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 http://issues.jalview.org/browse/JAL-1694 to get notified when we make some progress. Jim. 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. > http://mafft.cbrc.jp/alignment/server/ > 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, > http://mafft.cbrc.jp/alignment/server/spool/jalviewtestJan31.html > unless I weakened the security setting of Java. > > Then I unpacked the jalviewApplet.jar file and signed it with our (Osaka > University's) certificate. > http://mafft.cbrc.jp/alignment/server/spool/jalviewtestJan31osaka.html > It worked. The input sequence file in this example is > http://mafft.cbrc.jp/alignment/server/spool/dum.pir > > 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. > http://mafft.cbrc.jp/alignment/server/spool/jalviewtestApr6.html > > For another sequence file with simpler titles, it did work: > http://mafft.cbrc.jp/alignment/server/spool/dum-2.pir > http://mafft.cbrc.jp/alignment/server/spool/jalviewtestApr6-2.html > 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 > [email protected] > [email protected] > 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 | www.jalview.org | www.compbio.dundee.ac.uk The University of Dundee is registered Scottish charity: No.SC015096 _______________________________________________ Jalview-dev mailing list [email protected] http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-dev
