From 750715663d8f3c20224a861f678af1a10927bf28 Mon Sep 17 00:00:00 2001
From: Kevin Bui <kvb2univpitt@gmail.com>
Date: Wed, 15 Jun 2022 12:27:42 -0400
Subject: [PATCH 1/6] Added maven plugin to generate javadocs.

---
 pom.xml | 18 ++++++++++++++++++
 1 file changed, 18 insertions(+)

diff --git a/pom.xml b/pom.xml
index 269999c..13631aa 100644
--- a/pom.xml
+++ b/pom.xml
@@ -131,6 +131,24 @@
                     </execution>
                 </executions>
             </plugin>
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-javadoc-plugin</artifactId>
+                <version>3.4.0</version>
+                <configuration>
+                    <javadocExecutable>/usr/bin/javadoc</javadocExecutable>
+                    <!--<show>private</show>-->
+                    <nohelp>true</nohelp>
+                </configuration>
+                <executions>
+                    <execution>
+                        <id>attach-javadocs</id>
+                        <goals>
+                            <goal>jar</goal>
+                        </goals>
+                    </execution>
+                </executions>
+            </plugin>
         </plugins>
     </build>
 </project>

From 58772dd53d2c0a4c6eabbc8dc9c26896e9d2718d Mon Sep 17 00:00:00 2001
From: Kevin Bui <kvb2univpitt@gmail.com>
Date: Sun, 19 Jun 2022 14:22:15 -0400
Subject: [PATCH 2/6] Added javadocs for the main package.

---
 .../causal/cmd/AlgorithmRunException.java     |  2 +
 .../pitt/dbmi/causal/cmd/Applications.java    | 61 +++++++++++++
 .../java/edu/pitt/dbmi/causal/cmd/Args.java   | 86 ++++++++++++++++---
 .../dbmi/causal/cmd/CausalCmdApplication.java | 21 ++++-
 .../edu/pitt/dbmi/causal/cmd/CmdArgs.java     |  2 +
 .../edu/pitt/dbmi/causal/cmd/CmdOptions.java  | 80 +++++++++++++++++
 .../edu/pitt/dbmi/causal/cmd/CmdParams.java   |  1 +
 .../edu/pitt/dbmi/causal/cmd/CmdParser.java   | 60 +++++++++++++
 .../dbmi/causal/cmd/CmdParserException.java   |  2 +
 .../edu/pitt/dbmi/causal/cmd/DataTypes.java   |  1 +
 .../edu/pitt/dbmi/causal/cmd/Delimiters.java  |  2 +
 .../pitt/dbmi/causal/cmd/OptionFactory.java   | 24 ++++++
 .../pitt/dbmi/causal/cmd/ParseOptions.java    |  2 +
 .../dbmi/causal/cmd/ValidationException.java  |  1 +
 14 files changed, 332 insertions(+), 13 deletions(-)

diff --git a/src/main/java/edu/pitt/dbmi/causal/cmd/AlgorithmRunException.java b/src/main/java/edu/pitt/dbmi/causal/cmd/AlgorithmRunException.java
index 8a138b7..5b6e300 100644
--- a/src/main/java/edu/pitt/dbmi/causal/cmd/AlgorithmRunException.java
+++ b/src/main/java/edu/pitt/dbmi/causal/cmd/AlgorithmRunException.java
@@ -19,6 +19,8 @@
 package edu.pitt.dbmi.causal.cmd;
 
 /**
+ * The class {@code AlgorithmRunException} occurs when an algorithm that is
+ * attempted to run or was running failed.
  *
  * Oct 2, 2017 10:45:47 AM
  *
diff --git a/src/main/java/edu/pitt/dbmi/causal/cmd/Applications.java b/src/main/java/edu/pitt/dbmi/causal/cmd/Applications.java
index afc9a5a..60625e8 100644
--- a/src/main/java/edu/pitt/dbmi/causal/cmd/Applications.java
+++ b/src/main/java/edu/pitt/dbmi/causal/cmd/Applications.java
@@ -37,6 +37,8 @@
 import org.apache.commons.cli.Options;
 
 /**
+ * The class {@code Applications} is a utility class for displaying help
+ * information and for getting the application jar file information..
  *
  * Jan 8, 2019 12:04:29 PM
  *
@@ -49,6 +51,13 @@ public final class Applications {
     private Applications() {
     }
 
+    /**
+     * Print out help messages to terminal for options that are not satisfied..
+     *
+     * @param args user's input of options and arguments
+     * @param parseOptions options that has been parsed
+     * @param footer help message footer
+     */
     public static void showHelp(String[] args, ParseOptions parseOptions, String footer) {
         Options opts = parseOptions.getOptions();
         Options invalidOpts = parseOptions.getInvalidValueOptions();
@@ -88,6 +97,9 @@ public static void showHelp(String[] args, ParseOptions parseOptions, String foo
         }
     }
 
+    /**
+     * Print out a list of independence tests with descriptions to terminal..
+     */
     public static void showTestsAndDescriptions() {
         System.out.println("================================================================================");
         System.out.println("Independence Tests");
@@ -103,6 +115,9 @@ public static void showTestsAndDescriptions() {
                 });
     }
 
+    /**
+     * Print out a list of scores with descriptions to terminal..
+     */
     public static void showScoresAndDescriptions() {
         System.out.println("================================================================================");
         System.out.println("Scores");
@@ -118,6 +133,9 @@ public static void showScoresAndDescriptions() {
                 });
     }
 
+    /**
+     * Print out a list of algorithms with descriptions to terminal..
+     */
     public static void showAlgorithmsAndDescriptions() {
         System.out.println("================================================================================");
         System.out.println("Algorithms");
@@ -133,40 +151,83 @@ public static void showAlgorithmsAndDescriptions() {
                 });
     }
 
+    /**
+     * Print out help messages to terminal for the given options.
+     *
+     * @param options options to print out in help messages.
+     */
     public static void showHelp(Options options) {
         HelpFormatter formatter = new HelpFormatter();
         formatter.setWidth(-1);
         formatter.printHelp(getHelpTitle(), options, true);
     }
 
+    /**
+     * Print out help messages to terminal for the given options with message
+     * footer.
+     *
+     * @param options options to print out in help messages.
+     * @param footer message footer
+     */
     public static void showHelp(Options options, String footer) {
         HelpFormatter formatter = new HelpFormatter();
         formatter.setWidth(-1);
         formatter.printHelp(getHelpTitle(), null, options, footer, true);
     }
 
+    /**
+     * Get the application version.
+     *
+     * @return the application version
+     */
     public static String getVersion() {
         return String.format("Version %s", jarVersion());
     }
 
+    /**
+     * Formats the given {@link Date} into a date-time string.
+     *
+     * @param date the time value to be formatted into a date-time string.
+     * @return the formatted date-time string of the given Date
+     */
     public static String fmtDate(Date date) {
         return DF.format(date);
     }
 
+    /**
+     * Formats the current {@link Date} into a date-time string.
+     *
+     * @return the formatted date-time string of the current Date
+     */
     public static String fmtDateNow() {
         return fmtDate(new Date(System.currentTimeMillis()));
     }
 
+    /**
+     * et the application jar filename.
+     *
+     * @return the jar filename.
+     */
     public static String jarTitle() {
         return Applications.class.getPackage().getImplementationTitle();
     }
 
+    /**
+     * Get the application jar file version.
+     *
+     * @return the jar file version
+     */
     public static String jarVersion() {
         String version = Applications.class.getPackage().getImplementationVersion();
 
         return (version == null) ? "unknown" : version;
     }
 
+    /**
+     * Get the title for the help message.
+     *
+     * @return title of the help message
+     */
     private static String getHelpTitle() {
         String title = jarTitle();
         String version = jarVersion();
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 4c2b3d7..1c8fd0a 100644
--- a/src/main/java/edu/pitt/dbmi/causal/cmd/Args.java
+++ b/src/main/java/edu/pitt/dbmi/causal/cmd/Args.java
@@ -30,6 +30,8 @@
 import org.apache.commons.cli.ParseException;
 
 /**
+ * The class {@code Args} is a utility class for parsing, extracting, and
+ * manipulate command-line arguments .
  *
  * Mar 9, 2017 3:37:35 PM
  *
@@ -40,6 +42,13 @@ public final class Args {
     private Args() {
     }
 
+    /**
+     * Remove the given option from the command-line arguments.
+     *
+     * @param args command-line arguments
+     * @param option option to remove
+     * @return command-line arguments
+     */
     public static String[] removeLongOption(String[] args, String option) {
         CmdOptions cmdOptions = CmdOptions.getInstance();
         List<String> argsToKeep = new LinkedList<>();
@@ -63,9 +72,19 @@ public static String[] removeLongOption(String[] args, String option) {
             }
         }
 
-        return argsToKeep.toArray(new String[argsToKeep.size()]);
+        return argsToKeep.toArray(String[]::new);
     }
 
+    /**
+     * Parse options from command-line arguments by its multi-character name
+     * into argsMap.
+     *
+     * @param args command-line arguments
+     * @param options multi-character name options.
+     * @param argsMap holds options by name
+     * @throws ParseException whenever error occurs during parsing of a
+     * command-line.
+     */
     public static void parseLongOptions(String[] args, Options options, Map<String, String> argsMap) throws ParseException {
         CommandLine cmd = (new DefaultParser()).parse(options, args);
         options.getOptions().forEach(option -> {
@@ -76,6 +95,16 @@ public static void parseLongOptions(String[] args, Options options, Map<String,
         });
     }
 
+    /**
+     * Parse options from command-line arguments by its single-character name
+     * into argsMap.
+     *
+     * @param args command-line arguments
+     * @param options single-character name options.
+     * @param argsMap holds options by name
+     * @throws ParseException whenever error occurs during parsing of a
+     * command-line.
+     */
     public static void parse(String[] args, Options options, Map<String, String> argsMap) throws ParseException {
         CommandLine cmd = (new DefaultParser()).parse(options, args);
         options.getOptions().forEach(option -> {
@@ -91,6 +120,13 @@ public static void parse(String[] args, Options options, Map<String, String> arg
         });
     }
 
+    /**
+     * Extract multi-character name options from command-line arguments.
+     *
+     * @param args command-line arguments
+     * @param options multi-character name options.
+     * @return extracted command-line arguments
+     */
     public static String[] extractLongOptions(String[] args, Options options) {
         List<String> argsList = new LinkedList<>();
 
