November 2011 - galaxy-commits - lists.galaxyproject.org

commit/galaxy-central: jgoecks: Trackster: (a) give every Drawable unique id and (b) remove unused reference to jquery.scrollTo.
by Bitbucket 02 Nov '11

02 Nov '11

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/611ec861bde5/ changeset: 611ec861bde5 user: jgoecks date: 2011-11-02 22:48:22 summary: Trackster: (a) give every Drawable unique id and (b) remove unused reference to jquery.scrollTo. affected #: 2 files diff -r 9e90faf2cb1c58b19dc715243f4766223a6b3a47 -r 611ec861bde5a6c31eace77f94ab8024159cc77c static/scripts/trackster.js --- a/static/scripts/trackster.js +++ b/static/scripts/trackster.js @@ -654,6 +654,8 @@ * associated with a view and container. They optionally have a drag handle class. */ var Drawable = function(name, view, container, prefs, drag_handle_class) { + if (!Drawable.id_counter) { Drawable.id_counter = 0; } + this.id = Drawable.id_counter++; this.name = name; this.view = view; this.container = container; @@ -804,13 +806,11 @@ DrawableCollection.call(this, "DrawableGroup", name, view, container, prefs, "group-handle"); // HTML elements. - if (!DrawableGroup.id_counter) { DrawableGroup.id_counter = 0; } - var group_id = DrawableGroup.id_counter++ - this.container_div = $("<div/>").addClass("group").attr("id", "group_" + group_id).appendTo(this.container.content_div); + this.container_div = $("<div/>").addClass("group").attr("id", "group_" + this.id).appendTo(this.container.content_div); this.header_div = $("<div/>").addClass("track-header").appendTo(this.container_div); this.header_div.append($("<div/>").addClass(this.drag_handle_class)); this.name_div = $("<div/>").addClass("group-name menubutton popup").text(this.name).appendTo(this.header_div); - this.content_div = $("<div/>").addClass("content-div").attr("id", "group_" + group_id + "_content_div").appendTo(this.container_div); + this.content_div = $("<div/>").addClass("content-div").attr("id", "group_" + this.id + "_content_div").appendTo(this.container_div); // Set up containers/moving for group: register both container_div and content div as container // because both are used as containers (container div to recognize container, content_div to @@ -2329,9 +2329,6 @@ this.data_url_extra_params = {} this.data_query_wait = (data_query_wait ? data_query_wait : DEFAULT_DATA_QUERY_WAIT); this.dataset_check_url = converted_datasets_state_url; - - if (!Track.id_counter) { Track.id_counter = 0; } - this.id = Track.id_counter++; // // Create HTML element structure for track. diff -r 9e90faf2cb1c58b19dc715243f4766223a6b3a47 -r 611ec861bde5a6c31eace77f94ab8024159cc77c templates/tracks/browser.mako --- a/templates/tracks/browser.mako +++ b/templates/tracks/browser.mako @@ -42,7 +42,7 @@ <script type='text/javascript' src="${h.url_for('/static/scripts/excanvas.js')}"></script><![endif]--> -${h.js( "galaxy.base", "galaxy.panels", "json2", "jquery", "jstorage", "jquery.event.drag", "jquery.mousewheel", "jquery.autocomplete", "trackster", "trackster_ui", "jquery.ui.sortable.slider", "jquery.scrollTo", "farbtastic", "jquery.tipsy" )} +${h.js( "galaxy.base", "galaxy.panels", "json2", "jquery", "jstorage", "jquery.event.drag", "jquery.mousewheel", "jquery.autocomplete", "trackster", "trackster_ui", "jquery.ui.sortable.slider", "farbtastic", "jquery.tipsy" )} <script type="text/javascript"> // Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: John Duddy: Fix signature of slit method
by Bitbucket 02 Nov '11

02 Nov '11

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/9e90faf2cb1c/ changeset: 9e90faf2cb1c user: John Duddy date: 2011-11-02 22:15:08 summary: Fix signature of slit method affected #: 1 file diff -r 9a9479f7e53f31b7296dce641a8c3dd0ed2e230c -r 9e90faf2cb1c58b19dc715243f4766223a6b3a47 lib/galaxy/datatypes/data.py --- a/lib/galaxy/datatypes/data.py +++ b/lib/galaxy/datatypes/data.py @@ -462,15 +462,16 @@ dataset.peek = 'file does not exist' dataset.blurb = 'file purged from disk' - def split( input_files, subdir_generator_function, split_params): + def split( cls, input_datasets, subdir_generator_function, split_params): """ Split the input files by line. """ if split_params is None: return - if len(input_files) > 1: + if len(input_datasets) > 1: raise Exception("Text file splitting does not support multiple files") + input_files = [ds.file_name for ds in input_datasets] lines_per_file = None chunk_size = None @@ -534,7 +535,7 @@ part_file.close() raise f.close() - split = staticmethod(split) + split = classmethod(split) class LineCount( Text ): """ Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: natefoo: The "How to Cite Galaxy" link was being read from screencasts_url, not citation_url.
by Bitbucket 02 Nov '11

02 Nov '11

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/9a9479f7e53f/ changeset: 9a9479f7e53f user: natefoo date: 2011-11-02 21:39:08 summary: The "How to Cite Galaxy" link was being read from screencasts_url, not citation_url. affected #: 2 files diff -r 3e2cebfac37fafe251e314f4dfeb51ae816d8dda -r 9a9479f7e53f31b7296dce641a8c3dd0ed2e230c templates/webapps/galaxy/base_panels.mako --- a/templates/webapps/galaxy/base_panels.mako +++ b/templates/webapps/galaxy/base_panels.mako @@ -114,7 +114,7 @@ ['Support', app.config.get( "support_url", "http://wiki.g2.bx.psu.edu/Support" ), "_blank" ], ['Galaxy Wiki', app.config.get( "wiki_url", "http://wiki.g2.bx.psu.edu/" ), "_blank" ], ['Video tutorials (screencasts)', app.config.get( "screencasts_url", "http://galaxycast.org" ), "_blank" ], - ['How to Cite Galaxy', app.config.get( "screencasts_url", "http://wiki.g2.bx.psu.edu/Citing%20Galaxy" ), "_blank" ] + ['How to Cite Galaxy', app.config.get( "citation_url", "http://wiki.g2.bx.psu.edu/Citing%20Galaxy" ), "_blank" ] ] tab( "help", "Help", None, menu_options=menu_options) %> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: natefoo: Allow administrators to impersonate other users. Useful for debugging, but be aware that this gives said administrator a full session as the user, with the ability to do anything as that user (the user does not gain the administrator's privileges, however).
by Bitbucket 02 Nov '11

02 Nov '11

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/3e2cebfac37f/ changeset: 3e2cebfac37f user: natefoo date: 2011-11-02 18:37:33 summary: Allow administrators to impersonate other users. Useful for debugging, but be aware that this gives said administrator a full session as the user, with the ability to do anything as that user (the user does not gain the administrator's privileges, however). affected #: 4 files diff -r 1bae407d0d51aa07e026896fee8db5f525e71eac -r 3e2cebfac37fafe251e314f4dfeb51ae816d8dda lib/galaxy/config.py --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -71,6 +71,7 @@ self.allow_user_creation = string_as_bool( kwargs.get( "allow_user_creation", "True" ) ) self.allow_user_deletion = string_as_bool( kwargs.get( "allow_user_deletion", "False" ) ) self.allow_user_dataset_purge = string_as_bool( kwargs.get( "allow_user_dataset_purge", "False" ) ) + self.allow_user_impersonation = string_as_bool( kwargs.get( "allow_user_impersonation", "False" ) ) self.new_user_dataset_access_role_default_private = string_as_bool( kwargs.get( "new_user_dataset_access_role_default_private", "False" ) ) self.template_path = resolve_path( kwargs.get( "template_path", "templates" ), self.root ) self.template_cache = resolve_path( kwargs.get( "template_cache_path", "database/compiled_templates" ), self.root ) diff -r 1bae407d0d51aa07e026896fee8db5f525e71eac -r 3e2cebfac37fafe251e314f4dfeb51ae816d8dda lib/galaxy/web/controllers/admin.py --- a/lib/galaxy/web/controllers/admin.py +++ b/lib/galaxy/web/controllers/admin.py @@ -1029,6 +1029,27 @@ id=trans.security.encode_id( repository.id ), message=message, status=status ) ) + @web.expose + @web.require_admin + def impersonate( self, trans, email=None, **kwd ): + if not trans.app.config.allow_user_impersonation: + return trans.show_error_message( "User impersonation is not enabled in this instance of Galaxy." ) + message = '' + status = 'done' + emails = None + if email is not None: + user = trans.sa_session.query( trans.app.model.User ).filter_by( email=email ).first() + if user: + trans.set_user( user ) + message = 'You are now logged in as %s, <a target="_top" href="%s">return to the home page</a>' % ( email, url_for( controller='root' ) ) + emails = [] + else: + message = 'Invalid user selected' + status = 'error' + if emails is None: + emails = [ u.email for u in trans.sa_session.query( trans.app.model.User ).enable_eagerloads( False ).all() ] + return trans.fill_template( 'admin/impersonate.mako', emails=emails, message=message, status=status ) + def __get_relative_install_dir( self, trans, repository ): # Get the directory where the repository is install. tool_shed = self.__clean_tool_shed_url( repository.tool_shed ) diff -r 1bae407d0d51aa07e026896fee8db5f525e71eac -r 3e2cebfac37fafe251e314f4dfeb51ae816d8dda templates/webapps/galaxy/admin/index.mako --- a/templates/webapps/galaxy/admin/index.mako +++ b/templates/webapps/galaxy/admin/index.mako @@ -46,6 +46,9 @@ <div class="toolTitle"><a href="${h.url_for( controller='admin', action='users', webapp=webapp )}" target="galaxy_main">Manage users</a></div><div class="toolTitle"><a href="${h.url_for( controller='admin', action='groups', webapp=webapp )}" target="galaxy_main">Manage groups</a></div><div class="toolTitle"><a href="${h.url_for( controller='admin', action='roles', webapp=webapp )}" target="galaxy_main">Manage roles</a></div> + %if trans.app.config.allow_user_impersonation: + <div class="toolTitle"><a href="${h.url_for( controller='admin', action='impersonate', webapp=webapp )}" target="galaxy_main">Impersonate a user</a></div> + %endif </div></div><div class="toolSectionPad"></div> diff -r 1bae407d0d51aa07e026896fee8db5f525e71eac -r 3e2cebfac37fafe251e314f4dfeb51ae816d8dda universe_wsgi.ini.sample --- a/universe_wsgi.ini.sample +++ b/universe_wsgi.ini.sample @@ -405,6 +405,9 @@ # Allow administrators to delete accounts. #allow_user_deletion = False +# Allow administrators to log in as other users (useful for debugging) +#allow_user_impersonation = False + # Allow users to remove their datasets from disk immediately (otherwise, # datasets will be removed after a time period specified by an administrator in # the cleanup scripts run via cron) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: natefoo: Fix a typo in tasks.
by Bitbucket 02 Nov '11

02 Nov '11

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/1bae407d0d51/ changeset: 1bae407d0d51 user: natefoo date: 2011-11-02 18:28:43 summary: Fix a typo in tasks. affected #: 1 file diff -r b22ee1d4143247e2b0d8f0974e71cc4682efa401 -r 1bae407d0d51aa07e026896fee8db5f525e71eac lib/galaxy/jobs/__init__.py --- a/lib/galaxy/jobs/__init__.py +++ b/lib/galaxy/jobs/__init__.py @@ -1123,7 +1123,7 @@ def __get_runner_name( self, job_wrapper ): if self.app.config.use_tasked_jobs and job_wrapper.tool.parallelism is not None and not isinstance(job_wrapper, TaskWrapper): - runnner_name = "tasks" + runner_name = "tasks" else: runner_name = ( job_wrapper.get_job_runner().split(":", 1) )[0] return runner_name Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jgoecks: Fix vertical scrolling via keyboard in Trackster.
by Bitbucket 01 Nov '11

01 Nov '11

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/b22ee1d41432/ changeset: b22ee1d41432 user: jgoecks date: 2011-11-01 22:51:53 summary: Fix vertical scrolling via keyboard in Trackster. affected #: 3 files diff -r 0abcd5c667ac1f6199baa9df20d9c8847d7b8908 -r b22ee1d4143247e2b0d8f0974e71cc4682efa401 static/scripts/jquery.scrollTo.js --- a/static/scripts/jquery.scrollTo.js +++ /dev/null @@ -1,215 +0,0 @@ -/** - * jQuery.ScrollTo - * Copyright (c) 2007-2009 Ariel Flesler - aflesler(at)gmail(dot)com | http://flesler.blogspot.com - * Dual licensed under MIT and GPL. - * Date: 5/25/2009 - * - * @projectDescription Easy element scrolling using jQuery. - * http://flesler.blogspot.com/2007/10/jqueryscrollto.html - * Works with jQuery +1.2.6. Tested on FF 2/3, IE 6/7/8, Opera 9.5/6, Safari 3, Chrome 1 on WinXP. - * - * @author Ariel Flesler - * @version 1.4.2 - * - * @id jQuery.scrollTo - * @id jQuery.fn.scrollTo - * @param {String, Number, DOMElement, jQuery, Object} target Where to scroll the matched elements. - * The different options for target are: - * - A number position (will be applied to all axes). - * - A string position ('44', '100px', '+=90', etc ) will be applied to all axes - * - A jQuery/DOM element ( logically, child of the element to scroll ) - * - A string selector, that will be relative to the element to scroll ( 'li:eq(2)', etc ) - * - A hash { top:x, left:y }, x and y can be any kind of number/string like above. -* - A percentage of the container's dimension/s, for example: 50% to go to the middle. - * - The string 'max' for go-to-end. - * @param {Number} duration The OVERALL length of the animation, this argument can be the settings object instead. - * @param {Object,Function} settings Optional set of settings or the onAfter callback. - * @option {String} axis Which axis must be scrolled, use 'x', 'y', 'xy' or 'yx'. - * @option {Number} duration The OVERALL length of the animation. - * @option {String} easing The easing method for the animation. - * @option {Boolean} margin If true, the margin of the target element will be deducted from the final position. - * @option {Object, Number} offset Add/deduct from the end position. One number for both axes or { top:x, left:y }. - * @option {Object, Number} over Add/deduct the height/width multiplied by 'over', can be { top:x, left:y } when using both axes. - * @option {Boolean} queue If true, and both axis are given, the 2nd axis will only be animated after the first one ends. - * @option {Function} onAfter Function to be called after the scrolling ends. - * @option {Function} onAfterFirst If queuing is activated, this function will be called after the first scrolling ends. - * @return {jQuery} Returns the same jQuery object, for chaining. - * - * @desc Scroll to a fixed position - * @example $('div').scrollTo( 340 ); - * - * @desc Scroll relatively to the actual position - * @example $('div').scrollTo( '+=340px', { axis:'y' } ); - * - * @dec Scroll using a selector (relative to the scrolled element) - * @example $('div').scrollTo( 'p.paragraph:eq(2)', 500, { easing:'swing', queue:true, axis:'xy' } ); - * - * @ Scroll to a DOM element (same for jQuery object) - * @example var second_child = document.getElementById('container').firstChild.nextSibling; - * $('#container').scrollTo( second_child, { duration:500, axis:'x', onAfter:function(){ - * alert('scrolled!!'); - * }}); - * - * @desc Scroll on both axes, to different values - * @example $('div').scrollTo( { top: 300, left:'+=200' }, { axis:'xy', offset:-20 } ); - */ -;(function( $ ){ - - var $scrollTo = $.scrollTo = function( target, duration, settings ){ - $(window).scrollTo( target, duration, settings ); - }; - - $scrollTo.defaults = { - axis:'xy', - duration: parseFloat($.fn.jquery) >= 1.3 ? 0 : 1 - }; - - // Returns the element that needs to be animated to scroll the window. - // Kept for backwards compatibility (specially for localScroll & serialScroll) - $scrollTo.window = function( scope ){ - return $(window)._scrollable(); - }; - - // Hack, hack, hack :) - // Returns the real elements to scroll (supports window/iframes, documents and regular nodes) - $.fn._scrollable = function(){ - return this.map(function(){ - var elem = this, - isWin = !elem.nodeName || $.inArray( elem.nodeName.toLowerCase(), ['iframe','#document','html','body'] ) != -1; - - if( !isWin ) - return elem; - - var doc = (elem.contentWindow || elem).document || elem.ownerDocument || elem; - - return $.browser.safari || doc.compatMode == 'BackCompat' ? - doc.body : - doc.documentElement; - }); - }; - - $.fn.scrollTo = function( target, duration, settings ){ - if( typeof duration == 'object' ){ - settings = duration; - duration = 0; - } - if( typeof settings == 'function' ) - settings = { onAfter:settings }; - - if( target == 'max' ) - target = 9e9; - - settings = $.extend( {}, $scrollTo.defaults, settings ); - // Speed is still recognized for backwards compatibility - duration = duration || settings.speed || settings.duration; - // Make sure the settings are given right - settings.queue = settings.queue && settings.axis.length > 1; - - if( settings.queue ) - // Let's keep the overall duration - duration /= 2; - settings.offset = both( settings.offset ); - settings.over = both( settings.over ); - - return this._scrollable().each(function(){ - var elem = this, - $elem = $(elem), - targ = target, toff, attr = {}, - win = $elem.is('html,body'); - - switch( typeof targ ){ - // A number will pass the regex - case 'number': - case 'string': - if( /^([+-]=)?\d+(\.\d+)?(px|%)?$/.test(targ) ){ - targ = both( targ ); - // We are done - break; - } - // Relative selector, no break! - targ = $(targ,this); - case 'object': - // DOMElement / jQuery - if( targ.is || targ.style ) - // Get the real position of the target - toff = (targ = $(targ)).offset(); - } - $.each( settings.axis.split(''), function( i, axis ){ - var Pos = axis == 'x' ? 'Left' : 'Top', - pos = Pos.toLowerCase(), - key = 'scroll' + Pos, - old = elem[key], - max = $scrollTo.max(elem, axis); - - if( toff ){// jQuery / DOMElement - attr[key] = toff[pos] + ( win ? 0 : old - $elem.offset()[pos] ); - - // If it's a dom element, reduce the margin - if( settings.margin ){ - attr[key] -= parseInt(targ.css('margin'+Pos)) || 0; - attr[key] -= parseInt(targ.css('border'+Pos+'Width')) || 0; - } - - attr[key] += settings.offset[pos] || 0; - - if( settings.over[pos] ) - // Scroll to a fraction of its width/height - attr[key] += targ[axis=='x'?'width':'height']() * settings.over[pos]; - }else{ - var val = targ[pos]; - // Handle percentage values - attr[key] = val.slice && val.slice(-1) == '%' ? - parseFloat(val) / 100 * max - : val; - } - - // Number or 'number' - if( /^\d+$/.test(attr[key]) ) - // Check the limits - attr[key] = attr[key] <= 0 ? 0 : Math.min( attr[key], max ); - - // Queueing axes - if( !i && settings.queue ){ - // Don't waste time animating, if there's no need. - if( old != attr[key] ) - // Intermediate animation - animate( settings.onAfterFirst ); - // Don't animate this axis again in the next iteration. - delete attr[key]; - } - }); - - animate( settings.onAfter ); - - function animate( callback ){ - $elem.animate( attr, duration, settings.easing, callback && function(){ - callback.call(this, target, settings); - }); - }; - - }).end(); - }; - - // Max scrolling position, works on quirks mode - // It only fails (not too badly) on IE, quirks mode. - $scrollTo.max = function( elem, axis ){ - var Dim = axis == 'x' ? 'Width' : 'Height', - scroll = 'scroll'+Dim; - - if( !$(elem).is('html,body') ) - return elem[scroll] - $(elem)[Dim.toLowerCase()](); - - var size = 'client' + Dim, - html = elem.ownerDocument.documentElement, - body = elem.ownerDocument.body; - - return Math.max( html[scroll], body[scroll] ) - - Math.min( html[size] , body[size] ); - - }; - - function both( val ){ - return typeof val == 'object' ? val : { top:val, left:val }; - }; - -})( jQuery ); \ No newline at end of file diff -r 0abcd5c667ac1f6199baa9df20d9c8847d7b8908 -r b22ee1d4143247e2b0d8f0974e71cc4682efa401 static/scripts/packed/jquery.scrollTo.js --- a/static/scripts/packed/jquery.scrollTo.js +++ /dev/null @@ -1,1 +0,0 @@ -(function(c){var a=c.scrollTo=function(f,e,d){c(window).scrollTo(f,e,d)};a.defaults={axis:"xy",duration:parseFloat(c.fn.jquery)>=1.3?0:1};a.window=function(d){return c(window)._scrollable()};c.fn._scrollable=function(){return this.map(function(){var e=this,d=!e.nodeName||c.inArray(e.nodeName.toLowerCase(),["iframe","#document","html","body"])!=-1;if(!d){return e}var f=(e.contentWindow||e).document||e.ownerDocument||e;return c.browser.safari||f.compatMode=="BackCompat"?f.body:f.documentElement})};c.fn.scrollTo=function(f,e,d){if(typeof e=="object"){d=e;e=0}if(typeof d=="function"){d={onAfter:d}}if(f=="max"){f=9000000000}d=c.extend({},a.defaults,d);e=e||d.speed||d.duration;d.queue=d.queue&&d.axis.length>1;if(d.queue){e/=2}d.offset=b(d.offset);d.over=b(d.over);return this._scrollable().each(function(){var l=this,j=c(l),k=f,i,g={},m=j.is("html,body");switch(typeof k){case"number":case"string":if(/^([+-]=)?\d+(\.\d+)?(px|%)?$/.test(k)){k=b(k);break}k=c(k,this);case"object":if(k.is||k.style){i=(k=c(k)).offset()}}c.each(d.axis.split(""),function(q,r){var s=r=="x"?"Left":"Top",u=s.toLowerCase(),p="scroll"+s,o=l[p],n=a.max(l,r);if(i){g[p]=i[u]+(m?0:o-j.offset()[u]);if(d.margin){g[p]-=parseInt(k.css("margin"+s))||0;g[p]-=parseInt(k.css("border"+s+"Width"))||0}g[p]+=d.offset[u]||0;if(d.over[u]){g[p]+=k[r=="x"?"width":"height"]()*d.over[u]}}else{var t=k[u];g[p]=t.slice&&t.slice(-1)=="%"?parseFloat(t)/100*n:t}if(/^\d+$/.test(g[p])){g[p]=g[p]<=0?0:Math.min(g[p],n)}if(!q&&d.queue){if(o!=g[p]){h(d.onAfterFirst)}delete g[p]}});h(d.onAfter);function h(n){j.animate(g,e,d.easing,n&&function(){n.call(this,f,d)})}}).end()};a.max=function(j,i){var h=i=="x"?"Width":"Height",e="scroll"+h;if(!c(j).is("html,body")){return j[e]-c(j)[h.toLowerCase()]()}var g="client"+h,f=j.ownerDocument.documentElement,d=j.ownerDocument.body;return Math.max(f[e],d[e])-Math.min(f[g],d[g])};function b(d){return typeof d=="object"?d:{top:d,left:d}}})(jQuery); \ No newline at end of file diff -r 0abcd5c667ac1f6199baa9df20d9c8847d7b8908 -r b22ee1d4143247e2b0d8f0974e71cc4682efa401 static/scripts/trackster_ui.js --- a/static/scripts/trackster_ui.js +++ b/static/scripts/trackster_ui.js @@ -154,14 +154,14 @@ break case 38: var change = Math.round(view.viewport_container.height()/15.0); - view.viewport_container.scrollTo('-=' + change + 'px'); + view.viewport_container.scrollTop( view.viewport_container.scrollTop() - 20); break; case 39: view.move_fraction(-0.25); break; case 40: var change = Math.round(view.viewport_container.height()/15.0); - view.viewport_container.scrollTo('+=' + change + 'px'); + view.viewport_container.scrollTop( view.viewport_container.scrollTop() + 20); break; } }); Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: richard_burhans: consolidated make_html_table for tabular datatypes
by Bitbucket 01 Nov '11

