Merge branch 'master' of github.com:BoiseState/CS321_Bioinformatics

.github/workflows/gradle.yml

@@ -9,8 +9,10 @@
 # - Java 17 (LTS; officially supported since Gradle 7.3)
 # - Java 18 (deprecated; officially supported since Gradle 7.5)
 # - Java 19 (deprecated; officially supported since Gradle 7.6)
-# - Java 20 (current; will be deprecated in September 2023; officially supported since Gradle 8.1)
-# - Java 21 (LTS; to be released in September 2023; not officially supported by Gradle)
+# - Java 20 (deprecated; officially supported since Gradle 8.1)
+# - Java 21 (current; LTS; officially supported since Gradle 8.4)
+# - Java 22 (to be released in March 2024; not officially supported by Gradle)
+# - Java 23 (to be released in September 2024; not officially supported by Gradle)
 name: CS321 Bioinformatics CI with Gradle
 
 on:
@@ -26,17 +28,17 @@ jobs:
 
     strategy:
       matrix:
-        java: [ '8', '11', '15', '16', '17', '18', '19', '20' ]
+        java: [ '8', '11', '15', '16', '17', '18', '19', '20', '21' ]
     name: Java version ${{ matrix.Java }}
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
     - name: Set up JDK ${{ matrix.Java }}
-      uses: actions/setup-java@v2
+      uses: actions/setup-java@v3
       with:
         java-version: ${{ matrix.java }}
         # the distribution can be either 'adopt' or 'zulu'
-        distribution: 'adopt'
+        distribution: 'zulu'
     - name: Grant execute permission for gradlew
       run: chmod +x gradlew
 

