@sjcrh/proteinpaint-client 2.76.2 → 2.77.1

package/dist/{HicApp-e713aa40.js → HicApp-5ed85d49.js}

@@ -1 +1 @@
-import{_ as t}from"./tslib.es6-c3c2d88f.js";import{m as i,h as s,ah as e,ag as o,I as r,W as a,f as h,b as n,d as l,M as c,Z as p,ad as d,ae as u,o as f,ai as m}from"./app-6fb77603.js";import{d as g,a as y}from"./axis-747c801e.js";import{p as x}from"./pointer-c7475677.js";import{b as v}from"./block.lazyload-d2951c91.js";import{C as w}from"./ColorScale-b991fc9e.js";import{h as b}from"./parseData-292648dd.js";import"./axisstyle-fac7f76b.js";class k{constructor(){this.views=["genome","chrpair","detail","horizontal"];this.type="store";this.defaultState={defaultNmeth:"NONE",loading:true,minBinNum_bp:200,minFragSpan:200,initialBinNum:20,settings:{widthHeightPx:800}}}}const D=i(k);k.prototype.actions={view_create(t){if(!t.view)throw Error("view_create: missing view");if(!this.views.some((i=>i==t.view)))throw Error(`view_create: unknown view = ${t.view}`);this.state.currView=t.view;const i=Object.assign(this.state,t.config);this.state=i},view_update(t){if(t.view){if(!this.views.some((i=>i==t.view)))throw Error(`view_update: unknown view = ${t.view}`);const i=Object.assign(this.state[t.view],t.config);this.state[t.view]=i}else{const i=Object.assign(this.state,t.config);this.state=i}},loading_active(t){this.state.loading=t.active}};class M{constructor(t){this.hasStatePreMain=true;this.type="loadingOverlay",this.app=t.app,this.loadingDiv=t.loadingDiv}reactsTo(t){if(t.type.startsWith("loading"))return true;else return false}getState(t){return t}init(){this.loadingDiv.append("div").attr("class","sjpp-spinner").style("display","")}main(t){const i=this.app.getState(t).loading;this.loadingDiv.style("display",i?"":"none")}}const V=s(M);class z{colorizeElement(t,i,s,e,o,r,a,h,n){if(s>=0){const t=s>=h?0:s<=a?255:Math.floor(255*(h-s)/h);const i=`rgb(255, ${t}, ${t})`;if(n==="genome"){e.ctx.fillStyle=i;e.ctx2.fillStyle=i}else{e.fillStyle=i}}else{const t=s<=a?255:Math.floor(255*(h+s)/h);const i=`rgb(${t}, ${t}, 255)`;if(n==="genome"){e.ctx.fillStyle=i;e.ctx2.fillStyle=i}else{e.fillStyle=i}}if(n==="genome"){e.ctx.fillRect(i,t,o,r);e.ctx2.fillRect(t,i,o,r)}else{e.fillRect(t,i,o,r)}}}class R{constructor(t){this.error=t}getResolution(t,i){if(t.currView=="genome")return i["bpresolution"][0];if(t.currView=="chrpair"){const s=this.getChrPairResolution(i,t.x,t.y,t.minBinNum_bp);return s}else if(t.currView=="detail"){const s=Math.max(t.x.stop-t.x.start,t.y.stop-t.y.start);let e=this.findResFromArray(s,t.minBinNum_bp,i.bpresolution);if(e==null&&!i.enzyme){e=i.bpresolution[i.bpresolution.length-1]}return e}else{this.error(`Unknown view: ${t.currView}`);throw`Unknown view: ${t.currView}`}}getChrPairResolution(t,i,s,e){const o=t.genome.chrlookup[i.chr.toUpperCase()].len;const r=t.genome.chrlookup[s.chr.toUpperCase()].len;const a=Math.max(o,r);const h=this.findResFromArray(a,e,t.bpresolution);if(h==null){this.error(`No suitable resolution for ${i.chr}-${s.chr} pair.`);return}return h}findResFromArray(t,i,s,e){let o=null;for(const e of s){if(t/e>i){o=e;break}}if(e&&o==null){o=s[s.length-1]}return o}getDefaultViewSpan(t,i,s,e,o){const r=this.getChrPairResolution(t,i,s,o);if(!r)return;return r*e}}class ${constructor(t,i){this.error=t;this.resolution=new R(this.error);this.minBinNum_bp=i}setPosition(t,i,s,e,o,r,a){const h=this.resolution.getChrPairResolution(r,e,o,this.minBinNum_bp);const n=h*a;let l=Math.max(1,Math.floor(t*h/s)-n/2);let c=Math.max(1,Math.floor(i*h/s)-n/2);{const t=r.genome.chrlookup[e.chr.toUpperCase()].len;if(l+n>=t){l=t-n}const i=r.genome.chrlookup[o.chr.toUpperCase()].len;if(c+n>i){c=i-n}}const p={chr:e.chr,start:l,stop:l+n};const d={chr:o.chr,start:c,stop:c+n};return[p,d]}}class C{formatData(t,i,s,e,o,r){const a=[];for(const[h,n,l]of i){const i=Math.floor(h/e)*s;const c=Math.floor(n/e)*s;if(t=="genome"){a.push([i,c,l])}if(t=="chrpair"){const t=o?i:c;const s=o?c:i;a.push([t,s,l]);if(r){a.push([s,t,l])}}}return a}}class L{constructor(t,i,s){this.chrorder=t;this.chrx=i;this.chry=s}isFirstX(){if(this.chrx==this.chry)return true;return this.chrorder.indexOf(this.chrx)<this.chrorder.indexOf(this.chry)}}class S{constructor(t){this.binpx=1;this.axispad=10;this.axisLabelFontSize=15;this.calcResolution=null;this.data=[];this.app=t.app;this.hic=t.hic;this.plotDiv=t.plotDiv;this.items=t.items;this.parent=t.parent;this.chrxlen=this.hic.genome.chrlookup[this.parent("state").x.chr.toUpperCase()].len;this.chrylen=this.hic.genome.chrlookup[this.parent("state").y.chr.toUpperCase()].len;this.maxchrlen=Math.max(this.chrxlen,this.chrylen);this.colorizeElement=new z;this.positions=new $(t.error,this.parent("state").minBinNum_bp);this.formattedData=new C}setDefaultBinpx(){if(this.calcResolution==null)return;while(this.binpx*this.maxchrlen/this.calcResolution<600){this.binpx++}}renderAxes(){if(this.calcResolution==null)return;const t=this.plotDiv.yAxis.append("svg");const i=Math.ceil(this.chrylen/this.calcResolution)*this.binpx;t.attr("width",100).attr("height",this.axispad*2+i);t.append("g").attr("data-testid","sjpp-chrpair-svg-y").attr("transform","translate(80,"+(this.axispad+i/2)+")").append("text").text(this.parent("state").y.chr).attr("text-anchor","middle").attr("font-size",this.axisLabelFontSize).attr("font-family",e).attr("dominant-baseline","central").attr("transform","rotate(90)");o({axis:t.append("g").attr("transform",`translate(1, ${this.axispad})`).call(g(r().domain([0,this.chrylen]).range([0,i])).tickFormat(a(".2s"))),showline:true});const s=this.plotDiv.xAxis.append("svg").style("margin-top","-4px");const h=Math.ceil(this.chrxlen/this.calcResolution)*this.binpx;s.attr("height",100).attr("width",this.axispad*2+h);s.append("text").attr("data-testid","sjpp-chrpair-svg-x").text(this.parent("state").x.chr).attr("font-size",this.axisLabelFontSize).attr("font-family",e).attr("x",this.axispad+h/2).attr("text-anchor","middle").attr("y",60);o({axis:s.append("g").attr("transform","translate("+this.axispad+",1)").call(y(r().domain([0,this.chrxlen]).range([0,h])).tickFormat(a(".2s"))),showline:true})}renderCanvas(){const i=this.initDetailView.bind(this);this.canvas=this.plotDiv.plot.append("canvas").attr("data-testid","sjpp-chrpair-canvas").style("margin",this.axispad+"px").on("click",(function(s){return t(this,void 0,void 0,(function*(){const[t,e]=x(s,this);i(t,e)}))})).node();this.canvas.width=Math.ceil(this.chrxlen/this.calcResolution)*this.binpx;this.canvas.height=Math.ceil(this.chrylen/this.calcResolution)*this.binpx;this.ctx=this.canvas.getContext("2d")}initDetailView(t,i){const[s,e]=this.positions.setPosition(t,i,this.binpx,this.parent("state").x,this.parent("state").y,this.hic,this.parent("state").initialBinNum);this.app.dispatch({type:"view_create",view:"detail",config:{x:s,y:e}})}render(){this.calcResolution=this.parent("calcResolution");this.setDefaultBinpx();this.renderAxes();this.renderCanvas();this.update(this.items)}update(t){this.items=t;const i=new L(this.hic.chrorder,this.parent("state").x.chr,this.parent("state").y.chr).isFirstX();const s=this.parent("state").x.chr===this.parent("state").y.chr;this.data=this.formattedData.formatData("chrpair",t.items,this.binpx,this.calcResolution,i,s);this.ctx.clearRect(0,0,this.canvas.width,this.canvas.height);for(const[t,i,s]of this.data){this.colorizeElement.colorizeElement(t,i,s,this.ctx,this.binpx,this.binpx,this.parent("min"),this.parent("max"),"chrpair")}this.app.dispatch({type:"loading_active",active:false})}}class B{constructor(t){this.maxPercentage=5;this.subPanelPxWidth=600;this.borderColor="rgba(200,0,0,.1)";this.app=t.app;this.hic=t.hic;this.plotDiv=t.plotDiv;this.items=t.items;this.parent=t.parent}setRunPpTracks(){const t=[{type:"hicstraw",file:this.hic.file,url:this.hic.url,name:this.hic.name,enzyme:this.hic.enzyme,maxpercentage:this.maxPercentage,pyramindup:1}];if(this.hic.tklst){for(const i of this.hic.tklst){t.push(i)}}h(this.hic.genome,t);return t}setRunPpArgs(t){const i={holder:this.plotDiv.plot,hostURL:this.hic.hostURL,jwt:this.hic.jwt,genome:this.hic.genome,nobox:1,tklst:t};const s=this.parent("state");if(s.x.chr==s.y.chr&&Math.max(s.x.start,s.y.start)<Math.min(s.x.stop,s.y.stop)){i["chr"]=s.x.chr;i["start"]=Math.min(s.x.start,s.y.start);i["stop"]=Math.max(s.x.stop,s.y.stop)}else{i["chr"]=s.x.chr;i["start"]=s.x.start;i["stop"]=s.x.stop;i["width"]=this.subPanelPxWidth;i["subpanels"]=[{chr:s.y.chr,start:s.y.start,stop:s.y.stop,width:this.subPanelPxWidth,leftpad:10,leftborder:this.borderColor}]}return i}render(){const t=this.setRunPpTracks();const i=this.setRunPpArgs(t);v(i)}}class N{constructor(t,i,s,e,o,r){this.leftheadw=20;this.rightheadw=40;this.lpad=1;this.rpad=1;this.firstRender=true;this.app=t;this.hic=i;this.width=s;this.bbmargin=e;this.holder=o;this.isYblock=r;this.bbw=this.leftheadw+this.lpad+this.width+this.rpad+this.rightheadw+2*this.bbmargin;this.defaultLeft=this.bbmargin+this.leftheadw+this.lpad;this.defaultTop=this.bbmargin+this.rightheadw+this.rpad}setArgs(t){const i={hostURL:this.hic.hostURL,genome:this.hic.genome,holder:this.holder,noresize:true,nobox:true,butrowbottom:true,style:{margin:`${this.bbmargin}px`},width:this.width,leftheadw:this.leftheadw,chr:t.chr,start:t.start,stop:t.stop,rightheadw:this.rightheadw,tklst:[],rotated:this.isYblock,showreverse:this.isYblock};h(this.hic.genome,i.tklst);return i}setMethods(t,i,s){const e={onloadalltk_always:()=>{this.onload(t,i,s)},onpanning:t=>this.onpanning(t,i)};if(this.isYblock){e["onsetheight"]=t=>{this.holder.transition().style("left",`${t+this.bbmargin+30}px`)}}return e}onload(t,i,s){this.bbw=this.block.leftheadw+this.block.lpad+this.block.width+this.block.rpad+this.block.rightheadw+2*this.bbmargin;if(this.isYblock){s.transition().style("height",`${this.bbw}px`);t.style("height",`${this.bbw}px`)}else t.style("width",`${this.bbw}px`);if(this.isYblock){this.defaultTop=this.bbmargin+this.block.rightheadw+this.block.rpad;i.style("top",`${this.defaultTop}px`)}else{this.defaultLeft=this.bbmargin+this.block.leftheadw+this.block.lpad;i.style("left",`${this.defaultLeft}px`)}const e={[this.isYblock?"y":"x"]:{chr:this.block.rglst[0].chr,start:this.block.rglst[0].start,stop:this.block.rglst[0].stop}};if(this.firstRender==false){this.app.dispatch({type:"view_update",config:e})}else{this.firstRender=false}}onpanning(t,i){if(!this.isYblock)i.style("left",`${t+this.defaultLeft}px`);else i.style("top",`${-t+this.defaultTop}px`)}loadBlock(i,s,e,o){return t(this,void 0,void 0,(function*(){const r=this.setArgs(i);const a=this.isYblock?this.setMethods(s,e,o):this.setMethods(s,e);const h=Object.assign(r,a);yield v(h).then((i=>t(this,void 0,void 0,(function*(){this.block=i}))))}))}}class P{constructor(t){this.obj={rglst:[]};this.errList=t}isFragData(t,i){if(i!=null)return;if(!t.enzyme){i=t.bpresolution[t.bpresolution.length-1];return}}formatFragArgs(t,i){const s={getdata:1,getBED:1,file:t,rglst:[i]};return s}getBedData(i){return t(this,void 0,void 0,(function*(){try{return yield n("tkbedj",{method:"POST",body:JSON.stringify(i)})}catch(t){this.errList.push(t.message||t);if(t.stack)console.error(t.stack)}}))}getXFragData(i,s,e){return t(this,void 0,void 0,(function*(){this.isFragData(i,s);if(!i.enzymefile)return;const t=this.formatFragArgs(i.enzymefile,e);return yield this.getBedData(t)}))}getYFragData(i,s){return t(this,void 0,void 0,(function*(){const t=this.formatFragArgs(i.enzymefile,s);return yield this.getBedData(t)}))}fetchData(i,s,e,o,r,a){return t(this,void 0,void 0,(function*(){const t={matrixType:s.matrixType,file:i.file,url:i.url,pos1:this.determinePosition(i,o,a===null||a===void 0?void 0:a.x),pos2:this.determinePosition(i,r,a===null||a===void 0?void 0:a.y),nmeth:s.nmeth,resolution:e};if(a)t["isfrag"]=true;try{const i=n("hicdata?",{method:"POST",body:JSON.stringify(t)});if(i.error){this.errList.push(i.error)}return i}catch(t){this.errList.push(t.message||t);if(t.stack)console.error(t.stack)}}))}determinePosition(t,i,s){if(s){return`${t.nochr?i.chr.replace("chr",""):i.chr}:${s.start}:${s.stop}`}else{return`${t.nochr?i.chr.replace("chr",""):i.chr}:${i.start}:${i.stop}`}}}class E{constructor(t,i){this.id2coord=new Map;this.min=null;this.max=null;this.items=[];this.errLst=t;for(const t of i){if(!t.rest||!t.rest[0]){this.errLst.push("items[].rest data problem")}const i=Number.parseInt(t.rest[0]);if(Number.isNaN(i)){this.errLst.push(`${t.start}.${t.stop} invalid fragment id: ${t.rest[0]}`)}this.id2coord.set(i,[t.start,t.stop]);if(this.min==null){this.min=i;this.max=i}else{this.min=Math.min(this.min,i);this.max=Math.max(this.max,i)}}}}class _{constructor(t,i,s){this.frag={x:{},y:{}};this.hic=t;this.errList=i;this.dataFetcher=new P(i);this.parent=s}getFragData(i,s){return t(this,void 0,void 0,(function*(){try{const t=yield this.dataFetcher.getXFragData(this.hic,this.parent("calcResolution"),i);if(t){if(!t.items){this.errList.push(`No fragment data returned for ${i.chr}:${i.start}-${i.stop}`);return}const e=new E(this.errList,t.items);if(this.errList.length)return;this.frag.x={id2coord:e.id2coord,start:e.min,stop:e.max};const o=yield this.dataFetcher.getYFragData(this.hic,s);if(this.errList.length)return;if(o){if(!o.items){this.errList.push(`No fragment data returned for ${s.chr}:${s.start}-${s.stop}`);return}const t=new E(this.errList,o.items);if(this.errList.length)return;this.frag.y={id2coord:new Map,start:t.min,stop:t.max};this.determineMap(t.id2coord,i,s)}}}catch(t){this.errList.push(t.message||t);if(t.stack)console.error(t.stack)}}))}determineMap(t,i,s){if(i.chr==s.chr){for(const[i,s]of t){this.frag.x["id2coord"].set(i,s)}this.frag.y["id2coord"]=this.frag.x["id2coord"]}else{this.frag.y["id2coord"]=t}}getData(i,s,e){return t(this,void 0,void 0,(function*(){return yield this.dataFetcher.fetchData(this.hic,this.parent("state")["detail"],this.parent("calcResolution"),i,s,e)}))}}class j{constructor(t,i){this.hic=t;this.errlist=i}getCoordinates(t,i,s,e,o,r){const a=new L(this.hic.chrorder,t.chr,i.chr).isFirstX();const h=t.chr==i.chr;const n=o/(t.stop-t.start);const l=o/(i.stop-i.start);const c=this.calculateCoordinates(a,h,n,l,e,t,i,s,r);return c}calculateCoordinates(t,i,s,e,o,r,a,h,n){const l=[];for(const[c,p,d]of h.items){let h,u,f,m;if(n){const i=t?c:p;const s=t?p:c;if(n.x.id2coord.has(i)){const[t,s]=n.x.id2coord.get(i);h=t;f=s-t}else{this.errlist.push(`[x id error] x: ${i} y: ${s}`);continue}{const t=i+o;if(n.x.id2coord.has(t)){const[i,s]=n.x.id2coord.get(t);f=s-h}}if(n.y.id2coord.has(s)){const[t,i]=n.y.id2coord.get(s);u=t;m=i-t}else{this.errlist.push(`[y id error] x: ${i} y: ${s}`);continue}{const t=s+o;if(n.y.id2coord.has(t)){const[i,s]=n.y.id2coord.get(t);m=s-u}}}else{h=t?c:p;u=t?p:c;f=o;m=o}if(i){if(h>r.start-f&&h<r.stop&&u>a.start-m&&u<a.stop){l.push([Math.floor((h-r.start)*s),Math.floor((u-a.start)*e),Math.ceil(f*s),Math.ceil(m*e),d])}if(u>r.start-m&&u<r.stop&&h>a.start&&h<a.stop){l.push([Math.floor((u-r.start)*s),Math.floor((h-a.start)*e),Math.ceil(m*s),Math.ceil(f*e),d])}continue}l.push([Math.floor((h-r.start)*s),Math.floor((u-a.start)*e),Math.ceil(f*s),Math.ceil(m*e),d])}return l}}class