@sjcrh/proteinpaint-client 2.187.0 → 2.188.1

package/dist/block.tk.hicstraw-LEZUZHLF.js

@@ -0,0 +1,822 @@
+import {
+  hicparsefragdata,
+  hicparsestat
+} from "./chunk-ONAYJVN2.js";
+import {
+  ColorScale
+} from "./chunk-2XPDA6NL.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-LSEFWW72.js";
+import "./chunk-GHWHLSUX.js";
+import "./chunk-HYOEWQ5P.js";
+import "./chunk-HBW42TDT.js";
+import "./chunk-G6O3URDN.js";
+import "./chunk-FN5XPUPH.js";
+import "./chunk-KWM6B3NL.js";
+import "./chunk-UCLS2SVB.js";
+import "./chunk-AY4UBGLC.js";
+import "./chunk-2P6Z7JFC.js";
+import {
+  dofetch2
+} from "./chunk-MYWJQRTD.js";
+import "./chunk-MVTCBVSX.js";
+import "./chunk-B43MTEYB.js";
+import "./chunk-2T7VYQLY.js";
+import "./chunk-FDK4UJMN.js";
+import {
+  bplen
+} from "./chunk-X7GDCYND.js";
+import "./chunk-SJC2C77V.js";
+import "./chunk-C3SYSMNE.js";
+import "./chunk-KSGA62R2.js";
+import "./chunk-LOZEKOES.js";
+import "./chunk-TOU7EVFQ.js";
+import "./chunk-OAWQ6LOO.js";
+import "./chunk-NMBIT4IK.js";
+import "./chunk-KYBIQBXE.js";
+import "./chunk-I6Y4O3RR.js";
+import {
+  rgb
+} from "./chunk-OMR2DT66.js";
+import "./chunk-DQC5FFGV.js";
+import "./chunk-HFNDKYVF.js";
+
+// src/block.tk.hicstraw.ts
+var defaultnmeth = "NONE";
+var minimumbinnum_bp = 200;
+var minimumbinnum_frag = 200;
+var labyspace = 5;
+var insidedomaincolor = "102,102,102";
+var docurl_text = "https://github.com/stjude/proteinpaint/wiki/Interaction-Tracks:-Hi%E2%80%90C-and-Arc#text-data-copy--paste";
+function loadTk(tk, block) {
+  block.tkcloakon(tk);
+  block.block_setheight();
+  Promise.resolve().then(() => {
+    if (!tk.uninitialized) return;
+    delete tk.uninitialized;
+    makeTk(tk, block);
+    if (tk.textdata || tk.bedfile || tk.bedurl) return;
+    return dofetch2("hicstat?" + (tk.file ? "file=" + tk.file : "url=" + tk.url)).then((data) => {
+      if (data.error) throw data.error;
+      const err = hicparsestat(tk.hic, data.out);
+      if (err) throw err;
+    });
+  }).then(() => {
+    return setResolution(tk, block);
+  }).then(() => {
+    return mayLoadDomainoverlay(tk);
+  }).then(() => {
+    if (tk.textdata) return textdata_load(tk, block);
+    if (tk.bedfile || tk.bedurl) return bedfile_load(tk, block);
+    updateNormalizationArray(tk.hic);
+    return loadStrawdata(tk, block);
+  }).then(() => {
+    if (tk.data.length == 0) {
+      tk.height_main = 100;
+      tk.img.attr("width", 0);
+      throw tk.name + ": no data in view range";
+    }
+    drawCanvas(tk, block);
+  }).catch((err) => {
+    if (err.stack) {
+      console.error(err.stack);
+    }
+    return typeof err == "string" ? err : err.message;
+  }).then((errmsg) => {
+    block.tkcloakoff(tk, { error: errmsg });
+    block.block_setheight();
+  });
+}
+function setResolution(tk, block) {
+  const regions = [];
+  let x = 0;
+  for (let i = block.startidx; i <= block.stopidx; i++) {
+    const r = block.rglst[i];
+    regions.push({
+      chr: r.chr,
+      start: r.start,
+      stop: r.stop,
+      width: r.width,
+      x: x + (i == 0 ? 0 : 1) * block.regionspace
+    });
+    x += block.regionspace + r.width;
+  }
+  for (const r of block.subpanels) {
+    regions.push({
+      chr: r.chr,
+      start: r.start,
+      stop: r.stop,
+      width: r.width,
+      x: x + r.leftpad
+    });
+    x += r.leftpad + r.width;
+  }
+  tk.regions = regions;
+  if (tk.textdata || tk.bedfile || tk.bedurl) {
+    return;
+  }
+  const maxbpwidth = Math.max(...regions.map((i) => i.stop - i.start));
+  let resolution_bp = null;
+  for (const res of tk.hic.bpresolution) {
+    if (maxbpwidth / res > minimumbinnum_bp) {
+      resolution_bp = res;
