From: Jim Procter
')
+ $('#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/help/html/colourSchemes/abovePID.html b/help/html/colourSchemes/abovePID.html
index 614764b..8adacc9 100755
--- a/help/html/colourSchemes/abovePID.html
+++ b/help/html/colourSchemes/abovePID.html
@@ -35,10 +35,10 @@ td {
Colouring above a percentage identity threshold
'+JSON.stringify(JSON.parse(data),null,4)+'
Selecting this option causes the colour scheme to be applied to - only those residues that occur in that column more than a certain - percentage of the time. For instance selecting the threshold to be - 100 will only colour those columns with 100 % identity. This - threshold option can be applied to the Zappo, Taylor, Hydrophobicity - and User colour schemes.
+ only those residues that occur in that column at least a certain + percentage of the time. For instance, selecting the threshold to be + 100 will only colour those columns with 100% identity, and selecting 50 will shade residues appearing in least 50% of the rows (or sequences) in each column. +The percentage calculation may include or exclude gaps in the column, depending on the option selected for the consensus calculation.
+With a threshold of 0, colouring is unchanged.