@sjcrh/proteinpaint-client 2.166.0 → 2.167.0

package/dist/HicApp-6AYCPCW6.js

@@ -0,0 +1,2218 @@
+import {
+  blocklazyload
+} from "./chunk-NCL2K6UD.js";
+import {
+  hicParseFile
+} from "./chunk-KHOR7BCS.js";
+import {
+  ColorScale,
+  axisstyle,
+  first_genetrack_tolist,
+  font,
+  newpane,
+  showErrorsWithCounter,
+  tkt
+} from "./chunk-PX7A6LBY.js";
+import "./chunk-HJ6L54YS.js";
+import {
+  dofetch3
+} from "./chunk-6ADTREVX.js";
+import "./chunk-DKI7YOTJ.js";
+import {
+  bplen
+} from "./chunk-6VQ4C735.js";
+import {
+  Menu
+} from "./chunk-TGZA4ETW.js";
+import "./chunk-5MWX5HUZ.js";
+import "./chunk-IQIXGTQV.js";
+import "./chunk-ZFFHOEBE.js";
+import {
+  getAppInit,
+  getCompInit,
+  getStoreInit
+} from "./chunk-DDOM4XYV.js";
+import "./chunk-7NTZWOJV.js";
+import "./chunk-LD45BCVM.js";
+import "./chunk-RA5EXEHB.js";
+import "./chunk-2MN5JLZB.js";
+import {
+  axisBottom,
+  axisRight
+} from "./chunk-LOZEKOES.js";
+import "./chunk-TOU7EVFQ.js";
+import {
+  format,
+  linear
+} from "./chunk-W2IWHXLL.js";
+import "./chunk-5OHXYXLD.js";
+import "./chunk-UJUXE42U.js";
+import "./chunk-OMR2DT66.js";
+import {
+  pointer_default,
+  select_default
+} from "./chunk-NDWTN4U5.js";
+import "./chunk-HFNDKYVF.js";
+
+// tracks/hic/HicStore.ts
+var HicStore = class {
+  constructor() {
+    this.views = ["genome", "chrpair", "detail", "horizontal"];
+    this.type = "store";
+    this.defaultState = {
+      defaultNmeth: "NONE",
+      loading: true,
+      minBinNum_bp: 200,
+      minFragSpan: 200,
+      initialBinNum: 20,
+      settings: {
+        widthHeightPx: 800
+      }
+    };
+  }
+};
+var hicStoreInit = getStoreInit(HicStore);
+HicStore.prototype.actions = {
+  view_create(action) {
+    if (!action.view) throw Error("view_create: missing view");
+    if (!this.views.some((v) => v == action.view)) throw Error(`view_create: unknown view = ${action.view}`);
+    this.state.currView = action.view;
+    const opts = Object.assign(this.state, action.config);
+    this.state = opts;
+  },
+  view_update(action) {
+    if (action.view) {
+      if (!this.views.some((v) => v == action.view)) throw Error(`view_update: unknown view = ${action.view}`);
+      const opts = Object.assign(this.state[action.view], action.config);
+      this.state[action.view] = opts;
+    } else {
+      const opts = Object.assign(this.state, action.config);
+      this.state = opts;
+    }
+  },
+  loading_active(action) {
+    this.state.loading = action.active;
+  }
+};
+
+// tracks/hic/dom/LoadingOverlay.ts
+var LoadingOverlay = class {
+  constructor(opts) {
+    this.hasStatePreMain = true;
+    this.type = "loadingOverlay";
+    this.app = opts.app;
+    this.loadingDiv = opts.loadingDiv;
+  }
+  reactsTo(action) {
+    if (action.type.startsWith("loading")) return true;
+    else return false;
+  }
+  getState(appState) {
+    return appState;
+  }
+  init() {
+    this.loadingDiv.append("div").attr("class", "sjpp-spinner").style("display", "");
+  }
+  main(appState) {
+    const loading = this.app.getState(appState).loading;
+    this.loadingDiv.style("display", loading ? "" : "none");
+  }
+};
+var loadingInit = getCompInit(LoadingOverlay);
+
+// tracks/hic/dom/ColorizeElement.ts
+var ColorizeElement = class {
+  colorizeElement(xCoord, yCoord, v, obj, width, height, bpMinV, bpMaxV, currView) {
+    if (v >= 0) {
+      const p = v >= bpMaxV ? 0 : v <= bpMinV ? 255 : Math.floor(255 * (bpMaxV - v) / bpMaxV);
+      const positiveFill = `rgb(255, ${p}, ${p})`;
+      if (currView === "genome") {
+        obj.ctx.fillStyle = positiveFill;
+        obj.ctx2.fillStyle = positiveFill;
+      } else {
+        obj.fillStyle = positiveFill;
+      }
+    } else {
+      const p = v <= bpMinV ? 255 : Math.floor(255 * (bpMaxV + v) / bpMaxV);
+      const negativeFill = `rgb(${p}, ${p}, 255)`;
+      if (currView === "genome") {
+        obj.ctx.fillStyle = negativeFill;
+        obj.ctx2.fillStyle = negativeFill;
+      } else {
+        obj.fillStyle = negativeFill;
+      }
+    }
+    if (currView === "genome") {
