escher-1.3.1.min.js

/**
 * almond 0.2.6 Copyright (c) 2011-2012, The Dojo Foundation All Rights Reserved.
 * Available via the MIT or new BSD license.
 * see: http://github.com/jrburke/almond for details
 */

/**
 * vkBeautify - javascript plugin to pretty-print or minify text in XML, JSON, CSS and SQL formats.
 *
 * Version - 0.99.00.beta
 * Copyright (c) 2012 Vadim Kiryukhin
 * vkiryukhin @ gmail.com
 * http://www.eslinstructor.net/vkbeautify/
 *
 * Dual licensed under the MIT and GPL licenses:
 *   http://www.opensource.org/licenses/mit-license.php
 *   http://www.gnu.org/licenses/gpl.html
 *
 *   Pretty print
 *
 *        vkbeautify.xml(text [,indent_pattern]);
 *        vkbeautify.json(text [,indent_pattern]);
 *        vkbeautify.css(text [,indent_pattern]);
 *        vkbeautify.sql(text [,indent_pattern]);
 *
 *        @text - String; text to beatufy;
 *        @indent_pattern - Integer | String;
 *                Integer:  number of white spaces;
 *                String:   character string to visualize indentation ( can also be a set of white spaces )
 *   Minify
 *
 *        vkbeautify.xmlmin(text [,preserve_comments]);
 *        vkbeautify.jsonmin(text);
 *        vkbeautify.cssmin(text [,preserve_comments]);
 *        vkbeautify.sqlmin(text);
 *
 *        @text - String; text to minify;
 *        @preserve_comments - Bool; [optional];
 *                Set this flag to true to prevent removing comments from @text ( minxml and mincss functions only. )
 *
 *   Examples:
 *        vkbeautify.xml(text); // pretty print XML
 *        vkbeautify.json(text, 4 ); // pretty print JSON
 *        vkbeautify.css(text, '. . . .'); // pretty print CSS
 *        vkbeautify.sql(text, '----'); // pretty print SQL
 *
 *        vkbeautify.xmlmin(text, true);// minify XML, preserve comments
 *        vkbeautify.jsonmin(text);// minify JSON
 *        vkbeautify.cssmin(text);// minify CSS, remove comments ( default )
 *        vkbeautify.sqlmin(text);// minify SQL
 *
 */

/*! @source http://purl.eligrey.com/github/FileSaver.js/blob/master/FileSaver.js */

/**
 * complete.ly 1.0.0
 * MIT Licensing
 * Copyright (c) 2013 Lorenzo Puccetti
 * 
 * This Software shall be used for doing good things, not bad things.
 *
 * Liberally modified by Zachary King (c) 2014.
 * 
 **/

//     Underscore.js 1.8.3
//     http://underscorejs.org
//     (c) 2009-2015 Jeremy Ashkenas, DocumentCloud and Investigative Reporters & Editors
//     Underscore may be freely distributed under the MIT license.

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w(e,t,r){function u(e){return e.replace(n,"\\$1")}var i="(^|[\\s\\(\\)])",s="([\\s\\(\\)]|$)",o=i+u(t)+s;return e.replace(new RegExp(o,"g"),"$1"+r+"$2")}function E(e,t,n,r){var i,s,o,u;if(t===null){for(i in e){s=e[i],s.data=null,s.data_string="";for(o in s.segments)u=s.segments[o],u.data=null;s.gene_string=null}return!1}for(i in e){s=e[i];var a=t[s.bigg_id]||t[s.name]||null,f=p(a,n,r),l=d(a),c=m(a,f);s.data=f,s.data_string=c,s.reverse_flux=l,s.gene_string=null;for(o in s.segments)u=s.segments[o],u.data=s.data,u.reverse_flux=s.reverse_flux}return!0}function S(e,t,n,r){var i;if(t===null){for(i in e)e[i].data=null,e[i].data_string="";return!1}for(i in e){var s=e[i],o=t[s.bigg_id]||t[s.name]||null,u=p(o,n,r),a=m(o,u);s.data=u,s.data_string=a}return!0}function x(t,n,r,i,s,o){if(n===null){for(var u in t){var a=t[u];a.data=null,a.data_string="",a.reverse_flux=!1;for(var f in a.segments){var l=a.segments[f];l.data=null}a.gene_string=null}return!1}var c=[null];for(var u in n){for(var h in n[u]){c=n[u][h].map(function(){return null});break}break}for(var u in t){var a=t[u],g=a.gene_reaction_rule,y,w,E=n[a.bigg_id];typeof E!="undefined"?(w=E,y=b(g,w,o)):(w={},y=e.clone(c));var S=p(y,r,s),x=d(y),T=m(y,S);a.data=S,a.data_string=T,a.reverse_flux=x;for(var f in a.segments){var l=a.segments[f];l.data=a.data,l.reverse_flux=a.reverse_flux}a.gene_string=v(g,w,a.genes,r,i,s)}return!0}function T(e){var t=Number(e);return isNaN(t)||parseFloat(e)!=t?null:t}var t=function(e){return e},n=/([.*+?^=!:${}()|\[\]\/\\])/g,r=/\n\s*\n/g,i=/\n\s*(\)*)\s*$/,s=/([\(\) ])(?:and|or)([\)\( 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t={x:e.x,y:e.y};this.place(t)}function d(e){this.placed_div.place(e),this.direction_arrow.set_location(e),this.direction_arrow.show()}function v(){this.map.deselect_text_labels();var e=this.map.select_single_node();if(e==null)return!1;var t={x:e.x,y:e.y};return this.reload(e,t,!1),!0}function m(t,n,r){function H(e,t){for(var n in t)if(t[n].bigg_id==e)return!0;return!1}if(!r&&!t){console.error("No selected node, and not starting from scratch");return}this.place(n),this.completely.input.blur(),this.completely.repaint();if(this.map.cobra_model===null){this.completely.setText("Cannot add: No model.");return}var s=this.settings.get_option("identifiers_on_map")=="name",o=this.settings.get_option("allow_building_duplicate_reactions"),u=[],a=this.map.cobra_model.reactions,f=this.map.cobra_model.metabolites,l=this.map.reactions,c=this.map.has_data_on_reactions,h=this.map.reaction_data,p=this.map.reaction_data_styles,d=t?s?t.name:t.bigg_id:"",v=function(e,t){return e.replace(new RegExp("(^| 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t={x:d3.mouse(e)[0],y:d3.mouse(e)[1]};this.map.deselect_nodes(),this.map.deselect_text_labels(),this.reload(null,t,!0),this.show_target(this.map,t)}.bind(this,this.map.sel.node())),this.map.sel.classed("start-reaction-cursor",!0)):(this.map.sel.on("click.start_reaction",null),this.map.sel.classed("start-reaction-cursor",!1),this.hide_target())}function y(){this.target_coords&&this.map.sel.selectAll(".start-reaction-target").remove(),this.target_coords=null}function b(e,t){var n=e.sel.selectAll(".start-reaction-target").data([12,5]);n.enter().append("circle").classed("start-reaction-target",!0).attr("r",function(e){return e}).style("stroke-width",4),n.style("visibility","visible").attr("transform","translate("+t.x+","+t.y+")"),this.target_coords=t}var s=e.make_class();return 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e=function(){var e=d3.event,t=.5;e.stopPropagation(),e.preventDefault(),e.returnValue=!1;var r=function(e,r){var i=n.isUndefined(e)?r:-e/1.5;return i*t},i={x:this.window_translate.x-r(e.wheelDeltaX,e.deltaX),y:this.window_translate.y-r(e.wheelDeltaY,e.deltaY)};this.go_to(this.window_scale,i,!1)}.bind(this);this.zoom_container.on("mousewheel.escher",e),this.zoom_container.on("DOMMouseScroll.escher",e),this.zoom_container.on("wheel.escher",e)}}function f(t,r){e.check_undefined(arguments,["scale","translate"]);var i=this._use_3d_transform;if(!t)throw new Error("Bad scale value");if(!(!!r&&"x"in r&&"y"in r&&!isNaN(r.x)&&!isNaN(r.y)))return console.error("Bad translate value");this.window_scale=t,this.window_translate=r;if(!n.isNull(this._zoom_behavior)){this._zoom_behavior.scale(t);var s=[r.x,r.y];this._zoom_behavior.translate(s)}i?(n.isNull(this._zoom_timeout)||window.clearTimeout(this._zoom_timeout),this._go_to_3d(t,r,this._svg_scale,this._svg_translate),this._zoom_timeout=n.delay(function(){this._go_to_svg(t,r)}.bind(this),100)):this._go_to_svg(t,r),this.callback_manager.run("go_to")}function l(t,n,r,i){var s=t/r,o=e.c_minus_c(n,e.c_times_scalar(i,s)),u="translate("+o.x+"px,"+o.y+"px) "+"scale("+s+")";this.css3_transform_container.style("transform",u),this.css3_transform_container.style("-webkit-transform",u),this.css3_transform_container.style("transform-origin","0 0"),this.css3_transform_container.style("-webkit-transform-origin","0 0")}function c(){this.css3_transform_container.style("transform",null),this.css3_transform_container.style("-webkit-transform",null),this.css3_transform_container.style("transform-origin",null),this.css3_transform_container.style("-webkit-transform-origin",null)}function h(e,t){this.callback_manager.run("svg_start"),n.defer(function(){this._clear_3d(),this.zoomed_sel.attr("transform","translate("+t.x+","+t.y+") "+"scale("+e+")"),this._svg_scale=this.window_scale,this._svg_translate=this.window_translate,n.defer(function(){this.callback_manager.run("svg_finish")}.bind(this))}.bind(this))}function p(t){var n=this.get_size(),r={x:n.width/2-((n.width/2-this.window_translate.x)*t+this.window_translate.x),y:n.height/2-((n.height/2-this.window_translate.y)*t+this.window_translate.y)};this.go_to(this.window_scale*t,e.c_plus_c(this.window_translate,r))}function d(){this.zoom_by(1.5)}function v(){this.zoom_by(.667)}function m(){return{width:parseInt(this.selection.style("width"),10),height:parseInt(this.selection.style("height"),10)}}function g(e){var t=120,n=this.get_size(),r={x:{min:-this.window_translate.x/this.window_scale+t/this.window_scale,max:-this.window_translate.x/this.window_scale+(n.width-t)/this.window_scale},y:{min:-this.window_translate.y/this.window_scale+t/this.window_scale,max:-this.window_translate.y/this.window_scale+(n.height-t)/this.window_scale}};e.x<r.x.min?(this.window_translate.x=this.window_translate.x-(e.x-r.x.min)*this.window_scale,this.go_to(this.window_scale,this.window_translate)):e.x>r.x.max&&(this.window_translate.x=this.window_translate.x-(e.x-r.x.max)*this.window_scale,this.go_to(this.window_scale,this.window_translate)),e.y<r.y.min?(this.window_translate.y=this.window_translate.y-(e.y-r.y.min)*this.window_scale,this.go_to(this.window_scale,this.window_translate)):e.y>r.y.max&&(this.window_translate.y=this.window_translate.y-(e.y-r.y.max)*this.window_scale,this.go_to(this.window_scale,this.window_translate))}var r=e.make_class();return r.prototype={init:i,set_scroll_behavior:s,set_use_3d_transform:o,_update_scroll:a,toggle_pan_drag:u,go_to:f,_go_to_3d:l,_clear_3d:c,_go_to_svg:h,zoom_by:p,zoom_in:d,zoom_out:v,get_size:m,translate_off_screen:g},r}),n("Draw",["utils","data_styles","CallbackManager"],function(e,t,n){function i(e,t){this.behavior=e,this.settings=t,this.callback_manager=new n}function s(e){e.append("rect").attr("class","membrane"),this.callback_manager.run("create_membrane",this,e)}function o(e){e.attr("width",function(e){return e.width}).attr("height",function(e){return e.height}).attr("transform",function(e){return"translate("+e.x+","+e.y+")"}).style("stroke-width",function(e){return 10}).attr("rx",function(e){return 20}).attr("ry",function(e){return 20}),this.callback_manager.run("update_membrane",this,e)}function u(e){e.append("g").attr("id",function(e){return"r"+e.reaction_id}).attr("class","reaction").call(this.create_reaction_label.bind(this)),this.callback_manager.run("create_reaction",this,e);return}function a(t,n,r,i,s,o){t.select(".reaction-label-group").call(function(e){return this.update_reaction_label(e,o)}.bind(this)),e.draw_a_nested_object(t,".segment-group","segments","segment_id",this.create_segment.bind(this),function(e){return this.update_segment(e,n,r,i,s,o)}.bind(this),function(e){e.remove()}),this.callback_manager.run("update_reaction",this,t)}function f(e){var t=e.append("g").attr("class","reaction-label-group");t.append("title"),t.append("text").attr("class","reaction-label label"),t.append("g").attr("class","all-genes-label-group"),this.callback_manager.run("create_reaction_label",this,e)}function l(e,n){var r=d3.format(".4g"),i=this.settings.get_option("identifiers_on_map"),s=i=="bigg_id"?"name":"bigg_id",o=this.settings.get_option("reaction_styles"),u=this.settings.get_option("show_gene_reaction_rules"),a=this.settings.get_option("hide_all_labels"),f=this.settings.get_option("gene_font_size"),l=this.behavior.label_mousedown,c=this.behavior.label_mouseover,h=this.behavior.label_mouseout;e.attr("transform",function(e){return"translate("+e.label_x+","+e.label_y+")"}).call(this.behavior.turn_off_drag).call(this.behavior.reaction_label_drag);var p=e.select(".reaction-label").attr("visibility",a?"hidden":"visible");a||(p.text(function(e){var t=e[i];return n&&o.indexOf("text")!=-1&&(t+=" "+e.data_string),t}).on("mousedown",l).on("mouseover",c).on("mouseout",h),e.select("title").text(function(e){return e[s]}));var d=e.select(".all-genes-label-group").selectAll(".gene-label-group").data(function(e){var n="gene_string"in e&&e.gene_string!==null&&u&&!a&&o.indexOf("text")!==-1,r="gene_reaction_rule"in e&&e.gene_reaction_rule!==null&&u&&!a;return n?e.gene_string:r?t.gene_string_for_data(e.gene_reaction_rule,null,e.genes,null,i,null):[]}),v=d.enter().append("g").attr("class","gene-label-group");v.append("text").attr("class","gene-label").style("font-size",f+"px"),v.append("title"),d.attr("transform",function(e,t){return"translate(0, "+f*1.5*(t+1)+")"}),d.select("text").text(function(e){return e.text}),d.select("title").text(function(e){return e[s]}),d.exit().remove(),this.callback_manager.run("update_reaction_label",this,e)}function c(e){var t=e.append("g").attr("class","segment-group").attr("id",function(e){return"s"+e.segment_id});t.append("path").attr("class","segment"),t.append("g").attr("class","arrowheads"),t.append("g").attr("class","stoichiometry-labels"),this.callback_manager.run("create_segment",this,e)}function h(t,n,r,i,s,o){var u=this.settings.get_option("reaction_styles"),a=o&&u.indexOf("size")!=-1,f=o&&u.indexOf("color")!=-1,l=this.settings.get_option("reaction_no_data_size"),c=this.settings.get_option("reaction_no_data_color"),h=this.settings.get_option("highlight_missing"),p=this.settings.get_option("hide_secondary_metabolites"),d=this.settings.get_option("primary_metabolite_radius"),v=this.settings.get_option("secondary_metabolite_radius"),m=function(e,t){var r=20,i=13;return t&&(i=e===null?l:n.reaction_size(e),isNaN(i)&&(i=l),r=i*2),{width:r,height:i}},g=function(e,t,n,r){var i=t||n>0?e.height:0,s=r?d:v;return s+i+10};t.selectAll(".segment").datum(function(){return this.parentNode.__data__}).style("visibility",function(e){var t=i[e.from_node_id],n=i[e.to_node_id];return p&&(n["node_type"]=="metabolite"&&!n.node_is_primary||t["node_type"]=="metabolite"&&!t.node_is_primary)?"hidden":null}).attr("d",function(e){if(e.from_node_id===null||e.to_node_id===null)return null;var t=i[e.from_node_id],n=i[e.to_node_id],r=e.b1,s=e.b2;if(t["node_type"]=="metabolite"){var o=m(e.data,a),u=g(o,e.reversibility,e.from_node_coefficient,t.node_is_primary),f=r===null?n:r;t=b(u,t,f,"start")}if(n["node_type"]=="metabolite"){var o=m(e.data,a),u=g(o,e.reversibility,e.to_node_coefficient,n.node_is_primary),f=s===null?t:s;n=b(u,f,n,"end")}var l="M"+t.x+","+t.y+" ";return r!==null&&s!==null&&(l+="C"+r.x+","+r.y+" "+s.x+","+s.y+" "),l+=n.x+","+n.y,l}).style("stroke",function(e){var t=this.parentNode.parentNode.__data__.bigg_id,i=h&&r!==null&&!(t in r.reactions);if(i)return"red";if(f){var s=e.data;return s===null?c:n.reaction_color(s)}return null}).style("stroke-width",function(e){if(a){var t=e.data;return t===null?l:n.reaction_size(t)}return null});var y=t.select(".arrowheads").selectAll(".arrowhead").data(function(t){var n=[],r=i[t.from_node_id],s=t.b1,o=i[t.to_node_id],u=t.b2;if(p&&(o["node_type"]=="metabolite"&&!o.node_is_primary||r["node_type"]=="metabolite"&&!r.node_is_primary))return n;if(r.node_type=="metabolite"&&(t.reversibility||t.from_node_coefficient>0)){var f=m(t.data,a),l=g(f,t.reversibility,t.from_node_coefficient,r.node_is_primary),c=s===null?o:s,h=e.to_degrees(e.get_angle([r,c]))+90,d=b(l,r,c,"start");n.push({data:t.data,x:d.x,y:d.y,size:f,rotation:h,show_arrowhead_flux:t.from_node_coefficient<0==t.reverse_flux||t.data==0})}if(o.node_type=="metabolite"&&(t.reversibility||t.to_node_coefficient>0)){var f=m(t.data,a),l=g(f,t.reversibility,t.to_node_coefficient,o.node_is_primary),c=u===null?r:u,h=e.to_degrees(e.get_angle([o,c]))+90,d=b(l,c,o,"end");n.push({data:t.data,x:d.x,y:d.y,size:f,rotation:h,show_arrowhead_flux:t.to_node_coefficient<0==t.reverse_flux||t.data==0})}return n});y.enter().append("path").classed("arrowhead",!0),y.attr("d",function(e){return"M"+[-e.size.width/2,0]+" L"+[0,e.size.height]+" L"+[e.size.width/2,0]+" Z"}).attr("transform",function(e){return"translate("+e.x+","+e.y+")rotate("+e.rotation+")"}).style("fill",function(e){if(f){if(e.show_arrowhead_flux){var t=e.data;return t===null?c:n.reaction_color(t)}return"#FFFFFF"}return null}).style("stroke",function(e){if(f){var t=e.data;return t===null?c:n.reaction_color(t)}return null}),y.exit().remove();var w=t.select(".stoichiometry-labels").selectAll(".stoichiometry-label").data(function(t){var n=[],r=i[t.from_node_id],s=t.b1,o=i[t.to_node_id],u=t.b2,f=1.5;if(p&&(o["node_type"]=="metabolite"&&!o.node_is_primary||r["node_type"]=="metabolite"&&!r.node_is_primary))return n;if(r.node_type=="metabolite"&&Math.abs(t.from_node_coefficient)!=1){var l=m(t.data,a),c=f*g(l,!1,0,o.node_is_primary),h=s===null?o:s;h=e.c_plus_c(h,e.rotate_coords(h,.5,r));var d=b(c,r,h,"start");d=e.c_plus_c(d,{x:0,y:7}),n.push({coefficient:Math.abs(t.from_node_coefficient),x:d.x,y:d.y,data:t.data})}if(o.node_type=="metabolite"&&Math.abs(t.to_node_coefficient)!