[galaxy-commits] commit/galaxy-central: 2 new changesets

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/78eaaca131e3/ Changeset: 78eaaca131e3 User: dan Date: 2013-10-07 23:00:22 Summary: Fix for history updater when setting metadata Affected #: 1 file diff -r 4db4660f5b121eee69a822b9c1294e4316855715 -r 78eaaca131e3251ba9cc78f7546ace6a713a4f02 static/scripts/mvc/history/history-model.js --- a/static/scripts/mvc/history/history-model.js +++ b/static/scripts/mvc/history/history-model.js @@ -152,7 +152,8 @@ var timeout; // set up to keep pulling if this history in run/queue state if( ( history.get( 'state' ) === HistoryDatasetAssociation.STATES.RUNNING ) - || ( history.get( 'state' ) === HistoryDatasetAssociation.STATES.QUEUED ) ){ + || ( history.get( 'state' ) === HistoryDatasetAssociation.STATES.QUEUED ) + || ( history.get( 'state' ) === HistoryDatasetAssociation.STATES.SETTING_METADATA )){ //|| ( history.hdas.running() ) ){ timeout = history.updateAfterDelay(); https://bitbucket.org/galaxy/galaxy-central/commits/f76c280cdee5/ Changeset: f76c280cdee5 User: dan Date: 2013-10-07 23:00:29 Summary: Pack scripts Affected #: 11 files diff -r 78eaaca131e3251ba9cc78f7546ace6a713a4f02 -r f76c280cdee539b65315ac583f93bfa52feb790d static/scripts/packed/galaxy.base.js --- a/static/scripts/packed/galaxy.base.js +++ b/static/scripts/packed/galaxy.base.js @@ -1,1 +1,1 @@ -(function(){var b=0;var c=["ms","moz","webkit","o"];for(var a=0;a<c.length&&!window.requestAnimationFrame;++a){window.requestAnimationFrame=window[c[a]+"RequestAnimationFrame"];window.cancelRequestAnimationFrame=window[c[a]+"CancelRequestAnimationFrame"]}if(!window.requestAnimationFrame){window.requestAnimationFrame=function(h,e){var d=new Date().getTime();var f=Math.max(0,16-(d-b));var g=window.setTimeout(function(){h(d+f)},f);b=d+f;return g}}if(!window.cancelAnimationFrame){window.cancelAnimationFrame=function(d){clearTimeout(d)}}}());if(!Array.indexOf){Array.prototype.indexOf=function(c){for(var b=0,a=this.length;b<a;b++){if(this[b]==c){return b}}return -1}}function obj_length(c){if(c.length!==undefined){return c.length}var b=0;for(var a in c){b++}return b}$.fn.makeAbsolute=function(a){return this.each(function(){var b=$(this);var c=b.position();b.css({position:"absolute",marginLeft:0,marginTop:0,top:c.top,left:c.left,right:$(window).width()-(c.left+b.width())});if(a){b.remove().appendTo("body")}})};function make_popupmenu(b,c){var a=(b.data("menu_options"));b.data("menu_options",c);if(a){return}b.bind("click.show_popup",function(d){$(".popmenu-wrapper").remove();setTimeout(function(){var g=$("<ul class='dropdown-menu' id='"+b.attr("id")+"-menu'></ul>");var f=b.data("menu_options");if(obj_length(f)<=0){$("<li>No Options.</li>").appendTo(g)}$.each(f,function(j,i){if(i){var l=i.action||i;g.append($("<li></li>").append($("<a>").attr("href",i.url).html(j).click(l)))}else{g.append($("<li></li>").addClass("head").append($("<a href='#'></a>").html(j)))}});var h=$("<div class='popmenu-wrapper' style='position: absolute;left: 0; top: -1000;'></div>").append(g).appendTo("body");var e=d.pageX-h.width()/2;e=Math.min(e,$(document).scrollLeft()+$(window).width()-$(h).width()-5);e=Math.max(e,$(document).scrollLeft()+5);h.css({top:d.pageY,left:e})},10);setTimeout(function(){var f=function(h){$(h).bind("click.close_popup",function(){$(".popmenu-wrapper").remove();h.unbind("click.close_popup")})};f($(window.document));f($(window.top.document));for(var e=window.top.frames.length;e--;){var g=$(window.top.frames[e].document);f(g)}},50);return false})}function make_popup_menus(a){a=a||document;$(a).find("div[popupmenu]").each(function(){var b={};var d=$(this);d.find("a").each(function(){var g=$(this),i=g.get(0),e=i.getAttribute("confirm"),f=i.getAttribute("href"),h=i.getAttribute("target");if(!f){b[g.text()]=null}else{b[g.text()]={url:f,action:function(){if(!e||confirm(e)){var j;if(h==="demo"){if(j===undefined||j.closed){j=window.open(f,h);j.creator=self}}else{g.trigger("click")}}}}}});var c=$(a).find("#"+d.attr("popupmenu"));c.find("a").bind("click",function(f){f.stopPropagation();return true});make_popupmenu(c,b);c.addClass("popup");d.remove()})}function naturalSort(j,h){var p=/(-?[0-9\.]+)/g,k=j.toString().toLowerCase()||"",g=h.toString().toLowerCase()||"",l=String.fromCharCode(0),n=k.replace(p,l+"$1"+l).split(l),e=g.replace(p,l+"$1"+l).split(l),d=(new Date(k)).getTime(),o=d?(new Date(g)).getTime():null;if(o){if(d<o){return -1}else{if(d>o){return 1}}}var m,f;for(var i=0,c=Math.max(n.length,e.length);i<c;i++){m=parseFloat(n[i])||n[i];f=parseFloat(e[i])||e[i];if(m<f){return -1}else{if(m>f){return 1}}}return 0}$.fn.refresh_select2=function(){var b=$(this);var a={width:"resolve",closeOnSelect:!b.is("[MULTIPLE]")};return b.select2(a)};function replace_big_select_inputs(a,c,b){if(!jQuery.fn.select2){return}if(a===undefined){a=20}if(c===undefined){c=3000}b=b||$("select");b.each(function(){var e=$(this);var d=e.find("option").length;if((d<a)||(d>c)){return}if(e.hasClass("no-autocomplete")){return}e.refresh_select2()})}$.fn.make_text_editable=function(g){var d=("num_cols" in g?g.num_cols:30),c=("num_rows" in g?g.num_rows:4),e=("use_textarea" in g?g.use_textarea:false),b=("on_finish" in g?g.on_finish:null),f=("help_text" in g?g.help_text:null);var a=$(this);a.addClass("editable-text").click(function(l){if($(this).children(":input").length>0){return}a.removeClass("editable-text");var i=function(m){a.find(":input").remove();if(m!==""){a.text(m)}else{a.html("<br>")}a.addClass("editable-text");if(b){b(m)}};var h=a.text(),k,j;if(e){k=$("<textarea/>").attr({rows:c,cols:d}).text($.trim(h)).keyup(function(m){if(m.keyCode===27){i(h)}});j=$("<button/>").text("Done").click(function(){i(k.val());return false})}else{k=$("<input type='text'/>").attr({value:$.trim(h),size:d}).blur(function(){i(h)}).keyup(function(m){if(m.keyCode===27){$(this).trigger("blur")}else{if(m.keyCode===13){i($(this).val())}}})}a.text("");a.append(k);if(j){a.append(j)}k.focus();k.select();l.stopPropagation()});if(f){a.attr("title",f).tooltip()}return a};function async_save_text(d,f,e,a,c,h,i,g,b){if(c===undefined){c=30}if(i===undefined){i=4}$("#"+d).click(function(){if($("#renaming-active").length>0){return}var l=$("#"+f),k=l.text(),j;if(h){j=$("<textarea></textarea>").attr({rows:i,cols:c}).text($.trim(k))}else{j=$("<input type='text'></input>").attr({value:$.trim(k),size:c})}j.attr("id","renaming-active");j.blur(function(){$(this).remove();l.show();if(b){b(j)}});j.keyup(function(n){if(n.keyCode===27){$(this).trigger("blur")}else{if(n.keyCode===13){var m={};m[a]=$(this).val();$(this).trigger("blur");$.ajax({url:e,data:m,error:function(){alert("Text editing for elt "+f+" failed")},success:function(o){if(o!==""){l.text(o)}else{l.html("<em>None</em>")}if(b){b(j)}}})}}});if(g){g(j)}l.hide();j.insertAfter(l);j.focus();j.select();return})}function init_history_items(d,a,c){var b=function(){try{var e=$.jStorage.get("history_expand_state");if(e){for(var g in e){$("#"+g+" div.historyItemBody").show()}}}catch(f){$.jStorage.deleteKey("history_expand_state")}if($.browser.mozilla){$("div.historyItemBody").each(function(){if(!$(this).is(":visible")){$(this).find("pre.peek").css("overflow","hidden")}})}d.each(function(){var j=this.id,h=$(this).children("div.historyItemBody"),i=h.find("pre.peek");$(this).find(".historyItemTitleBar > .historyItemTitle").wrap("<a href='javascript:void(0);'></a>").click(function(){var k;if(h.is(":visible")){if($.browser.mozilla){i.css("overflow","hidden")}h.slideUp("fast");if(!c){k=$.jStorage.get("history_expand_state");if(k){delete k[j];$.jStorage.set("history_expand_state",k)}}}else{h.slideDown("fast",function(){if($.browser.mozilla){i.css("overflow","auto")}});if(!c){k=$.jStorage.get("history_expand_state");if(!k){k={}}k[j]=true;$.jStorage.set("history_expand_state",k)}}return false})});$("#top-links > a.toggle").click(function(){var h=$.jStorage.get("history_expand_state");if(!h){h={}}$("div.historyItemBody:visible").each(function(){if($.browser.mozilla){$(this).find("pre.peek").css("overflow","hidden")}$(this).slideUp("fast");if(h){delete h[$(this).parent().attr("id")]}});$.jStorage.set("history_expand_state",h)}).show()};b()}function commatize(b){b+="";var a=/(\d+)(\d{3})/;while(a.test(b)){b=b.replace(a,"$1,$2")}return b}function reset_tool_search(a){var c=$("#galaxy_tools").contents();if(c.length===0){c=$(document)}$(this).removeClass("search_active");c.find(".toolTitle").removeClass("search_match");c.find(".toolSectionBody").hide();c.find(".toolTitle").show();c.find(".toolPanelLabel").show();c.find(".toolSectionWrapper").each(function(){if($(this).attr("id")!=="recently_used_wrapper"){$(this).show()}else{if($(this).hasClass("user_pref_visible")){$(this).show()}}});c.find("#search-no-results").hide();c.find("#search-spinner").hide();if(a){var b=c.find("#tool-search-query");b.val("search tools")}}var GalaxyAsync=function(a){this.url_dict={};this.log_action=(a===undefined?false:a)};GalaxyAsync.prototype.set_func_url=function(a,b){this.url_dict[a]=b};GalaxyAsync.prototype.set_user_pref=function(a,b){var c=this.url_dict[arguments.callee];if(c===undefined){return false}$.ajax({url:c,data:{pref_name:a,pref_value:b},error:function(){return false},success:function(){return true}})};GalaxyAsync.prototype.log_user_action=function(c,b,d){if(!this.log_action){return}var a=this.url_dict[arguments.callee];if(a===undefined){return false}$.ajax({url:a,data:{action:c,context:b,params:d},error:function(){return false},success:function(){return true}})};$(document).ready(function(){$("select[refresh_on_change='true']").change(function(){var a=$(this),e=a.val(),d=false,c=a.attr("refresh_on_change_values");if(c){c=c.split(",");var b=a.attr("last_selected_value");if($.inArray(e,c)===-1&&$.inArray(b,c)===-1){return}}$(window).trigger("refresh_on_change");$(document).trigger("convert_to_values");a.get(0).form.submit()});$(":checkbox[refresh_on_change='true']").click(function(){var a=$(this),e=a.val(),d=false,c=a.attr("refresh_on_change_values");if(c){c=c.split(",");var b=a.attr("last_selected_value");if($.inArray(e,c)===-1&&$.inArray(b,c)===-1){return}}$(window).trigger("refresh_on_change");a.get(0).form.submit()});$("a[confirm]").click(function(){return confirm($(this).attr("confirm"))});if($.fn.tooltip){$(".unified-panel-header [title]").tooltip({placement:"bottom"});$("[title]").tooltip({placement:"top"})}make_popup_menus();replace_big_select_inputs(20,1500);$("a").click(function(){var b=$(this);var c=(parent.frames&&parent.frames.galaxy_main);if((b.attr("target")=="galaxy_main")&&(!c)){var a=b.attr("href");if(a.indexOf("?")==-1){a+="?"}else{a+="&"}a+="use_panels=True";b.attr("href",a);b.attr("target","_self")}return b})}); \ No newline at end of file +(function(){var b=0;var c=["ms","moz","webkit","o"];for(var a=0;a<c.length&&!window.requestAnimationFrame;++a){window.requestAnimationFrame=window[c[a]+"RequestAnimationFrame"];window.cancelRequestAnimationFrame=window[c[a]+"CancelRequestAnimationFrame"]}if(!window.requestAnimationFrame){window.requestAnimationFrame=function(h,e){var d=new Date().getTime();var f=Math.max(0,16-(d-b));var g=window.setTimeout(function(){h(d+f)},f);b=d+f;return g}}if(!window.cancelAnimationFrame){window.cancelAnimationFrame=function(d){clearTimeout(d)}}}());if(!Array.indexOf){Array.prototype.indexOf=function(c){for(var b=0,a=this.length;b<a;b++){if(this[b]==c){return b}}return -1}}function obj_length(c){if(c.length!==undefined){return c.length}var b=0;for(var a in c){b++}return b}$.fn.makeAbsolute=function(a){return this.each(function(){var b=$(this);var c=b.position();b.css({position:"absolute",marginLeft:0,marginTop:0,top:c.top,left:c.left,right:$(window).width()-(c.left+b.width())});if(a){b.remove().appendTo("body")}})};function make_popupmenu(b,c){var a=(b.data("menu_options"));b.data("menu_options",c);if(a){return}b.bind("click.show_popup",function(d){$(".popmenu-wrapper").remove();setTimeout(function(){var g=$("<ul class='dropdown-menu' id='"+b.attr("id")+"-menu'></ul>");var f=b.data("menu_options");if(obj_length(f)<=0){$("<li>No Options.</li>").appendTo(g)}$.each(f,function(j,i){if(i){var l=i.action||i;g.append($("<li></li>").append($("<a>").attr("href",i.url).html(j).click(l)))}else{g.append($("<li></li>").addClass("head").append($("<a href='#'></a>").html(j)))}});var h=$("<div class='popmenu-wrapper' style='position: absolute;left: 0; top: -1000;'></div>").append(g).appendTo("body");var e=d.pageX-h.width()/2;e=Math.min(e,$(document).scrollLeft()+$(window).width()-$(h).width()-5);e=Math.max(e,$(document).scrollLeft()+5);h.css({top:d.pageY,left:e})},10);setTimeout(function(){var f=function(h){$(h).bind("click.close_popup",function(){$(".popmenu-wrapper").remove();h.unbind("click.close_popup")})};f($(window.document));f($(window.top.document));for(var e=window.top.frames.length;e--;){var g=$(window.top.frames[e].document);f(g)}},50);return false})}function make_popup_menus(a){a=a||document;$(a).find("div[popupmenu]").each(function(){var b={};var d=$(this);d.find("a").each(function(){var g=$(this),i=g.get(0),e=i.getAttribute("confirm"),f=i.getAttribute("href"),h=i.getAttribute("target");if(!f){b[g.text()]=null}else{b[g.text()]={url:f,action:function(){if(!e||confirm(e)){if(h){window.open(f,h)}else{g.click()}}}}}});var c=$(a).find("#"+d.attr("popupmenu"));c.find("a").bind("click",function(f){f.stopPropagation();return true});make_popupmenu(c,b);c.addClass("popup");d.remove()})}function naturalSort(j,h){var p=/(-?[0-9\.]+)/g,k=j.toString().toLowerCase()||"",g=h.toString().toLowerCase()||"",l=String.fromCharCode(0),n=k.replace(p,l+"$1"+l).split(l),e=g.replace(p,l+"$1"+l).split(l),d=(new Date(k)).getTime(),o=d?(new Date(g)).getTime():null;if(o){if(d<o){return -1}else{if(d>o){return 1}}}var m,f;for(var i=0,c=Math.max(n.length,e.length);i<c;i++){m=parseFloat(n[i])||n[i];f=parseFloat(e[i])||e[i];if(m<f){return -1}else{if(m>f){return 1}}}return 0}$.fn.refresh_select2=function(){var b=$(this);var a={width:"resolve",closeOnSelect:!b.is("[MULTIPLE]")};return b.select2(a)};function replace_big_select_inputs(a,c,b){if(!jQuery.fn.select2){return}if(a===undefined){a=20}if(c===undefined){c=3000}b=b||$("select");b.each(function(){var e=$(this);var d=e.find("option").length;if((d<a)||(d>c)){return}if(e.hasClass("no-autocomplete")){return}e.refresh_select2()})}$.fn.make_text_editable=function(g){var d=("num_cols" in g?g.num_cols:30),c=("num_rows" in g?g.num_rows:4),e=("use_textarea" in g?g.use_textarea:false),b=("on_finish" in g?g.on_finish:null),f=("help_text" in g?g.help_text:null);var a=$(this);a.addClass("editable-text").click(function(l){if($(this).children(":input").length>0){return}a.removeClass("editable-text");var i=function(m){a.find(":input").remove();if(m!==""){a.text(m)}else{a.html("<br>")}a.addClass("editable-text");if(b){b(m)}};var h=a.text(),k,j;if(e){k=$("<textarea/>").attr({rows:c,cols:d}).text($.trim(h)).keyup(function(m){if(m.keyCode===27){i(h)}});j=$("<button/>").text("Done").click(function(){i(k.val());return false})}else{k=$("<input type='text'/>").attr({value:$.trim(h),size:d}).blur(function(){i(h)}).keyup(function(m){if(m.keyCode===27){$(this).trigger("blur")}else{if(m.keyCode===13){i($(this).val())}}})}a.text("");a.append(k);if(j){a.append(j)}k.focus();k.select();l.stopPropagation()});if(f){a.attr("title",f).tooltip()}return a};function async_save_text(d,f,e,a,c,h,i,g,b){if(c===undefined){c=30}if(i===undefined){i=4}$("#"+d).click(function(){if($("#renaming-active").length>0){return}var l=$("#"+f),k=l.text(),j;if(h){j=$("<textarea></textarea>").attr({rows:i,cols:c}).text($.trim(k))}else{j=$("<input type='text'></input>").attr({value:$.trim(k),size:c})}j.attr("id","renaming-active");j.blur(function(){$(this).remove();l.show();if(b){b(j)}});j.keyup(function(n){if(n.keyCode===27){$(this).trigger("blur")}else{if(n.keyCode===13){var m={};m[a]=$(this).val();$(this).trigger("blur");$.ajax({url:e,data:m,error:function(){alert("Text editing for elt "+f+" failed")},success:function(o){if(o!==""){l.text(o)}else{l.html("<em>None</em>")}if(b){b(j)}}})}}});if(g){g(j)}l.hide();j.insertAfter(l);j.focus();j.select();return})}function init_history_items(d,a,c){var b=function(){try{var e=$.jStorage.get("history_expand_state");if(e){for(var g in e){$("#"+g+" div.historyItemBody").show()}}}catch(f){$.jStorage.deleteKey("history_expand_state")}if($.browser.mozilla){$("div.historyItemBody").each(function(){if(!$(this).is(":visible")){$(this).find("pre.peek").css("overflow","hidden")}})}d.each(function(){var j=this.id,h=$(this).children("div.historyItemBody"),i=h.find("pre.peek");$(this).find(".historyItemTitleBar > .historyItemTitle").wrap("<a href='javascript:void(0);'></a>").click(function(){var k;if(h.is(":visible")){if($.browser.mozilla){i.css("overflow","hidden")}h.slideUp("fast");if(!c){k=$.jStorage.get("history_expand_state");if(k){delete k[j];$.jStorage.set("history_expand_state",k)}}}else{h.slideDown("fast",function(){if($.browser.mozilla){i.css("overflow","auto")}});if(!c){k=$.jStorage.get("history_expand_state");if(!k){k={}}k[j]=true;$.jStorage.set("history_expand_state",k)}}return false})});$("#top-links > a.toggle").click(function(){var h=$.jStorage.get("history_expand_state");if(!h){h={}}$("div.historyItemBody:visible").each(function(){if($.browser.mozilla){$(this).find("pre.peek").css("overflow","hidden")}$(this).slideUp("fast");if(h){delete h[$(this).parent().attr("id")]}});$.jStorage.set("history_expand_state",h)}).show()};b()}function commatize(b){b+="";var a=/(\d+)(\d{3})/;while(a.test(b)){b=b.replace(a,"$1,$2")}return b}function reset_tool_search(a){var c=$("#galaxy_tools").contents();if(c.length===0){c=$(document)}$(this).removeClass("search_active");c.find(".toolTitle").removeClass("search_match");c.find(".toolSectionBody").hide();c.find(".toolTitle").show();c.find(".toolPanelLabel").show();c.find(".toolSectionWrapper").each(function(){if($(this).attr("id")!=="recently_used_wrapper"){$(this).show()}else{if($(this).hasClass("user_pref_visible")){$(this).show()}}});c.find("#search-no-results").hide();c.find("#search-spinner").hide();if(a){var b=c.find("#tool-search-query");b.val("search tools")}}var GalaxyAsync=function(a){this.url_dict={};this.log_action=(a===undefined?false:a)};GalaxyAsync.prototype.set_func_url=function(a,b){this.url_dict[a]=b};GalaxyAsync.prototype.set_user_pref=function(a,b){var c=this.url_dict[arguments.callee];if(c===undefined){return false}$.ajax({url:c,data:{pref_name:a,pref_value:b},error:function(){return false},success:function(){return true}})};GalaxyAsync.prototype.log_user_action=function(c,b,d){if(!this.log_action){return}var a=this.url_dict[arguments.callee];if(a===undefined){return false}$.ajax({url:a,data:{action:c,context:b,params:d},error:function(){return false},success:function(){return true}})};$(document).ready(function(){$("select[refresh_on_change='true']").change(function(){var a=$(this),e=a.val(),d=false,c=a.attr("refresh_on_change_values");if(c){c=c.split(",");var b=a.attr("last_selected_value");if($.inArray(e,c)===-1&&$.inArray(b,c)===-1){return}}$(window).trigger("refresh_on_change");$(document).trigger("convert_to_values");a.get(0).form.submit()});$(":checkbox[refresh_on_change='true']").click(function(){var a=$(this),e=a.val(),d=false,c=a.attr("refresh_on_change_values");if(c){c=c.split(",");var b=a.attr("last_selected_value");if($.inArray(e,c)===-1&&$.inArray(b,c)===-1){return}}$(window).trigger("refresh_on_change");a.get(0).form.submit()});$("a[confirm]").click(function(){return confirm($(this).attr("confirm"))});if($.fn.tooltip){$(".unified-panel-header [title]").tooltip({placement:"bottom"});$("[title]").tooltip({placement:"top"})}make_popup_menus();replace_big_select_inputs(20,1500);$("a").click(function(){var b=$(this);var c=(parent.frames&&parent.frames.galaxy_main);if((b.attr("target")=="galaxy_main")&&(!c)){var a=b.attr("href");if(a.indexOf("?")==-1){a+="?"}else{a+="&"}a+="use_panels=True";b.attr("href",a);b.attr("target","_self")}return b})}); \ No newline at end of file diff -r 78eaaca131e3251ba9cc78f7546ace6a713a4f02 -r f76c280cdee539b65315ac583f93bfa52feb790d static/scripts/packed/galaxy.grids.js --- a/static/scripts/packed/galaxy.grids.js +++ b/static/scripts/packed/galaxy.grids.js @@ -1,1 +1,1 @@ -jQuery.ajaxSettings.traditional=true;var Grid=Backbone.Model.extend({defaults:{url_base:"",async:false,async_ops:[],categorical_filters:[],filters:{},sort_key:null,show_item_checkboxes:false,cur_page:1,num_pages:1,operation:undefined,item_ids:undefined},can_async_op:function(a){return _.indexOf(this.attributes.async_ops,a)!==-1},add_filter:function(e,f,b){if(b){var c=this.attributes.filters[e],a;if(c===null||c===undefined){a=f}else{if(typeof(c)=="string"){if(c=="All"){a=f}else{var d=[];d[0]=c;d[1]=f;a=d}}else{a=c;a.push(f)}}this.attributes.filters[e]=a}else{this.attributes.filters[e]=f}},remove_filter:function(b,e){var a=this.attributes.filters[b];if(a===null||a===undefined){return false}var d=true;if(typeof(a)==="string"){if(a=="All"){d=false}else{delete this.attributes.filters[b]}}else{var c=_.indexOf(a,e);if(c!==-1){a.splice(c,1)}else{d=false}}return d},get_url_data:function(){var a={async:this.attributes.async,sort:this.attributes.sort_key,page:this.attributes.cur_page,show_item_checkboxes:this.attributes.show_item_checkboxes};if(this.attributes.operation){a.operation=this.attributes.operation}if(this.attributes.item_ids){a.id=this.attributes.item_ids}var b=this;_.each(_.keys(b.attributes.filters),function(c){a["f-"+c]=b.attributes.filters[c]});return a}});function init_operation_buttons(){$("input[name=operation]:submit").each(function(){$(this).click(function(){var b=$(this).val();var a=[];$("input[name=id]:checked").each(function(){a.push($(this).val())});do_operation(b,a)})})}function init_grid_controls(){init_operation_buttons();$(".submit-image").each(function(){$(this).mousedown(function(){$(this).addClass("gray-background")});$(this).mouseup(function(){$(this).removeClass("gray-background")})});$(".sort-link").each(function(){$(this).click(function(){set_sort_condition($(this).attr("sort_key"));return false})});$(".page-link > a").each(function(){$(this).click(function(){set_page($(this).attr("page_num"));return false})});$(".categorical-filter > a").each(function(){$(this).click(function(){set_categorical_filter($(this).attr("filter_key"),$(this).attr("filter_val"));return false})});$(".text-filter-form").each(function(){$(this).submit(function(){var d=$(this).attr("column_key");var c=$("#input-"+d+"-filter");var e=c.val();c.val("");add_filter_condition(d,e,true);return false})});var a=$("#input-tags-filter");if(a.length){a.autocomplete(history_tag_autocomplete_url,{selectFirst:false,autoFill:false,highlight:false,mustMatch:false})}var b=$("#input-name-filter");if(b.length){b.autocomplete(history_name_autocomplete_url,{selectFirst:false,autoFill:false,highlight:false,mustMatch:false})}$(".advanced-search-toggle").each(function(){$(this).click(function(){$("#standard-search").slideToggle("fast");$("#advanced-search").slideToggle("fast");return false})})}function init_grid_elements(){$(".grid").each(function(){var b=$(this).find("input.grid-row-select-checkbox");var a=$(this).find("span.grid-selected-count");var c=function(){a.text($(b).filter(":checked").length)};$(b).each(function(){$(this).change(c)});c()});$(".label").each(function(){var a=$(this).attr("href");if(a!==undefined&&a.indexOf("operation=")!=-1){$(this).click(function(){do_operation_from_href($(this).attr("href"));return false})}});$(".community_rating_star").rating({});make_popup_menus()}function go_page_one(){var a=grid.get("cur_page");if(a!==null&&a!==undefined&&a!=="all"){grid.set("cur_page",1)}}function add_filter_condition(c,e,a){if(e===""){return false}grid.add_filter(c,e,a);var d=$("<span>"+e+"<a href='javascript:void(0);'><span class='delete-search-icon' /></a></span>");d.addClass("text-filter-val");d.click(function(){grid.remove_filter(c,e);$(this).remove();go_page_one();update_grid()});var b=$("#"+c+"-filtering-criteria");b.append(d);go_page_one();update_grid()}function add_tag_to_grid_filter(c,b){var a=c+(b!==undefined&&b!==""?":"+b:"");$("#advanced-search").show("fast");add_filter_condition("tags",a,true)}function set_sort_condition(f){var e=grid.get("sort_key");var d=f;if(e.indexOf(f)!==-1){if(e.substring(0,1)!=="-"){d="-"+f}else{}}$(".sort-arrow").remove();var c=(d.substring(0,1)=="-")?"↑":"↓";var a=$("<span>"+c+"</span>").addClass("sort-arrow");var b=$("#"+f+"-header");b.append(a);grid.set("sort_key",d);go_page_one();update_grid()}function set_categorical_filter(b,d){var a=grid.get("categorical_filters")[b],c=grid.get("filters")[b];$("."+b+"-filter").each(function(){var h=$.trim($(this).text());var f=a[h];var g=f[b];if(g==d){$(this).empty();$(this).addClass("current-filter");$(this).append(h)}else{if(g==c){$(this).empty();var e=$("<a href='#'>"+h+"</a>");e.click(function(){set_categorical_filter(b,g)});$(this).removeClass("current-filter");$(this).append(e)}}});grid.add_filter(b,d);go_page_one();update_grid()}function set_page(a){$(".page-link").each(function(){var g=$(this).attr("id"),e=parseInt(g.split("-")[2],10),c=grid.get("cur_page"),f;if(e===a){f=$(this).children().text();$(this).empty();$(this).addClass("inactive-link");$(this).text(f)}else{if(e===c){f=$(this).text();$(this).empty();$(this).removeClass("inactive-link");var d=$("<a href='#'>"+f+"</a>");d.click(function(){set_page(e)});$(this).append(d)}}});var b=true;if(a==="all"){grid.set("cur_page",a);b=false}else{grid.set("cur_page",parseInt(a,10))}update_grid(b)}function do_operation(b,a){b=b.toLowerCase();grid.set({operation:b,item_ids:a});if(grid.can_async_op(b)){update_grid(true)}else{go_to_URL()}}function do_operation_from_href(c){var f=c.split("?");if(f.length>1){var a=f[1];var e=a.split("&");var b=null;var g=-1;for(var d=0;d<e.length;d++){if(e[d].indexOf("operation")!=-1){b=e[d].split("=")[1]}else{if(e[d].indexOf("id")!=-1){g=e[d].split("=")[1]}}}do_operation(b,g);return false}}function go_to_URL(){grid.set("async",false);window.location=grid.get("url_base")+"?"+$.param(grid.get_url_data())}function update_grid(a){if(!grid.get("async")){go_to_URL();return}var b=(grid.get("operation")?"POST":"GET");$(".loading-elt-overlay").show();$.ajax({type:b,url:grid.get("url_base"),data:grid.get_url_data(),error:function(){alert("Grid refresh failed")},success:function(d){var c=d.split("*****");$("#grid-table-body").html(c[0]);$("#grid-table-footer").html(c[1]);$("#grid-table-body").trigger("update");init_grid_elements();init_operation_buttons();make_popup_menus();$(".loading-elt-overlay").hide();var e=$.trim(c[2]);if(e!==""){$("#grid-message").html(e).show();setTimeout(function(){$("#grid-message").hide()},5000)}},complete:function(){grid.set({operation:undefined,item_ids:undefined})}})}function check_all_items(){var a=document.getElementById("check_all"),b=document.getElementsByTagName("input"),d=0,c;if(a.checked===true){for(c=0;c<b.length;c++){if(b[c].name.indexOf("id")!==-1){b[c].checked=true;d++}}}else{for(c=0;c<b.length;c++){if(b[c].name.indexOf("id")!==-1){b[c].checked=false}}}init_grid_elements()}function submit_operation(b,c){var a=$('input[name="id"]:checked').length;if(!a>0){return false}if(c!="None"&&c!=""){if(!confirm(c)){return false}}$("#operation").val(b.value);b.form.submit();return true}; \ No newline at end of file +jQuery.ajaxSettings.traditional=true;var Grid=Backbone.Model.extend({defaults:{url_base:"",async:false,async_ops:[],categorical_filters:[],filters:{},sort_key:null,show_item_checkboxes:false,cur_page:1,num_pages:1,operation:undefined,item_ids:undefined},can_async_op:function(a){return _.indexOf(this.attributes.async_ops,a)!==-1},add_filter:function(e,f,b){if(b){var c=this.attributes.filters[e],a;if(c===null||c===undefined){a=f}else{if(typeof(c)=="string"){if(c=="All"){a=f}else{var d=[];d[0]=c;d[1]=f;a=d}}else{a=c;a.push(f)}}this.attributes.filters[e]=a}else{this.attributes.filters[e]=f}},remove_filter:function(b,e){var a=this.attributes.filters[b];if(a===null||a===undefined){return false}var d=true;if(typeof(a)==="string"){if(a=="All"){d=false}else{delete this.attributes.filters[b]}}else{var c=_.indexOf(a,e);if(c!==-1){a.splice(c,1)}else{d=false}}return d},get_url_data:function(){var a={async:this.attributes.async,sort:this.attributes.sort_key,page:this.attributes.cur_page,show_item_checkboxes:this.attributes.show_item_checkboxes};if(this.attributes.operation){a.operation=this.attributes.operation}if(this.attributes.item_ids){a.id=this.attributes.item_ids}var b=this;_.each(_.keys(b.attributes.filters),function(c){a["f-"+c]=b.attributes.filters[c]});return a}});function init_operation_buttons(){$("input[name=operation]:submit").each(function(){$(this).click(function(){var b=$(this).val();var a=[];$("input[name=id]:checked").each(function(){a.push($(this).val())});do_operation(b,a)})})}function init_grid_controls(){init_operation_buttons();$(".submit-image").each(function(){$(this).mousedown(function(){$(this).addClass("gray-background")});$(this).mouseup(function(){$(this).removeClass("gray-background")})});$(".sort-link").each(function(){$(this).click(function(){set_sort_condition($(this).attr("sort_key"));return false})});$(".page-link > a").each(function(){$(this).click(function(){set_page($(this).attr("page_num"));return false})});$(".categorical-filter > a").each(function(){$(this).click(function(){set_categorical_filter($(this).attr("filter_key"),$(this).attr("filter_val"));return false})});$(".text-filter-form").each(function(){$(this).submit(function(){var d=$(this).attr("column_key");var c=$("#input-"+d+"-filter");var e=c.val();c.val("");add_filter_condition(d,e,true);return false})});var a=$("#input-tags-filter");if(a.length){a.autocomplete(history_tag_autocomplete_url,{selectFirst:false,autoFill:false,highlight:false,mustMatch:false})}var b=$("#input-name-filter");if(b.length){b.autocomplete(history_name_autocomplete_url,{selectFirst:false,autoFill:false,highlight:false,mustMatch:false})}$(".advanced-search-toggle").each(function(){$(this).click(function(){$("#standard-search").slideToggle("fast");$("#advanced-search").slideToggle("fast");return false})})}function init_grid_elements(){$(".grid").each(function(){var b=$(this).find("input.grid-row-select-checkbox");var a=$(this).find("span.grid-selected-count");var c=function(){a.text($(b).filter(":checked").length)};$(b).each(function(){$(this).change(c)});c()});$(".label").each(function(){var a=$(this).attr("href");if(a!==undefined&&a.indexOf("operation=")!=-1){$(this).click(function(){do_operation_from_href($(this).attr("href"));return false})}});if($(".community_rating_star").length!==0){$(".community_rating_star").rating({})}make_popup_menus()}function go_page_one(){var a=grid.get("cur_page");if(a!==null&&a!==undefined&&a!=="all"){grid.set("cur_page",1)}}function add_filter_condition(c,e,a){if(e===""){return false}grid.add_filter(c,e,a);var d=$("<span>"+e+"<a href='javascript:void(0);'><span class='delete-search-icon' /></a></span>");d.addClass("text-filter-val");d.click(function(){grid.remove_filter(c,e);$(this).remove();go_page_one();update_grid()});var b=$("#"+c+"-filtering-criteria");b.append(d);go_page_one();update_grid()}function add_tag_to_grid_filter(c,b){var a=c+(b!==undefined&&b!==""?":"+b:"");$("#advanced-search").show("fast");add_filter_condition("tags",a,true)}function set_sort_condition(f){var e=grid.get("sort_key");var d=f;if(e.indexOf(f)!==-1){if(e.substring(0,1)!=="-"){d="-"+f}else{}}$(".sort-arrow").remove();var c=(d.substring(0,1)=="-")?"↑":"↓";var a=$("<span>"+c+"</span>").addClass("sort-arrow");var b=$("#"+f+"-header");b.append(a);grid.set("sort_key",d);go_page_one();update_grid()}function set_categorical_filter(b,d){var a=grid.get("categorical_filters")[b],c=grid.get("filters")[b];$("."+b+"-filter").each(function(){var h=$.trim($(this).text());var f=a[h];var g=f[b];if(g==d){$(this).empty();$(this).addClass("current-filter");$(this).append(h)}else{if(g==c){$(this).empty();var e=$("<a href='#'>"+h+"</a>");e.click(function(){set_categorical_filter(b,g)});$(this).removeClass("current-filter");$(this).append(e)}}});grid.add_filter(b,d);go_page_one();update_grid()}function set_page(a){$(".page-link").each(function(){var g=$(this).attr("id"),e=parseInt(g.split("-")[2],10),c=grid.get("cur_page"),f;if(e===a){f=$(this).children().text();$(this).empty();$(this).addClass("inactive-link");$(this).text(f)}else{if(e===c){f=$(this).text();$(this).empty();$(this).removeClass("inactive-link");var d=$("<a href='#'>"+f+"</a>");d.click(function(){set_page(e)});$(this).append(d)}}});var b=true;if(a==="all"){grid.set("cur_page",a);b=false}else{grid.set("cur_page",parseInt(a,10))}update_grid(b)}function do_operation(b,a){b=b.toLowerCase();grid.set({operation:b,item_ids:a});if(grid.can_async_op(b)){update_grid(true)}else{go_to_URL()}}function do_operation_from_href(c){var f=c.split("?");if(f.length>1){var a=f[1];var e=a.split("&");var b=null;var g=-1;for(var d=0;d<e.length;d++){if(e[d].indexOf("operation")!=-1){b=e[d].split("=")[1]}else{if(e[d].indexOf("id")!=-1){g=e[d].split("=")[1]}}}do_operation(b,g);return false}}function go_to_URL(){grid.set("async",false);window.location=grid.get("url_base")+"?"+$.param(grid.get_url_data())}function update_grid(a){if(!grid.get("async")){go_to_URL();return}var b=(grid.get("operation")?"POST":"GET");$(".loading-elt-overlay").show();$.ajax({type:b,url:grid.get("url_base"),data:grid.get_url_data(),error:function(){alert("Grid refresh failed")},success:function(d){var c=d.split("*****");$("#grid-table-body").html(c[0]);$("#grid-table-footer").html(c[1]);$("#grid-table-body").trigger("update");init_grid_elements();init_operation_buttons();make_popup_menus();$(".loading-elt-overlay").hide();var e=$.trim(c[2]);if(e!==""){$("#grid-message").html(e).show();setTimeout(function(){$("#grid-message").hide()},5000)}},complete:function(){grid.set({operation:undefined,item_ids:undefined})}})}function check_all_items(){var a=document.getElementById("check_all"),b=document.getElementsByTagName("input"),d=0,c;if(a.checked===true){for(c=0;c<b.length;c++){if(b[c].name.indexOf("id")!==-1){b[c].checked=true;d++}}}else{for(c=0;c<b.length;c++){if(b[c].name.indexOf("id")!==-1){b[c].checked=false}}}init_grid_elements()}function submit_operation(b,c){var a=$('input[name="id"]:checked').length;if(!a>0){return false}if(c!="None"&&c!=""){if(!confirm(c)){return false}}$("#operation").val(b.value);b.form.submit();return true}; \ No newline at end of file diff -r 78eaaca131e3251ba9cc78f7546ace6a713a4f02 -r f76c280cdee539b65315ac583f93bfa52feb790d static/scripts/packed/galaxy.modal.js --- a/static/scripts/packed/galaxy.modal.js +++ b/static/scripts/packed/galaxy.modal.js @@ -1,1 +1,1 @@ -define(["libs/backbone/backbone-relational"],function(){var a=Backbone.View.extend({el_main:"#everything",defaults:{title:"galaxy-modal",body:"No content available."},initialize:function(b){if(b){this.create(b)}},show:function(c){if(c){this.create(c)}var b=(this.$el).find(".modal-body");b.css("max-height",$(document).height()/2);if(this.visible){this.$el.show()}else{this.$el.fadeIn("fast")}this.visible=true},hide:function(){this.$el.fadeOut("fast");this.visible=false},create:function(c){c=_.defaults(c,this.defaults);if(c.body=="progress"){c.body='<div class="progress progress-striped active"><div class="progress-bar progress-bar-info" style="width:100%"></div></div>'}if(this.$el){this.$el.remove()}this.setElement(this.template(c.title));var b=(this.$el).find(".modal-body");var e=(this.$el).find(".modal-footer");var d=(this.$el).find(".buttons");b.append($(c.body));if(c.height){b.css("height",c.height)}if(c.buttons){$.each(c.buttons,function(f,g){d.append($('<button id="'+String(f).toLowerCase()+'"></button>').text(f).click(g)).append(" ")})}else{e.hide()}$(this.el_main).append($(this.el))},enable:function(b){$(this.el).find("#"+String(b).toLowerCase()).prop("disabled",false)},disable:function(b){$(this.el).find("#"+String(b).toLowerCase()).prop("disabled",true)},template:function(b){return'<div class="modal in"><div class="modal-backdrop in" style="z-index: -1;"></div><div class="modal-dialog"><div class="modal-content"><div class="modal-header"><span><h3 class="title">'+b+'</h3></span></div><div class="modal-body"></div><div class="modal-footer"><div class="buttons" style="float: right;"></div></div></div</div></div>'}});return{GalaxyModal:a}}); \ No newline at end of file +define(["libs/backbone/backbone-relational"],function(){var a=Backbone.View.extend({elMain:"#everything",optionsDefaults:{title:"galaxy-modal",body:"No content available."},initialize:function(b){if(b){this.create(b)}},show:function(c){this.initialize(c);var b=(this.$el).find(".modal-body");b.css("max-height",$(document).height()/2);if(this.visible){this.$el.show()}else{this.$el.fadeIn("fast")}this.visible=true},hide:function(){this.$el.fadeOut("fast");this.visible=false},create:function(c){c=_.defaults(c,this.optionsDefault);if(c.body=="progress"){c.body='<div class="progress progress-striped active"><div class="progress-bar progress-bar-info" style="width:100%"></div></div>'}if(this.$el){this.$el.remove()}this.setElement(this.template(c.title));var b=(this.$el).find(".modal-body");var e=(this.$el).find(".modal-footer");var d=(this.