//get list of IDs of selected sequences -public String getSelectedSequences() - -// list of IDs of selected sequences terminated by sep or, if sep is null, '¬' (¬) -public String getSelectedSequences(sep) - -// get selected sequences as alignment as format with or without start-end suffix -public String getSelectedSequencesAsAlignment(String format, boolean suffix) - -// get selected sequences as alignment from given view as format with or without start-end suffix -public String getSelectedSequencesAsAlignmentFrom(AlignFrame alf, String format, boolean suffix) - -// get alignment as format -public String getAlignment(String format) - -// get alignment as format with jalview -// start-end sequence suffix appended -public String getAlignment(String format, String suffix) - -// get alignment displayed in alf as format -public String getAlignmentFrom(AlignFrame alf, String format) - -// get alignment displayed in alf as format -// with jalview start-end sequence suffix appended -public String getAlignmentFrom(AlignFrame alf, String format, String suffix) - -// add the given features or annotation to the current alignment -public void loadAnnotation(String annotation) - -// add the given features or annotation to the given alignment view -public void loadAnnotationFrom(AlignFrame alf, String annotation) - -// get the sequence features in the given format (Jalview or GFF) -public String getFeatures(String format) - -// get the sequence features in alf in the given format (Jalview or GFF) -public String getFeaturesFrom(AlignFrame alf, String format) - -// get current alignment's annotation as an annotation file -public String getAnnotation() - -// get alignment view alf's annotation as an annotation file -public String getAnnotationFrom(AlignFrame alf) - -// create a new view and return the alignFrame instance -public AlignFrame newView() - -// create a new view named name and return the alignFrame instance -public AlignFrame newView(String name) - -// create a new view on alf and return the alignFrame instance -public AlignFrame newViewFrom(AlignFrame alf) - -// create a new view named name on alf -// and return the alignFrame instance -public AlignFrame newViewFrom(AlignFrame alf, String name) - -// load a new alignment -public AlignFrame loadAlignment(String text, String title) - -// return separator separated list of feature groups -// on the current alignment -public String getFeatureGroups() - -// return separator separated list of feature groups on alf -public String getFeatureGroupsOn(AlignFrame alf) - -// return separator separated list of feature groups -// either visible or hidden -public String getFeatureGroupsOfState(boolean state) - -// return separator separated list of feature groups -// either visible or hidden on alf -public String getFeatureGroupsOfStateOn(AlignFrame alf, boolean state) - -// set the separator separated list of feature groups as -// visible or hidden on the current alignment -public void setFeatureGroupState(String groupList, boolean state) - -// set the separator separated list of feature groups -// as visible or hidden on alf -public void setFeatureGroupStateOn(AlignFrame alf, String groupList, boolean state) - -// helper functions - -// convert list to a separator separated array -public String arrayToSeparatorList(String[] list) - -// get a string array from a list -public String[] separatorListToArray(String list) - -// get the current separator -public String getSeparator() - -// set the current separator -public void setSeparator(String) - -//// JalviewLite global state methods and fields - -// return the build date as a string -public static String getBuildDate() - -// return the JalviewLite version as a string -public static String getVersion() - -// debug flag - controls output to standard out -public static boolean debug - -