01 Nov '11

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/0abcd5c667ac/ changeset: 0abcd5c667ac user: richard_burhans date: 2011-11-01 20:52:53 summary: consolidated make_html_table for tabular datatypes affected #: 3 files diff -r 33e2ae31dddd0f494841aaa7f408aac9312b031b -r 0abcd5c667ac1f6199baa9df20d9c8847d7b8908 lib/galaxy/datatypes/genetics.py --- a/lib/galaxy/datatypes/genetics.py +++ b/lib/galaxy/datatypes/genetics.py @@ -192,27 +192,9 @@ Tabular.__init__( self, **kwd ) self.column_names = [] - def make_html_table( self, dataset, skipchars=[] ): - """ - Create HTML table, used for displaying peek - """ - out = ['<table cellspacing="0" cellpadding="3">'] - comments = [] - try: - # Generate column header - out.append( '<tr>' ) - for i, name in enumerate( self.column_names ): - out.append( '<th>%s.%s</th>' % ( str( i+1 ), name ) ) - if dataset.metadata.columns - len( self.column_names ) > 0: - for i in range( len( self.column_names ), dataset.metadata.columns ): - out.append( '<th>%s</th>' % str( i+1 ) ) - out.append( '</tr>' ) - out.append( self.make_html_peek_rows( dataset, skipchars=skipchars ) ) - out.append( '</table>' ) - out = "".join( out ) - except Exception, exc: - out = "Can't create peek %s" % exc - return out + def display_peek( self, dataset ): + """Returns formated html of peek""" + return Tabular.make_html_table( self, dataset, column_names=self.column_names ) def get_mime(self): """Returns the mime type of the datatype""" diff -r 33e2ae31dddd0f494841aaa7f408aac9312b031b -r 0abcd5c667ac1f6199baa9df20d9c8847d7b8908 lib/galaxy/datatypes/interval.py --- a/lib/galaxy/datatypes/interval.py +++ b/lib/galaxy/datatypes/interval.py @@ -219,33 +219,9 @@ os.write(fd, '%s\n' % '\t'.join(tmp) ) os.close(fd) return open(temp_name) - def make_html_table( self, dataset, skipchars=[] ): - """Create HTML table, used for displaying peek""" - out = ['<table cellspacing="0" cellpadding="3">'] - comments = [] - try: - # Generate column header - out.append('<tr>') - for i in range( 1, dataset.metadata.columns+1 ): - if i == dataset.metadata.chromCol: - out.append( '<th>%s.Chrom</th>' % i ) - elif i == dataset.metadata.startCol: - out.append( '<th>%s.Start</th>' % i ) - elif i == dataset.metadata.endCol: - out.append( '<th>%s.End</th>' % i ) - elif dataset.metadata.strandCol and i == dataset.metadata.strandCol: - out.append( '<th>%s.Strand</th>' % i ) - elif dataset.metadata.nameCol and i == dataset.metadata.nameCol: - out.append( '<th>%s.Name</th>' % i ) - else: - out.append( '<th>%s</th>' % i ) - out.append('</tr>') - out.append( self.make_html_peek_rows( dataset, skipchars=skipchars ) ) - out.append( '</table>' ) - out = "".join( out ) - except Exception, exc: - out = "Can't create peek %s" % str( exc ) - return out + def display_peek( self, dataset ): + """Returns formated html of peek""" + return Tabular.make_html_table( self, dataset, column_parameter_alias={'chromCol':'Chrom', 'startCol':'Start', 'endCol':'End', 'strandCol':'Strand', 'nameCol':'Name'} ) def ucsc_links( self, dataset, type, app, base_url ): """ Generate links to UCSC genome browser sites based on the dbkey @@ -617,21 +593,9 @@ except: pass Tabular.set_meta( self, dataset, overwrite = overwrite, skip = i ) - def make_html_table( self, dataset, skipchars=[] ): - """Create HTML table, used for displaying peek""" - out = ['<table cellspacing="0" cellpadding="3">'] - comments = [] - try: - # Generate column header - out.append( '<tr>' ) - for i, name in enumerate( self.column_names ): - out.append( '<th>%s.%s</th>' % ( str( i+1 ), name ) ) - out.append( self.make_html_peek_rows( dataset, skipchars=skipchars ) ) - out.append( '</table>' ) - out = "".join( out ) - except Exception, exc: - out = "Can't create peek %s" % exc - return out + def display_peek( self, dataset ): + """Returns formated html of peek""" + return Tabular.make_html_table( self, dataset, column_names=self.column_names ) def get_estimated_display_viewport( self, dataset ): """ Return a chrom, start, stop tuple for viewing a file. There are slight differences between gff 2 and gff 3 @@ -1081,7 +1045,8 @@ link = self._get_remote_call_url( redirect_url, site_name, dataset, type, app, base_url ) ret_val.append( ( site_name, link ) ) return ret_val - def make_html_table( self, dataset ): + def display_peek( self, dataset ): + """Returns formated html of peek""" return Tabular.make_html_table( self, dataset, skipchars=['track', '#'] ) def set_meta( self, dataset, overwrite = True, **kwd ): max_data_lines = None diff -r 33e2ae31dddd0f494841aaa7f408aac9312b031b -r 0abcd5c667ac1f6199baa9df20d9c8847d7b8908 lib/galaxy/datatypes/tabular.py --- a/lib/galaxy/datatypes/tabular.py +++ b/lib/galaxy/datatypes/tabular.py @@ -168,24 +168,46 @@ """Create HTML table, used for displaying peek""" out = ['<table cellspacing="0" cellpadding="3">'] try: - out.append( self.make_html_peek_header( dataset, kwargs ) ) - out.append( self.make_html_peek_rows( dataset, kwargs ) ) + out.append( self.make_html_peek_header( dataset, **kwargs ) ) + out.append( self.make_html_peek_rows( dataset, **kwargs ) ) out.append( '</table>' ) out = "".join( out ) except Exception, exc: out = "Can't create peek %s" % str( exc ) return out - def make_html_peek_header( self, dataset, skipchars=[] ): + def make_html_peek_header( self, dataset, skipchars=[], column_names=[], column_number_format='%s', column_parameter_alias={}, **kwargs ): out = [] try: + column_headers = [None] * dataset.metadata.columns + + # fill in empty headers with data from column_names + for i in range( min( dataset.metadata.columns, len( column_names ) ) ): + if column_headers[i] is None and column_names[i] is not None: + column_headers[i] = column_names[i] + + # fill in empty headers from ColumnParameters set in the metadata + for name, spec in dataset.metadata.spec.items(): + if isinstance( spec.param, metadata.ColumnParameter ): + try: + i = int( getattr( dataset.metadata, name ) ) - 1 + except: + i = -1 + if 0 <= i < dataset.metadata.columns and column_headers[i] is None: + column_headers[i] = column_parameter_alias.get(name, name) + out.append( '<tr>' ) - for i in range( 1, dataset.metadata.columns+1 ): - out.append( '<th>%s</th>' % str( i ) ) + for i, header in enumerate( column_headers ): + out.append( '<th>' ) + if header is None: + out.append( column_number_format % str( i + 1 ) ) + else: + out.append( '%s.%s' % ( str( i + 1 ), escape( header ) ) ) + out.append( '</th>' ) out.append( '</tr>' ) except Exception, exc: raise Exception, "Can't create peek header %s" % str( exc ) return "".join( out ) - def make_html_peek_rows( self, dataset, skipchars=[] ): + def make_html_peek_rows( self, dataset, skipchars=[], **kwargs ): out = [] try: if not dataset.peek: @@ -235,26 +257,9 @@ 'Superorder', 'Order', 'Suborder', 'Superfamily', 'Family', 'Subfamily', 'Tribe', 'Subtribe', 'Genus', 'Subgenus', 'Species', 'Subspecies' ] - def make_html_table( self, dataset, skipchars=[] ): - """Create HTML table, used for displaying peek""" - out = ['<table cellspacing="0" cellpadding="3">'] - comments = [] - try: - # Generate column header - out.append( '<tr>' ) - for i, name in enumerate( self.column_names ): - out.append( '<th>%s.%s</th>' % ( str( i+1 ), name ) ) - # This data type requires at least 24 columns in the data - if dataset.metadata.columns - len( self.column_names ) > 0: - for i in range( len( self.column_names ), dataset.metadata.columns ): - out.append( '<th>%s</th>' % str( i+1 ) ) - out.append( '</tr>' ) - out.append( self.make_html_peek_rows( dataset, skipchars=skipchars ) ) - out.append( '</table>' ) - out = "".join( out ) - except Exception, exc: - out = "Can't create peek %s" % exc - return out + def display_peek( self, dataset ): + """Returns formated html of peek""" + return Tabular.make_html_table( self, dataset, column_names=self.column_names ) class Sam( Tabular ): file_ext = 'sam' @@ -264,25 +269,10 @@ self.column_names = ['QNAME', 'FLAG', 'RNAME', 'POS', 'MAPQ', 'CIGAR', 'MRNM', 'MPOS', 'ISIZE', 'SEQ', 'QUAL', 'OPT' ] - def make_html_table( self, dataset, skipchars=[] ): - """Create HTML table, used for displaying peek""" - out = ['<table cellspacing="0" cellpadding="3">'] - try: - # Generate column header - out.append( '<tr>' ) - for i, name in enumerate( self.column_names ): - out.append( '<th>%s.%s</th>' % ( str( i+1 ), name ) ) - # This data type requires at least 11 columns in the data - if dataset.metadata.columns - len( self.column_names ) > 0: - for i in range( len( self.column_names ), dataset.metadata.columns ): - out.append( '<th>%s</th>' % str( i+1 ) ) - out.append( '</tr>' ) - out.append( self.make_html_peek_rows( dataset, skipchars=skipchars ) ) - out.append( '</table>' ) - out = "".join( out ) - except Exception, exc: - out = "Can't create peek %s" % exc - return out + def display_peek( self, dataset ): + """Returns formated html of peek""" + return Tabular.make_html_table( self, dataset, column_names=self.column_names ) + def sniff( self, filename ): """ Determines whether the file is in SAM format @@ -376,29 +366,9 @@ def init_meta( self, dataset, copy_from=None ): Tabular.init_meta( self, dataset, copy_from=copy_from ) - def make_html_table( self, dataset, skipchars=[] ): - """Create HTML table, used for displaying peek""" - out = ['<table cellspacing="0" cellpadding="3">'] - comments = [] - try: - # Generate column header - out.append('<tr>') - for i in range( 1, dataset.metadata.columns+1 ): - if i == dataset.metadata.chromCol: - out.append( '<th>%s.Chrom</th>' % i ) - elif i == dataset.metadata.startCol: - out.append( '<th>%s.Start</th>' % i ) - elif i == dataset.metadata.baseCol: - out.append( '<th>%s.Base</th>' % i ) - else: - out.append( '<th>%s</th>' % i ) - out.append('</tr>') - out.append( self.make_html_peek_rows( dataset, skipchars=skipchars ) ) - out.append( '</table>' ) - out = "".join( out ) - except Exception, exc: - out = "Can't create peek %s" % str( exc ) - return out + def display_peek( self, dataset ): + """Returns formated html of peek""" + return Tabular.make_html_table( self, dataset, column_parameter_alias={'chromCol':'Chrom', 'startCol':'Start', 'baseCol':'Base'} ) def repair_methods( self, dataset ): """Return options for removing errors along with a description""" @@ -464,21 +434,9 @@ def sniff( self, filename ): headers = get_headers( filename, '\n', count=1 ) return headers[0][0].startswith("##fileformat=VCF") + def display_peek( self, dataset ): + """Returns formated html of peek""" + return Tabular.make_html_table( self, dataset, column_names=self.column_names ) - def make_html_table( self, dataset, skipchars=[] ): - """Create HTML table, used for displaying peek""" - out = ['<table cellspacing="0" cellpadding="3">'] - try: - # Generate column header - out.append( '<tr>' ) - for i, name in enumerate( self.column_names ): - out.append( '<th>%s.%s</th>' % ( str( i+1 ), name ) ) - out.append( self.make_html_peek_rows( dataset, skipchars=skipchars ) ) - out.append( '</table>' ) - out = "".join( out ) - except Exception, exc: - out = "Can't create peek %s" % exc - return out - def get_track_type( self ): return "VcfTrack", {"data": "tabix", "index": "summary_tree"} Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jgoecks: Remove debugging statements from f34a17e508e5.
by Bitbucket 01 Nov '11

01 Nov '11

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/33e2ae31dddd/ changeset: 33e2ae31dddd user: jgoecks date: 2011-11-01 18:43:10 summary: Remove debugging statements from f34a17e508e5. affected #: 1 file diff -r 9c7e4bb081b5db8850d4ad7854f721c4c9376552 -r 33e2ae31dddd0f494841aaa7f408aac9312b031b lib/galaxy/web/controllers/tracks.py --- a/lib/galaxy/web/controllers/tracks.py +++ b/lib/galaxy/web/controllers/tracks.py @@ -852,7 +852,6 @@ # Recursive function to set param value. def set_value( param_dict, group_name, group_index, param_name, param_value ): - print "searching", param_dict if group_name in param_dict: param_dict[ group_name ][ group_index ][ param_name ] = param_value return True @@ -866,7 +865,6 @@ if isinstance( value, dict ): return_val = set_value( value, group_name, group_index, param_name, param_value) if return_val: - print "setting parameter", param_dict return return_val return False Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jgoecks: Fix bug introduced in f34a17e508e5.
by Bitbucket 01 Nov '11

01 Nov '11

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/9c7e4bb081b5/ changeset: 9c7e4bb081b5 user: jgoecks date: 2011-11-01 18:40:21 summary: Fix bug introduced in f34a17e508e5. affected #: 1 file diff -r f34a17e508e5bc07d761eeb8c36a3d076ce9ecf1 -r 9c7e4bb081b5db8850d4ad7854f721c4c9376552 lib/galaxy/web/controllers/tracks.py --- a/lib/galaxy/web/controllers/tracks.py +++ b/lib/galaxy/web/controllers/tracks.py @@ -925,7 +925,7 @@ else: message = 'Attributes updated' new_dataset.set_meta() - new_dataset.datatype.after_setting_metadata( data ) + new_dataset.datatype.after_setting_metadata( new_dataset ) trans.sa_session.flush() Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jgoecks: Trackster: (a) refactor tool data functionality into TiledTrack class so that it is generally available; (b) enable VcfTracks to work with tools; and (c) more robust parameter setting. Enable Unified Genotyper to work with Trackster.
by Bitbucket 01 Nov '11

