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biojs-vis-pdbviewer

Version:

A BioJS 2.0 component to view protein structures

github.com/sillitoe/biojs-vis-pdbviewer

sillitoe/biojs-vis-pdbviewer

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g=c-e,f=e+b.collisionHeight-d-c,h;b.collisionHeight>d?0<g&&0>=f?(h=a.top+g+b.collisionHeight-d-c,a.top+=g-h):0<f&&0>=g?a.top=c:g>f?a.top=c+d-b.collisionHeight:a.top=c:0<g?a.top+=g:0<f?a.top-=f:a.top=A(a.top-e,a.top)}},flip:{left:function(a,b){var c=b.within,d=c.offset.left+c.scrollLeft,e=c.width,g=c.isWindow?c.scrollLeft:c.offset.left,f=a.left-b.collisionPosition.marginLeft,c=f-g,h=f+b.collisionWidth-e-g,f="left"===b.my[0]?-b.elemWidth:"right"===b.my[0]?b.elemWidth:0,k="left"===b.at[0]?b.targetWidth: "right"===b.at[0]?-b.targetWidth:0,l=-2*b.offset[0];if(0>c){if(d=a.left+f+k+l+b.collisionWidth-e-d,0>d||d<r(c))a.left+=f+k+l}else if(0<h&&(d=a.left-b.collisionPosition.marginLeft+f+k+l-g,0<d||r(d)<h))a.left+=f+k+l},top:function(a,b){var c=b.within,d=c.offset.top+c.scrollTop,e=c.height,c=c.isWindow?c.scrollTop:c.offset.top,f=a.top-b.collisionPosition.marginTop,h=f-c,f=f+b.collisionHeight-e-c,k="top"===b.my[1]?-b.elemHeight:"bottom"===b.my[1]?b.elemHeight:0,l="top"===b.at[1]?b.targetHeight:"bottom"=== b.at[1]?-b.targetHeight:0,m=-2*b.offset[1],n,q;0>h?(q=a.top+k+l+m+b.collisionHeight-e-d,a.top+k+l+m>h&&(0>q||q<r(h))&&(a.top+=k+l+m)):0<f&&(n=a.top-b.collisionPosition.marginTop+k+l+m-c,a.top+k+l+m>f&&(0<n||r(n)<f)&&(a.top+=k+l+m))}},flipfit:{left:function(){h.ui.position.flip.left.apply(this,arguments);h.ui.position.fit.left.apply(this,arguments)},top:function(){h.ui.position.flip.top.apply(this,arguments);h.ui.position.fit.top.apply(this,arguments)}}};var s,y,t,F,G,H=document.getElementsByTagName("body")[0], I=document.createElement("div");s=document.createElement(H?"div":"body");t={visibility:"hidden",width:0,height:0,border:0,margin:0,background:"none"};H&&h.extend(t,{position:"absolute",left:"-1000px",top:"-1000px"});for(G in t)s.style[G]=t[G];s.appendChild(I);y=H||document.documentElement;y.insertBefore(s,y.firstChild);I.style.cssText="position: absolute; left: 10.7432222px;";F=h(I).offset().left;h.support.offsetFractions=10<F&&11>F;s.innerHTML="";y.removeChild(s);if(!1!==h.uiBackCompat){var K=jQuery, ba=K.fn.position;K.fn.position=function(a){if(!a||!a.offset)return ba.call(this,a);var b=a.offset.split(" "),c=a.at.split(" ");return 1===b.length&&(b[1]=b[0]),/^\d/.test(b[0])&&(b[0]="+"+b[0]),/^\d/.test(b[1])&&(b[1]="+"+b[1]),1===c.length&&(/left|center|right/.test(c[0])?c[1]="center":(c[1]=c[0],c[0]="center")),ba.call(this,K.extend(a,{at:c[0]+b[0]+" "+c[1]+b[1],offset:void 0}))}}}catch(fb){System.out.println("coremenu failed to load jQuery.ui.position -- jQuery version conflict?")}if(!jQuery.ui.menu)try{var k= jQuery,L=!1;k.widget("ui.menu",{version:"1.9.2",defaultElement:"<ul>",delay:300,options:{icons:{submenu:"ui-icon-carat-1-e"},menus:"ul",position:{my:"left top",at:"right top"},role:"menu",blur:null,focus:null,select:null},_create:function(){this.activeMenu=this.element;this.element.uniqueId().addClass("ui-menu ui-widget ui-widget-content ui-corner-all").toggleClass("ui-menu-icons",!!this.element.find(".ui-icon").length).attr({role:this.options.role,tabIndex:0}).bind("click"+this.eventNamespace,k.proxy(function(a){this.options.disabled&& a.preventDefault()},this));this.options.disabled&&this.element.addClass("ui-state-disabled").attr("aria-disabled","true");this._on({"mousedown .ui-menu-item > a":function(a){a.preventDefault()},"click .ui-state-disabled > a":function(a){a.preventDefault()},"click .ui-menu-item:has(a)":function(a){var b=k(a.target).closest(".ui-menu-item");!L&&b.not(".ui-state-disabled").length&&(L=!0,this.select(a),b.has(".ui-menu").length?this.expand(a):this.element.is(":focus")||(this.element.trigger("focus",[!0]), this.active&&1===this.active.parents(".ui-menu").length&&clearTimeout(this.timer)))},"mouseenter .ui-menu-item":function(a){var b=k(a.currentTarget);b.siblings().children(".ui-state-active").removeClass("ui-state-active");this.focus(a,b)},mouseleave:"collapseAll","mouseleave .ui-menu":"collapseAll",focus:function(a,b){var c=this.active||this.element.children(".ui-menu-item").eq(0);b||this.focus(a,c)},blur:function(a){this._delay(function(){k.contains(this.element[0],this.document[0].activeElement)|| this.collapseAll(a)})},keydown:"_keydown"});this.refresh();this._on(this.document,{click:function(a){k(a.target).closest(".ui-menu").length||this.collapseAll(a);L=!1}})},_destroy:function(){this.element.removeAttr("aria-activedescendant").find(".ui-menu").andSelf().removeClass("ui-menu ui-widget ui-widget-content ui-corner-all ui-menu-icons").removeAttr("role").removeAttr("tabIndex").removeAttr("aria-labelledby").removeAttr("aria-expanded").removeAttr("aria-hidden").removeAttr("aria-disabled").removeUniqueId().show(); this.element.find(".ui-menu-item").removeClass("ui-menu-item").removeAttr("role").removeAttr("aria-disabled").children("a").removeUniqueId().removeClass("ui-corner-all ui-state-hover").removeAttr("tabIndex").removeAttr("role").removeAttr("aria-haspopup").children().each(function(){var a=k(this);a.data("ui-menu-submenu-carat")&&a.remove()});this.element.find(".ui-menu-divider").removeClass("ui-menu-divider ui-widget-content")},_keydown:function(a){function b(a){return a.replace(/[\-\[\]{}()*+?.,\\\^$|#\s]/g, "\\$&")}var c,d,e,f,h=!0;switch(a.keyCode){case k.ui.keyCode.PAGE_UP:this.previousPage(a);break;case k.ui.keyCode.PAGE_DOWN:this.nextPage(a);break;case k.ui.keyCode.HOME:this._move("first","first",a);break;case k.ui.keyCode.END:this._move("last","last",a);break;case k.ui.keyCode.UP:this.previous(a);break;case k.ui.keyCode.DOWN:this.next(a);break;case k.ui.keyCode.LEFT:this.collapse(a);break;case k.ui.keyCode.RIGHT:this.active&&!this.active.is(".ui-state-disabled")&&this.expand(a);break;case k.ui.keyCode.ENTER:case k.ui.keyCode.SPACE:this._activate(a); break;case k.ui.keyCode.ESCAPE:this.collapse(a);break;default:h=!1,c=this.previousFilter||"",d=String.fromCharCode(a.keyCode),e=!1,clearTimeout(this.filterTimer),d===c?e=!0:d=c+d,f=RegExp("^"+b(d),"i"),c=this.activeMenu.children(".ui-menu-item").filter(function(){return f.test(k(this).children("a").text())}),c=e&&-1!==c.index(this.active.next())?this.active.nextAll(".ui-menu-item"):c,c.length||(d=String.fromCharCode(a.keyCode),f=RegExp("^"+b(d),"i"),c=this.activeMenu.children(".ui-menu-item").filter(function(){return f.test(k(this).children("a").text())})), c.length?(this.focus(a,c),1<c.length?(this.previousFilter=d,this.filterTimer=this._delay(function(){delete this.previousFilter},1E3)):delete this.previousFilter):delete this.previousFilter}h&&a.preventDefault()},_activate:function(a){this.active.is(".ui-state-disabled")||(this.active.children("a[aria-haspopup='true']").length?this.expand(a):this.select(a))},refresh:function(){var a,b=this.options.icons.submenu;a=this.element.find(this.options.menus);a.filter(":not(.ui-menu)").addClass("ui-menu ui-widget ui-widget-content ui-corner-all").hide().attr({role:this.options.role, "aria-hidden":"true","aria-expanded":"false"}).each(function(){var a=k(this),d=a.prev("a"),e=k("<span>").addClass("ui-menu-icon ui-icon "+b).data("ui-menu-submenu-carat",!0);d.attr("aria-haspopup","true").prepend(e);a.attr("aria-labelledby",d.attr("id"))});a=a.add(this.element);a.children(":not(.ui-menu-item):has(a)").addClass("ui-menu-item").attr("role","presentation").children("a").uniqueId().addClass("ui-corner-all").attr({tabIndex:-1,role:this._itemRole()});a.children(":not(.ui-menu-item)").each(function(){var