@sjcrh/proteinpaint-client 2.200.0 → 2.201.0

package/dist/svgraph-55XRIYJW.js

@@ -0,0 +1,1387 @@
+import {
+  appear2 as appear,
+  colorantisense,
+  disappear2 as disappear,
+  font,
+  getdomaintypes,
+  keyupEnter,
+  sayerror,
+  to_svg
+} from "./chunk-K6OVOHIZ.js";
+import {
+  genomic2gm,
+  rna2gmcoord
+} from "./chunk-HJ6L54YS.js";
+import "./chunk-XFAL46LZ.js";
+import "./chunk-HQAJVJCQ.js";
+import {
+  Menu
+} from "./chunk-HYOEWQ5P.js";
+import "./chunk-6QCYT6G2.js";
+import "./chunk-FN5XPUPH.js";
+import "./chunk-IIT367QZ.js";
+import "./chunk-RZGEKL77.js";
+import "./chunk-ZFJUVP2N.js";
+import "./chunk-R3ARQMM4.js";
+import {
+  dofetch3
+} from "./chunk-4USLEUNR.js";
+import "./chunk-4WF3XDQP.js";
+import "./chunk-X6VTVZY7.js";
+import "./chunk-M3J4MINX.js";
+import "./chunk-PF4DSFDR.js";
+import "./chunk-L44P5N4U.js";
+import {
+  proteinDomainColorScale
+} from "./chunk-GEQUQ3GG.js";
+import "./chunk-WPHUM5S5.js";
+import "./chunk-75T7ESEO.js";
+import {
+  link_default,
+  simulation_default,
+  x_default,
+  y_default
+} from "./chunk-2KXLYFAO.js";
+import "./chunk-LOZEKOES.js";
+import "./chunk-VQZ2Z5YU.js";
+import {
+  linear
+} from "./chunk-UJELJXJG.js";
+import "./chunk-FXQXCOII.js";
+import "./chunk-TLT4YIG3.js";
+import "./chunk-5R63Q5KH.js";
+import {
+  pointer_default,
+  select_default
+} from "./chunk-I6Y4O3RR.js";
+import {
+  rgb
+} from "./chunk-Q5RDQNIT.js";
+import "./chunk-DQC5FFGV.js";
+import "./chunk-HFNDKYVF.js";
+
+// src/hm2.legend.js
+function hm2legend(hm, rectFillFxn, textFxn, iconStroke, itemOpacity) {
+  let currlinex = 0;
+  let currliney = 0;
+  let defaults;
+  let currG;
+  init();
+  function main(g) {
+    currG = g;
+    currlinex = hm.legendpadleft;
+    currliney = 0;
+    g.selectAll("g").remove();
+    g.attr("transform", hm.legendontop ? null : "translate(0," + hm.svgh + ")").on(
+      "mouseover.tphm2",
+      hm.handlers.legend.mouseover
+    );
+    const l = g.selectAll("g").data(hm.h.legend);
+    l.exit().remove();
+    l.enter().append("g").each(addGroup);
+    return currliney + hm.legendlineh + hm.legendpadbtm;
+  }
+  function init() {
+    defaults = {
+      legendontop: true,
+      legendh: 0,
+      legendlineh: 25,
+      legendpadx: 5,
+      legendpadleft: 150,
+      legendpadright: 20,
+      legendpadbtm: 30,
+      legendfontsize: 12,
+      legendiconh: 10,
+      legendiconw: 10,
+      samplecount4legend: true,
+      legendhangleft: 1,
+      legendlinesep: false,
+      legendmutationorder: [
+        "M",
+        "E",
+        "F",
+        "N",
+        "S",
+        "D",
+        "I",
+        "P",
+        "L",
+        "Intron",
+        "ITD",
+        "DEL",
+        "NLOSS",
+        "CLOSS",
+        "Utr3",
+        "Utr5",
+        "X",
+        "noncoding",
+        "Fuserna",
+        "SV",
+        "CNV_amp",
+        "CNV_loss",
+        "snv",
+        "mnv"
+      ]
+    };
+    for (let key in defaults) {
+      if (!(key in hm)) hm[key] = defaults[key];
+    }
+  }
+  function addGroup(d, i) {
+    if (!d.items || !d.items.length) return;
+    currlinex = 0;
+    currliney += hm.legendlineh;
+    let g = select_default(this);
+    const leftdist = hm.legendhangleft ? hm.legendpadleft + hm.legendhangleft - hm.legendpadx : hm.legendpadleft;
+    const grplabel = g.append("text").attr("transform", "translate(" + leftdist + "," + (currliney + hm.legendiconh / 2) + ")").attr("text-anchor", hm.legendhangleft ? "end" : "start").attr("font-weight", 700).attr("font-size", hm.legendfontsize).attr("dominant-baseline", "central").text(d.text + (hm.samplecount4legend ? " (sample count)" : ""));
+    if (hm.linesep) {
+      currlinex = hm.legendpadleft;
+      currliney += hm.legendlineh;
+    } else if (hm.legendhangleft) {
+      currlinex = leftdist + 2 * hm.legendpadx;
+    } else {
+      currlinex += hm.legendpadleft + grplabel.node().getBBox().width + 2 * hm.legendpadx;
+    }
+    if (d.sorter) d.items.sort(d.sorter);
+    g.selectAll("g").data(d.items).enter().append("g").each(addItem);
+  }
+  function addItem(d, i) {
+    let g = select_default(this).attr("transform", "translate(" + currlinex + "," + currliney + ")").style("opacity", itemOpacity);
+    const itemlabel = g.append("text").attr("transform", "translate(" + (hm.legendiconw + hm.legendpadx / 2) + "," + hm.legendiconh / 2 + ")").attr("font-size", hm.legendfontsize).attr("dominant-baseline", "central").each(function(d2) {
+      const t = select_default(this);
+      if (typeof d2.text == "string") {
+        t.text(textFxn(d2));
+      } else if (Array.isArray(d2.text)) {
+        t.selectAll("tspan").data(d2.text).enter().append("tspan").text((d3) => d3).attr("dominant-baseline", "central").attr("x", function(dd, i2) {
+          if (i2 == 0) {
+            select_default(this).attr("font-weight", 700);
+            d2.lastx = select_default(this).node().getComputedTextLength() + 10;
+            return 0;
+          } else if (d2.lastx) {
+            return d2.lastx;
+          }
+        });
+      }
+    });
+    const bbox = itemlabel.node().getBBox();
+    currlinex += hm.legendiconw + bbox.width + 2.5 * hm.legendpadx;
+    if (hm.legendlinesep || currlinex > hm.svgw - hm.legendpadright) {
+      currliney += hm.legendlineh;
+      const leftdist = !hm.legendhangleft ? hm.legendpadleft : hm.legendpadleft + hm.legendhangleft + hm.legendpadx;
+      g.attr("transform", "translate(" + leftdist + "," + currliney + ")");
+      currlinex = hm.legendiconw + bbox.width + 2.5 * hm.legendpadx + hm.legendpadleft;
+      if (hm.legendhangleft) currlinex = hm.legendiconw + bbox.width + 2.5 * hm.legendpadx + leftdist;
+      else currlinex = hm.legendiconw + bbox.width + 2.5 * hm.legendpadx + hm.legendpadleft;
+    }
+    g.append("rect").attr("height", hm.legendiconh).attr("width", hm.legendiconw).attr("y", hm.legendfontsize - bbox.height + (bbox.height - hm.legendiconh) / 2).attr("fill", rectFillFxn).attr("stroke", iconStroke).attr("shape-rendering", "crispEdges");
+  }
+  main.defaults = defaults;
+  main.finalizePos = function(h) {
+    currG.transition().duration(hm.duration).attr("transform", hm.legendontop ? null : "translate(0," + (hm.svgh + h) + ")");
+  };
+  return main;
+}
+
+// src/svgraph.js
+function svgraph_default(arg) {
+  const outborder = "#ddd";
+  const pairlst = arg.pairlst;
+  const genome = arg.genome;
+  const errdiv = arg.holder.append("div");
+  const waitdiv = arg.holder.append("div");
+  const tmp = arg.holder.append("div").style("display", "inline-block").style("border", "solid 1px " + outborder);
+  const svgdiv = tmp.append("div").style("margin", "10px");
+  const buttdiv = tmp.append("div").style("margin-top", "5px").style("padding", "10px 20px").style("background-color", "#ededed");
+  const domaindiv = tmp.append("div").style("margin", "10px").style("display", "none");
+  const colormenu = new Menu({ padding: "10px" });
+  function err(m) {
+    sayerror(errdiv, m);
+  }