+      break;
+    }
+  }
+  return Promise.resolve().then(() => {
+    if (resolution_bp) {
+      return;
+    }
+    if (!tk.hic.enzymefile || !tk.hic.fragresolution?.length) {
+      resolution_bp = tk.hic.bpresolution[tk.hic.bpresolution.length - 1];
+      return;
+    }
+    const tasks = [];
+    for (const r of regions) {
+      const arg = {
+        getdata: 1,
+        getBED: 1,
+        file: tk.hic.enzymefile,
+        rglst: [{ chr: r.chr, start: r.start, stop: r.stop }],
+        genome: block.genome.name
+      };
+      tasks.push(
+        dofetch2("tkbedj", { method: "POST", body: JSON.stringify(arg) }).then((data) => {
+          if (data.error) throw data.error;
+          if (!data.items) throw ".items[] missing at mapping coord to fragment index";
+          const [err, map, start, stop] = hicparsefragdata(data.items);
+          if (err) throw err;
+          r.frag = {
+            id2coord: map,
+            startidx: start,
+            stopidx: stop
+          };
+          return;
+        })
+      );
+    }
+    return Promise.all(tasks);
+  }).then(() => {
+    let resolution_frag;
+    if (!resolution_bp) {
+      const maxfragspan = Math.max(...regions.map((i) => i.frag.stopidx - i.frag.startidx));
+      for (const v of tk.hic.fragresolution) {
+        if (maxfragspan / v > minimumbinnum_frag) {
+          resolution_frag = v;
+          break;
+        }
+      }
+      if (!resolution_frag) {
+        resolution_frag = tk.hic.fragresolution[tk.hic.fragresolution.length - 1];
+      }
+    }
+    tk.resolution_bp = resolution_bp;
+    tk.resolution_frag = resolution_frag;
+    if (resolution_bp) {
+      tk.label_resolution.text("Resolution: " + bplen(resolution_bp));
+    } else {
+      tk.label_resolution.text("Resolution: " + resolution_frag + " fragment" + (resolution_frag > 1 ? "s" : ""));
+    }
+    return;
+  });
+}
+function mayLoadDomainoverlay(tk) {
+  if (!tk.domainoverlay || !tk.domainoverlay.inuse) return;
+  return Promise.resolve().then(() => {
+    const tasks = [];
+    for (const r of tk.regions) {
+      const arg = { getdata: 1, getBED: 1, rglst: [{ chr: r.chr, start: r.start, stop: r.stop }] };
+      if (tk.domainoverlay.file) {
+        arg.file = tk.domainoverlay.file;
+      } else {
+        arg.url = tk.domainoverlay.url;
+      }
+      tasks.push(
+        dofetch2("tkbedj", { method: "POST", body: JSON.stringify(arg) }).then((data) => {
+          if (data.error) throw data.error;
+          if (!data.items || data.items.length == 0) return;
+          r.domainlst = data.items;
+        })
+      );
+    }
+    return Promise.all(tasks);
+  });
+}
+function textdata_load(tk, block) {
+  tk.data = [];
+  for (const i of tk.textdata.lst) {
+    const point = coordpair2plotpoint(i.chr1, i.start1, i.stop1, i.chr2, i.start2, i.stop2, block);
+    if (point) {
+      point.push(i.value);
+      tk.data.push(point);
+    }
+  }
+}
+function coordpair2plotpoint(chr1, start1, stop1, chr2, start2, stop2, block) {
+  let left1 = map_point(chr1, start1, block);
+  let left2 = map_point(chr1, stop1, block);
+  if (left1 == -1 && left2 == -1) return;
+  if (left1 == -1) left1 = left2;
+  else if (left2 == -1) left2 = left1;
+  let right1 = map_point(chr2, start2, block);
+  let right2 = map_point(chr2, stop2, block);
+  if (right1 == -1 && right2 == -1) return;
+  if (right1 == -1) right1 = right2;
+  else if (right2 == -1) right2 = right1;
+  if (left1 < right1) return [left1, left2, right1, right2];
+  return [right1, right2, left1, left2];
+}
+function map_point(chr, pos, block) {
+  const lst = block.seekcoord(chr, pos);
