phylotree/dist/phylotree.min.js

A JavaScript library for developing applications and interactive visualizations involving [phylogenetic trees](https://en.wikipedia.org/wiki/Phylogenetic_tree), written as an extension of the [D3](http://d3js.org) [hierarchy layout](https://github.com/d3/

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n={layout:"left-to-right",logger:console,branches:"step",scaling:!0,bootstrap:!1,"color-fill":!0,"font-size":14,"internal-names":!1,selectable:!0,"restricted-selectable":!1,collapsible:!0,"left-right-spacing":"fixed-step","top-bottom-spacing":"fixed-step","left-offset":0,"show-scale":"top","draw-size-bubbles":!1,"bubble-styler":this.radius_pad_for_bubbles,"binary-selectable":!1,"is-radial":!1,"attribute-list":[],"max-radius":768,"annular-limit":.38196601125010515,compression:.2,"align-tips":!1,"maximum-per-node-spacing":100,"minimum-per-node-spacing":2,"maximum-per-level-spacing":100,"minimum-per-level-spacing":10,node_circle_size:rt(3),transitions:null,brush:!0,reroot:!0,hide:!0,"label-nodes-with-name":!1,zoom:!1,"show-menu":!0,"show-labels":!0,"node-styler":null,"edge-styler":null,"node-span":null};this.ensure_size_is_in_px=function(t){return"number"==typeof t?t+"px":t},this.options=r.defaults(e,n),this.font_size=this.options["font-size"],this.offsets=[0,this.font_size/2],this.shown_font_size=this.font_size,this.width=this.options.width||800,this.height=this.options.height||600,this.node_styler=this.options["node-styler"],this.edge_styler=this.options["edge-styler"],this.nodeSpan=this.options["node-span"],this.nodeSpan||(this.nodeSpan=function(t){return 1}),this.rescale_nodeSpan=this.phylotree.nodes.children.map((t=>{if(l(t)||this.showInternalName(t))return this.nodeSpan(t)})).reduce((function(t,e){return Math.min(e,t||1e200)}),null)||1,this.initialize_svg(this.container),this.links=this.phylotree.nodes.links(),this.initializeEdgeLabels(),this.update(),nt()}pad_height(){return this.draw_scale_bar?this.scale_bar_font_size+25:0}pad_width(){this.label_width=this._label_width(this.shown_font_size);const t=this.options["show-labels"]?this.label_width:0;return 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n=0,s=this.svg.selectAll("."+R["tree-container"]).data([0]);if(s=s.enter().append("g").attr("class",R["tree-container"]).merge(s).attr("transform",(t=>this.d3PhylotreeSvgTranslate([this.offsets[1]+this.options["left-offset"],this.pad_height()]))),this.draw_scale_bar){let t=this.svg.selectAll("."+R["tree-scale-bar"]).data([0]);t.enter().append("g").attr("class",R["tree-scale-bar"]).style("font-size",this.ensure_size_is_in_px(this.scale_bar_font_size)).merge(t).attr("transform",(t=>this.d3PhylotreeSvgTranslate([this.offsets[1]+this.options["left-offset"],this.pad_height()-10]))).call(this.draw_scale_bar),t.selectAll("text").style("text-anchor","end")}else this.svg.selectAll("."+R["tree-scale-bar"]).remove();s=this.svg.selectAll("."