=1){var l=m(t.data,a),c=f*g(l,!1,0,o.node_is_primary),h=u===null?r:u;h=e.c_plus_c(h,e.rotate_coords(h,.5,o));var d=b(c,h,o,"end");d=e.c_plus_c(d,{x:0,y:7}),n.push({coefficient:Math.abs(t.to_node_coefficient),x:d.x,y:d.y,data:t.data})}return n});w.enter().append("text").attr("class","stoichiometry-label").attr("text-anchor","middle"),w.attr("transform",function(e){return"translate("+e.x+","+e.y+")"}).text(function(e){return e.coefficient}).style("fill",function(e){if(f){var t=e.data;return t===null?c:n.reaction_color(t)}return null}),w.exit().remove(),this.callback_manager.run("update_segment",this,t)}function p(e){var t=e.append("g").attr("id",function(e){return e.bezier_id}).attr("class",function(e){return"bezier"});t.append("path").attr("class","connect-line"),t.append("circle").attr("class",function(e){return"bezier-circle "+e.bezier}).style("stroke-width",String(1)+"px").attr("r",String(7)+"px"),this.callback_manager.run("create_bezier",this,e)}function d(e,t,n,r,i,s,o){var u=this.settings.get_option("hide_secondary_metabolites");if(!t){e.attr("visibility","hidden");return}e.attr("visibility","visible"),e.style("visibility",function(e){var t=o[e.reaction_id].segments[e.segment_id],n=s[t.from_node_id],r=s[t.to_node_id];return u&&(r["node_type"]=="metabolite"&&!r.node_is_primary||n["node_type"]=="metabolite"&&!n.node_is_primary)?"hidden":null}),e.select(".bezier-circle").call(this.behavior.turn_off_drag).call(n).on("mouseover",r).on("mouseout",i).attr("transform",function(e){return e.x==null||e.y==null?"":"translate("+e.x+","+e.y+")"}),e.select(".connect-line").attr("d",function(e){var t,n=o[e.reaction_id].segments[e.segment_id];return t=e.bezier=="b1"?s[n.from_node_id]:s[n.to_node_id],e.x==null||e.y==null||t.x==null||t.y==null?"":"M"+e.x+", "+e.y+" "+t.x+","+t.y}),this.callback_manager.run("update_bezier",this,e)}function v(e,t,n){var r=e.append("g").attr("class","node").attr("id",function(e){return"n"+e.node_id});r.append("circle").attr("class",function(e){var t="node-circle";return e.node_type!==null&&(t+=" "+e.node_type+"-circle"),t});var i=r.filter(function(e){return e.node_type=="metabolite"});i.append("text").attr("class","node-label label"),i.append("title"),this.callback_manager.run("create_node",this,e)}function m(e,t,n,r,i,s,o,u,a){var f=this.settings.get_option("hide_secondary_metabolites"),l=this.settings.get_option("primary_metabolite_radius"),c=this.settings.get_option("secondary_metabolite_radius"),h=this.settings.get_option("marker_radius"),p=this.settings.get_option("hide_all_labels"),d=this.settings.get_option("identifiers_on_map"),v=d=="bigg_id"?"name":"bigg_id",m=this.settings.get_option("metabolite_styles"),g={color:this.settings.get_option("metabolite_no_data_color"),size:this.settings.get_option("metabolite_no_data_size")},y=e.select(".node-circle").attr("transform",function(e){return"translate("+e.x+","+e.y+")"}).style("visibility",function(e){return f&&!e.node_is_primary?"hidden":null}).attr("r",function(e){if(e.node_type=="metabolite"){var r=n&&m.indexOf("size")!=-1;if(r){var i=e.data;return i===null?g.size:t.metabolite_size(i)}return e.node_is_primary?l:c}return h}).style("fill",function(e){if(e.node_type=="metabolite"){var r=n&&m.indexOf("color")!=-1;if(r){var i=e.data;return i===null?g.color:t.metabolite_color(i)}return null}return null}).call(this.behavior.turn_off_drag).call(u).on("mousedown",r).on("click",i).on("mouseover",s).on("mouseout",o),b=e.select(".node-label").attr("visibility",p?"hidden":"visible");p||(b.style("visibility",function(e){return f&&!e.node_is_primary?"hidden":null}).attr("transform",function(e){return"translate("+e.label_x+","+e.label_y+")"}).text(function(e){var t=e[d];return n&&m.indexOf("text")!=-1&&(t+=" "+e.data_string),t}).call(this.behavior.turn_off_drag).call(a),e.select("title").text(function(e){return e[v]})),this.callback_manager.run("update_node",this,e)}function g(e){e.append("g").attr("id",function(e){return"l"+e.text_label_id}).attr("class","text-label").append("text").attr("class","label"),this.callback_manager.run("create_text_label",this,e)}function y(e){var t=this.behavior.text_label_mousedown,n=this.behavior.text_label_click,r=this.behavior.selectable_drag,i=this.behavior.turn_off_drag;e.select(".label").text(function(e){return e.text}).attr("transform",function(e){return"translate("+e.x+","+e.y+")"}).on("mousedown",t).on("click",n).call(i).call(r),this.callback_manager.run("update_text_label",this,e)}function b(t,n,r,i){e.check_undefined(arguments,["reaction_arrow_displacement","start","end","displace"]);var s=t,o=e.distance(n,r),u,a;return(!s||!o)&&console.error("Bad value"),i=="start"?(u=n.x+s*(r.x-n.x)/o,a=n.y+s*(r.y-n.y)/o):i=="end"?(u=r.x-s*(r.x-n.x)/o,a=r.y-s*(r.y-n.y)/o):console.error("bad displace value: "+i),{x:u,y:a}}var r=e.make_class();return r.prototype={init:i,create_reaction:u,update_reaction:a,create_bezier:p,update_bezier:d,create_node:v,update_node:m,create_text_label:g,update_text_label:y,create_membrane:s,update_membrane:o,create_reaction_label:f,update_reaction_label:l,create_segment:c,update_segment:h},r}),n("build",["utils"],function(e){function t(t,r,i,o,u,a,f,c){c=Math.PI/180*c;var h=String(++a.reactions),p={x:u.x,y:u.y},d=300,v=[p,e.c_plus_c(p,{x:d,y:0})],m={x:(v[0].x+v[1].x)/2,y:(v[0].y+v[1].y)/2},g;Math.abs(c)<Math.PI/4||Math.abs(c-Math.PI)<Math.PI/4?g={x:-50,y:-40}:g={x:30,y:10};var y=20,b=e.clone(r);e.extend(b,{label_x:m.x+g.x,label_y:m.y+g.y,segments:{}});var w=[],E=[],S=0,x=0,T=!1;for(var N in b.metabolites){var C=i[N],k=b.metabolites[N],L=C.formula,A={coefficient:k,bigg_id:N,name:C.name};if(k<0){A.index=S;var O=/C([0-9]+)/.exec(L);u.bigg_id==A.bigg_id?w.push([A.index,Infinity]):O&&f.indexOf(e.decompartmentalize(A.bigg_id)[0])==-1&&w.push([A.index,parseInt(O[1])]),S++}else{A.index=x;var O=/C([0-9]+)/.exec(L);u.bigg_id==A.bigg_id?(E.push([A.index,Infinity]),T=!0):O&&f.indexOf(e.decompartmentalize(A.bigg_id)[0])==-1&&E.push([A.index,parseInt(O[1])]),x++}b.metabolites[N]=A}var M=function(e,t){return t[1]>e[1]?t:e},_=w.reduce(M,[0,0])[0],D=E.reduce(M,[0,0])[0];for(var N in b.metabolites){var C=b.metabolites[N];C.coefficient<0?(C.index==_&&(C.is_primary=!0),C.count=S+1):(C.index==D&&(C.is_primary=!0),C.count=x+1)}var P={},H=[{node_type:"anchor_reactants",dis:{x:y*(T?1:-1),y:0}},{node_type:"center",dis:{x:0,y:0}},{node_type:"anchor_products",dis:{x:y*(T?-1:1),y:0}}],B={};H.map(function(e){var t=String(++a.nodes),n=e.node_type=="center"?"midmarker":"multimarker";P[t]={node_type:n,x:m.x+e.dis.x,y:m.y+e.dis.y,connected_segments:[],name:null,bigg_id:null,label_x:null,label_y:null,node_is_primary:null},B[e.node_type]=t});var j=[[B.anchor_reactants,B.center],[B.anchor_products,B.center]];j.map(function(e){var t=e[0],n=e[1],r=String(++a.segments);b.segments[r]={b1:null,b2:null,from_node_id:t,to_node_id:n,from_node_coefficient:null,to_node_coefficient:null,reversibility:b.reversibility,data:b.data,reverse_flux:b.reverse_flux},P[t].connected_segments.push({segment_id:r,reaction_id:h}),P[n].connected_segments.push({segment_id:r,reaction_id:h})});var F=P;for(var N in b.metabolites){var C=b.metabolites[N],I,q;C.coefficient<0?(I=_,q=B.anchor_reactants):(I=D,q=B.anchor_products);var R=s(C,I,v,m,d,T);if(u.bigg_id==C.bigg_id){var U=String(++a.segments);b.segments[U]={b1:R.b1,b2:R.b2,from_node_id:q,to_node_id:o,from_node_coefficient:null,to_node_coefficient:C.coefficient,reversibility:b.reversibility,data:b.data,reverse_flux:b.reverse_flux},u.connected_segments.push({segment_id:U,reaction_id:h}),F[q].connected_segments.push({segment_id:U,reaction_id:h})}else{var U=String(++a.segments),z=String(++a.nodes);b.segments[U]={b1:R.b1,b2:R.b2,from_node_id:q,to_node_id:z,from_node_coefficient:null,to_node_coefficient:C.coefficient,reversibility:b.reversibility,data:b.data,reverse_flux:b.reverse_flux},F[z]={connected_segments:[{segment_id:U,reaction_id:h}],x:R.circle.x,y:R.circle.y,node_is_primary:Boolean(C.is_primary),label_x:R.circle.x+g.x,label_y:R.circle.y+g.y,name:C.name,bigg_id:C.bigg_id,node_type:"metabolite"},F[q].connected_segments.push({segment_id:U,reaction_id:h})}}var W=[];for(var t in b.metabolites)W.push({bigg_id:t,coefficient:b.metabolites[t].coefficient});b.metabolites=W;var X={};X[h]=b;var V=l(X);return F[o]=u,n(F,X,V,c,p),{new_reactions:X,new_beziers:V,new_nodes:F}}function n(t,n,r,s,o){var a=function(t){return t===null?null:e.rotate_coords(t,s,o)},f=[],l=[];for(var c in t){var h=t[c],p=a({x:h.x,y:h.y}),d=i(h,n,p);h.connected_segments.map(function(t){var i=n[t.reaction_id];if(i===undefined)return;var s=t.segment_id,o=i.segments[s];if(o.to_node_id==c&&o.b2){var f=a(o.b2),l=u(s,"b2");o.b2=e.c_plus_c(o.b2,f),r[l].x=o.b2.x,r[l].y=o.b2.y}else if(o.from_node_id==c&&o.b1){var f=a(o.b1),l=u(s,"b1");o.b1=e.c_plus_c(o.b1,f),r[l].x=o.b1.x,r[l].y=o.b1.y}}),l=e.unique_concat([l,d.reaction_ids]),f.push(c)}return{node_ids:f,reaction_ids:l}}function r(t,n,r,s,o){var a=i(t,r,o);return t.connected_segments.map(function(t){var i=r[t.reaction_id];if(i===undefined)return;var f=t.segment_id,l=i.segments[f];[["b1","from_node_id"],["b2","to_node_id"]].forEach(function(t){var r=t[0],i=t[1];if(l[i]==n&&l[r]){l[r]=e.c_plus_c(l[r],o);var a=s[u(f,r)];a.x=l[r].x,a.y=l[r].y}}),a.reaction_ids.indexOf(t.reaction_id)<0&&a.reaction_ids.push(t.reaction_id)}),a}function i(e,t,n){e.x=e.x+n.x,e.y=e.y+n.y,e.label_x=e.label_x+n.x,e.label_y=e.label_y+n.y;var r=[];return e.connected_segments.map(function(i){var s=t[i.reaction_id];r.indexOf(i.reaction_id)<0&&(r.push(i.reaction_id),e.node_type=="midmarker"&&(s.label_x=s.label_x+n.x,s.label_y=s.label_y+n.y))}),{reaction_ids:r}}function s(t,n,r,i,s,o){var u=r[0],r=[e.c_minus_c(r[0],u),e.c_minus_c(r[1],u)],i=e.c_minus_c(i,u),a=80,f=.4,l=.25,c=a*.7,h=40,p=Math.min(2,t.count-1),d,v,m;t.is_primary?d=20:(d=10,t.index>n?v=t.index-1:v=t.index);var g=s-d,y=[{x:d,y:0},{x:g,y:0}],b,w,E,S;t.coefficient<0!=o&&t.is_primary?(b={x:y[0].x,y:y[0].y},E={x:i.x*(1-f)+y[0].x*f,y:i.y*(1-f)+y[0].y*f},S={x:i.x*l+b.x*(1-l),y:i.y*l+b.y*(1-l)},w={x:r[0].x,y:r[0].y}):t.coefficient<0!=o?(b={x:y[0].x+h,y:y[0].y+(c*v-c*(p-1)/2)},E={x:i.x*(1-f)+y[0].x*f,y:i.y*(1-f)+y[0].y*f},S={x:i.x*l+b.x*(1-l),y:i.y*l+b.y*(1-l)},w={x:r[0].x+h,y:r[0].y+(a*v-a*(p-1)/2)}):t.coefficient>0!=o&&t.is_primary?(b={x:y[1].x,y:y[1].y},E={x:i.x*(1-f)+y[1].x*f,y:i.y*(1-f)+y[1].y*f},S={x:i.x*l+b.x*(1-l),y:i.y*l+b.y*(1-l)},w={x:r[1].x,y:r[1].y}):t.coefficient>0!=o&&(b={x:y[1].x-h,y:y[1].y+(c*v-c*(p-1)/2)},E={x:i.x*(1-f)+y[1].x*f,y:i.y*(1-f)+y[1].y*f},S={x:i.x*l+b.x*(1-l),y:i.y*l+b.y*(1-l)},w={x:r[1].x-h,y:r[1].y+(a*v-a*(p-1)/2)});var x={};return x.b1=e.c_plus_c(u,E),x.b2=e.c_plus_c(u,S),x.circle=e.c_plus_c(u,w),x}function o(e,t,n){var r=String(++e.text_labels),i={text:t,x:n.x,y:n.y};return{id:r,label:i}}function u(e,t){return e+"_"+t}function a(e){var t=[];for(var n in e){var r=e[n];for(var i in r.segments){var s=r.segments[i];["b1","b2"].forEach(function(e){var n=s[e];n!==null&&t.push(u(i,e))})}}return t}function f(e,t){var n={};for(var r in e){var i=e[r];["b1","b2"].forEach(function(e){var s=i[e];if(s!==null){var o=u(r,e);n[o]={bezier:e,x:s.x,y:s.y,reaction_id:t,segment_id:r}}})}return n}function l(t){var n={};for(var r in t){var i=t[r],s=f(i.segments,r);e.extend(n,s)}return n}return{new_reaction:t,rotate_nodes:n,move_node_and_dependents:r,new_text_label:o,bezier_id_for_segment_id:u,bezier_ids_for_reaction_ids:a,new_beziers_for_segments:f,new_beziers_for_reactions:l}}),n("Behavior",["utils","build"],function(e,t){function r(e,t){this.map=e,this.undo_stack=t,this.empty_behavior=function(){},this.rotation_mode_enabled=!1,this.rotation_drag=d3.behavior.drag(),this.selectable_mousedown=null,this.text_label_mousedown=null,this.text_label_click=null,this.selectable_drag=this.empty_behavior,this.node_mouseover=null,this.node_mouseout=null,this.label_mousedown=null,this.label_mouseover=null,this.label_mouseout=null,this.bezier_drag=this.empty_behavior,this.bezier_mouseover=null,this.bezier_mouseout=null,this.reaction_label_drag=this.empty_behavior,this.node_label_drag=this.empty_behavior,this.turn_everything_on()}function i(){this.toggle_selectable_click(!0),this.toggle_selectable_drag(!0),this.toggle_label_drag(!0),this.toggle_label_mousedown(!0)}function s(){this.toggle_selectable_click(!1),this.toggle_selectable_drag(!1),this.toggle_label_drag(!1),this.toggle_label_mousedown(!1)}function o(n){function g(){var e=this.map.sel.selectAll("#rotation-center").data([0]),t=e.enter().append("g").attr("id","rotation-center");t.append("path").attr("d","M-32 0 L32 0").attr("class","rotation-center-line"),t.append("path").attr("d","M0 -32 L0 32").attr("class","rotation-center-line"),e.attr("transform","translate("+this.center.x+","+this.center.y+")").attr("visibility","visible"),e.call(d3.behavior.drag().on("drag",function(e){var t=d3.transform(e.attr("transform")),n=[d3.event.dx+t.translate[0],d3.event.dy+t.translate[1]];e.attr("transform","translate("+n+")"),this.center={x:n[0],y:n[1]}}.bind(this,e))),e.on("mouseover",function(){var e=parseFloat(this.selectAll("path").style("stroke-width"));this.selectAll("path").style("stroke-width",e*2+"px")}.bind(e)),e.on("mouseout",function(){this.selectAll("path").style("stroke-width",null)}.bind(e))}function y(e){this.map.sel.select("#rotation-center").attr("visibility","hidden")}function b(t){var n=[],r=[];for(var i in t){var s=t[i];s.x!==undefined&&n.push(s.x),s.y!==undefined&&r.push(s.y)}return{x:e.mean(n),y:e.mean(r)}}n===undefined?this.rotation_mode_enabled=!this.rotation_mode_enabled:this.rotation_mode_enabled=n;var r=this.map.sel.selectAll(".node-circle"),i=this.map.sel.selectAll("#canvas");if(this.rotation_mode_enabled){this.map.callback_manager.run("start_rotation");var s=this.map.get_selected_nodes();if(Object.keys(s).length==0){console.warn("No selected nodes");return}this.center=b(s),g.call(this);var o=this.map,u=Object.keys(s),a=this.map.reactions,f=this.map.nodes,l=this.map.beziers,c=function(e){d3.event.sourceEvent.stopPropagation()},h=function(e,n,r,i){var u=t.rotate_nodes(s,a,l,n,i);o.draw_these_nodes(u.node_ids),o.draw_these_reactions(u.reaction_ids)},p=function(e){},d=function(e,n,r){var i={};u.forEach(function(e){i[e]=f[e]});var s=t.rotate_nodes(i,a,l,-n,r);o.draw_these_nodes(s.node_ids),o.draw_these_reactions(s.reaction_ids)},v=function(e,n,r){var i={};u.forEach(function(e){i[e]=f[e]});var s=t.rotate_nodes(i,a,l,n,r);o.draw_these_nodes(s.node_ids),o.draw_these_reactions(s.reaction_ids)},m=function(){return this.center}.bind(this);this.rotation_drag=this._get_generic_angular_drag(c,h,p,d,v,m,this.map.sel),i.call(this.rotation_drag),this.selectable_drag=this.rotation_drag}else y.call(this),r.on("mousedown.center",null),i.on("mousedown.center",null),i.on("mousedown.drag",null),i.on("touchstart.drag",null),this.rotation_drag=null,this.selectable_drag=null}function u(e){e===undefined&&(e=this.selectable_mousedown==null);if(e){var t=this.map;this.selectable_mousedown=function(e){d3.event.stopPropagation()},this.selectable_click=function(e){d3.event.stopPropagation();if(d3.event.defaultPrevented)return;t.select_selectable(this,e)},this.node_mouseover=function(e){d3.select(this).style("stroke-width",null);var t=parseFloat(d3.select(this).style("stroke-width"));d3.select(this.parentNode).classed("selected")||d3.select(this).style("stroke-width",t*3+"px")},this.node_mouseout=function(e){d3.select(this).style("stroke-width",null)}}else this.selectable_mousedown=null,this.selectable_click=null,this.node_mouseover=null,this.node_mouseout=null,this.map.sel.select("#nodes").selectAll(".node-circle").style("stroke-width",null)}function a(e){e===undefined&&(e=this.text_edit_mousedown==null);if(e){var t=this.map,n=this.selection;this.text_label_mousedown=function(){if(d3.event.defaultPrevented)return;var e=d3.transform(d3.select(this).attr("transform")).translate,n={x:e[0],y:e[1]};t.callback_manager.run("edit_text_label",null,d3.select(this),n),d3.event.stopPropagation()},this.text_label_click=null,this.map.sel.select("#text-labels").selectAll(".label").classed("edit-text-cursor",!0),this.map.sel.on("mousedown.new_text_label",function(e){d3.event.preventDefault();var t={x:d3.mouse(e)[0],y:d3.mouse(e)[1]};this.map.callback_manager.run("new_text_label",null,t)}.bind(this,this.map.sel.node()))}else this.text_label_mousedown=this.selectable_mousedown,this.text_label_click=this.selectable_click,this.map.sel.select("#text-labels").selectAll(".label").classed("edit-text-cursor",!1),this.map.sel.on("mousedown.new_text_label",null),this.map.callback_manager.run("hide_text_label_editor")}function f(e){e===undefined&&(e=this.selectable_drag===this.empty_behavior),e?(this.selectable_drag=this._get_selectable_drag(this.map,this.undo_stack),this.bezier_drag=this._get_bezier_drag(this.map,this.undo_stack)):(this.selectable_drag=this.empty_behavior,this.bezier_drag=this.empty_behavior)}function l(e){e===undefined&&(e=this.label_drag===this.empty_behavior),e?(this.reaction_label_drag=this._get_reaction_label_drag(this.map),this.node_label_drag=this._get_node_label_drag(this.map)):(this.reaction_label_drag=this.empty_behavior,this.node_label_drag=this.empty_behavior)}function c(e){e===undefined&&(e=this.label_mousedown==null);if(e){var t=this.map;this.label_mousedown=function(e){},this.label_mouseover=function(e){},this.label_mouseout=function(e){}}else this.label_mousedown=null,this.label_mouseover=null,this.label_mouseout=null,this.map.sel.select(".node-label,.reaction-label").style("fill",null)}function h(e){e===undefined&&(e=this.bezier_drag===this.empty_behavior),e?