a= k(this);/[^\-\u00e2\u20ac\u201d\u00e2\u20ac\u201c\s]/.test(a.text())||a.addClass("ui-widget-content ui-menu-divider")});a.children(".ui-state-disabled").attr("aria-disabled","true");this.active&&!k.contains(this.element[0],this.active[0])&&this.blur()},_itemRole:function(){return{menu:"menuitem",listbox:"option"}[this.options.role]},focus:function(a,b){var c;this.blur(a,a&&"focus"===a.type);this._scrollIntoView(b);this.active=b.first();c=this.active.children("a").addClass("ui-state-focus");this.options.role&& this.element.attr("aria-activedescendant",c.attr("id"));this.active.parent().closest(".ui-menu-item").children("a:first").addClass("ui-state-active");a&&"keydown"===a.type?this._close():this.timer=this._delay(function(){this._close()},this.delay);c=b.children(".ui-menu");c.length&&/^mouse/.test(a.type)&&this._startOpening(c);this.activeMenu=b.parent();this._trigger("focus",a,{item:b})},_scrollIntoView:function(a){var b,c,d,e,f,h;this._hasScroll()&&(b=parseFloat(k.css(this.activeMenu[0],"borderTopWidth"))|| 0,c=parseFloat(k.css(this.activeMenu[0],"paddingTop"))||0,d=a.offset().top-this.activeMenu.offset().top-b-c,e=this.activeMenu.scrollTop(),f=this.activeMenu.height(),h=a.height(),0>d?this.activeMenu.scrollTop(e+d):d+h>f&&this.activeMenu.scrollTop(e+d-f+h))},blur:function(a,b){b||clearTimeout(this.timer);this.active&&(this.active.children("a").removeClass("ui-state-focus"),this.active=null,this._trigger("blur",a,{item:this.active}))},_startOpening:function(a){clearTimeout(this.timer);"true"===a.attr("aria-hidden")&& (this.timer=this._delay(function(){this._close();this._open(a)},this.delay))},_open:function(a){var b=k.extend({of:this.active},this.options.position);clearTimeout(this.timer);this.element.find(".ui-menu").not(a.parents(".ui-menu")).hide().attr("aria-hidden","true");a.show().removeAttr("aria-hidden").attr("aria-expanded","true").position(b)},collapseAll:function(a,b){clearTimeout(this.timer);this.timer=this._delay(function(){var c=b?this.element:k(a&&a.target).closest(this.element.find(".ui-menu")); c.length||(c=this.element);this._close(c);this.blur(a);this.activeMenu=c},this.delay)},_close:function(a){a||(a=this.active?this.active.parent():this.element);a.find(".ui-menu").hide().attr("aria-hidden","true").attr("aria-expanded","false").end().find("a.ui-state-active").removeClass("ui-state-active")},collapse:function(a){var b=this.active&&this.active.parent().closest(".ui-menu-item",this.element);b&&b.length&&(this._close(),this.focus(a,b))},expand:function(a){var b=this.active&&this.active.children(".ui-menu ").children(".ui-menu-item").first(); b&&b.length&&(this._open(b.parent()),this._delay(function(){this.focus(a,b)}))},next:function(a){this._move("next","first",a)},previous:function(a){this._move("prev","last",a)},isFirstItem:function(){return this.active&&!this.active.prevAll(".ui-menu-item").length},isLastItem:function(){return this.active&&!this.active.nextAll(".ui-menu-item").length},_move:function(a,b,c){var d;this.active&&("first"===a||"last"===a?d=this.active["first"===a?"prevAll":"nextAll"](".ui-menu-item").eq(-1):d=this.active[a+ "All"](".ui-menu-item").eq(0));if(!d||!d.length||!this.active)d=this.activeMenu.children(".ui-menu-item")[b]();this.focus(c,d)},nextPage:function(a){var b,c,d;this.active?this.isLastItem()||(this._hasScroll()?(c=this.active.offset().top,d=this.element.height(),this.active.nextAll(".ui-menu-item").each(function(){return b=k(this),0>b.offset().top-c-d}),this.focus(a,b)):this.focus(a,this.activeMenu.children(".ui-menu-item")[this.active?"last":"first"]())):this.next(a)},previousPage:function(a){var b, c,d;this.active?this.isFirstItem()||(this._hasScroll()?