From c4feeb1aeebff7cb4399c99e1c4e9edf9140c2e4 Mon Sep 17 00:00:00 2001
From: Kevin Bui <kvb2univpitt@gmail.com>
Date: Sat, 10 Dec 2022 15:05:31 -0500
Subject: [PATCH 1/7] Fixed list-to-array conversion.

---
 src/main/java/edu/pitt/dbmi/causal/cmd/Args.java | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/main/java/edu/pitt/dbmi/causal/cmd/Args.java b/src/main/java/edu/pitt/dbmi/causal/cmd/Args.java
index 1c8fd0a..1663dfe 100644
--- a/src/main/java/edu/pitt/dbmi/causal/cmd/Args.java
+++ b/src/main/java/edu/pitt/dbmi/causal/cmd/Args.java
@@ -72,7 +72,7 @@ public static String[] removeLongOption(String[] args, String option) {
             }
         }
 
-        return argsToKeep.toArray(String[]::new);
+        return argsToKeep.stream().toArray(String[]::new);
     }
 
     /**
@@ -143,7 +143,7 @@ public static String[] extractLongOptions(String[] args, Options options) {
             }
         });
 
-        return argsList.toArray(String[]::new);
+        return argsList.stream().toArray(String[]::new);
     }
 
     /**
@@ -179,7 +179,7 @@ public static String[] extractOptions(String[] args, Options options) {
             }
         });
 
-        return argsList.toArray(String[]::new);
+        return argsList.stream().toArray(String[]::new);
     }
 
     /**

From b45dca7d57e32795dfff342248bfd42577aa9d3e Mon Sep 17 00:00:00 2001
From: Kevin Bui <kvb2univpitt@gmail.com>
Date: Sat, 10 Dec 2022 20:19:29 -0500
Subject: [PATCH 2/7] Bumped up project version number.

---
 pom.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pom.xml b/pom.xml
index c98fb3c..16ef83b 100644
--- a/pom.xml
+++ b/pom.xml
@@ -3,7 +3,7 @@
     <modelVersion>4.0.0</modelVersion>
     <groupId>edu.pitt.dbmi</groupId>
     <artifactId>causal-cmd</artifactId>
-    <version>1.4.1-SNAPSHOT</version>
+    <version>1.4.2</version>
     <packaging>jar</packaging>
 
     <properties>

From 36a00de37ad9e3d0c7b8df9f848ee49c2c246441 Mon Sep 17 00:00:00 2001
From: Kevin Bui <kvb2univpitt@gmail.com>
Date: Sat, 10 Dec 2022 20:27:06 -0500
Subject: [PATCH 3/7] Enable code to compile under Java 8.

---
 pom.xml | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/pom.xml b/pom.xml
index 16ef83b..835c64c 100644
--- a/pom.xml
+++ b/pom.xml
@@ -7,10 +7,9 @@
     <packaging>jar</packaging>
 
     <properties>
-        <java.version>11</java.version>
         <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
-        <maven.compiler.source>11</maven.compiler.source>
-        <maven.compiler.target>11</maven.compiler.target>
+        <maven.compiler.source>1.8</maven.compiler.source>
+        <maven.compiler.target>1.8</maven.compiler.target>
     </properties>
 
     <dependencies>

From e41a668d8452801abbfaddee15c24ea596e11aa1 Mon Sep 17 00:00:00 2001
From: Kevin Bui <kvb2univpitt@gmail.com>
Date: Sat, 10 Dec 2022 20:33:36 -0500
Subject: [PATCH 4/7] Updated dependencies to their latest version.

---
 pom.xml | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/pom.xml b/pom.xml
index 835c64c..3144d48 100644
--- a/pom.xml
+++ b/pom.xml
@@ -45,7 +45,7 @@
         <dependency>
             <groupId>org.junit.jupiter</groupId>
             <artifactId>junit-jupiter-engine</artifactId>
-            <version>5.8.2</version>
+            <version>5.9.1</version>
             <scope>test</scope>
         </dependency>
     </dependencies>
@@ -59,7 +59,7 @@
             </plugin>
             <plugin>
                 <artifactId>maven-resources-plugin</artifactId>
-                <version>3.2.0</version>
+                <version>3.3.0</version>
                 <executions>
                     <execution>
                         <id>copy-dist-resources</id>
@@ -82,7 +82,7 @@
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-jar-plugin</artifactId>
-                <version>3.2.2</version>
+                <version>3.3.0</version>
                 <configuration>
                     <archive>
                         <manifest>
@@ -94,7 +94,7 @@
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-assembly-plugin</artifactId>
-                <version>3.3.0</version>
+                <version>3.4.2</version>
                 <executions>
                     <execution>
                         <phase>package</phase>
@@ -133,7 +133,7 @@
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-javadoc-plugin</artifactId>
-                <version>3.4.0</version>
+                <version>3.4.1</version>
                 <configuration>
                     <javadocExecutable>/usr/bin/javadoc</javadocExecutable>
                     <!--<show>private</show>-->

From f2e9e153f72340772c9c2e11c09877bc3c41675a Mon Sep 17 00:00:00 2001
From: Kevin Bui <kvb2univpitt@gmail.com>
Date: Sat, 10 Dec 2022 21:15:00 -0500
Subject: [PATCH 5/7] Fixed code formatting.

---
 .../pitt/dbmi/causal/cmd/CausalCmdApplication.java  |  2 +-
 src/main/java/edu/pitt/dbmi/causal/cmd/CmdArgs.java | 13 +++++++------
 .../java/edu/pitt/dbmi/causal/cmd/CmdOptions.java   |  3 +--
 .../java/edu/pitt/dbmi/causal/cmd/CmdParams.java    |  2 +-
 .../edu/pitt/dbmi/causal/cmd/data/DataFiles.java    |  2 +-
 .../java/edu/pitt/dbmi/causal/cmd/util/GraphIO.java |  4 ++--
 6 files changed, 13 insertions(+), 13 deletions(-)

diff --git a/src/main/java/edu/pitt/dbmi/causal/cmd/CausalCmdApplication.java b/src/main/java/edu/pitt/dbmi/causal/cmd/CausalCmdApplication.java
index e02eac7..74c6fb6 100644
--- a/src/main/java/edu/pitt/dbmi/causal/cmd/CausalCmdApplication.java
+++ b/src/main/java/edu/pitt/dbmi/causal/cmd/CausalCmdApplication.java
@@ -137,7 +137,7 @@ private static void runTetrad(CmdArgs cmdArgs) throws AlgorithmRunException, Val
             Files.deleteIfExists(outTxtFile);
         }
 