+R["tree-container"]).data([0]),this.updateCollapsedClades(t);let i=s.selectAll(J(R)).data(this.links.filter(Y),(t=>t.target.id||(t.target.id=++n)));i.exit().remove(),i=i.enter().insert("path",":first-child").merge(i).each((function(n){e.drawEdge(this,n,t)}));let o=s.selectAll(F(R)).data(this.phylotree.nodes.descendants().filter(U),(t=>t.id||(t.id=++n)));if(o.exit().remove(),o=o.enter().append("g").attr("class",this.reclassNode).merge(o).attr("transform",(t=>{const e="right-to-left"==this.options.layout&&l(t);return t.screen_x=E(t),t.screen_y=S(t),this.d3PhylotreeSvgTranslate([e?0:t.screen_x,t.screen_y])})).each((function(n){e.drawNode(this,n,t)})).attr("transform",(t=>{if(!r.isUndefined(t.screen_x)&&!r.isUndefined(t.screen_y))return"translate("+t.screen_x+","+t.screen_y+")"})),this.options["label-nodes-with-name"]&&(o=o.attr("id",(t=>"node-"+t.name))),this.resizeSvg(this.phylotree,this.svg,t),this.options.brush){var h=s.selectAll("."+R["tree-selection-brush"]).data([0]).enter().insert("g",":first-child").attr("class",R["tree-selection-brush"]),d=a.brush().on("brush",((t,e)=>{var n=t.selection,s=this.links.filter(Y).filter(((t,e)=>t.source.screen_x>=n[0][0]&&t.source.screen_x<=n[1][0]&&t.source.screen_y>=n[0][1]&&t.source.screen_y<=n[1][1]&&t.target.screen_x>=n[0][0]&&t.target.screen_x<=n[1][0]&&t.target.screen_y>=n[0][1]&&t.target.screen_y<=n[1][1])).map((t=>t.target));this.modifySelection(this.phylotree.links.map((t=>t.target)),"tag",!1,s.length>0,"false"),this.modifySelection(s,"tag",!1,!1,"true")})).on("end",(()=>{}));h.call(d)}if(this.syncEdgeLabels(),this.options.zoom){let t=a.zoom().scaleExtent([.1,10]).on("zoom",(t=>{a.select("."+R["tree-container"]).attr("transform",(e=>t.transform)),a.select("."+R["tree-scale-bar"]).attr("transform",(e=>{let n=t.transform;return n.y-=10,n}))}));this.svg.call(t)}return this}_handle_single_node_layout(t){let 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this.tree_layout(t.children[i])&&n++,n>=e&&!s&&(this._handle_single_node_layout(t),s=!0)}0==n?(t.notshown=!0,t.x=void 0):s||this._handle_single_node_layout(t)}else t.x=t.children.map(this.tree_layout.bind(this)).reduce(((t,n)=>"number"==typeof n?t+n:(e+=1,t)),0),e==t.children.length?(t.notshown=!0,t.x=void 0):t.x/=t.children.length-e}do_lr(t){if(this.radial()&&t&&(this.offsets[1]=0),"fixed-step"==this.options["left-right-spacing"])this.size[1]=this.max_depth*this.fixed_width[1],this.scales[1]=(this.size[1]-this.offsets[1]-this.options["left-offset"])/this._extents[1][1],this.label_width=this._label_width(this.shown_font_size),this.radial()&&(this.label_width*=2);else{this.label_width=this._label_width(this.shown_font_size),t=!0;let e=this.size[1]-this.offsets[1]-this.options["left-offset"];.5*e<this.label_width&&(this.shown_font_size*=.5*e/this.label_width,this.label_width=.5*e),this.scales[1]=(this.size[1]-this.offsets[1]-this.options["left-offset"]-this.label_width)/this._extents[1][1]}}placenodes(){this._extents=[[0,0],[0,0]],this.x=0,this.last_span=0,this.last_node=null,this.last_span=0,this.save_x=this.x,this.save_span=.5*this.last_span,this.do_scaling=this.options.scaling;this.is_under_collapsed_parent=!1,this.max_depth=1,this.phylotree.nodes.x=this.tree_layout(this.phylotree.nodes,this.do_scaling),this.max_depth=a.max(this.phylotree.nodes.descendants(),(t=>t.depth)),this.do_scaling;let t=!1;if(this.draw_scale_bar=this.options["show-scale"]&&this.do_scaling,this.offsets[1]=Math.max(this.font_size,-this._extents[1][0]*this.fixed_width[0]),"fixed-step"==this.options["top-bottom-spacing"]?