Merge pull request #1722 from cmu-phil/development

Updating to 7.6.2

data-reader/pom.xml

@@ -5,16 +5,16 @@
     <parent>
         <groupId>io.github.cmu-phil</groupId>
         <artifactId>tetrad</artifactId>
-        <version>7.6.1</version>
+        <version>7.6.2-SNAPSHOT</version>
     </parent>
     <!--    <groupId>io.github.cmu-phil</groupId>-->
     <artifactId>data-reader</artifactId>
     <packaging>jar</packaging>
 
     <properties>
         <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
-        <maven.compiler.source>1.8</maven.compiler.source>
-        <maven.compiler.target>1.8</maven.compiler.target>
+        <maven.compiler.source>17</maven.compiler.source>
+        <maven.compiler.target>17</maven.compiler.target>
     </properties>
 
     <build>
@@ -24,8 +24,8 @@
                 <artifactId>maven-compiler-plugin</artifactId>
                 <version>3.11.0</version>
                 <configuration>
-                    <source>1.8</source>
-                    <target>1.8</target>
+                    <source>17</source>
+                    <target>17</target>
                 </configuration>
             </plugin>
         </plugins>

data-reader/src/main/java/edu/pitt/dbmi/data/reader/ContinuousData.java

@@ -25,8 +25,18 @@
  */
 public interface ContinuousData extends Data {
 
+    /**
+     * Get the data columns.
+     *
+     * @return the data columns.
+     */
     DataColumn[] getDataColumns();
 
+    /**
+     * Get the data.
+     *
+     * @return the data.
+     */
     double[][] getData();
 
 }

data-reader/src/main/java/edu/pitt/dbmi/data/reader/DataColumn.java

@@ -28,35 +28,35 @@ public interface DataColumn {
     /**
      * Get the column's name.
      *
-     * @return
+     * @return the column's name.
      */
     String getName();
 
     /**
      * Get the column's number.
      *
-     * @return
+     * @return the column's number.
      */
     int getColumnNumber();
 
     /**
      * True if this column was not read in from source such as file.
      *
-     * @return
+     * @return true if this column was not read in from source such as file.
      */
     boolean isGenerated();
 
     /**
      * True if the datatype is discrete.
      *
-     * @return
+     * @return true if the datatype is discrete.
      */
     boolean isDiscrete();
 
     /**
      * Set true for discrete datatype.
      *
-     * @param discrete
+     * @param discrete true for discrete datatype.
      */
     void setDiscrete(boolean discrete);
 

data-reader/src/main/java/edu/pitt/dbmi/data/reader/DataColumns.java

@@ -38,6 +38,13 @@ public final class DataColumns {
     private DataColumns() {
     }
 
+    /**
+     * Update data columns with metadata.
+     *
+     * @param dataColumns data columns
+     * @param metadata    metadata
+     * @return updated data columns
+     */
     public static DataColumn[] update(DataColumn[] dataColumns, Metadata metadata) {
         Map<String, ColumnMetadata> columnMetadataMap = DataColumns.getColumnMetadataMap(metadata);
 

data-reader/src/main/java/edu/pitt/dbmi/data/reader/DataFileReader.java

@@ -31,16 +31,52 @@
  */
 public abstract class DataFileReader implements DataReader {
 
+    /**
+     * The buffer size for reading data file.
+     */
     protected static final int BUFFER_SIZE = 1024 * 1024;
 
+    /**
+     * The newline character.
+     */
     protected static final byte LINE_FEED = '\n';
+
+    /**
+     * The carriage return character.
+     */
     protected static final byte CARRIAGE_RETURN = '\r';
+
+    /**
+     * The space character.
+     */
     protected static final byte SPACE_CHAR = Delimiter.SPACE.getByteValue();
+
+    /**
+     * The data file.
+     */
     protected final Path dataFile;
+
+    /**
+     * The delimiter.
+     */
     protected final Delimiter delimiter;
+
+    /**
+     * The quote character.
+     */
     protected byte quoteCharacter;
+
+    /**
+     * The comment marker.
+     */
     protected String commentMarker;
 
+    /**
+     * Constructor.
+     *
+     * @param dataFile  the data file
+     * @param delimiter the delimiter
+     */
     public DataFileReader(Path dataFile, Delimiter delimiter) {
         this.dataFile = dataFile;
         this.delimiter = delimiter;
@@ -52,7 +88,7 @@ public DataFileReader(Path dataFile, Delimiter delimiter) {
      * Counts number of column from the first non-blank line.
      *
      * @return the number of column from the first non-blank line
-     * @throws IOException
+     * @throws IOException if an I/O error occurs
      */
     protected int countNumberOfColumns() throws IOException {
         int count = 0;
@@ -148,7 +184,7 @@ protected int countNumberOfColumns() throws IOException {
      * Counts number of non-blank lines.
      *
      * @return the number of non-blank and non-commented lines
-     * @throws IOException
+     * @throws IOException if an I/O error occurs
      */
     protected int countNumberOfLines() throws IOException {
         int count = 0;
@@ -214,13 +250,23 @@ protected int countNumberOfLines() throws IOException {
         return count;
     }
 