+  const noset = /* @__PURE__ */ new Set();
+  const nolst = [];
+  for (const point of pairlst) {
+    if (point.a.gm) {
+      const n = point.a.gm.isoform;
+      if (genome.isoformcache.has(n)) {
+        point.a.gm = genome.isoformmatch(n, point.a.chr, point.a.position);
+      } else {
+        noset.add(n);
+        nolst.push(point.a);
+      }
+    }
+    if (point.b.gm) {
+      const n = point.b.gm.isoform;
+      if (genome.isoformcache.has(n)) {
+        point.b.gm = genome.isoformmatch(n, point.b.chr, point.b.position);
+      } else {
+        noset.add(n);
+        nolst.push(point.b);
+      }
+    }
+  }
+  if (noset.size == 0) {
+    validate();
+    return;
+  }
+  const loadlst = [];
+  for (const n of noset) {
+    loadlst.push(n);
+  }
+  dofetch3("isoformlst", { method: "POST", body: JSON.stringify({ genome: genome.name, lst: loadlst }) }).then((data) => {
+    if (data.error) throw { message: data.error };
+    for (const ilst of data.lst) {
+      if (ilst[0]) {
+        genome.isoformcache.set(ilst[0].isoform.toUpperCase(), ilst);
+      }
+    }
+    const errlst = [];
+    for (const node of nolst) {
+      const gm = genome.isoformmatch(node.gm.isoform, node.chr, node.position);
+      if (!gm) {
+        errlst.push(node.gm.isoform);
+        delete node.gm;
+      } else {
+        node.gm = gm;
+      }
+    }
+    if (errlst.length) {
+      err("invalid isoform: " + errlst.join(","));
+    }
+    validate();
+  }).catch((e) => {
+    err(e.message);
+    if (e.stack) console.log(e.stack);
+  });
+  async function validate() {
+    for (const point of pairlst) {
+      if (point.a.strand == void 0) {
+        point.a.strand = point.a.gm.strand;
+      }
+      if (point.b.strand == void 0) {
+        point.b.strand = point.b.gm.strand;
+      }
+    }
+    for (const p of pairlst) {
+      let e = nodecheck(p.a);
+      if (e) {
+        return err(e);
+      }
+      e = nodecheck(p.b);
+      if (e) {
+        return err(e);
+      }
+    }
+    for (let i = 1; i < pairlst.length; i++) {
+      const curr = pairlst[i].a;
+      const prev = pairlst[i - 1].b;
+      if (curr.chr != prev.chr)
+        return err("Error: mismatched chromosome at multi-seg breakpoint " + i + ": " + curr.chr + " != " + prev.chr);
+      if (curr.strand != prev.strand) return err("Error: mismatched strand at multi-seg breakpoint " + i);
+      if (curr.gm) {
+        if (prev.gm) {
+          if (curr.gm.isoform != prev.gm.isoform) {
+            return err(
+              "Error: mismatched gene in two breakpoints: " + prev.gm.symbol + " " + prev.gm.isoform + ", " + curr.gm.symbol + " " + curr.gm.isoform
+            );
+          }
+        } else {
+          prev.gm = curr.gm;
+          err("In multi-segment at " + i + ", 5' breakpoint is joined to the same gene model of 3'");
+          const t = genomic2gm(prev.position, curr.gm, 5);
+          prev.exonbp = t.rnapos;
+          prev.codon = t.aapos;
+          prev.atintron = t.atintron;
+          prev.exon = t.atexon;
+          prev.atutr3 = t.atutr3;
+          prev.atutr5 = t.atutr5;
+          prev.atupstream = t.atupstream;
+          prev.atdownstream = t.atdownstream;
+        }
+      } else {
+        if (prev.gm) {
+          curr.gm = prev.gm;
+          err("In multi-segment at " + i + ", 3' breakpoint is joined to the same gene model of 5'");
+          const t = genomic2gm(curr.position, prev.gm, 5);
+          curr.exonbp = t.rnapos;
+          curr.codon = t.aapos;
+          curr.atintron = t.atintron;
+          curr.exon = t.atexon;
+          curr.atutr3 = t.atutr3;
+          curr.atutr5 = t.atutr5;
+          curr.atupstream = t.atupstream;
+          curr.atdownstream = t.atdownstream;
+        }
+      }
+    }
+    const noset2 = /* @__PURE__ */ new Set();
+    for (const point of pairlst) {
+      if (point.a.gm && !point.a.gm.pdomains) {
+        noset2.add(point.a.gm.isoform);
+      }
+      if (point.b.gm && !point.b.gm.pdomains) {
+        noset2.add(point.b.gm.isoform);
+      }
+    }
+    if (noset2.size == 0) {
+      new draw();
+      return;
+    }
+    const loadlst2 = [];
+    for (const n of noset2) {
+      loadlst2.push(n);
+    }
+    waitdiv.style("margin", "5px").text("Loading protein domains ...");
+    const datalst = await getPdomains(loadlst2);
+    for (const i of datalst) {
+      const s = proteinDomainColorScale();
+      for (const d of i.pdomains) {
+        if (!d.color) {
+          d.color = s(d.name + d.description);
+        }
+      }
+      const n = i.name.toUpperCase();
+      if (genome.isoformcache.has(n)) {
+        for (const ii of genome.isoformcache.get(n)) {
+          ii.pdomains = i.pdomains;
+          ii.domain_hidden = {};
+        }
+      }
+    }
+    new draw();
+  }
+  async function getPdomains(loadlst2) {
+    const data = await dofetch3("pdomain", {
+      method: "POST",
+      body: JSON.stringify({ genome: genome.name, isoforms: loadlst2 })
+    });
+    if (data.error) throw data.error;
+    else waitdiv.remove();
+    return data.lst;
+  }
+  function draw() {
+    const scaffold = [];
+    let scfid = 0;
+    for (let i = 0; i < pairlst.length; i++) {
+      const point = pairlst[i];
+      let scf;
+      if (i > 0) {
+        scf = scaffold[scaffold.length - 1];
+      }
+      if (point.a.gm) {
+        if (!scf) {
+          scf = {
+            gm: point.a.gm,
+            strand: point.a.gm.strand,
+            id: scfid++,
+            name: point.a.name ? point.a.name : point.a.gm.name
+          };
+          if (point.a.gm.coding) {
+            scf.aalen = point.a.gm.cdslen / 3;
+          } else {
+            if (!point.a.gm.rnalen) {
+              err("no aacount or rnalen for " + point.a.gm.symbol + " " + point.a.gm.isoform);
+              return;
+            }
+            scf.bplen = point.a.gm.rnalen;
+          }
+        }
+        if (point.a.atutr3) {
+          scf.utr3bp = point.a.atutr3.total;
+        }
+        if (point.a.atutr5) {
+          scf.utr5bp = point.a.atutr5.total;
+        }
+        if (point.a.atupstream) {
+          scf.upstream = Math.max(scf.upstream ? scf.upstream : 0, point.a.atupstream.off);
+        }
+        if (point.a.atdownstream) {
+          scf.downstream = Math.max(scf.downstream ? scf.downstream : 0, point.a.atdownstream.off);
+        }
+      } else {
+        if (!scf) {
+          scf = {
+            chr: point.a.chr,
+            id: scfid++,
+            start: point.a.position,
+            stop: point.a.position,
+            name: point.a.name ? point.a.name : point.a.chr
+          };
+        }
+        scf.start = Math.min(scf.start, point.a.position);
+        scf.stop = Math.max(scf.stop, point.a.position);
+      }
+      point.a.scfid = scf.id;
+      if (i == 0) {
+        scaffold.push(scf);
+      }
+      if (point.interstitial) {
+        scf = {
+          nontemplate: true,
+          id: scfid++
+        };
+        if (point.interstitial.aalen) {