+  for (const r of lst) {
+    if (r.ridx != void 0) {
+      if (r.x > 0 && r.x < block.width) return r.x;
+    } else if (r.subpanelidx != void 0) {
+      return r.x;
+    }
+  }
+  return -1;
+}
+function bedfile_load(tk, block) {
+  const arg = {
+    getdata: 1,
+    getBED: 1,
+    rglst: tk.regions.map((i) => {
+      return { chr: i.chr, start: i.start, stop: i.stop };
+    }),
+    genome: block.genome.name
+  };
+  if (tk.bedfile) {
+    arg.file = tk.bedfile;
+  } else {
+    arg.url = tk.bedurl;
+    if (tk.bedindexURL) arg.indexURL = tk.bedindexURL;
+  }
+  return dofetch2("tkbedj", { method: "POST", body: JSON.stringify(arg) }).then((data) => {
+    if (data.error) throw data.error;
+    tk.data = [];
+    if (!data.items) {
+      return;
+    }
+    const usedlines = /* @__PURE__ */ new Set();
+    for (const i of data.items) {
+      const skipline = i.chr + " " + i.start + " " + i.stop + " " + i.rest[0] + " " + i.rest[1] + " " + i.rest[2];
+      if (usedlines.has(skipline)) continue;
+      const thisline = i.rest[0] + " " + i.rest[1] + " " + i.rest[2] + " " + i.chr + " " + i.start + " " + i.stop;
+      usedlines.add(thisline);
+      const chr2 = i.rest[0];
+      const start2 = Number.parseInt(i.rest[1]);
+      const stop2 = Number.parseInt(i.rest[2]);
+      if (Number.isNaN(start2)) throw "invalid start2 position: " + i.rest[1];
+      if (Number.isNaN(stop2)) throw "invalid stop2 position: " + i.rest[2];
+      const value = Number.parseFloat(i.rest[3]);
+      if (Number.isNaN(value)) throw "invalid value: " + i.rest[3];
+      const point = coordpair2plotpoint(i.chr, i.start, i.stop, chr2, start2, stop2, block);
+      if (point) {
+        point.push(value);
+        tk.data.push(point);
+      }
+    }
+  });
+}
+function updateNormalizationArray(hic) {
+  if (hic.normalization?.length > 0 && !hic.normalization.includes(defaultnmeth)) {
+    hic.normalization.unshift(defaultnmeth);
+  }
+}
+function loadStrawdata(tk, block) {
+  const resolution_bp = tk.resolution_bp;
+  const resolution_frag = tk.resolution_frag;
+  for (const r of tk.regions) {
+    r._str = (tk.hic.nochr ? r.chr.replace("chr", "") : r.chr) + ":" + (resolution_bp ? r.start + ":" + r.stop : r.frag.startidx + ":" + r.frag.stopidx);
+  }
+  const tasks = [];
+  for (const [i, r] of tk.regions.entries()) {
+    const par = {
+      jwt: block.jwt,
+      file: tk.file,
+      url: tk.url,
+      pos1: r._str,
+      pos2: r._str,
+      nmeth: tk.normalizationmethod,
+      mincutoff: tk.mincutoff
+    };
+    if (resolution_bp) {
+      par.resolution = resolution_bp;
+    } else {
+      par.resolution = resolution_frag;
+      par.isfrag = true;
+    }
+    tasks.push(
+      dofetch2("hicdata", {
+        method: "POST",
+        body: JSON.stringify(par)
+      }).then((data) => {
+        if (data.error) throw data.error;
+        if (!data.items || data.items.length == 0) {
+          return null;
+        }
+        return {
+          items: data.items,
+          regionidx: i
+        };
+      })
+    );
+  }
+  for (let i = 0; i < tk.regions.length - 1; i++) {
+    for (let j = i + 1; j < tk.regions.length; j++) {
+      const par = {
+        jwt: block.jwt,
+        file: tk.file,
+        url: tk.url,
+        pos1: tk.regions[i]._str,
+        pos2: tk.regions[j]._str,
+        nmeth: tk.normalizationmethod,
+        mincutoff: tk.mincutoff
+      };
+      if (resolution_bp) {
+        par.resolution = resolution_bp;
+      } else {
+        par.resolution = resolution_frag;
+        par.isfrag = true;
+      }
+      tasks.push(
+        dofetch2("hicdata", {
+          method: "POST",
