input for newest jalview applet?

Dear Dr Katoh.

Thanks for your email - it's great to hear that you've been able to update the applet on the MAFFT serer. I also have to thank you for revealing this bug in Jalview's file parsing mechanism: the problem is that it misidentifies a file as RNAML if it encounters '<..>' in the first line (which is the case in your complex sequence name example).

We'll try and get a patch out as soon as possible. There are a couple of hurdles, however, so I can't promise it'll be fixed in the next couple of days. If you'd like to register on our bugtracker, you can hit the 'watch' button on to get notified when we make some progress.



On 11/04/2015 07:28, Kazutaka Katoh wrote:

Dear Dr Procter and Prof Barton,

I'm using the Jalview applet in the mafft web service.
Thank you very much for this useful applet!

Today I'm writing to you because I have two problems in running two recent versions of the applet.

1. About one week ago, I downloaded the applet.
Time stamp = Jan31; md5 = 189ae364ea6a82cda9cd6c4727b74f1c.
This version did not work, seemingly due to a security problem,
unless I weakened the security setting of Java.

Then I unpacked the jalviewApplet.jar file and signed it with our (Osaka University's) certificate.
It worked. The input sequence file in this example is

2. Today, I downloaded a newer version.
time stamp = Apr6; md5 = 333b5d1560fb4e71fa54ff56fdd1d416
Now there is no security problem. However, when trying to open the same sequence file, it did not work.

For another sequence file with simpler titles, it did work:
I guess the first input file (dum.pir) has characters that are incompatible with the Apr6 version.

I'm not completely sure if I correctly installed the applet into our server. Is this difference in behavior between two versions as expected? If so, I'm wondering if the newest version could open dum.pir, too, since it is more useful if more flexible sequence titles are allowed. Or, do you think it's ok to keep using the Jan31 version signed with Osaka Univ's certificate? Users may feel it strange..

I would appreciate any of your suggestions.

Best regards,
Kazutaka Katoh
IFReC, Osaka University
Suita 565-0871, Japan

Dr JB Procter, Jalview Coordinator, The Barton Group
Division of Computational Biology, College of Life Sciences
University of Dundee, Dundee DD1 5EH, UK.
+44 1382 388734 | |
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