-        try ( PrintStream out = new PrintStream(new BufferedOutputStream(Files.newOutputStream(outTxtFile, StandardOpenOption.CREATE)), true)) {
+        try (PrintStream out = new PrintStream(new BufferedOutputStream(Files.newOutputStream(outTxtFile, StandardOpenOption.CREATE)), true)) {
             writeOutParameters(cmdArgs, out);
 
             if (!cmdArgs.isSkipValidation()) {
diff --git a/src/main/java/edu/pitt/dbmi/causal/cmd/CmdArgs.java b/src/main/java/edu/pitt/dbmi/causal/cmd/CmdArgs.java
index 9a9b538..80cf7d5 100644
--- a/src/main/java/edu/pitt/dbmi/causal/cmd/CmdArgs.java
+++ b/src/main/java/edu/pitt/dbmi/causal/cmd/CmdArgs.java
@@ -79,7 +79,7 @@ public class CmdArgs {
      * by the data reader.
      */
     protected String commentMarker;
-    
+
     /**
      * Indicates whether the first line in the data file is a header.
      */
@@ -89,7 +89,7 @@ public class CmdArgs {
      * Type of data in the dataset.
      */
     protected DataType dataType;
-    
+
     /**
      * Data delimiter.
      */
@@ -99,12 +99,12 @@ public class CmdArgs {
      * Algorithm class.
      */
     protected Class algorithmClass;
-    
+
     /**
      * Score class.
      */
     protected Class scoreClass;
-    
+
     /**
      * Independence test class.
      */
@@ -119,14 +119,15 @@ public class CmdArgs {
      * Indicates whether or not to skip data validation.
      */
     protected boolean skipValidation;
-    
+
     /**
      * Indicates whether to output the search graph in JSON format.
      */
     protected boolean jsonGraph;
 
     /**
-     * Maximum number of threads can be used by algorithm, score, or independence test.
+     * Maximum number of threads can be used by algorithm, score, or
+     * independence test.
      */
     protected int numOfThreads;
 
diff --git a/src/main/java/edu/pitt/dbmi/causal/cmd/CmdOptions.java b/src/main/java/edu/pitt/dbmi/causal/cmd/CmdOptions.java
index 834130a..bed8499 100644
--- a/src/main/java/edu/pitt/dbmi/causal/cmd/CmdOptions.java
+++ b/src/main/java/edu/pitt/dbmi/causal/cmd/CmdOptions.java
@@ -165,12 +165,11 @@ public List<Option> getBaseOptions() {
         opts.add(options.get(CmdParams.DIR_OUT));
 
 //        opts.add(options.get(CmdParams.THREAD));
-
         // data validation options
         opts.add(options.get(CmdParams.SKIP_VALIDATION));
 
         opts.add(options.get(CmdParams.EXPERIMENTAL));
-        
+
         opts.add(options.get(CmdParams.DEFAULT));
 
         return opts;
diff --git a/src/main/java/edu/pitt/dbmi/causal/cmd/CmdParams.java b/src/main/java/edu/pitt/dbmi/causal/cmd/CmdParams.java
index d4acf59..bd99fac 100644
--- a/src/main/java/edu/pitt/dbmi/causal/cmd/CmdParams.java
+++ b/src/main/java/edu/pitt/dbmi/causal/cmd/CmdParams.java
@@ -78,7 +78,7 @@ public final class CmdParams {
     public static final String EXTRACT_STRUCT_MODEL = "extract-struct-model";
 
     public static final String EXPERIMENTAL = "experimental";
-    
+
     public static final String DEFAULT = "default";
 
     private CmdParams() {
diff --git a/src/main/java/edu/pitt/dbmi/causal/cmd/data/DataFiles.java b/src/main/java/edu/pitt/dbmi/causal/cmd/data/DataFiles.java
index 3e94a78..9e3e1a5 100644
--- a/src/main/java/edu/pitt/dbmi/causal/cmd/data/DataFiles.java
+++ b/src/main/java/edu/pitt/dbmi/causal/cmd/data/DataFiles.java
@@ -245,7 +245,7 @@ public static Set<String> readInVariablesToExclude(CmdArgs cmdArgs, PrintStream
         Path file = cmdArgs.getExcludeVariableFile();
         if (file != null) {
             LogMessages.readingFileStart(file, LOGGER, out);
-            try ( Stream<String> stream = Files.lines(file)) {
+            try (Stream<String> stream = Files.lines(file)) {
                 stream
                         .map(e -> e.trim())
                         .filter(e -> !e.isEmpty())
diff --git a/src/main/java/edu/pitt/dbmi/causal/cmd/util/GraphIO.java b/src/main/java/edu/pitt/dbmi/causal/cmd/util/GraphIO.java
index 94aca24..4cf6853 100644
--- a/src/main/java/edu/pitt/dbmi/causal/cmd/util/GraphIO.java
+++ b/src/main/java/edu/pitt/dbmi/causal/cmd/util/GraphIO.java
@@ -49,7 +49,7 @@ private GraphIO() {
      */
     public static void writeAsTXT(Graph graph, Path path) throws IOException {
         Scanner scanner = new Scanner(graph.toString());
-        try ( PrintStream out = new PrintStream(Files.newOutputStream(path), true)) {
+        try (PrintStream out = new PrintStream(Files.newOutputStream(path), true)) {
             while (scanner.hasNextLine()) {
                 out.println(scanner.nextLine().trim());
             }
@@ -65,7 +65,7 @@ public static void writeAsTXT(Graph graph, Path path) throws IOException {
      */
     public static void writeAsJSON(Graph graph, Path path) throws IOException {
         Gson gson = new GsonBuilder().setPrettyPrinting().create();
-        try ( PrintStream out = new PrintStream(Files.newOutputStream(path), true)) {
+        try (PrintStream out = new PrintStream(Files.newOutputStream(path), true)) {
             out.println(gson.toJson(graph));
         }
     }

From 631961b5c6e6bd29d959efc99f8113f319fb3cd3 Mon Sep 17 00:00:00 2001
From: Kevin Bui <kvb2univpitt@gmail.com>
Date: Sat, 10 Dec 2022 21:21:29 -0500
Subject: [PATCH 6/7] Fixed txt output file deletion. See issue #78.

---
 .../java/edu/pitt/dbmi/causal/cmd/CausalCmdApplication.java     | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/main/java/edu/pitt/dbmi/causal/cmd/CausalCmdApplication.java b/src/main/java/edu/pitt/dbmi/causal/cmd/CausalCmdApplication.java
index 74c6fb6..96b804e 100644
--- a/src/main/java/edu/pitt/dbmi/causal/cmd/CausalCmdApplication.java
+++ b/src/main/java/edu/pitt/dbmi/causal/cmd/CausalCmdApplication.java
@@ -166,7 +166,7 @@ private static void runTetrad(CmdArgs cmdArgs) throws AlgorithmRunException, Val
 
                     Path outGraphFile = Paths.get(outDir, fileName);
                     if (Files.exists(outGraphFile)) {
-                        Files.deleteIfExists(outTxtFile);
+                        Files.deleteIfExists(outGraphFile);
                     }
 
                     GraphIO.writeAsJSON(graphs[i], outGraphFile);

From 75d85254044958267b28f417d578e5590bea08b6 Mon Sep 17 00:00:00 2001
From: Kevin Bui <kvb2univpitt@gmail.com>
Date: Sat, 10 Dec 2022 22:57:00 -0500
Subject: [PATCH 7/7] Added more documentations.