(this.bezier_drag=this._get_bezier_drag(this.map),this.bezier_mouseover=function(e){d3.select(this).style("stroke-width",String(3)+"px")},this.bezier_mouseout=function(e){d3.select(this).style("stroke-width",String(1)+"px")}):(this.bezier_drag=this.empty_behavior,this.bezier_mouseover=null,this.bezier_mouseout=null)}function p(e){e.on("mousedown.drag",null),e.on("touchstart.drag",null)}function d(n,r){function c(t,r){var i=n.nodes[r],s=n.nodes[t],o=[];return i.connected_segments.forEach(function(i){var u;try{u=n.reactions[i.reaction_id].segments[i.segment_id];if(u===undefined)throw new Error("undefined segment")}catch(a){console.warn("Could not find connected segment "+i.segment_id);return}if(u.from_node_id==r)u.from_node_id=t;else{if(u.to_node_id!=r){console.error("Segment does not connect to dragged node");return}u.to_node_id=t}s.connected_segments.push(i),o.push(e.clone(i));return}),n.delete_node_data([r]),n.sel.selectAll(".node-to-combine").classed("node-to-combine",!1),n.draw_everything(),o}var i=d3.behavior.drag(),s=null,o=null,u=null,a=null,f=null,l=function(e,t){var r=n.text_labels[e];r.x=r.x+t.x,r.y=r.y+t.y};return i.on("dragstart",function(e){d3.event.sourceEvent.stopPropagation(),o={x:0,y:0};if(d3.select(this).attr("class").indexOf("label")==-1){var t=this.parentNode.__data__,r=t.bigg_id,i=this.parentNode;s=window.setTimeout(function(){i.parentNode.insertBefore(i,i.parentNode.firstChild)},200),n.sel.selectAll(".metabolite-circle").on("mouseover.combine",function(e){e.bigg_id==r&&e.node_id!=t.node_id&&d3.select(this).style("stroke-width",String(12)+"px").classed("node-to-combine",!0)}).on("mouseout.combine",function(e){e.bigg_id==r&&n.sel.selectAll(".node-to-combine").style("stroke-width",String(2)+"px").classed("node-to-combine",!1)})}}),i.on("drag",function(r){d3.select(this.parentNode).classed("selected")||n.select_selectable(this,r);var i={};d3.select(this).attr("class").indexOf("label")==-1?(i.type="node",i.id=this.parentNode.__data__.node_id):(i.type="label",i.id=this.__data__.text_label_id);var s=n.get_selected_node_ids(),c=n.get_selected_text_label_ids();u=[],f=[],i["type"]=="node"&&s.indexOf(i["id"])==-1?u.push(i.id):i["type"]=="label"&&c.indexOf(i["id"])==-1?f.push(i.id):(u=s,f=c),a=[];var h={x:d3.event.dx,y:d3.event.dy};o=e.c_plus_c(o,h),u.forEach(function(r){var i=n.nodes[r],s=t.move_node_and_dependents(i,r,n.reactions,n.beziers,h);a=e.unique_concat([a,s.reaction_ids])}),f.forEach(function(e){l(e,h)}),n.draw_these_nodes(u),n.draw_these_reactions(a),n.draw_these_text_labels(f)}),i.on("dragend",function(){if(u===null){o=null,u=null,f=null,a=null,s=null;return}var i=[];n.sel.selectAll(".node-to-combine").each(function(e){i.push(e.node_id)});if(i.length==1){var h=i[0],p=this.parentNode.__data__.node_id,d=e.clone(n.nodes[p]),v=c(h,p);r.push(function(){n.nodes[p]=d;var e=n.nodes[h],t=[];v.forEach(function(r){var i=n.reactions[r.reaction_id].segments[r.segment_id];i.from_node_id==h?i.from_node_id=p:i.to_node_id==h?i.to_node_id=p:console.error("Segment does not connect to fixed node"),e.connected_segments=e.connected_segments.filter(function(e){return e.reaction_id!=r.reaction_id||e.segment_id!=r.segment_id}),t.indexOf(r.reaction_id)==-1&&t.push(r.reaction_id)}),n.draw_these_nodes([p]),n.draw_these_reactions(t)},function(){c(h,p)})}else{var m=e.clone(o),g=e.clone(u),y=e.clone(f),b=e.clone(a);r.push(function(){g.forEach(function(r){var i=n.nodes[r];t.move_node_and_dependents(i,r,n.reactions,n.beziers,e.c_times_scalar(m,-1))}),y.forEach(function(t){l(t,e.c_times_scalar(m,-1))}),n.draw_these_nodes(g),n.draw_these_reactions(b),n.draw_these_text_labels(y)},function(){g.forEach(function(e){var r=n.nodes[e];t.move_node_and_dependents(r,e,n.reactions,n.beziers,m)}),y.forEach(function(e){l(e,m)}),n.draw_these_nodes(g),n.draw_these_reactions(b),n.draw_these_text_labels(y)})}n.sel.selectAll(".metabolite-circle").on("mouseover.combine",null).on("mouseout.combine",null),window.clearTimeout(s),o=null,u=null,f=null,a=null,s=null}),i}function v(t){var n=function(n,r,i,s,o){var u=t.reactions[n].segments[r];u[i]=e.c_plus_c(u[i],o),t.beziers[s].x=u[i].x,t.beziers[s].y=u[i].y},r=function(e){e.dragging=!0},i=function(e,r,i){n(e.reaction_id,e.segment_id,e.bezier,e.bezier_id,r),t.draw_these_reactions([e.reaction_id],!1),t.draw_these_beziers([e.bezier_id])},s=function(e){e.dragging=!1},o=function(r,i){n(r.reaction_id,r.segment_id,r.bezier,r.bezier_id,e.c_times_scalar(i,-1)),t.draw_these_reactions([r.reaction_id],!1),t.draw_these_beziers([r.bezier_id])},u=function(e,r){n(e.reaction_id,e.segment_id,e.bezier,e.bezier_id,r),t.draw_these_reactions([e.reaction_id],!1),t.draw_these_beziers([e.bezier_id])};return this._get_generic_drag(r,i,s,o,u,this.map.sel)}function m(t){var n=function(e,n){var 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0!==t.minLength&&e.length<t.minLength?this.createError(d.STRING_LENGTH_SHORT,{length:e.length,minimum:t.minLength}).prefixWith(null,"minLength"):void 0!==t.maxLength&&e.length>t.maxLength?this.createError(d.STRING_LENGTH_LONG,{length:e.length,maximum:t.maxLength}).prefixWith(null,"maxLength"):null},p.prototype.validateStringPattern=function(e,t){if("string"!=typeof e||void 0===t.pattern)return null;var n=new RegExp(t.pattern);return n.test(e)?null:this.createError(d.STRING_PATTERN,{pattern:t.pattern}).prefixWith(null,"pattern")},p.prototype.validateArray=function(e,t,n){return Array.isArray(e)?this.validateArrayLength(e,t,n)||this.validateArrayUniqueItems(e,t,n)||this.validateArrayItems(e,t,n)||null:null},p.prototype.validateArrayLength=function(e,t){var n;return void 0!==t.minItems&&e.length<t.minItems&&(n=this.createError(d.ARRAY_LENGTH_SHORT,{length:e.length,minimum:t.minItems}).prefixWith(null,"minItems"),this.handleError(n))?n:void 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for(i=0;i<e.length;i++)if(r=this.validateAll(e[i],t.items,[i],["items"],n+"/"+i))return r;return null},p.prototype.validateObject=function(e,t,n){return"object"!=typeof e||null===e||Array.isArray(e)?null:this.validateObjectMinMaxProperties(e,t,n)||this.validateObjectRequiredProperties(e,t,n)||this.validateObjectProperties(e,t,n)||this.validateObjectDependencies(e,t,n)||null},p.prototype.validateObjectMinMaxProperties=function(e,t){var n,r=Object.keys(e);return void 0!==t.minProperties&&r.length<t.minProperties&&(n=this.createError(d.OBJECT_PROPERTIES_MINIMUM,{propertyCount:r.length,minimum:t.minProperties}).prefixWith(null,"minProperties"),this.handleError(n))?n:void 0!==t.maxProperties&&r.length>t.maxProperties&&(n=this.createError(d.OBJECT_PROPERTIES_MAXIMUM,{propertyCount:r.length,maximum:t.maxProperties}).prefixWith(null,"maxProperties"),this.handleError(n))?n:null},p.prototype.validateObjectRequiredProperties=function(e,t){if(void 0!==t.required)for(var n=0;n<t.required.length;n++){var r=t.required[n];if(void 0===e[r]){var i=this.createError(d.OBJECT_REQUIRED,{key:r}).prefixWith(null,""+n).prefixWith(null,"required");if(this.handleError(i))return i}}return null},p.prototype.validateObjectProperties=function(e,t,n){var r;for(var i in e){var s=n+"/"+i.replace(/~/g,"~0").replace(/\//g,"~1"),o=!1;if(void 0!==t.properties&&void 0!==t.properties[i]&&(o=!0,r=this.validateAll(e[i],t.properties[i],[i],["properties",i],s)))return r;if(void 0!==t.patternProperties)for(var u in t.patternProperties){var a=new RegExp(u);if(a.test(i)&&(o=!0,r=this.validateAll(e[i],t.patternProperties[u],[i],["patternProperties",u],s)))return r}if(o)this.trackUnknownProperties&&(this.knownPropertyPaths[s]=!0,delete this.unknownPropertyPaths[s]);else if(void 0!==t.additionalProperties){if(this.trackUnknownProperties&&(this.knownPropertyPaths[s]=!0,delete this.unknownPropertyPaths[s]),"boolean"==typeof t.additionalProperties){if(!t.additionalProperties&&(r=this.createError(d.OBJECT_ADDITIONAL_PROPERTIES,{}).prefixWith(i,"additionalProperties"),this.handleError(r)))return r}else if(r=this.validateAll(e[i],t.additionalProperties,[i],["additionalProperties"],s))return r}else this.trackUnknownProperties&&!this.knownPropertyPaths[s]&&(this.unknownPropertyPaths[s]=!0)}return null},p.prototype.validateObjectDependencies=function(e,t,n){var r;if(void 0!==t.dependencies)for(var i in t.dependencies)if(void 0!==e[i]){var s=t.dependencies[i];if("string"==typeof s){if(void 0===e[s]&&(r=this.createError(d.OBJECT_DEPENDENCY_KEY,{key:i,missing:s}).prefixWith(null,i).prefixWith(null,"dependencies"),this.handleError(r)))return r}else if(Array.isArray(s))for(var o=0;o<s.length;o++){var u=s[o];if(void 0===e[u]&&(r=this.createError(d.OBJECT_DEPENDENCY_KEY,{key:i,missing:u}).prefixWith(null,""+o).prefixWith(null,i).prefixWith(null,"dependencies"),this.handleError(r)))return r}else if(r=this.validateAll(e,s,[],["dependencies",i],n))return r}return null},p.prototype.validateCombinations=function(e,t,n){return this.validateAllOf(e,t,n)||this.validateAnyOf(e,t,n)||this.validateOneOf(e,t,n)||this.validateNot(e,t,n)||null},p.prototype.validateAllOf=function(e,t,n){if(void 0===t.allOf)return null;for(var r,i=0;i<t.allOf.length;i++){var s=t.allOf[i];if(r=this.validateAll(e,s,[],["allOf",i],n))return r}return null},p.prototype.validateAnyOf=function(e,t,n){if(void 0===t.anyOf)return null;var r,i,s=[],o=this.errors.length;this.trackUnknownProperties&&(r=this.unknownPropertyPaths,i=this.knownPropertyPaths);for(var u=!0,a=0;a<t.anyOf.length;a++){this.trackUnknownProperties&&(this.unknownPropertyPaths={},this.knownPropertyPaths={});var f=t.anyOf[a],l=this.errors.length,c=this.validateAll(e,f,[],["anyOf",a],n);if(null===c&&l===this.errors.length){if(this.errors=this.errors.slice(0,o),this.trackUnknownProperties){for(var h in this.knownPropertyPaths)i[h]=!0,delete r[h];for(var p in this.unknownPropertyPaths)i[p]||(r[p]=!0);u=!1;continue}return null}c&&s.push(c.prefixWith(null,""+a).prefixWith(null,"anyOf"))}return this.trackUnknownProperties&&(this.unknownPropertyPaths=r,this.knownPropertyPaths=i),u?(s=s.concat(this.errors.slice(o)),this.errors=this.errors.slice(0,o),this.createError(d.ANY_OF_MISSING,{},"","/anyOf",s)):void 0},p.prototype.validateOneOf=function(e,t,n){if(void 0===t.oneOf)return null;var r,i,s=null,o=[],u=this.errors.length;this.trackUnknownProperties&&(r=this.unknownPropertyPaths,i=this.knownPropertyPaths);for(var a=0;a<t.oneOf.length;a++){this.trackUnknownProperties&&(this.unknownPropertyPaths={},this.knownPropertyPaths={});var f=t.oneOf[a],l=this.errors.length,c=this.validateAll(e,f,[],["oneOf",a],n);if(null===c&&l===this.errors.length){if(null!==s)return this.errors=this.errors.slice(0,u),this.createError(d.ONE_OF_MULTIPLE,{index1:s,index2:a},"","/oneOf");if(s=a,this.trackUnknownProperties){for(var h in this.knownPropertyPaths)i[h]=!0,delete r[h];for(var p in this.unknownPropertyPaths)i[p]||(r[p]=!0)}}else c&&o.push(c)}return this.trackUnknownProperties&&(this.unknownPropertyPaths=r,this.knownPropertyPaths=i),null===s?(o=o.concat(this.errors.slice(u)),this.errors=this.errors.slice(0,u),this.createError(d.ONE_OF_MISSING,{},"","/oneOf",o)):(this.errors=this.errors.slice(0,u),null)},p.prototype.validateNot=function(e,t,n){if(void 0===t.not)return null;var r,i,s=this.errors.length;this.trackUnknownProperties&&(r=this.unknownPropertyPaths,i=this.knownPropertyPaths,this.unknownPropertyPaths={},this.knownPropertyPaths={});var o=this.validateAll(e,t.not,null,null,n),u=this.errors.slice(s);return this.errors=this.errors.slice(0,s),this.trackUnknownProperties&&(this.unknownPropertyPaths=r,this.knownPropertyPaths=i),null===o&&0===u.length?this.createError(d.NOT_PASSED,{},"","/not"):null},p.prototype.validateHypermedia=function(e,t,r){if(!t.links)return null;for(var i,s=0;s<t.links.length;s++){var o=t.links[s];if("describedby"===o.rel){for(var u=new n(o.href),a=!0,f=0;f<u.varNames.length;f++)if(!(u.varNames[f]in e)){a=!1;break}if(a){var l=u.fillFromObject(e),c={$ref:l};if(i=this.validateAll(e,c,[],["links",s],r))return i}}}};var d={INVALID_TYPE:0,ENUM_MISMATCH:1,ANY_OF_MISSING:10,ONE_OF_MISSING:11,ONE_OF_MULTIPLE:12,NOT_PASSED:13,NUMBER_MULTIPLE_OF:100,NUMBER_MINIMUM:101,NUMBER_MINIMUM_EXCLUSIVE:102,NUMBER_MAXIMUM:103,NUMBER_MAXIMUM_EXCLUSIVE:104,STRING_LENGTH_SHORT:200,STRING_LENGTH_LONG:201,STRING_PATTERN:202,OBJECT_PROPERTIES_MINIMUM:300,OBJECT_PROPERTIES_MAXIMUM:301,OBJECT_REQUIRED:302,OBJECT_ADDITIONAL_PROPERTIES:303,OBJECT_DEPENDENCY_KEY:304,ARRAY_LENGTH_SHORT:400,ARRAY_LENGTH_LONG:401,ARRAY_UNIQUE:402,ARRAY_ADDITIONAL_ITEMS:403,FORMAT_CUSTOM:500,KEYWORD_CUSTOM:501,CIRCULAR_REFERENCE:600,UNKNOWN_PROPERTY:1e3},v={};for(var m in d)v[d[m]]=m;var g={INVALID_TYPE:"Invalid type: {type} (expected {expected})",ENUM_MISMATCH:"No enum match for: {value}",ANY_OF_MISSING:'Data does not match any schemas from "anyOf"',ONE_OF_MISSING:'Data does not match any schemas from "oneOf"',ONE_OF_MULTIPLE:'Data is valid against more than one schema from "oneOf": indices {index1} and {index2}',NOT_PASSED:'Data matches schema from "not"',NUMBER_MULTIPLE_OF:"Value {value} is not a multiple of {multipleOf}",NUMBER_MINIMUM:"Value {value} is less than minimum {minimum}",NUMBER_MINIMUM_EXCLUSIVE:"Value {value} is equal to exclusive minimum {minimum}",NUMBER_MAXIMUM:"Value {value} is greater than maximum {maximum}",NUMBER_MAXIMUM_EXCLUSIVE:"Value {value} is equal to exclusive maximum {maximum}",STRING_LENGTH_SHORT:"String is too short ({length} chars), minimum {minimum}",STRING_LENGTH_LONG:"String is too long ({length} chars), maximum {maximum}",STRING_PATTERN:"String does not match pattern: {pattern}",OBJECT_PROPERTIES_MINIMUM:"Too few properties defined ({propertyCount}), minimum {minimum}",OBJECT_PROPERTIES_MAXIMUM:"Too many properties defined ({propertyCount}), maximum {maximum}",OBJECT_REQUIRED:"Missing required property: {key}",OBJECT_ADDITIONAL_PROPERTIES:"Additional properties not allowed",OBJECT_DEPENDENCY_KEY:"Dependency failed - key must exist: {missing} (due to key: {key})",ARRAY_LENGTH_SHORT:"Array is too short ({length}), minimum {minimum}",ARRAY_LENGTH_LONG:"Array is too long ({length}), maximum {maximum}",ARRAY_UNIQUE:"Array items are not unique (indices {match1} and {match2})",ARRAY_ADDITIONAL_ITEMS:"Additional items not allowed",FORMAT_CUSTOM:"Format validation failed ({message})",KEYWORD_CUSTOM:"Keyword failed: {key} ({message})",CIRCULAR_REFERENCE:"Circular $refs: {urls}",UNKNOWN_PROPERTY:"Unknown property (not in schema)"};a.prototype=Object.create(Error.prototype),a.prototype.constructor=a,a.prototype.name="ValidationError",a.prototype.prefixWith=function(e,t){if(null!==e&&(e=e.replace(/~/g,"~0").replace(/\//g,"~1"),this.dataPath="/"+e+this.dataPath),null!==t&&(t=t.replace(/~/g,"~0").replace(/\//g,"~1"),this.schemaPath="/"+t+this.schemaPath),null!==this.subErrors)for(var n=0;n<this.subErrors.length;n++)this.subErrors[n].prefixWith(e,t);return this};var y={},b=l();return b.addLanguage("en-gb",g),b.tv4=b,b}),n("Map",["utils","Draw","Behavior","Scale","build","UndoStack","CallbackManager","KeyManager","Canvas","data_styles","SearchIndex","lib/bacon","lib/tv4"],function(e,t,n,r,i,s,o,u,a,f,l,c,h){function d(i,f,c,h,p,d,v,m,g,y,b){if(v===null){var w=h.get_size();v={x:-w.width,y:-w.height,width:w.width*3,height:w.height*3}}g===undefined||g===null||g==""?g="new_map":g=String(g),y===undefined||y===null||y==""?y=e.generate_map_id():y=String(y),b===undefined||b===null?b="":b=String(b),this.callback_manager=new o,this.svg=i,this.defs=e.setup_defs(i,f),this.canvas=new a(c,v),this.setup_containers(c),this.sel=c,this.zoom_container=h,this.settings=p,this.cobra_model=d,this.largest_ids={reactions:-1,nodes:-1,segments:-1,text_labels:-1},this.scale=new r,this.calc_data_stats("reaction"),this.calc_data_stats("metabolite"),this.scale.connect_to_settings(this.settings,this,q.bind(this)),this.undo_stack=new s,this.behavior=new n(this,this.undo_stack),this.draw=new t(this.behavior,this.settings),this.key_manager=new u(this.settings.get_option("unique_map_id")),this.enable_search=m,this.search_index=new l,this.map_name=g,this.map_id=y,this.map_description=b;var E={x:0,y:0},S=1;this.beziers_enabled=!1,this.has_data_on_reactions=!1,this.has_data_on_nodes=!1,this.nodes={},this.reactions={},this.beziers={},this.text_labels={},this.apply_reaction_data_to_map(null),this.apply_metabolite_data_to_map(null),this.apply_gene_data_to_map(null),this.rotation_on=!1,this.debug=!1}function v(t,n,r,s,o,u,a,f){function P(e,t){return t===undefined&&(t=0),e===undefined?t:Math.max.apply(null,Object.keys(e).map(function(e){return parseInt(e)}).concat([t]))}var l=t[1].canvas,c=t[0].map_name,h=t[0].map_id,d=t[0].map_description.replace(/(\nLast Modified.*)+$/g,"")+"\nLast Modified "+Date(Date.now()).toString(),v=new p(n,r,s,o,u,a,l,f,c,h,d);v.reactions=t[1].reactions,v.nodes=t[1].nodes,v.text_labels=t[1].text_labels;for(var m in v.nodes){var g=v.nodes[m];g.connected_segments=[];if(f){if(g.node_type!