//get list of IDs of selected sequences +public String getSelectedSequences() + +// list of IDs of selected sequences terminated by sep or, if sep is null, '¬' (¬) +public String getSelectedSequences(sep) + +// get list of selected sequences from specific alignFrame. (2.7) +public String getSelectedSequencesFrom(AlignFrame alf) +public String getSelectedSequencesFrom(AlignFrame alf, String sep) + +// highlight a position in a specific sequence or a column in an alignment containing it +// provide ID sequence to highlight, integer (range highlighting will be supported in future versions) +// and flag indicating if position is an alignment column or given according to sequence numbering (2.7) +public void highlight(String sequenceId, String position, String alignedPosition) +public void highlightIn(AlignFrame alf, String sequenceId, String position, String alignedPosition) + + +// select regions of the currrent alignment frame using a list of sequence ids and a list of +// column numbers and ranges (with minus sign indicating start-end) (separated by default separator) (2.7) +public void select(String sequenceIds, String columns) +public void select(String sequenceIds, String columns, String sep) +public void selectIn(AlignFrame alf, String sequenceIds, String columns) +public void selectIn(AlignFrame alf, String sequenceIds, String columns, String sep) + + +// get selected sequences as alignment as format with or without start-end suffix +public String getSelectedSequencesAsAlignment(String format, boolean suffix) + +// get selected sequences as alignment from given view as format with or without start-end suffix +public String getSelectedSequencesAsAlignmentFrom(AlignFrame alf, String format, boolean suffix) + +// get a separator separated list of sequence IDs reflecting the order of the current alignment (2.7) +public String getAlignmentOrder(); +public String getAlignmentOrderFrom(AlignFrame alf); +public String getAlignmentOrderFrom(AlignFrame alf, String sep); + +// re-order the current alignment using the given list of sequence IDs separated by sep +// undoName - is string to use when referring to ordering action in undo buffer +// returns 'true' if alignment was actually reordered. empty string if alignment did not contain sequences. +// (v2.7) +public String orderBy(String order, String undoName) +public String orderBy(String order, String undoName, String sep) +String orderAlignmentBy(AlignFrame alf, String order, String undoName, String sep) + + +// get alignment as format +public String getAlignment(String format) + +// get alignment as format with jalview +// start-end sequence suffix appended +public String getAlignment(String format, String suffix) + +// get alignment displayed in alf as format +public String getAlignmentFrom(AlignFrame alf, String format) + +// get alignment displayed in alf as format +// with jalview start-end sequence suffix appended +public String getAlignmentFrom(AlignFrame alf, String format, String suffix) + +// add the given features or annotation to the current alignment +public void loadAnnotation(String annotation) + +// add the given features or annotation to the given alignment view +public void loadAnnotationFrom(AlignFrame alf, String annotation) + +// get the sequence features in the given format (Jalview or GFF) +public String getFeatures(String format) + +// get the sequence features in alf in the given format (Jalview or GFF) +public String getFeaturesFrom(AlignFrame alf, String format) + +// get current alignment's annotation as an annotation file +public String getAnnotation() + +// get alignment view alf's annotation as an annotation file +public String getAnnotationFrom(AlignFrame alf) + +// create a new view and return the alignFrame instance +public AlignFrame newView() + +// create a new view named name and return the alignFrame instance +public AlignFrame newView(String name) + +// create a new view on alf and return the alignFrame instance +public AlignFrame newViewFrom(AlignFrame alf) + +// create a new view named name on alf +// and return the alignFrame instance +public AlignFrame newViewFrom(AlignFrame alf, String name) + +// load a new alignment +public AlignFrame loadAlignment(String text, String title) + + +// register a javascript function to handle any alignment mouseover events +// listener is name of javascript function which will be called +// with arguments [jalview.appletgui.AlignFrame,String(sequence id), +// String(column in alignment), String(position in sequence)] +// (v2.7) +public void setMouseoverListener(String listener) + +// register a javascript function to handle mouseover events for specific alignframe +// (v2.7) +public void setMouseoverListener(AlignFrame af, String listener) + +// register a javascript function to handle alignment selection events. +// Events are generated when the user completes a selection event, or when +// the user deselects all selected regions. +// listener is name of javascript function that will be called with arguments +// [jalview.appletgui.AlignFrame, String(sequence set id), +// String(separator separated list of sequences which were selected), +// String(separator separated list of column ranges)] +// (v2.7) +public void setSelectionListener(String listener) + +// register a selection listener for a specific alignment frame +// (v2.7) +public void setSelectionListener(AlignFrame af, String listener) + +// register a javascript function to handle events normally routed +// to a Jmol structure viewer. +// listener is a javascript function called with several different types +// of arguments, dependent on the type of structure callback event. +// See jalview.javascript.MouseOverStructureListener for full details or +// the embedded Jmol example. +// modelSet - is a separator separated list of PDB file URIs that this viewer is handling (where position in list equals model number in Jmol). +// (v2.7) +public void setStructureListener(String listener, String modelSet) + +// remove any callback using the given listener function and associated with +// the given alignFrame (or null for all callbacks) (v2.7) +public void removeJavascriptListener(AlignFrame af, String listener) + +// send a mouseover message to all the alignment windows associated with the +// given residue in the pdbfile (v2.7) +public void mouseOverStructure(String pdbResNum, String chain, String pdbfile) + +// bind a pdb file to a sequence in the given alignFrame - this will be searched +// for sequences matching sequenceId. The PDB file in pdbFile is either the contents +// of a PDB file or a URI that can be used to retrieve the file, and the pdbEntryString +// is the user friendly name (or PDBID) shown in jalview's user interface. +// returns true if binding was as success (v2.7) +public boolean addPdbFile(AlignFrame alFrame, + String sequenceId, String pdbEntryString, String pdbFile) + +// adjust horizontal/vertical scroll in alf to the make +// the given location the top left hand corner for given current view (v2.7) +public void scrollViewToIn(AlignFrame alf, String topRow, String leftHandColumn) + + +// return separator separated list of feature groups +// on the current alignment +public String getFeatureGroups() + +// return separator separated list of feature groups on alf +public String getFeatureGroupsOn(AlignFrame alf) + +// return separator separated list of feature groups +// either visible or hidden +public String getFeatureGroupsOfState(boolean state) + +// return separator separated list of feature groups +// either visible or hidden on alf +public String getFeatureGroupsOfStateOn(AlignFrame alf, boolean state) + +// set the separator separated list of feature groups as +// visible or hidden on the current alignment +public void setFeatureGroupState(String groupList, boolean state) + +// set the separator separated list of feature groups +// as visible or hidden on alf +public void setFeatureGroupStateOn(AlignFrame alf, String groupList, boolean state) + +// helper functions + +// Asynchronously retrieve next chunk of a large packet of data made available +// for a JalviewLite event handler, or the empty string if no more data is available. +// messageclass and viewId are keys used to retrieve a specific message related +// to an event. +// Use this in a javascript timer or GUI update thread to retrieve data without +// blocking the JalviewLite applet. DO NOT USE IN THE CALLBACK THAT HANDLED THE EVENT +// (v2.7) +public String getJsMessage(String messageclass, String viewId) + + +// convert list to a separator separated array +public String arrayToSeparatorList(String[] list) + +// get a string array from a list +public String[] separatorListToArray(String list) + +// get the current separator +public String getSeparator() + +// set the current separator +public void setSeparator(String) + +//// JalviewLite global state methods and fields + +// return the build date as a string +public static String getBuildDate() + +// return the JalviewLite version as a string +public static String getVersion() + +// debug flag - controls output to standard out +public static boolean debug + +