+          scf.aalen = point.interstitial.aalen;
+          scf.name = scf.aalen + " AA insertion";
+        } else if (point.interstitial.bplen) {
+          scf.aalen = point.interstitial.bplen / 3;
+          scf.name = scf.bplen + " bp insertion";
+        }
+        scaffold.push(scf);
+        point.interstitial.scfid = scf.id;
+      }
+      if (point.b.gm) {
+        scf = {
+          gm: point.b.gm,
+          strand: point.b.gm.strand,
+          id: scfid++,
+          name: point.b.name ? point.b.name : point.b.gm.symbol
+        };
+        if (point.b.gm.coding) {
+          scf.aalen = point.b.gm.cdslen / 3;
+        } else {
+          if (!point.b.gm.rnalen) {
+            err("no aacount or rnalen for " + point.b.gm.symbol + " " + point.b.gm.isoform);
+            return;
+          }
+          scf.bplen = point.b.gm.rnalen;
+        }
+        if (point.b.atutr3) {
+          scf.utr3bp = point.b.atutr3.total;
+        }
+        if (point.b.atutr5) {
+          scf.utr5bp = point.b.atutr5.total;
+        }
+        if (point.b.atupstream) {
+          scf.upstream = Math.max(scf.upstream ? scf.upstream : 0, point.b.atupstream.off);
+        }
+        if (point.b.atdownstream) {
+          scf.downstream = Math.max(scf.downstream ? scf.downstream : 0, point.b.atdownstream.off);
+        }
+      } else {
+        scf = {
+          chr: point.b.chr,
+          id: scfid++,
+          start: point.b.position,
+          stop: point.b.position,
+          name: point.b.name ? point.b.name : point.b.chr
+        };
+        scf.start = Math.min(scf.start, point.b.position);
+        scf.stop = Math.max(scf.stop, point.b.position);
+      }
+      point.b.scfid = scf.id;
+      scaffold.push(scf);
+    }
+    for (const s of scaffold) {
+      s.nodes = [];
+      s.clipid0 = Math.ceil(Math.random() * 1e5);
+      s.clipid = "url(#" + s.clipid0 + ")";
+    }
+    for (const s of scaffold) {
+      if (!s.gm) continue;
+      const g = {
+        name: s.gm.name,
+        isoform: s.gm.isoform,
+        codingstart: s.gm.codingstart,
+        codingstop: s.gm.codingstop,
+        strand: s.gm.strand,
+        aaseq: s.gm.aaseq,
+        exon: s.gm.exon,
+        utr3: s.gm.utr3,
+        utr5: s.gm.utr5,
+        cdslen: s.gm.cdslen,
+        pdomains: [],
+        domain_hidden: s.gm.domain_hidden
+      };
+      if (s.gm.pdomains) {
+        for (const a of s.gm.pdomains) {
+          const b = {};
+          for (const k in a) {
+            b[k] = a[k];
+          }
+          g.pdomains.push(b);
+        }
+      }
+      s.gm = g;
+    }
+    const connheight = 90, pad4 = 5, regionthick = 3;
+    for (const s of scaffold) {
+      s.idealy = connheight * s.id + (pad4 + regionthick) * 2 * s.id;
+    }
+    this.width = this.width0 = 400;
+    const dragwidth = 20, dragheight = 20, toppad = 70, bottompad = 70, proteinheight = 26, pad2 = 5, pad3 = 5, scffontsize = 15, nodefontsize = 13, descfontsize = 12, pad5 = 5, pad6 = 3, pad7 = 10;
+    let height = toppad + bottompad + proteinheight * scaffold.length + (pad4 * 2 + regionthick * 2 + connheight) * (scaffold.length - 1);
+    let leftpad = 40, rightpad = 40;
+    const data = { nodes: [], links: [] };
+    for (let i = 0; i < pairlst.length; i++) {
+      const point = pairlst[i];
+      const left = copynode(point.a, scaffold, data);
+      left.x = this.width / 2;
+      left.y = height / 2;
+      let midleft = null, midright = null;
+      if (point.interstitial) {
+        const _scf = scaffold[point.interstitial.scfid];
+        midleft = {
+          nontemplate: true,
+          scfid: point.interstitial.scfid,
+          softlink3: left,
+          x: arg.quiet ? this.width / 2 : 0,
+          y: arg.quiet ? _scf.idealy : height / 2
+        };
+        left.softlink5 = midleft;
+        data.nodes.push(midleft);
+        _scf.nodes.push(midleft);
+        midright = {
+          nontemplate: true,
+          scfid: point.interstitial.scfid,
+          x: arg.quiet ? this.width / 2 : 0,
+          y: arg.quiet ? _scf.idealy : height / 2
+        };
+        data.nodes.push(midright);
+        _scf.nodes.push(midright);
+        midleft.hardlink = midright;
+        midright.hardlink = midleft;
+      }
+      const right = copynode(point.b, scaffold, data);
+      right.x = this.width / 2;
+      right.y = height / 2;
+      if (midright) {
+        midright.softlink5 = right;
+        right.softlink3 = midright;
+        data.links.push({
+          source: data.nodes.length - 4,
+          target: data.nodes.length - 3
+        });
+        data.links.push({
+          source: data.nodes.length - 2,
+          target: data.nodes.length - 1
+        });
+      } else {
+        left.softlink5 = right;
+        right.softlink3 = left;
+        data.links.push({
+          source: data.nodes.length - 2,
+          target: data.nodes.length - 1
+        });
+      }
+      if (i > 0) {
+        const prev = data.nodes[data.nodes.length - 3 - (point.interstitial ? 2 : 0)];
+        left.hardlink = prev;
+        prev.hardlink = left;
+      }
+    }
+    let gmmaxaa = 0, chrmaxspan = 0;
+    for (const scf of scaffold) {
+      if (scf.gm) {
+        scf.aatotal = (scf.aalen ? scf.aalen : scf.bplen / 3) + ((scf.utr3bp ? scf.utr3bp : 0) + (scf.utr5bp ? scf.utr5bp : 0) + (scf.upstream ? scf.upstream : 0) + (scf.downstream ? scf.downstream : 0)) / 3;
+        gmmaxaa = Math.max(gmmaxaa, scf.aatotal);
+      } else if (scf.nontemplate) {
+        gmmaxaa = Math.max(gmmaxaa, scf.aalen);
+      } else {
+        chrmaxspan = Math.max(chrmaxspan, scf.stop - scf.start);
+      }
+    }
+    if (chrmaxspan == 0) {
+      chrmaxspan = 1e3;
+    }
+    let chrsegml = 0;
+    for (const s of scaffold) {
+      if (!s.gm && !s.nontemplate) {
+        s.start -= chrmaxspan;
+        s.stop += chrmaxspan;
+        chrsegml = Math.max(chrsegml, s.stop - s.start);
+      }
+    }
+    let maxgmpxwidth = this.width;
+    let maxchrpxwidth = this.width * 0.7;
+    for (const scf of scaffold) {
+      if (scf.gm) {
+        scf.pxwidth = maxgmpxwidth * scf.aatotal / gmmaxaa;
+        scf.scale = linear().domain([0, scf.aatotal]).range([0, scf.pxwidth]);
+      } else if (scf.nontemplate) {
+        scf.pxwidth = maxgmpxwidth * scf.aalen / gmmaxaa;
+        scf.scale = linear().domain([0, scf.aalen]).range([0, scf.pxwidth]);
+      } else {
+        scf.pxwidth = maxchrpxwidth * (scf.stop - scf.start) / chrsegml;
+        scf.scale = linear().domain([scf.start, scf.stop]).range([0, scf.pxwidth]);
+      }
+      if (scf.nontemplate) {
+        scf.nodes[0].xoff = 0;
+        scf.nodes[1].xoff = scf.pxwidth;
+        continue;
+      }
+      for (const n of scf.nodes) {
+        if (!scf.gm) {
+          n.xoff = scf.scale(n.position);
+          continue;
+        }
+        if (n.atupstream) {
+          n.aaoff = (scf.upstream - n.atupstream.off) / 3;
+        } else if (n.atutr5) {
+          n.aaoff = (scf.upstream ? scf.upstream / 3 : 0) + n.atutr5.off / 3;