$el).find(".buttons");b.append($(c.body));if(c.height){b.css("height",c.height)}if(c.buttons){$.each(c.buttons,function(f,g){d.append($('<button id="'+String(f).toLowerCase()+'"></button>').text(f).click(g)).append(" ")})}else{e.hide()}$(this.elMain).append($(this.el))},enable:function(b){$(this.el).find("#"+String(b).toLowerCase()).prop("disabled",false)},disable:function(b){$(this.el).find("#"+String(b).toLowerCase()).prop("disabled",true)},scrollTop:function(){return $(this.el).find(".modal-body").scrollTop()},template:function(b){return'<div class="modal in"><div class="modal-backdrop in" style="z-index: -1;"></div><div class="modal-dialog"><div class="modal-content"><div class="modal-header"><span><h3 class="title">'+b+'</h3></span></div><div class="modal-body"></div><div class="modal-footer"><div class="buttons" style="float: right;"></div></div></div</div></div>'}});return{GalaxyModal:a}}); \ No newline at end of file diff -r 78eaaca131e3251ba9cc78f7546ace6a713a4f02 -r f76c280cdee539b65315ac583f93bfa52feb790d static/scripts/packed/mvc/data.js --- a/static/scripts/packed/mvc/data.js +++ b/static/scripts/packed/mvc/data.js @@ -1,1 +1,1 @@ -define(["libs/backbone/backbone-relational"],function(){var d=Backbone.RelationalModel.extend({});var e=Backbone.RelationalModel.extend({defaults:{id:"",type:"",name:"",hda_ldda:"hda",metadata:null},initialize:function(){this.on("change",this._set_metadata,this)},_set_metadata:function(){var i=new d();_.each(_.keys(this.attributes),function(j){if(j.indexOf("metadata_")===0){var l=j.split("metadata_")[1];i.set(l,this.attributes[j]);delete this.attributes[j]}},this);this.set("metadata",i,{silent:true})},get_metadata:function(i){return this.attributes.metadata.get(i)},urlRoot:galaxy_config.root+"api/datasets"});var c=e.extend({defaults:_.extend({},e.prototype.defaults,{chunk_url:null,first_data_chunk:null,chunk_index:-1,at_eof:false}),initialize:function(i){e.prototype.initialize.call(this);this.attributes.chunk_index=(this.attributes.first_data_chunk?1:0)},get_next_chunk:function(){if(this.attributes.at_eof){return null}var i=this,j=$.Deferred();$.getJSON(this.attributes.chunk_url,{chunk:i.attributes.chunk_index++}).success(function(k){var l;if(k.ck_data!==""){l=k}else{i.attributes.at_eof=true;l=null}j.resolve(l)});return j}});var g=Backbone.Collection.extend({model:e});var f=Backbone.View.extend({initialize:function(i){new b(i)},render:function(){var m=$("<table/>").attr({id:"content_table",cellpadding:0});this.$el.append(m);var i=this.model.get_metadata("column_names");if(i){m.append("<tr><th>"+i.join("</th><th>")+"</th></tr>")}var k=this.model.get("first_data_chunk");if(k){this._renderChunk(k)}var j=this,n=_.find(this.$el.parents(),function(o){return $(o).css("overflow")==="auto"}),l=false;if(!n){n=window}n=$(n);n.scroll(function(){if(!l&&(j.$el.height()-n.scrollTop()-n.height()<=0)){l=true;$.when(j.model.get_next_chunk()).then(function(o){if(o){j._renderChunk(o);l=false}})}});$("#loading_indicator").ajaxStart(function(){$(this).show()}).ajaxStop(function(){$(this).hide()})},_renderCell:function(k,i,l){var j=this.model.get_metadata("column_types");if(l!==undefined){return $("<td>").attr("colspan",l).addClass("stringalign").text(k)}else{if(j[i]==="str"||j==="list"){return $("<td>").addClass("stringalign").text(k)}else{return $("<td>").text(k)}}},_renderRow:function(i){var j=i.split("\t"),l=$("<tr>"),k=this.model.get_metadata("columns");if(j.length===k){_.each(j,function(n,m){l.append(this._renderCell(n,m))},this)}else{if(j.length>k){_.each(j.slice(0,k-1),function(n,m){l.append(this._renderCell(n,m))},this);l.append(this._renderCell(j.slice(k-1).join("\t"),k-1))}else{if(k>5&&j.length===k-1){_.each(j,function(n,m){l.append(this._renderCell(n,m))},this);l.append($("<td>"))}else{l.append(this._renderCell(i,0,k))}}}return l},_renderChunk:function(i){var j=this.$el.find("table");_.each(i.ck_data.split("\n"),function(k,l){j.append(this._renderRow(k))},this)}});var b=Backbone.View.extend({col:{chrom:null,start:null,end:null},url_viz:null,dataset_id:null,genome_build:null,data_type:null,initialize:function(k){var j=k.model.attributes;var m=k.model.attributes.metadata.attributes;if(typeof j.data_type!=="undefined"){this.data_type=j.data_type}else{console.log("TabularButtonTrackster : Data type missing.")}if(this.data_type=="bed"){if(typeof m.chromCol!=="undefined"||typeof m.startCol!=="undefined"||typeof m.endCol!=="undefined"){this.col.chrom=m.chromCol-1;this.col.start=m.startCol-1;this.col.end=m.endCol-1}else{console.log("TabularButtonTrackster : Bed-file metadata incomplete.")}}if(this.data_type=="vcf"){function l(o,p){for(var n=0;n<p.length;n++){if(p[n].match(o)){return n}}return -1}this.col.chrom=l("Chrom",m.column_names);this.col.start=l("Pos",m.column_names);this.col.end=null;if(this.col.chrom==-1||this.col.start==-1){console.log("TabularButtonTrackster : VCF-file metadata incomplete.")}}if(this.col.chrom===null){console.log("TabularButtonTrackster : Chromosome column undefined.");return}if(typeof k.model.attributes.id==="undefined"){console.log("TabularButtonTrackster : Dataset identification is missing.")}else{this.dataset_id=k.model.attributes.id}if(typeof k.model.attributes.url_viz==="undefined"){console.log("TabularButtonTrackster : Url for visualization controller is missing.")}else{this.url_viz=k.model.attributes.url_viz}if(typeof k.model.attributes.genome_build!=="undefined"){this.genome_build=k.model.attributes.genome_build}var i=new IconButtonView({model:new IconButton({title:"Visualize",icon_class:"chart_curve",id:"btn_viz"})});this.$el.append(i.render().$el);$("#btn_viz").hide()},events:{"mouseover tr":"btn_viz_show",mouseleave:"btn_viz_hide"},btn_viz_show:function(n){function m(s){return !isNaN(parseFloat(s))&&isFinite(s)}if(this.col.chrom===null){return}var r=$(n.target).parent();var o=r.children().eq(this.col.chrom).html();var i=r.children().eq(this.col.start).html();var k=this.col.end?r.children().eq(this.col.end).html():i;if(!o.match("^#")&&o!==""&&m(i)){var q={dataset_id:this.dataset_id,gene_region:o+":"+i+"-"+k};var l=r.offset();var j=l.left-10;var p=l.top-$(window).scrollTop();$("#btn_viz").css({position:"fixed",top:p+"px",left:j+"px"});$("#btn_viz").off("click");$("#btn_viz").click(this.create_trackster_action(this.url_viz,q,this.genome_build));$("#btn_viz").show()}else{$("#btn_viz").hide()}},btn_viz_hide:function(){$("#btn_viz").hide()},create_trackster_action:function(i,k,j){return function(){var l={};if(j){l["f-dbkey"]=j}$.ajax({url:i+"/list_tracks?"+$.param(l),dataType:"html",error:function(){alert(("Could not add this dataset to browser")+".")},success:function(m){var n=window.parent;n.show_modal(("View Data in a New or Saved Visualization"),"",{Cancel:function(){n.hide_modal()},"View in saved visualization":function(){n.show_modal(("Add Data to Saved Visualization"),m,{Cancel:function(){n.hide_modal()},"Add to visualization":function(){$(n.document).find("input[name=id]:checked").each(function(){var o=$(this).val();k.id=o;n.Galaxy.frame_manager.frame_new({title:"Trackster",type:"url",content:i+"/trackster?"+$.param(k)});n.hide_modal()})}})},"View in new visualization":function(){var o=i+"/trackster?"+$.param(k);n.Galaxy.frame_manager.frame_new({title:"Trackster",type:"url",content:o});n.hide_modal()}})}});return false}}});var a=function(l,j,m,i){var k=new j({model:new l(m)});k.render();if(i){i.append(k.$el)}return k};var h=function(k,i){var j=$("<div/>").appendTo(i);return new f({el:j,model:new c(k)}).render()};return{Dataset:e,TabularDataset:c,DatasetCollection:g,TabularDatasetChunkedView:f,createTabularDatasetChunkedView:h}}); \ No newline at end of file +define(["libs/backbone/backbone-relational"],function(){var d=Backbone.RelationalModel.extend({});var e=Backbone.RelationalModel.extend({defaults:{id:"",type:"",name:"",hda_ldda:"hda",metadata:null},initialize:function(){this.on("change",this._set_metadata,this)},_set_metadata:function(){var i=new d();_.each(_.keys(this.attributes),function(j){if(j.indexOf("metadata_")===0){var l=j.split("metadata_")[1];i.set(l,this.attributes[j]);delete this.attributes[j]}},this);this.set("metadata",i,{silent:true})},get_metadata:function(i){return this.attributes.metadata.get(i)},urlRoot:galaxy_config.root+"api/datasets"});var c=e.extend({defaults:_.extend({},e.prototype.defaults,{chunk_url:null,first_data_chunk:null,chunk_index:-1,at_eof:false}),initialize:function(i){e.prototype.initialize.call(this);this.attributes.chunk_index=(this.attributes.first_data_chunk?1:0)},get_next_chunk:function(){if(this.attributes.at_eof){return null}var i=this,j=$.Deferred();$.getJSON(this.attributes.chunk_url,{chunk:i.attributes.chunk_index++}).success(function(k){var l;if(k.ck_data!==""){l=k}else{i.attributes.at_eof=true;l=null}j.resolve(l)});return j}});var g=Backbone.Collection.extend({model:e});var f=Backbone.View.extend({initialize:function(i){new b(i)},render:function(){var m=$("<table/>").attr({id:"content_table",cellpadding:0});this.$el.append(m);var i=this.model.get_metadata("column_names");if(i){m.append("<tr><th>"+i.join("</th><th>")+"</th></tr>")}var k=this.model.get("first_data_chunk");if(k){this._renderChunk(k)}var j=this,n=_.find(this.$el.parents(),function(o){return $(o).css("overflow")==="auto"}),l=false;if(!n){n=window}n=$(n);n.scroll(function(){if(!l&&(j.$el.height()-n.scrollTop()-n.height()<=0)){l=true;$.when(j.model.get_next_chunk()).then(function(o){if(o){j._renderChunk(o);l=false}})}});$("#loading_indicator").ajaxStart(function(){$(this).show()}).ajaxStop(function(){$(this).hide()})},_renderCell:function(l,i,m){var j=$("<td>").text(l);var k=this.model.get_metadata("column_types");if(m!==undefined){j.attr("colspan",m).addClass("stringalign")}else{if(k!==undefined&&i<k.length){if(k[i]==="str"||k==="list"){j.addClass("stringalign")}}}return j},_renderRow:function(i){var j=i.split("\t"),l=$("<tr>"),k=this.model.get_metadata("columns");if(j.length===k){_.each(j,function(n,m){l.append(this._renderCell(n,m))},this)}else{if(j.length>k){_.each(j.slice(0,k-1),function(n,m){l.append(this._renderCell(n,m))},this);l.append(this._renderCell(j.slice(k-1).join("\t"),k-1))}else{if(k>5&&j.length===k-1){_.each(j,function(n,m){l.append(this._renderCell(n,m))},this);l.append($("<td>"))}else{l.append(this._renderCell(i,0,k))}}}return l},_renderChunk:function(i){var j=this.$el.find("table");_.each(i.ck_data.split("\n"),function(k,l){j.append(this._renderRow(k))},this)}});var b=Backbone.View.extend({col:{chrom:null,start:null,end:null},url_viz:null,dataset_id:null,genome_build:null,data_type:null,initialize:function(k){var j=k.model.attributes;var m=k.model.attributes.metadata.attributes;if(typeof j.data_type!=="undefined"){this.data_type=j.data_type}else{console.log("TabularButtonTrackster : Data type missing.")}if(this.data_type=="bed"){if(typeof m.chromCol!=="undefined"||typeof m.startCol!=="undefined"||typeof m.endCol!=="undefined"){this.col.chrom=m.chromCol-1;this.col.start=m.startCol-1;this.col.end=m.endCol-1}else{console.log("TabularButtonTrackster : Bed-file metadata incomplete.")}}if(this.data_type=="vcf"){function l(o,p){for(var n=0;n<p.length;n++){if(p[n].match(o)){return n}}return -1}this.col.chrom=l("Chrom",m.column_names);this.col.start=l("Pos",m.column_names);this.col.end=null;if(this.col.chrom==-1||this.col.start==-1){console.log("TabularButtonTrackster : VCF-file metadata incomplete.")}}if(this.col.chrom===null){console.log("TabularButtonTrackster : Chromosome column undefined.");return}if(typeof k.model.attributes.id==="undefined"){console.log("TabularButtonTrackster : Dataset identification is missing.")}else{this.dataset_id=k.model.attributes.id}if(typeof k.model.attributes.url_viz==="undefined"){console.log("TabularButtonTrackster : Url for visualization controller is missing.")}else{this.url_viz=k.model.attributes.url_viz}if(typeof k.model.attributes.genome_build!=="undefined"){this.genome_build=k.model.attributes.genome_build}var i=new IconButtonView({model:new IconButton({title:"Visualize",icon_class:"chart_curve",id:"btn_viz"})});this.$el.append(i.render().$el);$("#btn_viz").hide()},events:{"mouseover tr":"btn_viz_show",mouseleave:"btn_viz_hide"},btn_viz_show:function(n){function m(s){return !isNaN(parseFloat(s))&&isFinite(s)}if(this.col.chrom===null){return}var r=$(n.target).parent();var o=r.children().eq(this.col.chrom).html();var i=r.children().eq(this.col.start).html();var k=this.col.end?r.children().eq(this.col.end).html():i;if(!o.match("^#")&&o!==""&&m(i)){var q={dataset_id:this.dataset_id,gene_region:o+":"+i+"-"+k};var l=r.offset();var j=l.left-10;var p=l.top-$(window).scrollTop();$("#btn_viz").css({position:"fixed",top:p+"px",left:j+"px"});$("#btn_viz").off("click");$("#btn_viz").click(this.create_trackster_action(this.url_viz,q,this.genome_build));$("#btn_viz").show()}else{$("#btn_viz").hide()}},btn_viz_hide:function(){$("#btn_viz").hide()},create_trackster_action:function(i,k,j){return function(){var l={};if(j){l["f-dbkey"]=j}$.ajax({url:i+"/list_tracks?"+$.param(l),dataType:"html",error:function(){alert(("Could not add this dataset to browser")+".")},success:function(m){var n=window.parent;n.Galaxy.modal.show({title:"View Data in a New or Saved Visualization",buttons:{Cancel:function(){n.Galaxy.modal.hide()},"View in saved visualization":function(){n.Galaxy.modal.show({title:"Add Data to Saved Visualization",body:m,buttons:{Cancel:function(){n.Galaxy.modal.hide()},"Add to visualization":function(){$(n.document).find("input[name=id]:checked").each(function(){n.Galaxy.modal.hide();var o=$(this).val();k.id=o;n.Galaxy.frame_manager.frame_new({title:"Trackster",type:"url",content:i+"/trackster?"+$.param(k)})})}}})},"View in new visualization":function(){n.Galaxy.modal.hide();var o=i+"/trackster?"+$.param(k);n.Galaxy.frame_manager.frame_new({title:"Trackster",type:"url",content:o})}}})}});return false}}});var a=function(l,j,m,i){var k=new j({model:new l(m)});k.render();if(i){i.append(k.$el)}return k};var h=function(k,i){var j=$("<div/>").appendTo(i);return new f({el:j,model:new c(k)}).render()};return{Dataset:e,TabularDataset:c,DatasetCollection:g,TabularDatasetChunkedView:f,createTabularDatasetChunkedView:h}}); \ No newline at end of file diff -r 78eaaca131e3251ba9cc78f7546ace6a713a4f02 -r f76c280cdee539b65315ac583f93bfa52feb790d static/scripts/packed/mvc/dataset/hda-edit.js --- a/static/scripts/packed/mvc/dataset/hda-edit.js +++ b/static/scripts/packed/mvc/dataset/hda-edit.js @@ -1,1 +1,1 @@ -var HDAEditView=HDABaseView.extend(LoggableMixin).extend({initialize:function(a){HDABaseView.prototype.initialize.call(this,a);this.defaultPrimaryActionButtonRenderers=[this._render_showParamsButton,this._render_rerunButton]},_setUpBehaviors:function(c){HDABaseView.prototype._setUpBehaviors.call(this,c);var a=this,b=this.urls.purge,d=c.find("#historyItemPurger-"+this.model.get("id"));if(d){d.attr("href",["javascript","void(0)"].join(":"));d.click(function(e){var f=jQuery.ajax(b);f.success(function(i,g,h){a.model.set("purged",true);a.trigger("purged",a)});f.error(function(h,g,i){a.trigger("error",_l("Unable to purge this dataset"),h,g,i)})})}},_render_warnings:function(){return $(jQuery.trim(HDABaseView.templates.messages(_.extend(this.model.toJSON(),{urls:this.urls}))))},_render_titleButtons:function(){var a=$('<div class="historyItemButtons"></div>');a.append(this._render_displayButton());a.append(this._render_editButton());a.append(this._render_deleteButton());return a},_render_editButton:function(){if((this.model.get("state")===HistoryDatasetAssociation.STATES.NEW)||(this.model.get("state")===HistoryDatasetAssociation.STATES.UPLOAD)||(this.model.get("state")===HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(!this.model.get("accessible"))){this.editButton=null;return null}var c=this.model.get("purged"),a=this.model.get("deleted"),b={title:_l("Edit Attributes"),href:this.urls.edit,target:"galaxy_main",icon_class:"edit"};if(a||c){b.enabled=false;if(c){b.title=_l("Cannot edit attributes of datasets removed from disk")}else{if(a){b.title=_l("Undelete dataset to edit attributes")}}}this.editButton=new IconButtonView({model:new IconButton(b)});return this.editButton.render().$el},_render_deleteButton:function(){if((this.model.get("state")===HistoryDatasetAssociation.STATES.NEW)||(this.model.get("state")===HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(!this.model.get("accessible"))){this.deleteButton=null;return null}var a=this,b=a.urls["delete"],c={title:_l("Delete"),href:b,id:"historyItemDeleter-"+this.model.get("id"),icon_class:"delete",on_click:function(){$.ajax({url:b,type:"POST",error:function(){a.$el.show()},success:function(){a.model.set({deleted:true})}})}};if(this.model.get("deleted")||this.model.get("purged")){c={title:_l("Dataset is already deleted"),icon_class:"delete",enabled:false}}this.deleteButton=new IconButtonView({model:new IconButton(c)});return this.deleteButton.render().$el},_render_hdaSummary:function(){var a=_.extend(this.model.toJSON(),{urls:this.urls});if(this.model.get("metadata_dbkey")==="?"&&!this.model.isDeletedOrPurged()){_.extend(a,{dbkey_unknown_and_editable:true})}return HDABaseView.templates.hdaSummary(a)},_render_errButton:function(){if(this.model.get("state")!==HistoryDatasetAssociation.STATES.ERROR){this.errButton=null;return null}this.errButton=new IconButtonView({model:new IconButton({title:_l("View or report this error"),href:this.urls.report_error,target:"galaxy_main",icon_class:"bug"})});return this.errButton.render().$el},_render_rerunButton:function(){this.rerunButton=new IconButtonView({model:new IconButton({title:_l("Run this job again"),href:this.urls.rerun,target:"galaxy_main",icon_class:"arrow-circle"})});return this.rerunButton.render().$el},_render_visualizationsButton:function(){var a=this.model.get("visualizations");if((!this.model.hasData())||(_.isEmpty(a))){this.visualizationsButton=null;return null}if(_.isObject(a[0])){return this._render_visualizationsFrameworkButton(a)}if(!this.urls.visualization){this.visualizationsButton=null;return null}var c=this.model.get("dbkey"),f=this.urls.visualization,d={},g={dataset_id:this.model.get("id"),hda_ldda:"hda"};if(c){g.dbkey=c}this.visualizationsButton=new IconButtonView({model:new IconButton({title:_l("Visualize"),href:this.urls.visualization,icon_class:"chart_curve"})});var b=this.visualizationsButton.render().$el;b.addClass("visualize-icon");function e(h){switch(h){case"trackster":return create_trackster_action_fn(f,g,c);case"scatterplot":return create_scatterplot_action_fn(f,g);default:return function(){Galaxy.frame_manager.frame_new({title:"Visualization",type:"url",content:f+"/"+h+"?"+$.param(g)})}}}if(a.length===1){b.attr("title",a[0]);b.click(e(a[0]))}else{_.each(a,function(i){var h=i.charAt(0).toUpperCase()+i.slice(1);d[_l(h)]=e(i)});make_popupmenu(b,d)}return b},_render_visualizationsFrameworkButton:function(a){if(!(this.model.hasData())||!(a&&!_.isEmpty(a))){this.visualizationsButton=null;return null}this.visualizationsButton=new IconButtonView({model:new IconButton({title:_l("Visualize"),icon_class:"chart_curve"})});var c=this.visualizationsButton.render().$el;c.addClass("visualize-icon");if(_.keys(a).length===1){c.attr("title",_.keys(a)[0]);c.attr("href",_.values(a)[0])}else{var d=[];_.each(a,function(e){d.push(e)});var b=new PopupMenu(c,d)}return c},_render_secondaryActionButtons:function(b){var c=$("<div/>"),a=this;c.attr("style","float: right;").attr("id","secondary-actions-"+this.model.get("id"));_.each(b,function(d){c.append(d.call(a))});return c},_render_tagButton:function(){if(!(this.model.hasData())||(!this.urls.tags.get)){this.tagButton=null;return null}this.tagButton=new IconButtonView({model:new IconButton({title:_l("Edit dataset tags"),target:"galaxy_main",href:this.urls.tags.get,icon_class:"tags"})});return this.tagButton.render().$el},_render_annotateButton:function(){if(!(this.model.hasData())||(!this.urls.annotation.get)){this.annotateButton=null;return null}this.annotateButton=new IconButtonView({model:new IconButton({title:_l("Edit dataset annotation"),target:"galaxy_main",icon_class:"annotate"})});return this.annotateButton.render().$el},_render_tagArea:function(){if(!this.urls.tags.set){return null}return $(HDAEditView.templates.tagArea(_.extend(this.model.toJSON(),{urls:this.urls})).trim())},_render_annotationArea:function(){if(!this.urls.annotation.get){return null}return $(HDAEditView.templates.annotationArea(_.extend(this.model.toJSON(),{urls:this.urls})).trim())},_render_body_error:function(a){HDABaseView.prototype._render_body_error.call(this,a);var b=a.find("#primary-actions-"+this.model.get("id"));b.prepend(this._render_errButton())},_render_body_ok:function(a){a.append(this._render_hdaSummary());if(this.model.isDeletedOrPurged()){a.append(this._render_primaryActionButtons([this._render_downloadButton,this._render_showParamsButton,this._render_rerunButton]));return}a.append(this._render_primaryActionButtons([this._render_downloadButton,this._render_showParamsButton,this._render_rerunButton,this._render_visualizationsButton]));a.append(this._render_secondaryActionButtons([this._render_tagButton,this._render_annotateButton]));a.append('<div class="clear"/>');a.append(this._render_tagArea());a.append(this._render_annotationArea());a.append(this._render_displayAppArea());this._render_displayApps(a);a.append(this._render_peek())},events:{"click .historyItemTitle":"toggleBodyVisibility","click a.icon-button.tags":"loadAndDisplayTags","click a.icon-button.annotate":"loadAndDisplayAnnotation"},loadAndDisplayTags:function(c){this.log(this+".loadAndDisplayTags",c);var a=this,d=this.$el.find(".tag-area"),b=d.find(".tag-elt");if(d.is(":hidden")){if(!jQuery.trim(b.html())){$.ajax({url:this.urls.tags.get,error:function(g,e,f){a.log("Tagging failed",g,e,f);a.trigger("error",_l("Tagging failed"),g,e,f)},success:function(e){b.html(e);b.find("[title]").tooltip();d.slideDown("fast")}})}else{d.slideDown("fast")}}else{d.slideUp("fast")}return false},loadAndDisplayAnnotation:function(b){this.log(this+".loadAndDisplayAnnotation",b);var d=this.$el.find(".annotation-area"),c=d.find(".annotation-elt"),a=this.urls.annotation.set;if(d.is(":hidden")){if(!jQuery.trim(c.html())){$.ajax({url:this.urls.annotation.get,error:function(){view.log("Annotation failed",xhr,status,error);view.trigger("error",_l("Annotation failed"),xhr,status,error)},success:function(e){if(e===""){e="<em>"+_l("Describe or add notes to dataset")+"</em>"}c.html(e);d.find("[title]").tooltip();async_save_text(c.attr("id"),c.attr("id"),a,"new_annotation",18,true,4);d.slideDown("fast")}})}else{d.slideDown("fast")}}else{d.slideUp("fast")}return false},toString:function(){var a=(this.model)?(this.model+""):("(no model)");return"HDAView("+a+")"}});HDAEditView.templates={tagArea:Handlebars.templates["template-hda-tagArea"],annotationArea:Handlebars.templates["template-hda-annotationArea"]};function create_scatterplot_action_fn(a,b){action=function(){Galaxy.frame_manager.frame_new({title:"Scatterplot",type:"url",content:a+"/scatterplot?"+$.param(b),location:"center"});$("div.popmenu-wrapper").remove();return false};return action}function create_trackster_action_fn(a,c,b){return function(){var d={};if(b){d["f-dbkey"]=b}$.ajax({url:a+"/list_tracks?"+$.param(d),dataType:"html",error:function(){alert(_l("Could not add this dataset to browser")+".")},success:function(e){var f=window.parent;f.show_modal(_l("View Data in a New or Saved Visualization"),"",{Cancel:function(){f.hide_modal()},"View in saved visualization":function(){f.show_modal(_l("Add Data to Saved Visualization"),e,{Cancel:function(){f.hide_modal()},"Add to visualization":function(){$(f.document).find("input[name=id]:checked").each(function(){var g=$(this).val();c.id=g;f.hide_modal();Galaxy.frame_manager.frame_new({title:"Trackster",type:"url",content:a+"/trackster?"+$.param(c)})})}})},"View in new visualization":function(){f.hide_modal();Galaxy.frame_manager.frame_new({title:"Trackster",type:"url",content:a+"/trackster?"+$.param(c)})}})}});return false}}; \ No newline at end of file +var HDAEditView=HDABaseView.extend(LoggableMixin).extend({initialize:function(a){HDABaseView.prototype.initialize.call(this,a);this.defaultPrimaryActionButtonRenderers=[this._render_showParamsButton,this._render_rerunButton]},_setUpBehaviors:function(c){HDABaseView.prototype._setUpBehaviors.call(this,c);var a=this,b=this.urls.purge,d=c.find("#historyItemPurger-"+this.model.get("id"));if(d){d.attr("href",["javascript","void(0)"].join(":"));d.click(function(e){var f=jQuery.ajax(b);f.success(function(i,g,h){a.model.set("purged",true);a.trigger("purged",a)});f.error(function(h,g,i){a.trigger("error",_l("Unable to purge this dataset"),h,g,i)})})}},_render_warnings:function(){return $(jQuery.trim(HDABaseView.templates.messages(_.extend(this.model.toJSON(),{urls:this.urls}))))},_render_titleButtons:function(){var a=$('<div class="historyItemButtons"></div>');a.append(this._render_displayButton());a.append(this._render_editButton());a.append(this._render_deleteButton());return a},_render_editButton:function(){if((this.model.get("state")===HistoryDatasetAssociation.STATES.NEW)||(this.model.get("state")===HistoryDatasetAssociation.STATES.UPLOAD)||(this.model.get("state")===HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(!this.model.get("accessible"))){this.editButton=null;return null}var c=this.model.get("purged"),a=this.model.get("deleted"),b={title:_l("Edit Attributes"),href:this.urls.edit,target:"galaxy_main",icon_class:"edit"};if(a||c){b.enabled=false;if(c){b.title=_l("Cannot edit attributes of datasets removed from disk")}else{if(a){b.title=_l("Undelete dataset to edit attributes")}}}this.editButton=new IconButtonView({model:new IconButton(b)});return this.editButton.render().$el},_render_deleteButton:function(){if((this.model.get("state")===HistoryDatasetAssociation.STATES.NEW)||(this.model.get("state")===HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(!this.model.get("accessible"))){this.deleteButton=null;return null}var a=this,b=a.urls["delete"],c={title:_l("Delete"),href:b,id:"historyItemDeleter-"+this.model.get("id"),icon_class:"delete",on_click:function(){$.ajax({url:b,type:"POST",error:function(){a.$el.show()},success:function(){a.model.set({deleted:true})}})}};if(this.model.get("deleted")||this.model.get("purged")){c={title:_l("Dataset is already deleted"),icon_class:"delete",enabled:false}}this.deleteButton=new IconButtonView({model:new IconButton(c)});return this.deleteButton.render().$el},_render_hdaSummary:function(){var a=_.extend(this.model.toJSON(),{urls:this.urls});if(this.model.get("metadata_dbkey")==="?"&&!this.model.isDeletedOrPurged()){_.extend(a,{dbkey_unknown_and_editable:true})}return HDABaseView.templates.hdaSummary(a)},_render_errButton:function(){if(this.model.get("state")!==HistoryDatasetAssociation.STATES.ERROR){this.errButton=null;return null}this.errButton=new IconButtonView({model:new IconButton({title:_l("View or report this error"),href:this.urls.report_error,target:"galaxy_main",icon_class:"bug"})});return this.errButton.render().$el},_render_rerunButton:function(){this.rerunButton=new IconButtonView({model:new IconButton({title:_l("Run this job again"),href:this.urls.rerun,target:"galaxy_main",icon_class:"arrow-circle"})});return this.rerunButton.render().$el},_render_visualizationsButton:function(){var a=this.model.get("visualizations");if((!this.model.hasData())||(_.isEmpty(a))){this.visualizationsButton=null;return null}if(_.isObject(a[0])){return this._render_visualizationsFrameworkButton(a)}if(!this.urls.visualization){this.visualizationsButton=null;return null}var c=this.model.get("dbkey"),f=this.urls.visualization,d={},g={dataset_id:this.model.get("id"),hda_ldda:"hda"};if(c){g.dbkey=c}this.visualizationsButton=new IconButtonView({model:new IconButton({title:_l("Visualize"),href:this.urls.visualization,icon_class:"chart_curve"})});var b=this.visualizationsButton.render().$el;b.addClass("visualize-icon");function e(h){switch(h){case"trackster":return create_trackster_action_fn(f,g,c);case"scatterplot":return create_scatterplot_action_fn(f,g);default:return function(){Galaxy.frame_manager.frame_new({title:"Visualization",type:"url",content:f+"/"+h+"?"+$.param(g)})}}}if(a.length===1){b.attr("title",a[0]);b.click(e(a[0]))}else{_.each(a,function(i){var h=i.charAt(0).toUpperCase()+i.slice(1);d[_l(h)]=e(i)});make_popupmenu(b,d)}return b},_render_visualizationsFrameworkButton:function(a){if(!(this.model.hasData())||!(a&&!_.isEmpty(a))){this.visualizationsButton=null;return null}this.visualizationsButton=new IconButtonView({model:new IconButton({title:_l("Visualize"),icon_class:"chart_curve"})});var c=this.visualizationsButton.render().$el;c.addClass("visualize-icon");if(_.keys(a).length===1){c.attr("title",_.keys(a)[0]);c.attr("href",_.values(a)[0])}else{var d=[];_.each(a,function(e){d.push(e)});var b=new PopupMenu(c,d)}return c},_render_secondaryActionButtons:function(b){var c=$("<div/>"),a=this;c.attr("style","float: right;").attr("id","secondary-actions-"+this.model.get("id"));_.each(b,function(d){c.append(d.call(a))});return c},_render_tagButton:function(){if(!(this.model.hasData())||(!this.urls.tags.get)){this.tagButton=null;return null}this.tagButton=new IconButtonView({model:new IconButton({title:_l("Edit dataset tags"),target:"galaxy_main",href:this.urls.tags.get,icon_class:"tags"})});return this.tagButton.render().$el},_render_annotateButton:function(){if(!(this.model.hasData())||(!this.urls.annotation.get)){this.annotateButton=null;return null}this.annotateButton=new IconButtonView({model:new IconButton({title:_l("Edit dataset annotation"),target:"galaxy_main",icon_class:"annotate"})});return this.annotateButton.render().$el},_render_tagArea:function(){if(!this.urls.tags.set){return null}return $(HDAEditView.templates.tagArea(_.extend(this.model.toJSON(),{urls:this.urls})).trim())},_render_annotationArea:function(){if(!this.urls.annotation.get){return null}return $(HDAEditView.templates.annotationArea(_.extend(this.model.toJSON(),{urls:this.urls})).trim())},_render_body_error:function(a){HDABaseView.prototype._render_body_error.call(this,a);var b=a.find("#primary-actions-"+this.model.get("id"));b.prepend(this._render_errButton())},_render_body_ok:function(a){a.append(this._render_hdaSummary());if(this.model.isDeletedOrPurged()){a.append(this._render_primaryActionButtons([this._render_downloadButton,this._render_showParamsButton,this._render_rerunButton]));return}a.append(this._render_primaryActionButtons([this._render_downloadButton,this._render_showParamsButton,this._render_rerunButton,this._render_visualizationsButton]));a.append(this._render_secondaryActionButtons([this._render_tagButton,this._render_annotateButton]));a.append('<div class="clear"/>');a.append(this._render_tagArea());a.append(this._render_annotationArea());a.append(this._render_displayAppArea());this._render_displayApps(a);a.append(this._render_peek())},events:{"click .historyItemTitle":"toggleBodyVisibility","click a.icon-button.tags":"loadAndDisplayTags","click a.icon-button.annotate":"loadAndDisplayAnnotation"},loadAndDisplayTags:function(c){this.log(this+".loadAndDisplayTags",c);var a=this,d=this.$el.find(".tag-area"),b=d.find(".tag-elt");if(d.is(":hidden")){if(!jQuery.trim(b.html())){$.ajax({url:this.urls.tags.get,error:function(g,e,f){a.log("Tagging failed",g,e,f);a.trigger("error",_l("Tagging failed"),g,e,f)},success:function(e){b.html(e);b.find("[title]").tooltip();d.slideDown("fast")}})}else{d.slideDown("fast")}}else{d.slideUp("fast")}return false},loadAndDisplayAnnotation:function(b){this.log(this+".loadAndDisplayAnnotation",b);var d=this.$el.find(".annotation-area"),c=d.find(".annotation-elt"),a=this.urls.annotation.set;if(d.is(":hidden")){if(!jQuery.trim(c.html())){$.ajax({url:this.urls.annotation.get,error:function(){view.log("Annotation failed",xhr,status,error);view.trigger("error",_l("Annotation failed"),xhr,status,error)},success:function(e){if(e===""){e="<em>"+_l("Describe or add notes to dataset")+"</em>"}c.html(e);d.find("[title]").tooltip();async_save_text(c.attr("id"),c.attr("id"),a,"new_annotation",18,true,4);d.slideDown("fast")}})}else{d.slideDown("fast")}}else{d.slideUp("fast")}return false},toString:function(){var a=(this.model)?(this.model+""):("(no model)");return"HDAView("+a+")"}});HDAEditView.templates={tagArea:Handlebars.templates["template-hda-tagArea"],annotationArea:Handlebars.templates["template-hda-annotationArea"]};function create_scatterplot_action_fn(a,b){action=function(){Galaxy.frame_manager.frame_new({title:"Scatterplot",type:"url",content:a+"/scatterplot?"+$.param(b),location:"center"});$("div.popmenu-wrapper").remove();return false};return action}function create_trackster_action_fn(a,c,b){return function(){var d={};if(b){d["f-dbkey"]=b}$.ajax({url:a+"/list_tracks?"+$.param(d),dataType:"html",error:function(){alert(("Could not add this dataset to browser")+".")},success:function(e){var f=window.parent;f.Galaxy.modal.show({title:"View Data in a New or Saved Visualization",buttons:{Cancel:function(){f.Galaxy.modal.hide()},"View in saved visualization":function(){f.Galaxy.modal.show({title:"Add Data to Saved Visualization",body:e,buttons:{Cancel:function(){f.Galaxy.modal.hide()},"Add to visualization":function(){$(f.document).find("input[name=id]:checked").each(function(){f.Galaxy.modal.hide();var g=$(this).val();c.id=g;f.Galaxy.frame_manager.frame_new({title:"Trackster",type:"url",content:a+"/trackster?"+$.param(c)})})}}})},"View in new visualization":function(){f.Galaxy.modal.hide();var g=a+"/trackster?"+$.param(c);f.Galaxy.frame_manager.frame_new({title:"Trackster",type:"url",content:g})}}})}});return false}}; \ No newline at end of file diff -r 78eaaca131e3251ba9cc78f7546ace6a713a4f02 -r f76c280cdee539b65315ac583f93bfa52feb790d static/scripts/packed/mvc/history/history-model.js --- a/static/scripts/packed/mvc/history/history-model.js +++ b/static/scripts/packed/mvc/history/history-model.js @@ -1,1 +1,1 @@ -var History=Backbone.Model.extend(LoggableMixin).extend({defaults:{id:null,name:"Unnamed History",state:"new",diskSize:0,deleted:false},urlRoot:"api/histories/",url:function(){return this.urlRoot+this.get("id")},initialize:function(b,c,a){a=a||null;this.log(this+".initialize:",b,c);this.hdas=new HDACollection();this.updateTimeoutId=null;if(c&&_.isArray(c)){this.hdas.add(c);this.checkForUpdates();if(this.hdas.length>0){this.updateDisplayApplications()}}this.hdas.bind("state:ready",function(e,f,d){if(e.get("force_history_refresh")){this.updateAfterDelay()}},this);if(this.logger){this.bind("all",function(d){this.log(this+"",arguments)},this)}},hdaIdsFromStateIds:function(){return _.reduce(_.values(this.get("state_ids")),function(b,a){return b.concat(a)})},updateAfterDelay:function(){var a=this;this.updateTimeoutId=setTimeout(function(){a.stateUpdater()},History.UPDATE_DELAY);return this.updateTimeoutId},checkForUpdates:function(){if(this.hdas.running().length){this.updateAfterDelay()}else{this.trigger("ready")}return this},stateUpdater:function(){var c=this,a=this.get("state"),b=this.get("state_ids");jQuery.ajax("api/histories/"+this.get("id")).success(function(d){c.set(d);c.log("current history state:",c.get("state"),"(was)",a,"new size:",c.get("nice_size"));var f=[];_.each(_.keys(d.state_ids),function(h){var g=_.difference(d.state_ids[h],b[h]);f=f.concat(g)});if(f.length){c.fetchHdaUpdates(f).done(function(){e(c)})}else{e(c)}function e(h){var g;if((h.get("state")===HistoryDatasetAssociation.STATES.RUNNING)||(h.get("state")===HistoryDatasetAssociation.STATES.QUEUED)){g=h.updateAfterDelay()}else{this.updateTimeoutId=null;h.trigger("ready")}return g}}).error(function(g,d,e){if(g.status===502){setTimeout(function(){c.log("Bad Gateway error. Retrying...");c.stateUpdater()},History.UPDATE_DELAY)}else{if(!((g.readyState===0)&&(g.status===0))){c.log("stateUpdater error:",e,"responseText:",g.responseText);var f=_l("An error occurred while getting updates from the server.")+" "+_l("Please contact a Galaxy administrator if the problem persists.");c.trigger("error",f,g,d,e)}}})},fetchHdaUpdates:function(c){var a=this,b=jQuery.ajax({url:this.url()+"/contents?"+jQuery.param({ids:c.join(",")}),error:function(i,d,e){if((i.readyState===0)&&(i.status===0)){return}var g=JSON.parse(i.responseText);if(_.isArray(g)){var f=_.groupBy(g,function(j){if(_.has(j,"error")){return"errored"}return"ok"});a.log("fetched, errored datasets:",f.errored);a.updateHdas(g)}else{a.log("Error updating hdas from api history contents",c,i,d,e,g);var h=_l("An error occurred while getting dataset details from the server.")+" "+_l("Please contact a Galaxy administrator if the problem persists.");a.trigger("error",h,i,d,e)}},success:function(e,d,f){a.log(a+".fetchHdaUpdates, success:",d,f);a.updateHdas(e)}});return b},updateHdas:function(a){var c=this,b=[];c.log(c+".updateHdas:",a);_.each(a,function(e,f){var d=c.hdas.get(e.id);if(d){c.log("found existing model in list for id "+e.id+", updating...:");d.set(e)}else{c.log("NO existing model for id "+e.id+", creating...:");b.push(e)}});if(b.length){c.addHdas(b)}},addHdas:function(a){var b=this;_.each(a,function(c,d){var e=b.hdas.hidToCollectionIndex(c.hid);c.history_id=b.get("id");b.hdas.add(new HistoryDatasetAssociation(c),{at:e,silent:true})});b.hdas.trigger("add",a)},updateDisplayApplications:function(a){this.log(this+"updateDisplayApplications:",a);var c=this,b=(a&&_.isArray(a))?({hda_ids:a.join(",")}):({});c.log(this+": fetching display application data");jQuery.ajax("history/get_display_application_links",{data:b,success:function(f,d,e){_.each(f,function(h){var g=c.hdas.get(h.id);if(g){g.set(h)}})},error:function(g,d,e){if(!((g.readyState===0)&&(g.status===0))){c.log("Error fetching display applications:",a,g,d,e);var f=_l("An error occurred while getting display applications from the server.")+" "+_l("Please contact a Galaxy administrator if the problem persists.");c.trigger("error",f,g,d,e)}}})},toString:function(){var a=(this.get("name"))?(","+this.get("name")):("");return"History("+this.get("id")+a+")"}});History.UPDATE_DELAY=4000;var HistoryCollection=Backbone.Collection.extend(LoggableMixin).extend({model:History,urlRoot:"api/histories"}); \ No newline at end of file +var History=Backbone.Model.extend(LoggableMixin).extend({defaults:{id:null,name:"Unnamed History",state:"new",diskSize:0,deleted:false},urlRoot:"api/histories/",url:function(){return this.urlRoot+this.get("id")},initialize:function(b,c,a){a=a||null;this.log(this+".initialize:",b,c);this.hdas=new HDACollection();this.updateTimeoutId=null;if(c&&_.isArray(c)){this.hdas.add(c);this.checkForUpdates();if(this.hdas.length>0){this.updateDisplayApplications()}}this.hdas.bind("state:ready",function(e,f,d){if(e.get("force_history_refresh")){this.updateAfterDelay()}},this);if(this.logger){this.bind("all",function(d){this.log(this+"",arguments)},this)}},hdaIdsFromStateIds:function(){return _.reduce(_.values(this.get("state_ids")),function(b,a){return b.concat(a)})},updateAfterDelay:function(){var a=this;this.updateTimeoutId=setTimeout(function(){a.stateUpdater()},History.UPDATE_DELAY);return this.updateTimeoutId},checkForUpdates:function(){if(this.hdas.running().length){this.updateAfterDelay()}else{this.trigger("ready")}return this},stateUpdater:function(){var c=this,a=this.get("state"),b=this.get("state_ids");jQuery.ajax("api/histories/"+this.get("id")).success(function(d){c.set(d);c.log("current history state:",c.get("state"),"(was)",a,"new size:",c.get("nice_size"));var f=[];_.each(_.keys(d.state_ids),function(h){var g=_.difference(d.state_ids[h],b[h]);f=f.concat(g)});if(f.length){c.fetchHdaUpdates(f).done(function(){e(c)})}else{e(c)}function e(h){var g;if((h.get("state")===HistoryDatasetAssociation.STATES.RUNNING)||(h.get("state")===HistoryDatasetAssociation.STATES.QUEUED)||(h.get("state")===HistoryDatasetAssociation.STATES.SETTING_METADATA)){g=h.updateAfterDelay()}else{this.updateTimeoutId=null;h.trigger("ready")}return g}}).error(function(g,d,e){if(g.status===502){setTimeout(function(){c.log("Bad Gateway error. Retrying...");c.stateUpdater()},History.UPDATE_DELAY)}else{if(!