Tweaks for HDDBSCAN support

build.gradle

@@ -61,6 +61,7 @@ dependencies {
     }
     implementation group: 'com.github.quickhull3d', name: 'quickhull3d', version: '1.0.0'
     implementation group: 'org.apache.commons', name: 'commons-math3', version: '3.6.1'
+    implementation group: 'org.apache.commons', name: 'commons-lang3', version: '3.14.0'
     implementation group: 'org.zeromq', name: 'jeromq', version: '0.6.0'
     implementation group: 'com.fasterxml.jackson.core', name: 'jackson-annotations', version: '2.17.0'
     implementation group: 'com.fasterxml.jackson.core', name: 'jackson-databind', version: '2.17.0'
@@ -71,6 +72,7 @@ dependencies {
     implementation group: 'org.slf4j', name: 'slf4j-api', version: '2.0.12'
 
     testImplementation 'org.junit.jupiter:junit-jupiter:5.10.2'
+    testImplementation 'org.junit.platform:junit-platform-suite:1.10.2'
     testRuntimeOnly 'org.junit.platform:junit-platform-launcher:1.10.2'
 }
 

gradle.properties

@@ -8,5 +8,5 @@ org.gradle.java.installations.auto-detect=true
 
 # Project Build Properties
 env=dev
-javafx.version=21.0.2
+javafx.version=21.0.3
 javafx.static.version=21-ea+11.2

nbactions-assembly.xml

@@ -0,0 +1,37 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<actions>
+        <action>
+            <actionName>run</actionName>
+            <packagings>
+                <packaging>jar</packaging>
+            </packagings>
+            <goals>
+                <goal>clean</goal>
+                <goal>javafx:run</goal>
+            </goals>
+            <properties>
+                <exec.executable>java</exec.executable>
+                <exec.vmArgs>-Dprism.maxvram=2G</exec.vmArgs>
+                <exec.args>${exec.vmArgs}</exec.args>
+                <exec.mainClass>edu.jhuapl.trinity.TrinityMain</exec.mainClass>
+            </properties>
+        </action>
+        <action>
+            <actionName>debug</actionName>
+            <packagings>
+                <packaging>jar</packaging>
+            </packagings>
+            <goals>
+                <goal>clean</goal>
+                <goal>javafx:run@debug</goal>
+            </goals>
+            <properties>
+                <skipTests>true</skipTests>
+                <exec.executable>java</exec.executable>
+                <jpda.listen>true</jpda.listen>
+                <jpda.address>8000</jpda.address>
+                <exec.vmArgs>-Dprism.maxvram=2G</exec.vmArgs>
+                <exec.args>${exec.vmArgs} -Xdebug -Xrunjdwp:transport=dt_socket,server=n,address=8000 -classpath %classpath edu.jhuapl.trinity.App</exec.args>
+            </properties>
+        </action>
+    </actions>