01 Nov '11

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/f34a17e508e5/ changeset: f34a17e508e5 user: jgoecks date: 2011-11-01 15:49:34 summary: Trackster: (a) refactor tool data functionality into TiledTrack class so that it is generally available; (b) enable VcfTracks to work with tools; and (c) more robust parameter setting. Enable Unified Genotyper to work with Trackster. affected #: 6 files diff -r 4ba5c0b16190a9977fdefa3b4df508d033929903 -r f34a17e508e5bc07d761eeb8c36a3d076ce9ecf1 lib/galaxy/visualization/tracks/data_providers.py --- a/lib/galaxy/visualization/tracks/data_providers.py +++ b/lib/galaxy/visualization/tracks/data_providers.py @@ -135,10 +135,137 @@ { 'name' : attrs[ 'name' ], 'type' : column_types[viz_col_index], \ 'index' : attrs[ 'index' ] } ) return filters + +# +# -- Base mixins and providers -- +# + +class FilterableMixin: + def get_filters( self ): + """ Returns a dataset's filters. """ + + # is_ functions taken from Tabular.set_meta + def is_int( column_text ): + try: + int( column_text ) + return True + except: + return False + def is_float( column_text ): + try: + float( column_text ) + return True + except: + if column_text.strip().lower() == 'na': + return True #na is special cased to be a float + return False + + # + # Get filters. + # TODOs: + # (a) might be useful to move this into each datatype's set_meta method; + # (b) could look at first N lines to ensure GTF attribute types are consistent. + # + filters = [] + # HACK: first 8 fields are for drawing, so start filter column index at 9. + filter_col = 8 + if isinstance( self.original_dataset.datatype, Gff ): + # Can filter by score and GTF attributes. + filters = [ { 'name': 'Score', + 'type': 'int', + 'index': filter_col, + 'tool_id': 'Filter1', + 'tool_exp_name': 'c6' } ] + filter_col += 1 + if isinstance( self.original_dataset.datatype, Gtf ): + # Create filters based on dataset metadata. + for name, a_type in self.original_dataset.metadata.attribute_types.items(): + if a_type in [ 'int', 'float' ]: + filters.append( + { 'name': name, + 'type': a_type, + 'index': filter_col, + 'tool_id': 'gff_filter_by_attribute', + 'tool_exp_name': name } ) + filter_col += 1 + + ''' + # Old code: use first line in dataset to find attributes. + for i, line in enumerate( open(self.original_dataset.file_name) ): + if not line.startswith('#'): + # Look at first line for attributes and types. + attributes = parse_gff_attributes( line.split('\t')[8] ) + for attr, value in attributes.items(): + # Get attribute type. + if is_int( value ): + attr_type = 'int' + elif is_float( value ): + attr_type = 'float' + else: + attr_type = 'str' + # Add to filters. + if attr_type is not 'str': + filters.append( { 'name': attr, 'type': attr_type, 'index': filter_col } ) + filter_col += 1 + break + ''' + elif isinstance( self.original_dataset.datatype, Bed ): + # Can filter by score column only. + filters = [ { 'name': 'Score', + 'type': 'int', + 'index': filter_col, + 'tool_id': 'Filter1', + 'tool_exp_name': 'c5' + } ] + + return filters + + +class TabixDataProvider( FilterableMixin, TracksDataProvider ): + """ + Tabix index data provider for the Galaxy track browser. + """ + + col_name_data_attr_mapping = { 4 : { 'index': 4 , 'name' : 'Score' } } + + def get_iterator( self, chrom, start, end ): + start, end = int(start), int(end) + if end >= (2<<29): + end = (2<<29 - 1) # Tabix-enforced maximum + + bgzip_fname = self.dependencies['bgzip'].file_name + + # if os.path.getsize(self.converted_dataset.file_name) == 0: + # return { 'kind': messages.ERROR, 'message': "Tabix converted size was 0, meaning the input file had invalid values." } + tabix = ctabix.Tabixfile(bgzip_fname, index_filename=self.converted_dataset.file_name) + + # If chrom is not found in indexes, try removing the first three + # characters (e.g. 'chr') and see if that works. This enables the + # provider to handle chrome names defined as chrXXX and as XXX. + chrom = str(chrom) + if chrom not in tabix.contigs and chrom.startswith("chr") and (chrom[3:] in tabix.contigs): + chrom = chrom[3:] + + return tabix.fetch(reference=chrom, start=start, end=end) + + def get_data( self, chrom, start, end, start_val=0, max_vals=None, **kwargs ): + iterator = self.get_iterator( chrom, start, end ) + return self.process_data( iterator, start_val, max_vals, **kwargs ) + + def write_data_to_file( self, chrom, start, end, filename ): + iterator = self.get_iterator( chrom, start, end ) + out = open( filename, "w" ) + for line in iterator: + out.write( "%s\n" % line ) + out.close() + +# +# -- BED data providers -- +# class BedDataProvider( TracksDataProvider ): """ - Abstract class that processes BED data from text format to payload format. + Abstract class that processes BED data from native format to payload format. Payload format: [ uid (offset), start, end, name, strand, thick_start, thick_end, blocks ] """ @@ -220,7 +347,166 @@ for line in iterator: out.write( "%s\n" % line ) out.close() - + +class BedTabixDataProvider( TabixDataProvider, BedDataProvider ): + """ + Provides data from a BED file indexed via tabix. + """ + pass + +class RawBedDataProvider( BedDataProvider ): + """ + Provide data from BED file. + + NOTE: this data provider does not use indices, and hence will be very slow + for large datasets. + """ + + def get_iterator( self, chrom, start, end ): + def line_filter_iter(): + for line in open( self.original_dataset.file_name ): + feature = line.split() + feature_chrom = feature[0] + feature_start = int( feature[1] ) + feature_end = int( feature[2] ) + if feature_chrom != chrom or feature_start > int( end ) or feature_end < int( start ): + continue + yield line + return line_filter_iter() + +# +# -- VCF data providers -- +# + +class VcfDataProvider( TracksDataProvider ): + """ + Abstract class that processes VCF data from native format to payload format. + + Payload format: TODO + """ + + col_name_data_attr_mapping = { 'Qual' : { 'index': 6 , 'name' : 'Qual' } } + + + def get_iterator( self, chrom, start, end ): + raise "Unimplemented Method" + + def get_data( self, chrom, start, end, start_val=0, max_vals=None, **kwargs ): + iterator = self.get_iterator( chrom, start, end ) + return self.process_data( iterator, start_val, max_vals, **kwargs ) + + def process_data( self, iterator, start_val=0, max_vals=None, **kwargs ): + """ + Returns a dict with the following attributes: + data - a list of variants with the format + [<guid>, <start>, <end>, <name>, cigar, seq] + + message - error/informative message + """ + rval = [] + message = None + + def get_mapping( ref, alt ): + """ + Returns ( offset, new_seq, cigar ) tuple that defines mapping of + alt to ref. Cigar format is an array of [ op_index, length ] pairs + where op_index is the 0-based index into the string "MIDNSHP=X" + """ + + cig_ops = "MIDNSHP=X" + + ref_len = len( ref ) + alt_len = len( alt ) + + # Substitutions? + if ref_len == alt_len: + return 0, alt, [ [ cig_ops.find( "M" ), ref_len ] ] + + # Deletions? + alt_in_ref_index = ref.find( alt ) + if alt_in_ref_index != -1: + return alt_in_ref_index, ref[ alt_in_ref_index + 1: ], [ [ cig_ops.find( "D" ), ref_len - alt_len ] ] + + # Insertions? + ref_in_alt_index = alt.find( ref ) + if ref_in_alt_index != -1: + return ref_in_alt_index, alt[ ref_in_alt_index + 1: ], [ [ cig_ops.find( "I" ), alt_len - ref_len ] ] + + # Pack data. + for count, line in enumerate( iterator ): + if count < start_val: + continue + if max_vals and count-start_val >= max_vals: + message = ERROR_MAX_VALS % ( max_vals, "features" ) + break + + feature = line.split() + start = int( feature[1] ) - 1 + ref = feature[3] + alts = feature[4] + + # HACK? alts == '.' --> monomorphism. + if alts == '.': + alts = ref + + # Pack variants. + for alt in alts.split(","): + offset, new_seq, cigar = get_mapping( ref, alt ) + start += offset + end = start + len( new_seq ) + + # Pack line. + payload = [ hash( line ), + start, + end, + # ID: + feature[2], + cigar, + new_seq, + float( feature[5] )] + rval.append(payload) + + return { 'data': rval, 'message': message } + + def write_data_to_file( self, chrom, start, end, filename ): + iterator = self.get_iterator( chrom, start, end ) + out = open( filename, "w" ) + for line in iterator: + out.write( "%s\n" % line ) + out.close() + +class VcfTabixDataProvider( TabixDataProvider, VcfDataProvider ): + """ + Provides data from a VCF file indexed via tabix. + """ + pass + +class RawVcfDataProvider( VcfDataProvider ): + """ + Provide data from VCF file. + + NOTE: this data provider does not use indices, and hence will be very slow + for large datasets. + """ + + def get_iterator( self, chrom, start, end ): + def line_filter_iter(): + for line in open( self.original_dataset.file_name ): + if line.startswith("#"): + continue + variant = line.split() + variant_chrom, variant_start, id, ref, alts = variant[ 0:5 ] + variant_start = int( variant_start ) + longest_alt = -1 + for alt in alts: + if len( alt ) > longest_alt: + longest_alt = len( alt ) + variant_end = variant_start + abs( len( ref ) - longest_alt ) + if variant_chrom != chrom or variant_start > int( end ) or variant_end < int( start ): + continue + yield line + return line_filter_iter() + class SummaryTreeDataProvider( TracksDataProvider ): """ Summary tree data provider for the Galaxy track browser. @@ -485,118 +771,7 @@ else: f = open( self.original_dataset.file_name ) return f, BigWigFile(file=f) - -class FilterableMixin: - def get_filters( self ): - """ Returns a dataset's filters. """ - - # is_ functions taken from Tabular.set_meta - def is_int( column_text ): - try: - int( column_text ) - return True - except: - return False - def is_float( column_text ): - try: - float( column_text ) - return True - except: - if column_text.strip().lower() == 'na': - return True #na is special cased to be a float - return False - - # - # Get filters. - # TODOs: - # (a) might be useful to move this into each datatype's set_meta method; - # (b) could look at first N lines to ensure GTF attribute types are consistent. - # - filters = [] - # HACK: first 8 fields are for drawing, so start filter column index at 9. - filter_col = 8 - if isinstance( self.original_dataset.datatype, Gff ): - # Can filter by score and GTF attributes. - filters = [ { 'name': 'Score', - 'type': 'int', - 'index': filter_col, - 'tool_id': 'Filter1', - 'tool_exp_name': 'c6' } ] - filter_col += 1 - if isinstance( self.original_dataset.datatype, Gtf ): - # Create filters based on dataset metadata. - for name, a_type in self.original_dataset.metadata.attribute_types.items(): - if a_type in [ 'int', 'float' ]: - filters.append( - { 'name': name, - 'type': a_type, - 'index': filter_col, - 'tool_id': 'gff_filter_by_attribute', - 'tool_exp_name': name } ) - filter_col += 1 - - ''' - # Old code: use first line in dataset to find attributes. - for i, line in enumerate( open(self.original_dataset.file_name) ): - if not line.startswith('#'): - # Look at first line for attributes and types. - attributes = parse_gff_attributes( line.split('\t')[8] ) - for attr, value in attributes.items(): - # Get attribute type. - if is_int( value ): - attr_type = 'int' - elif is_float( value ): - attr_type = 'float' - else: - attr_type = 'str' - # Add to filters. - if attr_type is not 'str': - filters.append( { 'name': attr, 'type': attr_type, 'index': filter_col } ) - filter_col += 1 - break - ''' - elif isinstance( self.original_dataset.datatype, Bed ): - # Can filter by score column only. - filters = [ { 'name': 'Score', - 'type': 'int', - 'index': filter_col, - 'tool_id': 'Filter1', - 'tool_exp_name': 'c5' - } ] - - return filters - -class TabixDataProvider( FilterableMixin, TracksDataProvider ): - """ - Tabix index data provider for the Galaxy track browser. - """ - - col_name_data_attr_mapping = { 4 : { 'index': 4 , 'name' : 'Score' } } - - def get_iterator( self, chrom, start, end ): - start, end = int(start), int(end) - if end >= (2<<29): - end = (2<<29 - 1) # Tabix-enforced maximum - - bgzip_fname = self.dependencies['bgzip'].file_name - - # if os.path.getsize(self.converted_dataset.file_name) == 0: - # return { 'kind': messages.ERROR, 'message': "Tabix converted size was 0, meaning the input file had invalid values." } - tabix = ctabix.Tabixfile(bgzip_fname, index_filename=self.converted_dataset.file_name) - - # If chrom is not found in indexes, try removing the first three - # characters (e.g. 'chr') and see if that works. This enables the - # provider to handle chrome names defined as chrXXX and as XXX. - chrom = str(chrom) - if chrom not in tabix.contigs and chrom.startswith("chr") and (chrom[3:] in tabix.contigs): - chrom = chrom[3:] - - return tabix.fetch(reference=chrom, start=start, end=end) - - def get_data( self, chrom, start, end, start_val=0, max_vals=None, **kwargs ): - iterator = self.get_iterator( chrom, start, end ) - return self.process_data( iterator, start_val, max_vals, **kwargs ) - + class IntervalIndexDataProvider( FilterableMixin, TracksDataProvider ): """ Interval index files used only for GFF files. @@ -658,86 +833,6 @@ results.append( payload ) return { 'data': results, 'message': message } - -class VcfDataProvider( TabixDataProvider ): - """ - VCF data provider. Payload format uses the read format. - """ - - col_name_data_attr_mapping = { 'Qual' : { 'index': 6 , 'name' : 'Qual' } } - - def process_data( self, iterator, start_val=0, max_vals=sys.maxint, **kwargs ): - """ - Returns a dict with the following attributes: - data - a list of variants with the format - [<guid>, <start>, <end>, <name>, cigar, seq] - - message - error/informative message - """ - rval = [] - message = None - - def get_mapping( ref, alt ): - """ - Returns ( offset, new_seq, cigar ) tuple that defines mapping of - alt to ref. Cigar format is an array of [ op_index, length ] pairs - where op_index is the 0-based index into the string "MIDNSHP=X" - """ - - cig_ops = "MIDNSHP=X" - - ref_len = len( ref ) - alt_len = len( alt ) - - # Substitutions? - if ref_len == alt_len: - return 0, alt, [ [ cig_ops.find( "M" ), ref_len ] ] - - # Deletions? - alt_in_ref_index = ref.find( alt ) - if alt_in_ref_index != -1: - return alt_in_ref_index, ref[ alt_in_ref_index + 1: ], [ [ cig_ops.find( "D" ), ref_len - alt_len ] ] - - # Insertions? - ref_in_alt_index = alt.find( ref ) - if ref_in_alt_index != -1: - return ref_in_alt_index, alt[ ref_in_alt_index + 1: ], [ [ cig_ops.find( "I" ), alt_len - ref_len ] ] - - # Pack data. - for count, line in enumerate( iterator ): - if count < start_val: - continue - if count-start_val >= max_vals: - message = ERROR_MAX_VALS % ( "max_vals", "features" ) - break - - feature = line.split() - start = int( feature[1] ) - 1 - ref = feature[3] - alts = feature[4] - - # HACK? alts == '.' --> monomorphism. - if alts == '.': - alts = ref - - # Pack variants. - for alt in alts.split(","): - offset, new_seq, cigar = get_mapping( ref, alt ) - start += offset - end = start + len( new_seq ) - - # Pack line. - payload = [ hash( line ), - start, - end, - # ID: - feature[2], - cigar, - new_seq, - float( feature[5] )] - rval.append(payload) - - return { 'data': rval, 'message': message } class GFFDataProvider( TracksDataProvider ): """ @@ -769,40 +864,16 @@ offset += feature.raw_size return { 'data': results, 'message': message } - -class BedTabixDataProvider( TabixDataProvider, BedDataProvider ): - """ - Provides data from a BED file indexed via tabix. - """ - pass - -class RawBedDataProvider( BedDataProvider ): - """ - Provide data from BED file. - - NOTE: this data provider does not use indices, and hence will be very slow - for large datasets. - """ - - def get_iterator( self, chrom, start, end ): - def line_filter_iter(): - for line in open( self.original_dataset.file_name ): - feature = line.split() - feature_chrom, feature_start, feature_end = feature[ 0:3 ] - if feature_chrom != chrom or feature_start > end or feature_end < start: - continue - yield line - return line_filter_iter() - + # -# Helper methods. +# -- Helper methods. -- # # Mapping from dataset type name to a class that can fetch data from a file of that # type. First key is converted dataset type; if result is another dict, second key # is original dataset type. TODO: This needs to be more flexible. dataset_type_name_to_data_provider = { - "tabix": { Vcf: VcfDataProvider, Bed: BedTabixDataProvider, "default" : TabixDataProvider }, + "tabix": { Vcf: VcfTabixDataProvider, Bed: BedTabixDataProvider, "default" : TabixDataProvider }, "interval_index": IntervalIndexDataProvider, "bai": BamDataProvider, "summary_tree": SummaryTreeDataProvider, diff -r 4ba5c0b16190a9977fdefa3b4df508d033929903 -r f34a17e508e5bc07d761eeb8c36a3d076ce9ecf1 lib/galaxy/web/controllers/tracks.py --- a/lib/galaxy/web/controllers/tracks.py +++ b/lib/galaxy/web/controllers/tracks.py @@ -465,10 +465,14 @@ data = GFFDataProvider( original_dataset=dataset ).get_data( chrom, low, high, **kwargs ) data[ 'dataset_type' ] = 'interval_index' data[ 'extra_info' ] = None - if isinstance( dataset.datatype, Bed ): + elif isinstance( dataset.datatype, Bed ): data = RawBedDataProvider( original_dataset=dataset ).get_data( chrom, low, high, **kwargs ) data[ 'dataset_type' ] = 'interval_index' data[ 'extra_info' ] = None + elif isinstance( dataset.datatype, Vcf ): + data = RawVcfDataProvider( original_dataset=dataset ).get_data( chrom, low, high, **kwargs ) + data[ 'dataset_type' ] = 'tabix' + data[ 'extra_info' ] = None return data @web.json @@ -586,7 +590,7 @@ data_provider = data_provider_class( converted_dataset=converted_dataset, original_dataset=dataset, dependencies=deps ) # Get and return data from data_provider. - result = data_provider.get_data( chrom, low, high, int(start_val), int(max_vals), **kwargs ) + result = data_provider.get_data( chrom, low, high, int( start_val ), int( max_vals ), **kwargs ) result.update( { 'dataset_type': tracks_dataset_type, 'extra_info': extra_info } ) return result @@ -840,6 +844,45 @@ # Set input datasets for tool. If running on region, extract and use subset # when possible. # + + def set_param_value( param_dict, param_name, param_value ): + """ + Set new parameter value in a parameter dictionary. + """ + + # Recursive function to set param value. + def set_value( param_dict, group_name, group_index, param_name, param_value ): + print "searching", param_dict + if group_name in param_dict: + param_dict[ group_name ][ group_index ][ param_name ] = param_value + return True + elif param_name in param_dict: + param_dict[ param_name ] = param_value + return True + else: + # Recursive search. + return_val = False + for name, value in param_dict.items(): + if isinstance( value, dict ): + return_val = set_value( value, group_name, group_index, param_name, param_value) + if return_val: + print "setting parameter", param_dict + return return_val + return False + + # Parse parameter name if necessary. + if param_name.find( "|" ) == -1: + # Non-grouping parameter. + group_name = group_index = None + else: + # Grouping parameter. + group, param_name = param_name.split( "|" ) + index = group.rfind( "_" ) + group_name = group[ :index ] + group_index = int( group[ index + 1: ] ) + + return set_value( param_dict, group_name, group_index, param_name, param_value ) + for jida in original_job.input_datasets: input_dataset = jida.dataset if input_dataset is None: #optional dataset and dataset wasn't selected @@ -875,10 +918,20 @@ new_dataset.set_size() new_dataset.info = "Data subset for trackster" new_dataset.set_dataset_state( trans.app.model.Dataset.states.OK ) + + # Set metadata. + if trans.app.config.set_metadata_externally: + trans.app.datatypes_registry.set_external_metadata_tool.tool_action.execute( trans.app.datatypes_registry.set_external_metadata_tool, trans, incoming = { 'input1':new_dataset } ) + else: + message = 'Attributes updated' + new_dataset.set_meta() + new_dataset.datatype.after_setting_metadata( data ) + trans.sa_session.flush() - + # Add dataset to tool's parameters. - tool_params[ jida.name ] = new_dataset + if not set_param_value( tool_params, jida.name, new_dataset ): + return to_json_string( { "error" : True, "message" : "error setting parameter %s" % jida.name } ) # # Execute tool and handle outputs. diff -r 4ba5c0b16190a9977fdefa3b4df508d033929903 -r f34a17e508e5bc07d761eeb8c36a3d076ce9ecf1 static/scripts/packed/trackster.js --- a/static/scripts/packed/trackster.js +++ b/static/scripts/packed/trackster.js @@ -1,1 +1,1 @@ -var class_module=function(b,a){var c=function(){var f=arguments[0];for(var e=1;e<arguments.length;e++){var d=arguments[e];for(key in d){f[key]=d[key]}}return f};a.extend=c};var requestAnimationFrame=(function(){return window.requestAnimationFrame||window.webkitRequestAnimationFrame||window.mozRequestAnimationFrame||window.oRequestAnimationFrame||window.msRequestAnimationFrame||function(b,a){window.setTimeout(b,1000/60)}})();var BEFORE=1001,CONTAINS=1002,OVERLAP_START=1003,OVERLAP_END=1004,CONTAINED_BY=1005,AFTER=1006;var compute_overlap=function(e,b){var g=e[0],f=e[1],d=b[0],c=b[1],a;if(g<d){if(f<d){a=BEFORE}else{if(f<=c){a=OVERLAP_START}else{a=CONTAINS}}}else{if(g>c){a=AFTER}else{if(f<=c){a=CONTAINED_BY}else{a=OVERLAP_END}}}return a};var is_overlap=function(c,b){var a=compute_overlap(c,b);return(a!==BEFORE&&a!==AFTER)};var get_random_color=function(a){if(!a){a="#ffffff"}if(typeof(a)==="string"){a=[a]}for(var j=0;j<a.length;j++){a[j]=parseInt(a[j].slice(1),16)}var m=function(t,s,i){return((t*299)+(s*587)+(i*114))/1000};var e=function(u,t,v,r,i,s){return(Math.max(u,r)-Math.min(u,r))+(Math.max(t,i)-Math.min(t,i))+(Math.max(v,s)-Math.min(v,s))};var g,n,f,k,p,h,q,c,d,b,o,l=false;do{g=Math.random()*16777215;n=g|16711680;f=g|65280;k=g|255;d=m(n,f,k);l=true;for(var j=0;j<a.length;j++){p=a[j];h=p|16711680;q=p|65280;c=p|255;b=m(h,q,c);o=e(n,f,k,h,q,c);if((Math.abs(d-b)<125)||(o<500)){l=false;break}}}while(!l);return"#"+(16777216+g).toString(16).substr(1,6)};var trackster_module=function(f,Y){var p=f("class").extend,s=f("slotting"),M=f("painters");var af=function(ag,ah){this.document=ag;this.default_font=ah!==undefined?ah:"9px Monaco, Lucida Console, monospace";this.dummy_canvas=this.new_canvas();this.dummy_context=this.dummy_canvas.getContext("2d");this.dummy_context.font=this.default_font;this.char_width_px=this.dummy_context.measureText("A").width;this.patterns={};this.load_pattern("right_strand","/visualization/strand_right.png");this.load_pattern("left_strand","/visualization/strand_left.png");this.load_pattern("right_strand_inv","/visualization/strand_right_inv.png");this.load_pattern("left_strand_inv","/visualization/strand_left_inv.png")};p(af.prototype,{load_pattern:function(ag,ak){var ah=this.patterns,ai=this.dummy_context,aj=new Image();aj.src=image_path+ak;aj.onload=function(){ah[ag]=ai.createPattern(aj,"repeat")}},get_pattern:function(ag){return this.patterns[ag]},new_canvas:function(){var ag=this.document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(ag)}ag.manager=this;return ag}});var n={};var l=function(ag,ah){n[ag.attr("id")]=ah};var m=function(ag,ai,ak,aj){ak=".group";var ah={};n[ag.attr("id")]=aj;ag.bind("drag",{handle:"."+ai,relative:true},function(at,au){var ar=$(this);var ax=$(this).parent(),ao=ax.children(),aq=n[$(this).attr("id")],an,am,av,al,ap;am=$(this).parents(ak);if(am.length!