From: BobHanson
+JalviewJS Button Examples
+Try out JalviewJS by pressing one of the buttons below.
+Original Java (requires SeaMonkey browser)
+
+
+ + | +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 | +
+
+ | +Displays an RFAM RNA fold family with + secondary structure annotation | +
+
+ + | +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 + |
+
+
+
+ + | +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 | +
+
+ | +Displays an RFAM RNA fold family with + secondary structure annotation | +
+
+ + | +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 + |
+
+
+This simple page illustrates how one can embed the JalviewJS desktop into a web page.
+The basic idea is that we have something interesting to say — some sort of scientific context — something we want to get
+across to our visitors with more than just text and images. The idea is to have a dynamic page that will involve user interaction.
+
++We start with a Jalview desktop. You can't see it, because I have placed it in a div tag with style width:0px;height:0px just after the period that ends this sentence.
+
++The idea is NOT to teach visitors how to use Jalview. The idea is to seamlessly integrate components of Jalview that can be used to enrich a discussion. +Like JSmol in Proteopedia. +For example, in the space to the right, after a few seconds, you will see an alignment frame. This alignment is for 15 genes that code for one of the domains in the ferredoxin family (NIR_SIR_ferr (PF03460)). + +What you see initially is just the first few residues. Doesn't look like much of an alignment, does it? But scroll to the right. +See the big block of red color? That's the Ferredoxin folddomain. + + |
+
+
++The alignment frame will appear here momentarily. When it does, you can go ahead and manipulate the alignment with your mouse. + |
+
+
+||||
+
| |||||
+
+
+jalview-strucddtureviewer-div
+
+ |
+
+One more thing. Let's take a look at the 3D structure of one these proteins. Ferredoxins are important, because they have
+iron-sulfur clusters that can accept and deliver electrons in metabolic processes. Let's see if we can find it.
+ |
'+JSON.stringify(JSON.parse(data),null,4)+'
')
+ $('#facebox .loading').remove()
+ $('#facebox .body').children().fadeIn('normal')
+ $('#facebox').css('left', $(window).width() / 2 - ($('#facebox .popup').width() / 2))
+ $(document).trigger('reveal.facebox').trigger('afterReveal.facebox')
+ },
+
+ close: function() {
+ $(document).trigger('close.facebox')
+ return false
+ }
+ })
+
+ /*
+ * Public, $.fn methods
+ */
+
+ $.fn.facebox = function(settings) {
+ if ($(this).length == 0) return
+
+ init(settings)
+
+ function clickHandler() {
+ $.facebox.loading(true)
+
+ // support for rel="facebox.inline_popup" syntax, to add a class
+ // also supports deprecated "facebox[.inline_popup]" syntax
+ var klass = this.rel.match(/facebox\[?\.(\w+)\]?/)
+ if (klass) klass = klass[1]
+
+ fillFaceboxFromHref(this.href, klass)
+ return false
+ }
+
+ return this.bind('click.facebox', clickHandler)
+ }
+
+ /*
+ * Private methods
+ */
+
+ // called one time to setup facebox on this page
+ function init(settings) {
+ if ($.facebox.settings.inited) return true
+ else $.facebox.settings.inited = true
+
+ $(document).trigger('init.facebox')
+ makeCompatible()
+
+ var imageTypes = $.facebox.settings.imageTypes.join('|')
+ $.facebox.settings.imageTypesRegexp = new RegExp('\.(' + imageTypes + ')$', 'i')
+
+ if (settings) $.extend($.facebox.settings, settings)
+ $('body').append($.facebox.settings.faceboxHtml)
+
+ var preload = [ new Image(), new Image() ]
+ preload[0].src = $.facebox.settings.closeImage
+ preload[1].src = $.facebox.settings.loadingImage
+