+      obj.ctx.fillRect(yCoord, xCoord, width, height);
+      obj.ctx2.fillRect(xCoord, yCoord, width, height);
+    } else {
+      obj.fillRect(xCoord, yCoord, width, height);
+    }
+  }
+};
+
+// tracks/hic/data/Resolution.ts
+var Resolution = class {
+  constructor(error) {
+    this.error = error;
+  }
+  getResolution(state, hic) {
+    if (state.currView == "genome") return hic["bpresolution"][0];
+    if (state.currView == "chrpair") {
+      const resolution = this.getChrPairResolution(hic, state.x, state.y, state.minBinNum_bp);
+      return resolution;
+    } else if (state.currView == "detail") {
+      const maxBpWidth = Math.max(state.x.stop - state.x.start, state.y.stop - state.y.start);
+      let resolution = this.findResFromArray(maxBpWidth, state.minBinNum_bp, hic.bpresolution);
+      if (resolution == null && !hic.enzyme) {
+        resolution = hic.bpresolution[hic.bpresolution.length - 1];
+      }
+      return resolution;
+    } else {
+      this.error(`Unknown view: ${state.currView}`);
+      throw `Unknown view: ${state.currView}`;
+    }
+  }
+  getChrPairResolution(hic, x, y, minBinNum_bp) {
+    const chrxlen = hic.genome.chrlookup[x.chr.toUpperCase()].len;
+    const chrylen = hic.genome.chrlookup[y.chr.toUpperCase()].len;
+    const maxchrlen = Math.max(chrxlen, chrylen);
+    const resolution = this.findResFromArray(maxchrlen, minBinNum_bp, hic.bpresolution);
+    if (resolution == null) {
+      this.error(`No suitable resolution for ${x.chr}-${y.chr} pair.`);
+      return;
+    }
+    return resolution;
+  }
+  findResFromArray(max, defaultValue, resolutionArray, returnNum) {
+    let resolution = null;
+    for (const res of resolutionArray) {
+      if (max / res > defaultValue) {
+        resolution = res;
+        break;
+      }
+    }
+    if (returnNum && resolution == null) {
+      resolution = resolutionArray[resolutionArray.length - 1];
+    }
+    return resolution;
+  }
+  getDefaultViewSpan(hic, x, y, initialBinNum, minBinNum_bp) {
+    const chrpairResolution = this.getChrPairResolution(hic, x, y, minBinNum_bp);
+    if (!chrpairResolution) return;
+    return chrpairResolution * initialBinNum;
+  }
+};
+
+// tracks/hic/data/Positions.ts
+var Positions = class {
+  constructor(error, minBinNum_bp) {
+    this.error = error;
+    this.resolution = new Resolution(this.error);
+    this.minBinNum_bp = minBinNum_bp;
+  }
+  /**
+   *
+   * @param x x coordinate of pointer
+   * @param y y coordinate of pointer
+   * @param binpx
+   * @param chrx x chr from state
+   * @param chry y chr from state
+   * @param hic
+   * @param initialBinNum Set in the state
+   * @returns
+   */
+  setPosition(x, y, binpx, chrx, chry, hic, initialBinNum) {
+    const resolution = this.resolution.getChrPairResolution(hic, chrx, chry, this.minBinNum_bp);
+    const viewrangebpw = resolution * initialBinNum;
+    let coordx = Math.max(1, Math.floor(x * resolution / binpx) - viewrangebpw / 2);
+    let coordy = Math.max(1, Math.floor(y * resolution / binpx) - viewrangebpw / 2);
+    {
+      const lenx = hic.genome.chrlookup[chrx.chr.toUpperCase()].len;
+      if (coordx + viewrangebpw >= lenx) {
+        coordx = lenx - viewrangebpw;
+      }
+      const leny = hic.genome.chrlookup[chry.chr.toUpperCase()].len;
+      if (coordy + viewrangebpw > leny) {
+        coordy = leny - viewrangebpw;
+      }
+    }
+    const xObj = {
+      chr: chrx.chr,
+      start: coordx,
+      stop: coordx + viewrangebpw
+    };
+    const yObj = {
+      chr: chry.chr,
+      start: coordy,
+      stop: coordy + viewrangebpw
+    };
+    return [xObj, yObj];
+  }
+};
+
+// tracks/hic/data/GridElementsFormattedData.ts
+var GridElementsFormattedData = class {
+  /**
+   * Format the data for the grid elements.
+   * @param items The data to format.
+   * @param binpx The bin size in pixels.
+   * @param resolution The resolution.
+   * @param isFirstChrX Whether the first chromosome is X. Used for chrpair view.
+   * @param isIntraChr Whether the data is intra-chromosomal. Used for chrpair view
+   * @returns The formatted data.