==0){av=am.position().top;al=av+am.outerHeight();if(au.offsetY<av){$(this).insertBefore(am);var aw=n[am.attr("id")];aw.remove_drawable(aq);aw.container.add_drawable_before(aq,aw);return}else{if(au.offsetY>al){$(this).insertAfter(am);var aw=n[am.attr("id")];aw.remove_drawable(aq);aw.container.add_drawable(aq);return}}}am=null;for(ap=0;ap<ao.length;ap++){an=$(ao.get(ap));av=an.position().top;al=av+an.outerHeight();if(an.is(ak)&&this!==an.get(0)&&au.offsetY>=av&&au.offsetY<=al){if(au.offsetY-av<al-au.offsetY){an.find(".content-div").prepend(this)}else{an.find(".content-div").append(this)}if(aq.container){aq.container.remove_drawable(aq)}n[an.attr("id")].add_drawable(aq);return}}for(ap=0;ap<ao.length;ap++){if(au.offsetY<$(ao.get(ap)).position().top){break}}if(ap===ao.length){if(this!==ao.get(ap-1)){ax.append(this);n[ax.attr("id")].move_drawable(aq,ap)}}else{if(this!==ao.get(ap)){$(this).insertBefore(ao.get(ap));n[ax.attr("id")].move_drawable(aq,(au.deltaY>0?ap-1:ap))}}}).bind("dragstart",function(){ah["border-top"]=ag.css("border-top");ah["border-bottom"]=ag.css("border-bottom");$(this).css({"border-top":"1px solid blue","border-bottom":"1px solid blue"})}).bind("dragend",function(){$(this).css(ah)})};Y.moveable=m;var ae=16,H=9,E=20,T=H+2,z=100,J=12000,R=200,C=5,v=10,L=5000,w=100,o="There was an error in indexing this dataset. 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S.prototype.load_data.call(this,ag,aj,ak,ah,ai)}});var q=function(aj,ah,ag,ai,ak){this.name=aj;this.view=ah;this.container=ag;this.config=new G({track:this,params:[{key:"name",label:"Name",type:"text",default_value:aj}],saved_values:ai,onchange:function(){this.track.set_name(this.track.config.values.name)}});this.prefs=this.config.values;this.drag_handle_class=ak;this.is_overview=false};p(q.prototype,{init:function(){},request_draw:function(){},_draw:function(){},to_json:function(){},update_track_icons:function(){},set_name:function(ag){this.old_name=this.name;this.name=ag;this.name_div.text(this.name)},revert_name:function(){this.name=this.old_name;this.name_div.text(this.name)},remove:function(){this.container.remove_drawable(this);this.container_div.fadeOut("slow",function(){$(this).remove();view.update_intro_div();view.has_changes=true})}});var y=function(ak,aj,ah,ag,ai,al){q.call(this,aj,ah,ag,ai,al);this.obj_type=ak;this.drawables=[]};p(y.prototype,q.prototype,{init:function(){for(var ag=0;ag<this.drawables.length;ag++){this.drawables[ag].init()}},_draw:function(){for(var ag=0;ag<this.drawables.length;ag++){this.drawables[ag]._draw()}},to_json:function(){var ah=[];for(var ag=0;ag<this.drawables.length;ag++){ah.push(this.drawables[ag].to_json())}return{name:this.name,prefs:this.prefs,obj_type:this.obj_type,drawables:ah}},add_drawable:function(ag){this.drawables.push(ag);ag.container=this},add_drawable_before:function(ai,ag){var ah=this.drawables.indexOf(ag);if(ah!=-1){this.drawables.splice(ah,0,ai);return true}return false},remove_drawable:function(ah){var ag=this.drawables.indexOf(ah);if(ag!=-1){this.drawables.splice(ag,1);ah.container=null;return true}return false},move_drawable:function(ah,ai){var ag=this.drawables.indexOf(ah);if(ag!=-1){this.drawables.splice(ag,1);this.drawables.splice(ai,0,ah);return true}return false}});var Q=function(aj,ah,ag,ai){y.call(this,"DrawableGroup",aj,ah,ag,ai,"group-handle");if(!Q.id_counter){Q.id_counter=0}var ak=Q.id_counter++;this.container_div=$("<div/>").addClass("group").attr("id","group_"+ak).appendTo(this.container.content_div);this.header_div=$("<div/>").addClass("track-header").appendTo(this.container_div);this.header_div.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("group-name menubutton popup").text(this.name).appendTo(this.header_div);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+ak+"_content_div").appendTo(this.container_div);l(this.container_div,this);l(this.content_div,this);m(this.container_div,this.drag_handle_class,".group",this);this.update_track_icons()};p(Q.prototype,q.prototype,y.prototype,{update_track_icons:function(){var ah=this;var ag={};ag["Edit configuration"]=function(){var ak=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},ai=function(){ah.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},aj=function(al){if((al.keyCode||al.which)===27){ak()}else{if((al.keyCode||al.which)===13){ai()}}};$(window).bind("keypress.check_enter_esc",aj);show_modal("Configure Group",ah.config.build_form(),{Cancel:ak,OK:ai})};ag.Remove=function(){ah.remove()};make_popupmenu(ah.name_div,ag)}});var ad=function(ag,aj,ai,ah){y.call(this,"View");this.container=ag;this.chrom=null;this.vis_id=ai;this.dbkey=ah;this.title=aj;this.label_tracks=[];this.tracks_to_be_redrawn=[];this.max_low=0;this.max_high=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.load_chroms_deferred=null;this.init();this.canvas_manager=new af(ag.get(0).ownerDocument);this.reset()};p(ad.prototype,y.prototype,{init:function(){var ai=this.container,ag=this;this.top_container=$("<div/>").addClass("top-container").appendTo(ai);this.browser_content_div=$("<div/>").addClass("content").css("position","relative").appendTo(ai);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(ai);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;l(this.viewport_container,ag);this.intro_div=$("<div/>").addClass("intro");var aj=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){add_tracks()});this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a/>").attr("href","javascript:void(0);").attr("title","Close overview").addClass("icon-button overview-close tooltip").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").addClass("no-autocomplete").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var ah=function(ak){if(ak.type==="focusout"||(ak.keyCode||ak.which)===13||(ak.keyCode||ak.which)===27){if((ak.keyCode||ak.which)!==27){ag.go_to($(this).val())}$(this).hide();$(this).val("");ag.location_span.show();ag.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ah).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").appendTo(this.nav_controls);this.location_span.click(function(){ag.location_span.hide();ag.chrom_select.hide();ag.nav_input.val(ag.chrom+":"+ag.low+"-"+ag.high);ag.nav_input.css("display","inline-block");ag.nav_input.select();ag.nav_input.focus()});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a id='zoom-out' />").click(function(){ag.zoom_out();ag.request_redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a id='zoom-in' />").click(function(){ag.zoom_in();ag.request_redraw()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){ag.change_chrom(ag.chrom_select.val())});this.browser_content_div.click(function(ak){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(ak){ag.zoom_in(ak.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(ak,al){this.current_x=al.offsetX}).bind("drag",function(ak,am){var an=am.offsetX-this.current_x;this.current_x=am.offsetX;var al=Math.round(an/ag.viewport_container.width()*(ag.max_high-ag.max_low));ag.move_delta(-al)});this.overview_close.click(function(){ag.reset_overview()});this.viewport_container.bind("draginit",function(ak,al){if(ak.clientX>ag.viewport_container.width()-16){return false}}).bind("dragstart",function(ak,al){al.original_low=ag.low;al.current_height=ak.clientY;al.current_x=al.offsetX}).bind("drag",function(am,ao){var ak=$(this);var ap=ao.offsetX-ao.current_x;var al=ak.scrollTop()-(am.clientY-ao.current_height);ak.scrollTop(al);ao.current_height=am.clientY;ao.current_x=ao.offsetX;var an=Math.round(ap/ag.viewport_container.width()*(ag.high-ag.low));ag.move_delta(an)}).bind("mousewheel",function(am,ao,al,ak){if(al){var an=Math.round(-al/ag.viewport_container.width()*(ag.high-ag.low));ag.move_delta(an)}});this.top_labeltrack.bind("dragstart",function(ak,al){return $("<div />").css({height:ag.browser_content_div.height()+ag.top_labeltrack.height()+ag.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(ao,ap){$(ap.proxy).css({left:Math.min(ao.pageX,ap.startX),width:Math.abs(ao.pageX-ap.startX)});var al=Math.min(ao.pageX,ap.startX)-ag.container.offset().left,ak=Math.max(ao.pageX,ap.startX)-ag.container.offset().left,an=(ag.high-ag.low),am=ag.viewport_container.width();ag.update_location(Math.round(al/am*an)+ag.low,Math.round(ak/am*an)+ag.low)}).bind("dragend",function(ap,aq){var al=Math.min(ap.pageX,aq.startX),ak=Math.max(ap.pageX,aq.startX),an=(ag.high-ag.low),am=ag.viewport_container.width(),ao=ag.low;ag.low=Math.round(al/am*an)+ao;ag.high=Math.round(ak/am*an)+ao;$(aq.proxy).remove();ag.request_redraw()});this.add_label_track(new ac(this,{content_div:this.top_labeltrack}));this.add_label_track(new ac(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){ag.resize_window()});$(document).bind("redraw",function(){ag.redraw()});this.reset();$(window).trigger("resize");this.update_intro_div()},update_intro_div:function(){if(this.num_tracks===0){this.intro_div.appendTo(this.viewport_container)}else{this.intro_div.remove()}},update_location:function(ag,ah){this.location_span.text(commatize(ag)+" - "+commatize(ah));this.nav_input.val(this.chrom+":"+commatize(ag)+"-"+commatize(ah))},load_chroms:function(ai){ai.num=w;$.extend(ai,(this.vis_id!==undefined?{vis_id:this.vis_id}:{dbkey:this.dbkey}));var ag=this,ah=$.Deferred();$.ajax({url:chrom_url,data:ai,dataType:"json",success:function(ak){if(ak.chrom_info.length===0){alert("Invalid chromosome: "+ai.chrom);return}if(ak.reference){ag.add_label_track(new A(ag))}ag.chrom_data=ak.chrom_info;var an='<option value="">Select Chrom/Contig</option>';for(var am=0,aj=ag.chrom_data.length;am<aj;am++){var al=ag.chrom_data[am].chrom;an+='<option value="'+al+'">'+al+"</option>"}if(ak.prev_chroms){an+='<option value="previous">Previous '+w+"</option>"}if(ak.next_chroms){an+='<option value="next">Next '+w+"</option>"}ag.chrom_select.html(an);ag.chrom_start_index=ak.start_index;ah.resolve(ak)},error:function(){alert("Could not load chroms for this dbkey:",ag.dbkey)}});return ah},change_chrom:function(al,ah,an){if(!al||al==="None"){return}var ai=this;if(al==="previous"){ai.load_chroms({low:this.chrom_start_index-w});return}if(al==="next"){ai.load_chroms({low:this.chrom_start_index+w});return}var am=$.grep(ai.chrom_data,function(ao,ap){return ao.chrom===al})[0];if(am===undefined){ai.load_chroms({chrom:al},function(){ai.change_chrom(al,ah,an)});return}else{if(al!==ai.chrom){ai.chrom=al;ai.chrom_select.val(ai.chrom);ai.max_high=am.len-1;ai.reset();ai.request_redraw(true);for(var ak=0,ag=ai.drawables.length;ak<ag;ak++){var aj=ai.drawables[ak];if(aj.init){aj.init()}}}if(ah!==undefined&&an!==undefined){ai.low=Math.max(ah,0);ai.high=Math.min(an,ai.max_high)}ai.reset_overview();ai.request_redraw()}},go_to:function(ak){ak=ak.replace(/ |,/g,"");var ao=this,ag,aj,ah=ak.split(":"),am=ah[0],an=ah[1];if(an!==undefined){try{var al=an.split("-");ag=parseInt(al[0],10);aj=parseInt(al[1],10)}catch(ai){return false}}ao.change_chrom(am,ag,aj)},move_fraction:function(ai){var ag=this;var ah=ag.high-ag.low;this.move_delta(ai*ah)},move_delta:function(ai){var ag=this;var ah=ag.high-ag.low;if(ag.low-ai<ag.max_low){ag.low=ag.max_low;ag.high=ag.max_low+ah}else{if(ag.high-ai>ag.max_high){ag.high=ag.max_high;ag.low=ag.max_high-ah}else{ag.high-=ai;ag.low-=ai}}ag.request_redraw()},add_drawable:function(ag){y.prototype.add_drawable.call(this,ag);ag.init();this.has_changes=true;this.update_intro_div()},add_label_track:function(ag){ag.view=this;ag.init();this.label_tracks.push(ag)},remove_drawable:function(ai,ah){y.prototype.remove_drawable.call(this,ai);if(ah){var ag=this;ai.container_div.fadeOut("slow",function(){$(this).remove();ag.update_intro_div()});this.has_changes=true}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(ao,ag,an,ah){var am=this,ak=(ah?[ah]:am.drawables),ai;var ah;for(var al=0;al<ak.length;al++){ah=ak[al];ai=-1;for(var aj=0;aj<am.tracks_to_be_redrawn.length;aj++){if(am.tracks_to_be_redrawn[aj][0]===ah){ai=aj;break}}if(ai<0){am.tracks_to_be_redrawn.push([ah,ag,an])}else{am.tracks_to_be_redrawn[al][1]=ag;am.tracks_to_be_redrawn[al][2]=an}}requestAnimationFrame(function(){am._redraw(ao)})},_redraw:function(aq){var an=this.low,aj=this.high;if(an<this.max_low){an=this.max_low}if(aj>this.max_high){aj=this.max_high}var ap=this.high-this.low;if(this.high!==0&&ap<this.min_separation){aj=an+this.min_separation}this.low=Math.floor(an);this.high=Math.ceil(aj);this.resolution=Math.pow(C,Math.ceil(Math.log((this.high-this.low)/R)/Math.log(C)));this.zoom_res=Math.pow(v,Math.max(0,Math.ceil(Math.log(this.resolution,v)/Math.log(v))));var ag=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var am=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ar=13;this.overview_box.css({left:ag,width:Math.max(ar,am)}).show();if(am<ar){this.overview_box.css("left",ag-(ar-am)/2)}if(this.overview_highlight){this.overview_highlight.css({left:ag,width:am})}this.update_location(this.low,this.high);if(!aq){var ai,ah,ao;for(var ak=0,al=this.tracks_to_be_redrawn.length;ak<al;ak++){ai=this.tracks_to_be_redrawn[ak][0];ah=this.tracks_to_be_redrawn[ak][1];ao=this.tracks_to_be_redrawn[ak][2];if(ai){ai._draw(ah,ao)}}this.tracks_to_be_redrawn=[];for(ak=0,al=this.label_tracks.length;ak<al;ak++){this.label_tracks[ak]._draw()}}},zoom_in:function(ah,ai){if(this.max_high===0||this.high-this.low<this.min_separation){return}var aj=this.high-this.low,ak=aj/2+this.low,ag=(aj/this.zoom_factor)/2;if(ah){ak=ah/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(ak-ag);this.high=Math.round(ak+ag);this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ah=this.high-this.low,ai=ah/2+this.low,ag=(ah*this.zoom_factor)/2;this.low=Math.round(ai-ag);this.high=Math.round(ai+ag);this.request_redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.nav_container.width(this.container.width());this.request_redraw()},set_overview:function(ai){if(this.overview_drawable){if(this.overview_drawable.dataset_id===ai.dataset_id){return}this.overview_viewport.find(".track").remove()}var ah=ai.copy({content_div:this.overview_viewport}),ag=this;ah.header_div.hide();ah.is_overview=true;ag.overview_drawable=ah;this.overview_drawable.postdraw_actions=function(){ag.overview_highlight.show().height(ag.overview_drawable.content_div.height());ag.overview_viewport.height(ag.overview_drawable.content_div.height()+ag.overview_box.outerHeight());ag.overview_close.show();ag.resize_window()};this.overview_drawable.init();ag.has_changes=true},reset_overview:function(){$(".tipsy").remove();this.overview_viewport.find(".track-tile").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide();view.resize_window();view.overview_drawable=null}});var r=function(ai,am){this.track=ai;this.name=am.name;this.params=[];var au=am.params;for(var aj=0;aj<au.length;aj++){var ao=au[aj],ah=ao.name,at=ao.label,ak=unescape(ao.html),av=ao.value,aq=ao.type;if(aq==="number"){this.params[this.params.length]=new g(ah,at,ak,av,ao.min,ao.max)}else{if(aq=="select"){this.params[this.params.length]=new O(ah,at,ak,av)}else{console.log("WARNING: unrecognized tool parameter type:",ah,aq)}}}this.parent_div=$("<div/>").addClass("dynamic-tool").hide();this.parent_div.bind("drag",function(ax){ax.stopPropagation()}).click(function(ax){ax.stopPropagation()}).bind("dblclick",function(ax){ax.stopPropagation()});var ar=$("<div class='tool-name'>").appendTo(this.parent_div).text(this.name);var ap=this.params;var an=this;$.each(this.params,function(ay,aB){var aA=$("<div>").addClass("param-row").appendTo(an.parent_div);var ax=$("<div>").addClass("param-label").text(aB.label).appendTo(aA);var az=$("<div/>").addClass("slider").html(aB.html).appendTo(aA);az.find(":input").val(aB.value);$("<div style='clear: both;'/>").appendTo(aA)});this.parent_div.find("input").click(function(){$(this).select()});var aw=$("<div>").addClass("param-row").appendTo(this.parent_div);var al=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(aw);var ag=$("<input type='submit'>").attr("value","Run on visible region").css("margin-left","3em").appendTo(aw);var an=this;ag.click(function(){an.run_on_region()});al.click(function(){an.run_on_dataset()})};p(r.prototype,{get_param_values_dict:function(){var ag={};this.parent_div.find(":input").each(function(){var ah=$(this).attr("name"),ai=$(this).val();ag[ah]=JSON.stringify(ai)});return ag},get_param_values:function(){var ah=[];var ag={};this.parent_div.find(":input").each(function(){var ai=$(this).attr("name"),aj=$(this).val();if(ai){ah[ah.length]=aj}});return ah},run_on_dataset:function(){var ag=this;ag.run({dataset_id:this.track.original_dataset_id,tool_id:ag.name},null,function(ah){show_modal(ag.name+" is Running",ag.name+" is running on the complete dataset. Tool outputs are in dataset's history.",{Close:hide_modal})})},run_on_region:function(){var ah={dataset_id:this.track.original_dataset_id,chrom:this.track.view.chrom,low:this.track.view.low,high:this.track.view.high,tool_id:this.name},ak=this.track,ai=ah.tool_id+ak.tool_region_and_parameters_str(ah.chrom,ah.low,ah.high),ag,al;if(ak.container===view){var aj=new Q(this.name,this.track.view,this.track.container);ak.container.add_drawable(aj);ak.container.remove_drawable(ak);aj.add_drawable(ak);ak.container_div.appendTo(aj.content_div);ag=aj}else{ag=ak.container}if(ak instanceof e){al=new V(ai,view,ag,"hda");al.change_mode(ak.mode);ag.add_drawable(al)}al.content_div.text("Starting job.");this.run(ah,al,function(am){al.dataset_id=am.dataset_id;al.content_div.text("Running job.");al.init()})},run:function(ah,ai,aj){$.extend(ah,this.get_param_values_dict());var ag=function(){$.getJSON(rerun_tool_url,ah,function(ak){if(ak==="no converter"){ai.container_div.addClass("error");ai.content_div.text(K)}else{if(ak.error){ai.container_div.addClass("error");ai.content_div.text(x+ak.message)}else{if(ak==="pending"){ai.container_div.addClass("pending");ai.content_div.text("Converting input data so that it can be used quickly with tool.");setTimeout(ag,2000)}else{aj(ak)}}}})};ag()}});var O=function(ah,ag,ai,aj){this.name=ah;this.label=ag;this.html=ai;this.value=aj};var g=function(ai,ah,ak,al,aj,ag){O.call(this,ai,ah,ak,al);this.min=aj;this.max=ag};var h=function(ah,ag,ai,aj){this.name=ah;this.index=ag;this.tool_id=ai;this.tool_exp_name=aj};var W=function(ah,ag,ai,aj){h.call(this,ah,ag,ai,aj);this.low=-Number.MAX_VALUE;this.high=Number.MAX_VALUE;this.min=Number.MAX_VALUE;this.max=-Number.MAX_VALUE;this.container=null;this.slider=null;this.slider_label=null};p(W.prototype,{applies_to:function(ag){if(ag.length>this.index){return true}return false},keep:function(ag){if(!this.applies_to(ag)){return true}var ah=ag[this.index];return(isNaN(ah)||(ah>=this.low&&ah<=this.high))},update_attrs:function(ah){var ag=false;if(!this.applies_to(ah)){return ag}if(ah[this.index]<this.min){this.min=Math.floor(ah[this.index]);ag=true}if(ah[this.index]>this.max){this.max=Math.ceil(ah[this.index]);ag=true}return ag},update_ui_elt:function(){if(this.min!=this.max){this.container.show()}else{this.container.hide()}var ai=function(al,aj){var ak=aj-al;return(ak<=2?0.01:1)};var ah=this.slider.slider("option","min"),ag=this.slider.slider("option","max");if(this.min<ah||this.max>ag){this.slider.slider("option","min",this.min);this.slider.slider("option","max",this.max);this.slider.slider("option","step",ai(this.min,this.max));this.slider.slider("option","values",[this.min,this.max])}}});var ab=function(ar,az){this.track=ar;this.filters=[];for(var au=0;au<az.length;au++){var av=az[au],aA=av.name,ag=av.type,ai=av.index,ay=av.tool_id,ax=av.tool_exp_name;if(ag==="int"||ag==="float"){this.filters[au]=new W(aA,ai,ay,ax)}else{console.log("ERROR: unsupported filter: ",aA,ag)}}var aj=function(aB,aC,aD){aB.click(function(){var aE=aC.text();max=parseFloat(aD.slider("option","max")),input_size=(max<=1?4:max<=1000000?max.toString().length:6),multi_value=false;if(aD.slider("option","values")){input_size=2*input_size+1;multi_value=true}aC.text("");$("<input type='text'/>").attr("size",input_size).attr("maxlength",input_size).attr("value",aE).appendTo(aC).focus().select().click(function(aF){aF.stopPropagation()}).blur(function(){$(this).remove();aC.text(aE)}).keyup(function(aJ){if(aJ.keyCode===27){$(this).trigger("blur")}else{if(aJ.keyCode===13){var aH=aD.slider("option","min"),aF=aD.slider("option","max"),aI=function(aK){return(isNaN(aK)||aK>aF||aK<aH)},aG=$(this).val();if(!multi_value){aG=parseFloat(aG);if(aI(aG)){alert("Parameter value must be in the range ["+aH+"-"+aF+"]");return $(this)}}else{aG=aG.split("-");aG=[parseFloat(aG[0]),parseFloat(aG[1])];if(aI(aG[0])||aI(aG[1])){alert("Parameter value must be in the range ["+aH+"-"+aF+"]");return $(this)}}aD.slider((multi_value?"values":"value"),aG)}}})})};this.parent_div=$("<div/>").addClass("filters").hide();this.parent_div.bind("drag",function(aB){aB.stopPropagation()}).click(function(aB){aB.stopPropagation()}).bind("dblclick",function(aB){aB.stopPropagation()}).bind("keydown",function(aB){aB.stopPropagation()});var aw=$("<div/>").addClass("sliders").appendTo(this.parent_div);var ao=this;$.each(this.filters,function(aE,aG){aG.container=$("<div/>").addClass("filter-row slider-row").appendTo(aw);var aF=$("<div/>").addClass("elt-label").appendTo(aG.container);var aD=$("<span/>").addClass("slider-name").text(aG.name+" ").appendTo(aF);var aC=$("<span/>");var aI=$("<span/>").addClass("slider-value").appendTo(aF).append("[").append(aC).append("]");var aB=$("<div/>").addClass("slider").appendTo(aG.container);aG.control_element=$("<div/>").attr("id",aG.name+"-filter-control").appendTo(aB);var aH=[0,0];aG.control_element.slider({range:true,min:Number.MAX_VALUE,max:-Number.MIN_VALUE,values:[0,0],slide:function(aK,aL){var aJ=aL.values;aC.text(aJ[0]+"-"+aJ[1]);aG.low=aJ[0];aG.high=aJ[1];ao.track.request_draw(true,true)},change:function(aJ,aK){aG.control_element.slider("option","slide").call(aG.control_element,aJ,aK)}});aG.slider=aG.control_element;aG.slider_label=aC;aj(aI,aC,aG.control_element);$("<div style='clear: both;'/>").appendTo(aG.container)});if(this.filters.length!==0){var al=$("<div/>").addClass("param-row").appendTo(aw);var an=$("<input type='submit'/>").attr("value","Run on complete dataset").appendTo(al);var ah=this;an.click(function(){ah.run_on_dataset()})}var aq=$("<div/>").addClass("display-controls").appendTo(this.parent_div),at,am,ap,ak={Transparency:function(aB){ao.alpha_filter=aB},Height:function(aB){ao.height_filter=aB}};$.each(ak,function(aD,aC){at=$("<div/>").addClass("filter-row").appendTo(aq),am=$("<span/>").addClass("elt-label").text(aD+":").appendTo(at),ap=$("<select/>").attr("name",aD+"_dropdown").css("float","right").appendTo(at);$("<option/>").attr("value",-1).text("== None ==").appendTo(ap);for(var aB=0;aB<ao.filters.length;aB++){$("<option/>").attr("value",aB).text(ao.filters[aB].name).appendTo(ap)}ap.change(function(){$(this).children("option:selected").each(function(){var aE=parseInt($(this).val());ak[aD]((aE>=0?ao.filters[aE]:null));ao.track.request_draw(true,true)})});$("<div style='clear: both;'/>").appendTo(at)});$("<div style='clear: both;'/>").appendTo(this.parent_div)};p(ab.prototype,{reset_filters:function(){for(var ag=0;ag<this.filters.length;ag++){filter=this.filters[ag];filter.slider.slider("option","values",[filter.min,filter.max])}this.alpha_filter=null;this.height_filter=null},run_on_dataset:function(){var ao=function(at,aq,ar){if(!(aq in at)){at[aq]=ar}return at[aq]};var ai={},ag,ah,aj;for(var ak=0;ak<this.filters.length;ak++){ag=this.filters[ak];if(ag.tool_id){if(ag.min!=ag.low){ah=ao(ai,ag.tool_id,[]);ah[ah.length]=ag.tool_exp_name+" >= "+ag.low}if(ag.max!