@@ -107,9 +143,17 @@ public static String[] extractLongOptions(String[] args, Options options) {
             }
         });
 
-        return argsList.toArray(new String[argsList.size()]);
+        return argsList.toArray(String[]::new);
     }
 
+    /**
+     * Extract both multi-character name and single-character name options from
+     * command-line arguments.
+     *
+     * @param args command-line arguments
+     * @param options multi-character name and single-character name options.
+     * @return command-line arguments
+     */
     public static String[] extractOptions(String[] args, Options options) {
         List<String> argsList = new LinkedList<>();
 
@@ -135,15 +179,15 @@ public static String[] extractOptions(String[] args, Options options) {
             }
         });
 
-        return argsList.toArray(new String[argsList.size()]);
+        return argsList.toArray(String[]::new);
     }
 
     /**
-     * Parse the long parameters from the command inputs to map where the
-     * parameters are map keys and parameter values are map values.
+     * Extract multi-character name options into a parameter-argument
+     * collection.
      *
-     * @param args
-     * @return
+     * @param args command-line arguments
+     * @return parameter-argument collection
      */
     public static Map<String, String> toMapLongOptions(String[] args) {
         Map<String, String> map = new HashMap<>();
@@ -171,11 +215,11 @@ public static Map<String, String> toMapLongOptions(String[] args) {
     }
 
     /**
-     * Parse the command inputs to map where the parameters are map keys and
-     * parameter values are map values.
+     * Extract multi-character name and and single-character name options into a
+     * parameter-argument collection.
      *
-     * @param args
-     * @return
+     * @param args command-line arguments
+     * @return parameter-argument collection
      */
     public static Map<String, String> toMapOptions(String[] args) {
         Map<String, String> map = new HashMap<>();
@@ -204,6 +248,13 @@ public static Map<String, String> toMapOptions(String[] args) {
         return map;
     }
 
+    /**
+     * Check if the given option is in the command-line arguments.
+     *
+     * @param args command-line arguments
+     * @param option option to check for
+     * @return true if the given option is found in the command-line arguments
+     */
     public static boolean hasLongParam(String[] args, String option) {
         if (isEmpty(args)) {
             return false;
@@ -215,10 +266,23 @@ public static boolean hasLongParam(String[] args, String option) {
                 .anyMatch(option::equals);
     }
 
+    /**
+     * Test if the command-line arguments has any parameters or arguments.
+     *
+     * @param args command-line arguments
+     * @return true if the command-line arguments has not parameters or
+     * arguments
+     */
     public static boolean isEmpty(String[] args) {
         return (args == null || args.length == 0);
     }
 
+    /**
+     * Remove extract spaces in the parameter names and arguments.
+     *
+     * @param args command-line arguments
+     * @return command-line arguments
+     */
     public static String[] clean(String[] args) {
         return (args == null)
                 ? new String[0]
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 faef6b6..f196658 100644
--- a/src/main/java/edu/pitt/dbmi/causal/cmd/CausalCmdApplication.java
+++ b/src/main/java/edu/pitt/dbmi/causal/cmd/CausalCmdApplication.java
@@ -41,6 +41,7 @@
 import org.slf4j.LoggerFactory;
 
 /**
+ * The class {@code CausalCmdApplication} is the main application .
  *
  * Mar 8, 2017 6:11:17 PM
  *
@@ -55,7 +56,9 @@ public class CausalCmdApplication {
     public static boolean showExperimental;
 
     /**
-     * @param args the command line arguments
+     * Main executable method.
+     *
+     * @param args command-line arguments
      */
     public static void main(String[] args) {
         args = Args.clean(args);
@@ -108,6 +111,14 @@ public static void main(String[] args) {
         }
     }
 
+    /**
+     * Run Tetrad algorithm.
+     *
+     * @param cmdArgs command-line parameters and argument values.
+     * @throws AlgorithmRunException whenever algorithm fails to run
+     * @throws ValidationException whenever data validation fails
+     * @throws IOException whenever unable to read or write file
+     */
     private static void runTetrad(CmdArgs cmdArgs) throws AlgorithmRunException, ValidationException, IOException {
         String outDir = cmdArgs.getOutDirectory().toString();
         String prefix = cmdArgs.getFilePrefix();
@@ -118,7 +129,7 @@ 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()) {
@@ -156,6 +167,12 @@ private static void runTetrad(CmdArgs cmdArgs) throws AlgorithmRunException, Val
         }
     }
 
+    /**
+     * Write out the command-line parameters and arguments to output stream.
+     *
+     * @param cmdArgs command-line parameters and arguments
+     * @param out output stream writer
+     */
     private static void writeOutParameters(CmdArgs cmdArgs, PrintStream out) {
         Class algoClass = cmdArgs.getAlgorithmClass();
         Class indTestClass = cmdArgs.getTestClass();
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 d2d7199..9e54a6e 100644
--- a/src/main/java/edu/pitt/dbmi/causal/cmd/CmdArgs.java
+++ b/src/main/java/edu/pitt/dbmi/causal/cmd/CmdArgs.java
@@ -25,6 +25,8 @@
 import java.util.Map;
 
 /**
+ * The class {@code CmdArgs} holds values extracted from the command-line
+ * arguments.
  *
  * Sep 24, 2017 10:10:21 PM
  *
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 ce13d6f..2fd41cd 100644
--- a/src/main/java/edu/pitt/dbmi/causal/cmd/CmdOptions.java
+++ b/src/main/java/edu/pitt/dbmi/causal/cmd/CmdOptions.java
@@ -34,6 +34,7 @@
 import org.apache.commons.cli.Options;
 
 /**
+ * The class {@code CmdOptions} is a class for storing command-line options.
  *
  * Aug 27, 2017 10:42:03 PM
  *
@@ -50,6 +51,11 @@ private CmdOptions() {
         addOptionalOptions();
     }
 
+    /**
+     * Get an instance of the command-line options.
+     *
+     * @return
+     */
     public static CmdOptions getInstance() {
         if (instance == null) {
             instance = new CmdOptions();
@@ -58,18 +64,40 @@ public static CmdOptions getInstance() {
         return instance;
     }
 
+    /**
+     * Destroy the instance of the command-line options.
+     */
     public static void clear() {
         instance = null;
     }
 
+    /**
+     * Get multi-character name options for a given name..
+     *
+     * @param param multi-character name
+     * @return
+     */
     public Option getLongOption(String param) {
         return options.get(param);
     }
 
+    /**
+     * Test if the command-line options has an option with the given
+     * multi-character name.
+     *
+     * @param param multi-character name
+     * @return true if the command-line options contains the option with the
+     * given multi-character name.
+     */
     public boolean hasLongParam(String param) {
         return options.containsKey(param);
     }
 
+    /**
+     * Get all the stored command-line options.
+     *
+     * @return command-line options
+     */
     public Options getOptions() {
         Options opts = new Options();
         options.entrySet().forEach(e -> {
@@ -79,6 +107,11 @@ public Options getOptions() {
         return opts;
     }
 
+    /**
+     * Get all the application main command-line options.
+     *
+     * @return command-line options
+     */
     public Options getMainOptions() {
         List<Option> optList = getBaseOptions();
         optList.add(options.get(CmdParams.HELP));
@@ -91,6 +124,12 @@ public Options getMainOptions() {
         return toOptions(optList);
     }
 
+    /**
+     * Add a list of options to the {@code Options} object.
+     *
+     * @param optionList list of options
+     * @return the Options object containing the given list of options.
+     */
     public Options toOptions(List<Option> optionList) {
         Options opts = new Options();
 
@@ -101,6 +140,11 @@ public Options toOptions(List<Option> optionList) {
         return opts;
     }
 
+    /**
+     * Get all the application base command-line options.
+     *
+     * @return list of command-line options.
+     */
     public List<Option> getBaseOptions() {
         List<Option> opts = new LinkedList<>();
 
@@ -130,6 +174,9 @@ public List<Option> getBaseOptions() {
         return opts;
     }
 
+    /**
+     * Add application optional options to the stored options.
+     */
     private void addOptionalOptions() {
         options.put(CmdParams.QUOTE_CHAR, Option.builder().longOpt(CmdParams.QUOTE_CHAR).desc("Single character denotes quote.").hasArg().argName("character").build());
         options.put(CmdParams.MISSING_MARKER, Option.builder().longOpt(CmdParams.MISSING_MARKER).desc("Denotes missing value.").hasArg().argName("string").build());
@@ -186,6 +233,9 @@ private void addOptionalOptions() {
         });
     }
 
+    /**
+     * Add application required options to the stored options.
+     */
     private void addRequiredOptions() {
         options.put(CmdParams.ALGORITHM, Option.builder().longOpt(CmdParams.ALGORITHM).desc(getAlgorithmDesc()).hasArg().argName("string").required().build());
         options.put(CmdParams.DATASET, Option.builder().longOpt(CmdParams.DATASET).desc("Dataset. Multiple files are seperated by commas.").hasArg().argName("files").required().build());
@@ -193,6 +243,11 @@ private void addRequiredOptions() {
         options.put(CmdParams.DATA_TYPE, Option.builder().longOpt(CmdParams.DATA_TYPE).desc(getDataTypeDesc()).hasArg().argName("string").required().build());
     }
 
+    /**
+     * Get the application required options from the stored options.
+     *
+     * @return
+     */
     public List<Option> getRequiredOptions() {
         return options.entrySet().stream()
                 .filter(e -> e.getValue().isRequired())
@@ -200,26 +255,51 @@ public List<Option> getRequiredOptions() {
                 .collect(Collectors.toList());
     }
 
+    /**
+     * Get the names of all the datatypes.
+     *
+     * @return
+     */
     private String getDataTypeDesc() {
         return "Data type: " + DataTypes.getInstance().getNames().stream()
                 .collect(Collectors.joining(", "));
     }
 
+    /**
+     * Get the names of all the delimiters.
+     *
+     * @return
+     */
     private String getDelimiterDesc() {
         return "Delimiter: " + Delimiters.getInstance().getNames().stream()
                 .collect(Collectors.joining(", "));
     }
 
+    /**
+     * Get the names of all the scores.
+     *
+     * @return
+     */
     private String getScoreDesc() {
         return "Score: " + TetradScores.getInstance().getCommands().stream()
                 .collect(Collectors.joining(", "));
     }
 
+    /**
+     * Get the names of all the independence test.
+     *
+     * @return
+     */
     private String getIndependenceTestDesc() {
         return "Independence Test: " + TetradIndependenceTests.getInstance().getCommands().stream()
                 .collect(Collectors.joining(", "));
     }
 