((g.readyState===0)&&(g.status===0))){c.log("stateUpdater error:",e,"responseText:",g.responseText);var f=_l("An error occurred while getting updates from the server.")+" "+_l("Please contact a Galaxy administrator if the problem persists.");c.trigger("error",f,g,d,e)}}})},fetchHdaUpdates:function(c){var a=this,b=jQuery.ajax({url:this.url()+"/contents?"+jQuery.param({ids:c.join(",")}),error:function(i,d,e){if((i.readyState===0)&&(i.status===0)){return}var g=JSON.parse(i.responseText);if(_.isArray(g)){var f=_.groupBy(g,function(j){if(_.has(j,"error")){return"errored"}return"ok"});a.log("fetched, errored datasets:",f.errored);a.updateHdas(g)}else{a.log("Error updating hdas from api history contents",c,i,d,e,g);var h=_l("An error occurred while getting dataset details from the server.")+" "+_l("Please contact a Galaxy administrator if the problem persists.");a.trigger("error",h,i,d,e)}},success:function(e,d,f){a.log(a+".fetchHdaUpdates, success:",d,f);a.updateHdas(e)}});return b},updateHdas:function(a){var c=this,b=[];c.log(c+".updateHdas:",a);_.each(a,function(e,f){var d=c.hdas.get(e.id);if(d){c.log("found existing model in list for id "+e.id+", updating...:");d.set(e)}else{c.log("NO existing model for id "+e.id+", creating...:");b.push(e)}});if(b.length){c.addHdas(b)}},addHdas:function(a){var b=this;_.each(a,function(c,d){var e=b.hdas.hidToCollectionIndex(c.hid);c.history_id=b.get("id");b.hdas.add(new HistoryDatasetAssociation(c),{at:e,silent:true})});b.hdas.trigger("add",a)},updateDisplayApplications:function(a){this.log(this+"updateDisplayApplications:",a);var c=this,b=(a&&_.isArray(a))?({hda_ids:a.join(",")}):({});c.log(this+": fetching display application data");jQuery.ajax("history/get_display_application_links",{data:b,success:function(f,d,e){_.each(f,function(h){var g=c.hdas.get(h.id);if(g){g.set(h)}})},error:function(g,d,e){if(!((g.readyState===0)&&(g.status===0))){c.log("Error fetching display applications:",a,g,d,e);var f=_l("An error occurred while getting display applications from the server.")+" "+_l("Please contact a Galaxy administrator if the problem persists.");c.trigger("error",f,g,d,e)}}})},toString:function(){var a=(this.get("name"))?(","+this.get("name")):("");return"History("+this.get("id")+a+")"}});History.UPDATE_DELAY=4000;var HistoryCollection=Backbone.Collection.extend(LoggableMixin).extend({model:History,urlRoot:"api/histories"}); \ No newline at end of file diff -r 78eaaca131e3251ba9cc78f7546ace6a713a4f02 -r f76c280cdee539b65315ac583f93bfa52feb790d static/scripts/packed/utils/config.js --- a/static/scripts/packed/utils/config.js +++ b/static/scripts/packed/utils/config.js @@ -1,1 +1,1 @@ -define(["libs/underscore","viz/trackster/util"],function(b,e){var c=Backbone.Model.extend({initialize:function(f){var g=this.get("key");this.set("id",g);var h=b.find(c.known_settings_defaults,function(i){return i.key===g});if(h){this.set(b.extend({},h,f))}if(this.get("type")==="color"&&!this.get("value")){this.set("value",e.get_random_color())}this.on("change:value",this.cast_value,this)},cast_value:function(){var f=this.get("type"),g=this.get("value");if(f==="float"){g=parseFloat(g)}else{if(f==="int"){g=parseInt(g,10)}}this.set("value")}},{known_settings_defaults:[{key:"name",label:"Name",type:"text",default_value:""},{key:"color",label:"Color",type:"color",default_value:null},{key:"min_value",label:"Min Value",type:"float",default_value:null},{key:"max_value",label:"Max Value",type:"float",default_value:null},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:32,hidden:true},{key:"pos_color",label:"Positive Color",type:"color",default_value:"#FF8C00"},{key:"neg_color",label:"Negative Color",type:"color",default_value:"#4169E1"},{key:"block_color",label:"Block color",type:"color",default_value:null},{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},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:null},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true}]});var d=Backbone.Collection.extend({model:c,to_key_value_dict:function(){var f={};this.each(function(g){f[g.get("key")]=g.get("value")});return f},get_value:function(f){var g=this.get(f);if(g){return g.get("value")}return undefined}},{from_config_dict:function(g){var f=b.map(b.keys(g),function(h){return{key:h,value:g[h]}});return new d(f)}});var a=Backbone.View.extend({className:"config-settings-view",render:function(){var i=this.model;var f=this.$el;var h;function g(n,j){for(var r=0;r<n.length;r++){h=n[r];if(h.hidden){continue}var l="param_"+r;var v=i.values[h.key];var x=$("<div class='form-row' />").appendTo(j);x.append($("<label />").attr("for",l).text(h.label+":"));if(type==="bool"){x.append($('<input type="checkbox" />').attr("id",l).attr("name",l).attr("checked",v))}else{if(type==="text"){x.append($('<input type="text"/>').attr("id",l).val(v).click(function(){$(this).select()}))}else{if(type==="select"){var t=$("<select />").attr("id",l);for(var p=0;p<h.options.length;p++){$("<option/>").text(h.options[p].label).attr("value",h.options[p].value).appendTo(t)}t.val(v);x.append(t)}else{if(type==="color"){var w=$("<div/>").appendTo(x),s=$("<input />").attr("id",l).attr("name",l).val(v).css("float","left").appendTo(w).click(function(z){$(".tooltip").removeClass("in");var y=$(this).siblings(".tooltip").addClass("in");y.css({left:$(this).position().left+$(this).width()+5,top:$(this).position().top-($(y).height()/2)+($(this).height()/2)}).show();y.click(function(A){A.stopPropagation()});$(document).bind("click.color-picker",function(){y.hide();$(document).unbind("click.color-picker")});z.stopPropagation()}),q=$("<a href='javascript:void(0)'/>").addClass("icon-button arrow-circle").appendTo(w).attr("title","Set new random color").tooltip(),u=$("<div class='tooltip right' style='position: absolute;' />").appendTo(w).hide(),m=$("<div class='tooltip-inner' style='text-align: inherit'></div>").appendTo(u),k=$("<div class='tooltip-arrow'></div>").appendTo(u),o=$.farbtastic(m,{width:100,height:100,callback:s,color:v});w.append($("<div/>").css("clear","both"));(function(y){q.click(function(){y.setColor(e.get_random_color())})})(o)}else{x.append($("<input />").attr("id",l).attr("name",l).val(v))}}}}if(h.help){x.append($("<div class='help'/>").text(h.help))}}}g(this.params,f);return this},render_in_modal:function(){var h=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},f=function(){this.update_from_form();hide_modal();$(window).unbind("keypress.check_enter_esc")},g=function(i){if((i.keyCode||i.which)===27){h()}else{if((i.keyCode||i.which)===13){f()}}};$(window).bind("keypress.check_enter_esc",g);if(this.$el.children().length===0){this.render()}show_modal("Configure",drawable.config.build_form(),{Cancel:h,OK:f})},update_from_form:function(){var f=this;this.collection.each(function(h,g){if(!h.get("hidden")){var j="param_"+g;var i=f.$el.find("#"+j).val();if(type==="bool"){i=container.find("#"+j).is(":checked")}h.set("value",i)}})}});return{ConfigSettingCollection:d,ConfigSettingCollectionView:a}}); \ No newline at end of file +define(["libs/underscore","viz/trackster/util"],function(b,e){var c=Backbone.Model.extend({initialize:function(f){var g=this.get("key");this.set("id",g);var h=b.find(c.known_settings_defaults,function(i){return i.key===g});if(h){this.set(b.extend({},h,f))}if(this.get("type")==="color"&&!this.get("value")){this.set("value",e.get_random_color())}this.on("change:value",this.cast_value,this)},cast_value:function(){var f=this.get("type"),g=this.get("value");if(f==="float"){g=parseFloat(g)}else{if(f==="int"){g=parseInt(g,10)}}this.set("value")}},{known_settings_defaults:[{key:"name",label:"Name",type:"text",default_value:""},{key:"color",label:"Color",type:"color",default_value:null},{key:"min_value",label:"Min Value",type:"float",default_value:null},{key:"max_value",label:"Max Value",type:"float",default_value:null},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:32,hidden:true},{key:"pos_color",label:"Positive Color",type:"color",default_value:"#FF8C00"},{key:"neg_color",label:"Negative Color",type:"color",default_value:"#4169E1"},{key:"block_color",label:"Block color",type:"color",default_value:null},{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},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:null},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true}]});var d=Backbone.Collection.extend({model:c,to_key_value_dict:function(){var f={};this.each(function(g){f[g.get("key")]=g.get("value")});return f},get_value:function(f){var g=this.get(f);if(g){return g.get("value")}return undefined}},{from_config_dict:function(g){var f=b.map(b.keys(g),function(h){return{key:h,value:g[h]}});return new d(f)}});var a=Backbone.View.extend({className:"config-settings-view",render:function(){var i=this.model;var f=this.$el;var h;function g(n,j){for(var r=0;r<n.length;r++){h=n[r];if(h.hidden){continue}var l="param_"+r;var v=i.values[h.key];var x=$("<div class='form-row' />").appendTo(j);x.append($("<label />").attr("for",l).text(h.label+":"));if(type==="bool"){x.append($('<input type="checkbox" />').attr("id",l).attr("name",l).attr("checked",v))}else{if(type==="text"){x.append($('<input type="text"/>').attr("id",l).val(v).click(function(){$(this).select()}))}else{if(type==="select"){var t=$("<select />").attr("id",l);for(var p=0;p<h.options.length;p++){$("<option/>").text(h.options[p].label).attr("value",h.options[p].value).appendTo(t)}t.val(v);x.append(t)}else{if(type==="color"){var w=$("<div/>").appendTo(x),s=$("<input />").attr("id",l).attr("name",l).val(v).css("float","left").appendTo(w).click(function(z){$(".tooltip").removeClass("in");var y=$(this).siblings(".tooltip").addClass("in");y.css({left:$(this).position().left+$(this).width()+5,top:$(this).position().top-($(y).height()/2)+($(this).height()/2)}).show();y.click(function(A){A.stopPropagation()});$(document).bind("click.color-picker",function(){y.hide();$(document).unbind("click.color-picker")});z.stopPropagation()}),q=$("<a href='javascript:void(0)'/>").addClass("icon-button arrow-circle").appendTo(w).attr("title","Set new random color").tooltip(),u=$("<div class='tooltip right' style='position: absolute;' />").appendTo(w).hide(),m=$("<div class='tooltip-inner' style='text-align: inherit'></div>").appendTo(u),k=$("<div class='tooltip-arrow'></div>").appendTo(u),o=$.farbtastic(m,{width:100,height:100,callback:s,color:v});w.append($("<div/>").css("clear","both"));(function(y){q.click(function(){y.setColor(e.get_random_color())})})(o)}else{x.append($("<input />").attr("id",l).attr("name",l).val(v))}}}}if(h.help){x.append($("<div class='help'/>").text(h.help))}}}g(this.params,f);return this},render_in_modal:function(){var h=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},f=function(){this.update_from_form();hide_modal();$(window).unbind("keypress.check_enter_esc")},g=function(i){if((i.keyCode||i.which)===27){h()}else{if((i.keyCode||i.which)===13){f()}}};$(window).bind("keypress.check_enter_esc",g);if(this.$el.children().length===0){this.render()}Galaxy.modal.show({title:"Configure",body:drawable.config.build_form(),buttons:{Cancel:h,OK:f}})},update_from_form:function(){var f=this;this.collection.each(function(h,g){if(!h.get("hidden")){var j="param_"+g;var i=f.$el.find("#"+j).val();if(type==="bool"){i=container.find("#"+j).is(":checked")}h.set("value",i)}})}});return{ConfigSettingCollection:d,ConfigSettingCollectionView:a}}); \ No newline at end of file diff -r 78eaaca131e3251ba9cc78f7546ace6a713a4f02 -r f76c280cdee539b65315ac583f93bfa52feb790d static/scripts/packed/viz/trackster/filters.js --- a/static/scripts/packed/viz/trackster/filters.js +++ b/static/scripts/packed/viz/trackster/filters.js @@ -1,1 +1,1 @@ -define(["libs/underscore"],function(c){var f=c.extend;var a=function(g){this.manager=null;this.name=g.name;this.index=g.index;this.tool_id=g.tool_id;this.tool_exp_name=g.tool_exp_name};f(a.prototype,{to_dict:function(){return{name:this.name,index:this.index,tool_id:this.tool_id,tool_exp_name:this.tool_exp_name}}});var d=function(i,h,g){return $("<a/>").attr("href","javascript:void(0);").attr("title",i).addClass("icon-button").addClass(h).tooltip().click(g)};var e=function(o){a.call(this,o);this.low=("low" in o?o.low:-Number.MAX_VALUE);this.high=("high" in o?o.high:Number.MAX_VALUE);this.min=("min" in o?o.min:Number.MAX_VALUE);this.max=("max" in o?o.max:-Number.MAX_VALUE);this.container=null;this.slider=null;this.slider_label=null;var k=function(p,q,r){p.click(function(){var w=q.text(),u=parseFloat(r.slider("option","max")),t=(u<=1?4:u<=1000000?u.toString().length:6),v=false,s=$(this).parents(".slider-row");s.addClass("input");if(r.slider("option","values")){t=2*t+1;v=true}q.text("");$("<input type='text'/>").attr("size",t).attr("maxlength",t).attr("value",w).appendTo(q).focus().select().click(function(x){x.stopPropagation()}).blur(function(){$(this).remove();q.text(w);s.removeClass("input")}).keyup(function(B){if(B.keyCode===27){$(this).trigger("blur")}else{if(B.keyCode===13){var z=r.slider("option","min"),x=r.slider("option","max"),A=function(C){return(isNaN(C)||C>x||C<z)},y=$(this).val();if(!v){y=parseFloat(y);if(A(y)){alert("Parameter value must be in the range ["+z+"-"+x+"]");return $(this)}}else{y=y.split("-");y=[parseFloat(y[0]),parseFloat(y[1])];if(A(y[0])||A(y[1])){alert("Parameter value must be in the range ["+z+"-"+x+"]");return $(this)}}r.slider((v?"values":"value"),y);s.removeClass("input")}}})})};var h=this;h.parent_div=$("<div/>").addClass("filter-row slider-row");var g=$("<div/>").addClass("elt-label").appendTo(h.parent_div),m=$("<span/>").addClass("slider-name").text(h.name+" ").appendTo(g),i=$("<span/>").text(this.low+"-"+this.high),j=$("<span/>").addClass("slider-value").appendTo(g).append("[").append(i).append("]");h.values_span=i;var l=$("<div/>").addClass("slider").appendTo(h.parent_div);h.control_element=$("<div/>").attr("id",h.name+"-filter-control").appendTo(l);h.control_element.slider({range:true,min:this.min,max:this.max,step:this.get_slider_step(this.min,this.max),values:[this.low,this.high],slide:function(p,q){h.slide(p,q)},change:function(p,q){h.control_element.slider("option","slide").call(h.control_element,p,q)}});h.slider=h.control_element;h.slider_label=i;k(j,i,h.control_element);var n=$("<div/>").addClass("display-controls").appendTo(h.parent_div);this.transparency_icon=d("Use filter for data transparency","layer-transparent",function(){if(h.manager.alpha_filter!==h){h.manager.alpha_filter=h;h.manager.parent_div.find(".layer-transparent").removeClass("active").hide();h.transparency_icon.addClass("active").show()}else{h.manager.alpha_filter=null;h.transparency_icon.removeClass("active")}h.manager.track.request_draw({force:true,clear_after:true})}).appendTo(n).hide();this.height_icon=d("Use filter for data height","arrow-resize-090",function(){if(h.manager.height_filter!==h){h.manager.height_filter=h;h.manager.parent_div.find(".arrow-resize-090").removeClass("active").hide();h.height_icon.addClass("active").show()}else{h.manager.height_filter=null;h.height_icon.removeClass("active")}h.manager.track.request_draw({force:true,clear_after:true})}).appendTo(n).hide();h.parent_div.hover(function(){h.transparency_icon.show();h.height_icon.show()},function(){if(h.manager.alpha_filter!==h){h.transparency_icon.hide()}if(h.manager.height_filter!==h){h.height_icon.hide()}});$("<div style='clear: both;'/>").appendTo(h.parent_div)};f(e.prototype,{to_dict:function(){var g=a.prototype.to_dict.call(this);return f(g,{type:"number",min:this.min,max:this.max,low:this.low,high:this.high})},copy:function(){return new e({name:this.name,index:this.index,tool_id:this.tool_id,tool_exp_name:this.tool_exp_name})},get_slider_step:function(i,g){var h=g-i;return(h<=2?0.01:1)},slide:function(i,j){var h=j.values;this.values_span.text(h[0]+"-"+h[1]);this.low=h[0];this.high=h[1];var g=this;setTimeout(function(){if(h[0]===g.low&&h[1]===g.high){g.manager.track.request_draw({force:true,clear_after:true})}},25)},applies_to:function(g){if(g.length>this.index){return true}return false},_keep_val:function(g){return(isNaN(g)||(g>=this.low&&g<=this.high))},keep:function(h){if(!this.applies_to(h)){return true}var k=this;var l=h[this.index];if(l instanceof Array){var j=true;for(var g=0;g<l.length;g++){if(!this._keep_val(l[g])){j=false;break}}return j}else{return this._keep_val(h[this.index])}},update_attrs:function(k){var g=false;if(!this.applies_to(k)){return g}var h=k[this.index];if(!(h instanceof Array)){h=[h]}for(var j=0;j<h.length;j++){var l=h[j];if(l<this.min){this.min=Math.floor(l);g=true}if(l>this.max){this.max=Math.ceil(l);g=true}}return g},update_ui_elt:function(){if(this.min<this.max){this.parent_div.show()}else{this.parent_div.hide()}var h=this.slider.slider("option","min"),g=this.slider.slider("option","max");if(this.min<h||this.max>g){this.slider.slider("option","min",this.min);this.slider.slider("option","max",this.max);this.slider.slider("option","step",this.get_slider_step(this.min,this.max));this.slider.slider("option","values",[this.min,this.max])}}});var b=function(j,p){this.track=j;this.alpha_filter=null;this.height_filter=null;this.filters=[];this.parent_div=$("<div/>").addClass("filters").hide();this.parent_div.bind("drag",function(i){i.stopPropagation()}).click(function(i){i.stopPropagation()}).bind("dblclick",function(i){i.stopPropagation()}).bind("keydown",function(i){i.stopPropagation()});if(p&&"filters" in p){var g=("alpha_filter" in p?p.alpha_filter:null),k=("height_filter" in p?p.height_filter:null),m=p.filters,h;for(var n=0;n<m.length;n++){if(m[n].type==="number"){h=new e(m[n]);this.add_filter(h);if(h.name===g){this.alpha_filter=h;h.transparency_icon.addClass("active").show()}if(h.name===k){this.height_filter=h;h.height_icon.addClass("active").show()}}else{console.log("ERROR: unsupported filter: ",name,type)}}if("visible" in p&&p.visible){this.parent_div.show()}}if(this.filters.length!==0){var q=$("<div/>").addClass("param-row").appendTo(this.parent_div);var o=$("<input type='submit'/>").attr("value","Run on complete dataset").appendTo(q);var l=this;o.click(function(){l.run_on_dataset()})}};f(b.prototype,{show:function(){this.parent_div.show()},hide:function(){this.parent_div.hide()},toggle:function(){this.parent_div.toggle()},visible:function(){return this.parent_div.is(":visible")},to_dict:function(){var k={},j=[],h;for(var g=0;g<this.filters.length;g++){h=this.filters[g];j.push(h.to_dict())}k.filters=j;k.alpha_filter=(this.alpha_filter?this.alpha_filter.name:null);k.height_filter=(this.height_filter?this.height_filter.name:null);k.visible=this.parent_div.is(":visible");return k},copy:function(h){var j=new b(h);for(var g=0;g<this.filters.length;g++){j.add_filter(this.filters[g].copy())}return j},add_filter:function(g){g.manager=this;this.parent_div.append(g.parent_div);this.filters.push(g)},remove_all:function(){this.filters=[];this.parent_div.children().remove()},init_filters:function(){for(var g=0;g<this.filters.length;g++){var h=this.filters[g];h.update_ui_elt()}},clear_filters:function(){for(var g=0;g<this.filters.length;g++){var h=this.filters[g];h.slider.slider("option","values",[h.min,h.max])}this.alpha_filter=null;this.height_filter=null;this.parent_div.find(".icon-button").hide()},run_on_dataset:function(){var n=function(q,i,p){if(!(i in q)){q[i]=p}return q[i]};var m={},o,g;for(var l=0;l<this.filters.length;l++){o=this.filters[l];if(o.tool_id){if(o.min!==o.low){g=n(m,o.tool_id,[]);g[g.length]=o.tool_exp_name+" >= "+o.low}if(o.max!==o.high){g=n(m,o.tool_id,[]);g[g.length]=o.tool_exp_name+" <= "+o.high}}}var h=[];for(var k in m){h[h.length]=[k,m[k]]}(function j(u,r){var p=r[0],q=p[0],t=p[1],s="("+t.join(") and (")+")",i={cond:s,input:u,target_dataset_id:u,tool_id:q};r=r.slice(1);$.getJSON(run_tool_url,i,function(v){if(v.error){show_modal("Filter Dataset","Error running tool "+q,{Close:hide_modal})}else{if(r.length===0){show_modal("Filtering Dataset","Filter(s) are running on the complete dataset. Outputs are in dataset's history.",{Close:hide_modal})}else{j(v.dataset_id,r)}}})})(this.track.dataset_id,h)}});return{FiltersManager:b,NumberFilter:e}}); \ No newline at end of file +define(["libs/underscore"],function(c){var f=c.extend;var a=function(g){this.manager=null;this.name=g.name;this.index=g.index;this.tool_id=g.tool_id;this.tool_exp_name=g.tool_exp_name};f(a.prototype,{to_dict:function(){return{name:this.name,index:this.index,tool_id:this.tool_id,tool_exp_name:this.tool_exp_name}}});var d=function(i,h,g){return $("<a/>").attr("href","javascript:void(0);").attr("title",i).addClass("icon-button").addClass(h).tooltip().click(g)};var e=function(o){a.call(this,o);this.low=("low" in o?o.low:-Number.MAX_VALUE);this.high=("high" in o?o.high:Number.MAX_VALUE);this.min=("min" in o?o.min:Number.MAX_VALUE);this.max=("max" in o?o.max:-Number.MAX_VALUE);this.container=null;this.slider=null;this.slider_label=null;var k=function(p,q,r){p.click(function(){var w=q.text(),u=parseFloat(r.slider("option","max")),t=(u<=1?4:u<=1000000?u.toString().length:6),v=false,s=$(this).parents(".slider-row");s.addClass("input");if(r.slider("option","values")){t=2*t+1;v=true}q.text("");$("<input type='text'/>").attr("size",t).attr("maxlength",t).attr("value",w).appendTo(q).focus().select().click(function(x){x.stopPropagation()}).blur(function(){$(this).remove();q.text(w);s.removeClass("input")}).keyup(function(B){if(B.keyCode===27){$(this).trigger("blur")}else{if(B.keyCode===13){var z=r.slider("option","min"),x=r.slider("option","max"),A=function(C){return(isNaN(C)||C>x||C<z)},y=$(this).val();if(!v){y=parseFloat(y);if(A(y)){alert("Parameter value must be in the range ["+z+"-"+x+"]");return $(this)}}else{y=y.split("-");y=[parseFloat(y[0]),parseFloat(y[1])];if(A(y[0])||A(y[1])){alert("Parameter value must be in the range ["+z+"-"+x+"]");return $(this)}}r.slider((v?"values":"value"),y);s.removeClass("input")}}})})};var h=this;h.parent_div=$("<div/>").addClass("filter-row slider-row");var g=$("<div/>").addClass("elt-label").appendTo(h.parent_div),m=$("<span/>").addClass("slider-name").text(h.name+" ").appendTo(g),i=$("<span/>").text(this.low+"-"+this.high),j=$("<span/>").addClass("slider-value").appendTo(g).append("[").append(i).append("]");h.values_span=i;var l=$("<div/>").addClass("slider").appendTo(h.parent_div);h.control_element=$("<div/>").attr("id",h.name+"-filter-control").appendTo(l);h.control_element.slider({range:true,min:this.min,max:this.max,step:this.get_slider_step(this.min,this.max),values:[this.low,this.high],slide:function(p,q){h.slide(p,q)},change:function(p,q){h.control_element.slider("option","slide").call(h.control_element,p,q)}});h.slider=h.control_element;h.slider_label=i;k(j,i,h.control_element);var n=$("<div/>").addClass("display-controls").appendTo(h.parent_div);this.transparency_icon=d("Use filter for data transparency","layer-transparent",function(){if(h.manager.alpha_filter!==h){h.manager.alpha_filter=h;h.manager.parent_div.find(".layer-transparent").removeClass("active").hide();h.transparency_icon.addClass("active").show()}else{h.manager.alpha_filter=null;h.transparency_icon.removeClass("active")}h.manager.track.request_draw({force:true,clear_after:true})}).appendTo(n).hide();this.height_icon=d("Use filter for data height","arrow-resize-090",function(){if(h.manager.height_filter!==h){h.manager.height_filter=h;h.manager.parent_div.find(".arrow-resize-090").removeClass("active").hide();h.height_icon.addClass("active").show()}else{h.manager.height_filter=null;h.height_icon.removeClass("active")}h.manager.track.request_draw({force:true,clear_after:true})}).appendTo(n).hide();h.parent_div.hover(function(){h.transparency_icon.show();h.height_icon.show()},function(){if(h.manager.alpha_filter!==h){h.transparency_icon.hide()}if(h.manager.height_filter!==h){h.height_icon.hide()}});$("<div style='clear: both;'/>").appendTo(h.parent_div)};f(e.prototype,{to_dict:function(){var g=a.prototype.to_dict.call(this);return f(g,{type:"number",min:this.min,max:this.max,low:this.low,high:this.high})},copy:function(){return new e({name:this.name,index:this.index,tool_id:this.tool_id,tool_exp_name:this.tool_exp_name})},get_slider_step:function(i,g){var h=g-i;return(h<=2?0.01:1)},slide:function(i,j){var h=j.values;this.values_span.text(h[0]+"-"+h[1]);this.low=h[0];this.high=h[1];var g=this;setTimeout(function(){if(h[0]===g.low&&h[1]===g.high){g.manager.track.request_draw({force:true,clear_after:true})}},25)},applies_to:function(g){if(g.length>this.index){return true}return false},_keep_val:function(g){return(isNaN(g)||(g>=this.low&&g<=this.high))},keep:function(h){if(!this.applies_to(h)){return true}var k=this;var l=h[this.index];if(l instanceof Array){var j=true;for(var g=0;g<l.length;g++){if(!this._keep_val(l[g])){j=false;break}}return j}else{return this._keep_val(h[this.index])}},update_attrs:function(k){var g=false;if(!this.applies_to(k)){return g}var h=k[this.index];if(!(h instanceof Array)){h=[h]}for(var j=0;j<h.length;j++){var l=h[j];if(l<this.min){this.min=Math.floor(l);g=true}if(l>this.max){this.max=Math.ceil(l);g=true}}return g},update_ui_elt:function(){if(this.min<this.max){this.parent_div.show()}else{this.parent_div.hide()}var h=this.slider.slider("option","min"),g=this.slider.slider("option","max");if(this.min<h||this.max>g){this.slider.slider("option","min",this.min);this.slider.slider("option","max",this.max);this.slider.slider("option","step",this.get_slider_step(this.min,this.max));this.slider.slider("option","values",[this.min,this.max])}}});var b=function(j,p){this.track=j;this.alpha_filter=null;this.height_filter=null;this.filters=[];this.parent_div=$("<div/>").addClass("filters").hide();this.parent_div.bind("drag",function(i){i.stopPropagation()}).click(function(i){i.stopPropagation()}).bind("dblclick",function(i){i.stopPropagation()}).bind("keydown",function(i){i.stopPropagation()});if(p&&"filters" in p){var g=("alpha_filter" in p?p.alpha_filter:null),k=("height_filter" in p?p.height_filter:null),m=p.filters,h;for(var n=0;n<m.length;n++){if(m[n].type==="number"){h=new e(m[n]);this.add_filter(h);if(h.name===g){this.alpha_filter=h;h.transparency_icon.addClass("active").show()}if(h.name===k){this.height_filter=h;h.height_icon.addClass("active").show()}}else{console.log("ERROR: unsupported filter: ",name,type)}}if("visible" in p&&p.visible){this.parent_div.show()}}if(this.filters.length!==0){var q=$("<div/>").addClass("param-row").appendTo(this.parent_div);var o=$("<input type='submit'/>").attr("value","Run on complete dataset").appendTo(q);var l=this;o.click(function(){l.run_on_dataset()})}};f(b.prototype,{show:function(){this.parent_div.show()},hide:function(){this.parent_div.hide()},toggle:function(){this.parent_div.toggle()},visible:function(){return this.parent_div.is(":visible")},to_dict:function(){var k={},j=[],h;for(var g=0;g<this.filters.length;g++){h=this.filters[g];j.push(h.to_dict())}k.filters=j;k.alpha_filter=(this.alpha_filter?this.alpha_filter.name:null);k.height_filter=(this.height_filter?this.height_filter.name:null);k.visible=this.parent_div.is(":visible");return k},copy:function(h){var j=new b(h);for(var g=0;g<this.filters.length;g++){j.add_filter(this.filters[g].copy())}return j},add_filter:function(g){g.manager=this;this.parent_div.append(g.parent_div);this.filters.push(g)},remove_all:function(){this.filters=[];this.parent_div.children().remove()},init_filters:function(){for(var g=0;g<this.filters.length;g++){var h=this.filters[g];h.update_ui_elt()}},clear_filters:function(){for(var g=0;g<this.filters.length;g++){var h=this.filters[g];h.slider.slider("option","values",[h.min,h.max])}this.alpha_filter=null;this.height_filter=null;this.parent_div.find(".icon-button").hide()},run_on_dataset:function(){var n=function(q,i,p){if(!(i in q)){q[i]=p}return q[i]};var m={},o,g;for(var l=0;l<this.filters.length;l++){o=this.filters[l];if(o.tool_id){if(o.min!==o.low){g=n(m,o.tool_id,[]);g[g.length]=o.tool_exp_name+" >= "+o.low}if(o.max!==o.high){g=n(m,o.tool_id,[]);g[g.length]=o.tool_exp_name+" <= "+o.high}}}var h=[];for(var k in m){h[h.length]=[k,m[k]]}(function j(u,r){var p=r[0],q=p[0],t=p[1],s="("+t.join(") and (")+")",i={cond:s,input:u,target_dataset_id:u,tool_id:q};r=r.slice(1);$.getJSON(run_tool_url,i,function(v){if(v.error){Galaxy.modal.show({title:"Filter Dataset",body:"Error running tool "+q,buttons:{Close:Galaxy.modal.hide()}})}else{if(r.length===0){Galaxy.modal.show({title:"Filtering Dataset",body:"Filter(s) are running on the complete dataset. Outputs are in dataset's history.",buttons:{Close:Galaxy.modal.hide()}})}else{j(v.dataset_id,r)}}})})(this.track.dataset_id,h)}});return{FiltersManager:b,NumberFilter:e}}); \ No newline at end of file diff -r 78eaaca131e3251ba9cc78f7546ace6a713a4f02 -r f76c280cdee539b65315ac583f93bfa52feb790d static/scripts/packed/viz/trackster/painters.js --- a/static/scripts/packed/viz/trackster/painters.js +++ b/static/scripts/packed/viz/trackster/painters.js @@ -1,1 +1,1 @@ -define(["libs/underscore"],function(_){var extend=_.extend;var BEFORE=1001,CONTAINS=1002,OVERLAP_START=1003,OVERLAP_END=1004,CONTAINED_BY=1005,AFTER=1006;var compute_overlap=function(first_region,second_region){var first_start=first_region[0],first_end=first_region[1],second_start=second_region[0],second_end=second_region[1],overlap;if(first_start<second_start){if(first_end<=second_start){overlap=BEFORE}else{if(first_end<=second_end){overlap=OVERLAP_START}else{overlap=CONTAINS}}}else{if(first_start>second_end){overlap=AFTER}else{if(first_end<=second_end){overlap=CONTAINED_BY}else{overlap=OVERLAP_END}}}return overlap};var is_overlap=function(first_region,second_region){var overlap=compute_overlap(first_region,second_region);return(overlap!==BEFORE&&overlap!==AFTER)};var dashedLine=function(ctx,x1,y1,x2,y2,dashLen){if(dashLen===undefined){dashLen=4}var dX=x2-x1;var dY=y2-y1;var dashes=Math.floor(Math.sqrt(dX*dX+dY*dY)/dashLen);var dashX=dX/dashes;var dashY=dY/dashes;var q;for(q=0;q<dashes;q++,x1+=dashX,y1+=dashY){if(q%2!==0){continue}ctx.fillRect(x1,y1,dashLen,1)}};var drawDownwardEquilateralTriangle=function(ctx,down_vertex_x,down_vertex_y,side_len){var x1=down_vertex_x-side_len/2,x2=down_vertex_x+side_len/2,y=down_vertex_y-Math.sqrt(side_len*3/2);ctx.beginPath();ctx.moveTo(x1,y);ctx.lineTo(x2,y);ctx.lineTo(down_vertex_x,down_vertex_y);ctx.lineTo(x1,y);ctx.strokeStyle=this.fillStyle;ctx.fill();ctx.stroke();ctx.closePath()};var Scaler=function(default_val){this.default_val=(default_val?default_val:1)};Scaler.prototype.gen_val=function(input){return this.default_val};var Painter=function(data,view_start,view_end,prefs,mode){this.data=data;this.view_start=view_start;this.view_end=view_end;this.prefs=extend({},this.default_prefs,prefs);this.mode=mode};Painter.prototype.default_prefs={};Painter.prototype.draw=function(ctx,width,height,w_scale){};var LinePainter=function(data,view_start,view_end,prefs,mode){Painter.call(this,data,view_start,view_end,prefs,mode);if(this.prefs.min_value===undefined){this.prefs.min_value=_.min(_.map(this.data,function(d){return d[1]}))||0}if(this.prefs.max_value===undefined){this.prefs.max_value=_.max(_.map(this.data,function(d){return d[1]}))||0}};LinePainter.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Histogram",color:"#000",overflow_color:"#F66"};LinePainter.prototype.draw=function(ctx,width,height,w_scale){var in_path=false,min_value=this.prefs.min_value,max_value=this.prefs.max_value,vertical_range=max_value-min_value,height_px=height,view_start=this.view_start,mode=this.mode,data=this.data;ctx.save();var y_zero=Math.round(height+min_value/vertical_range*height);if(mode!=="Intensity"){ctx.fillStyle="#aaa";ctx.fillRect(0,y_zero,width,1)}ctx.beginPath();var x_scaled,y,delta_x_px;if(data.length>1){delta_x_px=Math.ceil((data[1][0]-data[0][0])*w_scale)}else{delta_x_px=10}var painter_color=this.prefs.block_color||this.prefs.color,pref_color=parseInt(painter_color.slice(1),16),pref_r=(pref_color&16711680)>>16,pref_g=(pref_color&65280)>>8,pref_b=pref_color&255,top_overflow=false,bot_overflow=false;for(var i=0,len=data.length;i<len;i++){ctx.fillStyle=ctx.strokeStyle=painter_color;top_overflow=bot_overflow=false;x_scaled=Math.round((data[i][0]-view_start)*w_scale);y=data[i][1];if(y===null){if(in_path&&mode==="Filled"){ctx.lineTo(x_scaled,height_px)}in_path=false;continue}if(y<min_value){bot_overflow=true;y=min_value}else{if(y>max_value){top_overflow=true;y=max_value}}if(mode==="Histogram"){y=Math.round(y/vertical_range*height_px);ctx.fillRect(x_scaled,y_zero,delta_x_px,-y)}else{if(mode==="Intensity"){var saturation=(y-min_value)/vertical_range,new_r=Math.round(pref_r+(255-pref_r)*(1-saturation)),new_g=Math.round(pref_g+(255-pref_g)*(1-saturation)),new_b=Math.round(pref_b+(255-pref_b)*(1-saturation));ctx.fillStyle="rgb("+new_r+","+new_g+","+new_b+")";ctx.fillRect(x_scaled,0,delta_x_px,height_px)}else{y=Math.round(height_px-(y-min_value)/vertical_range*height_px);if(in_path){ctx.lineTo(x_scaled,y)}else{in_path=true;if(mode==="Filled"){ctx.moveTo(x_scaled,height_px);ctx.lineTo(x_scaled,y)}else{ctx.moveTo(x_scaled,y)}}}}ctx.fillStyle=this.prefs.overflow_color;if(top_overflow||bot_overflow){var overflow_x;if(mode==="Histogram"||mode==="Intensity"){overflow_x=delta_x_px}else{x_scaled-=2;overflow_x=4}if(top_overflow){ctx.fillRect(x_scaled,0,overflow_x,3)}if(bot_overflow){ctx.fillRect(x_scaled,height_px-3,overflow_x,3)}}ctx.fillStyle=painter_color}if(mode==="Filled"){if(in_path){ctx.lineTo(x_scaled,y_zero);ctx.lineTo(0,y_zero)}ctx.fill()}else{ctx.stroke()}ctx.restore()};var FeaturePositionMapper=function(slot_height){this.feature_positions={};this.slot_height=slot_height;this.translation=0;this.y_translation=0};FeaturePositionMapper.prototype.map_feature_data=function(feature_data,slot,x_start,x_end){if(!this.feature_positions[slot]){this.feature_positions[slot]=[]}this.feature_positions[slot].push({data:feature_data,x_start:x_start,x_end:x_end})};FeaturePositionMapper.prototype.get_feature_data=function(x,y){var slot=Math.floor((y-this.y_translation)/this.slot_height),feature_dict;if(!this.feature_positions[slot]){return null}x+=this.translation;for(var i=0;i<this.feature_positions[slot].length;i++){feature_dict=this.feature_positions[slot][i];if(x>=feature_dict.x_start&&x<=feature_dict.x_end){return feature_dict.data}}};var FeaturePainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler){Painter.call(this,data,view_start,view_end,prefs,mode);this.alpha_scaler=(alpha_scaler?alpha_scaler:new Scaler());this.height_scaler=(height_scaler?height_scaler:new Scaler())};FeaturePainter.prototype.default_prefs={block_color:"#FFF",connector_color:"#FFF"};extend(FeaturePainter.prototype,{get_required_height:function(rows_required,width){var required_height=this.get_row_height(),y_scale=required_height,mode=this.mode;if(mode==="no_detail"||mode==="Squish"||mode==="Pack"){required_height=rows_required*y_scale}return required_height+this.get_top_padding(width)+this.get_bottom_padding(width)},get_top_padding:function(width){return 0},get_bottom_padding:function(width){return Math.max(Math.round(this.get_row_height()/2),5)},draw:function(ctx,width,height,w_scale,slots){var data=this.data,view_start=this.view_start,view_end=this.view_end;ctx.save();ctx.fillStyle=this.prefs.block_color;ctx.textAlign="right";var y_scale=this.get_row_height(),feature_mapper=new FeaturePositionMapper(y_scale),x_draw_coords;for(var i=0,len=data.length;i<len;i++){var feature=data[i],feature_uid=feature[0],feature_start=feature[1],feature_end=feature[2],slot=(slots&&slots[feature_uid]!==undefined?slots[feature_uid]:null);if((feature_start<view_end&&feature_end>view_start)&&(this.mode==="Dense"||slot!==null)){x_draw_coords=this.draw_element(ctx,this.mode,feature,slot,view_start,view_end,w_scale,y_scale,width);feature_mapper.map_feature_data(feature,slot,x_draw_coords[0],x_draw_coords[1])}}ctx.restore();feature_mapper.y_translation=this.get_top_padding(width);return feature_mapper},draw_element:function(ctx,mode,feature,slot,tile_low,tile_high,w_scale,y_scale,width){console.log("WARNING: Unimplemented function.");return[0,0]}});var DENSE_TRACK_HEIGHT=10,NO_DETAIL_TRACK_HEIGHT=3,SQUISH_TRACK_HEIGHT=5,PACK_TRACK_HEIGHT=10,NO_DETAIL_FEATURE_HEIGHT=1,DENSE_FEATURE_HEIGHT=9,SQUISH_FEATURE_HEIGHT=3,PACK_FEATURE_HEIGHT=9,LABEL_SPACING=2,CONNECTOR_COLOR="#ccc";var LinkedFeaturePainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler){FeaturePainter.call(this,data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler);this.draw_background_connector=true;this.draw_individual_connectors=false};extend(LinkedFeaturePainter.prototype,FeaturePainter.prototype,{get_row_height:function(){var mode=this.mode,height;if(mode==="Dense"){height=DENSE_TRACK_HEIGHT}else{if(mode==="no_detail"){height=NO_DETAIL_TRACK_HEIGHT}else{if(mode==="Squish"){height=SQUISH_TRACK_HEIGHT}else{height=PACK_TRACK_HEIGHT}}}return height},draw_element:function(ctx,mode,feature,slot,tile_low,tile_high,w_scale,y_scale,width){var feature_uid=feature[0],feature_start=feature[1],feature_end=feature[2],feature_name=feature[3],feature_strand=feature[4],f_start=Math.floor(Math.max(0,(feature_start-tile_low-0.5)*w_scale)),f_end=Math.ceil(Math.min(width,Math.max(0,(feature_end-tile_low-0.5)*w_scale))),draw_start=f_start,draw_end=f_end,y_center=(mode==="Dense"?0:(0+slot))*y_scale+this.get_top_padding(width),thickness,y_start,thick_start=null,thick_end=null,block_color=(!feature_strand||feature_strand==="+"||feature_strand==="."