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Unverified Commit 19550c18 authored by Matthieu Muffato's avatar Matthieu Muffato
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Cleaned up the root /lib directory

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LICENSE.txt
View file @ 19550c18
......@@ -207,7 +207,9 @@ ENSEMBL GUIHIVE PROJECT SUBCOMPONENTS
The Ensembl Guihive Project includes a number of subcomponents with
separate copyright notices and license terms. Your use of the source
code for these subcomponents is subject to the terms and conditions
stated in the subcomponent source code. Below, a summary of the
stated in the subcomponent source code.
All of the files found under lib/ are local copies of external libraries
and are covered by their own terms and conditions. Below, a summary of the
licensing terms of these subcomponents is presented. This list may
not be exhaustive and by no means should be taken as the final licensing
terms of the subcomponents used in this project. Refer to the source code of
......
index.html
View file @ 19550c18
......@@ -22,7 +22,8 @@
<!-- Twitter bootstrap JS -->
<script src="./lib/bootstrap/js/bootstrap.min.js"></script>
<script src="./lib/version_picker.js"></script>
<!-- Local javascripts -->
<script src="./javascript/version_picker.js"></script>
</head>
......
lib/ColVis.min.js deleted 100644 → 0
View file @ 3425de1f
/*
* File: ColVis.min.js
* Version: 1.0.8
* Author: Allan Jardine (www.sprymedia.co.uk)
*
* Copyright 2010-2012 Allan Jardine, all rights reserved.
*
* This source file is free software, under either the GPL v2 license or a
* BSD (3 point) style license, as supplied with this software.
*
* This source file 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 license files for details.
*/
(function(d){ColVis=function(a,b){(!this.CLASS||"ColVis"!=this.CLASS)&&alert("Warning: ColVis must be initialised with the keyword 'new'");"undefined"==typeof b&&(b={});this.s={dt:null,oInit:b,fnStateChange:null,activate:"click",sAlign:"left",buttonText:"Show / hide columns",hidden:!0,aiExclude:[],abOriginal:[],bShowAll:!1,sShowAll:"Show All",bRestore:!1,sRestore:"Restore original",iOverlayFade:500,fnLabel:null,sSize:"auto",bCssPosition:!1};this.dom={wrapper:null,button:null,collection:null,background:null,
catcher:null,buttons:[],restore:null};ColVis.aInstances.push(this);this.s.dt=a;this._fnConstruct();return this};ColVis.prototype={fnRebuild:function(){for(var a=this.dom.buttons.length-1;0<=a;a--)null!==this.dom.buttons[a]&&this.dom.collection.removeChild(this.dom.buttons[a]);this.dom.buttons.splice(0,this.dom.buttons.length);this.dom.restore&&this.dom.restore.parentNode(this.dom.restore);this._fnAddButtons();this._fnDrawCallback()},_fnConstruct:function(){this._fnApplyCustomisation();var a=this,
b,c;this.dom.wrapper=document.createElement("div");this.dom.wrapper.className="ColVis TableTools";this.dom.button=this._fnDomBaseButton(this.s.buttonText);this.dom.button.className+=" ColVis_MasterButton";this.dom.wrapper.appendChild(this.dom.button);this.dom.catcher=this._fnDomCatcher();this.dom.collection=this._fnDomCollection();this.dom.background=this._fnDomBackground();this._fnAddButtons();b=0;for(c=this.s.dt.aoColumns.length;b<c;b++)this.s.abOriginal.push(this.s.dt.aoColumns[b].bVisible);this.s.dt.aoDrawCallback.push({fn:function(){a._fnDrawCallback.call(a)},
