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 are not compatible with these settings, so if you find that you cannot see any of the examples on the left, try the unsigned applet examples. +

For additional deployment notes, see below.

Applet Parameters

The applet takes the following initialisation parameters.

@@ -185,6 +187,12 @@ var _gaq = _gaq || [];_gaq.push(["_setAccount", "UA-9060947-1"]);_gaq.push(["_tr + + + + + @@ -234,7 +242,7 @@ var _gaq = _gaq || [];_gaq.push(["_setAccount", "UA-9060947-1"]);_gaq.push(["_tr + Propensity, Strand Propensity, Turn Propensity, Buried Index, Nucleotide, T-Coffee Scores, RNA Helices @@ -308,7 +316,7 @@ var _gaq = _gaq || [];_gaq.push(["_setAccount", "UA-9060947-1"]);_gaq.push(["_tr - + - @@ -391,11 +399,14 @@ var _gaq = _gaq || [];_gaq.push(["_setAccount", "UA-9060947-1"]);_gaq.push(["_tr + + - + - + @@ -403,29 +414,29 @@ var _gaq = _gaq || [];_gaq.push(["_setAccount", "UA-9060947-1"]);_gaq.push(["_tr - + - + - + - + - + - + @@ -589,8 +600,14 @@ var _gaq = _gaq || [];_gaq.push(["_setAccount", "UA-9060947-1"]);_gaq.push(["_tr new line in an alignment file must be entered as a parameter) - - + + + + + + + +

The file to open, must be on same server as the applet.
file2	fileName	A second file to open. If one file is nucleotide and the other peptide, and at least one peptide sequence + is the translation of one of the nucleotide sequences, then alignments will be displayed linked in a split frame (since 2.8.3).
sequence1, sequence2, sequence3	defaultColour	One of: Clustal, Blosum62, % Identity, Hydrophobic, Zappo, Taylor, Helix - Propensity, Strand Propensity, Turn Propensity, Buried Index, Nucleotide	Default is no colour.
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 @@ -321,12 +329,12 @@ 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 2.8.3)
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