Fixed conflicts and bumped up update-version number.

pom.xml

@@ -3,7 +3,7 @@
     <modelVersion>4.0.0</modelVersion>
     <groupId>edu.pitt.dbmi</groupId>
     <artifactId>causal-cmd</artifactId>
-    <version>1.4.0</version>
+    <version>1.4.1</version>
     <packaging>jar</packaging>
 
     <properties>
@@ -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>

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
  *

src/main/java/edu/pitt/dbmi/causal/cmd/Applications.java

@@ -37,18 +37,30 @@
 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
  *
  * @author Kevin V. Bui ([email protected])
  */
 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() {
     }
 
+    /**
+     * 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 +100,9 @@ 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 +118,9 @@ 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 +136,9 @@ 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 +154,83 @@ 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();

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]