=ag.high){ah=ao(ai,ag.tool_id,[]);ah[ah.length]=ag.tool_exp_name+" <= "+ag.high}}}var am=[];for(var ap in ai){am[am.length]=[ap,ai[ap]]}var an=am.length;(function al(ax,au){var ar=au[0],at=ar[0],aw=ar[1],av="("+aw.join(") and (")+")",aq={cond:av,input:ax,target_dataset_id:ax,tool_id:at},au=au.slice(1);$.getJSON(run_tool_url,aq,function(ay){if(ay.error){show_modal("Filter Dataset","Error running tool "+at,{Close:hide_modal})}else{if(au.length===0){show_modal("Filtering Dataset","Filter(s) are running on the complete dataset. Outputs are in dataset's history.",{Close:hide_modal})}else{al(ay.dataset_id,au)}}})})(this.track.dataset_id,am)}});var D=function(ag,ah){M.Scaler.call(this,ah);this.filter=ag};D.prototype.gen_val=function(ag){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_val}return((parseFloat(ag[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var G=function(ag){this.track=ag.track;this.params=ag.params;this.values={};this.restore_values((ag.saved_values?ag.saved_values:{}));this.onchange=ag.onchange};p(G.prototype,{restore_values:function(ag){var ah=this;$.each(this.params,function(ai,aj){if(ag[aj.key]!==undefined){ah.values[aj.key]=ag[aj.key]}else{ah.values[aj.key]=aj.default_value}})},build_form:function(){var ah=this;var ag=$("<div />");$.each(this.params,function(al,aj){if(!aj.hidden){var ai="param_"+al;var an=ah.values[aj.key];var aq=$("<div class='form-row' />").appendTo(ag);aq.append($("<label />").attr("for",ai).text(aj.label+":"));if(aj.type==="bool"){aq.append($('<input type="checkbox" />').attr("id",ai).attr("name",ai).attr("checked",an))}else{if(aj.type==="text"){aq.append($('<input type="text"/>').attr("id",ai).val(an).click(function(){$(this).select()}))}else{if(aj.type==="color"){var am=$("<input />").attr("id",ai).attr("name",ai).val(an);var ao=$("<div class='tipsy tipsy-north' style='position: absolute;' />").hide();var ak=$("<div style='background-color: black; padding: 10px;'></div>").appendTo(ao);var ap=$("<div/>").appendTo(ak).farbtastic({width:100,height:100,callback:am,color:an});$("<div />").append(am).append(ao).appendTo(aq).bind("click",function(ar){ao.css({left:$(this).position().left+($(am).width()/2)-60,top:$(this).position().top+$(this.height)}).show();$(document).bind("click.color-picker",function(){ao.hide();$(document).unbind("click.color-picker")});ar.stopPropagation()})}else{aq.append($("<input />").attr("id",ai).attr("name",ai).val(an))}}}}});return ag},update_from_form:function(ag){var ai=this;var ah=false;$.each(this.params,function(aj,al){if(!al.hidden){var am="param_"+aj;var ak=ag.find("#"+am).val();if(al.type==="float"){ak=parseFloat(ak)}else{if(al.type==="int"){ak=parseInt(ak)}else{if(al.type==="bool"){ak=ag.find("#"+am).is(":checked")}}}if(ak!==ai.values[al.key]){ai.values[al.key]=ak;ah=true}}});if(ah){this.onchange()}}});var b=function(ag,aj,ai,ah,ak){this.track=ag;this.index=aj;this.low=aj*R*ai;this.high=(aj+1)*R*ai;this.resolution=ai;this.canvas=$("<div class='track-tile'/>").append(ah);this.data=ak;this.stale=false};b.prototype.predisplay_actions=function(){};var k=function(ag,aj,ai,ah,ak,al){b.call(this,ag,aj,ai,ah,ak);this.max_val=al};p(k.prototype,b.prototype);var P=function(ag,ak,aj,ai,am,an,al,ah){b.call(this,ag,ak,aj,ai,am);this.mode=an;this.message=al;this.feature_mapper=ah};p(P.prototype,b.prototype);P.prototype.predisplay_actions=function(){var ah=this,ag={};if(ah.mode!=="Pack"){return}$(this.canvas).mousemove(function(at){var an=$(this).offset(),ar=at.pageX-an.left,aq=at.pageY-an.top,ax=ah.feature_mapper.get_feature_data(ar,aq),ao=(ax?ax[0]:null);$(this).siblings(".feature-popup").each(function(){if(!ao||$(this).attr("id")!==ao.toString()){$(this).remove()}});if(ax){var aj=ag[ao];if(!aj){var ao=ax[0],au={name:ax[3],start:ax[1],end:ax[2],strand:ax[4]},am=ah.track.filters_manager.filters,al;for(var ap=0;ap<am.length;ap++){al=am[ap];au[al.name]=ax[al.index]}var aj=$("<div/>").attr("id",ao).addClass("feature-popup"),aw,av,ay=$("<table/>").appendTo(aj),az;for(aw in au){av=au[aw];az=$("<tr/>").appendTo(ay);$("<th/>").appendTo(az).text(aw);$("<td/>").attr("align","left").appendTo(az).text(typeof(av)=="number"?aa(av,2):av)}ag[ao]=aj}aj.appendTo($(ah.canvas).parent());var ak=ar+parseInt(ah.canvas.css("left"))+7,ai=aq+parseInt(ah.canvas.css("top"))+7;aj.css("left",ak+"px").css("top",ai+"px")}else{if(!at.isPropagationStopped()){at.stopPropagation();$(this).siblings().each(function(){$(this).trigger(at)})}}}).mouseleave(function(){$(this).siblings(".feature-popup").remove()})};var i=function(aj,ar,ak,an,at,ai,ah){q.call(this,aj,ar,ak,{},"draghandle");this.data_url=(ai?ai:default_data_url);this.data_url_extra_params={};this.data_query_wait=(ah?ah:L);this.dataset_check_url=converted_datasets_state_url;if(!i.id_counter){i.id_counter=0}this.id=i.id_counter++;this.container_div=$("<div />").addClass("track").attr("id","track_"+this.id).css("position","relative");if(an){this.header_div=$("<div class='track-header' />").appendTo(this.container_div);if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(this.header_div)}this.name_div=$("<div/>").addClass("track-name").appendTo(this.header_div).text(this.name).attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase());this.icons_div=$("<div/>").css("float","left").appendTo(this.header_div).hide();this.settings_icon=$("<a/>").attr("href","javascript:void(0);").attr("title","Edit settings").addClass("icon-button settings-icon").tipsy({gravity:"s"}).appendTo(this.icons_div);this.overview_icon=$("<a/>").attr("href","javascript:void(0);").attr("title","Set as overview").addClass("icon-button overview-icon").tipsy({gravity:"s"}).appendTo(this.icons_div);this.filters_icon=$("<a/>").attr("href","javascript:void(0);").attr("title","Filters").addClass("icon-button filters-icon").tipsy({gravity:"s"}).appendTo(this.icons_div).hide();this.tools_icon=$("<a/>").attr("href","javascript:void(0);").attr("title","Tools").addClass("icon-button tools-icon").tipsy({gravity:"s"}).appendTo(this.icons_div).hide();this.remove_icon=$("<a/>").attr("href","javascript:void(0);").attr("title","Remove").addClass("icon-button remove-icon").tipsy({gravity:"s"}).appendTo(this.icons_div);var al=this;this.header_div.dblclick(function(au){au.stopPropagation()});this.settings_icon.click(function(){var aw=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},au=function(){al.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},av=function(ax){if((ax.keyCode||ax.which)===27){aw()}else{if((ax.keyCode||ax.which)===13){au()}}};$(window).bind("keypress.check_enter_esc",av);show_modal("Configure Track",al.config.build_form(),{Cancel:aw,OK:au})});this.overview_icon.click(function(){al.view.set_overview(al)});this.filters_icon.click(function(){al.filters_div.toggle();al.filters_manager.reset_filters()});this.tools_icon.click(function(){al.dynamic_tool_div.toggle();if(al.dynamic_tool_div.is(":visible")){al.set_name(al.name+al.tool_region_and_parameters_str())}else{al.revert_name()}$(".tipsy").remove()});this.remove_icon.click(function(){$(".tipsy").remove();al.remove()});if(al.display_modes!==undefined){if(al.mode_div===undefined){al.mode_div=$("<div class='right-float menubutton popup' />").appendTo(al.header_div);var am=(al.config&&al.config.values.mode?al.config.values.mode:al.display_modes[0]);al.mode=am;al.mode_div.text(am);var ag={};for(var ao=0,aq=al.display_modes.length;ao<aq;ao++){var ap=al.display_modes[ao];ag[ap]=function(au){return function(){al.change_mode(au)}}(ap)}make_popupmenu(al.mode_div,ag)}else{al.mode_div.hide()}this.header_div.append($("<div/>").css("clear","both"));this.container_div.hover(function(){al.icons_div.show()},function(){al.icons_div.hide()})}}this.content_div=$("<div class='track-content'>").appendTo(this.container_div);this.container.content_div.append(this.container_div)};p(i.prototype,q.prototype,{get_type:function(){if(this instanceof ac){return"LabelTrack"}else{if(this instanceof A){return"ReferenceTrack"}else{if(this instanceof j){return"LineTrack"}else{if(this instanceof X){return"ReadTrack"}else{if(this instanceof V){return"ToolDataFeatureTrack"}else{if(this instanceof U){return"VcfTrack"}else{if(this instanceof e){return"FeatureTrack"}}}}}}}return""},init:function(){var ag=this;ag.enabled=false;ag.tile_cache.clear();ag.data_manager.clear();ag.initial_canvas=undefined;ag.content_div.css("height","auto");ag.container_div.removeClass("nodata error pending");if(!ag.dataset_id){return}$.getJSON(converted_datasets_state_url,{hda_ldda:ag.hda_ldda,dataset_id:ag.dataset_id,chrom:ag.view.chrom},function(ah){if(!ah||ah==="error"||ah.kind==="error"){ag.container_div.addClass("error");ag.content_div.text(o);if(ah.message){var ai=$(" <a href='javascript:void(0);'></a>").text("View error").click(function(){show_modal("Trackster Error","<pre>"+ah.message+"</pre>",{Close:hide_modal})});ag.content_div.append(ai)}}else{if(ah==="no converter"){ag.container_div.addClass("error");ag.content_div.text(K)}else{if(ah==="no data"||(ah.data!==undefined&&(ah.data===null||ah.data.length===0))){ag.container_div.addClass("nodata");ag.content_div.text(F)}else{if(ah==="pending"){ag.container_div.addClass("pending");ag.content_div.text(t);setTimeout(function(){ag.init()},ag.data_query_wait)}else{if(ah.status==="data"){if(ah.valid_chroms){ag.valid_chroms=ah.valid_chroms;ag.update_track_icons()}ag.content_div.text(Z);if(ag.view.chrom){ag.content_div.text("");ag.content_div.css("height",ag.height_px+"px");ag.enabled=true;$.when(ag.predraw_init()).done(function(){ag.container_div.removeClass("nodata error pending");ag.request_draw()})}}}}}}});this.update_track_icons()},predraw_init:function(){}});var N=function(ai,ao,aj,al,ap,an,am,ah,ag){i.call(this,ai,ao,aj,al,ap,ah,ag);var ak=this,ao=ak.view;m(ak.container_div,ak.drag_handle_class,".group",ak);this.filters_manager=new ab(this,(an!==undefined?an:{}));this.filters_available=false;this.filters_visible=false;this.tool=(am!==undefined&&obj_length(am)>0?new r(this,am):undefined);if(this.header_div){if(this.filters_manager){this.filters_div=this.filters_manager.parent_div;this.header_div.after(this.filters_div)}if(this.tool){this.dynamic_tool_div=this.tool.parent_div;this.header_div.after(this.dynamic_tool_div)}}};p(N.prototype,q.prototype,i.prototype,{copy:function(ag){return new this.constructor(this.name,this.view,ag,this.hda_ldda,this.dataset_id,this.prefs,this.filters,this.tool)},to_json:function(){return{track_type:this.get_type(),name:this.name,hda_ldda:this.hda_ldda,dataset_id:this.dataset_id,prefs:this.prefs,mode:this.mode,}},change_mode:function(ah){var ag=this;ag.mode_div.text(ah);ag.mode=ah;ag.config.values.mode=ah;ag.tile_cache.clear();ag.request_draw();return ag},update_track_icons:function(){var ag=this;if(ag.filters_available>0){ag.filters_icon.show()}else{ag.filters_icon.hide()}if(ag.tool){ag.tools_icon.show()}else{ag.tools_icon.hide()}},_gen_tile_cache_key:function(ah,ai,ag){return ah+"_"+ai+"_"+ag},request_draw:function(ah,ag){this.view.request_redraw(false,ah,ag,this)},_draw:function(ai,aq){if(!this.enabled){return}if(!(this instanceof A)&&(!this.dataset_id)){return}var ap=this.view.low,am=this.view.high,an=am-ap,aj=this.view.container.width(),au=aj/an,al=this.view.resolution,at=$("<div style='position: relative;'></div>");if(this.is_overview){ap=this.view.max_low;am=this.view.max_high;al=Math.pow(C,Math.ceil(Math.log((view.max_high-view.max_low)/R)/Math.log(C)));au=aj/(view.max_high-view.max_low)}if(!aq){this.content_div.children().remove()}this.content_div.append(at);this.max_height=0;var ah=Math.floor(ap/al/R);var ao=true;var ar=[];var ag=0;while((ah*R*al)<am){tile=this.draw_helper(ai,aj,ah,al,at,au);if(tile){ar.push(tile)}else{ao=false}ah+=1;ag++}var ak=this;if(ao){ak.postdraw_actions(ar,aj,au,aq)}},postdraw_actions:function(ak,al,am,ag){var ai=this;var aj=false;for(var ah=0;ah<ak.length;ah++){if(ak[ah].message){aj=true;break}}if(aj){for(var ah=0;ah<ak.length;ah++){tile=ak[ah];if(!tile.message){tile.canvas.css("padding-top",E)}}}},draw_helper:function(ah,ai,aj,am,at,ax,au,an){var ak=this,ar=this._gen_tile_cache_key(ai,ax,aj),ao=aj*R*am,aw=ao+R*am;var ap=(ah?undefined:ak.tile_cache.get(ar));if(ap){ak.show_tile(ap,at,ax);return ap}var aq=function(ay){return("isResolved" in ay)};var al=true;var ag=ak.data_manager.get_data(ao,aw,ak.mode,am,ak.data_url_extra_params);if(aq(ag)){al=false}var av;if(view.reference_track&&ax>view.canvas_manager.char_width_px){av=view.reference_track.data_manager.get_data(ao,aw,ak.mode,am,view.reference_track.data_url_extra_params);if(aq(av)){al=false}}if(al){p(ag,an);var ap=ak.draw_tile(ag,ak.mode,am,aj,ax,av);if(ap!==undefined){ak.tile_cache.set(ar,ap);ak.show_tile(ap,at,ax)}return ap}$.when(ag,av).then(function(){view.request_redraw(false,false,false,ak)});return null},show_tile:function(am,ao,ap){var ai=this,ah=am.canvas,al=ah;if(am.message){var aq=$("<div/>"),an=$("<div/>").addClass("tile-message").text(am.message).css({height:E-1,width:am.canvas.width}).appendTo(aq),ak=$("<a href='javascript:void(0);'/>").addClass("icon more-down").appendTo(an),ag=$("<a href='javascript:void(0);'/>").addClass("icon more-across").appendTo(an);aq.append(ah);al=aq;ak.click(function(){am.stale=true;ai.data_manager.get_more_data(am.low,am.high,ai.mode,am.resolution,{},ai.data_manager.DEEP_DATA_REQ);ai.request_draw()}).dblclick(function(ar){ar.stopPropagation()});ag.click(function(){am.stale=true;ai.data_manager.get_more_data(am.low,am.high,ai.mode,am.resolution,{},ai.data_manager.BROAD_DATA_REQ);ai.request_draw()}).dblclick(function(ar){ar.stopPropagation()})}am.predisplay_actions();var aj=(am.low-(this.is_overview?this.view.max_low:this.view.low))*ap;if(this.left_offset){aj-=this.left_offset}al.css({position:"absolute",top:0,left:aj,height:""});ao.append(al);ai.max_height=Math.max(ai.max_height,al.height());ai.content_div.css("height",ai.max_height+"px");ao.children().css("height",ai.max_height+"px")},_get_tile_bounds:function(ag,ah){var aj=ag*R*ah,ak=R*ah,ai=(aj+ak<=this.view.max_high?aj+ak:this.view.max_high);return[aj,ai]},tool_region_and_parameters_str:function(ai,ag,aj){var ah=this,ak=(ai!==undefined&&ag!==undefined&&aj!==undefined?ai+":"+ag+"-"+aj:"all");return" - region=["+ak+"], parameters=["+ah.tool.get_param_values().join(", ")+"]"}});var ac=function(ah,ag){i.call(this,"label",ah,ag,false,{});this.container_div.addClass("label-track")};p(ac.prototype,i.prototype,{init:function(){this.enabled=true},_draw:function(){var ai=this.view,aj=ai.high-ai.low,am=Math.floor(Math.pow(10,Math.floor(Math.log(aj)/Math.log(10)))),ag=Math.floor(ai.low/am)*am,ak=this.view.container.width(),ah=$("<div style='position: relative; height: 1.3em;'></div>");while(ag<ai.high){var al=(ag-ai.low)/aj*ak;ah.append($("<div class='label'>"+commatize(ag)+"</div>").css({position:"absolute",left:al-1}));ag+=am}this.content_div.children(":first").remove();this.content_div.append(ah)}});var A=function(ag){N.call(this,"reference",ag,{content_div:ag.top_labeltrack},false,{});ag.reference_track=this;this.left_offset=200;this.height_px=12;this.container_div.addClass("reference-track");this.content_div.css("background","none");this.content_div.css("min-height","0px");this.content_div.css("border","none");this.data_url=reference_url;this.data_url_extra_params={dbkey:ag.dbkey};this.data_manager=new I(B,this,false);this.tile_cache=new c(u)};p(A.prototype,q.prototype,N.prototype,{init:function(){this.enabled=true},draw_tile:function(aq,am,al,ah,ar){var ak=this,ai=R*al;if(ar>this.view.canvas_manager.char_width_px){if(aq.data===null){ak.content_div.css("height","0px");return}var aj=this.view.canvas_manager.new_canvas();var ap=aj.getContext("2d");aj.width=Math.ceil(ai*ar+ak.left_offset);aj.height=ak.height_px;ap.font=ap.canvas.manager.default_font;ap.textAlign="center";aq=aq.data;for(var an=0,ao=aq.length;an<ao;an++){var ag=Math.round(an*ar);ap.fillText(aq[an],ag+ak.left_offset,10)}return new b(ak,ah,al,aj,aq)}this.content_div.css("height","0px")}});var j=function(al,aj,ai,am,ag,ak){var ah=this;this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";N.call(this,al,aj,ai,true,ak);this.min_height_px=16;this.max_height_px=400;this.height_px=80;this.hda_ldda=am;this.dataset_id=ag;this.original_dataset_id=ag;this.data_manager=new S(B,this);this.tile_cache=new c(u);this.left_offset=0;this.config=new G({track:this,params:[{key:"name",label:"Name",type:"text",default_value:al},{key:"color",label:"Color",type:"color",default_value:get_random_color()},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:this.height_px,hidden:true}],saved_values:ak,onchange:function(){ah.set_name(ah.prefs.name);ah.vertical_range=ah.prefs.max_value-ah.prefs.min_value;$("#linetrack_"+ah.dataset_id+"_minval").text(ah.prefs.min_value);$("#linetrack_"+ah.dataset_id+"_maxval").text(ah.prefs.max_value);ah.tile_cache.clear();ah.request_draw()}});this.prefs=this.config.values;this.height_px=this.config.values.height;this.vertical_range=this.config.values.max_value-this.config.values.min_value;this.add_resize_handle()};p(j.prototype,q.prototype,N.prototype,{add_resize_handle:function(){var ag=this;var aj=false;var ai=false;var ah=$("<div class='track-resize'>");$(ag.container_div).hover(function(){aj=true;ah.show()},function(){aj=false;if(!ai){ah.hide()}});ah.hide().bind("dragstart",function(ak,al){ai=true;al.original_height=$(ag.content_div).height()}).bind("drag",function(al,am){var ak=Math.min(Math.max(am.original_height+am.deltaY,ag.min_height_px),ag.max_height_px);$(ag.content_div).css("height",ak);ag.height_px=ak;ag.request_draw(true)}).bind("dragend",function(ak,al){ag.tile_cache.clear();ai=false;if(!aj){ah.hide()}ag.config.values.height=ag.height_px}).appendTo(ag.container_div)},predraw_init:function(){var ag=this;ag.vertical_range=undefined;return $.getJSON(ag.data_url,{stats:true,chrom:ag.view.chrom,low:null,high:null,hda_ldda:ag.hda_ldda,dataset_id:ag.dataset_id},function(ah){ag.container_div.addClass("line-track");var aj=ah.data;if(isNaN(parseFloat(ag.prefs.min_value))||isNaN(parseFloat(ag.prefs.max_value))){ag.prefs.min_value=aj.min;ag.prefs.max_value=aj.max;$("#track_"+ag.dataset_id+"_minval").val(ag.prefs.min_value);$("#track_"+ag.dataset_id+"_maxval").val(ag.prefs.max_value)}ag.vertical_range=ag.prefs.max_value-ag.prefs.min_value;ag.total_frequency=aj.total_frequency;ag.container_div.find(".yaxislabel").remove();var ak=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+ag.dataset_id+"_minval").text(aa(ag.prefs.min_value,3));var ai=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+ag.dataset_id+"_maxval").text(aa(ag.prefs.max_value,3));ai.css({position:"absolute",top:"24px",left:"10px"});ai.prependTo(ag.container_div);ak.css({position:"absolute",bottom:"2px",left:"10px"});ak.prependTo(ag.container_div)})},draw_tile:function(at,al,ak,ai,ar){if(this.vertical_range===undefined){return}var ag=this._get_tile_bounds(ai,ak),am=ag[0],aq=ag[1],ah=Math.ceil((aq-am)*ar),ao=this.height_px;var aj=this.view.canvas_manager.new_canvas();aj.width=ah,aj.height=ao;var ap=aj.getContext("2d");var an=new M.LinePainter(at.data,am,aq,this.prefs,al);an.draw(ap,ah,ao);return new b(this.track,ai,ak,aj,at.data)}});var e=function(ag,am,ah,al,ao,an,aj,ak){var ai=this;this.display_modes=["Auto","Histogram","Dense","Squish","Pack"];N.call(this,ag,am,ah,true,an,aj,ak);this.config=new G({track:this,params:[{key:"name",label:"Name",type:"text",default_value:ag},{key:"block_color",label:"Block color",type:"color",default_value:get_random_color()},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:an,onchange:function(){ai.set_name(ai.prefs.name);ai.tile_cache.clear();ai.request_draw()}});this.prefs=this.config.values;this.height_px=0;this.container_div.addClass("feature-track");this.hda_ldda=al;this.dataset_id=ao;this.original_dataset_id=ao;this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.inc_slots={};this.start_end_dct={};this.tile_cache=new c(d);this.data_manager=new S(20,this);this.left_offset=200;this.painter=M.LinkedFeaturePainter};p(e.prototype,q.prototype,N.prototype,{postdraw_actions:function(aw,ag,ax,av){N.prototype.postdraw_actions.call(this,aw,av);var aj=this;if(av){var al=aj.content_div.children();var am=false;for(var ak=al.length-1,aq=0;ak>=aq;ak--){var ai=$(al[ak]);if(am){ai.remove()}else{if(ai.children().length!==0){am=true}}}}if(aj.mode=="Histogram"){var ap=-1;for(var ak=0;ak<aw.length;ak++){var au=aw[ak].max_val;if(au>ap){ap=au}}for(var ak=0;ak<aw.length;ak++){var at=aw[ak];if(at.max_val!==ap){at.canvas.remove();aj.draw_helper(true,ag,at.index,at.resolution,at.canvas.parent(),ax,[],{max:ap})}}}if(aj.filters_manager){var ah=aj.filters_manager.filters;for(var ao=0;ao<ah.length;ao++){ah[ao].update_ui_elt()}var an=false,ar;for(var ak=0;ak<aw.length;ak++){if(aw[ak].data.length){ar=aw[ak].data[0];for(var ao=0;ao<ah.length;ao++){if(ah[ao].applies_to(ar)){an=true;break}}}}if(aj.filters_available!==an){aj.filters_available=an;if(!aj.filters_available){aj.filters_div.hide()}aj.update_track_icons()}}},update_auto_mode:function(ag){if(this.mode=="Auto"){if(ag=="no_detail"){ag="feature spans"}else{if(ag=="summary_tree"){ag="coverage histogram"}}this.mode_div.text("Auto ("+ag+")")}},incremental_slots:function(ak,ah,aj){var ai=this.view.canvas_manager.dummy_context,ag=this.inc_slots[ak];if(!ag||(ag.mode!==aj)){ag=new (s.FeatureSlotter)(ak,aj==="Pack",z,function(al){return ai.measureText(al)});ag.mode=aj;this.inc_slots[ak]=ag}return ag.slot_features(ah)},get_summary_tree_data:function(ak,an,ai,aw){if(aw>ai-an){aw=ai-an}var ar=Math.floor((ai-an)/aw),av=[],aj=0;var al=0,am=0,aq,au=0,ao=[],at,ap;var ah=function(az,ay,aA,ax){az[0]=ay+aA*ax;az[1]=ay+(aA+1)*ax};while(au<aw&&al!==ak.length){var ag=false;for(;au<aw&&!ag;au++){ah(ao,an,au,ar);for(am=al;am<ak.length;am++){aq=ak[am].slice(1,3);if(is_overlap(aq,ao)){ag=true;break}}if(ag){break}}data_start_index=am;av[av.length]=at=[ao[0],0];for(;am<ak.length;am++){aq=ak[am].slice(1,3);if(is_overlap(aq,ao)){at[1]++}else{break}}if(at[1]>aj){aj=at[1]}au++}return{max:aj,delta:ar,data:av}},draw_tile:function(av,ay,aC,aG,aq,aj){var az=this,al=az._get_tile_bounds(aG,aC),aJ=al[0],ah=al[1],ax=ah-aJ,aA=Math.ceil(ax*aq),aP=25,ak=this.left_offset,aw,am;if(ay==="Auto"){if(av.dataset_type==="summary_tree"){ay=av.dataset_type}else{if(av.extra_info==="no_detail"||az.is_overview){ay="no_detail"}else{var aO=av.data;if(this.view.high-this.view.low>J){ay="Squish"}else{ay="Pack"}}}this.update_auto_mode(ay)}if(ay==="summary_tree"||ay==="Histogram"){am=this.summary_draw_height;this.container_div.find(".yaxislabel").remove();var ag=$("<div />").addClass("yaxislabel");ag.text(av.max);ag.css({position:"absolute",top:"24px",left:"10px",color:this.prefs.label_color});ag.prependTo(this.container_div);var ai=this.view.canvas_manager.new_canvas();ai.width=aA+ak;ai.height=am+T;if(av.dataset_type!