+          body: JSON.stringify(par)
+        }).then((data) => {
+          if (data.error) throw { message: data.error };
+          if (!data.items || data.items.length == 0) {
+            return null;
+          }
+          return {
+            items: data.items,
+            leftregionidx: i,
+            rightregionidx: j
+          };
+        })
+      );
+    }
+  }
+  return Promise.all(tasks).then((data) => {
+    return parseStrawData(data, resolution_bp, resolution_frag, tk, block);
+  });
+}
+function parseStrawData(datalst, resolution_bp, resolution_frag, tk, block) {
+  tk.data = [];
+  for (const data of datalst) {
+    if (!data) {
+      continue;
+    }
+    let r_left, r_right, fs_left, fs_right;
+    let firstisleft = false;
+    if (data.regionidx != void 0) {
+      r_left = r_right = tk.regions[data.regionidx];
+      fs_left = fs_right = r_left.width / (r_left.stop - r_left.start);
+      firstisleft = true;
+    } else {
+      r_left = tk.regions[data.leftregionidx];
+      fs_left = r_left.width / (r_left.stop - r_left.start);
+      r_right = tk.regions[data.rightregionidx];
+      fs_right = r_right.width / (r_right.stop - r_right.start);
+      firstisleft = tk.hic.chrorder.indexOf(r_left.chr) < tk.hic.chrorder.indexOf(r_right.chr);
+    }
+    for (const [n1, n2, v] of data.items) {
+      let coord1, coord2, span1, span2;
+      if (resolution_frag) {
+        const idx_left = firstisleft ? n1 : n2;
+        const idx_right = firstisleft ? n2 : n1;
+        let a = r_left.frag.id2coord.get(idx_left);
+        if (!a) {
+          a = r_right.frag.id2coord.get(idx_left);
+          if (!a) return "unknown frag id in region " + data.leftregionidx + ": " + idx_left;
+        }
+        coord1 = a[0];
+        span1 = a[1] - a[0];
+        if (r_left.frag.id2coord.has(idx_left + resolution_frag)) {
+          const x = r_left.frag.id2coord.get(idx_left + resolution_frag);
+          span1 = x[1] - coord1;
+        }
+        let b = r_right.frag.id2coord.get(idx_right);
+        if (!b) {
+          b = r_left.frag.id2coord.get(idx_right);
+          if (!b) return "unknown frag id in region " + data.rightregionidx + ": " + idx_right;
+        }
+        coord2 = b[0];
+        span2 = b[1] - b[0];
+        if (r_right.frag.id2coord.has(idx_right + resolution_frag)) {
+          const x = r_right.frag.id2coord.get(idx_right + resolution_frag);
+          span2 = x[1] - coord2;
+        }
+      } else {
+        coord1 = firstisleft ? n1 : n2;
+        coord2 = firstisleft ? n2 : n1;
+        span1 = span2 = resolution_bp;
+      }
+      let insidedomain = false;
+      if (tk.domainoverlay && tk.domainoverlay.inuse) {
+        if (data.regionidx != void 0) {
+          if (r_left.domainlst) {
+            if (r_left.domainlst.find((i) => i.start <= coord1 && i.stop >= coord2)) {
+              insidedomain = true;
+            }
+          }
+        } else {
+        }
+      }
+      if (data.leftregionidx != void 0 && r_left.chr == r_right.chr) {
+        if (coord1 > r_left.start - span1 && coord1 < r_left.stop && coord2 > r_right.start - span2 && coord2 < r_right.stop) {
+          const left1 = r_left.x + fs_left * (coord1 - r_left.start);
+          const left2 = left1 + fs_left * span1;
+          const right1 = r_right.x + fs_right * (coord2 - r_right.start);
+          const right2 = right1 + fs_right * span2;
+          tk.data.push([left1, left2, right1, right2, v, insidedomain]);
+        }
+        if (coord2 > r_left.start - span2 && coord2 < r_left.stop && coord1 > r_right.start && coord1 < r_right.stop) {
+          const left1 = r_left.x + fs_left * (coord2 - r_left.start);
