@sjcrh/proteinpaint-client 2.203.0 → 2.203.1

package/dist/mds.samplescatterplot-ZAIEWPO4.js

@@ -1,1544 +0,0 @@
-import {
-  blocklazyload
-} from "./chunk-OGQMELRU.js";
-import {
-  d3lasso
-} from "./chunk-JH73IL4C.js";
-import {
-  schemeCategory20
-} from "./chunk-V2OJLJSK.js";
-import {
-  getsjcharts
-} from "./chunk-MKAF2BHB.js";
-import {
-  appear2 as appear,
-  disappear2 as disappear,
-  export_data,
-  filterInit,
-  first_genetrack_tolist,
-  getVocabFromSamplesArray,
-  keyupEnter,
-  make_table_2col,
-  newpane,
-  sayerror,
-  tab_wait,
-  tkt
-} from "./chunk-GQQ4R6BI.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-XFAL46LZ.js";
-import "./chunk-7AYGTMED.js";
-import {
-  Menu
-} from "./chunk-ELJX3QIQ.js";
-import "./chunk-7BLXK3GI.js";
-import "./chunk-VSSZJHOR.js";
-import "./chunk-5RUVBYLK.js";
-import {
-  dofetch,
-  dofetch2
-} from "./chunk-HENLCRVM.js";
-import {
-  getFilteredSamples
-} from "./chunk-4WF3XDQP.js";
-import "./chunk-7UFK4GVI.js";
-import "./chunk-4QBRVM4V.js";
-import "./chunk-H6INPPUC.js";
-import "./chunk-PF4DSFDR.js";
-import "./chunk-IMYSFDE5.js";
-import "./chunk-W5J3LTYS.js";
-import {
-  identity,
-  zoom_default
-} from "./chunk-4ZL6IBXM.js";
-import {
-  linear,
-  ordinal
-} from "./chunk-OZVWP4ZR.js";
-import "./chunk-FXQXCOII.js";
-import "./chunk-TLT4YIG3.js";
-import "./chunk-5R63Q5KH.js";
-import {
-  select_default
-} from "./chunk-I6Y4O3RR.js";
-import "./chunk-Q5RDQNIT.js";
-import "./chunk-DQC5FFGV.js";
-import "./chunk-HFNDKYVF.js";
-
-// common/uncollide.js
-function getDefaults(opts) {
-  const defaults = {
-    waitTime: 0,
-    pad: 5,
-    nameKey: "",
-    steps: [
-      {
-        type: "restyle",
-        applyTo: "all",
-        // or just the minColliders
-        css: {
-          selector: "text",
-          key: "font-size",
-          value: "12px"
-        }
-      },
-      /*{
-      	type: 'restyle',
-      	css: {
-      		selector: 'text',
-      		key: 'text-anchor',
-      		value: 'start'
-      	}
-      },*/
-      {
-        type: "move",
-        repeat: 2,
-        pad: 0,
-        css: {
-          selector: "text"
-        },
-        boxSorter: (a, b) => {
-          if (a.x1 > b.x1) return -1;
-          if (b.x1 > a.x1) return 1;
-          if (a.y1 > b.y1) return -1;
-          if (b.y1 > a.y1) return 1;
-          return 0;
-        }
-      }
-    ]
-  };
-  return Object.assign(defaults, opts);
-}
-async function uncollide(labels, _opts = {}) {
-  if (!labels || !labels.size()) return;
-  const opts = getDefaults(_opts);
-  if (!opts.steps || !opts.steps.length) return;
-  if (!opts.svg) opts.svg = labels.node().closest("svg");
-  await sleep(opts.waitTime);
-  opts.svgBox = opts.svg.getBoundingClientRect();
-  const boxes = getBoxes(labels, opts);
-  const minNonZeroCollisions = trackCollisions(boxes);
-  window.boxes = boxes;
-  if (minNonZeroCollisions) {
-    const step = opts.steps.shift();
-    const adjustees = step.applyTo == "all" ? boxes : step.type == "move" ? boxes.filter((b) => b.collisions.length) : boxes.filter((b) => b.collisions.length === minNonZeroCollisions);
-    if (adjustees.length) {
-      if (step.boxSorter) adjustees.sort(step.boxSorter);
-      for (const box of adjustees) {
-        const b = getBoxes(box.label, opts)[0];
-        Object.assign(box, b);
-        trackOverlaps(box, boxes.filter((b2) => b2 != box));
-        await adjusters[step.type](box, step, boxes, opts);
-      }
-    }
-    if (typeof step.repeat == "number" && step.repeat > 0) {
-      step.repeat += -1;
-      opts.steps.unshift(step);
-    }
-    if (opts.steps.length) setTimeout(() => uncollide(labels, opts), 0);
-    else boxes.forEach(showBox);
-  } else boxes.forEach(showBox);
-}
-function getBoxes(labels, opts) {
-  const boxes = [];
-  labels.each(function(data) {
-    const elem = this;
-    const bbox = elem.getBoundingClientRect();
-    const box = {
-      elem,
-      label: select_default(elem),
-      x1: bbox.x - opts.svgBox.x,
-      x2: bbox.x - opts.svgBox.x + bbox.width,
-      y1: bbox.y - opts.svgBox.y,
-      y2: bbox.y - opts.svgBox.y + bbox.height,
-      width: bbox.width,
-      height: bbox.height
-    };
-    box.maxFree = {
-      n: Math.max(box.y1, 0),
-      s: Math.max(opts.svgBox.y + opts.svgBox.height - box.y2, 0),
-      e: Math.max(opts.svgBox.x + opts.svgBox.width - box.x2, 0),
-      w: Math.max(box.x1, 0)
-    };
-    box.corners = {};
-    box.overlapSum = 0;
-    box.collisions = [];
-    box.maxOverlaps = {};
-    if (opts.nameKey) box.name = data[opts.nameKey];
-    detectSvgOverflow(box, opts.svgBox);
-    boxes.push(box);
-  });
-  return boxes;
-}
-function trackCollisions(boxes) {
-  let minNonZeroCollisions = 0;
-  for (const box of boxes) {
-    const numCollisions = trackOverlaps(box, boxes.filter((b) => b != box));
-    if (minNonZeroCollisions === 0 || numCollisions > 0 && numCollisions < minNonZeroCollisions) {
-      minNonZeroCollisions = numCollisions;
-    }
-  }
-  boxes.sort(sortBoxes);
-  return minNonZeroCollisions;
-}
-function sortBoxes(a, b) {
-  return a.collisions.length - b.collisions.length;
-}
-function trackOverlaps(box, boxes) {
-  const x1 = box.x1, x2 = box.x2;
-  const y1 = box.y1, y2 = box.y2;
-  for (const b of boxes) {
-    if (b === box) continue;
-    const free = {};
-    if (b.x2 < x1) {
-      free.w = x1 - b.x2;
-    } else if (b.x1 > x2) {
-      free.e = b.x1 - x2;
-    }
-    if (b.y2 < y1) {
-      free.n = y1 - b.y2;
-    } else if (b.y1 > y2) {
-      free.s = b.y1 - y2;
-    }
-    const corners = {};
-    if (Object.keys(free).length) {
-      if ("n" in free && free.n < box.maxFree.n) box.maxFree.n = free.n;
-      if ("s" in free && free.s < box.maxFree.s) box.maxFree.s = free.s;
-      if ("e" in free && free.e < box.maxFree.e) box.maxFree.e = free.e;
-      if ("w" in free && free.w < box.maxFree.w) box.maxFree.w = free.w;
-    } else {
-      if (b.x1 <= x1 && x2 <= b.x2) {
-        if (b.x1 <= x1 && x1 <= b.x2) {
-          const dx = b.x2 - x1;
-          if (!("x" in box.maxOverlaps) || box.maxOverlaps.x.val < dx) box.maxOverlaps.x = { val: dx, dir: "w" };
-          if (b.y1 <= y1 && y1 <= b.y2) {
-            const dy = b.y2 - y1;
-            corners.nw = dx * dy;
-            if (!("y" in box.maxOverlaps) || box.maxOverlaps.y.val < dy) box.maxOverlaps.y = { val: dy, dir: "n" };
-          }
-          if (b.y1 <= y2 && y2 <= b.y2) {
-            const dy = y2 - b.y1;
-            corners.sw = dx * dy;
-            if (!("y" in box.maxOverlaps) || box.maxOverlaps.y.val < dy) box.maxOverlaps.y = { val: dy, dir: "s" };
-          }
-        }
-        if (b.x1 <= x2 && x2 <= b.x2) {
-          const dx = x2 - b.x1;
-          if (!("x" in box.maxOverlaps) || box.maxOverlaps.x.val < dx) box.maxOverlaps.x = { val: dx, dir: "e" };
-          if (b.y1 <= y1 && y1 <= b.y2) {
-            const dy = b.y2 - y1;
-            corners.ne = dx * dy;
-            if (!("y" in box.maxOverlaps) || box.maxOverlaps.y.val < dy) box.maxOverlaps.y = { val: dy, dir: "n" };
-          }
-          if (b.y1 <= y2 && y2 <= b.y2) {
-            const dy = y2 - b.y1;
-            corners.se = dx * dy;
-            if (!("y" in box.maxOverlaps) || box.maxOverlaps.y.val < dy) box.maxOverlaps.y = { val: dy, dir: "s" };
-          }
-        }
-      } else {
-        if (x1 <= b.x1 && b.x1 <= x2) {
-          const dx = x2 - b.x1;
-          if (!("x" in box.maxOverlaps) || box.maxOverlaps.x.val < dx) box.maxOverlaps.x = { val: dx, dir: "e" };
-          if (y1 <= b.y1 && b.y1 <= y2) {
-            const dy = y2 - b.y1;
-            corners.se = dx * dy;
-            if (!("y" in box.maxOverlaps) || box.maxOverlaps.y.val < dy) box.maxOverlaps.y = { val: dy, dir: "s" };
-          }
-          if (y1 <= b.y2 && b.y2 <= y2) {
-            const dy = b.y2 - y1;
-            corners.ne = dx * dy;
-            if (!("y" in box.maxOverlaps) || box.maxOverlaps.y.val < dy) box.maxOverlaps.y = { val: dy, dir: "n" };
-          }
-        }