="metabolite")continue;v.search_index.insert("n"+m,{name:g.bigg_id,data:{type:"metabolite",node_id:m}}),v.search_index.insert("n_name"+m,{name:g.name,data:{type:"metabolite",node_id:m}})}}for(var y in v.reactions){var b=v.reactions[y];if(f){v.search_index.insert("r"+y,{name:b.bigg_id,data:{type:"reaction",reaction_id:y}}),v.search_index.insert("r_name"+y,{name:b.name,data:{type:"reaction",reaction_id:y}});for(var w in b.genes){var E=b.genes[w];v.search_index.insert("r"+y+"_g"+w,{name:E.bigg_id,data:{type:"reaction",reaction_id:y}}),v.search_index.insert("r"+y+"_g_name"+w,{name:E.name,data:{type:"reaction",reaction_id:y}})}}var S=[];for(var x in b.segments){var T=b.segments[x];T.reversibility=b.reversibility;if(!(T.from_node_id in v.nodes&&T.to_node_id in v.nodes)){console.warn("Bad node references in segment "+x+". Deleting segment."),S.push(x);continue}var N=v.nodes[T.from_node_id],C=v.nodes[T.to_node_id];b.metabolites.forEach(function(e){e.bigg_id==N.bigg_id?T.from_node_coefficient=e.coefficient:e.bigg_id==C.bigg_id&&(T.to_node_coefficient=e.coefficient)}),[N,C].forEach(function(e){e.connected_segments.push({segment_id:x,reaction_id:y})});var k=v.nodes[T.from_node_id],L=v.nodes[T.to_node_id];if(k["node_type"]=="metabolite"||L["node_type"]=="metabolite"){var A=e.c_plus_c(k,e.c_times_scalar(e.c_minus_c(L,k),.5));T.b1===null&&(T.b1=A),T.b2===null&&(T.b2=A)}}S.forEach(function(e){delete b.segments[e]})}if(f)for(var O in v.text_labels){var M=v.text_labels[O];v.search_index.insert("l"+O,{name:M.text,data:{type:"text_label",text_label_id:O}})}v.beziers=i.new_beziers_for_reactions(v.reactions),v.largest_ids.reactions=P(v.reactions),v.largest_ids.nodes=P(v.nodes),v.largest_ids.text_labels=P(v.text_labels);var _=0;for(var D in v.reactions)_=P(v.reactions[D].segments,_);return v.largest_ids.segments=_,v.apply_reaction_data_to_map(null),v.apply_metabolite_data_to_map(null),v.apply_gene_data_to_map(null),v}function m(e){e.append("g").attr("id","reactions"),e.append("g").attr("id","nodes"),e.append("g").attr("id","beziers"),e.append("g").attr("id","text-labels")}function g(){this.sel.select("#reactions").selectAll(".reaction").remove(),this.sel.select("#nodes").selectAll(".node").remove(),this.sel.select("#beziers").selectAll(".bezier").remove(),this.sel.select("#text-labels").selectAll(".text-label").remove()}function y(e,t){this.callback_manager.run("set_status",null,e),window.clearTimeout(this._status_timer),this._status_timer=null,t!==undefined&&(this._status_timer=window.setTimeout(function(){this.callback_manager.run("set_status",null,"")}.bind(this),t))}function b(){this.reactions={},this.beziers={},this.nodes={},this.text_labels={},this.map_name="new_map",this.map_id=e.generate_map_id(),this.map_description="",this.apply_reaction_data_to_map(null),this.apply_metabolite_data_to_map(null),this.apply_gene_data_to_map(null),this.draw_everything()}function w(){return this.cobra_model!==null}function E(){this.draw_all_reactions(!0,!0),this.draw_all_nodes(!0),this.draw_all_text_labels()}function S(e,t){e===undefined&&(e=!0),t===undefined&&(t=!0);var n=[];for(var r in this.reactions)n.push(r);this.draw_these_reactions(n,!1),e&&this.beziers_enabled&&this.draw_all_beziers(),t&&this.clear_deleted_reactions(e)}function x(t,n){n===undefined&&(n=!0);var r=e.object_slice_for_ids_ref(this.reactions,t),s=function(e){return this.draw.update_reaction(e,this.scale,this.cobra_model,this.nodes,this.defs,this.has_data_on_reactions)}.bind(this);e.draw_an_object(this.sel,"#reactions",".reaction",r,"reaction_id",this.draw.create_reaction.bind(this.draw),s);if(n){var o=i.bezier_ids_for_reaction_ids(r);this.draw_these_beziers(o)}}function T(t){function n(t){e.draw_a_nested_object(t,".segment-group","segments","segment_id",null,null,function(e){e.remove()})}t===undefined&&(t=!0),e.draw_an_object(this.sel,"#reactions",".reaction",this.reactions,"reaction_id",null,n,function(e){e.remove()}),t==1&&this.clear_deleted_beziers()}function N(e){e===undefined&&(e=!0);var t=[];for(var n in this.nodes)t.push(n);this.draw_these_nodes(t),e&&this.clear_deleted_nodes()}function C(t){var n=e.object_slice_for_ids_ref(this.nodes,t),r=function(e){return this.draw.create_node(e,this.nodes,this.reactions)}.bind(this),i=function(e){return this.draw.update_node(e,this.scale,this.has_data_on_nodes,this.behavior.selectable_mousedown,this.behavior.selectable_click,this.behavior.node_mouseover,this.behavior.node_mouseout,this.behavior.selectable_drag,this.behavior.node_label_drag)}.bind(this);e.draw_an_object(this.sel,"#nodes",".node",n,"node_id",r,i)}function k(){e.draw_an_object(this.sel,"#nodes",".node",this.nodes,"node_id",null,null,function(e){e.remove()})}function L(){var e=[];for(var t in this.text_labels)e.push(t);this.draw_these_text_labels(e),this.clear_deleted_text_labels()}function A(t){var n=e.object_slice_for_ids_ref(this.text_labels,t),r=function(e){return this.draw.update_text_label(e,this.behavior)}.bind(this);e.draw_an_object(this.sel,"#text-labels",".text-label",n,"text_label_id",this.draw.create_text_label.bind(this.draw),r)}function O(){e.draw_an_object(this.sel,"#text-labels",".text-label",this.text_labels,"text_label_id",null,null,function(e){e.remove()})}function M(){var e=[];for(var t in this.beziers)e.push(t);this.draw_these_beziers(e),this.clear_deleted_beziers()}function _(t){var n=e.object_slice_for_ids_ref(this.beziers,t),r=function(e){return this.draw.update_bezier(e,this.beziers_enabled,this.behavior.bezier_drag,this.behavior.bezier_mouseover,this.behavior.bezier_mouseout,this.nodes,this.reactions)}.bind(this);e.draw_an_object(this.sel,"#beziers",".bezier",n,"bezier_id",this.draw.create_bezier.bind(this.draw),r)}function D(){e.draw_an_object(this.sel,"#beziers",".bezier",this.beziers,"bezier_id",null,null,function(e){e.remove()})}function P(){this.toggle_beziers(!0)}function H(){this.toggle_beziers(!1)}function B(e){e===undefined?this.beziers_enabled=!this.beziers_enabled:this.beziers_enabled=e,this.draw_all_beziers(),this.callback_manager.run("toggle_beziers",null,this.beziers_enabled)}function j(e){var t=this.settings.get_option("reaction_styles"),n=this.settings.get_option("reaction_compare_style"),r=f.apply_reaction_data_to_reactions(this.reactions,e,t,n);return this.has_data_on_reactions=r,this.calc_data_stats("reaction")}function F(e){var t=this.settings.get_option("metabolite_styles"),n=this.settings.get_option("metabolite_compare_style"),r=f.apply_metabolite_data_to_nodes(this.nodes,e,t,n);return this.has_data_on_nodes=r,this.calc_data_stats("metabolite")}function I(e){var t=this.settings.get_option("reaction_styles"),n=this.settings.get_option("reaction_compare_style"),r=this.settings.get_option("identifiers_on_map"),i=this.settings.get_option("and_method_in_gene_reaction_rule"),s=f.apply_gene_data_to_reactions(this.reactions,e,t,r,n,i);return this.has_data_on_reactions=s,this.calc_data_stats("reaction")}function q(){return this.data_statistics}function R(t){function l(e){return function(t){return e.apply(null,t)}}if(["reaction","metabolite"].indexOf(t)==-1)throw new Error("Bad type "+t);"data_statistics"in this?t in this.data_statistics||(this.data_statistics[t]={}):(this.data_statistics={},this.data_statistics[t]={});var n=!0,r=[];if(t=="metabolite")for(var i in this.nodes){var s=this.nodes[i];s.data!==null&&r.push(s.data)}else if(t=="reaction")for(var o in this.reactions){var u=this.reactions[o];u.data!==null&&r.push(u.data)}var a=e.quartiles(r),f=[["min",l(Math.min)],["max",l(Math.max)],["mean",e.mean],["Q1",function(){return a[0]}],["median",function(){return a[1]}],["Q3",function(){return a[2]}]];return f.forEach(function(e){var i,s=e[0];if(r.length==0)i=null;else{var o=e[1];i=o(r)}i!=this.data_statistics[t][s]&&(n=!1),this.data_statistics[t][s]=i}.bind(this)),t=="reaction"?this.callback_manager.run("calc_data_stats__reaction",null,!n):this.callback_manager.run("calc_data_stats__metabolite",null,!n),!n}function U(e){var t=this.nodes[e],n={x:t.x,y:t.y};return n}function z(){var e=[];return this.sel.select("#nodes").selectAll(".selected").each(function(t){e.push(t.node_id)}),e}function W(){var e={},t=this;return this.sel.select("#nodes").selectAll(".selected").each(function(t){e[t.node_id]=this.nodes[t.node_id]}.bind(this)),e}function X(){var e=[];return this.sel.select("#text-labels").selectAll(".selected").each(function(t){e.push(t.text_label_id)}),e}function V(){var e={},t=this;return this.sel.select("#text-labels").selectAll(".selected").each(function(t){e[t.text_label_id]=this.text_labels[t.text_label_id]}.bind(this)),e}function $(){this.sel.selectAll("#nodes,#text-labels").selectAll(".node,.text-label").classed("selected",!0)}function J(){this.sel.selectAll(".selected").classed("selected",!1)}function K(){var e=this.sel.selectAll("#nodes,#text-labels").selectAll(".node,.text-label");e.classed("selected",function(){return!d3.select(this).classed("selected")})}function Q(e){this.deselect_text_labels();var t=this.sel.select("#nodes").selectAll(".node"),n,r;t.classed("selected",function(t){var i=String(t.node_id)==String(e);return i&&(r=t,n={x:t.x,y:t.y}),i}),this.sel.selectAll(".start-reaction-target").style("visibility","hidden"),this.callback_manager.run("select_metabolite_with_id",null,r,n)}function G(e,t){var n=this.sel.selectAll("#nodes,#text-labels").selectAll(".node,.text-label"),r=this.key_manager.held_keys.shift,i;d3.select(e).attr("class").indexOf("text-label")==-1?i=e.parentNode:i=e,r?d3.select(i).classed("selected",!d3.select(i).classed("selected")):(n.classed("selected",!1),d3.select(i).classed("selected",!0));var s=this.sel.select("#nodes").selectAll(".selected"),o=0,u,a;s.each(function(e){a=e,u={x:e.x,y:e.y},o++}),this.callback_manager.run("select_selectable",null,o,a,u)}function Y(){var e=null,t=this,n=this.sel.select("#nodes").selectAll(".selected");return n.classed("selected",function(t,n){return n==0?(e=t,!0):!1}),e}function Z(){var e=this.sel.select("#nodes").selectAll(".node");e.classed("selected",!1),this.callback_manager.run("deselect_nodes")}function et(e,t){this.deselect_nodes();var n=this.sel.select("#text-labels").selectAll(".text-label");n.classed("selected",function(e){return t===e});var r=this.sel.select("#text-labels").selectAll(".selected"),i;r.each(function(e){i={x:e.x,y:e.y}}),this.callback_manager.run("select_text_label")}function tt(){var e=this.sel.select("#text-labels").selectAll(".text-label");e.classed("selected",!1)}function nt(){var e=this.get_selected_nodes(),t=this.get_selected_text_labels();(Object.keys(e).length>=1||Object.keys(t).length>=1)&&this.delete_selectable(e,t,!0)}function rt(t,n,r){var s=this.segments_and_reactions_for_nodes(t),o=s.segment_objs_w_segments,u=s.reactions,a=e.clone(t),f=e.clone(o),l=e.clone(u),c=e.clone(n),h=function(e,n,i,s){this.delete_node_data(Object.keys(t)),this.delete_segment_data(i),this.delete_reaction_data(Object.keys(n)),this.delete_text_label_data(Object.keys(s));var o=!1,u=!1;this.has_data_on_reactions&&(o=this.calc_data_stats("reaction")),this.has_data_on_nodes&&(u=this.calc_data_stats("metabolite")),r&&(o?this.draw_all_reactions(!0,!0):this.clear_deleted_reactions(),u?this.draw_all_nodes(!0):this.clear_deleted_nodes(),this.clear_deleted_text_labels())}.bind(this);h(t,u,o,n),this.undo_stack.push(function(){this.extend_nodes(a),this.extend_reactions(l);var s=Object.keys(l);for(var h in f){var p=f[h],d=p.segment;this.reactions[p.reaction_id].segments[p.segment_id]=d,[d.from_node_id,d.to_node_id].forEach(function(e){if(e in a)return;var t=this.nodes[e];t.connected_segments.push({reaction_id:p.reaction_id,segment_id:p.segment_id})}.bind(this));var v=p.segment_id,m=p.reaction_id,g={};g[v]=p.segment,e.extend(this.beziers,i.new_beziers_for_segments(g,m)),s.indexOf(p.reaction_id)==-1&&s.push(p.reaction_id)}if(this.has_data_on_reactions){var y=this.calc_data_stats("reaction");y?this.draw_all_reactions(!0,!1):this.draw_these_reactions(s)}else r&&this.draw_these_reactions(s);if(this.has_data_on_nodes){var y=this.calc_data_stats("metabolite");r&&(y?this.draw_all_nodes(!1):this.draw_these_nodes(Object.keys(a)))}else r&&this.draw_these_nodes(Object.keys(a));e.extend(this.text_labels,c),r&&this.draw_these_text_labels(Object.keys(c)),n=e.clone(c),t=e.clone(a),o=e.clone(f),u=e.clone(l)}.bind(this),function(){h(t,u,o,n)}.bind(this))}function it(e){e.forEach(function(e){if(this.enable_search&&this.nodes[e].node_type=="metabolite"){var t=this.search_index.remove("n"+e)&&this.search_index.remove("n_name"+e);t||console.warn("Could not find deleted metabolite in search index")}delete this.nodes[e]}.bind(this))}function st(e){for(var t in e){var n=e[t],r=this.reactions[n.reaction_id];if(!(n.segment_id in r.segments))return;var s=r.segments[n.segment_id];[s.from_node_id,s.to_node_id].forEach(function(e){if(!(e in this.nodes))return;var t=this.nodes[e];t.connected_segments=t.connected_segments.filter(function(e){return e.segment_id!=n.segment_id})}.bind(this)),["b1","b2"].forEach(function(e){var t=i.bezier_id_for_segment_id(n.segment_id,e);delete this.beziers[t]}.bind(this)),delete r.segments[n.segment_id]}}function ot(e){e.forEach(function(e){var t=this.reactions[e];for(var n in t.segments)["b1","b2"].forEach(function(e){var t=i.bezier_id_for_segment_id(n,e);delete this.beziers[t]}.bind(this));delete this.reactions[e];var r=this.search_index.remove("r"+e)&&this.search_index.remove("r_name"+e);r||console.warn("Could not find deleted reaction "+e+" in search index");for(var s in t.genes){var r=this.search_index.remove("r"+e+"_g"+s)&&this.search_index.remove("r"+e+"_g_name"+s);r||console.warn("Could not find deleted gene "+s+" in search index")}}.bind(this))}function ut(e){e.forEach(function(e){delete this.text_labels[e];var t=this.search_index.remove("l"+e);t||console.warn("Could not find deleted text label in search index")}.bind(this))}function at(t,n,r){function m(e,t){this.extend_nodes(e);if(this.has_data_on_nodes){var n=this.apply_metabolite_data_to_nodes(e);n?this.draw_all_nodes(!1):this.draw_these_nodes([t])}else this.draw_these_nodes([t])}if(!this.cobra_model)return console.error("No CobraModel. Cannot build new reaction");var i=e.clone(this.cobra_model.reactions[t]);for(var s in i.metabolites){var o=i.metabolites[s],u=this.cobra_model.metabolites[s];if(o<0){var a=String(++this.largest_ids.nodes),f={x:30,y:10},l={connected_segments:[],x:n.x,y:n.y,node_is_primary:!0,label_x:n.x+f.x,label_y:n.y+f.y,name:u.name,bigg_id:s,node_type:"metabolite"},c={};c[a]=l;break}}m.apply(this,[c,a]);var h=e.clone(c),p=this.new_reaction_for_metabolite(t,a,r,!1),d=p.redo,v=p.undo;return this.undo_stack.push(function(){v(),this.delete_node_data(Object.keys(c)),c=e.clone(h),this.clear_deleted_nodes(),this.deselect_nodes()}.bind(this),function(){m.apply(this,[c,a]),d()}.bind(this)),null}function ft(t){if(this.enable_search)for(var n in t){var r=t[n];if(r.node_type!="metabolite")continue;this.search_index.insert("n"+n,{name:r.bigg_id,data:{type:"metabolite",node_id:n}}),this.search_index.insert("n_name"+n,{name:r.name,data:{type:"metabolite",node_id:n}})}e.extend(this.nodes,t)}function lt(t){if(this.enable_search)for(var n in t){var r=t[n];this.search_index.insert("r"+n,{name:r.bigg_id,data:{type:"reaction",reaction_id:n}}),this.search_index.insert("r_name"+n,{name:r.name,data:{type:"reaction",reaction_id:n}});for(var i in r.genes){var s=r.genes[i];this.search_index.insert("r"+n+"_g"+i,{name:s.bigg_id,data:{type:"reaction",reaction_id:n}}),this.search_index.insert("r"+n+"_g_name"+i,{name:s.name,data:{type:"reaction",reaction_id:n}})}}e.extend(this.reactions,t)}function ct(t,n,r,s){function g(t,n,r,i){this.extend_reactions(n),e.extend(this.beziers,r),this.delete_node_data([i]),this.extend_nodes(t);if(this.has_data_on_reactions){var s=this.calc_data_stats("reaction");s?this.draw_all_reactions(!0,!1):this.draw_these_reactions(Object.keys(n))}else this.draw_these_reactions(Object.keys(n));if(this.has_data_on_nodes){var s=this.calc_data_stats("metabolite");s?this.draw_all_nodes(!1):this.draw_these_nodes(Object.keys(t))}else this.draw_these_nodes(Object.keys(t));for(var o in t){var u=t[o];if(u.node_is_primary&&o!=i){this.select_metabolite_with_id(o);var a={x:u.x,y:u.y};this.zoom_container&&this.zoom_container.translate_off_screen(a)}}}s===undefined&&(s=!0);var o=this.nodes[n],u=this.cobra_model.reactions[t],a=i.new_reaction(t,u,this.cobra_model.metabolites,n,e.clone(o),this.largest_ids,this.cobra_model.cofactors,r),f=a.new_nodes,l=a.new_reactions,c=a.new_beziers;g.apply(this,[f,l,c,n]);var h=e.clone(f),p=e.clone(l),d=e.clone(c),v=function(){delete f[n],this.delete_node_data(Object.keys(f)),this.delete_reaction_data(Object.keys(l)),Q.apply(this,[n]),f=e.clone(h),l=e.clone(p),c=e.clone(d);if(this.has_data_on_reactions){var t=this.calc_data_stats("reaction");t?this.draw_all_reactions(!0,!0):this.draw_these_reactions(Object.keys(l))}else this.clear_deleted_reactions(!0);if(this.has_data_on_nodes){var t=this.calc_data_stats("metabolite");t?this.draw_all_nodes(!0):this.draw_these_nodes(Object.keys(f))}else this.clear_deleted_nodes()}.bind(this),m=function(){g.apply(this,[f,l,c,n])}.bind(this);return s&&this.undo_stack.push(v,m),{undo:v,redo:m}}function ht(){var e=this.get_selected_nodes(),t=Object.keys(e)[0],n=e[t],r=this.reactions,i=this.nodes,s=[],o;i[t].connected_segments.forEach(function(e){o=[e.reaction_id];var n;try{n=r[e.reaction_id].segments[e.segment_id];if(n===undefined)throw new Error("undefined segment")}catch(i){console.warn("Could not find connected segment "+e.segment_id);return}s.push(n.from_node_id==t?n.to_node_id:n.from_node_id)});if(s.length!