+          const left2 = left1 + fs_left * span2;
+          const right1 = r_right.x + fs_right * (coord1 - r_right.start);
+          const right2 = right1 + fs_right * span1;
+          tk.data.push([left1, left2, right1, right2, v, insidedomain]);
+        }
+      } else {
+        const left1 = r_left.x + fs_left * (coord1 - r_left.start);
+        const left2 = left1 + fs_left * span1;
+        const right1 = r_right.x + fs_right * (coord2 - r_right.start);
+        const right2 = right1 + fs_right * span2;
+        tk.data.push([left1, left2, right1, right2, v, insidedomain]);
+      }
+    }
+  }
+  drawCanvas(tk, block);
+  return;
+}
+function drawCanvas(tk, block) {
+  if (tk.data.length == 0) return;
+  let rgbstring;
+  {
+    const t = rgb(tk.color);
+    rgbstring = t.r + "," + t.g + "," + t.b;
+  }
+  const canvas = tk.hiddencanvas.node();
+  const canvaswidth = block.width + block.subpanels.reduce((i, j) => i + j.leftpad + j.width, 0);
+  let canvasheight = 0;
+  if (tk.mode_hm) {
+    canvasheight = Math.min(
+      canvaswidth,
+      tk.data.reduce((i, j) => Math.max(i, (j[3] - j[0]) / 2), 0)
+    );
+  } else if (tk.mode_arc) {
+    for (const i of tk.data) {
+      const arcxspan = (i[2] + i[3]) / 2 - (i[0] + i[1]) / 2;
+      const h = arcxspan / 2 / Math.tan((Math.PI - tk.arcangle / 2) / 2);
+      canvasheight = Math.max(canvasheight, h);
+    }
+  }
+  canvas.width = canvaswidth;
+  canvas.height = canvasheight;
+  const ctx = canvas.getContext("2d");
+  if (window.devicePixelRatio > 1) {
+    canvas.width = canvaswidth * window.devicePixelRatio;
+    canvas.height = canvasheight * window.devicePixelRatio;
+    ctx.scale(window.devicePixelRatio, window.devicePixelRatio);
+  }
+  let maxv;
+  {
+    const values = tk.data.map((i) => i[4]);
+    values.sort((i, j) => i - j);
+    maxv = values[Math.floor(values.length * tk.percentile_max / 100)];
+  }
+  resize_label(tk, block);
+  for (const [left1, left2, right1, right2, value, insidedomain] of tk.data) {
+    if (value < tk.mincutoff) {
+      continue;
+    }
+    let color;
+    if (insidedomain) {
+      color = "rgba(" + insidedomaincolor + "," + (value / maxv).toFixed(2) + ")";
+    } else {
+      color = "rgba(" + rgbstring + "," + (value / maxv).toFixed(2) + ")";
+    }
+    if (tk.mode_hm) {
+      ctx.fillStyle = color;
+      ctx.beginPath();
+      let x1, y1, x2, y2, x3, y3, x4, y4;
+      if (tk.pyramidup) {
+        x1 = (left1 + right2) / 2;
+        y1 = canvasheight - (right2 - left1) / 2;
+        x2 = (left1 + right1) / 2;
+        y2 = canvasheight - (right1 - left1) / 2;
+        x3 = (left2 + right1) / 2;
+        y3 = canvasheight - (right1 - left2) / 2;
+        x4 = (left2 + right2) / 2;
+        y4 = canvasheight - (right2 - left2) / 2;
+      } else {
+        x1 = (left2 + right1) / 2;
+        y1 = (right1 - left2) / 2;
+        x2 = (left1 + right1) / 2;
+        y2 = (right1 - left1) / 2;
+        x3 = (left1 + right2) / 2;
+        y3 = (right2 - left1) / 2;
+        x4 = (left2 + right2) / 2;
+        y4 = (right2 - left2) / 2;
+      }
+      ctx.moveTo(x1, y1);
+      ctx.lineTo(x2, y2);
+      ctx.lineTo(x3, y3);
+      ctx.lineTo(x4, y4);
+      ctx.closePath();
+      ctx.fill();
+    } else if (tk.mode_arc) {
+      const a = (left1 + left2) / 2;
+      const b = (right1 + right2) / 2;
+      const arcxspan = Math.abs(a - b);
+      const centerx = Math.min(a, b) + arcxspan / 2;
+      const radius = arcxspan / 2 / Math.sin(tk.arcangle / 2);
+      let centery, startangle, endangle;
+      if (tk.pyramidup) {
+        centery = canvasheight + radius * Math.cos(tk.arcangle / 2);
