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Maven central release and minor documentation updates
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‎README.md

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# index4j
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[![License](https://img.shields.io/badge/License-Apache%202.0-blue.svg)](https://opensource.org/licenses/Apache-2.0)
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[![Maven Central Version](https://img.shields.io/maven-central/v/com.dynatrace.index4j/indices)](https://central.sonatype.com/artifact/com.dynatrace.index4j/indices)
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[![javadoc](https://javadoc.io/badge2/com.dynatrace.index4j/indices/javadoc.svg)](https://javadoc.io/doc/com.dynatrace.index4j/indices)
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This repository is a Java library developed by Dynatrace that implements the FM-Index succinct data structure. The FM-Index takes
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advantage of the relationship between the suffix array and the Burrows-Wheeler transform to enable both compression and
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fast queries.
@@ -23,7 +27,21 @@ In addition, this repository also contains further data structures for working w
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## First steps
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TODO add dependency on maven
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To add a dependency on `index4j` using Maven, use the following:
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```
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<dependency>
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<groupId>com.dynatrace.index4j</groupId>
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<artifactId>indices</artifactId>
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<version>0.1.0</version>
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</dependency>
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```
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To add the dependency using Gradle:
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```
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implementation group: 'com.dynatrace.index4j', name: 'indices', version: '0.1.0'
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```
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## Supported data structures
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‎build.gradle

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plugins {
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id 'io.github.gradle-nexus.publish-plugin' version '2.0.0'
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id 'signing'
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id 'java-library'
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id 'maven-publish'
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id 'org.sonarqube' version '6.0.1.5171'
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}
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sonarqube {
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properties {
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property 'sonar.projectKey', 'dynatrace-oss_index4j'
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property 'sonar.organization', 'dynatrace-oss'
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property 'sonar.host.url', 'https://sonarcloud.io'
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}
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}
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nexusPublishing {
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packageGroup = 'com.dynatrace'
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useStaging = true
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repositories {
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sonatype {
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nexusUrl = uri('https://oss.sonatype.org/service/local/')
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snapshotRepositoryUrl = uri('https://oss.sonatype.org/content/repositories/snapshots/')
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username = System.getenv('OSSRH_USERNAME')
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password = System.getenv('OSSRH_PASSWORD')
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}
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}
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}

‎indices/build.gradle

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@@ -104,29 +104,61 @@ test {
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java {
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toolchain {
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languageVersion.set(JavaLanguageVersion.of(17))
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languageVersion.set(JavaLanguageVersion.of(21))
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}
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withSourcesJar()
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withJavadocJar()
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}
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jar {
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archiveBaseName.set('research-succinct-ds')
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}
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javadoc {
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failOnError true
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title 'index4j ' + project.version + ' API'
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}
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group = 'com.dynatrace.index4j'
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version = '0.1.0'
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gradlePlugin { automatedPublishing = false }
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publishing {
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publications {
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mavenJava(MavenPublication) {
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groupId = 'com.dynatrace.research'
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artifactId = 'succinct-ds'
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from components.java
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pom {
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name = 'com.dynatrace.index4j:index4j'
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description = 'index4j: A Dynatrace FM-Index library for Java'
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url = 'https://github.com/dynatrace-oss/index4j'
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licenses {
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license {
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name = 'The Apache License, Version 2.0'
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url = 'http://www.apache.org/licenses/LICENSE-2.0.txt'
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}
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}
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developers {
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developer {
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id = 'Dynatrace'
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name = 'Dynatrace LLC'
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email = 'opensource@dynatrace.com'
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}
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}
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scm {
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connection = 'scm:git:git://github.com/dynatrace-oss/index4j.git'
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developerConnection = 'scm:git:ssh://github.com/dynatrace-oss/index4j.git'
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url = 'https://github.com/dynatrace-oss/index4j'
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}
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}
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}
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}
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}
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tasks.withType(PublishToMavenLocal) {
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doFirst {
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println "Publishing '${publication.name}' to maven local with the following artifacts:"
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publication.artifacts.each { artifact -> println(" ${artifact.file}") }
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}
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signing {
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useInMemoryPgpKeys(System.getenv('GPG_PRIVATE_KEY'), System.getenv('GPG_PASSPHRASE'))
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sign publishing.publications.mavenJava
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}
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static def readJavaLicense(file, licenseName) {