?this.prefs.block_color:this.prefs.reverse_strand_color);label_color=this.prefs.label_color;ctx.globalAlpha=this.alpha_scaler.gen_val(feature);if(mode==="Dense"){slot=1}if(mode==="no_detail"){ctx.fillStyle=block_color;ctx.fillRect(f_start,y_center+5,f_end-f_start,NO_DETAIL_FEATURE_HEIGHT)}else{var feature_ts=feature[5],feature_te=feature[6],feature_blocks=feature[7],full_height=true;if(feature_ts&&feature_te){thick_start=Math.floor(Math.max(0,(feature_ts-tile_low)*w_scale));thick_end=Math.ceil(Math.min(width,Math.max(0,(feature_te-tile_low)*w_scale)))}var thin_height,thick_height;if(mode==="Squish"){thin_height=1;thick_height=SQUISH_FEATURE_HEIGHT;full_height=false}else{if(mode==="Dense"){thin_height=5;thick_height=DENSE_FEATURE_HEIGHT}else{thin_height=5;thick_height=PACK_FEATURE_HEIGHT}}if(!feature_blocks){ctx.fillStyle=block_color;ctx.fillRect(f_start,y_center+1,f_end-f_start,thick_height);if(feature_strand&&full_height){if(feature_strand==="+"){ctx.fillStyle=ctx.canvas.manager.get_pattern("right_strand_inv")}else{if(feature_strand==="-"){ctx.fillStyle=ctx.canvas.manager.get_pattern("left_strand_inv")}}ctx.fillRect(f_start,y_center+1,f_end-f_start,thick_height)}}else{var cur_y_center,cur_height;if(mode==="Squish"||mode==="Dense"){cur_y_center=y_center+Math.floor(SQUISH_FEATURE_HEIGHT/2)+1;cur_height=1}else{if(feature_strand){cur_y_center=y_center;cur_height=thick_height}else{cur_y_center+=(SQUISH_FEATURE_HEIGHT/2)+1;cur_height=1}}if(this.draw_background_connector){if(mode==="Squish"||mode==="Dense"){ctx.fillStyle=CONNECTOR_COLOR}else{if(feature_strand){if(feature_strand==="+"){ctx.fillStyle=ctx.canvas.manager.get_pattern("right_strand")}else{if(feature_strand==="-"){ctx.fillStyle=ctx.canvas.manager.get_pattern("left_strand")}}}else{ctx.fillStyle=CONNECTOR_COLOR}}ctx.fillRect(f_start,cur_y_center,f_end-f_start,cur_height)}var start_and_height;for(var k=0,k_len=feature_blocks.length;k<k_len;k++){var block=feature_blocks[k],block_start=Math.floor(Math.max(0,(block[0]-tile_low-0.5)*w_scale)),block_end=Math.ceil(Math.min(width,Math.max((block[1]-tile_low-0.5)*w_scale))),last_block_start,last_block_end;if(block_start>block_end){continue}ctx.fillStyle=block_color;ctx.fillRect(block_start,y_center+(thick_height-thin_height)/2+1,block_end-block_start,thin_height);if(thick_start!==undefined&&feature_te>feature_ts&&!(block_start>thick_end||block_end<thick_start)){var block_thick_start=Math.max(block_start,thick_start),block_thick_end=Math.min(block_end,thick_end);ctx.fillRect(block_thick_start,y_center+1,block_thick_end-block_thick_start,thick_height);if(feature_blocks.length===1&&mode==="Pack"){if(feature_strand==="+"){ctx.fillStyle=ctx.canvas.manager.get_pattern("right_strand_inv")}else{if(feature_strand==="-"){ctx.fillStyle=ctx.canvas.manager.get_pattern("left_strand_inv")}}if(block_thick_start+14<block_thick_end){block_thick_start+=2;block_thick_end-=2}ctx.fillRect(block_thick_start,y_center+1,block_thick_end-block_thick_start,thick_height)}}if(this.draw_individual_connectors&&last_block_start){this.draw_connector(ctx,last_block_start,last_block_end,block_start,block_end,y_center)}last_block_start=block_start;last_block_end=block_end}if(mode==="Pack"){ctx.globalAlpha=1;ctx.fillStyle="white";var hscale_factor=this.height_scaler.gen_val(feature),new_height=Math.ceil(thick_height*hscale_factor),ws_height=Math.round((thick_height-new_height)/2);if(hscale_factor!==1){ctx.fillRect(f_start,cur_y_center+1,f_end-f_start,ws_height);ctx.fillRect(f_start,cur_y_center+thick_height-ws_height+1,f_end-f_start,ws_height)}}}ctx.globalAlpha=1;if(feature_name&&mode==="Pack"&&feature_start>tile_low){ctx.fillStyle=label_color;if(tile_low===0&&f_start-ctx.measureText(feature_name).width<0){ctx.textAlign="left";ctx.fillText(feature_name,f_end+LABEL_SPACING,y_center+8);draw_end+=ctx.measureText(feature_name).width+LABEL_SPACING}else{ctx.textAlign="right";ctx.fillText(feature_name,f_start-LABEL_SPACING,y_center+8);draw_start-=ctx.measureText(feature_name).width+LABEL_SPACING}}}ctx.globalAlpha=1;return[draw_start,draw_end]}});var ReadPainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler,ref_seq,base_color_fn){FeaturePainter.call(this,data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler);this.ref_seq=(ref_seq?ref_seq.data:null);this.base_color_fn=base_color_fn};extend(ReadPainter.prototype,FeaturePainter.prototype,{get_row_height:function(){var height,mode=this.mode;if(mode==="Dense"){height=DENSE_TRACK_HEIGHT}else{if(mode==="Squish"){height=SQUISH_TRACK_HEIGHT}else{height=PACK_TRACK_HEIGHT;if(this.prefs.show_insertions){height*=2}}}return height},_parse_cigar:function(cigar_str){var cigar_ops="MIDNSHP=X";var blocks=[[0,0]],cur_block=blocks[0],base_pos=0,parsed_cigar=_.map(cigar_str.match(/[0-9]+[MIDNSHP=X]/g),function(op){var op_len=parseInt(op.slice(0,-1),10),op_char=op.slice(-1);if(op_char==="N"){if(cur_block[1]!==0){cur_block=[base_pos+op_len,base_pos+op_len];blocks.push(cur_block)}}else{if("ISHP".indexOf(op_char)===-1){cur_block[1]+=op_len;base_pos+=op_len}}return[cigar_ops.indexOf(op_char),op_len]});return{blocks:blocks,cigar:parsed_cigar}},draw_read:function(ctx,mode,w_scale,y_center,tile_low,tile_high,feature_start,cigar,strand,read_seq){ctx.textAlign="center";var tile_region=[tile_low,tile_high],base_offset=0,seq_offset=0,gap=Math.round(w_scale/2),char_width_px=ctx.canvas.manager.char_width_px,block_color=(strand==="+"?this.prefs.block_color:this.prefs.reverse_strand_color),pack_mode=(mode==="Pack");var draw_last=[];if(!cigar){cigar=[[0,read_seq.length]]}for(var cig_id=0,len=cigar.length;cig_id<len;cig_id++){var cig=cigar[cig_id],cig_op="MIDNSHP=X"[cig[0]],cig_len=cig[1];var seq_start=feature_start+base_offset,s_start=Math.floor(Math.max(-0.5*w_scale,(seq_start-tile_low-0.5)*w_scale)),s_end=Math.floor(Math.max(0,(seq_start+cig_len-tile_low-0.5)*w_scale));if(s_start===s_end){s_end+=1}switch(cig_op){case"H":break;case"S":seq_offset+=cig_len;break;case"M":case"=":case"X":if(is_overlap([seq_start,seq_start+cig_len],tile_region)){ctx.fillStyle=block_color;ctx.fillRect(s_start,y_center+(pack_mode?1:4),s_end-s_start,(pack_mode?PACK_FEATURE_HEIGHT:SQUISH_FEATURE_HEIGHT));var seq=read_seq.slice(seq_offset,seq_offset+cig_len),ref_char,read_char;for(var c=0,str_len=seq.length;c<str_len;c++){if(seq_start+c>=tile_low&&seq_start+c<=tile_high){ref_char=(this.ref_seq?this.ref_seq[seq_start-tile_low+c]:null);read_char=seq[c];if((ref_char&&(!this.prefs.show_differences||(read_char.toLowerCase!=="n"&&(ref_char.toLowerCase()!==read_char.toLowerCase()))))||(!ref_char&&!this.prefs.show_differences)){var c_start=Math.floor(Math.max(0,(seq_start+c-tile_low)*w_scale));ctx.fillStyle=this.base_color_fn(seq[c]);if(pack_mode&&w_scale>char_width_px){ctx.fillText(seq[c],c_start,y_center+9)}else{if(w_scale>0.05){ctx.fillRect(c_start-gap,y_center+(pack_mode?1:4),Math.max(1,Math.round(w_scale)),(pack_mode?PACK_FEATURE_HEIGHT:SQUISH_FEATURE_HEIGHT))}}}}}}seq_offset+=cig_len;base_offset+=cig_len;break;case"N":ctx.fillStyle=CONNECTOR_COLOR;ctx.fillRect(s_start,y_center+5,s_end-s_start,1);base_offset+=cig_len;break;case"D":ctx.fillStyle="black";ctx.fillRect(s_start,y_center+4,s_end-s_start,3);base_offset+=cig_len;break;case"P":break;case"I":var insert_x_coord=s_start-gap;if(is_overlap([seq_start,seq_start+cig_len],tile_region)){var seq=read_seq.slice(seq_offset,seq_offset+cig_len);if(this.prefs.show_insertions){var x_center=s_start-(s_end-s_start)/2;if((mode==="Pack"||this.mode==="Auto")&&read_seq!==undefined&&w_scale>char_width_px){ctx.fillStyle="yellow";ctx.fillRect(x_center-gap,y_center-9,s_end-s_start,9);draw_last[draw_last.length]={type:"triangle",data:[insert_x_coord,y_center+4,5]};ctx.fillStyle=CONNECTOR_COLOR;switch(compute_overlap([seq_start,seq_start+cig_len],tile_region)){case (OVERLAP_START):seq=seq.slice(tile_low-seq_start);break;case (OVERLAP_END):seq=seq.slice(0,seq_start-tile_high);break;case (CONTAINED_BY):break;case (CONTAINS):seq=seq.slice(tile_low-seq_start,seq_start-tile_high);break}for(var c=0,str_len=seq.length;c<str_len;c++){var c_start=Math.floor(Math.max(0,(seq_start+c-tile_low)*w_scale));ctx.fillText(seq[c],c_start-(s_end-s_start)/2,y_center)}}else{ctx.fillStyle="yellow";ctx.fillRect(x_center,y_center+(this.mode!=="Dense"?2:5),s_end-s_start,(mode!=="Dense"?SQUISH_FEATURE_HEIGHT:DENSE_FEATURE_HEIGHT))}}else{if((mode==="Pack"||this.mode==="Auto")&&read_seq!==undefined&&w_scale>char_width_px){draw_last.push({type:"text",data:[seq.length,insert_x_coord,y_center+9]})}else{}}}seq_offset+=cig_len;break}}ctx.fillStyle="yellow";var item,type,data;for(var i=0;i<draw_last.length;i++){item=draw_last[i];type=item.type;data=item.data;if(type==="text"){ctx.save();ctx.font="bold "+ctx.font;ctx.fillText(data[0],data[1],data[2]);ctx.restore()}else{if(type==="triangle"){drawDownwardEquilateralTriangle(ctx,data[0],data[1],data[2])}}}},draw_element:function(ctx,mode,feature,slot,tile_low,tile_high,w_scale,y_scale,width){var feature_uid=feature[0],feature_start=feature[1],feature_end=feature[2],feature_name=feature[3],f_start=Math.floor(Math.max(-0.5*w_scale,(feature_start-tile_low-0.5)*w_scale)),f_end=Math.ceil(Math.min(width,Math.max(0,(feature_end-tile_low-0.5)*w_scale))),y_center=(mode==="Dense"?0:(0+slot))*y_scale,label_color=this.prefs.label_color;if(feature[5] instanceof Array){var b1_start=Math.floor(Math.max(0,(feature[4][0]-tile_low)*w_scale)),b1_end=Math.ceil(Math.min(width,Math.max(0,(feature[4][1]-tile_low)*w_scale))),b2_start=Math.floor(Math.max(0,(feature[5][0]-tile_low)*w_scale)),b2_end=Math.ceil(Math.min(width,Math.max(0,(feature[5][1]-tile_low)*w_scale))),connector=true;if(feature[4][1]>=tile_low&&feature[4][0]<=tile_high&&feature[4][2]){this.draw_read(ctx,mode,w_scale,y_center,tile_low,tile_high,feature[4][0],feature[4][2],feature[4][3],feature[4][4])}else{connector=false}if(feature[5][1]>=tile_low&&feature[5][0]<=tile_high&&feature[5][2]){this.draw_read(ctx,mode,w_scale,y_center,tile_low,tile_high,feature[5][0],feature[5][2],feature[5][3],feature[5][4])}else{connector=false}if(connector&&b2_start>b1_end){ctx.fillStyle=CONNECTOR_COLOR;dashedLine(ctx,b1_end,y_center+5,b2_start,y_center+5)}}else{this.draw_read(ctx,mode,w_scale,y_center,tile_low,tile_high,feature_start,feature[4],feature[5],feature[6])}if(mode==="Pack"&&feature_start>=tile_low&&feature_name!=="."){ctx.fillStyle=this.prefs.label_color;if(tile_low===0&&f_start-ctx.measureText(feature_name).width<0){ctx.textAlign="left";ctx.fillText(feature_name,f_end+LABEL_SPACING,y_center+8)}else{ctx.textAlign="right";ctx.fillText(feature_name,f_start-LABEL_SPACING,y_center+8)}}return[0,0]}});var RefBasedReadPainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler,ref_seq,base_color_fn){ReadPainter.call(this,data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler,ref_seq,base_color_fn)};extend(RefBasedReadPainter.prototype,ReadPainter.prototype,FeaturePainter,{draw_read:function(ctx,mode,w_scale,y_center,tile_low,tile_high,feature_start,cigar,strand,read_seq){ctx.textAlign="center";var tile_region=[tile_low,tile_high],base_offset=0,seq_offset=0,gap=Math.round(w_scale/2),char_width_px=ctx.canvas.manager.char_width_px,block_color=(strand==="+"?this.prefs.block_color:this.prefs.reverse_strand_color),pack_mode=(mode==="Pack"),drawing_blocks=[];var draw_last=[];var t=this._parse_cigar(cigar);cigar=t.cigar;drawing_blocks=t.blocks;for(var i=0;i<drawing_blocks.length;i++){var block=drawing_blocks[i];if(is_overlap([feature_start+block[0],feature_start+block[1]],tile_region)){var s_start=Math.floor(Math.max(-0.5*w_scale,(feature_start+block[0]-tile_low-0.5)*w_scale)),s_end=Math.floor(Math.max(0,(feature_start+block[1]-tile_low-0.5)*w_scale));if(s_start===s_end){s_end+=1}ctx.fillStyle=block_color;ctx.fillRect(s_start,y_center+(pack_mode?1:4),s_end-s_start,(pack_mode?PACK_FEATURE_HEIGHT:SQUISH_FEATURE_HEIGHT))}}for(var cig_id=0,len=cigar.length;cig_id<len;cig_id++){var cig=cigar[cig_id],cig_op="MIDNSHP=X"[cig[0]],cig_len=cig[1];var seq_start=feature_start+base_offset,s_start=Math.floor(Math.max(0,-0.5*w_scale,(seq_start-tile_low-0.5)*w_scale)),s_end=Math.floor(Math.max(0,(seq_start+cig_len-tile_low-0.5)*w_scale));if(s_start===s_end){s_end+=1}switch(cig_op){case"H":case"S":case"P":break;case"M":base_offset+=cig_len;break;case"=":case"X":if(is_overlap([seq_start,seq_start+cig_len],tile_region)){var cur_seq="";if(cig_op==="X"){cur_seq=read_seq.slice(seq_offset,seq_offset+cig_len)}else{if(this.ref_seq){cur_seq=this.ref_seq.slice(Math.max(0,seq_start-tile_low),Math.min(seq_start-tile_low+cig_len,tile_high-tile_low))}}var start_pos=Math.max(seq_start,tile_low);for(var c=0;c<cur_seq.length;c++){if(cur_seq&&!this.prefs.show_differences||cig_op==="X"){var c_start=Math.floor(Math.max(0,(start_pos+c-tile_low)*w_scale));ctx.fillStyle=this.base_color_fn(cur_seq[c]);if(pack_mode&&w_scale>char_width_px){ctx.fillText(cur_seq[c],c_start,y_center+9)}else{if(w_scale>0.05){ctx.fillRect(c_start-gap,y_center+(pack_mode?1:4),Math.max(1,Math.round(w_scale)),(pack_mode?PACK_FEATURE_HEIGHT:SQUISH_FEATURE_HEIGHT))}}}}}if(cig_op==="X"){seq_offset+=cig_len}base_offset+=cig_len;break;case"N":ctx.fillStyle=CONNECTOR_COLOR;ctx.fillRect(s_start,y_center+5,s_end-s_start,1);base_offset+=cig_len;break;case"D":ctx.fillStyle="black";ctx.fillRect(s_start,y_center+4,s_end-s_start,3);base_offset+=cig_len;break;case"I":var insert_x_coord=s_start-gap;if(is_overlap([seq_start,seq_start+cig_len],tile_region)){var seq=read_seq.slice(seq_offset,seq_offset+cig_len);if(this.prefs.show_insertions){var x_center=s_start-(s_end-s_start)/2;if((mode==="Pack"||this.mode==="Auto")&&read_seq!==undefined&&w_scale>char_width_px){ctx.fillStyle="yellow";ctx.fillRect(x_center-gap,y_center-9,s_end-s_start,9);draw_last[draw_last.length]={type:"triangle",data:[insert_x_coord,y_center+4,5]};ctx.fillStyle=CONNECTOR_COLOR;switch(compute_overlap([seq_start,seq_start+cig_len],tile_region)){case (OVERLAP_START):seq=seq.slice(tile_low-seq_start);break;case (OVERLAP_END):seq=seq.slice(0,seq_start-tile_high);break;case (CONTAINED_BY):break;case (CONTAINS):seq=seq.slice(tile_low-seq_start,seq_start-tile_high);break}for(var c=0,str_len=seq.length;c<str_len;c++){var c_start=Math.floor(Math.max(0,(seq_start+c-tile_low)*w_scale));ctx.fillText(seq[c],c_start-(s_end-s_start)/2,y_center)}}else{ctx.fillStyle="yellow";ctx.fillRect(x_center,y_center+(this.mode!=="Dense"?2:5),s_end-s_start,(mode!=="Dense"?SQUISH_FEATURE_HEIGHT:DENSE_FEATURE_HEIGHT))}}else{if((mode==="Pack"||this.mode==="Auto")&&read_seq!==undefined&&w_scale>char_width_px){draw_last.push({type:"text",data:[seq.length,insert_x_coord,y_center+9]})}else{}}}seq_offset+=cig_len;break}}ctx.fillStyle="yellow";var item,type,data;for(var i=0;i<draw_last.length;i++){item=draw_last[i];type=item.type;data=item.data;if(type==="text"){ctx.save();ctx.font="bold "+ctx.font;ctx.fillText(data[0],data[1],data[2]);ctx.restore()}else{if(type==="triangle"){drawDownwardEquilateralTriangle(ctx,data[0],data[1],data[2])}}}}});var ArcLinkedFeaturePainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler){LinkedFeaturePainter.call(this,data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler);this.longest_feature_length=this.calculate_longest_feature_length();this.draw_background_connector=false;this.draw_individual_connectors=true};extend(ArcLinkedFeaturePainter.prototype,FeaturePainter.prototype,LinkedFeaturePainter.prototype,{calculate_longest_feature_length:function(){var longest_feature_length=0;for(var i=0,len=this.data.length;i<len;i++){var feature=this.data[i],feature_start=feature[1],feature_end=feature[2];longest_feature_length=Math.max(longest_feature_length,feature_end-feature_start)}return longest_feature_length},get_top_padding:function(width){var view_range=this.view_end-this.view_start,w_scale=width/view_range;return Math.min(128,Math.ceil((this.longest_feature_length/2)*w_scale))},draw_connector:function(ctx,block1_start,block1_end,block2_start,block2_end,y_center){var x_center=(block1_end+block2_start)/2,radius=block2_start-x_center;var angle1=Math.PI,angle2=0;if(radius>0){ctx.beginPath();ctx.arc(x_center,y_center,block2_start-x_center,Math.PI,0);ctx.stroke()}}});var Color=function(rgb,a){if(Array.isArray(rgb)){this.rgb=rgb}else{if(rgb.length==6){this.rgb=rgb.match(/.{2}/g).map(function(c){return parseInt(c,16)})}else{if(rgb.length==7){this.rgb=rgb.substring(1,7).match(/.{2}/g).map(function(c){return parseInt(c,16)})}else{this.rgb=rgb.split("").map(function(c){return parseInt(c+c,16)})}}}this.alpha=typeof(a)==="number"?a:1};Color.prototype={eval:function(){return this},toCSS:function(){if(this.alpha<1){return"rgba("+this.rgb.map(function(c){return Math.round(c)}).concat(this.alpha).join(", ")+")"}else{return"#"+this.rgb.map(function(i){i=Math.round(i);i=(i>255?255:(i<0?0:i)).toString(16);return i.length===1?"0"+i:i}).join("")}},toHSL:function(){var r=this.rgb[0]/255,g=this.rgb[1]/255,b=this.rgb[2]/255,a=this.alpha;var max=Math.max(r,g,b),min=Math.min(r,g,b);var h,s,l=(max+min)/2,d=max-min;if(max===min){h=s=0}else{s=l>0.5?d/(2-max-min):d/(max+min);switch(max){case r:h=(g-b)/d+(g<b?6:0);break;case g:h=(b-r)/d+2;break;case b:h=(r-g)/d+4;break}h/=6}return{h:h*360,s:s,l:l,a:a}},toARGB:function(){var argb=[Math.round(this.alpha*255)].concat(this.rgb);return"#"+argb.map(function(i){i=Math.round(i);i=(i>255?255:(i<0?0:i)).toString(16);return i.length===1?"0"+i:i}).join("")},mix:function(color2,weight){color1=this;var p=weight;var w=p*2-1;var a=color1.toHSL().a-color2.toHSL().a;var w1=(((w*a==-1)?w:(w+a)/(1+w*a))+1)/2;var w2=1-w1;var rgb=[color1.rgb[0]*w1+color2.rgb[0]*w2,color1.rgb[1]*w1+color2.rgb[1]*w2,color1.rgb[2]*w1+color2.rgb[2]*w2];var alpha=color1.alpha*p+color2.alpha*(1-p);return new Color(rgb,alpha)}};var LinearRamp=function(start_color,end_color,start_value,end_value){this.start_color=new Color(start_color);this.end_color=new Color(end_color);this.start_value=start_value;this.end_value=end_value;this.value_range=end_value-start_value};LinearRamp.prototype.map_value=function(value){value=Math.max(value,this.start_value);value=Math.min(value,this.end_value);value=(value-this.start_value)/this.value_range;return this.start_color.mix(this.end_color,1-value).toCSS()};var SplitRamp=function(start_color,middle_color,end_color,start_value,end_value){this.positive_ramp=new LinearRamp(middle_color,end_color,0,end_value);this.negative_ramp=new LinearRamp(middle_color,start_color,0,-start_value);this.start_value=start_value;this.end_value=end_value};SplitRamp.prototype.map_value=function(value){value=Math.max(value,this.start_value);value=Math.min(value,this.end_value);if(value>=0){return this.positive_ramp.map_value(value)}else{return this.negative_ramp.map_value(-value)}};var DiagonalHeatmapPainter=function(data,view_start,view_end,prefs,mode){Painter.call(this,data,view_start,view_end,prefs,mode);var i,len;if(this.prefs.min_value===undefined){var min_value=Infinity;for(i=0,len=this.data.length;i<len;i++){min_value=Math.min(min_value,this.data[i][5])}this.prefs.min_value=min_value}if(this.prefs.max_value===undefined){var max_value=-Infinity;for(i=0,len=this.data.length;i<len;i++){max_value=Math.max(max_value,this.data[i][5])}this.prefs.max_value=max_value}};DiagonalHeatmapPainter.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Heatmap",pos_color:"#FF8C00",neg_color:"#4169E1"};DiagonalHeatmapPainter.prototype.draw=function(ctx,width,height,w_scale){var min_value=this.prefs.min_value,max_value=this.prefs.max_value,value_range=max_value-min_value,height_px=height,view_start=this.view_start,mode=this.mode,data=this.data,invsqrt2=1/Math.sqrt(2);var ramp=(new SplitRamp(this.prefs.neg_color,"#FFFFFF",this.prefs.pos_color,min_value,max_value));var d,s1,e1,s2,e2,value;var scale=function(p){return(p-view_start)*w_scale};ctx.save();ctx.rotate(-45*Math.PI/180);ctx.scale(invsqrt2,invsqrt2);for(var i=0,len=data.length;i<len;i++){d=data[i];s1=scale(d[1]);e1=scale(d[2]);s2=scale(d[4]);e2=scale(d[5]);value=d[6];ctx.fillStyle=(ramp.map_value(value));ctx.fillRect(s1,s2,(e1-s1),(e2-s2))}ctx.restore()};var VariantPainter=function(data,view_start,view_end,prefs,mode,base_color_fn){Painter.call(this,data,view_start,view_end,prefs,mode);this.base_color_fn=base_color_fn;this.divider_height=1};extend(VariantPainter.prototype,Painter.prototype,{get_row_height:function(){var mode=this.mode,height;if(mode==="Dense"){height=DENSE_TRACK_HEIGHT}else{if(mode==="Squish"){height=SQUISH_TRACK_HEIGHT}else{height=PACK_TRACK_HEIGHT}}return height},get_required_height:function(num_samples){var height=this.prefs.summary_height;if(this.prefs.show_sample_data){height+=this.divider_height+num_samples*this.get_row_height()}return height},draw:function(ctx,width,height,w_scale){ctx.save();var locus_data,pos,id,ref,alt,qual,filter,sample_gts,allele_counts,variant,draw_x_start,char_x_start,draw_y_start,genotype,base_px=Math.max(1,Math.floor(w_scale)),row_height=(this.mode==="Squish"?SQUISH_TRACK_HEIGHT:PACK_TRACK_HEIGHT),feature_height=(w_scale<0.1?row_height:(this.mode==="Squish"?SQUISH_FEATURE_HEIGHT:PACK_FEATURE_HEIGHT)),j;if(this.prefs.show_sample_data){ctx.fillStyle="#F3F3F3";ctx.globalAlpha=1;ctx.fillRect(0,this.prefs.summary_height-this.divider_height,width,this.divider_height)}ctx.textAlign="center";for(var i=0;i<this.data.length;i++){locus_data=this.data[i];pos=locus_data[1];alt=locus_data[4].split(",");sample_gts=locus_data[7].split(",");allele_counts=locus_data.slice(8);if(pos<this.view_start||pos>this.view_end){continue}draw_x_start=Math.floor(Math.max(-0.5*w_scale,(pos-this.view_start-0.5)*w_scale));char_x_start=Math.floor(Math.max(0,(pos-this.view_start)*w_scale));ctx.fillStyle="#999999";ctx.globalAlpha=1;ctx.fillRect(draw_x_start,0,base_px,this.prefs.summary_height);draw_y_start=this.prefs.summary_height;for(j=0;j<alt.length;j++){ctx.fillStyle=this.base_color_fn(alt[j]);allele_frac=allele_counts/sample_gts.length;draw_height=Math.ceil(this.prefs.summary_height*allele_frac);ctx.fillRect(draw_x_start,draw_y_start-draw_height,base_px,draw_height);draw_y_start-=draw_height}if(!this.prefs.show_sample_data){continue}draw_y_start=this.prefs.summary_height+this.divider_height;for(j=0;j<sample_gts.length;j++,draw_y_start+=row_height){genotype=(sample_gts[j]?sample_gts[j].split(/\/|\|/):["0","0"]);variant=null;if(genotype[0]===genotype[1]){if(genotype[0]==="."){}else{if(genotype[0]!=="0"){variant=alt[parseInt(genotype[0],10)-1];ctx.globalAlpha=1}}}else{variant=(genotype[0]!=="0"?genotype[0]:genotype[1]);variant=alt[parseInt(variant,10)-1];ctx.globalAlpha=0.5}if(variant){ctx.fillStyle=this.base_color_fn(variant);if(this.mode==="Squish"||w_scale<ctx.canvas.manager.char_width_px){ctx.fillRect(draw_x_start,draw_y_start+1,base_px,feature_height)}else{ctx.fillText(variant,char_x_start,draw_y_start+row_height)}}}}ctx.restore()}});return{Scaler:Scaler,LinePainter:LinePainter,LinkedFeaturePainter:LinkedFeaturePainter,ReadPainter:ReadPainter,RefBasedReadPainter:RefBasedReadPainter,ArcLinkedFeaturePainter:ArcLinkedFeaturePainter,DiagonalHeatmapPainter:DiagonalHeatmapPainter,VariantPainter:VariantPainter}}); \ No newline at end of file +define(["libs/underscore"],function(_){var extend=_.extend;var BEFORE=1001,CONTAINS=1002,OVERLAP_START=1003,OVERLAP_END=1004,CONTAINED_BY=1005,AFTER=1006;var compute_overlap=function(first_region,second_region){var first_start=first_region[0],first_end=first_region[1],second_start=second_region[0],second_end=second_region[1],overlap;if(first_start<second_start){if(first_end<=second_start){overlap=BEFORE}else{if(first_end<=second_end){overlap=OVERLAP_START}else{overlap=CONTAINS}}}else{if(first_start>second_end){overlap=AFTER}else{if(first_end<=second_end){overlap=CONTAINED_BY}else{overlap=OVERLAP_END}}}return overlap};var is_overlap=function(first_region,second_region){var overlap=compute_overlap(first_region,second_region);return(overlap!==BEFORE&&overlap!==AFTER)};var dashedLine=function(ctx,x1,y1,x2,y2,dashLen){if(dashLen===undefined){dashLen=4}var dX=x2-x1;var dY=y2-y1;var dashes=Math.floor(Math.sqrt(dX*dX+dY*dY)/dashLen);var dashX=dX/dashes;var dashY=dY/dashes;var q;for(q=0;q<dashes;q++,x1+=dashX,y1+=dashY){if(q%2!==0){continue}ctx.fillRect(x1,y1,dashLen,1)}};var drawDownwardEquilateralTriangle=function(ctx,down_vertex_x,down_vertex_y,side_len){var x1=down_vertex_x-side_len/2,x2=down_vertex_x+side_len/2,y=down_vertex_y-Math.sqrt(side_len*3/2);ctx.beginPath();ctx.moveTo(x1,y);ctx.lineTo(x2,y);ctx.lineTo(down_vertex_x,down_vertex_y);ctx.lineTo(x1,y);ctx.strokeStyle=this.fillStyle;ctx.fill();ctx.stroke();ctx.closePath()};var Scaler=function(default_val){this.default_val=(default_val?default_val:1)};Scaler.prototype.gen_val=function(input){return this.default_val};var Painter=function(data,view_start,view_end,prefs,mode){this.data=data;this.view_start=view_start;this.view_end=view_end;this.prefs=extend({},this.default_prefs,prefs);this.mode=mode};Painter.prototype.default_prefs={};Painter.prototype.draw=function(ctx,width,height,w_scale){};var LinePainter=function(data,view_start,view_end,prefs,mode){Painter.call(this,data,view_start,view_end,prefs,mode);if(this.prefs.min_value===undefined){this.prefs.min_value=_.min(_.map(this.data,function(d){return d[1]}))||0}if(this.prefs.max_value===undefined){this.prefs.max_value=_.max(_.map(this.data,function(d){return d[1]}))||0}};LinePainter.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Histogram",color:"#000",overflow_color:"#F66"};LinePainter.prototype.draw=function(ctx,width,height,w_scale){var in_path=false,min_value=this.prefs.min_value,max_value=this.prefs.max_value,vertical_range=max_value-min_value,height_px=height,view_start=this.view_start,mode=this.mode,data=this.data;ctx.save();var y_zero=Math.round(height+min_value/vertical_range*height);if(mode!=="Intensity"){ctx.fillStyle="#aaa";ctx.fillRect(0,y_zero,width,1)}ctx.beginPath();var x_scaled,y,delta_x_px;if(data.length>1){delta_x_px=Math.ceil((data[1][0]-data[0][0])*w_scale)}else{delta_x_px=10}var painter_color=this.prefs.block_color||this.prefs.color,pref_color=parseInt(painter_color.slice(1),16),pref_r=(pref_color&16711680)>>16,pref_g=(pref_color&65280)>>8,pref_b=pref_color&255,top_overflow=false,bot_overflow=false;for(var i=0,len=data.length;i<len;i++){ctx.fillStyle=ctx.strokeStyle=painter_color;top_overflow=bot_overflow=false;x_scaled=Math.round((data[i][0]-view_start)*w_scale);y=data[i][1];if(y===null){if(in_path&&mode==="Filled"){ctx.lineTo(x_scaled,height_px)}in_path=false;continue}if(y<min_value){bot_overflow=true;y=min_value}else{if(y>max_value){top_overflow=true;y=max_value}}if(mode==="Histogram"){y=Math.round(y/vertical_range*height_px);ctx.fillRect(x_scaled,y_zero,delta_x_px,-y)}else{if(mode==="Intensity"){var saturation=(y-min_value)/vertical_range,new_r=Math.round(pref_r+(255-pref_r)*(1-saturation)),new_g=Math.round(pref_g+(255-pref_g)*(1-saturation)),new_b=Math.round(pref_b+(255-pref_b)*(1-saturation));ctx.fillStyle="rgb("+new_r+","+new_g+","+new_b+")";ctx.fillRect(x_scaled,0,delta_x_px,height_px)}else{y=Math.round(height_px-(y-min_value)/vertical_range*height_px);if(in_path){ctx.lineTo(x_scaled,y)}else{in_path=true;if(mode==="Filled"){ctx.moveTo(x_scaled,height_px);ctx.lineTo(x_scaled,y)}else{ctx.moveTo(x_scaled,y)}}}}ctx.fillStyle=this.prefs.overflow_color;if(top_overflow||bot_overflow){var overflow_x;if(mode==="Histogram"||mode==="Intensity"){overflow_x=delta_x_px}else{x_scaled-=2;overflow_x=4}if(top_overflow){ctx.fillRect(x_scaled,0,overflow_x,3)}if(bot_overflow){ctx.fillRect(x_scaled,height_px-3,overflow_x,3)}}ctx.fillStyle=painter_color}if(mode==="Filled"){if(in_path){ctx.lineTo(x_scaled,y_zero);ctx.lineTo(0,y_zero)}ctx.fill()}else{ctx.stroke()}ctx.restore()};var FeaturePositionMapper=function(slot_height){this.feature_positions={};this.slot_height=slot_height;this.translation=0;this.y_translation=0};FeaturePositionMapper.prototype.map_feature_data=function(feature_data,slot,x_start,x_end){if(!this.feature_positions[slot]){this.feature_positions[slot]=[]}this.feature_positions[slot].push({data:feature_data,x_start:x_start,x_end:x_end})};FeaturePositionMapper.prototype.get_feature_data=function(x,y){var slot=Math.floor((y-this.y_translation)/this.slot_height),feature_dict;if(!this.feature_positions[slot]){return null}x+=this.translation;for(var i=0;i<this.feature_positions[slot].length;i++){feature_dict=this.feature_positions[slot][i];if(x>=feature_dict.x_start&&x<=feature_dict.x_end){return feature_dict.data}}};var FeaturePainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler){Painter.call(this,data,view_start,view_end,prefs,mode);this.alpha_scaler=(alpha_scaler?alpha_scaler:new Scaler());this.height_scaler=(height_scaler?height_scaler:new Scaler())};FeaturePainter.prototype.default_prefs={block_color:"#FFF",connector_color:"#FFF"};extend(FeaturePainter.prototype,{get_required_height:function(rows_required,width){var required_height=this.get_row_height(),y_scale=required_height,mode=this.mode;if(mode==="no_detail"||mode==="Squish"||mode==="Pack"){required_height=rows_required*y_scale}return required_height+this.get_top_padding(width)+this.get_bottom_padding(width)},get_top_padding:function(width){return 0},get_bottom_padding:function(width){return Math.max(Math.round(this.get_row_height()/2),5)},draw:function(ctx,width,height,w_scale,slots){var data=this.data,view_start=this.view_start,view_end=this.view_end;ctx.save();ctx.fillStyle=this.prefs.block_color;ctx.textAlign="right";var y_scale=this.get_row_height(),feature_mapper=new FeaturePositionMapper(y_scale),x_draw_coords;for(var i=0,len=data.length;i<len;i++){var feature=data[i],feature_uid=feature[0],feature_start=feature[1],feature_end=feature[2],slot=(slots&&slots[feature_uid]!==undefined?slots[feature_uid]:null);if((feature_start<view_end&&feature_end>view_start)&&(this.mode==="Dense"||slot!==null)){x_draw_coords=this.draw_element(ctx,this.mode,feature,slot,view_start,view_end,w_scale,y_scale,width);feature_mapper.map_feature_data(feature,slot,x_draw_coords[0],x_draw_coords[1])}}ctx.restore();feature_mapper.y_translation=this.get_top_padding(width);return feature_mapper},draw_element:function(ctx,mode,feature,slot,tile_low,tile_high,w_scale,y_scale,width){return[0,0]}});var DENSE_TRACK_HEIGHT=10,NO_DETAIL_TRACK_HEIGHT=3,SQUISH_TRACK_HEIGHT=5,PACK_TRACK_HEIGHT=10,NO_DETAIL_FEATURE_HEIGHT=1,DENSE_FEATURE_HEIGHT=9,SQUISH_FEATURE_HEIGHT=3,PACK_FEATURE_HEIGHT=9,LABEL_SPACING=2,CONNECTOR_COLOR="#ccc";var LinkedFeaturePainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler){FeaturePainter.call(this,data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler);this.draw_background_connector=true;this.draw_individual_connectors=false};extend(LinkedFeaturePainter.prototype,FeaturePainter.prototype,{get_row_height:function(){var mode=this.mode,height;if(mode==="Dense"){height=DENSE_TRACK_HEIGHT}else{if(mode==="no_detail"){height=NO_DETAIL_TRACK_HEIGHT}else{if(mode==="Squish"){height=SQUISH_TRACK_HEIGHT}else{height=PACK_TRACK_HEIGHT}}}return height},draw_element:function(ctx,mode,feature,slot,tile_low,tile_high,w_scale,y_scale,width){var feature_uid=feature[0],feature_start=feature[1],feature_end=feature[2],feature_name=feature[3],feature_strand=feature[4],f_start=Math.floor(Math.max(0,(feature_start-tile_low-0.5)*w_scale)),f_end=Math.ceil(Math.min(width,Math.max(0,(feature_end-tile_low-0.5)*w_scale))),draw_start=f_start,draw_end=f_end,y_center=(mode==="Dense"?0:(0+slot))*y_scale+this.get_top_padding(width),thickness,y_start,thick_start=null,thick_end=null,block_color=(!feature_strand||feature_strand==="+"||feature_strand==="."?this.prefs.block_color:this.prefs.reverse_strand_color);label_color=this.prefs.label_color;ctx.globalAlpha=this.alpha_scaler.gen_val(feature);if(mode==="Dense"){slot=1}if(mode==="no_detail"){ctx.fillStyle=block_color;ctx.fillRect(f_start,y_center+5,f_end-f_start,NO_DETAIL_FEATURE_HEIGHT)}else{var feature_ts=feature[5],feature_te=feature[6],feature_blocks=feature[7],full_height=true;if(feature_ts&&feature_te){thick_start=Math.floor(Math.max(0,(feature_ts-tile_low)*w_scale));thick_end=Math.ceil(Math.min(width,Math.max(0,(feature_te-tile_low)*w_scale)))}var thin_height,thick_height;if(mode==="Squish"){thin_height=1;thick_height=SQUISH_FEATURE_HEIGHT;full_height=false}else{if(mode==="Dense"){thin_height=5;thick_height=DENSE_FEATURE_HEIGHT}else{thin_height=5;thick_height=PACK_FEATURE_HEIGHT}}if(!feature_blocks){ctx.fillStyle=block_color;ctx.fillRect(f_start,y_center+1,f_end-f_start,thick_height);if(feature_strand&&full_height){if(feature_strand==="+"){ctx.fillStyle=ctx.canvas.manager.get_pattern("right_strand_inv")}else{if(feature_strand==="-"){ctx.fillStyle=ctx.canvas.manager.get_pattern("left_strand_inv")}}ctx.fillRect(f_start,y_center+1,f_end-f_start,thick_height)}}else{var cur_y_center,cur_height;if(mode==="Squish"||mode==="Dense"){cur_y_center=y_center+Math.floor(SQUISH_FEATURE_HEIGHT/2)+1;cur_height=1}else{if(feature_strand){cur_y_center=y_center;cur_height=thick_height}else{cur_y_center+=(SQUISH_FEATURE_HEIGHT/2)+1;cur_height=1}}if(this.draw_background_connector){if(mode==="Squish"||mode==="Dense"){ctx.fillStyle=CONNECTOR_COLOR}else{if(feature_strand){if(feature_strand==="+"){ctx.fillStyle=ctx.canvas.manager.get_pattern("right_strand")}else{if(feature_strand==="-"){ctx.fillStyle=ctx.canvas.manager.get_pattern("left_strand")}}}else{ctx.fillStyle=CONNECTOR_COLOR}}ctx.fillRect(f_start,cur_y_center,f_end-f_start,cur_height)}var start_and_height;for(var k=0,k_len=feature_blocks.length;k<k_len;k++){var block=feature_blocks[k],block_start=Math.floor(Math.max(0,(block[0]-tile_low-0.5)*w_scale)),block_end=Math.ceil(Math.min(width,Math.max((block[1]-tile_low-0.5)*w_scale))),last_block_start,last_block_end;if(block_start>block_end){continue}ctx.fillStyle=block_color;ctx.fillRect(block_start,y_center+(thick_height-thin_height)/2+1,block_end-block_start,thin_height);if(thick_start!==undefined&&feature_te>feature_ts&&!(block_start>thick_end||block_end<thick_start)){var block_thick_start=Math.max(block_start,thick_start),block_thick_end=Math.min(block_end,thick_end);ctx.fillRect(block_thick_start,y_center+1,block_thick_end-block_thick_start,thick_height);if(feature_blocks.length===1&&mode==="Pack"){if(feature_strand==="+"){ctx.fillStyle=ctx.canvas.manager.get_pattern("right_strand_inv")}else{if(feature_strand==="-"){ctx.fillStyle=ctx.canvas.manager.get_pattern("left_strand_inv")}}if(block_thick_start+14<block_thick_end){block_thick_start+=2;block_thick_end-=2}ctx.fillRect(block_thick_start,y_center+1,block_thick_end-block_thick_start,thick_height)}}if(this.draw_individual_connectors&&last_block_start){this.draw_connector(ctx,last_block_start,last_block_end,block_start,block_end,y_center)}last_block_start=block_start;last_block_end=block_end}if(mode==="Pack"){ctx.globalAlpha=1;ctx.fillStyle="white";var hscale_factor=this.height_scaler.gen_val(feature),new_height=Math.ceil(thick_height*hscale_factor),ws_height=Math.round((thick_height-new_height)/2);if(hscale_factor!==1){ctx.fillRect(f_start,cur_y_center+1,f_end-f_start,ws_height);ctx.fillRect(f_start,cur_y_center+thick_height-ws_height+1,f_end-f_start,ws_height)}}}ctx.globalAlpha=1;if(feature_name&&mode==="Pack"&&feature_start>tile_low){ctx.fillStyle=label_color;if(tile_low===0&&f_start-ctx.measureText(feature_name).width<0){ctx.textAlign="left";ctx.fillText(feature_name,f_end+LABEL_SPACING,y_center+8);draw_end+=ctx.measureText(feature_name).width+LABEL_SPACING}else{ctx.textAlign="right";ctx.fillText(feature_name,f_start-LABEL_SPACING,y_center+8);draw_start-=ctx.measureText(feature_name).width+LABEL_SPACING}}}ctx.globalAlpha=1;return[draw_start,draw_end]}});var ReadPainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler,ref_seq,base_color_fn){FeaturePainter.call(this,data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler);this.ref_seq=(ref_seq?ref_seq.data:null);this.base_color_fn=base_color_fn};extend(ReadPainter.prototype,FeaturePainter.prototype,{get_row_height:function(){var height,mode=this.mode;if(mode==="Dense"){height=DENSE_TRACK_HEIGHT}else{if(mode==="Squish"){height=SQUISH_TRACK_HEIGHT}else{height=PACK_TRACK_HEIGHT;if(this.prefs.show_insertions){height*=2}}}return height},_parse_cigar:function(cigar_str){var cigar_ops="MIDNSHP=X";var blocks=[[0,0]],cur_block=blocks[0],base_pos=0,parsed_cigar=_.map(cigar_str.match(/[0-9]+[MIDNSHP=X]/g),function(op){var op_len=parseInt(op.slice(0,-1),10),op_char=op.slice(-1);if(op_char==="N"){if(cur_block[1]!==0){cur_block=[base_pos+op_len,base_pos+op_len];blocks.push(cur_block)}}else{if("ISHP".indexOf(op_char)===-1){cur_block[1]+=op_len;base_pos+=op_len}}return[cigar_ops.indexOf(op_char),op_len]});return{blocks:blocks,cigar:parsed_cigar}},draw_read:function(ctx,mode,w_scale,y_center,tile_low,tile_high,feature_start,cigar,strand,read_seq){ctx.textAlign="center";var tile_region=[tile_low,tile_high],base_offset=0,seq_offset=0,gap=Math.round(w_scale/2),char_width_px=ctx.canvas.manager.char_width_px,block_color=(strand==="+"?this.prefs.block_color:this.prefs.reverse_strand_color),pack_mode=(mode==="Pack");var draw_last=[];if(!cigar){cigar=[[0,read_seq.length]]}for(var cig_id=0,len=cigar.length;cig_id<len;cig_id++){var cig=cigar[cig_id],cig_op="MIDNSHP=X"[cig[0]],cig_len=cig[1];var seq_start=feature_start+base_offset,s_start=Math.floor(Math.max(-0.5*w_scale,(seq_start-tile_low-0.5)*w_scale)),s_end=Math.floor(Math.max(0,(seq_start+cig_len-tile_low-0.5)*w_scale));if(s_start===s_end){s_end+=1}switch(cig_op){case"H":break;case"S":seq_offset+=cig_len;break;case"M":case"=":case"X":if(is_overlap([seq_start,seq_start+cig_len],tile_region)){ctx.fillStyle=block_color;ctx.fillRect(s_start,y_center+(pack_mode?1:4),s_end-s_start,(pack_mode?PACK_FEATURE_HEIGHT:SQUISH_FEATURE_HEIGHT));var seq=read_seq.slice(seq_offset,seq_offset+cig_len),ref_char,read_char;for(var c=0,str_len=seq.length;c<str_len;c++){if(seq_start+c>=tile_low&&seq_start+c<=tile_high){ref_char=(this.ref_seq?this.ref_seq[seq_start-tile_low+c]:null);read_char=seq[c];if((ref_char&&(!this.prefs.show_differences||(read_char.toLowerCase!=="n"&&(ref_char.toLowerCase()!==read_char.toLowerCase()))))||(!ref_char&&!this.prefs.show_differences)){var c_start=Math.floor(Math.max(0,(seq_start+c-tile_low)*w_scale));ctx.fillStyle=this.base_color_fn(seq[c]);if(pack_mode&&w_scale>char_width_px){ctx.fillText(seq[c],c_start,y_center+9)}else{if(w_scale>0.05){ctx.fillRect(c_start-gap,y_center+(pack_mode?1:4),Math.max(1,Math.round(w_scale)),(pack_mode?PACK_FEATURE_HEIGHT:SQUISH_FEATURE_HEIGHT))}}}}}}seq_offset+=cig_len;base_offset+=cig_len;break;case"N":ctx.fillStyle=CONNECTOR_COLOR;ctx.fillRect(s_start,y_center+5,s_end-s_start,1);base_offset+=cig_len;break;case"D":ctx.fillStyle="black";ctx.fillRect(s_start,y_center+4,s_end-s_start,3);base_offset+=cig_len;break;case"P":break;case"I":var insert_x_coord=s_start-gap;if(is_overlap([seq_start,seq_start+cig_len],tile_region)){var seq=read_seq.slice(seq_offset,seq_offset+cig_len);if(this.prefs.show_insertions){var x_center=s_start-(s_end-s_start)/2;if((mode==="Pack"||this.mode==="Auto")&&read_seq!