Biojava
The BioJava Project is an open source project dedicated to providing Java tools for processing biological data. This will include objects for manipulating sequences, file parsers, CORBA interoperability, DAS, access to ACeDB, dynamic programming, and simple statistical routines.The BioJava library is useful for automating many daily and mundane bioinformatics tasks. As the library matures, the BioJava libraries will provide a foundation upon which both free software and commercial packages can be developed.
JMOL
Jmol is a molecule viewer for use in chemistry and biochemistry. It is free and open source. It can be used as a teaching tool or in research. It is Java based and runs on Windows, Mac OS X, Linux and Unix systems. There is a standalone application and a development tool kit that can be integrated into other Java applications. The most notable feature is an applet that can be integrated into web pages to display molecules in a variety of ways. For example, molecules can be displayed as "ball and stick" models, "space filling models", etc. Jmol supports a wide range of molecular file formats, including Protein Data Bank (pdb), Crystallographic Information File (cif), MDL Molfile (mol), and Chemical Markup Language (CML).
FPV
FPV is protein visualization software built using Java 3D API. FPV reads PDB files as input. It can load large molecules (e.g. 3000-4000 amino acids) and has a few display modes: spacefill, backbone, bonds, ribbon. It is available with source code.
MyDoggy
MyDoggy is a Java docking framework to be used in cross-platform Swing applications. MyDoggy is an IntelliJ Idea like docking framework for managing secondary windows within the main window. MyDoggy allows to move,resize or extract those secondary windows. Also, MyDoggy provides support for content management of the main window. Like Eclipse, MyDoggy supports the concept of "prospective" using mydoggy groups.
JFreeChart
JFreeChart is an open-source framework for the programming language Java, which allows the creation of complex charts in a simple way.JFreeChart also works with GNU Classpath, a free software implementation of the standard class library for the Java programming language.
Neobio
NeoBio is a library of bioinformatics algorithms implemented in Java.The current version consists mainly of (pairwise) sequence alignment algorithms such as the classical dynamic programming methods of Needleman & Wunsch (global alignment) and Smith & Waterman (local alignment).