/java/edu/cmu/tetrad/sem/SemProposition.java
@@ -196,6 +196,12 @@ public String toString() {
         return buf.toString();
     }
 
+    /**
+     * Writes the object to the specified ObjectOutputStream.
+     *
+     * @param out The ObjectOutputStream to write the object to.
+     * @throws IOException If an I/O error occurs.
+     */
     @Serial
     private void writeObject(ObjectOutputStream out) throws IOException {
         try {
@@ -207,6 +213,14 @@ private void writeObject(ObjectOutputStream out) throws IOException {
         }
     }
 
+    /**
+     * Reads the object from the specified ObjectInputStream. This method is used during deserialization
+     * to restore the state of the object.
+     *
+     * @param in The ObjectInputStream to read the object from.
+     * @throws IOException            If an I/O error occurs.
+     * @throws ClassNotFoundException If the class of the serialized object cannot be found.
+     */
     @Serial
     private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
         try {
diff --git a/tetrad-lib/src/main/java/edu/cmu/tetrad/sem/SemUpdater.java b/tetrad-lib/src/main/java/edu/cmu/tetrad/sem/SemUpdater.java
index 92bda2f2a2..7dc3eb00f3 100644
--- a/tetrad-lib/src/main/java/edu/cmu/tetrad/sem/SemUpdater.java
+++ b/tetrad-lib/src/main/java/edu/cmu/tetrad/sem/SemUpdater.java
@@ -247,6 +247,12 @@ private SemGraph createManipulatedGraph(Graph graph) {
         return updatedGraph;
     }
 
+    /**
+     * Writes the object to the specified ObjectOutputStream.
+     *
+     * @param out The ObjectOutputStream to write the object to.
+     * @throws IOException If an I/O error occurs.
+     */
     @Serial
     private void writeObject(ObjectOutputStream out) throws IOException {
         try {
@@ -258,6 +264,14 @@ private void writeObject(ObjectOutputStream out) throws IOException {
         }
     }
 
+    /**
+     * Reads the object from the specified ObjectInputStream. This method is used during deserialization
+     * to restore the state of the object.
+     *
+     * @param in The ObjectInputStream to read the object from.
+     * @throws IOException            If an I/O error occurs.
+     * @throws ClassNotFoundException If the class of the serialized object cannot be found.
+     */
     @Serial
     private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
         try {
diff --git a/tetrad-lib/src/main/java/edu/cmu/tetrad/sem/StandardizedSemIm.java b/tetrad-lib/src/main/java/edu/cmu/tetrad/sem/StandardizedSemIm.java
index 367821656a..85435905c0 100644
--- a/tetrad-lib/src/main/java/edu/cmu/tetrad/sem/StandardizedSemIm.java
+++ b/tetrad-lib/src/main/java/edu/cmu/tetrad/sem/StandardizedSemIm.java
@@ -1045,6 +1045,12 @@ public String toString() {
         }
     }
 
+    /**
+     * Writes the object to the specified ObjectOutputStream.
+     *
+     * @param out The ObjectOutputStream to write the object to.
+     * @throws IOException If an I/O error occurs.
+     */
     @Serial
     private void writeObject(ObjectOutputStream out) throws IOException {
         try {
@@ -1056,6 +1062,14 @@ private void writeObject(ObjectOutputStream out) throws IOException {
         }
     }
 
+    /**
+     * Reads the object from the specified ObjectInputStream. This method is used during deserialization
+     * to restore the state of the object.
+     *
+     * @param in The ObjectInputStream to read the object from.
+     * @throws IOException            If an I/O error occurs.
+     * @throws ClassNotFoundException If the class of the serialized object cannot be found.
+     */
     @Serial
     private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
         try {
diff --git a/tetrad-lib/src/main/java/edu/cmu/tetrad/study/gene/tetrad/gene/graph/StoredLagGraphParams.java b/tetrad-lib/src/main/java/edu/cmu/tetrad/study/gene/tetrad/gene/graph/StoredLagGraphParams.java
index cbe5ecb86a..231586af47 100755
--- a/tetrad-lib/src/main/java/edu/cmu/tetrad/study/gene/tetrad/gene/graph/StoredLagGraphParams.java
+++ b/tetrad-lib/src/main/java/edu/cmu/tetrad/study/gene/tetrad/gene/graph/StoredLagGraphParams.java
@@ -86,6 +86,12 @@ public void setFilename(String filename) {
         this.filename = filename;
     }
 
+    /**
+     * Writes the object to the specified ObjectOutputStream.
+     *
+     * @param out The ObjectOutputStream to write the object to.
+     * @throws IOException If an I/O error occurs.
+     */
     @Serial
     private void writeObject(ObjectOutputStream out) throws IOException {
         try {
@@ -97,6 +103,14 @@ private void writeObject(ObjectOutputStream out) throws IOException {
         }
     }
 
