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## Notes on applet deployment

Required Dependency Downloads
Dependency | Description
--- | ---
JalviewApplet.jar | Main Jalview Applet Jar
JmolApplet-14.6.4_2016.10.26.jar | Jmol Applet Jar
java-json.jar | Required for BioJSON Generation
json_simple-1.1.jar | Required for BioJSON Generation

To run Jalview applet in your web page download the Jars listed above. The snippet below shows a minimal code for embedding Jalview applet into a web page.

    <applet code="jalview.bin.JalviewLite" width="756" height="560" archive="jalviewApplet.jar,JmolApplet-14.6.4_2016.10.26.jar,java-json.jar,json_simple-1.1.jar">
    	<param name="permissions" value="sandbox" />
    	<param name="file" value="plantfdx.fa" />
    	<param name="features" value="plantfdx.features" />
    	<param name="userDefinedColour" value="C=yellow; R,K,H=FF5555; D,E=5555FF" />
    	<param name="showFullId" value="false" />
    	<param name="embedded" value="true" />
    	<param name="linkLabel_1" value="Uniprot" />
    	<param name="linkUrl_1"	value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$" />
    	<param name="linkLabel_2" value="EMBL-EBI Search" />
    	<param name="linkUrl_2"	value="http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$" />
    	<param name="APPLICATION_URL" value="http://www.jalview.org/services/launchApp" />
    </applet>

- View full list of supported applet parameters here.
- Package all your data files into a single (or multiple) zip / jar files. This is very useful to reduce download time of large data files. The applet archive tag can take multiple entries separated by commas, eg

      <applet code="jalview.bin.JalviewLite" archive="jalviewApplet.jar, mydata.zip">

- Use Jalview for input to a HTML form. For an example of how to code this using Javascript, click here.
- Embed Jalview into the web page, without the "Start Jalview" button by setting the embed parameter to true;
  <param name="embedded" value="true">
- For more examples, see the links to the left.

Applet Release History
Release | New Features / required changes
--- | ---
- 2.9 (Latest) | Split Views for cDNA and Protein alignments Specify second alignment with 'file2' parameter, and set cDNA/Protein column scaling with scaleProteinAsCdna Jmol compatibility updated to Jmol 14.2.x series - download the JmolApplet here The Jmol jar must be updated from 'JmolApplet-12.2.4.jar' to 'JmolApplet-14.2.14_2015.06.11.jar' in the applet archive argument as highlighted in red below:
      archive="jalviewApplet.jar,JmolApplet-14.2.14_2015.06.11.jar,java-json.jar,json_simple-1.1.jar"
- BioJson - A Json file format for representing a single multiple sequence alignment. Biojson uses the following external libraries: java-json and json_simple-1.1. Hence the jar files highlighted in red must be included in the applet archive argument as follows:
      archive="jalviewApplet.jar,JmolApplet-14.2.14_2015.06.11.jar,java-json.jar,json_simple-1.1.jar"
- 2.8 | Normalised sequence logo display RNA secondary structure annotation row Jmol compatibility updated to Jmol 12.2.x series - download the JmolApplet here To use Jmol as the structure viewer for Jalview, you must include the jar file in the applet archive argument thus:
      archive="jalviewApplet.jar,Jmol-12.2.4.jar"
Jmol 12.2.x requires at least Java 1.6 to run in the clients web browser. If the client does not have Java 1.6, or if the Jmol-12.2.jar is not added to the archive, the original Jalview structure viewer will still be available.
2.7 | Javascript callbacks capabilities oninit parameter and methods for registering javascript handlers for selections, mouseovers and linking to Jmol applets on the page. To use javascript callbacks, ensure the applet tag includes the 'mayscript' attribute - either as a parameter (<param name="mayscript" value="true"/;gt;) or as a bare attribute in the applet html tag). New jalviewLite java api methods for selecting, highlighting, scrolling and reordering sequences in an alignment view. **NEW FEATURES** in Jalview 2.6 Jmol compatibility updated to Jmol 12.1.x series Jalview 2.6 works only with Jmol version 12.1.13 or later. You can use the JmolApplet.jar from the Jmol binary distribution available at the Jmol Sourceforge site, or download the Jmol applet from here Minimum recommended version of Java runtime for the applet is now 1.5 (JalviewLite v2.6 without the Jmol viewer may work ok on earlier Java environments but compatibility can no-longer be guaranteed).
2.5 | New parameters to control display of tree annotation, width of alignment columns, and to disable the jalview button and check for Jmol on startup.
2.4 | New applet API methods for feature display control, views, and obtaining current selection via javascript. Group show and hide parameters: "showfeaturegroups" and "hidefeaturegroups". Both take a list of feature group names (separarated by "|" by default) to hide or show on the displayed alignment. Regular expressions can be used in URL links for sequence IDs. "debug" parameter to control verbosity of the applet's console output. "showbutton" parameter to disable launch button and open JalviewLite immediatly. "nojmol" parameter to disable check for Jmol classes.
- 2.3 | Note that Parameter "PDBFile" now takes the PDB file followed by a space separated list of alignment sequence ids to associate the structure to. It is also possible to associate multiple PDB files by adding an incremental value to PDBFile (up to 10). It is also possible to map specific sequences to specific chains by using the following notation:
                  <param name="PDBFile" value="First.pdb SeqA SeqB
                  SeqC">

                  <param name="PDBFile2" value="Second.pdb
                  A=SeqA B=SeqB C=SeqC">

                  <param name="PDBFile3" value="Third.pdb
                  D=SeqX B=SeqY C=SeqZ">
Note parameter "PDBSeq" is no longer required. Jalview 2.3 was updated to work with Jmol 11. See the versions archive if you want to download the old Jmol applet.
- 2.1 | Jalview Applet can read and display JPred secondary structure annotation directly via the jnetfile parameter. Param "UserDefinedColour" - specify your own colours for each residue using a semi colon separated list. Multiple residues can be assigned the same colour using commas. eg:
      <param name="userDefinedColour"
                  value="D,E=red; K,R,H=0022FF; C=yellow">
- Param "showFeatureSettings" - this will display the feature settings window when the applet starts. Param "Application_URL" value="http://www.jalview.org/services/launchApp" This calls a servlet which creates a JNLP file with the alignment file, annotations file and features file of the applet as arguments. If the user has Java installed, the returned JNLP file should start up the full Jalview Application. BUT this does not currently work for alignment files added to the applet in a zip file. Look at the XML comments in the file downloaded from The LaunchApp page for full documentation. Alignment file can be a series of parameters using eg PFAM format
      <param name="sequence1"
                  value="Q93XJ9_SOLTU/11-26 TSFLPRKPVVTSLKAI">

                  <param name="sequence2" value="FER1_PEA/14-29 TSFLRTQPMPMSVTTT">
(All the usual Jalview File formats are valid, however each new line in an alignment file must be entered as a parameter)