Protein Alignment Tool

Mac OS X 10.5 - Java 2D pipeline

admin — Sun, 02 Mar 2008 07:04:25 +0000

I came across this post when doing some fiddling with the “Overview” panel used by PAT.

The basic problem is that there is a bug in the drawImage() method call leading to very poor performance on 10.5. The post above provides some help until the bug is fixed.

Mylyn rocks!

admin — Wed, 06 Feb 2008 21:44:33 +0000

I first started to use Mylyn a few weeks back and have integrated it with trac, which was very easy to do.

Eclipse live provides free access to a webinar by Mik Kersten, the creator of Mylyn.

Zotero: The Next-Generation Research Tool

admin — Tue, 08 Jan 2008 18:50:55 +0000

Zotero is an interesting Firefox add-on and a possible replacement for tools like EndNote. It is an open source sollution to collecting and managing research sources. It runs completely within the Firefox browser and works offline too.

Mac OS X - Java 6 :-(

admin — Mon, 29 Oct 2007 16:13:56 +0000

Many of us have been waiting patiently (or not) for Apple to release Java 6. With 10.5 we thought perhaps this would happen. Apparently Java 6 is still AWOL.

http://www.theserverside.com/news/thread.tss?thread_id=47375

What is the holdup on this?

build.xml

admin — Wed, 29 Aug 2007 06:10:19 +0000

I found a bug in my build.xml script. I let Eclipse compile all my source with the exception of Version.java which is dynamically built by Ant and then compiled before I generate the project JAR file. The problem is that even though my Eclipse project settings were set to 5.0, I didn’t set the target in the javac task in the build file. This resulted in a Bad Version Number error if I built the project on a machine where Java 6 was the default.

Java Web Start with JARs signed by multiple certificates

admin — Thu, 09 Aug 2007 04:53:44 +0000

This is a problem I ran into when adding activation.jar and mail.jar (both from Sun) to my .jnlp file. It turns out that these JAR files are already signed by Sun. All JAR files within a JNLP file must be signed by the same certificate - the way around it is to have multiple JNLP files and use the extension keyword. For details see this post from Kirill Grouchnikov’s Blog.

A SEquence Globally Unique IDentifier (SEGUID) Proteome Database

admin — Wed, 01 Aug 2007 17:26:57 +0000

Protein sequences stored in UniProt have a CRC64 checksum. This means that it is possible to take an arbitrary sequence (with or without a known identifier), calculate the CRC64 checksum for it, and then search UniProt for that specific sequence. There are two problems with this:

UniProt does not provide any web services for querying their database. I’ll check again, but, I don’t see it
There is a low possibility of collision; that is, two sequences may produce the same CRC64 checksum.

On Nature Precedings I came across A SEquence Globally Unique IDentifier (SEGUID) Proteome Database that solves the two problems above.

Eclipse Europa (3.3.0) - Discovered odd behaviour with Ant input task

admin — Sun, 22 Jul 2007 21:03:54 +0000

My Ant build script stopped working when I moved from Elipse-3.2.2 to
Eclipse 3.3.0. It was failing with a null pointer on the input task.
By process of elimination I discovered that if a defaultvalue was set
in the input task, then it would fail. That is odd for sure. I
downloaded Ant 1.7.0 and had no problem executing my build script,
therefore, the problem had to be with Eclipse 3.30. Through
experimentation I discovered that by setting Ant to run in the same JRE
as the workspace the input task succeeded!

Thank you to JAVASOFT Software Engineering

admin — Mon, 16 Jul 2007 16:28:01 +0000

A big thank you to JAVASOFT Software Engineering for granting me a non-commercial license to the Synthetica look and feel.