VRaptor 2 is a Web-based MVC and IOC framework based on many frameworks and ideas (Seam, Stripes, Webwork, Hibernate Annotations, etc). It makes full use of Java 5 Annotations. It favors convention over configuration, because configuration in XML/properties/annotations is always easy to make mistakes and repetitive (aka copy and paste in many places). This framework uses a more imperative approach, instead of having many XML files to configure lifecycle and other properties. Most of the settings go inside plain Java objects (POJO), so the team knows exactly what is going on and where.
Spring Batch Advanced Launcher (SBAL) is a tool based on Spring Batch. It allows launching batches from the command line. A set of advanced functionality is provided to allow enterprise deployment as an alternative to the CommandLineJobRunner. it provides advanced features like displaying the batch version, running resource validations, and configuring logging. It also defines a standard directory structure for deployments.
Icwri is a lightweight, very simple, service-oriented Java built-in script. It can help Java developers build some application interfaces in a service-oriented style. It can also help non-technical people join the development team to write their own application scripts to enforce business rules and decisions. Icwri service providers and consumers can be either Icwri scripts or Java classes. An Icwri script can run all alone, but the primary purpose of Icwri script is to have an assistant language of Java. It can run on any system with JDK/JRE 1.5 or above installed. It does not support Java SE 6 Script Engine because of the service-oriented design and the requirement to support Java SE 1.5 users.
JCons provides a library that bring color to your Java console. The Java console gives no methods to change the foreground or background color. With help of this library, one can make error messages red and success messages green, for example. Most Unix terminals can deal with ESC sequences, so they are used to make the Java console colorful.
Isobel is a framework to build complex information retrieval and analysis systems. Isobel can be functionally divided in two subsytems, Isobel Gatherer (the crawling and filtering subsystem) and Isobel Analyzer (the analysis subsystem). The two subsytems can also be used separately. Isobel Gatherer offers ready-to-use services like content fetching, scheduling, document format conversion, Hyperlink graph storage and analysis, content storage and indexing. A programmer may easily add new services. Isobel Analyzer uses the IBM UIMA architecture to reuse the analysis components developed for this architecture.
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.