Formatting fixes

amplab · Oct 17, 2016 · 33477e5 · 33477e5
1 parent d3c2011
commit 33477e5
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Showing 100 changed files with 1,118 additions and 1,072 deletions.
diff --git a/assembly/src/main/assembly/assembly.xml b/assembly/src/main/assembly/assembly.xml
@@ -1,6 +1,6 @@
 <assembly
-  xmlns="http://maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.0"
   xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+  xmlns="http://maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.0"
   xsi:schemaLocation="http://maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.0 http://maven.apache.org/xsd/assembly-1.1.0.xsd">
   <id>assembly</id>
   <formats>

diff --git a/core/src/main/java/edu/berkeley/cs/succinct/SuccinctCore.java b/core/src/main/java/edu/berkeley/cs/succinct/SuccinctCore.java
@@ -11,6 +11,7 @@ public abstract class SuccinctCore implements Serializable {
 
   // Logger
   public final static Logger LOG = Logger.getLogger(Logger.GLOBAL_LOGGER_NAME);
+
   static {
     final Handler consoleHandler = new ConsoleHandler();
     consoleHandler.setFormatter(new Formatter() {
@@ -24,6 +25,8 @@ public String format(LogRecord record) {
     LOG.setLevel(Level.OFF);
   }
 
+  // Alphabet map
+  protected transient int[] alphabet;
   // Metadata
   private transient int originalSize;
   private transient int alphabetSize;
@@ -32,9 +35,6 @@ public String format(LogRecord record) {
   private transient int samplingRateNPA;
   private transient int sampleBitWidth;
 
-  // Alphabet map
-  protected transient int[] alphabet;
-
   public SuccinctCore() {
   }
 
@@ -138,22 +138,22 @@ public int getSampleBitWidth() {
   }
 
   /**
-   * Find a character in the alphabet.
+   * Set the sample bit width.
    *
-   * @param c The character to find.
-   * @return The position of the character in the alphabet (if it exists), -ve value otherwise.
+   * @param sampleBitWidth The sample bit width to set.
    */
-  public int findCharacter(int c) {
-    return Arrays.binarySearch(alphabet, 1, alphabet.length, c);
+  public void setSampleBitWidth(int sampleBitWidth) {
+    this.sampleBitWidth = sampleBitWidth;
   }
 
   /**
-   * Set the sample bit width.
+   * Find a character in the alphabet.
    *
-   * @param sampleBitWidth The sample bit width to set.
+   * @param c The character to find.
+   * @return The position of the character in the alphabet (if it exists), -ve value otherwise.
    */
-  public void setSampleBitWidth(int sampleBitWidth) {
-    this.sampleBitWidth = sampleBitWidth;
+  public int findCharacter(int c) {
+    return Arrays.binarySearch(alphabet, 1, alphabet.length, c);
   }
 
   protected int baseSize() {

diff --git a/core/src/main/java/edu/berkeley/cs/succinct/SuccinctIndexedFile.java b/core/src/main/java/edu/berkeley/cs/succinct/SuccinctIndexedFile.java
@@ -44,8 +44,8 @@ public interface SuccinctIndexedFile extends SuccinctFile {
    * Get random access into record.
    *
    * @param recordId The record id.
-   * @param offset Offset into record.
-   * @param length Number of bytes to fetch.
+   * @param offset   Offset into record.
+   * @param length   Number of bytes to fetch.
    * @return The extracted data.
    */
   byte[] extractRecordBytes(int recordId, int offset, int length);
@@ -62,8 +62,8 @@ public interface SuccinctIndexedFile extends SuccinctFile {
    * Get random access into record.
    *
    * @param recordId The record id.
-   * @param offset Offset into record.
-   * @param length Number of bytes to fetch.
+   * @param offset   Offset into record.
+   * @param length   Number of bytes to fetch.
    * @return The extracted data.
    */
   String extractRecord(int recordId, int offset, int length);

diff --git a/core/src/main/java/edu/berkeley/cs/succinct/buffers/SuccinctBuffer.java b/core/src/main/java/edu/berkeley/cs/succinct/buffers/SuccinctBuffer.java
@@ -47,10 +47,6 @@ public SuccinctBuffer() {
     super();
   }
 
-  @Override public int getCoreSize() {
-    return core.limit();
-  }
-
   /**
    * Constructor to initialize SuccinctCore from input byte array.
    *
@@ -139,6 +135,10 @@ public SuccinctBuffer(ByteBuffer buf) {
     mapFromCore();
   }
 