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+c.fn["inner"+b]=function(){return this[0]?parseFloat(c.css(this[0],d,"padding")):null};c.fn["outer"+b]=function(e){return this[0]?parseFloat(c.css(this[0],d,e?"margin":"border")):null};c.fn[d]=function(e){var f=this[0];if(!f)return e==null?null:this;if(c.isFunction(e))return this.each(function(l){var k=c(this);k[d](e.call(this,l,k[d]()))});if(c.isWindow(f))return f.document.compatMode==="CSS1Compat"&&f.document.documentElement["client"+b]||f.document.body["client"+b];else if(f.nodeType===9)return Math.max(f.documentElement["client"+ +b],f.body["scroll"+b],f.documentElement["scroll"+b],f.body["offset"+b],f.documentElement["offset"+b]);else if(e===B){f=c.css(f,d);var h=parseFloat(f);return c.isNaN(h)?f:h}else return this.css(d,typeof e==="string"?e:e+"px")}})})(window); diff --git a/examples/javascript/jquery.blockUI.js b/examples/javascript/jquery.blockUI.js new file mode 100644 index 0000000..502a2e8 --- /dev/null +++ b/examples/javascript/jquery.blockUI.js @@ -0,0 +1,490 @@ +ï»¿/*! + * jQuery blockUI plugin + * Version 2.37 (29-JAN-2011) + * @requires jQuery v1.2.3 or later + * + * Examples at: http://malsup.com/jquery/block/ + * Copyright (c) 2007-2010 M. Alsup + * Dual licensed under the MIT and GPL licenses: + * http://www.opensource.org/licenses/mit-license.php + * http://www.gnu.org/licenses/gpl.html + * + * Thanks to Amir-Hossein Sobhi for some excellent contributions! + */ + +;(function($) { + +if (/1\.(0|1|2)\.(0|1|2)/.test($.fn.jquery) || /^1.1/.test($.fn.jquery)) { + alert('blockUI requires jQuery v1.2.3 or later! You are using v' + $.fn.jquery); + return; +} + +$.fn._fadeIn = $.fn.fadeIn; + +var noOp = function() {}; + +// this bit is to ensure we don't call setExpression when we shouldn't (with extra muscle to handle +// retarded userAgent strings on Vista) +var mode = document.documentMode || 0; +var setExpr = $.browser.msie && (($.browser.version < 8 && !mode) || mode < 8); +var ie6 = $.browser.msie && /MSIE 6.0/.test(navigator.userAgent) && !mode; + +// global $ methods for blocking/unblocking the entire page +$.blockUI = function(opts) { install(window, opts); }; +$.unblockUI = function(opts) { remove(window, opts); }; + +// convenience method for quick growl-like notifications (http://www.google.com/search?q=growl) +$.growlUI = function(title, message, timeout, onClose) { + var $m = $('

'); + if (title) $m.append('

'+title+'

'); + if (message) $m.append('

'+message+'

'); + if (timeout == undefined) timeout = 3000; + $.blockUI({ + message: $m, fadeIn: 700, fadeOut: 1000, centerY: false, + timeout: timeout, showOverlay: false, + onUnblock: onClose, + css: $.blockUI.defaults.growlCSS + }); +}; + +// plugin method for blocking element content +$.fn.block = function(opts) { + return this.unblock({ fadeOut: 0 }).each(function() { + if ($.css(this,'position') == 'static') + this.style.position = 'relative'; + if ($.browser.msie) + this.style.zoom = 1; // force 'hasLayout' + install(this, opts); + }); +}; + +// plugin method for unblocking element content +$.fn.unblock = function(opts) { + return this.each(function() { + remove(this, opts); + }); +}; + +$.blockUI.version = 2.37; // 2nd generation blocking at no extra cost! + +// override these in your code to change the default behavior and style +$.blockUI.defaults = { + // message displayed when blocking (use null for no message) + message: '

Please wait...