+        } else if (n.atutr3) {
+          n.aaoff = (scf.upstream ? scf.upstream / 3 : 0) + (scf.utr5bp ? scf.utr5bp / 3 : 0) + (scf.aalen ? scf.aalen : scf.bplen / 3) + n.atutr3.off / 3;
+        } else if (n.atdownstream) {
+          n.aaoff = (scf.upstream ? scf.upstream / 3 : 0) + (scf.utr5bp ? scf.utr5bp / 3 : 0) + (scf.aalen ? scf.aalen : scf.bplen / 3) + (scf.utr3bp ? scf.utr3bp / 3 : 0) + n.atdownstream.off / 3;
+        } else {
+          n.aaoff = (scf.upstream ? scf.upstream / 3 : 0) + (scf.utr5bp ? scf.utr5bp / 3 : 0) + (n.codon ? n.codon : n.exonbp / 3);
+        }
+        n.xoff = scf.scale(n.aaoff);
+      }
+      scf.nodes.sort((a, b) => {
+        if (!scf.gm) return a.position - b.position;
+        if (a.atupstream) {
+          if (b.atupstream) return a.atupstream.off - b.atupstream.off;
+          return -1;
+        }
+        if (a.atutr5) {
+          if (b.atupstream) return 1;
+          if (b.atutr5) return a.atutr5.off - b.atutr5.off;
+          return -1;
+        }
+        if (a.atutr3) {
+          if (b.atupstream || b.atutr5) return 1;
+          if (b.atutr3) return a.atutr3.off - b.atutr3.off;
+          if (b.atdownstream) return -1;
+          return 1;
+        }
+        if (a.atdownstream) {
+          if (b.atdownstream) return a.atdownstream.off - b.atdownstream.off;
+          return 1;
+        }
+        if (b.atupstream || b.atutr5) return 1;
+        if (b.atdownstream || b.atutr3) return -1;
+        if (a.exonbp) return a.exonbp - b.exonbp;
+        return a.codon - b.codon;
+      });
+    }
+    for (const s of scaffold) {
+      if (s.gm && s.gm.pdomains) {
+        s.gm.pdomains.forEach(function(i) {
+          i.__scf = s;
+        });
+      }
+    }
+    data.nodes[0].hardlink = {};
+    data.nodes[data.nodes.length - 1].hardlink = {};
+    const setheadtail = () => {
+      let n = data.nodes[0];
+      let scf = scaffold[n.scfid];
+      if (scf.gm) {
+        if (n.strand != scf.gm.strand) {
+          n.hardlink.xoff = scf.pxwidth;
+        } else {
+          n.hardlink.xoff = 0;
+        }
+      } else {
+        if (n.strand == "+") {
+          n.hardlink.xoff = 0;
+        } else {
+          n.hardlink.xoff = scf.pxwidth;
+        }
+      }
+      n = data.nodes[data.nodes.length - 1];
+      scf = scaffold[n.scfid];
+      if (scf.gm) {
+        if (n.strand != scf.gm.strand) {
+          n.hardlink.xoff = 0;
+        } else {
+          n.hardlink.xoff = scf.pxwidth;
+        }
+      } else {
+        if (n.strand == "+") {
+          n.hardlink.xoff = scf.pxwidth;
+        } else {
+          n.hardlink.xoff = 0;
+        }
+      }
+    };
+    setheadtail();
+    const svg = svgdiv.append("svg");
+    const g0 = svg.append("g");
+    const simulation = simulation_default(data.nodes).force("link", link_default().links(data.links));
+    const scfg = g0.selectAll().data(scaffold).enter().append("g");
+    const link = g0.selectAll().data(data.links).enter().append("line").attr("stroke", "black").attr("stroke-dasharray", "3,2");
+    const node = g0.selectAll().data(data.nodes).enter().append("g");
+    const nodelabel = node.filter((d) => d.label).append("text").text((d) => d.label).attr("font-family", font).attr("font-size", nodefontsize).attr("fill", "black").each(function(d) {
+      d.labelwidth = this.getBBox().width;
+    });
+    const nodelabel2 = node.filter((d) => d.antisense).append("text").text("antisense").attr("font-family", font).attr("font-size", nodefontsize).attr("fill", colorantisense).each(function(d) {
+      d.labelwidth = Math.max(this.getBBox().width, d.labelwidth);
+    });
+    for (const d of data.nodes) {
+      if (!d.labelwidth) {
+        continue;
+      }
+      leftpad = Math.max(leftpad, d.labelwidth - d.xoff);
+      rightpad = Math.max(rightpad, d.labelwidth - scaffold[d.scfid].pxwidth + d.xoff);
+    }
+    const nodebar = node.append("rect").attr("height", regionthick).attr("fill", (d) => d.antisense ? colorantisense : "black");
+    const scftick = scfg.append("line").attr("y1", (d, i) => i % 2 == 0 ? -pad6 : proteinheight).attr("stroke", "black").attr("stroke-opacity", 0).attr("shape-rendering", "crispEdges");
+    const nontmp = scfg.filter((d) => d.nontemplate);
+    nontmp.append("rect").attr("clip-path", (d) => d.clipid).attr("fill", "black");
+    const chrbar = scfg.filter((d) => !d.gm && !d.nontemplate);
+    chrbar.append("rect").attr("fill", "white").attr("clip-path", (d) => d.clipid);
+    const chrbarline1 = chrbar.append("line").attr("clip-path", (d) => d.clipid).attr("stroke", "black");
+    const chrbarline2 = chrbar.append("line").attr("clip-path", (d) => d.clipid).attr("stroke", "black");
+    const protein = scfg.filter((d) => d.gm);
+    const pupstream = protein.filter((d) => d.upstream).append("line").attr("clip-path", (d) => d.clipid).attr("stroke", "#545454").attr("stroke-dasharray", "2,1");
+    const p5utr = protein.filter((d) => d.utr5bp).append("line").attr("clip-path", (d) => d.clipid).attr("stroke", "#858585");
+    const p3utr = protein.filter((d) => d.utr3bp).append("line").attr("clip-path", (d) => d.clipid).attr("stroke", "#858585");
+    const pdownstream = protein.filter((d) => d.downstream).append("line").attr("clip-path", (d) => d.clipid).attr("stroke", "#545454").attr("stroke-dasharray", "2,1");
+    const pbg = protein.append("rect").attr("clip-path", (d) => d.clipid).attr("fill", "white");
+    const allpdomain = protein.filter((d) => d.gm.pdomains).selectAll().data((d) => d.gm.pdomains).enter().append("rect").attr("clip-path", (d) => d.__scf.clipid).attr("fill", (d) => d.color);
+    const exonboundary = protein.filter((d) => d.gm.exon.length > 1).selectAll().data((d) => {
+      let cum = 0;
+      const lst = [];
+      let utr5len = 0;
+      if (d.gm.utr5) {
+        for (const e of d.gm.utr5) {
+          utr5len += e[1] - e[0];
+        }
+      }
+      const cdslen = d.gm.cdslen || 0;
+      for (let i = 0; i < d.gm.exon.length - 1; i++) {
+        const e = d.gm.exon[i];
+        cum += e[1] - e[0];
+        const boundary = {
+          rnabp: cum,
+          scf: d
+        };
+        if (cum < utr5len) {
+          if (d.utr5bp) {
+            boundary.utr5 = true;
+          } else {
+            continue;
+          }
+        } else if (cum > utr5len + cdslen) {
+          if (d.utr3bp) {
+            boundary.utr3 = true;
+          } else {
+            continue;
+          }
+        }
+        if (!d.utr5bp) {
+          boundary.rnabp = cum - utr5len;
+        }
+        lst.push(boundary);
+      }
+      return lst;
+    }).enter().append("line").attr("clip-path", (boundary) => boundary.scf.clipid).attr("stroke", "black").attr("stroke-dasharray", "3,2").attr("shape-rendering", "crispEdges").attr("y1", (boundary) => {
+      return boundary.utr5 || boundary.utr3 ? proteinheight / 4 : 0;
+    }).attr("y2", (boundary) => {
+      return boundary.utr5 || boundary.utr3 ? proteinheight * 3 / 4 : proteinheight;