+  @Override public int getCoreSize() {
+    return core.limit();
+  }
+
   /**
    * Lookup NPA at specified index.
    *

diff --git a/core/src/main/java/edu/berkeley/cs/succinct/buffers/SuccinctFileBuffer.java b/core/src/main/java/edu/berkeley/cs/succinct/buffers/SuccinctFileBuffer.java
@@ -201,8 +201,7 @@ public SuccinctFileBuffer() {
     s = lookupNPA(s);
     int byte1 = lookupC(s);
 
-    return (short) ((byte0 << 8) |
-      (byte1 & 0xFF));
+    return (short) ((byte0 << 8) | (byte1 & 0xFF));
   }
 
   /**

diff --git a/core/src/main/java/edu/berkeley/cs/succinct/examples/SuccinctShell.java b/core/src/main/java/edu/berkeley/cs/succinct/examples/SuccinctShell.java
@@ -112,7 +112,8 @@ public static void main(String[] args) throws IOException {
             results.put(result.getOffset(), result.getLength());
           }
         } catch (RegExParsingException e) {
-          System.err.println("Could not parse regular expression: [" + cmdArray[1] + "]: " + e.getMessage());
+          System.err.println(
+            "Could not parse regular expression: [" + cmdArray[1] + "]: " + e.getMessage());
           continue;
         }
         System.out.println("Result size = " + results.size());

diff --git a/core/src/main/java/edu/berkeley/cs/succinct/regex/RegExMatch.java b/core/src/main/java/edu/berkeley/cs/succinct/regex/RegExMatch.java
@@ -78,13 +78,11 @@ public boolean contains(RegExMatch r) {
     return r.begin() >= begin() && r.end() <= end();
   }
 
-  @Override
-  public String toString() {
+  @Override public String toString() {
     return "(" + offset + ", " + length + ")";
   }
 
-  @Override
-  public int compareTo(RegExMatch o) {
+  @Override public int compareTo(RegExMatch o) {
     if (offset == o.getOffset()) {
       return length - o.getLength();
     }

diff --git a/core/src/main/java/edu/berkeley/cs/succinct/regex/SuccinctRegEx.java b/core/src/main/java/edu/berkeley/cs/succinct/regex/SuccinctRegEx.java
@@ -23,7 +23,7 @@ public class SuccinctRegEx {
    * @throws RegExParsingException
    */
   public SuccinctRegEx(SuccinctFile succinctFile, String regExString, boolean greedy)
-      throws RegExParsingException {
+    throws RegExParsingException {
     this.succinctFile = succinctFile;
     this.regExString = regExString;
     this.regEx = parse();

diff --git a/core/src/main/java/edu/berkeley/cs/succinct/regex/SuccinctRegExMatch.java b/core/src/main/java/edu/berkeley/cs/succinct/regex/SuccinctRegExMatch.java
@@ -21,7 +21,7 @@ public SuccinctRegExMatch(long first, long second, int length) {
   /**
    * Constructor to initialize Regex Match.
    *
-   * @param range Input range.
+   * @param range  Input range.
    * @param length Length of the match.
    */
   public SuccinctRegExMatch(Range range, int length) {

diff --git a/core/src/main/java/edu/berkeley/cs/succinct/regex/executor/RegExExecutor.java b/core/src/main/java/edu/berkeley/cs/succinct/regex/executor/RegExExecutor.java
@@ -17,16 +17,12 @@ public abstract class RegExExecutor {
   protected TreeSet<RegExMatch> finalResults;
   protected boolean greedy;
 
-  enum SortType {
-    FRONT_SORTED,
-    END_SORTED
-  }
 
   /**
    * Constructor to initialize RegExExecutor.
    *
    * @param succinctFile The input SuccinctFile.
-   * @param regEx The input regular expression.
+   * @param regEx        The input regular expression.
    */
   RegExExecutor(SuccinctFile succinctFile, RegEx regEx, boolean greedy) {
     this.succinctFile = succinctFile;
@@ -100,7 +96,8 @@ protected TreeSet<RegExMatch> regexWildcard(TreeSet<RegExMatch> left, TreeSet<Re
 
       // Greedy match
       RegExMatch lastMatch = null;
-      while (rightEntry != null && succinctFile.sameRecord(leftEntry.getOffset(), rightEntry.getOffset())) {
+      while (rightEntry != null && succinctFile
+        .sameRecord(leftEntry.getOffset(), rightEntry.getOffset())) {
         lastMatch = rightEntry;
         rightEntry = right.higher(rightEntry);
       }
@@ -117,4 +114,9 @@ protected TreeSet<RegExMatch> regexWildcard(TreeSet<RegExMatch> left, TreeSet<Re
 