+    /**
+     * Get the names of all the algorithms.
+     *
+     * @return
+     */
     private String getAlgorithmDesc() {
         return "Algorithm: " + TetradAlgorithms.getInstance().getCommands().stream()
                 .collect(Collectors.joining(", "));
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 ff1c1ad..33bed47 100644
--- a/src/main/java/edu/pitt/dbmi/causal/cmd/CmdParams.java
+++ b/src/main/java/edu/pitt/dbmi/causal/cmd/CmdParams.java
@@ -19,6 +19,7 @@
 package edu.pitt.dbmi.causal.cmd;
 
 /**
+ * The class {@code CmdParams} contains all the command-line parameter names.
  *
  * Sep 7, 2017 4:52:54 PM
  *
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 40bef43..364b66c 100644
--- a/src/main/java/edu/pitt/dbmi/causal/cmd/CmdParser.java
+++ b/src/main/java/edu/pitt/dbmi/causal/cmd/CmdParser.java
@@ -47,6 +47,8 @@
 import org.apache.commons.cli.ParseException;
 
 /**
+ * The class {@code CmdParser} is a utility class for parsing and extractiong
+ * command-line options.
  *
  * Sep 15, 2017 11:34:22 AM
  *
@@ -73,6 +75,14 @@ public static CmdArgs parse(String[] args) throws CmdParserException {
         return cmdArgs;
     }
 
+    /**
+     * Parse command-line options.
+     *
+     * @param cmd
+     * @param parseOptions
+     * @param cmdArgs
+     * @throws CmdParserException
+     */
     private static void parseOptionalOptions(CommandLine cmd, ParseOptions parseOptions, CmdArgs cmdArgs) throws CmdParserException {
         cmdArgs.knowledgeFile = cmd.hasOption(CmdParams.KNOWLEDGE)
                 ? getValidFile(cmd.getOptionValue(CmdParams.KNOWLEDGE), parseOptions, CmdParams.KNOWLEDGE)
@@ -126,6 +136,14 @@ private static void parseOptionalOptions(CommandLine cmd, ParseOptions parseOpti
         cmdArgs.parameters = getValidParameters(cmd, cmdArgs, parseOptions);
     }
 
+    /**
+     * Parse the required command-line options.
+     *
+     * @param cmd
+     * @param parseOptions
+     * @param cmdArgs
+     * @throws CmdParserException
+     */
     private static void parseRequiredOptions(CommandLine cmd, ParseOptions parseOptions, CmdArgs cmdArgs) throws CmdParserException {
         cmdArgs.dataType = DataTypes.getInstance().get(cmd.getOptionValue(CmdParams.DATA_TYPE));
         cmdArgs.delimiter = Delimiters.getInstance().get(cmd.getOptionValue(CmdParams.DELIMITER));
@@ -151,6 +169,13 @@ private static void parseRequiredOptions(CommandLine cmd, ParseOptions parseOpti
         }
     }
 
+    /**
+     * Get the options for the help message.
+     *
+     * @param args
+     * @return
+     * @throws CmdParserException
+     */
     public static ParseOptions getHelpOptions(String[] args) throws CmdParserException {
         CmdOptions cmdOptions = CmdOptions.getInstance();
 
@@ -338,6 +363,11 @@ private static List<String> getAlgorithmRelatedParameters(Algorithm algorithm) {
         return params;
     }
 
+    /**
+     * Add options for manipulating Tetrad output graph.
+     *
+     * @param opts
+     */
     private static void addGraphManipulationOptions(Options opts) {
         opts.addOption(CmdOptions.getInstance().getLongOption(CmdParams.CHOOSE_DAG_IN_PATTERN));
         opts.addOption(CmdOptions.getInstance().getLongOption(CmdParams.CHOOSE_MAG_IN_PAG));
@@ -466,6 +496,16 @@ private static Map<String, String> getValidParameters(CommandLine cmd, CmdArgs c
         return parameters;
     }
 
+    /**
+     * 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
+     */
     private static int getValidThreadNumber(String value, ParseOptions parseOptions, String cmdParam) throws CmdParserException {
         int numOfThreads = 0;
 
@@ -489,6 +529,16 @@ private static int getValidThreadNumber(String value, ParseOptions parseOptions,
         return numOfThreads;
     }
 
+    /**
+     * 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
+     */
     private static char getValidChar(String quoteChar, ParseOptions parseOptions, String cmdParam) throws CmdParserException {
         char c = 0;
 
@@ -506,6 +556,16 @@ private static char getValidChar(String quoteChar, ParseOptions parseOptions, St
         return c;
     }
 
+    /**
+     * 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
+     */
     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/CmdParserException.java b/src/main/java/edu/pitt/dbmi/causal/cmd/CmdParserException.java
index fa83d95..4edf774 100644
--- a/src/main/java/edu/pitt/dbmi/causal/cmd/CmdParserException.java
+++ b/src/main/java/edu/pitt/dbmi/causal/cmd/CmdParserException.java
@@ -19,6 +19,8 @@
 package edu.pitt.dbmi.causal.cmd;
 
 /**
+ * The class {@code CmdParserException} occurs when it fails to parse
+ * command-line options.
  *
  * Sep 15, 2017 12:26:52 PM
  *
diff --git a/src/main/java/edu/pitt/dbmi/causal/cmd/DataTypes.java b/src/main/java/edu/pitt/dbmi/causal/cmd/DataTypes.java
index 80b677d..9b01d27 100644
--- a/src/main/java/edu/pitt/dbmi/causal/cmd/DataTypes.java
+++ b/src/main/java/edu/pitt/dbmi/causal/cmd/DataTypes.java
@@ -26,6 +26,7 @@
 import java.util.stream.Collectors;
 
 /**
+ * The class {@code DataTypes} contains the data types supported by Tetrad.
  *
  * Jan 8, 2019 11:28:17 AM
  *
diff --git a/src/main/java/edu/pitt/dbmi/causal/cmd/Delimiters.java b/src/main/java/edu/pitt/dbmi/causal/cmd/Delimiters.java
index 5302626..7baaea3 100644
--- a/src/main/java/edu/pitt/dbmi/causal/cmd/Delimiters.java
+++ b/src/main/java/edu/pitt/dbmi/causal/cmd/Delimiters.java
@@ -26,6 +26,8 @@
 import java.util.stream.Collectors;
 
 /**
+ * The class {@code Delimiters} contains the data delimiters supported by
+ * Tetrad.
  *
  * Jan 8, 2019 11:29:32 AM
  *
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 3fb7b76..070ddf8 100644
--- a/src/main/java/edu/pitt/dbmi/causal/cmd/OptionFactory.java
+++ b/src/main/java/edu/pitt/dbmi/causal/cmd/OptionFactory.java
@@ -26,6 +26,8 @@
 import org.apache.commons.cli.Option;
 
 /**
+ * The class {@code OptionFactory} is a class that helps creating command-line
+ * options.
  *
  * Sep 15, 2017 1:45:16 PM
  *
@@ -36,6 +38,11 @@ public final class OptionFactory {
     private OptionFactory() {
     }
 
+    /**
+     * Create the required options for the help message.
+     *
+     * @return
+     */
     public static Option createRequiredHelpOpt() {
         Option opt = CmdOptions.getInstance().getLongOption(CmdParams.HELP);
 
@@ -48,6 +55,12 @@ public static Option createRequiredHelpOpt() {
                 .build();
     }
 
+    /**
+     * Create the required indepedence test options.
+     *
+     * @param dataType
+     * @return
+     */
     public static Option createRequiredTestOpt(DataType dataType) {
         List<String> commands = TetradIndependenceTests.getInstance().getCommands(dataType);
         Option opt = CmdOptions.getInstance().getLongOption(CmdParams.TEST);
@@ -62,6 +75,12 @@ public static Option createRequiredTestOpt(DataType dataType) {
                 .build();
     }
 
+    /**
+     * Create the required score options.
+     *
+     * @param dataType
+     * @return
+     */
     public static Option createRequiredScoreOpt(DataType dataType) {
         List<String> commands = TetradScores.getInstance().getCommands(dataType);
         Option opt = CmdOptions.getInstance().getLongOption(CmdParams.SCORE);
@@ -76,6 +95,11 @@ public static Option createRequiredScoreOpt(DataType dataType) {
                 .build();
     }
 
+    /**
+     * Create the required option for the number of category for mixed data.
+     *
+     * @return
+     */
     public static Option createRequiredNumCategoryOpt() {
         Option opt = CmdOptions.getInstance().getLongOption(CmdParams.NUM_CATEGORIES);
 
diff --git a/src/main/java/edu/pitt/dbmi/causal/cmd/ParseOptions.java b/src/main/java/edu/pitt/dbmi/causal/cmd/ParseOptions.java
index 5c6fbcb..b7a72ec 100644
--- a/src/main/java/edu/pitt/dbmi/causal/cmd/ParseOptions.java
+++ b/src/main/java/edu/pitt/dbmi/causal/cmd/ParseOptions.java
@@ -21,6 +21,8 @@
 import org.apache.commons.cli.Options;
 
 /**
+ * The class {@code ParseOptions} holds the command-line options that have been
+ * parsed.
  *
  * Oct 6, 2017 11:36:39 AM
  *
diff --git a/src/main/java/edu/pitt/dbmi/causal/cmd/ValidationException.java b/src/main/java/edu/pitt/dbmi/causal/cmd/ValidationException.java
index 6f26a13..cb27a82 100644
--- a/src/main/java/edu/pitt/dbmi/causal/cmd/ValidationException.java
+++ b/src/main/java/edu/pitt/dbmi/causal/cmd/ValidationException.java
@@ -19,6 +19,7 @@
 package edu.pitt.dbmi.causal.cmd;
 
 /**
+ * The class {@code ValidationException} occurs when data validation fails.
  *
  * Sep 27, 2017 12:15:27 PM
  *

From cfe09d64bf466e6803214d1cbc808ba746907741 Mon Sep 17 00:00:00 2001
From: Kevin Bui <kvb2univpitt@gmail.com>
Date: Sat, 2 Jul 2022 09:53:07 -0600
Subject: [PATCH 3/6] Added the default flag to use Tetrad default parameter
 values.