sName:"ColVis"});d(this.s.dt.oInstance).bind("column-reorder",function(d,g,f){b=0;for(c=a.s.aiExclude.length;b<c;b++)a.s.aiExclude[b]=f.aiInvertMapping[a.s.aiExclude[b]];d=a.s.abOriginal.splice(f.iFrom,1)[0];a.s.abOriginal.splice(f.iTo,0,d);a.fnRebuild()})},_fnApplyCustomisation:function(){var a=this.s.oInit;"undefined"!=typeof a.activate&&(this.s.activate=a.activate);"undefined"!=typeof a.buttonText&&(this.s.buttonText=a.buttonText);"undefined"!=typeof a.aiExclude&&(this.s.aiExclude=a.aiExclude);
"undefined"!=typeof a.bRestore&&(this.s.bRestore=a.bRestore);"undefined"!=typeof a.sRestore&&(this.s.sRestore=a.sRestore);"undefined"!=typeof a.bShowAll&&(this.s.bShowAll=a.bShowAll);"undefined"!=typeof a.sShowAll&&(this.s.sShowAll=a.sShowAll);"undefined"!=typeof a.sAlign&&(this.s.sAlign=a.sAlign);"undefined"!=typeof a.fnStateChange&&(this.s.fnStateChange=a.fnStateChange);"undefined"!=typeof a.iOverlayFade&&(this.s.iOverlayFade=a.iOverlayFade);"undefined"!=typeof a.fnLabel&&(this.s.fnLabel=a.fnLabel);
"undefined"!=typeof a.sSize&&(this.s.sSize=a.sSize);"undefined"!=typeof a.bCssPosition&&(this.s.bCssPosition=a.bCssPosition)},_fnDrawCallback:function(){for(var a=this.s.dt.aoColumns,b=0,c=a.length;b<c;b++)null!==this.dom.buttons[b]&&(a[b].bVisible?d("input",this.dom.buttons[b]).attr("checked","checked"):d("input",this.dom.buttons[b]).removeAttr("checked"))},_fnAddButtons:function(){for(var a,b=","+this.s.aiExclude.join(",")+",",c=0,d=this.s.dt.aoColumns.length;c<d;c++)-1==b.indexOf(","+c+",")?(a=
this._fnDomColumnButton(c),this.dom.buttons.push(a),this.dom.collection.appendChild(a)):this.dom.buttons.push(null);this.s.bRestore&&(a=this._fnDomRestoreButton(),a.className+=" ColVis_Restore",this.dom.buttons.push(a),this.dom.collection.appendChild(a));this.s.bShowAll&&(a=this._fnDomShowAllButton(),a.className+=" ColVis_ShowAll",this.dom.buttons.push(a),this.dom.collection.appendChild(a))},_fnDomRestoreButton:function(){var a=this,b=document.createElement("button"),c=document.createElement("span");
b.className=!this.s.dt.bJUI?"ColVis_Button TableTools_Button":"ColVis_Button TableTools_Button ui-button ui-state-default";b.appendChild(c);d(c).html('<span class="ColVis_title">'+this.s.sRestore+"</span>");d(b).click(function(){for(var b=0,c=a.s.abOriginal.length;b<c;b++)a.s.dt.oInstance.fnSetColumnVis(b,a.s.abOriginal[b],!1);a._fnAdjustOpenRows();a.s.dt.oInstance.fnAdjustColumnSizing(!1);a.s.dt.oInstance.fnDraw(!1)});return b},_fnDomShowAllButton:function(){var a=this,b=document.createElement("button"),
c=document.createElement("span");b.className=!this.s.dt.bJUI?"ColVis_Button TableTools_Button":"ColVis_Button TableTools_Button ui-button ui-state-default";b.appendChild(c);d(c).html('<span class="ColVis_title">'+this.s.sShowAll+"</span>");d(b).click(function(){for(var b=0,c=a.s.abOriginal.length;b<c;b++)-1===a.s.aiExclude.indexOf(b)&&a.s.dt.oInstance.fnSetColumnVis(b,!0,!1);a._fnAdjustOpenRows();a.s.dt.oInstance.fnAdjustColumnSizing(!1);a.s.dt.oInstance.fnDraw(!1)});return b},_fnDomColumnButton:function(a){var b=