‎indices/src/main/java/com/dynatrace/bitsequence/RrrVector.java

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/*
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* Copyright 2024 Dynatrace LLC
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* Copyright 2024-2025 Dynatrace LLC
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*
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* Licensed under the Apache License, Version 2.0 (the "License");
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* you may not use this file except in compliance with the License.
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* bits is sparse. For example, a bit sequence of size 2^31 (2,147,483,648) bits stored with a
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* sample rate of 256 requires the following amount of bits depending on the sparseness:
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*
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* <p>
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*
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* <table border="1">
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* <tr align="center">
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* <caption>Compression ratio by number of bits set and size</caption>
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* <tr style = "text-align: center;">
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* <td>Number of set bits </td> <td>Size in bits</td> <td>Compression ratio</td>
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* </tr>
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* <tr align="right">
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* <tr style = "text-align: right;">
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* <td>1%</td> <td>809,837,056</td><td>2.65x</td>
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* </tr>
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* <tr align="right">
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* <tr style = "text-align: right;">
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* <td>5%</td> <td>1,063,113,216</td><td>2.01x</td>
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* </tr>
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* <tr align="right">
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* <tr style = "text-align: right;">
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* <td>10%</td> <td>1,353,711,936</td><td>1.58x</td>
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* </tr>
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* </table>
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* Serializes this object to an {@code ObjectOutput} stream.
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*
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* @param objectOutput The stream to which the object will be written
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* @throws IOException if an I/O error occurs.
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*/
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public void write(ObjectOutput objectOutput) throws IOException {
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objectOutput.writeByte(SERIAL_VERSION_V0);
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*
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* @param objectInput The stream from which to read
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* @return The deserialized instance of this object
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* @throws IOException if an I/O error occurs.
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*/
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public static RrrVector read(ObjectInput objectInput) throws IOException {
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checkSerialVersion(SERIAL_VERSION_V0, objectInput.readByte());

‎indices/src/main/java/com/dynatrace/fm/FmIndex.java

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/*
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* Copyright 2024 Dynatrace LLC
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* Copyright 2024-2025 Dynatrace LLC
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*
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* Licensed under the Apache License, Version 2.0 (the "License");
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* you may not use this file except in compliance with the License.
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* Serializes this object to an {@code ObjectOutput} stream.
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*
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* @param objectOutput The stream to which the object will be written
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* @throws IOException if an I/O error occurs
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*/
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public void write(ObjectOutput objectOutput) throws IOException {
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objectOutput.writeByte(SERIAL_VERSION_V0);
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* Deserializes an {@code FM-index} from an {@code ObjectInput} stream.
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*
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* @param objectInput The stream from which to read from
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* @return The deserialized instance of this object
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* @return The deserialized instance of this object\
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* @throws IOException if an I/O error occurs
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*/
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public static FmIndex read(ObjectInput objectInput) throws IOException {
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checkSerialVersion(SERIAL_VERSION_V0, objectInput.readByte());

‎indices/src/main/java/com/dynatrace/fm/FmIndexBuilder.java

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/*
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* Copyright 2024 Dynatrace LLC
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* Copyright 2024-2025 Dynatrace LLC
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*
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* Licensed under the Apache License, Version 2.0 (the "License");
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* you may not use this file except in compliance with the License.
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private int sampleRate = 32;
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private boolean enableExtraction = true;
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/** Builds a new FmIndexBuilder with a {@code sampleRate} of 32 and extraction enabled. */
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public FmIndexBuilder() {}
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/**
2528
* Sets the sampling rate for the FM-Index. The lower the value of the sample rate, the higher
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* the memory consumption but the higher the query throughput. The default value is 32. A value

‎indices/src/main/java/com/dynatrace/intsequence/IntVector.java

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/*
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* Copyright 2024 Dynatrace LLC
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* Copyright 2024-2025 Dynatrace LLC
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*
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* Licensed under the Apache License, Version 2.0 (the "License");
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* you may not use this file except in compliance with the License.
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* Serializes this object to an {@code ObjectOutput} stream.
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*
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* @param objectOutput The stream to which the object will be written
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* @throws IOException if an I/O error occurs
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*/
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public void write(ObjectOutput objectOutput) throws IOException {
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objectOutput.writeByte(SERIAL_VERSION_V0);
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207208
*
208209
* @param objectInput The stream from which to read from
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* @return The deserialized instance of the object
211+
* @throws IOException if an I/O error occurs
210212
*/
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public static IntVector read(ObjectInput objectInput) throws IOException {
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checkSerialVersion(SERIAL_VERSION_V0, objectInput.readByte());