---
 .../dbmi/causal/cmd/CausalCmdApplication.java |   7 +-
 .../edu/pitt/dbmi/causal/cmd/CmdArgs.java     |   6 +
 .../edu/pitt/dbmi/causal/cmd/CmdOptions.java  |   4 +
 .../edu/pitt/dbmi/causal/cmd/CmdParams.java   |   2 +
 .../edu/pitt/dbmi/causal/cmd/CmdParser.java   | 107 +++++++++++-------
 .../pitt/dbmi/causal/cmd/tetrad/Tetrad.java   |  27 -----
 .../cmd/CausalCmdApplicationMetadataTest.java |   6 +-
 .../causal/cmd/CausalCmdApplicationTest.java  |  24 ++--
 .../edu/pitt/dbmi/causal/cmd/TestFiles.java   |  13 +++
 9 files changed, 112 insertions(+), 84 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 f196658..55a841d 100644
--- a/src/main/java/edu/pitt/dbmi/causal/cmd/CausalCmdApplication.java
+++ b/src/main/java/edu/pitt/dbmi/causal/cmd/CausalCmdApplication.java
@@ -20,7 +20,6 @@
 
 import edu.cmu.tetrad.graph.Graph;
 import edu.pitt.dbmi.causal.cmd.data.DataValidations;
-import edu.pitt.dbmi.causal.cmd.tetrad.Tetrad;
 import edu.pitt.dbmi.causal.cmd.tetrad.TetradAlgorithms;
 import edu.pitt.dbmi.causal.cmd.tetrad.TetradIndependenceTests;
 import edu.pitt.dbmi.causal.cmd.tetrad.TetradRunner;
@@ -129,7 +128,7 @@ 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()) {
@@ -232,8 +231,8 @@ private static void writeOutParameters(CmdArgs cmdArgs, PrintStream out) {
         out.println();
         out.println("Algorithm Parameters");
         out.println("--------------------------------------------------------------------------------");
-        Tetrad.getParameterValues(cmdArgs)
-                .forEach((k, v) -> out.printf("%s: %s%n", k, WordUtil.toYesOrNo(v)));
+        cmdArgs.getParameters().forEach((k, v) -> out.printf("%s: %s%n", k, WordUtil.toYesOrNo(v)));
+
         out.println();
         out.println();
     }
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 9e54a6e..5bb477a 100644
--- a/src/main/java/edu/pitt/dbmi/causal/cmd/CmdArgs.java
+++ b/src/main/java/edu/pitt/dbmi/causal/cmd/CmdArgs.java
@@ -74,6 +74,8 @@ public class CmdArgs {
     protected boolean extractStructModel;
 
     protected boolean experimental;
+    
+    protected boolean defaultParamValues;
 
     protected Map<String, String> parameters;
 
@@ -200,6 +202,10 @@ public boolean isExperimental() {
         return experimental;
     }
 
+    public boolean isDefaultParamValues() {
+        return defaultParamValues;
+    }
+
     public Map<String, String> getParameters() {
         return parameters;
     }
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 2fd41cd..73f7f77 100644
--- a/src/main/java/edu/pitt/dbmi/causal/cmd/CmdOptions.java
+++ b/src/main/java/edu/pitt/dbmi/causal/cmd/CmdOptions.java
@@ -170,6 +170,8 @@ public List<Option> getBaseOptions() {
         opts.add(options.get(CmdParams.SKIP_VALIDATION));
 
         opts.add(options.get(CmdParams.EXPERIMENTAL));
+        
+        opts.add(options.get(CmdParams.DEFAULT));
 
         return opts;
     }
@@ -218,6 +220,8 @@ private void addOptionalOptions() {
 
         options.put(CmdParams.EXPERIMENTAL, new Option(null, CmdParams.EXPERIMENTAL, false, "Show experimental algorithms, tests, and scores."));
 
+        options.put(CmdParams.DEFAULT, new Option(null, CmdParams.DEFAULT, false, "Use Tetrad default parameter values."));
+
         // tetrad parameters
         ParamDescriptions paramDescs = ParamDescriptions.getInstance();
         Set<String> params = paramDescs.getNames();
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 33bed47..d4acf59 100644
--- a/src/main/java/edu/pitt/dbmi/causal/cmd/CmdParams.java
+++ b/src/main/java/edu/pitt/dbmi/causal/cmd/CmdParams.java
@@ -78,6 +78,8 @@ 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/CmdParser.java b/src/main/java/edu/pitt/dbmi/causal/cmd/CmdParser.java
index 364b66c..bb02fdc 100644
--- a/src/main/java/edu/pitt/dbmi/causal/cmd/CmdParser.java
+++ b/src/main/java/edu/pitt/dbmi/causal/cmd/CmdParser.java
@@ -36,9 +36,11 @@
 import java.nio.file.Paths;
 import java.util.Collections;
 import java.util.HashMap;
+import java.util.HashSet;
 import java.util.LinkedList;
 import java.util.List;
 import java.util.Map;
+import java.util.Set;
 import java.util.TreeMap;
 import org.apache.commons.cli.CommandLine;
 import org.apache.commons.cli.DefaultParser;
@@ -133,6 +135,8 @@ private static void parseOptionalOptions(CommandLine cmd, ParseOptions parseOpti
 
         cmdArgs.experimental = cmd.hasOption(CmdParams.EXPERIMENTAL);
 
+        cmdArgs.defaultParamValues = cmd.hasOption(CmdParams.DEFAULT);
+
         cmdArgs.parameters = getValidParameters(cmd, cmdArgs, parseOptions);
     }
 
@@ -300,7 +304,7 @@ private static ParseOptions getValidOptions(String[] args, Options options) thro
             scoreClass = TetradScores.getInstance().getClass(scoreCmd);
         }
 
-        List<String> params = new LinkedList<>();
+        Set<String> params = new HashSet<>();
         try {
             params.addAll(getAlgorithmRelatedParameters(AlgorithmFactory.create(algorithmClass, indTestClass, scoreClass)));
         } catch (IllegalAccessException | InstantiationException exception) {
@@ -334,15 +338,15 @@ 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 to get parameters from
-     * @return list of parameters for the algorithm, test and score
+     * @param algorithm
+     * @return
      */
-    private static List<String> getAlgorithmRelatedParameters(Algorithm algorithm) {
+    private static Set<String> getAlgorithmRelatedParameters(Algorithm algorithm) {
         if (algorithm == null) {
-            return Collections.EMPTY_LIST;
+            return Collections.EMPTY_SET;
         }
 
-        List<String> params = new LinkedList<>();
+        Set<String> params = new HashSet<>();
 
         // add algorithm parameters
         params.addAll(algorithm.getParameters());
@@ -396,27 +400,52 @@ private static String extractName(Class clazz) {
         return fields[fields.length - 1];
     }
 
-    private static Map<String, String> getValidParameters(CommandLine cmd, CmdArgs cmdArgs, ParseOptions parseOptions) throws CmdParserException {
-        Map<String, String> parameters = new TreeMap<>(String.CASE_INSENSITIVE_ORDER);
-
-        List<String> params = new LinkedList<>();
+    /**
+     * Get all the parameters related to the selected algorithm, test, and
+     * score.
+     *
+     * @param cmdArgs
+     * @param parseOptions
+     * @return
+     * @throws CmdParserException
+     */
+    private static Set<String> getAllRelatedParameters(CmdArgs cmdArgs, ParseOptions parseOptions) throws CmdParserException {
         try {
-            params.addAll(getAlgorithmRelatedParameters(AlgorithmFactory.create(cmdArgs.getAlgorithmClass(), cmdArgs.getTestClass(), cmdArgs.getScoreClass())));
+            return getAlgorithmRelatedParameters(AlgorithmFactory.create(cmdArgs.getAlgorithmClass(), cmdArgs.getTestClass(), cmdArgs.getScoreClass()));
         } catch (IllegalAccessException | InstantiationException exception) {
             throw new CmdParserException(parseOptions, exception);
         }
+    }
 
-        // add --numCategories to validate with other tetrad parameters
-        if (cmd.hasOption(CmdParams.NUM_CATEGORIES)) {
-            params.add(CmdParams.NUM_CATEGORIES);
-        }
+    /**
+     * Get all the parameters for algorithm, test, and score. Use default values
+     * 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
+     */
+    private static Map<String, String> getValidParameters(CommandLine cmd, CmdArgs cmdArgs, ParseOptions parseOptions) throws CmdParserException {
+        Map<String, String> parametersWithValues = new TreeMap<>(String.CASE_INSENSITIVE_ORDER);
+
+        Set<String> parameters = getAllRelatedParameters(cmdArgs, parseOptions);
+
+        setParametersAndValues(parametersWithValues, parameters, cmdArgs.defaultParamValues);
+        setUserParameterValues(parametersWithValues, parameters, cmd, parseOptions);
+
+        return parametersWithValues;
+    }
 
+    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();
         Options invalidOpts = parseOptions.getInvalidValueOptions();
-        ParamDescriptions paramDescs = ParamDescriptions.getInstance();
-        for (String param : params) {
-            ParamDescription paramDesc = paramDescs.get(param);
+        for (String param : parameters) {
             if (cmd.hasOption(param)) {
+                ParamDescription paramDesc = paramDescriptions.get(param);
                 String value = cmd.getOptionValue(param);
                 Option opt = opts.getOption(param);
                 Object type = opt.getType();
@@ -471,29 +500,31 @@ private static Map<String, String> getValidParameters(CommandLine cmd, CmdArgs c
                         value = "true";
                     }
                 }
-                parameters.put(param, value);
-            } else {
-                Serializable defaultValue = paramDesc.getDefaultValue();
-                String value = (defaultValue instanceof Boolean)
-                        ? Boolean.FALSE.toString()
-                        : defaultValue.toString();
-                parameters.put(param, value);
-            }
-        };
-
-        // remove --numCategories parameter after validation
-        if (parameters.containsKey(CmdParams.NUM_CATEGORIES)) {
-            String value = parameters.remove(CmdParams.NUM_CATEGORIES);
-            try {
-                cmdArgs.numCategories = Integer.parseInt(value);
-            } catch (NumberFormatException exception) {
-                invalidOpts.addOption(opts.getOption(CmdParams.NUM_CATEGORIES));
-                String errMsg = String.format("The value '%s' for parameter %s is not a integer.", value, CmdParams.NUM_CATEGORIES);
-                throw new CmdParserException(parseOptions, new NumberFormatException(errMsg));
+                parametersWithValues.put(param, value);
             }
         }
+    }
 
