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Genomics Inform > Volume 6(1); 2008 > Article
Refactoring the Code for Visualizing Protein Database Information in a 3D Viewer for Software Reusability.
Yoo Jin Chun, Seong Il Ham, San Duk Yang, Arang Rhie, Hyun Seok Park
1Institute of Bioinformatics, Macrogen Inc., Seoul 153-023, Korea.
2Department of Computer Science, Ewha Womans University, Seoul 120-750, Korea.
3Department of Architectural Engineering, Yonsei University, Seoul, 120-749, Korea.
We have released five Java Application Programming Interface (API) packages for viewing three-dimensional structures of proteins from the Protein Data Bank. To this end, the user interface of an earlier version has been refactored in an object-oriented fashion, in which refactoring is the process of changing a software system to improve its internal structure, without altering the external behavior. Various GUI design and features have been provided conveniently thanks to the Model-View-Control (MVC)model, which is an architectural pattern used in software engineering. Availability: The source code and API specification can be downloaded from
Keywords: API; Bioinformatics; Protein structure visualization; Refactoring
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