+    /**
+     * Reads the object from the specified ObjectInputStream. This method is used during deserialization
+     * to restore the state of the object.
+     *
+     * @param in The ObjectInputStream to read the object from.
+     * @throws IOException            If an I/O error occurs.
+     * @throws ClassNotFoundException If the class of the serialized object cannot be found.
+     */
     @Serial
     private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
         try {
diff --git a/tetrad-lib/src/main/java/edu/cmu/tetrad/study/gene/tetrad/gene/history/BooleanFunction.java b/tetrad-lib/src/main/java/edu/cmu/tetrad/study/gene/tetrad/gene/history/BooleanFunction.java
index e912b3053c..8e76d3c7ae 100644
--- a/tetrad-lib/src/main/java/edu/cmu/tetrad/study/gene/tetrad/gene/history/BooleanFunction.java
+++ b/tetrad-lib/src/main/java/edu/cmu/tetrad/study/gene/tetrad/gene/history/BooleanFunction.java
@@ -306,6 +306,12 @@ public String toString() {
         return buf.toString();
     }
 
+    /**
+     * Writes the object to the specified ObjectOutputStream.
+     *
+     * @param out The ObjectOutputStream to write the object to.
+     * @throws IOException If an I/O error occurs.
+     */
     @Serial
     private void writeObject(ObjectOutputStream out) throws IOException {
         try {
@@ -317,6 +323,14 @@ private void writeObject(ObjectOutputStream out) throws IOException {
         }
     }
 
+    /**
+     * Reads the object from the specified ObjectInputStream. This method is used during deserialization
+     * to restore the state of the object.
+     *
+     * @param in The ObjectInputStream to read the object from.
+     * @throws IOException            If an I/O error occurs.
+     * @throws ClassNotFoundException If the class of the serialized object cannot be found.
+     */
     @Serial
     private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
         try {
diff --git a/tetrad-lib/src/main/java/edu/cmu/tetrad/study/gene/tetrad/gene/history/DishModel.java b/tetrad-lib/src/main/java/edu/cmu/tetrad/study/gene/tetrad/gene/history/DishModel.java
index 94d5565e9a..065fa4d227 100644
--- a/tetrad-lib/src/main/java/edu/cmu/tetrad/study/gene/tetrad/gene/history/DishModel.java
+++ b/tetrad-lib/src/main/java/edu/cmu/tetrad/study/gene/tetrad/gene/history/DishModel.java
@@ -156,6 +156,12 @@ public void setDishBumpStDev(double dishBumpStDev) {
         this.dishBumpStDev = dishBumpStDev;
     }
 
+    /**
+     * Writes the object to the specified ObjectOutputStream.
+     *
+     * @param out The ObjectOutputStream to write the object to.
+     * @throws IOException If an I/O error occurs.
+     */
     @Serial
     private void writeObject(ObjectOutputStream out) throws IOException {
         try {
@@ -167,6 +173,14 @@ private void writeObject(ObjectOutputStream out) throws IOException {
         }
     }
 
+    /**
+     * Reads the object from the specified ObjectInputStream. This method is used during deserialization
+     * to restore the state of the object.
+     *
+     * @param in The ObjectInputStream to read the object from.
+     * @throws IOException            If an I/O error occurs.
+     * @throws ClassNotFoundException If the class of the serialized object cannot be found.
+     */
     @Serial
     private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
         try {
diff --git a/tetrad-lib/src/main/java/edu/cmu/tetrad/study/gene/tetrad/gene/history/GeneHistory.java b/tetrad-lib/src/main/java/edu/cmu/tetrad/study/gene/tetrad/gene/history/GeneHistory.java
index 3297e898a3..30e793d9b6 100644
--- a/tetrad-lib/src/main/java/edu/cmu/tetrad/study/gene/tetrad/gene/history/GeneHistory.java
+++ b/tetrad-lib/src/main/java/edu/cmu/tetrad/study/gene/tetrad/gene/history/GeneHistory.java
@@ -285,6 +285,12 @@ public void initialize() {
         this.step = -1;
     }
 
+    /**
+     * Writes the object to the specified ObjectOutputStream.
+     *
+     * @param out The ObjectOutputStream to write the object to.
+     * @throws IOException If an I/O error occurs.
+     */
     @Serial
     private void writeObject(ObjectOutputStream out) throws IOException {
         try {
@@ -296,6 +302,14 @@ private void writeObject(ObjectOutputStream out) throws IOException {
         }
     }
 