==undefined&&w_scale>char_width_px){ctx.fillStyle="yellow";ctx.fillRect(x_center-gap,y_center-9,s_end-s_start,9);draw_last[draw_last.length]={type:"triangle",data:[insert_x_coord,y_center+4,5]};ctx.fillStyle=CONNECTOR_COLOR;switch(compute_overlap([seq_start,seq_start+cig_len],tile_region)){case (OVERLAP_START):seq=seq.slice(tile_low-seq_start);break;case (OVERLAP_END):seq=seq.slice(0,seq_start-tile_high);break;case (CONTAINED_BY):break;case (CONTAINS):seq=seq.slice(tile_low-seq_start,seq_start-tile_high);break}for(var c=0,str_len=seq.length;c<str_len;c++){var c_start=Math.floor(Math.max(0,(seq_start+c-tile_low)*w_scale));ctx.fillText(seq[c],c_start-(s_end-s_start)/2,y_center)}}else{ctx.fillStyle="yellow";ctx.fillRect(x_center,y_center+(this.mode!=="Dense"?2:5),s_end-s_start,(mode!=="Dense"?SQUISH_FEATURE_HEIGHT:DENSE_FEATURE_HEIGHT))}}else{if((mode==="Pack"||this.mode==="Auto")&&read_seq!==undefined&&w_scale>char_width_px){draw_last.push({type:"text",data:[seq.length,insert_x_coord,y_center+9]})}else{}}}seq_offset+=cig_len;break}}ctx.fillStyle="yellow";var item,type,data;for(var i=0;i<draw_last.length;i++){item=draw_last[i];type=item.type;data=item.data;if(type==="text"){ctx.save();ctx.font="bold "+ctx.font;ctx.fillText(data[0],data[1],data[2]);ctx.restore()}else{if(type==="triangle"){drawDownwardEquilateralTriangle(ctx,data[0],data[1],data[2])}}}},draw_element:function(ctx,mode,feature,slot,tile_low,tile_high,w_scale,y_scale,width){var feature_uid=feature[0],feature_start=feature[1],feature_end=feature[2],feature_name=feature[3],f_start=Math.floor(Math.max(-0.5*w_scale,(feature_start-tile_low-0.5)*w_scale)),f_end=Math.ceil(Math.min(width,Math.max(0,(feature_end-tile_low-0.5)*w_scale))),y_center=(mode==="Dense"?0:(0+slot))*y_scale,label_color=this.prefs.label_color;if(feature[5] instanceof Array){var b1_start=Math.floor(Math.max(0,(feature[4][0]-tile_low)*w_scale)),b1_end=Math.ceil(Math.min(width,Math.max(0,(feature[4][1]-tile_low)*w_scale))),b2_start=Math.floor(Math.max(0,(feature[5][0]-tile_low)*w_scale)),b2_end=Math.ceil(Math.min(width,Math.max(0,(feature[5][1]-tile_low)*w_scale))),connector=true;if(feature[4][1]>=tile_low&&feature[4][0]<=tile_high&&feature[4][2]){this.draw_read(ctx,mode,w_scale,y_center,tile_low,tile_high,feature[4][0],feature[4][2],feature[4][3],feature[4][4])}else{connector=false}if(feature[5][1]>=tile_low&&feature[5][0]<=tile_high&&feature[5][2]){this.draw_read(ctx,mode,w_scale,y_center,tile_low,tile_high,feature[5][0],feature[5][2],feature[5][3],feature[5][4])}else{connector=false}if(connector&&b2_start>b1_end){ctx.fillStyle=CONNECTOR_COLOR;dashedLine(ctx,b1_end,y_center+5,b2_start,y_center+5)}}else{this.draw_read(ctx,mode,w_scale,y_center,tile_low,tile_high,feature_start,feature[4],feature[5],feature[6])}if(mode==="Pack"&&feature_start>=tile_low&&feature_name!=="."){ctx.fillStyle=this.prefs.label_color;if(tile_low===0&&f_start-ctx.measureText(feature_name).width<0){ctx.textAlign="left";ctx.fillText(feature_name,f_end+LABEL_SPACING,y_center+8)}else{ctx.textAlign="right";ctx.fillText(feature_name,f_start-LABEL_SPACING,y_center+8)}}return[0,0]}});var RefBasedReadPainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler,ref_seq,base_color_fn){ReadPainter.call(this,data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler,ref_seq,base_color_fn)};extend(RefBasedReadPainter.prototype,ReadPainter.prototype,FeaturePainter,{draw_read:function(ctx,mode,w_scale,y_center,tile_low,tile_high,feature_start,cigar,strand,read_seq){ctx.textAlign="center";var tile_region=[tile_low,tile_high],base_offset=0,seq_offset=0,gap=Math.round(w_scale/2),char_width_px=ctx.canvas.manager.char_width_px,block_color=(strand==="+"?this.prefs.block_color:this.prefs.reverse_strand_color),pack_mode=(mode==="Pack"),drawing_blocks=[];var draw_last=[];var t=this._parse_cigar(cigar);cigar=t.cigar;drawing_blocks=t.blocks;for(var i=0;i<drawing_blocks.length;i++){var block=drawing_blocks[i];if(is_overlap([feature_start+block[0],feature_start+block[1]],tile_region)){var s_start=Math.floor(Math.max(-0.5*w_scale,(feature_start+block[0]-tile_low-0.5)*w_scale)),s_end=Math.floor(Math.max(0,(feature_start+block[1]-tile_low-0.5)*w_scale));if(s_start===s_end){s_end+=1}ctx.fillStyle=block_color;ctx.fillRect(s_start,y_center+(pack_mode?1:4),s_end-s_start,(pack_mode?PACK_FEATURE_HEIGHT:SQUISH_FEATURE_HEIGHT))}}for(var cig_id=0,len=cigar.length;cig_id<len;cig_id++){var cig=cigar[cig_id],cig_op="MIDNSHP=X"[cig[0]],cig_len=cig[1];var seq_start=feature_start+base_offset,s_start=Math.floor(Math.max(0,-0.5*w_scale,(seq_start-tile_low-0.5)*w_scale)),s_end=Math.floor(Math.max(0,(seq_start+cig_len-tile_low-0.5)*w_scale));if(s_start===s_end){s_end+=1}switch(cig_op){case"H":case"S":case"P":break;case"M":base_offset+=cig_len;break;case"=":case"X":if(is_overlap([seq_start,seq_start+cig_len],tile_region)){var cur_seq="";if(cig_op==="X"){cur_seq=read_seq.slice(seq_offset,seq_offset+cig_len)}else{if(this.ref_seq){cur_seq=this.ref_seq.slice(Math.max(0,seq_start-tile_low),Math.min(seq_start-tile_low+cig_len,tile_high-tile_low))}}var start_pos=Math.max(seq_start,tile_low);for(var c=0;c<cur_seq.length;c++){if(cur_seq&&!this.prefs.show_differences||cig_op==="X"){var c_start=Math.floor(Math.max(0,(start_pos+c-tile_low)*w_scale));ctx.fillStyle=this.base_color_fn(cur_seq[c]);if(pack_mode&&w_scale>char_width_px){ctx.fillText(cur_seq[c],c_start,y_center+9)}else{if(w_scale>0.05){ctx.fillRect(c_start-gap,y_center+(pack_mode?1:4),Math.max(1,Math.round(w_scale)),(pack_mode?PACK_FEATURE_HEIGHT:SQUISH_FEATURE_HEIGHT))}}}}}if(cig_op==="X"){seq_offset+=cig_len}base_offset+=cig_len;break;case"N":ctx.fillStyle=CONNECTOR_COLOR;ctx.fillRect(s_start,y_center+5,s_end-s_start,1);base_offset+=cig_len;break;case"D":ctx.fillStyle="black";ctx.fillRect(s_start,y_center+4,s_end-s_start,3);base_offset+=cig_len;break;case"I":var insert_x_coord=s_start-gap;if(is_overlap([seq_start,seq_start+cig_len],tile_region)){var seq=read_seq.slice(seq_offset,seq_offset+cig_len);if(this.prefs.show_insertions){var x_center=s_start-(s_end-s_start)/2;if((mode==="Pack"||this.mode==="Auto")&&read_seq!==undefined&&w_scale>char_width_px){ctx.fillStyle="yellow";ctx.fillRect(x_center-gap,y_center-9,s_end-s_start,9);draw_last[draw_last.length]={type:"triangle",data:[insert_x_coord,y_center+4,5]};ctx.fillStyle=CONNECTOR_COLOR;switch(compute_overlap([seq_start,seq_start+cig_len],tile_region)){case (OVERLAP_START):seq=seq.slice(tile_low-seq_start);break;case (OVERLAP_END):seq=seq.slice(0,seq_start-tile_high);break;case (CONTAINED_BY):break;case (CONTAINS):seq=seq.slice(tile_low-seq_start,seq_start-tile_high);break}for(var c=0,str_len=seq.length;c<str_len;c++){var c_start=Math.floor(Math.max(0,(seq_start+c-tile_low)*w_scale));ctx.fillText(seq[c],c_start-(s_end-s_start)/2,y_center)}}else{ctx.fillStyle="yellow";ctx.fillRect(x_center,y_center+(this.mode!=="Dense"?2:5),s_end-s_start,(mode!=="Dense"?SQUISH_FEATURE_HEIGHT:DENSE_FEATURE_HEIGHT))}}else{if((mode==="Pack"||this.mode==="Auto")&&read_seq!==undefined&&w_scale>char_width_px){draw_last.push({type:"text",data:[seq.length,insert_x_coord,y_center+9]})}else{}}}seq_offset+=cig_len;break}}ctx.fillStyle="yellow";var item,type,data;for(var i=0;i<draw_last.length;i++){item=draw_last[i];type=item.type;data=item.data;if(type==="text"){ctx.save();ctx.font="bold "+ctx.font;ctx.fillText(data[0],data[1],data[2]);ctx.restore()}else{if(type==="triangle"){drawDownwardEquilateralTriangle(ctx,data[0],data[1],data[2])}}}}});var ArcLinkedFeaturePainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler){LinkedFeaturePainter.call(this,data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler);this.longest_feature_length=this.calculate_longest_feature_length();this.draw_background_connector=false;this.draw_individual_connectors=true};extend(ArcLinkedFeaturePainter.prototype,FeaturePainter.prototype,LinkedFeaturePainter.prototype,{calculate_longest_feature_length:function(){var longest_feature_length=0;for(var i=0,len=this.data.length;i<len;i++){var feature=this.data[i],feature_start=feature[1],feature_end=feature[2];longest_feature_length=Math.max(longest_feature_length,feature_end-feature_start)}return longest_feature_length},get_top_padding:function(width){var view_range=this.view_end-this.view_start,w_scale=width/view_range;return Math.min(128,Math.ceil((this.longest_feature_length/2)*w_scale))},draw_connector:function(ctx,block1_start,block1_end,block2_start,block2_end,y_center){var x_center=(block1_end+block2_start)/2,radius=block2_start-x_center;var angle1=Math.PI,angle2=0;if(radius>0){ctx.beginPath();ctx.arc(x_center,y_center,block2_start-x_center,Math.PI,0);ctx.stroke()}}});var Color=function(rgb,a){if(Array.isArray(rgb)){this.rgb=rgb}else{if(rgb.length==6){this.rgb=rgb.match(/.{2}/g).map(function(c){return parseInt(c,16)})}else{if(rgb.length==7){this.rgb=rgb.substring(1,7).match(/.{2}/g).map(function(c){return parseInt(c,16)})}else{this.rgb=rgb.split("").map(function(c){return parseInt(c+c,16)})}}}this.alpha=typeof(a)==="number"?a:1};Color.prototype={eval:function(){return this},toCSS:function(){if(this.alpha<1){return"rgba("+this.rgb.map(function(c){return Math.round(c)}).concat(this.alpha).join(", ")+")"}else{return"#"+this.rgb.map(function(i){i=Math.round(i);i=(i>255?255:(i<0?0:i)).toString(16);return i.length===1?"0"+i:i}).join("")}},toHSL:function(){var r=this.rgb[0]/255,g=this.rgb[1]/255,b=this.rgb[2]/255,a=this.alpha;var max=Math.max(r,g,b),min=Math.min(r,g,b);var h,s,l=(max+min)/2,d=max-min;if(max===min){h=s=0}else{s=l>0.5?d/(2-max-min):d/(max+min);switch(max){case r:h=(g-b)/d+(g<b?6:0);break;case g:h=(b-r)/d+2;break;case b:h=(r-g)/d+4;break}h/=6}return{h:h*360,s:s,l:l,a:a}},toARGB:function(){var argb=[Math.round(this.alpha*255)].concat(this.rgb);return"#"+argb.map(function(i){i=Math.round(i);i=(i>255?255:(i<0?0:i)).toString(16);return i.length===1?"0"+i:i}).join("")},mix:function(color2,weight){color1=this;var p=weight;var w=p*2-1;var a=color1.toHSL().a-color2.toHSL().a;var w1=(((w*a==-1)?w:(w+a)/(1+w*a))+1)/2;var w2=1-w1;var rgb=[color1.rgb[0]*w1+color2.rgb[0]*w2,color1.rgb[1]*w1+color2.rgb[1]*w2,color1.rgb[2]*w1+color2.rgb[2]*w2];var alpha=color1.alpha*p+color2.alpha*(1-p);return new Color(rgb,alpha)}};var LinearRamp=function(start_color,end_color,start_value,end_value){this.start_color=new Color(start_color);this.end_color=new Color(end_color);this.start_value=start_value;this.end_value=end_value;this.value_range=end_value-start_value};LinearRamp.prototype.map_value=function(value){value=Math.max(value,this.start_value);value=Math.min(value,this.end_value);value=(value-this.start_value)/this.value_range;return this.start_color.mix(this.end_color,1-value).toCSS()};var SplitRamp=function(start_color,middle_color,end_color,start_value,end_value){this.positive_ramp=new LinearRamp(middle_color,end_color,0,end_value);this.negative_ramp=new LinearRamp(middle_color,start_color,0,-start_value);this.start_value=start_value;this.end_value=end_value};SplitRamp.prototype.map_value=function(value){value=Math.max(value,this.start_value);value=Math.min(value,this.end_value);if(value>=0){return this.positive_ramp.map_value(value)}else{return this.negative_ramp.map_value(-value)}};var DiagonalHeatmapPainter=function(data,view_start,view_end,prefs,mode){Painter.call(this,data,view_start,view_end,prefs,mode);var i,len;if(this.prefs.min_value===undefined){var min_value=Infinity;for(i=0,len=this.data.length;i<len;i++){min_value=Math.min(min_value,this.data[i][5])}this.prefs.min_value=min_value}if(this.prefs.max_value===undefined){var max_value=-Infinity;for(i=0,len=this.data.length;i<len;i++){max_value=Math.max(max_value,this.data[i][5])}this.prefs.max_value=max_value}};DiagonalHeatmapPainter.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Heatmap",pos_color:"#FF8C00",neg_color:"#4169E1"};DiagonalHeatmapPainter.prototype.draw=function(ctx,width,height,w_scale){var min_value=this.prefs.min_value,max_value=this.prefs.max_value,value_range=max_value-min_value,height_px=height,view_start=this.view_start,mode=this.mode,data=this.data,invsqrt2=1/Math.sqrt(2);var ramp=(new SplitRamp(this.prefs.neg_color,"#FFFFFF",this.prefs.pos_color,min_value,max_value));var d,s1,e1,s2,e2,value;var scale=function(p){return(p-view_start)*w_scale};ctx.save();ctx.rotate(-45*Math.PI/180);ctx.scale(invsqrt2,invsqrt2);for(var i=0,len=data.length;i<len;i++){d=data[i];s1=scale(d[1]);e1=scale(d[2]);s2=scale(d[4]);e2=scale(d[5]);value=d[6];ctx.fillStyle=(ramp.map_value(value));ctx.fillRect(s1,s2,(e1-s1),(e2-s2))}ctx.restore()};var VariantPainter=function(data,view_start,view_end,prefs,mode,base_color_fn){Painter.call(this,data,view_start,view_end,prefs,mode);this.base_color_fn=base_color_fn;this.divider_height=1};extend(VariantPainter.prototype,Painter.prototype,{get_row_height:function(){var mode=this.mode,height;if(mode==="Dense"){height=DENSE_TRACK_HEIGHT}else{if(mode==="Squish"){height=SQUISH_TRACK_HEIGHT}else{height=PACK_TRACK_HEIGHT}}return height},get_required_height:function(num_samples){var height=this.prefs.summary_height;if(num_samples>1&&this.prefs.show_sample_data){height+=this.divider_height+num_samples*this.get_row_height()}return height},draw:function(ctx,width,height,w_scale){ctx.save();var locus_data,pos,id,ref,alt,qual,filter,sample_gts,allele_counts,variant,draw_x_start,char_x_start,draw_y_start,genotype,base_px=Math.max(1,Math.floor(w_scale)),num_samples=(this.data.length?this.data[0][7].split(",").length:0),row_height=(this.mode==="Squish"?SQUISH_TRACK_HEIGHT:PACK_TRACK_HEIGHT),feature_height=(w_scale<0.1?row_height:(this.mode==="Squish"?SQUISH_FEATURE_HEIGHT:PACK_FEATURE_HEIGHT)),draw_summary=true,j;if(num_samples===1){row_height=feature_height=(w_scale<ctx.canvas.manager.char_width_px?this.prefs.summary_height:row_height);draw_summary=false}if(this.prefs.show_sample_data&&draw_summary){ctx.fillStyle="#F3F3F3";ctx.globalAlpha=1;ctx.fillRect(0,this.prefs.summary_height-this.divider_height,width,this.divider_height)}ctx.textAlign="center";for(var i=0;i<this.data.length;i++){locus_data=this.data[i];pos=locus_data[1];alt=locus_data[4].split(",");sample_gts=locus_data[7].split(",");allele_counts=locus_data.slice(8);if(pos<this.view_start||pos>this.view_end){continue}draw_x_start=Math.floor(Math.max(-0.5*w_scale,(pos-this.view_start-0.5)*w_scale));char_x_start=Math.floor(Math.max(0,(pos-this.view_start)*w_scale));if(draw_summary){ctx.fillStyle="#999999";ctx.globalAlpha=1;ctx.fillRect(draw_x_start,0,base_px,this.prefs.summary_height);draw_y_start=this.prefs.summary_height;for(j=0;j<alt.length;j++){ctx.fillStyle=this.base_color_fn(alt[j]);allele_frac=allele_counts/sample_gts.length;draw_height=Math.ceil(this.prefs.summary_height*allele_frac);ctx.fillRect(draw_x_start,draw_y_start-draw_height,base_px,draw_height);draw_y_start-=draw_height}}if(!this.prefs.show_sample_data){continue}draw_y_start=(draw_summary?this.prefs.summary_height+this.divider_height:0);for(j=0;j<sample_gts.length;j++,draw_y_start+=row_height){genotype=(sample_gts[j]?sample_gts[j].split(/\/|\|/):["0","0"]);variant=null;if(genotype[0]===genotype[1]){if(genotype[0]==="."){}else{if(genotype[0]!=="0"){variant=alt[parseInt(genotype[0],10)-1];ctx.globalAlpha=1}}}else{variant=(genotype[0]!=="0"?genotype[0]:genotype[1]);variant=alt[parseInt(variant,10)-1];ctx.globalAlpha=0.5}if(variant){ctx.fillStyle=this.base_color_fn(variant);if(this.mode==="Squish"||w_scale<ctx.canvas.manager.char_width_px){ctx.fillRect(draw_x_start,draw_y_start+1,base_px,feature_height)}else{ctx.fillText(variant,char_x_start,draw_y_start+row_height)}}}}ctx.restore()}});return{Scaler:Scaler,LinePainter:LinePainter,LinkedFeaturePainter:LinkedFeaturePainter,ReadPainter:ReadPainter,RefBasedReadPainter:RefBasedReadPainter,ArcLinkedFeaturePainter:ArcLinkedFeaturePainter,DiagonalHeatmapPainter:DiagonalHeatmapPainter,VariantPainter:VariantPainter}}); \ No newline at end of file diff -r 78eaaca131e3251ba9cc78f7546ace6a713a4f02 -r f76c280cdee539b65315ac583f93bfa52feb790d static/scripts/packed/viz/trackster/tracks.js --- a/static/scripts/packed/viz/trackster/tracks.js +++ b/static/scripts/packed/viz/trackster/tracks.js @@ -1,1 +1,1 @@ -define(["libs/underscore","viz/visualization","viz/trackster/util","viz/trackster/slotting","viz/trackster/painters","viz/trackster/filters","mvc/data","mvc/tools"],function(ac,w,j,s,L,h,X,R){var o=ac.extend;var l={};var i=function(ad,ae){l[ad.attr("id")]=ae};var k=function(ad,af,ah,ag){ah=".group";var ae={};l[ad.attr("id")]=ag;ad.bind("drag",{handle:"."+af,relative:true},function(ap,aq){var ao=$(this),au=$(this).parent(),al=au.children(),an=l[$(this).attr("id")],ak,aj,ar,ai,am;aj=$(this).parents(ah);if(aj.length!==0){ar=aj.position().top;ai=ar+aj.outerHeight();if(aq.offsetY<ar){$(this).insertBefore(aj);var at=l[aj.attr("id")];at.remove_drawable(an);at.container.add_drawable_before(an,at);return}else{if(aq.offsetY>ai){$(this).insertAfter(aj);var at=l[aj.attr("id")];at.remove_drawable(an);at.container.add_drawable(an);return}}}aj=null;for(am=0;am<al.length;am++){ak=$(al.get(am));ar=ak.position().top;ai=ar+ak.outerHeight();if(ak.is(ah)&&this!==ak.get(0)&&aq.offsetY>=ar&&aq.offsetY<=ai){if(aq.offsetY-ar<ai-aq.offsetY){ak.find(".content-div").prepend(this)}else{ak.find(".content-div").append(this)}if(an.container){an.container.remove_drawable(an)}l[ak.attr("id")].add_drawable(an);return}}for(am=0;am<al.length;am++){ak=$(al.get(am));if(aq.offsetY<ak.position().top&&!(ak.hasClass("reference-track")||ak.hasClass("intro"))){break}}if(am===al.length){if(this!==al.get(am-1)){au.append(this);l[au.attr("id")].move_drawable(an,am)}}else{if(this!==al.get(am)){$(this).insertBefore(al.get(am));l[au.attr("id")].move_drawable(an,(aq.deltaY>0?am-1:am))}}}).bind("dragstart",function(){ae["border-top"]=ad.css("border-top");ae["border-bottom"]=ad.css("border-bottom");$(this).css({"border-top":"1px solid blue","border-bottom":"1px solid blue"})}).bind("dragend",function(){$(this).css(ae)})};var aa=16,G=9,D=20,z=100,I=12000,S=400,K=5000,v=100,m="Cannot display dataset due to an error. ",J="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",E="No data for this chrom/contig.",u="Preparing data. This can take a while for a large dataset. If the visualization is saved and closed, preparation will continue in the background.",x="Tool cannot be rerun: ",a="Loading data...",U="Ready for display",Q=10,H=20,A=["Histogram","Line","Filled","Intensity"];function V(ae,ad){if(!ad){ad=0}var af=Math.pow(10,ad);return Math.round(ae*af)/af}var p=function(ae,ad,ag){if(!p.id_counter){p.id_counter=0}this.id=p.id_counter++;this.name=ag.name;this.view=ae;this.container=ad;this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name}],saved_values:ag.prefs,onchange:function(){this.track.set_name(this.track.config.values.name)}});this.prefs=this.config.values;this.drag_handle_class=ag.drag_handle_class;this.is_overview=false;this.action_icons={};this.content_visible=true;this.container_div=this.build_container_div();this.header_div=this.build_header_div();if(this.header_div){this.container_div.append(this.header_div);this.icons_div=$("<div/>").css("float","left").hide().appendTo(this.header_div);this.build_action_icons(this.action_icons_def);this.header_div.append($("<div style='clear: both'/>"));this.header_div.dblclick(function(ah){ah.stopPropagation()});var af=this;this.container_div.hover(function(){af.icons_div.show()},function(){af.icons_div.hide()});$("<div style='clear: both'/>").appendTo(this.container_div)}};p.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(ad){if(ad.content_visible){ad.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle");ad.hide_contents();ad.content_visible=false}else{ad.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand");ad.content_visible=true;ad.show_contents()}}},{name:"settings_icon",title:"Edit settings",css_class:"settings-icon",on_click_fn:function(ae){var ag=function(){Galaxy.modal.hide();$(window).unbind("keypress.check_enter_esc")},ad=function(){ae.config.update_from_form($(Galaxy.modal.el));Galaxy.modal.hide();$(window).unbind("keypress.check_enter_esc")},af=function(ah){if((ah.keyCode||ah.which)===27){ag()}else{if((ah.keyCode||ah.which)===13){ad()}}};$(window).bind("keypress.check_enter_esc",af);Galaxy.modal.show({title:"Configure",body:ae.config.build_form(),buttons:{Cancel:ag,Ok:ad}})}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(ad){$(".tooltip").remove();ad.remove()}}];o(p.prototype,{init:function(){},changed:function(){this.view.changed()},can_draw:function(){if(this.enabled&&this.content_visible){return true}return false},request_draw:function(){},_draw:function(ad){},to_dict:function(){},set_name:function(ad){this.old_name=this.name;this.name=ad;this.name_div.text(this.name)},revert_name:function(){if(this.old_name){this.name=this.old_name;this.name_div.text(this.name)}},remove:function(){this.changed();this.container.remove_drawable(this);var ad=this.view;this.container_div.hide(0,function(){$(this).remove();ad.update_intro_div()})},build_container_div:function(){},build_header_div:function(){},add_action_icon:function(ae,aj,ai,ah,ad,ag){var af=this;this.action_icons[ae]=$("<a/>").attr("href","javascript:void(0);").attr("title",aj).addClass("icon-button").addClass(ai).tooltip().click(function(){ah(af)}).appendTo(this.icons_div);if(ag){this.action_icons[ae].hide()}},build_action_icons:function(ad){var af;for(var ae=0;ae<ad.length;ae++){af=ad[ae];this.add_action_icon(af.name,af.title,af.css_class,af.on_click_fn,af.prepend,af.hide)}},update_icons:function(){},hide_contents:function(){},show_contents:function(){},get_drawables:function(){}});var y=function(ae,ad,af){p.call(this,ae,ad,af);this.obj_type=af.obj_type;this.drawables=[]};o(y.prototype,p.prototype,{unpack_drawables:function(af){this.drawables=[];var ae;for(var ad=0;ad<af.length;ad++){ae=n(af[ad],this.view,this);this.add_drawable(ae)}},init:function(){for(var ad=0;ad<this.drawables.length;ad++){this.drawables[ad].init()}},_draw:function(ad){for(var ae=0;ae<this.drawables.length;ae++){this.drawables[ae]._draw(ad)}},to_dict:function(){var ae=[];for(var ad=0;ad<this.drawables.length;ad++){ae.push(this.drawables[ad].to_dict())}return{name:this.name,prefs:this.prefs,obj_type:this.obj_type,drawables:ae}},add_drawable:function(ad){this.drawables.push(ad);ad.container=this;this.changed()},add_drawable_before:function(af,ad){this.changed();var ae=this.drawables.indexOf(ad);if(ae!==-1){this.drawables.splice(ae,0,af);return true}return false},replace_drawable:function(af,ad,ae){var ag=this.drawables.indexOf(af);if(ag!==-1){this.drawables[ag]=ad;if(ae){af.container_div.replaceWith(ad.container_div)}this.changed()}return ag},remove_drawable:function(ae){var ad=this.drawables.indexOf(ae);if(ad!==-1){this.drawables.splice(ad,1);ae.container=null;this.changed();return true}return false},move_drawable:function(ae,af){var ad=this.drawables.indexOf(ae);if(ad!==-1){this.drawables.splice(ad,1);this.drawables.splice(af,0,ae);this.changed();return true}return false},get_drawables:function(){return this.drawables},get_tracks:function(ag){var ad=this.drawables.slice(0),ae=[],af;while(ad.length!==0){af=ad.shift();if(af instanceof ag){ae.push(af)}else{if(af.drawables){ad=ad.concat(af.drawables)}}}return ae}});var P=function(ae,ad,ag){o(ag,{obj_type:"DrawableGroup",drag_handle_class:"group-handle"});y.call(this,ae,ad,ag);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div);i(this.container_div,this);i(this.content_div,this);k(this.container_div,this.drag_handle_class,".group",this);this.filters_manager=new h.FiltersManager(this);this.header_div.after(this.filters_manager.parent_div);this.saved_filters_managers=[];if("drawables" in ag){this.unpack_drawables(ag.drawables)}if("filters" in ag){var af=this.filters_manager;this.filters_manager=new h.FiltersManager(this,ag.filters);af.parent_div.replaceWith(this.filters_manager.parent_div);if(ag.filters.visible){this.setup_multitrack_filtering()}}};o(P.prototype,p.prototype,y.prototype,{action_icons_def:[p.prototype.action_icons_def[0],p.prototype.action_icons_def[1],{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(ad){$(".tooltip").remove();ad.show_composite_track()}},{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ad){if(ad.filters_manager.visible()){ad.filters_manager.clear_filters();ad._restore_filter_managers()}else{ad.setup_multitrack_filtering();ad.request_draw({clear_tile_cache:true})}ad.filters_manager.toggle()}},p.prototype.action_icons_def[2]],build_container_div:function(){var ad=$("<div/>").addClass("group").attr("id","group_"+this.id);if(this.container){this.container.content_div.append(ad)}return ad},build_header_div:function(){var ad=$("<div/>").addClass("track-header");ad.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("track-name").text(this.name).appendTo(ad);return ad},hide_contents:function(){this.tiles_div.hide()},show_contents:function(){this.tiles_div.show();this.request_draw()},update_icons:function(){var af=this.drawables.length;if(af===0){this.action_icons.composite_icon.hide();this.action_icons.filters_icon.hide()}else{if(af===1){if(this.drawables[0] instanceof e){this.action_icons.composite_icon.show()}this.action_icons.filters_icon.hide()}else{var am,al,aj,ap=true,ah=this.drawables[0].get_type(),ad=0;for(am=0;am<af;am++){aj=this.drawables[am];if(aj.get_type()!==ah){can_composite=false;break}if(aj instanceof c){ad++}}if(ap||ad===1){this.action_icons.composite_icon.show()}else{this.action_icons.composite_icon.hide();$(".tooltip").remove()}if(ad>1&&ad===this.drawables.length){var aq={},ae;aj=this.drawables[0];for(al=0;al<aj.filters_manager.filters.length;al++){ae=aj.filters_manager.filters[al];aq[ae.name]=[ae]}for(am=1;am<this.drawables.length;am++){aj=this.drawables[am];for(al=0;al<aj.filters_manager.filters.length;al++){ae=aj.filters_manager.filters[al];if(ae.name in aq){aq[ae.name].push(ae)}}}this.filters_manager.remove_all();var ag,ai,ak,an;for(var ao in aq){ag=aq[ao];if(ag.length===ad){ai=new h.NumberFilter({name:ag[0].name,index:ag[0].index});this.filters_manager.add_filter(ai)}}if(this.filters_manager.filters.length>0){this.action_icons.filters_icon.show()}else{this.action_icons.filters_icon.hide()}}else{this.action_icons.filters_icon.hide()}}}},_restore_filter_managers:function(){for(var ad=0;ad<this.drawables.length;ad++){this.drawables[ad].filters_manager=this.saved_filters_managers[ad]}this.saved_filters_managers=[]},setup_multitrack_filtering:function(){if(this.filters_manager.filters.length>0){this.saved_filters_managers=[];for(var ad=0;ad<this.drawables.length;ad++){drawable=this.drawables[ad];this.saved_filters_managers.push(drawable.filters_manager);drawable.filters_manager=this.filters_manager}}this.filters_manager.init_filters()},show_composite_track:function(){var ae=new e(this.view,this.view,{name:this.name,drawables:this.drawables});var ad=this.container.replace_drawable(this,ae,true);ae.request_draw()},add_drawable:function(ad){y.prototype.add_drawable.call(this,ad);this.update_icons()},remove_drawable:function(ad){y.prototype.remove_drawable.call(this,ad);this.update_icons()},to_dict:function(){if(this.filters_manager.visible()){this._restore_filter_managers()}var ad=o(y.prototype.to_dict.call(this),{filters:this.filters_manager.to_dict()});if(this.filters_manager.visible()){this.setup_multitrack_filtering()}return ad},request_draw:function(ad){ac.each(this.drawables,function(ae){ae.request_draw(ad)})}});var Y=Backbone.View.extend({initialize:function(ad){o(ad,{obj_type:"View"});y.call(this,"View",ad.container,ad);this.chrom=null;this.vis_id=ad.vis_id;this.dbkey=ad.dbkey;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.render();this.canvas_manager=new w.CanvasManager(this.container.get(0).ownerDocument);this.reset();this.config=new F({track:this,params:[{key:"a_color",label:"A Color",type:"color",default_value:"#FF0000"},{key:"c_color",label:"C Color",type:"color",default_value:"#00FF00"},{key:"g_color",label:"G Color",type:"color",default_value:"#0000FF"},{key:"t_color",label:"T Color",type:"color",default_value:"#FF00FF"},{key:"n_color",label:"N Color",type:"color",default_value:"#AAAAAA"}],saved_values:ad.prefs,onchange:function(){track.request_redraw({clear_tile_cache:true})}})},render:function(){this.requested_redraw=false;var af=this.container,ad=this;this.top_container=$("<div/>").addClass("top-container").appendTo(af);this.browser_content_div=$("<div/>").addClass("content").css("position","relative").appendTo(af);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(af);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;i(this.viewport_container,ad);this.intro_div=$("<div/>").addClass("intro").appendTo(this.viewport_container).hide();var ag=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){w.select_datasets(galaxy_config.root+"visualization/list_current_history_datasets",galaxy_config.root+"api/datasets",{"f-dbkey":ad.dbkey},function(ah){ac.each(ah,function(ai){ad.add_drawable(n(ai,ad,ad))})})});this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("trackster-nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("trackster-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").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var ae=function(ah){if(ah.type==="focusout"||(ah.keyCode||ah.which)===13||(ah.keyCode||ah.which)===27){if((ah.keyCode||ah.which)!==27){ad.go_to($(this).val())}$(this).hide();$(this).val("");ad.location_span.show();ad.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ae).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").attr("original-title","Click to change location").tooltip({placement:"bottom"}).appendTo(this.nav_controls);this.location_span.click(function(){ad.location_span.hide();ad.chrom_select.hide();ad.nav_input.val(ad.chrom+":"+ad.low+"-"+ad.high);ad.nav_input.css("display","inline-block");ad.nav_input.select();ad.nav_input.focus();ad.nav_input.autocomplete({source:function(aj,ah){var ak=[],ai=$.map(ad.get_tracks(c),function(al){return al.data_manager.search_features(aj.term).success(function(am){ak=ak.concat(am)})});$.when.apply($,ai).done(function(){ah($.map(ak,function(al){return{label:al[0],value:al[1]}}))})}})});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a/>").attr("id","zoom-out").attr("title","Zoom out").tooltip({placement:"bottom"}).click(function(){ad.zoom_out();ad.request_redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a/>").attr("id","zoom-in").attr("title","Zoom in").tooltip({placement:"bottom"}).click(function(){ad.zoom_in();ad.request_redraw()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){ad.change_chrom(ad.chrom_select.val())});this.browser_content_div.click(function(ah){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(ah){ad.zoom_in(ah.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(ah,ai){this.current_x=ai.offsetX}).bind("drag",function(ah,aj){var ak=aj.offsetX-this.current_x;this.current_x=aj.offsetX;var ai=Math.round(ak/ad.viewport_container.width()*(ad.max_high-ad.max_low));ad.move_delta(-ai)});this.overview_close.click(function(){ad.reset_overview()});this.viewport_container.bind("draginit",function(ah,ai){if(ah.clientX>ad.viewport_container.width()-16){return false}}).bind("dragstart",function(ah,ai){ai.original_low=ad.low;ai.current_height=ah.clientY;ai.current_x=ai.offsetX}).bind("drag",function(aj,al){var ah=$(this);var am=al.offsetX-al.current_x;var ai=ah.scrollTop()-(aj.clientY-al.current_height);ah.scrollTop(ai);al.current_height=aj.clientY;al.current_x=al.offsetX;var ak=Math.round(am/ad.viewport_container.width()*(ad.high-ad.low));ad.move_delta(ak)}).bind("mousewheel",function(aj,al,ai,ah){if(ai){ai*=50;var ak=Math.round(-ai/ad.viewport_container.width()*(ad.high-ad.low));ad.move_delta(ak)}});this.top_labeltrack.bind("dragstart",function(ah,ai){return $("<div />").css({height:ad.browser_content_div.height()+ad.top_labeltrack.height()+ad.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(al,am){$(am.proxy).css({left:Math.min(al.pageX,am.startX)-ad.container.offset().left,width:Math.abs(al.pageX-am.startX)});var ai=Math.min(al.pageX,am.startX)-ad.container.offset().left,ah=Math.max(al.pageX,am.startX)-ad.container.offset().left,ak=(ad.high-ad.low),aj=ad.viewport_container.width();ad.update_location(Math.round(ai/aj*ak)+ad.low,Math.round(ah/aj*ak)+ad.low)}).bind("dragend",function(am,an){var ai=Math.min(am.pageX,an.startX),ah=Math.max(am.pageX,an.startX),ak=(ad.high-ad.low),aj=ad.viewport_container.width(),al=ad.low;ad.low=Math.round(ai/aj*ak)+al;ad.high=Math.round(ah/aj*ak)+al;$(an.proxy).remove();ad.request_redraw()});this.add_label_track(new W(this,{content_div:this.top_labeltrack}));this.add_label_track(new W(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){if(this.resize_timer){clearTimeout(this.resize_timer)}this.resize_timer=setTimeout(function(){ad.resize_window()},500)});$(document).bind("redraw",function(){ad.redraw()});this.reset();$(window).trigger("resize")},get_base_color:function(ad){return this.config.values[ad.toLowerCase()+"_color"]||this.config.values.n_color}});o(Y.prototype,y.prototype,{changed:function(){this.has_changes=true},update_intro_div:function(){if(this.drawables.length===0){this.intro_div.show()}else{this.intro_div.hide()}},trigger_navigate:function(ae,ag,ad,ah){if(this.timer){clearTimeout(this.timer)}if(ah){var af=this;this.timer=setTimeout(function(){af.trigger("navigate",ae+":"+ag+"-"+ad)},500)}else{view.trigger("navigate",ae+":"+ag+"-"+ad)}},update_location:function(ad,af){this.location_span.text(commatize(ad)+" - "+commatize(af));this.nav_input.val(this.chrom+":"+commatize(ad)+"-"+commatize(af));var ae=view.chrom_select.val();if(ae!==""){this.trigger_navigate(ae,view.low,view.high,true)}},load_chroms:function(af){af.num=v;var ad=this,ae=$.Deferred();$.ajax({url:galaxy_config.root+"api/genomes/"+this.dbkey,data:af,dataType:"json",success:function(ah){if(ah.chrom_info.length===0){return}if(ah.reference){ad.add_label_track(new B(ad))}ad.chrom_data=ah.chrom_info;var ak='<option value="">Select Chrom/Contig</option>';for(var aj=0,ag=ad.chrom_data.length;aj<ag;aj++){var ai=ad.chrom_data[aj].chrom;ak+='<option value="'+ai+'">'+ai+"</option>"}if(ah.prev_chroms){ak+='<option value="previous">Previous '+v+"</option>"}if(ah.next_chroms){ak+='<option value="next">Next '+v+"</option>"}ad.chrom_select.html(ak);ad.chrom_start_index=ah.start_index;ae.resolve(ah.chrom_info)},error:function(){alert("Could not load chroms for this dbkey:",ad.dbkey)}});return ae},change_chrom:function(ai,ae,ak){var af=this;if(!af.chrom_data){af.load_chroms_deferred.then(function(){af.change_chrom(ai,ae,ak)});return}if(!ai||ai==="None"){return}if(ai==="previous"){af.load_chroms({low:this.chrom_start_index-v});return}if(ai==="next"){af.load_chroms({low:this.chrom_start_index+v});return}var aj=$.grep(af.chrom_data,function(al,am){return al.chrom===ai})[0];if(aj===undefined){af.load_chroms({chrom:ai},function(){af.change_chrom(ai,ae,ak)});return}else{if(ai!==af.chrom){af.chrom=ai;af.chrom_select.val(af.chrom);af.max_high=aj.len-1;af.reset();for(var ah=0,ad=af.drawables.length;ah<ad;ah++){var ag=af.drawables[ah];if(ag.init){ag.init()}}if(af.reference_track){af.reference_track.init()}}if(ae&&ak){af.low=Math.max(ae,0);af.high=Math.min(ak,af.max_high)}else{af.low=0;af.high=af.max_high}af.reset_overview();af.request_redraw()}},go_to:function(ah){ah=ah.replace(/,/g,"");ah=ah.replace(/:|\-/g," ");var ae=ah.split(/\s+/),ag=ae[0],af=(ae[1]?parseInt(ae[1],10):null),ad=(ae[2]?parseInt(ae[2],10):null);if(!ad){af=af-15;ad=af+15}this.change_chrom(ag,af,ad)},move_fraction:function(af){var ad=this;var ae=ad.high-ad.low;this.move_delta(af*ae)},move_delta:function(ag){var ad=this;var af=ad.high-ad.low;if(ad.low-ag<ad.max_low){ad.low=ad.max_low;ad.high=ad.max_low+af}else{if(ad.high-ag>ad.max_high){ad.high=ad.max_high;ad.low=ad.max_high-af}else{ad.high-=ag;ad.low-=ag}}ad.request_redraw({data_fetch:false});if(this.redraw_on_move_fn){clearTimeout(this.redraw_on_move_fn)}this.redraw_on_move_fn=setTimeout(function(){ad.request_redraw()},200);var ae=ad.chrom_select.val();this.trigger_navigate(ae,ad.low,ad.high,true)},add_drawable:function(ad){y.prototype.add_drawable.call(this,ad);ad.init();this.changed();this.update_intro_div()},add_label_track:function(ad){ad.view=this;ad.init();this.label_tracks.push(ad)},remove_drawable:function(af,ae){y.prototype.remove_drawable.call(this,af);if(ae){var ad=this;af.container_div.hide(0,function(){$(this).remove();ad.update_intro_div()})}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(ae,af){var ad=this,ag=(af?[af]:ad.drawables);ac.each(ag,function(ah){var ai=ac.find(ad.tracks_to_be_redrawn,function(aj){return aj[0]===ah});if(ai){ai[1]=ae}else{ad.tracks_to_be_redrawn.push([ah,ae])}});if(!this.requested_redraw){requestAnimationFrame(function(){ad._redraw()});this.requested_redraw=true}},_redraw:function(){this.requested_redraw=false;var ad=this.low,ah=this.high;if(ad<this.max_low){ad=this.max_low}if(ah>this.max_high){ah=this.max_high}var ae=this.high-this.low;if(this.high!==0&&ae<this.min_separation){ah=ad+this.min_separation}this.low=Math.floor(ad);this.high=Math.ceil(ah);this.update_location(this.low,this.high);this.resolution_px_b=this.viewport_container.width()/(this.high-this.low);var ag=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ai=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var af=13;this.overview_box.css({left:ag,width:Math.max(af,ai)}).show();if(ai<af){this.overview_box.css("left",ag-(af-ai)/2)}if(this.overview_highlight){this.overview_highlight.css({left:ag,width:ai})}ac.each(this.tracks_to_be_redrawn,function(al){var aj=al[0],ak=al[1];if(aj){aj._draw(ak)}});this.tracks_to_be_redrawn=[];ac.each(this.label_tracks,function(aj){aj._draw()})},zoom_in:function(ae,af){if(this.max_high===0||this.high-this.low<=this.min_separation){return}var ag=this.high-this.low,ah=ag/2+this.low,ad=(ag/this.zoom_factor)/2;if(ae){ah=ae/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(ah-ad);this.high=Math.round(ah+ad);this.changed();this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ae=this.high-this.low,af=ae/2+this.low,ad=(ae*this.zoom_factor)/2;this.low=Math.round(af-ad);this.high=Math.round(af+ad);this.changed();this.request_redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.request_redraw()},set_overview:function(af){if(this.overview_drawable){if(this.overview_drawable.dataset.id===af.dataset.id){return}this.overview_viewport.find(".track").remove()}var ae=af.copy({content_div:this.overview_viewport}),ad=this;ae.header_div.hide();ae.is_overview=true;ad.overview_drawable=ae;this.overview_drawable.postdraw_actions=function(){ad.overview_highlight.show().height(ad.overview_drawable.content_div.height());ad.overview_viewport.height(ad.overview_drawable.content_div.height()+ad.overview_box.outerHeight());ad.overview_close.show();ad.resize_window()};ad.overview_drawable.request_draw();this.changed()},reset_overview:function(){$(".tooltip").