+    });
+    const pbox = protein.append("rect").attr("clip-path", (d) => d.clipid).attr("stroke-dasharray", (d) => d.bplen ? "4,2" : "none").attr("fill", "none").attr("stroke", "black");
+    const scflabel = scfg.append("text").text((d) => d.name).attr("font-family", font).attr("fill", "black").attr("font-size", scffontsize).attr("dominant-baseline", "central").each(function(d) {
+      d.chimericlabelw = d.labelwidth = this.getBBox().width;
+    });
+    for (const s of scaffold) {
+      rightpad = Math.max(rightpad, pad3 + s.labelwidth);
+    }
+    const scflabel2 = scfg.filter((d) => !d.nontemplate).append("text").attr("fill", "#858585").attr("fill-opacity", 0).attr("font-size", nodefontsize).attr("font-family", font).attr("text-anchor", "middle").attr("dominant-baseline", (d) => d.id % 2 == 0 ? "auto" : "hanging").text((d) => {
+      if (d.gm) {
+        if (d.nodes.length == 1) {
+          const n2 = d.nodes[0];
+          let what;
+          if (n2.atupstream) what = n2.atupstream.off + " bp upstream";
+          else if (n2.atdownstream) what = n2.atdownstream.off + " bp downstream";
+          else if (n2.atutr3) what = n2.atutr3.off + " bp in 3' UTR";
+          else if (n2.atutr5) what = n2.atutr5.off + " bp in 5' UTR";
+          else {
+            what = n2.codon ? n2.codon + " AA" : n2.exonbp + " bp";
+          }
+          if (n2.softlink5) return "ends at " + what;
+          return "starts at " + what;
+        }
+        let n = d.nodes[0];
+        let what1;
+        if (n.atupstream) what1 = n.atupstream.off + " bp upstream";
+        else if (n.atdownstream) what1 = n.atdownstream.off + " bp downstream";
+        else if (n.atutr3) what1 = n.atutr3.off + " bp in 3' UTR";
+        else if (n.atutr5) what1 = n.atutr5.off + " bp in 5' UTR";
+        else {
+          if (n.betweencodon) {
+            what1 = (n.codonsideN ? n.codon + 1 : n.codon) + " AA";
+          } else {
+            what1 = n.exonbp ? n.exonbp + " bp " : n.codon + " AA";
+          }
+        }
+        n = d.nodes[1];
+        let what2;
+        if (n.atupstream) what2 = n.atupstream.off + " bp upstream";
+        else if (n.atdownstream) what2 = n.atdownstream.off + " bp downstream";
+        else if (n.atutr3) what2 = n.atutr3.off + " bp in 3' UTR";
+        else if (n.atutr5) what2 = n.atutr5.off + " bp in 5' UTR";
+        else what2 = n.codon ? n.codon + " AA" : n.exonbp + " bp";
+        return "from " + what1 + " to " + what2;
+      }
+      if (d.nodes.length == 1) {
+        const n = d.nodes[0];
+        if (n.softlink5) return "ends at " + n.position + " bp";
+        return "starts at " + n.position + " bp";
+      }
+      return "from " + d.nodes[0].position + " bp to " + d.nodes[1].position + " bp";
+    }).each(function(d) {
+      d.chimericlabelw = Math.max(this.getBBox().width, d.chimericlabelw);
+    });
+    const scflabel3 = scfg.filter((d) => d.nodes[0].antisense).append("text").text("antisense").attr("fill", colorantisense).attr("fill-opacity", 0).attr("font-size", nodefontsize).attr("font-family", font).attr("text-anchor", "middle").attr("dominant-baseline", (d) => d.id % 2 == 0 ? "auto" : "hanging").each(function(d) {
+      d.chimericlabelw = Math.max(this.getBBox().width, d.chimericlabelw);
+    });
+    const scfcliprect = scfg.append("defs").append("clipPath").attr("id", (d) => d.clipid0).append("rect").attr("x", 0).attr("y", 0);
+    const scfkick = scfg.append("rect").attr("clip-path", (d) => d.clipid).attr("fill", "white").attr("fill-opacity", 0).on("mousemove", (event, d) => {
+      if (!d.gm) {
+        return;
+      }
+      let aa = d.scale.invert(pointer_default(event)[0]);
+      let pstr = null;
+      const domainlst = [];
+      if (d.upstream) {
+        if (aa * 3 < d.upstream) {
+          pstr = Math.floor(aa * 3) + " bp upstream of " + d.name;
+        } else {
+          aa -= d.upstream / 3;
+        }
+      }
+      if (!pstr) {
+        if (d.utr5bp) {
+          if (aa * 3 < d.utr5bp) {
+            pstr = Math.floor(aa * 3) + " bp in 5' UTR of " + d.name;
+          } else {
+            aa -= d.utr5bp / 3;
+          }
+        }
+      }
+      if (!pstr) {
+        if (d.aalen) {
+          if (aa <= d.aalen) {
+            const i = Math.floor(aa);
+            pstr = (d.gm.aaseq ? d.gm.aaseq[i] : "amino acid ") + i + " of " + d.name;
+            if (d.gm.pdomains) {
+              for (const dm of d.gm.pdomains) {
+                if (dm.start <= aa && dm.stop >= aa && !(dm.name + dm.description in d.gm.domain_hidden)) {
+                  domainlst.push(dm);
+                }
+              }
+            }
+          } else {
+            aa -= d.aalen;
+          }
+        } else {
+          if (aa * 3 < d.bplen) {
+            pstr = Math.floor(aa * 3) + " bp in " + d.name;
+          }
+          aa -= d.bplen / 3;
+        }
+      }
+      if (!pstr) {
+        if (d.utr3bp) {
+          if (aa * 3 < d.utr3bp) {
+            pstr = Math.floor(aa * 3) + " bp in 3' UTR of " + d.name;
+          } else {
+            aa -= d.utr3bp / 3;
+          }
+        }
+      }
+      if (!pstr) {
+        pstr = Math.floor(aa * 3) + " bp downstream of " + d.name;
+      }
+      gsays.selectAll("*").remove();
+      gsays.append("text").text(pstr).attr("dominant-baseline", "hanging").attr("font-family", font).attr("font-size", descfontsize);
+      let vsp = 5;
+      for (let i = 0; i < domainlst.length; i++) {
+        const dg = gsays.append("g").attr("transform", "translate(0," + (descfontsize + vsp) * (i + 1) + ")");
+        const dm = domainlst[i];
+        const col = dm.color;
+        dg.append("rect").attr("width", descfontsize).attr("height", descfontsize).attr("fill", col).attr("stroke", rgb(col).darker(2).toString());
+        let w;
+        dg.append("text").text(dm.name).attr("x", descfontsize + 5).attr("dominant-baseline", "hanging").attr("font-family", font).attr("font-size", descfontsize).attr("fill", "black").each(function() {
+          w = this.getBBox().width;
+        });
+        dg.append("text").text(dm.description).attr("x", descfontsize + 5 + w + 5).attr("dominant-baseline", "hanging").attr("font-family", font).attr("font-size", descfontsize).attr("fill", "#858585");
+      }
+      svg.attr(
+        "height",
+        height - bottompad + Math.max(bottompad, pad7 + (descfontsize + vsp) * (domainlst.length + 1))
+      );
+    }).on("mouseout", () => {
+      gsays.selectAll("*").remove();
+      svg.attr("height", height);
+    });
+    const gsays = svg.append("g");
+    const drag = svg.append("text").text("drag to resize").attr("class", "sja_svgtext").attr("fill", "black").attr("font-size", 12).attr("text-anchor", "end").on("mousedown", (event) => {
+      const b = select_default(document.body);
+      const x0 = event.clientX, y0 = event.clientY;
+      b.on("mousemove", (event2) => {
+        event2.preventDefault();
+        this.width = this.width0 + event2.clientX - x0;