+   */
+  formatData(view, items, binpx, resolution, isFirstChrX, isIntraChr) {
+    const formattedData = [];
+    for (const [xCoord, yCoord, value] of items) {
+      const xPx = Math.floor(xCoord / resolution) * binpx;
+      const yPx = Math.floor(yCoord / resolution) * binpx;
+      if (view == "genome") {
+        formattedData.push([xPx, yPx, value]);
+      }
+      if (view == "chrpair") {
+        const x = isFirstChrX ? xPx : yPx;
+        const y = isFirstChrX ? yPx : xPx;
+        formattedData.push([x, y, value]);
+        if (isIntraChr) {
+          formattedData.push([y, x, value]);
+        }
+      }
+    }
+    return formattedData;
+  }
+};
+
+// tracks/hic/data/FirstChrX.ts
+var FirstChrX = class {
+  constructor(chrorder, chrx, chry) {
+    this.chrorder = chrorder;
+    this.chrx = chrx;
+    this.chry = chry;
+  }
+  isFirstX() {
+    if (this.chrx == this.chry) return true;
+    return this.chrorder.indexOf(this.chrx) < this.chrorder.indexOf(this.chry);
+  }
+};
+
+// tracks/hic/chrpair/ChrPairView.ts
+var ChrPairView = class {
+  constructor(opts) {
+    this.binpx = 1;
+    /** padding on the ends of x/y chr coordinate axes */
+    this.axispad = 10;
+    this.axisLabelFontSize = 15;
+    this.calcResolution = null;
+    this.data = [];
+    this.app = opts.app;
+    this.hic = opts.hic;
+    this.plotDiv = opts.plotDiv;
+    this.items = opts.items;
+    this.parent = opts.parent;
+    this.chrxlen = this.hic.genome.chrlookup[this.parent("state").x.chr.toUpperCase()].len;
+    this.chrylen = this.hic.genome.chrlookup[this.parent("state").y.chr.toUpperCase()].len;
+    this.maxchrlen = Math.max(this.chrxlen, this.chrylen);
+    this.colorizeElement = new ColorizeElement();
+    this.positions = new Positions(opts.error, this.parent("state").minBinNum_bp);
+    this.formattedData = new GridElementsFormattedData();
+  }
+  setDefaultBinpx() {
+    if (this.calcResolution == null) return;
+    while (this.binpx * this.maxchrlen / this.calcResolution < 600) {
+      this.binpx++;
+    }
+  }
+  renderAxes() {
+    if (this.calcResolution == null) return;
+    const svgY = this.plotDiv.yAxis.append("svg");
+    const h = Math.ceil(this.chrylen / this.calcResolution) * this.binpx;
+    svgY.attr("width", 100).attr("height", this.axispad * 2 + h);
+    svgY.append("g").attr("data-testid", "sjpp-chrpair-svg-y").attr("transform", "translate(80," + (this.axispad + h / 2) + ")").append("text").text(this.parent("state").y.chr).attr("text-anchor", "middle").attr("font-size", this.axisLabelFontSize).attr("font-family", font).attr("dominant-baseline", "central").attr("transform", "rotate(90)");
+    axisstyle({
+      axis: svgY.append("g").attr("transform", `translate(1, ${this.axispad})`).call(axisRight(linear().domain([0, this.chrylen]).range([0, h])).tickFormat(format(".2s"))),
+      showline: true
+    });
+    const svgX = this.plotDiv.xAxis.append("svg").style("margin-top", "-4px");
+    const w = Math.ceil(this.chrxlen / this.calcResolution) * this.binpx;
+    svgX.attr("height", 100).attr("width", this.axispad * 2 + w);
+    svgX.append("text").attr("data-testid", "sjpp-chrpair-svg-x").text(this.parent("state").x.chr).attr("font-size", this.axisLabelFontSize).attr("font-family", font).attr("x", this.axispad + w / 2).attr("text-anchor", "middle").attr("y", 60);
+    axisstyle({
+      axis: svgX.append("g").attr("transform", "translate(" + this.axispad + ",1)").call(axisBottom(linear().domain([0, this.chrxlen]).range([0, w])).tickFormat(format(".2s"))),
+      showline: true
+    });
+  }
+  renderCanvas() {
+    const initDetailView = this.initDetailView.bind(this);
+    this.canvas = this.plotDiv.plot.append("canvas").attr("data-testid", "sjpp-chrpair-canvas").style("margin", this.axispad + "px").on("click", async function(event) {
+      const [x, y] = pointer_default(event, this);
+      initDetailView(x, y);
+    }).node();
+    this.canvas.width = Math.ceil(this.chrxlen / this.calcResolution) * this.binpx;
+    this.canvas.height = Math.ceil(this.chrylen / this.calcResolution) * this.binpx;
+    this.ctx = this.canvas.getContext("2d");
+  }
+  initDetailView(x, y) {
+    const [xObj, yObj] = this.positions.setPosition(
+      x,
+      y,
+      this.binpx,
+      this.parent("state").x,
+      this.parent("state").y,
+      this.hic,
+      this.parent("state").initialBinNum
+    );
+    this.app.dispatch({
+      type: "view_create",
+      view: "detail",
+      config: {
+        x: xObj,
+        y: yObj
+      }
+    });
+  }
+  render() {
+    this.calcResolution = this.parent("calcResolution");
+    this.setDefaultBinpx();
+    this.renderAxes();
+    this.renderCanvas();
