SearchAssist is a simple but practical search engine application that uses a ternary search tree. It uses Java's dynamic loading feature to make the search engine highly customizable, and uses takes Mozilla bookmarks as input. A Swing UI allows users to enter search words and view the results.
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.
JHighlight is an embeddable Java syntax highlighting library that supports Java, Groovy, C++, HTML, XHTML, XML, and LZX languages and outputs to XHTML. The library can be used in several ways: embedded into another tool (for instance a blog or forum), through the command-line to generate highlighted files locally, or as a servlet filter to highlight source files on your server on-the- fly. It also supports RIFE templates tags and highlights them clearly so that you can easily identify the difference between your RIFE markup and the actual marked up source.
jSieve is a Java implementation of the Sieve mail filtering language defined by RFC 3028. Sieve is an extensible mail filtering language. Its limited expressiveness (no loops or variables and no tests with side effects) allows user created scripts to be run safely on email servers. Sieve is targeted at the final delivery phase (where an incoming email is transferred to a user's mailbox). jSieve is implemented as a language processor that can be plugged into any Internet mail application to add Sieve support.