Added more documentations.

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

@@ -54,7 +54,7 @@ private CmdOptions() {
     /**
      * Get an instance of the command-line options.
      *
-     * @return
+     * @return CmdOptions instance
      */
     public static CmdOptions getInstance() {
         if (instance == null) {
@@ -75,7 +75,7 @@ public static void clear() {
      * Get multi-character name options for a given name..
      *
      * @param param multi-character name
-     * @return
+     * @return command-line option
      */
     public Option getLongOption(String param) {
         return options.get(param);
@@ -249,7 +249,7 @@ private void addRequiredOptions() {
     /**
      * Get the application required options from the stored options.
      *
-     * @return
+     * @return required command-line options
      */
     public List<Option> getRequiredOptions() {
         return options.entrySet().stream()
@@ -261,7 +261,7 @@ public List<Option> getRequiredOptions() {
     /**
      * Get the names of all the datatypes.
      *
-     * @return
+     * @return datatype description
      */
     private String getDataTypeDesc() {
         return "Data type: " + DataTypes.getInstance().getNames().stream()
@@ -271,7 +271,7 @@ private String getDataTypeDesc() {
     /**
      * Get the names of all the delimiters.
      *
-     * @return
+     * @return names of delimiters
      */
     private String getDelimiterDesc() {
         return "Delimiter: " + Delimiters.getInstance().getNames().stream()
@@ -281,7 +281,7 @@ private String getDelimiterDesc() {
     /**
      * Get the names of all the scores.
      *
-     * @return
+     * @return description for score
      */
     private String getScoreDesc() {
         return "Score: " + TetradScores.getInstance().getCommands().stream()
@@ -291,7 +291,7 @@ private String getScoreDesc() {
     /**
      * Get the names of all the independence test.
      *
-     * @return
+     * @return description for test of independence
      */
     private String getIndependenceTestDesc() {
         return "Independence Test: " + TetradIndependenceTests.getInstance().getCommands().stream()
@@ -301,7 +301,7 @@ private String getIndependenceTestDesc() {
     /**
      * Get the names of all the algorithms.
      *
-     * @return
+     * @return description for algorithm
      */
     private String getAlgorithmDesc() {
         return "Algorithm: " + TetradAlgorithms.getInstance().getCommands().stream()

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

@@ -61,6 +61,13 @@ public final class CmdParser {
     private CmdParser() {
     }
 
+    /**
+     * Parse user input command
+     *
+     * @param args user input command
+     * @return user input command values
+     * @throws CmdParserException when an error occurs while parsing
+     */
     public static CmdArgs parse(String[] args) throws CmdParserException {
         CmdArgs cmdArgs = new CmdArgs();
 