+    this.update(this.items);
+  }
+  update(items) {
+    this.items = items;
+    const firstisx = new FirstChrX(this.hic.chrorder, this.parent("state").x.chr, this.parent("state").y.chr).isFirstX();
+    const isintrachr = this.parent("state").x.chr === this.parent("state").y.chr;
+    this.data = this.formattedData.formatData(
+      "chrpair",
+      items.items,
+      this.binpx,
+      this.calcResolution,
+      firstisx,
+      isintrachr
+    );
+    this.ctx.clearRect(0, 0, this.canvas.width, this.canvas.height);
+    for (const [x, y, v] of this.data) {
+      this.colorizeElement.colorizeElement(
+        x,
+        y,
+        v,
+        this.ctx,
+        this.binpx,
+        //width
+        this.binpx,
+        //height
+        this.parent("min"),
+        this.parent("max"),
+        "chrpair"
+      );
+    }
+    this.app.dispatch({ type: "loading_active", active: false });
+  }
+};
+
+// tracks/hic/horizontal/HorizontalView.ts
+var HorizontalView = class {
+  constructor(opts) {
+    /** Defaults*/
+    this.maxPercentage = 5;
+    this.subPanelPxWidth = 600;
+    this.borderColor = "rgba(200,0,0,.1)";
+    this.app = opts.app;
+    this.hic = opts.hic;
+    this.plotDiv = opts.plotDiv;
+    this.items = opts.items;
+    this.parent = opts.parent;
+  }
+  setRunPpTracks() {
+    const tracks = [
+      {
+        type: "hicstraw",
+        file: this.hic.file,
+        url: this.hic.url,
+        name: this.hic.name,
+        enzyme: this.hic.enzyme,
+        maxpercentage: this.maxPercentage,
+        pyramindup: 1
+      }
+    ];
+    if (this.hic.tklst) {
+      for (const t of this.hic.tklst) {
+        tracks.push(t);
+      }
+    }
+    first_genetrack_tolist(this.hic.genome, tracks);
+    return tracks;
+  }
+  setRunPpArgs(tracks) {
+    const arg = {
+      holder: this.plotDiv.plot,
+      hostURL: this.hic.hostURL,
+      jwt: this.hic.jwt,
+      genome: this.hic.genome,
+      nobox: 1,
+      tklst: tracks
+    };
+    const state = this.parent("state");
+    if (state.x.chr == state.y.chr && Math.max(state.x.start, state.y.start) < Math.min(state.x.stop, state.y.stop)) {
+      arg["chr"] = state.x.chr;
+      arg["start"] = Math.min(state.x.start, state.y.start);
+      arg["stop"] = Math.max(state.x.stop, state.y.stop);
+    } else {
+      arg["chr"] = state.x.chr;
+      arg["start"] = state.x.start;
+      arg["stop"] = state.x.stop;
+      arg["width"] = this.subPanelPxWidth;
+      arg["subpanels"] = [
+        {
+          chr: state.y.chr,
+          start: state.y.start,
+          stop: state.y.stop,
+          width: this.subPanelPxWidth,
+          leftpad: 10,
+          leftborder: this.borderColor
+        }
+      ];
+    }
+    return arg;
+  }
+  render() {
+    const tracks = this.setRunPpTracks();
+    const arg = this.setRunPpArgs(tracks);
+    blocklazyload(arg);
+  }
+  // update() {
+  // 	//Not required.
+  // 	//If controls are added back. Implement changes here.
+  // }
+};
+
+// tracks/hic/detail/DetailBlock.ts
+var DetailBlock = class {
+  constructor(app, hic, blockwidth, bbmargin, holder, isYblock) {
+    /** Defaults */
+    this.leftheadw = 20;
+    this.rightheadw = 40;
+    this.lpad = 1;
+    this.rpad = 1;
+    this.firstRender = true;
+    this.app = app;
+    this.hic = hic;
+    this.width = blockwidth;
+    this.bbmargin = bbmargin;
+    this.holder = holder;
+    this.isYblock = isYblock;
+    this.bbw = this.leftheadw + this.lpad + this.width + this.rpad + this.rightheadw + 2 * this.bbmargin;
+    this.defaultLeft = this.bbmargin + this.leftheadw + this.lpad;
+    this.defaultTop = this.bbmargin + this.rightheadw + this.rpad;
+  }
+  setArgs(chrObj) {
+    const runPpArgs = {
+      hostURL: this.hic.hostURL,
+      genome: this.hic.genome,
+      holder: this.holder,
+      noresize: true,
+      nobox: true,
+      butrowbottom: true,
+      style: {
+        margin: `${this.bbmargin}px`
+      },
+      width: this.width,
+      leftheadw: this.leftheadw,
+      chr: chrObj.chr,
+      start: chrObj.start,
+      stop: chrObj.stop,
+      rightheadw: this.rightheadw,
+      tklst: [],
+      rotated: this.isYblock,
+      showreverse: this.isYblock
+    };
+    first_genetrack_tolist(this.hic.genome, runPpArgs.tklst);
+    return runPpArgs;
+  }
+  setMethods(canvasHolder, canvas, sheath) {
+    const runPpMethods = {
+      onloadalltk_always: () => {
+        this.onload(canvasHolder, canvas, sheath);
+      },
+      onpanning: (xoff) => this.onpanning(xoff, canvas)
+    };
+    if (this.isYblock) {
+      runPpMethods["onsetheight"] = (bbh) => {
+        this.holder.transition().style("left", `${bbh + this.bbmargin + 30}px`);
+      };