this,c=this.s.dt.aoColumns[a],e=document.createElement("button"),g=document.createElement("span"),f=this.s.dt;e.className=!f.bJUI?"ColVis_Button TableTools_Button":"ColVis_Button TableTools_Button ui-button ui-state-default";e.appendChild(g);c=null===this.s.fnLabel?c.sTitle:this.s.fnLabel(a,c.sTitle,c.nTh);d(g).html('<span class="ColVis_radio"><input type="checkbox"/></span><span class="ColVis_title">'+c+"</span>");d(e).click(function(c){var e=!d("input",this).is(":checked");"input"==c.target.nodeName.toLowerCase()&&
(e=d("input",this).is(":checked"));c=d.fn.dataTableExt.iApiIndex;d.fn.dataTableExt.iApiIndex=b._fnDataTablesApiIndex.call(b);f.oFeatures.bServerSide&&(""!==f.oScroll.sX||""!==f.oScroll.sY)?(b.s.dt.oInstance.fnSetColumnVis(a,e,!1),b.s.dt.oInstance.fnAdjustColumnSizing(!1),b.s.dt.oInstance.oApi._fnScrollDraw(b.s.dt),b._fnDrawCallback()):b.s.dt.oInstance.fnSetColumnVis(a,e);d.fn.dataTableExt.iApiIndex=c;null!==b.s.fnStateChange&&b.s.fnStateChange.call(b,a,e)});return e},_fnDataTablesApiIndex:function(){for(var a=
0,b=this.s.dt.oInstance.length;a<b;a++)if(this.s.dt.oInstance[a]==this.s.dt.nTable)return a;return 0},_fnDomBaseButton:function(a){var b=this,c=document.createElement("button"),e=document.createElement("span"),g="mouseover"==this.s.activate?"mouseover":"click";c.className=!this.s.dt.bJUI?"ColVis_Button TableTools_Button":"ColVis_Button TableTools_Button ui-button ui-state-default";c.appendChild(e);e.innerHTML=a;d(c).bind(g,function(a){b._fnCollectionShow();a.preventDefault()});return c},_fnDomCollection:function(){var a=
document.createElement("div");a.style.display="none";a.className=!this.s.dt.bJUI?"ColVis_collection TableTools_collection":"ColVis_collection TableTools_collection ui-buttonset ui-buttonset-multi";this.s.bCssPosition||(a.style.position="absolute");d(a).css("opacity",0);return a},_fnDomCatcher:function(){var a=this,b=document.createElement("div");b.className="ColVis_catcher TableTools_catcher";d(b).click(function(){a._fnCollectionHide.call(a,null,null)});return b},_fnDomBackground:function(){var a=
this,b=document.createElement("div");b.style.position="absolute";b.style.left="0px";b.style.top="0px";b.className="ColVis_collectionBackground TableTools_collectionBackground";d(b).css("opacity",0);d(b).click(function(){a._fnCollectionHide.call(a,null,null)});"mouseover"==this.s.activate&&d(b).mouseover(function(){a.s.overcollection=!1;a._fnCollectionHide.call(a,null,null)});return b},_fnCollectionShow:function(){var a=this,b,c;b=d(this.dom.button).offset();var e=this.dom.collection,g=this.dom.background,
f=parseInt(b.left,10),h=parseInt(b.top+d(this.dom.button).outerHeight(),10);this.s.bCssPosition||(e.style.top=h+"px",e.style.left=f+"px");e.style.display="block";d(e).css("opacity",0);c=d(window).height();var i=d(document).height(),j=d(window).width(),h=d(document).width();g.style.height=(c>i?c:i)+"px";g.style.width=(j<h?j:h)+"px";c=this.dom.catcher.style;c.height=d(this.dom.button).outerHeight()+"px";c.width=d(this.dom.button).outerWidth()+"px";c.top=b.top+"px";c.left=f+"px";document.body.appendChild(g);