', + + title: null, // title string; only used when theme == true + draggable: true, // only used when theme == true (requires jquery-ui.js to be loaded) + + theme: false, // set to true to use with jQuery UI themes + + // styles for the message when blocking; if you wish to disable + // these and use an external stylesheet then do this in your code: + // $.blockUI.defaults.css = {}; + css: { + padding: 0, + margin: 0, + width: '30%', + top: '40%', + left: '35%', + textAlign: 'center', + color: '#000', + border: '3px solid #aaa', + backgroundColor:'#fff', + cursor: 'wait' + }, + + // minimal style set used when themes are used + themedCSS: { + width: '30%', + top: '40%', + left: '35%' + }, + + // styles for the overlay + overlayCSS: { + backgroundColor: '#000', + opacity: 0.6, + cursor: 'wait' + }, + + // styles applied when using $.growlUI + growlCSS: { + width: '350px', + top: '10px', + left: '', + right: '10px', + border: 'none', + padding: '5px', + opacity: 0.6, + cursor: 'default', + color: '#fff', + backgroundColor: '#000', + '-webkit-border-radius': '10px', + '-moz-border-radius': '10px', + 'border-radius': '10px' + }, + + // IE issues: 'about:blank' fails on HTTPS and javascript:false is s-l-o-w + // (hat tip to Jorge H. N. de Vasconcelos) + iframeSrc: /^https/i.test(window.location.href || '') ? 'javascript:false' : 'about:blank', + + // force usage of iframe in non-IE browsers (handy for blocking applets) + forceIframe: false, + + // z-index for the blocking overlay + baseZ: 1000, + + // set these to true to have the message automatically centered + centerX: true, // <-- only effects element blocking (page block controlled via css above) + centerY: true, + + // allow body element to be stetched in ie6; this makes blocking look better + // on "short" pages. disable if you wish to prevent changes to the body height + allowBodyStretch: true, + + // enable if you want key and mouse events to be disabled for content that is blocked + bindEvents: true, + + // be default blockUI will supress tab navigation from leaving blocking content + // (if bindEvents is true) + constrainTabKey: true, + + // fadeIn time in millis; set to 0 to disable fadeIn on block + fadeIn: 200, + + // fadeOut time in millis; set to 0 to disable fadeOut on unblock + fadeOut: 400, + + // time in millis to wait before auto-unblocking; set to 0 to disable auto-unblock + timeout: 0, + + // disable if you don't want to show the overlay + showOverlay: true, + + // if true, focus will be placed in the first available input field when + // page blocking + focusInput: true, + + // suppresses the use of overlay styles on FF/Linux (due to performance issues with opacity) + applyPlatformOpacityRules: true, + + // callback method invoked when fadeIn has completed and blocking message is visible + onBlock: null, + + // callback method invoked when unblocking has completed; the callback is + // passed the element that has been unblocked (which is the window object for page + // blocks) and the options that were passed to the unblock call: + // onUnblock(element, options) + onUnblock: null, + + // don't ask; if you really must know: http://groups.google.com/group/jquery-en/browse_thread/thread/36640a8730503595/2f6a79a77a78e493#2f6a79a77a78e493 + quirksmodeOffsetHack: 4, + + // class name of the message block + blockMsgClass: 'blockMsg' +}; + +// private data and functions follow... + +var pageBlock = null; +var pageBlockEls = []; + +function install(el, opts) { + var full = (el == window); + var msg = opts && opts.message !== undefined ? opts.message : undefined; + opts = $.extend({}, $.blockUI.defaults, opts || {}); + opts.overlayCSS = $.extend({}, $.blockUI.defaults.overlayCSS, opts.overlayCSS || {}); + var css = $.extend({}, $.blockUI.defaults.css, opts.css || {}); + var themedCSS = $.extend({}, $.blockUI.defaults.themedCSS, opts.themedCSS || {}); + msg = msg === undefined ? opts.message : msg; + + // remove the current block (if there is one) + if (full && pageBlock) + remove(window, {fadeOut:0}); + + // if an existing element is being used as the blocking content then we capture + // its current place in the DOM (and current display style) so we can restore + // it when we unblock + if (msg && typeof msg != 'string' && (msg.parentNode || msg.jquery)) { + var node = msg.jquery ? msg[0] : msg; + var data = {}; + $(el).data('blockUI.history', data); + data.el = node; + data.parent = node.parentNode; + data.display = node.style.display; + data.position = node.style.position; + if (data.parent) + data.parent.removeChild(node); + } + + var z = opts.baseZ; + + // blockUI uses 3 layers for blocking, for simplicity they are all used on every platform; + // layer1 is the iframe layer which is used to supress bleed through of underlying content + // layer2 is the overlay layer which has opacity and a wait cursor (by default) + // layer3 is the message content that is displayed while blocking + + var lyr1 = ($.browser.msie || opts.forceIframe) + ? $('') + : $(''); + var lyr2 = $(''); + + var lyr3, s; + if (opts.theme && full) { + s = ''; + } + else if (opts.theme) { + s = ''; + } + else if (full) { + s = ''; + } + else { + s = ''; + } + lyr3 = $(s); + + // if we have a message, style it + if (msg) { + if (opts.theme) { + lyr3.css(themedCSS); + lyr3.addClass('ui-widget-content'); + } + else + lyr3.css(css); + } + + // style the overlay + if (!opts.applyPlatformOpacityRules || !