---
 .../edu/pitt/dbmi/causal/cmd/CmdOptions.java  | 16 +--
 .../edu/pitt/dbmi/causal/cmd/CmdParser.java   | 99 ++++++++++++-------
 .../pitt/dbmi/causal/cmd/OptionFactory.java   | 14 +--
 .../pitt/dbmi/causal/cmd/data/DataFiles.java  | 51 +++++-----
 .../dbmi/causal/cmd/data/DataValidations.java | 14 +--
 .../pitt/dbmi/causal/cmd/tetrad/Tetrad.java   |  4 +-
 .../causal/cmd/tetrad/TetradAlgorithms.java   | 35 +++----
 .../cmd/tetrad/TetradIndependenceTests.java   | 44 +++++----
 .../dbmi/causal/cmd/tetrad/TetradRunner.java  | 32 +++---
 .../dbmi/causal/cmd/tetrad/TetradScores.java  | 44 +++++----
 .../pitt/dbmi/causal/cmd/util/DateTime.java   | 10 ++
 .../pitt/dbmi/causal/cmd/util/FileUtils.java  |  7 ++
 .../pitt/dbmi/causal/cmd/util/GraphIO.java    | 12 +--
 .../dbmi/causal/cmd/util/LogMessages.java     | 44 ++++-----
 .../pitt/dbmi/causal/cmd/util/WordUtil.java   |  4 +-
 15 files changed, 241 insertions(+), 189 deletions(-)

diff --git a/src/main/java/edu/pitt/dbmi/causal/cmd/CmdOptions.java b/src/main/java/edu/pitt/dbmi/causal/cmd/CmdOptions.java
index bed8499..c4bbc35 100644
--- a/src/main/java/edu/pitt/dbmi/causal/cmd/CmdOptions.java
+++ b/src/main/java/edu/pitt/dbmi/causal/cmd/CmdOptions.java
@@ -54,7 +54,7 @@ private CmdOptions() {
     /**
      * Get an instance of the command-line options.
      *
-     * @return
+     * @return CmdOptions instance
      */
     public static CmdOptions getInstance() {
         if (instance == null) {
@@ -75,7 +75,7 @@ public static void clear() {
      * Get multi-character name options for a given name..
      *
      * @param param multi-character name
-     * @return
+     * @return command-line option
      */
     public Option getLongOption(String param) {
         return options.get(param);
@@ -249,7 +249,7 @@ private void addRequiredOptions() {
     /**
      * Get the application required options from the stored options.
      *
-     * @return
+     * @return required command-line options
      */
     public List<Option> getRequiredOptions() {
         return options.entrySet().stream()
@@ -261,7 +261,7 @@ public List<Option> getRequiredOptions() {
     /**
      * Get the names of all the datatypes.
      *
-     * @return
+     * @return datatype description
      */
     private String getDataTypeDesc() {
         return "Data type: " + DataTypes.getInstance().getNames().stream()
@@ -271,7 +271,7 @@ private String getDataTypeDesc() {
     /**
      * Get the names of all the delimiters.
      *
-     * @return
+     * @return names of delimiters
      */
     private String getDelimiterDesc() {
         return "Delimiter: " + Delimiters.getInstance().getNames().stream()
@@ -281,7 +281,7 @@ private String getDelimiterDesc() {
     /**
      * Get the names of all the scores.
      *
-     * @return
+     * @return description for score
      */
     private String getScoreDesc() {
         return "Score: " + TetradScores.getInstance().getCommands().stream()
@@ -291,7 +291,7 @@ private String getScoreDesc() {
     /**
      * Get the names of all the independence test.
      *
-     * @return
+     * @return description for test of independence
      */
     private String getIndependenceTestDesc() {
         return "Independence Test: " + TetradIndependenceTests.getInstance().getCommands().stream()
@@ -301,7 +301,7 @@ private String getIndependenceTestDesc() {
     /**
      * Get the names of all the algorithms.
      *
-     * @return
+     * @return description for algorithm
      */
     private String getAlgorithmDesc() {
         return "Algorithm: " + TetradAlgorithms.getInstance().getCommands().stream()
diff --git a/src/main/java/edu/pitt/dbmi/causal/cmd/CmdParser.java b/src/main/java/edu/pitt/dbmi/causal/cmd/CmdParser.java
index bb02fdc..fd97a94 100644
--- a/src/main/java/edu/pitt/dbmi/causal/cmd/CmdParser.java
+++ b/src/main/java/edu/pitt/dbmi/causal/cmd/CmdParser.java
@@ -61,6 +61,13 @@ public final class CmdParser {
     private CmdParser() {
     }
 
+    /**
+     * Parse user input command
+     *
+     * @param args user input command
+     * @return user input command values
+     * @throws CmdParserException when an error occurs while parsing
+     */
     public static CmdArgs parse(String[] args) throws CmdParserException {
         CmdArgs cmdArgs = new CmdArgs();
 
@@ -80,10 +87,10 @@ public static CmdArgs parse(String[] args) throws CmdParserException {
     /**
      * Parse command-line options.
      *
-     * @param cmd
-     * @param parseOptions
-     * @param cmdArgs
-     * @throws CmdParserException
+     * @param cmd command-line input
+     * @param parseOptions command-line options
+     * @param cmdArgs parsed command line arguments and values
+     * @throws CmdParserException when an error occurs while parsing
      */
     private static void parseOptionalOptions(CommandLine cmd, ParseOptions parseOptions, CmdArgs cmdArgs) throws CmdParserException {
         cmdArgs.knowledgeFile = cmd.hasOption(CmdParams.KNOWLEDGE)
@@ -143,10 +150,10 @@ private static void parseOptionalOptions(CommandLine cmd, ParseOptions parseOpti
     /**
      * Parse the required command-line options.
      *
-     * @param cmd
-     * @param parseOptions
-     * @param cmdArgs
-     * @throws CmdParserException
+     * @param cmd command-line input
+     * @param parseOptions command-line options
+     * @param cmdArgs parsed command line arguments and values
+     * @throws CmdParserException when an error occurs while parsing
      */
     private static void parseRequiredOptions(CommandLine cmd, ParseOptions parseOptions, CmdArgs cmdArgs) throws CmdParserException {
         cmdArgs.dataType = DataTypes.getInstance().get(cmd.getOptionValue(CmdParams.DATA_TYPE));
@@ -176,9 +183,9 @@ private static void parseRequiredOptions(CommandLine cmd, ParseOptions parseOpti
     /**
      * Get the options for the help message.
      *
-     * @param args
-     * @return
-     * @throws CmdParserException
+     * @param args user input command
+     * @return parsed command-line options
+     * @throws CmdParserException when an error occurs while parsing
      */
     public static ParseOptions getHelpOptions(String[] args) throws CmdParserException {
         CmdOptions cmdOptions = CmdOptions.getInstance();
@@ -338,8 +345,8 @@ private static ParseOptions getValidOptions(String[] args, Options options) thro
      * Get the parameters for the algorithm, the algorithm's test, algorithm's
      * score and bootstrap.
      *
-     * @param algorithm
-     * @return
+     * @param algorithm algorithm to get the parameters for
+     * @return set of parameters related to the given algorithm
      */
     private static Set<String> getAlgorithmRelatedParameters(Algorithm algorithm) {
         if (algorithm == null) {
@@ -370,7 +377,7 @@ private static Set<String> getAlgorithmRelatedParameters(Algorithm algorithm) {
     /**
      * Add options for manipulating Tetrad output graph.
      *
-     * @param opts
+     * @param opts options to add to
      */
     private static void addGraphManipulationOptions(Options opts) {
         opts.addOption(CmdOptions.getInstance().getLongOption(CmdParams.CHOOSE_DAG_IN_PATTERN));
@@ -393,6 +400,12 @@ private static String getValidPrefix(CommandLine cmd, CmdArgs cmdArgs, ParseOpti
         }
     }
 