+        startangle = Math.PI + (Math.PI - tk.arcangle) / 2;
+        endangle = startangle + tk.arcangle;
+      } else {
+        centery = -radius * Math.cos(tk.arcangle / 2);
+        startangle = (Math.PI - tk.arcangle) / 2;
+        endangle = startangle + tk.arcangle;
+      }
+      ctx.strokeStyle = color;
+      ctx.beginPath();
+      ctx.arc(centerx, centery, radius, startangle, endangle);
+      ctx.stroke();
+    }
+  }
+  tk.img.attr("width", canvaswidth).attr("height", canvasheight).attr("xlink:href", canvas.toDataURL());
+  tk.colorScale.domain = [0, maxv];
+  tk.colorScale.markedValue = tk.mincutoff;
+  tk.colorScale.updateScale();
+  tk.height_main = tk.toppad + Math.max(tk.left_labelheight, canvasheight) + tk.bottompad;
+}
+function resize_label(tk, block) {
+  tk.leftLabelMaxwidth = tk.colorScale.barwidth;
+  tk.tklabel.each(function() {
+    tk.leftLabelMaxwidth = Math.max(tk.leftLabelMaxwidth, this.getBBox().width);
+  });
+  if (tk.label_resolution) {
+    tk.label_resolution.each(function() {
+      tk.leftLabelMaxwidth = Math.max(tk.leftLabelMaxwidth, this.getBBox().width);
+    });
+  }
+  block.setllabel();
+}
+function makeTk(tk, block) {
+  if (tk.textdata) {
+    if (!tk.textdata.raw) throw ".raw missing from textdata";
+    const err = textdata_parseraw(tk, block);
+    if (err) throw "Error with text data: " + err;
+  }
+  if (tk.mode_hm == void 0) tk.mode_hm = true;
+  if (tk.mode_arc == void 0) tk.mode_arc = false;
+  if (tk.mode_hm && tk.mode_arc) {
+    tk.mode_arc = false;
+  } else if (!tk.mode_hm && !tk.mode_arc) {
+    tk.mode_hm = true;
+  }
+  if (!tk.color) tk.color = "#ff0000";
+  tk.arcangle = Math.PI / 2;
+  if (tk.pyramidup == void 0) tk.pyramidup = true;
+  tk.hic.genome = block.genome;
+  if (tk.hic.enzyme) {
+    if (block.genome.hicenzymefragment) {
+      const e = block.genome.hicenzymefragment.find((i) => i.enzyme.toUpperCase() == tk.hic.enzyme.toUpperCase());
+      if (e) {
+        tk.hic.enzymefile = e.file;
+      } else {
+        block.error("unknown Hi-C enzyme: " + tk.hic.enzyme);
+        delete tk.hic.enzyme;
+      }
+    } else {
+      block.error("Hi-C enzyme fragment not available for this genome");
+      delete tk.hic.enzyme;
+    }
+  }
+  if (!tk.percentile_max) {
+    tk.percentile_max = 90;
+  }
+  if (tk.mincutoff == void 0) {
+    tk.mincutoff = 0;
+  }
+  if (!tk.normalizationmethod) {
+    tk.normalizationmethod = defaultnmeth;
+  }
+  let laby = labyspace + block.labelfontsize;
+  if (tk.file || tk.url) {
+    tk.label_resolution = block.maketklefthandle(tk, laby).attr("class", null);
+    laby += labyspace + block.labelfontsize;
+  }
+  {
+    const barheight = 14;
+    const barwidth = 100;
+    const space = 1;
+    const holder = tk.gleft.append("g").attr("transform", `scale(1), translate(${block.tkleftlabel_xshift - barwidth}, ${laby})`);
+    tk.colorScale = new ColorScale({
+      barheight,
+      barwidth,
+      //data will update after loading data
+      domain: [0, 1],
+      fontSize: 12,
+      height: 45,
+      width: 120,
+      holder,
+      colors: ["white", tk.color],
+      position: `6,${barheight + space}`,
+      ticks: 2,
+      tickSize: 2,
+      markedValue: tk.mincutoff
+    });
+    laby += barheight + 10 + block.labelfontsize;
+  }
+  laby += 10;
+  tk.left_labelheight = laby;
+  tk.img = tk.glider.append("image");
+  tk.hiddencanvas = block.holder.append("canvas").style("display", "none");
+  tk.config_handle = block.maketkconfighandle(tk).on("click", () => {
+    configPanel(tk, block);
+  });
+}
+function configPanel(tk, block) {
+  tk.tkconfigtip.clear().showunder(tk.config_handle.node());