F{constructor(t){this.calcResolution=null;this.binpx=2;this.bbmargin=1;this.app=t.app;this.hic=t.hic;this.plotDiv=t.plotDiv;this.sheath=t.plotDiv.yAxis.append("div").style("position","relative").style("width","200px").style("height","800px");this.rotor=this.sheath.append("div").style("position","absolute").style("bottom","0px").style("transform","rotate(-90deg)").style("transform-origin","left bottom");this.data=t.data;this.parent=t.parent;this.errList=this.parent("errList");this.resolution=new R(t.error);this.colorizeElement=new z;this.viewRangeBpW=this.resolution.getDefaultViewSpan(this.hic,this.parent("state").x,this.parent("state").y,this.parent("state").initialBinNum,this.parent("state").minBinNum_bp);this.dataMapper=new _(this.hic,t.error,t.parent);this.coordinates=new j(this.hic,this.errList)}renderCanvas(t){this.canvasHolder=this.plotDiv.plot.append("div").style("position","relative").style("width",`${this.xBlock.bbw}px`).style("height",`${this.yBlock.bbw}px`).style("overflow","hidden");this.canvas=this.canvasHolder.append("canvas").style("display","block").style("position","absolute").attr("data-testid","sjpp-hic-detail-canvas").attr("width",t).attr("height",t).on("mousedown",(t=>{const i=l(document.body);const s=t.clientX;const e=t.clientY;const o=Number.parseInt(this.canvas.style("left"));const r=Number.parseInt(this.canvas.style("top"));i.on("mousemove",(t=>{const i=t.clientX-s;const a=t.clientY-e;this.xBlock.block.panning(i);this.yBlock.block.panning(a);this.canvas.style("left",`${o+i}px`).style("top",`${r+a}px`)}));i.on("mouseup",(t=>{i.on("mousemove",null).on("mouseup",null);const o=t.clientX-s;const r=t.clientY-e;console.log(o);this.xBlock.block.pannedby(o);this.yBlock.block.pannedby(r)}))}))}render(){return t(this,void 0,void 0,(function*(){this.calcResolution=this.parent("calcResolution");const t=this.parent("state");this.xBlock=new N(this.app,this.hic,t.settings.widthHeightPx,this.bbmargin,this.plotDiv.xAxis,false);this.yBlock=new N(this.app,this.hic,t.settings.widthHeightPx,this.bbmargin,this.rotor,true);this.renderCanvas(t.settings.widthHeightPx);yield this.xBlock.loadBlock(t.x,this.canvasHolder,this.canvas);yield this.yBlock.loadBlock(t.y,this.canvasHolder,this.canvas,this.sheath);this.update(this.data)}))}update(i){return t(this,void 0,void 0,(function*(){if(i.items.length==0){this.app.dispatch({type:"loading_active",active:false});return}this.data=i;const t=this.parent("state");const s=Number.parseInt(this.canvas.attr("width"));const e=Number.parseInt(this.canvasHolder.style("width"))-s+t.settings.widthHeightPx;this.canvasHolder.style("width",`${e}px`).style("height",`${e}px`);this.canvas.attr("width",`${t.settings.widthHeightPx}px`).attr("height",`${t.settings.widthHeightPx}px`);if(this.xBlock.block.width!=t.settings.widthHeightPx){this.xBlock.block.width=t.settings.widthHeightPx;this.yBlock.block.width=t.settings.widthHeightPx;this.xBlock.block.zoom2px(0,s);this.yBlock.block.zoom2px(0,s)}this.ctx=this.canvas.node().getContext("2d");const o=this.coordinates.getCoordinates(t.x,t.y,this.parent("data"),this.parent("calcResolution"),t.settings.widthHeightPx,this.parent("fragData"));this.coords=o;this.ctx.clearRect(0,0,t.settings.widthHeightPx,t.settings.widthHeightPx);for(const[t,i,s,e,o]of this.coords){this.colorizeElement.colorizeElement(t,i,o,this.ctx,s,e,this.parent("min"),this.parent("max"),"detail")}this.app.dispatch({type:"loading_active",active:false})}))}}class T{constructor(t,i){this.label=t;this.width=i}}class A{constructor(t,i,s,e){this.chromosomeMatrix=new Map;this.chromosomeList=[];this.xoff=0;this.yoff=0;this.chr2px=[];this.chrlst=t;let o=this.chrlst.length;for(const t of this.chrlst){const r=Math.ceil(s[t.toUpperCase()].len/i)*e;const a=new T(t,r);this.chromosomeList.push(a);this.chr2px[t]=r;o+=r}this.totalpx=o;for(let t=0;t<this.chrlst.length;t++){const o=this.chrlst[t];this.chromosomeMatrix.set(o,new Map);let r=0;for(let a=0;a<=t;a++){const t=this.chrlst[a];const h=s[o.toUpperCase()].len;const n=s[t.toUpperCase()].len;const l=Math.ceil(h/i)*e;const c=Math.ceil(n/i)*e;this.chromosomeMatrix.get(o).set(t,{x:this.xoff,y:r,xbins:l,ybins:c,data:[]});r+=this.chr2px[t]+A.borderWidth}this.yoff=r;this.xoff+=this.chr2px[o]+A.borderWidth}}}A.checkerFill="#DEF3FA";A.spaceColor="#CCC";A.fontSize=15;A.font=e;A.borderWidth=1;A.defaultChrLabWidth=100;class O{constructor(t){this.grid=new A(t.hic.chrlst,t.resolution||t.hic.bpresolution[0],t.hic.genome.chrlookup,1)}}class U{constructor(t,i,s,e){this.svg=t;this.layerMap=i.attr("transform",`translate(${A.defaultChrLabWidth}, ${A.fontSize})`);this.layerSv=s.attr("transform",`translate(${A.defaultChrLabWidth}, ${A.fontSize})`);this.grid=e}render(){this.renderAxisX(this.grid);this.renderAxisY(this.grid);this.svg.attr("width",A.defaultChrLabWidth+this.grid.xoff).attr("height",A.fontSize+this.grid.yoff)}renderAxisX(t){let i=0;this.grid.chromosomeList.forEach(((s,e)=>{const o=s.width;if(e%2===0){this.layerMap.append("rect").attr("x",i).attr("width",o).attr("height",A.fontSize).attr("y",-A.fontSize).attr("fill",A.checkerFill)}this.layerMap.append("text").attr("font-family",A.font).attr("text-anchor","middle").attr("font-size",12).attr("x",i+o/2).text(s.label);i+=o;this.layerSv.append("line").attr("x1",i).attr("x2",i).attr("y2",t.totalpx).attr("stroke",A.spaceColor).attr("shape-rendering","crispEdges");i+=A.borderWidth}))}renderAxisY(t){let i=0;this.grid.chromosomeList.forEach(((s,e)=>{const o=s.width;if(e%2===0){this.layerMap.append("rect").attr("x",-A.defaultChrLabWidth).attr("width",A.defaultChrLabWidth).attr("height",o).attr("y",i).attr("fill",A.checkerFill)}this.layerMap.append("text").attr("font-family",A.font).attr("text-anchor","end").attr("dominant-baseline","central").attr("font-size",12).attr("y",i+o/2).text(s.label);i+=o;this.layerSv.append("line").attr("x2",t.totalpx).attr("y1",i).attr("y2",i).attr("stroke",A.spaceColor).attr("shape-rendering","crispEdges");i+=A.borderWidth}))}}class H{constructor(){this.chrx_tip=new c({border:"solid 1px #ccc",padding:"0px",offsetX:0,offsetY:0});this.chry_tip=new c({border:"solid 1px #ccc",padding:"0px",offsetX:0,offsetY:0})}render(t,i,s){const e=t.node().getBoundingClientRect();this.chrx_tip.clear().show(e.left,e.top).d.style("top",null).style("bottom",window.innerHeight-e.top-window.pageYOffset+"px").text(i);this.chry_tip.clear().show(e.left,e.top).d.style("left",null).style("right",document.body.clientWidth-e.left-window.pageXOffset+"px").text(s)}}class W{constructor(t,i){this.app=i;this.layerMap=t;this.tooltips=new H}render(i,s,e,o){i.canvas=o.append("canvas").style("display","none").node();i.ctx=i.canvas.getContext("2d");i.canvas.width=i.xbins;i.canvas.height=i.ybins;i.img=this.layerMap.append("image").attr("width",i.canvas.width).attr("height",i.canvas.height).attr("x",i.x).attr("y",i.y).on("click",(()=>t(this,void 0,void 0,(function*(){yield this.app.dispatch({type:"view_create",view:"chrpair",config:{x:{chr:s},y:{chr:e}}})})))).on("mouseover",(()=>{this.tooltips.render(i.img,s,e)}));if(s!=e){i.canvas2=o.append("canvas").style("display","none").node();i.canvas2.width=i.ybins;i.canvas2.height=i.xbins;i.ctx2=i.canvas2.getContext("2d");i.img2=this.layerMap.append("image").attr("width",i.canvas2.width).attr("height",i.canvas2.height).attr("x",i.y).attr("y",i.x).on("click",(()=>t(this,void 0,void 0,(function*(){yield this.app.dispatch({type:"view_create",view:"chrpair",config:{x:{chr:e},y:{chr:s}}})})))).on("mouseover",(()=>{this.tooltips.render(i.img2,e,s)}))}else{i.ctx2=i.ctx}}}class Y{constructor(t,i,s){this.grid=t;this.gridElementRenderer=new W(i,s)}render(t){for(const[i,s]of this.grid.chromosomeMatrix){for(const[e,o]of s){this.gridElementRenderer.render(o,i,e,t)}}}}class I{constructor(t){this.tip=new c;this.pica_x=new c({border:"solid 1px #ccc",padding:"0px",offsetX:0,offsetY:0});this.pica_y=new c({border:"solid 1px #ccc",padding:"0px",offsetX:0,offsetY:0});this.chr2px={};this.lead2follow=new Map;this.values=[];this.defaultChrLabWidth=100;this.borderwidth=1;this.default_maxVPerc=5;this.fontsize=15;this.xoff=0;this.yoff=0;this.binpx=1;this.atdev_chrnum=8;this.min=0;this.max=0;this.app=t.app;this.hic=t.hic;this.plotDiv=t.plotDiv;this.data=t.data;this.parent=t.parent;this.resolution=t.resolution||t.hic.bpresolution[0];this.svg=this.plotDiv.plot.append("svg").attr("data-testid","sjpp-hic-genome-svg");this.layer_map=this.svg.append("g").attr("data-testid","sjpp-hic-layerMap-g");this.layer_sv=this.svg.append("g").attr("data-testid","sjpp-hic-layerSv-g");this.colorizeElement=new z;this.viewModel=new O(t);this.viewRender=new U(this.svg,this.layer_map,this.layer_sv,this.viewModel.grid);this.gridElementsRenderer=new Y(this.viewModel.grid,this.layer_map,this.app);this.gridFormattedData=new C}makeSv(){const t=new Set;const i=8;for(const s of this.hic.sv.items){const e=this.lead2follow.get(s.chr1);if(!e){t.add(s.chr1);continue}const o=e.get(s.chr2);if(!o){t.add(s.chr2);continue}const r=s.position1/this.resolution;const a=s.position2/this.resolution;this.layer_sv.append("circle").attr("stroke","black").attr("fill","white").attr("fill-opacity",0).attr("cx",o.x+r).attr("cy",o.y+a).attr("r",i).on("mouseover",(t=>{this.tooltipSv(t,s)})).on("mouseout",(()=>{this.tip.hide()})).on("click",(()=>{this.clickSv(s)}));if(o.img2){this.layer_sv.append("circle").attr("stroke","black").attr("fill","whilte").attr("fill-opacity",0).attr("cy",o.x+r).attr("cx",o.y+a).attr("r",i).on("mouseover",(t=>{this.tooltipSv(t,s)})).on("mouseout",(()=>{this.tip.hide()})).on("click",(()=>{this.clickSv(s)}))}}}tooltipSv(t,i){this.tip.clear().show(t.clientX,t.clientY).d.append("div").text(i.chr1==i.chr2?`${i.chr1}:${i.position1}-${i.position2}`:`${i.chr1}:${i.position1}>${i.chr2}:${i.position2}`)}clickSv(t){const i=5e5;const s=600;const e="rgba(200,0,0,.1)";const o=p({x:100,y:100});o.header.text(this.hic.name+" "+(t.chr1==t.chr2?`${t.chr1}:${t.position1}-${t.position2}`:`${t.chr1}:${t.position1}>${t.chr2}:${t.position2}`));const r=[{type:d.hicstraw,file:this.hic.file,enzyme:this.hic.enzyme,maxpercentage:this.default_maxVPerc,pyramidup:1,name:this.hic.name}];if(this.hic.tklst){for(const t of this.hic.tklst){r.push(t)}}h(this.hic.genome,r);const a={holder:o.body,hostURL:this.hic.hostURL,jwt:this.hic.jwt,genome:this.hic.genome,nobox:1,tklst:r};if(t.chr1==t.chr2&&Math.abs(t.position2-t.position1)<i*2){a.chr=t.chr1;const i=Math.abs(t.position2-t.position1);a.start=Math.max(1,Math.min(t.position1,t.position2)-i);a.stop=Math.min(this.hic.genome.chrlookup[t.chr1.toUpperCase()].len,Math.max(t.position1,t.position2)+i)}else{a.chr=t.chr1;a.start=Math.max(1,t.position1-i/2);a.stop=Math.min(this.hic.genome.chrlookup[t.chr1.toUpperCase()].len,t.position1+i/2);a.width=s;a.subpanels=[{chr:t.chr2,start:Math.max(1,t.position2-i/2),stop:Math.min(this.hic.genome.chrlookup[t.chr2.toUpperCase()].len,t.position2+i/2),width:s,leftpad:10,leftborder:e}]}v(a)}render(){this.viewRender.render();this.gridElementsRenderer.render(this.hic.holder);if(this.hic.sv&&this.hic.sv.items){this.makeSv()}this.update(this.data)}update(t){this.data=t;this.min=this.parent("min");this.max=this.parent("max");for(const t of this.data){if(!this.hic.chrlst.includes(t.lead)||!this.hic.chrlst.includes(t.follow))continue;const i=this.viewModel.grid.chromosomeMatrix.get(t.lead).get(t.follow);if(!i)continue;i.ctx.clearRect(0,0,i.canvas.width,i.canvas.height);if(i.canvas2){i.ctx2.clearRect(0,0,i.canvas2.width,i.canvas.height)}i.data=this.gridFormattedData.formatData("genome",t.items,this.binpx,this.resolution);for(const[t,s,e]of i.data){this.colorizeElement.colorizeElement(t,s,e,i,this.binpx,this.binpx,this.min,this.max,"genome")}i.img.attr("xlink:href",i.canvas.toDataURL());if(i.canvas2){i.img2.attr("xlink:href",i.canvas2.toDataURL())}}this.app.dispatch({type:"loading_active",active:false})}}class X{constructor(t,i,s,e){this.holder=t;this.normalization=i;this.defaultNmeth=s;this.callback=e}render(){var i;if(!((i=this.normalization)===null||i===void 0?void 0:i.length)){this.nmethSelect=this.holder.text(this.defaultNmeth)}else{this.nmethSelect=this.holder.style("margin-right","10px").append("select").on("change",(()=>t(this,void 0,void 0,(function*(){const t=this.nmethSelect.node().value;this.callback(t,"nmeth")}))));for(const t of this.normalization){this.nmethSelect.append("option").text(t)}}}update(t){const i=this.nmethSelect.node().options;if(!i)return;const s=Array.from(i).find((i=>i.value===t));if(!s)throw`Invalid normalization method: ${t}`;s.selected=true}}class J{constructor(t,i,s){this.holder=t;this.value=i;this.callback=s}render(i){const s=this.holder.style("margin-right","10px").append("input").attr("type","number").style("width",i&&"width"in i?i.width:"80px").style("margin-left","0px").attr("type","number").property("value",this.value).on("keyup",(i=>t(this,void 0,void 0,(function*(){if(i.code!="Enter")return;const t=i.target.value;this.callback(t)}))));return s}}class Z{constructor(t,i){this.values=[{label:"Observed",value:"observed"},{label:"Expected",value:"expected"},{label:"Observed/Expected",value:"oe"},{label:"Log(Observed/Expected)",value:"log(oe)"}];this.holder=t;this.callback=i}render(){this.matrixSelect=this.holder.style("margin-right","10px").append("select").on("change",(()=>t(this,void 0,void 0,(function*(){this.callback(this.matrixSelect.node().value,"matrixType")}))));for(const t of this.values){this.matrixSelect.append("option").text(t.label).attr("value",t.value)}}update(t){const i=this.matrixSelect.node().options;if(!i)return;const s=Array.from(i).find((i=>i.value===t));if(!s)throw`Invalid normalization method: ${t}`;s.selected=true}}class G{constructor(t){this.zoomBlockCallback=t=>{const i=this.parent("detail");i.xBlock.block.zoomblock(2,t);i.yBlock.block.zoomblock(2,t)};this.minCallback=t=>{if(Number(t)>Number(this.parent("max"))){this.error("Min cutoff cannot be greater than max cutoff")}else{this.parent("min",Number(t));this.reColorHeatmap();this.parent("infoBar").update()}};this.maxCallback=t=>{if(Number(t)<Number(this.parent("min"))){this.error(`Max cutoff cannot be less than min cutoff`)}else if(Number(t)<0){this.error(`Max cutoff cannot be less than 0`)}else{this.parent("max",Number(t));this.reColorHeatmap();this.parent("infoBar").update()}};this.reColorHeatmap=()=>{if(this.parent("activeView")=="genome"){const t=this.parent("genome");const i=t.viewRender.grid.chromosomeMatrix;if(!i)return;for(const[t,s]of i){for(const[t,i]of s){if(!i)continue;for(const[t,s,e]of i.data){this.colorizeElement.colorizeElement(t,s,e,i,1,1,this.parent("min"),this.parent("max"),"genome")}i.img.attr("xlink:href",i.canvas.toDataURL());if(i.canvas2){i.img2.attr("xlink:href",i.canvas2.toDataURL())}}}}else if(this.parent("activeView")=="chrpair"){const t=this.parent("chrpair");for(const[i,s,e]of t.data){this.colorizeElement.colorizeElement(i,s,e,t.ctx,t.binpx,t.binpx,this.parent("min"),this.parent("max"),"chrpair")}}else if(this.parent("activeView")=="detail"){const t=this.parent("detail");for(const[i,s,e,o,r]of t.coords){this.colorizeElement.colorizeElement(i,s,r,t.ctx,e,o,this.parent("min"),this.parent("max"),"detail")}}};this.dropdownCallback=(t,i)=>{const s=this.app.getState();this.app.dispatch({type:"view_update",view:s.currView,config:{[i]:t}})};this.type="controlPanel";this.controls={};this.app=t.app;this.controlsDiv=t.controlsDiv;this.hic=t.hic;this.colorizeElement=new z;this.parent=t.parent;this.error=t.error}getState(t){return t}addLabel(t,i){return t.append("td").style("color","#858585").style("font-size",".8em").style("vertical-align",i.toUpperCase()=="VIEW"?"top":"middle").text(i.toUpperCase())}init(){const i=this.app.getState();const s=this.controlsDiv.style("background","rgb(253, 250, 244)").style("vertical-align","top").style("padding","5px").style("border","solid 0.5px #ccc");let e=true;this.controlsDiv.append("button").style("display","block").style("border","none").style("font-size","1.5em").style("background","none").html("&#8801;").on("click",(()=>{e=!e;o.style("display",e?"block":"none")}));const o=s.append("div").attr("class","sjpp-hic-menu").style("display",e?"block":"none");const r=o.append("table").style("border-spacing","3px");this.controls.normalizationRow=r.append("tr");this.addLabel(this.controls.normalizationRow,"NORMALIZATION");this.controls.nmeth=new X(this.controls.normalizationRow.append("td").attr("class","sjpp-nmeth-select"),this.hic.normalization,i.defaultNmeth,this.dropdownCallback);this.controls.nmeth.render();this.controls.minCutoffRow=r.append("tr");this.controls.minCutoffLabel=this.addLabel(this.controls.minCutoffRow,"");this.controls.inputBpMinV=new J(this.controls.minCutoffRow.append("td"),this.parent("min"),this.minCallback).render({width:"120px"});this.controls.maxCutoffRow=r.append("tr");this.controls.maxCutoffLabel=this.addLabel(this.controls.maxCutoffRow,"");this.controls.inputBpMaxV=new J(this.controls.maxCutoffRow.append("td"),this.parent("max"),this.maxCallback).render({width:"120px"});this.controls.matrixTypeRow=r.append("tr");this.addLabel(this.controls.matrixTypeRow,"matrix type");this.controls.matrixType=new Z(this.controls.matrixTypeRow.append("td"),this.dropdownCallback);this.controls.matrixType.render();this.controls.widthRow=r.append("tr");this.addLabel(this.controls.widthRow,"WIDTH / height");this.controls.width=this.controls.widthRow.append("td");this.controls.width.style("margin-right","10px").append("input").attr("type","number").style("width","80px").style("margin-left","0px").attr("type","number").property("value",i.width).on("keyup",(i=>t(this,void 0,void 0,(function*(){if(i.code!