Hi all, I think that Andrew is referring to the T-Coffee web server http://tcoffee.crg.cat in which I've recently added Jalview as an option to display the alignment produced by T-Coffee.
To render the applet in a similar way we do in our web server, you can use the following applet definition: <applet id="applet" code="jalview.bin.JalviewLite" width="800" height="600" archive="public/jalviewApplet.jar"> <param name="file" value="http://path-to-your-alignment-file-to-display-in-fasta-format";> <param name="embedded" value="true"> <param name="showFeatureSettings" value="false"> <param name="widthScale" value="1.4"> <param name="heightScale" value="1.4"> <param name="nojmol" value="true" > <param name="linkLabel_1" value="SRS"> <param name="linkUrl_1" value="http://srs.ebi.ac.uk/srs7bin/cgi-bin/wgetz?-e+[uniprot-all:$SEQUENCE_ID$]+-vn+2";> <param name="linkLabel_2" value="Uniprot"> <param name="linkUrl_2" value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$";> </applet> The alignment to be showed have to specified using the parameter "file". You can find the explanation for all the available applet parameters at this page: http://www.jalview.org/examples/appletParameters.html Regarding the second part of your question, frankly I haven't understood which is your goal. Cheers, Paolo On Mar 9, 2012, at 6:34 PM, Geoff Barton wrote: Dear Andrew, I'm glad you are finding jalview useful in your studies. I'm not sure which particular site you are referring to when you say the Jalview applet embedded in T-Coffee. Jalview is used on many sites as an applet including alignment methods at EBI and elsewhere. If you join and reply to the [email protected]<mailto:[email protected]> mailing list then someone should be able to help you more. Kind regards, Geoff On 09/03/2012 17:30, Andrew Gerwin wrote: Hello, I have a question pertaining to the applet version of JalView that is embedded in T-Coffee. I am a high school co-op student working in the University of Guelph's Molecular and Cellular Biology department with the promoter sequences of CBF genes in grape plants. Recently I discovered JalView as part of T-Coffee and I was intrigued with the vast number of features at my disposal. Currently, I am primarily interested in the applet version (JalViewLite) but I may soon, with approval from my professor, choose to download and use the full version. Which of the four links under the applet category on the JalView site will direct me to the same JalView applet that T-Coffee exports to? Additionally, once loaded, what steps can be taken to completely clear all the data in the applet so that the alignment results of T-Coffee and/or Genomatix DiAlign may display in a similar way as when T-Coffee exports the data directly to the applet? Thanks for your help. Sincerely, Andrew Gerwin -- Geoff Barton, Professor of Bioinformatics, College of Life Sciences University of Dundee, Scotland, UK. [email protected]<mailto:[email protected]> Tel:+44 1382 385860/388731 (Fax:385764) www.compbio.dundee.ac.uk<http://www.compbio.dundee.ac.uk/> The University of Dundee is registered Scottish charity: No.SC015096 _______________________________________________ Jalview-discuss mailing list [email protected]<mailto:[email protected]> http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss
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