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 q=R.Tool.extend({defaults:{track:null},initialize:function(ad){if(ad.tool_state!==undefined){this.set("hidden",ad.tool_state.hidden)}this.remove_inputs(["data","hidden_data","conditional"])},state_dict:function(ad){return ac.extend(this.get_inputs_dict(),{hidden:!this.is_visible()})}});var t=Backbone.View.extend({events:{"change input":"update_value"},render:function(){var af=this.$el.addClass("param-row"),ag=this.model;var ad=$("<div>").addClass("param-label").text(ag.get("label")).appendTo(af);var ae=$("<div/>").addClass("param-input").html(ag.get("html")).appendTo(af);ae.find(":input").val(ag.get("value"));$("<div style='clear: both;'/>").appendTo(af)},update_value:function(ad){this.model.set_value($(ad.target).val())}});var ab=Backbone.View.extend({initialize:function(ad){this.model.on("change:hidden",this.set_visible,this)},render:function(){var ae=this;tool=this.model,parent_div=this.$el.addClass("dynamic-tool").hide();parent_div.bind("drag",function(ai){ai.stopPropagation()}).click(function(ai){ai.stopPropagation()}).bind("dblclick",function(ai){ai.stopPropagation()}).keydown(function(ai){ai.stopPropagation()});var af=$("<div class='tool-name'>").appendTo(parent_div).text(tool.get("name"));tool.get("inputs").each(function(aj){var ai=new t({model:aj});ai.render();parent_div.append(ai.$el)});parent_div.find("input").click(function(){$(this).select()});var ag=$("<div>").addClass("param-row").appendTo(parent_div);var ah=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(ag);var ad=$("<input type='submit'>").attr("value","Run on visible region").css("margin-left","3em").appendTo(ag);ad.click(function(){ae.run_on_region()});ah.click(function(){ae.run_on_dataset()});if(tool.is_visible()){this.$el.show()}},set_visible:function(){if(this.model.is_visible()){this.$el.show()}else{this.$el.hide()}},update_params:function(){for(var ad=0;ad<this.params.length;ad++){this.params[ad].update_value()}},run_on_dataset:function(){var ad=this.model;this.run({target_dataset_id:this.model.get("track").dataset.id,action:"rerun",tool_id:ad.id},null,function(ae){Galaxy.modal.show({title:ad.get("name")+" is Running",body:ad.get("name")+" is running on the complete dataset. Tool outputs are in dataset's history.",buttons:{Close:function(){Galaxy.modal.hide()}}})})},run_on_region:function(){var ae=this.model.get("track"),ah=this.model,aj=new w.GenomeRegion({chrom:ae.view.chrom,start:ae.view.low,end:ae.view.high}),ak={target_dataset_id:ae.dataset.id,action:"rerun",tool_id:ah.id,regions:[aj.toJSON()]},ai=ae,am=ak.tool_id+ai.tool_region_and_parameters_str(aj),ad;if(ai.container===view){var al=new P(view,view,{name:this.name});var ag=ai.container.replace_drawable(ai,al,false);al.container_div.insertBefore(ai.view.content_div.children()[ag]);al.add_drawable(ai);ai.container_div.appendTo(al.content_div);ad=al}else{ad=ai.container}var af=new ai.constructor(view,ad,{name:am,hda_ldda:"hda"});af.init_for_tool_data();af.change_mode(ai.mode);af.set_filters_manager(ai.filters_manager.copy(af));af.update_icons();ad.add_drawable(af);af.tiles_div.text("Starting job.");this.run(ak,af,function(an){af.set_dataset(new X.Dataset(an));af.tiles_div.text("Running job.");af.init()})},run:function(ad,af,ag){ad.inputs=this.model.get_inputs_dict();var ae=new j.ServerStateDeferred({ajax_settings:{url:galaxy_config.root+"api/tools",data:JSON.stringify(ad),dataType:"json",contentType:"application/json",type:"POST"},interval:2000,success_fn:function(ah){return ah!=="pending"}});$.when(ae.go()).then(function(ah){if(ah==="no converter"){af.container_div.addClass("error");af.content_div.text(J)}else{if(ah.error){af.container_div.addClass("error");af.content_div.text(x+ah.message)}else{ag(ah)}}})}});var C=function(ad,ae){L.Scaler.call(this,ae);this.filter=ad};C.prototype.gen_val=function(ad){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(ad[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var F=function(ad){this.track=ad.track;this.params=ad.params;this.values={};this.restore_values((ad.saved_values?ad.saved_values:{}));this.onchange=ad.onchange};o(F.prototype,{set_param_default_value:function(ae,ad){var af=ac.find(this.params,function(ag){return ag.key===ae});if(af){af.default_value=ad}},set_param_value:function(ad,ae){var af=ac.find(this.params,function(ag){return ag.key===ad});if(af){if(typeof ae==="string"||ae instanceof String){if(ae.trim()===""){ae=af.default_value}else{if(af.type==="float"){ae=parseFloat(ae)}else{if(af.type==="int"){ae=parseInt(ae,10)}}}}}if(this.values[ad]!==ae){this.values[ad]=ae;return true}else{return false}},restore_values:function(ad){var ae=this;$.each(this.params,function(af,ag){if(ad[ag.key]!==undefined){ae.values[ag.key]=ad[ag.key]}else{ae.values[ag.key]=ag.default_value}})},build_form:function(){var ag=this;var ad=$("<div />");var af;function ae(al,ah){for(var ap=0;ap<al.length;ap++){af=al[ap];if(af.hidden){continue}var aj="param_"+ap;var au=ag.values[af.key];var aw=$("<div class='form-row' />").appendTo(ah);aw.append($("<label />").attr("for",aj).text(af.label+":"));if(af.type==="bool"){aw.append($('<input type="checkbox" />').attr("id",aj).attr("name",aj).attr("checked",au))}else{if(af.type==="text"){aw.append($('<input type="text"/>').attr("id",aj).val(au).click(function(){$(this).select()}))}else{if(af.type==="select"){var ar=$("<select />").attr("id",aj);for(var an=0;an<af.options.length;an++){$("<option/>").text(af.options[an].label).attr("value",af.options[an].value).appendTo(ar)}ar.val(au);aw.append(ar)}else{if(af.type==="color"){var av=$("<div/>").appendTo(aw),aq=$("<input />").attr("id",aj).attr("name",aj).val(au).css("float","left").appendTo(av).click(function(ay){$(".tooltip").removeClass("in");var ax=$(this).siblings(".tooltip").addClass("in");ax.css({left:$(this).position().left+$(this).width()+5,top:$(this).position().top-($(ax).height()/2)+($(this).height()/2)}).show();ax.click(function(az){az.stopPropagation()});$(document).bind("click.color-picker",function(){ax.hide();$(document).unbind("click.color-picker")});ay.stopPropagation()}),ao=$("<a href='javascript:void(0)'/>").addClass("icon-button arrow-circle").appendTo(av).attr("title","Set new random color").tooltip(),at=$("<div class='tooltip right' style='position: absolute;' />").appendTo(av).hide(),ak=$("<div class='tooltip-inner' style='text-align: inherit'></div>").appendTo(at),ai=$("<div class='tooltip-arrow'></div>").appendTo(at),am=$.farbtastic(ak,{width:100,height:100,callback:aq,color:au});av.append($("<div/>").css("clear","both"));(function(ax){ao.click(function(){ax.setColor(j.get_random_color())})})(am)}else{aw.append($("<input />").attr("id",aj).attr("name",aj).val(au))}}}}if(af.help){aw.append($("<div class='help'/>").text(af.help))}}}ae(this.params,ad);return ad},update_from_form:function(ad){var af=this;var ae=false;$.each(this.params,function(ag,ai){if(!ai.hidden){var aj="param_"+ag;var ah=ad.find("#"+aj).val();if(ai.type==="bool"){ah=ad.find("#"+aj).is(":checked")}ae=af.set_param_value(ai.key,ah)||ae}});if(ae){this.onchange();this.track.changed()}}});var b=function(ad,ag,ah,ae,af){this.track=ad;this.region=ag;this.low=ag.get("start");this.high=ag.get("end");this.w_scale=ah;this.html_elt=$("<div class='track-tile'/>").append(ae).height($(ae).attr("height"));this.data=af;this.stale=false};b.prototype.predisplay_actions=function(){};var M=function(ad,ag,ah,ae,af){b.call(this,ad,ag,ah,ae,af)};M.prototype.predisplay_actions=function(){};var O=function(ag,an,ap,af,ai,aj,aq,ae,am){b.call(this,ag,an,ap,af,ai);this.mode=aj;this.all_slotted=ae;this.feature_mapper=am;this.has_icons=false;if(aq){this.has_icons=true;var ak=this;af=this.html_elt.children()[0],message_div=$("<div/>").addClass("tile-message").css({height:D-1,width:af.width}).prependTo(this.html_elt);var al=new w.GenomeRegion({chrom:ag.view.chrom,start:this.low,end:this.high}),ao=ai.length,ah=$("<a href='javascript:void(0);'/>").addClass("icon more-down").attr("title","For speed, only the first "+ao+" features in this region were obtained from server. Click to get more data including depth").tooltip().appendTo(message_div),ad=$("<a href='javascript:void(0);'/>").addClass("icon more-across").attr("title","For speed, only the first "+ao+" features in this region were obtained from server. Click to get more data excluding depth").tooltip().appendTo(message_div);ah.click(function(){ak.stale=true;ag.data_manager.get_more_data(al,ag.mode,1/ak.w_scale,{},ag.data_manager.DEEP_DATA_REQ);$(".tooltip").hide();ag.request_draw()}).dblclick(function(ar){ar.stopPropagation()});ad.click(function(){ak.stale=true;ag.data_manager.get_more_data(al,ag.mode,1/ak.w_scale,{},ag.data_manager.BROAD_DATA_REQ);$(".tooltip").hide();ag.request_draw()}).dblclick(function(ar){ar.stopPropagation()})}};o(O.prototype,b.prototype);O.prototype.predisplay_actions=function(){var ae=this,ad={};if(ae.mode!=="Pack"){return}$(this.html_elt).hover(function(){this.hovered=true;$(this).mousemove()},function(){this.hovered=false;$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()}).mousemove(function(ap){if(!this.hovered){return}var ak=$(this).offset(),ao=ap.pageX-ak.left,an=ap.pageY-ak.top,au=ae.feature_mapper.get_feature_data(ao,an),al=(au?au[0]:null);$(this).parents(".track-content").children(".overlay").children(".feature-popup").each(function(){if(!al||$(this).attr("id")!==al.toString()){$(this).remove()}});if(au){var ag=ad[al];if(!ag){var al=au[0],aq={name:au[3],start:au[1],end:au[2],strand:au[4]},aj=ae.track.filters_manager.filters,ai;for(var am=0;am<aj.length;am++){ai=aj[am];aq[ai.name]=au[ai.index]}var ag=$("<div/>").attr("id",al).addClass("feature-popup"),av=$("<table/>"),at,ar,aw;for(at in aq){ar=aq[at];aw=$("<tr/>").appendTo(av);$("<th/>").appendTo(aw).text(at);$("<td/>").attr("align","left").appendTo(aw).text(typeof(ar)==="number"?V(ar,2):ar)}ag.append($("<div class='feature-popup-inner'>").append(av));ad[al]=ag}ag.appendTo($(this).parents(".track-content").children(".overlay"));var ah=ao+parseInt(ae.html_elt.css("left"))-ag.width()/2,af=an+parseInt(ae.html_elt.css("top"))+7;ag.css("left",ah+"px").css("top",af+"px")}else{if(!ap.isPropagationStopped()){ap.stopPropagation();$(this).siblings().each(function(){$(this).trigger(ap)})}}}).mouseleave(function(){$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()})};var f=function(ae,ad,af){o(af,{drag_handle_class:"draghandle"});p.call(this,ae,ad,af);this.dataset=null;if(af.dataset){this.dataset=(af.dataset instanceof Backbone.Model?af.dataset:X.Dataset.findOrCreate(af.dataset))}this.dataset_check_type="converted_datasets_state";this.data_url_extra_params={};this.data_query_wait=("data_query_wait" in af?af.data_query_wait:K);this.data_manager=("data_manager" in af?af.data_manager:new w.GenomeDataManager({dataset:this.dataset,genome:new w.Genome({key:ae.dbkey,chroms_info:{chrom_info:ae.chrom_data}}),data_mode_compatible:this.data_and_mode_compatible,can_subset:this.can_subset}));this.min_height_px=16;this.max_height_px=800;this.visible_height_px=0;this.content_div=$("<div class='track-content'>").appendTo(this.container_div);if(this.container){this.container.content_div.append(this.container_div);if(!("resize" in af)||af.resize){this.add_resize_handle()}}};o(f.prototype,p.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},p.prototype.action_icons_def[0],{name:"overview_icon",title:"Set as overview",css_class:"overview-icon",on_click_fn:function(ad){ad.view.set_overview(ad)}},p.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ad){if(ad.filters_manager.visible()){ad.filters_manager.clear_filters()}else{ad.filters_manager.init_filters()}ad.filters_manager.toggle()}},{name:"tools_icon",title:"Tool",css_class:"hammer",on_click_fn:function(ad){ad.tool.toggle();if(ad.tool.is_visible()){ad.set_name(ad.name+ad.tool_region_and_parameters_str())}else{ad.revert_name()}$(".tooltip").remove()}},{name:"param_space_viz_icon",title:"Tool parameter space visualization",css_class:"arrow-split",on_click_fn:function(ad){var ag='<strong>Tool</strong>: <%= track.tool.name %><br/><strong>Dataset</strong>: <%= track.name %><br/><strong>Region(s)</strong>: <select name="regions"><option value="cur">current viewing area</option><option value="bookmarks">bookmarks</option><option value="both">current viewing area and bookmarks</option></select>',af=ac.template(ag,{track:ad});var ai=function(){Galaxy.modal.hide();$(window).unbind("keypress.check_enter_esc")},ae=function(){var ak=$('select[name="regions"] option:selected').val(),am,aj=new w.GenomeRegion({chrom:view.chrom,start:view.low,end:view.high}),al=ac.map($(".bookmark"),function(an){return new w.GenomeRegion({from_str:$(an).children(".position").text()})});if(ak==="cur"){am=[aj]}else{if(ak==="bookmarks"){am=al}else{am=[aj].concat(al)}}Galaxy.modal.hide();window.location.href=galaxy_config.root+"visualization/sweepster?"+$.param({dataset_id:ad.dataset.id,hda_ldda:ad.dataset.get("hda_ldda"),regions:JSON.stringify(new Backbone.Collection(am).toJSON())})},ah=function(aj){if((aj.keyCode||aj.which)===27){ai()}else{if((aj.keyCode||aj.which)===13){ae()}}};Galaxy.modal.show({title:"Visualize tool parameter space and output from different parameter settings?",body:af,buttons:{No:ai,Yes:ae}})}},p.prototype.action_icons_def[2]],can_draw:function(){return this.dataset&&p.prototype.can_draw.call(this)},build_container_div:function(){return $("<div/>").addClass("track").attr("id","track_"+this.id).css("position","relative")},build_header_div:function(){var ad=$("<div class='track-header'/>");if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(ad)}this.name_div=$("<div/>").addClass("track-name").appendTo(ad).text(this.name).attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase());return ad},set_dataset:function(ad){this.dataset=ad;this.data_manager.set("dataset",ad)},on_resize:function(){this.request_draw({clear_tile_cache:true})},add_resize_handle:function(){var ad=this;var ag=false;var af=false;var ae=$("<div class='track-resize'>");$(ad.container_div).hover(function(){if(ad.content_visible){ag=true;ae.show()}},function(){ag=false;if(!af){ae.hide()}});ae.hide().bind("dragstart",function(ah,ai){af=true;ai.original_height=$(ad.content_div).height()}).bind("drag",function(ai,aj){var ah=Math.min(Math.max(aj.original_height+aj.deltaY,ad.min_height_px),ad.max_height_px);$(ad.tiles_div).css("height",ah);ad.visible_height_px=(ad.max_height_px===ah?0:ah);ad.on_resize()}).bind("dragend",function(ah,ai){ad.tile_cache.clear();af=false;if(!ag){ae.hide()}ad.config.values.height=ad.visible_height_px;ad.changed()}).appendTo(ad.container_div)},set_display_modes:function(ag,aj){this.display_modes=ag;this.mode=(aj?aj:(this.config&&this.config.values.mode?this.config.values.mode:this.display_modes[0]));this.action_icons.mode_icon.attr("title","Set display mode (now: "+this.mode+")");var ae=this,ah={};for(var af=0,ad=ae.display_modes.length;af<ad;af++){var ai=ae.display_modes[af];ah[ai]=function(ak){return function(){ae.change_mode(ak);ae.icons_div.show();ae.container_div.mouseleave(function(){ae.icons_div.hide()})}}(ai)}make_popupmenu(this.action_icons.mode_icon,ah)},build_action_icons:function(){p.prototype.build_action_icons.call(this,this.action_icons_def);if(this.display_modes!==undefined){this.set_display_modes(this.display_modes)}},hide_contents:function(){this.tiles_div.hide();this.container_div.find(".yaxislabel, .track-resize").hide()},show_contents:function(){this.tiles_div.show();this.container_div.find(".yaxislabel, .track-resize").show();this.request_draw()},get_type:function(){if(this instanceof W){return"LabelTrack"}else{if(this instanceof B){return"ReferenceTrack"}else{if(this instanceof g){return"LineTrack"}else{if(this instanceof T){return"ReadTrack"}else{if(this instanceof Z){return"VariantTrack"}else{if(this instanceof e){return"CompositeTrack"}else{if(this instanceof c){return"FeatureTrack"}}}}}}}return""},init:function(af){var ae=this;ae.enabled=false;ae.tile_cache.clear();ae.data_manager.clear();ae.tiles_div.css("height","auto");ae.tiles_div.text("").children().remove();ae.container_div.removeClass("nodata error pending");if(!ae.dataset.id){return}var ad=$.Deferred(),ag={hda_ldda:ae.dataset.get("hda_ldda"),data_type:this.dataset_check_type,chrom:ae.view.chrom,retry:af};$.getJSON(this.dataset.url(),ag,function(ah){if(!ah||ah==="error"||ah.kind==="error"){ae.container_div.addClass("error");ae.tiles_div.text(m);if(ah.message){ae.tiles_div.append($("<a href='javascript:void(0);'></a>").text("View error").click(function(){Galaxy.modal.show({title:"Trackster Error",body:"<pre>"+ah.message+"</pre>",buttons:{Close:function(){Galaxy.modal.hide()}}})}));ae.tiles_div.append($("<span/>").text(" "));ae.tiles_div.append($("<a href='javascript:void(0);'></a>").text("Try again").click(function(){ae.init(true)}))}}else{if(ah==="no converter"){ae.container_div.addClass("error");ae.tiles_div.text(J)}else{if(ah==="no data"||(ah.data!==undefined&&(ah.data===null||ah.data.length===0))){ae.container_div.addClass("nodata");ae.tiles_div.text(E)}else{if(ah==="pending"){ae.container_div.addClass("pending");ae.tiles_div.html(u);setTimeout(function(){ae.init()},ae.data_query_wait)}else{if(ah==="data"||ah.status==="data"){if(ah.valid_chroms){ae.valid_chroms=ah.valid_chroms;ae.update_icons()}ae.tiles_div.text(U);if(ae.view.chrom){ae.tiles_div.text("");ae.tiles_div.css("height",ae.visible_height_px+"px");ae.enabled=true;$.when.apply($,ae.predraw_init()).done(function(){ad.resolve();ae.container_div.removeClass("nodata error pending");ae.request_draw()})}else{ad.resolve()}}}}}}});this.update_icons();return ad},predraw_init:function(){var ad=this;return $.getJSON(ad.dataset.url(),{data_type:"data",stats:true,chrom:ad.view.chrom,low:0,high:ad.view.max_high,hda_ldda:ad.dataset.get("hda_ldda")},function(ae){ad.container_div.addClass("line-track");var ag=ae.data;if(ag&&ag.min&&ag.max){var af=ag.min,ah=ag.max;af=Math.floor(Math.min(0,Math.max(af,ag.mean-2*ag.sd)));ah=Math.ceil(Math.max(0,Math.min(ah,ag.mean+2*ag.sd)));ad.config.set_param_default_value("min_value",af);ad.config.set_param_default_value("max_value",ah);ad.prefs.min_value=af;ad.prefs.max_value=ah}})},get_drawables:function(){return this}});var N=function(af,ae,ah){f.call(this,af,ae,ah);var ad=this;k(ad.container_div,ad.drag_handle_class,".group",ad);this.filters_manager=new h.FiltersManager(this,("filters" in ah?ah.filters:null));this.data_manager.set("filters_manager",this.filters_manager);this.filters_available=false;this.tool=(ah.tool?new q(ac.extend(ah.tool,{track:this,tool_state:ah.tool_state})):null);this.tile_cache=new w.Cache(Q);this.left_offset=0;if(this.header_div){this.set_filters_manager(this.filters_manager);if(this.tool){var ag=new ab({model:this.tool});ag.render();this.dynamic_tool_div=ag.$el;this.header_div.after(this.dynamic_tool_div)}}this.tiles_div=$("<div/>").addClass("tiles").appendTo(this.content_div);this.overlay_div=$("<div/>").addClass("overlay").appendTo(this.content_div);if(ah.mode){this.change_mode(ah.mode)}};o(N.prototype,p.prototype,f.prototype,{action_icons_def:f.prototype.action_icons_def.concat([{name:"show_more_rows_icon",title:"To minimize track height, not all feature rows are displayed. Click to display more rows.",css_class:"exclamation",on_click_fn:function(ad){$(".tooltip").remove();ad.slotters[ad.view.resolution_px_b].max_rows*=2;ad.request_draw({clear_tile_cache:true})},hide:true}]),copy:function(ad){var ae=this.to_dict();o(ae,{data_manager:this.data_manager});var af=new this.constructor(this.view,ad,ae);af.change_mode(this.mode);af.enabled=this.enabled;return af},set_filters_manager:function(ad){this.filters_manager=ad;this.header_div.after(this.filters_manager.parent_div)},to_dict:function(){return{track_type:this.get_type(),name:this.name,dataset:{id:this.dataset.id,hda_ldda:this.dataset.get("hda_ldda")},prefs:this.prefs,mode:this.mode,filters:this.filters_manager.to_dict(),tool_state:(this.tool?this.tool.state_dict():{})}},set_min_max:function(){var ad=this;return $.getJSON(ad.dataset.url(),{data_type:"data",stats:true,chrom:ad.view.chrom,low:0,high:ad.view.max_high,hda_ldda:ad.dataset.get("hda_ldda")},function(ae){var ag=ae.data;if(isNaN(parseFloat(ad.prefs.min_value))||isNaN(parseFloat(ad.prefs.max_value))){var af=ag.min,ah=ag.max;af=Math.floor(Math.min(0,Math.max(af,ag.mean-2*ag.sd)));ah=Math.ceil(Math.max(0,Math.min(ah,ag.mean+2*ag.sd)));ad.prefs.min_value=af;ad.prefs.max_value=ah}})},change_mode:function(ae){var ad=this;ad.mode=ae;ad.config.values.mode=ae;if(ae==="Auto"){this.data_manager.clear()}ad.request_draw({clear_tile_cache:true});this.action_icons.mode_icon.attr("title","Set display mode (now: "+ad.mode+")");return ad},update_icons:function(){var ad=this;if(ad.filters_available){ad.action_icons.filters_icon.show()}else{ad.action_icons.filters_icon.hide()}if(ad.tool){ad.action_icons.tools_icon.show();ad.action_icons.param_space_viz_icon.show()}else{ad.action_icons.tools_icon.hide();ad.action_icons.param_space_viz_icon.hide()}},_gen_tile_cache_key:function(ae,ad){return ae+"_"+ad},request_draw:function(ad){if(ad&&ad.clear_tile_cache){this.tile_cache.clear()}this.view.request_redraw(ad,this)},before_draw:function(){this.max_height_px=0},_draw:function(ar){if(!this.can_draw()){return}var ao=ar&&ar.clear_after,am=this.view.low,ah=this.view.high,ak=ah-am,ae=this.view.container.width(),aq=this.view.resolution_px_b,ag=1/aq;if(this.is_overview){am=this.view.max_low;ah=this.view.max_high;aq=ae/(view.max_high-view.max_low);ag=1/aq}this.before_draw();this.tiles_div.children().addClass("remove");var ad=Math.floor(am/(ag*S)),al,an,ai,aj=[],ap=[];while((ad*S*ag)<ah){al=Math.floor(ad*S*ag);an=new w.GenomeRegion({chrom:this.view.chrom,start:al,end:Math.min(al+Math.ceil(S*ag),this.view.max_high)});ai=this.draw_helper(an,aq,ar);aj.push(ai);$.when(ai).then(function(at){ap.push(at)});ad+=1}if(!ao){this.tiles_div.children(".remove").removeClass("remove").remove()}var af=this;$.when.apply($,aj).then(function(){af.tiles_div.children(".remove").remove();ap=ac.filter(ap,function(at){return at!==null});if(ap.length!==0){af.postdraw_actions(ap,ae,aq,ao)}})},_add_yaxis_label:function(ag,ai){var ae=this,ah=(ag==="max"?"top":"bottom"),aj=(ag==="max"?"max":"min"),ad=(ag==="max"?"max_value":"min_value"),ai=ai||function(){ae.request_draw({clear_tile_cache:true})},af=this.container_div.find(".yaxislabel."+ah);if(af.length!==0){af.text(ae.prefs[ad])}else{af=$("<div/>").text(ae.prefs[ad]).make_text_editable({num_cols:12,on_finish:function(ak){$(".tooltip").remove();ae.config.set_param_value(ad,ak);ai()},help_text:"Set "+aj+" value"}).addClass("yaxislabel "+ah).css("color",this.prefs.label_color);this.container_div.prepend(af)}},postdraw_actions:function(ag,ah,aj,ad){var af=ac.filter(ag,function(ak){return(ak instanceof M)});if(af.length>0){this.max_height_px=0;var ae=this;ac.each(ag,function(ak){if(!(ak instanceof M)){ak.html_elt.remove();ae.draw_helper(ak.region,aj,{force:true,mode:"Coverage"})}});ae._add_yaxis_label("max")}else{this.container_div.find(".yaxislabel").remove();var ai=ac.find(ag,function(ak){return ak.has_icons});if(ai){ac.each(ag,function(ak){if(!ak.has_icons){ak.html_elt.css("padding-top",D)}})}}},get_mode:function(ad){return this.mode},update_auto_mode:function(ad){},_get_drawables:function(){return[this]},draw_helper:function(am,ap,aq){if(!aq){aq={}}var ae=aq.force,ao=!(aq.data_fetch===false),aj=aq.mode||this.mode,ag=1/ap,af=this,ah=this._get_drawables(),an=this._gen_tile_cache_key(ap,am),ai=function(ar){return(ar&&"track" in ar)};var ak=(ae?undefined:af.tile_cache.get_elt(an));if(ak){if(ai(ak)){af.show_tile(ak,ap)}return ak}if(!ao){return null}var al=function(){var ar=(ac.find(A,function(au){return au===aj})?"Coverage":aj);var at=ac.map(ah,function(au){return au.data_manager.get_data(am,ar,ag,af.data_url_extra_params)});if(view.reference_track){at.push(view.reference_track.data_manager.get_data(am,aj,ag,view.reference_track.data_url_extra_params))}return at};var ad=$.Deferred();af.tile_cache.set_elt(an,ad);$.when.apply($,al()).then(function(){var ar=al(),ax=ar,aD;if(view.reference_track){aD=view.reference_track.data_manager.subset_entry(ar.pop(),am)}var ay=[],av=[];ac.each(ah,function(aI,aF){var aH=aI.mode,aG=ax[aF];if(aH==="Auto"){aH=aI.get_mode(aG);aI.update_auto_mode(aH)}ay.push(aH);av.push(aI.get_canvas_height(aG,aH,ap,at))});var aw=af.view.canvas_manager.new_canvas(),az=am.get("start"),aE=am.get("end"),au=0,at=Math.ceil((aE-az)*ap)+af.left_offset,aB=ac.max(av),aA;aw.width=at;aw.height=(aq.height||aB);var aC=aw.getContext("2d");aC.translate(af.left_offset,0);if(ah.length>1){aC.globalAlpha=0.5;aC.globalCompositeOperation="source-over"}ac.each(ah,function(aG,aF){aA=aG.draw_tile(ax[aF],aC,ay[aF],am,ap,aD)});if(aA!==undefined){af.tile_cache.set_elt(an,aA);af.show_tile(aA,ap)}ad.resolve(aA)});return ad},get_canvas_height:function(ad,af,ag,ae){return this.visible_height_px},_draw_line_track_tile:function(ad,af,ai,ah,aj){var ag=af.canvas,ae=new L.LinePainter(ad.data,ah.get("start"),ah.get("end"),this.prefs,ai);ae.draw(af,ag.width,ag.height,aj);return new M(this,ah,aj,ag,ad.data)},draw_tile:function(ad,ae,ah,ag,ai,af){},show_tile:function(af,ai){var ae=this,ad=af.html_elt;af.predisplay_actions();var ah=(af.low-(this.is_overview?this.view.max_low:this.view.low))*ai;if(this.left_offset){ah-=this.left_offset}ad.css({position:"absolute",top:0,left:ah});if(ad.hasClass("remove")){ad.removeClass("remove")}else{this.tiles_div.append(ad)}af.html_elt.height("auto");this.max_height_px=Math.max(this.max_height_px,af.html_elt.height());af.html_elt.parent().children().css("height",this.max_height_px+"px");var ag=this.max_height_px;if(this.visible_height_px!==0){ag=Math.min(this.max_height_px,this.visible_height_px)}this.tiles_div.css("height",ag+"px")},tool_region_and_parameters_str:function(ag){var ad=this,af=(ag!==undefined?ag.toString():"all"),ae=ac.values(ad.tool.get_inputs_dict()).join(", ");return" - region=["+af+"], parameters=["+ae+"]"},data_and_mode_compatible:function(ad,ae){if(ae==="Auto"){return true}else{if(ae==="Coverage"){return ad.dataset_type==="bigwig"}else{if(ad.dataset_type==="bigwig"||ad.extra_info==="no_detail"){return false}else{return true}}}},can_subset:function(ad){if(ad.message||ad.extra_info==="no_detail"){return false}else{if(ad.dataset_type==="bigwig"){return(ad.data[1][0]-ad.data[0][0]===1)}}return true},init_for_tool_data:function(){this.data_manager.set("data_type","raw_data");this.data_query_wait=1000;this.dataset_check_type="state"}});var W=function(ae,ad){var af={resize:false};f.call(this,ae,ad,af);this.container_div.addClass("label-track")};o(W.prototype,f.prototype,{build_header_div:function(){},init:function(){this.enabled=true},predraw_init:function(){},_draw:function(ah){var af=this.view,ag=af.high-af.low,ak=Math.floor(Math.pow(10,Math.floor(Math.log(ag)/Math.log(10)))),ad=Math.floor(af.low/ak)*ak,ai=this.view.container.width(),ae=$("<div style='position: relative; height: 1.3em;'></div>");while(ad<af.high){var aj=(ad-af.low)/ag*ai;ae.append($("<div class='label'>"+commatize(ad)+"</div>").css({position:"absolute",left:aj-1}));ad+=ak}this.content_div.children(":first").remove();this.content_div.append(ae)}});var e=function(ae,ad,ah){this.display_modes=A;N.call(this,ae,ad,ah);this.drawables=[];if("drawables" in ah){var ag;for(var af=0;af<ah.drawables.length;af++){ag=ah.drawables[af];this.drawables[af]=n(ag,ae,null);if(ag.left_offset>this.left_offset){this.left_offset=ag.left_offset}}this.enabled=true}ac.each(this.drawables,function(ai){if(ai instanceof c||ai instanceof T){ai.change_mode("Coverage")}});this.update_icons();this.obj_type="CompositeTrack"};o(e.prototype,N.prototype,{action_icons_def:[{name:"composite_icon",title:"Show individual tracks",css_class:"layers-stack",on_click_fn:function(ad){$(".tooltip").remove();ad.show_group()}}].concat(N.prototype.action_icons_def),to_dict:y.prototype.to_dict,add_drawable:y.prototype.add_drawable,unpack_drawables:y.prototype.unpack_drawables,change_mode:function(ad){N.prototype.change_mode.call(this,ad);for(var ae=0;ae<this.drawables.length;ae++){this.drawables[ae].change_mode(ad)}},init:function(){var af=[];for(var ae=0;ae<this.drawables.length;ae++){af.push(this.drawables[ae].init())}var ad=this;$.when.apply($,af).then(function(){ad.enabled=true;ad.request_draw()})},update_icons:function(){this.action_icons.filters_icon.hide();this.action_icons.tools_icon.hide();this.action_icons.param_space_viz_icon.hide()},can_draw:p.prototype.can_draw,_get_drawables:function(){return this.drawables},show_group:function(){var ag=new P(this.view,this.container,{name:this.name}),ad;for(var af=0;af<this.drawables.length;af++){ad=this.drawables[af];ad.update_icons();ag.add_drawable(ad);ad.container=ag;ag.content_div.append(ad.container_div)}var ae=this.container.replace_drawable(this,ag,true);ag.request_draw({clear_tile_cache:true})},before_draw:function(){N.prototype.before_draw.call(this);var ae=ac.min(ac.map(this.drawables,function(af){return af.prefs.min_value})),ad=ac.max(ac.map(this.drawables,function(af){return af.prefs.max_value}));this.prefs.min_value=ae;this.prefs.max_value=ad;ac.each(this.drawables,function(af){af.prefs.min_value=ae;af.prefs.max_value=ad})},update_all_min_max:function(){var ad=this;ac.each(this.drawables,function(ae){ae.prefs.min_value=ad.prefs.min_value;ae.prefs.max_value=ad.prefs.max_value});this.request_draw({clear_tile_cache:true})},postdraw_actions:function(aj,ad,am,ai){N.prototype.postdraw_actions.call(this,aj,ad,am,ai);var ah=-1;for(var af=0;af<aj.length;af++){var ak=aj[af].html_elt.find("canvas").height();if(ak>ah){ah=ak}}for(var af=0;af<aj.length;af++){var ag=aj[af];if(ag.html_elt.find("canvas").height()!==ah){this.draw_helper(ag.region,am,{force:true,height:ah});ag.html_elt.remove()}}var ae=this,al=function(){ae.update_all_min_max()};this._add_yaxis_label("min",al);this._add_yaxis_label("max",al)}});var B=function(ad){N.call(this,ad,{content_div:ad.top_labeltrack},{resize:false});ad.reference_track=this;this.left_offset=200;this.visible_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=galaxy_config.root+"api/genomes//"+this.view.dbkey;this.data_url_extra_params={reference:true};this.data_manager=new w.GenomeReferenceDataManager({data_url:this.data_url,can_subset:this.can_subset});this.hide_contents()};o(B.prototype,p.prototype,N.prototype,{build_header_div:function(){},init:function(){this.data_manager.clear();this.enabled=true},predraw_init:function(){},can_draw:p.prototype.can_draw,draw_helper:function(ae,af,ad){if(af>this.view.canvas_manager.char_width_px){this.tiles_div.show();return N.prototype.draw_helper.call(this,ae,af,ad)}else{this.tiles_div.hide();return null}},can_subset:function(ad){return true},draw_tile:function(af,al,ag,ai,am){var ae=this.data_manager.subset_entry(af,ai),ak=ae.data;var ad=al.canvas;al.font=al.canvas.manager.default_font;al.textAlign="center";for(var ah=0,aj=ak.length;ah<aj;ah++){al.fillStyle=this.view.get_base_color(ak[ah]);al.fillText(ak[ah],Math.floor(ah*am),10)}return new b(this,ai,am,ad,ae)}});var g=function(af,ae,ag){var ad=this;this.display_modes=A;this.mode="Histogram";N.call(this,af,ae,ag);this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"color",label:"Color",type:"color",default_value:j.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:32,hidden:true}],saved_values:ag.prefs,onchange:function(){ad.set_name(ad.prefs.name);ad.request_redraw({clear_tile_cache:true})}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height};o(g.prototype,p.prototype,N.prototype,{before_draw:function(){},draw_tile:function(ad,ae,ag,af,ah){return this._draw_line_track_tile(ad,ae,ag,af,ah)},can_subset:function(ad){return(ad.data[1][0]-ad.data[0][0]===1)},postdraw_actions:function(ae,af,ag,ad){this._add_yaxis_label("max");this._add_yaxis_label("min")}});var r=function(af,ae,ag){var ad=this;this.display_modes=["Heatmap"];this.mode="Heatmap";N.call(this,af,ae,ag);this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"pos_color",label:"Positive Color",type:"color",default_value:"#FF8C00"},{key:"neg_color",label:"Negative Color",type:"color",default_value:"#4169E1"},{key:"min_value",label:"Min Value",type:"float",default_value:-1},{key:"max_value",label:"Max Value",type:"float",default_value:1},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:500,hidden:true}],saved_values:ag.prefs,onchange:function(){ad.set_name(ad.prefs.name);this.request_redraw({clear_tile_cache:true})}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height};o(r.prototype,p.prototype,N.prototype,{draw_tile:function(ad,af,ai,ah,aj){var ag=af.canvas,ae=new L.DiagonalHeatmapPainter(ad.data,ah.get("start"),ah.get("end"),this.prefs,ai);ae.draw(af,ag.width,ag.height,aj);return new b(this,ah,aj,ag,ad.data)}});var c=function(ag,af,ai){var ae=this;this.display_modes=["Auto","Coverage","Dense","Squish","Pack"];N.call(this,ag,af,ai);var ah=j.get_random_color(),ad=j.get_random_color([ah,"#FFFFFF"]);this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block color",type:"color",default_value:ah},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:ad},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true,help:"Show the number of items in each bin when drawing summary histogram"},{key:"min_value",label:"Histogram minimum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"connector_style",label:"Connector style",type:"select",default_value:"fishbones",options:[{label:"Line with arrows",value:"fishbone"},{label:"Arcs",value:"arcs"}]},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:this.visible_height_px,hidden:true}],saved_values:ai.prefs,onchange:function(){ae.set_name(ae.prefs.name);ae.set_painter_from_config();ae.request_draw({clear_tile_cache:true})}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height;this.container_div.addClass("feature-track");this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.slotters={};this.start_end_dct={};this.left_offset=200;this.set_painter_from_config()};o(c.prototype,p.prototype,N.prototype,{set_painter_from_config:function(){if(this.config.values.connector_style==="arcs"){this.painter=L.ArcLinkedFeaturePainter}else{this.painter=L.LinkedFeaturePainter}},postdraw_actions:function(an,af,ao,am){N.prototype.postdraw_actions.call(this,an,af,ao,am);var ah=this,ai;if(ah.filters_manager){var ag=ah.filters_manager.filters;for(var ak=0;ak<ag.length;ak++){ag[ak].update_ui_elt()}var aj=false,al,ae;for(ai=0;ai<an.length;ai++){if(an[ai].data.length){al=an[ai].data[0];for(var ak=0;ak<ag.length;ak++){ae=ag[ak];if(ae.applies_to(al)&&ae.min!==ae.max){aj=true;break}}}}if(ah.filters_available!==aj){ah.filters_available=aj;if(!ah.filters_available){ah.filters_manager.hide()}ah.update_icons()}}if(an[0] instanceof O){var ad=true;for(ai=0;ai<an.length;ai++){if(!an[ai].all_slotted){ad=false;break}}if(!ad){this.action_icons.show_more_rows_icon.show()}else{this.action_icons.show_more_rows_icon.hide()}}else{this.action_icons.show_more_rows_icon.hide()}},update_auto_mode:function(ad){var ad;if(this.mode==="Auto"){if(ad==="no_detail"){ad="feature spans"}this.action_icons.mode_icon.attr("title","Set display mode (now: Auto/"+ad+")")}},incremental_slots:function(ah,ad,ag){var ae=this.view.canvas_manager.dummy_context,af=this.slotters[ah];if(!af||(af.mode!==ag)){af=new (s.FeatureSlotter)(ah,ag,z,function(ai){return ae.measureText(ai)});this.slotters[ah]=af}return af.slot_features(ad)},get_mode:function(ad){if(ad.extra_info==="no_detail"||this.is_overview){mode="no_detail"}else{if(this.view.high-this.view.low>I){mode="Squish"}else{mode="Pack"}}return mode},get_canvas_height:function(ad,ah,ai,ae){if(ah==="Coverage"||ad.dataset_type==="bigwig"){return this.summary_draw_height}else{var ag=this.incremental_slots(ai,ad.data,ah);var af=new (this.painter)(null,null,null,this.prefs,ah);return Math.max(aa,af.get_required_height(ag,ae))}},draw_tile:function(an,ar,ap,ag,ak,af){var aq=this,ae=ar.canvas,ay=ag.get("start"),ad=ag.get("end"),ah=this.left_offset;if(an.dataset_type==="bigwig"){return this._draw_line_track_tile(an,ar,ap,ag,ak)}var aj=[],ao=this.slotters[ak].slots;all_slotted=true;if(an.data){var al=this.filters_manager.filters;for(var at=0,av=an.data.length;at<av;at++){var ai=an.data[at];var au=false;var am;for(var ax=0,aC=al.length;ax<aC;ax++){am=al[ax];am.update_attrs(ai);if(!am.keep(ai)){au=true;break}}if(!au){aj.push(ai);if(!(ai[0] in ao)){all_slotted=false}}}}var aB=(this.filters_manager.alpha_filter?new C(this.filters_manager.alpha_filter):null),az=(this.filters_manager.height_filter?new C(this.filters_manager.height_filter):null),aA=new (this.painter)(aj,ay,ad,this.prefs,ap,aB,az,af,function(aD){return aq.view.get_base_color(aD)});var aw=null;ar.fillStyle=this.prefs.block_color;ar.font=ar.canvas.manager.default_font;ar.textAlign="right";if(an.data){aw=aA.draw(ar,ae.width,ae.height,ak,ao);aw.translation=-ah}return new O(aq,ag,ak,ae,an.data,ap,an.message,all_slotted,aw)}});var Z=function(ae,ad,af){this.display_modes=["Auto","Coverage","Dense","Squish","Pack"];N.call(this,ae,ad,af);this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"color",label:"Histogram color",type:"color",default_value:j.get_random_color()},{key:"show_sample_data",label:"Show sample data",type:"bool",default_value:true},{key:"show_labels",label:"Show summary and sample labels",type:"bool",default_value:true},{key:"summary_height",label:"Locus summary height",type:"float",default_value:20},{key:"mode",type:"string",default_value:this.mode,hidden:true}],saved_values:af.prefs,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.request_draw({clear_tile_cache:true})}});this.prefs=this.config.values;this.painter=L.VariantPainter;this.summary_draw_height=30;this.left_offset=30};o(Z.prototype,p.prototype,N.prototype,{draw_tile:function(ad,ag,ai,ah,aj){if(ad.dataset_type==="bigwig"){return this._draw_line_track_tile(ad,ag,"Histogram",ah,aj)}else{var af=this.view,ae=new (this.painter)(ad.data,ah.get("start"),ah.get("end"),this.prefs,ai,function(ak){return af.get_base_color(ak)});ae.draw(ag,ag.canvas.width,ag.canvas.height,aj);return new b(this,ah,aj,ag.canvas,ad.data)}},get_canvas_height:function(ad,ah,ai,af){if(ad.dataset_type==="bigwig"){return this.summary_draw_height}else{var ag=new (this.painter)(null,null,null,this.prefs,ah);var ae=(this.dataset.get_metadata("sample_names")?this.dataset.get_metadata("sample_names").length:0);if(ae===0&&ad.data.length!