+    }
+    return runPpMethods;
+  }
+  onload(canvasHolder, canvas, sheath) {
+    this.bbw = this.block.leftheadw + this.block.lpad + this.block.width + this.block.rpad + this.block.rightheadw + 2 * this.bbmargin;
+    if (this.isYblock) {
+      sheath.transition().style("height", `${this.bbw}px`);
+      canvasHolder.style("height", `${this.bbw}px`);
+    } else canvasHolder.style("width", `${this.bbw}px`);
+    if (this.isYblock) {
+      this.defaultTop = this.bbmargin + this.block.rightheadw + this.block.rpad;
+      canvas.style("top", `${this.defaultTop}px`);
+    } else {
+      this.defaultLeft = this.bbmargin + this.block.leftheadw + this.block.lpad;
+      canvas.style("left", `${this.defaultLeft}px`);
+    }
+    const config = {
+      [this.isYblock ? "y" : "x"]: {
+        chr: this.block.rglst[0].chr,
+        start: this.block.rglst[0].start,
+        stop: this.block.rglst[0].stop
+      }
+    };
+    if (this.firstRender == false) {
+      this.app.dispatch({
+        type: "view_update",
+        config
+      });
+    } else {
+      this.firstRender = false;
+    }
+  }
+  onpanning(xoff, canvas) {
+    if (!this.isYblock) canvas.style("left", `${xoff + this.defaultLeft}px`);
+    else canvas.style("top", `${-xoff + this.defaultTop}px`);
+  }
+  async loadBlock(chrObj, canvasHolder, canvas, sheath) {
+    const runPpArgs = this.setArgs(chrObj);
+    const runPpMethods = this.isYblock ? this.setMethods(canvasHolder, canvas, sheath) : this.setMethods(canvasHolder, canvas);
+    const args = Object.assign(runPpArgs, runPpMethods);
+    await blocklazyload(args).then(async (block) => {
+      this.block = block;
+    });
+  }
+};
+
+// tracks/hic/data/DetailDataFetcher.ts
+var DetailDataFetcher = class {
+  constructor(errList) {
+    this.obj = {
+      rglst: []
+    };
+    this.errList = errList;
+  }
+  isFragData(hic, resolution) {
+    if (resolution != null) return;
+    if (!hic.enzyme) {
+      resolution = hic.bpresolution[hic.bpresolution.length - 1];
+      return;
+    }
+  }
+  formatFragArgs(enzymefile, chr) {
+    const arg = {
+      getdata: 1,
+      getBED: 1,
+      file: enzymefile,
+      rglst: [chr]
+    };
+    return arg;
+  }
+  /**
+   * @param arg Formated obj from either fn above
+   * @param errList
+   * @returns
+   */
+  async getBedData(arg) {
+    try {
+      return await dofetch3("tkbedj", { method: "POST", body: JSON.stringify(arg) });
+    } catch (e) {
+      this.errList.push(e.message || e);
+      if (e.stack) console.error(e.stack);
+    }
+  }
+  async getXFragData(hic, resolution, chrx) {
+    this.isFragData(hic, resolution);
+    if (!hic.enzymefile) return;
+    const reqArgs = this.formatFragArgs(hic.enzymefile, chrx);
+    return await this.getBedData(reqArgs);
+  }
+  async getYFragData(hic, chry) {
+    const reqArgs = this.formatFragArgs(hic.enzymefile, chry);
+    return await this.getBedData(reqArgs);
+  }
+  /**
+   * Separate request from data fetch
+   * Returns the additional fragment data
+   * @param fragCoords
+   */
+  async fetchData(hic, detailView, resolution, x, y, fragCoords) {
+    const fragStrawArgs = {
+      matrixType: detailView.matrixType,
+      file: hic.file,
+      url: hic.url,
+      pos1: this.determinePosition(hic, x, fragCoords?.x),
+      pos2: this.determinePosition(hic, y, fragCoords?.y),
+      nmeth: detailView.nmeth,
+      resolution
+    };
+    if (fragCoords) fragStrawArgs["isfrag"] = true;
+    try {
+      const data = dofetch3("hicdata?", {
+        method: "POST",
+        body: JSON.stringify(fragStrawArgs)
+      });
+      if (data.error) {
+        this.errList.push(data.error);
+      }
+      return data;
+    } catch (e) {
+      this.errList.push(e.message || e);
+      if (e.stack) console.error(e.stack);
+    }
+  }
+  determinePosition(hic, chr, fragCoord) {
+    if (fragCoord) {
+      return `${hic.nochr ? chr.chr.replace("chr", "") : chr.chr}:${fragCoord.start}:${fragCoord.stop}`;
+    } else {
+      return `${hic.nochr ? chr.chr.replace("chr", "") : chr.chr}:${chr.start}:${chr.stop}`;
+    }
+  }
+};
+
+// tracks/hic/data/ParseFragData.ts
+var ParseFragData = class {
+  constructor(errLst, items) {
+    this.id2coord = /* @__PURE__ */ new Map();
+    this.min = null;
+    this.max = null;
+    this.items = [];
+    this.errLst = errLst;
+    for (const i of items) {
+      if (!i.rest || !i.rest[0]) {
+        this.errLst.push("items[].rest data problem");
+      }
+      const id = Number.parseInt(i.rest[0]);
+      if (Number.isNaN(id)) {
+        this.errLst.push(`${i.start}.${i.stop} invalid fragment id: ${i.rest[0]}`);
+      }
+      this.id2coord.set(id, [i.start, i.stop]);