=1){console.error("Only connected nodes with a single reaction can be selected");return}var u=s[0],a=[t],f=[];i[u].connected_segments.forEach(function(e){var n;try{n=r[e.reaction_id].segments[e.segment_id];if(n===undefined)throw new Error("undefined segment")}catch(s){console.warn("Could not find connected segment "+e.segment_id);return}var o=n.from_node_id==u?n.to_node_id:n.from_node_id,f=i[o];f.node_type=="metabolite"&&o!=t&&a.push(String(o))});for(var l=0;l<a.length;l++)if(i[a[l]].connected_segments.length>1){console.error("Only connected nodes with a single reaction can be selected");return}for(var c in e)if(c!=t&&a.indexOf(c)==-1){console.warn("Selected nodes are not on the same reaction");return}var h=[],p=a.length-1,d=i[a[p]],v=d.node_is_primary,m={x:d.x,y:d.y,label_x:d.label_x,label_y:d.label_y};d.connected_segments.length>1&&console.warn("Too many connected segments for node "+d.node_id);var g=d.connected_segments[0],y;try{y=r[g.reaction_id].segments[g.segment_id];if(y===undefined)throw new Error("undefined segment")}catch(b){console.error("Could not find connected segment "+g.segment_id);return}var w={b1:y.b1,b2:y.b2},E;a.forEach(function(e){var t=i[e],n=t.node_is_primary,s={x:t.x,y:t.y,label_x:t.label_x,label_y:t.label_y},o=t.connected_segments[0],u=r[o.reaction_id].segments[o.segment_id],a={b1:u.b1,b2:u.b2};t.node_is_primary=v,t.x=m.x,t.y=m.y,t.label_x=m.label_x,t.label_y=m.label_y,u.b1=w.b1,u.b2=w.b2,v=n,m=s,w=a,t.node_is_primary&&(E=e),h.push(e)});var S=i[u].connected_segments,p=S.length-1,x=[S[p]];S.forEach(function(e,t){if(p==t)return;x.push(e)}),i[u].connected_segments=x,this.draw_these_nodes(h),this.draw_these_reactions(o),this.select_metabolite_with_id(E);return}function pt(){var e=this.get_selected_node_ids(),t=function(e){var t={},n=this.settings.get_option("hide_secondary_metabolites");e.forEach(function(e){if(!(e in this.nodes)){console.warn("Could not find node: "+e);return}var n=this.nodes[e];n.node_type=="metabolite"&&(n.node_is_primary=!n.node_is_primary,t[e]=n)}.bind(this)),this.draw_these_nodes(Object.keys(t));if(n){var r=this.segments_and_reactions_for_nodes(t),i={};for(var s in r.segment_objs_w_segments){var o=r.segment_objs_w_segments[s].reaction_id;i[o]=!0}this.draw_these_reactions(Object.keys(i))}}.bind(this);t(e),this.undo_stack.push(function(){t(e)},function(){t(e)})}function dt(t){var n={},r={},i={},s=this.reactions;for(var o in t){var u=t[o];u.connected_segments.forEach(function(t){var r;try{r=s[t.reaction_id].segments[t.segment_id];if(r===undefined)throw new Error("undefined segment")}catch(o){console.warn("Could not find connected segments for node");return}var u=e.clone(t);u.segment=e.clone(r),n[t.segment_id]=u,t.reaction_id in i||(i[t.reaction_id]=[]),i[t.reaction_id].push(t.segment_id)})}for(var a in i){var f=s[a],l=i[a],c=!0;for(var h in f.segments)l.indexOf(h)==-1&&(c=!1);c&&(r[a]=f)}return{segment_objs_w_segments:n,reactions:r}}function vt(e,t){var n=i.new_text_label(this.largest_ids,t,e);this.text_labels[n.id]=n.label;var r=this.draw_these_text_labels([n.id]);return this.search_index.insert("l"+n.id,{name:t,data:{type:"text_label",text_label_id:n.id}}),n.id}function mt(e,t,n){var r=this.text_labels[e].text,i=function(t,n){this.text_labels[e].text=t,n&&this.draw_these_text_labels([e]);var r="l"+e,i=this.search_index.remove(r);i||console.warn("Could not find modified text label in search index"),this.search_index.insert(r,{name:t,data:{type:"text_label",text_label_id:e}})}.bind(this);i(t,n),this.undo_stack.push(function(){i(r,n)},function(){i(t,n)})}function gt(e){this._zoom_extent(e,"nodes")}function yt(e){this._zoom_extent(e,"canvas")}function bt(e,t){e===undefined&&(e=t=="nodes"?.2:0),t===undefined&&(t="canvas");var n,r,i=this.get_size();e*=i.height;if(t=="nodes"){var s={x:null,y:null},o={x:null,y:null};for(var u in this.nodes){var a=this.nodes[u];s.x===null&&(s.x=a.x),s.y===null&&(s.y=a.y),o.x===null&&(o.x=a.x),o.y===null&&(o.y=a.y),s.x=Math.min(s.x,a.x),s.y=Math.min(s.y,a.y),o.x=Math.max(o.x,a.x),o.y=Math.max(o.y,a.y)}n=Math.min((i.width-e*2)/(o.x-s.x),(i.height-e*2)/(o.y-s.y)),r={x:-(s.x*n)+e+(i.width-e*2-(o.x-s.x)*n)/2,y:-(s.y*n)+e+(i.height-e*2-(o.y-s.y)*n)/2}}else{if(t!="canvas")return console.error("Did not recognize mode");n=Math.min((i.width-e*2)/this.canvas.width,(i.height-e*2)/this.canvas.height),r={x:-(this.canvas.x*n)+e+(i.width-e*2-this.canvas.width*n)/2,y:-(this.canvas.y*n)+e+(i.height-e*2-this.canvas.height*n)/2}}return this.zoom_container.go_to(n,r),null}function wt(){return this.zoom_container.get_size()}function Et(e){var t=this.reactions[e],n=.5,r=this.get_size(),i={x:-t.label_x*n+r.width/2,y:-t.label_y*n+r.height/2};this.zoom_container.go_to(n,i)}function St(e){var t=this.nodes[e],n=.5,r=this.get_size(),i={x:-t.label_x*n+r.width/2,y:-t.label_y*n+r.height/2};this.zoom_container.go_to(n,i)}function xt(e){var t=this.text_labels[e],n=.5,r=this.get_size(),i={x:-t.x*n+r.width/2,y:-t.y*n+r.height/2};this.zoom_container.go_to(n,i)}function Tt(e){this.highlight(this.sel.selectAll("#r"+e).selectAll("text"))}function Nt(e){this.highlight(this.sel.selectAll("#n"+e).selectAll("text"))}function Ct(e){this.highlight(this.sel.selectAll("#l"+e).selectAll("text"))}function kt(e){this.sel.selectAll(".highlight").classed("highlight",!1),e!==null&&e.classed("highlight",!0)}function Lt(){e.download_json(this.map_for_export(),this.map_name)}function At(){var t=[{map_name:this.map_name,map_id:this.map_id,map_description:this.map_description,homepage:"https://escher.github.io",schema:"https://escher.github.io/escher/jsonschema/1-0-0#"},{reactions:e.clone(this.reactions),nodes:e.clone(this.nodes),text_labels:e.clone(this.text_labels),canvas:this.canvas.size_and_location()}];for(var n in t[1].reactions){var r=t[1].reactions[n],i={};["name","bigg_id","reversibility","label_x","label_y","gene_reaction_rule","genes","metabolites"].forEach(function(e){i[e]=r[e]}),i.segments={};for(var s in r.segments){var o=r.segments[s],u={};["from_node_id","to_node_id","b1","b2"].forEach(function(e){u[e]=o[e]}),i.segments[s]=u}t[1].reactions[n]=i}for(var a in t[1].nodes){var f=t[1].nodes[a],l={},c;f.node_type=="metabolite"?c=["node_type","x","y","bigg_id","name","label_x","label_y","node_is_primary"]:c=["node_type","x","y"],c.forEach(function(e){l[e]=f[e]}),t[1].nodes[a]=l}for(var p in t[1].text_labels){var d=t[1].text_labels[p],v={},c=["x","y","text"];c.forEach(function(e){v[e]=d[e]}),t[1].text_labels[p]=v}var m=t[1].canvas,g={},c=["x","y","width","height"];return c.forEach(function(e){g[e]=m[e]}),t[1].canvas=g,this.debug&&d3.json("jsonschema/1-0-0",function(e,n){if(e)throw new Error(e);h.validate(t,n)||console.warn(h.error)}),t}function Ot(){this.callback_manager.run("before_svg_export");var t=this.zoom_container.window_scale,n=this.zoom_container.window_translate,r=this.canvas.size_and_location(),i={w:this.canvas.mouse_node.attr("width"),h:this.canvas.mouse_node.attr("height"),transform:this.canvas.mouse_node.attr("transform")};this.zoom_container.go_to(1,{x:-r.x,y:-r.y},!1),this.svg.attr("width",r.width),this.svg.attr("height",r.height),this.canvas.mouse_node.attr("width","0px"),this.canvas.mouse_node.attr("height","0px"),this.canvas.mouse_node.attr("transform",null);var s=this.sel.selectAll(".multimarker-circle,.midmarker-circle,#canvas").style("visibility","hidden");e.download_svg("saved_map",this.svg,!0),this.zoom_container.go_to(t,n,!1),this.svg.attr("width",null),this.svg.attr("height",null),this.canvas.mouse_node.attr("width",i.w),this.canvas.mouse_node.attr("height",i.h),this.canvas.mouse_node.attr("transform",i.transform),s.style("visibility",null),this.callback_manager.run("after_svg_export")}function Mt(){this.callback_manager.run("before_convert_map");if(!this.has_cobra_model())throw Error("No COBRA model loaded.");var e=this.cobra_model,t={},n=["name","gene_reaction_rule","genes"],r={},i=["name"],s;for(var o in this.reactions){var u=this.reactions[o];s=!1;for(var a in e.reactions){var f=e.reactions[a];f.bigg_id==u.bigg_id&&(n.forEach(function(e){u[e]=f[e]}),s=!0)}s||(t[o]=!0)}for(var l in this.nodes){var c=this.nodes[l];if(c.node_type!="metabolite")continue;s=!1;for(var h in e.metabolites){var p=e.metabolites[h];p.bigg_id==c.bigg_id&&(i.forEach(function(e){c[e]=p[e]}),s=!0)}s||(r[l]=!0)}var d=Object.keys(t).length,v=Object.keys(r).length,m=3e3;d==0&&v==0?this.set_status("Successfully converted attributes.",m):v==0?(this.set_status("Converted attributes, but count not find "+d+" reactions in the model.",m),this.settings.set_conditional("highlight_missing",!0)):d==0?(this.set_status("Converted attributes, but count not find "+v+" metabolites in the model.",m),this.settings.set_conditional("highlight_missing",!0)):(this.set_status("Converted attributes, but count not find "+d+" reactions and "+v+" metabolites in the model.",m),this.settings.set_conditional("highlight_missing",!0)),this.draw_everything(),this.callback_manager.run("after_convert_map")}var p=e.make_class();return p.from_data=v,p.prototype={init:d,setup_containers:m,reset_containers:g,set_status:y,clear_map:b,select_all:$,select_none:J,invert_selection:K,select_selectable:G,select_metabolite_with_id:Q,select_single_node:Y,deselect_nodes:Z,select_text_label:et,deselect_text_labels:tt,new_reaction_from_scratch:at,extend_nodes:ft,extend_reactions:lt,new_reaction_for_metabolite:ct,cycle_primary_node:ht,toggle_selected_node_primary:pt,new_text_label:vt,edit_text_label:mt,delete_selected:nt,delete_selectable:rt,delete_node_data:it,delete_segment_data:st,delete_reaction_data:ot,delete_text_label_data:ut,get_selected_node_ids:z,get_selected_nodes:W,get_selected_text_label_ids:X,get_selected_text_labels:V,segments_and_reactions_for_nodes:dt,draw_everything:E,draw_all_reactions:S,draw_these_reactions:x,clear_deleted_reactions:T,draw_all_nodes:N,draw_these_nodes:C,clear_deleted_nodes:k,draw_all_text_labels:L,draw_these_text_labels:A,clear_deleted_text_labels:O,draw_all_beziers:M,draw_these_beziers:_,clear_deleted_beziers:D,toggle_beziers:B,hide_beziers:H,show_beziers:P,has_cobra_model:w,apply_reaction_data_to_map:j,apply_metabolite_data_to_map:F,apply_gene_data_to_map:I,get_data_statistics:q,calc_data_stats:R,zoom_extent_nodes:gt,zoom_extent_canvas:yt,_zoom_extent:bt,get_size:wt,zoom_to_reaction:Et,zoom_to_node:St,zoom_to_text_label:xt,highlight_reaction:Tt,highlight_node:Nt,highlight_text_label:Ct,highlight:kt,save:Lt,map_for_export:At,save_svg:Ot,convert_map:Mt},p}),n("Brush",["utils"],function(e){function n(e,t,n,r){this.brush_sel=e.append("g").attr("id","brush-container");var i=this.brush_sel.node(),s=e.select(r).node().nextSibling;i!==s&&i.parentNode.insertBefore(i,s),this.enabled=t,this.map=n}function r(){return this.map.sel.select(".brush").empty()}function i(e){e===undefined&&(e=!this.enabled),e?this.selection_brush=this.setup_selection_brush():this.brush_sel.selectAll(".brush").remove()}function s(){var e=this.brush_sel,t=this.map.sel.selectAll("#nodes,#text-labels"),n=this.map.canvas.size_and_location(),r=n.width,i=n.height,s=n.x,o=n.y;e.selectAll("g").remove();var u=d3.svg.brush().x(d3.scale.identity().domain([s,s+r])).y(d3.scale.identity().domain([o,o+i])).on("brush",function(e){var n=e.held_keys.shift,r=d3.event.target.extent(),i;n?i=t.selectAll(".node:not(.selected),.text-label:not(.selected)"):i=t.selectAll(".node,.text-label"),i.classed("selected",function(e){var t=e.x,n=e.y;return r[0][0]<=t&&t<r[1][0]&&r[0][1]<=n&&n<r[1][1]})}.bind(null,this.map.key_manager)).on("brushend",function(){d3.event.target.clear(),d3.select(this).call(d3.event.target)}),a=e.append("g").attr("class","brush").call(u);return e.selectAll(".background").classed("cursor-grab",!1).classed("cursor-grabbing",!1).style("cursor",null),a}var t=e.make_class();return t.prototype={init:n,toggle:i,setup_selection_brush:s},t}),n("ui",["utils","data_styles"],function(e,t){function n(e,t){var n=e.append("button"),r=n.append("span");"id"in t&&n.attr("id",t.id),"classes"in t&&n.attr("class",t.classes),"key_text"in t&&"text"in t&&t.key_text!==null?r.text(t.text+t.key_text):"text"in t&&r.text(t.text),"icon"in t&&r.classed(t.icon,!0),"key"in t&&o(n,t.key),n.attr("title",t.tooltip)}function r(e){var t=e.append("li").attr("class","btn-group-vertical").attr("data-toggle","buttons");return{button:function(e){var n=t.append("label").attr("class","btn btn-default");n.append("input").attr("type","radio");var r=n.append("span");return"id"in e&&n.attr("id",e.id),"key_text"in e&&"text"in e&&e.key_text!==null?r.text(e.text+e.key_text):"text"in e&&r.text(e.text),"icon"in e&&r.classed(e.icon,!0),"key"in e&&o(n,e.key),"tooltip"in e&&n.attr("title",e.tooltip),this}}}function i(e){var t=e.attr("class","btn-group-vertical");return{button:function(e){var n=t.append("button").attr("class","btn btn-default"),r=n.append("span");return"id"in e&&n.attr("id",e.id),"key_text"in e&&"text"in e&&e.key_text!==null?r.text(e.text+e.key_text):"text"in e&&r.text(e.text),"icon"in e&&r.classed(e.icon,!0),"key"in e&&o(n,e.key),"tooltip"in e&&n.attr("title",e.tooltip),this}}}function s(e,t,n){n===undefined&&(n=!1);var r=e.append("li").attr("class","dropdown");r.append("button").text(t+" ").attr("class","btn btn-link btn-sm dropdown-button").attr("data-toggle","dropdown").append("b").attr("class","caret");var i=r.append("ul").attr("class","dropdown-menu").classed("pull-right",n).attr("role","menu").attr("aria-labelledby","dLabel");return{dropdown:r,button:function(e){var t=i.append("li").attr("role","presentation").datum(e),n=t.append("a").attr("href","#"),r=n.append("span").attr("class","dropdown-button-icon"),s=n.append("span").attr("class","dropdown-button-text");"id"in e&&t.attr("id",e.id),"key_text"in e&&"text"in e&&e.key_text!==null?s.text(" "+e.text+e.key_text):"text"in e&&s.text(" "+e.text),"icon"in e&&r.classed(e.icon,!0);if("key"in e)o(n,e.key);else if("input"in e){var f=e.input,l=f.accept_csv?a(n,t,f.pre_fn,f.fn,f.failure_fn):u(n,t,f.pre_fn,f.fn,f.failure_fn);"assign"in f&&"key"in f&&(f.assign[f.key]=l)}return this},divider:function(){return i.append("li").attr("role","presentation").attr("class","divider"),this}}}function o(e,t){e.on("click",function(){t.fn.call(t.target)})}function u(t,n,r,i,s){var o=n.append("input").attr("type","file").style("display","none").on("change",function(){e.load_json(this.files[0],function(e,t){i(e,t),this.value=""}.bind(this),r,s)});return t.on("click",function(e){o.node().click()}),function(){o.node().click()}}function a(n,r,i,s,o){var u=r.append("input").attr("type","file").style("display","none").on("change",function(){e.load_json_or_csv(this.files[0],t.csv_converter,function(e,t){s(e,t),this.value=""}.bind(this),i,o)});return n.on("click",function(e){u.node().click()}),function(){u.node().click()}}return{individual_button:n,radio_button_group:r,button_group:i,dropdown_menu:s,set_json_input_button:u,set_json_or_csv_input_button:a}}),n("SearchBar",["utils","CallbackManager"],function(e,t){function r(n,r,i){var s=n.attr("class","search-container").style("display","none");this.input=s.append("input").attr("class","search-bar");var o=s.append("div").attr("class","btn-group btn-group-sm");o.append("button").attr("class","btn btn-default").on("click",this.previous.bind(this)).append("span").attr("class","glyphicon glyphicon-chevron-left"),o.append("button").attr("class","btn btn-default").on("click",this.next.bind(this)).append("span").attr("class","glyphicon glyphicon-chevron-right"),this.counter=s.append("div").attr("class","search-counter"),s.append("button").attr("class","btn btn-sm btn-default close-button").on("click",function(){this.toggle(!1)}.bind(this)).append("span").attr("class","glyphicon glyphicon-remove"),this.callback_manager=new t,this.selection=s,this.map=i,this.search_index=r,this.current=1,this.results=null;var u=function(e){this.current=1,this.results=this.search_index.find(e.value),this.update()}.bind(this,this.input.node());this.input.on("input",e.debounce(u,200))}function i(){return this.selection.style("display")!="none"}function s(e){e===undefined?this.is_active=!this.is_active:this.is_active=e,this.is_active?