==0){ae=ad.data[0][7].match(/,/g);if(ae===null){ae=1}else{ae=ae.length+1}}return ag.get_required_height(ae)}},predraw_init:function(){var ad=[f.prototype.predraw_init.call(this)];if(!this.dataset.get_metadata("sample_names")){ad.push(this.dataset.fetch())}return ad},postdraw_actions:function(ag,ah,aj,ae){N.prototype.postdraw_actions.call(this,ag,ah,aj,ae);var af=ac.filter(ag,function(ak){return(ak instanceof M)});if(af.length===0&&this.prefs.show_labels){var ad;if(this.container_div.find(".yaxislabel.variant").length===0){ad=this.prefs.summary_height/2;this.tiles_div.prepend($("<div/>").text("Summary").addClass("yaxislabel variant top").css({"font-size":ad+"px",top:(this.prefs.summary_height-ad)/2+"px"}));if(this.prefs.show_sample_data){var ai=this.dataset.get("metadata").get("sample_names").join("<br/>");this.tiles_div.prepend($("<div/>").html(ai).addClass("yaxislabel variant top sample").css({top:this.prefs.summary_height+2,}))}}ad=(this.mode==="Squish"?5:10)+"px";$(this.tiles_div).find(".sample").css({"font-size":ad,"line-height":ad});$(this.tiles_div).find(".yaxislabel").css("color",this.prefs.label_color)}else{this.container_div.find(".yaxislabel.variant").remove()}}});var T=function(af,ae,ah){c.call(this,af,ae,ah);var ag=j.get_random_color(),ad=j.get_random_color([ag,"#ffffff"]);this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block and sense strand color",type:"color",default_value:ag},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:ad},{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},{key:"min_value",label:"Histogram minimum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"}],saved_values:ah.prefs,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.request_draw({clear_tile_cache:true})}});this.prefs=this.config.values;this.painter=(af.reference_track?L.RefBasedReadPainter:L.ReadPainter);this.update_icons()};o(T.prototype,p.prototype,N.prototype,c.prototype);var d={CompositeTrack:e,DrawableGroup:P,DiagonalHeatmapTrack:r,FeatureTrack:c,LineTrack:g,ReadTrack:T,VariantTrack:Z,VcfTrack:Z};var n=function(af,ae,ad){if("copy" in af){return af.copy(ad)}else{var ag=af.obj_type;if(!ag){ag=af.track_type}return new d[ag](ae,ad,af)}};return{TracksterView:Y,DrawableGroup:P,LineTrack:g,FeatureTrack:c,DiagonalHeatmapTrack:r,ReadTrack:T,VariantTrack:Z,CompositeTrack:e,object_from_template:n}}); \ No newline at end of file +define(["libs/underscore","viz/visualization","viz/trackster/util","viz/trackster/slotting","viz/trackster/painters","viz/trackster/filters","mvc/data","mvc/tools"],function(ac,w,j,s,L,h,X,R){var o=ac.extend;var l={};var i=function(ad,ae){l[ad.attr("id")]=ae};var k=function(ad,af,ah,ag){ah=".group";var ae={};l[ad.attr("id")]=ag;ad.bind("drag",{handle:"."+af,relative:true},function(ap,aq){var ao=$(this),au=$(this).parent(),al=au.children(),an=l[$(this).attr("id")],ak,aj,ar,ai,am;aj=$(this).parents(ah);if(aj.length!==0){ar=aj.position().top;ai=ar+aj.outerHeight();if(aq.offsetY<ar){$(this).insertBefore(aj);var at=l[aj.attr("id")];at.remove_drawable(an);at.container.add_drawable_before(an,at);return}else{if(aq.offsetY>ai){$(this).insertAfter(aj);var at=l[aj.attr("id")];at.remove_drawable(an);at.container.add_drawable(an);return}}}aj=null;for(am=0;am<al.length;am++){ak=$(al.get(am));ar=ak.position().top;ai=ar+ak.outerHeight();if(ak.is(ah)&&this!==ak.get(0)&&aq.offsetY>=ar&&aq.offsetY<=ai){if(aq.offsetY-ar<ai-aq.offsetY){ak.find(".content-div").prepend(this)}else{ak.find(".content-div").append(this)}if(an.container){an.container.remove_drawable(an)}l[ak.attr("id")].add_drawable(an);return}}for(am=0;am<al.length;am++){ak=$(al.get(am));if(aq.offsetY<ak.position().top&&!(ak.hasClass("reference-track")||ak.hasClass("intro"))){break}}if(am===al.length){if(this!==al.get(am-1)){au.append(this);l[au.attr("id")].move_drawable(an,am)}}else{if(this!==al.get(am)){$(this).insertBefore(al.get(am));l[au.attr("id")].move_drawable(an,(aq.deltaY>0?am-1:am))}}}).bind("dragstart",function(){ae["border-top"]=ad.css("border-top");ae["border-bottom"]=ad.css("border-bottom");$(this).css({"border-top":"1px solid blue","border-bottom":"1px solid blue"})}).bind("dragend",function(){$(this).css(ae)})};var aa=16,G=9,D=20,z=100,I=12000,S=400,K=5000,v=100,m="Cannot display dataset due to an error. ",J="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",E="No data for this chrom/contig.",u="Preparing data. This can take a while for a large dataset. If the visualization is saved and closed, preparation will continue in the background.",x="Tool cannot be rerun: ",a="Loading data...",U="Ready for display",Q=10,H=20,A=["Histogram","Line","Filled","Intensity"];function V(ae,ad){if(!ad){ad=0}var af=Math.pow(10,ad);return Math.round(ae*af)/af}var p=function(ae,ad,ag){if(!p.id_counter){p.id_counter=0}this.id=p.id_counter++;this.name=ag.name;this.view=ae;this.container=ad;this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name}],saved_values:ag.prefs,onchange:function(){this.track.set_name(this.track.config.values.name)}});this.prefs=this.config.values;this.drag_handle_class=ag.drag_handle_class;this.is_overview=false;this.action_icons={};this.content_visible=true;this.container_div=this.build_container_div();this.header_div=this.build_header_div();if(this.header_div){this.container_div.append(this.header_div);this.icons_div=$("<div/>").css("float","left").hide().appendTo(this.header_div);this.build_action_icons(this.action_icons_def);this.header_div.append($("<div style='clear: both'/>"));this.header_div.dblclick(function(ah){ah.stopPropagation()});var af=this;this.container_div.hover(function(){af.icons_div.show()},function(){af.icons_div.hide()});$("<div style='clear: both'/>").appendTo(this.container_div)}};p.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(ad){if(ad.content_visible){ad.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle");ad.hide_contents();ad.content_visible=false}else{ad.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand");ad.content_visible=true;ad.show_contents()}}},{name:"settings_icon",title:"Edit settings",css_class:"settings-icon",on_click_fn:function(ae){var ag=function(){Galaxy.modal.hide();$(window).unbind("keypress.check_enter_esc")},ad=function(){ae.config.update_from_form($(Galaxy.modal.el));Galaxy.modal.hide();$(window).unbind("keypress.check_enter_esc")},af=function(ah){if((ah.keyCode||ah.which)===27){ag()}else{if((ah.keyCode||ah.which)===13){ad()}}};$(window).bind("keypress.check_enter_esc",af);Galaxy.modal.show({title:"Configure",body:ae.config.build_form(),buttons:{Cancel:ag,Ok:ad}})}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(ad){$(".tooltip").remove();ad.remove()}}];o(p.prototype,{init:function(){},changed:function(){this.view.changed()},can_draw:function(){if(this.enabled&&this.content_visible){return true}return false},request_draw:function(){},_draw:function(ad){},to_dict:function(){},set_name:function(ad){this.old_name=this.name;this.name=ad;this.name_div.text(this.name)},revert_name:function(){if(this.old_name){this.name=this.old_name;this.name_div.text(this.name)}},remove:function(){this.changed();this.container.remove_drawable(this);var ad=this.view;this.container_div.hide(0,function(){$(this).remove();ad.update_intro_div()})},build_container_div:function(){},build_header_div:function(){},add_action_icon:function(ae,aj,ai,ah,ad,ag){var af=this;this.action_icons[ae]=$("<a/>").attr("href","javascript:void(0);").attr("title",aj).addClass("icon-button").addClass(ai).tooltip().click(function(){ah(af)}).appendTo(this.icons_div);if(ag){this.action_icons[ae].hide()}},build_action_icons:function(ad){var af;for(var ae=0;ae<ad.length;ae++){af=ad[ae];this.add_action_icon(af.name,af.title,af.css_class,af.on_click_fn,af.prepend,af.hide)}},update_icons:function(){},hide_contents:function(){},show_contents:function(){},get_drawables:function(){}});var y=function(ae,ad,af){p.call(this,ae,ad,af);this.obj_type=af.obj_type;this.drawables=[]};o(y.prototype,p.prototype,{unpack_drawables:function(af){this.drawables=[];var ae;for(var ad=0;ad<af.length;ad++){ae=n(af[ad],this.view,this);this.add_drawable(ae)}},init:function(){for(var ad=0;ad<this.drawables.length;ad++){this.drawables[ad].init()}},_draw:function(ad){for(var ae=0;ae<this.drawables.length;ae++){this.drawables[ae]._draw(ad)}},to_dict:function(){var ae=[];for(var ad=0;ad<this.drawables.length;ad++){ae.push(this.drawables[ad].to_dict())}return{name:this.name,prefs:this.prefs,obj_type:this.obj_type,drawables:ae}},add_drawable:function(ad){this.drawables.push(ad);ad.container=this;this.changed()},add_drawable_before:function(af,ad){this.changed();var ae=this.drawables.indexOf(ad);if(ae!==-1){this.drawables.splice(ae,0,af);return true}return false},replace_drawable:function(af,ad,ae){var ag=this.drawables.indexOf(af);if(ag!==-1){this.drawables[ag]=ad;if(ae){af.container_div.replaceWith(ad.container_div)}this.changed()}return ag},remove_drawable:function(ae){var ad=this.drawables.indexOf(ae);if(ad!==-1){this.drawables.splice(ad,1);ae.container=null;this.changed();return true}return false},move_drawable:function(ae,af){var ad=this.drawables.indexOf(ae);if(ad!==-1){this.drawables.splice(ad,1);this.drawables.splice(af,0,ae);this.changed();return true}return false},get_drawables:function(){return this.drawables},get_tracks:function(ag){var ad=this.drawables.slice(0),ae=[],af;while(ad.length!==0){af=ad.shift();if(af instanceof ag){ae.push(af)}else{if(af.drawables){ad=ad.concat(af.drawables)}}}return ae}});var P=function(ae,ad,ag){o(ag,{obj_type:"DrawableGroup",drag_handle_class:"group-handle"});y.call(this,ae,ad,ag);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div);i(this.container_div,this);i(this.content_div,this);k(this.container_div,this.drag_handle_class,".group",this);this.filters_manager=new h.FiltersManager(this);this.header_div.after(this.filters_manager.parent_div);this.saved_filters_managers=[];if("drawables" in ag){this.unpack_drawables(ag.drawables)}if("filters" in ag){var af=this.filters_manager;this.filters_manager=new h.FiltersManager(this,ag.filters);af.parent_div.replaceWith(this.filters_manager.parent_div);if(ag.filters.visible){this.setup_multitrack_filtering()}}};o(P.prototype,p.prototype,y.prototype,{action_icons_def:[p.prototype.action_icons_def[0],p.prototype.action_icons_def[1],{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(ad){$(".tooltip").remove();ad.show_composite_track()}},{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ad){if(ad.filters_manager.visible()){ad.filters_manager.clear_filters();ad._restore_filter_managers()}else{ad.setup_multitrack_filtering();ad.request_draw({clear_tile_cache:true})}ad.filters_manager.toggle()}},p.prototype.action_icons_def[2]],build_container_div:function(){var ad=$("<div/>").addClass("group").attr("id","group_"+this.id);if(this.container){this.container.content_div.append(ad)}return ad},build_header_div:function(){var ad=$("<div/>").addClass("track-header");ad.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("track-name").text(this.name).appendTo(ad);return ad},hide_contents:function(){this.tiles_div.hide()},show_contents:function(){this.tiles_div.show();this.request_draw()},update_icons:function(){var af=this.drawables.length;if(af===0){this.action_icons.composite_icon.hide();this.action_icons.filters_icon.hide()}else{if(af===1){if(this.drawables[0] instanceof e){this.action_icons.composite_icon.show()}this.action_icons.filters_icon.hide()}else{var am,al,aj,ap=true,ah=this.drawables[0].get_type(),ad=0;for(am=0;am<af;am++){aj=this.drawables[am];if(aj.get_type()!==ah){can_composite=false;break}if(aj instanceof c){ad++}}if(ap||ad===1){this.action_icons.composite_icon.show()}else{this.action_icons.composite_icon.hide();$(".tooltip").remove()}if(ad>1&&ad===this.drawables.length){var aq={},ae;aj=this.drawables[0];for(al=0;al<aj.filters_manager.filters.length;al++){ae=aj.filters_manager.filters[al];aq[ae.name]=[ae]}for(am=1;am<this.drawables.length;am++){aj=this.drawables[am];for(al=0;al<aj.filters_manager.filters.length;al++){ae=aj.filters_manager.filters[al];if(ae.name in aq){aq[ae.name].push(ae)}}}this.filters_manager.remove_all();var ag,ai,ak,an;for(var ao in aq){ag=aq[ao];if(ag.length===ad){ai=new h.NumberFilter({name:ag[0].name,index:ag[0].index});this.filters_manager.add_filter(ai)}}if(this.filters_manager.filters.length>0){this.action_icons.filters_icon.show()}else{this.action_icons.filters_icon.hide()}}else{this.action_icons.filters_icon.hide()}}}},_restore_filter_managers:function(){for(var ad=0;ad<this.drawables.length;ad++){this.drawables[ad].filters_manager=this.saved_filters_managers[ad]}this.saved_filters_managers=[]},setup_multitrack_filtering:function(){if(this.filters_manager.filters.length>0){this.saved_filters_managers=[];for(var ad=0;ad<this.drawables.length;ad++){drawable=this.drawables[ad];this.saved_filters_managers.push(drawable.filters_manager);drawable.filters_manager=this.filters_manager}}this.filters_manager.init_filters()},show_composite_track:function(){var ae=new e(this.view,this.view,{name:this.name,drawables:this.drawables});var ad=this.container.replace_drawable(this,ae,true);ae.request_draw()},add_drawable:function(ad){y.prototype.add_drawable.call(this,ad);this.update_icons()},remove_drawable:function(ad){y.prototype.remove_drawable.call(this,ad);this.update_icons()},to_dict:function(){if(this.filters_manager.visible()){this._restore_filter_managers()}var ad=o(y.prototype.to_dict.call(this),{filters:this.filters_manager.to_dict()});if(this.filters_manager.visible()){this.setup_multitrack_filtering()}return ad},request_draw:function(ad){ac.each(this.drawables,function(ae){ae.request_draw(ad)})}});var Y=Backbone.View.extend({initialize:function(ad){o(ad,{obj_type:"View"});y.call(this,"View",ad.container,ad);this.chrom=null;this.vis_id=ad.vis_id;this.dbkey=ad.dbkey;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.render();this.canvas_manager=new w.CanvasManager(this.container.get(0).ownerDocument);this.reset();this.config=new F({track:this,params:[{key:"a_color",label:"A Color",type:"color",default_value:"#FF0000"},{key:"c_color",label:"C Color",type:"color",default_value:"#00FF00"},{key:"g_color",label:"G Color",type:"color",default_value:"#0000FF"},{key:"t_color",label:"T Color",type:"color",default_value:"#FF00FF"},{key:"n_color",label:"N Color",type:"color",default_value:"#AAAAAA"}],saved_values:ad.prefs,onchange:function(){track.request_redraw({clear_tile_cache:true})}})},render:function(){this.requested_redraw=false;var af=this.container,ad=this;this.top_container=$("<div/>").addClass("top-container").appendTo(af);this.browser_content_div=$("<div/>").addClass("content").css("position","relative").appendTo(af);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(af);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;i(this.viewport_container,ad);this.intro_div=$("<div/>").addClass("intro").appendTo(this.viewport_container).hide();var ag=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){w.select_datasets(galaxy_config.root+"visualization/list_current_history_datasets",galaxy_config.root+"api/datasets",{"f-dbkey":ad.dbkey},function(ah){ac.each(ah,function(ai){ad.add_drawable(n(ai,ad,ad))})})});this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("trackster-nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("trackster-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").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var ae=function(ah){if(ah.type==="focusout"||(ah.keyCode||ah.which)===13||(ah.keyCode||ah.which)===27){if((ah.keyCode||ah.which)!==27){ad.go_to($(this).val())}$(this).hide();$(this).val("");ad.location_span.show();ad.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ae).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").attr("original-title","Click to change location").tooltip({placement:"bottom"}).appendTo(this.nav_controls);this.location_span.click(function(){ad.location_span.hide();ad.chrom_select.hide();ad.nav_input.val(ad.chrom+":"+ad.low+"-"+ad.high);ad.nav_input.css("display","inline-block");ad.nav_input.select();ad.nav_input.focus();ad.nav_input.autocomplete({source:function(aj,ah){var ak=[],ai=$.map(ad.get_tracks(c),function(al){return al.data_manager.search_features(aj.term).success(function(am){ak=ak.concat(am)})});$.when.apply($,ai).done(function(){ah($.map(ak,function(al){return{label:al[0],value:al[1]}}))})}})});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a/>").attr("id","zoom-out").attr("title","Zoom out").tooltip({placement:"bottom"}).click(function(){ad.zoom_out();ad.request_redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a/>").attr("id","zoom-in").attr("title","Zoom in").tooltip({placement:"bottom"}).click(function(){ad.zoom_in();ad.request_redraw()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){ad.change_chrom(ad.chrom_select.val())});this.browser_content_div.click(function(ah){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(ah){ad.zoom_in(ah.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(ah,ai){this.current_x=ai.offsetX}).bind("drag",function(ah,aj){var ak=aj.offsetX-this.current_x;this.current_x=aj.offsetX;var ai=Math.round(ak/ad.viewport_container.width()*(ad.max_high-ad.max_low));ad.move_delta(-ai)});this.overview_close.click(function(){ad.reset_overview()});this.viewport_container.bind("draginit",function(ah,ai){if(ah.clientX>ad.viewport_container.width()-16){return false}}).bind("dragstart",function(ah,ai){ai.original_low=ad.low;ai.current_height=ah.clientY;ai.current_x=ai.offsetX}).bind("drag",function(aj,al){var ah=$(this);var am=al.offsetX-al.current_x;var ai=ah.scrollTop()-(aj.clientY-al.current_height);ah.scrollTop(ai);al.current_height=aj.clientY;al.current_x=al.offsetX;var ak=Math.round(am/ad.viewport_container.width()*(ad.high-ad.low));ad.move_delta(ak)}).bind("mousewheel",function(aj,al,ai,ah){if(ai){ai*=50;var ak=Math.round(-ai/ad.viewport_container.width()*(ad.high-ad.low));ad.move_delta(ak)}});this.top_labeltrack.bind("dragstart",function(ah,ai){return $("<div />").css({height:ad.browser_content_div.height()+ad.top_labeltrack.height()+ad.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(al,am){$(am.proxy).css({left:Math.min(al.pageX,am.startX)-ad.container.offset().left,width:Math.abs(al.pageX-am.startX)});var ai=Math.min(al.pageX,am.startX)-ad.container.offset().left,ah=Math.max(al.pageX,am.startX)-ad.container.offset().left,ak=(ad.high-ad.low),aj=ad.viewport_container.width();ad.update_location(Math.round(ai/aj*ak)+ad.low,Math.round(ah/aj*ak)+ad.low)}).bind("dragend",function(am,an){var ai=Math.min(am.pageX,an.startX),ah=Math.max(am.pageX,an.startX),ak=(ad.high-ad.low),aj=ad.viewport_container.width(),al=ad.low;ad.low=Math.round(ai/aj*ak)+al;ad.high=Math.round(ah/aj*ak)+al;$(an.proxy).remove();ad.request_redraw()});this.add_label_track(new W(this,{content_div:this.top_labeltrack}));this.add_label_track(new W(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){if(this.resize_timer){clearTimeout(this.resize_timer)}this.resize_timer=setTimeout(function(){ad.resize_window()},500)});$(document).bind("redraw",function(){ad.redraw()});this.reset();$(window).trigger("resize")},get_base_color:function(ad){return this.config.values[ad.toLowerCase()+"_color"]||this.config.values.n_color}});o(Y.prototype,y.prototype,{changed:function(){this.has_changes=true},update_intro_div:function(){if(this.drawables.length===0){this.intro_div.show()}else{this.intro_div.hide()}},trigger_navigate:function(ae,ag,ad,ah){if(this.timer){clearTimeout(this.timer)}if(ah){var af=this;this.timer=setTimeout(function(){af.trigger("navigate",ae+":"+ag+"-"+ad)},500)}else{view.trigger("navigate",ae+":"+ag+"-"+ad)}},update_location:function(ad,af){this.location_span.text(commatize(ad)+" - "+commatize(af));this.nav_input.val(this.chrom+":"+commatize(ad)+"-"+commatize(af));var ae=view.chrom_select.val();if(ae!==""){this.trigger_navigate(ae,view.low,view.high,true)}},load_chroms:function(af){af.num=v;var ad=this,ae=$.Deferred();$.ajax({url:galaxy_config.root+"api/genomes/"+this.dbkey,data:af,dataType:"json",success:function(ah){if(ah.chrom_info.length===0){return}if(ah.reference){ad.add_label_track(new B(ad))}ad.chrom_data=ah.chrom_info;var ak='<option value="">Select Chrom/Contig</option>';for(var aj=0,ag=ad.chrom_data.length;aj<ag;aj++){var ai=ad.chrom_data[aj].chrom;ak+='<option value="'+ai+'">'+ai+"</option>"}if(ah.prev_chroms){ak+='<option value="previous">Previous '+v+"</option>"}if(ah.next_chroms){ak+='<option value="next">Next '+v+"</option>"}ad.chrom_select.html(ak);ad.chrom_start_index=ah.start_index;ae.resolve(ah.chrom_info)},error:function(){alert("Could not load chroms for this dbkey:",ad.dbkey)}});return ae},change_chrom:function(ai,ae,ak){var af=this;if(!af.chrom_data){af.load_chroms_deferred.then(function(){af.change_chrom(ai,ae,ak)});return}if(!ai||ai==="None"){return}if(ai==="previous"){af.load_chroms({low:this.chrom_start_index-v});return}if(ai==="next"){af.load_chroms({low:this.chrom_start_index+v});return}var aj=$.grep(af.chrom_data,function(al,am){return al.chrom===ai})[0];if(aj===undefined){af.load_chroms({chrom:ai},function(){af.change_chrom(ai,ae,ak)});return}else{if(ai!==af.chrom){af.chrom=ai;af.chrom_select.val(af.chrom);af.max_high=aj.len-1;af.reset();for(var ah=0,ad=af.drawables.length;ah<ad;ah++){var ag=af.drawables[ah];if(ag.init){ag.init()}}if(af.reference_track){af.reference_track.init()}}if(ae&&ak){af.low=Math.max(ae,0);af.high=Math.min(ak,af.max_high)}else{af.low=0;af.high=af.max_high}af.reset_overview();af.request_redraw()}},go_to:function(ah){ah=ah.replace(/,/g,"");ah=ah.replace(/:|\-/g," ");var ae=ah.split(/\s+/),ag=ae[0],af=(ae[1]?parseInt(ae[1],10):null),ad=(ae[2]?parseInt(ae[2],10):null);if(!ad){af=af-15;ad=af+15}this.change_chrom(ag,af,ad)},move_fraction:function(af){var ad=this;var ae=ad.high-ad.low;this.move_delta(af*ae)},move_delta:function(ag){var ad=this;var af=ad.high-ad.low;if(ad.low-ag<ad.max_low){ad.low=ad.max_low;ad.high=ad.max_low+af}else{if(ad.high-ag>ad.max_high){ad.high=ad.max_high;ad.low=ad.max_high-af}else{ad.high-=ag;ad.low-=ag}}ad.request_redraw({data_fetch:false});if(this.redraw_on_move_fn){clearTimeout(this.redraw_on_move_fn)}this.redraw_on_move_fn=setTimeout(function(){ad.request_redraw()},200);var ae=ad.chrom_select.val();this.trigger_navigate(ae,ad.low,ad.high,true)},add_drawable:function(ad){y.prototype.add_drawable.call(this,ad);ad.init();this.changed();this.update_intro_div()},add_label_track:function(ad){ad.view=this;ad.init();this.label_tracks.push(ad)},remove_drawable:function(af,ae){y.prototype.remove_drawable.call(this,af);if(ae){var ad=this;af.container_div.hide(0,function(){$(this).remove();ad.update_intro_div()})}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(ae,af){var ad=this,ag=(af?[af]:ad.drawables);ac.each(ag,function(ah){var ai=ac.find(ad.tracks_to_be_redrawn,function(aj){return aj[0]===ah});if(ai){ai[1]=ae}else{ad.tracks_to_be_redrawn.push([ah,ae])}});if(!this.requested_redraw){requestAnimationFrame(function(){ad._redraw()});this.requested_redraw=true}},_redraw:function(){this.requested_redraw=false;var ad=this.low,ah=this.high;if(ad<this.max_low){ad=this.max_low}if(ah>this.max_high){ah=this.max_high}var ae=this.high-this.low;if(this.high!==0&&ae<this.min_separation){ah=ad+this.min_separation}this.low=Math.floor(ad);this.high=Math.ceil(ah);this.update_location(this.low,this.high);this.resolution_px_b=this.viewport_container.width()/(this.high-this.low);var ag=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ai=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var af=13;this.overview_box.css({left:ag,width:Math.max(af,ai)}).show();if(ai<af){this.overview_box.css("left",ag-(af-ai)/2)}if(this.overview_highlight){this.overview_highlight.css({left:ag,width:ai})}ac.each(this.tracks_to_be_redrawn,function(al){var aj=al[0],ak=al[1];if(aj){aj._draw(ak)}});this.tracks_to_be_redrawn=[];ac.each(this.label_tracks,function(aj){aj._draw()})},zoom_in:function(ae,af){if(this.max_high===0||this.high-this.low<=this.min_separation){return}var ag=this.high-this.low,ah=ag/2+this.low,ad=(ag/this.zoom_factor)/2;if(ae){ah=ae/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(ah-ad);this.high=Math.round(ah+ad);this.changed();this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ae=this.high-this.low,af=ae/2+this.low,ad=(ae*this.zoom_factor)/2;this.low=Math.round(af-ad);this.high=Math.round(af+ad);this.changed();this.request_redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.request_redraw()},set_overview:function(af){if(this.overview_drawable){if(this.overview_drawable.dataset.id===af.dataset.id){return}this.overview_viewport.find(".track").remove()}var ae=af.copy({content_div:this.overview_viewport}),ad=this;ae.header_div.hide();ae.is_overview=true;ad.overview_drawable=ae;this.overview_drawable.postdraw_actions=function(){ad.overview_highlight.show().height(ad.overview_drawable.content_div.height());ad.overview_viewport.height(ad.overview_drawable.content_div.height()+ad.overview_box.outerHeight());ad.overview_close.show();ad.resize_window()};ad.overview_drawable.request_draw();this.changed()},reset_overview:function(){$(".tooltip").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 q=R.Tool.extend({defaults:{track:null},initialize:function(ad){if(ad.tool_state!==undefined){this.set("hidden",ad.tool_state.hidden)}this.remove_inputs(["data","hidden_data","conditional"])},state_dict:function(ad){return ac.extend(this.get_inputs_dict(),{hidden:!this.is_visible()})}});var t=Backbone.View.extend({events:{"change input":"update_value"},render:function(){var af=this.$el.addClass("param-row"),ag=this.model;var ad=$("<div>").addClass("param-label").text(ag.get("label")).appendTo(af);var ae=$("<div/>").addClass("param-input").html(ag.get("html")).appendTo(af);ae.find(":input").val(ag.get("value"));$("<div style='clear: both;'/>").appendTo(af)},update_value:function(ad){this.model.set_value($(ad.target).val())}});var ab=Backbone.View.extend({initialize:function(ad){this.model.on("change:hidden",this.set_visible,this)},render:function(){var ae=this;tool=this.model,parent_div=this.$el.addClass("dynamic-tool").hide();parent_div.bind("drag",function(ai){ai.stopPropagation()}).click(function(ai){ai.stopPropagation()}).bind("dblclick",function(ai){ai.stopPropagation()}).keydown(function(ai){ai.stopPropagation()});var af=$("<div class='tool-name'>").appendTo(parent_div).text(tool.get("name"));tool.get("inputs").each(function(aj){var ai=new t({model:aj});ai.render();parent_div.append(ai.$el)});parent_div.find("input").click(function(){$(this).select()});var ag=$("<div>").addClass("param-row").appendTo(parent_div);var ah=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(ag);var ad=$("<input type='submit'>").attr("value","Run on visible region").css("margin-left","3em").appendTo(ag);ad.click(function(){ae.run_on_region()});ah.click(function(){ae.run_on_dataset()});if(tool.is_visible()){this.$el.show()}},set_visible:function(){if(this.model.is_visible()){this.$el.show()}else{this.$el.hide()}},update_params:function(){for(var ad=0;ad<this.params.length;ad++){this.params[ad].update_value()}},run_on_dataset:function(){var ad=this.model;this.run({target_dataset_id:this.model.get("track").dataset.id,action:"rerun",tool_id:ad.id},null,function(ae){Galaxy.modal.show({title:ad.get("name")+" is Running",body:ad.get("name")+" is running on the complete dataset. Tool outputs are in dataset's history.",buttons:{Close:function(){Galaxy.modal.hide()}}})})},run_on_region:function(){var ae=this.model.get("track"),ah=this.model,aj=new w.GenomeRegion({chrom:ae.view.chrom,start:ae.view.low,end:ae.view.high}),ak={target_dataset_id:ae.dataset.id,action:"rerun",tool_id:ah.id,regions:[aj.toJSON()]},ai=ae,am=ak.tool_id+ai.tool_region_and_parameters_str(aj),ad;if(ai.container===view){var al=new P(view,view,{name:this.name});var ag=ai.container.replace_drawable(ai,al,false);al.container_div.insertBefore(ai.view.content_div.children()[ag]);al.add_drawable(ai);ai.container_div.appendTo(al.content_div);ad=al}else{ad=ai.container}var af=new ai.constructor(view,ad,{name:am,hda_ldda:"hda"});af.init_for_tool_data();af.change_mode(ai.mode);af.set_filters_manager(ai.filters_manager.copy(af));af.update_icons();ad.add_drawable(af);af.tiles_div.text("Starting job.");this.run(ak,af,function(an){af.set_dataset(new X.Dataset(an));af.tiles_div.text("Running job.");af.init()})},run:function(ad,af,ag){ad.inputs=this.model.get_inputs_dict();var ae=new j.ServerStateDeferred({ajax_settings:{url:galaxy_config.root+"api/tools",data:JSON.stringify(ad),dataType:"json",contentType:"application/json",type:"POST"},interval:2000,success_fn:function(ah){return ah!=="pending"}});$.when(ae.go()).then(function(ah){if(ah==="no converter"){af.container_div.addClass("error");af.content_div.text(J)}else{if(ah.error){af.container_div.addClass("error");af.content_div.text(x+ah.message)}else{ag(ah)}}})}});var C=function(ad,ae){L.Scaler.call(this,ae);this.filter=ad};C.prototype.gen_val=function(ad){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(ad[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var F=function(ad){this.track=ad.track;this.params=ad.params;this.values={};this.restore_values((ad.saved_values?ad.saved_values:{}));this.onchange=ad.onchange};o(F.prototype,{set_param_default_value:function(ae,ad){var af=ac.find(this.params,function(ag){return ag.key===ae});if(af){af.default_value=ad}},set_param_value:function(ad,ae){var af=ac.find(this.params,function(ag){return ag.key===ad});if(af){if(typeof ae==="string"||ae instanceof String){if(ae.trim()===""){ae=af.default_value}else{if(af.type==="float"){ae=parseFloat(ae)}else{if(af.type==="int"){ae=parseInt(ae,10)}}}}}if(this.values[ad]!==ae){this.values[ad]=ae;return true}else{return false}},restore_values:function(ad){var ae=this;$.each(this.params,function(af,ag){if(ad[ag.key]!==undefined){ae.values[ag.key]=ad[ag.key]}else{ae.values[ag.key]=ag.default_value}})},build_form:function(){var ag=this;var ad=$("<div />");var af;function ae(al,ah){for(var ap=0;ap<al.length;ap++){af=al[ap];if(af.hidden){continue}var aj="param_"+ap;var au=ag.values[af.key];var aw=$("<div class='form-row' />").appendTo(ah);aw.append($("<label />").attr("for",aj).text(af.label+":"));if(af.type==="bool"){aw.append($('<input type="checkbox" />').attr("id",aj).attr("name",aj).attr("checked",au))}else{if(af.type==="text"){aw.append($('<input type="text"/>').attr("id",aj).val(au).click(function(){$(this).select()}))}else{if(af.type==="select"){var ar=$("<select />").attr("id",aj);for(var an=0;an<af.options.length;an++){$("<option/>").text(af.options[an].label).attr("value",af.options[an].value).appendTo(ar)}ar.val(au);aw.append(ar)}else{if(af.type==="color"){var av=$("<div/>").appendTo(aw),aq=$("<input />").attr("id",aj).attr("name",aj).val(au).css("float","left").appendTo(av).click(function(ay){$(".tooltip").removeClass("in");var ax=$(this).siblings(".tooltip").addClass("in");ax.css({left:$(this).position().left+$(this).width()+5,top:$(this).position().top+Galaxy.modal.scrollTop()-($(ax).height()/2)+($(this).height()/2)}).show();ax.click(function(az){az.stopPropagation()});$(document).bind("click.color-picker",function(){ax.hide();$(document).unbind("click.color-picker")});ay.stopPropagation()}),ao=$("<a href='javascript:void(0)'/>").addClass("icon-button arrow-circle").appendTo(av).attr("title","Set new random color").tooltip(),at=$("<div class='tooltip right' style='position: absolute;' />").appendTo(av).hide(),ak=$("<div class='tooltip-inner' style='text-align: inherit'></div>").appendTo(at),ai=$("<div class='tooltip-arrow'></div>").appendTo(at),am=$.farbtastic(ak,{width:100,height:100,callback:aq,color:au});av.append($("<div/>").css("clear","both"));(function(ax){ao.click(function(){ax.setColor(j.get_random_color())})})(am)}else{aw.append($("<input />").attr("id",aj).attr("name",aj).val(au))}}}}if(af.help){aw.append($("<div class='help'/>").text(af.help))}}}ae(this.params,ad);return ad},update_from_form:function(ad){var af=this;var ae=false;$.each(this.params,function(ag,ai){if(!ai.hidden){var aj="param_"+ag;var ah=ad.find("#"+aj).val();if(ai.type==="bool"){ah=ad.find("#"+aj).is(":checked")}ae=af.set_param_value(ai.key,ah)||ae}});if(ae){this.onchange();this.track.changed()}}});var b=function(ad,ag,ah,ae,af){this.track=ad;this.region=ag;this.low=ag.get("start");this.high=ag.get("end");this.w_scale=ah;this.html_elt=$("<div class='track-tile'/>").append(ae).height($(ae).attr("height"));this.data=af;this.stale=false};b.prototype.predisplay_actions=function(){};var M=function(ad,ag,ah,ae,af){b.call(this,ad,ag,ah,ae,af)};M.prototype.predisplay_actions=function(){};var O=function(ag,an,ap,af,ai,aj,aq,ae,am){b.call(this,ag,an,ap,af,ai);this.mode=aj;this.all_slotted=ae;this.feature_mapper=am;this.has_icons=false;if(aq){this.has_icons=true;var ak=this;af=this.html_elt.children()[0],message_div=$("<div/>").addClass("tile-message").css({height:D-1,width:af.width}).prependTo(this.html_elt);var al=new w.GenomeRegion({chrom:ag.view.chrom,start:this.low,end:this.high}),ao=ai.length,ah=$("<a href='javascript:void(0);'/>").addClass("icon more-down").attr("title","For speed, only the first "+ao+" features in this region were obtained from server. Click to get more data including depth").tooltip().appendTo(message_div),ad=$("<a href='javascript:void(0);'/>").addClass("icon more-across").attr("title","For speed, only the first "+ao+" features in this region were obtained from server. Click to get more data excluding depth").tooltip().appendTo(message_div);ah.click(function(){ak.stale=true;ag.data_manager.get_more_data(al,ag.mode,1/ak.w_scale,{},ag.data_manager.DEEP_DATA_REQ);$(".tooltip").hide();ag.request_draw()}).dblclick(function(ar){ar.stopPropagation()});ad.click(function(){ak.stale=true;ag.data_manager.get_more_data(al,ag.mode,1/ak.w_scale,{},ag.data_manager.BROAD_DATA_REQ);$(".tooltip").hide();ag.request_draw()}).dblclick(function(ar){ar.stopPropagation()})}};o(O.prototype,b.prototype);O.prototype.predisplay_actions=function(){var ae=this,ad={};if(ae.mode!=="Pack"){return}$(this.html_elt).hover(function(){this.hovered=true;$(this).mousemove()},function(){this.hovered=false;$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()}).mousemove(function(ap){if(!this.hovered){return}var ak=$(this).offset(),ao=ap.pageX-ak.left,an=ap.pageY-ak.top,au=ae.feature_mapper.get_feature_data(ao,an),al=(au?au[0]:null);$(this).parents(".track-content").children(".overlay").children(".feature-popup").each(function(){if(!al||$(this).attr("id")!==al.toString()){$(this).remove()}});if(au){var ag=ad[al];if(!ag){var al=au[0],aq={name:au[3],start:au[1],end:au[2],strand:au[4]},aj=ae.track.filters_manager.filters,ai;for(var am=0;am<aj.length;am++){ai=aj[am];aq[ai.name]=au[ai.index]}var ag=$("<div/>").attr("id",al).addClass("feature-popup"),av=$("<table/>"),at,ar,aw;for(at in aq){ar=aq[at];aw=$("<tr/>").appendTo(av);$("<th/>").appendTo(aw).text(at);$("<td/>").attr("align","left").appendTo(aw).text(typeof(ar)==="number"?V(ar,2):ar)}ag.append($("<div class='feature-popup-inner'>").append(av));ad[al]=ag}ag.appendTo($(this).parents(".track-content").children(".overlay"));var ah=ao+parseInt(ae.html_elt.css("left"))-ag.width()/2,af=an+parseInt(ae.html_elt.css("top"))+7;ag.css("left",ah+"px").css("top",af+"px")}else{if(!ap.isPropagationStopped()){ap.stopPropagation();$(this).siblings().each(function(){$(this).trigger(ap)})}}}).mouseleave(function(){$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()})};var f=function(ae,ad,af){o(af,{drag_handle_class:"draghandle"});p.call(this,ae,ad,af);this.dataset=null;if(af.dataset){this.dataset=(af.dataset instanceof Backbone.Model?af.dataset:X.Dataset.findOrCreate(af.dataset))}this.dataset_check_type="converted_datasets_state";this.data_url_extra_params={};this.data_query_wait=("data_query_wait" in af?af.data_query_wait:K);this.data_manager=("data_manager" in af?af.data_manager:new w.GenomeDataManager({dataset:this.dataset,genome:new w.Genome({key:ae.dbkey,chroms_info:{chrom_info:ae.chrom_data}}),data_mode_compatible:this.data_and_mode_compatible,can_subset:this.can_subset}));this.min_height_px=16;this.max_height_px=800;this.visible_height_px=0;this.content_div=$("<div class='track-content'>").appendTo(this.container_div);if(this.container){this.container.content_div.append(this.container_div);if(!("resize" in af)||af.resize){this.add_resize_handle()}}};o(f.prototype,p.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},p.prototype.action_icons_def[0],{name:"overview_icon",title:"Set as overview",css_class:"overview-icon",on_click_fn:function(ad){ad.view.set_overview(ad)}},p.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ad){if(ad.filters_manager.visible()){ad.filters_manager.clear_filters()}else{ad.filters_manager.init_filters()}ad.filters_manager.toggle()}},{name:"tools_icon",title:"Tool",css_class:"hammer",on_click_fn:function(ad){ad.tool.toggle();if(ad.tool.is_visible()){ad.set_name(ad.name+ad.tool_region_and_parameters_str())}else{ad.revert_name()}$(".tooltip").remove()}},{name:"param_space_viz_icon",title:"Tool parameter space visualization",css_class:"arrow-split",on_click_fn:function(ad){var ag='<strong>Tool</strong>: <%= track.tool.name %><br/><strong>Dataset</strong>: <%= track.name %><br/><strong>Region(s)</strong>: <select name="regions"><option value="cur">current viewing area</option><option value="bookmarks">bookmarks</option><option value="both">current viewing area and bookmarks</option></select>',af=ac.template(ag,{track:ad});var ai=function(){Galaxy.modal.hide();$(window).unbind("keypress.check_enter_esc")},ae=function(){var ak=$('select[name="regions"] option:selected').val(),am,aj=new w.GenomeRegion({chrom:view.chrom,start:view.low,end:view.high}),al=ac.map($(".bookmark"),function(an){return new w.GenomeRegion({from_str:$(an).children(".position").text()})});if(ak==="cur"){am=[aj]}else{if(ak==="bookmarks"){am=al}else{am=[aj].concat(al)}}Galaxy.modal.hide();window.location.href=galaxy_config.root+"visualization/sweepster?"