Jstacs

Jstacs is an open-source Java library for statistical analysis of biological sequences. It provides efficient sequence data structures and a broad set of generative and discriminative models for parameter learning, along with tools to assess and compare classifiers on test datasets or via cross-validation using multiple performance measures.

For more information including an API documentation, code examples, FAQs, binaries and a cookbook visit http://www.jstacs.de.

Prerequisites

• Java 17
• Apache Maven 3.6+
• Maven downloads dependencies from configured repositories: ensure network access for the first build.

Repository layout

• src/main/java -- core Java sources under the de.jstacs package
• src/main/resources -- runtime assets (native libs, package docs, etc.)

Building via Maven

This repository builds the core library only (no project modules).

mvn clean package

To install into your local maven repository:

mvn clean install

By default, Javadoc generation is skipped during regular builds and installs.

Building Javadoc on demand

Generate HTML Javadoc into target/site/apidocs:

mvn javadoc:javadoc -Dmaven.javadoc.skip=false

Build and attach the Javadoc JAR:

mvn javadoc:jar -Dmaven.javadoc.skip=false

The jar is created in folder target/.

Organization of the library

Jstacs core classes may be found in sub-packages of de.jstacs.

A list of projects that are based on Jstacs, including binaries documentation of user parameters is available at http://jstacs.de/index.php/Projects.

Building upon Jstacs, JstacsFX visualizes parameters and results in a JavaFX-based GUI that is built upon the generic de.jstacs.tools.JstacsTool class.

Licensing information

Jstacs is free software: you can redistribute it and/or modify under the terms of the GNU General Public License version 3 or (at your option) any later version as published by the Free Software Foundation.

For more information, please read LICENSE.