="Enter")return;const t=i.target.value;this.app.dispatch({type:"view_update",config:{settings:{widthHeightPx:Number.parseInt(t)}}})}))));const a=r.append("tr");this.addLabel(a,"VIEW");const h=a.append("td");this.controls.view=h.append("span").style("padding-right","5px").style("display","block");this.controls.genomeViewBtn=h.append("button").style("display","none").style("padding","2px").style("margin-top","4px").html("&#8810; Genome").on("click",(()=>t(this,void 0,void 0,(function*(){yield this.app.dispatch({type:"view_create",view:"genome",config:{x:{},y:{}}})}))));this.controls.chrpairViewBtn=h.append("button").style("display","none").style("padding","2px").style("margin","4px 0px").on("click",(()=>t(this,void 0,void 0,(function*(){const t=this.app.getState();yield this.app.dispatch({type:"view_create",view:"chrpair",config:{x:{chr:t.x.chr},y:{chr:t.y.chr}}})}))));this.controls.horizontalViewBtn=h.append("button").style("display","none").style("padding","2px").style("margin","4px 0px").html("Horizontal View &#8811;").on("click",(()=>t(this,void 0,void 0,(function*(){yield this.app.dispatch({type:"view_create",view:"horizontal"})}))));this.controls.detailViewBtn=h.append("button").style("display","none").style("padding","2px").style("margin","4px 0px").html("&#8810; Detailed View").on("click",(()=>t(this,void 0,void 0,(function*(){yield this.app.dispatch({type:"view_create",view:"detail"})}))));this.controls.zoomDiv=r.append("tr").style("display",i.currView=="detail"?"contents":"none");this.addLabel(this.controls.zoomDiv,"ZOOM");const n=this.controls.zoomDiv.append("td");this.controls.zoomIn=n.append("button").style("margin-right","10px").text("In").on("click",(()=>{this.zoomBlockCallback(false)}));this.controls.zoomOut=n.append("button").style("margin-right","10px").text("Out").on("click",(()=>{this.zoomBlockCallback(true)}))}showBtns(){const t=this.app.getState();this.controls.genomeViewBtn.style("display",t.currView==="genome"?"none":"inline-block");if(t.currView==="detail"){this.controls.chrpairViewBtn.html(`&#8810; Entire ${t.x.chr}-${t.y.chr}`).style("display","block");this.controls.horizontalViewBtn.style("display","block");this.controls.zoomDiv.style("display","contents");this.controls.detailViewBtn.style("display","none")}else if(t.currView==="horizontal"){this.controls.chrpairViewBtn.html(`&#8810; Entire ${t.x.chr}-${t.y.chr}`).style("display","block");this.controls.detailViewBtn.style("display","block");this.controls.horizontalViewBtn.style("display","none");this.controls.zoomDiv.style("display","none")}else{this.controls.chrpairViewBtn.style("display","none");this.controls.horizontalViewBtn.style("display","none");this.controls.detailViewBtn.style("display","none");this.controls.zoomDiv.style("display","none");this.controls.widthRow.style("display","none")}}showHideControls(){const t=this.app.getState();this.controls.normalizationRow.style("display",t.currView=="horizontal"?"none":"");this.controls.minCutoffRow.style("display",t.currView=="horizontal"?"none":"");this.controls.maxCutoffRow.style("display",t.currView=="horizontal"?"none":"");this.controls.matrixTypeRow.style("display",t.currView=="horizontal"?"none":"");this.controls.widthRow.style("display",t.currView=="detail"?"contents":"none")}main(t){const i=this.app.getState(t);this.controls.nmeth.update(i[i.currView].nmeth);this.controls.matrixType.update(i[i.currView].matrixType);this.controls.zoomDiv.style("display",i.currView=="detail"?"contents":"none");if(i.currView=="chrpair"){this.controls.view.text(`${i.x.chr}-${i.y.chr} Pair`)}else{this.controls.view.text(i.currView.charAt(0).toUpperCase()+i.currView.slice(1))}const s=this.parent("absMin")<1e-5?Number(this.parent("absMin")).toExponential(1):Number(this.parent("absMin").toFixed(6));const e=this.parent("absMax")<1e-5?Number(this.parent("absMax")).toExponential(1):Number(this.parent("absMax").toFixed(6));this.controls.width.select("input").property("value",i.settings.widthHeightPx);this.controls.inputBpMinV.property("value",this.parent("min"));this.controls.inputBpMaxV.property("value",this.parent("max"));this.controls.minCutoffLabel.html(`MIN CUTOFF <br>(>= ${s})`);this.controls.maxCutoffLabel.html(`MAX CUTOFF <br>(<= ${e})`);this.showBtns();this.showHideControls()}}const q=s(G);class K{constructor(t){this.startColor="white";this.endColor="red";this.addLabel=t=>this.labelRow.append("td").style("color","#858585").style("font-size",".8em").style("text-align","center").style("vertical-align","middle").text(t.toUpperCase());this.addValue=t=>this.valueRow.append("td").style("font-size","1em").style("text-align","center").style("vertical-align","middle").text(t);this.type="infoBar";this.app=t.app;this.hic=t.hic;const i=t.infoBarDiv;this.labelRow=i.append("tr");this.valueRow=i.append("tr");this.parent=t.parent}render(){return t(this,void 0,void 0,(function*(){this.addLabel("Version");this.addValue(this.hic.version);this.addLabel("Enzyme");this.addValue(this.hic.enzyme||"N/A");this.addLabel("Resolution");this.resolutionDiv=this.addValue("");this.colorScaleLabel=this.addLabel("Scale");this.colorScaleDiv=this.valueRow.append("td");this.colorScale=new w({barheight:14,barwidth:85,data:[this.parent("min"),this.parent("max")],fontSize:12,height:35,width:120,holder:this.colorScaleDiv,startColor:this.startColor,endColor:this.endColor,position:"20,0",ticks:2,tickSize:3,markedValue:1});this.colorScale.render();this.update()}))}update(){const t=this.parent("calcResolution");let i;if(t<this.hic.bpresolution[this.hic.bpresolution.length-1]){i=`${t} fragment${t>1?"s":""}`}else{i=u(t)}this.resolutionDiv.text(i);if(this.parent("state").currView=="horizontal"){this.colorScaleLabel.style("display","none");this.colorScaleDiv.style("display","none")}else{this.colorScaleLabel.style("display","");this.colorScaleDiv.style("display","");const t=this.parent("min");const i=this.parent("max");if(t<0){this.colorScale.startColor="blue";this.colorScale.data=[t,i]}else{this.colorScale.startColor="white";this.colorScale.data=[0,i]}this.colorScale.markedValue=t;this.colorScale.updateScale()}}}class Q{constructor(t,i){this.hic=t;this.percentile=i?i/100:.99}sortData(t){const i=[];if((t===null||t===void 0?void 0:t.items)&&(t===null||t===void 0?void 0:t.items.length)){for(const s of t.items){i.push(s[2])}}else{const s=new Set;for(const e of t){if(e.lead=="chrM"&&!e.items.length||e.lead=="chrY"&&!e.items.length){s.add(e.lead);continue}for(const t of e.items){i.push(t[2])}}if(s.size){for(const t of s){const i=this.hic.chrlst.indexOf(t);this.hic.chrlst.splice(i,1)}}}const s=i.sort(((t,i)=>t-i));const e=s[Math.floor(s.length*this.percentile)];const o=s[0];return[o,e,s[s.length-1]]}}class tt{constructor(t,i,s=[]){this.data=[];this.hic=t;this.debugmode=i;this.errList=s||[]}getData(i){return t(this,void 0,void 0,(function*(){if(this.data.length)this.data=[];if(!(i===null||i===void 0?void 0:i.matrixType))i.matrixType="observed";try{const t=yield n("hicgenome?",{method:"POST",body:JSON.stringify({chrlst:this.hic.chrlst,nmeth:i.nmeth,resolution:i.resolution,matrixType:i.matrixType,file:this.hic.file,url:this.hic.url,nochr:this.hic.nochr})});if(t.error){const i=t.error.split("\n");for(const t of i){this.errList.push(t)}}return t.data}catch(t){this.errList.push(t.message||t);if(t.stack)console.error(t.stack)}}))}}class it{constructor(t,i,s=[]){this.hic=t;this.debugmode=i;this.errList=s||[]}getData(i){return t(this,void 0,void 0,(function*(){if(!(i===null||i===void 0?void 0:i.matrixType))i.matrixType="observed";const t={matrixType:i.matrixType,file:this.hic.file,url:this.hic.url,pos1:this.hic.nochr?i.lead.replace("chr",""):i.lead,pos2:this.hic.nochr?i.follow.replace("chr",""):i.follow,nmeth:i.nmeth,resolution:i.resolution};try{const s=yield n("hicdata?",{method:"POST",body:JSON.stringify(t)});if(s.error){throw Error(`${i.lead} - ${i.follow}: ${s.error.error}`)}if(!s.items||s.items.length==0)return;return s}catch(t){this.errList.push(t.message||t);if(t.stack)console.error(t.stack)}}))}}class st{constructor(t){this.components={controls:[]};this.genomeData=[];this.calcResolution=null;this.firstRender=true;this.min=0;this.absMin=0;this.max=0;this.absMax=0;this.hasStatePreMain=true;this.type="view";this.hic=t.hic;this.state=t.state;this.dom=t.dom;this.errList=t.errList;this.plotDiv=this.dom.plotDiv.append("table").classed("sjpp-hic-plot-main",true);const i=this.plotDiv.append("tr");const s=this.plotDiv.append("tr");this.plotDiv={plot:i.append("td").classed("sjpp-hic-plot",true).attr("data-testid","sjpp-hic-plot"),yAxis:i.append("td").classed("sjpp-hic-plot-yaxis",true).attr("data-testid","sjpp-hic-yaxis"),xAxis:s.append("td").classed("sjpp-hic-plot-xaxis",true).attr("data-testid","sjpp-hic-xaxis"),blank:s.append("td")};this.app=t.app;this.dataMapper=new Q(this.hic,t.state.maxCutoffPercentile);this.activeView=this.state.currView;this.error=t.error;this.resolution=new R(this.error);this.parent=t=>this[t];this.detailDataMapper=new _(this.hic,this.errList,this.parent)}getState(t){return t}reactsTo(t){if(t.type.startsWith("view"))return true;else return false}initView(){const t={plotDiv:this.plotDiv,hic:this.hic,app:this.app,parent:t=>this[t]};if(this.state.currView=="genome"){t["data"]=this.data;this.genome=new I(t);this.genome.render()}else if(this.state.currView==="chrpair"){t["items"]=this.data;this.chrpair=new S(t);this.chrpair.render()}else if(this.state.currView==="detail"){t["data"]=this.data;this.detail=new F(t);this.detail.render()}else if(this.state.currView==="horizontal"){this.horizontal=new B(t);this.horizontal.render()}else{throw Error(`Unknown view: ${this.state.currView}`)}}fetchData(i){var s,e,o,r,a,h;return t(this,void 0,void 0,(function*(){if((s=this.data)===null||s===void 0?void 0:s.length)this.data=[];if(this.state.currView=="genome"){if(this.activeView!="genome"&&((e=this.genomeData)===null||e===void 0?void 0:e.length))this.data=this.genomeData;else{const t=new tt(this.hic,true,this.errList);this.genomeData=yield t.getData(i);this.data=this.genomeData}}else if(this.state.currView=="detail"){this.data=yield this.detailDataMapper.getData(this.state.x,this.state.y,this.fragData)}else{if(!((r=(o=this.state)===null||o===void 0?void 0:o.x)===null||r===void 0?void 0:r.chr)||!((h=(a=this.state)===null||a===void 0?void 0:a.y)===null||h===void 0?void 0:h.chr)){this.errList.push(`No positions provided for ${this.activeView} view.`);return}else{const t=this.state.x;const s=this.state.y;i["lead"]=`${t.start&&t.stop?`${t.chr}:${t.start}-${t.stop}`:t.chr}`;i["follow"]=`${s.start&&s.stop?`${s.chr}:${s.start}-${s.stop}`:s.chr}`}const t=new it(this.hic,true,this.errList);this.data=yield t.getData(i)}}))}setResolution(i){return t(this,void 0,void 0,(function*(){const t=this.app.getState(i);this.calcResolution=this.resolution.getResolution(t,this.hic);if(t.currView=="detail"&&this.calcResolution==null){yield this.detailDataMapper.getFragData(t.x,t.y);this.fragData=this.detailDataMapper.frag;const i=Math.min(this.fragData.x.stop-this.fragData.x.start,this.fragData.y.stop-this.fragData.y.start);this.calcResolution=this.resolution.findResFromArray(i,t.minFragSpan,this.hic.fragresolution,true)}else{this.fragData=null}return this.calcResolution}))}setDataArgs(i){return t(this,void 0,void 0,(function*(){const t=this.app.getState(i);const s=t[t.currView];const e={nmeth:s.nmeth,resolution:yield this.setResolution(i),matrixType:s.matrixType};if(t.currView=="chrpair"){e["lead"]=t.x.chr;e["follow"]=t.y.chr}return e}))}getViewData(i){var s,e,o,r,a;return t(this,void 0,void 0,(function*(){const t=yield this.setDataArgs(i);yield this.fetchData(t);if(((s=this.data)===null||s===void 0?void 0:s.length)>0||((o=(e=this.data)===null||e===void 0?void 0:e.items)===null||o===void 0?void 0:o.length)>0){const[t,i,s]=this.dataMapper.sortData(this.data);this.min=this.absMin=t;this.max=i;this.absMax=s}else{if(this.state.currView!="genome"){const t=this.app.getState(i);const s=((r=t.x)===null||r===void 0?void 0:r.start)?`${t.x.chr}:${t.x.start}-${t.x.stop}`:t.x.chr;const e=((a=t.y)===null||a===void 0?void 0:a.start)?`${t.y.chr}:${t.y.start}-${t.y.stop}`:t.y.chr;this.errList.push(`No data returned for ${s} and ${e}`)}}}))}init(){return t(this,void 0,void 0,(function*(){this.components={controls:yield q({app:this.app,controlsDiv:this.dom.controlsDiv,hic:this.hic,parent:(t,i)=>{if(i)this[t]=i;return this[t]},error:this.error.bind(this)})};this.infoBar=new K({app:this.app,infoBarDiv:this.dom.infoBarDiv.append("table").style("border-spacing","3px"),hic:this.hic,parent:t=>this[t]});this.infoBar.render()}))}main(i){return t(this,void 0,void 0,(function*(){if(this.errList.length){this.app.dispatch({type:"loading_active",active:false});return}const t=this.app.getState(i);if(this.firstRender==true){this.firstRender=false;yield this.getViewData(i);this.initView()}else{if(t.currView!="horizontal"){this.app.dispatch({type:"loading_active",active:true});yield this.getViewData(i)}if(this.activeView!