+    /**
+     * Extract class name.
+     *
+     * @param clazz class to extract name from
+     * @return class name
+     */
     private static String extractName(Class clazz) {
         String name = clazz.getName();
         String[] fields = name.toLowerCase().split("\\.");
@@ -404,10 +417,11 @@ private static String extractName(Class clazz) {
      * Get all the parameters related to the selected algorithm, test, and
      * score.
      *
-     * @param cmdArgs
-     * @param parseOptions
-     * @return
-     * @throws CmdParserException
+     * @param cmdArgs parsed command line arguments and values
+     * @param parseOptions command-line options
+     * @return set of parameters relating to the given algorithm, test and score
+     * from the command-line.
+     * @throws CmdParserException when an error occurs while parsing
      */
     private static Set<String> getAllRelatedParameters(CmdArgs cmdArgs, ParseOptions parseOptions) throws CmdParserException {
         try {
@@ -422,11 +436,11 @@ private static Set<String> getAllRelatedParameters(CmdArgs cmdArgs, ParseOptions
      * for the parameters if user use the "--default" flag. Replace any value if
      * user explicitly specified with parameter-arg input or flag.
      *
-     * @param cmd
-     * @param cmdArgs
-     * @param parseOptions
-     * @return
-     * @throws CmdParserException
+     * @param cmd command-line input
+     * @param cmdArgs parsed command line arguments and values
+     * @param parseOptions command-line options
+     * @return a collection of valid parameters
+     * @throws CmdParserException when an error occurs while parsing
      */
     private static Map<String, String> getValidParameters(CommandLine cmd, CmdArgs cmdArgs, ParseOptions parseOptions) throws CmdParserException {
         Map<String, String> parametersWithValues = new TreeMap<>(String.CASE_INSENSITIVE_ORDER);
@@ -439,6 +453,15 @@ private static Map<String, String> getValidParameters(CommandLine cmd, CmdArgs c
         return parametersWithValues;
     }
 
+    /**
+     * Set parameters based on user's input.
+     *
+     * @param parametersWithValues set of parameters and values
+     * @param parameters set of parameters
+     * @param cmd command-line input
+     * @param parseOptions command-line options
+     * @throws CmdParserException when an error occurs while parsing
+     */
     private static void setUserParameterValues(Map<String, String> parametersWithValues, Set<String> parameters, CommandLine cmd, ParseOptions parseOptions) throws CmdParserException {
         ParamDescriptions paramDescriptions = ParamDescriptions.getInstance();
         Options opts = parseOptions.getOptions();
@@ -531,11 +554,11 @@ private static void setParametersAndValues(Map<String, String> parametersWithVal
      * Extract the thread number from the command-line option and check to make
      * sure the number is valid.
      *
-     * @param value
-     * @param parseOptions
-     * @param cmdParam
-     * @return
-     * @throws CmdParserException
+     * @param value number of threads taken from the command-line
+     * @param parseOptions command-line options
+     * @param cmdParam command-line parameter
+     * @return number of thread from the command-line input that is valid
+     * @throws CmdParserException when an error occurs while parsing
      */
     private static int getValidThreadNumber(String value, ParseOptions parseOptions, String cmdParam) throws CmdParserException {
         int numOfThreads = 0;
@@ -564,11 +587,11 @@ private static int getValidThreadNumber(String value, ParseOptions parseOptions,
      * Extract the delimiter charactor from the command-line option and make
      * sure the character is valid.
      *
-     * @param quoteChar
-     * @param parseOptions
-     * @param cmdParam
-     * @return
-     * @throws CmdParserException
+     * @param quoteChar character from the command-line
+     * @param parseOptions command-line options
+     * @param cmdParam command-line parameter
+     * @return character from the command-line input that is valid
+     * @throws CmdParserException when an error occurs while parsing
      */
     private static char getValidChar(String quoteChar, ParseOptions parseOptions, String cmdParam) throws CmdParserException {
         char c = 0;
@@ -591,11 +614,11 @@ private static char getValidChar(String quoteChar, ParseOptions parseOptions, St
      * Extract the file location from the command-line option and make sure the
      * file is valid.
      *
-     * @param filePath
-     * @param parseOptions
-     * @param cmdParam
-     * @return
-     * @throws CmdParserException
+     * @param filePath path to where the file is from the command-line input
+     * @param parseOptions command-line options
+     * @param cmdParam command-line parameter
+     * @return the path of the file from the command-line input that exists
+     * @throws CmdParserException when an error occurs while parsing
      */
     private static Path getValidFile(String filePath, ParseOptions parseOptions, String cmdParam) throws CmdParserException {
         Path file = Paths.get(filePath);
diff --git a/src/main/java/edu/pitt/dbmi/causal/cmd/OptionFactory.java b/src/main/java/edu/pitt/dbmi/causal/cmd/OptionFactory.java
index 070ddf8..4af0237 100644
--- a/src/main/java/edu/pitt/dbmi/causal/cmd/OptionFactory.java
+++ b/src/main/java/edu/pitt/dbmi/causal/cmd/OptionFactory.java
@@ -41,7 +41,7 @@ private OptionFactory() {
     /**
      * Create the required options for the help message.
      *
-     * @return
+     * @return required options
      */
     public static Option createRequiredHelpOpt() {
         Option opt = CmdOptions.getInstance().getLongOption(CmdParams.HELP);
@@ -56,10 +56,10 @@ public static Option createRequiredHelpOpt() {
     }
 
