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java2script/SwingJS for bioinformatics: Reintroducing Jalview on the Web as JalviewJS
Abstract
We have successfully developed the technology used to produce JSmol with Jmol [1, 2] to produce JalviewJS with Jalview [3] for the integration and visualisation of biological sequence and three-dimensional structures and other data within an evolutionary alignment framework. java2script/SwingJS [4] has been used to produce well over 600 JavaScript apps from Java code bases involving over 5000 Java classes (including Java applets and full Java applications -- see, for example, Physlet Physics [5] and SwingJS Examples [6]). This is not a "total rewrite". This is a minor tweaking of a Java program to be "JavaScript compatible" with automated co-production of Java class files and their JavaScript equivalents simultaneously. java2script/SwingJS is breakthrough technology that allows open-source developers to produce multiple flavors of their programs (Java desktop power application, fully contextualized JavaScript web page-based embedded app, and self-contained progressive web app) from the same Java code base. Little or no actual programming is done in JavaScript. The java2script transpiler rides along with the Eclipse Java compiler to produce the JavaScript "class" files, which then "run" on a web page using the SwingJS equivalent of the Java Virtual Machine. We will discuss how this technology allows the Jalview Desktop (3000+ Java classes) to be used within a rich web-based environment, and how easy it is for any developer to do this themselves. [1] https://sourceforge.net/projects/jmol/files/Jmol [2] https://github.com/BobHanson/Jmol-SwingJS [3] http://www.jalview.org/ [4] https://github.com/BobHanson/java2script [5] https://www.compadre.org/physlets [6] https://chemapps.stolaf.edu/swingjs/site/swingjs/examples
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“Launched in late 2019, JalviewJS is the Jalview application compiled to JavaScript [2] and adapted to run in-page either as the full-featured “Desktop” application or as interactive MSA visualization components designed for embedding in web pages.”
From Alignment of Biological Sequences with Jalview (2021) · cites this paper as [2]
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Alignment of Biological Sequences with Jalview
Procter, J. B., Carstairs, G. M., Soares, B., Mourão, K., Ofoegbu, T. C., Barton, D., Lui, L., Menard, A., Sherstnev, N., Roldan-Martinez, D., et al. (2021) · Methods in Molecular Biology · doi:10.1007/978-1-0716-1036-7_13 · Cited by 221
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Metadata
- Authors
- Hanson, R. M., Barton, G. J., Procter, J., Carstairs, M., & Soares, B.
- Publisher
- F1000 Research Ltd
- Published
- 2019-09-03
- Cited by
- 0
- References
- 0
- Licence
- creativecommons.org/licenses/by/4.0/ (tdm)
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- Hanson, R. M., Barton, G. J., Procter, J., Carstairs, M., & Soares, B. (2019). java2script/SwingJS for bioinformatics: Reintroducing Jalview on the Web as JalviewJS. https://doi.org/10.7490/f1000research.1117456.1
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