X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=blobdiff_plain;f=examples%2FappletDeployment.html;h=e9c22e563394fd0a81254cbb082b6151dc7b58b4;hp=a7653ed0747290b32df89230ab888f79806a7bce;hb=5104921c5c24afc2066ad6dc127f2dcb9e07daa5;hpb=62908e93f175753769436fd62193773b9f3ad26f diff --git a/examples/appletDeployment.html b/examples/appletDeployment.html index a7653ed..e9c22e5 100644 --- a/examples/appletDeployment.html +++ b/examples/appletDeployment.html @@ -18,30 +18,83 @@ --> - + -

Notes on applet deployment

- - -

**NEW FEATURES** in Jalview 2.9

+

Notes on applet deployment

+ + + + + + + + + + + + + + + + + + + + + + +
Required Dependency Downloads
DependencyDescription
JalviewApplet.jar Main Jalview Applet Jar
JmolApplet-14.6.4_2016.10.26.jar Jmol Applet Jar
java-json.jarRequired for BioJSON Generation
json_simple-1.1.jarRequired for BioJSON Generation
+ +

To run Jalview applet in your web page download the Jars listed above. The snippet below shows a minimal code for embedding Jalview applet into a web page. +


+<applet code="jalview.bin.JalviewLite" width="756" height="560" archive="jalviewApplet.jar,JmolApplet-14.6.4_2016.10.26.jar,java-json.jar,json_simple-1.1.jar">
+	<param name="permissions" value="sandbox" />
+	<param name="file" value="plantfdx.fa" />
+	<param name="features" value="plantfdx.features" />
+	<param name="userDefinedColour" value="C=yellow; R,K,H=FF5555; D,E=5555FF" />
+	<param name="showFullId" value="false" />
+	<param name="embedded" value="true" />
+	<param name="linkLabel_1" value="Uniprot" />
+	<param name="linkUrl_1"	value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$" />
+	<param name="linkLabel_2" value="EMBL-EBI Search" />
+	<param name="linkUrl_2"	value="http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$" />
+	<param name="APPLICATION_URL" value="http://www.jalview.org/services/launchApp" />
+</applet>
+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Applet Release History
ReleaseNew Features / required changes
2.9
(Latest)
  • Split Views for cDNA and Protein alignments
    Specify second alignment with 'file2' parameter, and set cDNA/Protein column scaling with scaleProteinAsCdna
    • @@ -54,9 +107,11 @@ 
    archive="jalviewApplet.jar,JmolApplet-14.2.14_2015.06.11.jar,java-json.jar,json_simple-1.1.jar"
-

-

**NEW FEATURES** in Jalview 2.8

-
    +
2.8
  • Normalised sequence logo display
  • RNA secondary structure annotation row @@ -71,9 +126,11 @@ original Jalview structure viewer will still be available.
    • -
-

**NEW FEATURES** in Jalview 2.7

-
    +
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).
    • @@ -86,13 +143,17 @@ 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

-
    +
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.
+
2.4
  • New applet API methods for feature display control, views, and obtaining current selection via javascript.
  • Group show and hide parameters: "showfeaturegroups" and @@ -104,9 +165,11 @@
  • "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

-
    +
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 @@ -126,12 +189,13 @@
  • 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 + +
2.1
    +
  • Jalview Applet can read and display JPred secondary structure annotation directly via the jnetfile parameter.
  • Param "UserDefinedColour" - specify your own colours for each residue using a semi colon @@ -158,5 +222,9 @@ <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)
    • -
+
+ +