-        if (x1 <= b.x2 && b.x2 <= x2) {
-          const dx = b.x2 - x1;
-          if (!("x" in box.maxOverlaps) || box.maxOverlaps.x.val < dx) box.maxOverlaps.x = { val: dx, dir: "w" };
-          if (y1 <= b.y1 && b.y1 <= y2) {
-            const dy = y2 - b.y1;
-            corners.sw = dx * dy;
-            if (!("y" in box.maxOverlaps) || box.maxOverlaps.y.val < dy) box.maxOverlaps.y = { val: dy, dir: "s" };
-          }
-          if (y1 <= b.y2 && b.y2 <= y2) {
-            const dy = b.y2 - y1;
-            corners.nw = dx * dy;
-            if (!("y" in box.maxOverlaps) || box.maxOverlaps.y.val < dy) box.maxOverlaps.y = { val: dy, dir: "n" };
-          }
-        }
-      }
-    }
-    const keys = Object.keys(corners);
-    if (keys.length) {
-      box.collisions.push({ box: b.name, corners: keys });
-      for (const k of keys) {
-        if (!box.corners[k]) box.corners[k] = { against: [], sum: 0 };
-        box.corners[k].against.push(b.name);
-        box.corners[k].sum += corners[k];
-        box.overlapSum += corners[k];
-      }
-    }
-  }
-  return box.collisions.length;
-}
-function detectSvgOverflow(box, svgBox) {
-  const x1 = box.x1, x2 = box.x2;
-  const y1 = box.y1, y2 = box.y2;
-  const corners = [];
-  if (x1 < 0) {
-    box.maxOverlaps.x = { val: Math.abs(x1), dir: "w" };
-    corners.push("w");
-    box.corners.w = { against: [], sum: Math.abs(x1) * box.height };
-    box.overlapSum += box.corners.w.sum;
-  }
-  const dx = x2 - svgBox.width;
-  if (dx > 0 && (!box.maxOverlaps.x || box.maxOverlaps.x.val < dx)) {
-    box.maxOverlaps.x = { val: dx, dir: "e" };
-    corners.push("e");
-    box.corners.e = { against: ["svgbox"], sum: dx * box.height };
-    box.overlapSum += box.corners.e.sum;
-  }
-  if (y1 < 0) {
-    box.maxOverlaps.y = { val: Math.abs(y1), dir: "n" };
-    corners.push("n");
-    box.corners.n = { against: ["svgbox"], sum: Math.abs(y1) };
-    box.overlapSum += box.corners.n.sum;
-  }
-  const dy = y2 - svgBox.height;
-  if (dy > 0 && (!box.maxOverlaps.y || box.maxOverlaps.y.val < dy)) {
-    box.maxOverlaps.y = { val: dy, dir: "s" };
-    corners.push("s");
-    box.corners.s = { against: ["svgbox"], sum: dy * box.height };
-    box.overlapSum += box.corners.s.sum;
-  }
-  if (corners.length) box.collisions.push({ box: "svg", corners });
-}
-async function restyle(box, step, boxes, opts) {
-  const preAdjustedVal = /* @__PURE__ */ new Map();
-  box.label.selectAll(step.css.selector).each(function(d) {
-    const s = select_default(this);
-    preAdjustedVal.set(this, s.attr(step.css.key));
-    s.attr(step.css.key, step.css.value);
-  });
-  await sleep(opts.waitTime);
-  const adjustedBox = getBoxes(box.label, opts)[0];
-  const i = boxes.indexOf(box);
-  trackOverlaps(adjustedBox, boxes.filter((b) => b != box));
-  if (step.applyTo == "all") {
-    Object.assign(box, adjustedBox);
-  } else {
-    if (adjustedBox.overlapSum >= box.overlapSum) {
-      box.label.selectAll(step.css.selector).each(function(d) {
-        select_default(this).attr(step.css.key, preAdjustedVal.get(this));
-      });
-    } else {
-      Object.assign(box, adjustedBox);
-    }
-  }
-}
-async function move(box, step, boxes, opts) {
-  const freeDirections = Object.keys(box.maxFree).filter((dir) => box.maxFree[dir] > 0);
-  if (!freeDirections.length) return;
-  const preAdjustedVal = /* @__PURE__ */ new Map();
-  if (box.maxOverlaps.y && box.maxOverlaps.y.val > 0) {
-    if (box.maxOverlaps.y.dir == "s" && freeDirections.includes("n")) {
-      box.label.selectAll(step.css.selector).each(function(d) {
-        const s = select_default(this);
-        preAdjustedVal.set(this, s.attr("y") || 0);
-        s.attr("y", Math.max(-box.maxFree.n, -box.maxOverlaps.y.val) - step.pad);
-      });
-    }
-    if (box.maxOverlaps.y.dir == "n" && freeDirections.includes("s")) {
-      box.label.selectAll(step.css.selector).each(function(d) {
-        const s = select_default(this);
-        preAdjustedVal.set(this, s.attr("y") || 0);
-        s.attr("y", Math.min(box.maxFree.s, box.maxOverlaps.y.val) + step.pad);
-      });
-    }
-  }
-  if (preAdjustedVal.size) {
-    await sleep(opts.waitTime);
-    const adjustedBox2 = getBoxes(box.label, opts)[0];
-    trackOverlaps(adjustedBox2, boxes.filter((b) => b != box));
-    if (adjustedBox2.overlapSum >= box.overlapSum) {
-      box.label.selectAll(step.css.selector).each(function(d) {
-        select_default(this).attr("y", preAdjustedVal.get(this));
-      });
-    } else {
-      Object.assign(box, adjustedBox2);
-      if (!box.collisions.length) return;
-    }
-  }
-  if (box.maxOverlaps.x && box.maxOverlaps.x.val > 0) {
-    if (box.maxOverlaps.x.dir == "e" && freeDirections.includes("w")) {
-      box.label.selectAll(step.css.selector).each(function(d) {
-        const s = select_default(this);
-        preAdjustedVal.set(this, s.attr("x") || 0);
-        s.attr("x", Math.max(-box.maxFree.w, -box.maxOverlaps.x.val) - step.pad);
-      });
-    }
-    if (box.maxOverlaps.x.dir == "w" && freeDirections.includes("e")) {
-      box.label.selectAll(step.css.selector).each(function(d) {
-        const s = select_default(this);
-        preAdjustedVal.set(this, s.attr("x") || 0);
-        s.attr("x", Math.min(box.maxFree.e, box.maxOverlaps.x.val) + step.pad);
-      });
-    }
-  }
-  if (!preAdjustedVal.size) return;
-  await sleep(opts.waitTime);
-  const adjustedBox = getBoxes(box.label, opts)[0];
-  trackOverlaps(adjustedBox, boxes.filter((b) => b != box));
-  if (adjustedBox.overlapSum >= box.overlapSum) {
-    box.label.selectAll(step.css.selector).each(function(d) {
-      select_default(this).attr("x", preAdjustedVal.get(this));
-    });
-  } else {
-    Object.assign(box, adjustedBox);
-  }
-}
-var adjusters = { restyle, move };
-function showBox(box) {
-  return;
-  const rect = select_default(box.elem.closest("svg")).append("rect").attr("x", box.x1).attr("y", box.y1).attr("width", box.width).attr("height", box.height).style("stroke", "blue").style("fill", "transparent");
-}
-function sleep(ms) {
-  return new Promise((resolve) => setTimeout(resolve, ms));
-}
-
-// src/mds.samplescatterplot.js
-var radius = 3;
-var radius_tiny = 0.7;
-var userdotcolor = "black";
-async function init(obj, holder, debugmode) {
-  if (debugmode) {
-    window.obj = obj;
-  }
-  if (!obj.lasso)
-    obj.lasso = {
-      postSelectMenuOptions: [
-        /*{
-             label: 'Do something', 
-             callback({samples, sample_attributes, sample2dot}) {....}
-          },*/
-        {
-          label: "List samples",
-          callback: "listSamples"
-          // will indicate to use the default callback of listing the samples
-        }
-      ]
-    };
-  obj.menu = new Menu({ padding: "2px" });
-  obj.menu2 = new Menu({ padding: "10px" });
-  obj.tip = new Menu({ padding: "5px" });
-  obj.errordiv = holder.append("div").style("margin", "10px");
-  obj.sayerror = (e) => {
-    sayerror(obj.errordiv, typeof e == "string" ? e : e.message);
-    if (e.stack) console.log(e.stack);
-  };
-  const _table = holder.append("table").style("border-spacing", "20px");
-  const tr1 = _table.append("tr");
-  const tr1td1 = tr1.append("td").style("vertical-align", "top");
-  const tr1td2 = tr1.append("td").style("vertical-align", "top");
-  {
-    let searchStr2 = function(data, str) {
-      let found_flag = false;
-      let vals = Object.values(data).filter((a) => a != null && typeof a != "number");
-      let new_vals = vals.filter((a) => typeof a != "object").map((x) => x.toLowerCase());
-      new_vals.forEach((v) => {
-        if (v.toLowerCase().includes(str)) return found_flag = true;
-      });
-      if (!found_flag) {
-        vals.forEach((v) => {
-          if (v && typeof v == "object") {
-            const obj_vals = Object.values(v).filter((a) => a != null && typeof a != "number").map((x) => x.toLowerCase());
-            obj_vals.forEach((ov) => {
-              if (ov.toLowerCase().includes(str)) return found_flag = true;
-            });