-        return parameters;
+    /**
+     * Add all the parameters with values.
+     *
+     * @param parametersWithValues holds parameters along with their values
+     * @param parameters parameters to add
+     * @param useDefaultValues true if default values should be used for boolean
+     * parameters. Else, the values for the boolean parameters are false.
+     */
+    private static void setParametersAndValues(Map<String, String> parametersWithValues, Set<String> parameters, boolean useDefaultValues) {
+        ParamDescriptions paramDescriptions = ParamDescriptions.getInstance();
+        for (String param : parameters) {
+            ParamDescription paramDesc = paramDescriptions.get(param);
+            Serializable defaultValue = paramDesc.getDefaultValue();
+            String value = useDefaultValues
+                    ? String.valueOf(defaultValue)
+                    : (defaultValue instanceof Boolean)
+                            ? Boolean.FALSE.toString()
+                            : String.valueOf(defaultValue);
+            parametersWithValues.put(param, value);
+        }
     }
 
     /**
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 0963ff7..a185ebe 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
@@ -18,14 +18,11 @@
  */
 package edu.pitt.dbmi.causal.cmd.tetrad;
 
-import edu.cmu.tetrad.algcomparison.algorithm.Algorithm;
-import edu.cmu.tetrad.algcomparison.algorithm.AlgorithmFactory;
 import edu.cmu.tetrad.util.ParamDescription;
 import edu.cmu.tetrad.util.ParamDescriptions;
 import edu.cmu.tetrad.util.Parameters;
 import edu.pitt.dbmi.causal.cmd.CmdArgs;
 import java.util.Map;
-import java.util.TreeMap;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
@@ -70,28 +67,4 @@ public static Parameters getParameters(CmdArgs cmdArgs) {
         return parameters;
     }
 
-    public static Map<String, String> getParameterValues(CmdArgs cmdArgs) {
-        Map<String, String> params = new TreeMap<>();
-
-        Class algoClass = cmdArgs.getAlgorithmClass();
-        Class indTestClass = cmdArgs.getTestClass();
-        Class scoreClass = cmdArgs.getScoreClass();
-
-        Algorithm algorithm;
-        try {
-            algorithm = AlgorithmFactory.create(algoClass, indTestClass, scoreClass);
-        } catch (IllegalAccessException | InstantiationException exception) {
-            algorithm = null;
-            LOGGER.error("Unable to construct algorithm object.", exception);
-        }
-
-        if (algorithm != null) {
-            ParamDescriptions paramDesc = ParamDescriptions.getInstance();
-            algorithm.getParameters().forEach(e -> params.put(e, String.valueOf(paramDesc.get(e).getDefaultValue())));
-        }
-        cmdArgs.getParameters().forEach((k, v) -> params.put(k, v));
-
-        return params;
-    }
-
 }
diff --git a/src/test/java/edu/pitt/dbmi/causal/cmd/CausalCmdApplicationMetadataTest.java b/src/test/java/edu/pitt/dbmi/causal/cmd/CausalCmdApplicationMetadataTest.java
index e568689..058ec77 100644
--- a/src/test/java/edu/pitt/dbmi/causal/cmd/CausalCmdApplicationMetadataTest.java
+++ b/src/test/java/edu/pitt/dbmi/causal/cmd/CausalCmdApplicationMetadataTest.java
@@ -49,7 +49,7 @@ public void testGFCIWithMixedData() throws IOException {
             "--algorithm", "gfci",
             "--test", "cg-lr-test",
             "--score", "cg-bic-score",
-            "--verbose",
+            "--default",
             "--out", dirOut
         };
         CausalCmdApplication.main(args);
@@ -68,7 +68,7 @@ public void testGFCIWithDiscreteData() throws IOException {
             "--algorithm", "gfci",
             "--test", "g-square-test",
             "--score", "bdeu-score",
-            "--verbose",
+            "--default",
             "--out", dirOut
         };
         CausalCmdApplication.main(args);
@@ -87,7 +87,7 @@ public void testGFCIWithContinuousData() throws IOException {
             "--algorithm", "gfci",
             "--test", "fisher-z-test",
             "--score", "sem-bic-score",
-            "--verbose",
+            "--default",
             "--out", dirOut
         };
         CausalCmdApplication.main(args);
diff --git a/src/test/java/edu/pitt/dbmi/causal/cmd/CausalCmdApplicationTest.java b/src/test/java/edu/pitt/dbmi/causal/cmd/CausalCmdApplicationTest.java
index 229127c..6e3887e 100644
--- a/src/test/java/edu/pitt/dbmi/causal/cmd/CausalCmdApplicationTest.java
+++ b/src/test/java/edu/pitt/dbmi/causal/cmd/CausalCmdApplicationTest.java
@@ -45,7 +45,7 @@ public void testExperimentalAlgorithm() throws IOException {
             "--delimiter", "tab",
             "--data-type", "discrete",
             "--algorithm", "rfci-bsc",
-            "--verbose",
+            "--default",
             "--experimental",
             "--out", dirOut
         };
@@ -64,7 +64,7 @@ public void testGFCIWithContinuousMissingData() throws IOException {
             "--test", "fisher-z-test",
             "--score", "sem-bic-score",
             "--missing", "*",
-            "--verbose",
+            "--default",
             "--out", dirOut
         };
         CausalCmdApplication.main(args);
@@ -81,7 +81,7 @@ public void testGFCIWithContinuousDataAndChooseMagInPag() throws IOException {
             "--algorithm", "gfci",
             "--test", "fisher-z-test",
             "--score", "sem-bic-score",
-            "--verbose",
+            "--default",
             "--choose-mag-in-pag",
             "--out", dirOut
         };
@@ -100,7 +100,7 @@ public void testFaskVoteWithMultipleContinuousData() throws IOException {
             "--algorithm", "fask-vote",
             "--test", "fisher-z-test",
             "--score", "sem-bic-score",
-            "--verbose",
+            "--default",
             "--out", dirOut
         };
         CausalCmdApplication.main(args);
@@ -119,7 +119,7 @@ public void testGFCIWithContinuousDataAndVariablesToExclude() throws IOException
             "--algorithm", "gfci",
             "--test", "fisher-z-test",
             "--score", "sem-bic-score",
-            "--verbose",
+            "--default",
             "--out", dirOut
         };
         CausalCmdApplication.main(args);
@@ -136,7 +136,7 @@ public void testFGESCovariance() throws IOException {
             "--algorithm", "gfci",
             "--test", "fisher-z-test",
             "--score", "sem-bic-score",
-            "--verbose",
+            "--default",
             "--out", dirOut
         };
         CausalCmdApplication.main(args);
@@ -155,7 +155,7 @@ public void testGFCIWithContinuousDataAndKnowledge() throws IOException {
             "--algorithm", "gfci",
             "--test", "fisher-z-test",
             "--score", "sem-bic-score",
-            "--verbose",
+            "--default",
             "--out", dirOut
         };
         CausalCmdApplication.main(args);
@@ -173,7 +173,7 @@ public void testGFCIWithNoHeaderContinuousData() throws IOException {
             "--algorithm", "gfci",
             "--test", "fisher-z-test",
             "--score", "sem-bic-score",
-            "--verbose",
+            "--default",
             "--out", dirOut
         };
         CausalCmdApplication.main(args);
@@ -191,7 +191,7 @@ public void testGFCIWithMixedData() throws IOException {
             "--algorithm", "gfci",
             "--test", "cg-lr-test",
             "--score", "cg-bic-score",
-            "--verbose",
+            "--default",
             "--out", dirOut
         };
         CausalCmdApplication.main(args);
@@ -209,7 +209,7 @@ public void testGFCIWithDiscreteData() throws IOException {
             "--test", "g-square-test",
             "--score", "bdeu-score",
             "--faithfulnessAssumed",
-            "--verbose",
+            "--default",
             "--out", dirOut
         };
         CausalCmdApplication.main(args);
@@ -228,7 +228,7 @@ public void testGFCIWithContinuousData() throws IOException {
             "--score", "sem-bic-score",
             "--penaltyDiscount", "1.0",
             "--semBicStructurePrior", "0.01",
-            "--verbose",
+            "--default",
             "--out", dirOut
         };
         CausalCmdApplication.main(args);
@@ -245,7 +245,7 @@ public void testGRaSPWithContinuousData() throws IOException {
             "--algorithm", "grasp",
             "--test", "fisher-z-test",
             "--score", "sem-bic-score",
-            "--verbose",
+            "--default",
             "--out", dirOut
         };
         CausalCmdApplication.main(args);
diff --git a/src/test/java/edu/pitt/dbmi/causal/cmd/TestFiles.java b/src/test/java/edu/pitt/dbmi/causal/cmd/TestFiles.java
index ddf865a..dde282f 100644
--- a/src/test/java/edu/pitt/dbmi/causal/cmd/TestFiles.java
+++ b/src/test/java/edu/pitt/dbmi/causal/cmd/TestFiles.java
@@ -22,6 +22,8 @@
 import java.nio.file.Files;
 import java.nio.file.Path;
 import java.nio.file.Paths;
+import java.util.LinkedList;
+import java.util.List;
 
 /**
  *
@@ -86,4 +88,15 @@ public static Path createSubDir(Path dir, String name) throws IOException {
         return Files.createDirectory(Paths.get(dir.toString(), name));
     }
 
+    public static List<String> readFileLineByLine(Path file) {
+        List<String> allLines = new LinkedList<>();
+
+        try {
+            allLines.addAll(Files.readAllLines(file));
+        } catch (IOException exception) {
+        }
+
+        return allLines;
+    }
+
 }

From 1c272c33ecaafdddc85b9a077bc4de40a9573798 Mon Sep 17 00:00:00 2001
From: Kevin Bui <kvb2univpitt@gmail.com>
Date: Sat, 9 Jul 2022 15:36:00 -0600
Subject: [PATCH 4/6] Added more javadocs.

