X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=examples%2FappletParameters.html;h=b9af1df5304eb8cec8f6886e450429b87b6b6a00;hb=ab43013b7e357b84b4abade0dba949668dfb2a0e;hp=4779046313e6892d99f7aabae2807513e89b0874;hpb=8a41714a5c8428bac75034c7c40428ea2d16c2d2;p=jalview.git diff --git a/examples/appletParameters.html b/examples/appletParameters.html index 4779046..b9af1df 100644 --- a/examples/appletParameters.html +++ b/examples/appletParameters.html @@ -1,7 +1,7 @@ - + - -Applet Parameters + Applet Parameters + - - - - - + + + + + - + - - - + + + - - - - + +
- +
-

- Quick Links:

-

-

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.

@@ -234,7 +236,7 @@ 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 +310,7 @@ var _gaq = _gaq || [];_gaq.push(["_setAccount", "UA-9060947-1"]);_gaq.push(["_tr - + - @@ -589,8 +591,14 @@ var _gaq = _gaq || [];_gaq.push(["_setAccount", "UA-9060947-1"]);_gaq.push(["_tr new line in an alignment file must be entered as a parameter) - - + + + + + + + +
defaultColour One of:
Clustal, Blosum62, % Identity, Hydrophobic, Zappo, Taylor, Helix - Propensity, Strand Propensity, Turn Propensity, Buried Index, Nucleotide		 Default is no colour.
linkLabel_1UniprotEMBL-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 +323,12 @@ 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=$SEQUENCE_ID$