-          }
-        });
-      }
-      return found_flag;
-    };
-    var searchStr = searchStr2;
-    const row = tr1td2.append("div").style("margin-bottom", "5px");
-    row.append("input").attr("type", "text").attr("placeholder", "Search sample").style("width", "200px").on("keyup", (event2) => {
-      const str0 = event2.target.value;
-      if (!str0) {
-        obj.dotselection.transition().attr("r", radius);
-        return;
-      }
-      const str = str0.toLowerCase();
-      obj.dotselection.filter((d) => searchStr2(d, str)).transition().attr("r", radius * 2);
-      obj.dotselection.filter((d) => !searchStr2(d, str)).transition().attr("r", 1);
-    });
-  }
-  const legend_div = tr1td2.append("div").style("overflow-x", "hidden").style("overflow-y", "auto").style("height", "100vh");
-  obj.legendtable = legend_div.append("table").style("border-spacing", "5px");
-  obj.filterDiv = tr1td1.append("div").style("position", "relative");
-  const scatterdiv = tr1td1.append("div").style("position", "relative");
-  obj.scattersvg = scatterdiv.append("svg");
-  obj.scattersvg_resizehandle = scatterdiv.append("div");
-  obj.scattersvg_buttons = scatterdiv.append("div");
-  try {
-    await get_data(obj);
-    finish_setup(obj);
-    init_dotcolor_legend(obj);
-    init_plot(obj);
-  } catch (e) {
-    if (e.stack) console.log(e.stack);
-    obj.sayerror(e.message || e);
-  }
-}
-async function get_data(obj) {
-  if (obj.dslabel) {
-    const lst = ["genome=" + obj.genome.name, "dslabel=" + obj.dslabel];
-    if (obj.analysisdata) {
-      if (obj.analysisdata.subset) {
-        if (!obj.analysisdata.subset.key) throw ".subset.key missing";
-        if (!obj.analysisdata.subset.value) throw ".subset.value missing";
-        lst.push("subsetkey=" + obj.analysisdata.subset.key);
-        lst.push("subsetvalue=" + obj.analysisdata.subset.value);
-      }
-    }
-    const data = await dofetch2("mdssamplescatterplot?" + lst.join("&"));
-    if (data.error) throw data.error;
-    if (!data.dots) throw "server error";
-    obj.sample2dot = /* @__PURE__ */ new Map();
-    for (const dot of data.dots) {
-      obj.sample2dot.set(dot.sample, dot);
-    }
-    combine_clientserverdata(obj, data);
-    obj.colorbyattributes = data.colorbyattributes;
-    obj.colorbygeneexpression = data.colorbygeneexpression;
-    obj.tracks = data.tracks;
-    obj.querykey = data.querykey;
-    obj.sample_attributes = obj.mds.sampleAttribute.attributes;
-    return;
-  }
-  const ad = obj.analysisdata;
-  if (obj.disco || ad.disco) {
-    const disco = obj.disco || ad.disco;
-    obj.mds = obj.genome.datasets[disco.dslabel];
-  } else if (obj.mds) {
-    obj.mds = obj.genome.datasets[obj.mds.dslabel];
-  }
-  if (!ad) throw "both .analysisdata{} and .dslabel are missing";
-  if (ad.samples) {
-    if (!Array.isArray(ad.samples)) throw ".analysisdata.samples is not array";
-    obj.dots = ad.samples;
-  } else if (ad.tabular_data) {
-    let lines = ad.tabular_data.split("\n");
-    if (lines.length < 2) throw "at least 2 rows, header row + at least 1 sample data must be supplied";
-    ad.samples = [];
-    const headers = lines.shift().split("	");
-    if (headers.length < 3) throw "at least 3 columns are required with X, Y and sample name";
-    ad.samplekey = headers[2];
-    let xi = headers.indexOf("x");
-    if (xi == -1) xi = headers.indexOf("X");
-    if (xi == -1) throw '"X" or "x" column missing from tabular data';
-    let yi = headers.indexOf("y");
-    if (yi == -1) yi = headers.indexOf("Y");
-    if (yi == -1) throw '"Y" or "y" column missing from tabular data';
-    for (const line of lines) {
-      const values = line.split("	");
-      const sample = {};
-      for (const [i, v] of values.entries()) {
-        if (i == xi) sample.x = Number.parseFloat(v);
-        else if (i == yi) sample.y = Number.parseFloat(v);
-        else sample[headers[i]] = v;
-      }
-      ad.samples.push(sample);
-    }
-    obj.dots = ad.samples;
-    if (ad.sample_attributes == void 0) {
-      ad.sample_attributes = {};
-      for (const [i, key] of headers.entries()) {
-        if (i <= 2) continue;
-        ad.sample_attributes[key] = { label: key };
-      }
-    }
-    if (!ad.colorbyattributes && headers.length > 3) ad.colorbyattributes = [{ key: headers[3] }];
-  } else {
-    throw "unknown data encoding in .analysisdata{}";
-  }
-  obj.sample2dot = /* @__PURE__ */ new Map();
-  for (const d of obj.dots) {
-    if (!Number.isFinite(d.x) || !Number.isFinite(d.y)) throw "non-numeric x/y for a sample";
-    if (ad.samplekey) {
-      d.sample = d[ad.samplekey];
-      delete d[ad.samplekey];
-    }
-    if (ad.sample_attributes) {
-      d.s = {};
-      for (const k in ad.sample_attributes) {
-        d.s[k] = d[k];
-        delete d[k];
-      }
-    }
-    obj.sample2dot.set(d.sample, d);
-  }
-  obj.sample_attributes = ad.sample_attributes;
-  obj.colorbyattributes = ad.colorbyattributes;
-  obj.attr_levels = ad.attr_levels;
-  if (ad.user_samples) {
-    if (!Array.isArray(ad.user_samples)) throw ".user_samples[] is not array";
-    obj.dots_user = [];
-    for (const d of ad.user_samples) {
-      if (!Number.isFinite(d.x) || !Number.isFinite(d.y)) throw "non-numeric x/y for a USER sample";
-      if (ad.samplekey) {
-        d.sample = d[ad.samplekey];
-        delete d[ad.samplekey];
-      }
-      if (!d.color) d.color = userdotcolor;
-      obj.dots_user.push(d);
-    }
-  }
-  if (!obj.filterApi) {
-    obj.filterApi = filterInit({
-      btn: obj.filterDiv.append("div"),
-      btnLabel: "Filter",
-      emptyLabel: "+New Filter",
-      holder: obj.filterDiv.append("div"),
-      vocab: getVocabFromSamplesArray(ad),
-      //termdbConfig: opts.termdbConfig,
-      debug: true,
-      callback(filter) {
-        obj.filteredSamples = getFilteredSamples(ad.samples, filter);
-        if (obj.dotselection._groups[0].length != obj.filteredSamples.size) {
-          obj.dotselection.transition().attr("r", (d) => obj.filteredSamples.has(d.sample) ? radius : 0).style("opacity", (d) => obj.filteredSamples.has(d.sample) ? 1 : 0);
-        } else {
-          obj.dotselection.transition().attr("r", radius).style("opacity", 1);
-        }
-        update_dotcolor_legend(obj);
-      }
-    });
-    obj.filterApi.main({ type: "tvslst", join: "", lst: [] });
-    obj.filteredSamples = [];
-  }
-}
-function combine_clientserverdata(obj, data) {
-  if (!obj.analysisdata) {
-    obj.dots = data.dots;
-    return;
-  }
-  if (!obj.analysisdata.str) throw ".analysisdata.str missing while trying to combine client/server data";
-  const analysis = /* @__PURE__ */ new Map();
-  obj.dots_user = [];
-  for (const line of obj.analysisdata.str.trim().split("\n")) {
-    const l = line.split("	");
-    if (l.length < 3) {
-      continue;
-    }
-    const sample = l[2];
-    if (!sample) continue;
-    const j = {
-      x: Number(l[0]),
-      y: Number(l[1])
-    };
-    if (Number.isNaN(j.x) || Number.isNaN(j.y)) continue;
-    if (l[3]) {
-      j.sample = sample;
-      j.color = userdotcolor;
-      obj.dots_user.push(j);
-      continue;
-    }
-    analysis.set(sample, j);
-  }
-  obj.dots = [];
-  for (const i of data.dots) {
-    const j = analysis.get(i.sample);
-    if (!j) continue;
-    i.x = j.x;
-    i.y = j.y;
-    obj.dots.push(i);
-  }
-}
-function finish_setup(obj) {
-  if (obj.colorbyattributes) {
-    if (!Array.isArray(obj.colorbyattributes)) throw ".colorbyattributes[] is not array";
-    if (!obj.sample_attributes) throw ".sample_attributes{} missing when .colorbyattributes is defined";
-    for (const a of obj.colorbyattributes) {
-      if (typeof a != "object") throw "one of .colorbyattributes[] is not array";
-      if (!a.key) throw ".key missing from one of .colorbyattributes[]";
-      const a2 = obj.sample_attributes[a.key];
-      if (!a2) throw "unknown key from .colorbyattributes: " + a.key;
-      a.label = a2.label;
-      a.values = a2.values;
-      if (!a.values) {
-        a.values = {};
-        for (const d of obj.dots) {