+        setpxsize();
+        if (chimeric) {
+          tochimeric(false);
+        } else {
+          simulation.restart();
+        }
+      });
+      b.on("mouseup", () => {
+        this.width0 = this.width;
+        b.on("mousemove", null).on("mouseup", null);
+      });
+    });
+    const setpxsize = () => {
+      for (const s of scaffold) {
+        s.idealy = connheight * s.id + (pad4 + regionthick) * 2 * s.id;
+      }
+      height = toppad + bottompad + proteinheight * scaffold.length + (pad4 * 2 + regionthick * 2 + connheight) * (scaffold.length - 1);
+      simulation.force("x", x_default(this.width / 2)).force("y", y_default(height / 2));
+      maxgmpxwidth = this.width;
+      maxchrpxwidth = this.width * 0.7;
+      for (const scf of scaffold) {
+        if (scf.gm) {
+          scf.pxwidth = maxgmpxwidth * scf.aatotal / gmmaxaa;
+        } else if (scf.nontemplate) {
+          scf.pxwidth = maxgmpxwidth * scf.aalen / gmmaxaa;
+        } else {
+          scf.pxwidth = maxchrpxwidth * (scf.stop - scf.start) / chrsegml;
+        }
+        scf.scale.range([0, scf.pxwidth]);
+        if (scf.nontemplate) {
+          scf.nodes[1].xoff = scf.pxwidth;
+          continue;
+        }
+        for (const n of scf.nodes) {
+          if (!scf.gm) {
+            n.xoff = scf.scale(n.position);
+            continue;
+          }
+          n.xoff = scf.scale(n.aaoff);
+        }
+      }
+      setheadtail();
+      nodebar.attr("x", (d) => Math.min(d.xoff, d.hardlink.xoff) - d.xoff).attr("width", (d) => Math.abs(d.xoff - d.hardlink.xoff)).attr("y", (d) => {
+        if (d.softlink5) return proteinheight + pad4;
+        return -pad4 - regionthick;
+      });
+      scftick.attr("y2", (d, i) => i % 2 == 0 ? 0 : proteinheight + pad6);
+      nontmp.select("rect").attr("width", (d) => d.pxwidth).attr("height", proteinheight);
+      chrbar.select("rect").attr("width", (d) => d.pxwidth).attr("height", proteinheight);
+      chrbarline1.attr("x2", (d) => d.pxwidth);
+      chrbarline2.attr("x2", (d) => d.pxwidth).attr("y1", proteinheight).attr("y2", proteinheight);
+      pupstream.attr("x2", (d) => d.scale(d.upstream / 3)).attr("y1", proteinheight / 2).attr("y2", proteinheight / 2).attr("stroke-width", proteinheight / 5);
+      pdownstream.attr("x1", (d) => {
+        return d.scale(
+          (d.upstream ? d.upstream / 3 : 0) + (d.utr5bp ? d.utr5bp / 3 : 0) + (d.aalen ? d.aalen : d.bplen / 3) + (d.utr3bp ? d.utr3bp / 3 : 0)
+        );
+      }).attr("x2", (d) => {
+        return d.scale(
+          (d.upstream ? d.upstream / 3 : 0) + (d.utr5bp ? d.utr5bp / 3 : 0) + (d.aalen ? d.aalen : d.bplen / 3) + (d.utr3bp ? d.utr3bp / 3 : 0) + d.downstream / 3
+        );
+      }).attr("y1", proteinheight / 2).attr("y2", proteinheight / 2).attr("stroke-width", proteinheight / 5);
+      p5utr.attr("x1", (d) => d.upstream ? d.scale(d.upstream / 3) : 0).attr("x2", (d) => d.scale(((d.upstream ? d.upstream : 0) + d.utr5bp) / 3)).attr("y1", proteinheight / 2).attr("y2", proteinheight / 2).attr("stroke-width", Math.floor(proteinheight / 2) + 0.5);
+      p3utr.attr("x1", (d) => {
+        return d.scale(
+          (d.upstream ? d.upstream / 3 : 0) + (d.utr5bp ? d.utr5bp / 3 : 0) + (d.aalen ? d.aalen : d.bplen / 3)
+        );
+      }).attr("x2", (d) => {
+        return d.scale(
+          (d.upstream ? d.upstream / 3 : 0) + (d.utr5bp ? d.utr5bp / 3 : 0) + (d.aalen ? d.aalen : d.bplen / 3) + (d.utr3bp ? d.utr3bp / 3 : 0)
+        );
+      }).attr("y1", proteinheight / 2).attr("y2", proteinheight / 2).attr("stroke-width", Math.floor(proteinheight / 2) + 0.5);
+      pbg.attr("x", (d) => {
+        return d.scale((d.upstream ? d.upstream / 3 : 0) + (d.utr5bp ? d.utr5bp / 3 : 0));
+      }).attr("width", (d) => d.scale(d.aalen ? d.aalen : d.bplen / 3) - d.scale(0)).attr("height", proteinheight);
+      allpdomain.attr("x", (d) => {
+        const scf = d.__scf;
+        return scf.scale((scf.upstream ? scf.upstream / 3 : 0) + (scf.utr5bp ? scf.utr5bp / 3 : 0) + d.start);
+      }).attr("width", (d) => {
+        const scf = d.__scf;
+        return scf.scale(d.stop) - scf.scale(d.start);
+      }).attr("height", proteinheight);
+      exonboundary.attr("x1", (boundary) => {
+        const scf = boundary.scf;
+        boundary.x = scf.scale((scf.upstream ? scf.upstream / 3 : 0) + boundary.rnabp / 3);
+        return boundary.x;
+      }).attr("x2", (boundary) => {
+        return boundary.x;
+      });
+      pbox.attr("x", (d) => {
+        return d.scale((d.upstream ? d.upstream / 3 : 0) + (d.utr5bp ? d.utr5bp / 3 : 0));
+      }).attr("width", (d) => d.scale(d.aalen ? d.aalen : d.bplen / 3) - d.scale(0)).attr("height", proteinheight);
+      scflabel.attr("x", (d) => d.pxwidth + pad3).attr("y", proteinheight / 2);
+      scflabel2.attr(
+        "y",
+        (d) => d.id % 2 == 0 ? -pad6 * 2 - scffontsize - pad6 : proteinheight + pad6 * 2 + scffontsize + pad6
+      );
+      scflabel3.attr(
+        "y",
+        (d) => d.id % 2 == 0 ? -pad6 * 2 - scffontsize - pad6 - nodefontsize - pad6 : proteinheight + pad6 * 2 + scffontsize + pad6 + nodefontsize + pad6
+      );
+      scfcliprect.attr("height", proteinheight).attr("width", (d) => d.pxwidth + pad3 + d.labelwidth);
+      scfkick.attr("width", (d) => d.pxwidth).attr("height", proteinheight);
+      svg.attr("width", this.width + leftpad + rightpad).attr("height", height);
+      g0.attr("transform", "translate(" + leftpad + "," + toppad + ")");
+      gsays.attr("transform", "translate(" + leftpad + "," + (height - bottompad + pad7) + ")");
+      drag.attr("x", leftpad + this.width + rightpad - 5).attr("y", height - 7);
+    };
+    setpxsize();
+    simulation.on("tick", () => {
+      const scf2ymean = [];
+      for (const s of scaffold) {
+        let sum = 0;
+        for (const d of s.nodes) {
+          sum += d.y;
+        }
+        scf2ymean[s.id] = sum / s.nodes.length;
+      }
+      for (const scf of scaffold) {
+        let y = scf2ymean[scf.id];
+        let changed = false;
+        if (y > scf.idealy) {
+          y -= Math.min(15, y - scf.idealy);
+          changed = true;
+        } else if (y < scf.idealy) {
+          y += Math.min(15, scf.idealy - y);
+          changed = true;
+        }
+        if (changed) {
+          scf2ymean[scf.id] = y;
+          for (const n of scf.nodes) {
+            n.y = y;
+          }
+        }
+      }
+      for (const scf of scaffold) {
+        const n0 = scf.nodes[0];
+        if (n0.x < n0.xoff) {
+          n0.x += Math.min(10, n0.xoff - n0.x);
+        } else if (n0.x > this.width - scf.pxwidth + n0.xoff) {
+          n0.x -= Math.min(10, n0.x - (this.width - scf.pxwidth + n0.xoff));
+        }
+        for (let i = 1; i < scf.nodes.length; i++) {
+          scf.nodes[i].x = n0.x + (scf.nodes[i].xoff - n0.xoff);
+        }
+      }
+      scfg.attr("transform", (scf) => "translate(" + (scf.nodes[0].x - scf.nodes[0].xoff) + "," + scf.nodes[0].y + ")");