+  if (tk.textdata) {
+    tk.tkconfigtip.d.append("div").attr("class", "sja_menuoption").attr("data-testid", "sjpp-edit-interaction-data").style("margin-bottom", "10px").text("Edit interaction data").on("click", () => {
+      textdata_editUI(tk, block);
+    });
+  }
+  {
+    const row = tk.tkconfigtip.d.append("div").style("margin-bottom", "10px");
+    row.append("span").text("Change color");
+    row.append("input").style("margin-left", "5px").attr("type", "color").property("value", tk.color).on("change", (event) => {
+      tk.color = event.target.value;
+      tk.colorScale.colors[tk.colorScale.colors.length - 1] = tk.color;
+      tk.colorScale.updateScale();
+      drawCanvas(tk, block);
+    });
+  }
+  {
+    const row = tk.tkconfigtip.d.append("div").style("margin-bottom", "10px");
+    row.append("input").attr("type", "number").style("width", "40px").property("value", tk.percentile_max).on("keyup", (event) => {
+      if (event.code != "Enter" && event.code != "NumpadEnter") return;
+      const v = Number.parseFloat(event.target.value);
+      if (Number.isNaN(v) || v <= 0 || v >= 100) {
+        alert("Please enter a value between 0 and 100");
+        return;
+      }
+      tk.percentile_max = v;
+      drawCanvas(tk, block);
+    });
+    row.append("span").html("&nbsp;percentile for color scale max");
+  }
+  {
+    const row = tk.tkconfigtip.d.append("div").style("margin-bottom", "10px");
+    row.append("input").attr("type", "number").style("width", "50px").property("value", tk.mincutoff).on("keyup", (event) => {
+      if (event.code != "Enter" && event.code != "NumpadEnter") return;
+      const v = Number.parseFloat(event.target.value);
+      if (Number.isNaN(v)) {
+        alert("Please enter a valid number");
+        return;
+      }
+      tk.mincutoff = v;
+      loadTk(tk, block);
+    });
+    row.append("span").html("&nbsp;for minimum cutoff value");
+    row.append("div").style("font-size", ".8em").style("opacity", 0.5).html("Interactions with scores &le; cutoff will not be shown.");
+  }
+  if (tk.file || tk.url) {
+    const normalization = tk.hic.normalization;
+    const row = tk.tkconfigtip.d.append("div").style("margin-bottom", "10px");
+    row.append("span").html("Normalization&nbsp;");
+    if (tk.hic.normalization.length > 0) {
+      const s = row.append("select").on("change", () => {
+        const ss = s.node();
+        tk.normalizationmethod = ss.options[ss.selectedIndex].innerHTML;
+        loadTk(tk, block);
+      });
+      for (const method of normalization) s.append("option").text(method);
+      for (const o of s.node().options) {
+        if (o.innerHTML == tk.normalizationmethod) {
+          o.selected = true;
+          break;
+        }
+      }
+    } else {
+      row.append("span").text(defaultnmeth);
+    }
+  }
+  if (tk.domainoverlay) {
+    const row = tk.tkconfigtip.d.append("div").style("margin-bottom", "10px");
+    row.append("span").html("Overlay with " + tk.domainoverlay.name + " domains&nbsp;");
+    row.append("button").text(tk.domainoverlay.inuse ? "No" : "Yes").on("click", () => {
+      tk.tkconfigtip.hide();
+      tk.domainoverlay.inuse = !tk.domainoverlay.inuse;
+      loadTk(tk, block);
+    });
+  }
+  {
+    const row = tk.tkconfigtip.d.append("div").style("margin-bottom", "10px");
+    const id = Math.random().toString();
+    row.append("input").attr("name", id).attr("id", id + "1").attr("type", "radio").property("checked", tk.mode_hm).on("change", (event) => {
+      if (event.target.checked) {
+        tk.mode_hm = true;
+        tk.mode_arc = false;
+      } else {
+        tk.mode_hm = false;