=t.currView){if(this.activeView=="genome"){this.genome.svg.remove()}else{this.plotDiv.xAxis.selectAll("*").remove();this.plotDiv.yAxis.selectAll("*").remove();this.plotDiv.plot.selectAll("*").remove()}this.activeView=t.currView;this.initView()}else{this[t.currView].update(this.data)}}this.infoBar.update();if(this.errList.length){this.error(this.errList);this.app.dispatch({type:"loading_active",active:false})}}))}}const et=s(st);class ot{constructor(t){this.views=["genome","chrpair","detail","horizontal"];this.errList=[];this.type="app";this.hic={enzyme:t.enzyme,file:t.file,url:t.url,genome:t.genome,holder:t.holder,hostUrl:t.hostUrl,jwt:t.jwt,position1:t.position1,position2:t.position2,maxCutoffPercentile:t.maxCutoffPercentile,name:"name"in t?t.name:"Hi-C",tklist:"tklst"in t?t.tklst:[],state:"state"in t?t.state:{}};this.dom={errorDiv:t.holder.append("div").classed("sjpp-hic-error",true),controlsDiv:t.holder.append("div").classed("sjpp-hic-controls",true).style("display","inline-block"),infoBarDiv:t.holder.append("div").classed("sjpp-hic-infobar",true).style("display","inline-block").style("vertical-align","top").style("padding","5px").style("border","solid 0.5px #ccc"),loadingDiv:l("body").append("div").attr("id","sjpp-loading-overlay"),plotDiv:t.holder.append("div").classed("sjpp-hic-main",true).style("display","inline-block"),tip:new c}}error(i){return t(this,void 0,void 0,(function*(){if(i&&typeof i=="string")this.errList.push(i);m(this.errList,this.dom.errorDiv);this.errList=[]}))}determineView(){if(!this.hic.position1&&!this.hic.position2&&!this.hic.state.currView)this.hic.state.currView="genome";if(!this.hic.position1&&this.hic.position2)this.errList.push("Missing first position");if(this.hic.position1&&!this.hic.position2)this.errList.push("Missing second position");if(this.hic.position1&&this.hic.position2){const t=this.hic.position1.split(/[:-]/);const i=this.hic.position2.split(/[:-]/);this.hic.state.x={chr:t[0]};this.hic.state.y={chr:i[0]};if(!Number.isNaN(+t[1])&&!Number.isNaN(+t[2])){this.hic.state.x.start=+t[1];this.hic.state.x.stop=+t[2];this.hic.state.y.start=+i[1];this.hic.state.y.stop=+i[2];this.hic.state.currView="detail"}else{this.hic.state.currView="chrpair"}}else{if(!this.views.some((t=>t===this.hic.state.currView)))this.error(`Unknown view: ${this.hic.state.currView}`);else return this.hic.state.currView}}getViewsConfig(){var t,i,s;if(this.hic.maxCutoffPercentile)this.hic.state.maxCutoffPercentile=this.hic.maxCutoffPercentile;let e;if(((t=this.hic["normalization"])===null||t===void 0?void 0:t.length)>0){if(!this.hic["normalization"].includes("NONE"))this.hic["normalization"].unshift("NONE");e=this.hic["normalization"][0]}else{e="NONE"}if(this.hic.state.currView){if(!this.hic.state[this.hic.state.currView])this.hic.state[this.hic.state.currView]={};if(!((i=this.hic.state[this.hic.state.currView])===null||i===void 0?void 0:i.matrixType)){this.hic.state[this.hic.state.currView].matrixType="observed"}if(!((s=this.hic.state[this.hic.state.currView])===null||s===void 0?void 0:s.nmeth)){this.hic.state[this.hic.state.currView].nmeth=e}}for(const t of this.views){if(!this.hic.state[t]){this.hic.state[t]={matrixType:"observed",nmeth:e}}}}init(){return t(this,void 0,void 0,(function*(){this.determineView();try{yield b(this.hic,true,this.errList);this.getViewsConfig();this.store=yield D({app:this.api,state:this.hic.state});this.state=yield this.store.copyState();this.components={loadingOverlay:yield V({app:this.api,loadingDiv:this.dom.loadingDiv}),view:yield et({app:this.api,state:this.state,dom:this.dom,hic:this.hic,errList:this.errList,error:this.error})};yield this.api.dispatch()}catch(t){console.error(t.stack||t)}}))}main(){if(this.errList.length){this.error(this.errList);this.dom.loadingDiv.style("display","none");return}}}const rt=f(ot);export{rt as hicInit};
+import{_ as t}from"./tslib.es6-c3c2d88f.js";import{m as i,h as s,ah as e,ag as o,I as r,W as a,f as h,b as n,d as l,M as c,Z as p,ad as d,ae as u,o as f,ai as m}from"./app-0de0ae35.js";import{d as g,a as y}from"./axis-747c801e.js";import{p as x}from"./pointer-c7475677.js";import{b as v}from"./block.lazyload-19a55cac.js";import{C as w}from"./ColorScale-23c17654.js";import{h as b}from"./parseData-05ab5f81.js";import"./axisstyle-fac7f76b.js";class k{constructor(){this.views=["genome","chrpair","detail","horizontal"];this.type="store";this.defaultState={defaultNmeth:"NONE",loading:true,minBinNum_bp:200,minFragSpan:200,initialBinNum:20,settings:{widthHeightPx:800}}}}const D=i(k);k.prototype.actions={view_create(t){if(!t.view)throw Error("view_create: missing view");if(!this.views.some((i=>i==t.view)))throw Error(`view_create: unknown view = ${t.view}`);this.state.currView=t.view;const i=Object.assign(this.state,t.config);this.state=i},view_update(t){if(t.view){if(!this.views.some((i=>i==t.view)))throw Error(`view_update: unknown view = ${t.view}`);const i=Object.assign(this.state[t.view],t.config);this.state[t.view]=i}else{const i=Object.assign(this.state,t.config);this.state=i}},loading_active(t){this.state.loading=t.active}};class M{constructor(t){this.hasStatePreMain=true;this.type="loadingOverlay",this.app=t.app,this.loadingDiv=t.loadingDiv}reactsTo(t){if(t.type.startsWith("loading"))return true;else return false}getState(t){return t}init(){this.loadingDiv.append("div").attr("class","sjpp-spinner").style("display","")}main(t){const i=this.app.getState(t).loading;this.loadingDiv.style("display",i?"":"none")}}const V=s(M);class z{colorizeElement(t,i,s,e,o,r,a,h,n){if(s>=0){const t=s>=h?0:s<=a?255:Math.floor(255*(h-s)/h);const i=`rgb(255, ${t}, ${t})`;if(n==="genome"){e.ctx.fillStyle=i;e.ctx2.fillStyle=i}else{e.fillStyle=i}}else{const t=s<=a?255:Math.floor(255*(h+s)/h);const i=`rgb(${t}, ${t}, 255)`;if(n==="genome"){e.ctx.fillStyle=i;e.ctx2.fillStyle=i}else{e.fillStyle=i}}if(n==="genome"){e.ctx.fillRect(i,t,o,r);e.ctx2.fillRect(t,i,o,r)}else{e.fillRect(t,i,o,r)}}}class R{constructor(t){this.error=t}getResolution(t,i){if(t.currView=="genome")return i["bpresolution"][0];if(t.currView=="chrpair"){const s=this.getChrPairResolution(i,t.x,t.y,t.minBinNum_bp);return s}else if(t.currView=="detail"){const s=Math.max(t.x.stop-t.x.start,t.y.stop-t.y.start);let e=this.findResFromArray(s,t.minBinNum_bp,i.bpresolution);if(e==null&&!i.enzyme){e=i.bpresolution[i.bpresolution.length-1]}return e}else{this.error(`Unknown view: ${t.currView}`);throw`Unknown view: ${t.currView}`}}getChrPairResolution(t,i,s,e){const o=t.genome.chrlookup[i.chr.toUpperCase()].len;const r=t.genome.chrlookup[s.chr.toUpperCase()].len;const a=Math.max(o,r);const h=this.findResFromArray(a,e,t.bpresolution);if(h==null){this.error(`No suitable resolution for ${i.chr}-${s.chr} pair.`);return}return h}findResFromArray(t,i,s,e){let o=null;for(const e of s){if(t/e>i){o=e;break}}if(e&&o==null){o=s[s.length-1]}return o}getDefaultViewSpan(t,i,s,e,o){const r=this.getChrPairResolution(t,i,s,o);if(!r)return;return r*e}}class ${constructor(t,i){this.error=t;this.resolution=new R(this.error);this.minBinNum_bp=i}setPosition(t,i,s,e,o,r,a){const h=this.resolution.getChrPairResolution(r,e,o,this.minBinNum_bp);const n=h*a;let l=Math.max(1,Math.floor(t*h/s)-n/2);let c=Math.max(1,Math.floor(i*h/s)-n/2);{const t=r.genome.chrlookup[e.chr.toUpperCase()].len;if(l+n>=t){l=t-n}const i=r.genome.chrlookup[o.chr.toUpperCase()].len;if(c+n>i){c=i-n}}const p={chr:e.chr,start:l,stop:l+n};const d={chr:o.chr,start:c,stop:c+n};return[p,d]}}class C{formatData(t,i,s,e,o,r){const a=[];for(const[h,n,l]of i){const i=Math.floor(h/e)*s;const c=Math.floor(n/e)*s;if(t=="genome"){a.push([i,c,l])}if(t=="chrpair"){const t=o?i:c;const s=o?c:i;a.push([t,s,l]);if(r){a.push([s,t,l])}}}return a}}class L{constructor(t,i,s){this.chrorder=t;this.chrx=i;this.chry=s}isFirstX(){if(this.chrx==this.chry)return true;return this.chrorder.indexOf(this.chrx)<this.chrorder.indexOf(this.chry)}}class S{constructor(t){this.binpx=1;this.axispad=10;this.axisLabelFontSize=15;this.calcResolution=null;this.data=[];this.app=t.app;this.hic=t.hic;this.plotDiv=t.plotDiv;this.items=t.items;this.parent=t.parent;this.chrxlen=this.hic.genome.chrlookup[this.parent("state").x.chr.toUpperCase()].len;this.chrylen=this.hic.genome.chrlookup[this.parent("state").y.chr.toUpperCase()].len;this.maxchrlen=Math.max(this.chrxlen,this.chrylen);this.colorizeElement=new z;this.positions=new $(t.error,this.parent("state").minBinNum_bp);this.formattedData=new C}setDefaultBinpx(){if(this.calcResolution==null)return;while(this.binpx*this.maxchrlen/this.calcResolution<600){this.binpx++}}renderAxes(){if(this.calcResolution==null)return;const t=this.plotDiv.yAxis.append("svg");const i=Math.ceil(this.chrylen/this.calcResolution)*this.binpx;t.attr("width",100).attr("height",this.axispad*2+i);t.append("g").attr("data-testid","sjpp-chrpair-svg-y").attr("transform","translate(80,"+(this.axispad+i/2)+")").append("text").text(this.parent("state").y.chr).attr("text-anchor","middle").attr("font-size",this.axisLabelFontSize).attr("font-family",e).attr("dominant-baseline","central").attr("transform","rotate(90)");o({axis:t.append("g").attr("transform",`translate(1, ${this.axispad})`).call(g(r().domain([0,this.chrylen]).range([0,i])).tickFormat(a(".2s"))),showline:true});const s=this.plotDiv.xAxis.append("svg").style("margin-top","-4px");const h=Math.ceil(this.chrxlen/this.calcResolution)*this.binpx;s.attr("height",100).attr("width",this.axispad*2+h);s.append("text").attr("data-testid","sjpp-chrpair-svg-x").text(this.parent("state").x.chr).attr("font-size",this.axisLabelFontSize).attr("font-family",e).attr("x",this.axispad+h/2).attr("text-anchor","middle").attr("y",60);o({axis:s.append("g").attr("transform","translate("+this.axispad+",1)").call(y(r().domain([0,this.chrxlen]).range([0,h])).tickFormat(a(".2s"))),showline:true})}renderCanvas(){const i=this.initDetailView.bind(this);this.canvas=this.plotDiv.plot.append("canvas").attr("data-testid","sjpp-chrpair-canvas").style("margin",this.axispad+"px").on("click",(function(s){return t(this,void 0,void 0,(function*(){const[t,e]=x(s,this);i(t,e)}))})).node();this.canvas.width=Math.ceil(this.chrxlen/this.calcResolution)*this.binpx;this.canvas.height=Math.ceil(this.chrylen/this.calcResolution)*this.binpx;this.ctx=this.canvas.getContext("2d")}initDetailView(t,i){const[s,e]=this.positions.setPosition(t,i,this.binpx,this.parent("state").x,this.parent("state").y,this.hic,this.parent("state").initialBinNum);this.app.dispatch({type:"view_create",view:"detail",config:{x:s,y:e}})}render(){this.calcResolution=this.parent("calcResolution");this.setDefaultBinpx();this.renderAxes();this.renderCanvas();this.update(this.items)}update(t){this.items=t;const i=new L(this.hic.chrorder,this.parent("state").x.chr,this.parent("state").y.chr).isFirstX();const s=this.parent("state").x.chr===this.parent("state").y.chr;this.data=this.formattedData.formatData("chrpair",t.items,this.binpx,this.calcResolution,i,s);this.ctx.clearRect(0,0,this.canvas.width,this.canvas.height);for(const[t,i,s]of this.data){this.colorizeElement.colorizeElement(t,i,s,this.ctx,this.binpx,this.binpx,this.parent("min"),this.parent("max"),"chrpair")}this.app.dispatch({type:"loading_active",active:false})}}class B{constructor(t){this.maxPercentage=5;this.subPanelPxWidth=600;this.borderColor="rgba(200,0,0,.1)";this.app=t.app;this.hic=t.hic;this.plotDiv=t.plotDiv;this.items=t.items;this.parent=t.parent}setRunPpTracks(){const t=[{type:"hicstraw",file:this.hic.file,url:this.hic.url,name:this.hic.name,enzyme:this.hic.enzyme,maxpercentage:this.maxPercentage,pyramindup:1}];if(this.hic.tklst){for(const i of this.hic.tklst){t.push(i)}}h(this.hic.genome,t);return t}setRunPpArgs(t){const i={holder:this.plotDiv.plot,hostURL:this.hic.hostURL,jwt:this.hic.jwt,genome:this.hic.genome,nobox:1,tklst:t};const s=this.parent("state");if(s.x.chr==s.y.chr&&Math.max(s.x.start,s.y.start)<Math.min(s.x.stop,s.y.stop)){i["chr"]=s.x.chr;i["start"]=Math.min(s.x.start,s.y.start);i["stop"]=Math.max(s.x.stop,s.y.stop)}else{i["chr"]=s.x.chr;i["start"]=s.x.start;i["stop"]=s.x.stop;i["width"]=this.subPanelPxWidth;i["subpanels"]=[{chr:s.y.chr,start:s.y.start,stop:s.y.stop,width:this.subPanelPxWidth,leftpad:10,leftborder:this.borderColor}]}return i}render(){const t=this.setRunPpTracks();const i=this.setRunPpArgs(t);v(i)}}class N{constructor(t,i,s,e,o,r){this.leftheadw=20;this.rightheadw=40;this.lpad=1;this.rpad=1;this.firstRender=true;this.app=t;this.hic=i;this.width=s;this.bbmargin=e;this.holder=o;this.isYblock=r;this.bbw=this.leftheadw+this.lpad+this.width+this.rpad+this.rightheadw+2*this.bbmargin;this.defaultLeft=this.bbmargin+this.leftheadw+this.lpad;this.defaultTop=this.bbmargin+this.rightheadw+this.rpad}setArgs(t){const i={hostURL:this.hic.hostURL,genome:this.hic.genome,holder:this.holder,noresize:true,nobox:true,butrowbottom:true,style:{margin:`${this.bbmargin}px`},width:this.width,leftheadw:this.leftheadw,chr:t.chr,start:t.start,stop:t.stop,rightheadw:this.rightheadw,tklst:[],rotated:this.isYblock,showreverse:this.isYblock};h(this.hic.genome,i.tklst);return i}setMethods(t,i,s){const e={onloadalltk_always:()=>{this.onload(t,i,s)},onpanning:t=>this.onpanning(t,i)};if(this.isYblock){e["onsetheight"]=t=>{this.holder.transition().style("left",`${t+this.bbmargin+30}px`)}}return e}onload(t,i,s){this.bbw=this.block.leftheadw+this.block.lpad+this.block.width+this.block.rpad+this.block.rightheadw+2*this.bbmargin;if(this.isYblock){s.transition().style("height",`${this.bbw}px`);t.style("height",`${this.bbw}px`)}else t.style("width",`${this.bbw}px`);if(this.isYblock){this.defaultTop=this.bbmargin+this.block.rightheadw+this.block.rpad;i.style("top",`${this.defaultTop}px`)}else{this.defaultLeft=this.bbmargin+this.block.leftheadw+this.block.lpad;i.style("left",`${this.defaultLeft}px`)}const e={[this.isYblock?"y":"x"]:{chr:this.block.rglst[0].chr,start:this.block.rglst[0].start,stop:this.block.rglst[0].stop}};if(this.firstRender==false){this.app.dispatch({type:"view_update",config:e})}else{this.firstRender=false}}onpanning(t,i){if(!this.isYblock)i.style("left",`${t+this.defaultLeft}px`);else i.style("top",`${-t+this.defaultTop}px`)}loadBlock(i,s,e,o){return t(this,void 0,void 0,(function*(){const r=this.setArgs(i);const a=this.isYblock?this.setMethods(s,e,o):this.setMethods(s,e);const h=Object.assign(r,a);yield v(h).then((i=>t(this,void 0,void 0,(function*(){this.block=i}))))}))}}class P{constructor(t){this.obj={rglst:[]};this.errList=t}isFragData(t,i){if(i!