="summary_tree"){var ar=this.get_summary_tree_data(av.data,aJ,ah,200);if(av.max){ar.max=av.max}av=ar}var aL=new M.SummaryTreePainter(av,aJ,ah,this.prefs);var aB=ai.getContext("2d");aB.translate(ak,T);aL.draw(aB,aA,am);return new k(az,aG,aC,ai,av.data,av.max)}var aw,ao=1;if(ay==="no_detail"||ay==="Squish"||ay==="Pack"){ao=this.incremental_slots(aq,av.data,ay);aw=this.inc_slots[aq].slots}var ap=[];if(av.data){var at=this.filters_manager.filters;for(var aD=0,aF=av.data.length;aD<aF;aD++){var an=av.data[aD];var aE=false;var au;for(var aI=0,aN=at.length;aI<aN;aI++){au=at[aI];au.update_attrs(an);if(!au.keep(an)){aE=true;break}}if(!aE){ap.push(an)}}}var aM=(this.filters_manager.alpha_filter?new D(this.filters_manager.alpha_filter):null);var aK=(this.filters_manager.height_filter?new D(this.filters_manager.height_filter):null);var aL=new (this.painter)(ap,aJ,ah,this.prefs,ay,aM,aK,aj);var am=Math.max(ae,aL.get_required_height(ao));var ai=this.view.canvas_manager.new_canvas();var aH=null;ai.width=aA+ak;ai.height=am;var aB=ai.getContext("2d");aB.fillStyle=this.prefs.block_color;aB.font=aB.canvas.manager.default_font;aB.textAlign="right";this.container_div.find(".yaxislabel").remove();if(av.data){aB.translate(ak,0);aH=aL.draw(aB,aA,am,aw);aH.translation=-ak}return new P(az,aG,aC,ai,av.data,ay,av.message,aH)}});var U=function(ak,ai,ah,am,ag,aj,al){e.call(this,ak,ai,ah,am,ag,aj,al);this.config=new G({track:this,params:[{key:"name",label:"Name",type:"text",default_value:ak},{key:"block_color",label:"Block color",type:"color",default_value:get_random_color()},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:aj,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=M.ReadPainter};p(U.prototype,q.prototype,N.prototype,e.prototype);var X=function(ak,ai,ah,am,ag,aj,al){e.call(this,ak,ai,ah,am,ag,aj,al);this.config=new G({track:this,params:[{key:"name",label:"Name",type:"text",default_value:ak},{key:"block_color",label:"Block color",type:"color",default_value:get_random_color()},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:aj,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=M.ReadPainter;this.update_track_icons()};p(X.prototype,q.prototype,N.prototype,e.prototype);var V=function(ak,ai,ah,am,ag,aj,al){e.call(this,ak,ai,ah,am,ag,aj,al,{});this.data_url=raw_data_url;this.data_query_wait=1000;this.dataset_check_url=dataset_state_url};p(V.prototype,q.prototype,N.prototype,e.prototype,{predraw_init:function(){var ah=this;var ag=function(){if(ah.data_manager.size()===0){setTimeout(ag,300)}else{ah.data_url=default_data_url;ah.data_query_wait=L;ah.dataset_state_url=converted_datasets_state_url;$.getJSON(ah.dataset_state_url,{dataset_id:ah.dataset_id,hda_ldda:ah.hda_ldda},function(ai){})}};ag()}});Y.View=ad;Y.DrawableGroup=Q;Y.LineTrack=j;Y.FeatureTrack=e;Y.ReadTrack=X;Y.VcfTrack=U};var slotting_module=function(c,b){var e=c("class").extend;var d=2,a=5;b.FeatureSlotter=function(i,h,f,g){this.slots={};this.start_end_dct={};this.w_scale=i;this.include_label=h;this.max_rows=f;this.measureText=g};e(b.FeatureSlotter.prototype,{slot_features:function(m){var p=this.w_scale,s=this.slots,h=this.start_end_dct,y=[],A=[],n=0,z=this.max_rows;for(var w=0,x=m.length;w<x;w++){var l=m[w],o=l[0];if(s[o]!==undefined){n=Math.max(n,s[o]);A.push(s[o])}else{y.push(w)}}var q=function(F,G){for(var E=0;E<=z;E++){var C=false,H=h[E];if(H!==undefined){for(var B=0,D=H.length;B<D;B++){var i=H[B];if(G>i[0]&&F<i[1]){C=true;break}}}if(!C){return E}}return -1};for(var w=0,x=y.length;w<x;w++){var l=m[y[w]],o=l[0],u=l[1],f=l[2],r=l[3],g=Math.floor(u*p),k=Math.ceil(f*p),v=this.measureText(r).width,j;if(r!==undefined&&this.include_label){v+=(d+a);if(g-v>=0){g-=v;j="left"}else{k+=v;j="right"}}var t=q(g,k);if(t>=0){if(h[t]===undefined){h[t]=[]}h[t].push([g,k]);s[o]=t;n=Math.max(n,t)}else{}}return n+1}})};var painters_module=function(i,w){var t=i("class").extend;var o=function(H,z,F,y,E,C){if(C===undefined){C=4}var B=y-z;var A=E-F;var D=Math.floor(Math.sqrt(B*B+A*A)/C);var I=B/D;var G=A/D;var x;for(x=0;x<D;x++,z+=I,F+=G){if(x%2!==0){continue}H.fillRect(z,F,C,1)}};var p=function(A,z,x,D){var C=z-D/2,B=z+D/2,E=x-Math.sqrt(D*3/2);A.beginPath();A.moveTo(C,E);A.lineTo(B,E);A.lineTo(z,x);A.lineTo(C,E);A.strokeStyle=this.fillStyle;A.fill();A.stroke();A.closePath()};var d=function(x){this.default_val=(x?x:1)};d.prototype.gen_val=function(x){return this.default_val};var l=function(z,B,x,y,A){this.data=z;this.view_start=B;this.view_end=x;this.prefs=t({},this.default_prefs,y);this.mode=A};l.prototype.default_prefs={};var u=function(z,B,x,y,A){l.call(this,z,B,x,y,A)};u.prototype.default_prefs={show_counts:false};u.prototype.draw=function(M,z,L){var E=this.view_start,O=this.view_end-this.view_start,N=z/O;var J=this.data.data,I=this.data.delta,G=this.data.max,B=L;delta_x_px=Math.ceil(I*N);M.save();for(var C=0,D=J.length;C<D;C++){var H=Math.floor((J[C][0]-E)*N);var F=J[C][1];if(!F){continue}var K=F/G*L;if(F!==0&&K<1){K=1}M.fillStyle=this.prefs.block_color;M.fillRect(H,B-K,delta_x_px,K);var A=4;if(this.prefs.show_counts&&(M.measureText(F).width+A)<delta_x_px){M.fillStyle=this.prefs.label_color;M.textAlign="center";M.fillText(F,H+(delta_x_px/2),10)}}M.restore()};var b=function(x,B,D,E,z){l.call(this,x,B,D,E,z);if(this.prefs.min_value===undefined){var F=Infinity;for(var y=0,A=this.data.length;y<A;y++){F=Math.min(F,this.data[y][1])}this.prefs.min_value=F}if(this.prefs.max_value===undefined){var C=-Infinity;for(var y=0,A=this.data.length;y<A;y++){C=Math.max(C,this.data[y][1])}this.prefs.max_value=C}};b.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Histogram",color:"#000",overflow_color:"#F66"};b.prototype.draw=function(M,L,J){var E=false,G=this.prefs.min_value,C=this.prefs.max_value,I=C-G,x=J,z=this.view_start,K=this.view_end-this.view_start,A=L/K,H=this.mode,S=this.data;M.save();var T=Math.round(J+G/I*J);if(H!=="Intensity"){M.fillStyle="#aaa";M.fillRect(0,T,L,1)}M.beginPath();var Q,D,B;if(S.length>1){B=Math.ceil((S[1][0]-S[0][0])*A)}else{B=10}for(var N=0,O=S.length;N<O;N++){M.fillStyle=this.prefs.color;Q=Math.round((S[N][0]-z)*A);D=S[N][1];var P=false,F=false;if(D===null){if(E&&H==="Filled"){M.lineTo(Q,x)}E=false;continue}if(D<G){F=true;D=G}else{if(D>C){P=true;D=C}}if(H==="Histogram"){D=Math.round(D/I*x);M.fillRect(Q,T,B,-D)}else{if(H==="Intensity"){D=255-Math.floor((D-G)/I*255);M.fillStyle="rgb("+D+","+D+","+D+")";M.fillRect(Q,0,B,x)}else{D=Math.round(x-(D-G)/I*x);if(E){M.lineTo(Q,D)}else{E=true;if(H==="Filled"){M.moveTo(Q,x);M.lineTo(Q,D)}else{M.moveTo(Q,D)}}}}M.fillStyle=this.prefs.overflow_color;if(P||F){var R;if(H==="Histogram"||H==="Intensity"){R=B}else{Q-=2;R=4}if(P){M.fillRect(Q,0,R,3)}if(F){M.fillRect(Q,x-3,R,3)}}M.fillStyle=this.prefs.color}if(H==="Filled"){if(E){M.lineTo(Q,T);M.lineTo(0,T)}M.fill()}else{M.stroke()}M.restore()};var 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F=this.height_scaler.gen_val(U),O=Math.ceil(S*F),am=Math.round((S-O)/2);if(F!==1){L.fillRect(aa,I+1,M-aa,am);L.fillRect(aa,I+S-am+1,M-aa,am)}}}L.globalAlpha=1;if(C==="Pack"&&ah>N){L.fillStyle=ac;if(N===0&&aa-L.measureText(P).width<0){L.textAlign="left";L.fillText(P,M+j,X+8);ak+=L.measureText(P).width+j}else{L.textAlign="right";L.fillText(P,aa-j,X+8);Y-=L.measureText(P).width+j}}}L.globalAlpha=1;return[Y,ak]}});var s=function(A,D,x,z,C,E,B,y){n.call(this,A,D,x,z,C,E,B);this.ref_seq=(y?y.data:null)};s.prototype.default_prefs=t({},n.prototype.default_prefs,{show_insertions:false});t(s.prototype,n.prototype,{get_row_height:function(){var x,y=this.mode;if(y==="Dense"){x=c}else{if(y==="Squish"){x=k}else{x=v;if(this.prefs.show_insertions){x*=2}}}return x},draw_read:function(U,P,L,Z,A,T,I,F,E){U.textAlign="center";var S=this,z=[Z,A],O=0,V=0,R=0,x=U.canvas.manager.char_width_px;var ae=[];if((P==="Pack"||this.mode==="Auto")&&F!==undefined&&L>x){R=Math.round(L/2)}if(!I){I=[[0,F.length]]}for(var 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ag=an;if(aj===this.DEEP_DATA_REQ){$.extend(al,{start_val:ao.data.length+1})}else{if(aj===this.BROAD_DATA_REQ){ag=(ao.max_high?ao.max_high:ao.data[ao.data.length-1][2])+1}}var af=this,ak=this.load_data(ag,ai,am,ah,al);new_data_available=$.Deferred();this.set_data(an,ai,am,new_data_available);$.when(ak).then(function(ap){if(ap.data){ap.data=ao.data.concat(ap.data);if(ap.max_low){ap.max_low=ao.max_low}if(ap.message){ap.message=ap.message.replace(/[0-9]+/,ap.data.length)}}af.set_data(an,ai,am,ap);new_data_available.resolve(ap)});return new_data_available},get_data_from_cache:function(af,ag,ah){return this.get(this.gen_key(af,ag,ah))},set_data:function(ag,ah,ai,af){return this.set(this.gen_key(ag,ah,ai),af)},gen_key:function(af,ah,ai){var ag=af+"_"+ah+"_"+ai;return ag},split_key:function(af){return af.split("_")}});var I=function(ag,af,ah){S.call(this,ag,af,ah)};p(I.prototype,S.prototype,c.prototype,{load_data:function(af,ai,aj,ag,ah){if(ag>1){return{data:null}}return S.prototype.load_data.call(this,af,ai,aj,ag,ah)}});var q=function(ai,ag,af,ah,aj){this.name=ai;this.view=ag;this.container=af;this.config=new G({track:this,params:[{key:"name",label:"Name",type:"text",default_value:ai}],saved_values:ah,onchange:function(){this.track.set_name(this.track.config.values.name)}});this.prefs=this.config.values;this.drag_handle_class=aj;this.is_overview=false};p(q.prototype,{init:function(){},request_draw:function(){},_draw:function(){},to_json:function(){},update_track_icons:function(){},set_name:function(af){this.old_name=this.name;this.name=af;this.name_div.text(this.name)},revert_name:function(){this.name=this.old_name;this.name_div.text(this.name)},remove:function(){this.container.remove_drawable(this);this.container_div.fadeOut("slow",function(){$(this).remove();view.update_intro_div();view.has_changes=true})}});var y=function(aj,ai,ag,af,ah,ak){q.call(this,ai,ag,af,ah,ak);this.obj_type=aj;this.drawables=[]};p(y.prototype,q.prototype,{init:function(){for(var af=0;af<this.drawables.length;af++){this.drawables[af].init()}},_draw:function(){for(var af=0;af<this.drawables.length;af++){this.drawables[af]._draw()}},to_json:function(){var ag=[];for(var af=0;af<this.drawables.length;af++){ag.push(this.drawables[af].to_json())}return{name:this.name,prefs:this.prefs,obj_type:this.obj_type,drawables:ag}},add_drawable:function(af){this.drawables.push(af);af.container=this},add_drawable_before:function(ah,af){var ag=this.drawables.indexOf(af);if(ag!=-1){this.drawables.splice(ag,0,ah);return true}return false},remove_drawable:function(ag){var af=this.drawables.indexOf(ag);if(af!=-1){this.drawables.splice(af,1);ag.container=null;return true}return false},move_drawable:function(ag,ah){var af=this.drawables.indexOf(ag);if(af!=-1){this.drawables.splice(af,1);this.drawables.splice(ah,0,ag);return true}return false}});var Q=function(ai,ag,af,ah){y.call(this,"DrawableGroup",ai,ag,af,ah,"group-handle");if(!Q.id_counter){Q.id_counter=0}var aj=Q.id_counter++;this.container_div=$("<div/>").addClass("group").attr("id","group_"+aj).appendTo(this.container.content_div);this.header_div=$("<div/>").addClass("track-header").appendTo(this.container_div);this.header_div.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("group-name menubutton popup").text(this.name).appendTo(this.header_div);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+aj+"_content_div").appendTo(this.container_div);l(this.container_div,this);l(this.content_div,this);m(this.container_div,this.drag_handle_class,".group",this);this.update_track_icons()};p(Q.prototype,q.prototype,y.prototype,{update_track_icons:function(){var ag=this;var af={};af["Edit configuration"]=function(){var aj=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},ah=function(){ag.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},ai=function(ak){if((ak.keyCode||ak.which)===27){aj()}else{if((ak.keyCode||ak.which)===13){ah()}}};$(window).bind("keypress.check_enter_esc",ai);show_modal("Configure Group",ag.config.build_form(),{Cancel:aj,OK:ah})};af.Remove=function(){ag.remove()};make_popupmenu(ag.name_div,af)}});var ac=function(af,ai,ah,ag){y.call(this,"View");this.container=af;this.chrom=null;this.vis_id=ah;this.dbkey=ag;this.title=ai;this.label_tracks=[];this.tracks_to_be_redrawn=[];this.max_low=0;this.max_high=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.load_chroms_deferred=null;this.init();this.canvas_manager=new ae(af.get(0).ownerDocument);this.reset()};p(ac.prototype,y.prototype,{init:function(){var ah=this.container,af=this;this.top_container=$("<div/>").addClass("top-container").appendTo(ah);this.browser_content_div=$("<div/>").addClass("content").css("position","relative").appendTo(ah);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(ah);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;l(this.viewport_container,af);this.intro_div=$("<div/>").addClass("intro");var ai=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){add_tracks()});this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a/>").attr("href","javascript:void(0);").attr("title","Close overview").addClass("icon-button overview-close tooltip").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").addClass("no-autocomplete").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var ag=function(aj){if(aj.type==="focusout"||(aj.keyCode||aj.which)===13||(aj.keyCode||aj.which)===27){if((aj.keyCode||aj.which)!==27){af.go_to($(this).val())}$(this).hide();$(this).val("");af.location_span.show();af.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ag).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").appendTo(this.nav_controls);this.location_span.click(function(){af.location_span.hide();af.chrom_select.hide();af.nav_input.val(af.chrom+":"+af.low+"-"+af.high);af.nav_input.css("display","inline-block");af.nav_input.select();af.nav_input.focus()});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a id='zoom-out' />").click(function(){af.zoom_out();af.request_redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a id='zoom-in' />").click(function(){af.zoom_in();af.request_redraw()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){af.change_chrom(af.chrom_select.val())});this.browser_content_div.click(function(aj){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(aj){af.zoom_in(aj.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(aj,ak){this.current_x=ak.offsetX}).bind("drag",function(aj,al){var am=al.offsetX-this.current_x;this.current_x=al.offsetX;var ak=Math.round(am/af.viewport_container.width()*(af.max_high-af.max_low));af.move_delta(-ak)});this.overview_close.click(function(){af.reset_overview()});this.viewport_container.bind("draginit",function(aj,ak){if(aj.clientX>af.viewport_container.width()-16){return false}}).bind("dragstart",function(aj,ak){ak.original_low=af.low;ak.current_height=aj.clientY;ak.current_x=ak.offsetX}).bind("drag",function(al,an){var aj=$(this);var ao=an.offsetX-an.current_x;var ak=aj.scrollTop()-(al.clientY-an.current_height);aj.scrollTop(ak);an.current_height=al.clientY;an.current_x=an.offsetX;var am=Math.round(ao/af.viewport_container.width()*(af.high-af.low));af.move_delta(am)}).bind("mousewheel",function(al,an,ak,aj){if(ak){var am=Math.round(-ak/af.viewport_container.width()*(af.high-af.low));af.move_delta(am)}});this.top_labeltrack.bind("dragstart",function(aj,ak){return $("<div />").css({height:af.browser_content_div.height()+af.top_labeltrack.height()+af.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(an,ao){$(ao.proxy).css({left:Math.min(an.pageX,ao.startX),width:Math.abs(an.pageX-ao.startX)});var ak=Math.min(an.pageX,ao.startX)-af.container.offset().left,aj=Math.max(an.pageX,ao.startX)-af.container.offset().left,am=(af.high-af.low),al=af.viewport_container.width();af.update_location(Math.round(ak/al*am)+af.low,Math.round(aj/al*am)+af.low)}).bind("dragend",function(ao,ap){var ak=Math.min(ao.pageX,ap.startX),aj=Math.max(ao.pageX,ap.startX),am=(af.high-af.low),al=af.viewport_container.width(),an=af.low;af.low=Math.round(ak/al*am)+an;af.high=Math.round(aj/al*am)+an;$(ap.proxy).remove();af.request_redraw()});this.add_label_track(new ab(this,{content_div:this.top_labeltrack}));this.add_label_track(new ab(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){af.resize_window()});$(document).bind("redraw",function(){af.redraw()});this.reset();$(window).trigger("resize");this.update_intro_div()},update_intro_div:function(){if(this.num_tracks===0){this.intro_div.appendTo(this.viewport_container)}else{this.intro_div.remove()}},update_location:function(af,ag){this.location_span.text(commatize(af)+" - "+commatize(ag));this.nav_input.val(this.chrom+":"+commatize(af)+"-"+commatize(ag))},load_chroms:function(ah){ah.num=w;$.extend(ah,(this.vis_id!==undefined?{vis_id:this.vis_id}:{dbkey:this.dbkey}));var af=this,ag=$.Deferred();$.ajax({url:chrom_url,data:ah,dataType:"json",success:function(aj){if(aj.chrom_info.length===0){alert("Invalid chromosome: "+ah.chrom);return}if(aj.reference){af.add_label_track(new A(af))}af.chrom_data=aj.chrom_info;var am='<option value="">Select Chrom/Contig</option>';for(var al=0,ai=af.chrom_data.length;al<ai;al++){var ak=af.chrom_data[al].chrom;am+='<option value="'+ak+'">'+ak+"</option>"}if(aj.prev_chroms){am+='<option value="previous">Previous '+w+"</option>"}if(aj.next_chroms){am+='<option value="next">Next '+w+"</option>"}af.chrom_select.html(am);af.chrom_start_index=aj.start_index;ag.resolve(aj)},error:function(){alert("Could not load chroms for this dbkey:",af.dbkey)}});return ag},change_chrom:function(ak,ag,am){if(!ak||ak==="None"){return}var ah=this;if(ak==="previous"){ah.load_chroms({low:this.chrom_start_index-w});return}if(ak==="next"){ah.load_chroms({low:this.chrom_start_index+w});return}var al=$.grep(ah.chrom_data,function(an,ao){return an.chrom===ak})[0];if(al===undefined){ah.load_chroms({chrom:ak},function(){ah.change_chrom(ak,ag,am)});return}else{if(ak!==ah.chrom){ah.chrom=ak;ah.chrom_select.val(ah.chrom);ah.max_high=al.len-1;ah.reset();ah.request_redraw(true);for(var aj=0,af=ah.drawables.length;aj<af;aj++){var ai=ah.drawables[aj];if(ai.init){ai.init()}}}if(ag!==undefined&&am!==undefined){ah.low=Math.max(ag,0);ah.high=Math.min(am,ah.max_high)}ah.reset_overview();ah.request_redraw()}},go_to:function(aj){aj=aj.replace(/ |,/g,"");var an=this,af,ai,ag=aj.split(":"),al=ag[0],am=ag[1];if(am!==undefined){try{var ak=am.split("-");af=parseInt(ak[0],10);ai=parseInt(ak[1],10)}catch(ah){return false}}an.change_chrom(al,af,ai)},move_fraction:function(ah){var af=this;var ag=af.high-af.low;this.move_delta(ah*ag)},move_delta:function(ah){var af=this;var ag=af.high-af.low;if(af.low-ah<af.max_low){af.low=af.max_low;af.high=af.max_low+ag}else{if(af.high-ah>af.max_high){af.high=af.max_high;af.low=af.max_high-ag}else{af.high-=ah;af.low-=ah}}af.request_redraw()},add_drawable:function(af){y.prototype.add_drawable.call(this,af);af.init();this.has_changes=true;this.update_intro_div()},add_label_track:function(af){af.view=this;af.init();this.label_tracks.push(af)},remove_drawable:function(ah,ag){y.prototype.remove_drawable.call(this,ah);if(ag){var af=this;ah.container_div.fadeOut("slow",function(){$(this).remove();af.update_intro_div()});this.has_changes=true}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(an,af,am,ag){var al=this,aj=(ag?[ag]:al.drawables),ah;var ag;for(var ak=0;ak<aj.length;ak++){ag=aj[ak];ah=-1;for(var ai=0;ai<al.tracks_to_be_redrawn.length;ai++){if(al.tracks_to_be_redrawn[ai][0]===ag){ah=ai;break}}if(ah<0){al.tracks_to_be_redrawn.push([ag,af,am])}else{al.tracks_to_be_redrawn[ak][1]=af;al.tracks_to_be_redrawn[ak][2]=am}}requestAnimationFrame(function(){al._redraw(an)})},_redraw:function(ap){var am=this.low,ai=this.high;if(am<this.max_low){am=this.max_low}if(ai>this.max_high){ai=this.max_high}var ao=this.high-this.low;if(this.high!==0&&ao<this.min_separation){ai=am+this.min_separation}this.low=Math.floor(am);this.high=Math.ceil(ai);this.resolution=Math.pow(C,Math.ceil(Math.log((this.high-this.low)/R)/Math.log(C)));this.zoom_res=Math.pow(v,Math.max(0,Math.ceil(Math.log(this.resolution,v)/Math.log(v))));var af=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var al=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var aq=13;this.overview_box.css({left:af,width:Math.max(aq,al)}).show();if(al<aq){this.overview_box.css("left",af-(aq-al)/2)}if(this.overview_highlight){this.overview_highlight.css({left:af,width:al})}this.update_location(this.low,this.high);if(!ap){var ah,ag,an;for(var aj=0,ak=this.tracks_to_be_redrawn.length;aj<ak;aj++){ah=this.tracks_to_be_redrawn[aj][0];ag=this.tracks_to_be_redrawn[aj][1];an=this.tracks_to_be_redrawn[aj][2];if(ah){ah._draw(ag,an)}}this.tracks_to_be_redrawn=[];for(aj=0,ak=this.label_tracks.length;aj<ak;aj++){this.label_tracks[aj]._draw()}}},zoom_in:function(ag,ah){if(this.max_high===0||this.high-this.low<this.min_separation){return}var ai=this.high-this.low,aj=ai/2+this.low,af=(ai/this.zoom_factor)/2;if(ag){aj=ag/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(aj-af);this.high=Math.round(aj+af);this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ag=this.high-this.low,ah=ag/2+this.low,af=(ag*this.zoom_factor)/2;this.low=Math.round(ah-af);this.high=Math.round(ah+af);this.request_redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.nav_container.width(this.container.width());this.request_redraw()},set_overview:function(ah){if(this.overview_drawable){if(this.overview_drawable.dataset_id===ah.dataset_id){return}this.overview_viewport.find(".track").remove()}var ag=ah.copy({content_div:this.overview_viewport}),af=this;ag.header_div.hide();ag.is_overview=true;af.overview_drawable=ag;this.overview_drawable.postdraw_actions=function(){af.overview_highlight.show().height(af.overview_drawable.content_div.height());af.overview_viewport.height(af.overview_drawable.content_div.height()+af.overview_box.outerHeight());af.overview_close.show();af.resize_window()};this.overview_drawable.init();af.has_changes=true},reset_overview:function(){$(".tipsy").remove();this.overview_viewport.find(".track-tile").