@@ -80,10 +87,10 @@ public static CmdArgs parse(String[] args) throws CmdParserException {
     /**
      * Parse command-line options.
      *
-     * @param cmd
-     * @param parseOptions
-     * @param cmdArgs
-     * @throws CmdParserException
+     * @param cmd command-line input
+     * @param parseOptions command-line options
+     * @param cmdArgs parsed command line arguments and values
+     * @throws CmdParserException when an error occurs while parsing
      */
     private static void parseOptionalOptions(CommandLine cmd, ParseOptions parseOptions, CmdArgs cmdArgs) throws CmdParserException {
         cmdArgs.knowledgeFile = cmd.hasOption(CmdParams.KNOWLEDGE)
@@ -143,10 +150,10 @@ private static void parseOptionalOptions(CommandLine cmd, ParseOptions parseOpti
     /**
      * Parse the required command-line options.
      *
-     * @param cmd
-     * @param parseOptions
-     * @param cmdArgs
-     * @throws CmdParserException
+     * @param cmd command-line input
+     * @param parseOptions command-line options
+     * @param cmdArgs parsed command line arguments and values
+     * @throws CmdParserException when an error occurs while parsing
      */
     private static void parseRequiredOptions(CommandLine cmd, ParseOptions parseOptions, CmdArgs cmdArgs) throws CmdParserException {
         cmdArgs.dataType = DataTypes.getInstance().get(cmd.getOptionValue(CmdParams.DATA_TYPE));
@@ -176,9 +183,9 @@ private static void parseRequiredOptions(CommandLine cmd, ParseOptions parseOpti
     /**
      * Get the options for the help message.
      *
-     * @param args
-     * @return
-     * @throws CmdParserException
+     * @param args user input command
+     * @return parsed command-line options
+     * @throws CmdParserException when an error occurs while parsing
      */
     public static ParseOptions getHelpOptions(String[] args) throws CmdParserException {
         CmdOptions cmdOptions = CmdOptions.getInstance();
@@ -338,8 +345,8 @@ private static ParseOptions getValidOptions(String[] args, Options options) thro
      * Get the parameters for the algorithm, the algorithm's test, algorithm's
      * score and bootstrap.
      *
-     * @param algorithm
-     * @return
+     * @param algorithm algorithm to get the parameters for
+     * @return set of parameters related to the given algorithm
      */
     private static Set<String> getAlgorithmRelatedParameters(Algorithm algorithm) {
         if (algorithm == null) {
@@ -370,7 +377,7 @@ private static Set<String> getAlgorithmRelatedParameters(Algorithm algorithm) {
     /**
      * Add options for manipulating Tetrad output graph.
      *
-     * @param opts
+     * @param opts options to add to
      */
     private static void addGraphManipulationOptions(Options opts) {
         opts.addOption(CmdOptions.getInstance().getLongOption(CmdParams.CHOOSE_DAG_IN_PATTERN));
@@ -393,6 +400,12 @@ private static String getValidPrefix(CommandLine cmd, CmdArgs cmdArgs, ParseOpti
         }
     }
 
+    /**
+     * Extract class name.
+     *
+     * @param clazz class to extract name from
+     * @return class name
+     */
     private static String extractName(Class clazz) {
         String name = clazz.getName();
         String[] fields = name.toLowerCase().split("\\.");
@@ -404,10 +417,11 @@ private static String extractName(Class clazz) {
      * Get all the parameters related to the selected algorithm, test, and
      * score.
      *
-     * @param cmdArgs
-     * @param parseOptions
-     * @return
-     * @throws CmdParserException
+     * @param cmdArgs parsed command line arguments and values
+     * @param parseOptions command-line options
+     * @return set of parameters relating to the given algorithm, test and score
+     * from the command-line.
+     * @throws CmdParserException when an error occurs while parsing
      */
     private static Set<String> getAllRelatedParameters(CmdArgs cmdArgs, ParseOptions parseOptions) throws CmdParserException {
         try {
@@ -422,11 +436,11 @@ private static Set<String> getAllRelatedParameters(CmdArgs cmdArgs, ParseOptions
      * for the parameters if user use the "--default" flag. Replace any value if
      * user explicitly specified with parameter-arg input or flag.
      *
-     * @param cmd
-     * @param cmdArgs
-     * @param parseOptions
-     * @return
-     * @throws CmdParserException
+     * @param cmd command-line input
+     * @param cmdArgs parsed command line arguments and values
+     * @param parseOptions command-line options
+     * @return a collection of valid parameters
+     * @throws CmdParserException when an error occurs while parsing
      */
     private static Map<String, String> getValidParameters(CommandLine cmd, CmdArgs cmdArgs, ParseOptions parseOptions) throws CmdParserException {
         Map<String, String> parametersWithValues = new TreeMap<>(String.CASE_INSENSITIVE_ORDER);
@@ -439,6 +453,15 @@ private static Map<String, String> getValidParameters(CommandLine cmd, CmdArgs c
         return parametersWithValues;
     }
 
