Hawron is a GUI tool for the Apache XML Web Development Framework Cocoon and pure Java. It mainly supports the "Offline Generation Part" of Cocoon, but an embedded Servlet Container (Jetty) for Cocoon's default environment is included. Hawron tries to help Cocoon users with some extra features like publishing offline generated files (ftp, sftp) and editing content (embedded OpenOffice).
JAM (JavaGen Ant Modules) allows Java/J2EE developers to create robust, test-driven build environments with just a few lines of Ant script. Builds are simplified with a standard set of commands that you customize for your project. The Maven-to-Ant bridge manages classpaths, dependencies, versioning, and resource downloads automatically. JAM modules support JBoss, Tomcat 5, Resin, Oracle OC4J, JUnit, Cactus, XDoclet, CVS, Axis, Castor, JMX EJBs, and Hibernate.
While the author of BSAX-J has not yet come to a final conclusion about the need for a binary XML format, BSAX is his idea of one possible encoding that leverages other XML prior art (SAX events and UTF-8, in particular). It is complete in that it can be used to perform round-trip conversions from textual XML to SAX events to BSAX binary streams, and back to SAX events and textual XML. The test code in the distribution does exactly that for a simple example XML file, and measures the difference in file size (the file is slightly smaller for the BSAX encoding of the sample file) and the difference in read time (the read time is significantly faster for the sample file).
OpenArm is an implementation of the Open Group's Application Response Measurement (ARM) standard. It provides a complete implementation of the ARM 4.0 Java interfaces, as well as ARM agent functionality that allows you to record your transaction events as log4J logging events, JMS messages, SNMP traps, JMX notifications, or as records in a relational database.
Morph is a Java framework that eases the internal interoperability of an application. As information flows through an application, it undergoes multiple transformations. Morph provides a standard way to implement these transformations. In addition to providing a framework for performing transformations, Morph provides implementations of many common transformations. It has been built from the ground up for flexibility and extensibility, and it integrates seamlessly with dependency injection frameworks such as Spring, PicoContainer, and Hivemind.
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.