(this.size[0]=this._extents[0][1]*this.fixed_width[0],this.scales[0]=this.fixed_width[0]):(this.scales[0]=(this.size[0]-this.pad_height())/this._extents[0][1],t=!0),this.shown_font_size=Math.min(this.font_size,this.scales[0]),this.radial()){this.draw_branch=r.partial(L,this.radial_center),this.edge_placer=T;let e=null,n=null,s=null,i=0,a=this._extents[0][1]*this.scales[0],o=function(t,e,n,s,i){return i=i||0,Math.sqrt((e-t)*(e-t)+2*(t+i)*(e+i)*(1-Math.cos(n-s)))},l=0;this.phylotree.nodes.each((t=>{let e=t.x*this.scales[0];t.angle=2*Math.PI*e/a,t.text_angle=t.angle-Math.PI/2,t.text_angle=t.text_angle>0&&t.text_angle<Math.PI,t.text_align=t.text_angle?"end":"start",t.text_angle=(t.text_angle?180:0)+180*t.angle/Math.PI})),this.do_lr(t),this.phylotree.nodes.each((t=>{t.radius=t.y*this.scales[1]/this.size[1],l=Math.max(t.radius,l)}));let h=0;this.phylotree.nodes.each((t=>{if(!t.children){let a=t.x*this.scales[0];if(null!==e){let r=a-n,d=o(t.radius,s,t.angle,e,h),c=d>0?r/d:10*this.options["max-radius"];if(c>this.options["max-radius"]){let n=r/this.options["max-radius"],a=t.radius+s,o=t.radius*s-(n*n-(s-t.radius)*(s-t.radius))/2/(1-Math.cos(e-t.angle)),d=Math.sqrt(a*a-4*o);h=Math.min(this.options["annular-limit"]*l,(-a+d)/2),i=this.options["max-radius"]}else i=Math.max(i,c)}e=t.angle,n=a,s=t.radius}})),this.radius=Math.min(this.options["max-radius"],Math.max(a/2/Math.PI,i)),t&&(this.radius=Math.min(this.radius,.5*(Math.min(a,this._extents[1][1]*this.scales[1])-this.label_width)-this.radius*h)),this.radial_center=this.radius_pad_for_bubbles=this.radius,this.draw_branch=r.partial(L,this.radial_center);let d=1;h&&(d=l/(l+h),this.radius*=d),this.phylotree.nodes.each((t=>{if(A(t,this.radius,h,this.radial_center,this.scales,this.size),l=Math.max(l,t.radius),this.options["draw-size-bubbles"]?this.radius_pad_for_bubbles=Math.max(this.radius_pad_for_bubbles,t.radius+this.nodeBubbleSize(t)):this.radius_pad_for_bubbles=Math.max(this.radius_pad_for_bubbles,t.radius),t.collapsed){t.collapsed=t.collapsed.map((t=>{let e={};return e.x=t[0],e.y=t[1],e=A(e,this.radius,h,this.radial_center,this.scales,this.size),[e.x,e.y]}));let e=t.collapsed[1];t.collapsed=t.collapsed.filter((function(n,s){return s<3||s>t.collapsed.length-4||Math.sqrt(Math.pow(n[0]-e[0],2)+Math.pow(n[1]-e[1],2))>3&&(e=n,!0)}))}})),this.size[0]=this.radial_center+this.radius/d,this.size[1]=this.radial_center+this.radius/d}else this.do_lr(),this.draw_branch=C,this.edge_placer=O,this.right_most_leaf=0,this.phylotree.nodes.each((t=>{if(t.x*=this.scales[0],t.y*=.8*this.scales[1],"right-to-left"==this.options.layout&&(t.y=this._extents[1][1]*this.scales[1]-t.y),l(t)&&(this.right_most_leaf=Math.max(this.right_most_leaf,t.y+this.nodeBubbleSize(t))),t.collapsed){t.collapsed.forEach((t=>{t[0]*=this.scales[0],t[1]*=.8*this.scales[1]}));let e=t.collapsed[1][0];t.collapsed=t.collapsed.filter((function(n,s){return s<3||s>t.collapsed.length-4||n[0]-e>3&&(e=n[0],!0)}))}}));if(this.draw_scale_bar){let t,e;if(this.radial()){if(e=Math.min(this.radius/5,50),t=Math.pow(10,Math.ceil(Math.log(this._extents[1][1]*e/this.radius)/Math.log(10))),e=t*(this.radius/this._extents[1][1]),e<30){let n=Math.ceil(30/e);e*=n,t*=n}}else