(c=this.active.offset().top,d=this.element.height(),this.active.prevAll(".ui-menu-item").each(function(){return b=k(this),0<b.offset().top-c+d}),this.focus(a,b)):this.focus(a,this.activeMenu.children(".ui-menu-item").first())):this.next(a)},_hasScroll:function(){return this.element.outerHeight()<this.element.prop("scrollHeight")},select:function(a){this.active=this.active||k(a.target).closest(".ui-menu-item");var b={item:this.active};this.active.has(".ui-menu").length|| this.collapseAll(a,!0);this._trigger("select",a,b)}})}catch(gb){System.out.println("JSmolMenu failed to load jQuery.ui.menu -- jQuery version conflict?")}var m=Jmol.Swing;m.menuInitialized||(m.menuCounter=0,m.menuInitialized=1,m.__getMenuStyle=function(a){return"\t.jmolPopupMenu{font-family:Arial,sans-serif;font-size:11px;position:absolute;z-index:"+Jmol._getZ(a,"menu")+'}\t.jmolPopupMenu,.jmolPopupMenu .ui-corner-all{border-radius:5px}\t.jmolPopupMenu,.jmolPopupMenu .ui-widget-content{border:1px solid #a6c9e2;background-color:#fcfdfd;color:#222}\t.jmolPopupMenu a{color:#222;font-size:10px;}\t.jmolPopupMenu input[type="checkbox"]{vertical-align:middle;}\t.jmolPopupMenu,.jmolPopupMenu .ui-menu{list-style:none;padding:2px;margin:0;display:block;outline:none;box-shadow:1px 1px 5px rgba(50,50,50,0.75)}\t.jmolPopupMenu .ui-menu{margin-top:-3px;position:absolute}\t.jmolPopupMenu .ui-menu-item{cursor:pointer;margin:0 2ex 0 0;padding:0;width:100%}\t.jmolPopupMenu .ui-menu-divider{margin:3px 1px;height:0;font-size:0;line-height:0;border-width:1px 0 0 0}\t.jmolPopupMenu .ui-menu-item a{text-decoration:none;display:block;padding:0.05em 0.4em;white-space:nowrap;border:1px solid transparent}\t.jmolPopupMenu .ui-menu-icons{position:relative}\t.jmolPopupMenu .ui-menu-icons .ui-menu-item a{position:relative;padding-left:2em}\t.jmolPopupMenu .ui-icon{display:block;text-indent:-99999px;overflow:hidden;background-repeat:no-repeat;position:absolute;top:.2em;left:.2em}\t.jmolPopupMenu .ui-menu-icon{position:static;float:right}\t.jmolPopupMenu 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a:hover{background-color:transparent!important;border-color:transparent!important}\t.jmolPopupMenu .ui-state-disabled .ui-icon{filter:Alpha(Opacity=35)}'}, m.setMenu=function(a){m.__getMenuStyle&&Jmol.$after("head","<style>"+m.__getMenuStyle(a.applet)+"</style>");m.__getStyle=null;a.tainted=!0;a.popupMenu=a;a.id="top";a.id=m.getMenuID(a);a.applet._menus||(a.applet._menus={});a.applet._menus[a.name]=a;Jmol.$after("body",'<ul id="'+a.id+'" class="jmolPopupMenu"></ul>');a.setContainer(Jmol.$("#"+a.id))},m.showMenu=function(a,b,c){Jmol._showMenuCallback&&Jmol._showMenuCallback(a,b,c);a.tainted&&(a.container.html(a.toHTML()),a.tainted=!1,m.bindMenuActionCommands(a, !0));a.setPosition();a.container.hide().menu().menu("refresh").show();a.visible=!0;a.timestamp=System.currentTimeMillis();a.dragBind(!0);a.container.unbind("clickoutjsmol");a.container.bind("clickoutjsmol 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a.id,function(){a.itemListener?(a.selected=a.btnType==javajs.swing.JMenuItem.TYPE_CHECKBOX?Jmol.$prop(a.id+"-cb","checked"):!0,m.hideMenus(a.applet),a.itemListener.itemStateChanged({getSource:function(){return a}})):a.actionListener&&(m.hideMenus(a.applet),a.actionListener.actionPerformed({getSource:function(){return a},getActionCommand:function(){return a.actionCommand}}))})});u("javajs.api");O(javajs.api,"GenericMenuInterface");u("JSV.api");x(["javajs.api.GenericMenuInterface"],"JSV.api.JSVPopupMenu", null,function(){O(JSV.api,"JSVPopupMenu",javajs.api.GenericMenuInterface)});u("JSV.js2d");x(["JSV.popup.JSVGenericPopup"],"JSV.js2d.JsPopup",["JSV.popup.JSVPopupResourceBundle","J.popup.JSSwingPopupHelper"],function(){c$=N(JSV.js2d,"JsPopup",JSV.popup.JSVGenericPopup);B(c$,function(){C(this,JSV.js2d.JsPopup,[]);this.helper=new J.popup.JSSwingPopupHelper(this)});l(c$,"jpiInitialize",function(a,b){var c=new 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