+      if (this.min == null) {
+        this.min = id;
+        this.max = id;
+      } else {
+        this.min = Math.min(this.min, id);
+        this.max = Math.max(this.max, id);
+      }
+    }
+  }
+};
+
+// tracks/hic/data/DetailDataMapper.ts
+var DetailDataMapper = class {
+  constructor(hic, errList, parent) {
+    this.frag = {
+      x: {},
+      y: {}
+    };
+    this.hic = hic;
+    this.errList = errList;
+    this.dataFetcher = new DetailDataFetcher(errList);
+    this.parent = parent;
+  }
+  async getFragData(chrx, chry) {
+    try {
+      const xFragData = await this.dataFetcher.getXFragData(this.hic, this.parent("calcResolution"), chrx);
+      if (xFragData) {
+        if (!xFragData.items) {
+          this.errList.push(`No fragment data returned for ${chrx.chr}:${chrx.start}-${chrx.stop}`);
+          return;
+        }
+        const xParse = new ParseFragData(this.errList, xFragData.items);
+        if (this.errList.length) return;
+        this.frag.x = {
+          id2coord: xParse.id2coord,
+          start: xParse.min,
+          stop: xParse.max
+        };
+        const yFragData = await this.dataFetcher.getYFragData(this.hic, chry);
+        if (this.errList.length) return;
+        if (yFragData) {
+          if (!yFragData.items) {
+            this.errList.push(`No fragment data returned for ${chry.chr}:${chry.start}-${chry.stop}`);
+            return;
+          }
+          const yParse = new ParseFragData(this.errList, yFragData.items);
+          if (this.errList.length) return;
+          this.frag.y = {
+            id2coord: /* @__PURE__ */ new Map(),
+            start: yParse.min,
+            stop: yParse.max
+          };
+          this.determineMap(yParse.id2coord, chrx, chry);
+        }
+      }
+    } catch (e) {
+      this.errList.push(e.message || e);
+      if (e.stack) console.error(e.stack);
+    }
+  }
+  determineMap(map, chrx, chry) {
+    if (chrx.chr == chry.chr) {
+      for (const [id, pos] of map) {
+        this.frag.x["id2coord"].set(id, pos);
+      }
+      this.frag.y["id2coord"] = this.frag.x["id2coord"];
+    } else {
+      this.frag.y["id2coord"] = map;
+    }
+  }
+  async getData(chrx, chry, fragCoords) {
+    return await this.dataFetcher.fetchData(
+      this.hic,
+      this.parent("state")["detail"],
+      this.parent("calcResolution"),
+      chrx,
+      chry,
+      fragCoords
+    );
+  }
+};
+
+// tracks/hic/data/DetailCoodinates.ts
+var DetailCoordinates = class {
+  constructor(hic, errlist) {
+    this.hic = hic;
+    this.errlist = errlist;
+  }
+  getCoordinates(chrx, chry, data, resolution, widthHeightPx, fragData) {
+    const isFirstX = new FirstChrX(this.hic.chrorder, chrx.chr, chry.chr).isFirstX();
+    const isintrachr = chrx.chr == chry.chr;
+    const xpxbp = widthHeightPx / (chrx.stop - chrx.start);
+    const ypxbp = widthHeightPx / (chry.stop - chry.start);
+    const list = this.calculateCoordinates(isFirstX, isintrachr, xpxbp, ypxbp, resolution, chrx, chry, data, fragData);
+    return list;
+  }
+  calculateCoordinates(isFirstX, isintrachr, xpxbp, ypxbp, resolution, chrx, chry, data, fragData) {
+    const list = [];
+    for (const [xCoord, yCoord, value] of data.items) {
+      let coord1, coord2, span1, span2;
+      if (fragData) {
+        const idx_start = isFirstX ? xCoord : yCoord;
+        const idy_start = isFirstX ? yCoord : xCoord;
+        if (fragData.x.id2coord.has(idx_start)) {
+          const [a, b] = fragData.x.id2coord.get(idx_start);
+          coord1 = a;
+          span1 = b - a;
+        } else {
+          this.errlist.push(`[x id error] x: ${idx_start} y: ${idy_start}`);
+          continue;
+        }
+        {
+          const id_stop = idx_start + resolution;
+          if (fragData.x.id2coord.has(id_stop)) {
+            const ab = fragData.x.id2coord.get(id_stop);
+            span1 = ab[1] - coord1;
+          }
+        }
+        if (fragData.y.id2coord.has(idy_start)) {
+          const [a, b] = fragData.y.id2coord.get(idy_start);
+          coord2 = a;
+          span2 = b - a;
+        } else {
+          this.errlist.push(`[y id error] x: ${idx_start} y: ${idy_start}`);
+          continue;
+        }
+        {
+          const id_stop = idy_start + resolution;
+          if (fragData.y.id2coord.has(id_stop)) {
+            const ab = fragData.y.id2coord.get(id_stop);
+            span2 = ab[1] - coord2;
+          }
+        }
+      } else {
+        coord1 = isFirstX ? xCoord : yCoord;
+        coord2 = isFirstX ? yCoord : xCoord;
+        span1 = resolution;
+        span2 = resolution;
+      }
+      if (isintrachr) {