+        tk.mode_arc = true;
+      }
+      drawCanvas(tk, block);
+      block.block_setheight();
+    });
+    row.append("label").attr("for", id + "1").attr("class", "sja_clbtext").html("&nbsp;Heatmap");
+    row.append("input").style("margin-left", "10px").attr("name", id).attr("id", id + "2").attr("type", "radio").property("checked", tk.mode_arc).on("change", (event) => {
+      if (event.target.checked) {
+        tk.mode_hm = false;
+        tk.mode_arc = true;
+      } else {
+        tk.mode_hm = true;
+        tk.mode_arc = false;
+      }
+      drawCanvas(tk, block);
+      block.block_setheight();
+    });
+    row.append("label").attr("for", id + "2").attr("class", "sja_clbtext").html("&nbsp;Arc");
+    row.append("span").style("margin-left", "10px").style("opacity", 0.5).text("for showing interactions.");
+  }
+  {
+    tk.tkconfigtip.d.append("div").style("margin", "20px 0px").append("button").text("Point " + (tk.pyramidup ? "down" : "up")).on("click", () => {
+      tk.pyramidup = !tk.pyramidup;
+      drawCanvas(tk, block);
+      tk.tkconfigtip.hide();
+    });
+  }
+  if (tk.hic.version) {
+    tk.tkconfigtip.d.append("div").style("opacity", 0.5).text("HiC file version: " + tk.hic.version);
+  }
+}
+function textdata_editUI(tk, block) {
+  tk.tkconfigtip.d.transition().style("left", Number.parseInt(tk.tkconfigtip.d.style("left")) - 500 + "px");
+  tk.tkconfigtip.clear();
+  const d = tk.tkconfigtip.d.append("div");
+  const ta = d.append("textarea").attr("cols", 50).attr("rows", 10);
+  ta.property("value", tk.textdata.raw);
+  const row2 = d.append("div").style("margin-top", "10px");
+  row2.append("button").text("Update").on("click", () => {
+    const text = ta.property("value");
+    if (!text) {
+      window.alert("Enter text interaction data");
+      return;
+    }
+    tk.textdata.raw = text;
+    const err = textdata_parseraw(tk, block);
+    if (err) {
+      window.alert(err);
+      return;
+    }
+    loadTk(tk, block);
+    tk.tkconfigtip.hide();
+  });
+  row2.append("span").style("margin-left", "5px").html("<a href=" + docurl_text + " target=_blank>Text data format</a>");
+  row2.append("button").style("margin-left", "30px").text("Cancel").on("click", () => tk.tkconfigtip.hide());
+}
+function textdata_parseraw(tk, block) {
+  tk.textdata.lst = [];
+  const lines = tk.textdata.raw.trim().split(/\r?\n/);
+  for (let i = 0; i < lines.length; i++) {
+    const line = lines[i].trim();
+    if (!line) continue;
+    const l = line.split(/[\t\s]+/);
+    const chr1 = l[0];
+    if (!block.genome.chrlookup[chr1.toUpperCase()]) return "wrong chrA name at line " + (i + 1);
+    const start1 = Number.parseInt(l[1]);
+    if (Number.isNaN(start1)) return "invalid startA at line " + (i + 1);
+    const stop1 = Number.parseInt(l[2]);
+    if (Number.isNaN(stop1)) return "invalid stopA name at line " + (i + 1);
+    const chr2 = l[3];
+    if (!block.genome.chrlookup[chr2.toUpperCase()]) return "wrong chrB name at line " + (i + 1);
+    const start2 = Number.parseInt(l[4]);
+    if (Number.isNaN(start2)) return "invalid startB at line " + (i + 1);
+    const stop2 = Number.parseInt(l[5]);
+    if (Number.isNaN(stop2)) return "invalid stopB at line " + (i + 1);
+    const value = Number.parseFloat(l[7]);
+    if (Number.isNaN(value)) return "invalid value (8th column) at line " + (i + 1);
+    tk.textdata.lst.push({
+      chr1,
+      start1,
+      stop1,
+      chr2,
+      start2,
+      stop2,
+      value
+    });
+  }
+  if (tk.textdata.lst.length == 0) return "No data points from text input";
+}
+export {
+  loadTk
+};
+//# sourceMappingURL=block.tk.hicstraw-LEZUZHLF.js.map