ProteomeCommons.org IO Framework is a proper Java framework for handling spectra and peak lists. The framework can read and write to a number of different spectra and peak list formats, and it provides a simple, intuitive Java object model for working with spectra or peak lists. All classes support two methods of handling peak list and spectrum data: in-memory or stream. The goal of this framework is to support all the popular MS and MSMS data formats, and to eliminate any time or effort involved in figuring out how to read and write peak list or spectrum files.
ProteomeCommons.org Java Analysis Framework is a framework for referencing common mass spectrometry data such as atoms and residues. This framework provides a programmer with an easy-to-use library for writing programs that rely on common mass spectrometry data. The framework also contains utilities such as an isotope calculator and a reference for residue abbreviations.
tadedon is a set of utilities that form a foundation for applications written with one of the many Java frameworks, such as GWT, GIN, Guice, Google App Engine, commons-configuration, and many others. It lets you specify the default configuration of your application and upgrade it automatically on each new release. It can redirect all java.util.logging to slf4j and easily configure logback. It can bind application configuration in a Guice module. It supports @PostConstruct and @PreDestroy annotations (JSR 250) in Guice applications. It lets you annotate your methods with @Transactional annotation. It supports Guice injector stage in your Web application. It lets you test your Guice managed servlets and filters without needing a real servlet container. It lets you use Guice Matchers for matching super class, interface, and type literal annotations. It can inject event bus to your GWT applications with the help of GIN.
J4ME is a library to help with J2ME development. It includes a UI framework for professional-looking and intuitive interfaces, a logging framework to help debugging platform-specific issues found on different phones, a Bluetooth GPS integrated into the JSR-179 Location API, and a library of missing J2ME methods and helpful collections for small devices.