-          const v = d.s[a.key];
-          if (v == void 0 || v == null) continue;
-          a.values[v] = {};
-        }
-      }
-      const cf = ordinal(schemeCategory20);
-      for (const k in a.values) {
-        if (!a.values[k].color) a.values[k].color = cf(k);
-      }
-      if (obj.analysisdata) {
-        const ad = obj.analysisdata.sample_attributes;
-        if (ad[a.key].values == void 0) ad[a.key].values = a.values;
-      }
-    }
-  }
-  if (obj.attr_levels) {
-    if (!Array.isArray(obj.attr_levels)) throw ".attr_levels[] is not array";
-    if (obj.attr_levels.length < 2) throw ".attr_levels[] array has less than 2 items";
-    if (!obj.sample_attributes) throw ".sample_attributes is missing when .attr_levels is defined";
-    for (const l of obj.attr_levels) {
-      if (!l.key) throw ".key missing from one of attr_levels[]";
-      const register = obj.sample_attributes[l.key];
-      if (!register) throw ".attr_levels key missing from sample_attributes{}: " + l.key;
-      if (!register.values) {
-        register.values = {};
-        for (const d of obj.dots) {
-          const v = d.s[l.key];
-          if (v == void 0 || v == null || register.values[v]) continue;
-          register.values[v] = {};
-        }
-        const cf = ordinal(schemeCategory20);
-        for (const k in register.values) {
-          if (!register.values[k].color) register.values[k].color = cf(k);
-        }
-        register.orderByCount = true;
-      }
-      if (l.label) {
-      }
-    }
-  }
-}
-function init_plot(obj) {
-  const rootholder = obj.scattersvg.node().closest(".sja_root_holder");
-  let minx = obj.dots[0].x, maxx = minx, miny = obj.dots[0].y, maxy = miny;
-  for (const d of [...obj.dots, ...obj.dots_user || []]) {
-    minx = Math.min(minx, d.x);
-    maxx = Math.max(maxx, d.x);
-    miny = Math.min(miny, d.y);
-    maxy = Math.max(maxy, d.y);
-  }
-  let xscale = obj.xscale = linear().domain([minx, maxx]);
-  let yscale = obj.yscale = linear().domain([miny, maxy]);
-  if (!obj.dimensions) obj.dimensions = {};
-  if (!("autoResize" in obj.dimensions)) obj.dimensions.autoResize = true;
-  if (!("minWidth" in obj.dimensions)) obj.dimensions.minWidth = 300;
-  if (!("minHeight" in obj.dimensions)) obj.dimensions.minHeight = 300;
-  let currBbox;
-  const estlegendwidth = 250;
-  const bbox = rootholder.getBoundingClientRect();
-  let toppad = 30, bottompad = 50, leftpad = 100, rightpad = 30, vpad = 20, width = obj.dimensions.width ? obj.dimensions.width : Math.max(obj.dimensions.minWidth, 0.75 * (bbox.width - estlegendwidth)), height = obj.dimensions.height ? obj.dimensions.height : Math.max(obj.dimensions.minHeight, Math.min(1.2 * width, 0.5 * bbox.height)), fontsize = 18;
-  const svg = obj.scattersvg;
-  const dotg = obj.dotg = svg.append("g").attr("transform", "translate(" + (leftpad + vpad) + "," + toppad + ")");
-  const dots = dotg.selectAll().data(obj.dots).enter().append("g").attr("class", "sample_dot");
-  const circles = dots.append("circle").attr("stroke", "none").attr("r", radius).on("mouseover", (event2, d) => {
-    event2.target.setAttribute("stroke", "white");
-    const lst = [{ k: "Sample", v: d.sample }];
-    if (obj.sample_attributes) {
-      for (const attrkey in obj.sample_attributes) {
-        const attr = obj.sample_attributes[attrkey];
-        const v = d.s[attrkey];
-        lst.push({
-          k: attr.label,
-          v: d.s[attrkey]
-        });
-      }
-    }
-    make_table_2col(obj.tip.clear().d, lst);
-    obj.tip.show(event2.clientX, event2.clientY);
-  }).on("mouseout", (event2, d) => {
-    event2.target.setAttribute("stroke", "none");
-    obj.tip.hide();
-  }).on("click", (event2, d) => {
-    click_dot(d, obj, event2);
-  });
-  obj.dotselection = circles;
-  let userdots, usercircles, userlabelg, userlabels, userlabel_borders;
-  const userlabel_grp = obj.userlabel_grp = { userlabels, userlabel_borders };
-  if (obj.dots_user) {
-    userdots = dotg.selectAll().data(obj.dots_user).enter().append("g").attr("class", "sample_dot");
-    usercircles = userdots.append("circle").attr("stroke", "none").attr("fill", (d) => d.color).attr("r", radius).on("mouseover", (event2, d) => {
-      const lst = [{ k: "Sample", v: d.sample }];
-      if (obj.sample_attributes) {
-        for (const attrkey in obj.sample_attributes) {
-          const attr = obj.sample_attributes[attrkey];
-          if (d[attrkey])
-            lst.push({
-              k: attr.label,
-              v: d[attrkey]
-            });
-        }
-      }
-      make_table_2col(obj.tip.clear().d, lst);
-      obj.tip.show(event2.clientX, event2.clientY);
-      Object.values(userlabel_grp).forEach(
-        (labels) => labels.filter((i) => i.sample == d.sample).attr("font-weight", "bold")
-      );
-    }).on("mouseout", (event2, d) => {
-      obj.tip.hide();
-      Object.values(userlabel_grp).forEach(
-        (labels) => labels.filter((i) => i.sample == d.sample).attr("font-weight", "normal")
-      );
-    });
-    userlabelg = dotg.selectAll().data(obj.dots_user).enter().append("g").attr("class", "userlabelg");
-    userlabel_grp.userlabel_borders = userlabelg.append("text").attr("fill", "#fff").attr("font-size", fontsize).attr("stroke", "white").attr("stroke-width", "3px").text((d) => d.sample).attr("text-anchor", "end");
-    userlabel_grp.userlabels = userlabelg.append("text").attr("fill", (d) => d.color).attr("font-size", fontsize).text((d) => d.sample).on("mouseover", (event2, d) => {
-      usercircles.filter((i) => i.sample == d.sample).attr("r", radius * 2);
-      svg.style("cursor", "move");
-      const lst = [{ k: "Sample", v: d.sample }];
-      if (obj.sample_attributes) {
-        for (const attrkey in obj.sample_attributes) {
-          const attr = obj.sample_attributes[attrkey];
-          if (d[attrkey])
-            lst.push({
-              k: attr.label,
-              v: d[attrkey]
-            });
-        }
-      }
-      make_table_2col(obj.tip.clear().d, lst);
-      obj.tip.show(event2.clientX, event2.clientY);
-    }).on("mouseout", (event2, d) => {
-      usercircles.filter((i) => i.sample == d.sample).attr("r", radius);
-      svg.style("cursor", "auto");
-      obj.tip.hide();
-    }).on("mousedown", (event2, d) => {
-      event2.preventDefault();
-      event2.stopPropagation();
-      const b = select_default(document.body);
-      const x = event2.clientX;
-      const y = event2.clientY;
-      xscale = obj.zoomed_scale && obj.zoomed_scale > 1 ? obj.new_xscale : obj.xscale;
-      yscale = obj.zoomed_scale && obj.zoomed_scale > 1 ? obj.new_yscale : obj.yscale;
-      const g = userlabelg.filter((i) => i.sample == d.sample);
-      const [x1, y1] = g.attr("transform").match(/[\d\.]+/g).map(Number);
-      b.on("mousemove", (event3) => {
-        g.attr("transform", "translate(" + (x1 + event3.clientX - x) + "," + (y1 + event3.clientY - y) + ")");
-      });
-      b.on("mouseup", (event3) => {
-        b.on("mousemove", null).on("mouseup", null);
-        d.x_ = xscale.invert(x1 + event3.clientX - x);
-        d.y_ = yscale.invert(y1 + event3.clientY - y);
-      });
-    }).on("dblclick", (event2, d) => {
-      obj.menu2.clear().show(event2.clientX - 90, event2.clientY);
-      obj.menu2.d.append("input").attr("type", "text").property("value", d.sample).style("display", "block").style("margin-bottom", "5px").on("keyup", (event3) => {
-        if (!keyupEnter(event3)) return;
-        const v = event3.target.value;
-        Object.values(userlabel_grp).forEach((labels) => labels.filter((i) => i.sample == d.sample).text(v));
-        d.sample = v;
-        obj.menu2.hide();
-      });
-      obj.menu2.d.append("input").attr("type", "color").property("value", d.color).on("change", (event3) => {
-        const v = event3.target.value;
-        Object.values(userlabel_grp).forEach((labels) => labels.filter((i) => i.sample == d.sample).attr("fill", v));
-        usercircles.filter((i) => i.sample == d.sample).attr("fill", v);