(this.selection.style("display",null),this.counter.text(""),this.input.node().value="",this.input.node().focus(),this.escape=this.map.key_manager.add_escape_listener(function(){this.toggle(!1)}.bind(this),"settings"),this.enter=this.map.key_manager.add_enter_listener(function(){this.next()}.bind(this),"settings"),this.callback_manager.run("show")):(this.map.highlight(null),this.selection.style("display","none"),this.results=null,this.escape&&this.escape.clear(),this.escape=null,this.enter&&this.enter.clear(),this.enter=null,this.callback_manager.run("hide"))}function o(){if(this.results==null)this.counter.text(""),this.map.highlight(null);else if(this.results.length==0)this.counter.text("0 / 0"),this.map.highlight(null);else{this.counter.text(this.current+" / "+this.results.length);var e=this.results[this.current-1];if(e.type=="reaction")this.map.zoom_to_reaction(e.reaction_id),this.map.highlight_reaction(e.reaction_id);else if(e.type=="metabolite")this.map.zoom_to_node(e.node_id),this.map.highlight_node(e.node_id);else{if(e.type!="text_label")throw new Error("Bad search index data type: "+e.type);this.map.zoom_to_text_label(e.text_label_id),this.map.highlight_text_label(e.text_label_id)}}}function u(){if(this.results==null)return;this.current==this.results.length?this.current=1:this.current+=1,this.update()}function a(){if(this.results==null)return;this.current==1?this.current=this.results.length:this.current-=1,this.update()}var n=e.make_class();return n.prototype={init:r,is_visible:i,toggle:s,update:o,next:u,previous:a},n}),n("Settings",["utils","lib/bacon"],function(e,t){function r(e,n,r){this.set_option=e,this.get_option=n,this.status_bus=new t.Bus,this.force_update_bus=new t.Bus,t.Observable.prototype.convert_to_conditional_stream=i,t.Observable.prototype.force_update_with_bus=s,this.busses={},this.streams={};for(var u=0,a=r.length;u<a;u++){var f=r[u],l=o(f,n(f),e,this.status_bus,this.force_update_bus);this.busses[f]=l.bus,this.streams[f]=l.stream}}function i(e){var n=e.map(function(e){return e=="hold"}).not().toProperty(!0),r=e.scan(!1,function(e,t){return e==0&&(t=="accepted"||t=="rejected")}).not(),i=e.scan(!1,function(e,t){return e==0&&t=="hold"}).not(),s=t.combineAsArray(this,e),o=s.scan([],function(e,t){if(t[1]=="hold")return e.push(t[0]),e;if(t[1]=="accept")return e;if(t[1]=="reject")return[];if(t[1]=="rejected"||t[1]=="accepted")return[t[0]];throw Error("bad status "+t[1])}).filter(n).filter(r).filter(i).flatMap(function(e){return t.fromArray(e)}),u=this.filter(n);return u.merge(o)}function s(e){return t.combineAsArray(this,e.toProperty(!1)).map(function(e){return e[0]})}function o(e,n,r,i,s){var o=new t.Bus,u=o.convert_to_conditional_stream(i).force_update_with_bus(s);return u.onValue(function(t){r(e,t)}),o.push(n),{bus:o,stream:u}}function u(e,t){if(!(e in this.busses))throw new Error("Invalid setting name");this.busses[e].push(t)}function a(){this.status_bus.push("hold")}function f(){this.status_bus.push("reject"),this.status_bus.push("rejected"),this.force_update_bus.push(!0)}function l(){this.status_bus.push("accept"),this.status_bus.push("accepted")}var n=e.make_class();return n.prototype={init:r,set_conditional:u,hold_changes:a,abandon_changes:f,accept_changes:l},n}),n("ScaleEditor",["utils","lib/bacon"],function(e,t){function r(e,t,n,r){var i="grad"+t+this.unique_string;this.w=400,this.h=30,this.x=20,this.input_width=90,this.input_height=24;var s=e.append("div").attr("class","scale-editor");this.data_not_loaded=s.append("div").attr("class","data-not-loaded").text((t=="reaction"?"Reaction and gene":"Metabolite")+" data not loaded"),this.input_label_group=s.append("div").attr("class","input-label-group");var o=s.append("div").style("top",this.input_height*3+56+10+"px").attr("class","no-data");o.append("span").text("Styles for "+t+"s with no data").attr("class","no-data-heading"),this.no_data_container=o.append("div");var u=s.append("div").attr("class","centered");this.add_group=u.append("div"),this.trash_group=u.append("div").attr("class","trash-container");var a=u.append("svg").attr("class","scale-svg");this.input_group=u.append("div").attr("class","input-container"),this.gradient=a.append("defs").append("linearGradient").attr("id",i),a.append("rect").attr("class","rect").attr("fill","url(#"+i+")").attr("width",this.w+"px").attr("height",this.h+"px").attr("x",this.x+"px"),this.pickers_group=a.append("g"),this.type=t,this.settings=n,this.get_data_statistics=r;var f=this.settings.get_option("unique_map_id");this.unique_string=f===null?"":"."+f,this.no_data={},["color","size"].forEach(function(e){this.no_data[e]=null,this.settings.streams[this.type+"_no_data_"+e].onValue(function(t){this.no_data[e]=t,this.update_no_data()}.bind(this))}.bind(this)),this.settings.streams[t+"_scale"].onValue(function(e){this.scale=e,this.update()}.bind(this))}function i(){var e=this.scale,t=this.get_data_statistics()[this.type],n=14,r=35,i=this.x,s=this._data_not_loaded();s&&(e=[{type:"min",color:null,size:null},{type:"max",color:null,size:null}],t={min:0,max:1});var o=d3.scale.linear().domain([0,this.w]).range([t.min,t.max]),u=d3.scale.linear().domain([0,this.w]).range([0,t.max-t.min]),a=function(e,t){this.input_group.selectAll(".input-set").each(function(t){d3.select(this).classed("selected-set",e===t)})}.bind(this),f=function(e){return e.type=="value"?e.value:t[e.type]},l=function(e){this.settings.set_conditional(this.type+"_scale",e),this.scale=e,this.update()}.bind(this),c=e.map(function(e){return{frac:(f(e)-t.min)/(t.max-t.min),color:e.color}}).filter(function(e){return e.frac>=0&&e.frac<=1}).sort(function(e,t){return e.frac-t.frac}),h=this.gradient.selectAll("stop").data(c);h.enter().append("stop"),h.attr("offset",function(e){return e.frac*100+"%"}).style("stop-color",function(e){return e.color===null?"#F1ECFA":e.color}),h.exit().remove(),this.data_not_loaded.style("visibility",s?null:"hidden");var p=this.pickers_group.selectAll(".picker").data(e),d=d3.behavior.drag();d.on("drag",function(r,i){["value","min","max"].indexOf(e[i].type)===-1&&(e[i].value=f(r),e[i].type="value");var s=e[i].value+u(d3.event.dx),o=u(n+2);s>t.max-o&&(s=t.max-o),s<t.min+o&&(s=t.min+o),s=Math.floor(s*100)/100,e[i].value=s,this.settings.set_conditional(this.type+"_scale",e),this.scale=e,this.update()}.bind(this)),p.enter().append("g").attr("class","picker").style("cursor","pointer").append("rect"),p.select("rect").attr("x",function(e,r){var s=f(e),u=n+2;return e.type=="value"&&s<=t.min?o.invert(t.min)-n/2+i-u:e.type=="value"&&s>=t.max?o.invert(t.max)-n/2+i+u:o.invert(s)-n/2+i}).attr("width",n+"px").attr("height",r+"px").call(d).on("mousedown",a),p.exit().remove();var v=this.trash_group.selectAll("span").data(e);v.enter().append("span"),v.attr("class",function(e,t){return e.type=="min"||e.type=="max"?null:"trash glyphicon glyphicon-trash"}).style("left",function(e){return o.invert(f(e))-n/2+i+"px"}).on("click",function(t,n){if(t.type=="min"||t.type=="max")return;e=e.slice(0,n).concat(e.slice(n+1)),this.settings.set_conditional(this.type+"_scale",e),this.scale=e,this.update()}.bind(this)),v.exit().remove();var m=this.add_group.selectAll(".add").data(["add"]);m.enter().append("span").attr("class","add glyphicon glyphicon-plus"),m.on("click",function(r){if(s)return;var i=(t.max+t.min)/2,o=u(n+2),a=0;for(var c=0,h=e.length;c<h;c++){var p=f(e[c]);Math.abs(p-i)<o&&(i+=o,i>t.max-o&&(i=t.max-o),i<t.min+o&&(i=t.min+o)),i>p&&(a=c)}e.push({type:"value",value:i,color:e[a].color,size:e[a].size}),l(e)}.bind(this)),m.exit().remove();var g=this.input_label_group.selectAll(".row-label").data(["Value:","Color:","Size:"]);g.enter().append("div").attr("class","row-label").style("height",this.input_height+"px").style("line-height",this.input_height+"px"),g.style("top",function(e,t){return 56+t*this.input_height+"px"}.bind(this)).text(function(e){return e}),g.exit().remove();var y=this.input_group.selectAll(".input-set").data(e),b=y.enter().append("div").attr("class","input-set");b.append("input").attr("class","domain-input").style("width",this.input_width+"px"),b.append("select").attr("class","domain-type-picker"),b.append("input").attr("class","color-input").style("width",this.input_width+"px"),b.append("input").attr("type","color").style("visibility",function(){return this.type=="text"?"hidden":null}).attr("class","color-picker"),b.append("input").attr("class","size-input").style("width",this.input_width+"px"),y.style("height",this.input_height*3+"px").style("width",this.input_width+"px").style("left",function(e){var r=f(e),s=n+2,u;return e.type=="value"&&r<=t.min?u=o.invert(t.min)-n/2+i-s:e.type=="value"&&r>=t.max?u=o.invert(t.max)-n/2+i+s:u=o.invert(r)-n/2+i,u+this.input_width>this.w+this.x&&(u=u-this.input_width+n/2),u+"px"}.bind(this)).on("mousedown",a);var w=d3.format(".4g");y.select(".domain-input").style("height",this.input_height+"px").each(function(e,t){e.type=="value"?(this.value=f(e),this.disabled=!1):(this.value=e.type+" ("+w(f(e))+")",this.disabled=!0)}).on("change",function(t,r){var i=u(n+2),s=parseFloat(this.value);e[r].value=s,l(e)});var E=y.select(".domain-type-picker"),S=["value"].concat(Object.keys(t)).filter(function(e){return e!="min"&&e!="max"}),x=E.selectAll("option").data(S);x.enter().append("option"),x.attr("value",function(e){return e}).text(function(e){return e}),x.exit().remove(),E.style("visibility",function(e){return e.type=="min"||e.type=="max"?"hidden":null}).style("left",this.input_width-20+"px").style("width","20px").each(function(e,t){var n=0;d3.select(this).selectAll("option").each(function(t,r){this.value==e.type&&(n=r)}),this.selectedIndex=n}).on("change",function(n,r){this.value=="value"&&(e[r].value=t[n.type]),e[r].type=this.value,l(e)}),y.select(".color-input").style("height",this.input_height+"px").style("top",this.input_height+"px").each(function(e,t){this.value=e.color===null?"":e.color,this.disabled=e.color===null}).on("change",function(t,n){e[n].color=this.value,l(e)}),y.select(".color-picker").style("left",this.input_width-this.input_height+"px").style("top",this.input_height+"px").style("width",this.input_height+"px").style("height",this.input_height+"px").each(function(e,t){this.value=e.color===null?"#dddddd":e.color,this.disabled=e.color===null}).on("change",function(t,n){e[n].color=this.value,l(e)}),y.select(".size-input").style("height",this.input_height+"px").style("top",this.input_height*2+"px").each(function(e,t){this.value=e.size===null?"":e.size,this.disabled=e.size===null}).on("change",function(t,n){e[n].size=parseFloat(this.value),l(e)}),y.exit().remove()}function s(){var e=this.no_data,t=this._data_not_loaded(),n=40,r=this.no_data_container.selectAll(".input-group").data([["color","Color:"],["size","Size:"]]),i=r.enter().append("div").attr("class","input-group");i.append("span"),i.append("input"),i.append("input").attr("type","color").style("visibility",function(e){return this.type=="text"||e[0]!="color"?"hidden":null}).attr("class","color-picker"),r.select("span").text(function(e){return e[1]}).style("height",this.input_height+"px").style("line-height",this.input_height+"px").style("left",function(e,t){return(n+this.input_width+10)*t+"px"}.bind(this));var s=function(e){return this.settings.get_option(this.type+"_no_data_"+e)}.bind(this);r.select("input").style("left",function(e,t){return n+(n+this.input_width+10)*t+"px"}.bind(this)).style("height",this.input_height+"px").style("width",this.input_width+"px").each(function(n){this.value=t?"":e[n[0]],this.disabled=t}).on("change",function(e){var t=d3.event.target.value;e[0]=="size"&&(t=parseFloat(t)),this.no_data[e[0]]=t,this.settings.set_conditional(this.type+"_no_data_"+e[0],t),this.update_no_data()}.bind(this)),r.select(".color-picker").style("left",function(e,t){return(n+this.input_width)*(t+1)-this.input_height+"px"}.bind(this)).style("width",this.input_height+"px").style("height",this.input_height+"px").each(function(n,r){this.value=t?"#dddddd":e[n[0]],this.disabled=t}).on("change",function(e,t){var n=d3.event.target.value;this.no_data[e[0]]=n,this.settings.set_conditional(this.type+"_no_data_"+e[0],n),this.update_no_data()}.bind(this)),r.exit().remove()}function o(){var e=this.get_data_statistics()[this.type];return e.max===null||e.min===null}var n=e.make_class();return n.prototype={init:r,update:i,update_no_data:s,_data_not_loaded:o},n}),n("SettingsMenu",["utils","CallbackManager","ScaleEditor"],function(e,t,n){function i(e,r,i,s){this.sel=e,this.settings=r,this.draw=!1;var o=this.settings.get_option("unique_map_id");this.unique_string=o===null?"":"."+o;var u=e.append("div").attr("class","settings-box-background").style("display","none"),a=u.append("div").attr("class","settings-box-container").style("display","none");a.append("button").attr("class","btn btn-sm btn-default settings-button").on("click",function(){this.accept_changes()}.bind(this)).append("span").attr("class","glyphicon glyphicon-ok"),a.append("button").attr("class","btn btn-sm btn-default settings-button settings-button-close").on("click",function(){this.abandon_changes()}.bind(this)).append("span").attr("class","glyphicon glyphicon-remove");var f=a.append("div").attr("class","settings-box");f.append("div").text("Tip: Hover over an option to see more details about it.").classed("settings-tip",!0),f.append("hr"),f.append("div").text("View and build options").attr("class","settings-section-heading-large"),this.view_gui(f.append("div")),f.append("hr"),f.append("div").text("Reactions").attr("class","settings-section-heading-large");var l=new n(f.append("div"),"reaction",this.settings,i.get_data_statistics.bind(i));i.callback_manager.set("calc_data_stats__reaction",function(e){e&&(l.update(),l.update_no_data())}),f.append("div").text("Reaction or Gene data").attr("class","settings-section-heading"),this.style_gui(f.append("div"),"reaction",function(e){s&&(s("reaction",e),l.update(),l.update_no_data())}),f.append("hr"),f.append("div").text("Metabolites").attr("class","settings-section-heading-large");var c=new n(f.append("div"),"metabolite",this.settings,i.get_data_statistics.bind(i));i.callback_manager.set("calc_data_stats__metabolite",function(e){e&&(c.update(),c.update_no_data())}),f.append("div").text("Metabolite data").attr("class","settings-section-heading"),this.style_gui(f.append("div"),"metabolite",function(e){s&&(s("metabolite",e),c.update(),c.update_no_data())}),this.callback_manager=new t,this.map=i,this.selection=a,this.background=u}function s(){return this.selection.style("display")!="none"}function o(e){e===undefined&&(e=!this.is_visible()),e?(this.hold_changes(),this.selection.style("display","inline-block"),this.background.style("display","block"),this.selection.select("input").node().focus(),this.escape=this.map.key_manager.add_escape_listener(function(){this.abandon_changes()}.bind(this),"settings"),this.enter=this.map.key_manager.add_enter_listener(function(){this.accept_changes()}.bind(this),"settings"),this.callback_manager.run("show")):(this.draw&&this.map.draw_everything(),this.selection.style("display","none"),this.background.style("display","none"),this.escape&&this.escape.clear(),this.enter&&this.enter.clear(),this.escape=null,this.enter=null,this.callback_manager.run("hide"))}function u(){this.settings.hold_changes()}function a(){this.draw=!1,this.settings.abandon_changes(),this.toggle(!1)}function f(){this.sel.selectAll("input").each(function(e){this.blur()}),this.draw=!0,this.settings.accept_changes(),this.toggle(!1)}function l(e,t,n){var r=e.append("table").attr("class","settings-table"),i=this.settings;r.append("tr").call(function(e){e.append("td").text("Options:").attr("class","options-label").attr("title","Options for "+t+" data.");var r=e.append("td"),s=[["Absolute value","abs","If checked, use the absolute value when calculating colors and sizes of "+t+"s on the map"],["Size","size","If checked, then size the "+(t=="metabolite"?"radius of metabolite circles ":"thickness of reaction lines ")+"according to the value of the "+t+" data"],["Color","color","If checked, then color the "+(t=="metabolite"?"metabolite circles ":"reaction lines ")+"according to the value of the "+t+" data"],["Text (Show data in label)","text","If checked, then show data values in the "+t+" "+"labels"]],o=r.selectAll(".option-group").data(s),u=o.enter().append("label").attr("class","option-group"),a=[],f=function(){var e=[];return r.selectAll("input").each(function(t){this.checked&&e.push(t[1])}),e};u.append("input").attr("type","checkbox").on("change",function(e){i.set_conditional(t+"_styles",f()),e[1]=="abs"&&n(this.checked)}).each(function(e){i.streams[t+"_styles"].onValue(function(t){this.checked=t.indexOf(e[1])!