+ $('#facebox').find('.b:first, .bl').each(function() {
+ preload.push(new Image())
+ preload.slice(-1).src = $(this).css('background-image').replace(/url\((.+)\)/, '$1')
+ })
+
+ $('#facebox .close').click($.facebox.close)
+ $('#facebox .close_image').attr('src', $.facebox.settings.closeImage)
+ }
+
+ // getPageScroll() by quirksmode.com
+ function getPageScroll() {
+ var xScroll, yScroll;
+ if (self.pageYOffset) {
+ yScroll = self.pageYOffset;
+ xScroll = self.pageXOffset;
+ } else if (document.documentElement && document.documentElement.scrollTop) { // Explorer 6 Strict
+ yScroll = document.documentElement.scrollTop;
+ xScroll = document.documentElement.scrollLeft;
+ } else if (document.body) {// all other Explorers
+ yScroll = document.body.scrollTop;
+ xScroll = document.body.scrollLeft;
+ }
+ return new Array(xScroll,yScroll)
+ }
+
+ // Adapted from getPageSize() by quirksmode.com
+ function getPageHeight() {
+ var windowHeight
+ if (self.innerHeight) { // all except Explorer
+ windowHeight = self.innerHeight;
+ } else if (document.documentElement && document.documentElement.clientHeight) { // Explorer 6 Strict Mode
+ windowHeight = document.documentElement.clientHeight;
+ } else if (document.body) { // other Explorers
+ windowHeight = document.body.clientHeight;
+ }
+ return windowHeight
+ }
+
+ // Backwards compatibility
+ function makeCompatible() {
+ var $s = $.facebox.settings
+
+ $s.loadingImage = $s.loading_image || $s.loadingImage
+ $s.closeImage = $s.close_image || $s.closeImage
+ $s.imageTypes = $s.image_types || $s.imageTypes
+ $s.faceboxHtml = $s.facebox_html || $s.faceboxHtml
+ }
+
+ // Figures out what you want to display and displays it
+ // formats are:
+ // div: #id
+ // image: blah.extension
+ // ajax: anything else
+ function fillFaceboxFromHref(href, klass) {
+ // div
+ if (href.match(/#/)) {
+ var url = window.location.href.split('#')[0]
+ var target = href.replace(url,'')
+ if (target == '#') return
+ $.facebox.reveal($(target).html(), klass)
+
+ // image
+ } else if (href.match($.facebox.settings.imageTypesRegexp)) {
+ fillFaceboxFromImage(href, klass)
+ // ajax
+ } else {
+ fillFaceboxFromAjax(href, klass)
+ }
+ }
+
+ function fillFaceboxFromImage(href, klass) {
+ var image = new Image()
+ image.onload = function() {
+ $.facebox.reveal('', klass)
+ }
+ image.src = href
+ }
+
+ function fillFaceboxFromAjax(href, klass) {
+ $.get(href, function(data) { $.facebox.reveal(data, klass) })
+ }
+
+ function skipOverlay() {
+ return $.facebox.settings.overlay == false || $.facebox.settings.opacity === null
+ }
+
+ function showOverlay() {
+ if (skipOverlay()) return
+
+ if ($('#facebox_overlay').length == 0)
+ $("body").append('')
+
+ $('#facebox_overlay').hide().addClass("facebox_overlayBG")
+ .css('opacity', $.facebox.settings.opacity)
+ .click(function() { $(document).trigger('close.facebox') })
+ .fadeIn(200)
+ return false
+ }
+
+ function hideOverlay() {
+ if (skipOverlay()) return
+
+ $('#facebox_overlay').fadeOut(200, function(){
+ $("#facebox_overlay").removeClass("facebox_overlayBG")
+ $("#facebox_overlay").addClass("facebox_hide")
+ $("#facebox_overlay").remove()
+ })
+
+ return false
+ }
+
+ /*
+ * Bindings
+ */
+
+ $(document).bind('close.facebox', function() {
+ $(document).unbind('keydown.facebox')
+ $('#facebox').fadeOut(function() {
+ $('#facebox .content').removeClass().addClass('content')
+ $('#facebox .loading').remove()
+ $(document).trigger('afterClose.facebox')
+ })
+ hideOverlay()
+ })
+
+})(jQuery);
diff --git a/site-resources/javascript/jalview.js b/site-resources/javascript/jalview.js
new file mode 100644
index 0000000..1c1f1c2
--- /dev/null
+++ b/site-resources/javascript/jalview.js
@@ -0,0 +1,380 @@
+/**
