Applet Parameters

Discussion Mailing List

Please send problems
and bug reports to the discussion list.

Quick Links:

Download the applet jar file from here

Parameters are described below

The javascript API is described here

Useful to know!!

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 2.7.1

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 2.5

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.
-
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)
-

- + + + + + + +

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.

+ + + + + + + + + + + + + + + + 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. @@ -148,10 +115,18 @@ + Propensity, Strand Propensity, Turn Propensity, Buried Index, Nucleotide, Purine/Pyrimidine, T-Coffee Scores, RNA Helices + + + + + + + + @@ -184,6 +159,11 @@ + + + + + @@ -222,7 +202,7 @@ - + - @@ -285,7 +265,102 @@ - -

<param name=""	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, @@ -125,8 +91,9 @@	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 @@ -235,12 +215,12 @@ 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=$SEQUENCE_ID$
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. (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)
normaliseLogo	true of 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 2.7.1)
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)