From cb597de858c70703321daa67adef5089957e9f55 Mon Sep 17 00:00:00 2001 From: hansonr Date: Fri, 17 May 2019 13:41:49 -0500 Subject: [PATCH] Jalview-JS/JAL-3253-applet more argument parsing allows for web component as well as deprecated adds applets-nocore.html for testing; sets applets.html to be with core loading, for demo. --- site-resources/applets-nocore.html | 230 ++++++++++++++++++++++++++++ site-resources/applets.html | 3 +- site-resources/javascript/JalviewApplet.js | 112 -------------- site-resources/swingjs/JalviewApplet.js | 68 ++++---- 4 files changed, 269 insertions(+), 144 deletions(-) create mode 100644 site-resources/applets-nocore.html delete mode 100644 site-resources/javascript/JalviewApplet.js diff --git a/site-resources/applets-nocore.html b/site-resources/applets-nocore.html new file mode 100644 index 0000000..f63f78d --- /dev/null +++ b/site-resources/applets-nocore.html @@ -0,0 +1,230 @@ + + + +SwingJS test Jalview + + + + + + + +

+

JalviewJS Button Examples

+Try out JalviewJS by pressing one of the buttons below. +Original Java (requires SeaMonkey browser) +

+

 

+

+

Ferredoxins, chloroplast precursor related UniRef50 + cluster

+
(15 sequences x 150 residues) +

+ + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + +User Defined Colours, loads an associated + Newick format tree file which is used to sort the alignment, and + group consensus and sequence logos are shown below the alignment.
+ + + + + + + + + + + + + + + +Displays a features file on the alignment
+ + + + + + + + + + + + + + + + +Associates PDB file 1GAQ with sequence + FER1_MAIZE
+ + + + + + + + + + + + + + + Displays a Multiple Sequence Alignment + Based JPred Prediction for a Sequence
+

+

RF00031 RFAM Alignment with per sequence secondary + structure

+

+ + + + + +
+ + + + + + + + + +Displays an RFAM RNA fold family with + secondary structure annotation
+

+

Linked Protein and cDNA alignments for a family of Steroid Receptors

+

+ + + + + +
+ + + + + + + + + + + + + + + +Displays a split window view showing aligned protein + and a reconstructed cDNA alignment.
Proteins were aligned with Muscle (version 3.8.31, + via the Jalview Desktop).
Data retrieved from Uniprot and + ENA, after Thornton, Need and Crews, Science 19 + September 2003: 301 (5640), 1714-1717 +
+
+
+ + + + + diff --git a/site-resources/applets.html b/site-resources/applets.html index 613aac7..9ff05dd 100644 --- a/site-resources/applets.html +++ b/site-resources/applets.html @@ -10,7 +10,8 @@ if (!self.SwingJS)alert('swingjs2.js was not found. It needs to be in swingjs fo JalviewInfo = { code: null, main: "jalview.bin.Jalview", - core: "NONE", + //core: "NONE", + core:"_jalview", resourcePath: "examples", readyFunction: null, serverURL: 'https://chemapps.stolaf.edu/jmol/jsmol/php/jsmol.php', diff --git a/site-resources/javascript/JalviewApplet.js b/site-resources/javascript/JalviewApplet.js deleted file mode 100644 index 576b891..0000000 --- a/site-resources/javascript/JalviewApplet.js +++ /dev/null @@ -1,112 +0,0 @@ -Jalview = {} - - -$(document).ready(function() { - Jalview.processAllAppletElements(); -}); - - -var currentPage = "applets"; - -Jalview.processAllAppletElements = function() { - var apps = document.getElementsByTagName("applet"); - for (var i = apps.length; --i >= 0;) { - processAppletElement(apps[i]); - } -} - -Jalview.jvid = 0; - -Jalview.doStartJalview = function(e) { - var element = e.target.appletElement; - var text = element.outerHTML; - - var Info = self.JalviewInfo || { -code: null, -main: "jalview.bin.Jalview", -core: "NONE", - width: 850, - height: 550, - readyFunction: null, - serverURL: 'https://chemapps.stolaf.edu/jmol/jsmol/php/jsmol.php', - j2sPath: 'swingjs/j2s', - console:'sysoutdiv', - allowjavascript: true - } - -var addParam = function(key,value) { - args.push("name=\"" + key + "\" value=\"" + value + "\""); -} - -var id = "JVApplet" + jvid++; -var args = text.replace(/[\n\t]/g, " ").split(" or tag. + + // To set Jalview application tags, use Info.args="......." + + // To set preferences, use "jalview_" prefix with all-upper-case names: + + //Info.jalview_SCREEN_X= 10,Info.jalview_SCREEN_Y= 10; + //Info.jalview_EMBEDDED= true; + //Info.jalview_SCREEN_WIDTH = 400; + //Info.jalview_SCREEN_HEIGHT = 100; + +var text = element.outerHTML; var code = element.getAttribute("code"); var parent = element.parentElement; -if (code != "jalview.bin.JalviewLite") { +if (code != "jalview.bin.JalviewLite" && text.indexOf("