---
 .../pitt/dbmi/causal/cmd/Applications.java    |  3 +
 .../dbmi/causal/cmd/CausalCmdApplication.java | 11 ++-
 .../edu/pitt/dbmi/causal/cmd/CmdArgs.java     | 71 ++++++++++++++++++-
 .../edu/pitt/dbmi/causal/cmd/Delimiters.java  | 11 ++-
 .../pitt/dbmi/causal/cmd/data/DataFiles.java  | 56 ++++++++++++++-
 .../dbmi/causal/cmd/data/DataValidations.java | 22 ++++++
 .../pitt/dbmi/causal/cmd/tetrad/Tetrad.java   |  7 ++
 .../causal/cmd/tetrad/TetradAlgorithms.java   | 57 +++++++++++++++
 .../cmd/tetrad/TetradIndependenceTests.java   | 60 ++++++++++++++++
 .../dbmi/causal/cmd/tetrad/TetradRunner.java  | 29 ++++++++
 .../dbmi/causal/cmd/tetrad/TetradScores.java  | 59 +++++++++++++++
 .../pitt/dbmi/causal/cmd/util/DateTime.java   |  1 +
 .../pitt/dbmi/causal/cmd/util/FileUtils.java  |  1 +
 .../pitt/dbmi/causal/cmd/util/GraphIO.java    | 20 +++++-
 .../dbmi/causal/cmd/util/LogMessages.java     | 52 ++++++++++++++
 .../pitt/dbmi/causal/cmd/util/WordUtil.java   |  7 ++
 16 files changed, 460 insertions(+), 7 deletions(-)

diff --git a/src/main/java/edu/pitt/dbmi/causal/cmd/Applications.java b/src/main/java/edu/pitt/dbmi/causal/cmd/Applications.java
index 60625e8..c187d3b 100644
--- a/src/main/java/edu/pitt/dbmi/causal/cmd/Applications.java
+++ b/src/main/java/edu/pitt/dbmi/causal/cmd/Applications.java
@@ -46,6 +46,9 @@
  */
 public final class Applications {
 
+    /**
+     * Use to convert {@link Date} into a date-time string.
+     */
     private static final DateFormat DF = new SimpleDateFormat("EEE, MMMM dd, yyyy hh:mm:ss a");
 
     private Applications() {
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 55a841d..e02eac7 100644
--- a/src/main/java/edu/pitt/dbmi/causal/cmd/CausalCmdApplication.java
+++ b/src/main/java/edu/pitt/dbmi/causal/cmd/CausalCmdApplication.java
@@ -48,10 +48,19 @@
  */
 public class CausalCmdApplication {
 
+    /**
+     * Logger for the class {@code CausalCmdApplication}.
+     */
     private static final Logger LOGGER = LoggerFactory.getLogger(CausalCmdApplication.class);
 
+    /**
+     * Help message footer.
+     */
     public static final String FOOTER = "Use --help for guidance list of options.  Use --help-all to show all options.";
 
+    /**
+     * Indicate whether to show experimental algorithms, tests and scores.
+     */
     public static boolean showExperimental;
 
     /**
@@ -128,7 +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 5bb477a..9a9b538 100644
--- a/src/main/java/edu/pitt/dbmi/causal/cmd/CmdArgs.java
+++ b/src/main/java/edu/pitt/dbmi/causal/cmd/CmdArgs.java
@@ -34,31 +34,100 @@
  */
 public class CmdArgs {
 
+    /**
+     * Data set files.
+     */
     protected List<Path> datasetFiles;
+
+    /**
+     * Knowledge file.
+     */
     protected Path knowledgeFile;
+
+    /**
+     * File contains a list of variables to exclude when reading in data.
+     */
     protected Path excludeVariableFile;
+
+    /**
+     * Metadata file.
+     */
     protected Path metadataFile;
+
+    /**
+     * Directory to where
+     */
     protected Path outDirectory;
 
+    /**
+     * Prefix file name of output files.
+     */
     protected String filePrefix;
 
+    /**
+     * Quote character.
+     */
     protected char quoteChar;
+
+    /**
+     * A placeholder for missing value in dataset.
+     */
     protected String missingValueMarker;
+
+    /**
+     * A line in the data file that begins with comment marker will be ignored
+     * by the data reader.
+     */
     protected String commentMarker;
+    
+    /**
+     * Indicates whether the first line in the data file is a header.
+     */
     protected boolean hasHeader;
 
+    /**
+     * Type of data in the dataset.
+     */
     protected DataType dataType;
+    
+    /**
+     * Data delimiter.
+     */
     protected Delimiter delimiter;
 
+    /**
+     * Algorithm class.
+     */
     protected Class algorithmClass;
+    
+    /**
+     * Score class.
+     */
     protected Class scoreClass;
+    
+    /**
+     * Independence test class.
+     */
     protected Class testClass;
 
+    /**
+     * Number of discrete values.
+     */
     protected int numCategories;
 
+    /**
+     * 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.
+     */
     protected int numOfThreads;
 
     // graph manipulations
@@ -74,7 +143,7 @@ public class CmdArgs {
     protected boolean extractStructModel;
 
     protected boolean experimental;
-    
+
     protected boolean defaultParamValues;
 
     protected Map<String, String> parameters;
diff --git a/src/main/java/edu/pitt/dbmi/causal/cmd/Delimiters.java b/src/main/java/edu/pitt/dbmi/causal/cmd/Delimiters.java
index 7baaea3..105039a 100644
--- a/src/main/java/edu/pitt/dbmi/causal/cmd/Delimiters.java
+++ b/src/main/java/edu/pitt/dbmi/causal/cmd/Delimiters.java
@@ -26,8 +26,8 @@
 import java.util.stream.Collectors;
 
 /**
- * The class {@code Delimiters} contains the data delimiters supported by
- * Tetrad.
+ * The class {@code Delimiters} contains the data delimiters supported by the
+ * data reader.
  *
  * Jan 8, 2019 11:29:32 AM
  *
@@ -35,8 +35,15 @@
  */
 public final class Delimiters {
 
+    /**
+     * An instance of this class.
+     */
     private static final Delimiters INSTANCE = new Delimiters();
 
+    /**
+     * A data structure that holds different types of delimiters by delimiter
+     * name.
+     */
     private final Map<String, Delimiter> delimiters = new TreeMap<>(String.CASE_INSENSITIVE_ORDER);
 
     private Delimiters() {
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 6f652b8..3e94a78 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
@@ -53,6 +53,8 @@
 import org.slf4j.LoggerFactory;
 
 /**
+ * The class {@code DataFiles} is a utility class for reading various data
+ * files.
  *
  * Jan 14, 2019 11:25:47 AM
  *
@@ -60,11 +62,22 @@
  */
 public final class DataFiles {
 
+    /**
+     * The logger for the class {@code DataFiles}.
+     */
     private static final Logger LOGGER = LoggerFactory.getLogger(DataFiles.class);
 
     private DataFiles() {
     }
 
+    /**
+     * Read in metadata file.
+     *
+     * @param cmdArgs
+     * @param out
+     * @return
+     * @throws IOException
+     */
     public static Metadata readInMetadata(CmdArgs cmdArgs, PrintStream out) throws IOException {
         Path file = cmdArgs.getMetadataFile();
         if (file == null) {
@@ -78,6 +91,14 @@ public static Metadata readInMetadata(CmdArgs cmdArgs, PrintStream out) throws I
         }
     }
 
+    /**
+     * Read in knowledge file.
+     *
+     * @param cmdArgs
+     * @param out
+     * @return
+     * @throws IOException
+     */
     public static IKnowledge readInKnowledge(CmdArgs cmdArgs, PrintStream out) throws IOException {
         Path file = cmdArgs.getKnowledgeFile();
         if (file == null) {
@@ -91,6 +112,15 @@ public static IKnowledge readInKnowledge(CmdArgs cmdArgs, PrintStream out) throw
         }
     }
 
+    /**
+     * Read in datasets files.
+     *
+     * @param cmdArgs
+     * @param out
+     * @return
+     * @throws IOException
+     * @throws AlgorithmRunException
+     */
     public static List<DataModel> readInDatasets(CmdArgs cmdArgs, PrintStream out) throws IOException, AlgorithmRunException {
         DataType dataType = cmdArgs.getDataType();
         switch (dataType) {
@@ -106,6 +136,14 @@ public static List<DataModel> readInDatasets(CmdArgs cmdArgs, PrintStream out) t
         }
     }
 
+    /**
+     * Read in tabular dataset files.
+     *
+     * @param cmdArgs
+     * @param out
+     * @return
+     * @throws IOException
+     */
     private static List<DataModel> readInTabularData(CmdArgs cmdArgs, PrintStream out) throws IOException {
         List<DataModel> dataModels = new LinkedList<>();
 
@@ -163,6 +201,14 @@ private static List<DataModel> readInTabularData(CmdArgs cmdArgs, PrintStream ou
         return dataModels;
     }
 
+    /**
+     * Read in covariances files.
+     *
+     * @param cmdArgs
+     * @param out
+     * @return
+     * @throws IOException
+     */
     private static List<DataModel> readInCovarianceFile(CmdArgs cmdArgs, PrintStream out) throws IOException {
         List<DataModel> dataModels = new LinkedList<>();
 
@@ -185,13 +231,21 @@ private static List<DataModel> readInCovarianceFile(CmdArgs cmdArgs, PrintStream
         return dataModels;
     }
 
+    /**
+     * Read in exclude-variable file.
+     *
+     * @param cmdArgs
+     * @param out
+     * @return
+     * @throws IOException
+     */
     public static Set<String> readInVariablesToExclude(CmdArgs cmdArgs, PrintStream out) throws IOException {
         Set<String> variablesToExclude = new HashSet<>();
 
         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/data/DataValidations.java b/src/main/java/edu/pitt/dbmi/causal/cmd/data/DataValidations.java
index 1e289af..6ad62ba 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
@@ -45,6 +45,7 @@
 import org.slf4j.LoggerFactory;
 
 /**
+ * The class {@code DataValidations} is a utility class for validating data.
  *
  * Jan 9, 2019 2:17:36 PM
  *
@@ -57,6 +58,13 @@ public final class DataValidations {
     private DataValidations() {
     }
 
+    /**
+     * Validate tabular dataset and covariance data.
+     *
+     * @param cmdArgs
+     * @param out
+     * @throws ValidationException
+     */
     public static void validate(CmdArgs cmdArgs, PrintStream out) throws ValidationException {
         DataType dataType = cmdArgs.getDataType();
         switch (dataType) {
@@ -74,6 +82,13 @@ public static void validate(CmdArgs cmdArgs, PrintStream out) throws ValidationE
         }
     }
 
+    /**
+     * Validate tabular dataset.
+     *
+     * @param cmdArgs
+     * @param out
+     * @throws ValidationException
+     */
     private static void validateTabularData(CmdArgs cmdArgs, PrintStream out) throws ValidationException {
         try {
             Delimiter delimiter = cmdArgs.getDelimiter();
@@ -126,6 +141,13 @@ private static void validateTabularData(CmdArgs cmdArgs, PrintStream out) throws
         }
     }
 