‎indices/src/main/java/com/dynatrace/intsequence/VariableWidthIntVector.java

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/*
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* Copyright 2024 Dynatrace LLC
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* Copyright 2024-2025 Dynatrace LLC
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*
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* Licensed under the Apache License, Version 2.0 (the "License");
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* you may not use this file except in compliance with the License.
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}
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5353
/**
54-
* Sets the value at {@code position} with {@value} using the minimum number of bits possible.
54+
* Sets the value at {@code position} with {@code value} using the minimum number of bits
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* possible.
5556
*
5657
* @param position The absolute position in bit counts
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* @param value The value to write
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8586
}
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8788
/**
88-
* Sets the value at {@code position} with {@value} using the given number of bits.
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* Sets the value at {@code position} with {@code value} using the given number of bits.
8990
*
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* @param position The absolute position in bit counts
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* @param value The value to write
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* Serializes this object to an {@code ObjectOutput} stream.
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*
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* @param objectOutput The stream to which the object will be written
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* @throws IOException if an I/O error occurs
174176
*/
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public void write(ObjectOutput objectOutput) throws IOException {
176178
objectOutput.writeByte(SERIAL_VERSION_V0);
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185187
*
186188
* @param objectInput The stream from which to read from
187189
* @return The deserialized instance of this object
190+
* @throws IOException if an I/O error occurs
188191
*/
189192
public static VariableWidthIntVector read(ObjectInput objectInput) throws IOException {
190193
checkSerialVersion(SERIAL_VERSION_V0, objectInput.readByte());

‎indices/src/main/java/com/dynatrace/run/Runner.java

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/*
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* Copyright 2024 Dynatrace LLC
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* Copyright 2024-2025 Dynatrace LLC
33
*
44
* Licensed under the Apache License, Version 2.0 (the "License");
55
* you may not use this file except in compliance with the License.
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2222
import java.nio.file.Files;
2323
import java.nio.file.Path;
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25+
/** A simple Main class template to build and query an FM-Index. */
2526
public final class Runner {
2627

2728
private Runner() {
2829
// Main class
2930
}
3031

32+
/**
33+
* Example Main class which builds an FM-Index of the given file and sample rate and then
34+
* queries the number of times the string "INFO" appears.
35+
*
36+
* @param args An array of size two, where the first string is the location of the input file
37+
* and the second is the sample rate for the FM-Index.
38+
* @throws IOException if the file does not exist
39+
* @throws IllegalArgumentException if the arguments are not correctly supplied
40+
*/
3141
public static void main(String[] args) throws IOException {
3242

3343
if (args.length < 2) {

‎indices/src/main/java/com/dynatrace/suffixarray/SuffixArray.java

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/*
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* Copyright 2024 Dynatrace LLC
2+
* Copyright 2024-2025 Dynatrace LLC
33
*
44
* Licensed under the Apache License, Version 2.0 (the "License");
55
* you may not use this file except in compliance with the License.
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168168
* Serializes this object to an {@code ObjectOutput} stream.
169169
*
170170
* @param objectOutput The stream to which the object will be written
171+
* @throws IOException if an I/O error occurs
171172
*/
172173
public void write(ObjectOutput objectOutput) throws IOException {
173174
objectOutput.writeByte(SERIAL_VERSION_V0);
@@ -185,6 +186,7 @@ public void write(ObjectOutput objectOutput) throws IOException {
185186
*
186187
* @param objectInput The stream from which to read from
187188
* @return The deserialized instance of this object
189+
* @throws IOException if an I/O error occurs
188190
*/
189191
public static SuffixArray read(ObjectInput objectInput) throws IOException {
190192
checkSerialVersion(SERIAL_VERSION_V0, objectInput.readByte());

‎indices/src/main/java/com/dynatrace/wavelet/WaveletFixedBlockBoosting.java

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/*
2-
* Copyright 2024 Dynatrace LLC
2+
* Copyright 2024-2025 Dynatrace LLC
33
*
44
* Licensed under the Apache License, Version 2.0 (the "License");
55
* you may not use this file except in compliance with the License.
@@ -282,6 +282,7 @@ private static long restoreCodeFromBlockHeader(
282282
*
283283
* @param objectInput The stream from which to read from
284284
* @return The deserialized instance of this object
285+
* @throws IOException if an I/O error occurs
285286
*/
286287
public static WaveletFixedBlockBoosting read(ObjectInput objectInput) throws IOException {
287288
checkSerialVersion(SERIAL_VERSION_V0, objectInput.readByte());
@@ -1540,6 +1541,7 @@ public long inverseSelect(long position) {
15401541
* Serializes this object to an {@code ObjectOutput} stream.
15411542
*
15421543
* @param objectOutput The stream to which the object will be written
1544+
* @throws IOException if an I/O error occurs
15431545
*/
15441546
public void write(ObjectOutput objectOutput) throws IOException {
15451547
objectOutput.writeByte(SERIAL_VERSION_V0);

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