+    /**
+     * Reads the object from the specified ObjectInputStream. This method is used during deserialization
+     * to restore the state of the object.
+     *
+     * @param in The ObjectInputStream to read the object from.
+     * @throws IOException            If an I/O error occurs.
+     * @throws ClassNotFoundException If the class of the serialized object cannot be found.
+     */
     @Serial
     private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
         try {
diff --git a/tetrad-lib/src/main/java/edu/cmu/tetrad/study/gene/tetrad/gene/history/IndexedConnectivity.java b/tetrad-lib/src/main/java/edu/cmu/tetrad/study/gene/tetrad/gene/history/IndexedConnectivity.java
index d1db22bd89..2929628ff2 100644
--- a/tetrad-lib/src/main/java/edu/cmu/tetrad/study/gene/tetrad/gene/history/IndexedConnectivity.java
+++ b/tetrad-lib/src/main/java/edu/cmu/tetrad/study/gene/tetrad/gene/history/IndexedConnectivity.java
@@ -238,6 +238,12 @@ public String toString() {
         return buf.toString();
     }
 
+    /**
+     * Writes the object to the specified ObjectOutputStream.
+     *
+     * @param out The ObjectOutputStream to write the object to.
+     * @throws IOException If an I/O error occurs.
+     */
     @Serial
     private void writeObject(ObjectOutputStream out) throws IOException {
         try {
@@ -249,6 +255,14 @@ private void writeObject(ObjectOutputStream out) throws IOException {
         }
     }
 
+    /**
+     * Reads the object from the specified ObjectInputStream. This method is used during deserialization
+     * to restore the state of the object.
+     *
+     * @param in The ObjectInputStream to read the object from.
+     * @throws IOException            If an I/O error occurs.
+     * @throws ClassNotFoundException If the class of the serialized object cannot be found.
+     */
     @Serial
     private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
         try {
diff --git a/tetrad-lib/src/main/java/edu/cmu/tetrad/study/gene/tetrad/gene/history/IndexedLagGraph.java b/tetrad-lib/src/main/java/edu/cmu/tetrad/study/gene/tetrad/gene/history/IndexedLagGraph.java
index e682ab3979..a02ee85ae6 100644
--- a/tetrad-lib/src/main/java/edu/cmu/tetrad/study/gene/tetrad/gene/history/IndexedLagGraph.java
+++ b/tetrad-lib/src/main/java/edu/cmu/tetrad/study/gene/tetrad/gene/history/IndexedLagGraph.java
@@ -234,6 +234,12 @@ public String toString() {
         return buf.toString();
     }
 
+    /**
+     * Writes the object to the specified ObjectOutputStream.
+     *
+     * @param out The ObjectOutputStream to write the object to.
+     * @throws IOException If an I/O error occurs.
+     */
     @Serial
     private void writeObject(ObjectOutputStream out) throws IOException {
         try {
@@ -245,6 +251,14 @@ private void writeObject(ObjectOutputStream out) throws IOException {
         }
     }
 
+    /**
+     * Reads the object from the specified ObjectInputStream. This method is used during deserialization
+     * to restore the state of the object.
+     *
+     * @param in The ObjectInputStream to read the object from.
+     * @throws IOException            If an I/O error occurs.
+     * @throws ClassNotFoundException If the class of the serialized object cannot be found.
+     */
     @Serial
     private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
         try {
diff --git a/tetrad-lib/src/main/java/edu/cmu/tetrad/study/gene/tetrad/gene/history/IndexedParent.java b/tetrad-lib/src/main/java/edu/cmu/tetrad/study/gene/tetrad/gene/history/IndexedParent.java
index f3b14e53b1..e0765bb2e1 100644
--- a/tetrad-lib/src/main/java/edu/cmu/tetrad/study/gene/tetrad/gene/history/IndexedParent.java
+++ b/tetrad-lib/src/main/java/edu/cmu/tetrad/study/gene/tetrad/gene/history/IndexedParent.java
@@ -125,6 +125,12 @@ public String toString() {
         return "IndexedParent, index = " + getIndex() + ", lag = " + getLag();
     }
 
+    /**
+     * Writes the object to the specified ObjectOutputStream.
+     *
+     * @param out The ObjectOutputStream to write the object to.
+     * @throws IOException If an I/O error occurs.
+     */
     @Serial
     private void writeObject(ObjectOutputStream out) throws IOException {
         try {
@@ -136,6 +142,14 @@ private void writeObject(ObjectOutputStream out) throws IOException {
         }
     }
 
