Classpath 0.92 has been released

Bling! Bling!. Mark Wielaard announced the GNU Classpath 0.92 release, with the following changes: an alternative awt peer implementation based on Escher that uses the X protocol directly. Various ImageIO providers for png, gif and bmp images. Support for reading and writing midi files and reading .au and .wav files have been added. Various tools and support classes have been added for jar, native2ascii, serialver, keytool, jarsigner. A GConf based util.peers backend has been added. Support for using alternative root certificate authorities with the security and crypto packages. Start of javax.management and runtime lang.managment runtime support. NIO channels now support scatter-gather operations. less than 1 minute read

Fortran and XML: FoX reads and writes CML

Mix one of the oldest and one of the latest computer technologies, and you get FoX (BSD license), a Fortran library for reading and writing Chemical Markup Language, and thus XML. Amazing, what Toby White achieved, though he did not start from scratch: “FoX evolved from the initial codebase of xmlf90, which was written largely by Alberto Garcia and Jon Wakelin.” (source: cml-discuss mailing list). less than 1 minute read

new Atom(Elements.CARBON);

Something I have not completely comfortable with about the CDK in the past, is the way Atom’s are constructed: less than 1 minute read

BlueObelisk components in Japanese

Technorati is nice in several ways, one being the feature to set up a watchlist. I have set watches on chemoinformatics, Jmol, Bioclipse and a few more. This allows me see the latest blog items on these topics. Often, the point to Asian blogs, mostly Chinese and Japanese, which I mostly find hard to read. Funny characters with Jmol somewhere in the sentence :) less than 1 minute read

CDK and the Java 6 beta

Recently, a second beta of Java 6 was released, which triggered a patch for the Debian java-package package. It was a Bioclipse bug report today, however, which made me patch my java-package setup and install the beta. 1 minute read

Context help in Bioclipse

The Eclipse Rich Client Platform (RCP) is very powerfull, and takes a lot of architectural things of your hand when developing a bio- and chemoinformatics GUIs. Bioclipse is based on it. One thing the RCP offers is a Help View which works with plain (X)HTML files, and one neat feature is the context help. It is help shown in the Help View when one focused on a specific GUI element. less than 1 minute read

Matrix support in Bioclipse

With chemometrics in mind (QSAR, data mining, …), I have started working on matrix support in Bioclipse, because the matrix is the important step between (bio-)molecular content and statistical analysis. I implemented this such that the actual matrix implementation can be freely chosen, that is, bc_statistical provides a IMatrixImplementation extension point. The plugin bc_jama provides a JAMA based extension for this, but other implementations are possible, and possibly useful. 1 minute read