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see 0))if(q){var s=0,v=q;for(q=null;j=v[s++];)j.call(t,b);b.fn.trigger&&b(t).trigger("ready").unbind("ready")}}},bindReady:function(){if(!p){p=true;if(t.readyState==="complete")return setTimeout(b.ready,1);if(t.addEventListener){t.addEventListener("DOMContentLoaded",u,false);E.addEventListener("load",b.ready,false)}else if(t.attachEvent){t.attachEvent("onreadystatechange",u);E.attachEvent("onload", +b.ready);var j=false;try{j=E.frameElement==null}catch(s){}t.documentElement.doScroll&&j&&a()}}},isFunction:function(j){return b.type(j)==="function"},isArray:Array.isArray||function(j){return b.type(j)==="array"},isWindow:function(j){return j&&typeof j==="object"&&"setInterval"in j},isNaN:function(j){return j==null||!r.test(j)||isNaN(j)},type:function(j){return j==null?String(j):R[y.call(j)]||"object"},isPlainObject:function(j){if(!j||b.type(j)!=="object"||j.nodeType||b.isWindow(j))return false;if(j.constructor&& +!F.call(j,"constructor")&&!F.call(j.constructor.prototype,"isPrototypeOf"))return false;for(var s in j);return s===B||F.call(j,s)},isEmptyObject:function(j){for(var s in j)return false;return true},error:function(j){throw j;},parseJSON:function(j){if(typeof j!=="string"||!j)return null;j=b.trim(j);if(C.test(j.replace(J,"@").replace(w,"]").replace(I,"")))return E.JSON&&E.JSON.parse?E.JSON.parse(j):(new Function("return "+j))();else b.error("Invalid JSON: "+j)},noop:function(){},globalEval:function(j){if(j&& +l.test(j)){var s=t.getElementsByTagName("head")[0]||t.documentElement,v=t.createElement("script");v.type="text/javascript";if(b.support.scriptEval)v.appendChild(t.createTextNode(j));else v.text=j;s.insertBefore(v,s.firstChild);s.removeChild(v)}},nodeName:function(j,s){return j.nodeName&&j.nodeName.toUpperCase()===s.toUpperCase()},each:function(j,s,v){var z,H=0,G=j.length,K=G===B||b.isFunction(j);if(v)if(K)for(z in j){if(s.apply(j[z],v)===false)break}else for(;Ha";var f=d.getElementsByTagName("*"),h=d.getElementsByTagName("a")[0],l=t.createElement("select"), +k=l.appendChild(t.createElement("option"));if(!(!f||!f.length||!h)){c.support={leadingWhitespace:d.firstChild.nodeType===3,tbody:!d.getElementsByTagName("tbody").length,htmlSerialize:!!d.getElementsByTagName("link").length,style:/red/.test(h.getAttribute("style")),hrefNormalized:h.getAttribute("href")==="/a",opacity:/^0.55$/.test(h.style.opacity),cssFloat:!!h.style.cssFloat,checkOn:d.getElementsByTagName("input")[0].value==="on",optSelected:k.selected,deleteExpando:true,optDisabled:false,checkClone:false, +scriptEval:false,noCloneEvent:true,boxModel:null,inlineBlockNeedsLayout:false,shrinkWrapBlocks:false,reliableHiddenOffsets:true};l.disabled=true;c.support.optDisabled=!k.disabled;b.type="text/javascript";try{b.appendChild(t.createTextNode("window."+e+"=1;"))}catch(o){}a.insertBefore(b,a.firstChild);if(E[e]){c.support.scriptEval=true;delete E[e]}try{delete b.test}catch(x){c.support.deleteExpando=false}a.removeChild(b);if(d.attachEvent&&d.fireEvent){d.attachEvent("onclick",function r(){c.support.noCloneEvent= +false;d.detachEvent("onclick",r)});d.cloneNode(true).fireEvent("onclick")}d=t.createElement("div");d.innerHTML="";a=t.createDocumentFragment();a.appendChild(d.firstChild);c.support.checkClone=a.cloneNode(true).cloneNode(true).lastChild.checked;c(function(){var r=t.createElement("div");r.style.width=r.style.paddingLeft="1px";t.body.appendChild(r);c.boxModel=c.support.boxModel=r.offsetWidth===2;if("zoom"in r.style){r.style.display="inline";r.style.zoom= +1;c.support.inlineBlockNeedsLayout=r.offsetWidth===2;r.style.display="";r.innerHTML="";c.support.shrinkWrapBlocks=r.offsetWidth!==2}r.innerHTML="
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