     /**
-     * Create the required indepedence test options.
+     * Create the required options for the test of independence.
      *
-     * @param dataType
-     * @return
+     * @param dataType data type
+     * @return options required options for the test of independence
      */
     public static Option createRequiredTestOpt(DataType dataType) {
         List<String> commands = TetradIndependenceTests.getInstance().getCommands(dataType);
@@ -78,8 +78,8 @@ public static Option createRequiredTestOpt(DataType dataType) {
     /**
      * Create the required score options.
      *
-     * @param dataType
-     * @return
+     * @param dataType data type
+     * @return options required options for the score
      */
     public static Option createRequiredScoreOpt(DataType dataType) {
         List<String> commands = TetradScores.getInstance().getCommands(dataType);
@@ -98,7 +98,7 @@ public static Option createRequiredScoreOpt(DataType dataType) {
     /**
      * Create the required option for the number of category for mixed data.
      *
-     * @return
+     * @return required option for number of categories.
      */
     public static Option createRequiredNumCategoryOpt() {
         Option opt = CmdOptions.getInstance().getLongOption(CmdParams.NUM_CATEGORIES);
diff --git a/src/main/java/edu/pitt/dbmi/causal/cmd/data/DataFiles.java b/src/main/java/edu/pitt/dbmi/causal/cmd/data/DataFiles.java
index 9e3e1a5..ef21097 100644
--- a/src/main/java/edu/pitt/dbmi/causal/cmd/data/DataFiles.java
+++ b/src/main/java/edu/pitt/dbmi/causal/cmd/data/DataFiles.java
@@ -73,10 +73,10 @@ private DataFiles() {
     /**
      * Read in metadata file.
      *
-     * @param cmdArgs
-     * @param out
-     * @return
-     * @throws IOException
+     * @param cmdArgs command-line arguments
+     * @param out output stream to write message to
+     * @return metadata
+     * @throws IOException when errors occur during reading file
      */
     public static Metadata readInMetadata(CmdArgs cmdArgs, PrintStream out) throws IOException {
         Path file = cmdArgs.getMetadataFile();
@@ -94,10 +94,10 @@ public static Metadata readInMetadata(CmdArgs cmdArgs, PrintStream out) throws I
     /**
      * Read in knowledge file.
      *
-     * @param cmdArgs
-     * @param out
-     * @return
-     * @throws IOException
+     * @param cmdArgs command-line arguments
+     * @param out output stream to write message to
+     * @return knowledge information from file
+     * @throws IOException when errors occur during reading file
      */
     public static IKnowledge readInKnowledge(CmdArgs cmdArgs, PrintStream out) throws IOException {
         Path file = cmdArgs.getKnowledgeFile();
@@ -115,11 +115,12 @@ public static IKnowledge readInKnowledge(CmdArgs cmdArgs, PrintStream out) throw
     /**
      * Read in datasets files.
      *
-     * @param cmdArgs
-     * @param out
-     * @return
-     * @throws IOException
-     * @throws AlgorithmRunException
+     * @param cmdArgs command-line arguments
+     * @param out output stream to write message to
+     * @return list of datasets read in from files
+     * @throws IOException when errors occur during reading file
+     * @throws AlgorithmRunException when dataset is not supported by the given
+     * algorithm from command-line
      */
     public static List<DataModel> readInDatasets(CmdArgs cmdArgs, PrintStream out) throws IOException, AlgorithmRunException {
         DataType dataType = cmdArgs.getDataType();
@@ -139,10 +140,10 @@ public static List<DataModel> readInDatasets(CmdArgs cmdArgs, PrintStream out) t
     /**
      * Read in tabular dataset files.
      *
-     * @param cmdArgs
-     * @param out
-     * @return
-     * @throws IOException
+     * @param cmdArgs command-line arguments
+     * @param out output stream to write message to
+     * @return list of datasets read in from files
+     * @throws IOException when errors occur during reading file
      */
     private static List<DataModel> readInTabularData(CmdArgs cmdArgs, PrintStream out) throws IOException {
         List<DataModel> dataModels = new LinkedList<>();
@@ -204,10 +205,10 @@ private static List<DataModel> readInTabularData(CmdArgs cmdArgs, PrintStream ou
     /**
      * Read in covariances files.
      *
-     * @param cmdArgs
-     * @param out
-     * @return
-     * @throws IOException
+     * @param cmdArgs command-line arguments
+     * @param out output stream to write message to
+     * @return list of datasets read in from files
+     * @throws IOException when errors occur during reading file
      */
     private static List<DataModel> readInCovarianceFile(CmdArgs cmdArgs, PrintStream out) throws IOException {
         List<DataModel> dataModels = new LinkedList<>();
@@ -234,10 +235,10 @@ private static List<DataModel> readInCovarianceFile(CmdArgs cmdArgs, PrintStream
     /**
      * Read in exclude-variable file.
      *
-     * @param cmdArgs
-     * @param out
-     * @return
-     * @throws IOException
+     * @param cmdArgs command-line arguments
+     * @param out output stream to write message to
+     * @return set of variables to exclude reading in
+     * @throws IOException when errors occur during reading file
      */
     public static Set<String> readInVariablesToExclude(CmdArgs cmdArgs, PrintStream out) throws IOException {
         Set<String> variablesToExclude = new HashSet<>();
diff --git a/src/main/java/edu/pitt/dbmi/causal/cmd/data/DataValidations.java b/src/main/java/edu/pitt/dbmi/causal/cmd/data/DataValidations.java
index 6ad62ba..cd0928a 100644
--- a/src/main/java/edu/pitt/dbmi/causal/cmd/data/DataValidations.java
+++ b/src/main/java/edu/pitt/dbmi/causal/cmd/data/DataValidations.java
@@ -61,9 +61,9 @@ private DataValidations() {
     /**
      * Validate tabular dataset and covariance data.
      *
-     * @param cmdArgs
-     * @param out
-     * @throws ValidationException
+     * @param cmdArgs command-line arguments
+     * @param out output stream to write message to
+     * @throws ValidationException when dataset validation fails
      */
     public static void validate(CmdArgs cmdArgs, PrintStream out) throws ValidationException {
         DataType dataType = cmdArgs.getDataType();
@@ -85,8 +85,8 @@ public static void validate(CmdArgs cmdArgs, PrintStream out) throws ValidationE
     /**
      * Validate tabular dataset.
      *
-     * @param cmdArgs
-     * @param out
+     * @param cmdArgs command-line arguments
+     * @param out output stream to write message to
      * @throws ValidationException
      */
     private static void validateTabularData(CmdArgs cmdArgs, PrintStream out) throws ValidationException {
@@ -144,8 +144,8 @@ private static void validateTabularData(CmdArgs cmdArgs, PrintStream out) throws
     /**
      * Validate covariance data.
      *
-     * @param cmdArgs
-     * @param out
+     * @param cmdArgs command-line arguments
+     * @param out output stream to write message to
      * @throws ValidationException
      */
     private static void validateCovariance(CmdArgs cmdArgs, PrintStream out) throws ValidationException {
diff --git a/src/main/java/edu/pitt/dbmi/causal/cmd/tetrad/Tetrad.java b/src/main/java/edu/pitt/dbmi/causal/cmd/tetrad/Tetrad.java
index c735b9a..e736cae 100644
--- a/src/main/java/edu/pitt/dbmi/causal/cmd/tetrad/Tetrad.java
+++ b/src/main/java/edu/pitt/dbmi/causal/cmd/tetrad/Tetrad.java
@@ -43,8 +43,8 @@ private Tetrad() {
     /**
      * Get Tetrad parameters from command-line input.
      *
-     * @param cmdArgs
-     * @return
+     * @param cmdArgs command-line arguments
+     * @return Tetrad parameters
      */
     public static Parameters getParameters(CmdArgs cmdArgs) {
         Parameters parameters = new Parameters();
diff --git a/src/main/java/edu/pitt/dbmi/causal/cmd/tetrad/TetradAlgorithms.java b/src/main/java/edu/pitt/dbmi/causal/cmd/tetrad/TetradAlgorithms.java
index f7548fa..622cdc0 100644
--- a/src/main/java/edu/pitt/dbmi/causal/cmd/tetrad/TetradAlgorithms.java
+++ b/src/main/java/edu/pitt/dbmi/causal/cmd/tetrad/TetradAlgorithms.java
@@ -60,16 +60,16 @@ private TetradAlgorithms() {
     /**
      * Get the instance of this class.
      *
-     * @return
+     * @return instance of TetradAlgorithms
      */
     public static TetradAlgorithms getInstance() {
         return INSTANCE;
     }
 