-        d.color = v;
-      });
-    });
-    userlabel_grp.userlabels.append("title").text("Double-click to edit");
-  }
-  assign_color4dots(obj);
-  function resize() {
-    bottompad = width / 20 + 20;
-    svg.attr("width", leftpad + vpad + width + rightpad).attr("height", toppad + height + vpad + bottompad);
-    const new_xscale = obj.zoomed_scale && obj.zoomed_scale > 1 ? obj.new_xscale : xscale;
-    const new_yscale = obj.zoomed_scale && obj.zoomed_scale > 1 ? obj.new_yscale : yscale;
-    new_xscale.range([0, width]);
-    new_yscale.range([height, 0]);
-    dots.attr("transform", (d) => "translate(" + new_xscale(d.x) + "," + new_yscale(d.y) + ")");
-    if (userdots) {
-      userdots.attr("transform", (d) => "translate(" + new_xscale(d.x) + "," + new_yscale(d.y) + ")");
-      userlabelg.attr("transform", (d) => {
-        const x = d.x_ ? new_xscale(d.x_) : new_xscale(d.x), y = d.y_ ? new_yscale(d.y_) : new_yscale(d.y);
-        let lw;
-        Object.values(userlabel_grp).forEach(
-          (labels) => labels.filter((i) => i.sample == d.sample).each(function() {
-            lw = this.getBBox().width;
-          }).attr("text-anchor", x + lw >= width ? "end" : "start")
-        );
-        return "translate(" + x + "," + y + ")";
-      });
-    }
-    currBbox = rootholder.getBoundingClientRect();
-    if (obj.userlabel_grp && userlabelg && userlabelg.size()) {
-      uncollide(userlabelg, { waitTime: 0, nameKey: "sample" });
-    }
-  }
-  resize();
-  obj.scattersvg_resizehandle.style("position", "absolute").style("right", "0px").style("bottom", "0px").attr("class", "sja_clbtext").text("drag to resize").on("mousedown", (event2) => {
-    event2.preventDefault();
-    const b = select_default(document.body);
-    const x = event2.clientX;
-    const y = event2.clientY;
-    const w0 = width;
-    const h0 = height;
-    b.on("mousemove", (event3) => {
-      width = w0 + event3.clientX - x;
-      height = h0 + event3.clientY - y;
-      resize();
-    });
-    b.on("mouseup", () => {
-      b.on("mousemove", null).on("mouseup", null);
-    });
-  });
-  function resetDimensions() {
-    const bbox2 = rootholder.getBoundingClientRect();
-    const w = width * bbox2.width / currBbox.width;
-    width = obj.dimensions.minWidth ? Math.max(obj.dimensions.minWidth, w) : w;
-    const h = height * bbox2.height / currBbox.height;
-    height = obj.dimensions.minHeight ? Math.max(obj.dimensions.minHeight, h) : h;
-    currBbox = bbox2;
-    resize();
-  }
-  let timeout;
-  if (obj.dimensions.autoResize) {
-    window.addEventListener("resize", () => {
-      if (timeout) clearTimeout(timeout);
-      timeout = setTimeout(resetDimensions, 50);
-    });
-  }
-  makeConfigPanel(obj);
-}
-function makeConfigPanel(obj) {
-  const svg = obj.scattersvg;
-  obj.scattersvg_buttons.style("position", "absolute").style("right", "0px").style("top", "0px");
-  obj.zoom_active = false;
-  const zoom_btn = obj.scattersvg_buttons.append("div").style("padding", "2px 5px").style("border", "1px solid #999").style("color", "#999").style("background-color", "#fff").style("cursor", "pointer").style("font-weight", "300").style("border-radius", "5px").style("text-align", "center").text("Pan / Zoom").on("click", zoomToggle);
-  const zoom_menu = obj.scattersvg_buttons.append("div").style("margin-top", "2px").style("padding", "2px 5px").style("border-radius", "5px").style("text-align", "center").style("display", obj.zoom_active ? "block" : "none").style("background-color", "#ddd");
-  const zoom_inout_div = zoom_menu.append("div").style("margin", "5px 2px");
-  zoom_inout_div.append("div").style("display", "block").style("padding", "2px 4px").style("font-size", "80%").text("Zoom");
-  zoom_inout_div.append("div").style("display", "block").style("padding", "2px").style("font-size", "70%").html('<p style="margin:1px;">Mouse wheel </br>or use these buttons</p>');
-  const zoom_in_btn = zoom_inout_div.append("button").style("margin", "1px").style("padding", "2px 7px").text("+");
-  const zoom_out_btn = zoom_inout_div.append("button").style("margin", "1px").style("padding", "2px 8px").text("-");
-  const pan_div = zoom_menu.append("div").style("margin", "5px 2px");
-  pan_div.append("div").style("display", "block").style("padding", "2px").style("font-size", "80%").text("Pan");
-  pan_div.append("div").style("display", "block").style("padding", "2px").style("font-size", "70%").html('<p style="margin:1px;">Mouse click </br>+ Mouse move</p>');
-  const reset_div = zoom_menu.append("div").style("margin", "5px 2px");
-  const reset_btn = reset_div.append("button").style("margin", "1px").style("padding", "2px 8px").text("Reset");
-  function zoomToggle() {
-    obj.zoom_active = obj.zoom_active ? false : true;
-    zoom_btn.style("border", obj.zoom_active ? "2px solid #000" : "1px solid #999").style("color", obj.zoom_active ? "#000" : "#999").style("background-color", obj.zoom_active ? "#eee" : "#fff").style("font-weight", obj.zoom_active ? "400" : "300");
-    lasso_btn.style("pointer-events", obj.zoom_active ? "none" : "auto");
-    zoom_menu.style("display", obj.zoom_active ? "block" : "none");
-    const zoom = zoom_default().scaleExtent([1, 5]).on("zoom", obj.zoom_active ? zoomed : null);
-    function zoomed(event2) {
-      obj.new_xscale = event2.transform.rescaleX(obj.xscale);
-      obj.new_yscale = event2.transform.rescaleY(obj.yscale);
-      obj.zoomed_scale = event2.transform.k;
-      const dots = obj.dotg.selectAll(".sample_dot");
-      dots.attr("transform", (d) => "translate(" + obj.new_xscale(d.x) + "," + obj.new_yscale(d.y) + ")");
-      const userlabelg = obj.dotg.selectAll(".userlabelg");
-      userlabelg.attr(
-        "transform",
-        (d) => "translate(" + obj.new_xscale(d.x_ || d.x) + "," + obj.new_yscale(d.y_ || d.y) + ")"
-      );
-    }
-    if (obj.zoom_active) svg.call(zoom);
-    else svg.on(".zoom", null);
-    zoom_in_btn.on("click", () => {
-      zoom.scaleBy(svg.transition().duration(750), 1.5);
-    });
-    zoom_out_btn.on("click", () => {
-      zoom.scaleBy(svg.transition().duration(750), 0.5);
-    });
-    reset_btn.on("click", () => {
-      svg.transition().duration(750).call(zoom.transform, identity);
-    });
-  }
-  const lasso_btn = obj.scattersvg_buttons.append("div").style("display", "block").style("padding", "2px 5px").style("margin-top", "5px").style("border", "1px solid #999").style("color", "#999").style("background-color", "#fff").style("cursor", "pointer").style("font-weight", "300").style("border-radius", "5px").style("text-align", "center").text("Lasso select").on("click", lassoToggle);
-  const lasso_menu = obj.scattersvg_buttons.append("div").style("margin-top", "2px").style("padding", "2px 5px").style("border-radius", "5px").style("text-align", "center").style("display", obj.lasso_active ? "block" : "none").style("background-color", "#ddd");
-  const lasso_div = lasso_menu.append("div").style("margin", "5px 2px");
-  lasso_div.append("div").style("display", "block").style("padding", "2px").style("font-size", "80%").text("Lasso usage");
-  lasso_div.append("div").style("display", "block").style("padding", "2px").style("font-size", "70%").html(
-    '<p style="margin:1px;">Mouse click </br>+ Mouse move <br>TIP: Release the mouse <br> when desired dots <br> are selected, without <br>closing the loop. </p>'
-  );
-  function lassoToggle() {
-    const dots = obj.dotg.selectAll("g");
-    obj.lasso_active = obj.lasso_active ? false : true;
-    zoom_btn.style("pointer-events", obj.lasso_active ? "none" : "auto");
-    lasso_menu.style("display", obj.lasso_active ? "block" : "none");
-    lasso_btn.style("border", obj.lasso_active ? "2px solid #000" : "1px solid #999").style("color", obj.lasso_active ? "#000" : "#999").style("background-color", obj.lasso_active ? "#eee" : "#fff").style("font-weight", obj.lasso_active ? "400" : "300");
-    lasso_select(obj, dots);
-    if (obj.lasso_active) return;
-    dots.selectAll("circle").classed("not_possible", false).classed("possible", false).attr("r", radius).style("fill-opacity", "1");