+      node.attr("transform", (d) => "translate(" + d.x + "," + d.y + ")");
+      nodelabel.attr("text-anchor", (d) => {
+        if (d.softlink3) {
+          return d.softlink3.x < d.x ? "start" : "end";
+        }
+        return d.softlink5.x < d.x ? "start" : "end";
+      }).attr("y", (d) => {
+        if (d.softlink3) return -pad4 - regionthick - pad2;
+        if (d.softlink5) return proteinheight + pad4 + regionthick + pad2;
+      }).attr("dominant-baseline", (d) => {
+        if (d.softlink3) return "auto";
+        if (d.softlink5) return "hanging";
+      });
+      nodelabel2.attr("text-anchor", (d) => {
+        if (d.softlink3) return d.softlink3.x < d.x ? "start" : "end";
+        return d.softlink5.x < d.x ? "start" : "end";
+      }).attr("y", (d) => {
+        if (d.softlink3) return -pad4 - regionthick - pad2 - nodefontsize - pad2 / 2;
+        if (d.softlink5) return proteinheight + pad4 + regionthick + pad2 + nodefontsize + pad2 / 2;
+      }).attr("dominant-baseline", (d) => {
+        if (d.softlink3) return "auto";
+        if (d.softlink5) return "hanging";
+      });
+      link.attr("x1", (d) => d.source.x).attr("y1", (d) => d.source.y + proteinheight + pad4 + regionthick).attr("x2", (d) => d.target.x).attr("y2", (d) => {
+        if (d.target.scfid == d.source.scfid) {
+          return d.source.y + proteinheight + pad4 + regionthick;
+        }
+        return d.target.y - pad4 - regionthick;
+      });
+    }).restart();
+    const dur = 500;
+    const tochimeric = (slow) => {
+      for (const scf of scaffold) {
+        const n0 = scf.nodes[0];
+        if (scf.nodes.length == 1) {
+          scf.chimericwidth = Math.abs(n0.xoff - n0.hardlink.xoff);
+        } else {
+          let min = n0.xoff, max = n0.xoff;
+          for (const n of scf.nodes) {
+            min = Math.min(min, n.xoff);
+            max = Math.max(max, n.xoff);
+          }
+          scf.chimericwidth = max - min;
+        }
+        let x = n0.xoff;
+        if (scf.nodes.length == 1) {
+          x = Math.min(x, n0.hardlink.xoff);
+        }
+        scf.chimericmidx = x + scf.chimericwidth / 2;
+      }
+      let topx = 0, midx = 0, botx = 0;
+      const labelspacing = pad5 * 2;
+      for (let i = 0; i < scaffold.length; i++) {
+        const scf = scaffold[i];
+        let thiscenterx = midx + pad5 * 2 + scf.chimericwidth / 2;
+        if (i % 2 == 0) {
+          thiscenterx = Math.max(thiscenterx, topx + labelspacing + scf.chimericlabelw / 2);
+          topx = thiscenterx + scf.chimericlabelw / 2;
+        } else {
+          thiscenterx = Math.max(thiscenterx, botx + labelspacing + scf.chimericlabelw / 2);
+          botx = thiscenterx + scf.chimericlabelw / 2;
+        }
+        scf.chimericcenterx = thiscenterx;
+        midx = thiscenterx + scf.chimericwidth / 2;
+        const n0 = scf.nodes[0];
+        let xshear = n0.xoff;
+        if (scf.nodes.length == 1) {
+          xshear = Math.min(n0.xoff, n0.hardlink.xoff);
+        }
+        scf.chimericx = thiscenterx - scf.chimericwidth / 2 - xshear;
+      }
+      scfcliprect.transition().duration(slow ? dur : 0).attr("x", (d) => {
+        const n0 = d.nodes[0];
+        if (d.nodes.length == 1) {
+          return Math.min(n0.xoff, n0.hardlink.xoff);
+        }
+        let min = n0.xoff;
+        for (const n of d.nodes) {
+          min = Math.min(min, n.xoff);
+        }
+        return min;
+      }).attr("width", (d) => d.chimericwidth);
+      scflabel.attr("text-anchor", "middle").attr("x", (d) => d.chimericmidx).attr("y", (d, i) => i % 2 == 0 ? -pad6 * 2 : proteinheight + pad6 * 2).attr("dominant-baseline", (d, i) => i % 2 == 0 ? "auto" : "hanging");
+      nodelabel.attr("fill-opacity", 0);
+      nodelabel2.attr("fill-opacity", 0);
+      nodebar.attr("fill-opacity", 0);
+      scftick.attr("stroke-opacity", 1).attr("x1", (d) => d.chimericmidx).attr("x2", (d) => d.chimericmidx);
+      scflabel2.attr("fill-opacity", 1).attr("x", (d) => d.chimericmidx);
+      scflabel3.attr("fill-opacity", 1).attr("x", (d) => d.chimericmidx);
+      const yset = (height - toppad * 2) / 2 - proteinheight / 2;
+      scfg.transition().duration(slow ? dur : 0).attr("transform", (d) => {
+        for (const n of d.nodes) {
+          n.x = d.chimericx + n.xoff;
+          n.y = yset;
+        }
+        return "translate(" + d.chimericx + "," + yset + ")";
+      });
+      node.transition().duration(slow ? dur : 0).attr("transform", (d) => "translate(" + d.x + "," + d.y + ")");
+      link.transition().duration(slow ? dur : 0).attr("x1", (d) => {
+        const s1 = scaffold[d.source.scfid];
+        const s2 = scaffold[d.target.scfid];
+        d.chimericx = (s1.chimericcenterx + s1.chimericwidth / 2 + s2.chimericcenterx - s2.chimericwidth / 2) / 2;
+        return d.chimericx;
+      }).attr("x2", (d) => d.chimericx).attr("y1", yset).attr("y2", yset + proteinheight);
+      const s = scaffold[scaffold.length - 1];
+      const w2 = s.chimericcenterx + Math.max(s.chimericlabelw / 2, s.chimericwidth / 2);
+      svg.transition().duration(slow ? dur : 0).attr("width", leftpad + w2 + rightpad);
+      drag.transition().duration(slow ? dur : 0).attr("x", leftpad + w2 + rightpad - dragwidth);
+    };
+    let chimeric = false;
+    buttdiv.append("button").text("Toggle chimeric view").on("click", () => {
+      chimeric = !chimeric;
+      if (chimeric) {
+        simulation.stop();
+        tochimeric(true);
+        return;
+      }
+      scfcliprect.transition().duration(dur).attr("x", 0).attr("width", (d) => d.pxwidth + pad3 + d.labelwidth);
+      scflabel.attr("text-anchor", "start").attr("dominant-baseline", "central").attr("x", (d) => d.pxwidth + pad3).attr("y", proteinheight / 2);
+      nodelabel.attr("fill-opacity", 1);
+      nodelabel2.attr("fill-opacity", 1);
+      nodebar.attr("fill-opacity", 1);
+      scftick.attr("stroke-opacity", 0);
+      scflabel2.attr("fill-opacity", 0);
+      scflabel3.attr("fill-opacity", 0);
+      svg.transition().duration(dur).attr("width", leftpad + this.width + rightpad);
+      drag.transition().duration(dur).attr("x", leftpad + this.width + rightpad - dragwidth);
+      simulation.alpha(0.3).restart();
+    });
+    const dgmlst = [];
+    for (const s of scaffold) {
+      if (s.gm && s.gm.pdomains) {
+        dgmlst.push(s);
+      }
+    }
+    if (dgmlst.length) {
+      let pdmshown = false;
+      buttdiv.append("button").text("Protein domains").on("click", () => {
+        if (!pdmshown) {
+          pdmshown = true;
+          for (const scf of dgmlst) {
+            const d = domaindiv.append("div").style("margin-bottom", "10px").style("padding", "10px");
+            d.append("div").style("margin-bottom", "10px").html(scf.gm.name + " " + scf.gm.isoform).append("div");
+            const lst = getdomaintypes(scf.gm);
+            for (const e of lst) {
+              const d2 = d.append("div");
