[Biojava-l] tiny problem with converting java 1.5 to 1.4

Recently I discussed that Biojava could be changed to Java version 1.5 without breaking compatibility since the novel tool Retroweaver allows to run Java 1.5 programs on older JREs. I started to use enums in my program and did not encounter any problems related to retroweaving. However there is o

[Biojava-l] BLAST (ncbi-blast, wu-blast, web-blast)

In the last weeks, we had many discussions on BLAST which shows that BLAST is of much interest. To my knowledge, there is no class in Biojava for invoking Blast searches yet. Therefore I would like to discuss the new BLAST API with you. It is a Java wrapper for local NCBI and local WU-blast and

[Biojava-l] 1.4 vs 1.5

Recently we had a discussion whether Biojava could use the novel features of Java1.5. Since I just have moved two larger applications (633 java files) to Java1.5 I would like to share my experiences with you. Applying the new features to the source code took me two days: This was worth doing beca

[Biojava-l] blast in an applet applet

If you installed blast locally you would need a cron job updating the blast database regularly. Perhaps it is easier to install a proxy server e.g. tiniproxy on the web server where the applet is stored. The proxy can redirect the blast request to any cgi server. ___

[Biojava-l] moving to java 1.5

Hi everyone, I followed the discussion on java 1.5. Is 1.5 installable on all MacOSX systems? There might be a problem with early OSX systems but I do not have a Mac to check it. It would be bad to break platform independence by moving to 1.5. By googling I found retroweaver, a converter of 1.5

[Biojava-l] (no subject)

The following looks like a bug to me. It occured with jre (SUN) 1.4 and 1.5 on X-Windows: I loaded the example "How do I display Features" http://www.biojava.org/docs/bj_in_anger/featgui.htm The sequence and the associated feature are displayed in a JFrame without error as described in the tutoria

[Biojava-l] (no subject)

Hi, I am currently working on an interface biojava <==> STRAP (http://www.charite.de/bioinf/strap/, http://www.charite.de/bioinf/strap/doc/index.pdf). First I create a GappedSequence object from a StrapProtein object. I include all STRAP anntotations and STRAP features. The features are subsets

[Biojava-l] biojava and STRAP

Hi, I would like to ask whether my program STRAP could benefit from BioJava and vice versa. Is it worth to develop converters to exchange objects like protein objects between both? http://www.charite.de/bioinf/strap/ STRAP is a multi purpose multiple sequences alignment tool. It contains wrapp