($.browser.mozilla && /Linux/.test(navigator.platform))) + lyr2.css(opts.overlayCSS); + lyr2.css('position', full ? 'fixed' : 'absolute'); + + // make iframe layer transparent in IE + if ($.browser.msie || opts.forceIframe) + lyr1.css('opacity',0.0); + + //$([lyr1[0],lyr2[0],lyr3[0]]).appendTo(full ? 'body' : el); + var layers = [lyr1,lyr2,lyr3], $par = full ? $('body') : $(el); + $.each(layers, function() { + this.appendTo($par); + }); + + if (opts.theme && opts.draggable && $.fn.draggable) { + lyr3.draggable({ + handle: '.ui-dialog-titlebar', + cancel: 'li' + }); + } + + // ie7 must use absolute positioning in quirks mode and to account for activex issues (when scrolling) + var expr = setExpr && (!$.boxModel || $('object,embed', full ? null : el).length > 0); + if (ie6 || expr) { + // give body 100% height + if (full && opts.allowBodyStretch && $.boxModel) + $('html,body').css('height','100%'); + + // fix ie6 issue when blocked element has a border width + if ((ie6 || !$.boxModel) && !full) { + var t = sz(el,'borderTopWidth'), l = sz(el,'borderLeftWidth'); + var fixT = t ? '(0 - '+t+')' : 0; + var fixL = l ? '(0 - '+l+')' : 0; + } + + // simulate fixed position + $.each([lyr1,lyr2,lyr3], function(i,o) { + var s = o[0].style; + s.position = 'absolute'; + if (i < 2) { + full ? s.setExpression('height','Math.max(document.body.scrollHeight, document.body.offsetHeight) - (jQuery.boxModel?0:'+opts.quirksmodeOffsetHack+') + "px"') + : s.setExpression('height','this.parentNode.offsetHeight + "px"'); + full ? s.setExpression('width','jQuery.boxModel && document.documentElement.clientWidth || document.body.clientWidth + "px"') + : s.setExpression('width','this.parentNode.offsetWidth + "px"'); + if (fixL) s.setExpression('left', fixL); + if (fixT) s.setExpression('top', fixT); + } + else if (opts.centerY) { + if (full) s.setExpression('top','(document.documentElement.clientHeight || document.body.clientHeight) / 2 - (this.offsetHeight / 2) + (blah = document.documentElement.scrollTop ? document.documentElement.scrollTop : document.body.scrollTop) + "px"'); + s.marginTop = 0; + } + else if (!opts.centerY && full) { + var top = (opts.css && opts.css.top) ? parseInt(opts.css.top) : 0; + var expression = '((document.documentElement.scrollTop ? document.documentElement.scrollTop : document.body.scrollTop) + '+top+') + "px"'; + s.setExpression('top',expression); + } + }); + } + + // show the message + if (msg) { + if (opts.theme) + lyr3.find('.ui-widget-content').append(msg); + else + lyr3.append(msg); + if (msg.jquery || msg.nodeType) + $(msg).show(); + } + + if (($.browser.msie || opts.forceIframe) && opts.showOverlay) + lyr1.show(); // opacity is zero + if (opts.fadeIn) { + var cb = opts.onBlock ? opts.onBlock : noOp; + var cb1 = (opts.showOverlay && !msg) ? cb : noOp; + var cb2 = msg ? cb : noOp; + if (opts.showOverlay) + lyr2._fadeIn(opts.fadeIn, cb1); + if (msg) + lyr3._fadeIn(opts.fadeIn, cb2); + } + else { + if (opts.showOverlay) + lyr2.show(); + if (msg) + lyr3.show(); + if (opts.onBlock) + opts.onBlock(); + } + + // bind key and mouse events + bind(1, el, opts); + + if (full) { + pageBlock = lyr3[0]; + pageBlockEls = $(':input:enabled:visible',pageBlock); + if (opts.focusInput) + setTimeout(focus, 20); + } + else + center(lyr3[0], opts.centerX, opts.centerY); + + if (opts.timeout) { + // auto-unblock + var to = setTimeout(function() { + full ? $.unblockUI(opts) : $(el).unblock(opts); + }, opts.timeout); + $(el).data('blockUI.timeout', to); + } +}; + +// remove the block +function remove(el, opts) { + var full = (el == window); + var $el = $(el); + var data = $el.data('blockUI.history'); + var to = $el.data('blockUI.timeout'); + if (to) { + clearTimeout(to); + $el.removeData('blockUI.timeout'); + } + opts = $.extend({}, $.blockUI.defaults, opts || {}); + bind(0, el, opts); // unbind events + + var els; + if (full) // crazy selector to handle odd field errors in ie6/7 + els = $('body').children().filter('.blockUI').add('body > .blockUI'); + else + els = $('.blockUI', el); + + if (full) + pageBlock = pageBlockEls = null; + + if (opts.fadeOut) { + els.fadeOut(opts.fadeOut); + setTimeout(function() { reset(els,data,opts,el); }, opts.fadeOut); + } + else + reset(els, data, opts, el); +}; + +// move blocking element back into the DOM where it started +function reset(els,data,opts,el) { + els.each(function(i,o) { + // remove via DOM calls so we don't lose event handlers + if (this.parentNode) + this.parentNode.removeChild(this); + }); + + if (data && data.el) { + data.el.style.display = data.display; + data.el.style.position = data.position; + if (data.parent) + data.parent.appendChild(data.el); + $(el).removeData('blockUI.history'); + } + + if (typeof opts.onUnblock == 'function') + opts.onUnblock(el,opts); +}; + +// bind/unbind the handler +function bind(b, el, opts) { + var full = el == window, $el = $(el); + + // don't bother unbinding if there is nothing to unbind + if (!b && (full && !pageBlock || !full && !