+$.param({dataset_id:ad.dataset.id,hda_ldda:ad.dataset.get("hda_ldda"),regions:JSON.stringify(new Backbone.Collection(am).toJSON())})},ah=function(aj){if((aj.keyCode||aj.which)===27){ai()}else{if((aj.keyCode||aj.which)===13){ae()}}};Galaxy.modal.show({title:"Visualize tool parameter space and output from different parameter settings?",body:af,buttons:{No:ai,Yes:ae}})}},p.prototype.action_icons_def[2]],can_draw:function(){return this.dataset&&p.prototype.can_draw.call(this)},build_container_div:function(){return $("<div/>").addClass("track").attr("id","track_"+this.id).css("position","relative")},build_header_div:function(){var ad=$("<div class='track-header'/>");if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(ad)}this.name_div=$("<div/>").addClass("track-name").appendTo(ad).text(this.name).attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase());return ad},set_dataset:function(ad){this.dataset=ad;this.data_manager.set("dataset",ad)},on_resize:function(){this.request_draw({clear_tile_cache:true})},add_resize_handle:function(){var ad=this;var ag=false;var af=false;var ae=$("<div class='track-resize'>");$(ad.container_div).hover(function(){if(ad.content_visible){ag=true;ae.show()}},function(){ag=false;if(!af){ae.hide()}});ae.hide().bind("dragstart",function(ah,ai){af=true;ai.original_height=$(ad.content_div).height()}).bind("drag",function(ai,aj){var ah=Math.min(Math.max(aj.original_height+aj.deltaY,ad.min_height_px),ad.max_height_px);$(ad.tiles_div).css("height",ah);ad.visible_height_px=(ad.max_height_px===ah?0:ah);ad.on_resize()}).bind("dragend",function(ah,ai){ad.tile_cache.clear();af=false;if(!ag){ae.hide()}ad.config.values.height=ad.visible_height_px;ad.changed()}).appendTo(ad.container_div)},set_display_modes:function(ag,aj){this.display_modes=ag;this.mode=(aj?aj:(this.config&&this.config.values.mode?this.config.values.mode:this.display_modes[0]));this.action_icons.mode_icon.attr("title","Set display mode (now: "+this.mode+")");var ae=this,ah={};for(var af=0,ad=ae.display_modes.length;af<ad;af++){var ai=ae.display_modes[af];ah[ai]=function(ak){return function(){ae.change_mode(ak);ae.icons_div.show();ae.container_div.mouseleave(function(){ae.icons_div.hide()})}}(ai)}make_popupmenu(this.action_icons.mode_icon,ah)},build_action_icons:function(){p.prototype.build_action_icons.call(this,this.action_icons_def);if(this.display_modes!==undefined){this.set_display_modes(this.display_modes)}},hide_contents:function(){this.tiles_div.hide();this.container_div.find(".yaxislabel, .track-resize").hide()},show_contents:function(){this.tiles_div.show();this.container_div.find(".yaxislabel, .track-resize").show();this.request_draw()},get_type:function(){if(this instanceof W){return"LabelTrack"}else{if(this instanceof B){return"ReferenceTrack"}else{if(this instanceof g){return"LineTrack"}else{if(this instanceof T){return"ReadTrack"}else{if(this instanceof Z){return"VariantTrack"}else{if(this instanceof e){return"CompositeTrack"}else{if(this instanceof c){return"FeatureTrack"}}}}}}}return""},init:function(af){var ae=this;ae.enabled=false;ae.tile_cache.clear();ae.data_manager.clear();ae.tiles_div.css("height","auto");ae.tiles_div.text("").children().remove();ae.container_div.removeClass("nodata error pending");if(!ae.dataset.id){return}var ad=$.Deferred(),ag={hda_ldda:ae.dataset.get("hda_ldda"),data_type:this.dataset_check_type,chrom:ae.view.chrom,retry:af};$.getJSON(this.dataset.url(),ag,function(ah){if(!ah||ah==="error"||ah.kind==="error"){ae.container_div.addClass("error");ae.tiles_div.text(m);if(ah.message){ae.tiles_div.append($("<a href='javascript:void(0);'></a>").text("View error").click(function(){Galaxy.modal.show({title:"Trackster Error",body:"<pre>"+ah.message+"</pre>",buttons:{Close:function(){Galaxy.modal.hide()}}})}));ae.tiles_div.append($("<span/>").text(" "));ae.tiles_div.append($("<a href='javascript:void(0);'></a>").text("Try again").click(function(){ae.init(true)}))}}else{if(ah==="no converter"){ae.container_div.addClass("error");ae.tiles_div.text(J)}else{if(ah==="no data"||(ah.data!==undefined&&(ah.data===null||ah.data.length===0))){ae.container_div.addClass("nodata");ae.tiles_div.text(E)}else{if(ah==="pending"){ae.container_div.addClass("pending");ae.tiles_div.html(u);setTimeout(function(){ae.init()},ae.data_query_wait)}else{if(ah==="data"||ah.status==="data"){if(ah.valid_chroms){ae.valid_chroms=ah.valid_chroms;ae.update_icons()}ae.tiles_div.text(U);if(ae.view.chrom){ae.tiles_div.text("");ae.tiles_div.css("height",ae.visible_height_px+"px");ae.enabled=true;$.when.apply($,ae.predraw_init()).done(function(){ad.resolve();ae.container_div.removeClass("nodata error pending");ae.request_draw()})}else{ad.resolve()}}}}}}});this.update_icons();return ad},predraw_init:function(){var ad=this;return $.getJSON(ad.dataset.url(),{data_type:"data",stats:true,chrom:ad.view.chrom,low:0,high:ad.view.max_high,hda_ldda:ad.dataset.get("hda_ldda")},function(ae){ad.container_div.addClass("line-track");var ag=ae.data;if(ag&&ag.min&&ag.max){var af=ag.min,ah=ag.max;af=Math.floor(Math.min(0,Math.max(af,ag.mean-2*ag.sd)));ah=Math.ceil(Math.max(0,Math.min(ah,ag.mean+2*ag.sd)));ad.config.set_param_default_value("min_value",af);ad.config.set_param_default_value("max_value",ah);ad.prefs.min_value=af;ad.prefs.max_value=ah}})},get_drawables:function(){return this}});var N=function(af,ae,ah){f.call(this,af,ae,ah);var ad=this;k(ad.container_div,ad.drag_handle_class,".group",ad);this.filters_manager=new h.FiltersManager(this,("filters" in ah?ah.filters:null));this.data_manager.set("filters_manager",this.filters_manager);this.filters_available=false;this.tool=(ah.tool?new q(ac.extend(ah.tool,{track:this,tool_state:ah.tool_state})):null);this.tile_cache=new w.Cache(Q);this.left_offset=0;if(this.header_div){this.set_filters_manager(this.filters_manager);if(this.tool){var ag=new ab({model:this.tool});ag.render();this.dynamic_tool_div=ag.$el;this.header_div.after(this.dynamic_tool_div)}}this.tiles_div=$("<div/>").addClass("tiles").appendTo(this.content_div);this.overlay_div=$("<div/>").addClass("overlay").appendTo(this.content_div);if(ah.mode){this.change_mode(ah.mode)}};o(N.prototype,p.prototype,f.prototype,{action_icons_def:f.prototype.action_icons_def.concat([{name:"show_more_rows_icon",title:"To minimize track height, not all feature rows are displayed. Click to display more rows.",css_class:"exclamation",on_click_fn:function(ad){$(".tooltip").remove();ad.slotters[ad.view.resolution_px_b].max_rows*=2;ad.request_draw({clear_tile_cache:true})},hide:true}]),copy:function(ad){var ae=this.to_dict();o(ae,{data_manager:this.data_manager});var af=new this.constructor(this.view,ad,ae);af.change_mode(this.mode);af.enabled=this.enabled;return af},set_filters_manager:function(ad){this.filters_manager=ad;this.header_div.after(this.filters_manager.parent_div)},to_dict:function(){return{track_type:this.get_type(),name:this.name,dataset:{id:this.dataset.id,hda_ldda:this.dataset.get("hda_ldda")},prefs:this.prefs,mode:this.mode,filters:this.filters_manager.to_dict(),tool_state:(this.tool?this.tool.state_dict():{})}},set_min_max:function(){var ad=this;return $.getJSON(ad.dataset.url(),{data_type:"data",stats:true,chrom:ad.view.chrom,low:0,high:ad.view.max_high,hda_ldda:ad.dataset.get("hda_ldda")},function(ae){var ag=ae.data;if(isNaN(parseFloat(ad.prefs.min_value))||isNaN(parseFloat(ad.prefs.max_value))){var af=ag.min,ah=ag.max;af=Math.floor(Math.min(0,Math.max(af,ag.mean-2*ag.sd)));ah=Math.ceil(Math.max(0,Math.min(ah,ag.mean+2*ag.sd)));ad.prefs.min_value=af;ad.prefs.max_value=ah}})},change_mode:function(ae){var ad=this;ad.mode=ae;ad.config.values.mode=ae;if(ae==="Auto"){this.data_manager.clear()}ad.request_draw({clear_tile_cache:true});this.action_icons.mode_icon.attr("title","Set display mode (now: "+ad.mode+")");return ad},update_icons:function(){var ad=this;if(ad.filters_available){ad.action_icons.filters_icon.show()}else{ad.action_icons.filters_icon.hide()}if(ad.tool){ad.action_icons.tools_icon.show();ad.action_icons.param_space_viz_icon.show()}else{ad.action_icons.tools_icon.hide();ad.action_icons.param_space_viz_icon.hide()}},_gen_tile_cache_key:function(ae,ad){return ae+"_"+ad},request_draw:function(ad){if(ad&&ad.clear_tile_cache){this.tile_cache.clear()}this.view.request_redraw(ad,this)},before_draw:function(){this.max_height_px=0},_draw:function(ar){if(!this.can_draw()){return}var ao=ar&&ar.clear_after,am=this.view.low,ah=this.view.high,ak=ah-am,ae=this.view.container.width(),aq=this.view.resolution_px_b,ag=1/aq;if(this.is_overview){am=this.view.max_low;ah=this.view.max_high;aq=ae/(view.max_high-view.max_low);ag=1/aq}this.before_draw();this.tiles_div.children().addClass("remove");var ad=Math.floor(am/(ag*S)),al,an,ai,aj=[],ap=[];while((ad*S*ag)<ah){al=Math.floor(ad*S*ag);an=new w.GenomeRegion({chrom:this.view.chrom,start:al,end:Math.min(al+Math.ceil(S*ag),this.view.max_high)});ai=this.draw_helper(an,aq,ar);aj.push(ai);$.when(ai).then(function(at){ap.push(at)});ad+=1}if(!ao){this.tiles_div.children(".remove").removeClass("remove").remove()}var af=this;$.when.apply($,aj).then(function(){af.tiles_div.children(".remove").remove();ap=ac.filter(ap,function(at){return at!==null});if(ap.length!==0){af.postdraw_actions(ap,ae,aq,ao)}})},_add_yaxis_label:function(ag,ai){var ae=this,ah=(ag==="max"?"top":"bottom"),aj=(ag==="max"?"max":"min"),ad=(ag==="max"?"max_value":"min_value"),ai=ai||function(){ae.request_draw({clear_tile_cache:true})},af=this.container_div.find(".yaxislabel."+ah);if(af.length!==0){af.text(ae.prefs[ad])}else{af=$("<div/>").text(ae.prefs[ad]).make_text_editable({num_cols:12,on_finish:function(ak){$(".tooltip").remove();ae.config.set_param_value(ad,ak);ai()},help_text:"Set "+aj+" value"}).addClass("yaxislabel "+ah).css("color",this.prefs.label_color);this.container_div.prepend(af)}},postdraw_actions:function(ag,ah,aj,ad){var af=ac.filter(ag,function(ak){return(ak instanceof M)});if(af.length>0){this.max_height_px=0;var ae=this;ac.each(ag,function(ak){if(!(ak instanceof M)){ak.html_elt.remove();ae.draw_helper(ak.region,aj,{force:true,mode:"Coverage"})}});ae._add_yaxis_label("max")}else{this.container_div.find(".yaxislabel").remove();var ai=ac.find(ag,function(ak){return ak.has_icons});if(ai){ac.each(ag,function(ak){if(!ak.has_icons){ak.html_elt.css("padding-top",D)}})}}},get_mode:function(ad){return this.mode},update_auto_mode:function(ad){},_get_drawables:function(){return[this]},draw_helper:function(am,ap,aq){if(!aq){aq={}}var ae=aq.force,ao=!(aq.data_fetch===false),aj=aq.mode||this.mode,ag=1/ap,af=this,ah=this._get_drawables(),an=this._gen_tile_cache_key(ap,am),ai=function(ar){return(ar&&"track" in ar)};var ak=(ae?undefined:af.tile_cache.get_elt(an));if(ak){if(ai(ak)){af.show_tile(ak,ap)}return ak}if(!ao){return null}var al=function(){var ar=(ac.find(A,function(au){return au===aj})?"Coverage":aj);var at=ac.map(ah,function(au){return au.data_manager.get_data(am,ar,ag,af.data_url_extra_params)});if(view.reference_track){at.push(view.reference_track.data_manager.get_data(am,aj,ag,view.reference_track.data_url_extra_params))}return at};var ad=$.Deferred();af.tile_cache.set_elt(an,ad);$.when.apply($,al()).then(function(){var ar=al(),ax=ar,aD;if(view.reference_track){aD=view.reference_track.data_manager.subset_entry(ar.pop(),am)}var ay=[],av=[];ac.each(ah,function(aI,aF){var aH=aI.mode,aG=ax[aF];if(aH==="Auto"){aH=aI.get_mode(aG);aI.update_auto_mode(aH)}ay.push(aH);av.push(aI.get_canvas_height(aG,aH,ap,at))});var aw=af.view.canvas_manager.new_canvas(),az=am.get("start"),aE=am.get("end"),au=0,at=Math.ceil((aE-az)*ap)+af.left_offset,aB=ac.max(av),aA;aw.width=at;aw.height=(aq.height||aB);var aC=aw.getContext("2d");aC.translate(af.left_offset,0);if(ah.length>1){aC.globalAlpha=0.5;aC.globalCompositeOperation="source-over"}ac.each(ah,function(aG,aF){aA=aG.draw_tile(ax[aF],aC,ay[aF],am,ap,aD)});if(aA!==undefined){af.tile_cache.set_elt(an,aA);af.show_tile(aA,ap)}ad.resolve(aA)});return ad},get_canvas_height:function(ad,af,ag,ae){return this.visible_height_px},_draw_line_track_tile:function(ad,af,ai,ah,aj){var ag=af.canvas,ae=new L.LinePainter(ad.data,ah.get("start"),ah.get("end"),this.prefs,ai);ae.draw(af,ag.width,ag.height,aj);return new M(this,ah,aj,ag,ad.data)},draw_tile:function(ad,ae,ah,ag,ai,af){},show_tile:function(af,ai){var ae=this,ad=af.html_elt;af.predisplay_actions();var ah=(af.low-(this.is_overview?this.view.max_low:this.view.low))*ai;if(this.left_offset){ah-=this.left_offset}ad.css({position:"absolute",top:0,left:ah});if(ad.hasClass("remove")){ad.removeClass("remove")}else{this.tiles_div.append(ad)}af.html_elt.height("auto");this.max_height_px=Math.max(this.max_height_px,af.html_elt.height());af.html_elt.parent().children().css("height",this.max_height_px+"px");var ag=this.max_height_px;if(this.visible_height_px!==0){ag=Math.min(this.max_height_px,this.visible_height_px)}this.tiles_div.css("height",ag+"px")},tool_region_and_parameters_str:function(ag){var ad=this,af=(ag!==undefined?ag.toString():"all"),ae=ac.values(ad.tool.get_inputs_dict()).join(", ");return" - region=["+af+"], parameters=["+ae+"]"},data_and_mode_compatible:function(ad,ae){if(ae==="Auto"){return true}else{if(ae==="Coverage"){return ad.dataset_type==="bigwig"}else{if(ad.dataset_type==="bigwig"||ad.extra_info==="no_detail"){return false}else{return true}}}},can_subset:function(ad){if(ad.message||ad.extra_info==="no_detail"){return false}else{if(ad.dataset_type==="bigwig"){return(ad.data[1][0]-ad.data[0][0]===1)}}return true},init_for_tool_data:function(){this.data_manager.set("data_type","raw_data");this.data_query_wait=1000;this.dataset_check_type="state"}});var W=function(ae,ad){var af={resize:false};f.call(this,ae,ad,af);this.container_div.addClass("label-track")};o(W.prototype,f.prototype,{build_header_div:function(){},init:function(){this.enabled=true},predraw_init:function(){},_draw:function(ah){var af=this.view,ag=af.high-af.low,ak=Math.floor(Math.pow(10,Math.floor(Math.log(ag)/Math.log(10)))),ad=Math.floor(af.low/ak)*ak,ai=this.view.container.width(),ae=$("<div style='position: relative; height: 1.3em;'></div>");while(ad<af.high){var aj=(ad-af.low)/ag*ai;ae.append($("<div class='label'>"+commatize(ad)+"</div>").css({position:"absolute",left:aj-1}));ad+=ak}this.content_div.children(":first").remove();this.content_div.append(ae)}});var e=function(ae,ad,ah){this.display_modes=A;N.call(this,ae,ad,ah);this.drawables=[];if("drawables" in ah){var ag;for(var af=0;af<ah.drawables.length;af++){ag=ah.drawables[af];this.drawables[af]=n(ag,ae,null);if(ag.left_offset>this.left_offset){this.left_offset=ag.left_offset}}this.enabled=true}ac.each(this.drawables,function(ai){if(ai instanceof c||ai instanceof T){ai.change_mode("Coverage")}});this.update_icons();this.obj_type="CompositeTrack"};o(e.prototype,N.prototype,{action_icons_def:[{name:"composite_icon",title:"Show individual tracks",css_class:"layers-stack",on_click_fn:function(ad){$(".tooltip").remove();ad.show_group()}}].concat(N.prototype.action_icons_def),to_dict:y.prototype.to_dict,add_drawable:y.prototype.add_drawable,unpack_drawables:y.prototype.unpack_drawables,change_mode:function(ad){N.prototype.change_mode.call(this,ad);for(var ae=0;ae<this.drawables.length;ae++){this.drawables[ae].change_mode(ad)}},init:function(){var af=[];for(var ae=0;ae<this.drawables.length;ae++){af.push(this.drawables[ae].init())}var ad=this;$.when.apply($,af).then(function(){ad.enabled=true;ad.request_draw()})},update_icons:function(){this.action_icons.filters_icon.hide();this.action_icons.tools_icon.hide();this.action_icons.param_space_viz_icon.hide()},can_draw:p.prototype.can_draw,_get_drawables:function(){return this.drawables},show_group:function(){var ag=new P(this.view,this.container,{name:this.name}),ad;for(var af=0;af<this.drawables.length;af++){ad=this.drawables[af];ad.update_icons();ag.add_drawable(ad);ad.container=ag;ag.content_div.append(ad.container_div)}var ae=this.container.replace_drawable(this,ag,true);ag.request_draw({clear_tile_cache:true})},before_draw:function(){N.prototype.before_draw.call(this);var ae=ac.min(ac.map(this.drawables,function(af){return af.prefs.min_value})),ad=ac.max(ac.map(this.drawables,function(af){return af.prefs.max_value}));this.prefs.min_value=ae;this.prefs.max_value=ad;ac.each(this.drawables,function(af){af.prefs.min_value=ae;af.prefs.max_value=ad})},update_all_min_max:function(){var ad=this;ac.each(this.drawables,function(ae){ae.prefs.min_value=ad.prefs.min_value;ae.prefs.max_value=ad.prefs.max_value});this.request_draw({clear_tile_cache:true})},postdraw_actions:function(aj,ad,am,ai){N.prototype.postdraw_actions.call(this,aj,ad,am,ai);var ah=-1;for(var af=0;af<aj.length;af++){var ak=aj[af].html_elt.find("canvas").height();if(ak>ah){ah=ak}}for(var af=0;af<aj.length;af++){var ag=aj[af];if(ag.html_elt.find("canvas").height()!==ah){this.draw_helper(ag.region,am,{force:true,height:ah});ag.html_elt.remove()}}var ae=this,al=function(){ae.update_all_min_max()};this._add_yaxis_label("min",al);this._add_yaxis_label("max",al)}});var B=function(ad){N.call(this,ad,{content_div:ad.top_labeltrack},{resize:false});ad.reference_track=this;this.left_offset=200;this.visible_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=galaxy_config.root+"api/genomes//"+this.view.dbkey;this.data_url_extra_params={reference:true};this.data_manager=new w.GenomeReferenceDataManager({data_url:this.data_url,can_subset:this.can_subset});this.hide_contents()};o(B.prototype,p.prototype,N.prototype,{build_header_div:function(){},init:function(){this.data_manager.clear();this.enabled=true},predraw_init:function(){},can_draw:p.prototype.can_draw,draw_helper:function(ae,af,ad){if(af>this.view.canvas_manager.char_width_px){this.tiles_div.show();return N.prototype.draw_helper.call(this,ae,af,ad)}else{this.tiles_div.hide();return null}},can_subset:function(ad){return true},draw_tile:function(af,al,ag,ai,am){var ae=this.data_manager.subset_entry(af,ai),ak=ae.data;var ad=al.canvas;al.font=al.canvas.manager.default_font;al.textAlign="center";for(var ah=0,aj=ak.length;ah<aj;ah++){al.fillStyle=this.view.get_base_color(ak[ah]);al.fillText(ak[ah],Math.floor(ah*am),10)}return new b(this,ai,am,ad,ae)}});var g=function(af,ae,ag){var ad=this;this.display_modes=A;this.mode="Histogram";N.call(this,af,ae,ag);this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"color",label:"Color",type:"color",default_value:j.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:32,hidden:true}],saved_values:ag.prefs,onchange:function(){ad.set_name(ad.prefs.name);ad.request_redraw({clear_tile_cache:true})}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height};o(g.prototype,p.prototype,N.prototype,{before_draw:function(){},draw_tile:function(ad,ae,ag,af,ah){return this._draw_line_track_tile(ad,ae,ag,af,ah)},can_subset:function(ad){return(ad.data[1][0]-ad.data[0][0]===1)},postdraw_actions:function(ae,af,ag,ad){this._add_yaxis_label("max");this._add_yaxis_label("min")}});var r=function(af,ae,ag){var ad=this;this.display_modes=["Heatmap"];this.mode="Heatmap";N.call(this,af,ae,ag);this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"pos_color",label:"Positive Color",type:"color",default_value:"#FF8C00"},{key:"neg_color",label:"Negative Color",type:"color",default_value:"#4169E1"},{key:"min_value",label:"Min Value",type:"float",default_value:-1},{key:"max_value",label:"Max Value",type:"float",default_value:1},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:500,hidden:true}],saved_values:ag.prefs,onchange:function(){ad.set_name(ad.prefs.name);this.request_redraw({clear_tile_cache:true})}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height};o(r.prototype,p.prototype,N.prototype,{draw_tile:function(ad,af,ai,ah,aj){var ag=af.canvas,ae=new L.DiagonalHeatmapPainter(ad.data,ah.get("start"),ah.get("end"),this.prefs,ai);ae.draw(af,ag.width,ag.height,aj);return new b(this,ah,aj,ag,ad.data)}});var c=function(ag,af,ai){var ae=this;this.display_modes=["Auto","Coverage","Dense","Squish","Pack"];N.call(this,ag,af,ai);var ah=j.get_random_color(),ad=j.get_random_color([ah,"#FFFFFF"]);this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block color",type:"color",default_value:ah},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:ad},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true,help:"Show the number of items in each bin when drawing summary histogram"},{key:"min_value",label:"Histogram minimum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"connector_style",label:"Connector style",type:"select",default_value:"fishbones",options:[{label:"Line with arrows",value:"fishbone"},{label:"Arcs",value:"arcs"}]},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:this.visible_height_px,hidden:true}],saved_values:ai.prefs,onchange:function(){ae.set_name(ae.prefs.name);ae.set_painter_from_config();ae.request_draw({clear_tile_cache:true})}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height;this.container_div.addClass("feature-track");this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.slotters={};this.start_end_dct={};this.left_offset=200;this.set_painter_from_config()};o(c.prototype,p.prototype,N.prototype,{set_painter_from_config:function(){if(this.config.values.connector_style==="arcs"){this.painter=L.ArcLinkedFeaturePainter}else{this.painter=L.LinkedFeaturePainter}},postdraw_actions:function(an,af,ao,am){N.prototype.postdraw_actions.call(this,an,af,ao,am);var ah=this,ai;if(ah.filters_manager){var ag=ah.filters_manager.filters;for(var ak=0;ak<ag.length;ak++){ag[ak].update_ui_elt()}var aj=false,al,ae;for(ai=0;ai<an.length;ai++){if(an[ai].data.length){al=an[ai].data[0];for(var ak=0;ak<ag.length;ak++){ae=ag[ak];if(ae.applies_to(al)&&ae.min!==ae.max){aj=true;break}}}}if(ah.filters_available!==aj){ah.filters_available=aj;if(!ah.filters_available){ah.filters_manager.hide()}ah.update_icons()}}if(an[0] instanceof O){var ad=true;for(ai=0;ai<an.length;ai++){if(!an[ai].all_slotted){ad=false;break}}if(!ad){this.action_icons.show_more_rows_icon.show()}else{this.action_icons.show_more_rows_icon.hide()}}else{this.action_icons.show_more_rows_icon.hide()}},update_auto_mode:function(ad){var ad;if(this.mode==="Auto"){if(ad==="no_detail"){ad="feature spans"}this.action_icons.mode_icon.attr("title","Set display mode (now: Auto/"+ad+")")}},incremental_slots:function(ah,ad,ag){var ae=this.view.canvas_manager.dummy_context,af=this.slotters[ah];if(!af||(af.mode!==ag)){af=new (s.FeatureSlotter)(ah,ag,z,function(ai){return ae.measureText(ai)});this.slotters[ah]=af}return af.slot_features(ad)},get_mode:function(ad){if(ad.extra_info==="no_detail"||this.is_overview){mode="no_detail"}else{if(this.view.high-this.view.low>I){mode="Squish"}else{mode="Pack"}}return mode},get_canvas_height:function(ad,ah,ai,ae){if(ah==="Coverage"||ad.dataset_type==="bigwig"){return this.summary_draw_height}else{var ag=this.incremental_slots(ai,ad.data,ah);var af=new (this.painter)(null,null,null,this.prefs,ah);return Math.max(aa,af.get_required_height(ag,ae))}},draw_tile:function(an,ar,ap,ag,ak,af){var aq=this,ae=ar.canvas,ay=ag.get("start"),ad=ag.get("end"),ah=this.left_offset;if(an.dataset_type==="bigwig"){return this._draw_line_track_tile(an,ar,ap,ag,ak)}var aj=[],ao=this.slotters[ak].slots;all_slotted=true;if(an.data){var al=this.filters_manager.filters;for(var at=0,av=an.data.length;at<av;at++){var ai=an.data[at];var au=false;var am;for(var ax=0,aC=al.length;ax<aC;ax++){am=al[ax];am.update_attrs(ai);if(!am.keep(ai)){au=true;break}}if(!au){aj.push(ai);if(!(ai[0] in ao)){all_slotted=false}}}}var aB=(this.filters_manager.alpha_filter?new C(this.filters_manager.alpha_filter):null),az=(this.filters_manager.height_filter?new C(this.filters_manager.height_filter):null),aA=new (this.painter)(aj,ay,ad,this.prefs,ap,aB,az,af,function(aD){return aq.view.get_base_color(aD)});var aw=null;ar.fillStyle=this.prefs.block_color;ar.font=ar.canvas.manager.default_font;ar.textAlign="right";if(an.data){aw=aA.draw(ar,ae.width,ae.height,ak,ao);aw.translation=-ah}return new O(aq,ag,ak,ae,an.data,ap,an.message,all_slotted,aw)}});var Z=function(ae,ad,af){this.display_modes=["Auto","Coverage","Dense","Squish","Pack"];N.call(this,ae,ad,af);this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"color",label:"Histogram color",type:"color",default_value:j.get_random_color()},{key:"show_sample_data",label:"Show sample data",type:"bool",default_value:true},{key:"show_labels",label:"Show summary and sample labels",type:"bool",default_value:true},{key:"summary_height",label:"Locus summary height",type:"float",default_value:20},{key:"mode",type:"string",default_value:this.mode,hidden:true}],saved_values:af.prefs,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.request_draw({clear_tile_cache:true})}});this.prefs=this.config.values;this.painter=L.VariantPainter;this.summary_draw_height=30;this.left_offset=30};o(Z.prototype,p.prototype,N.prototype,{draw_tile:function(ad,ag,ai,ah,aj){if(ad.dataset_type==="bigwig"){return this._draw_line_track_tile(ad,ag,"Histogram",ah,aj)}else{var af=this.view,ae=new (this.painter)(ad.data,ah.get("start"),ah.get("end"),this.prefs,ai,function(ak){return af.get_base_color(ak)});ae.draw(ag,ag.canvas.width,ag.canvas.height,aj);return new b(this,ah,aj,ag.canvas,ad.data)}},get_canvas_height:function(ad,ah,ai,af){if(ad.dataset_type==="bigwig"){return this.summary_draw_height}else{var ae=(this.dataset.get_metadata("sample_names")?this.dataset.get_metadata("sample_names").length:0);if(ae===0&&ad.data.length!==0){ae=ad.data[0][7].match(/,/g);if(ae===null){ae=1}else{ae=ae.length+1}}var ag=new (this.painter)(null,null,null,this.prefs,ah);return ag.get_required_height(ae)}},predraw_init:function(){var ad=[f.prototype.predraw_init.call(this)];if(!this.dataset.get_metadata("sample_names")){ad.push(this.dataset.fetch())}return ad},postdraw_actions:function(ah,ai,ak,ae){N.prototype.postdraw_actions.call(this,ah,ai,ak,ae);var ag=ac.filter(ah,function(al){return(al instanceof M)});var af=this.dataset.get_metadata("sample_names");if(ag.length===0&&this.prefs.show_labels&&af){var ad;if(this.container_div.find(".yaxislabel.variant").length===0){ad=this.prefs.summary_height/2;this.tiles_div.prepend($("<div/>").text("Summary").addClass("yaxislabel variant top").css({"font-size":ad+"px",top:(this.prefs.summary_height-ad)/2+"px"}));if(this.prefs.show_sample_data){var aj=af.join("<br/>");this.tiles_div.prepend($("<div/>").html(aj).addClass("yaxislabel variant top sample").css({top:this.prefs.summary_height+2,}))}}ad=(this.mode==="Squish"?5:10)+"px";$(this.tiles_div).find(".sample").css({"font-size":ad,"line-height":ad});$(this.tiles_div).find(".yaxislabel").css("color",this.prefs.label_color)}else{this.container_div.find(".yaxislabel.variant").remove()}}});var T=function(af,ae,ah){c.call(this,af,ae,ah);var ag=j.get_random_color(),ad=j.get_random_color([ag,"#ffffff"]);this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block and sense strand color",type:"color",default_value:ag},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:ad},{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},{key:"min_value",label:"Histogram minimum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"}],saved_values:ah.prefs,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.request_draw({clear_tile_cache:true})}});this.prefs=this.config.values;this.painter=(af.reference_track?L.RefBasedReadPainter:L.ReadPainter);this.update_icons()};o(T.prototype,p.prototype,N.prototype,c.prototype);var d={CompositeTrack:e,DrawableGroup:P,DiagonalHeatmapTrack:r,FeatureTrack:c,LineTrack:g,ReadTrack:T,VariantTrack:Z,VcfTrack:Z};var n=function(af,ae,ad){if("copy" in af){return af.copy(ad)}else{var ag=af.obj_type;if(!ag){ag=af.track_type}return new d[ag](ae,ad,af)}};return{TracksterView:Y,DrawableGroup:P,LineTrack:g,FeatureTrack:c,DiagonalHeatmapTrack:r,ReadTrack:T,VariantTrack:Z,CompositeTrack:e,object_from_template:n}}); \ No newline at end of file diff -r 78eaaca131e3251ba9cc78f7546ace6a713a4f02 -r f76c280cdee539b65315ac583f93bfa52feb790d static/scripts/packed/viz/trackster_ui.js --- a/static/scripts/packed/viz/trackster_ui.js +++ b/static/scripts/packed/viz/trackster_ui.js @@ -1,1 +1,1 @@ -define(["base","libs/underscore","viz/trackster/slotting","viz/trackster/painters","viz/trackster/tracks","viz/visualization"],function(a,f,e,c,d,h){var j=d.object_from_template;var b=function(l,k){if(!k){k={}}var m=new IconButtonCollection(f.map(l,function(n){return new IconButton(f.extend(n,k))}));return new IconButtonMenuView({collection:m})};var g=a.Base.extend({initialize:function(k){this.baseURL=k},createButtonMenu:function(){var k=this,l=b([{icon_class:"plus-button",title:"Add tracks",on_click:function(){h.select_datasets(galaxy_config.root+"visualization/list_current_history_datasets",galaxy_config.root+"api/datasets",{"f-dbkey":view.dbkey},function(m){f.each(m,function(n){view.add_drawable(j(n,view,view))})})}},{icon_class:"block--plus",title:"Add group",on_click:function(){view.add_drawable(new d.DrawableGroup(view,view,{name:"New Group"}))}},{icon_class:"bookmarks",title:"Bookmarks",on_click:function(){force_right_panel(($("div#right").css("right")=="0px"?"hide":"show"))}},{icon_class:"globe",title:"Circster",on_click:function(){window.location=k.baseURL+"visualization/circster?id="+view.vis_id}},{icon_class:"disk--arrow",title:"Save",on_click:function(){Galaxy.modal.show({title:"Saving...",body:"progress"});var m=[];$(".bookmark").each(function(){m.push({position:$(this).children(".position").text(),annotation:$(this).children(".annotation").text()})});var n=(view.overview_drawable?view.overview_drawable.name:null),o={view:view.to_dict(),viewport:{chrom:view.chrom,start:view.low,end:view.high,overview:n},bookmarks:m};$.ajax({url:galaxy_config.root+"visualization/save",type:"POST",dataType:"json",data:{id:view.vis_id,title:view.name,dbkey:view.dbkey,type:"trackster",vis_json:JSON.stringify(o)}}).success(function(p){Galaxy.modal.hide();view.vis_id=p.vis_id;view.has_changes=false;window.history.pushState({},"",p.url+window.location.hash)}).error(function(){Galaxy.modal.show({title:"Could Not Save",body:"Could not save visualization. Please try again later.",buttons:{Cancel:function(){Galaxy.modal.hide()}}})})}}],{tooltip_config:{placement:"bottom"}});this.buttonMenu=l;return l},add_bookmarks:function(){var k=this,l=this.baseURL;Galaxy.modal.show({title:"Select dataset for new bookmarks",body:"progress"});$.ajax({url:this.baseURL+"/visualization/list_histories",data:{"f-dbkey":view.dbkey},error:function(){alert("Grid failed")},success:function(m){Galaxy.modal.show({title:"Select dataset for new bookmarks",body:m,buttons:{Cancel:function(){Galaxy.modal.hide()},Insert:function(){$("input[name=id]:checked,input[name=ldda_ids]:checked").first().each(function(){var n,o=$(this).val();if($(this).attr("name")==="id"){n={hda_id:o}}else{n={ldda_id:o}}$.ajax({url:this.baseURL+"/visualization/bookmarks_from_dataset",data:n,dataType:"json"}).then(function(p){for(i=0;i<p.data.length;i++){var q=p.data[i];k.add_bookmark(q[0],q[1])}})});Galaxy.modal.hide()}}})}})},add_bookmark:function(o,m,k){var q=$("#right .unified-panel-body"),s=$("<div/>").addClass("bookmark").appendTo(q);var t=$("<div/>").addClass("position").appendTo(s),p=$("<a href=''/>").text(o).appendTo(t).click(function(){view.go_to(o);return false}),n=$("<div/>").text(m).appendTo(s);if(k){var r=$("<div/>").addClass("delete-icon-container").prependTo(s).click(function(){s.slideUp("fast");s.remove();view.has_changes=true;return false}),l=$("<a href=''/>").addClass("icon-button delete").appendTo(r);n.make_text_editable({num_rows:3,use_textarea:true,help_text:"Edit bookmark note"}).addClass("annotation")}view.has_changes=true;return s},create_visualization:function(p,k,o,q,n){var m=this,l=new d.TracksterView(p);l.editor=true;$.when(l.load_chroms_deferred).then(function(B){if(k){var z=k.chrom,r=k.start,w=k.end,t=k.overview;if(z&&(r!==undefined)&&w){l.change_chrom(z,r,w)}else{l.change_chrom(B[0].chrom)}}else{l.change_chrom(B[0].chrom)}if(o){var u,s,v;for(var x=0;x<o.length;x++){l.add_drawable(j(o[x],l,l))}}l.update_intro_div();var A;for(var x=0;x<l.drawables.length;x++){if(l.drawables[x].name===t){l.set_overview(l.drawables[x]);break}}if(q){var y;for(var x=0;x<q.length;x++){y=q[x];m.add_bookmark(y.position,y.annotation,n)}}l.has_changes=false});return l},init_keyboard_nav:function(k){$(document).keydown(function(l){if($(l.srcElement).is(":input")){return}switch(l.which){case 37:k.move_fraction(0.25);break;case 38:var m=Math.round(k.viewport_container.height()/15);k.viewport_container.scrollTop(k.viewport_container.scrollTop()-20);break;case 39:k.move_fraction(-0.25);break;case 40:var m=Math.round(k.viewport_container.height()/15);k.viewport_container.scrollTop(k.viewport_container.scrollTop()+20);break}})}});return{object_from_template:j,TracksterUI:g}}); \ No newline at end of file +define(["base","libs/underscore","viz/trackster/slotting","viz/trackster/painters","viz/trackster/tracks","viz/visualization"],function(a,f,e,c,d,h){var j=d.object_from_template;var b=function(l,k){if(!k){k={}}var m=new IconButtonCollection(f.map(l,function(n){return new IconButton(f.extend(n,k))}));return new IconButtonMenuView({collection:m})};var g=a.Base.extend({initialize:function(k){this.baseURL=k},createButtonMenu:function(){var k=this,l=b([{icon_class:"plus-button",title:"Add tracks",on_click:function(){h.select_datasets(galaxy_config.root+"visualization/list_current_history_datasets",galaxy_config.root+"api/datasets",{"f-dbkey":view.dbkey},function(m){f.each(m,function(n){view.add_drawable(j(n,view,view))})})}},{icon_class:"block--plus",title:"Add group",on_click:function(){view.add_drawable(new d.DrawableGroup(view,view,{name:"New Group"}))}},{icon_class:"bookmarks",title:"Bookmarks",on_click:function(){force_right_panel(($("div#right").css("right")=="0px"?"hide":"show"))}},{icon_class:"globe",title:"Circster",on_click:function(){window.location=k.baseURL+"visualization/circster?id="+view.vis_id}},{icon_class:"disk--arrow",title:"Save",on_click:function(){Galaxy.modal.show({title:"Saving...",body:"progress"});var m=[];$(".bookmark").each(function(){m.push({position:$(this).children(".position").text(),annotation:$(this).children(".annotation").text()})});var n=(view.overview_drawable?view.overview_drawable.name:null),o={view:view.to_dict(),viewport:{chrom:view.chrom,start:view.low,end:view.high,overview:n},bookmarks:m};$.ajax({url:galaxy_config.root+"visualization/save",type:"POST",dataType:"json",data:{id:view.vis_id,title:view.name,dbkey:view.dbkey,type:"trackster",vis_json:JSON.stringify(o)}}).success(function(p){Galaxy.modal.hide();view.vis_id=p.vis_id;view.has_changes=false;window.history.pushState({},"",p.url+window.location.hash)}).error(function(){Galaxy.modal.show({title:"Could Not Save",body:"Could not save visualization. Please try again later.",buttons:{Cancel:function(){Galaxy.modal.hide()}}})})}},{icon_class:"cross-circle",title:"Close",on_click:function(){window.location=galaxy_config.root+"visualization"}}],{tooltip_config:{placement:"bottom"}});this.buttonMenu=l;return l},add_bookmarks:function(){var k=this,l=this.baseURL;Galaxy.modal.show({title:"Select dataset for new bookmarks",body:"progress"});$.ajax({url:this.baseURL+"/visualization/list_histories",data:{"f-dbkey":view.dbkey},error:function(){alert("Grid failed")},success:function(m){Galaxy.modal.show({title:"Select dataset for new bookmarks",body:m,buttons:{Cancel:function(){Galaxy.modal.hide()},Insert:function(){$("input[name=id]:checked,input[name=ldda_ids]:checked").first().each(function(){var n,o=$(this).val();if($(this).attr("name")==="id"){n={hda_id:o}}else{n={ldda_id:o}}$.ajax({url:this.baseURL+"/visualization/bookmarks_from_dataset",data:n,dataType:"json"}).then(function(p){for(i=0;i<p.data.length;i++){var q=p.data[i];k.add_bookmark(q[0],q[1])}})});Galaxy.modal.hide()}}})}})},add_bookmark:function(o,m,k){var q=$("#right .unified-panel-body"),s=$("<div/>").addClass("bookmark").appendTo(q);var t=$("<div/>").addClass("position").appendTo(s),p=$("<a href=''/>").text(o).appendTo(t).click(function(){view.go_to(o);return false}),n=$("<div/>").text(m).appendTo(s);if(k){var r=$("<div/>").addClass("delete-icon-container").prependTo(s).click(function(){s.slideUp("fast");s.remove();view.has_changes=true;return false}),l=$("<a href=''/>").addClass("icon-button delete").appendTo(r);n.make_text_editable({num_rows:3,use_textarea:true,help_text:"Edit bookmark note"}).addClass("annotation")}view.has_changes=true;return s},create_visualization:function(p,k,o,q,n){var m=this,l=new d.TracksterView(p);l.editor=true;$.when(l.load_chroms_deferred).then(function(B){if(k){var z=k.chrom,r=k.start,w=k.end,t=k.overview;if(z&&(r!==undefined)&&w){l.change_chrom(z,r,w)}else{l.change_chrom(B[0].chrom)}}else{l.change_chrom(B[0].chrom)}if(o){var u,s,v;for(var x=0;x<o.length;x++){l.add_drawable(j(o[x],l,l))}}l.update_intro_div();var A;for(var x=0;x<l.drawables.length;x++){if(l.drawables[x].name===t){l.set_overview(l.drawables[x]);break}}if(q){var y;for(var x=0;x<q.length;x++){y=q[x];m.add_bookmark(y.position,y.annotation,n)}}l.has_changes=false});return l},init_keyboard_nav:function(k){$(document).keydown(function(l){if($(l.srcElement).is(":input")){return}switch(l.which){case 37:k.move_fraction(0.25);break;case 38:var m=Math.round(k.viewport_container.height()/15);k.viewport_container.scrollTop(k.viewport_container.scrollTop()-20);break;case 39:k.move_fraction(-0.25);break;case 40:var m=Math.round(k.viewport_container.height()/15);k.viewport_container.scrollTop(k.viewport_container.scrollTop()+20);break}})}});return{object_from_template:j,TracksterUI:g}}); \ No newline at end of file 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.