Applet Parameters

- Quick Links:

Download the applet jar file from here -

-
Parameters are described below
-
The javascript API is described here
-

Additional applet deployment notes are below.

+ +

JalviewLite Applet Parameter Documentation

+The JalviewLite applet is configured through a series of applet parameters, +which are described below. Once initialised, +the applet can be interacted with via its +Javascript API. +

Issues arising from tightening of Java Security default settings
JalviewLite is provided as a signed applet with 'sandbox' permissions and wildcards that allow it to be run from any website. Unfortunately, earlier versions of Java may not be compatible with these settings.

For additional deployment notes, see Applet Deployment.

Applet Parameters

The applet takes the following initialisation parameters.

@@ -174,11 +36,34 @@ var _gaq = _gaq || [];_gaq.push(["_setAccount", "UA-9060947-1"]);_gaq.push(["_tr + + + + + + + + + + + + + + + + href="http://www.compbio.dundee.ac.uk/~www-jpred/">JPred Concise + file will be added to the first sequence in the alignment.
+ jpredfile can be used interchangeably with this parameter. @@ -229,10 +115,18 @@ var _gaq = _gaq || [];_gaq.push(["_setAccount", "UA-9060947-1"]);_gaq.push(["_tr + Propensity, Strand Propensity, Turn Propensity, Buried Index, Nucleotide, Purine/Pyrimidine, T-Coffee Scores, RNA Helices + + + + + + + + @@ -265,6 +159,11 @@ var _gaq = _gaq || [];_gaq.push(["_setAccount", "UA-9060947-1"]);_gaq.push(["_tr + + + + + @@ -303,7 +202,7 @@ var _gaq = _gaq || [];_gaq.push(["_setAccount", "UA-9060947-1"]);_gaq.push(["_tr - + - @@ -386,11 +285,14 @@ var _gaq = _gaq || [];_gaq.push(["_setAccount", "UA-9060947-1"]);_gaq.push(["_tr + + - + - + @@ -398,29 +300,29 @@ var _gaq = _gaq || [];_gaq.push(["_setAccount", "UA-9060947-1"]);_gaq.push(["_tr - + - + - + - + - + - + @@ -461,146 +363,4 @@ var _gaq = _gaq || [];_gaq.push(["_setAccount", "UA-9060947-1"]);_gaq.push(["_tr

value="">	Description
permissions	sandbox	*This parameter is necessary, and must have the value sandbox* to allow the JalviewLite applet to run.**
file	fileName	The file to open, must be on same server as the applet.
file2	fileName	A second file to open and show linked in a Split Frame + view. If one file is nucleotide and the other peptide, and at + least one peptide sequence matches the translation of one of the + nucleotide sequences, then gaps will be inserted into the + sequences in this file to match the aligned columns for + corresponding positions in the primary alignment file. This + parameter is ignored if enableSplitFrame is set to false (since + 2.9). +
enableSplitFrame	true or false (default true)	Enable or disable the display of linked cDNA and Protein alignments in a split frame (since 2.9).
sequence1, sequence2, @@ -206,8 +91,9 @@ var _gaq = _gaq \|\| [];_gaq.push(["_setAccount", "UA-9060947-1"]);_gaq.push(["_tr	jnetfile	fileName	Secondary structure predictions from a Jnet Concise - file will be added to the first sequence in the alignment.
PDBfile(x)	defaultColour	One of: Clustal, Blosum62, % Identity, Hydrophobic, Zappo, Taylor, Helix - Propensity, Strand Propensity, Turn Propensity, Buried Index, Nucleotide	Default is no colour.
defaultColourNuc	A colour scheme (from the list above) to apply to Nucleotide alignments	This overrides defaultColour if it is specified.
defaultColourProt	A colour scheme (from the list above) to apply to Peptide alignments	This overrides defaultColour if it is specified.
userDefinedColour	Example: D,E=red; K,R,H=0022FF; c=yellow	Default is true.
showOccupancy	true or false	Default is true.
sortBy	Id , Pairwise Identity, or Length	Sorts the alignment on startup
linkLabel_1	Uniprot	EMBL-EBI Search	Right click on sequence id to see list of available links. Any new links MUST have $SEQUENCE_ID$ as part of the linkURL_n value. For multiple links, increment the label and url name by @@ -316,12 +215,12 @@ var _gaq = _gaq \|\| [];_gaq.push(["_setAccount", "UA-9060947-1"]);_gaq.push(["_tr Regex URL links are also applied to the description line (since Jalview 2.4.+).
+	+ linkUrl_1	- http://us.expasy.org/cgi-bin/ - niceprot.pl?$SEQUENCE_ID$ + http://www.ebi.ac.uk/ebisearch/ search.ebi?db=allebi&query=$SEQUENCE_ID$
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)
scaleProteinAsCdna	true or false (default is false)	Set true to shown protein residues the same width as their encoding codons. + For use with parameter file2 when showing a split frame of cDNA and protein. (since 2.9)
centrecolumnlabels	true of false (default is false)	true or 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)	true or 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	Indicate a text style to apply to uppercase sequence symbols. Currently, only bold is supported.
automaticScrolling	true of false (default is true)	true or 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)	true or 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)	true or 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)	true or 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)	true or 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)
normaliseSequenceLogo	true of false (default is false)	true or false (default is false)	When true, all sequence logos will be normalised (all symbol stacks add up to full height of annotation row), rather than being scaled according to the fraction of symbols identical to the consensus. (since 2.8)
oninit	Multiple sequences aligment scores file. Currently is supported only the T-Coffee score_ascii file format

Notes on applet deployment

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">

**NEW FEATURES** in Jalview 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.
-

**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.
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.

- **NEW FEATURES** in Jalview 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.

- **NEW FEATURES** in Jalview 2.1 -

Jalview Applet can read and display JNet 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)

- -