From: jprocter Date: Fri, 4 Nov 2011 16:09:09 +0000 (+0000) Subject: Merge branch 'JAL-980_jmol_patch' into develop X-Git-Tag: Jalview_2_9~561 X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=commitdiff_plain;h=88ba474b631ee8844b2212cf0ef1bff6a97ec7e1 Merge branch 'JAL-980_jmol_patch' into develop Conflicts: .classpath examples/appletParameters.html --- 88ba474b631ee8844b2212cf0ef1bff6a97ec7e1 diff --cc .classpath index 8af4838,d26fa6c..4e84fb8 --- a/.classpath +++ b/.classpath @@@ -39,11 -36,10 +37,13 @@@ - - - + ++ + + + ++ diff --cc examples/appletParameters.html index 5b0af6c,3cc5403..261bfa3 --- a/examples/appletParameters.html +++ b/examples/appletParameters.html @@@ -19,7 -19,7 +19,7 @@@ button by setting the embed parameter to true;
<param name="embedded" value="true"> -

**NEW FEATURES** in Jalview 2.7.1

Normalised sequence logo display
RNA secondary structure annotation row

**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 2.7.1

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.

**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
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 2.8

Normalised sequence logo display
RNA secondary structure annotation row

**NEW FEATURES** in Jalview 2.7.1

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.

**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
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.