Cylindrical BLAST Viewer / News: Recent posts

I have uploaded a new .zip file containing all that is needed to run this project: there is no need to figure out how to install Java3D. And the samples are bundled, along with batch scripts to see how everything is done. You will not need to search high and low looking for example data, or sit looking at a blank screen wondering what to do next.

Enjoy!

A new release was made on 5/28/2012, by the admin. This one has its settings all moved onto a single popup, to eliminate all the clutter, keep the multiple settings handy, and help us to remember what all can be changed. In addition, to help in determining what level of effort needs to be expended on the viewer, it will post statistics to Google Analytics. The events will be types (not name!) of files being opened, startup, and one or two error conditions.

The ClustalWConverter.java file, which had been downloadable as part of the 1.2 release, has been removed. It is still available in the CVS repository as self.lesfoster.cylindrical_viewer.data_source.ClustalWConverter.java.

It had been added to the release as a stopgap measure during some difficulties with CVS and a lack of time to diagnose the problem, on the part of myself.

The file has been downloaded several times. It had been added to fulfill the SourceForge requirement that all code used to make a release be available on the site. This would have constituted a one-file code drop.... read more

A new download has been added, that is identical to Version 1.1, except that it is compatible with a slightly later (1.3.2) version of Java3D. This also allows an upgrade to one minor version forward, of Open GL, which is the layer below Java3D (that is used by this project).

As before, the JVM (trademark Sun Microsystems) and Java3D have been included as a convenience.

This upgrade may allow full animation with anti-aliasing, without the skipping behavior seen in the past. CAUTION: the OpenGL upgrade requires suitable graphics card support. The author found that a mere video driver upgrade was sufficient to run the project on a circa 2002 system.

Recently, a new downloadable just for windows(tm) users was uploaded. This includes all the binary code for the Cylindrical BLAST Viewer, plus everything it should require to run. This includes the Sun(tm) Java(tm) 1.5.0_03 JVM, with extensions applied for Java3D 1.3.1. The sample file set is also included.

This download is contained in a .ZIP file, meaning you will need to unzip it. Within is a file called _README.txt, with further instructions. This downloadable is windows-specific, in that the JVM included is not compatible with any other platform.... read more

As of 4/27/2006, release 1.1 has been created. It contains bug fixes for bugs number 1470816, 1469831, 1469827, and 1469408. All defects refer to sourceforge-site-listed bugs. All have been marked "closed".

The latest version of the Cylindrical BLAST Viewer has been posted, in order to make a first, non-point release, with as many of the suggestions from early users included, as possible. Also, in releasing this, the developer has attempted to create something reasonably stable and useable.

The Cylindrical BLAST Viewer was brought to existence during a period from Jan-May 2005, as an independent research project for a graduate course of study. During this time, the author/developer received feedback from a number of people (call them 'commenters') who asked that specific features be added. Many of those (thing like suggested file formats) were addressed during the initial period, but some were left out due to time constraints. Of these, some were addressed in versions 0.2 and 0.3 (such as still more file formats, and the ability to startup the viewer using a sane set of command line arguments: namely, none).... read more

Latest release allows the user to open the viewer with no command line parameters, and select a file. At the time of file open, the appropriate "dentils" parameter may be selected. Further, it is no longer necessary to know the length of the axis at launch time (it will be read from the input file). Finally, it is now possible to read Microsoft Project(tm) files exported as XML.

A new release of the Cylindrical Viewer has been added to the download page. The new version can read the BlastOutput (NCBI BLASTP), ClustalW, and GeneMachine XML formats directly. The previous verson required that a user first convert all file types into a proprietary format. A schema is also offered for the proprietary format (cylinder).
This addition fixes an omission: there was no description of the required format in the past, just samples. And widely-used formats were not used. With 0.2, there is a hidden conversion using also-hidden XSLT translation style sheets, to alleviate this problem.