+    /**
+     * Sets the quote character.
+     *
+     * @param quoteCharacter the quote character
+     */
     @Override
     public void setQuoteCharacter(char quoteCharacter) {
         this.quoteCharacter = Character.isDefined(quoteCharacter)
                 ? (byte) quoteCharacter
                 : (byte) -1;
     }
 
+    /**
+     * Sets the comment marker.
+     *
+     * @param commentMarker the comment marker
+     */
     @Override
     public void setCommentMarker(String commentMarker) {
         this.commentMarker = (commentMarker == null)

data-reader/src/main/java/edu/pitt/dbmi/data/reader/DataReader.java

@@ -28,14 +28,14 @@ public interface DataReader {
     /**
      * Set the character that is used to group multiple words as one.
      *
-     * @param quoteCharacter
+     * @param quoteCharacter the quote character.
      */
     void setQuoteCharacter(char quoteCharacter);
 
     /**
      * Set the value to indicate a line is a comment to be ignored.
      *
-     * @param commentMarker
+     * @param commentMarker the comment marker.
      */
     void setCommentMarker(String commentMarker);
 

data-reader/src/main/java/edu/pitt/dbmi/data/reader/DataReaderException.java

@@ -18,13 +18,16 @@
  */
 package edu.pitt.dbmi.data.reader;
 
+import java.io.Serial;
+
 /**
  * Nov 6, 2018 2:26:59 PM
  *
  * @author Kevin V. Bui ([email protected])
  */
 public class DataReaderException extends RuntimeException {
 
+    @Serial
     private static final long serialVersionUID = 1123054334542973950L;
 
     /**

data-reader/src/main/java/edu/pitt/dbmi/data/reader/DatasetFileReader.java

@@ -27,14 +27,28 @@
  */
 public abstract class DatasetFileReader extends DataFileReader implements DatasetReader {
 
+    /**
+     * The missing data marker.
+     */
     protected String missingDataMarker;
 
+    /**
+     * Constructor.
+     *
+     * @param dataFile  the data file
+     * @param delimiter the delimiter
+     */
     public DatasetFileReader(Path dataFile, Delimiter delimiter) {
         super(dataFile, delimiter);
 
         this.missingDataMarker = "";
     }
 
+    /**
+     * Get the missing data marker.
+     *
+     * @param missingDataMarker the missing data marker
+     */
     @Override
     public void setMissingDataMarker(String missingDataMarker) {
         this.missingDataMarker = (missingDataMarker == null)

data-reader/src/main/java/edu/pitt/dbmi/data/reader/DatasetReader.java

@@ -25,14 +25,20 @@
  */
 public interface DatasetReader extends DataReader {
 
+    /**
+     * The missing data marker for continuous data.
+     */
     double CONTINUOUS_MISSING_VALUE = Double.NaN;
 
+    /**
+     * The missing data marker for discrete data.
+     */
     int DISCRETE_MISSING_VALUE = -99;
 
     /**
      * Set the value to indicate missing data.
      *
-     * @param missingDataMarker
+     * @param missingDataMarker the missing data marker.
      */
     void setMissingDataMarker(String missingDataMarker);
 

data-reader/src/main/java/edu/pitt/dbmi/data/reader/Delimiter.java

@@ -25,32 +25,80 @@
  */
 public enum Delimiter {
 
+    /**
+     * The tab delimiter.
+     */
     TAB("tab", '\t'),
+
+    /**
+     * The space delimiter.
+     */
     SPACE("space", ' '),
+
+    /**
+     * The whitespace delimiter.
+     */
     WHITESPACE("whitespace", ' '),
+
+    /**
+     * The comma delimiter.
+     */
     COMMA("comma", ','),
+
+    /**
+     * The colon delimiter.
+     */
     COLON("colon", ':'),
+
+    /**
+     * The semicolon delimiter.
+     */
     SEMICOLON("semicolon", ';'),
+
+    /**
+     * The pipe delimiter.
+     */
     PIPE("pipe", '|');
 
     private final String name;
     private final char value;
     private final byte byteValue;
 
+    /**
+     * Constructor.
+     *
+     * @param name  the name of the delimiter.
+     * @param value the value of the delimiter.
+     */
     Delimiter(String name, char value) {
         this.name = name;
         this.value = value;
         this.byteValue = (byte) value;
     }
 
+    /**
+     * Get the name of the delimiter.
+     *
+     * @return the name of the delimiter.
+     */
     public String getName() {
         return this.name;
     }
 
+    /**
+     * Get the value of the delimiter.
+     *
+     * @return the value of the delimiter.
+     */
     public char getValue() {
         return this.value;
     }
 
+    /**
+     * Get the byte value of the delimiter.
+     *
+     * @return the byte value of the delimiter.
+     */
     public byte getByteValue() {
         return this.byteValue;
     }

data-reader/src/main/java/edu/pitt/dbmi/data/reader/DiscreteData.java

@@ -25,8 +25,18 @@
  */
 public interface DiscreteData extends Data {
 
+    /**
+     * Get the discrete data columns.
+     *
+     * @return the discrete data columns.
+     */
     DiscreteDataColumn[] getDataColumns();
 
+    /**
+     * Get the discrete data.
+     *
+     * @return the discrete data.
+     */
     int[][] getData();
 
 }