t=this._extents[1][1],e=this.size[1]-this.offsets[1]-this.options["left-offset"]-this.shown_font_size;let n=a.scaleLinear().domain([0,t]).range([0,e]),s=a.format(".2f");if(this.draw_scale_bar=a.axisTop().scale(n).tickFormat((function(t){return 0===t?"":s(t)})),this.radial())this.draw_scale_bar.tickValues([t]);else{let t=function(t,e){return e?Math.round(t*(e=Math.pow(10,e)))/e:Math.round(t)},i=n.ticks();i=i.length>1?i[1]:i[0],this.draw_scale_bar.ticks(Math.min(10,t(e/(this.shown_font_size*s(i).length*2),0)))}}else this.draw_scale_bar=null;return this}spacing_x(t,e){return arguments.length?(this.fixed_width[0]!=t&&t>=this.options["minimum-per-node-spacing"]&&t<=this.options["maximum-per-node-spacing"]&&(this.fixed_width[0]=t,e||this.placenodes()),this):this.fixed_width[0]}spacing_y(t,e){return arguments.length?(this.fixed_width[1]!=t&&t>=this.options["minimum-per-level-spacing"]&&t<=this.options["maximum-per-level-spacing"]&&(this.fixed_width[1]=t,e||this.placenodes()),this):this.fixed_width[1]}_label_width(t){t=t||this.shown_font_size;let e=0;return this.phylotree.nodes.descendants().filter(U).forEach((n=>{let s=12+this._nodeLabel(n).length*t*.8;null!==n.angle&&(s*=Math.max(Math.abs(Math.cos(n.angle)),Math.abs(Math.sin(n.angle)))),e=Math.max(s,e)})),e}font_size(t){return arguments.length?(this.font_size=void 0===t?12:t,this):this.font_size}scale_bar_font_size(t){return arguments.length?(this.scale_bar_font_size=void 0===t?12:t,this):this.scale_bar_font_size}node_circle_size(t,e){return arguments.length?(this.options.node_circle_size=rt(void 0===t?3:t),this):this.options.node_circle_size}css(t){if(0===arguments.length)return this.css_classes;if(arguments.length>2){var e={};return e[t[0]]=t[1],this.css(e)}for(var n in R)n in t&&t[n]!=R[n]&&(R[n]=t[n]);return this}transitions(t){return void 0!==t?t:null!==this.options.transitions?this.options.transitions:this.phylotree.nodes.descendants().length<=300}css_classes(t,e){if(!arguments.length)return this.css_classes;let n=!1;for(var s in R)s in t&&t[s]!=this.css_classes[s]&&(n=!0,this.css_classes[s]=t[s]);return e&&n&&this.layout(),this}layout(t){return this.svg?(this.svg.selectAll("."+this.css_classes["tree-container"]+",."+this.css_classes["tree-scale-bar"]+",."+this.css_classes["tree-selection-brush"]),this.d3PhylotreeTriggerLayout(this),this.update()):(this.d3PhylotreeTriggerLayout(this),this)}handle_node_click(t,e){this.nodeDropdownMenu(t,this.container,this,this.options,e)}refresh(){if(this.svg){let t=this.svg.selectAll("."+this.css_classes["tree-container"]).selectAll(J(this.css_classes)).attr("class",this.reclassEdge.bind(this));this.edge_styler&&t.each((t=>{this.edge_styler(a.select(this),t)}))}return this}countHandler(t){return arguments.length?(this.count_listener_handler=t,this):this.count_listener_handler}style_nodes(t){return arguments.length?(this.node_styler=t,this):this.node_styler}style_edges(t){return arguments.length?