document.body.appendChild(e);document.body.appendChild(this.dom.catcher);if("auto"==this.s.sSize){i=[];this.dom.collection.style.width="auto";b=0;for(c=this.dom.buttons.length;b<c;b++)null!==this.dom.buttons[b]&&(this.dom.buttons[b].style.width="auto",i.push(d(this.dom.buttons[b]).outerWidth()));iMax=Math.max.apply(window,i);b=0;for(c=this.dom.buttons.length;b<c;b++)null!==this.dom.buttons[b]&&(this.dom.buttons[b].style.width=iMax+"px");this.dom.collection.style.width=iMax+"px"}this.s.bCssPosition||
(e.style.left="left"==this.s.sAlign?f+"px":f-d(e).outerWidth()+d(this.dom.button).outerWidth()+"px",b=d(e).outerWidth(),d(e).outerHeight(),f+b>h&&(e.style.left=h-b+"px"));setTimeout(function(){d(e).animate({opacity:1},a.s.iOverlayFade);d(g).animate({opacity:0.1},a.s.iOverlayFade,"linear",function(){jQuery.browser.msie&&jQuery.browser.version=="6.0"&&a._fnDrawCallback()})},10);this.s.hidden=!1},_fnCollectionHide:function(){var a=this;!this.s.hidden&&null!==this.dom.collection&&(this.s.hidden=!0,d(this.dom.collection).animate({opacity:0},
a.s.iOverlayFade,function(){this.style.display="none"}),d(this.dom.background).animate({opacity:0},a.s.iOverlayFade,function(){document.body.removeChild(a.dom.background);document.body.removeChild(a.dom.catcher)}))},_fnAdjustOpenRows:function(){for(var a=this.s.dt.aoOpenRows,b=this.s.dt.oApi._fnVisbleColumns(this.s.dt),c=0,d=a.length;c<d;c++)a[c].nTr.getElementsByTagName("td")[0].colSpan=b}};ColVis.fnRebuild=function(a){var b=null;"undefined"!=typeof a&&(b=a.fnSettings().nTable);for(var c=0,d=ColVis.aInstances.length;c<
d;c++)("undefined"==typeof a||b==ColVis.aInstances[c].s.dt.nTable)&&ColVis.aInstances[c].fnRebuild()};ColVis.aInstances=[];ColVis.prototype.CLASS="ColVis";ColVis.VERSION="1.0.8";ColVis.prototype.VERSION=ColVis.VERSION;"function"==typeof d.fn.dataTable&&"function"==typeof d.fn.dataTableExt.fnVersionCheck&&d.fn.dataTableExt.fnVersionCheck("1.7.0")?d.fn.dataTableExt.aoFeatures.push({fnInit:function(a){return(new ColVis(a,"undefined"==typeof a.oInit.oColVis?{}:a.oInit.oColVis)).dom.wrapper},cFeature:"C",
sFeature:"ColVis"}):alert("Warning: ColVis requires DataTables 1.7 or greater - www.datatables.net/download")})(jQuery);
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lib/jquery.tipsy.js deleted 100644 → 0
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// tipsy, facebook style tooltips for jquery
// version 1.0.0a
// (c) 2008-2010 jason frame [jason@onehackoranother.com]
// released under the MIT license
// Modified by Miguel Pignatelli [emepyc@gmail.com]
// Added support for svg elements
(function($) {
function maybeCall(thing, ctx) {
return (typeof thing == 'function') ? (thing.call(ctx)) : thing;
};
function isElementInDOM(ele) {
while (ele = ele.parentNode) {
if (ele == document) return true;
}
return false;
};
function Tipsy(element, options) {
this.$element = $(element);
this.options = options;
this.enabled = true;
this.fixTitle();
};
Tipsy.prototype = {
show: function() {
var title = this.getTitle();
if (title && this.enabled) {
var $tip = this.tip();
$tip.find('.tipsy-inner')[this.options.html ? 'html' : 'text'](title);
$tip[0].className = 'tipsy'; // reset classname in case of dynamic gravity
$tip.remove().css({top: 0, left: 0, visibility: 'hidden', display: 'block'}).prependTo(document.body);
var pos = $.extend({}, this.$element.offset(), {
width: this.$element[0].offsetWidth || 0,