=null)return;if(!t.enzyme){i=t.bpresolution[t.bpresolution.length-1];return}}formatFragArgs(t,i){const s={getdata:1,getBED:1,file:t,rglst:[i]};return s}getBedData(i){return t(this,void 0,void 0,(function*(){try{return yield n("tkbedj",{method:"POST",body:JSON.stringify(i)})}catch(t){this.errList.push(t.message||t);if(t.stack)console.error(t.stack)}}))}getXFragData(i,s,e){return t(this,void 0,void 0,(function*(){this.isFragData(i,s);if(!i.enzymefile)return;const t=this.formatFragArgs(i.enzymefile,e);return yield this.getBedData(t)}))}getYFragData(i,s){return t(this,void 0,void 0,(function*(){const t=this.formatFragArgs(i.enzymefile,s);return yield this.getBedData(t)}))}fetchData(i,s,e,o,r,a){return t(this,void 0,void 0,(function*(){const t={matrixType:s.matrixType,file:i.file,url:i.url,pos1:this.determinePosition(i,o,a===null||a===void 0?void 0:a.x),pos2:this.determinePosition(i,r,a===null||a===void 0?void 0:a.y),nmeth:s.nmeth,resolution:e};if(a)t["isfrag"]=true;try{const i=n("hicdata?",{method:"POST",body:JSON.stringify(t)});if(i.error){this.errList.push(i.error)}return i}catch(t){this.errList.push(t.message||t);if(t.stack)console.error(t.stack)}}))}determinePosition(t,i,s){if(s){return`${t.nochr?i.chr.replace("chr",""):i.chr}:${s.start}:${s.stop}`}else{return`${t.nochr?i.chr.replace("chr",""):i.chr}:${i.start}:${i.stop}`}}}class E{constructor(t,i){this.id2coord=new Map;this.min=null;this.max=null;this.items=[];this.errLst=t;for(const t of i){if(!t.rest||!t.rest[0]){this.errLst.push("items[].rest data problem")}const i=Number.parseInt(t.rest[0]);if(Number.isNaN(i)){this.errLst.push(`${t.start}.${t.stop} invalid fragment id: ${t.rest[0]}`)}this.id2coord.set(i,[t.start,t.stop]);if(this.min==null){this.min=i;this.max=i}else{this.min=Math.min(this.min,i);this.max=Math.max(this.max,i)}}}}class _{constructor(t,i,s){this.frag={x:{},y:{}};this.hic=t;this.errList=i;this.dataFetcher=new P(i);this.parent=s}getFragData(i,s){return t(this,void 0,void 0,(function*(){try{const t=yield this.dataFetcher.getXFragData(this.hic,this.parent("calcResolution"),i);if(t){if(!t.items){this.errList.push(`No fragment data returned for ${i.chr}:${i.start}-${i.stop}`);return}const e=new E(this.errList,t.items);if(this.errList.length)return;this.frag.x={id2coord:e.id2coord,start:e.min,stop:e.max};const o=yield this.dataFetcher.getYFragData(this.hic,s);if(this.errList.length)return;if(o){if(!o.items){this.errList.push(`No fragment data returned for ${s.chr}:${s.start}-${s.stop}`);return}const t=new E(this.errList,o.items);if(this.errList.length)return;this.frag.y={id2coord:new Map,start:t.min,stop:t.max};this.determineMap(t.id2coord,i,s)}}}catch(t){this.errList.push(t.message||t);if(t.stack)console.error(t.stack)}}))}determineMap(t,i,s){if(i.chr==s.chr){for(const[i,s]of t){this.frag.x["id2coord"].set(i,s)}this.frag.y["id2coord"]=this.frag.x["id2coord"]}else{this.frag.y["id2coord"]=t}}getData(i,s,e){return t(this,void 0,void 0,(function*(){return yield this.dataFetcher.fetchData(this.hic,this.parent("state")["detail"],this.parent("calcResolution"),i,s,e)}))}}class j{constructor(t,i){this.hic=t;this.errlist=i}getCoordinates(t,i,s,e,o,r){const a=new L(this.hic.chrorder,t.chr,i.chr).isFirstX();const h=t.chr==i.chr;const n=o/(t.stop-t.start);const l=o/(i.stop-i.start);const c=this.calculateCoordinates(a,h,n,l,e,t,i,s,r);return c}calculateCoordinates(t,i,s,e,o,r,a,h,n){const l=[];for(const[c,p,d]of h.items){let h,u,f,m;if(n){const i=t?c:p;const s=t?p:c;if(n.x.id2coord.has(i)){const[t,s]=n.x.id2coord.get(i);h=t;f=s-t}else{this.errlist.push(`[x id error] x: ${i} y: ${s}`);continue}{const t=i+o;if(n.x.id2coord.has(t)){const[i,s]=n.x.id2coord.get(t);f=s-h}}if(n.y.id2coord.has(s)){const[t,i]=n.y.id2coord.get(s);u=t;m=i-t}else{this.errlist.push(`[y id error] x: ${i} y: ${s}`);continue}{const t=s+o;if(n.y.id2coord.has(t)){const[i,s]=n.y.id2coord.get(t);m=s-u}}}else{h=t?c:p;u=t?p:c;f=o;m=o}if(i){if(h>r.start-f&&h<r.stop&&u>a.start-m&&u<a.stop){l.push([Math.floor((h-r.start)*s),Math.floor((u-a.start)*e),Math.ceil(f*s),Math.ceil(m*e),d])}if(u>r.start-m&&u<r.stop&&h>a.start&&h<a.stop){l.push([Math.floor((u-r.start)*s),Math.floor((h-a.start)*e),Math.ceil(m*s),Math.ceil(f*e),d])}continue}l.push([Math.floor((h-r.start)*s),Math.floor((u-a.start)*e),Math.ceil(f*s),Math.ceil(m*e),d])}return l}}class F{constructor(t){this.calcResolution=null;this.binpx=2;this.bbmargin=1;this.app=t.app;this.hic=t.hic;this.plotDiv=t.plotDiv;this.sheath=t.plotDiv.yAxis.append("div").style("position","relative").style("width","200px").style("height","800px");this.rotor=this.sheath.append("div").style("position","absolute").style("bottom","0px").style("transform","rotate(-90deg)").style("transform-origin","left bottom");this.data=t.data;this.parent=t.parent;this.errList=this.parent("errList");this.resolution=new R(t.error);this.colorizeElement=new z;this.viewRangeBpW=this.resolution.getDefaultViewSpan(this.hic,this.parent("state").x,this.parent("state").y,this.parent("state").initialBinNum,this.parent("state").minBinNum_bp);this.dataMapper=new _(this.hic,t.error,t.parent);this.coordinates=new j(this.hic,this.errList)}renderCanvas(t){this.canvasHolder=this.plotDiv.plot.append("div").style("position","relative").style("width",`${this.xBlock.bbw}px`).style("height",`${this.yBlock.bbw}px`).style("overflow","hidden");this.canvas=this.canvasHolder.append("canvas").style("display","block").style("position","absolute").attr("data-testid","sjpp-hic-detail-canvas").attr("width",t).attr("height",t).on("mousedown",(t=>{const i=l(document.body);const s=t.clientX;const e=t.clientY;const o=Number.parseInt(this.canvas.style("left"));const r=Number.parseInt(this.canvas.style("top"));i.on("mousemove",(t=>{const i=t.clientX-s;const a=t.clientY-e;this.xBlock.block.panning(i);this.yBlock.block.panning(a);this.canvas.style("left",`${o+i}px`).style("top",`${r+a}px`)}));i.on("mouseup",(t=>{i.on("mousemove",null).on("mouseup",null);const o=t.clientX-s;const r=t.clientY-e;console.log(o);this.xBlock.block.pannedby(o);this.yBlock.block.pannedby(r)}))}))}render(){return t(this,void 0,void 0,(function*(){this.calcResolution=this.parent("calcResolution");const t=this.parent("state");this.xBlock=new N(this.app,this.hic,t.settings.widthHeightPx,this.bbmargin,this.plotDiv.xAxis,false);this.yBlock=new N(this.app,this.hic,t.settings.widthHeightPx,this.bbmargin,this.rotor,true);this.renderCanvas(t.settings.widthHeightPx);yield this.xBlock.loadBlock(t.x,this.canvasHolder,this.canvas);yield this.yBlock.loadBlock(t.y,this.canvasHolder,this.canvas,this.sheath);this.update(this.data)}))}update(i){return t(this,void 0,void 0,(function*(){if(i.items.length==0){this.app.dispatch({type:"loading_active",active:false});return}this.data=i;const t=this.parent("state");const s=Number.parseInt(this.canvas.attr("width"));const e=Number.parseInt(this.canvasHolder.style("width"))-s+t.settings.widthHeightPx;this.canvasHolder.style("width",`${e}px`).style("height",`${e}px`);this.canvas.attr("width",`${t.settings.widthHeightPx}px`).attr("height",`${t.settings.widthHeightPx}px`);if(this.xBlock.block.width!=t.settings.widthHeightPx){this.xBlock.block.width=t.settings.widthHeightPx;this.yBlock.block.width=t.settings.widthHeightPx;this.xBlock.block.zoom2px(0,s);this.yBlock.block.zoom2px(0,s)}this.ctx=this.canvas.node().getContext("2d");const o=this.coordinates.getCoordinates(t.x,t.y,this.parent("data"),this.parent("calcResolution"),t.settings.widthHeightPx,this.parent("fragData"));this.coords=o;this.ctx.clearRect(0,0,t.settings.widthHeightPx,t.settings.widthHeightPx);for(const[t,i,s,e,o]of this.coords){this.colorizeElement.colorizeElement(t,i,o,this.ctx,s,e,this.parent("min"),this.parent("max"),"detail")}this.app.dispatch({type:"loading_active",active:false})}))}}class T{constructor(t,i){this.label=t;this.width=i}}class A{constructor(t,i,s,e){this.chromosomeMatrix=new Map;this.chromosomeList=[];this.xoff=0;this.yoff=0;this.chr2px=[];this.chrlst=t;let o=this.chrlst.length;for(const t of this.chrlst){const r=Math.ceil(s[t.toUpperCase()].len/i)*e;const a=new T(t,r);this.chromosomeList.push(a);this.chr2px[t]=r;o+=r}this.totalpx=o;for(let t=0;t<this.chrlst.length;t++){const o=this.chrlst[t];this.chromosomeMatrix.set(o,new Map);let r=0;for(let a=0;a<=t;a++){const t=this.chrlst[a];const h=s[o.toUpperCase()].len;const n=s[t.toUpperCase()].len;const l=Math.ceil(h/i)*e;const c=Math.ceil(n/i)*e;this.chromosomeMatrix.get(o).set(t,{x:this.xoff,y:r,xbins:l,ybins:c,data:[]});r+=this.chr2px[t]+A.borderWidth}this.yoff=r;this.xoff+=this.chr2px[o]+A.borderWidth}}}A.checkerFill="#DEF3FA";A.spaceColor="#CCC";A.fontSize=15;A.font=e;A.borderWidth=1;A.defaultChrLabWidth=100;class O{constructor(t){this.grid=new A(t.hic.chrlst,t.resolution||t.hic.bpresolution[0],t.hic.genome.chrlookup,1)}}class U{constructor(t,i,s,e){this.svg=t;this.layerMap=i.attr("transform",`translate(${A.defaultChrLabWidth}, ${A.fontSize})`);this.layerSv=s.attr("transform",`translate(${A.defaultChrLabWidth}, ${A.fontSize})`);this.grid=e}render(){this.renderAxisX(this.grid);this.renderAxisY(this.grid);this.svg.attr("width",A.defaultChrLabWidth+this.grid.xoff).attr("height",A.fontSize+this.grid.yoff)}renderAxisX(t){let i=0;this.grid.chromosomeList.forEach(((s,e)=>{const o=s.width;if(e%2===0){this.layerMap.append("rect").attr("x",i).attr("width",o).attr("height",A.fontSize).attr("y",-A.fontSize).attr("fill",A.checkerFill)}this.layerMap.append("text").attr("font-family",A.font).attr("text-anchor","middle").attr("font-size",12).attr("x",i+o/2).text(s.label);i+=o;this.layerSv.append("line").attr("x1",i).attr("x2",i).attr("y2",t.totalpx).attr("stroke",A.spaceColor).attr("shape-rendering","crispEdges");i+=A.borderWidth}))}renderAxisY(t){let i=0;this.grid.chromosomeList.forEach(((s,e)=>{const o=s.width;if(e%2===0){this.layerMap.append("rect").attr("x",-A.defaultChrLabWidth).attr("width",A.defaultChrLabWidth).attr("height",o).attr("y",i).attr("fill",A.checkerFill)}this.layerMap.append("text").attr("font-family",A.font).attr("text-anchor","end").attr("dominant-baseline","central").attr("font-size",12).attr("y",i+o/2).text(s.label);i+=o;this.layerSv.append("line").attr("x2",t.totalpx).attr("y1",i).attr("y2",i).attr("stroke",A.spaceColor).attr("shape-rendering","crispEdges");i+=A.borderWidth}))}}class H{constructor(){this.chrx_tip=new c({border:"solid 1px #ccc",padding:"0px",offsetX:0,offsetY:0});this.chry_tip=new c({border:"solid 1px #ccc",padding:"0px",offsetX:0,offsetY:0})}render(t,i,s){const e=t.node().getBoundingClientRect();this.chrx_tip.clear().show(e.left,e.top).d.style("top",null).style("bottom",window.innerHeight-e.top-window.pageYOffset+"px").text(i);this.chry_tip.clear().show(e.left,e.top).d.style("left",null).style("right",document.body.clientWidth-e.left-window.pageXOffset+"px").text(s)}}class W{constructor(t,i){this.app=i;this.layerMap=t;this.tooltips=new H}render(i,s,e,o){i.canvas=o.append("canvas").style("display","none").node();i.ctx=i.canvas.getContext("2d");i.canvas.width=i.xbins;i.canvas.height=i.ybins;i.img=this.layerMap.append("image").attr("width",i.canvas.width).attr("height",i.canvas.height).attr("x",i.x).attr("y",i.y).on("click",(()=>t(this,void 0,void 0,(function*(){yield this.app.dispatch({type:"view_create",view:"chrpair",config:{x:{chr:s},y:{chr:e}}})})))).on("mouseover",(()=>{this.tooltips.render(i.img,s,e)}));if(s!=e){i.canvas2=o.append("canvas").style("display","none").node();i.canvas2.width=i.ybins;i.canvas2.height=i.xbins;i.ctx2=i.canvas2.getContext("2d");i.img2=this.layerMap.append("image").attr("width",i.canvas2.width).attr("height",i.canvas2.height).attr("x",i.y).attr("y",i.x).on("click",(()=>t(this,void 0,void 0,(function*(){yield this.app.dispatch({type:"view_create",view:"chrpair",config:{x:{chr:e},y:{chr:s}}})})))).on("mouseover",(()=>{this.tooltips.render(i.img2,e,s)}))}else{i.ctx2=i.ctx}}}class Y{constructor(t,i,s){this.grid=t;this.gridElementRenderer=new W(i,s)}render(t){for(const[i,s]of this.grid.chromosomeMatrix){for(const[e,o]of s){this.gridElementRenderer.render(o,i,e,t)}}}}class I{constructor(t){this.tip=new c;this.pica_x=new c({border:"solid 1px #ccc",padding:"0px",offsetX:0,offsetY:0});this.pica_y=new c({border:"solid 1px #ccc",padding:"0px",offsetX:0,offsetY:0});this.chr2px={};this.lead2follow=new Map;this.values=[];this.defaultChrLabWidth=100;this.borderwidth=1;this.default_maxVPerc=5;this.fontsize=15;this.xoff=0;this.yoff=0;this.binpx=1;this.atdev_chrnum=8;this.min=0;this.max=0;this.app=t.app;this.hic=t.hic;this.plotDiv=t.plotDiv;this.data=t.data;this.parent=t.parent;this.resolution=t.resolution||t.hic.bpresolution[0];this.svg=this.plotDiv.plot.append("svg").attr("data-testid","sjpp-hic-genome-svg");this.layer_map=this.svg.append("g").attr("data-testid","sjpp-hic-layerMap-g");this.layer_sv=this.svg.append("g").attr("data-testid","sjpp-hic-layerSv-g");this.colorizeElement=new z;this.viewModel=new O(t);this.viewRender=new U(this.svg,this.layer_map,this.layer_sv,this.viewModel.grid);this.gridElementsRenderer=new Y(this.viewModel.grid,this.layer_map,this.app);this.gridFormattedData=new C}makeSv(){const t=new Set;const i=8;for(const s of this.hic.sv.items){const e=this.lead2follow.get(s.chr1);if(!e){t.add(s.chr1);continue}const o=e.get(s.chr2);if(!o){t.add(s.chr2);continue}const r=s.position1/this.resolution;const a=s.position2/this.resolution;this.layer_sv.append("circle").attr("stroke","black").attr("fill","white").attr("fill-opacity",0).attr("cx",o.x+r).attr("cy",o.y+a).attr("r",i).on("mouseover",(t=>{this.tooltipSv(t,s)})).on("mouseout",(()=>{this.tip.hide()})).on("click",(()=>{this.clickSv(s)}));if(o.img2){this.layer_sv.append("circle").attr("stroke","black").attr("fill","whilte").attr("fill-opacity",0).attr("cy",o.x+r).attr("cx",o.y+a).attr("r",i).on("mouseover",(t=>{this.tooltipSv(t,s)})).on("mouseout",(()=>{this.tip.hide()})).on("click",(()=>{this.clickSv(s)}))}}}tooltipSv(t,i){this.tip.clear().show(t.clientX,t.clientY).d.append("div").text(i.chr1==i.chr2?`${i.chr1}:${i.position1}-${i.position2}`:`${i.chr1}:${i.position1}>${i.chr2}:${i.position2}`)}clickSv(t){const i=5e5;const s=600;const e="rgba(200,0,0,.1)";const o=p({x:100,y:100});o.header.text(this.hic.name+" "+(t.chr1==t.chr2?`${t.chr1}:${t.position1}-${t.position2}`:`${t.chr1}:${t.position1}>${t.chr2}:${t.position2}`));const r=[{type:d.hicstraw,file:this.hic.file,enzyme:this.hic.enzyme,maxpercentage:this.default_maxVPerc,pyramidup:1,name:this.hic.name}];if(this.hic.tklst){for(const t of this.hic.tklst){r.push(t)}}h(this.hic.genome,r);const a={holder:o.body,hostURL:this.hic.hostURL,jwt:this.hic.jwt,genome:this.hic.genome,nobox:1,tklst:r};if(t.chr1==t.chr2&&Math.abs(t.position2-t.position1)<i*2){a.chr=t.chr1;const i=Math.abs(t.position2-t.position1);a.start=Math.max(1,Math.min(t.position1,t.position2)-i);a.stop=Math.min(this.hic.genome.chrlookup[t.chr1.toUpperCase()].len,Math.max(t.position1,t.position2)+i)}else{a.chr=t.chr1;a.start=Math.max(1,t.position1-i/2);a.stop=Math.min(this.hic.genome.chrlookup[t.chr1.toUpperCase()].len,t.position1+i/2);a.width=s;a.subpanels=[{chr:t.chr2,start:Math.max(1,t.position2-i/2),stop:Math.min(this.hic.genome.chrlookup[t.chr2.toUpperCase()].len,t.position2+i/2),width:s,leftpad:10,leftborder:e}]}v(a)}render(){this.viewRender.render();this.gridElementsRenderer.render(this.hic.holder);if(this.hic.sv&&this.hic.sv.items){this.makeSv()}this.update(this.data)}update(t){this.data=t;this.min=this.parent("min");this.max=this.parent("max");for(const t of this.data){if(!this.hic.chrlst.includes(t.lead)||!this.hic.chrlst.includes(t.follow))continue;const i=this.viewModel.grid.chromosomeMatrix.get(t.lead).get(t.follow);if(!i)continue;i.ctx.clearRect(0,0,i.canvas.width,i.canvas.height);if(i.canvas2){i.ctx2.clearRect(0,0,i.canvas2.width,i.canvas.height)}i.data=this.gridFormattedData.formatData("genome",t.items,this.binpx,this.resolution);for(const[t,s,e]of i.data){this.colorizeElement.colorizeElement(t,s,e,i,this.binpx,this.binpx,this.min,this.max,"genome")}i.img.attr("xlink:href",i.canvas.toDataURL());if(i.canvas2){i.img2.attr("xlink:href",i.canvas2.toDataURL())}}this.app.dispatch({type:"loading_active",active:false})}}class X{constructor(t,i,s,e){this.holder=t;this.normalization=i;this.defaultNmeth=s;this.callback=e}render(){var i;if(!