     return wildcardRes;
   }
+
+  enum SortType {
+    FRONT_SORTED,
+    END_SORTED
+  }
 }
diff --git a/core/src/main/java/edu/berkeley/cs/succinct/regex/executor/SuccinctBwdRegExExecutor.java b/core/src/main/java/edu/berkeley/cs/succinct/regex/executor/SuccinctBwdRegExExecutor.java
@@ -140,7 +140,8 @@ private HashSet<SuccinctRegExMatch> regexConcat(RegEx r, SuccinctRegExMatch righ
             String mgram = p.getPrimitiveStr();
             Range range = succinctFile.continueBwdSearch(mgram.toCharArray(), rightMatch);
             if (!range.empty()) {
-              concatResults.add(new SuccinctRegExMatch(range, rightMatch.getLength() + mgram.length()));
+              concatResults
+                .add(new SuccinctRegExMatch(range, rightMatch.getLength() + mgram.length()));
             }
             break;
           }
@@ -225,13 +226,14 @@ private HashSet<SuccinctRegExMatch> computeSeedToRepeat(RegEx r) {
     if (!greedy)
       return results;
 
-    TreeSet<SuccinctRegExMatch> initialRepeats = new TreeSet<>(new Comparator<SuccinctRegExMatch>() {
-      @Override public int compare(SuccinctRegExMatch o1, SuccinctRegExMatch o2) {
-        return (int) (o1.begin() - o2.begin());
-      }
-    });
+    TreeSet<SuccinctRegExMatch> initialRepeats =
+      new TreeSet<>(new Comparator<SuccinctRegExMatch>() {
+        @Override public int compare(SuccinctRegExMatch o1, SuccinctRegExMatch o2) {
+          return (int) (o1.begin() - o2.begin());
+        }
+      });
 
-    for (SuccinctRegExMatch result: results) {
+    for (SuccinctRegExMatch result : results) {
       initialRepeats.addAll(regexConcat(r, result));
     }
 
@@ -251,7 +253,7 @@ private HashSet<SuccinctRegExMatch> computeSeedToRepeat(RegEx r) {
       } else {
         // Remove subrange.
         HashSet<SuccinctRegExMatch> newSubRanges = new HashSet<>();
-        for (Iterator<SuccinctRegExMatch> i = results.iterator(); i.hasNext();) {
+        for (Iterator<SuccinctRegExMatch> i = results.iterator(); i.hasNext(); ) {
           SuccinctRegExMatch match = i.next();
           if (match.contains(start, end)) {
             i.remove();
@@ -274,7 +276,7 @@ private HashSet<SuccinctRegExMatch> computeSeedToRepeat(RegEx r) {
 
     // Remove subrange.
     HashSet<SuccinctRegExMatch> newSubRanges = new HashSet<>();
-    for (Iterator<SuccinctRegExMatch> i = results.iterator(); i.hasNext();) {
+    for (Iterator<SuccinctRegExMatch> i = results.iterator(); i.hasNext(); ) {
       SuccinctRegExMatch match = i.next();
       if (match.contains(start, end)) {
         i.remove();
@@ -316,7 +318,7 @@ private HashSet<SuccinctRegExMatch> regexRepeatOneOrMore(RegEx r) {
   /**
    * Repeat regular expression one or more times given right match.
    *
-   * @param r         The regular expression.
+   * @param r          The regular expression.
    * @param rightMatch The right match.
    * @return The results for repeat.
    */
@@ -341,11 +343,12 @@ private HashSet<SuccinctRegExMatch> regexRepeatOneOrMore(RegEx r, SuccinctRegExM
   /**
    * Repeat regular expression zero or more times given right match.
    *
-   * @param r         The regular expression.
+   * @param r          The regular expression.
    * @param rightMatch The right match.
    * @return The results for repeat.
    */
-  private HashSet<SuccinctRegExMatch> regexRepeatZeroOrMore(RegEx r, SuccinctRegExMatch rightMatch) {
+  private HashSet<SuccinctRegExMatch> regexRepeatZeroOrMore(RegEx r,
+    SuccinctRegExMatch rightMatch) {
     HashSet<SuccinctRegExMatch> repeatResults = new HashSet<>();
     if (rightMatch.empty()) {
       return repeatResults;
@@ -389,10 +392,10 @@ private HashSet<SuccinctRegExMatch> regexRepeatMinToMax(RegEx r, int min, int ma
   /**
    * Repeat the regular expression from min to max times given right match.
    *
-   * @param r         The regular expression.
+   * @param r          The regular expression.
    * @param rightMatch The right match.
-   * @param min       The minimum number of repetitions.
-   * @param max       The maximum number of repetitions.
+   * @param min        The minimum number of repetitions.
+   * @param max        The maximum number of repetitions.
    * @return The results for repeat.
    */
   private HashSet<SuccinctRegExMatch> regexRepeatMinToMax(RegEx r, SuccinctRegExMatch rightMatch,