     /**
-     * Get a list of command-line options.
+     * Get a list of command-line options for algorithms.
      *
-     * @return
+     * @return list of command-line options for algorithms
      */
     public List<String> getCommands() {
         List<String> list = CausalCmdApplication.showExperimental
@@ -82,8 +82,9 @@ public List<String> getCommands() {
     /**
      * Determine if the giving command is a validate command-line option.
      *
-     * @param command
-     * @return
+     * @param command command-line argument
+     * @return true if the giving command is a validate command-line option,
+     * otherwise false
      */
     public boolean hasCommand(String command) {
         if (command == null || command.isEmpty()) {
@@ -98,8 +99,8 @@ public boolean hasCommand(String command) {
     /**
      * Get the algorithm class from the command-line input.
      *
-     * @param command
-     * @return
+     * @param command algorithm command-line value
+     * @return algorithm class
      */
     public Class getAlgorithmClass(String command) {
         if (command == null || command.isEmpty()) {
@@ -116,8 +117,8 @@ public Class getAlgorithmClass(String command) {
     /**
      * Determine if the given algorithm class requires an independence test.
      *
-     * @param clazz
-     * @return
+     * @param clazz algorithm class
+     * @return true of the given algorithm requires test of dependence
      */
     public boolean requireIndependenceTest(Class clazz) {
         return AlgorithmAnnotations.getInstance().requireIndependenceTest(clazz);
@@ -126,8 +127,8 @@ public boolean requireIndependenceTest(Class clazz) {
     /**
      * Determine if the given algorithm class requires a score.
      *
-     * @param clazz
-     * @return
+     * @param clazz algorithm class
+     * @return true of the given algorithm requires score
      */
     public boolean requireScore(Class clazz) {
         return AlgorithmAnnotations.getInstance().requireScore(clazz);
@@ -136,8 +137,8 @@ public boolean requireScore(Class clazz) {
     /**
      * Determine if the given algorithm class accepts multiple datasets.
      *
-     * @param clazz
-     * @return
+     * @param clazz algorithm class
+     * @return true if algorithm can handle multiple datasets
      */
     public boolean acceptMultipleDataset(Class clazz) {
         return AlgorithmAnnotations.getInstance().acceptMultipleDataset(clazz);
@@ -146,8 +147,8 @@ public boolean acceptMultipleDataset(Class clazz) {
     /**
      * Determine if the given algorithm class accepts prior knowledge.
      *
-     * @param clazz
-     * @return
+     * @param clazz algorithm class
+     * @return true if algorithm supports knowledge
      */
     public boolean acceptKnowledge(Class clazz) {
         return AlgorithmAnnotations.getInstance().acceptKnowledge(clazz);
@@ -156,8 +157,8 @@ public boolean acceptKnowledge(Class clazz) {
     /**
      * Get the description for a given class.
      *
-     * @param clazz
-     * @return
+     * @param clazz algorithm class
+     * @return description for the given algorithm
      */
     public String getName(Class clazz) {
         return (clazz != null && clazz.isAnnotationPresent(Algorithm.class))
diff --git a/src/main/java/edu/pitt/dbmi/causal/cmd/tetrad/TetradIndependenceTests.java b/src/main/java/edu/pitt/dbmi/causal/cmd/tetrad/TetradIndependenceTests.java
index 2aac29a..486306c 100644
--- a/src/main/java/edu/pitt/dbmi/causal/cmd/tetrad/TetradIndependenceTests.java
+++ b/src/main/java/edu/pitt/dbmi/causal/cmd/tetrad/TetradIndependenceTests.java
@@ -99,9 +99,9 @@ private TetradIndependenceTests() {
     /**
      * Combine two lists of command-line options into one.
      *
-     * @param listA
-     * @param listB
-     * @return
+     * @param listA list to merge
+     * @param listB list to merge
+     * @return list containing values from listA and listB
      */
     private static List<String> mergeList(List<String> listA, List<String> listB) {
         return Stream.concat(listA.stream(), listB.stream())
@@ -112,7 +112,7 @@ private static List<String> mergeList(List<String> listA, List<String> listB) {
     /**
      * Get the instance of this class.
      *
-     * @return
+     * @return instance of TetradIndependenceTests
      */
     public static TetradIndependenceTests getInstance() {
         return INSTANCE;
@@ -121,8 +121,9 @@ public static TetradIndependenceTests getInstance() {
     /**
      * Determine if the giving command is a validate command-line option.
      *
-     * @param command
-     * @return
+     * @param command command-line argument
+     * @return true if the giving command is a validate command-line option,
+     * otherwise false
      */
     public boolean hasCommand(String command) {
         if (command == null || command.isEmpty()) {
@@ -138,9 +139,10 @@ public boolean hasCommand(String command) {
      * Determine if the giving command is a validate command-line option for a
      * giving datatype.
      *
-     * @param command
-     * @param dataType
-     * @return
+     * @param command command-line argument
+     * @param dataType data type
+     * @return true if the giving command is a validate command-line option for
+     * a giving datatype. Otherwise, false.
      */
     public boolean hasCommand(String command, DataType dataType) {
         if (command == null || command.isEmpty() || dataType == null) {
@@ -160,9 +162,9 @@ public boolean hasCommand(String command, DataType dataType) {
     }
 
     /**
-     * Get a list of command-line options.
+     * Get a list of command-line options for test of independence.
      *
-     * @return
+     * @return a list of command-line options for test of independence
      */
     public List<String> getCommands() {
         List<String> list = CausalCmdApplication.showExperimental
@@ -175,8 +177,8 @@ public List<String> getCommands() {
     /**
      * Get a list of command-line options for a giving datatype.
      *
-     * @param dataType
-     * @return
+     * @param dataType data type
+     * @return a list of command-line options for a giving datatype
      */
     public List<String> getCommands(DataType dataType) {
         Map<DataType, List<String>> map = CausalCmdApplication.showExperimental
@@ -191,8 +193,8 @@ public List<String> getCommands(DataType dataType) {
     /**
      * Get class for a giving command-line option.
      *
-     * @param command
-     * @return
+     * @param command command-line argument
+     * @return class for a giving command-line option
      */
     public Class getClass(String command) {
         if (command == null || command.isEmpty()) {
@@ -207,10 +209,10 @@ public Class getClass(String command) {
     }
 
     /**
-     * Get the name for a given class.
+     * Get the class name for test of independence.
      *
-     * @param clazz
-     * @return
+     * @param clazz test-of-independence class
+     * @return class name for test of independence.
      */
     public String getName(Class clazz) {
         return (clazz != null && clazz.isAnnotationPresent(TestOfIndependence.class))
@@ -219,10 +221,10 @@ public String getName(Class clazz) {
     }
 