(this.edge_styler=t.bind(this),this):this.edge_styler}itemSelected(t,e){return t[e]||!1}show(){return this.svg.node()}}r.extend(ot.prototype,$),r.extend(ot.prototype,X),r.extend(ot.prototype,K),r.extend(ot.prototype,st),r.extend(ot.prototype,at),r.extend(ot.prototype,H);let lt=class{constructor(t,e={}){this.newick_string="",this.nodes=[],this.links=[],this.parsed_tags=[],this.partitions=[],this.branch_length_accessor=z,this.branch_length=z,this.logger=e.logger||console,this.selection_attribute_name="selected";var n=e.type||void 0,s=[],i=this;if(r.isString(n))n in v?s=v[n](t,e):i.logger.error("type "+n+" not in registry! Available types are "+r.keys(v));else if(r.isFunction(n))try{s=n(t,e)}catch(t){i.logger.error("Could not parse custom format!")}else"root"==t.name?s={json:t,error:null}:"string"!=typeof t?s=t:"application/xml"==t.contentType?s=b(t):(this.newick_string=t,s=c(t,e));if(s.json){i.nodes=a.hierarchy(s.json);let t={};i.nodes.each((e=>{e.data.annotation&&(t[e.data.annotation]=!0)})),i.parsed_tags=Object.keys(t)}else i.nodes=[];return i.links=i.nodes.links(),this.hasBranchLengths()||(console.warn("Phylotree User Warning : NO BRANCH LENGTHS DETECTED, SETTING ALL LENGTHS TO 1"),this.setBranchLength((t=>1))),i}json(t){var e=0;this.traverse_and_compute((function(t){t.json_export_index=e++}),t);var n=new Array(e);return e=0,this.traverse_and_compute((function(t){let s=r.clone(t);delete s.json_export_index,t.parent&&(s.parent=t.parent.json_export_index),t.children&&(s.children=r.map(t.children,(function(t){return t.json_export_index}))),n[e++]=s}),t),this.traverse_and_compute((function(t){delete t.json_export_index}),t),JSON.stringify(n)}traverse_and_compute(t,e,n,s){return(e="pre-order"==(e=e||"post-order")?function(e){x(e,t,s)}:"in-order"==e?function(e){w(e,t,s)}:function(e){r.isUndefined(e)||y(e,t,s)})(n||this.nodes),this}get_parsed_tags(){return this.parsed_tags}update(t){this.nodes=t}render(t){return this.display=new ot(this,t),this.display}};function ht(t){var e=t.branch_length_accessor;if(!e)throw"A non-null branch lengths accessor function is required for this operation";var n=0;function s(t){for(var e=0;e<t.children.length;e++)for(var n=0;n<t.children.length;n++)e!=n&&r.each(t.children[n].cot_path_to_leaves_below,(function(s,i){t.children[e].cot_path_to_leaves_above&&(t.children[e].cot_path_to_leaves_above[i]=s+t.children[n].cot_computed_length)}))}return t.traverse_and_compute((function(s){if(s.cot_computed_length=e(s),s.parent&&r.isUndefined(s.cot_computed_length))throw"Non-null branch lengths are required for this operation: missing branch length at node "+s.data.name;t.isLeafNode(s)?(s.cot_leaf_index=n++,s.cot_path_to_leaves_below={},s.cot_path_to_leaves_below[s.cot_leaf_index]=0,s.cot_path_to_leaves_above={}):(s.cot_path_to_leaves_below={},s.cot_path_to_leaves_above={})})),t.traverse_and_compute((function(t){t.parent&&r.each(t.cot_path_to_leaves_below,(function(e,n){t.parent.cot_path_to_leaves_below[n]=e+t.cot_computed_length}))})),s(t.getRootNode()),t.traverse_and_compute((function(e){e.parent&&(r.each(e.parent.cot_path_to_leaves_above,(function(t,n){e.cot_path_to_leaves_above[n]=t+e.parent.cot_computed_length})),t.isLeafNode(e)||s(e))}),"pre-order"),n}function dt(t,e,n,s,i){var a=t.branch_length(e),r=!1;if(n||(s=e.data.rootToTip,i=0,r=!0),e.children)for(var o=0;o<e.children.length;o++)e.children[o]!