[Jalview-discuss] Jalview applet compatibility issue

[vincent ranwez]

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.
> 
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