+    /**
+     * Reads the object from the specified ObjectInputStream. This method is used during deserialization
+     * to restore the state of the object.
+     *
+     * @param in The ObjectInputStream to read the object from.
+     * @throws IOException            If an I/O error occurs.
+     * @throws ClassNotFoundException If the class of the serialized object cannot be found.
+     */
     @Serial
     private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
         try {
diff --git a/tetrad-lib/src/main/java/edu/cmu/tetrad/study/gene/tetrad/gene/history/LaggedEdge.java b/tetrad-lib/src/main/java/edu/cmu/tetrad/study/gene/tetrad/gene/history/LaggedEdge.java
index 3e9a48f25d..3bd1eb779e 100644
--- a/tetrad-lib/src/main/java/edu/cmu/tetrad/study/gene/tetrad/gene/history/LaggedEdge.java
+++ b/tetrad-lib/src/main/java/edu/cmu/tetrad/study/gene/tetrad/gene/history/LaggedEdge.java
@@ -99,6 +99,12 @@ public LaggedFactor getLaggedFactor() {
         return this.laggedFactor;
     }
 
+    /**
+     * Writes the object to the specified ObjectOutputStream.
+     *
+     * @param out The ObjectOutputStream to write the object to.
+     * @throws IOException If an I/O error occurs.
+     */
     @Serial
     private void writeObject(ObjectOutputStream out) throws IOException {
         try {
@@ -110,6 +116,14 @@ private void writeObject(ObjectOutputStream out) throws IOException {
         }
     }
 
+    /**
+     * Reads the object from the specified ObjectInputStream. This method is used during deserialization
+     * to restore the state of the object.
+     *
+     * @param in The ObjectInputStream to read the object from.
+     * @throws IOException            If an I/O error occurs.
+     * @throws ClassNotFoundException If the class of the serialized object cannot be found.
+     */
     @Serial
     private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
         try {
diff --git a/tetrad-lib/src/main/java/edu/cmu/tetrad/study/gene/tetrad/gene/history/Polynomial.java b/tetrad-lib/src/main/java/edu/cmu/tetrad/study/gene/tetrad/gene/history/Polynomial.java
index 1e26b5503b..a2a3ca780b 100644
--- a/tetrad-lib/src/main/java/edu/cmu/tetrad/study/gene/tetrad/gene/history/Polynomial.java
+++ b/tetrad-lib/src/main/java/edu/cmu/tetrad/study/gene/tetrad/gene/history/Polynomial.java
@@ -155,6 +155,12 @@ public String toString() {
         return buf.toString();
     }
 
+    /**
+     * Writes the object to the specified ObjectOutputStream.
+     *
+     * @param out The ObjectOutputStream to write the object to.
+     * @throws IOException If an I/O error occurs.
+     */
     @Serial
     private void writeObject(ObjectOutputStream out) throws IOException {
         try {
@@ -166,6 +172,14 @@ private void writeObject(ObjectOutputStream out) throws IOException {
         }
     }
 
+    /**
+     * Reads the object from the specified ObjectInputStream. This method is used during deserialization
+     * to restore the state of the object.
+     *
+     * @param in The ObjectInputStream to read the object from.
+     * @throws IOException            If an I/O error occurs.
+     * @throws ClassNotFoundException If the class of the serialized object cannot be found.
+     */
     @Serial
     private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
         try {
diff --git a/tetrad-lib/src/main/java/edu/cmu/tetrad/study/gene/tetrad/gene/history/PolynomialTerm.java b/tetrad-lib/src/main/java/edu/cmu/tetrad/study/gene/tetrad/gene/history/PolynomialTerm.java
index cd0c986265..0b6ae64bc4 100644
--- a/tetrad-lib/src/main/java/edu/cmu/tetrad/study/gene/tetrad/gene/history/PolynomialTerm.java
+++ b/tetrad-lib/src/main/java/edu/cmu/tetrad/study/gene/tetrad/gene/history/PolynomialTerm.java
@@ -180,6 +180,12 @@ public String toString() {
         return buf.toString();
     }
 
+    /**
+     * Writes the object to the specified ObjectOutputStream.
+     *
+     * @param out The ObjectOutputStream to write the object to.
+     * @throws IOException If an I/O error occurs.
+     */
     @Serial
     private void writeObject(ObjectOutputStream out) throws IOException {
         try {
@@ -191,6 +197,14 @@ private void writeObject(ObjectOutputStream out) throws IOException {
         }
     }
 