-  }
-}
-function assign_color4dots(obj) {
-  let byattr;
-  if (obj.colorbygeneexpression && obj.colorbygeneexpression.__inuse) {
-  } else if (obj.attr_levels) {
-    byattr = { key: obj.attr_levels[1].key };
-    byattr.values = obj.sample_attributes[byattr.key].values;
-  } else if (obj.colorbyattributes) {
-    byattr = { key: (obj.colorbyattributes.find((i) => i.__inuse) || obj.colorbyattributes[0]).key };
-    byattr.values = obj.sample_attributes[byattr.key].values;
-  }
-  obj.dotselection.transition().attr("fill", (d) => {
-    if (byattr) {
-      const v = d.s[byattr.key];
-      return byattr.values[v] ? byattr.values[v].color : "black";
-    }
-    return "#ccc";
-  });
-}
-function init_dotcolor_legend(obj) {
-  if (obj.attr_levels) {
-    legend_attr_levels(obj);
-    return;
-  }
-  if (obj.colorbyattributes) {
-    legend_flatlist(obj);
-    return;
-  }
-  if (obj.colorbygeneexpression) {
-  }
-}
-function legend_attr_levels(obj) {
-  const staydiv = obj.legendtable.append("tr").append("td").append("div").style("position", "relative");
-  const scrolldiv = staydiv.append("div");
-  const L1 = obj.attr_levels[0];
-  L1.v2c = /* @__PURE__ */ new Map();
-  L1.unannotated = 0;
-  for (const d of obj.dots) {
-    const v = d.s[L1.key];
-    if (v == void 0 || v == null) {
-      L1.unannotated++;
-      continue;
-    }
-    if (!L1.v2c.has(v)) L1.v2c.set(v, { dots: [] });
-    L1.v2c.get(v).dots.push(d);
-    if (L1.label) {
-      L1.v2c.get(v).label = d.s[L1.label];
-    }
-  }
-  for (const L1value of get_itemOrderList(L1, obj)) {
-    const L1o = L1.v2c.get(L1value);
-    const L1div = scrolldiv.append("div").style("margin-top", "20px").attr("class", "sja_lb_div");
-    L1div.append("div").attr("class", "sja_l1lb").html((L1o.label || L1value) + ' &nbsp;<span style="font-size:.8em">n=' + L1o.dots.length + "</span>").style("margin-top", "15px");
-    const L2 = obj.attr_levels[1];
-    if (L2) {
-      const L2values = obj.sample_attributes[L2.key].values;
-      L2.v2c = /* @__PURE__ */ new Map();
-      L2.unannotated = 0;
-      for (const d of L1o.dots) {
-        const v = d.s[L2.key];
-        if (v == void 0 || v == null) {
-          L2.unannotated++;
-          continue;
-        }
-        if (!L2.v2c.has(v)) {
-          const o = L2values[v];
-          if (o) {
-            o.dots = [];
-            L2.v2c.set(v, o);
-          }
-        }
-        if (L2.v2c.has(v)) {
-          L2.v2c.get(v).dots.push(d);
-          if (L2.label) {
-            L2.v2c.get(v).label = d.s[L2.label];
-          }
-        }
-      }
-      if (!obj.hide_subtype_legend) {
-        for (const L2value of get_itemOrderList(L2, obj)) {
-          const L2o = L2.v2c.get(L2value);
-          const cell = L1div.append("div").style("display", "inline-block").style("white-space", "nowrap").attr("class", "sja_clb").on("click", () => {
-            if (L2o.selected) {
-              L2o.selected = false;
-              cell.style("border", "");
-              let alloff2 = true;
-              for (const k in L2values) {
-                if (L2values[k].selected) alloff2 = false;
-              }
-              if (alloff2) {
-                obj.dotselection.transition().attr("r", radius);
-              } else {
-                obj.dotselection.filter((d) => d.s[L2.key] == L2value).transition().attr("r", radius_tiny);
-              }
-              return;
-            }
-            let alloff = true;
-            for (const k in L2values) {
-              if (L2values[k].selected) alloff = false;
-            }
-            L2o.selected = true;
-            cell.style("border", "solid 1px #858585");
-            if (alloff) {
-              obj.dotselection.transition().attr("r", (d) => d.s[L2.key] == L2value ? radius : radius_tiny);
-            } else {
-              obj.dotselection.filter((d) => d.s[L2.key] == L2value).transition().attr("r", radius);
-            }
-          });
-          cell.append("div").style("display", "inline-block").attr("class", "sja_mcdot").style("background", L2o.color).style("margin-right", "3px").text(L2o.dots.length);
-          cell.append("div").style("display", "inline-block").style("color", L2o.color).text(L2o.label || L2value);
-          L2o.cell = cell;
-        }
-      }
-      if (L2.unannotated) {
-        const d = L1div.append("div").style("margin-top", "20px");
-        d.append("div").text('Unannotated for "' + L2.key + '": ' + L2.unannotated);
-      }
-    }
-  }
-  if (L1.unannotated) {
-    const d = scrolldiv.append("div").style("margin-top", "20px");
-    d.append("div").html('Unannotated for "' + L1.key + '": ' + L1.unannotated);
-  }
-  if (L1.v2c.size > 10) {
-    scrolldiv.style("overflow-y", "scroll").style("height", "800px").style("resize", "vertical");
-  }
-}
-function get_itemOrderList(level, obj) {
-  const register = obj.sample_attributes[level.key];
-  if (!register.values || register.orderByCount) {
-    return [...level.v2c].sort((i, j) => j[1].dots.length - i[1].dots.length).map((i) => i[0]);
-  }
-  const lst = [];
-  for (const k in register.values) {
-    if (level.v2c.has(k)) lst.push(k);
-  }
-  return lst;
-}
-function legend_flatlist(obj) {
-  if (!obj.colorbyattributes.find((i) => i.__inuse)) obj.colorbyattributes[0].__inuse = true;
-  for (const attr of obj.colorbyattributes) {
-    const tr = obj.legendtable.append("tr");
-    attr.labelhandle = tr.append("td").append("div").style("white-space", "nowrap").text(attr.label).attr("class", "sja_clb").on("click", () => {
-      for (const attr2 of obj.colorbyattributes) {
-        attr2.__inuse = false;
-        attr2.labelhandle.style("background", "").style("border-bottom", "");
-      }
-      attr.__inuse = true;
-      attr.labelhandle.style("background", "#ededed").style("border-bottom", "solid 2px #858585");
-      assign_color4dots(obj);
-    });
-    if (attr.__inuse) {
-      attr.labelhandle.style("background", "#ededed").style("border-bottom", "solid 2px #858585");
-    }
-    for (const d of obj.dots) {
-      const v = d.s[attr.key];
-      if (v == void 0 || v == null) continue;
-      if (!attr.values[v]) attr.values[v] = { color: "black" };
-      attr.values[v].count = 1 + (attr.values[v].count || 0);
-    }
-    const cellholder = tr.append("td");
-    for (const value in attr.values) {
-      const o = attr.values[value];
-      if (o.count == 0 || o.count == void 0) continue;
-      const cell = cellholder.append("div").style("display", "inline-block").attr("class", "sja_clb").on("click", () => {
-        if (o.selected) {
-          o.selected = false;
-          cell.style("border", "");
-          let alloff2 = true;
-          for (const k in attr.values) {
-            if (attr.values[k].selected) alloff2 = false;
-          }
-          if (alloff2) {
-            obj.dotselection.transition().attr("r", radius);
-          } else {
-            obj.dotselection.filter((d) => d.s[attr.key] == value).transition().attr("r", radius_tiny);
-          }
-          return;
-        }
-        let alloff = true;
-        for (const k in attr.values) {
-          if (attr.values[k].selected) alloff = false;
-        }
-        o.selected = true;
-        cell.style("border", "solid 1px #858585");
-        if (alloff) {
-          obj.dotselection.transition().attr("r", (d) => d.s[attr.key] == value ? radius : radius_tiny);
-        } else {
-          obj.dotselection.filter((d) => d.s[attr.key] == value).transition().attr("r", radius);
-        }
-      });
-      cell.append("div").style("display", "inline-block").attr("class", "sja_mcdot").style("background", o.color).style("margin-right", "3px").text(o.count);
-      cell.append("div").style("display", "inline-block").style("color", o.color).text(o.name || value);
-      o.cell = cell;
-    }
-  }
-}
-function update_dotcolor_legend(obj) {
-  const filterd_dots = obj.dots.filter((d) => obj.filteredSamples.has(d.sample));