$el.data('blockUI.isBlocked'))) + return; + if (!full) + $el.data('blockUI.isBlocked', b); + + // don't bind events when overlay is not in use or if bindEvents is false + if (!opts.bindEvents || (b && !opts.showOverlay)) + return; + + // bind anchors and inputs for mouse and key events + var events = 'mousedown mouseup keydown keypress'; + b ? $(document).bind(events, opts, handler) : $(document).unbind(events, handler); + +// former impl... +// var $e = $('a,:input'); +// b ? $e.bind(events, opts, handler) : $e.unbind(events, handler); +}; + +// event handler to suppress keyboard/mouse events when blocking +function handler(e) { + // allow tab navigation (conditionally) + if (e.keyCode && e.keyCode == 9) { + if (pageBlock && e.data.constrainTabKey) { + var els = pageBlockEls; + var fwd = !e.shiftKey && e.target === els[els.length-1]; + var back = e.shiftKey && e.target === els[0]; + if (fwd || back) { + setTimeout(function(){focus(back)},10); + return false; + } + } + } + var opts = e.data; + // allow events within the message content + if ($(e.target).parents('div.' + opts.blockMsgClass).length > 0) + return true; + + // allow events for content that is not being blocked + return $(e.target).parents().children().filter('div.blockUI').length == 0; +}; + +function focus(back) { + if (!pageBlockEls) + return; + var e = pageBlockEls[back===true ? pageBlockEls.length-1 : 0]; + if (e) + e.focus(); +}; + +function center(el, x, y) { + var p = el.parentNode, s = el.style; + var l = ((p.offsetWidth - el.offsetWidth)/2) - sz(p,'borderLeftWidth'); + var t = ((p.offsetHeight - el.offsetHeight)/2) - sz(p,'borderTopWidth'); + if (x) s.left = l > 0 ? (l+'px') : '0'; + if (y) s.top = t > 0 ? (t+'px') : '0'; +}; + +function sz(el, p) { + return parseInt($.css(el,p))||0; +}; + +})(jQuery); diff --git a/examples/javascript/jquery.timer.js b/examples/javascript/jquery.timer.js new file mode 100644 index 0000000..fe9afe2 --- /dev/null +++ b/examples/javascript/jquery.timer.js @@ -0,0 +1,75 @@ +ï»¿/* + * + * jQuery Timer plugin v0.1 + * Matt Schmidt [http://www.mattptr.net] + * + * Licensed under the BSD License: + * http://mattptr.net/license/license.txt + * + */ + + jQuery.timer = function (interval, callback) + { + /** + * + * timer() provides a cleaner way to handle intervals + * + * @usage + * $.timer(interval, callback); + * + * + * @example + * $.timer(1000, function (timer) { + * alert("hello"); + * timer.stop(); + * }); + * @desc Show an alert box after 1 second and stop + * + * @example + * var second = false; + * $.timer(1000, function (timer) { + * if (!second) { + * alert('First time!'); + * second = true; + * timer.reset(3000); + * } + * else { + * alert('Second time'); + * timer.stop(); + * } + * }); + * @desc Show an alert box after 1 second and show another after 3 seconds + * + * + */ + + var interval = interval || 100; + + if (!callback) + return false; + + _timer = function (interval, callback) { + this.stop = function () { + clearInterval(self.id); + }; + + this.internalCallback = function () { + callback(self); + }; + + this.reset = function (val) { + if (self.id) + clearInterval(self.id); + + var val = val || 100; + this.id = setInterval(this.internalCallback, val); + }; + + this.interval = interval; + this.id = setInterval(this.internalCallback, this.interval); + + var self = this; + }; + + return new _timer(interval, callback); + }; \ No newline at end of file diff --git a/examples/javascript/jshashtable-2.1.js b/examples/javascript/jshashtable-2.1.js new file mode 100644 index 0000000..3b93622 --- /dev/null +++ b/examples/javascript/jshashtable-2.1.js @@ -0,0 +1,16 @@ +/** + * Copyright 2010 Tim Down. + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ +var Hashtable=(function(){var p="function";var n=(typeof Array.prototype.splice==p)?function(s,r){s.splice(r,1)}:function(u,t){var s,v,r;if(t===u.length-1){u.length=t}else{s=u.slice(t+1);u.length=t;for(v=0,r=s.length;v + Opening JalviewLite from Javascript + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/examples/jmol/Jmol.js b/examples/jmol/Jmol.js new file mode 100644 index 0000000..6962276 --- /dev/null +++ b/examples/jmol/Jmol.js @@ -0,0 +1,1705 @@ +/* Jmol 12.0 script library Jmol.js 9:48 PM 1/31/2011 Bob Hanson + + checkbox heirarchy -- see http://chemapps.stolaf.edu/jmol/docs/examples-11/check.htm + + based on: + * + * Copyright (C) 2004-2005 Miguel, Jmol Development, www.jmol.org + * + * Contact: hansonr@stolaf.edu + * + * This library is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public + * License as published by the Free Software Foundation; either + * version 2.1 of the License, or (at your option) any later version. + * + * This library 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 + * Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public + * License along with this library; if not, write to the Free Software + * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA + * 02111-1307 USA. + */ + +// for documentation see www.jmol.org/jslibrary + +try{if(typeof(_jmol)!="undefined")exit() + +// place "?NOAPPLET" on your command line to check applet control action with a textarea +// place "?JMOLJAR=xxxxx" to use a specific jar file + +// bob hanson -- jmolResize(w,h) -- resizes absolutely or by percent (w or h 0.5 means 50%) +// angel herraez -- update of jmolResize(w,h,targetSuffix) so it is not tied to first applet +// bob hanson -- jmolEvaluate -- evaluates molecular math 8:37 AM 2/23/2007 +// bob hanson -- jmolScriptMessage -- returns all "scriptStatus" messages 8:37 AM 2/23/2007 +// bob hanson -- jmolScriptEcho -- returns all "scriptEcho" messages 8:37 AM 2/23/2007 +// bob hanson -- jmolScriptWait -- 11:31 AM 5/2/2006 +// bob hanson -- remove trailing separatorHTML in radio groups -- 12:18 PM 5/6/2006 +// bob hanson -- adds support for dynamic DOM script nodes 7:04 AM 5/19/2006 +// bob hanson -- adds try/catch for wiki - multiple code passes 7:05 AM 5/19/2006 +// bob hanson -- auto-initiates to defaultdir/defaultjar -- change as desired. +// bob hanson -- adding save/restore orientation w/ and w/o delay 11:49 AM 5/25/2006 +// bob hanson -- adding AjaxJS service 11:16 AM 6/3/2006 +// bob hanson -- fix for iframes not available for finding applet +// bob hanson -- added applet fake ?NOAPPLET URL flag +// bob hanson -- added jmolSetCallback(calbackName, funcName) 3:32 PM 6/13/2006 +// used PRIOR to jmolApplet() or jmolAppletInline() +// added 4th array element in jmolRadioGroup -- title +// added and id around link, checkbox, radio, menu +// fixing AJAX loads for MSIE/Opera-Mozilla incompatibility +// -- renamed Jmol-11.js from Jmol-new.js; JmolApplet.jar from JmolAppletProto.jar +// renamed Jmol.js for Jmol 11 distribution +// -- modified jmolRestoreOrientation() to be immediate, no 1-second delay +// bob hanson -- jmolScriptWait always returns a string -- 11:23 AM 9/16/2006 +// bh -- jmolCommandInput() +// bh -- jmolSetTranslation(TF) -- forces translation even if there might be message callback issues +// bh -- minor fixes suggested by Angel +// bh -- adds jmolSetSyncId() and jmolGetSyncId() +// bh 3/2008 -- adds jmolAppendInlineScript() and jmolAppendInlineArray() +// bh 3/2008 -- fixes IE7 bug in relation to jmolLoadInlineArray() +// bh 6/2008 -- adds jmolSetAppletWindow() +// Angel H. 6/2008 -- added html tags to checkboxes and radio buttons [in jmolCheckbox() and _jmolRadio() functions] +// bh 7/2008 -- code fix "for(i..." not "for(var i..." +// bh 12/2008 -- jmolLoadInline, jmolLoadInlineArray, jmolLoadInlineScript, jmolAppendInlineScript, jmolAppendInlineArray all return error message or null (Jmol 11.7.16) +// bh 12/2008 -- jmolScriptWaitOutput() -- waits for script to complete and delivers output normally sent to console + +// bh 5/2009 -- Support for XHTML using jmolSetXHTML(id) +// ah & bh 6/2009 -- New jmolResizeApplet() more flexible, similar to jmolApplet() size syntax +// bh 11/2009 -- care in accessing top.document +// bh 12/2009 -- added jmolSetParameter(name, value) +// bh 12/2009 -- added PARAMS=name:value;name:value;name:value... for command line +// bh 12/2009 -- overhaul of target checking +// bh 1/2010 -- all _xxxx() methods ALWAYS have complete argument list +// bh 1/2010 -- adds option to run a JavaScript function from any Jmol control. +// This is accomplished by passing an array rather than a script: +// jmolHref([myfunc,"my param 1", "my param 2"], "testing") +// function myfunc(jmolControlObject, [myfunc,"my param 1", "my param 2"], target){...