+    /**
+     * Reads the object from the specified ObjectInputStream. This method is used during deserialization
+     * to restore the state of the object.
+     *
+     * @param in The ObjectInputStream to read the object from.
+     * @throws IOException            If an I/O error occurs.
+     * @throws ClassNotFoundException If the class of the serialized object cannot be found.
+     */
     @Serial
     private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
         try {
diff --git a/tetrad-lib/src/main/java/edu/cmu/tetrad/study/gene/tetrad/gene/simulation/MeasurementSimulator.java b/tetrad-lib/src/main/java/edu/cmu/tetrad/study/gene/tetrad/gene/simulation/MeasurementSimulator.java
index 640678d5da..f76c6fa0e2 100755
--- a/tetrad-lib/src/main/java/edu/cmu/tetrad/study/gene/tetrad/gene/simulation/MeasurementSimulator.java
+++ b/tetrad-lib/src/main/java/edu/cmu/tetrad/study/gene/tetrad/gene/simulation/MeasurementSimulator.java
@@ -975,6 +975,12 @@ class results in an inconsistent parameter set. jdramsey 12/22/01
         becomes an issue. jdramsey 12/22/01
         */
 
+    /**
+     * Writes the object to the specified ObjectOutputStream.
+     *
+     * @param out The ObjectOutputStream to write the object to.
+     * @throws IOException If an I/O error occurs.
+     */
     @Serial
     private void writeObject(ObjectOutputStream out) throws IOException {
         try {
@@ -986,6 +992,14 @@ private void writeObject(ObjectOutputStream out) throws IOException {
         }
     }
 
+    /**
+     * Reads the object from the specified ObjectInputStream. This method is used during deserialization
+     * to restore the state of the object.
+     *
+     * @param in The ObjectInputStream to read the object from.
+     * @throws IOException            If an I/O error occurs.
+     * @throws ClassNotFoundException If the class of the serialized object cannot be found.
+     */
     @Serial
     private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
         try {
diff --git a/tetrad-lib/src/main/java/edu/cmu/tetrad/study/gene/tetradapp/model/GenePm.java b/tetrad-lib/src/main/java/edu/cmu/tetrad/study/gene/tetradapp/model/GenePm.java
index 76bdd8507b..f636d84497 100644
--- a/tetrad-lib/src/main/java/edu/cmu/tetrad/study/gene/tetradapp/model/GenePm.java
+++ b/tetrad-lib/src/main/java/edu/cmu/tetrad/study/gene/tetradapp/model/GenePm.java
@@ -67,6 +67,12 @@ public LagGraph getLagGraph() {
         return this.lagGraph;
     }
 
+    /**
+     * Writes the object to the specified ObjectOutputStream.
+     *
+     * @param out The ObjectOutputStream to write the object to.
+     * @throws IOException If an I/O error occurs.
+     */
     @Serial
     private void writeObject(ObjectOutputStream out) throws IOException {
         try {
@@ -78,6 +84,14 @@ private void writeObject(ObjectOutputStream out) throws IOException {
         }
     }
 
+    /**
+     * Reads the object from the specified ObjectInputStream. This method is used during deserialization
+     * to restore the state of the object.
+     *
+     * @param in The ObjectInputStream to read the object from.
+     * @throws IOException            If an I/O error occurs.
+     * @throws ClassNotFoundException If the class of the serialized object cannot be found.
+     */
     @Serial
     private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
         try {
diff --git a/tetrad-lib/src/main/java/edu/cmu/tetrad/study/gene/tetradapp/model/MeasurementSimulatorParams.java b/tetrad-lib/src/main/java/edu/cmu/tetrad/study/gene/tetradapp/model/MeasurementSimulatorParams.java
index e779a7384a..fbcf73a0d0 100644
--- a/tetrad-lib/src/main/java/edu/cmu/tetrad/study/gene/tetradapp/model/MeasurementSimulatorParams.java
+++ b/tetrad-lib/src/main/java/edu/cmu/tetrad/study/gene/tetradapp/model/MeasurementSimulatorParams.java
@@ -370,6 +370,12 @@ public double[][][] getRawData() {
         return getSimulator().getRawData();
     }
 
+    /**
+     * Writes the object to the specified ObjectOutputStream.
+     *
+     * @param out The ObjectOutputStream to write the object to.
+     * @throws IOException If an I/O error occurs.
+     */
     @Serial
     private void writeObject(ObjectOutputStream out) throws IOException {
         try {
@@ -381,6 +387,14 @@ private void writeObject(ObjectOutputStream out) throws IOException {
         }
     }
 
+    /**
+     * Reads the object from the specified ObjectInputStream. This method is used during deserialization
+     * to restore the state of the object.
+     *
+     * @param in The ObjectInputStream to read the object from.
+     * @throws IOException            If an I/O error occurs.
+     * @throws ClassNotFoundException If the class of the serialized object cannot be found.
+     */
     @Serial
     private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
         try {
diff --git a/tetrad-lib/src/main/java/edu/cmu/tetrad/util/Matrix.java b/tetrad-lib/src/main/java/edu/cmu/tetrad/util/Matrix.java
index 492649a3e2..21ad683b99 100644
--- a/tetrad-lib/src/main/java/edu/cmu/tetrad/util/Matrix.java
+++ b/tetrad-lib/src/main/java/edu/cmu/tetrad/util/Matrix.java
@@ -629,6 +629,12 @@ public String toString() {
         }
     }
 