-  const attrs_list = Array.from(filterd_dots, (d) => d.s);
-  const key1 = obj.attr_levels?.[0].label || obj.attr_levels?.[0].key;
-  const l1_labs = [...new Set(Array.from(attrs_list, (a) => a[key1]))];
-  const key2 = obj.attr_levels?.[1].label || obj.attr_levels?.[1].key;
-  const l2_labs = [...new Set(Array.from(attrs_list, (a) => a[key2]))];
-  const legend_divs = obj.legendtable.node().querySelectorAll(".sja_lb_div");
-  for (const div1 of legend_divs) {
-    const l1_label = select_default(div1).select(".sja_l1lb").node().innerText.split(/\s{2}n=/)[0];
-    if (!l1_labs.includes(l1_label)) select_default(div1).style("display", "none");
-    else {
-      select_default(div1).style("display", "block");
-      const l2_divs = select_default(div1).node().querySelectorAll(".sja_clb");
-      for (const div2 of l2_divs) {
-        const clab = select_default(div2).node().querySelectorAll("div")[1];
-        if (!l2_labs.includes(clab.innerText)) select_default(div2).style("display", "none");
-        else select_default(div2).style("display", "inline-block");
-      }
-    }
-  }
-}
-function click_dot(dot, obj, event2) {
-  if (obj.dslabel) {
-    click_dot_mdsview(dot, obj, event2);
-    return;
-  }
-  if (obj.mds) {
-    click_dot_disco(dot, obj, event2);
-    return;
-  }
-}
-async function click_dot_disco(dot, obj, event2) {
-  const pane = newpane({ x: event2.clientX, y: event2.clientY });
-  pane.header.text(dot.sample);
-  const wait = tab_wait(pane.body);
-  try {
-    const sjcharts = await getsjcharts();
-    const arg = {
-      genome: obj.genome.name,
-      dslabel: obj.mds.label,
-      querykey: obj.mds.querykey,
-      getsample4disco: dot.sample
-    };
-    const data = await dofetch("/mdssvcnv", arg);
-    if (data.error) throw data.error;
-    if (!data.text) throw ".text missing";
-    const discoHolder = pane.body.append("div");
-    const renderer = await sjcharts.dtDisco({
-      holderSelector: discoHolder,
-      chromosomeType: obj.genome.name,
-      majorchr: obj.genome.majorchr,
-      settings: {
-        showControls: false,
-        selectedSamples: []
-      },
-      callbacks: {
-        geneLabelClick: {
-          type: "genomepaint",
-          hostURL: sessionStorage.getItem("hostURL") || "",
-          genome: obj.genome.name,
-          dslabel: obj.mds.label,
-          sample: dot.sample
-        }
-      }
-    });
-    const disco_arg = {
-      sampleName: dot.sample,
-      data: JSON.parse(data.text)
-    };
-    renderer.main(disco_arg);
-    wait.remove();
-  } catch (e) {
-    wait.text("Error: " + (e.message || e));
-    if (e.stack) console.log(e.stack);
-  }
-}
-function click_dot_mdsview(dot, obj, event2) {
-  const pane = newpane({ x: event2.clientX, y: event2.clientY });
-  pane.header.text(dot.sample);
-  const wait = pane.body.append("div").style("margin", "20px").text("Loading ...");
-  dofetch("/mdssvcnv", {
-    genome: obj.genome.name,
-    dslabel: obj.dslabel,
-    querykey: obj.querykey,
-    // TODO general track
-    gettrack4singlesample: dot.sample
-  }).then((data) => {
-    wait.remove();
-    launch_singlesample({
-      obj,
-      dot,
-      sampletracks: data.tracks,
-      holder: pane.body
-    });
-  });
-}
-function lasso_select(obj, dots) {
-  const svg = obj.scattersvg;
-  let lasso;
-  if (obj.lasso_active) {
-    lasso = d3lasso().items(dots.selectAll("circle")).targetArea(svg);
-    lasso.on("start", scatterplot_lasso_start).on("draw", scatterplot_lasso_draw).on("end", scatterplot_lasso_end);
-    svg.call(lasso);
-  } else {
-    svg.selectAll(".lasso").remove();
-    svg.on("mousedown.drag", null);
-  }
-  function scatterplot_lasso_start() {
-    if (!obj.lasso_active) return;
-    lasso.items().attr("r", 2).style("fill-opacity", ".5").classed("not_possible", true).classed("selected", false);
-  }
-  function scatterplot_lasso_draw() {
-    if (!obj.lasso_active) return;
-    lasso.possibleItems().attr("r", radius).style("fill-opacity", "1").classed("not_possible", false).classed("possible", true);
-  }
-  function scatterplot_lasso_end(event2) {
-    if (!obj.lasso_active) return;
-    const selected_samples = svg.selectAll(".possible").data().map((d) => d.sample);
-    if (selected_samples.length) show_lasso_menu(event2, selected_samples);
-    else obj.menu.hide();
-    lasso.items().classed("not_possible", false).classed("possible", false);
-    lasso.selectedItems().attr("r", radius);
-    lasso.notSelectedItems().attr("r", selected_samples.length == 0 ? radius : radius_tiny).style("fill-opacity", "1");
-  }
-  function show_lasso_menu(event2, samples) {
-    obj.menu.clear().show(event2.sourceEvent.clientX - 90, event2.sourceEvent.clientY);
-    if (obj.mds && obj.mds.gene2mutcount) {
-      obj.menu.d.append("div").attr("class", "sja_menuoption").text("Recurrently mutated genes").on("click", async () => {
-        obj.menu.hide();
-        await click_mutated_genes(obj, samples);
-      });
-    }
-    for (const opt of obj.lasso.postSelectMenuOptions) {
-      obj.menu.d.append("div").attr("class", "sja_menuoption").text(opt.label).on("click", async () => {
-        obj.menu.hide();
-        const arg = {
-          samples,
-          sample_attributes: obj.sample_attributes,
-          sample2dot: obj.sample2dot
-        };
-        if (opt.callback == "listSamples") printData(arg);
-        else opt.callback(arg);
-      });
-    }
-    obj.menu.d.append("div").attr("class", "sja_menuoption").text("Cancel").on("click", () => {
-      lasso.items().classed("not_possible", false).classed("possible", false).attr("r", radius).style("fill-opacity", "1");
-      obj.menu.hide();
-    });
-    obj.menu.d.append("div").style("padding", "10px").style("font-size", ".8em").style("width", "150px").text(samples.length + " samples selected");
-  }
-}
-function printData(obj) {
-  const { samples, sample_attributes, sample2dot } = obj;
-  const label_keys = Object.keys(sample_attributes);
-  let labels = label_keys.map((k) => sample_attributes[k].label ? sample_attributes[k].label : k);
-  labels.unshift("Sample");
-  const labels_str = labels.join("	");
-  const lst = [labels_str];
-  for (const s of samples) {
-    if (sample2dot.get(s).s) {
-      let sample_row = [];
-      sample_row.push(s);
-      for (const k of label_keys) sample_row.push(sample2dot.get(s).s[k]);
-      lst.push(sample_row.join("	"));
-    }
-  }
-  export_data("List of selected samples", [{ text: lst.join("\n") }]);
-}
-function click_mutated_genes(obj, samples) {
-  obj.pane = newpane({ x: event.clientX, y: event.clientY });
-  obj.pane.header.text("Recurrently Mutated Genes");
-  obj.pane.wait = tab_wait(obj.pane.body);
-  obj.pane.matrix_criteria_div = obj.pane.body.append("div");
-  obj.pane.sample_matrix_div = obj.pane.body.append("div");
-  init_mutation_type_control(obj, samples);
-}
-function init_mutation_type_control(obj, samples) {
-  let mutTypes = [], defaultTypes = [], selectedTypes = [], selected_cnv, nGenes = 15;
-  const holder = obj.pane.matrix_criteria_div;
-  if (obj.mds.mutCountType) {
-    mutTypes = obj.mds.mutCountType;
-    const non_cnv_types = mutTypes.filter((m) => !m.db_col.includes("cnv"));
-    const cnv_types = mutTypes.filter((m) => m.db_col.includes("cnv"));
-    const default_cnv = cnv_types.find((t) => t.default);
-    selected_cnv = default_cnv;
-    defaultTypes = mutTypes.filter((t) => t.default).map((t) => t.db_col);
-    selectedTypes = [...defaultTypes];
-    const buttonrow = holder.append("div").style("margin", "5px 20px");
-    const criteria_div = holder.append("div").style("margin", "5px 20px").style("padding", "5px").style("border-top", "solid 1px #ededed").style("border-bottom", "solid 1px #ededed").style("background-color", "#FCFBF7").style("font-size", ".8em");
-    buttonrow.append("span").style("margin-right", "20px").style("font-size", ".8em").text("MUTATION COUNT & NO. OF GENE CRITERIA").attr("class", "sja_clbtext").on("click", () => {
-      if (criteria_div.style("display") == "none") {
-        appear(criteria_div);