((i=this.normalization)===null||i===void 0?void 0:i.length)){this.nmethSelect=this.holder.text(this.defaultNmeth)}else{this.nmethSelect=this.holder.style("margin-right","10px").append("select").on("change",(()=>t(this,void 0,void 0,(function*(){const t=this.nmethSelect.node().value;this.callback(t,"nmeth")}))));for(const t of this.normalization){this.nmethSelect.append("option").text(t)}}}update(t){const i=this.nmethSelect.node().options;if(!i)return;const s=Array.from(i).find((i=>i.value===t));if(!s)throw`Invalid normalization method: ${t}`;s.selected=true}}class J{constructor(t,i,s){this.holder=t;this.value=i;this.callback=s}render(i){const s=this.holder.style("margin-right","10px").append("input").attr("type","number").style("width",i&&"width"in i?i.width:"80px").style("margin-left","0px").attr("type","number").property("value",this.value).on("keyup",(i=>t(this,void 0,void 0,(function*(){if(i.code!="Enter")return;const t=i.target.value;this.callback(t)}))));return s}}class Z{constructor(t,i){this.values=[{label:"Observed",value:"observed"},{label:"Expected",value:"expected"},{label:"Observed/Expected",value:"oe"},{label:"Log(Observed/Expected)",value:"log(oe)"}];this.holder=t;this.callback=i}render(){this.matrixSelect=this.holder.style("margin-right","10px").append("select").on("change",(()=>t(this,void 0,void 0,(function*(){this.callback(this.matrixSelect.node().value,"matrixType")}))));for(const t of this.values){this.matrixSelect.append("option").text(t.label).attr("value",t.value)}}update(t){const i=this.matrixSelect.node().options;if(!i)return;const s=Array.from(i).find((i=>i.value===t));if(!s)throw`Invalid normalization method: ${t}`;s.selected=true}}class G{constructor(t){this.zoomBlockCallback=t=>{const i=this.parent("detail");i.xBlock.block.zoomblock(2,t);i.yBlock.block.zoomblock(2,t)};this.minCallback=t=>{if(Number(t)>Number(this.parent("max"))){this.error("Min cutoff cannot be greater than max cutoff")}else{this.parent("min",Number(t));this.reColorHeatmap();this.parent("infoBar").update()}};this.maxCallback=t=>{if(Number(t)<Number(this.parent("min"))){this.error(`Max cutoff cannot be less than min cutoff`)}else if(Number(t)<0){this.error(`Max cutoff cannot be less than 0`)}else{this.parent("max",Number(t));this.reColorHeatmap();this.parent("infoBar").update()}};this.reColorHeatmap=()=>{if(this.parent("activeView")=="genome"){const t=this.parent("genome");const i=t.viewRender.grid.chromosomeMatrix;if(!i)return;for(const[t,s]of i){for(const[t,i]of s){if(!i)continue;for(const[t,s,e]of i.data){this.colorizeElement.colorizeElement(t,s,e,i,1,1,this.parent("min"),this.parent("max"),"genome")}i.img.attr("xlink:href",i.canvas.toDataURL());if(i.canvas2){i.img2.attr("xlink:href",i.canvas2.toDataURL())}}}}else if(this.parent("activeView")=="chrpair"){const t=this.parent("chrpair");for(const[i,s,e]of t.data){this.colorizeElement.colorizeElement(i,s,e,t.ctx,t.binpx,t.binpx,this.parent("min"),this.parent("max"),"chrpair")}}else if(this.parent("activeView")=="detail"){const t=this.parent("detail");for(const[i,s,e,o,r]of t.coords){this.colorizeElement.colorizeElement(i,s,r,t.ctx,e,o,this.parent("min"),this.parent("max"),"detail")}}};this.dropdownCallback=(t,i)=>{const s=this.app.getState();this.app.dispatch({type:"view_update",view:s.currView,config:{[i]:t}})};this.type="controlPanel";this.controls={};this.app=t.app;this.controlsDiv=t.controlsDiv;this.hic=t.hic;this.colorizeElement=new z;this.parent=t.parent;this.error=t.error}getState(t){return t}addLabel(t,i){return t.append("td").style("color","#858585").style("font-size",".8em").style("vertical-align",i.toUpperCase()=="VIEW"?"top":"middle").text(i.toUpperCase())}init(){const i=this.app.getState();const s=this.controlsDiv.style("background","rgb(253, 250, 244)").style("vertical-align","top").style("padding","5px").style("border","solid 0.5px #ccc");let e=true;this.controlsDiv.append("button").style("display","block").style("border","none").style("font-size","1.5em").style("background","none").html("&#8801;").on("click",(()=>{e=!e;o.style("display",e?"block":"none")}));const o=s.append("div").attr("class","sjpp-hic-menu").style("display",e?"block":"none");const r=o.append("table").style("border-spacing","3px");this.controls.normalizationRow=r.append("tr");this.addLabel(this.controls.normalizationRow,"NORMALIZATION");this.controls.nmeth=new X(this.controls.normalizationRow.append("td").attr("class","sjpp-nmeth-select"),this.hic.normalization,i.defaultNmeth,this.dropdownCallback);this.controls.nmeth.render();this.controls.minCutoffRow=r.append("tr");this.controls.minCutoffLabel=this.addLabel(this.controls.minCutoffRow,"");this.controls.inputBpMinV=new J(this.controls.minCutoffRow.append("td"),this.parent("min"),this.minCallback).render({width:"120px"});this.controls.maxCutoffRow=r.append("tr");this.controls.maxCutoffLabel=this.addLabel(this.controls.maxCutoffRow,"");this.controls.inputBpMaxV=new J(this.controls.maxCutoffRow.append("td"),this.parent("max"),this.maxCallback).render({width:"120px"});this.controls.matrixTypeRow=r.append("tr");this.addLabel(this.controls.matrixTypeRow,"matrix type");this.controls.matrixType=new Z(this.controls.matrixTypeRow.append("td"),this.dropdownCallback);this.controls.matrixType.render();this.controls.widthRow=r.append("tr");this.addLabel(this.controls.widthRow,"WIDTH / height");this.controls.width=this.controls.widthRow.append("td");this.controls.width.style("margin-right","10px").append("input").attr("type","number").style("width","80px").style("margin-left","0px").attr("type","number").property("value",i.width).on("keyup",(i=>t(this,void 0,void 0,(function*(){if(i.code!="Enter")return;const t=i.target.value;this.app.dispatch({type:"view_update",config:{settings:{widthHeightPx:Number.parseInt(t)}}})}))));const a=r.append("tr");this.addLabel(a,"VIEW");const h=a.append("td");this.controls.view=h.append("span").style("padding-right","5px").style("display","block");this.controls.genomeViewBtn=h.append("button").style("display","none").style("padding","2px").style("margin-top","4px").html("&#8810; Genome").on("click",(()=>t(this,void 0,void 0,(function*(){yield this.app.dispatch({type:"view_create",view:"genome",config:{x:{},y:{}}})}))));this.controls.chrpairViewBtn=h.append("button").style("display","none").style("padding","2px").style("margin","4px 0px").on("click",(()=>t(this,void 0,void 0,(function*(){const t=this.app.getState();yield this.app.dispatch({type:"view_create",view:"chrpair",config:{x:{chr:t.x.chr},y:{chr:t.y.chr}}})}))));this.controls.horizontalViewBtn=h.append("button").style("display","none").style("padding","2px").style("margin","4px 0px").html("Horizontal View &#8811;").on("click",(()=>t(this,void 0,void 0,(function*(){yield this.app.dispatch({type:"view_create",view:"horizontal"})}))));this.controls.detailViewBtn=h.append("button").style("display","none").style("padding","2px").style("margin","4px 0px").html("&#8810; Detailed View").on("click",(()=>t(this,void 0,void 0,(function*(){yield this.app.dispatch({type:"view_create",view:"detail"})}))));this.controls.zoomDiv=r.append("tr").style("display",i.currView=="detail"?"contents":"none");this.addLabel(this.controls.zoomDiv,"ZOOM");const n=this.controls.zoomDiv.append("td");this.controls.zoomIn=n.append("button").style("margin-right","10px").text("In").on("click",(()=>{this.zoomBlockCallback(false)}));this.controls.zoomOut=n.append("button").style("margin-right","10px").text("Out").on("click",(()=>{this.zoomBlockCallback(true)}))}showBtns(){const t=this.app.getState();this.controls.genomeViewBtn.style("display",t.currView==="genome"?"none":"inline-block");if(t.currView==="detail"){this.controls.chrpairViewBtn.html(`&#8810; Entire ${t.x.chr}-${t.y.chr}`).style("display","block");this.controls.horizontalViewBtn.style("display","block");this.controls.zoomDiv.style("display","contents");this.controls.detailViewBtn.style("display","none")}else if(t.currView==="horizontal"){this.controls.chrpairViewBtn.html(`&#8810; Entire ${t.x.chr}-${t.y.chr}`).style("display","block");this.controls.detailViewBtn.style("display","block");this.controls.horizontalViewBtn.style("display","none");this.controls.zoomDiv.style("display","none")}else{this.controls.chrpairViewBtn.style("display","none");this.controls.horizontalViewBtn.style("display","none");this.controls.detailViewBtn.style("display","none");this.controls.zoomDiv.style("display","none");this.controls.widthRow.style("display","none")}}showHideControls(){const t=this.app.getState();this.controls.normalizationRow.style("display",t.currView=="horizontal"?"none":"");this.controls.minCutoffRow.style("display",t.currView=="horizontal"?"none":"");this.controls.maxCutoffRow.style("display",t.currView=="horizontal"?"none":"");this.controls.matrixTypeRow.style("display",t.currView=="horizontal"?"none":"");this.controls.widthRow.style("display",t.currView=="detail"?"contents":"none")}main(t){const i=this.app.getState(t);this.controls.nmeth.update(i[i.currView].nmeth);this.controls.matrixType.update(i[i.currView].matrixType);this.controls.zoomDiv.style("display",i.currView=="detail"?"contents":"none");if(i.currView=="chrpair"){this.controls.view.text(`${i.x.chr}-${i.y.chr} Pair`)}else{this.controls.view.text(i.currView.charAt(0).toUpperCase()+i.currView.slice(1))}const s=this.parent("absMin")<1e-5?Number(this.parent("absMin")).toExponential(1):Number(this.parent("absMin").toFixed(6));const e=this.parent("absMax")<1e-5?Number(this.parent("absMax")).toExponential(1):Number(this.parent("absMax").toFixed(6));this.controls.width.select("input").property("value",i.settings.widthHeightPx);this.controls.inputBpMinV.property("value",this.parent("min"));this.controls.inputBpMaxV.property("value",this.parent("max"));this.controls.minCutoffLabel.html(`MIN CUTOFF <br>(>= ${s})`);this.controls.maxCutoffLabel.html(`MAX CUTOFF <br>(<= ${e})`);this.showBtns();this.showHideControls()}}const q=s(G);class K{constructor(t){this.startColor="white";this.endColor="red";this.addLabel=t=>this.labelRow.append("td").style("color","#858585").style("font-size",".8em").style("text-align","center").style("vertical-align","middle").text(t.toUpperCase());this.addValue=t=>this.valueRow.append("td").style("font-size","1em").style("text-align","center").style("vertical-align","middle").text(t);this.type="infoBar";this.app=t.app;this.hic=t.hic;const i=t.infoBarDiv;this.labelRow=i.append("tr");this.valueRow=i.append("tr");this.parent=t.parent}render(){return t(this,void 0,void 0,(function*(){this.addLabel("Version");this.addValue(this.hic.version);this.addLabel("Enzyme");this.addValue(this.hic.enzyme||"N/A");this.addLabel("Resolution");this.resolutionDiv=this.addValue("");this.colorScaleLabel=this.addLabel("Scale");this.colorScaleDiv=this.valueRow.append("td");this.colorScale=new w({barheight:14,barwidth:85,data:[this.parent("min"),this.parent("max")],fontSize:12,height:35,width:120,holder:this.colorScaleDiv,startColor:this.startColor,endColor:this.endColor,position:"20,0",ticks:2,tickSize:3,markedValue:1});this.colorScale.render();this.update()}))}update(){const t=this.parent("calcResolution");let i;if(t<this.hic.bpresolution[this.hic.bpresolution.length-1]){i=`${t} fragment${t>1?"s":""}`}else{i=u(t)}this.resolutionDiv.text(i);if(this.parent("state").currView=="horizontal"){this.colorScaleLabel.style("display","none");this.colorScaleDiv.style("display","none")}else{this.colorScaleLabel.style("display","");this.colorScaleDiv.style("display","");const t=this.parent("min");const i=this.parent("max");if(t<0){this.colorScale.startColor="blue";this.colorScale.data=[t,i]}else{this.colorScale.startColor="white";this.colorScale.data=[0,i]}this.colorScale.markedValue=t;this.colorScale.updateScale()}}}class Q{constructor(t,i){this.hic=t;this.percentile=i?i/100:.99}sortData(t){const i=[];if((t===null||t===void 0?void 0:t.items)&&(t===null||t===void 0?void 0:t.items.length)){for(const s of t.items){i.push(s[2])}}else{const s=new Set;for(const e of t){if(e.lead=="chrM"&&!e.items.length||e.lead=="chrY"&&!e.items.length){s.add(e.lead);continue}for(const t of e.items){i.push(t[2])}}if(s.size){for(const t of s){const i=this.hic.chrlst.indexOf(t);this.hic.chrlst.splice(i,1)}}}const s=i.sort(((t,i)=>t-i));const e=s[Math.floor(s.length*this.percentile)];const o=s[0];return[o,e,s[s.length-1]]}}class tt{constructor(t,i,s=[]){this.data=[];this.hic=t;this.debugmode=i;this.errList=s||[]}getData(i){return t(this,void 0,void 0,(function*(){if(this.data.length)this.data=[];if(!(i===null||i===void 0?void 0:i.matrixType))i.matrixType="observed";try{const t=yield n("hicgenome?",{method:"POST",body:JSON.stringify({chrlst:this.hic.chrlst,nmeth:i.nmeth,resolution:i.resolution,matrixType:i.matrixType,file:this.hic.file,url:this.hic.url,nochr:this.hic.nochr})});if(t.error){const i=t.error.split("\n");for(const t of i){this.errList.push(t)}}return t.data}catch(t){this.errList.push(t.message||t);if(t.stack)console.error(t.stack)}}))}}class it{constructor(t,i,s=[]){this.hic=t;this.debugmode=i;this.errList=s||[]}getData(i){return t(this,void 0,void 0,(function*(){if(!(i===null||i===void 0?void 0:i.matrixType))i.matrixType="observed";const t={matrixType:i.matrixType,file:this.hic.file,url:this.hic.url,pos1:this.hic.nochr?i.lead.replace("chr",""):i.lead,pos2:this.hic.nochr?i.follow.replace("chr",""):i.follow,nmeth:i.nmeth,resolution:i.resolution};try{const s=yield n("hicdata?",{method:"POST",body:JSON.stringify(t)});if(s.error){throw Error(`${i.lead} - ${i.follow}: ${s.error.error}`)}if(!s.items||s.items.length==0)return;return s}catch(t){this.errList.push(t.message||t);if(t.stack)console.error(t.stack)}}))}}class st{constructor(t){this.components={controls:[]};this.genomeData=[];this.calcResolution=null;this.firstRender=true;this.min=0;this.absMin=0;this.max=0;this.absMax=0;this.hasStatePreMain=true;this.type="view";this.hic=t.hic;this.state=t.state;this.dom=t.dom;this.errList=t.errList;this.plotDiv=this.dom.plotDiv.append("table").classed("sjpp-hic-plot-main",true);const i=this.plotDiv.append("tr");const s=this.plotDiv.append("tr");this.plotDiv={plot:i.append("td").classed("sjpp-hic-plot",true).attr("data-testid","sjpp-hic-plot"),yAxis:i.append("td").classed("sjpp-hic-plot-yaxis",true).attr("data-testid","sjpp-hic-yaxis"),xAxis:s.append("td").classed("sjpp-hic-plot-xaxis",true).attr("data-testid","sjpp-hic-xaxis"),blank:s.append("td")};this.app=t.app;this.dataMapper=new Q(this.hic,t.state.maxCutoffPercentile);this.activeView=this.state.currView;this.error=t.error;this.resolution=new R(this.error);this.parent=t=>this[t];this.detailDataMapper=new _(this.hic,this.errList,this.parent)}getState(t){return t}reactsTo(t){if(t.type.startsWith("view"))return true;else return false}initView(){const t={plotDiv:this.plotDiv,hic:this.hic,app:this.app,parent:t=>this[t]};if(this.state.currView=="genome"){t["data"]=this.data;this.genome=new I(t);this.genome.render()}else if(this.state.currView==="chrpair"){t["items"]=this.data;this.chrpair=new S(t);this.chrpair.render()}else if(this.state.currView==="detail"){t["data"]=this.data;this.detail=new F(t);this.detail.render()}else if(this.state.currView==="horizontal"){this.horizontal=new B(t);this.horizontal.render()}else{throw Error(`Unknown view: ${this.state.currView}`)}}fetchData(i){var s,e,o,r,a,h;return t(this,void 0,void 0,(function*(){if((s=this.data)===null||s===void 0?void 0:s.length)this.data=[];if(this.state.currView=="genome"){if(this.activeView!