+    /**
+     * Writes the object to the specified ObjectOutputStream.
+     *
+     * @param out The ObjectOutputStream to write the object to.
+     * @throws IOException If an I/O error occurs.
+     */
     @Serial
     private void writeObject(ObjectOutputStream out) throws IOException {
         try {
@@ -640,6 +646,14 @@ private void writeObject(ObjectOutputStream out) throws IOException {
         }
     }
 
+    /**
+     * Reads the object from the specified ObjectInputStream. This method is used during deserialization
+     * to restore the state of the object.
+     *
+     * @param in The ObjectInputStream to read the object from.
+     * @throws IOException            If an I/O error occurs.
+     * @throws ClassNotFoundException If the class of the serialized object cannot be found.
+     */
     @Serial
     private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
         try {
diff --git a/tetrad-lib/src/main/java/edu/cmu/tetrad/util/Parameters.java b/tetrad-lib/src/main/java/edu/cmu/tetrad/util/Parameters.java
index 518899a579..04aeb5e236 100644
--- a/tetrad-lib/src/main/java/edu/cmu/tetrad/util/Parameters.java
+++ b/tetrad-lib/src/main/java/edu/cmu/tetrad/util/Parameters.java
@@ -346,6 +346,12 @@ public void remove(String parameter) {
         parameters.remove(parameter);
     }
 
+    /**
+     * Writes the object to the specified ObjectOutputStream.
+     *
+     * @param out The ObjectOutputStream to write the object to.
+     * @throws IOException If an I/O error occurs.
+     */
     @Serial
     private void writeObject(ObjectOutputStream out) throws IOException {
         try {
@@ -357,6 +363,14 @@ private void writeObject(ObjectOutputStream out) throws IOException {
         }
     }
 
+    /**
+     * Reads the object from the specified ObjectInputStream. This method is used during deserialization
+     * to restore the state of the object.
+     *
+     * @param in The ObjectInputStream to read the object from.
+     * @throws IOException            If an I/O error occurs.
+     * @throws ClassNotFoundException If the class of the serialized object cannot be found.
+     */
     @Serial
     private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
         try {
diff --git a/tetrad-lib/src/main/java/edu/cmu/tetrad/util/Params.java b/tetrad-lib/src/main/java/edu/cmu/tetrad/util/Params.java
index 906078b4dd..9d0942e379 100644
--- a/tetrad-lib/src/main/java/edu/cmu/tetrad/util/Params.java
+++ b/tetrad-lib/src/main/java/edu/cmu/tetrad/util/Params.java
@@ -891,7 +891,7 @@ public final class Params {
      */
     public static final String ALLOW_TUCKS = "allowTucks";
     /**
-     * Constant <code>ALLOW_TUCKS="allowTucks
+     * Constant <code>ALLOW_TUCKS="allowTucks"</code>
      */
     public static final String EQUALITY_THRESHOLD = "equalityThreshold";
     /**
diff --git a/tetrad-lib/src/main/java/edu/cmu/tetrad/util/PointXy.java b/tetrad-lib/src/main/java/edu/cmu/tetrad/util/PointXy.java
index a514ca2993..687d4f90d4 100644
--- a/tetrad-lib/src/main/java/edu/cmu/tetrad/util/PointXy.java
+++ b/tetrad-lib/src/main/java/edu/cmu/tetrad/util/PointXy.java
@@ -127,6 +127,12 @@ public String toString() {
         return "Point<" + this.x + "," + this.y + ">";
     }
 
+    /**
+     * Writes the object to the specified ObjectOutputStream.
+     *
+     * @param out The ObjectOutputStream to write the object to.
+     * @throws IOException If an I/O error occurs.
+     */
     @Serial
     private void writeObject(ObjectOutputStream out) throws IOException {
         try {
@@ -138,6 +144,14 @@ private void writeObject(ObjectOutputStream out) throws IOException {
         }
     }
 
+    /**
+     * Reads the object from the specified ObjectInputStream. This method is used during deserialization
+     * to restore the state of the object.
+     *
+     * @param in The ObjectInputStream to read the object from.
+     * @throws IOException            If an I/O error occurs.
+     * @throws ClassNotFoundException If the class of the serialized object cannot be found.
+     */
     @Serial
     private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
         try {
diff --git a/tetrad-lib/src/main/java/edu/cmu/tetrad/util/Vector.java b/tetrad-lib/src/main/java/edu/cmu/tetrad/util/Vector.java
index e5d7af0b94..2a75c360cc 100644
--- a/tetrad-lib/src/main/java/edu/cmu/tetrad/util/Vector.java
+++ b/tetrad-lib/src/main/java/edu/cmu/tetrad/util/Vector.java
@@ -259,6 +259,12 @@ public double dot(Vector v2) {
         return sum;
     }
 