+              const cbox = d2.append("div").style("display", "inline-block").style("padding", "2px 3px").style("border", "solid 1px " + e.stroke).style("font-family", "Courier").style("margin-right", "10px").style("background-color", e.fill).style("cursor", "default").html("&nbsp;").on("click", (event) => {
+                if (scf.gm.domain_hidden[e.key]) {
+                  delete scf.gm.domain_hidden[e.key];
+                } else {
+                  scf.gm.domain_hidden[e.key] = 1;
+                }
+                allpdomain.filter((d3) => d3.__scf.clipid == scf.clipid && d3.name + d3.description == e.key).transition().attr("height", () => {
+                  if (e.key in scf.gm.domain_hidden) {
+                    event.target.innerHTML = "&times;";
+                    return 0;
+                  }
+                  event.target.innerHTML = "&nbsp;";
+                  return proteinheight;
+                });
+              });
+              const colorbtn = d2.append("input").attr("type", "color").style("display", "none").property("value", e.fill);
+              d2.append("span").text(e.name).attr("class", "sja_clbtext2").style("margin-right", "5px").property("title", "Click to edit color of this domain").on("click", (event) => {
+                colormenu.clear().showunder(event.target);
+                const input = colormenu.d.append("input").attr("type", "text").property("value", e.fill).style("width", "100px").on("keyup", (event2) => {
+                  if (!keyupEnter(event2)) return;
+                  const v = event2.target.value.trim();
+                  if (!v) return;
+                  cbox.style("background", v);
+                  allpdomain.filter((d3) => d3.__scf.clipid == scf.clipid && d3.name + d3.description == e.key).transition().attr("fill", v);
+                  scf.gm.pdomains.forEach((d3) => {
+                    if (d3.name + d3.description == e.key) {
+                      d3.color = v;
+                    }
+                  });
+                }).node();
+                input.focus();
+                input.select();
+                colormenu.d.append("div").style("margin-top", "10px").style("opacity", 0.5).style("font-size", ".8em").html("To change the color of this domain,<br>type in a new color and press ENTER.");
+              });
+              d2.append("span").text(e.description).style("font-size", ".7em").style("color", "#858585");
+            }
+          }
+        }
+        if (domaindiv.style("display") == "none") {
+          appear(domaindiv);
+        } else {
+          disappear(domaindiv);
+        }
+      });
+    }
+    buttdiv.append("button").text("SVG").on("click", () => {
+      const lst = scaffold.map((a) => a.name);
+      const legendG = svg.append("g").style("font-family", "Arial");
+      let legendGrps = [];
+      if (dgmlst.length) {
+        for (const scf of dgmlst) {
+          const grp = {
+            text: scf.gm.name + " " + scf.gm.isoform,
+            items: []
+          };
+          const lst2 = getdomaintypes(scf.gm);
+          for (const e of lst2) {
+            if (!(e.key in scf.gm.domain_hidden)) {
+              const text = [e.name, e.description];
+              if (text[1].length > 80) {
+                text[1] = text[1].substr(0, 77) + "...";
+              }
+              grp.items.push({
+                fill: e.fill,
+                text
+              });
+            }
+          }
+          legendGrps.push(grp);
+        }
+      }
+      const bbs = svg.node().getBBox();
+      const legendRenderer = hm2legend(
+        {
+          legendontop: false,
+          svgw: bbs.width,
+          svgh: bbs.height,
+          legendhangleft: false,
+          titleline: true,
+          legendpadleft: 10,
+          legendfontsize: 12,
+          legendlinesep: true,
+          samplecount4legend: false,
+          h: {
+            legend: legendGrps
+          },
+          handlers: {
+            legend: {
+              mouseover: () => {
+              }
+            }
+          }
+        },
+        (d) => d.fill,
+        (d) => d.text,
+        (d) => "#aaa"
+      );
+      legendRenderer(legendG);
+      const w = +svg.attr("width");
+      const h = +svg.attr("height");
+      const bbl = legendG.node().getBBox();
+      svg.attr("width", w + bbl.width).attr("height", h + bbl.height + 10);
+      drag.style("display", "none");
+      to_svg(svg.node(), lst.join("-"));
+      drag.style("display", "");
+      legendG.remove();
+      svg.attr("width", w).attr("height", h);
+    });
+    buttdiv.append("a").attr("href", "https://docs.google.com/document/d/1LgcMk_p1qyPgFPQChy4sLlU9GDL6oahffP7jJfD8ZwE/edit?usp=sharing").attr("target", "_blank").text("Help").style("padding-left", "10px");
+  }
+}
+function nodecheck(n) {
+  if (n.gm) {
+    if (!Number.isFinite(n.position)) {
+      if (!Number.isFinite(n.rnaposition)) {
+        if (!Number.isFinite(n.codon)) return "no position provided genome/rna/codon";
+        n.rnaposition = (n.gm.utr5 ? n.gm.utr5.reduce((i, j) => i + j[1] - j[0], 0) : 0) + n.codon * 3 - 1;
+      }
+      if (!Number.isFinite(n.rnaposition)) return "neither genomic or rna position given for node";
+      n.position = rna2gmcoord(n.rnaposition, n.gm);
+      if (n.position == null) return "cannot map rnaposition " + n.rnaposition + " to " + n.gm.isoform;
+    }
+    const t = genomic2gm(n.position, n.gm, 5);
+    n.exonbp = t.rnapos;
+    if (!Number.isFinite(n.codon)) n.codon = t.aapos;
+    n.atintron = t.atintron;
+    n.exon = t.atexon;
+    n.atutr3 = t.atutr3;
+    n.atutr5 = t.atutr5;
+    n.atupstream = t.atupstream;
+    n.atdownstream = t.atdownstream;
+  } else {
+    if (!n.chr || !n.position) {
+      return "missing genomic position for intergenic breakpoint";
+    }
+  }
+  return false;
+}
+function copynode(n, scaffold, data) {
+  const a = {};
+  for (const k in n) {
+    a[k] = n[k];
+  }
+  if (!a.gm) {
+    a.label = a.chr + ":" + a.position;
+  } else if (a.atupstream) {
+    a.label = a.atupstream.off + " bp upstream";
+  } else if (a.atdownstream) {
+    a.label = a.atdownstream.off + " bp downstream";
+  } else if (a.atutr3) {
+    if (a.atintron) {
+      a.label = "intron " + a.atintron + ", 3' UTR";
+    } else {
+      a.label = "3' UTR" + (a.exon ? ", exon " + a.exon : "");
+    }
+  } else if (a.atutr5) {
+    if (a.atintron) {
+      a.label = "intron " + a.atintron + ", 5' UTR";
+    } else {
+      a.label = "5' UTR" + (a.exon ? ", exon " + a.exon : "");
+    }
+  } else if (a.atintron) {
+    a.label = "intron " + a.atintron + (a.codon ? ", " + a.codon + " AA" : "");
+  } else {
+    a.label = (a.exon ? "exon " + a.exon + ", " : "") + (a.codon ? a.codon + " AA" : a.exonbp + " bp");
+  }
+  if (a.strand && a.gm) {
+    if (a.strand != a.gm.strand) {
+      a.antisense = true;
+    }
+  }
+  data.nodes.push(a);
+  scaffold[a.scfid].nodes.push(a);
+  return a;
+}
+export {
+  svgraph_default as default
+};
+//# sourceMappingURL=svgraph-55XRIYJW.js.map