+    /**
+     * Validate covariance data.
+     *
+     * @param cmdArgs
+     * @param out
+     * @throws ValidationException
+     */
     private static void validateCovariance(CmdArgs cmdArgs, PrintStream out) throws ValidationException {
         for (Path dataFile : cmdArgs.getDatasetFiles()) {
             Delimiter delimiter = cmdArgs.getDelimiter();
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 a185ebe..c735b9a 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
@@ -27,6 +27,7 @@
 import org.slf4j.LoggerFactory;
 
 /**
+ * The class {@code Tetrad} is a utility class for getting Tetrad parameters.
  *
  * Jan 14, 2019 4:27:15 PM
  *
@@ -39,6 +40,12 @@ public final class Tetrad {
     private Tetrad() {
     }
 
+    /**
+     * Get Tetrad parameters from command-line input.
+     *
+     * @param cmdArgs
+     * @return
+     */
     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 803b95c..f7548fa 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
@@ -30,6 +30,8 @@
 import java.util.stream.Collectors;
 
 /**
+ * The class {@code TetradAlgorithms} is a utility class for handling Tetrad
+ * algorithms.
  *
  * Sep 21, 2017 5:46:44 PM
  *
@@ -42,6 +44,9 @@ public final class TetradAlgorithms {
     private final Map<String, AnnotatedClass<Algorithm>> algorithms = new TreeMap<>(String.CASE_INSENSITIVE_ORDER);
     private final Map<String, AnnotatedClass<Algorithm>> nonExpAlgorithms = new TreeMap<>(String.CASE_INSENSITIVE_ORDER);
 
+    /**
+     * Private constructor.
+     */
     private TetradAlgorithms() {
         AlgorithmAnnotations.getInstance().getAnnotatedClasses().stream().forEach(e -> {
             String key = e.getAnnotation().command();
@@ -52,10 +57,20 @@ private TetradAlgorithms() {
         });
     }
 
+    /**
+     * Get the instance of this class.
+     *
+     * @return
+     */
     public static TetradAlgorithms getInstance() {
         return INSTANCE;
     }
 
+    /**
+     * Get a list of command-line options.
+     *
+     * @return
+     */
     public List<String> getCommands() {
         List<String> list = CausalCmdApplication.showExperimental
                 ? algorithms.keySet().stream().collect(Collectors.toList())
@@ -64,6 +79,12 @@ public List<String> getCommands() {
         return Collections.unmodifiableList(list);
     }
 
+    /**
+     * Determine if the giving command is a validate command-line option.
+     *
+     * @param command
+     * @return
+     */
     public boolean hasCommand(String command) {
         if (command == null || command.isEmpty()) {
             return false;
@@ -74,6 +95,12 @@ public boolean hasCommand(String command) {
                 : nonExpAlgorithms.containsKey(command);
     }
 
+    /**
+     * Get the algorithm class from the command-line input.
+     *
+     * @param command
+     * @return
+     */
     public Class getAlgorithmClass(String command) {
         if (command == null || command.isEmpty()) {
             return null;
@@ -86,22 +113,52 @@ public Class getAlgorithmClass(String command) {
         return (annotatedClass == null) ? null : annotatedClass.getClazz();
     }
 
+    /**
+     * Determine if the given algorithm class requires an independence test.
+     *
+     * @param clazz
+     * @return
+     */
     public boolean requireIndependenceTest(Class clazz) {
         return AlgorithmAnnotations.getInstance().requireIndependenceTest(clazz);
     }
 
+    /**
+     * Determine if the given algorithm class requires a score.
+     *
+     * @param clazz
+     * @return
+     */
     public boolean requireScore(Class clazz) {
         return AlgorithmAnnotations.getInstance().requireScore(clazz);
     }
 
+    /**
+     * Determine if the given algorithm class accepts multiple datasets.
+     *
+     * @param clazz
+     * @return
+     */
     public boolean acceptMultipleDataset(Class clazz) {
         return AlgorithmAnnotations.getInstance().acceptMultipleDataset(clazz);
     }
 
+    /**
+     * Determine if the given algorithm class accepts prior knowledge.
+     *
+     * @param clazz
+     * @return
+     */
     public boolean acceptKnowledge(Class clazz) {
         return AlgorithmAnnotations.getInstance().acceptKnowledge(clazz);
     }
 
+    /**
+     * Get the description for a given class.
+     *
+     * @param clazz
+     * @return
+     */
     public String getName(Class clazz) {
         return (clazz != null && clazz.isAnnotationPresent(Algorithm.class))
                 ? ((Algorithm) clazz.getAnnotation(Algorithm.class)).name()
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 dad3bac..2aac29a 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
@@ -34,6 +34,8 @@
 import java.util.stream.Stream;
 
 /**
+ * The class {@code TetradIndependenceTests} is a utility class for handling
+ * Tetrad independence tests.
  *
  * Sep 26, 2017 2:48:25 PM
  *
@@ -49,6 +51,9 @@ public final class TetradIndependenceTests {
     private final Map<DataType, List<String>> groupByDataType = new EnumMap<>(DataType.class);
     private final Map<DataType, List<String>> nonExpGroupByDataType = new EnumMap<>(DataType.class);
 
+    /**
+     * Private constructor.
+     */
     private TetradIndependenceTests() {
         TestOfIndependenceAnnotations.getInstance().getAnnotatedClasses().stream().forEach(e -> {
             String key = e.getAnnotation().command();
@@ -91,16 +96,34 @@ private TetradIndependenceTests() {
         nonExpGroupByDataType.put(DataType.Discrete, mergeList(nonExpGroupByDataType.get(DataType.Discrete), nonExpGroupByDataType.get(DataType.Mixed)));
     }
 
+    /**
+     * Combine two lists of command-line options into one.
+     *
+     * @param listA
+     * @param listB
+     * @return
+     */
     private static List<String> mergeList(List<String> listA, List<String> listB) {
         return Stream.concat(listA.stream(), listB.stream())
                 .sorted()
                 .collect(Collectors.toList());
     }
 
+    /**
+     * Get the instance of this class.
+     *
+     * @return
+     */
     public static TetradIndependenceTests getInstance() {
         return INSTANCE;
     }
 
+    /**
+     * Determine if the giving command is a validate command-line option.
+     *
+     * @param command
+     * @return
+     */
     public boolean hasCommand(String command) {
         if (command == null || command.isEmpty()) {
             return false;
@@ -111,6 +134,14 @@ public boolean hasCommand(String command) {
                 : nonExpTests.containsKey(command);
     }
 
+    /**
+     * Determine if the giving command is a validate command-line option for a
+     * giving datatype.
+     *
+     * @param command
+     * @param dataType
+     * @return
+     */
     public boolean hasCommand(String command, DataType dataType) {
         if (command == null || command.isEmpty() || dataType == null) {
             return false;
@@ -128,6 +159,11 @@ public boolean hasCommand(String command, DataType dataType) {
                 .anyMatch(e -> e.equalsIgnoreCase(command));
     }
 
+    /**
+     * Get a list of command-line options.
+     *
+     * @return
+     */
     public List<String> getCommands() {
         List<String> list = CausalCmdApplication.showExperimental
                 ? tests.keySet().stream().collect(Collectors.toList())
@@ -136,6 +172,12 @@ public List<String> getCommands() {
         return Collections.unmodifiableList(list);
     }
 
+    /**
+     * Get a list of command-line options for a giving datatype.
+     *
+     * @param dataType
+     * @return
+     */
     public List<String> getCommands(DataType dataType) {
         Map<DataType, List<String>> map = CausalCmdApplication.showExperimental
                 ? groupByDataType
@@ -146,6 +188,12 @@ public List<String> getCommands(DataType dataType) {
                 : Collections.EMPTY_LIST;
     }
 
+    /**
+     * Get class for a giving command-line option.
+     *
+     * @param command
+     * @return
+     */
     public Class getClass(String command) {
         if (command == null || command.isEmpty()) {
             return null;
@@ -158,12 +206,24 @@ public Class getClass(String command) {
         return (annotatedClass == null) ? null : annotatedClass.getClazz();
     }
 
+    /**
+     * Get the name for a given class.
+     *
+     * @param clazz
+     * @return
+     */
     public String getName(Class clazz) {
         return (clazz != null && clazz.isAnnotationPresent(TestOfIndependence.class))
                 ? ((TestOfIndependence) clazz.getAnnotation(TestOfIndependence.class)).name()
                 : "";
     }
 
+    /**
+     * Get the description for a given class.
+     *
+     * @param clazz
+     * @return
+     */
     public String getDescription(Class clazz) {
         return (clazz != null && clazz.isAnnotationPresent(TestOfIndependence.class))
                 ? ((TestOfIndependence) clazz.getAnnotation(TestOfIndependence.class)).description()
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 d08f5f9..c4dfd42 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
@@ -52,6 +52,8 @@
 import org.slf4j.LoggerFactory;
 
 /**
+ * The class {@code TetradRunner} is a class for handling running Tetrad search
+ * algorithms.
  *
  * Oct 23, 2017 11:24:07 AM
  *
@@ -65,11 +67,23 @@ public class TetradRunner {
 
     private final List<Graph> graphs;
 
+    /**
+     * Constructor.
+     *
+     * @param cmdArgs command-line inputs
+     */
     public TetradRunner(CmdArgs cmdArgs) {
         this.cmdArgs = cmdArgs;
         this.graphs = new LinkedList<>();
     }
 
+    /**
+     * Run algorithm.
+     *
+     * @param out
+     * @throws AlgorithmRunException
+     * @throws IOException
+     */
     public void runAlgorithm(PrintStream out) throws AlgorithmRunException, IOException {
         final List<DataModel> dataModels = DataFiles.readInDatasets(cmdArgs, out);
         final Algorithm algorithm = getAlgorithm(cmdArgs);
@@ -134,6 +148,14 @@ private boolean containsMissingValues(final List<DataModel> dataModels) {
         return hasMissingValues;
     }
 
+    /**
+     * Run search algorithm.
+     *
+     * @param algorithm
+     * @param parameters
+     * @param dataModels
+     * @return
+     */
     private List<Graph> runSearch(final Algorithm algorithm, final Parameters parameters, final List<DataModel> dataModels) {
         List<Graph> graphList = new LinkedList<>();
 
@@ -304,6 +326,13 @@ private Graph manipulateGraph(Graph graph) {
         return graph;
     }
 
