Jalview

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Download the applet jar file from here. Parameters are described - below, and the javascript API is described here. -

Quick Links:

Parameters are described below

The javascript API is described here

Package all your data files into a single (or multiple) zip / jar @@ -22,7 +19,7 @@ button by setting the embed parameter to true;
<param name="embedded" value="true">

**NEW FEATURES** in Jalview 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 - 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-12.1.13.jar"
```
Jmol 12.x requires at least Java 1.5 to run in the clients web browser. If the client does not have Java 1.5, or if the Jmol-12.1.13.jar is not added to the archive, the original Jalview structure viewer will still be available.
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).

**NEW FEATURES** in Jalview 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 - 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-12.1.13.jar"
```
Jmol 12.x requires at least Java 1.5 to run in the clients web browser. If the client does not have Java 1.5, or if the Jmol-12.1.13.jar is not added to the archive, the original Jalview structure viewer will still be available.
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).

**NEW FEATURES** in Jalview 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.

**NEW FEATURES** in Jalview 2.4

New applet API methods for feature display control, views, and obtaining current selection via javascript.