=-1}.bind(this))}),u.append("span").text(function(e){return e[0]}).attr("title",function(e){return e[2]})}),r.append("tr").call(function(e){e.append("td").text("Comparison:").attr("class","options-label").attr("title","The function that will be used to compare datasets, when paired data is loaded");var n=e.append("td").attr("title","The function that will be used to compare datasets, when paired data is loaded"),r=[["Fold Change","fold"],["Log2(Fold Change)","log2_fold"],["Difference","diff"]],s=n.selectAll(".option-group").data(r),o=s.enter().append("label").attr("class","option-group");o.append("input").attr("type","radio").attr("name",t+"_compare_style"+this.unique_string).attr("value",function(e){return e[1]}).on("change",function(){this.checked&&i.set_conditional(t+"_compare_style",this.value)}).each(function(){i.streams[t+"_compare_style"].onValue(function(e){this.checked=this.value==e}.bind(this))}),o.append("span").text(function(e){return e[0]})}.bind(this));if(t=="reaction"){var r=e.append("table").attr("class","settings-table").attr("title","The function that will be used to evaluate AND connections in gene reaction rules (AND connections generally connect components of an enzyme complex)");r.append("tr").call(function(e){e.append("td").text("Method for evaluating AND:").attr("class","options-label-wide");var t=e.append("td"),n=[["Mean","mean"],["Min","min"]],r=t.selectAll(".option-group").data(n),s=r.enter().append("label").attr("class","option-group"),o="and_method_in_gene_reaction_rule";s.append("input").attr("type","radio").attr("name",o+this.unique_string).attr("value",function(e){return e[1]}).on("change",function(){this.checked&&i.set_conditional(o,this.value)}).each(function(){i.streams[o].onValue(function(e){this.checked=this.value==e}.bind(this))}),s.append("span").text(function(e){return e[0]})}.bind(this))}}function c(e,t,n,r){var i=this.settings,s=e.append("table").attr("class","settings-table");s.append("tr").call(function(e){e.attr("title","The identifiers that are show in the reaction, gene, and metabolite labels on the map."),e.append("td").text("Identifiers:").attr("class","options-label");var t=e.append("td"),n=[["ID's","bigg_id"],["Descriptive names","name"]],r=t.selectAll(".option-group").data(n),s=r.enter().append("label").attr("class","option-group"),o="identifiers_on_map";s.append("input").attr("type","radio").attr("name",o+this.unique_string).attr("value",function(e){return e[1]}).on("change",function(){this.checked&&i.set_conditional(o,this.value)}).each(function(){i.streams[o].onValue(function(e){this.checked=this.value==e}.bind(this))}),s.append("span").text(function(e){return e[0]})}.bind(this));var o=[["scroll_behavior","Scroll to zoom (instead of scroll to pan)","If checked, then the scroll wheel and trackpad will control zoom rather than pan.",{zoom:!0,pan:!1}],["use_3d_transform","Responsive pan and zoom (best for latest Chrome, Firefox, and IE)","Depending on your browser, this option may help or hurt performance when panning and zooming."],["hide_secondary_metabolites","Hide secondary metabolites","If checked, then only the primary metabolites will be displayed."],["show_gene_reaction_rules","Show gene reaction rules","If checked, then gene reaction rules will be displayed below each reaction label. (Gene reaction rules are always shown when gene data is loaded.)"],["hide_all_labels","Hide reaction, gene, and metabolite labels","If checked, hide all reaction, gene, and metabolite labels"],["allow_building_duplicate_reactions","Allow duplicate reactions","If checked, then allow duplicate reactions during model building."],["highlight_missing","Highlight reactions not in model","If checked, then highlight in red all the reactions on the map that are not present in the loaded model."]],u=e.append("div").attr("class","settings-container").selectAll(".option-group").data(o),a=u.enter().append("label").attr("class","option-group full-line");a.append("input").attr("type","checkbox"),a.append("span"),u.attr("title",function(e){return e[2]}),u.select("input").on("change",function(e){if(e.length>=4){for(var t in e[3])if(e[3][t]==this.checked){i.set_conditional(e[0],t);break}}else i.set_conditional(e[0],this.checked)}).each(function(e){i.streams[e[0]].onValue(function(t){e.length>=4?this.checked=e[3][t]:this.checked=t}.bind(this))}),u.select("span").text(function(e){return e[1]}),u.exit().remove(),e.append("div").style("margin-top","16px").classed("settings-tip",!0).text("Tip: To increase map performance, turn off text boxes (i.e. labels and gene reaction rules).")}var r=e.make_class();return r.prototype={init:i,is_visible:s,toggle:o,hold_changes:u,abandon_changes:a,accept_changes:f,style_gui:l,view_gui:c},r}),n("TextEditInput",["utils","PlacedDiv","build"],function(e,t,n){function i(e,n,r){var i=e.append("div").attr("id","text-edit-input");this.placed_div=t(i,n),this.placed_div.hide(),this.input=i.append("input"),this.map=n,this.setup_map_callbacks(n),this.zoom_container=r,this.setup_zoom_callbacks(r)}function s(e){e.callback_manager.set("edit_text_label.text_edit_input",function(e,t){this.show(e,t)}.bind(this)),e.callback_manager.set("new_text_label.text_edit_input",function(e){this.active_target!==null&&this._accept_changes(this.active_target.target),this.hide(),this._add_and_edit(e)}.bind(this)),e.callback_manager.set("hide_text_label_editor.text_edit_input",function(){this.hide()}.bind(this))}function o(e){e.callback_manager.set("zoom.text_edit_input",function(){this.active_target&&this._accept_changes(this.active_target.target),this.hide()}.bind(this)),e.callback_manager.set("go_to.text_edit_input",function(){this.active_target&&this._accept_changes(this.active_target.target),this.hide()}.bind(this))}function u(){return this.placed_div.is_visible()}function a(e,t){this.active_target&&this._accept_changes(this.active_target.target),this.active_target={target:e,coords:t},e.each(function(e){this.input.node().value=e.text}.bind(this)),this.placed_div.place(t),this.input.node().focus(),this.escape=this.map.key_manager.add_escape_listener(function(){this._accept_changes(e),this.hide()}.bind(this)),this.enter=this.map.key_manager.add_enter_listener(function(e){this._accept_changes(e),this.hide()}.bind(this,e))}function f(){this.placed_div.hide(),this.input.attr("value",""),this.active_target=null,this.escape&&this.escape.clear(),this.escape=null,this.enter&&this.enter.clear(),this.enter=null}function l(e){if(this.input.node().value=="")e.each(function(e){var t={};t[e.text_label_id]=this.map.text_labels[e.text_label_id],this.map.delete_selectable({},t,!0)}.bind(this));else{var t=[];e.each(function(e){this.map.edit_text_label(e.text_label_id,this.input.node().value,!0),t.push(e.text_label_id)}.bind(this))}}function c(e){var t=this.map.new_text_label(e,""),n=this.map.sel.select("#text-labels").selectAll(".text-label").filter(function(e){return e.text_label_id==t});n.select("text").classed("edit-text-cursor",!0),this.show(n,e)}var r=e.make_class();return r.prototype={init:i,setup_map_callbacks:s,setup_zoom_callbacks:o,is_visible:u,show:a,hide:f,_accept_changes:l,_add_and_edit:c},r}),n("QuickJump",["utils"],function(e){function n(t,n){var r=t.append("select").attr("id","quick-jump-menu").attr("class","form-control");this.selector=r;var i=e.parse_url_components(window),s="map_name"in i?i.map_name:null,o="quick_jump_path"in i?i.quick_jump_path:null,u="quick_jump"in i?i.quick_jump:[],a="— Jump to map —",f=[a].concat(u);s!==null&&(f=f.filter(function(e){return e!=s})),r.selectAll("option").data(f).enter().append("option").text(function(e){return e.split(".").slice(-1)[0]}),r.style("display",f.length>1?"block":"none");var l=function(e){n(e,o,function(t){t?this.replace_state_for_map_name(e):this.reset_selection()}.bind(this))}.bind(this);r.on("change",function(){var e=this.options[this.selectedIndex].__data__;l(e)})}function r(){this.selector.node().selectedIndex=0}function i(e){var t=window.location.href.replace(/(map_name=)([^&]+)(&|$)/,"$1"+e+"$3");window.history.replaceState("Not implemented","",t)}var t=e.make_class();return t.prototype={init:n,reset_selection:r,replace_state_for_map_name:i},t}),n("Builder",["utils","BuildInput","ZoomContainer","Map","CobraModel","Brush","CallbackManager","ui","SearchBar","Settings","SettingsMenu","TextEditInput","QuickJump","data_styles"],function(e,t,n,r,i,s,o,u,a,f,l,c,h,p){function v(t,n,r,i,s){i||(i=d3.select("body").append("div")),s||(s={}),this.map_data=t,this.model_data=n,this.embedded_css=r,this.selection=i,this.selection.datum(this),this.options=e.set_options(s,{menu:"all",scroll_behavior:"pan",use_3d_transform:!1,enable_editing:!0,enable_keys:!0,enable_search:!0,fill_screen:!1,zoom_to_element:null,starting_reaction:null,never_ask_before_quit:!1,unique_map_id:null,primary_metabolite_radius:20,secondary_metabolite_radius:10,marker_radius:5,gene_font_size:18,hide_secondary_metabolites:!1,show_gene_reaction_rules:!1,hide_all_labels:!1,reaction_data:null,reaction_styles:["color","size","text"],reaction_compare_style:"log2_fold",reaction_scale:[{type:"min",color:"#c8c8c8",size:12},{type:"median",color:"#9696ff",size:20},{type:"max",color:"#ff0000",size:25}],reaction_no_data_color:"#dcdcdc",reaction_no_data_size:8,gene_data:null,and_method_in_gene_reaction_rule:"mean",metabolite_data:null,metabolite_styles:["color","size","text"],metabolite_compare_style:"log2_fold",metabolite_scale:[{type:"min",color:"#fffaf0",size:20},{type:"median",color:"#f1c470",size:30},{type:"max",color:"#800000",size:40}],metabolite_no_data_color:"#ffffff",metabolite_no_data_size:10,identifiers_on_map:"bigg_id",highlight_missing:!1,allow_building_duplicate_reactions:!1,first_load_callback:null},{primary_metabolite_radius:!0,secondary_metabolite_radius:!0,marker_radius:!0,gene_font_size:!0,reaction_no_data_size:!0,metabolite_no_data_size:!0});if(e.check_for_parent_tag(this.selection,"svg"))throw new Error("Builder cannot be placed within an svg node becuase UI elements are html-based.");var u=function(e,t){this.options[e]=t}.bind(this),a=function(e){return this.options[e]}.bind(this),l=["hide_secondary_metabolites","show_gene_reaction_rules","hide_all_labels","scroll_behavior","use_3d_transform","reaction_styles","reaction_compare_style","reaction_scale","reaction_no_data_color","reaction_no_data_size","and_method_in_gene_reaction_rule","metabolite_styles","metabolite_compare_style","metabolite_scale","metabolite_no_data_color","metabolite_no_data_size","identifiers_on_map","highlight_missing","allow_building_duplicate_reactions"];this.settings=new f(u,a,l),["reaction_scale","metabolite_scale"].forEach(function(e){this.settings.streams[e].onValue(function(t){["min","max"].forEach(function(n){var r=t.reduce(function(e,t){return e||t.type==n},!1);r||(t.push({type:n,color:"#ffffff",size:10}),this.settings.set_conditional(e,t))}.bind(this))}.bind(this))}.bind(this)),this.callback_manager=o(),this.options.first_load_callback!==null&&this.callback_manager.set("first_load",this.options.first_load_callback),this.load_model(this.model_data,!1),this.load_map(this.map_data,!1),this._update_data(!0,!0),this.settings.status_bus.onValue(function(e){if(e==="accepted"){this._update_data(!0,!0,["reaction","metabolite"],!1);if(this.zoom_container!==null){var t=this.settings.get_option("scroll_behavior");this.zoom_container.set_scroll_behavior(t),this.zoom_container.set_use_3d_transform(this.settings.get_option("use_3d_transform"))}this.map!==null&&(this.map.draw_all_nodes(!1),this.map.draw_all_reactions(!0,!1))}}.bind(this)),this.callback_manager.run("first_load",this)}function m(e,t){t===undefined&&(t=!0),e===null?this.cobra_model=null:this.cobra_model=i.from_cobra_json(e),this.map&&(this.map.cobra_model=this.cobra_model,t&&this._update_data(!0,!1),this.settings.get_option("highlight_missing")&&this.map.draw_all_reactions(!1,!1)),this.callback_manager.run("load_model",null,e,t)}function g(i,o){o===undefined&&(o=!0);var u=!0,f=!1;e.remove_child_nodes(this.selection),this.zoom_container=new n(this.selection,this.options.scroll_behavior,this.options.use_3d_transform,this.options.fill_screen);var h=this.zoom_container.zoomed_sel,p=this.zoom_container.svg;i!==null?this.map=r.from_data(i,p,this.embedded_css,h,this.zoom_container,this.settings,this.cobra_model,this.options.enable_search):this.map=new r(p,this.embedded_css,h,this.zoom_container,this.settings,this.cobra_model,null,this.options.enable_search),this.zoom_container.callback_manager.set("svg_start",function(){this.map.set_status("Drawing ...")}.bind(this)),this.zoom_container.callback_manager.set("svg_finish",function(){this.map.set_status("")}.bind(this)),o&&this._update_data(!1,!0),this.build_input=t(this.selection,this.map,this.zoom_container,this.settings),this.text_edit_input=c(this.selection,this.map,this.zoom_container),this.brush=new s(h,!1,this.map,".canvas-group"),this.map.canvas.callback_manager.set("resize",function(){this.brush.toggle(!0)}.bind(this)),this._setup_modes(this.map,this.brush,this.zoom_container);var d=this.selection.append("div").attr("class","search-menu-container").append("div").attr("class","search-menu-container-inline"),v=d.append("div"),m=d.append("div"),g=this.selection.append("div");this.search_bar=a(m,this.map.search_index,this.map),this.search_bar.callback_manager.set("show",function(){this.settings_bar.toggle(!1)}.bind(this));var y=this.selection.append("div");this.settings_bar=l(y,this.settings,this.map,function(e,t){var n=this.options[e+"_styles"];if(t&&n.indexOf("abs")==-1)n.push("abs");else if(!t){var r=n.indexOf("abs");r!=-1&&(this.options[e+"_styles"]=n.slice(0,r).concat(n.slice(r+1)))}this._update_data(!1,!0,e)}.bind(this)),this.settings_bar.callback_manager.set("show",function(){this.search_bar.toggle(!1)}.bind(this));var b=this._get_keys(this.map,this.zoom_container,this.search_bar,this.settings_bar,this.options.enable_editing);this.map.key_manager.assigned_keys=b,this.map.key_manager.input_list=[this.build_input,this.search_bar,this.settings_bar,this.text_edit_input],this.map.key_manager.update(),this.map.key_manager.toggle(this.options.enable_keys),this.options.menu=="all"?this._setup_menu(v,g,this.map,this.zoom_container,this.map.key_manager,b,this.options.enable_editing,this.options.enable_keys):this.options.menu=="zoom"&&this._setup_simple_zoom_buttons(g,b);if(this.options.zoom_to_element){var w=this.options.zoom_to_element.type,E=this.options.zoom_to_element.id;if(typeof w=="undefined"||["reaction","node"].indexOf(w)==-1)throw new Error('zoom_to_element type must be "reaction" or "node"');if(typeof E=="undefined")throw new Error("zoom_to_element must include id");w=="reaction"?this.map.zoom_to_reaction(E):w=="node"&&this.map.zoom_to_node(E)}else if(i!==null)this.map.zoom_extent_canvas();else if(this.options.starting_reaction!==null&&this.cobra_model!==null){var S=this.zoom_container.get_size(),x={x:S.width/2,y:S.height/4};this.map.new_reaction_from_scratch(this.options.starting_reaction,x,90),this.map.zoom_extent_nodes()}else this.map.zoom_extent_canvas();var T=this._setup_status(this.selection,this.map);this._setup_quick_jump(this.selection),this.options.enable_editing?this.zoom_mode():this.view_mode(),this.options.enable_editing&&this._setup_confirm_before_exit(),this.map.draw_everything()}function y(e){this.search_bar.toggle(!1),this.build_input.toggle(e=="build"),this.build_input.direction_arrow.toggle(e=="build"),this.options.menu=="all"&&this.options.enable_editing&&this._toggle_direction_buttons(e=="build"),this.brush.toggle(e=="brush"),this.zoom_container.toggle_pan_drag(e=="zoom"||e=="view"),this.map.canvas.toggle_resize(e=="zoom"||e=="brush"),e=="rotate"?(this.map.behavior.toggle_selectable_drag(!1),this.map.behavior.toggle_rotation_mode(!0)):(this.map.behavior.toggle_rotation_mode(e=="rotate"),this.map.behavior.toggle_selectable_drag(e=="brush")),this.map.behavior.toggle_selectable_click(e=="build"||e=="brush"),this.map.behavior.toggle_label_drag(e=="brush"),this.map.behavior.toggle_label_mousedown(e=="brush"),this.map.behavior.toggle_text_label_edit(e=="text"),this.map.behavior.toggle_bezier_drag(e=="brush"),(e=="view"||e=="text")&&this.map.select_none(),e=="rotate"&&this.map.deselect_text_labels(),this.map.draw_everything()}function b(){this.callback_manager.run("view_mode"),this._set_mode("view")}function w(){this.callback_manager.run("build_mode"),this._set_mode("build")}function E(){this.callback_manager.run("brush_mode"),this._set_mode("brush")}function S(){this.callback_manager.run("zoom_mode"),this._set_mode("zoom")}function x(){this.callback_manager.run("rotate_mode"),this._set_mode("rotate")}function T(){this.callback_manager.run("text_mode"),this._set_mode("text")}function N(e){this.options.reaction_data=e,this._update_data(!0,!0,"reaction"),this.map.set_status("")}function C(e,t){t&&this.settings.set_conditional("show_gene_reaction_rules",!1),this.options.gene_data=e,this._update_data(!0,!0,"reaction"),this.map.set_status("")}function k(e){this.options.metabolite_data=e,this._update_data(!0,!0,"metabolite"),this.map.set_status("")}function L(t,n,r,i){function c(t,n,r){var i={};return n!==null&&e.extend(i,n.reactions),r!==null&&e.extend(i,r.reactions,!0),p.import_and_check(t,"gene_data",i)}r===undefined&&(r=["reaction","metabolite"]),i===undefined&&(i=!0);var s=r.indexOf("metabolite")!=-1,o=r.indexOf("reaction")!=-1,u,a,f;s&&n&&this.map!==null&&(u=p.import_and_check(this.options.metabolite_data,"metabolite_data"),this.map.apply_metabolite_data_to_map(u),i&&this.map.draw_all_nodes(!1)),o&&(this.options.reaction_data!==null&&n&&this.map!==null?(a=p.import_and_check(this.options.reaction_data,"reaction_data"),this.map.apply_reaction_data_to_map(a),i&&this.map.draw_all_reactions(!1,!1)):this.options.gene_data!