+    /**
+     * Writes the object to the specified ObjectOutputStream.
+     *
+     * @param out The ObjectOutputStream to write the object to.
+     * @throws IOException If an I/O error occurs.
+     */
     @Serial
     private void writeObject(ObjectOutputStream out) throws IOException {
         try {
@@ -270,6 +276,14 @@ private void writeObject(ObjectOutputStream out) throws IOException {
         }
     }
 
+    /**
+     * Reads the object from the specified ObjectInputStream. This method is used during deserialization
+     * to restore the state of the object.
+     *
+     * @param in The ObjectInputStream to read the object from.
+     * @throws IOException            If an I/O error occurs.
+     * @throws ClassNotFoundException If the class of the serialized object cannot be found.
+     */
     @Serial
     private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
         try {
diff --git a/tetrad-lib/src/main/java/edu/cmu/tetrad/util/Version.java b/tetrad-lib/src/main/java/edu/cmu/tetrad/util/Version.java
index 14116fe2f9..0c529f6756 100644
--- a/tetrad-lib/src/main/java/edu/cmu/tetrad/util/Version.java
+++ b/tetrad-lib/src/main/java/edu/cmu/tetrad/util/Version.java
@@ -301,6 +301,12 @@ public String toString() {
 
     //===========================PRIVATE METHODS=========================//
 
+    /**
+     * Writes the object to the specified ObjectOutputStream.
+     *
+     * @param out The ObjectOutputStream to write the object to.
+     * @throws IOException If an I/O error occurs.
+     */
     @Serial
     private void writeObject(ObjectOutputStream out) throws IOException {
         try {
@@ -312,6 +318,14 @@ private void writeObject(ObjectOutputStream out) throws IOException {
         }
     }
 
+    /**
+     * Reads the object from the specified ObjectInputStream. This method is used during deserialization
+     * to restore the state of the object.
+     *
+     * @param in The ObjectInputStream to read the object from.
+     * @throws IOException            If an I/O error occurs.
+     * @throws ClassNotFoundException If the class of the serialized object cannot be found.
+     */
     @Serial
     private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
         try {
diff --git a/tetrad-lib/src/main/java/edu/cmu/tetrad/util/dist/ChiSquare.java b/tetrad-lib/src/main/java/edu/cmu/tetrad/util/dist/ChiSquare.java
index fb802f336d..d517141b5d 100644
--- a/tetrad-lib/src/main/java/edu/cmu/tetrad/util/dist/ChiSquare.java
+++ b/tetrad-lib/src/main/java/edu/cmu/tetrad/util/dist/ChiSquare.java
@@ -143,6 +143,12 @@ public String toString() {
         return "ChiSquare(" + this.df + ")";
     }
 
+    /**
+     * Writes the object to the specified ObjectOutputStream.
+     *
+     * @param out The ObjectOutputStream to write the object to.
+     * @throws IOException If an I/O error occurs.
+     */
     @Serial
     private void writeObject(ObjectOutputStream out) throws IOException {
         try {
@@ -154,6 +160,14 @@ private void writeObject(ObjectOutputStream out) throws IOException {
         }
     }
 
+    /**
+     * Reads the object from the specified ObjectInputStream. This method is used during deserialization
+     * to restore the state of the object.
+     *
+     * @param in The ObjectInputStream to read the object from.
+     * @throws IOException            If an I/O error occurs.
+     * @throws ClassNotFoundException If the class of the serialized object cannot be found.
+     */
     @Serial
     private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
         try {
diff --git a/tetrad-lib/src/main/java/edu/cmu/tetrad/util/dist/Normal.java b/tetrad-lib/src/main/java/edu/cmu/tetrad/util/dist/Normal.java
index 32c1ada925..7f284f5a01 100644
--- a/tetrad-lib/src/main/java/edu/cmu/tetrad/util/dist/Normal.java
+++ b/tetrad-lib/src/main/java/edu/cmu/tetrad/util/dist/Normal.java
@@ -155,6 +155,12 @@ public String toString() {
 
     //========================PRIVATE METHODS===========================//
 
+    /**
+     * Writes the object to the specified ObjectOutputStream.
+     *
+     * @param out The ObjectOutputStream to write the object to.
+     * @throws IOException If an I/O error occurs.
+     */
     @Serial
     private void writeObject(ObjectOutputStream out) throws IOException {
         try {
@@ -166,6 +172,14 @@ private void writeObject(ObjectOutputStream out) throws IOException {
         }
     }
 
