Jalview applet compatibility issue

Dear Jalview developper’s team,

Our team is relying on Jalview applet to display sequence alignments in two projects:

  1. OrthoMaM a database of othologuous mammalian molecular markers. The current OrthoMaM release (v6) is based on EnsEMBL v56. It now includes 6,056 exons and 12,777 CDS alignments for up to 36 species (http://www.orthomam.univ-montp2.fr/)
  2. MACSE an automatic solution to align protein-coding gene datasets containing non-functional sequences (pseudogenes) without disrupting the underlying codon structure. MACSE has also proved useful in detecting undocumented frameshifts in public database sequences and in aligning next-generation sequencing reads/contigs against a reference coding sequence (http://mbb.univ-montp2.fr/MBB/subsection/softExec.php?soft=macse)

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

We encounter the same compatibility issues on the demo page of your web site : http://www.jalview.org/examples/embedded.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.

sincerely yours,

Vincent

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!

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.

···

On 12/12/2011 08:42, vincent ranwez wrote:

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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