height: this.$element[0].offsetHeight || 0
});
if (typeof this.$element[0].nearestViewportElement == 'object') {
// SVG
var el = this.$element[0];
var located_element = $(el).children("text")[0];
var rect = located_element.getBoundingClientRect();
pos.width = rect.width;
pos.height = rect.height;
pos.left = rect.left;
}
var actualWidth = $tip[0].offsetWidth,
actualHeight = $tip[0].offsetHeight,
gravity = maybeCall(this.options.gravity, this.$element[0]);
var tp;
switch (gravity.charAt(0)) {
case 'n':
tp = {top: pos.top + pos.height + this.options.offset, left: pos.left + pos.width / 2 - actualWidth / 2};
break;
case 's':
tp = {top: pos.top - actualHeight - this.options.offset, left: pos.left + pos.width / 2 - actualWidth / 2};
break;
case 'e':
tp = {top: pos.top + pos.height / 2 - actualHeight / 2, left: pos.left - actualWidth - this.options.offset};
break;
case 'w':
tp = {top: pos.top + pos.height / 2 - actualHeight / 2, left: pos.left + pos.width + this.options.offset};
break;
}
if (gravity.length == 2) {
if (gravity.charAt(1) == 'w') {
tp.left = pos.left + pos.width / 2 - 15;
} else {
tp.left = pos.left + pos.width / 2 - actualWidth + 15;
}
}
$tip.css(tp).addClass('tipsy-' + gravity);
$tip.find('.tipsy-arrow')[0].className = 'tipsy-arrow tipsy-arrow-' + gravity.charAt(0);
if (this.options.className) {
$tip.addClass(maybeCall(this.options.className, this.$element[0]));
}
if (this.options.fade) {
$tip.stop().css({opacity: 0, display: 'block', visibility: 'visible'}).animate({opacity: this.options.opacity});
} else {
$tip.css({visibility: 'visible', opacity: this.options.opacity});
}
}
},
hide: function() {
if (this.options.fade) {
this.tip().stop().fadeOut(function() { $(this).remove(); });
} else {
this.tip().remove();
}
},
fixTitle: function() {
var $e = this.$element;
if ($e.attr('title') || typeof($e.attr('original-title')) != 'string') {
$e.attr('original-title', $e.attr('title') || '').removeAttr('title');
}
},
getTitle: function() {
var title, $e = this.$element, o = this.options;
this.fixTitle();
var title, o = this.options;
if (typeof o.title == 'string') {
title = $e.attr(o.title == 'title' ? 'original-title' : o.title);
} else if (typeof o.title == 'function') {
title = o.title.call($e[0]);
}
title = ('' + title).replace(/(^\s*|\s*$)/, "");
return title || o.fallback;
},
tip: function() {
if (!this.$tip) {
this.$tip = $('<div class="tipsy"></div>').html('<div class="tipsy-arrow"></div><div class="tipsy-inner"></div>');
this.$tip.data('tipsy-pointee', this.$element[0]);
}
return this.$tip;
},
validate: function() {
if (!this.$element[0].parentNode) {
this.hide();
this.$element = null;
this.options = null;
}
},
enable: function() { this.enabled = true; },
disable: function() { this.enabled = false; },
toggleEnabled: function() { this.enabled = !this.enabled; }
};
$.fn.tipsy = function(options) {
if (options === true) {
return this.data('tipsy');
} else if (typeof options == 'string') {
var tipsy = this.data('tipsy');
if (tipsy) tipsy[options]();
return this;
}
options = $.extend({}, $.fn.tipsy.defaults, options);
function get(ele) {
var tipsy = $.data(ele, 'tipsy');
if (!tipsy) {
tipsy = new Tipsy(ele, $.fn.tipsy.elementOptions(ele, options));
$.data(ele, 'tipsy', tipsy);