+    /**
+     * Reads the object from the specified ObjectInputStream. This method is used during deserialization
+     * to restore the state of the object.
+     *
+     * @param in The ObjectInputStream to read the object from.
+     * @throws IOException            If an I/O error occurs.
+     * @throws ClassNotFoundException If the class of the serialized object cannot be found.
+     */
     @Serial
     private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
         try {
diff --git a/tetrad-lib/src/main/java/edu/cmu/tetrad/util/dist/Split.java b/tetrad-lib/src/main/java/edu/cmu/tetrad/util/dist/Split.java
index 2767efd4f4..3c1d3e36b1 100644
--- a/tetrad-lib/src/main/java/edu/cmu/tetrad/util/dist/Split.java
+++ b/tetrad-lib/src/main/java/edu/cmu/tetrad/util/dist/Split.java
@@ -186,6 +186,12 @@ public int getNumParameters() {
         return 2;
     }
 
+    /**
+     * Writes the object to the specified ObjectOutputStream.
+     *
+     * @param out The ObjectOutputStream to write the object to.
+     * @throws IOException If an I/O error occurs.
+     */
     @Serial
     private void writeObject(ObjectOutputStream out) throws IOException {
         try {
@@ -197,6 +203,14 @@ private void writeObject(ObjectOutputStream out) throws IOException {
         }
     }
 
+    /**
+     * Reads the object from the specified ObjectInputStream. This method is used during deserialization
+     * to restore the state of the object.
+     *
+     * @param in The ObjectInputStream to read the object from.
+     * @throws IOException            If an I/O error occurs.
+     * @throws ClassNotFoundException If the class of the serialized object cannot be found.
+     */
     @Serial
     private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
         try {
diff --git a/tetrad-lib/src/main/java/edu/cmu/tetrad/util/dist/TruncatedNormal.java b/tetrad-lib/src/main/java/edu/cmu/tetrad/util/dist/TruncatedNormal.java
index 77dd4b4613..f51a79a5f6 100644
--- a/tetrad-lib/src/main/java/edu/cmu/tetrad/util/dist/TruncatedNormal.java
+++ b/tetrad-lib/src/main/java/edu/cmu/tetrad/util/dist/TruncatedNormal.java
@@ -176,6 +176,12 @@ public String toString() {
 
     //========================PRIVATE METHODS===========================//
 
+    /**
+     * Writes the object to the specified ObjectOutputStream.
+     *
+     * @param out The ObjectOutputStream to write the object to.
+     * @throws IOException If an I/O error occurs.
+     */
     @Serial
     private void writeObject(ObjectOutputStream out) throws IOException {
         try {
@@ -187,6 +193,14 @@ private void writeObject(ObjectOutputStream out) throws IOException {
         }
     }
 
+    /**
+     * Reads the object from the specified ObjectInputStream. This method is used during deserialization
+     * to restore the state of the object.
+     *
+     * @param in The ObjectInputStream to read the object from.
+     * @throws IOException            If an I/O error occurs.
+     * @throws ClassNotFoundException If the class of the serialized object cannot be found.
+     */
     @Serial
     private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
         try {
diff --git a/tetrad-lib/src/main/java/edu/cmu/tetrad/util/dist/Uniform.java b/tetrad-lib/src/main/java/edu/cmu/tetrad/util/dist/Uniform.java
index b2fec107df..e050632f75 100644
--- a/tetrad-lib/src/main/java/edu/cmu/tetrad/util/dist/Uniform.java
+++ b/tetrad-lib/src/main/java/edu/cmu/tetrad/util/dist/Uniform.java
@@ -157,6 +157,12 @@ public String toString() {
 
     //========================PRIVATE METHODS===========================//
 
+    /**
+     * Writes the object to the specified ObjectOutputStream.
+     *
+     * @param out The ObjectOutputStream to write the object to.
+     * @throws IOException If an I/O error occurs.
+     */
     @Serial
     private void writeObject(ObjectOutputStream out) throws IOException {
         try {
@@ -168,6 +174,14 @@ private void writeObject(ObjectOutputStream out) throws IOException {
         }
     }
 
+    /**
+     * Reads the object from the specified ObjectInputStream. This method is used during deserialization
+     * to restore the state of the object.
+     *
+     * @param in The ObjectInputStream to read the object from.
+     * @throws IOException            If an I/O error occurs.
+     * @throws ClassNotFoundException If the class of the serialized object cannot be found.
+     */
     @Serial
     private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
         try {