="genome"&&((e=this.genomeData)===null||e===void 0?void 0:e.length))this.data=this.genomeData;else{const t=new tt(this.hic,true,this.errList);this.genomeData=yield t.getData(i);this.data=this.genomeData}}else if(this.state.currView=="detail"){this.data=yield this.detailDataMapper.getData(this.state.x,this.state.y,this.fragData)}else{if(!((r=(o=this.state)===null||o===void 0?void 0:o.x)===null||r===void 0?void 0:r.chr)||!((h=(a=this.state)===null||a===void 0?void 0:a.y)===null||h===void 0?void 0:h.chr)){this.errList.push(`No positions provided for ${this.activeView} view.`);return}else{const t=this.state.x;const s=this.state.y;i["lead"]=`${t.start&&t.stop?`${t.chr}:${t.start}-${t.stop}`:t.chr}`;i["follow"]=`${s.start&&s.stop?`${s.chr}:${s.start}-${s.stop}`:s.chr}`}const t=new it(this.hic,true,this.errList);this.data=yield t.getData(i)}}))}setResolution(i){return t(this,void 0,void 0,(function*(){const t=this.app.getState(i);this.calcResolution=this.resolution.getResolution(t,this.hic);if(t.currView=="detail"&&this.calcResolution==null){yield this.detailDataMapper.getFragData(t.x,t.y);this.fragData=this.detailDataMapper.frag;const i=Math.min(this.fragData.x.stop-this.fragData.x.start,this.fragData.y.stop-this.fragData.y.start);this.calcResolution=this.resolution.findResFromArray(i,t.minFragSpan,this.hic.fragresolution,true)}else{this.fragData=null}return this.calcResolution}))}setDataArgs(i){return t(this,void 0,void 0,(function*(){const t=this.app.getState(i);const s=t[t.currView];const e={nmeth:s.nmeth,resolution:yield this.setResolution(i),matrixType:s.matrixType};if(t.currView=="chrpair"){e["lead"]=t.x.chr;e["follow"]=t.y.chr}return e}))}getViewData(i){var s,e,o,r,a;return t(this,void 0,void 0,(function*(){const t=yield this.setDataArgs(i);yield this.fetchData(t);if(((s=this.data)===null||s===void 0?void 0:s.length)>0||((o=(e=this.data)===null||e===void 0?void 0:e.items)===null||o===void 0?void 0:o.length)>0){const[t,i,s]=this.dataMapper.sortData(this.data);this.min=this.absMin=t;this.max=i;this.absMax=s}else{if(this.state.currView!="genome"){const t=this.app.getState(i);const s=((r=t.x)===null||r===void 0?void 0:r.start)?`${t.x.chr}:${t.x.start}-${t.x.stop}`:t.x.chr;const e=((a=t.y)===null||a===void 0?void 0:a.start)?`${t.y.chr}:${t.y.start}-${t.y.stop}`:t.y.chr;this.errList.push(`No data returned for ${s} and ${e}`)}}}))}init(){return t(this,void 0,void 0,(function*(){this.components={controls:yield q({app:this.app,controlsDiv:this.dom.controlsDiv,hic:this.hic,parent:(t,i)=>{if(i)this[t]=i;return this[t]},error:this.error.bind(this)})};this.infoBar=new K({app:this.app,infoBarDiv:this.dom.infoBarDiv.append("table").style("border-spacing","3px"),hic:this.hic,parent:t=>this[t]});this.infoBar.render()}))}main(i){return t(this,void 0,void 0,(function*(){if(this.errList.length){this.app.dispatch({type:"loading_active",active:false});return}const t=this.app.getState(i);if(this.firstRender==true){this.firstRender=false;yield this.getViewData(i);this.initView()}else{if(t.currView!="horizontal"){this.app.dispatch({type:"loading_active",active:true});yield this.getViewData(i)}if(this.activeView!=t.currView){if(this.activeView=="genome"){this.genome.svg.remove()}else{this.plotDiv.xAxis.selectAll("*").remove();this.plotDiv.yAxis.selectAll("*").remove();this.plotDiv.plot.selectAll("*").remove()}this.activeView=t.currView;this.initView()}else{this[t.currView].update(this.data)}}this.infoBar.update();if(this.errList.length){this.error(this.errList);this.app.dispatch({type:"loading_active",active:false})}}))}}const et=s(st);class ot{constructor(t){this.views=["genome","chrpair","detail","horizontal"];this.errList=[];this.type="app";this.hic={enzyme:t.enzyme,file:t.file,url:t.url,genome:t.genome,holder:t.holder,hostUrl:t.hostUrl,jwt:t.jwt,position1:t.position1,position2:t.position2,maxCutoffPercentile:t.maxCutoffPercentile,name:"name"in t?t.name:"Hi-C",tklist:"tklst"in t?t.tklst:[],state:"state"in t?t.state:{}};this.dom={errorDiv:t.holder.append("div").classed("sjpp-hic-error",true),controlsDiv:t.holder.append("div").classed("sjpp-hic-controls",true).style("display","inline-block"),infoBarDiv:t.holder.append("div").classed("sjpp-hic-infobar",true).style("display","inline-block").style("vertical-align","top").style("padding","5px").style("border","solid 0.5px #ccc"),loadingDiv:l("body").append("div").attr("id","sjpp-loading-overlay"),plotDiv:t.holder.append("div").classed("sjpp-hic-main",true).style("display","inline-block"),tip:new c}}error(i){return t(this,void 0,void 0,(function*(){if(i&&typeof i=="string")this.errList.push(i);m(this.errList,this.dom.errorDiv);this.errList=[]}))}determineView(){if(!this.hic.position1&&!this.hic.position2&&!this.hic.state.currView)this.hic.state.currView="genome";if(!this.hic.position1&&this.hic.position2)this.errList.push("Missing first position");if(this.hic.position1&&!this.hic.position2)this.errList.push("Missing second position");if(this.hic.position1&&this.hic.position2){const t=this.hic.position1.split(/[:-]/);const i=this.hic.position2.split(/[:-]/);this.hic.state.x={chr:t[0]};this.hic.state.y={chr:i[0]};if(!Number.isNaN(+t[1])&&!Number.isNaN(+t[2])){this.hic.state.x.start=+t[1];this.hic.state.x.stop=+t[2];this.hic.state.y.start=+i[1];this.hic.state.y.stop=+i[2];this.hic.state.currView="detail"}else{this.hic.state.currView="chrpair"}}else{if(!this.views.some((t=>t===this.hic.state.currView)))this.error(`Unknown view: ${this.hic.state.currView}`);else return this.hic.state.currView}}getViewsConfig(){var t,i,s;if(this.hic.maxCutoffPercentile)this.hic.state.maxCutoffPercentile=this.hic.maxCutoffPercentile;let e;if(((t=this.hic["normalization"])===null||t===void 0?void 0:t.length)>0){if(!this.hic["normalization"].includes("NONE"))this.hic["normalization"].unshift("NONE");e=this.hic["normalization"][0]}else{e="NONE"}if(this.hic.state.currView){if(!this.hic.state[this.hic.state.currView])this.hic.state[this.hic.state.currView]={};if(!((i=this.hic.state[this.hic.state.currView])===null||i===void 0?void 0:i.matrixType)){this.hic.state[this.hic.state.currView].matrixType="observed"}if(!((s=this.hic.state[this.hic.state.currView])===null||s===void 0?void 0:s.nmeth)){this.hic.state[this.hic.state.currView].nmeth=e}}for(const t of this.views){if(!this.hic.state[t]){this.hic.state[t]={matrixType:"observed",nmeth:e}}}}init(){return t(this,void 0,void 0,(function*(){this.determineView();try{yield b(this.hic,true,this.errList);this.getViewsConfig();this.store=yield D({app:this.api,state:this.hic.state});this.state=yield this.store.copyState();this.components={loadingOverlay:yield V({app:this.api,loadingDiv:this.dom.loadingDiv}),view:yield et({app:this.api,state:this.state,dom:this.dom,hic:this.hic,errList:this.errList,error:this.error})};yield this.api.dispatch()}catch(t){console.error(t.stack||t)}}))}main(){if(this.errList.length){this.error(this.errList);this.dom.loadingDiv.style("display","none");return}}}const rt=f(ot);export{rt as hicInit};

package/dist/{OrbitControls-2466d420.js → OrbitControls-604f40af.js}

@@ -1 +1 @@
-import{E as e,a as t,b as n,T as o,Q as a,S as i,V as s}from"./sampleScatter.rendererThree-ef289434.js";import"./app-6fb77603.js";const c={type:"change"};const r={type:"start"};const l={type:"end"};class m extends e{constructor(e,m){super();this.object=e;this.domElement=m;this.domElement.style.touchAction="none";this.enabled=true;this.target=new t;this.minDistance=0;this.maxDistance=Infinity;this.minZoom=0;this.maxZoom=Infinity;this.minPolarAngle=0;this.maxPolarAngle=Math.PI;this.minAzimuthAngle=-Infinity;this.maxAzimuthAngle=Infinity;this.enableDamping=false;this.dampingFactor=.05;this.enableZoom=true;this.zoomSpeed=1;this.enableRotate=true;this.rotateSpeed=1;this.enablePan=true;this.panSpeed=1;this.screenSpacePanning=true;this.keyPanSpeed=7;this.autoRotate=false;this.autoRotateSpeed=2;this.keys={LEFT:"ArrowLeft",UP:"ArrowUp",RIGHT:"ArrowRight",BOTTOM:"ArrowDown"};this.mouseButtons={LEFT:n.ROTATE,MIDDLE:n.DOLLY,RIGHT:n.PAN};this.touches={ONE:o.ROTATE,TWO:o.DOLLY_PAN};this.target0=this.target.clone();this.position0=this.object.position.clone();this.zoom0=this.object.zoom;this._domElementKeyEvents=null;this.getPolarAngle=function(){return d.phi};this.getAzimuthalAngle=function(){return d.theta};this.getDistance=function(){return this.object.position.distanceTo(this.target)};this.listenToKeyEvents=function(e){e.addEventListener("keydown",me);this._domElementKeyEvents=e};this.stopListenToKeyEvents=function(){this._domElementKeyEvents.removeEventListener("keydown",me);this._domElementKeyEvents=null};this.saveState=function(){u.target0.copy(u.target);u.position0.copy(u.object.position);u.zoom0=u.object.zoom};this.reset=function(){u.target.copy(u.target0);u.object.position.copy(u.position0);u.object.zoom=u.zoom0;u.object.updateProjectionMatrix();u.dispatchEvent(c);u.update();f=p.NONE};this.update=function(){const n=new t;const o=(new a).setFromUnitVectors(e.up,new t(0,1,0));const i=o.clone().invert();const s=new t;const r=new a;const l=2*Math.PI;return function e(){const t=u.object.position;n.copy(t).sub(u.target);n.applyQuaternion(o);d.setFromVector3(n);if(u.autoRotate&&f===p.NONE){x(I())}if(u.enableDamping){d.theta+=b.theta*u.dampingFactor;d.phi+=b.phi*u.dampingFactor}else{d.theta+=b.theta;d.phi+=b.phi}let a=u.minAzimuthAngle;let m=u.maxAzimuthAngle;if(isFinite(a)&&isFinite(m)){if(a<-Math.PI)a+=l;else if(a>Math.PI)a-=l;if(m<-Math.PI)m+=l;else if(m>Math.PI)m-=l;if(a<=m){d.theta=Math.max(a,Math.min(m,d.theta))}else{d.theta=d.theta>(a+m)/2?Math.max(a,d.theta):Math.min(m,d.theta)}}d.phi=Math.max(u.minPolarAngle,Math.min(u.maxPolarAngle,d.phi));d.makeSafe();d.radius*=E;d.radius=Math.max(u.minDistance,Math.min(u.maxDistance,d.radius));if(u.enableDamping===true){u.target.addScaledVector(g,u.dampingFactor)}else{u.target.add(g)}n.setFromSpherical(d);n.applyQuaternion(i);t.copy(u.target).add(n);u.object.lookAt(u.target);if(u.enableDamping===true){b.theta*=1-u.dampingFactor;b.phi*=1-u.dampingFactor;g.multiplyScalar(1-u.dampingFactor)}else{b.set(0,0,0);g.set(0,0,0)}E=1;if(y||s.distanceToSquared(u.object.position)>h||8*(1-r.dot(u.object.quaternion))>h){u.dispatchEvent(c);s.copy(u.object.position);r.copy(u.object.quaternion);y=false;return true}return false}}();this.dispose=function(){u.domElement.removeEventListener("contextmenu",fe);u.domElement.removeEventListener("pointerdown",ae);u.domElement.removeEventListener("pointercancel",se);u.domElement.removeEventListener("wheel",le);u.domElement.removeEventListener("pointermove",ie);u.domElement.removeEventListener("pointerup",se);if(u._domElementKeyEvents!==null){u._domElementKeyEvents.removeEventListener("keydown",me);u._domElementKeyEvents=null}};const u=this;const p={NONE:-1,ROTATE:0,DOLLY:1,PAN:2,TOUCH_ROTATE:3,TOUCH_PAN:4,TOUCH_DOLLY_PAN:5,TOUCH_DOLLY_ROTATE:6};let f=p.NONE;const h=1e-6;const d=new i;const b=new i;let E=1;const g=new t;let y=false;const O=new s;const P=new s;const T=new s;const v=new s;const A=new s;const L=new s;const w=new s;const N=new s;const j=new s;const M=[];const k={};function I(){return 2*Math.PI/60/60*u.autoRotateSpeed}function R(){return Math.pow(.95,u.zoomSpeed)}function x(e){b.theta-=e}function S(e){b.phi-=e}const Y=function(){const e=new t;return function t(n,o){e.setFromMatrixColumn(o,0);e.multiplyScalar(-n);g.add(e)}}();const D=function(){const e=new t;return function t(n,o){if(u.screenSpacePanning===true){e.setFromMatrixColumn(o,1)}else{e.setFromMatrixColumn(o,0);e.crossVectors(u.object.up,e)}e.multiplyScalar(n);g.add(e)}}();const _=function(){const e=new t;return function t(n,o){const a=u.domElement;if(u.object.isPerspectiveCamera){const t=u.object.position;e.copy(t).sub(u.target);let i=e.length();i*=Math.tan(u.object.fov/2*Math.PI/180);Y(2*n*i/a.clientHeight,u.object.matrix);D(2*o*i/a.clientHeight,u.object.matrix)}else if(u.object.isOrthographicCamera){Y(n*(u.object.right-u.object.left)/u.object.zoom/a.clientWidth,u.object.matrix);D(o*(u.object.top-u.object.bottom)/u.object.zoom/a.clientHeight,u.object.matrix)}else{console.warn("WARNING: OrbitControls.js encountered an unknown camera type - pan disabled.");u.enablePan=false}}}();function H(e){if(u.object.isPerspectiveCamera){E/=e}else if(u.object.isOrthographicCamera){u.object.zoom=Math.max(u.minZoom,Math.min(u.maxZoom,u.object.zoom*e));u.object.updateProjectionMatrix();y=true}else{console.warn("WARNING: OrbitControls.js encountered an unknown camera type - dolly/zoom disabled.");u.enableZoom=false}}function K(e){if(u.object.isPerspectiveCamera){E*=e}else if(u.object.isOrthographicCamera){u.object.zoom=Math.max(u.minZoom,Math.min(u.maxZoom,u.object.zoom/e));u.object.updateProjectionMatrix();y=true}else{console.warn("WARNING: OrbitControls.js encountered an unknown camera type - dolly/zoom disabled.");u.enableZoom=false}}function C(e){O.set(e.clientX,e.clientY)}function z(e){w.set(e.clientX,e.clientY)}function X(e){v.set(e.clientX,e.clientY)}function Z(e){P.set(e.clientX,e.clientY);T.subVectors(P,O).multiplyScalar(u.rotateSpeed);const t=u.domElement;x(2*Math.PI*T.x/t.clientHeight);S(2*Math.PI*T.y/t.clientHeight);O.copy(P);u.update()}function F(e){N.set(e.clientX,e.clientY);j.subVectors(N,w);if(j.y>0){H(R())}else if(j.y<0){K(R())}w.copy(N);u.update()}function U(e){A.set(e.clientX,e.clientY);L.subVectors(A,v).multiplyScalar(u.panSpeed);_(L.x,L.y);v.copy(A);u.update()}function V(e){if(e.deltaY<0){K(R())}else if(e.deltaY>0){H(R())}u.update()}function G(e){let t=false;switch(e.code){case u.keys.UP:if(e.ctrlKey||e.metaKey||e.shiftKey){S(2*Math.PI*u.rotateSpeed/u.domElement.clientHeight)}else{_(0,u.keyPanSpeed)}t=true;break;case u.keys.BOTTOM:if(e.ctrlKey||e.metaKey||e.shiftKey){S(-2*Math.PI*u.rotateSpeed/u.domElement.clientHeight)}else{_(0,-u.keyPanSpeed)}t=true;break;case u.keys.LEFT:if(e.ctrlKey||e.metaKey||e.shiftKey){x(2*Math.PI*u.rotateSpeed/u.domElement.clientHeight)}else{_(u.keyPanSpeed,0)}t=true;break;case u.keys.RIGHT:if(e.ctrlKey||e.metaKey||e.shiftKey){x(-2*Math.PI*u.rotateSpeed/u.domElement.clientHeight)}else{_(-u.keyPanSpeed,0)}t=true;break}if(t){e.preventDefault();u.update()}}function B(){if(M.length===1){O.set(M[0].pageX,M[0].pageY)}else{const e=.5*(M[0].pageX+M[1].pageX);const t=.5*(M[0].pageY+M[1].pageY);O.set(e,t)}}function W(){if(M.length===1){v.set(M[0].pageX,M[0].pageY)}else{const e=.5*(M[0].pageX+M[1].pageX);const t=.5*(M[0].pageY+M[1].pageY);v.set(e,t)}}function q(){const e=M[0].pageX-M[1].pageX;const t=M[0].pageY-M[1].pageY;const n=Math.sqrt(e*e+t*t);w.set(0,n)}function Q(){if(u.enableZoom)q();if(u.enablePan)W()}function J(){if(u.enableZoom)q();if(u.enableRotate)B()}function $(e){if(M.length==1){P.set(e.pageX,e.pageY)}else{const t=Ee(e);const n=.5*(e.pageX+t.x);const o=.5*(e.pageY+t.y);P.set(n,o)}T.subVectors(P,O).multiplyScalar(u.rotateSpeed);const t=u.domElement;x(2*Math.PI*T.x/t.clientHeight);S(2*Math.PI*T.y/t.clientHeight);O.copy(P)}function ee(e){if(M.length===1){A.set(e.pageX,e.pageY)}else{const t=Ee(e);const n=.5*(e.pageX+t.x);const o=.5*(e.pageY+t.y);A.set(n,o)}L.subVectors(A,v).multiplyScalar(u.panSpeed);_(L.x,L.y);v.copy(A)}function te(e){const t=Ee(e);const n=e.pageX-t.x;const o=e.pageY-t.y;const a=Math.sqrt(n*n+o*o);N.set(0,a);j.set(0,Math.pow(N.y/w.y,u.zoomSpeed));H(j.y);w.copy(N)}function ne(e){if(u.enableZoom)te(e);if(u.enablePan)ee(e)}function oe(e){if(u.enableZoom)te(e);if(u.enableRotate)$(e)}function ae(e){if(u.enabled===false)return;if(M.length===0){u.domElement.setPointerCapture(e.pointerId);u.domElement.addEventListener("pointermove",ie);u.domElement.addEventListener("pointerup",se)}he(e);if(e.pointerType==="touch"){ue(e)}else{ce(e)}}function ie(e){if(u.enabled===false)return;if(e.pointerType==="touch"){pe(e)}else{re(e)}}function se(e){de(e);if(M.length===0){u.domElement.releasePointerCapture(e.pointerId);u.domElement.removeEventListener("pointermove",ie);u.domElement.removeEventListener("pointerup",se)}u.dispatchEvent(l);f=p.NONE}function ce(e){let t;switch(e.button){case 0:t=u.mouseButtons.LEFT;break;case 1:t=u.mouseButtons.MIDDLE;break;case 2:t=u.mouseButtons.RIGHT;break;default:t=-1}switch(t){case n.DOLLY:if(u.enableZoom===false)return;z(e);f=p.DOLLY;break;case n.ROTATE:if(e.ctrlKey||e.metaKey||e.shiftKey){if(u.enablePan===false)return;X(e);f=p.PAN}else{if(u.enableRotate===false)return;C(e);f=p.ROTATE}break;case n.PAN:if(e.ctrlKey||e.metaKey||e.shiftKey){if(u.enableRotate===false)return;C(e);f=p.ROTATE}else{if(u.enablePan===false)return;X(e);f=p.PAN}break;default:f=p.NONE}if(f!