+    /**
+     * Set parameters based on user's input.
+     *
+     * @param parametersWithValues set of parameters and values
+     * @param parameters set of parameters
+     * @param cmd command-line input
+     * @param parseOptions command-line options
+     * @throws CmdParserException when an error occurs while parsing
+     */
     private static void setUserParameterValues(Map<String, String> parametersWithValues, Set<String> parameters, CommandLine cmd, ParseOptions parseOptions) throws CmdParserException {
         ParamDescriptions paramDescriptions = ParamDescriptions.getInstance();
         Options opts = parseOptions.getOptions();
@@ -531,11 +554,11 @@ private static void setParametersAndValues(Map<String, String> parametersWithVal
      * Extract the thread number from the command-line option and check to make
      * sure the number is valid.
      *
-     * @param value
-     * @param parseOptions
-     * @param cmdParam
-     * @return
-     * @throws CmdParserException
+     * @param value number of threads taken from the command-line
+     * @param parseOptions command-line options
+     * @param cmdParam command-line parameter
+     * @return number of thread from the command-line input that is valid
+     * @throws CmdParserException when an error occurs while parsing
      */
     private static int getValidThreadNumber(String value, ParseOptions parseOptions, String cmdParam) throws CmdParserException {
         int numOfThreads = 0;
@@ -564,11 +587,11 @@ private static int getValidThreadNumber(String value, ParseOptions parseOptions,
      * Extract the delimiter charactor from the command-line option and make
      * sure the character is valid.
      *
-     * @param quoteChar
-     * @param parseOptions
-     * @param cmdParam
-     * @return
-     * @throws CmdParserException
+     * @param quoteChar character from the command-line
+     * @param parseOptions command-line options
+     * @param cmdParam command-line parameter
+     * @return character from the command-line input that is valid
+     * @throws CmdParserException when an error occurs while parsing
      */
     private static char getValidChar(String quoteChar, ParseOptions parseOptions, String cmdParam) throws CmdParserException {
         char c = 0;
@@ -591,11 +614,11 @@ private static char getValidChar(String quoteChar, ParseOptions parseOptions, St
      * Extract the file location from the command-line option and make sure the
      * file is valid.
      *
-     * @param filePath
-     * @param parseOptions
-     * @param cmdParam
-     * @return
-     * @throws CmdParserException
+     * @param filePath path to where the file is from the command-line input
+     * @param parseOptions command-line options
+     * @param cmdParam command-line parameter
+     * @return the path of the file from the command-line input that exists
+     * @throws CmdParserException when an error occurs while parsing
      */
     private static Path getValidFile(String filePath, ParseOptions parseOptions, String cmdParam) throws CmdParserException {
         Path file = Paths.get(filePath);

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

@@ -41,7 +41,7 @@ private OptionFactory() {
     /**
      * Create the required options for the help message.
      *
-     * @return
+     * @return required options
      */
     public static Option createRequiredHelpOpt() {
         Option opt = CmdOptions.getInstance().getLongOption(CmdParams.HELP);
@@ -56,10 +56,10 @@ public static Option createRequiredHelpOpt() {
     }
 
     /**
-     * Create the required indepedence test options.
+     * Create the required options for the test of independence.
      *
-     * @param dataType
-     * @return
+     * @param dataType data type
+     * @return options required options for the test of independence
      */
     public static Option createRequiredTestOpt(DataType dataType) {
         List<String> commands = TetradIndependenceTests.getInstance().getCommands(dataType);
@@ -78,8 +78,8 @@ public static Option createRequiredTestOpt(DataType dataType) {
     /**
      * Create the required score options.
      *
-     * @param dataType
-     * @return
+     * @param dataType data type
+     * @return options required options for the score
      */
     public static Option createRequiredScoreOpt(DataType dataType) {
         List<String> commands = TetradScores.getInstance().getCommands(dataType);
@@ -98,7 +98,7 @@ public static Option createRequiredScoreOpt(DataType dataType) {
     /**
      * Create the required option for the number of category for mixed data.
      *
-     * @return
+     * @return required option for number of categories.
      */
     public static Option createRequiredNumCategoryOpt() {
         Option opt = CmdOptions.getInstance().getLongOption(CmdParams.NUM_CATEGORIES);