+        if (coord1 > chrx.start - span1 && coord1 < chrx.stop && coord2 > chry.start - span2 && coord2 < chry.stop) {
+          list.push([
+            Math.floor((coord1 - chrx.start) * xpxbp),
+            Math.floor((coord2 - chry.start) * ypxbp),
+            Math.ceil(span1 * xpxbp),
+            Math.ceil(span2 * ypxbp),
+            value
+          ]);
+        }
+        if (coord2 > chrx.start - span2 && coord2 < chrx.stop && coord1 > chry.start && coord1 < chry.stop) {
+          list.push([
+            Math.floor((coord2 - chrx.start) * xpxbp),
+            Math.floor((coord1 - chry.start) * ypxbp),
+            Math.ceil(span2 * xpxbp),
+            Math.ceil(span1 * ypxbp),
+            value
+          ]);
+        }
+        continue;
+      }
+      list.push([
+        Math.floor((coord1 - chrx.start) * xpxbp),
+        Math.floor((coord2 - chry.start) * ypxbp),
+        Math.ceil(span1 * xpxbp),
+        Math.ceil(span2 * ypxbp),
+        value
+      ]);
+    }
+    return list;
+  }
+};
+
+// tracks/hic/detail/DetailView.ts
+var DetailView = class {
+  constructor(opts) {
+    this.calcResolution = null;
+    /** Defaults **/
+    this.binpx = 2;
+    this.bbmargin = 1;
+    this.app = opts.app;
+    this.hic = opts.hic;
+    this.plotDiv = opts.plotDiv;
+    this.sheath = opts.plotDiv.yAxis.append("div").style("position", "relative").style("width", "200px").style("height", "800px");
+    this.rotor = this.sheath.append("div").style("position", "absolute").style("bottom", "0px").style("transform", "rotate(-90deg)").style("transform-origin", "left bottom");
+    this.data = opts.data;
+    this.parent = opts.parent;
+    this.errList = this.parent("errList");
+    this.resolution = new Resolution(opts.error);
+    this.colorizeElement = new ColorizeElement();
+    this.viewRangeBpW = this.resolution.getDefaultViewSpan(
+      this.hic,
+      this.parent("state").x,
+      this.parent("state").y,
+      this.parent("state").initialBinNum,
+      this.parent("state").minBinNum_bp
+    );
+    this.dataMapper = new DetailDataMapper(this.hic, opts.error, opts.parent);
+    this.coordinates = new DetailCoordinates(this.hic, this.errList);
+  }
+  renderCanvas(blockwidth) {
+    this.canvasHolder = this.plotDiv.plot.append("div").style("position", "relative").style("width", `${this.xBlock.bbw}px`).style("height", `${this.yBlock.bbw}px`).style("overflow", "hidden");
+    this.canvas = this.canvasHolder.append("canvas").style("display", "block").style("position", "absolute").attr("data-testid", "sjpp-hic-detail-canvas").attr("width", blockwidth).attr("height", blockwidth).on("mousedown", (event) => {
+      const body = select_default(document.body);
+      const x = event.clientX;
+      const y = event.clientY;
+      const oldx = Number.parseInt(this.canvas.style("left"));
+      const oldy = Number.parseInt(this.canvas.style("top"));
+      body.on("mousemove", (event2) => {
+        const xoff = event2.clientX - x;
+        const yoff = event2.clientY - y;
+        this.xBlock.block.panning(xoff);
+        this.yBlock.block.panning(yoff);
+        this.canvas.style("left", `${oldx + xoff}px`).style("top", `${oldy + yoff}px`);
+      });
+      body.on("mouseup", (event2) => {
+        body.on("mousemove", null).on("mouseup", null);
+        const xoff = event2.clientX - x;
+        const yoff = event2.clientY - y;
+        console.log(xoff);
+        this.xBlock.block.pannedby(xoff);
+        this.yBlock.block.pannedby(yoff);
+      });
+    });
+  }
+  async render() {
+    this.calcResolution = this.parent("calcResolution");
+    const state = this.parent("state");
+    this.xBlock = new DetailBlock(
+      this.app,
+      this.hic,
+      state.settings.widthHeightPx,
+      this.bbmargin,
+      this.plotDiv.xAxis,
+      false
+    );
+    this.yBlock = new DetailBlock(this.app, this.hic, state.settings.widthHeightPx, this.bbmargin, this.rotor, true);
+    this.renderCanvas(state.settings.widthHeightPx);
+    await this.xBlock.loadBlock(state.x, this.canvasHolder, this.canvas);
+    await this.yBlock.loadBlock(state.y, this.canvasHolder, this.canvas, this.sheath);
+    this.update(this.data);
+  }
+  async update(data) {
+    if (data.items.length == 0) {
+      this.app.dispatch({ type: "loading_active", active: false });
+      return;
+    }
+    this.data = data;
+    const state = this.parent("state");
+    const initialWidth = Number.parseInt(this.canvas.attr("width"));
+    const holderChange = Number.parseInt(this.canvasHolder.style("width")) - initialWidth + state.settings.widthHeightPx;
+    this.canvasHolder.style("width", `${holderChange}px`).style("height", `${holderChange}px`);