pom.xml

@@ -20,7 +20,7 @@
         <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
         <project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>
         <java.version>21</java.version>
-        <javafx.version>21.0.2</javafx.version>
+        <javafx.version>21.0.3</javafx.version>
         <javafx.static.version>21-ea+11.2</javafx.static.version>
         <maven.min.version>3.6.3</maven.min.version>
         <maven.compiler.source>${java.version}</maven.compiler.source>
@@ -40,19 +40,18 @@
         <git.commit.maven.plugin.version>8.0.2</git.commit.maven.plugin.version>
         <org.owasp.dependency-check-maven.plugin.version>9.0.10</org.owasp.dependency-check-maven.plugin.version>
         <junit.jupiter.version>5.10.2</junit.jupiter.version>
+        <junit.jupiter.platform.version>1.10.2</junit.jupiter.platform.version>
         <litfx.controls.version>0.1.3</litfx.controls.version>
         <fxyz3d.version>0.6.0</fxyz3d.version>
         <hansolo.charts.version>21.0.7</hansolo.charts.version>
         <quickhull3d.version>1.0.0</quickhull3d.version>
         <apache.commons.math3.version>3.6.1</apache.commons.math3.version>
+        <apache.commons.lang3.version>3.14.0</apache.commons.lang3.version>
         <zeromq.jeromq.version>0.6.0</zeromq.jeromq.version>
         <jackson.version>2.17.0</jackson.version>
         <sarxos.webcam.capture.version>0.3.12</sarxos.webcam.capture.version>
         <org.jflac.jflac-codec.version>1.5.2</org.jflac.jflac-codec.version>
         <slf4j.version>2.0.12</slf4j.version>
-        <license.organizationName>The Johns Hopkins University Applied Physics Laboratory LLC</license.organizationName>
-        <license.licenceFile>LICENSE.md</license.licenceFile>
-        <license.licenseName>apache_v2</license.licenseName>
         <mainClassName>edu.jhuapl.trinity.TrinityMain</mainClassName>
         <!-- Values for build.properties -->
         <trinity.title>Trinity</trinity.title>
@@ -96,14 +95,20 @@
         </dependency>
         <dependency>
             <groupId>org.junit.jupiter</groupId>
-            <artifactId>junit-jupiter-api</artifactId>
+            <artifactId>junit-jupiter</artifactId>
             <version>${junit.jupiter.version}</version>
             <scope>test</scope>
         </dependency>
         <dependency>
-            <groupId>org.junit.jupiter</groupId>
-            <artifactId>junit-jupiter-params</artifactId>
-            <version>${junit.jupiter.version}</version>
+            <groupId>org.junit.platform</groupId>
+            <artifactId>junit-platform-suite</artifactId>
+            <version>${junit.jupiter.platform.version}</version>
+            <scope>test</scope>
+        </dependency>
+        <dependency>
+            <groupId>org.junit.platform</groupId>
+            <artifactId>junit-platform-launcher</artifactId>
+            <version>${junit.jupiter.platform.version}</version>
             <scope>test</scope>
         </dependency>
         <dependency>
@@ -131,6 +136,11 @@
             <artifactId>commons-math3</artifactId>
             <version>${apache.commons.math3.version}</version>
         </dependency>
+        <dependency>
+            <groupId>org.apache.commons</groupId>
+            <artifactId>commons-lang3</artifactId>
+            <version>${apache.commons.lang3.version}</version>
+        </dependency>
         <dependency>
             <groupId>org.zeromq</groupId>
             <artifactId>jeromq</artifactId>
@@ -266,33 +276,6 @@
                     <mainClass>${mainClassName}</mainClass>
                 </configuration>
             </plugin>
-            <!-- Adding license header to file, and copying license into metadata -->
-            <!-- Currently only used Manually -->
-            <plugin>
-                <groupId>org.codehaus.mojo</groupId>
-                <artifactId>license-maven-plugin</artifactId>
-                <version>${codehaus.license.plugin.version}</version>
-                <configuration>
-                    <licenseName>apache_v2</licenseName>
-                    <canUpdateCopyright>false</canUpdateCopyright>
-                    <canUpdateDescription>false</canUpdateDescription>
-                    <roots>
-                        <root>src/main/java</root>
-                        <root>src/test/java</root>
-                    </roots>
-                    <excludes>
-                        <exclude>**/*.json</exclude>
-                    </excludes>
-                </configuration>
-                <executions>
-                    <execution>
-                        <phase>process-sources</phase>
-                        <goals>
-                            <goal>update-file-header</goal>
-                        </goals>
-                    </execution>
-                </executions>
-            </plugin>
             <plugin>
                 <groupId>io.github.git-commit-id</groupId>
                 <artifactId>git-commit-id-maven-plugin</artifactId>

src/main/java/com/clust4j/Clust4j.java

@@ -0,0 +1,77 @@
+/*******************************************************************************
+ *    Copyright 2015, 2016 Taylor G Smith
+ *
+ *    Licensed under the Apache License, Version 2.0 (the "License");
+ *    you may not use this file except in compliance with the License.
+ *    You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ *    Unless required by applicable law or agreed to in writing, software
+ *    distributed under the License is distributed on an "AS IS" BASIS,
+ *    WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ *    See the License for the specific language governing permissions and
+ *    limitations under the License.
+ *******************************************************************************/
+package com.clust4j;
+
+import java.io.FileInputStream;
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.io.ObjectInputStream;
+import java.io.ObjectOutputStream;
+
+/**
+ * The absolute super type for all clust4j objects (models and datasets)
+ * that should be able to commonly serialize their data.
+ *
+ * @author Taylor G Smith
+ */
+public abstract class Clust4j implements java.io.Serializable {
+    private static final long serialVersionUID = -4522135376738501625L;
+
+    /**
+     * Load a model from a FileInputStream
+     *
+     * @param fos
+     * @return
+     * @throws IOException
+     * @throws ClassNotFoundException
+     */
+    public static Clust4j loadObject(final FileInputStream fis) throws IOException, ClassNotFoundException {
+        ObjectInputStream in = null;
+        Clust4j bm = null;
+
+        try {
+            in = new ObjectInputStream(fis);
+            bm = (Clust4j) in.readObject();
+        } finally {
+            if (null != in)
+                in.close();
+
+            fis.close();
+        }
+
+        return bm;
+    }
+
+    /**
+     * Save a model to FileOutputStream
+     *
+     * @param fos
+     * @throws IOException
+     */
+    public void saveObject(final FileOutputStream fos) throws IOException {
+        ObjectOutputStream out = null;
+
+        try {
+            out = new ObjectOutputStream(fos);
+            out.writeObject(this);
+        } finally {
+            if (null != out)
+                out.close();
+
+            fos.close();
+        }
+    }
+}