     /**
-     * Get the description for a given class.
+     * Get the description for test of independence from class.
      *
-     * @param clazz
-     * @return
+     * @param clazz test-of-independence class
+     * @return description for test of independence
      */
     public String getDescription(Class clazz) {
         return (clazz != null && clazz.isAnnotationPresent(TestOfIndependence.class))
diff --git a/src/main/java/edu/pitt/dbmi/causal/cmd/tetrad/TetradRunner.java b/src/main/java/edu/pitt/dbmi/causal/cmd/tetrad/TetradRunner.java
index c4dfd42..9284dc1 100644
--- a/src/main/java/edu/pitt/dbmi/causal/cmd/tetrad/TetradRunner.java
+++ b/src/main/java/edu/pitt/dbmi/causal/cmd/tetrad/TetradRunner.java
@@ -80,9 +80,9 @@ public TetradRunner(CmdArgs cmdArgs) {
     /**
      * Run algorithm.
      *
-     * @param out
-     * @throws AlgorithmRunException
-     * @throws IOException
+     * @param out output stream to write message to
+     * @throws AlgorithmRunException when algorithm run fails
+     * @throws IOException when unable to read knowledge file
      */
     public void runAlgorithm(PrintStream out) throws AlgorithmRunException, IOException {
         final List<DataModel> dataModels = DataFiles.readInDatasets(cmdArgs, out);
@@ -129,8 +129,8 @@ public void runAlgorithm(PrintStream out) throws AlgorithmRunException, IOExcept
     /**
      * Determine if any of the data model contains missing values;
      *
-     * @param dataModels
-     * @return
+     * @param dataModels dataset
+     * @return true if data contains missing values
      */
     private boolean containsMissingValues(final List<DataModel> dataModels) {
         boolean hasMissingValues = false;
@@ -151,10 +151,10 @@ private boolean containsMissingValues(final List<DataModel> dataModels) {
     /**
      * Run search algorithm.
      *
-     * @param algorithm
-     * @param parameters
-     * @param dataModels
-     * @return
+     * @param algorithm Tetrad algorithm
+     * @param parameters algorithm, score, and test parameters
+     * @param dataModels list of dataset to run
+     * @return list of result search graphs
      */
     private List<Graph> runSearch(final Algorithm algorithm, final Parameters parameters, final List<DataModel> dataModels) {
         List<Graph> graphList = new LinkedList<>();
@@ -210,7 +210,7 @@ private List<Graph> runSearch(final Algorithm algorithm, final Parameters parame
     /**
      * Manipulating graphs.
      *
-     * @param graphs
+     * @param graph graph to manipulate
      * @author: Chirayu Wongchokprasitti, PhD
      */
     private Graph manipulateGraph(Graph graph) {
@@ -329,9 +329,10 @@ private Graph manipulateGraph(Graph graph) {
     /**
      * Get algorithm instance from command-line input.
      *
-     * @param cmdArgs
-     * @return
-     * @throws AlgorithmRunException
+     * @param cmdArgs command-line arguments
+     * @return algorithm from command-line
+     * @throws AlgorithmRunException whenever unable to algorithm from
+     * command-line
      */
     private Algorithm getAlgorithm(CmdArgs cmdArgs) throws AlgorithmRunException {
         try {
@@ -341,6 +342,11 @@ private Algorithm getAlgorithm(CmdArgs cmdArgs) throws AlgorithmRunException {
         }
     }
 
+    /**
+     * Get list of result graphs from search algorithms.
+     *
+     * @return list of result graphs from search algorithms
+     */
     public List<Graph> getGraphs() {
         return graphs;
     }
diff --git a/src/main/java/edu/pitt/dbmi/causal/cmd/tetrad/TetradScores.java b/src/main/java/edu/pitt/dbmi/causal/cmd/tetrad/TetradScores.java
index f7b297e..278afd4 100644
--- a/src/main/java/edu/pitt/dbmi/causal/cmd/tetrad/TetradScores.java
+++ b/src/main/java/edu/pitt/dbmi/causal/cmd/tetrad/TetradScores.java
@@ -98,9 +98,9 @@ private TetradScores() {
     /**
      * Combine two lists of command-line options into one.
      *
-     * @param listA
-     * @param listB
-     * @return
+     * @param listA list to merge
+     * @param listB list to merge
+     * @return list containing values from listA and listB
      */
     private static List<String> mergeList(List<String> listA, List<String> listB) {
         return Stream.concat(listA.stream(), listB.stream())
@@ -111,7 +111,7 @@ private static List<String> mergeList(List<String> listA, List<String> listB) {
     /**
      * Get the instance of this class.
      *
-     * @return
+     * @return instance of TetradScores
      */
     public static TetradScores getInstance() {
         return INSTANCE;
@@ -120,8 +120,9 @@ public static TetradScores getInstance() {
     /**
      * Determine if the giving command is a validate command-line option.
      *
-     * @param command
-     * @return
+     * @param command command-line argument
+     * @return true if the giving command is a validate command-line option,
+     * otherwise false
      */
     public boolean hasCommand(String command) {
         if (command == null || command.isEmpty()) {
@@ -137,9 +138,10 @@ public boolean hasCommand(String command) {
      * Determine if the giving command is a validate command-line option for a
      * giving datatype.
      *
-     * @param command
-     * @param dataType
-     * @return
+     * @param command command-line argument
+     * @param dataType data type
+     * @return true if the giving command is a validate command-line option for
+     * a giving datatype. Otherwise, false.
      */
     public boolean hasCommand(String command, DataType dataType) {
         if (command == null || command.isEmpty() || dataType == null) {
@@ -159,9 +161,9 @@ public boolean hasCommand(String command, DataType dataType) {
     }
 
     /**
-     * Get a list of command-line options.
+     * Get a list of command-line options for scores.
      *
-     * @return
+     * @return a list of command-line options for scores
      */
     public List<String> getCommands() {
         List<String> list = CausalCmdApplication.showExperimental
@@ -174,8 +176,8 @@ public List<String> getCommands() {
     /**
      * Get a list of command-line options for a giving datatype.
      *
-     * @param dataType
-     * @return
+     * @param dataType data type
+     * @return a list of command-line options for a giving datatype
      */
     public List<String> getCommands(DataType dataType) {
         Map<DataType, List<String>> map = CausalCmdApplication.showExperimental
@@ -190,8 +192,8 @@ public List<String> getCommands(DataType dataType) {
     /**
      * Get class for a giving command-line option.
      *
-     * @param command
-     * @return
+     * @param command command-line argument
+     * @return class for a giving command-line option
      */
     public Class getClass(String command) {
         if (command == null || command.isEmpty()) {
@@ -206,10 +208,10 @@ public Class getClass(String command) {
     }
 
     /**
-     * Get the name for a given class.
+     * Get the class name for score.
      *
-     * @param clazz
-     * @return
+     * @param clazz score class
+     * @return class name for score.
      */
     public String getName(Class clazz) {
         return (clazz != null && clazz.isAnnotationPresent(Score.class))
@@ -218,10 +220,10 @@ public String getName(Class clazz) {
     }
 
     /**
-     * Get the description for a given class.
+     * Get the score description from class.
      *
-     * @param clazz
-     * @return
+     * @param clazz score class
+     * @return description for score
      */
     public String getDescription(Class clazz) {
         return (clazz != null && clazz.isAnnotationPresent(Score.class))
diff --git a/src/main/java/edu/pitt/dbmi/causal/cmd/util/DateTime.java b/src/main/java/edu/pitt/dbmi/causal/cmd/util/DateTime.java
index 53e8768..d365a6d 100644
--- a/src/main/java/edu/pitt/dbmi/causal/cmd/util/DateTime.java
+++ b/src/main/java/edu/pitt/dbmi/causal/cmd/util/DateTime.java
@@ -36,10 +36,20 @@ public final class DateTime {
     private DateTime() {
     }
 