==null&&n&&this.map!==null?(f=c(this.options.gene_data,this.cobra_model,this.map),this.map.apply_gene_data_to_map(f),i&&this.map.draw_all_reactions(!1,!1)):n&&this.map!==null&&(this.map.apply_reaction_data_to_map(null),i&&this.map.draw_all_reactions(!1,!1))),this.update_model_timer&&window.clearTimeout(this.update_model_timer);var l=5;this.update_model_timer=window.setTimeout(function(){s&&t&&this.cobra_model!==null&&(u||(u=p.import_and_check(this.options.metabolite_data,"metabolite_data")),this.cobra_model.apply_metabolite_data(u,this.options.metabolite_styles,this.options.metabolite_compare_style)),o&&(this.options.reaction_data!==null&&t&&this.cobra_model!==null?(a||(a=p.import_and_check(this.options.reaction_data,"reaction_data")),this.cobra_model.apply_reaction_data(a,this.options.reaction_styles,this.options.reaction_compare_style)):this.options.gene_data!==null&&t&&this.cobra_model!==null?(f||(f=c(this.options.gene_data,this.cobra_model,this.map)),this.cobra_model.apply_gene_data(f,this.options.reaction_styles,this.options.identifiers_on_map,this.options.reaction_compare_style,this.options.and_method_in_gene_reaction_rule)):t&&this.cobra_model!==null&&this.cobra_model.apply_reaction_data(null,this.options.reaction_styles,this.options.reaction_compare_style)),this.callback_manager.run("update_data",null,t,n,r,i)}.bind(this),l)}function A(e,t,n,r,i,s,o,a){function b(e,t){function r(e){if(!("map_id"in e[0]&&"reactions"in e[1]&&"nodes"in e[1]&&"canvas"in e[1]))throw new Error("Bad map data.")}if(e){console.warn(e),this.map.set_status("Error loading map: "+e,2e3);return}try{r(t),this.load_map(t),this.map.set_status("Loaded map "+t[0].map_name,3e3)}catch(n){console.warn(n),this.map.set_status("Error loading map: "+n,2e3)}}function w(e,t){if(e){console.warn(e),this.map.set_status("Error loading model: "+e,2e3);return}try{this.load_model(t,!0),this.build_input.toggle(!1),"id"in t?this.map.set_status("Loaded model "+t.id,3e3):this.map.set_status("Loaded model (no model id)",3e3)}catch(n){console.warn(n),this.map.set_status("Error loading model: "+n,2e3)}}function E(e,t){if(e){console.warn(e),this.map.set_status("Could not parse file as JSON or CSV",2e3);return}t!==null&&this.set_gene_data(null),this.set_reaction_data(t)}function S(e,t){if(e){console.warn(e),this.map.set_status("Could not parse file as JSON or CSV",2e3);return}this.set_metabolite_data(t)}function x(e,t){if(e){console.warn(e),this.map.set_status("Could not parse file as JSON or CSV",2e3);return}t!==null&&this.set_reaction_data(null),this.settings.set_conditional("show_gene_reaction_rules",!0),this.set_gene_data(t)}var f=e.attr("id","menu").append("ul").attr("class","nav nav-pills");u.dropdown_menu(f,"Map").button({key:s.save,text:"Save map JSON",key_text:a?" (Ctrl+S)":null}).button({text:"Load map JSON",key_text:a?" (Ctrl+O)":null,input:{assign:i.assigned_keys.load,key:"fn",fn:b.bind(this),pre_fn:function(){n.set_status("Loading map ...")},failure_fn:function(){n.set_status("")}}}).button({key:s.save_svg,text:"Export as SVG",key_text:a?" (Ctrl+Shift+S)":null}).button({key:s.clear_map,text:"Clear map"});var l=u.dropdown_menu(f,"Model").button({text:"Load COBRA model JSON",key_text:a?" (Ctrl+M)":null,input:{assign:i.assigned_keys.load_model,key:"fn",fn:w.bind(this),pre_fn:function(){n.set_status("Loading model ...")},failure_fn:function(){n.set_status("")}}}).button({id:"convert_map",key:s.convert_map,text:"Update names and gene reaction rules using model"}).button({id:"clear_model",key:s.clear_model,text:"Clear model"}),c=function(){l.dropdown.selectAll("li").classed("escher-disabled",function(e){return e.id!="clear_model"&&e.id!="convert_map"||this.cobra_model!==null?null:!0}.bind(this))}.bind(this);c(),this.callback_manager.set("load_model",c);var h=u.dropdown_menu(f,"Data").button({input:{assign:i.assigned_keys.load_reaction_data,key:"fn",fn:E.bind(this),accept_csv:!0,pre_fn:function(){n.set_status("Loading reaction data ...")},failure_fn:function(){n.set_status("")}},text:"Load reaction data"}).button({key:s.clear_reaction_data,text:"Clear reaction data"}).divider().button({input:{fn:x.bind(this),accept_csv:!0,pre_fn:function(){n.set_status("Loading gene data ...")},failure_fn:function(){n.set_status("")}},text:"Load gene data"}).button({key:s.clear_gene_data,text:"Clear gene data"}).divider().button({input:{fn:S.bind(this),accept_csv:!0,pre_fn:function(){n.set_status("Loading metabolite data ...")},failure_fn:function(){n.set_status("")}},text:"Load metabolite data"}).button({key:s.clear_metabolite_data,text:"Clear metabolite data"}),p=function(){h.dropdown.selectAll("li").classed("escher-disabled",function(e){return e?e.text=="Clear reaction data"&&this.options.reaction_data===null?!0:e.text=="Clear gene data"&&this.options.gene_data===null?!0:e.text=="Clear metabolite data"&&this.options.metabolite_data===null?!0:null:null}.bind(this))}.bind(this);p(),this.callback_manager.set("update_data",p);var d=u.dropdown_menu(f,"Edit",!0);o?d.button({key:s.zoom_mode,id:"zoom-mode-menu-button",text:"Pan mode",key_text:a?" (Z)":null}).button({key:s.brush_mode,id:"brush-mode-menu-button",text:"Select mode",key_text:a?" (V)":null}).button({key:s.build_mode,id:"build-mode-menu-button",text:"Add reaction mode",key_text:a?" (N)":null}).button({key:s.rotate_mode,id:"rotate-mode-menu-button",text:"Rotate mode",key_text:a?" (R)":null}).button({key:s.text_mode,id:"text-mode-menu-button",text:"Text mode",key_text:a?" (T)":null}).divider().button({key:s.delete,text:"Delete",key_text:a?" (Del)":null}).button({key:s.undo,text:"Undo",key_text:a?" (Ctrl+Z)":null}).button({key:s.redo,text:"Redo",key_text:a?" (Ctrl+Shift+Z)":null}).button({key:s.toggle_primary,text:"Toggle primary/secondary",key_text:a?" (P)":null}).button({key:s.cycle_primary,text:"Rotate reactant locations",key_text:a?" (C)":null}).button({key:s.select_all,text:"Select all",key_text:a?" (Ctrl+A)":null}).button({key:s.select_none,text:"Select none",key_text:a?" (Ctrl+Shift+A)":null}).button({key:s.invert_selection,text:"Invert selection"}):d.button({key:s.view_mode,id:"view-mode-menu-button",text:"View mode"});var v=u.dropdown_menu(f,"View",!0).button({key:s.zoom_in,text:"Zoom in",key_text:a?" (Ctrl and +)":null}).button({key:s.zoom_out,text:"Zoom out",key_text:a?" (Ctrl and -)":null}).button({key:s.extent_nodes,text:"Zoom to nodes",key_text:a?" (Ctrl+0)":null}).button({key:s.extent_canvas,text:"Zoom to canvas",key_text:a?" (Ctrl+1)":null}).button({key:s.search,text:"Find",key_text:a?" (Ctrl+F)":null});o&&(v.button({key:s.toggle_beziers,id:"bezier-button",text:"Show control points",key_text:a?" (B)":null}),n.callback_manager.set("toggle_beziers.button",function(e){f.select("#bezier-button").select(".dropdown-button-text").text((e?"Hide":"Show")+" control points"+(a?" (B)":""))})),v.divider().button({key:s.show_settings,text:"Settings",key_text:a?" (Ctrl+,)":null}),f.append("a").attr("class","help-button").attr("target","#").attr("href","https://escher.readthedocs.org").text("?");var m=t.append("ul").attr("class","nav nav-pills nav-stacked").attr("id","button-panel");u.individual_button(m.append("li"),{key:s.zoom_in,icon:"glyphicon glyphicon-plus-sign",classes:"btn btn-default",tooltip:"Zoom in",key_text:a?" (Ctrl and +)":null}),u.individual_button(m.append("li"),{key:s.zoom_out,icon:"glyphicon glyphicon-minus-sign",classes:"btn btn-default",tooltip:"Zoom out",key_text:a?" (Ctrl and -)":null}),u.individual_button(m.append("li"),{key:s.extent_canvas,icon:"glyphicon glyphicon-resize-full",classes:"btn btn-default",tooltip:"Zoom to canvas",key_text:a?" (Ctrl+1)":null});if(o){u.radio_button_group(m.append("li")).button({key:s.zoom_mode,id:"zoom-mode-button",icon:"glyphicon glyphicon-move",tooltip:"Pan mode",key_text:a?" (Z)":null}).button({key:s.brush_mode,id:"brush-mode-button",icon:"glyphicon glyphicon-hand-up",tooltip:"Select mode",key_text:a?" (V)":null}).button({key:s.build_mode,id:"build-mode-button",icon:"glyphicon glyphicon-plus",tooltip:"Add reaction mode",key_text:a?" (N)":null}).button({key:s.rotate_mode,id:"rotate-mode-button",icon:"glyphicon glyphicon-repeat",tooltip:"Rotate mode",key_text:a?" (R)":null}).button({key:s.text_mode,id:"text-mode-button",icon:"glyphicon glyphicon-font",tooltip:"Text mode",key_text:a?" (T)":null}),this.direction_buttons=m.append("li");var g=u.button_group(this.direction_buttons).button({key:s.direction_arrow_left,icon:"glyphicon glyphicon-arrow-left",tooltip:"Direction arrow (←)"}).button({key:s.direction_arrow_right,icon:"glyphicon glyphicon-arrow-right",tooltip:"Direction arrow (→)"}).button({key:s.direction_arrow_up,icon:"glyphicon glyphicon-arrow-up",tooltip:"Direction arrow (↑)"}).button({key:s.direction_arrow_down,icon:"glyphicon glyphicon-arrow-down",tooltip:"Direction arrow (↓)"})}var y=function(e){$(this.selection.node()).find("#"+e).button("toggle");var t=["zoom-mode-menu-button","brush-mode-menu-button","build-mode-menu-button","rotate-mode-menu-button","view-mode-menu-button","text-mode-menu-button"];t.forEach(function(t){var n=t.replace("-menu","");this.selection.select("#"+t).select("span").classed("glyphicon",n==e).classed("glyphicon-ok",n==e)}.bind(this))};this.callback_manager.set("zoom_mode",y.bind(this,"zoom-mode-button")),this.callback_manager.set("brush_mode",y.bind(this,"brush-mode-button")),this.callback_manager.set("build_mode",y.bind(this,"build-mode-button")),this.callback_manager.set("rotate_mode",y.bind(this,"rotate-mode-button")),this.callback_manager.set("view_mode",y.bind(this,"view-mode-button")),this.callback_manager.set("text_mode",y.bind(this,"text-mode-button"))}function O(e,t){var n=e.append("div").attr("id","simple-button-panel");u.individual_button(n.append("div"),{key:t.zoom_in,text:"+",classes:"simple-button",tooltip:"Zoom in (Ctrl +)"}),u.individual_button(n.append("div"),{key:t.zoom_out,text:"–",classes:"simple-button",tooltip:"Zoom out (Ctrl -)"}),u.individual_button(n.append("div"),{key:t.extent_canvas,text:"↔",classes:"simple-button",tooltip:"Zoom to canvas (Ctrl 1)"})}function M(e){e===undefined&&(e=!this.direction_buttons.style("visibility")=="visible"),this.direction_buttons.style("visibility",e?"visible":"hidden")}function _(e,t){var n=e.append("div").attr("id","status");return t.callback_manager.set("set_status",function(e){n.html(e)}),n}function D(t){var n=function(t,n,r){if(this.options.enable_editing&&!this.options.never_ask_before_quit&&!confirm("You will lose any unsaved changes.\n\nAre you sure you want to switch maps?")){r&&r(!1);return}this.map.set_status("Loading map "+t+" ...");var i=e.name_to_url(t,n);d3.json(i,function(e,t){e&&(console.warn("Could not load data: "+e),r&&r(!1)),r&&r(!0),this.load_map(t),this.map.set_status("")}.bind(this))}.bind(this);this.quick_jump=h(t,n)}function P(e,t,n){var r={};e.callback_manager.set("start_rotation",function(){r.brush=t.enabled,t.toggle(!1),r.zoom=n.zoom_on,n.toggle_pan_drag(!1),r.selectable_mousedown=e.behavior.selectable_mousedown!=null,e.behavior.toggle_selectable_click(!1),r.label_mousedown=e.behavior.label_mousedown!=null,e.behavior.toggle_label_mousedown(!1)}),e.callback_manager.set("end_rotation",function(){t.toggle(r.brush),n.toggle_pan_drag(r.zoom),e.behavior.toggle_selectable_click(r.selectable_mousedown),e.behavior.toggle_label_mousedown(r.label_mousedown),r={}})}function H(t,n,r,i,s){var o={save:{key:83,modifiers:{control:!0},target:t,fn:t.save},save_svg:{key:83,modifiers:{control:!0,shift:!0},target:t,fn:t.save_svg},load:{key:79,modifiers:{control:!0},fn:null},convert_map:{fn:this.map.convert_map.bind(this.map)},clear_map:{fn:this.map.clear_map.bind(this.map)},load_model:{key:77,modifiers:{control:!0},fn:null},clear_model:{fn:this.load_model.bind(this,null,!0)},load_reaction_data:{fn:null},clear_reaction_data:{target:this,fn:function(){this.set_reaction_data(null)}},load_metabolite_data:{fn:null},clear_metabolite_data:{target:this,fn:function(){this.set_metabolite_data(null)}},load_gene_data:{fn:null},clear_gene_data:{fn:function(){this.set_gene_data(null,!0)}.bind(this)},zoom_in:{key:187,modifiers:{control:!0},target:n,fn:n.zoom_in},zoom_out:{key:189,modifiers:{control:!0},target:n,fn:n.zoom_out},extent_nodes:{key:48,modifiers:{control:!0},target:t,fn:t.zoom_extent_nodes},extent_canvas:{key:49,modifiers:{control:!0},target:t,fn:t.zoom_extent_canvas},search:{key:70,modifiers:{control:!0},fn:r.toggle.bind(r,!0)},view_mode:{fn:this.view_mode.bind(this),ignore_with_input:!0},show_settings:{key:188,modifiers:{control:!0},fn:i.toggle.bind(i)}};return s&&e.extend(o,{build_mode:{key:78,fn:this.build_mode.bind(this),ignore_with_input:!0},zoom_mode:{key:90,fn:this.zoom_mode.bind(this),ignore_with_input:!0},brush_mode:{key:86,fn:this.brush_mode.bind(this),ignore_with_input:!0},rotate_mode:{key:82,fn:this.rotate_mode.bind(this),ignore_with_input:!0},text_mode:{key:84,fn:this.text_mode.bind(this),ignore_with_input:!0},toggle_beziers:{key:66,target:t,fn:t.toggle_beziers,ignore_with_input:!0},"delete":{key:8,modifiers:{control:!0},target:t,fn:t.delete_selected,ignore_with_input:!0},delete_del:{key:46,modifiers:{control:!1},target:t,fn:t.delete_selected,ignore_with_input:!0},toggle_primary:{key:80,target:t,fn:t.toggle_selected_node_primary,ignore_with_input:!0},cycle_primary:{key:67,target:t,fn:t.cycle_primary_node,ignore_with_input:!0},direction_arrow_right:{key:39,fn:this.build_input.direction_arrow.right.bind(this.build_input.direction_arrow),ignore_with_input:!0},direction_arrow_down:{key:40,fn:this.build_input.direction_arrow.down.bind(this.build_input.direction_arrow),ignore_with_input:!0},direction_arrow_left:{key:37,fn:this.build_input.direction_arrow.left.bind(this.build_input.direction_arrow),ignore_with_input:!0},direction_arrow_up:{key:38,fn:this.build_input.direction_arrow.up.bind(this.build_input.direction_arrow),ignore_with_input:!0},undo:{key:90,modifiers:{control:!0},target:t.undo_stack,fn:t.undo_stack.undo},redo:{key:90,modifiers:{control:!0,shift:!0},target:t.undo_stack,fn:t.undo_stack.redo},select_all:{key:65,modifiers:{control:!0},fn:t.select_all.bind(t)},select_none:{key:65,modifiers:{control:!0,shift:!0},fn:t.select_none.bind(t)},invert_selection:{fn:t.invert_selection.bind(t)}}),o}function B(){window.onbeforeunload=function(e){return e=e||window.event,this.options.never_ask_before_quit?null:"You will lose any unsaved changes."}.bind(this)}var d=e.make_class();return d.prototype={init:v,load_map:g,load_model:m,_set_mode:y,view_mode:b,build_mode:w,brush_mode:E,zoom_mode:S,rotate_mode:x,text_mode:T,set_reaction_data:N,set_metabolite_data:k,set_gene_data:C,_update_data:L,_toggle_direction_buttons:M,_setup_menu:A,_setup_simple_zoom_buttons:O,_setup_status:_,_setup_quick_jump:D,_setup_modes:P,_get_keys:H,_setup_confirm_before_exit:B},d}),n("DataMenu",["utils"],function(e){return function(t){function s(e,t,n,r,i){n.node().addEventListener("change",function(){o(e,this.value,i,r)},!1);var s=t[0];u(t,n),o(e,s,i,r)}function o(t,r,i,s){e.load_the_file(t,r,function(e,t){if(e)return console.warn(e);n.data=t,s&&s(t)})}function u(e,t){t.selectAll(".menu-option").data(e).enter().append("option").attr("value",function(e){return e}).text(function(e){return e}),t.node().focus()}function a(){return n.data}var n=e.set_options(t,{selection:null,getdatafiles:null,datafiles:null,update_callback:null,target:null});if(n.selection===null)throw new Error("No selection provided for DataMenu");var r=n.selection.select(".data-menu");r.empty()&&(r=n.selection.append("div").attr("class","data-menu"));var i=r.append("form").append("select").attr("class","dropdown-menu");return n.getdatafiles?(n.datafiles&&console.warn("DataMenu: getdatafiles option overrides datafiles"),d3.json(n.getdatafiles,function(e,t){return e?console.warn(e):(s(n.target,t.data,i,n.update_callback,n.selection),null)})):n.datafiles?s(n.target,n.datafiles,i,n.update_callback,n.selection):console.warn("DataMenu: No datafiles given"),{update:u}}}),n("static",["utils"],function(e){function t(t,r,i,s,o){var u=e.parse_url_components(window,s),a=[],f=function(e){e(null)},l=function(e){e(null)};if(u.map_name){var c=n("map",u.map_name,i,t);c&&(f=function(e){d3.json(c,function(t,n){t&&console.warn(t),e(n)})})}if(u.model_name){var h=n("model",u.model_name,i,r);h&&(l=function(e){d3.json(h,function(t,n){t&&console.warn(t),e(n)})})}f(function(e){l(function(t){o(e,t,s)})})}function n(e,t,n,r){var i=n[e+"s"].filter(function(n){return n[e+"_name"]==t});if(i.length==0)throw new Error("Bad "+e+" "+t);return r+encodeURIComponent(i[0].organism)+"/"+encodeURIComponent(i[0][e+"_name"])+".json"}return{load_map_model_from_url:t}}),n("main",["Builder","Map","Behavior","KeyManager","DataMenu","UndoStack","CobraModel","utils","SearchIndex","Settings","data_styles","ui","static","ZoomContainer"],function(e,t,n,r,i,s,o,u,a,f,l,c,h,p){return{Builder:e,Map:t,Behavior:n,KeyManager:r,DataMenu:i,UndoStack:s,CobraModel:o,utils:u,SearchIndex:a,Settings:f,data_styles:l,ui:c,"static":h,ZoomContainer:p}}),t("main")});