Dear Jim, thanks to your advice we have found a solution that work on all tested web browser. Instead of <applet file="../alignDNA/ENSG00000000005_TNMD_sh.fasta" archive="../../../jalviewApplet.jar" code="jalview.bin.JalviewLite" height="450" width="640"> <param value="false" name="showFullId"><param value="true" name="embedded"><param value="nucleotide" name="defaultColour"> <param value="false" name="wrap"><param value="F2F2FF" name="RGB"><param value="http://www.jalview.org/services/launchApp"; name="APPLICATION_URL"> </applet> we now use: <applet archive="../../../jalviewApplet.jar" code="jalview.bin.JalviewLite" height="450" width="640"> <param value="../alignDNA/ENSG00000000005_TNMD_sh.fasta" name="file"><param value="nucleotide" name="defaultColour"><param value="false" name="showFullId"> <param value="F2F2FF" name="RGB"><param value="True" name="sortByTree"><param value="true" name="showSequenceLogo"><param value="true" name="showGroupConsensus"><param value="false" name="showConservation"><param value="false" name="showQuality"><param value="true" name="embedded"><param value="SRS" name="linkLabel_1"> <param value="http://srs.ebi.ac.uk/srs7bin/cgi-bin/wgetz?-e+[uniprot-all:$SEQUENCE_ID$]+-vn+2"; name="linkUrl_1"> <param value="Uniprot" name="linkLabel_2"><param value="http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID$"; name="linkUrl_2"> <param value="http://www.jalview.org/services/launchApp"; name="APPLICATION_URL"></applet>
I will be please to update our Jalview applet as soon as the next version that could handle stop codon "*" in AA alignments will be available. thanks for your help Vincent Le 12 déc. 2011 à 11:09, Jim Procter a écrit : > Dear Vincent. > > Thanks very much for contacting us. I recently heard about MACSE from an > attendee of the Jalview course two weeks ago, and it is a nice > coincidence that you have emailed, even more so in that you have found a > problem with Jalview! > > On 12/12/2011 08:42, vincent ranwez wrote: >> We are really pleased with Jalview functionality's but it seems that >> the applet as compatibility issues. Indeed the applet is not loaded >> with JRE1.5 and the following web browser: >> chrome 15.0.874.121, firefox 8.0.1, safari 5.0.5 > May I ask what OS you used to identify this problem ? Also, could you > verify that the 'Do I have java' link at http://www.java.com/ reports > that Java is working ? The reason I ask is that as far as I am aware, > firefox 8 and chrome (practically all versions) require JRE1.6. > >> We encounter the same compatibility issues on the demo page of your >> web site : http://www.jalview.org/examples/embedded.html > Do you find the same problems with the non embedded examples on > http://www.jalview.org/examples/applets.html ? >> >> It seems that the standard way to include embedded applet is now to >> rely on .class files. The last jalview release (2.7) does not provide >> such files, can you please provide those files or alternative >> solutions so that we can continue to benefit from your JalView applet. > Forgive me, but I am a little confused by this part of your email. If > you wish to deploy the unpacked .class file set on your site, then you > may simply unpack the jalviewApplet.jar into a directory using a > standard ZIP archiving tool or java's own jartool. Normally, however, > the JRE will be happy both ways, and the jar deployment method can > result in slightly faster applet startup times. > > On the other hand, the fact that you have mentioned this suggests > something else might be happening. Are there some specific .class files > that cannot be located in the jalviewApplet.jar, for which you are > seeing 'Class Not Found' exceptions ? > > Jim. > > ps. my question regarding .class files excludes requests in your > server's log for the SmarterJmolAdapter.class, which was mentioned in > this previous > thread:http://www.jalview.org/pipermail/jalview-discuss/2011-December/000729.html > > and can be solved by including the jmol applet jar at > http://www.jalview.org/examples/JmolApplet-12.1.13.jar on the classpath. > > _______________________________________________ > Jalview-discuss mailing list > [email protected] > http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss _______________________________________________ Jalview-discuss mailing list [email protected] http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss