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide();view.resize_window();view.overview_drawable=null}});var r=function(ah,al){this.track=ah;this.name=al.name;this.params=[];var at=al.params;for(var ai=0;ai<at.length;ai++){var an=at[ai],ag=an.name,ar=an.label,aj=unescape(an.html),au=an.value,ap=an.type;if(ap==="number"){this.params[this.params.length]=new g(ag,ar,aj,au,an.min,an.max)}else{if(ap=="select"){this.params[this.params.length]=new O(ag,ar,aj,au)}else{console.log("WARNING: unrecognized tool parameter type:",ag,ap)}}}this.parent_div=$("<div/>").addClass("dynamic-tool").hide();this.parent_div.bind("drag",function(aw){aw.stopPropagation()}).click(function(aw){aw.stopPropagation()}).bind("dblclick",function(aw){aw.stopPropagation()});var aq=$("<div class='tool-name'>").appendTo(this.parent_div).text(this.name);var ao=this.params;var am=this;$.each(this.params,function(ax,aA){var az=$("<div>").addClass("param-row").appendTo(am.parent_div);var aw=$("<div>").addClass("param-label").text(aA.label).appendTo(az);var ay=$("<div/>").addClass("slider").html(aA.html).appendTo(az);ay.find(":input").val(aA.value);$("<div style='clear: both;'/>").appendTo(az)});this.parent_div.find("input").click(function(){$(this).select()});var av=$("<div>").addClass("param-row").appendTo(this.parent_div);var ak=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(av);var af=$("<input type='submit'>").attr("value","Run on visible region").css("margin-left","3em").appendTo(av);var am=this;af.click(function(){am.run_on_region()});ak.click(function(){am.run_on_dataset()})};p(r.prototype,{get_param_values_dict:function(){var af={};this.parent_div.find(":input").each(function(){var ag=$(this).attr("name"),ah=$(this).val();af[ag]=JSON.stringify(ah)});return af},get_param_values:function(){var ag=[];var af={};this.parent_div.find(":input").each(function(){var ah=$(this).attr("name"),ai=$(this).val();if(ah){ag[ag.length]=ai}});return ag},run_on_dataset:function(){var af=this;af.run({dataset_id:this.track.original_dataset_id,tool_id:af.name},null,function(ag){show_modal(af.name+" is Running",af.name+" is running on the complete dataset. Tool outputs are in dataset's history.",{Close:hide_modal})})},run_on_region:function(){var ag={dataset_id:this.track.original_dataset_id,chrom:this.track.view.chrom,low:this.track.view.low,high:this.track.view.high,tool_id:this.name},aj=this.track,ah=ag.tool_id+aj.tool_region_and_parameters_str(ag.chrom,ag.low,ag.high),af;if(aj.container===view){var ai=new Q(this.name,this.track.view,this.track.container);aj.container.add_drawable(ai);aj.container.remove_drawable(aj);ai.add_drawable(aj);aj.container_div.appendTo(ai.content_div);af=ai}else{af=aj.container}var ak=new aj.constructor(ah,view,af,"hda");ak.init_for_tool_data();ak.change_mode(aj.mode);af.add_drawable(ak);ak.content_div.text("Starting job.");this.run(ag,ak,function(al){ak.dataset_id=al.dataset_id;ak.content_div.text("Running job.");ak.init()})},run:function(ag,ah,ai){$.extend(ag,this.get_param_values_dict());var af=function(){$.getJSON(rerun_tool_url,ag,function(aj){if(aj==="no converter"){ah.container_div.addClass("error");ah.content_div.text(K)}else{if(aj.error){ah.container_div.addClass("error");ah.content_div.text(x+aj.message)}else{if(aj==="pending"){ah.container_div.addClass("pending");ah.content_div.text("Converting input data so that it can be used quickly with tool.");setTimeout(af,2000)}else{ai(aj)}}}})};af()}});var O=function(ag,af,ah,ai){this.name=ag;this.label=af;this.html=ah;this.value=ai};var g=function(ah,ag,aj,ak,ai,af){O.call(this,ah,ag,aj,ak);this.min=ai;this.max=af};var h=function(ag,af,ah,ai){this.name=ag;this.index=af;this.tool_id=ah;this.tool_exp_name=ai};var V=function(ag,af,ah,ai){h.call(this,ag,af,ah,ai);this.low=-Number.MAX_VALUE;this.high=Number.MAX_VALUE;this.min=Number.MAX_VALUE;this.max=-Number.MAX_VALUE;this.container=null;this.slider=null;this.slider_label=null};p(V.prototype,{applies_to:function(af){if(af.length>this.index){return true}return false},keep:function(af){if(!this.applies_to(af)){return true}var ag=af[this.index];return(isNaN(ag)||(ag>=this.low&&ag<=this.high))},update_attrs:function(ag){var af=false;if(!this.applies_to(ag)){return af}if(ag[this.index]<this.min){this.min=Math.floor(ag[this.index]);af=true}if(ag[this.index]>this.max){this.max=Math.ceil(ag[this.index]);af=true}return af},update_ui_elt:function(){if(this.min!=this.max){this.container.show()}else{this.container.hide()}var ah=function(ak,ai){var aj=ai-ak;return(aj<=2?0.01:1)};var ag=this.slider.slider("option","min"),af=this.slider.slider("option","max");if(this.min<ag||this.max>af){this.slider.slider("option","min",this.min);this.slider.slider("option","max",this.max);this.slider.slider("option","step",ah(this.min,this.max));this.slider.slider("option","values",[this.min,this.max])}}});var aa=function(aq,ay){this.track=aq;this.filters=[];for(var at=0;at<ay.length;at++){var au=ay[at],az=au.name,af=au.type,ah=au.index,ax=au.tool_id,aw=au.tool_exp_name;if(af==="int"||af==="float"){this.filters[at]=new V(az,ah,ax,aw)}else{console.log("ERROR: unsupported filter: ",az,af)}}var ai=function(aA,aB,aC){aA.click(function(){var aD=aB.text();max=parseFloat(aC.slider("option","max")),input_size=(max<=1?4:max<=1000000?max.toString().length:6),multi_value=false;if(aC.slider("option","values")){input_size=2*input_size+1;multi_value=true}aB.text("");$("<input type='text'/>").attr("size",input_size).attr("maxlength",input_size).attr("value",aD).appendTo(aB).focus().select().click(function(aE){aE.stopPropagation()}).blur(function(){$(this).remove();aB.text(aD)}).keyup(function(aI){if(aI.keyCode===27){$(this).trigger("blur")}else{if(aI.keyCode===13){var aG=aC.slider("option","min"),aE=aC.slider("option","max"),aH=function(aJ){return(isNaN(aJ)||aJ>aE||aJ<aG)},aF=$(this).val();if(!multi_value){aF=parseFloat(aF);if(aH(aF)){alert("Parameter value must be in the range ["+aG+"-"+aE+"]");return $(this)}}else{aF=aF.split("-");aF=[parseFloat(aF[0]),parseFloat(aF[1])];if(aH(aF[0])||aH(aF[1])){alert("Parameter value must be in the range ["+aG+"-"+aE+"]");return $(this)}}aC.slider((multi_value?"values":"value"),aF)}}})})};this.parent_div=$("<div/>").addClass("filters").hide();this.parent_div.bind("drag",function(aA){aA.stopPropagation()}).click(function(aA){aA.stopPropagation()}).bind("dblclick",function(aA){aA.stopPropagation()}).bind("keydown",function(aA){aA.stopPropagation()});var av=$("<div/>").addClass("sliders").appendTo(this.parent_div);var an=this;$.each(this.filters,function(aD,aF){aF.container=$("<div/>").addClass("filter-row slider-row").appendTo(av);var aE=$("<div/>").addClass("elt-label").appendTo(aF.container);var aC=$("<span/>").addClass("slider-name").text(aF.name+" ").appendTo(aE);var aB=$("<span/>");var aH=$("<span/>").addClass("slider-value").appendTo(aE).append("[").append(aB).append("]");var aA=$("<div/>").addClass("slider").appendTo(aF.container);aF.control_element=$("<div/>").attr("id",aF.name+"-filter-control").appendTo(aA);var aG=[0,0];aF.control_element.slider({range:true,min:Number.MAX_VALUE,max:-Number.MIN_VALUE,values:[0,0],slide:function(aJ,aK){var aI=aK.values;aB.text(aI[0]+"-"+aI[1]);aF.low=aI[0];aF.high=aI[1];an.track.request_draw(true,true)},change:function(aI,aJ){aF.control_element.slider("option","slide").call(aF.control_element,aI,aJ)}});aF.slider=aF.control_element;aF.slider_label=aB;ai(aH,aB,aF.control_element);$("<div style='clear: both;'/>").appendTo(aF.container)});if(this.filters.length!==0){var ak=$("<div/>").addClass("param-row").appendTo(av);var am=$("<input type='submit'/>").attr("value","Run on complete dataset").appendTo(ak);var ag=this;am.click(function(){ag.run_on_dataset()})}var ap=$("<div/>").addClass("display-controls").appendTo(this.parent_div),ar,al,ao,aj={Transparency:function(aA){an.alpha_filter=aA},Height:function(aA){an.height_filter=aA}};$.each(aj,function(aC,aB){ar=$("<div/>").addClass("filter-row").appendTo(ap),al=$("<span/>").addClass("elt-label").text(aC+":").appendTo(ar),ao=$("<select/>").attr("name",aC+"_dropdown").css("float","right").appendTo(ar);$("<option/>").attr("value",-1).text("== None ==").appendTo(ao);for(var aA=0;aA<an.filters.length;aA++){$("<option/>").attr("value",aA).text(an.filters[aA].name).appendTo(ao)}ao.change(function(){$(this).children("option:selected").each(function(){var aD=parseInt($(this).val());aj[aC]((aD>=0?an.filters[aD]:null));an.track.request_draw(true,true)})});$("<div style='clear: both;'/>").appendTo(ar)});$("<div style='clear: both;'/>").appendTo(this.parent_div)};p(aa.prototype,{reset_filters:function(){for(var af=0;af<this.filters.length;af++){filter=this.filters[af];filter.slider.slider("option","values",[filter.min,filter.max])}this.alpha_filter=null;this.height_filter=null},run_on_dataset:function(){var an=function(ar,ap,aq){if(!(ap in ar)){ar[ap]=aq}return ar[ap]};var ah={},af,ag,ai;for(var aj=0;aj<this.filters.length;aj++){af=this.filters[aj];if(af.tool_id){if(af.min!=af.low){ag=an(ah,af.tool_id,[]);ag[ag.length]=af.tool_exp_name+" >= "+af.low}if(af.max!=af.high){ag=an(ah,af.tool_id,[]);ag[ag.length]=af.tool_exp_name+" <= "+af.high}}}var al=[];for(var ao in ah){al[al.length]=[ao,ah[ao]]}var am=al.length;(function ak(aw,at){var aq=at[0],ar=aq[0],av=aq[1],au="("+av.join(") and (")+")",ap={cond:au,input:aw,target_dataset_id:aw,tool_id:ar},at=at.slice(1);$.getJSON(run_tool_url,ap,function(ax){if(ax.error){show_modal("Filter Dataset","Error running tool "+ar,{Close:hide_modal})}else{if(at.length===0){show_modal("Filtering Dataset","Filter(s) are running on the complete dataset. Outputs are in dataset's history.",{Close:hide_modal})}else{ak(ax.dataset_id,at)}}})})(this.track.dataset_id,al)}});var D=function(af,ag){M.Scaler.call(this,ag);this.filter=af};D.prototype.gen_val=function(af){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_val}return((parseFloat(af[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var G=function(af){this.track=af.track;this.params=af.params;this.values={};this.restore_values((af.saved_values?af.saved_values:{}));this.onchange=af.onchange};p(G.prototype,{restore_values:function(af){var ag=this;$.each(this.params,function(ah,ai){if(af[ai.key]!==undefined){ag.values[ai.key]=af[ai.key]}else{ag.values[ai.key]=ai.default_value}})},build_form:function(){var ag=this;var af=$("<div />");$.each(this.params,function(ak,ai){if(!ai.hidden){var ah="param_"+ak;var am=ag.values[ai.key];var ap=$("<div class='form-row' />").appendTo(af);ap.append($("<label />").attr("for",ah).text(ai.label+":"));if(ai.type==="bool"){ap.append($('<input type="checkbox" />').attr("id",ah).attr("name",ah).attr("checked",am))}else{if(ai.type==="text"){ap.append($('<input type="text"/>').attr("id",ah).val(am).click(function(){$(this).select()}))}else{if(ai.type==="color"){var al=$("<input />").attr("id",ah).attr("name",ah).val(am);var an=$("<div class='tipsy tipsy-north' style='position: absolute;' />").hide();var aj=$("<div style='background-color: black; padding: 10px;'></div>").appendTo(an);var ao=$("<div/>").appendTo(aj).farbtastic({width:100,height:100,callback:al,color:am});$("<div />").append(al).append(an).appendTo(ap).bind("click",function(aq){an.css({left:$(this).position().left+($(al).width()/2)-60,top:$(this).position().top+$(this.height)}).show();$(document).bind("click.color-picker",function(){an.hide();$(document).unbind("click.color-picker")});aq.stopPropagation()})}else{ap.append($("<input />").attr("id",ah).attr("name",ah).val(am))}}}}});return af},update_from_form:function(af){var ah=this;var ag=false;$.each(this.params,function(ai,ak){if(!ak.hidden){var al="param_"+ai;var aj=af.find("#"+al).val();if(ak.type==="float"){aj=parseFloat(aj)}else{if(ak.type==="int"){aj=parseInt(aj)}else{if(ak.type==="bool"){aj=af.find("#"+al).is(":checked")}}}if(aj!==ah.values[ak.key]){ah.values[ak.key]=aj;ag=true}}});if(ag){this.onchange()}}});var b=function(af,ai,ah,ag,aj){this.track=af;this.index=ai;this.low=ai*R*ah;this.high=(ai+1)*R*ah;this.resolution=ah;this.canvas=$("<div class='track-tile'/>").append(ag);this.data=aj;this.stale=false};b.prototype.predisplay_actions=function(){};var k=function(af,ai,ah,ag,aj,ak){b.call(this,af,ai,ah,ag,aj);this.max_val=ak};p(k.prototype,b.prototype);var P=function(af,aj,ai,ah,al,am,ak,ag){b.call(this,af,aj,ai,ah,al);this.mode=am;this.message=ak;this.feature_mapper=ag};p(P.prototype,b.prototype);P.prototype.predisplay_actions=function(){var ag=this,af={};if(ag.mode!=="Pack"){return}$(this.canvas).mousemove(function(ar){var am=$(this).offset(),aq=ar.pageX-am.left,ap=ar.pageY-am.top,aw=ag.feature_mapper.get_feature_data(aq,ap),an=(aw?aw[0]:null);$(this).siblings(".feature-popup").each(function(){if(!an||$(this).attr("id")!==an.toString()){$(this).remove()}});if(aw){var ai=af[an];if(!ai){var an=aw[0],at={name:aw[3],start:aw[1],end:aw[2],strand:aw[4]},al=ag.track.filters_manager.filters,ak;for(var ao=0;ao<al.length;ao++){ak=al[ao];at[ak.name]=aw[ak.index]}var ai=$("<div/>").attr("id",an).addClass("feature-popup"),av,au,ax=$("<table/>").appendTo(ai),ay;for(av in at){au=at[av];ay=$("<tr/>").appendTo(ax);$("<th/>").appendTo(ay).text(av);$("<td/>").attr("align","left").appendTo(ay).text(typeof(au)=="number"?Z(au,2):au)}af[an]=ai}ai.appendTo($(ag.canvas).parent());var aj=aq+parseInt(ag.canvas.css("left"))+7,ah=ap+parseInt(ag.canvas.css("top"))+7;ai.css("left",aj+"px").css("top",ah+"px")}else{if(!ar.isPropagationStopped()){ar.stopPropagation();$(this).siblings().each(function(){$(this).trigger(ar)})}}}).mouseleave(function(){$(this).siblings(".feature-popup").remove()})};var i=function(ai,aq,aj,am,ar,ah,ag){q.call(this,ai,aq,aj,{},"draghandle");this.data_url=(ah?ah:default_data_url);this.data_url_extra_params={};this.data_query_wait=(ag?ag:L);this.dataset_check_url=converted_datasets_state_url;if(!i.id_counter){i.id_counter=0}this.id=i.id_counter++;this.container_div=$("<div />").addClass("track").attr("id","track_"+this.id).css("position","relative");if(am){this.header_div=$("<div class='track-header' />").appendTo(this.container_div);if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(this.header_div)}this.name_div=$("<div/>").addClass("track-name").appendTo(this.header_div).text(this.name).attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase());this.icons_div=$("<div/>").css("float","left").appendTo(this.header_div).hide();this.settings_icon=$("<a/>").attr("href","javascript:void(0);").attr("title","Edit settings").addClass("icon-button settings-icon").tipsy({gravity:"s"}).appendTo(this.icons_div);this.overview_icon=$("<a/>").attr("href","javascript:void(0);").attr("title","Set as overview").addClass("icon-button overview-icon").tipsy({gravity:"s"}).appendTo(this.icons_div);this.filters_icon=$("<a/>").attr("href","javascript:void(0);").attr("title","Filters").addClass("icon-button filters-icon").tipsy({gravity:"s"}).appendTo(this.icons_div).hide();this.tools_icon=$("<a/>").attr("href","javascript:void(0);").attr("title","Tools").addClass("icon-button tools-icon").tipsy({gravity:"s"}).appendTo(this.icons_div).hide();this.remove_icon=$("<a/>").attr("href","javascript:void(0);").attr("title","Remove").addClass("icon-button remove-icon").tipsy({gravity:"s"}).appendTo(this.icons_div);var ak=this;this.header_div.dblclick(function(at){at.stopPropagation()});this.settings_icon.click(function(){var av=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},at=function(){ak.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},au=function(aw){if((aw.keyCode||aw.which)===27){av()}else{if((aw.keyCode||aw.which)===13){at()}}};$(window).bind("keypress.check_enter_esc",au);show_modal("Configure Track",ak.config.build_form(),{Cancel:av,OK:at})});this.overview_icon.click(function(){ak.view.set_overview(ak)});this.filters_icon.click(function(){ak.filters_div.toggle();ak.filters_manager.reset_filters()});this.tools_icon.click(function(){ak.dynamic_tool_div.toggle();if(ak.dynamic_tool_div.is(":visible")){ak.set_name(ak.name+ak.tool_region_and_parameters_str())}else{ak.revert_name()}$(".tipsy").remove()});this.remove_icon.click(function(){$(".tipsy").remove();ak.remove()});if(ak.display_modes!==undefined){if(ak.mode_div===undefined){ak.mode_div=$("<div class='right-float menubutton popup' />").appendTo(ak.header_div);var al=(ak.config&&ak.config.values.mode?ak.config.values.mode:ak.display_modes[0]);ak.mode=al;ak.mode_div.text(al);var af={};for(var an=0,ap=ak.display_modes.length;an<ap;an++){var ao=ak.display_modes[an];af[ao]=function(at){return function(){ak.change_mode(at)}}(ao)}make_popupmenu(ak.mode_div,af)}else{ak.mode_div.hide()}this.header_div.append($("<div/>").css("clear","both"));this.container_div.hover(function(){ak.icons_div.show()},function(){ak.icons_div.hide()})}}this.content_div=$("<div class='track-content'>").appendTo(this.container_div);this.container.content_div.append(this.container_div)};p(i.prototype,q.prototype,{get_type:function(){if(this instanceof ab){return"LabelTrack"}else{if(this instanceof A){return"ReferenceTrack"}else{if(this instanceof j){return"LineTrack"}else{if(this instanceof W){return"ReadTrack"}else{if(this instanceof U){return"VcfTrack"}else{if(this instanceof e){return"FeatureTrack"}}}}}}return""},init:function(){var af=this;af.enabled=false;af.tile_cache.clear();af.data_manager.clear();af.initial_canvas=undefined;af.content_div.css("height","auto");af.container_div.removeClass("nodata error pending");if(!af.dataset_id){return}$.getJSON(converted_datasets_state_url,{hda_ldda:af.hda_ldda,dataset_id:af.dataset_id,chrom:af.view.chrom},function(ag){if(!ag||ag==="error"||ag.kind==="error"){af.container_div.addClass("error");af.content_div.text(o);if(ag.message){var ah=$(" <a href='javascript:void(0);'></a>").text("View error").click(function(){show_modal("Trackster Error","<pre>"+ag.message+"</pre>",{Close:hide_modal})});af.content_div.append(ah)}}else{if(ag==="no converter"){af.container_div.addClass("error");af.content_div.text(K)}else{if(ag==="no data"||(ag.data!==undefined&&(ag.data===null||ag.data.length===0))){af.container_div.addClass("nodata");af.content_div.text(F)}else{if(ag==="pending"){af.container_div.addClass("pending");af.content_div.text(t);setTimeout(function(){af.init()},af.data_query_wait)}else{if(ag.status==="data"){if(ag.valid_chroms){af.valid_chroms=ag.valid_chroms;af.update_track_icons()}af.content_div.text(Y);if(af.view.chrom){af.content_div.text("");af.content_div.css("height",af.height_px+"px");af.enabled=true;$.when(af.predraw_init()).done(function(){af.container_div.removeClass("nodata error pending");af.request_draw()})}}}}}}});this.update_track_icons()},predraw_init:function(){}});var N=function(aj,ah,ag,am,ai,al,ak){i.call(this,aj,ah,ag,am,ai);var af=this,ah=af.view;m(af.container_div,af.drag_handle_class,".group",af);this.filters_manager=new aa(this,(al!==undefined?al:{}));this.filters_available=false;this.filters_visible=false;this.tool=(ak!==undefined&&obj_length(ak)>0?new r(this,ak):undefined);if(this.header_div){if(this.filters_manager){this.filters_div=this.filters_manager.parent_div;this.header_div.after(this.filters_div)}if(this.tool){this.dynamic_tool_div=this.tool.parent_div;this.header_div.after(this.dynamic_tool_div)}}};p(N.prototype,q.prototype,i.prototype,{copy:function(af){return new this.constructor(this.name,this.view,af,this.hda_ldda,this.dataset_id,this.prefs,this.filters,this.tool)},to_json:function(){return{track_type:this.get_type(),name:this.name,hda_ldda:this.hda_ldda,dataset_id:this.dataset_id,prefs:this.prefs,mode:this.mode,}},change_mode:function(ag){var af=this;af.mode_div.text(ag);af.mode=ag;af.config.values.mode=ag;af.tile_cache.clear();af.request_draw();return af},update_track_icons:function(){var af=this;if(af.filters_available>0){af.filters_icon.show()}else{af.filters_icon.hide()}if(af.tool){af.tools_icon.show()}else{af.tools_icon.hide()}},_gen_tile_cache_key:function(ag,ah,af){return ag+"_"+ah+"_"+af},request_draw:function(ag,af){this.view.request_redraw(false,ag,af,this)},_draw:function(ah,ap){if(!this.enabled){return}if(!(this instanceof A)&&(!this.dataset_id)){return}var ao=this.view.low,al=this.view.high,am=al-ao,ai=this.view.container.width(),at=ai/am,ak=this.view.resolution,ar=$("<div style='position: relative;'></div>");if(this.is_overview){ao=this.view.max_low;al=this.view.max_high;ak=Math.pow(C,Math.ceil(Math.log((view.max_high-view.max_low)/R)/Math.log(C)));at=ai/(view.max_high-view.max_low)}if(!ap){this.content_div.children().remove()}this.content_div.append(ar);this.max_height=0;var ag=Math.floor(ao/ak/R);var an=true;var aq=[];var af=0;while((ag*R*ak)<al){tile=this.draw_helper(ah,ai,ag,ak,ar,at);if(tile){aq.push(tile)}else{an=false}ag+=1;af++}var aj=this;if(an){aj.postdraw_actions(aq,ai,at,ap)}},postdraw_actions:function(aj,ak,al,af){var ah=this;var ai=false;for(var ag=0;ag<aj.length;ag++){if(aj[ag].message){ai=true;break}}if(ai){for(var ag=0;ag<aj.length;ag++){tile=aj[ag];if(!tile.message){tile.canvas.css("padding-top",E)}}}},draw_helper:function(ag,ah,ai,al,ar,aw,at,am){var aj=this,aq=this._gen_tile_cache_key(ah,aw,ai),an=ai*R*al,av=an+R*al;var ao=(ag?undefined:aj.tile_cache.get(aq));if(ao){aj.show_tile(ao,ar,aw);return ao}var ap=function(ax){return("isResolved" in ax)};var ak=true;var af=aj.data_manager.get_data(an,av,aj.mode,al,aj.data_url_extra_params);if(ap(af)){ak=false}var au;if(view.reference_track&&aw>view.canvas_manager.char_width_px){au=view.reference_track.data_manager.get_data(an,av,aj.mode,al,view.reference_track.data_url_extra_params);if(ap(au)){ak=false}}if(ak){p(af,am);var ao=aj.draw_tile(af,aj.mode,al,ai,aw,au);if(ao!==undefined){aj.tile_cache.set(aq,ao);aj.show_tile(ao,ar,aw)}return ao}$.when(af,au).then(function(){view.request_redraw(false,false,false,aj)});return null},show_tile:function(al,an,ao){var ah=this,ag=al.canvas,ak=ag;if(al.message){var ap=$("<div/>"),am=$("<div/>").addClass("tile-message").text(al.message).css({height:E-1,width:al.canvas.width}).appendTo(ap),aj=$("<a href='javascript:void(0);'/>").addClass("icon more-down").appendTo(am),af=$("<a href='javascript:void(0);'/>").addClass("icon more-across").appendTo(am);ap.append(ag);ak=ap;aj.click(function(){al.stale=true;ah.data_manager.get_more_data(al.low,al.high,ah.mode,al.resolution,{},ah.data_manager.DEEP_DATA_REQ);ah.request_draw()}).dblclick(function(aq){aq.stopPropagation()});af.click(function(){al.stale=true;ah.data_manager.get_more_data(al.low,al.high,ah.mode,al.resolution,{},ah.data_manager.BROAD_DATA_REQ);ah.request_draw()}).dblclick(function(aq){aq.stopPropagation()})}al.predisplay_actions();var ai=(al.low-(this.is_overview?this.view.max_low:this.view.low))*ao;if(this.left_offset){ai-=this.left_offset}ak.css({position:"absolute",top:0,left:ai,height:""});an.append(ak);ah.max_height=Math.max(ah.max_height,ak.height());ah.content_div.css("height",ah.max_height+"px");an.children().css("height",ah.max_height+"px")},_get_tile_bounds:function(af,ag){var ai=af*R*ag,aj=R*ag,ah=(ai+aj<=this.view.max_high?ai+aj:this.view.max_high);return[ai,ah]},tool_region_and_parameters_str:function(ah,af,ai){var ag=this,aj=(ah!==undefined&&af!==undefined&&ai!==undefined?ah+":"+af+"-"+ai:"all");return" - region=["+aj+"], parameters=["+ag.tool.get_param_values().join(", ")+"]"},init_for_tool_data:function(){this.data_url=raw_data_url;this.data_query_wait=1000;this.dataset_check_url=dataset_state_url;this.predraw_init=function(){var ag=this;var af=function(){if(ag.data_manager.size()===0){setTimeout(af,300)}else{ag.data_url=default_data_url;ag.data_query_wait=L;ag.dataset_state_url=converted_datasets_state_url;$.getJSON(ag.dataset_state_url,{dataset_id:ag.dataset_id,hda_ldda:ag.hda_ldda},function(ah){})}};af()}}});var ab=function(ag,af){i.call(this,"label",ag,af,false,{});this.container_div.addClass("label-track")};p(ab.prototype,i.prototype,{init:function(){this.enabled=true},_draw:function(){var ah=this.view,ai=ah.high-ah.low,al=Math.floor(Math.pow(10,Math.floor(Math.log(ai)/Math.log(10)))),af=Math.floor(ah.low/al)*al,aj=this.view.container.width(),ag=$("<div style='position: relative; height: 1.3em;'></div>");while(af<ah.high){var ak=(af-ah.low)/ai*aj;ag.append($("<div class='label'>"+commatize(af)+"</div>").css({position:"absolute",left:ak-1}));af+=al}this.content_div.children(":first").remove();this.content_div.append(ag)}});var A=function(af){N.call(this,"reference",af,{content_div:af.top_labeltrack},false,{});af.reference_track=this;this.left_offset=200;this.height_px=12;this.container_div.addClass("reference-track");this.content_div.css("background","none");this.content_div.css("min-height","0px");this.content_div.css("border","none");this.data_url=reference_url;this.data_url_extra_params={dbkey:af.dbkey};this.data_manager=new I(B,this,false);this.tile_cache=new c(u)};p(A.prototype,q.prototype,N.prototype,{init:function(){this.enabled=true},draw_tile:function(ap,al,ak,ag,aq){var aj=this,ah=R*ak;if(aq>this.view.canvas_manager.char_width_px){if(ap.data===null){aj.content_div.css("height","0px");return}var ai=this.view.canvas_manager.new_canvas();var ao=ai.getContext("2d");ai.width=Math.ceil(ah*aq+aj.left_offset);ai.height=aj.height_px;ao.font=ao.canvas.manager.default_font;ao.textAlign="center";ap=ap.data;for(var am=0,an=ap.length;am<an;am++){var af=Math.round(am*aq);ao.fillText(ap[am],af+aj.left_offset,10)}return new b(aj,ag,ak,ai,ap)}this.content_div.css("height","0px")}});var j=function(ak,ai,ah,al,af,aj){var ag=this;this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";N.call(this,ak,ai,ah,true,aj);this.min_height_px=16;this.max_height_px=400;this.height_px=80;this.hda_ldda=al;this.dataset_id=af;this.original_dataset_id=af;this.data_manager=new S(B,this);this.tile_cache=new c(u);this.left_offset=0;this.config=new G({track:this,params:[{key:"name",label:"Name",type:"text",default_value:ak},{key:"color",label:"Color",type:"color",default_value:get_random_color()},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:this.height_px,hidden:true}],saved_values:aj,onchange:function(){ag.set_name(ag.prefs.name);ag.vertical_range=ag.prefs.max_value-ag.prefs.min_value;$("#linetrack_"+ag.dataset_id+"_minval").text(ag.prefs.min_value);$("#linetrack_"+ag.dataset_id+"_maxval").text(ag.prefs.max_value);ag.tile_cache.clear();ag.request_draw()}});this.prefs=this.config.values;this.height_px=this.config.values.height;this.vertical_range=this.config.values.max_value-this.config.values.min_value;this.add_resize_handle()};p(j.prototype,q.prototype,N.prototype,{add_resize_handle:function(){var af=this;var ai=false;var ah=false;var ag=$("<div class='track-resize'>");$(af.container_div).hover(function(){ai=true;ag.show()},function(){ai=false;if(!ah){ag.hide()}});ag.hide().bind("dragstart",function(aj,ak){ah=true;ak.original_height=$(af.content_div).height()}).bind("drag",function(ak,al){var aj=Math.min(Math.max(al.original_height+al.deltaY,af.min_height_px),af.max_height_px);$(af.content_div).css("height",aj);af.height_px=aj;af.request_draw(true)}).bind("dragend",function(aj,ak){af.tile_cache.clear();ah=false;if(!ai){ag.hide()}af.config.values.height=af.height_px}).appendTo(af.container_div)},predraw_init:function(){var af=this;af.vertical_range=undefined;return $.getJSON(af.data_url,{stats:true,chrom:af.view.chrom,low:null,high:null,hda_ldda:af.hda_ldda,dataset_id:af.dataset_id},function(ag){af.container_div.addClass("line-track");var ai=ag.data;if(isNaN(parseFloat(af.prefs.min_value))||isNaN(parseFloat(af.prefs.max_value))){af.prefs.min_value=ai.min;af.prefs.max_value=ai.max;$("#track_"+af.dataset_id+"_minval").val(af.prefs.min_value);$("#track_"+af.dataset_id+"_maxval").val(af.prefs.max_value)}af.vertical_range=af.prefs.max_value-af.prefs.min_value;af.total_frequency=ai.total_frequency;af.container_div.find(".yaxislabel").remove();var aj=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+af.dataset_id+"_minval").text(Z(af.prefs.min_value,3));var ah=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+af.dataset_id+"_maxval").text(Z(af.prefs.max_value,3));ah.css({position:"absolute",top:"24px",left:"10px"});ah.prependTo(af.container_div);aj.css({position:"absolute",bottom:"2px",left:"10px"});aj.prependTo(af.container_div)})},draw_tile:function(ar,ak,aj,ah,aq){if(this.vertical_range===undefined){return}var af=this._get_tile_bounds(ah,aj),al=af[0],ap=af[1],ag=Math.ceil((ap-al)*aq),an=this.height_px;var ai=this.view.canvas_manager.new_canvas();ai.width=ag,ai.height=an;var ao=ai.getContext("2d");var am=new M.LinePainter(ar.data,al,ap,this.prefs,ak);am.draw(ao,ag,an);return new b(this.track,ah,aj,ai,ar.data)}});var e=function(af,al,ag,ak,an,am,ai,aj){var ah=this;this.display_modes=["Auto","Histogram","Dense","Squish","Pack"];N.call(this,af,al,ag,true,am,ai,aj);this.config=new G({track:this,params:[{key:"name",label:"Name",type:"text",default_value:af},{key:"block_color",label:"Block color",type:"color",default_value:get_random_color()},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:am,onchange:function(){ah.set_name(ah.prefs.name);ah.tile_cache.clear();ah.request_draw()}});this.prefs=this.config.values;this.height_px=0;this.container_div.addClass("feature-track");this.hda_ldda=ak;this.dataset_id=an;this.original_dataset_id=an;this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.inc_slots={};this.start_end_dct={};this.tile_cache=new c(d);this.data_manager=new S(20,this);this.left_offset=200;this.painter=M.LinkedFeaturePainter};p(e.prototype,q.prototype,N.prototype,{postdraw_actions:function(av,af,aw,au){N.prototype.postdraw_actions.call(this,av,au);var ai=this;if(au){var ak=ai.content_div.children();var al=false;for(var aj=ak.length-1,ap=0;aj>=ap;aj--){var ah=$(ak[aj]);if(al){ah.remove()}else{if(ah.children().length!==0){al=true}}}}if(ai.mode=="Histogram"){var ao=-1;for(var aj=0;aj<av.length;aj++){var at=av[aj].max_val;if(at>ao){ao=at}}for(var aj=0;aj<av.length;aj++){var ar=av[aj];if(ar.max_val!==ao){ar.canvas.remove();ai.draw_helper(true,af,ar.index,ar.resolution,ar.canvas.parent(),aw,[],{max:ao})}}}if(ai.filters_manager){var ag=ai.filters_manager.filters;for(var an=0;an<ag.length;an++){ag[an].update_ui_elt()}var am=false,aq;for(var aj=0;aj<av.length;aj++){if(av[aj].data.length){aq=av[aj].data[0];for(var an=0;an<ag.length;an++){if(ag[an].applies_to(aq)){am=true;break}}}}if(ai.filters_available!==am){ai.filters_available=am;if(!ai.filters_available){ai.filters_div.hide()}ai.update_track_icons()}}},update_auto_mode:function(af){if(this.mode=="Auto"){if(af=="no_detail"){af="feature spans"}else{if(af=="summary_tree"){af="coverage histogram"}}this.mode_div.text("Auto ("+af+")")}},incremental_slots:function(aj,ag,ai){var ah=this.view.canvas_manager.dummy_context,af=this.inc_slots[aj];if(!af||(af.mode!==ai)){af=new (s.FeatureSlotter)(aj,ai==="Pack",z,function(ak){return ah.measureText(ak)});af.mode=ai;this.inc_slots[aj]=af}return af.slot_features(ag)},get_summary_tree_data:function(aj,am,ah,av){if(av>ah-am){av=ah-am}var aq=Math.floor((ah-am)/av),au=[],ai=0;var ak=0,al=0,ap,at=0,an=[],ar,ao;var ag=function(ay,ax,az,aw){ay[0]=ax+az*aw;ay[1]=ax+(az+1)*aw};while(at<av&&ak!==aj.length){var af=false;for(;at<av&&!af;at++){ag(an,am,at,aq);for(al=ak;al<aj.length;al++){ap=aj[al].slice(1,3);if(is_overlap(ap,an)){af=true;break}}if(af){break}}data_start_index=al;au[au.length]=ar=[an[0],0];for(;al<aj.length;al++){ap=aj[al].slice(1,3);if(is_overlap(ap,an)){ar[1]++}else{break}}if(ar[1]>ai){ai=ar[1]}at++}return{max:ai,delta:aq,data:au}},draw_tile:function(au,ax,aB,aF,ap,ai){var ay=this,ak=ay._get_tile_bounds(aF,aB),aI=ak[0],ag=ak[1],aw=ag-aI,az=Math.ceil(aw*ap),aO=25,aj=this.left_offset,av,al;if(ax==="Auto"){if(au.dataset_type==="summary_tree"){ax=au.dataset_type}else{if(au.extra_info==="no_detail"||ay.is_overview){ax="no_detail"}else{var aN=au.data;if(this.view.high-this.view.low>J){ax="Squish"}else{ax="Pack"}}}this.update_auto_mode(ax)}if(ax==="summary_tree"||ax==="Histogram"){al=this.summary_draw_height;this.container_div.find(".yaxislabel").remove();var af=$("<div />").addClass("yaxislabel");af.text(au.max);af.css({position:"absolute",top:"24px",left:"10px",color:this.prefs.label_color});af.prependTo(this.container_div);var ah=this.view.canvas_manager.new_canvas();ah.width=az+aj;ah.height=al+T;if(au.dataset_type!="summary_tree"){var aq=this.get_summary_tree_data(au.data,aI,ag,200);if(au.max){aq.max=au.max}au=aq}var aK=new M.SummaryTreePainter(au,aI,ag,this.prefs);var aA=ah.getContext("2d");aA.translate(aj,T);aK.draw(aA,az,al);return new k(ay,aF,aB,ah,au.data,au.max)}var av,an=1;if(ax==="no_detail"||ax==="Squish"||ax==="Pack"){an=this.incremental_slots(ap,au.data,ax);av=this.inc_slots[ap].slots}var ao=[];if(au.data){var ar=this.filters_manager.filters;for(var aC=0,aE=au.data.length;aC<aE;aC++){var am=au.data[aC];var aD=false;var at;for(var aH=0,aM=ar.length;aH<aM;aH++){at=ar[aH];at.update_attrs(am);if(!at.keep(am)){aD=true;break}}if(!aD){ao.push(am)}}}var aL=(this.filters_manager.alpha_filter?new D(this.filters_manager.alpha_filter):null);var aJ=(this.filters_manager.height_filter?new D(this.filters_manager.height_filter):null);var aK=new (this.painter)(ao,aI,ag,this.prefs,ax,aL,aJ,ai);var al=Math.max(ad,aK.get_required_height(an));var ah=this.view.canvas_manager.new_canvas();var aG=null;ah.width=az+aj;ah.height=al;var aA=ah.getContext("2d");aA.fillStyle=this.prefs.block_color;aA.font=aA.canvas.manager.default_font;aA.textAlign="right";this.container_div.find(".yaxislabel").remove();if(au.data){aA.translate(aj,0);aG=aK.draw(aA,az,al,av);aG.translation=-aj}return new P(ay,aF,aB,ah,au.data,ax,au.message,aG)}});var U=function(ak,ah,ag,am,af,aj,al,ai){e.call(this,ak,ah,ag,am,af,aj,al,ai);this.config=new G({track:this,params:[{key:"name",label:"Name",type:"text",default_value:ak},{key:"block_color",label:"Block color",type:"color",default_value:get_random_color()},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:aj,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=M.ReadPainter};p(U.prototype,q.prototype,N.prototype,e.prototype);var W=function(aj,ah,ag,al,af,ai,ak){e.call(this,aj,ah,ag,al,af,ai,ak);this.config=new G({track:this,params:[{key:"name",label:"Name",type:"text",default_value:aj},{key:"block_color",label:"Block color",type:"color",default_value:get_random_color()},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:ai,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=M.ReadPainter;this.update_track_icons()};p(W.prototype,q.prototype,N.prototype,e.prototype);X.View=ac;X.DrawableGroup=Q;X.LineTrack=j;X.FeatureTrack=e;X.ReadTrack=W;X.VcfTrack=U};var slotting_module=function(c,b){var e=c("class").extend;var d=2,a=5;b.FeatureSlotter=function(i,h,f,g){this.slots={};this.start_end_dct={};this.w_scale=i;this.include_label=h;this.max_rows=f;this.measureText=g};e(b.FeatureSlotter.prototype,{slot_features:function(m){var p=this.w_scale,s=this.slots,h=this.start_end_dct,y=[],A=[],n=0,z=this.max_rows;for(var w=0,x=m.length;w<x;w++){var l=m[w],o=l[0];if(s[o]!==undefined){n=Math.max(n,s[o]);A.push(s[o])}else{y.push(w)}}var q=function(F,G){for(var E=0;E<=z;E++){var C=false,H=h[E];if(H!==undefined){for(var B=0,D=H.length;B<D;B++){var i=H[B];if(G>i[0]&&F<i[1]){C=true;break}}}if(!C){return E}}return -1};for(var w=0,x=y.length;w<x;w++){var l=m[y[w]],o=l[0],u=l[1],f=l[2],r=l[3],g=Math.floor(u*p),k=Math.ceil(f*p),v=this.measureText(r).width,j;if(r!==undefined&&this.include_label){v+=(d+a);if(g-v>=0){g-=v;j="left"}else{k+=v;j="right"}}var t=q(g,k);if(t>=0){if(h[t]===undefined){h[t]=[]}h[t].push([g,k]);s[o]=t;n=Math.max(n,t)}else{}}return n+1}})};var painters_module=function(i,w){var t=i("class").extend;var o=function(H,z,F,y,E,C){if(C===undefined){C=4}var B=y-z;var A=E-F;var D=Math.floor(Math.sqrt(B*B+A*A)/C);var I=B/D;var G=A/D;var x;for(x=0;x<D;x++,z+=I,F+=G){if(x%2!==0){continue}H.fillRect(z,F,C,1)}};var p=function(A,z,x,D){var C=z-D/2,B=z+D/2,E=x-Math.sqrt(D*3/2);A.beginPath();A.moveTo(C,E);A.lineTo(B,E);A.lineTo(z,x);A.lineTo(C,E);A.strokeStyle=this.fillStyle;A.fill();A.stroke();A.closePath()};var d=function(x){this.default_val=(x?x:1)};d.prototype.gen_val=function(x){return this.default_val};var l=function(z,B,x,y,A){this.data=z;this.view_start=B;this.view_end=x;this.prefs=t({},this.default_prefs,y);this.mode=A};l.prototype.default_prefs={};var u=function(z,B,x,y,A){l.call(this,z,B,x,y,A)};u.prototype.default_prefs={show_counts:false};u.prototype.draw=function(M,z,L){var E=this.view_start,O=this.view_end-this.view_start,N=z/O;var J=this.data.data,I=this.data.delta,G=this.data.max,B=L;delta_x_px=Math.ceil(I*N);M.save();for(var C=0,D=J.length;C<D;C++){var H=Math.floor((J[C][0]-E)*N);var F=J[C][1];if(!F){continue}var K=F/G*L;if(F!==0&&K<1){K=1}M.fillStyle=this.prefs.block_color;M.fillRect(H,B-K,delta_x_px,K);var A=4;if(this.prefs.show_counts&&(M.measureText(F).width+A)<delta_x_px){M.fillStyle=this.prefs.label_color;M.textAlign="center";M.fillText(F,H+(delta_x_px/2),10)}}M.restore()};var b=function(x,B,D,E,z){l.call(this,x,B,D,E,z);if(this.prefs.min_value===undefined){var F=Infinity;for(var y=0,A=this.data.length;y<A;y++){F=Math.min(F,this.data[y][1])}this.prefs.min_value=F}if(this.prefs.max_value===undefined){var C=-Infinity;for(var y=0,A=this.data.length;y<A;y++){C=Math.max(C,this.data[y][1])}this.prefs.max_value=C}};b.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Histogram",color:"#000",overflow_color:"#F66"};b.prototype.draw=function(M,L,J){var E=false,G=this.prefs.min_value,C=this.prefs.max_value,I=C-G,x=J,z=this.view_start,K=this.view_end-this.view_start,A=L/K,H=this.mode,S=this.data;M.save();var T=Math.round(J+G/I*J);if(H!=="Intensity"){M.fillStyle="#aaa";M.fillRect(0,T,L,1)}M.beginPath();var Q,D,B;if(S.length>1){B=Math.ceil((S[1][0]-S[0][0])*A)}else{B=10}for(var N=0,O=S.length;N<O;N++){M.fillStyle=this.prefs.color;Q=Math.round((S[N][0]-z)*A);D=S[N][1];var P=false,F=false;if(D===null){if(E&&H==="Filled"){M.lineTo(Q,x)}E=false;continue}if(D<G){F=true;D=G}else{if(D>C){P=true;D=C}}if(H==="Histogram"){D=Math.round(D/I*x);M.fillRect(Q,T,B,-D)}else{if(H==="Intensity"){D=255-Math.floor((D-G)/I*255);M.fillStyle="rgb("+D+","+D+","+D+")";M.fillRect(Q,0,B,x)}else{D=Math.round(x-(D-G)/I*x);if(E){M.lineTo(Q,D)}else{E=true;if(H==="Filled"){M.moveTo(Q,x);M.lineTo(Q,D)}else{M.moveTo(Q,D)}}}}M.fillStyle=this.prefs.overflow_color;if(P||F){var R;if(H==="Histogram"||H==="Intensity"){R=B}else{Q-=2;R=4}if(P){M.fillRect(Q,0,R,3)}if(F){M.fillRect(Q,x-3,R,3)}}M.fillStyle=this.prefs.color}if(H==="Filled"){if(E){M.lineTo(Q,T);M.lineTo(0,T)}M.fill()}else{M.stroke()}M.restore()};var m=function(x){this.feature_positions={};this.slot_height=x;this.translation=0};m.prototype.map_feature_data=function(y,A,x,z){if(!this.feature_positions[A]){this.feature_positions[A]=[]}this.feature_positions[A].push({data:y,x_start:x,x_end:z})};m.prototype.get_feature_data=function(z,D){var C=Math.floor(D/this.slot_height),B;if(!this.feature_positions[C]){return null}z+=this.translation;for(var A=0;A<this.feature_positions[C].length;A++){B=this.feature_positions[C][A];if(z>=B.x_start&&z<=B.x_end){return B.data}}};var n=function(z,C,x,y,B,D,A){l.call(this,z,C,x,y,B);this.alpha_scaler=(D?D:new d());this.height_scaler=(A?A:new d())};n.prototype.default_prefs={block_color:"#FFF",connector_color:"#FFF"};t(n.prototype,{get_required_height:function(y){var x=y_scale=this.get_row_height(),z=this.mode;if(z==="no_detail"||z==="Squish"||z==="Pack"){x=y*y_scale}return x+Math.max(Math.round(y_scale/2),5)},draw:function(J,H,F,E){var 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D=ad-(H-ad)/2;if((P==="Pack"||this.mode==="Auto")&&F!==undefined&&L>x){U.fillStyle="yellow";U.fillRect(D-R,E-9,H-ad,9);ae[ae.length]={type:"triangle",data:[Y,E+4,5]};U.fillStyle=g;switch(compute_overlap([G,G+N],z)){case (OVERLAP_START):Q=Q.slice(Z-G);break;case (OVERLAP_END):Q=Q.slice(0,G-A);break;case (CONTAINED_BY):break;case (CONTAINS):Q=Q.slice(Z-G,G-A);break}for(var ab=0,y=Q.length;ab<y;ab++){var ac=Math.floor(Math.max(0,(G+ab-Z)*L));U.fillText(Q[ab],ac-(H-ad)/2,E)}}else{U.fillStyle="yellow";U.fillRect(D,E+(this.mode!=="Dense"?2:5),H-ad,(P!=="Dense"?e:r))}}else{if((P==="Pack"||this.mode==="Auto")&&F!==undefined&&L>x){ae.push({type:"text",data:[Q.length,Y,E+9]})}else{}}}V+=N;break;case"X":V+=N;break}}U.fillStyle="yellow";var aa,C,af;for(var W=0;W<ae.length;W++){aa=ae[W];C=aa.type;af=aa.data;if(C==="text"){U.save();U.font="bold "+U.font;U.fillText(af[0],af[1],af[2]);U.restore()}else{if(C=="triangle"){p(U,af[0],af[1],af[2])}}}},draw_element:function(Q,L,D,A,T,y,H,R,O){var G=D[0],P=D[1],z=D[2],I=D[3],C=Math.floor(Math.max(0,(P-T)*H)),E=Math.ceil(Math.min(O,Math.max(0,(z-T)*H))),B=(L==="Dense"?0:(0+A))*R,U=this.prefs.block_color,F=this.prefs.label_color,N=0;if((L==="Pack"||this.mode==="Auto")&&H>Q.canvas.manager.char_width_px){var N=Math.round(H/2)}Q.fillStyle=U;if(D[5] instanceof Array){var M=Math.floor(Math.max(0,(D[4][0]-T)*H)),K=Math.ceil(Math.min(O,Math.max(0,(D[4][1]-T)*H))),J=Math.floor(Math.max(0,(D[5][0]-T)*H)),x=Math.ceil(Math.min(O,Math.max(0,(D[5][1]-T)*H)));if(D[4][1]>=T&&D[4][0]<=y&&D[4][2]){this.draw_read(Q,L,H,T,y,D[4][0],D[4][2],D[4][3],B)}if(D[5][1]>=T&&D[5][0]<=y&&D[5][2]){this.draw_read(Q,L,H,T,y,D[5][0],D[5][2],D[5][3],B)}if(J>K){Q.fillStyle=g;o(Q,K-N,B+5,J-N,B+5)}}else{Q.fillStyle=U;this.draw_read(Q,L,H,T,y,P,D[4],D[5],B)}if(L==="Pack"&&P>T&&I!=="."){Q.fillStyle=this.prefs.label_color;var S=1;if(S===0&&C-Q.measureText(I).width<0){Q.textAlign="left";Q.fillText(I,E+j-N,B+8)}else{Q.textAlign="right";Q.fillText(I,C-j-N,B+8)}Q.fillStyle=U}return[0,0]}});w.Scaler=d;w.SummaryTreePainter=u;w.LinePainter=b;w.LinkedFeaturePainter=q;w.ReadPainter=s};(function(d){var c={};var b=function(e){return c[e]};var a=function(f,g){var e={};g(b,e);c[f]=e};a("class",class_module);a("slotting",slotting_module);a("painters",painters_module);a("trackster",trackster_module);for(key in c.trackster){d[key]=c.trackster[key]}})(window); \ No newline at end of file diff -r 4ba5c0b16190a9977fdefa3b4df508d033929903 -r f34a17e508e5bc07d761eeb8c36a3d076ce9ecf1 static/scripts/trackster.js --- a/static/scripts/trackster.js +++ b/static/scripts/trackster.js @@ -1577,8 +1577,7 @@ // Set name of track to include tool name, parameters, and region used. track_name = url_params.tool_id + current_track.tool_region_and_parameters_str(url_params.chrom, url_params.low, url_params.high), - container, - new_track; + container; // If track not in a group, create a group for it and add new track to group. If track // already in group, add track to group. @@ -1595,11 +1594,12 @@ else { container = current_track.container; } - if (current_track instanceof FeatureTrack) { - new_track = new ToolDataFeatureTrack(track_name, view, container, "hda"); - new_track.change_mode(current_track.mode); - container.add_drawable(new_track); - } + + // Create and init new track. + var new_track = new current_track.constructor(track_name, view, container, "hda"); + new_track.init_for_tool_data(); + new_track.change_mode(current_track.mode); + container.add_drawable(new_track); new_track.content_div.text("Starting job."); // Run tool. @@ -2316,7 +2316,6 @@ * ----> ReferenceTrack * ----> FeatureTrack * -------> ReadTrack - * -------> ToolDataFeatureTrack * -------> VcfTrack */ var Track = function(name, view, container, show_header, prefs, data_url, data_query_wait) { @@ -2476,9 +2475,6 @@ else if (this instanceof ReadTrack) { return "ReadTrack"; } - else if (this instanceof ToolDataFeatureTrack) { - return "ToolDataFeatureTrack"; - } else if (this instanceof VcfTrack) { return "VcfTrack"; } @@ -2562,8 +2558,8 @@ predraw_init: function() {} }); -var TiledTrack = function(name, view, container, show_header, prefs, filters_list, tool_dict, data_url, data_query_wait) { - Track.call(this, name, view, container, show_header, prefs, data_url, data_query_wait); +var TiledTrack = function(name, view, container, show_header, prefs, filters_list, tool_dict) { + Track.call(this, name, view, container, show_header, prefs); var track = this, view = track.view; @@ -2910,6 +2906,39 @@ region = (chrom !== undefined && low !== undefined && high !== undefined ? chrom + ":" + low + "-" + high : "all"); return " - region=[" + region + "], parameters=[" + track.tool.get_param_values().join(", ") + "]"; + }, + /** + * Set up track to receive tool data. + */ + init_for_tool_data: function() { + // Set up track to fetch initial data from raw data URL when the dataset--not the converted datasets-- + // is ready. + this.data_url = raw_data_url; + this.data_query_wait = 1000; + this.dataset_check_url = dataset_state_url; + + /** + * Predraw init sets up postdraw init. + */ + this.predraw_init = function() { + // Postdraw init: once data has been fetched, reset data url, wait time and start indexing. + var track = this; + var post_init = function() { + if (track.data_manager.size() === 0) { + // Track still drawing initial data, so do nothing. + setTimeout(post_init, 300); + } + else { + // Track drawing done: reset dataset check, data URL, wait time and get dataset state to start + // indexing. + track.data_url = default_data_url; + track.data_query_wait = DEFAULT_DATA_QUERY_WAIT; + track.dataset_state_url = converted_datasets_state_url; + $.getJSON(track.dataset_state_url, {dataset_id : track.dataset_id, hda_ldda: track.hda_ldda}, function(track_data) {}); + } + }; + post_init(); + } } }); @@ -3524,8 +3553,8 @@ } }); -var VcfTrack = function(name, view, container, hda_ldda, dataset_id, prefs, filters) { - FeatureTrack.call(this, name, view, container, hda_ldda, dataset_id, prefs, filters); +var VcfTrack = function(name, view, container, hda_ldda, dataset_id, prefs, filters, tool) { + FeatureTrack.call(this, name, view, container, hda_ldda, dataset_id, prefs, filters, tool); this.config = new DrawableConfig( { track: this, @@ -3546,13 +3575,11 @@ }); this.prefs = this.config.values; - this.painter = painters.ReadPainter; }; extend(VcfTrack.prototype, Drawable.prototype, TiledTrack.prototype, FeatureTrack.prototype); - var ReadTrack = function (name, view, container, hda_ldda, dataset_id, prefs, filters) { FeatureTrack.call(this, name, view, container, hda_ldda, dataset_id, prefs, filters); @@ -3581,44 +3608,6 @@ }; extend(ReadTrack.prototype, Drawable.prototype, TiledTrack.prototype, FeatureTrack.prototype); -/** - * Feature track that displays data generated from tool. - */ -var ToolDataFeatureTrack = function(name, view, container, hda_ldda, dataset_id, prefs, filters) { - FeatureTrack.call(this, name, view, container, hda_ldda, dataset_id, prefs, filters, {}); - - // Set up track to fetch initial data from raw data URL when the dataset--not the converted datasets-- - // is ready. - this.data_url = raw_data_url; - this.data_query_wait = 1000; - this.dataset_check_url = dataset_state_url; -}; - -extend(ToolDataFeatureTrack.prototype, Drawable.prototype, TiledTrack.prototype, FeatureTrack.prototype, { - /** - * For this track type, the predraw init sets up postdraw init. - */ - predraw_init: function() { - // Postdraw init: once data has been fetched, reset data url, wait time and start indexing. - var track = this; - var post_init = function() { - if (track.data_manager.size() === 0) { - // Track still drawing initial data, so do nothing. - setTimeout(post_init, 300); - } - else { - // Track drawing done: reset dataset check, data URL, wait time and get dataset state to start - // indexing. - track.data_url = default_data_url; - track.data_query_wait = DEFAULT_DATA_QUERY_WAIT; - track.dataset_state_url = converted_datasets_state_url; - $.getJSON(track.dataset_state_url, {dataset_id : track.dataset_id, hda_ldda: track.hda_ldda}, function(track_data) {}); - } - }; - post_init(); - } -}); - // Exports exports.View = View; diff -r 4ba5c0b16190a9977fdefa3b4df508d033929903 -r f34a17e508e5bc07d761eeb8c36a3d076ce9ecf1 templates/tracks/browser.mako --- a/templates/tracks/browser.mako +++ b/templates/tracks/browser.mako @@ -125,7 +125,7 @@ view = create_visualization( $("#browser-container"), "${config.get('title') | h}", "${config.get('vis_id')}", "${config.get('dbkey')}", JSON.parse('${ h.to_json_string( config.get( 'viewport', dict() ) ) }'), - JSON.parse('${ h.to_json_string( config['tracks'] ) }'), + JSON.parse('${ h.to_json_string( config['tracks'] ).replace("'", "\\'") }'), JSON.parse('${ h.to_json_string( config['bookmarks'] ) }') ); init_editor(); diff -r 4ba5c0b16190a9977fdefa3b4df508d033929903 -r f34a17e508e5bc07d761eeb8c36a3d076ce9ecf1 tools/gatk/unified_genotyper.xml --- a/tools/gatk/unified_genotyper.xml +++ b/tools/gatk/unified_genotyper.xml @@ -396,7 +396,7 @@ <data format="txt" name="output_metrics" label="${tool.name} on ${on_string} (metrics)" /><data format="txt" name="output_log" label="${tool.name} on ${on_string} (log)" /></outputs> -  + <trackster_conf/><tests><test><param name="reference_source_selector" value="history" /> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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