Applet Parameters

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 2.6

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 2.5

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.

showbutton

true

Show the jalview button on the page. When false, JalviewLite will open immediately.

sortByTree

true or false (default is false)

automatically sort the associated alignment view by the tree when a new tree is opened.

showTreeBootstraps

true or false (default is true)

show or hide branch bootstraps

showTreeDistances

true or false (default is true)

show or hide branch lengths

showUnlinkedTreeNodes

true or false (default is false)

indicate if unassociated nodes should be highlighted in the tree view

heightScale

1.0 or greater

Adjust the height of each cell in the alignment grid relative to the height of a character in the alignment font.

widthScale

1.0 or greater

Adjust the width of each cell in the alignment grid relative to the width of a character in the alignment font.

+ sortByTree true or false (default is false) automatically sort the associated alignment view by the tree when a new tree is opened. showTreeBootstrapstrue or false (default is true)show or hide branch bootstraps showTreeDistancestrue or false (default is true)show or hide branch lengths showUnlinkedTreeNodestrue or false (default is false)indicate if unassociated nodes should be highlighted in the tree view heightScale 1.0 or greater Adjust the height of each cell in the alignment grid relative to the height of a character in the alignment font. (since 2.5.1) + widthScale 1.0 or greater Adjust the width of each cell in the alignment grid relative to the width of a character in the alignment font. (since 2.5.1) centrecolumnlabels true of false (default is false) When true, text labels associated with a column in the alignment will be shown centered with respect to the column. (since 2.4) showUnconserved true of false (default is false) When true, only gaps and symbols different to the consensus sequence for a column will be shown. Useful for visualizing alignments exhibiting low sequence variation, where it is important to highlight mutations. (since 2.5) upperCase bold or other value Indicate a text style to apply to uppercase sequence symbols. Currently, only bold is supported. automaticScrolling true of false (default is true) When true, alignment panels will automatically scroll to show any regions of the alignment highlighted due to javascript events or when mousing over a position in an associated structure. (since 2.6) showGroupConsensus true of false (default is false) When true, shows consensus annotation row for any groups on the alignment. (since 2.7) showGroupConservation true of false (default is false) When true, shows amino-acid property conservation annotation row for any groups on the alignment. (since 2.7) showConsensusHistogram true of false (default is true) When true, shows the percentage occurence of the consensus symbol for each column as a histogram above the consensus sequence row. (since 2.7) showSequenceLogo true of false (default is false) When true, shows a sequence logo above the consensus sequence (overlaid above the Consensus Histogram, if visible, with symbols coloured using the alignment's default colourscheme). (since 2.7) oninit after_init() name of javascript function that will be called after the jalviewLite instance has completed its initialisation. (since 2.7) relaxedidmatch true or false (default is false) When true, use stem based matching to identify sequences that match features imported from a GFF or Jalview sequence features file, and for associating PDB data (passed on PDBfile parguments) with sequences (based on a given destination sequence ID). (since 2.7) alignpdbfiles true or false (default is false) When true, and jalviewLite is able to use jmol as a structure viewer, attempt to show a superposition of all structures loaded onto the alignment, superimposed using the aligned regions of corresponding sequences. [experimental] (since 2.7) externalstructureviewer true or false (default is false) re-route jmol colouring commands, selection and mouseover events to an external viewer using javascript callbacks. [experimental] (since 2.7) annotationcolour_max colour name or RGB hex triplet (default is red) Default colour used for maximum value when shading by annotation. (since 2.7) annotationcolour_min colour name or RGB hex triplet (default is orange) Default colour used for minimum value when shading by annotation. (since 2.7) jalviewhelpurl absolute or relative url or javascript function prefixed by javascript: (default is http://www.jalview.org/help.html) Optional parameter allowing modification of the default Jalview Help URL normally opened when JalviewLite's 'Help' menu item is selected. (since 2.7) resolvetocodebase True or False (False) Set to true to re-instate pre-JalviewLite 2.7 behaviour where relative URLs were prepended with the applet 'codebase' rather than the current document base URL before resolution. (since 2.7)