+    /**
+     * Get algorithm instance from command-line input.
+     *
+     * @param cmdArgs
+     * @return
+     * @throws AlgorithmRunException
+     */
     private Algorithm getAlgorithm(CmdArgs cmdArgs) throws AlgorithmRunException {
         try {
             return AlgorithmFactory.create(cmdArgs.getAlgorithmClass(), cmdArgs.getTestClass(), cmdArgs.getScoreClass());
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 264b39c..f7b297e 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
@@ -34,6 +34,7 @@
 import java.util.stream.Stream;
 
 /**
+ * The class {@code TetradScores} is a utility class for handling Tetrad scores.
  *
  * Sep 22, 2017 2:10:59 PM
  *
@@ -49,6 +50,9 @@ public final class TetradScores {
     private final Map<DataType, List<String>> groupByDataType = new EnumMap<>(DataType.class);
     private final Map<DataType, List<String>> nonExpGroupByDataType = new EnumMap<>(DataType.class);
 
+    /**
+     * Private constructor.
+     */
     private TetradScores() {
         ScoreAnnotations.getInstance().getAnnotatedClasses().stream().forEach(e -> {
             String key = e.getAnnotation().command();
@@ -91,16 +95,34 @@ private TetradScores() {
         nonExpGroupByDataType.put(DataType.Discrete, mergeList(nonExpGroupByDataType.get(DataType.Discrete), nonExpGroupByDataType.get(DataType.Mixed)));
     }
 
+    /**
+     * Combine two lists of command-line options into one.
+     *
+     * @param listA
+     * @param listB
+     * @return
+     */
     private static List<String> mergeList(List<String> listA, List<String> listB) {
         return Stream.concat(listA.stream(), listB.stream())
                 .sorted()
                 .collect(Collectors.toList());
     }
 
+    /**
+     * Get the instance of this class.
+     *
+     * @return
+     */
     public static TetradScores getInstance() {
         return INSTANCE;
     }
 
+    /**
+     * Determine if the giving command is a validate command-line option.
+     *
+     * @param command
+     * @return
+     */
     public boolean hasCommand(String command) {
         if (command == null || command.isEmpty()) {
             return false;
@@ -111,6 +133,14 @@ public boolean hasCommand(String command) {
                 : nonExpScores.containsKey(command);
     }
 
+    /**
+     * Determine if the giving command is a validate command-line option for a
+     * giving datatype.
+     *
+     * @param command
+     * @param dataType
+     * @return
+     */
     public boolean hasCommand(String command, DataType dataType) {
         if (command == null || command.isEmpty() || dataType == null) {
             return false;
@@ -128,6 +158,11 @@ public boolean hasCommand(String command, DataType dataType) {
                 .anyMatch(e -> e.equalsIgnoreCase(command));
     }
 
+    /**
+     * Get a list of command-line options.
+     *
+     * @return
+     */
     public List<String> getCommands() {
         List<String> list = CausalCmdApplication.showExperimental
                 ? scores.keySet().stream().collect(Collectors.toList())
@@ -136,6 +171,12 @@ public List<String> getCommands() {
         return Collections.unmodifiableList(list);
     }
 
+    /**
+     * Get a list of command-line options for a giving datatype.
+     *
+     * @param dataType
+     * @return
+     */
     public List<String> getCommands(DataType dataType) {
         Map<DataType, List<String>> map = CausalCmdApplication.showExperimental
                 ? groupByDataType
@@ -146,6 +187,12 @@ public List<String> getCommands(DataType dataType) {
                 : Collections.EMPTY_LIST;
     }
 
+    /**
+     * Get class for a giving command-line option.
+     *
+     * @param command
+     * @return
+     */
     public Class getClass(String command) {
         if (command == null || command.isEmpty()) {
             return null;
@@ -158,12 +205,24 @@ public Class getClass(String command) {
         return (annotatedClass == null) ? null : annotatedClass.getClazz();
     }
 
+    /**
+     * Get the name for a given class.
+     *
+     * @param clazz
+     * @return
+     */
     public String getName(Class clazz) {
         return (clazz != null && clazz.isAnnotationPresent(Score.class))
                 ? ((Score) clazz.getAnnotation(Score.class)).name()
                 : "";
     }
 
+    /**
+     * Get the description for a given class.
+     *
+     * @param clazz
+     * @return
+     */
     public String getDescription(Class clazz) {
         return (clazz != null && clazz.isAnnotationPresent(Score.class))
                 ? ((Score) clazz.getAnnotation(Score.class)).description()
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 36feefa..53e8768 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
@@ -23,6 +23,7 @@
 import java.util.Date;
 
 /**
+ * The class {@code DateTime} is used to format data-time to String.
  *
  * Mar 14, 2017 4:21:47 PM
  *
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 41c9522..1851066 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
@@ -23,6 +23,7 @@
 import java.nio.file.Path;
 
 /**
+ * The class {@code FileUtils} is a utility class for file management.
  *
  * Sep 15, 2017 4:03:38 PM
  *
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 dbb546d..94aca24 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
@@ -28,6 +28,8 @@
 import java.util.Scanner;
 
 /**
+ * The class {@code FileUtils} is a utility class for converting and writing out
+ * graph object.
  *
  * Jan 15, 2019 2:58:45 PM
  *
@@ -38,18 +40,32 @@ public final class GraphIO {
     private GraphIO() {
     }
 
+    /**
+     * Write out graph object to a text file.
+     *
+     * @param graph
+     * @param path
+     * @throws IOException
+     */
     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());
             }
         }
     }
 
+    /**
+     * Write out graph object to a JSON file.
+     *
+     * @param graph
+     * @param 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));
         }
     }
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 c67a1a8..aaf7ffb 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
@@ -30,6 +30,8 @@
 import org.slf4j.Logger;
 
 /**
+ * The class {@code LogMessages} is a utility class for writing out log
+ * messages.
  *
  * Jan 11, 2019 11:39:19 AM
  *
@@ -40,6 +42,14 @@ public final class LogMessages {
     private LogMessages() {
     }
 
+    /**
+     * Write out dataset information to log file.
+     *
+     * @param file
+     * @param dataModel
+     * @param logger
+     * @param out
+     */
     public static void dataInfo(Path file, DataModel dataModel, Logger logger, PrintStream out) {
         int row = 0;
         int col = 0;
@@ -58,18 +68,39 @@ public static void dataInfo(Path file, DataModel dataModel, Logger logger, Print
         logMessage(msg, logger, out);
     }
 
+    /**
+     * Log the end time of reading file.
+     *
+     * @param file
+     * @param logger
+     * @param out
+     */
     public static void readingFileEnd(Path file, Logger logger, PrintStream out) {
         String fileName = file.getFileName().toString();
         String msg = String.format("Finished reading in file %s.", fileName);
         logMessage(msg, logger, out);
     }
 
+    /**
+     * Log the start time of reading file.
+     *
+     * @param file
+     * @param logger
+     * @param out
+     */
     public static void readingFileStart(Path file, Logger logger, PrintStream out) {
         String fileName = file.getFileName().toString();
         String msg = String.format("Start reading in file %s.", fileName);
         logMessage(msg, logger, out);
     }
 
+    /**
+     * Log data validation results.
+     *
+     * @param groupedResults
+     * @param logger
+     * @param out
+     */
     public static void dataValidationResults(Map<ValidationCode, List<ValidationResult>> groupedResults, Logger logger, PrintStream out) {
         if (groupedResults.containsKey(ValidationCode.INFO)) {
             groupedResults.get(ValidationCode.INFO).stream()
@@ -97,18 +128,39 @@ public static void dataValidationResults(Map<ValidationCode, List<ValidationResu
         }
     }
 
+    /**
+     * Log the end time of the data validation.
+     *
+     * @param file
+     * @param logger
+     * @param out
+     */
     public static void dataValidationEnd(Path file, Logger logger, PrintStream out) {
         String fileName = file.getFileName().toString();
         String msg = String.format("End data validation on file %s.", fileName);
         logMessage(msg, logger, out);
     }
 
+    /**
+     * Log the start time of the data validation.
+     *
+     * @param file
+     * @param logger
+     * @param out
+     */
     public static void dataValidationStart(Path file, Logger logger, PrintStream out) {
         String fileName = file.getFileName().toString();
         String msg = String.format("Start data validation on file %s.", fileName);
         logMessage(msg, logger, out);
     }
 
+    /**
+     * Log message.
+     *
+     * @param message
+     * @param logger
+     * @param out
+     */
     public static void logMessage(String message, Logger logger, PrintStream out) {
         out.printf("%s: %s%n", DateTime.printNow(), message);
         logger.info(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 a47510a..e632a93 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
@@ -19,6 +19,7 @@
 package edu.pitt.dbmi.causal.cmd.util;
 
 /**
+ * The class {@code WordUtil} is a utility class for converting string values.
  *
  * Jan 9, 2019 11:30:13 AM
  *
@@ -29,6 +30,12 @@ public final class WordUtil {
     private WordUtil() {
     }
 
+    /**
+     * Convert true/false value to yes/no.
+     *
+     * @param value
+     * @return
+     */
     public static final String toYesOrNo(String value) {
         switch (value) {
             case "true":

From f79bb464c7bc444e61fd2aa7517507d0f0776092 Mon Sep 17 00:00:00 2001
From: Kevin Bui <kvb2univpitt@gmail.com>
Date: Sun, 10 Jul 2022 13:59:11 -0600
Subject: [PATCH 5/6] Removed thread option from command-line.

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

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 73f7f77..834130a 100644
--- a/src/main/java/edu/pitt/dbmi/causal/cmd/CmdOptions.java
+++ b/src/main/java/edu/pitt/dbmi/causal/cmd/CmdOptions.java
@@ -164,7 +164,7 @@ public List<Option> getBaseOptions() {
         opts.add(options.get(CmdParams.JSON_GRAPH));
         opts.add(options.get(CmdParams.DIR_OUT));
 
-        opts.add(options.get(CmdParams.THREAD));
+//        opts.add(options.get(CmdParams.THREAD));
 
         // data validation options
         opts.add(options.get(CmdParams.SKIP_VALIDATION));

From 75834d8d3fa033155ebc73f4664f6270326cb2bc Mon Sep 17 00:00:00 2001
From: Kevin Bui <kvb2univpitt@gmail.com>
Date: Sun, 10 Jul 2022 14:16:59 -0600
Subject: [PATCH 6/6] Bumped up update-version number.

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

diff --git a/pom.xml b/pom.xml
index 13631aa..c98fb3c 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>1.4.0-SNAPSHOT</version>
+    <version>1.4.1-SNAPSHOT</version>
     <packaging>jar</packaging>
 
     <properties>