}
return tipsy;
}
function enter() {
var tipsy = get(this);
tipsy.hoverState = 'in';
if (options.delayIn == 0) {
tipsy.show();
} else {
tipsy.fixTitle();
setTimeout(function() { if (tipsy.hoverState == 'in') tipsy.show(); }, options.delayIn);
}
};
function leave() {
var tipsy = get(this);
tipsy.hoverState = 'out';
if (options.delayOut == 0) {
tipsy.hide();
} else {
setTimeout(function() { if (tipsy.hoverState == 'out') tipsy.hide(); }, options.delayOut);
}
};
if (!options.live) this.each(function() { get(this); });
if (options.trigger != 'manual') {
var binder = options.live ? 'live' : 'bind',
eventIn = options.trigger == 'hover' ? 'mouseenter' : 'focus',
eventOut = options.trigger == 'hover' ? 'mouseleave' : 'blur';
this[binder](eventIn, enter)[binder](eventOut, leave);
}
return this;
};
$.fn.tipsy.defaults = {
className: null,
delayIn: 0,
delayOut: 0,
fade: false,
fallback: '',
gravity: 'n',
html: false,
live: false,
offset: 0,
opacity: 0.8,
title: 'title',
trigger: 'hover'
};
$.fn.tipsy.revalidate = function() {
$('.tipsy').each(function() {
var pointee = $.data(this, 'tipsy-pointee');
if (!pointee || !isElementInDOM(pointee)) {
$(this).remove();
}
});
};
// Overwrite this method to provide options on a per-element basis.
// For example, you could store the gravity in a 'tipsy-gravity' attribute:
// return $.extend({}, options, {gravity: $(ele).attr('tipsy-gravity') || 'n' });
// (remember - do not modify 'options' in place!)
$.fn.tipsy.elementOptions = function(ele, options) {
return $.metadata ? $.extend({}, options, $(ele).metadata()) : options;
};
$.fn.tipsy.autoNS = function() {
return $(this).offset().top > ($(document).scrollTop() + $(window).height() / 2) ? 's' : 'n';
};
$.fn.tipsy.autoWE = function() {
return $(this).offset().left > ($(document).scrollLeft() + $(window).width() / 2) ? 'e' : 'w';
};
/**
* yields a closure of the supplied parameters, producing a function that takes
* no arguments and is suitable for use as an autogravity function like so:
*
* @param margin (int) - distance from the viewable region edge that an
* element should be before setting its tooltip's gravity to be away
* from that edge.
* @param prefer (string, e.g. 'n', 'sw', 'w') - the direction to prefer
* if there are no viewable region edges effecting the tooltip's
* gravity. It will try to vary from this minimally, for example,
* if 'sw' is preferred and an element is near the right viewable
* region edge, but not the top edge, it will set the gravity for
* that element's tooltip to be 'se', preserving the southern
* component.
*/
$.fn.tipsy.autoBounds = function(margin, prefer) {
return function() {
var dir = {ns: prefer[0], ew: (prefer.length > 1 ? prefer[1] : false)},
boundTop = $(document).scrollTop() + margin,
boundLeft = $(document).scrollLeft() + margin,
$this = $(this);
if ($this.offset().top < boundTop) dir.ns = 'n';
if ($this.offset().left < boundLeft) dir.ew = 'w';
if ($(window).width() + $(document).scrollLeft() - $this.offset().left < margin) dir.ew = 'e';
if ($(window).height() + $(document).scrollTop() - $this.offset().top < margin) dir.ns = 's';
return dir.ns + (dir.ew ? dir.ew : '');
}
};
})(jQuery);
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