+    /**
+     * Print the current date-time.
+     *
+     * @return the current date-time
+     */
     public static String printNow() {
         return print(new Date(System.currentTimeMillis()));
     }
 
+    /**
+     *
+     * @param date date-time to format
+     * @return a formatted date-time
+     */
     public static String print(Date date) {
         return DF.format(date);
     }
diff --git a/src/main/java/edu/pitt/dbmi/causal/cmd/util/FileUtils.java b/src/main/java/edu/pitt/dbmi/causal/cmd/util/FileUtils.java
index 1851066..caf16d3 100644
--- a/src/main/java/edu/pitt/dbmi/causal/cmd/util/FileUtils.java
+++ b/src/main/java/edu/pitt/dbmi/causal/cmd/util/FileUtils.java
@@ -34,6 +34,13 @@ public class FileUtils {
     private FileUtils() {
     }
 
+    /**
+     * Determine if a given file exists.
+     *
+     * @param file file to determine if it exists or not
+     * @throws FileNotFoundException when file does not exist or when file is a
+     * directory
+     */
     public static void exists(Path file) throws FileNotFoundException {
         if (Files.notExists(file)) {
             throw new FileNotFoundException(String.format("File '%s' does not exist.", file.toString()));
diff --git a/src/main/java/edu/pitt/dbmi/causal/cmd/util/GraphIO.java b/src/main/java/edu/pitt/dbmi/causal/cmd/util/GraphIO.java
index 4cf6853..143b3fa 100644
--- a/src/main/java/edu/pitt/dbmi/causal/cmd/util/GraphIO.java
+++ b/src/main/java/edu/pitt/dbmi/causal/cmd/util/GraphIO.java
@@ -43,9 +43,9 @@ private GraphIO() {
     /**
      * Write out graph object to a text file.
      *
-     * @param graph
-     * @param path
-     * @throws IOException
+     * @param graph Tetrad graph
+     * @param path directory to write output text file
+     * @throws IOException when unable to create or write file
      */
     public static void writeAsTXT(Graph graph, Path path) throws IOException {
         Scanner scanner = new Scanner(graph.toString());
@@ -59,9 +59,9 @@ public static void writeAsTXT(Graph graph, Path path) throws IOException {
     /**
      * Write out graph object to a JSON file.
      *
-     * @param graph
-     * @param path
-     * @throws IOException
+     * @param graph Tetrad graph
+     * @param path directory to write output JSON file
+     * @throws IOException when unable to create or write file
      */
     public static void writeAsJSON(Graph graph, Path path) throws IOException {
         Gson gson = new GsonBuilder().setPrettyPrinting().create();
diff --git a/src/main/java/edu/pitt/dbmi/causal/cmd/util/LogMessages.java b/src/main/java/edu/pitt/dbmi/causal/cmd/util/LogMessages.java
index aaf7ffb..e55bf25 100644
--- a/src/main/java/edu/pitt/dbmi/causal/cmd/util/LogMessages.java
+++ b/src/main/java/edu/pitt/dbmi/causal/cmd/util/LogMessages.java
@@ -45,10 +45,10 @@ private LogMessages() {
     /**
      * Write out dataset information to log file.
      *
-     * @param file
-     * @param dataModel
-     * @param logger
-     * @param out
+     * @param file dataset file to log information about
+     * @param dataModel dataset read in from dataset file
+     * @param logger write log message to
+     * @param out output stream to write message to
      */
     public static void dataInfo(Path file, DataModel dataModel, Logger logger, PrintStream out) {
         int row = 0;
@@ -71,9 +71,9 @@ public static void dataInfo(Path file, DataModel dataModel, Logger logger, Print
     /**
      * Log the end time of reading file.
      *
-     * @param file
-     * @param logger
-     * @param out
+     * @param file file to log information about
+     * @param logger write log message to
+     * @param out output stream to write message to
      */
     public static void readingFileEnd(Path file, Logger logger, PrintStream out) {
         String fileName = file.getFileName().toString();
@@ -84,9 +84,9 @@ public static void readingFileEnd(Path file, Logger logger, PrintStream out) {
     /**
      * Log the start time of reading file.
      *
-     * @param file
-     * @param logger
-     * @param out
+     * @param file file to log information about
+     * @param logger write log message to
+     * @param out output stream to write message to
      */
     public static void readingFileStart(Path file, Logger logger, PrintStream out) {
         String fileName = file.getFileName().toString();
@@ -97,9 +97,9 @@ public static void readingFileStart(Path file, Logger logger, PrintStream out) {
     /**
      * Log data validation results.
      *
-     * @param groupedResults
-     * @param logger
-     * @param out
+     * @param groupedResults validation results
+     * @param logger write log message to
+     * @param out output stream to write message to
      */
     public static void dataValidationResults(Map<ValidationCode, List<ValidationResult>> groupedResults, Logger logger, PrintStream out) {
         if (groupedResults.containsKey(ValidationCode.INFO)) {
@@ -131,9 +131,9 @@ public static void dataValidationResults(Map<ValidationCode, List<ValidationResu
     /**
      * Log the end time of the data validation.
      *
-     * @param file
-     * @param logger
-     * @param out
+     * @param file data file to log information about
+     * @param logger write log message to
+     * @param out output stream to write message to
      */
     public static void dataValidationEnd(Path file, Logger logger, PrintStream out) {
         String fileName = file.getFileName().toString();
@@ -144,9 +144,9 @@ public static void dataValidationEnd(Path file, Logger logger, PrintStream out)
     /**
      * Log the start time of the data validation.
      *
-     * @param file
-     * @param logger
-     * @param out
+     * @param file data file to log information about
+     * @param logger write log message to
+     * @param out output stream to write message to
      */
     public static void dataValidationStart(Path file, Logger logger, PrintStream out) {
         String fileName = file.getFileName().toString();
@@ -157,9 +157,9 @@ public static void dataValidationStart(Path file, Logger logger, PrintStream out
     /**
      * Log message.
      *
-     * @param message
-     * @param logger
-     * @param out
+     * @param message message to write to log file
+     * @param logger write log message to
+     * @param out output stream to write message to
      */
     public static void logMessage(String message, Logger logger, PrintStream out) {
         out.printf("%s: %s%n", DateTime.printNow(), message);
diff --git a/src/main/java/edu/pitt/dbmi/causal/cmd/util/WordUtil.java b/src/main/java/edu/pitt/dbmi/causal/cmd/util/WordUtil.java
index e632a93..9af9c51 100644
--- a/src/main/java/edu/pitt/dbmi/causal/cmd/util/WordUtil.java
+++ b/src/main/java/edu/pitt/dbmi/causal/cmd/util/WordUtil.java
@@ -33,8 +33,8 @@ private WordUtil() {
     /**
      * Convert true/false value to yes/no.
      *
-     * @param value
-     * @return
+     * @param value true or false literal value
+     * @return yes literal value if the value literal is true, no otherwise.
      */
     public static final String toYesOrNo(String value) {
         switch (value) {