} +// and allows much more flexibility with responding to controls +// bh 4/2010 -- added jmolSetMemoryMb(nMb) +// ah 1/2011 -- wider detection of browsers; more browsers now use the object tag instead of the applet tag; +// fix of object tag (removed classid) accounts for change of behavior in Chrome +// bh 3/2011 -- added jmolLoadAjax_STOLAF_NIH + +var defaultdir = "." +var defaultjar = "JmolApplet.jar" + + +// Note added 12:41 PM 9/21/2008 by Bob Hanson, hansonr@stolaf.edu: + +// JMOLJAR=xxxxx.jar on the URL for this page will override +// the JAR file specified in the jmolInitialize() call. + +// The idea is that it can be very useful to test a web page with different JAR files +// Or for an expert user to substitute a signed applet for an unsigned one +// so as to use a broader range of models or to create JPEG files, for example. + +// If the JAR file is not in the current directory (has any sort of "/" in its name) +// then the user is presented with a warning and asked whether it is OK to change Jar files. +// The default action, if the user just presses "OK" is to NOT allow the change. +// The user must type the word "yes" in the prompt box for the change to be approved. + +// If you don't want people to be able to switch in their own JAR file on your page, +// simply set this next line to read "var allowJMOLJAR = false". + + +var undefined; // for IE 5 ... wherein undefined is undefined + +//////////////////////////////////////////////////////////////// +// Basic Scripting infrastruture +//////////////////////////////////////////////////////////////// + +function jmolInitialize(codebaseDirectory, fileNameOrUseSignedApplet) { + if (_jmol.initialized) + return; + _jmol.initialized = true; + if(_jmol.jmoljar) { + var f = _jmol.jmoljar; + if (f.indexOf("/") >= 0) { + alert ("This web page URL is requesting that the applet used be " + f + ". This is a possible security risk, particularly if the applet is signed, because signed applets can read and write files on your local machine or network.") + var ok = prompt("Do you want to use applet " + f + "? ","yes or no") + if (ok == "yes") { + codebaseDirectory = f.substring(0, f.lastIndexOf("/")); + fileNameOrUseSignedApplet = f.substring(f.lastIndexOf("/") + 1); + } else { + _jmolGetJarFilename(fileNameOrUseSignedApplet); + alert("The web page URL was ignored. Continuing using " + _jmol.archivePath + ' in directory "' + codebaseDirectory + '"'); + } + } else { + fileNameOrUseSignedApplet = f; + } + } + _jmolSetCodebase(codebaseDirectory); + _jmolGetJarFilename(fileNameOrUseSignedApplet); + _jmolOnloadResetForms(); +} + +function jmolSetTranslation(TF) { + _jmol.params.doTranslate = ''+TF; +} + +function _jmolGetJarFilename(fileNameOrFlag) { + _jmol.archivePath = + (typeof(fileNameOrFlag) == "string" ? fileNameOrFlag : (fileNameOrFlag ? "JmolAppletSigned" : "JmolApplet") + "0.jar"); +} + +function jmolSetDocument(doc) { + _jmol.currentDocument = doc; +} + +function jmolSetAppletColor(boxbgcolor, boxfgcolor, progresscolor) { + _jmolInitCheck(); + _jmol.params.boxbgcolor = boxbgcolor; + if (boxfgcolor) + _jmol.params.boxfgcolor = boxfgcolor + else if (boxbgcolor == "white" || boxbgcolor == "#FFFFFF") + _jmol.params.boxfgcolor = "black"; + else + _jmol.params.boxfgcolor = "white"; + if (progresscolor) + _jmol.params.progresscolor = progresscolor; + if (_jmol.debugAlert) + alert(" boxbgcolor=" + _jmol.params.boxbgcolor + + " boxfgcolor=" + _jmol.params.boxfgcolor + + " progresscolor=" + _jmol.params.progresscolor); +} + +function jmolSetAppletWindow(w) { + _jmol.appletWindow = w; +} + +function jmolApplet(size, script, nameSuffix) { + _jmolInitCheck(); + return _jmolApplet(size, null, script, nameSuffix); +} + +//////////////////////////////////////////////////////////////// +// Basic controls +//////////////////////////////////////////////////////////////// + +// undefined means it wasn't there; null means it was explicitly listed as null (so as to skip it) + +function jmolButton(script, label, id, title) { + _jmolInitCheck(); + id != undefined && id != null || (id = "jmolButton" + _jmol.buttonCount); + label != undefined && label != null || (label = script.substring(0, 32)); + ++_jmol.buttonCount; + var scriptIndex = _jmolAddScript(script); + var t = ""; + if (_jmol.debugAlert) + alert(t); + return _jmolDocumentWrite(t); +} + +function jmolCheckbox(scriptWhenChecked, scriptWhenUnchecked, + labelHtml, isChecked, id, title) { + _jmolInitCheck(); + id != undefined && id != null || (id = "jmolCheckbox" + _jmol.checkboxCount); + ++_jmol.checkboxCount; + if (scriptWhenChecked == undefined || scriptWhenChecked == null || + scriptWhenUnchecked == undefined || scriptWhenUnchecked == null) { + alert("jmolCheckbox requires two scripts"); + return; + } + if (labelHtml == undefined || labelHtml == null) { + alert("jmolCheckbox requires a label"); + return; + } + var indexChecked = _jmolAddScript(scriptWhenChecked); + var indexUnchecked = _jmolAddScript(scriptWhenUnchecked); + var eospan = "" + var t = "" + if (labelHtml.toLowerCase().indexOf("

Useful to know!!

Ferredoxins, chloroplast precursor related UniRef50 cluster
@@ -82,8 +82,8 @@

Notes

JalviewLite's Java API

'+title+'

'+message+'

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Useful to know!!

Ferredoxins, chloroplast precursor related UniRef50 cluster @@ -82,8 +82,8 @@

Notes

JalviewLite's Java API

'+title+'

'+message+'

Please wait...

Ferredoxins, chloroplast precursor related UniRef50 cluster
@@ -82,8 +82,8 @@