-      } else {
-        disappear(criteria_div);
-      }
-    });
-    const mut_div = criteria_div.append("div");
-    const mut_label_div = mut_div.append("div").style("display", "table-cell").style("width", "110px");
-    mut_label_div.append("div").text("Consequences").style("padding-right", "15px");
-    const mut_types_div = mut_div.append("div").style("display", "table-cell").style("border-left", "solid 1px #ededed");
-    non_cnv_types.forEach((type) => {
-      const m_div = mut_types_div.append("div");
-      const checkbox = m_div.append("input").attr("type", "checkbox").attr("name", "mut_type").attr("value", type.db_col).style("margin", "3px").style("margin-left", "4px").property("checked", type.default);
-      checkbox.on("change", () => {
-        if (checkbox.node().checked) {
-          selectedTypes.push(checkbox.node().value);
-        } else {
-          selectedTypes = selectedTypes.filter((t) => t !== checkbox.node().value);
-        }
-      });
-      m_div.append("label").attr("for", type.db_col).html(type.label);
-    });
-    const cnv_checkbox = mut_types_div.append("input").attr("type", "checkbox").attr("name", "noncnv").attr("value", "cnv").style("margin", "3px").style("margin-left", "4px").property("checked", default_cnv ? true : false).on("change", () => {
-      if (cnv_checkbox.node().checked) {
-        size_select.property("disabled", false);
-        ratio_select.property("disabled", false);
-      } else {
-        size_select.property("disabled", true);
-        ratio_select.property("disabled", true);
-      }
-    });
-    mut_types_div.append("label").attr("for", "cnv").text("CNV");
-    const cnv_options_div = mut_types_div.append("div").style("display", "block").style("padding", "3px 15px");
-    const cnv_size_cutoff = [...new Set(cnv_types.map((t) => t.sizecutoff))];
-    const cnv_ratio_cutoff = [...new Set(cnv_types.map((t) => t.log2cutoff))];
-    cnv_options_div.append("label").attr("for", "cnv_size").style("margin", "2px 10px").text("Size cutoff");
-    const size_select = cnv_options_div.append("select").attr("name", "cnv_size");
-    cnv_size_cutoff.forEach((size) => {
-      size_select.append("option").attr("value", size).text(size);
-    });
-    size_select.property("selectedIndex", default_cnv.sizecutoff == "1Mb" ? 0 : default_cnv.sizecutoff == "2Mb" ? 1 : 2);
-    cnv_options_div.append("label").attr("for", "log2_ratio").style("margin", "2px 10px").text("log2(ratio) cutoff");
-    const ratio_select = cnv_options_div.append("select").attr("name", "log2_ratio");
-    cnv_ratio_cutoff.forEach((ratio) => {
-      ratio_select.append("option").attr("value", ratio.toFixed(1)).text(ratio.toFixed(1));
-    });
-    ratio_select.property("selectedIndex", default_cnv.log2cutoff == 0.1 ? 0 : default_cnv.log2cutoff == 0.2 ? 1 : 2);
-    const gene_div = criteria_div.append("div").style("padding-top", "10px");
-    const gene_label_div = gene_div.append("div").style("display", "table-cell").style("width", "110px");
-    gene_label_div.append("div").text("No. of Genes").style("padding-right", "15px");
-    const gene_n_select_div = gene_div.append("div").style("display", "table-cell").style("padding", "3px").style("border-left", "solid 1px #ededed");
-    const gene_n = [10, 15, 20, 30, 40];
-    const gene_n_select = gene_n_select_div.append("select").attr("name", "gene_n");
-    gene_n.forEach((n) => {
-      gene_n_select.append("option").attr("value", n).text(n);
-    });
-    gene_n_select.property(
-      "selectedIndex",
-      gene_n.findIndex((n) => n == nGenes)
-    );
-    const calc_btn = criteria_div.append("button").style("margin", "10px").style("padding", "3px 10px").text("Calculate").on("click", () => {
-      const checked_boxes = mut_types_div.node().querySelectorAll("input:checked");
-      selectedTypes = [];
-      checked_boxes.forEach((checkbox) => {
-        if (checkbox.value !== "cnv" && !selectedTypes.includes(checkbox.value)) selectedTypes.push(checkbox.value);
-        else if (checkbox.value == "cnv") {
-          const selected_size = size_select.node().value;
-          const selected_ratio = ratio_select.node().value;
-          selected_cnv = cnv_types.find((t) => t.sizecutoff == selected_size && t.log2cutoff == selected_ratio);
-          selectedTypes.push(selected_cnv.db_col);
-        }
-      });
-      nGenes = gene_n_select.node().value;
-      get_mutation_count_data(obj, samples, selectedTypes, nGenes);
-      defaultTypes = [...selectedTypes];
-    });
-  } else defaultTypes = ["total"];
-  get_mutation_count_data(obj, samples, defaultTypes, nGenes);
-}
-async function get_mutation_count_data(obj, samples, selectedMutTypes, nGenes) {
-  try {
-    const arg = {
-      genome: obj.genome.name,
-      dslabel: obj.mds.label,
-      samples,
-      selectedMutTypes,
-      nGenes
-    };
-    const data = await dofetch2("mdsgenecount", { method: "POST", body: JSON.stringify(arg) });
-    if (data.error) throw data.error;
-    if (!data.genes) throw ".genes missing";
-    if (!data.genes.length) {
-      obj.pane.wait.html("No gene retrived with mutations.");
-      obj.pane.matrix_criteria_div.style("display", "none");
-      return;
-    }
-    make_sample_matrix({ obj, genes: data.genes, samples, holder: obj.pane.body });
-    obj.pane.wait.remove();
-  } catch (e) {
-    obj.pane.wait.text("Error: " + (e.message || e));
-    if (e.stack) console.log(e.stack);
-  }
-}
-function make_sample_matrix(args) {
-  const { obj, genes, samples } = args;
-  const holder = obj.pane.sample_matrix_div;
-  holder.selectAll("*").remove();
-  for (const g of genes) {
-    g.ismutation = true;
-    g.genename = g.gene;
-    g.label = g.gene;
-    delete g.gene;
-    g.querykeylst = ["svcnv", "snvindel"];
-    obj.features_on_rows ? g.height = 50 : g.width = 50;
-  }
-  const arg = {
-    genome: obj.genome,
-    dslabel: obj.mds.label,
-    features: genes,
-    features_on_rows: obj.features_on_rows,
-    ismutation_allsymbolic: true,
-    hostURL: sessionStorage.getItem("hostURL") || "",
-    limitbysamplesetgroup: { samples },
-    jwt: sessionStorage.getItem("jwt") || "",
-    holder: holder.append("div").style("margin", "20px")
-  };
-  import("./samplematrix-DFD3PNI4.js").then((_) => {
-    const m = new _.Samplematrix(arg);
-    m._pane = holder;
-  });
-}
-function launch_singlesample(p) {
-  const { obj, dot, sampletracks, holder } = p;
-  const arg = {
-    genome: obj.genome,
-    hostURL: sessionStorage.getItem("hostURL") || "",
-    jwt: sessionStorage.getItem("jwt") || "",
-    holder,
-    chr: obj.genome.defaultcoord.chr,
-    start: obj.genome.defaultcoord.start,
-    stop: obj.genome.defaultcoord.stop,
-    nobox: 1,
-    tklst: []
-  };
-  if (obj.tracks) {
-    for (const t of obj.tracks) arg.tklst.push(t);
-  }
-  const mdstk = obj.mds.queries[obj.querykey];
-  if (mdstk) {
-    const tk = {
-      singlesample: { name: dot.sample },
-      mds: obj.mds,
-      querykey: obj.querykey
-    };
-    for (const k in mdstk) {
-      tk[k] = mdstk[k];
-    }
-    arg.tklst.push(tk);
-    if (mdstk.checkexpressionrank) {
-      const et = {
-        type: tkt.mdsexpressionrank,
-        name: dot.sample + " gene expression rank",
-        //mds: tk.mds,
-        dslabel: obj.mds.label,
-        querykey: mdstk.checkexpressionrank.querykey,
-        sample: dot.sample
-      };
-      if (mdstk.groupsamplebyattr) {
-        const lst = mdstk.groupsamplebyattr.attrlst;
-        if (lst && lst.length) {
-          et.attributes = [];
-          for (const attr of lst) {
-            et.attributes.push({
-              k: attr.k,
-              label: attr.label,
-              kvalue: dot.s[attr.k]
-            });
-          }
-        }
-      }
-      arg.tklst.push(et);
-    }
-  }
-  if (sampletracks) {
-    for (const t of sampletracks) arg.tklst.push(t);
-  }
-  first_genetrack_tolist(obj.genome, arg.tklst);
-  blocklazyload(arg);
-}
-export {
-  init
-};
-//# sourceMappingURL=mds.samplescatterplot-ZAIEWPO4.js.map