==p.NONE){u.dispatchEvent(r)}}function re(e){switch(f){case p.ROTATE:if(u.enableRotate===false)return;Z(e);break;case p.DOLLY:if(u.enableZoom===false)return;F(e);break;case p.PAN:if(u.enablePan===false)return;U(e);break}}function le(e){if(u.enabled===false||u.enableZoom===false||f!==p.NONE)return;e.preventDefault();u.dispatchEvent(r);V(e);u.dispatchEvent(l)}function me(e){if(u.enabled===false||u.enablePan===false)return;G(e)}function ue(e){be(e);switch(M.length){case 1:switch(u.touches.ONE){case o.ROTATE:if(u.enableRotate===false)return;B();f=p.TOUCH_ROTATE;break;case o.PAN:if(u.enablePan===false)return;W();f=p.TOUCH_PAN;break;default:f=p.NONE}break;case 2:switch(u.touches.TWO){case o.DOLLY_PAN:if(u.enableZoom===false&&u.enablePan===false)return;Q();f=p.TOUCH_DOLLY_PAN;break;case o.DOLLY_ROTATE:if(u.enableZoom===false&&u.enableRotate===false)return;J();f=p.TOUCH_DOLLY_ROTATE;break;default:f=p.NONE}break;default:f=p.NONE}if(f!==p.NONE){u.dispatchEvent(r)}}function pe(e){be(e);switch(f){case p.TOUCH_ROTATE:if(u.enableRotate===false)return;$(e);u.update();break;case p.TOUCH_PAN:if(u.enablePan===false)return;ee(e);u.update();break;case p.TOUCH_DOLLY_PAN:if(u.enableZoom===false&&u.enablePan===false)return;ne(e);u.update();break;case p.TOUCH_DOLLY_ROTATE:if(u.enableZoom===false&&u.enableRotate===false)return;oe(e);u.update();break;default:f=p.NONE}}function fe(e){if(u.enabled===false)return;e.preventDefault()}function he(e){M.push(e)}function de(e){delete k[e.pointerId];for(let t=0;t<M.length;t++){if(M[t].pointerId==e.pointerId){M.splice(t,1);return}}}function be(e){let t=k[e.pointerId];if(t===undefined){t=new s;k[e.pointerId]=t}t.set(e.pageX,e.pageY)}function Ee(e){const t=e.pointerId===M[0].pointerId?M[1]:M[0];return k[t.pointerId]}u.domElement.addEventListener("contextmenu",fe);u.domElement.addEventListener("pointerdown",ae);u.domElement.addEventListener("pointercancel",se);u.domElement.addEventListener("wheel",le,{passive:false});this.update()}}export{m as OrbitControls};
+import{E as e,a as t,b as n,T as o,Q as a,S as i,V as s}from"./sampleScatter.rendererThree-b6db5a09.js";import"./app-0de0ae35.js";const c={type:"change"};const r={type:"start"};const l={type:"end"};class m extends e{constructor(e,m){super();this.object=e;this.domElement=m;this.domElement.style.touchAction="none";this.enabled=true;this.target=new t;this.minDistance=0;this.maxDistance=Infinity;this.minZoom=0;this.maxZoom=Infinity;this.minPolarAngle=0;this.maxPolarAngle=Math.PI;this.minAzimuthAngle=-Infinity;this.maxAzimuthAngle=Infinity;this.enableDamping=false;this.dampingFactor=.05;this.enableZoom=true;this.zoomSpeed=1;this.enableRotate=true;this.rotateSpeed=1;this.enablePan=true;this.panSpeed=1;this.screenSpacePanning=true;this.keyPanSpeed=7;this.autoRotate=false;this.autoRotateSpeed=2;this.keys={LEFT:"ArrowLeft",UP:"ArrowUp",RIGHT:"ArrowRight",BOTTOM:"ArrowDown"};this.mouseButtons={LEFT:n.ROTATE,MIDDLE:n.DOLLY,RIGHT:n.PAN};this.touches={ONE:o.ROTATE,TWO:o.DOLLY_PAN};this.target0=this.target.clone();this.position0=this.object.position.clone();this.zoom0=this.object.zoom;this._domElementKeyEvents=null;this.getPolarAngle=function(){return d.phi};this.getAzimuthalAngle=function(){return d.theta};this.getDistance=function(){return this.object.position.distanceTo(this.target)};this.listenToKeyEvents=function(e){e.addEventListener("keydown",me);this._domElementKeyEvents=e};this.stopListenToKeyEvents=function(){this._domElementKeyEvents.removeEventListener("keydown",me);this._domElementKeyEvents=null};this.saveState=function(){u.target0.copy(u.target);u.position0.copy(u.object.position);u.zoom0=u.object.zoom};this.reset=function(){u.target.copy(u.target0);u.object.position.copy(u.position0);u.object.zoom=u.zoom0;u.object.updateProjectionMatrix();u.dispatchEvent(c);u.update();f=p.NONE};this.update=function(){const n=new t;const o=(new a).setFromUnitVectors(e.up,new t(0,1,0));const i=o.clone().invert();const s=new t;const r=new a;const l=2*Math.PI;return function e(){const t=u.object.position;n.copy(t).sub(u.target);n.applyQuaternion(o);d.setFromVector3(n);if(u.autoRotate&&f===p.NONE){x(I())}if(u.enableDamping){d.theta+=b.theta*u.dampingFactor;d.phi+=b.phi*u.dampingFactor}else{d.theta+=b.theta;d.phi+=b.phi}let a=u.minAzimuthAngle;let m=u.maxAzimuthAngle;if(isFinite(a)&&isFinite(m)){if(a<-Math.PI)a+=l;else if(a>Math.PI)a-=l;if(m<-Math.PI)m+=l;else if(m>Math.PI)m-=l;if(a<=m){d.theta=Math.max(a,Math.min(m,d.theta))}else{d.theta=d.theta>(a+m)/2?Math.max(a,d.theta):Math.min(m,d.theta)}}d.phi=Math.max(u.minPolarAngle,Math.min(u.maxPolarAngle,d.phi));d.makeSafe();d.radius*=E;d.radius=Math.max(u.minDistance,Math.min(u.maxDistance,d.radius));if(u.enableDamping===true){u.target.addScaledVector(g,u.dampingFactor)}else{u.target.add(g)}n.setFromSpherical(d);n.applyQuaternion(i);t.copy(u.target).add(n);u.object.lookAt(u.target);if(u.enableDamping===true){b.theta*=1-u.dampingFactor;b.phi*=1-u.dampingFactor;g.multiplyScalar(1-u.dampingFactor)}else{b.set(0,0,0);g.set(0,0,0)}E=1;if(y||s.distanceToSquared(u.object.position)>h||8*(1-r.dot(u.object.quaternion))>h){u.dispatchEvent(c);s.copy(u.object.position);r.copy(u.object.quaternion);y=false;return true}return false}}();this.dispose=function(){u.domElement.removeEventListener("contextmenu",fe);u.domElement.removeEventListener("pointerdown",ae);u.domElement.removeEventListener("pointercancel",se);u.domElement.removeEventListener("wheel",le);u.domElement.removeEventListener("pointermove",ie);u.domElement.removeEventListener("pointerup",se);if(u._domElementKeyEvents!==null){u._domElementKeyEvents.removeEventListener("keydown",me);u._domElementKeyEvents=null}};const u=this;const p={NONE:-1,ROTATE:0,DOLLY:1,PAN:2,TOUCH_ROTATE:3,TOUCH_PAN:4,TOUCH_DOLLY_PAN:5,TOUCH_DOLLY_ROTATE:6};let f=p.NONE;const h=1e-6;const d=new i;const b=new i;let E=1;const g=new t;let y=false;const O=new s;const P=new s;const T=new s;const v=new s;const A=new s;const L=new s;const w=new s;const N=new s;const j=new s;const M=[];const k={};function I(){return 2*Math.PI/60/60*u.autoRotateSpeed}function R(){return Math.pow(.95,u.zoomSpeed)}function x(e){b.theta-=e}function S(e){b.phi-=e}const Y=function(){const e=new t;return function t(n,o){e.setFromMatrixColumn(o,0);e.multiplyScalar(-n);g.add(e)}}();const D=function(){const e=new t;return function t(n,o){if(u.screenSpacePanning===true){e.setFromMatrixColumn(o,1)}else{e.setFromMatrixColumn(o,0);e.crossVectors(u.object.up,e)}e.multiplyScalar(n);g.add(e)}}();const _=function(){const e=new t;return function t(n,o){const a=u.domElement;if(u.object.isPerspectiveCamera){const t=u.object.position;e.copy(t).sub(u.target);let i=e.length();i*=Math.tan(u.object.fov/2*Math.PI/180);Y(2*n*i/a.clientHeight,u.object.matrix);D(2*o*i/a.clientHeight,u.object.matrix)}else if(u.object.isOrthographicCamera){Y(n*(u.object.right-u.object.left)/u.object.zoom/a.clientWidth,u.object.matrix);D(o*(u.object.top-u.object.bottom)/u.object.zoom/a.clientHeight,u.object.matrix)}else{console.warn("WARNING: OrbitControls.js encountered an unknown camera type - pan disabled.");u.enablePan=false}}}();function H(e){if(u.object.isPerspectiveCamera){E/=e}else if(u.object.isOrthographicCamera){u.object.zoom=Math.max(u.minZoom,Math.min(u.maxZoom,u.object.zoom*e));u.object.updateProjectionMatrix();y=true}else{console.warn("WARNING: OrbitControls.js encountered an unknown camera type - dolly/zoom disabled.");u.enableZoom=false}}function K(e){if(u.object.isPerspectiveCamera){E*=e}else if(u.object.isOrthographicCamera){u.object.zoom=Math.max(u.minZoom,Math.min(u.maxZoom,u.object.zoom/e));u.object.updateProjectionMatrix();y=true}else{console.warn("WARNING: OrbitControls.js encountered an unknown camera type - dolly/zoom disabled.");u.enableZoom=false}}function C(e){O.set(e.clientX,e.clientY)}function z(e){w.set(e.clientX,e.clientY)}function X(e){v.set(e.clientX,e.clientY)}function Z(e){P.set(e.clientX,e.clientY);T.subVectors(P,O).multiplyScalar(u.rotateSpeed);const t=u.domElement;x(2*Math.PI*T.x/t.clientHeight);S(2*Math.PI*T.y/t.clientHeight);O.copy(P);u.update()}function F(e){N.set(e.clientX,e.clientY);j.subVectors(N,w);if(j.y>0){H(R())}else if(j.y<0){K(R())}w.copy(N);u.update()}function U(e){A.set(e.clientX,e.clientY);L.subVectors(A,v).multiplyScalar(u.panSpeed);_(L.x,L.y);v.copy(A);u.update()}function V(e){if(e.deltaY<0){K(R())}else if(e.deltaY>0){H(R())}u.update()}function G(e){let t=false;switch(e.code){case u.keys.UP:if(e.ctrlKey||e.metaKey||e.shiftKey){S(2*Math.PI*u.rotateSpeed/u.domElement.clientHeight)}else{_(0,u.keyPanSpeed)}t=true;break;case u.keys.BOTTOM:if(e.ctrlKey||e.metaKey||e.shiftKey){S(-2*Math.PI*u.rotateSpeed/u.domElement.clientHeight)}else{_(0,-u.keyPanSpeed)}t=true;break;case u.keys.LEFT:if(e.ctrlKey||e.metaKey||e.shiftKey){x(2*Math.PI*u.rotateSpeed/u.domElement.clientHeight)}else{_(u.keyPanSpeed,0)}t=true;break;case u.keys.RIGHT:if(e.ctrlKey||e.metaKey||e.shiftKey){x(-2*Math.PI*u.rotateSpeed/u.domElement.clientHeight)}else{_(-u.keyPanSpeed,0)}t=true;break}if(t){e.preventDefault();u.update()}}function B(){if(M.length===1){O.set(M[0].pageX,M[0].pageY)}else{const e=.5*(M[0].pageX+M[1].pageX);const t=.5*(M[0].pageY+M[1].pageY);O.set(e,t)}}function W(){if(M.length===1){v.set(M[0].pageX,M[0].pageY)}else{const e=.5*(M[0].pageX+M[1].pageX);const t=.5*(M[0].pageY+M[1].pageY);v.set(e,t)}}function q(){const e=M[0].pageX-M[1].pageX;const t=M[0].pageY-M[1].pageY;const n=Math.sqrt(e*e+t*t);w.set(0,n)}function Q(){if(u.enableZoom)q();if(u.enablePan)W()}function J(){if(u.enableZoom)q();if(u.enableRotate)B()}function $(e){if(M.length==1){P.set(e.pageX,e.pageY)}else{const t=Ee(e);const n=.5*(e.pageX+t.x);const o=.5*(e.pageY+t.y);P.set(n,o)}T.subVectors(P,O).multiplyScalar(u.rotateSpeed);const t=u.domElement;x(2*Math.PI*T.x/t.clientHeight);S(2*Math.PI*T.y/t.clientHeight);O.copy(P)}function ee(e){if(M.length===1){A.set(e.pageX,e.pageY)}else{const t=Ee(e);const n=.5*(e.pageX+t.x);const o=.5*(e.pageY+t.y);A.set(n,o)}L.subVectors(A,v).multiplyScalar(u.panSpeed);_(L.x,L.y);v.copy(A)}function te(e){const t=Ee(e);const n=e.pageX-t.x;const o=e.pageY-t.y;const a=Math.sqrt(n*n+o*o);N.set(0,a);j.set(0,Math.pow(N.y/w.y,u.zoomSpeed));H(j.y);w.copy(N)}function ne(e){if(u.enableZoom)te(e);if(u.enablePan)ee(e)}function oe(e){if(u.enableZoom)te(e);if(u.enableRotate)$(e)}function ae(e){if(u.enabled===false)return;if(M.length===0){u.domElement.setPointerCapture(e.pointerId);u.domElement.addEventListener("pointermove",ie);u.domElement.addEventListener("pointerup",se)}he(e);if(e.pointerType==="touch"){ue(e)}else{ce(e)}}function ie(e){if(u.enabled===false)return;if(e.pointerType==="touch"){pe(e)}else{re(e)}}function se(e){de(e);if(M.length===0){u.domElement.releasePointerCapture(e.pointerId);u.domElement.removeEventListener("pointermove",ie);u.domElement.removeEventListener("pointerup",se)}u.dispatchEvent(l);f=p.NONE}function ce(e){let t;switch(e.button){case 0:t=u.mouseButtons.LEFT;break;case 1:t=u.mouseButtons.MIDDLE;break;case 2:t=u.mouseButtons.RIGHT;break;default:t=-1}switch(t){case n.DOLLY:if(u.enableZoom===false)return;z(e);f=p.DOLLY;break;case n.ROTATE:if(e.ctrlKey||e.metaKey||e.shiftKey){if(u.enablePan===false)return;X(e);f=p.PAN}else{if(u.enableRotate===false)return;C(e);f=p.ROTATE}break;case n.PAN:if(e.ctrlKey||e.metaKey||e.shiftKey){if(u.enableRotate===false)return;C(e);f=p.ROTATE}else{if(u.enablePan===false)return;X(e);f=p.PAN}break;default:f=p.NONE}if(f!==p.NONE){u.dispatchEvent(r)}}function re(e){switch(f){case p.ROTATE:if(u.enableRotate===false)return;Z(e);break;case p.DOLLY:if(u.enableZoom===false)return;F(e);break;case p.PAN:if(u.enablePan===false)return;U(e);break}}function le(e){if(u.enabled===false||u.enableZoom===false||f!==p.NONE)return;e.preventDefault();u.dispatchEvent(r);V(e);u.dispatchEvent(l)}function me(e){if(u.enabled===false||u.enablePan===false)return;G(e)}function ue(e){be(e);switch(M.length){case 1:switch(u.touches.ONE){case o.ROTATE:if(u.enableRotate===false)return;B();f=p.TOUCH_ROTATE;break;case o.PAN:if(u.enablePan===false)return;W();f=p.TOUCH_PAN;break;default:f=p.NONE}break;case 2:switch(u.touches.TWO){case o.DOLLY_PAN:if(u.enableZoom===false&&u.enablePan===false)return;Q();f=p.TOUCH_DOLLY_PAN;break;case o.DOLLY_ROTATE:if(u.enableZoom===false&&u.enableRotate===false)return;J();f=p.TOUCH_DOLLY_ROTATE;break;default:f=p.NONE}break;default:f=p.NONE}if(f!==p.NONE){u.dispatchEvent(r)}}function pe(e){be(e);switch(f){case p.TOUCH_ROTATE:if(u.enableRotate===false)return;$(e);u.update();break;case p.TOUCH_PAN:if(u.enablePan===false)return;ee(e);u.update();break;case p.TOUCH_DOLLY_PAN:if(u.enableZoom===false&&u.enablePan===false)return;ne(e);u.update();break;case p.TOUCH_DOLLY_ROTATE:if(u.enableZoom===false&&u.enableRotate===false)return;oe(e);u.update();break;default:f=p.NONE}}function fe(e){if(u.enabled===false)return;e.preventDefault()}function he(e){M.push(e)}function de(e){delete k[e.pointerId];for(let t=0;t<M.length;t++){if(M[t].pointerId==e.pointerId){M.splice(t,1);return}}}function be(e){let t=k[e.pointerId];if(t===undefined){t=new s;k[e.pointerId]=t}t.set(e.pageX,e.pageY)}function Ee(e){const t=e.pointerId===M[0].pointerId?M[1]:M[0];return k[t.pointerId]}u.domElement.addEventListener("contextmenu",fe);u.domElement.addEventListener("pointerdown",ae);u.domElement.addEventListener("pointercancel",se);u.domElement.addEventListener("wheel",le,{passive:false});this.update()}}export{m as OrbitControls};