src/main/java/edu/pitt/dbmi/causal/cmd/data/DataFiles.java

@@ -73,10 +73,10 @@ private DataFiles() {
     /**
      * Read in metadata file.
      *
-     * @param cmdArgs
-     * @param out
-     * @return
-     * @throws IOException
+     * @param cmdArgs command-line arguments
+     * @param out output stream to write message to
+     * @return metadata
+     * @throws IOException when errors occur during reading file
      */
     public static Metadata readInMetadata(CmdArgs cmdArgs, PrintStream out) throws IOException {
         Path file = cmdArgs.getMetadataFile();
@@ -94,10 +94,10 @@ public static Metadata readInMetadata(CmdArgs cmdArgs, PrintStream out) throws I
     /**
      * Read in knowledge file.
      *
-     * @param cmdArgs
-     * @param out
-     * @return
-     * @throws IOException
+     * @param cmdArgs command-line arguments
+     * @param out output stream to write message to
+     * @return knowledge information from file
+     * @throws IOException when errors occur during reading file
      */
     public static IKnowledge readInKnowledge(CmdArgs cmdArgs, PrintStream out) throws IOException {
         Path file = cmdArgs.getKnowledgeFile();
@@ -115,11 +115,12 @@ public static IKnowledge readInKnowledge(CmdArgs cmdArgs, PrintStream out) throw
     /**
      * Read in datasets files.
      *
-     * @param cmdArgs
-     * @param out
-     * @return
-     * @throws IOException
-     * @throws AlgorithmRunException
+     * @param cmdArgs command-line arguments
+     * @param out output stream to write message to
+     * @return list of datasets read in from files
+     * @throws IOException when errors occur during reading file
+     * @throws AlgorithmRunException when dataset is not supported by the given
+     * algorithm from command-line
      */
     public static List<DataModel> readInDatasets(CmdArgs cmdArgs, PrintStream out) throws IOException, AlgorithmRunException {
         DataType dataType = cmdArgs.getDataType();
@@ -139,10 +140,10 @@ public static List<DataModel> readInDatasets(CmdArgs cmdArgs, PrintStream out) t
     /**
      * Read in tabular dataset files.
      *
-     * @param cmdArgs
-     * @param out
-     * @return
-     * @throws IOException
+     * @param cmdArgs command-line arguments
+     * @param out output stream to write message to
+     * @return list of datasets read in from files
+     * @throws IOException when errors occur during reading file
      */
     private static List<DataModel> readInTabularData(CmdArgs cmdArgs, PrintStream out) throws IOException {
         List<DataModel> dataModels = new LinkedList<>();
@@ -204,10 +205,10 @@ private static List<DataModel> readInTabularData(CmdArgs cmdArgs, PrintStream ou
     /**
      * Read in covariances files.
      *
-     * @param cmdArgs
-     * @param out
-     * @return
-     * @throws IOException
+     * @param cmdArgs command-line arguments
+     * @param out output stream to write message to
+     * @return list of datasets read in from files
+     * @throws IOException when errors occur during reading file
      */
     private static List<DataModel> readInCovarianceFile(CmdArgs cmdArgs, PrintStream out) throws IOException {
         List<DataModel> dataModels = new LinkedList<>();
@@ -234,10 +235,10 @@ private static List<DataModel> readInCovarianceFile(CmdArgs cmdArgs, PrintStream
     /**
      * Read in exclude-variable file.
      *
-     * @param cmdArgs
-     * @param out
-     * @return
-     * @throws IOException
+     * @param cmdArgs command-line arguments
+     * @param out output stream to write message to
+     * @return set of variables to exclude reading in
+     * @throws IOException when errors occur during reading file
      */
     public static Set<String> readInVariablesToExclude(CmdArgs cmdArgs, PrintStream out) throws IOException {
         Set<String> variablesToExclude = new HashSet<>();