README.md

@@ -43,9 +43,13 @@ Use the following command to check our installed JDK version:
 $ javac -version
 ```
 
-This project **does not work** with JDK 21.
+This project **does not work** with JDK 22.
 
-It is recommended to use either JDK 8, JDK 11 or JDK 17 or JDK 19 or 20.
+It is recommended to use any of the following versions:
+- JDK 8 (LTS)
+- JDK 11 (LTS)
+- JDK 17 (LTS)
+- JDK 21 (LTS)
 
 :book: See this [wiki page for additional details regarding the supported Java versions and links to download the correct JDK versions](https://github.com/BoiseState/CS321_Bioinformatics/wiki/Install-the-correct-JDK-version).
 

build.gradle

@@ -8,7 +8,9 @@ plugins {
 group 'cs321'
 version '1.0'
 
-sourceCompatibility = 1.8
+java {
+    sourceCompatibility = JavaVersion.VERSION_1_8
+}
 
 repositories {
     mavenCentral()

gradle/wrapper/gradle-wrapper.properties

@@ -1,6 +1,6 @@
 distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
-distributionUrl=https\://services.gradle.org/distributions/gradle-8.1.1-bin.zip
+distributionUrl=https\://services.gradle.org/distributions/gradle-8.4-bin.zip
 networkTimeout=10000
 zipStoreBase=GRADLE_USER_HOME
 zipStorePath=wrapper/dists

gradlew

@@ -85,9 +85,6 @@ done
 APP_BASE_NAME=${0##*/}
 APP_HOME=$( cd "${APP_HOME:-./}" && pwd -P ) || exit
 
-# Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script.
-DEFAULT_JVM_OPTS='"-Xmx64m" "-Xms64m"'
-
 # Use the maximum available, or set MAX_FD != -1 to use that value.
 MAX_FD=maximum
 
@@ -144,15 +141,15 @@ if ! "$cygwin" && ! "$darwin" && ! "$nonstop" ; then
     case $MAX_FD in #(
       max*)
         # In POSIX sh, ulimit -H is undefined. That's why the result is checked to see if it worked.
-        # shellcheck disable=SC3045 
+        # shellcheck disable=SC3045
         MAX_FD=$( ulimit -H -n ) ||
             warn "Could not query maximum file descriptor limit"
     esac
     case $MAX_FD in  #(
       '' | soft) :;; #(
       *)
         # In POSIX sh, ulimit -n is undefined. That's why the result is checked to see if it worked.
-        # shellcheck disable=SC3045 
+        # shellcheck disable=SC3045
         ulimit -n "$MAX_FD" ||
             warn "Could not set maximum file descriptor limit to $MAX_FD"
     esac
@@ -197,6 +194,10 @@ if "$cygwin" || "$msys" ; then
     done
 fi
 
+
+# Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script.
+DEFAULT_JVM_OPTS='"-Xmx64m" "-Xms64m"'
+
 # Collect all arguments for the java command;
 #   * $DEFAULT_JVM_OPTS, $JAVA_OPTS, and $GRADLE_OPTS can contain fragments of
 #     shell script including quotes and variable substitutions, so put them in

src/test/java/cs321/btree/BTreeTest.java

@@ -205,7 +205,8 @@ public void testInsertTenDuplicates() throws BTreeException, IOException {
 
         assertEquals(1, b.getSize());
         assertEquals(0, b.getHeight());
-        assertTrue(validateSearchTreeProperty(b));
+
+        assertTrue(validateBTreeInserts(b, new long[]{1, 1, 1, 1, 1, 1, 1, 1, 1, 1}));
     }
 
 
@@ -220,13 +221,17 @@ public void testInsertTenThousandObjects() throws BTreeException, IOException {
 
         BTree b = new BTree(2, testFilename);
 
+        long[] input = new long[10000];
+
         for (int i = 0; i < 10000; i++) {
+            input[i] = i;
             b.insert(new TreeObject(i));
         }
 
         assertEquals(10000, b.getSize());
         assertEquals(12, b.getHeight());
-        assertTrue(validateSearchTreeProperty(b));
+
+        assertTrue(validateBTreeInserts(b, input));
     }
 
     /**
@@ -242,24 +247,24 @@ public void testCLRSExample18_6() throws BTreeException, IOException {
 
         BTree b = new BTree(4, testFilename);
 
-        b.insert(new TreeObject(1)); //A
-        b.insert(new TreeObject(4)); //D
-        b.insert(new TreeObject(6)); //F
-        b.insert(new TreeObject(8)); //H
-        b.insert(new TreeObject(12)); //L
-        b.insert(new TreeObject(14)); //N
-        b.insert(new TreeObject(16)); //P
+        //                        A  D  F  H   L   N   P  B
+        long[] input = new long[]{1, 4, 6, 8, 12, 14, 16, 2};
+
+        for (int i = 0; i < input.length - 1; i++) {
+            b.insert(new TreeObject(input[i]));
+        }
 
         assertEquals(7, b.getSize());
         assertEquals(0, b.getHeight());
         assertEquals(1, b.getNumberOfNodes());
 
-        b.insert(new TreeObject(2)); //Insert 'B'
+        b.insert(new TreeObject(input[7])); //Insert 'B'
 
         assertEquals(8, b.getSize());
         assertEquals(1, b.getHeight());
         assertEquals(3, b.getNumberOfNodes());
-        assertTrue(validateSearchTreeProperty(b));
+
+        assertTrue(validateBTreeInserts(b, input));
     }
 
     /**
@@ -401,22 +406,21 @@ public void testInsertToNotLeaf() throws BTreeException, IOException {
 
         BTree b = new BTree(4, testFilename);
 
-        b.insert(new TreeObject(1)); //A
-        b.insert(new TreeObject(4)); //D
-        b.insert(new TreeObject(6)); //F
-        b.insert(new TreeObject(8)); //H
-        b.insert(new TreeObject(12)); //L
-        b.insert(new TreeObject(14)); //N
-        b.insert(new TreeObject(16)); //P
-        b.insert(new TreeObject(2)); //B
+        //                        A  D  F  H   L   N   P  B  H
+        long[] input = new long[]{1, 4, 6, 8, 12, 14, 16, 2, 8};
+
+        for (int i = 0; i < input.length - 1; i++) {
+            b.insert(new TreeObject(input[i]));
+        }
 
         //by inserting a duplicate into a non leaf node, another branch is tested.
-        b.insert(new TreeObject(8)); //H
+        b.insert(new TreeObject(input[8])); //H
 
         TreeObject obj = b.search(8);
 
         assertEquals(2, obj.getCount());
-        assertTrue(validateSearchTreeProperty(b));
+
+        assertTrue(validateBTreeInserts(b, input));
     }
 
 
@@ -426,8 +430,8 @@ public void testInsertToNotLeaf() throws BTreeException, IOException {
      * a full child.
      * Assertion is that key 'H' (8) has been counted twice in a search
      *
-     * @throws BTreeException
-     * @throws IOException
+     * @throws BTreeException Exception thrown when BTree encounters an unexpected problem
+     * @throws IOException Exception thrown when testing fails due to IO errors
      */
     @Test
     public void testInsertToNotLeafFullChild() throws BTreeException, IOException {
@@ -437,14 +441,14 @@ public void testInsertToNotLeafFullChild() throws BTreeException, IOException {
         //                        A  D  F  H   L  H
         long[] input = new long[]{1, 4, 6, 8, 12, 8};
 
-        for (int i = 0; i < input.length; i++) {
-            b.insert(new TreeObject(input[i]));
+        for (long l : input) {
+            b.insert(new TreeObject(l));
         }
 
         TreeObject obj = b.search(8);
 
         assertEquals(2, obj.getCount());
-        assertTrue(validateSearchTreeProperty(b));
+
         assertTrue(validateBTreeInserts(b, input));
     }
 
@@ -457,7 +461,7 @@ public void testInsertToNotLeafFullChild() throws BTreeException, IOException {
      * @return true if there are no keys in the BTree, or if the keys are indeed in sorted order.
      *
      */
-    private boolean validateSearchTreeProperty(BTree b) {
+    private boolean validateSearchTreeProperty(BTree b) throws IOException {
 
         long[] keys = b.getSortedKeyArray();
 
@@ -492,7 +496,7 @@ private boolean validateSearchTreeProperty(BTree b) {
      *
      * @return true if BTree in order traversal matches provide input
      */
-    private boolean validateBTreeInserts(BTree b, long[] inputKeys) {
+    private boolean validateBTreeInserts(BTree b, long[] inputKeys) throws IOException {
 
         long[] bTreeKeys = b.getSortedKeyArray();
 
@@ -522,7 +526,7 @@ private boolean validateBTreeInserts(BTree b, long[] inputKeys) {
 
         long prev = bTreeKeys[0];
 
-        for (int i = 0; i < inputKeys.length; i++) {
+        for (int i = 0; i < bTreeKeys.length; i++) {
             if (bTreeKeys[i] != inputNoDuplicates.get(i)) {
                 return false;
             }