=n?dt(t,e.children[o],e,s,i):r=!0;e.data.rtta=e.data.rootToTip-s+i,r&&(s-=a,i+=a),e.parent&&r&&dt(t,e.parent,e,s,i)}function ct(t){var e=t.reduce((function(t,e){return e[2]+t}),0),n=t.reduce((function(t,e){return e[2]*e[0]+t}),0),s=t.reduce((function(t,e){return e[2]*e[1]+t}),0),i=n/e,a=s/e,r=0,o=0,l=0;t.forEach((function(t){var e=t[0]-i;o+=t[2]*e*e,r+=t[2]*e*t[1],l+=t[2]*(t[1]-a)*(t[1]-a)}));var h=(s-n*(r/=o))/e,d=0;return t.forEach((function(t){var e=t[1]-h-r*t[0];d+=t[2]*e*e})),{intercept:h,slope:r,r2:1-d/l,"var (intercept)":Math.sqrt((1+n*n/(e*o))/e),"var (slope)":Math.sqrt(1/o)}}function ut(t){var e=t.branch_length_accessor,n=0;t.traverse_and_compute((s=>{if(s.parent&&(s.data._computed_length=e(s),!r.isNumber(s.data._computed_length)))throw"rootToTip cannot be run on trees with missing branch lengths";t.isLeafNode(s)&&(s.data.leaf_index=n++),"r2t"in s.data&&delete s.data.r2t})),t.traverse_and_compute((e=>{e.parent&&("r2t"in e.parent.data||(e.parent.data.r2t={}),t.isLeafNode(e)?e.parent.data.r2t[e.data.leaf_index]=e.data._computed_length:(r.each(e.data.r2t,(function(t,n){e.parent.data.r2t[n]=t+e.data._computed_length})),delete e.data.r2t),delete e.data._computed_length)}));var s=t.getRootNode().data.r2t;return t.traverse_and_compute((e=>{t.isLeafNode(e)&&(e.data.rootToTip=s[e.data.leaf_index]||0,delete e.data.leaf_index)})),delete t.getRootNode().data.r2t,t}lt.prototype.isLeafNode=l,lt.prototype.selectAllDescendants=h,lt.prototype.mrca=function(t){var e;return t=t.map((function(t){return"string"==typeof t?t:t.data.name})),this.traverse_and_compute((function(n){n.children?n.parent?(n.data.mrca=r.union(...n.descendants().map((t=>t.data.mrca))),e||n.data.mrca.length!=t.length||(e=n)):e||(e=n):n.data.mrca=r.intersection([n.data.name],t)})),e},lt.prototype.hasBranchLengths=function(){let t=this.branch_length;return!!t&&r.every(this.nodes.descendants(),(function(e){return!e.parent||!r.isUndefined(t(e))}))},lt.prototype.getBranchLengths=function(){let t=this.branch_length;return r.map(this.nodes.descendants(),(e=>t(e)))},lt.prototype.branchName=function(t){return arguments.length?(this.nodeLabel=t,this):this.nodeLabel},lt.prototype.normalizeBranchLengths=function(t){let e=this.branch_length,n=r.map(this.nodes.descendants(),(function(t){return e(t)?e(t):null}));const s=r.max(n),i=r.min(n);return r.each(this.nodes.descendants(),(t=>{let n=e(t);n&&e(t,(n-i)/(s-i))})),this},lt.prototype.scaleBranchLengths=function(t){let e=this.branch_length;return r.each(this.nodes.descendants(),(n=>{let s=e(n);s&&e(n,t(s))})),this},lt.prototype.getNewick=u,lt.prototype.resortChildren=function(t,e,n){return this.nodes.sum((function(t){return t.value})).sort(t),this.display&&(this.display.update_layout(this.nodes),this.display.update()),this},lt.prototype.setBranchLength=function(t){return arguments.length?(this.branch_length_accessor=t||z,this):this.branch_length_accessor},lt.prototype.maxParsimony=function(t,e){const n=r.partial((function(t,e){if(e.mp=[[0,0],[!1,!1]],l(e))e.mp[1][0]=e.mp[1][1]=e[t]||!1,e.mp[0][0]=e.mp[1][0]?1:0,e.mp[0][1]=1-e.mp[0][0];else{e.children.forEach(n);var s=e.children.reduce((function(t,e){return e.mp[0][0]+t}),0),i=e.children.reduce((function(t,e){return e.mp[0][1]+t}),0);e[t]?(e.mp[0][0]=i+1,e.mp[1][0]=!0,e.mp[0][1]=i,e.mp[1][1]=!0):(s<i+1?(e.mp[0][0]=s,e.mp[1][0]=