X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=examples%2FappletParameters.html;h=b9af1df5304eb8cec8f6886e450429b87b6b6a00;hb=ab43013b7e357b84b4abade0dba949668dfb2a0e;hp=af1ec8793b22b891af59f3135afa5f6094f90555;hpb=76417f8a84ca46eab2f7c07dca76d13017715829;p=jalview.git diff --git a/examples/appletParameters.html b/examples/appletParameters.html index af1ec87..b9af1df 100644 --- a/examples/appletParameters.html +++ b/examples/appletParameters.html @@ -1,7 +1,7 @@ - + - -Applet Parameters + Applet Parameters + - - - - - + + + + + - + - - + // close layer when click-out + document.onclick = mclose; + // --> + + @@ -87,83 +91,84 @@ document.onclick = mclose; - - - - + +
- +
-

- Quick Links:

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-

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.

@@ -171,6 +176,11 @@ document.onclick = mclose; + + + + + @@ -226,7 +236,7 @@ document.onclick = mclose; + Propensity, Strand Propensity, Turn Propensity, Buried Index, Nucleotide, T-Coffee Scores, RNA Helices @@ -546,7 +556,7 @@ document.onclick = mclose;
  • 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.
    • +
  • Jalview 2.3 was updated to work with Jmol 11. See the versions archive if you want to download the old Jmol applet.

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    @@ -581,8 +591,14 @@ document.onclick = mclose; new line in an alignment file must be entered as a parameter) - - + + + + + + + +
    value=""> Description
    permissionssandboxThis parameter is necessary, and must have the value sandbox to allow the JalviewLite applet to run.
    file fileNamedefaultColour One of:
    Clustal, Blosum62, % Identity, Hydrophobic, Zappo, Taylor, Helix - Propensity, Strand Propensity, Turn Propensity, Buried Index, Nucleotide    		 Default is no colour.