+    this.canvas.attr("width", `${state.settings.widthHeightPx}px`).attr("height", `${state.settings.widthHeightPx}px`);
+    if (this.xBlock.block.width != state.settings.widthHeightPx) {
+      this.xBlock.block.width = state.settings.widthHeightPx;
+      this.yBlock.block.width = state.settings.widthHeightPx;
+      this.xBlock.block.zoom2px(0, initialWidth);
+      this.yBlock.block.zoom2px(0, initialWidth);
+    }
+    this.ctx = this.canvas.node().getContext("2d");
+    const coords = this.coordinates.getCoordinates(
+      state.x,
+      state.y,
+      this.parent("data"),
+      this.parent("calcResolution"),
+      state.settings.widthHeightPx,
+      this.parent("fragData")
+    );
+    this.coords = coords;
+    this.ctx.clearRect(0, 0, state.settings.widthHeightPx, state.settings.widthHeightPx);
+    for (const [xCoord, yCoord, width, height, value] of this.coords) {
+      this.colorizeElement.colorizeElement(
+        xCoord,
+        yCoord,
+        value,
+        this.ctx,
+        width,
+        height,
+        this.parent("min"),
+        this.parent("max"),
+        "detail"
+      );
+    }
+    this.app.dispatch({ type: "loading_active", active: false });
+  }
+};
+
+// tracks/hic/axes/Chromosome.ts
+var Chromosome = class {
+  constructor(chr, width) {
+    this.label = chr;
+    this.width = width;
+  }
+};
+
+// tracks/hic/grid/Grid.ts
+var Grid = class _Grid {
+  constructor(chrlst, resolution, chrlookup, binpx) {
+    this.chromosomeMatrix = /* @__PURE__ */ new Map();
+    this.chromosomeList = [];
+    this.xoff = 0;
+    this.yoff = 0;
+    this.chr2px = [];
+    this.chrlst = chrlst;
+    let totalpx = this.chrlst.length;
+    for (const chr of this.chrlst) {
+      const w = Math.ceil(chrlookup[chr.toUpperCase()].len / resolution) * binpx;
+      const chromosome = new Chromosome(chr, w);
+      this.chromosomeList.push(chromosome);
+      this.chr2px[chr] = w;
+      totalpx += w;
+    }
+    this.totalpx = totalpx;
+    for (let i = 0; i < this.chrlst.length; i++) {
+      const chrx = this.chrlst[i];
+      this.chromosomeMatrix.set(chrx, /* @__PURE__ */ new Map());
+      let yoff = 0;
+      for (let j = 0; j <= i; j++) {
+        const chry = this.chrlst[j];
+        const chrxChrLen = chrlookup[chrx.toUpperCase()].len;
+        const chryChrLen = chrlookup[chry.toUpperCase()].len;
+        const xbins = Math.ceil(chrxChrLen / resolution) * binpx;
+        const ybins = Math.ceil(chryChrLen / resolution) * binpx;
+        this.chromosomeMatrix.get(chrx).set(chry, {
+          x: this.xoff,
+          y: yoff,
+          xbins,
+          ybins,
+          data: []
+          //Empty array of data to fill later
+        });
+        yoff += this.chr2px[chry] + _Grid.borderWidth;
+      }
+      this.yoff = yoff;
+      this.xoff += this.chr2px[chrx] + _Grid.borderWidth;
+    }
+  }
+  static {
+    this.checkerFill = "#DEF3FA";
+  }
+  static {
+    this.spaceColor = "#CCC";
+  }
+  static {
+    this.fontSize = 15;
+  }
+  static {
+    this.font = font;
+  }
+  static {
+    this.borderWidth = 1;
+  }
+  static {
+    this.defaultChrLabWidth = 100;
+  }
+};
+
+// tracks/hic/viewmodel/GridViewModel.ts
+var GridViewModel = class {
+  constructor(opts) {
+    this.grid = new Grid(opts.hic.chrlst, opts.resolution || opts.hic.bpresolution[0], opts.hic.genome.chrlookup, 1);
+  }
+};
+
+// tracks/hic/grid/GridRenderer.ts
+var GridRenderer = class {
+  constructor(svg, layerMap, layerSv, grid) {
+    this.svg = svg;
+    this.layerMap = layerMap.attr("transform", `translate(${Grid.defaultChrLabWidth}, ${Grid.fontSize})`);
+    this.layerSv = layerSv.attr("transform", `translate(${Grid.defaultChrLabWidth}, ${Grid.fontSize})`);
+    this.grid = grid;
+  }
+  render() {
+    this.renderAxisX(this.grid);
+    this.renderAxisY(this.grid);
+    this.svg.attr("width", Grid.defaultChrLabWidth + this.grid.xoff).attr("height", Grid.fontSize + this.grid.yoff);
+  }
+  renderAxisX(grid) {
+    let xoff = 0;
+    this.grid.chromosomeList.forEach((chr, index) => {
+      const chrw = chr.width;
+      if (index % 2 === 0) {
+        this.layerMap.append("rect").attr("x", xoff).attr("width", chrw).attr("height", Grid.fontSize).attr("y", -Grid.fontSize).attr("fill", Grid.checkerFill);
+      }
+      this.layerMap.append("text").attr("font-family", Grid.font).attr("text-anchor", "middle").attr("font-size", 12).attr("x", xoff + chrw / 2).text(chr.label);
+      xoff += chrw;
+      this.layerSv.append("line").attr("x1", xoff).attr("x2", xoff).attr("y2", grid.totalpx).attr("stroke", Grid.spaceColor).attr("shape-rendering", "crispEdges");
+      xoff += Grid.borderWidth;
+    });
+  }
+  renderAxisY(grid) {
+    let yoff = 0;
+    this.grid.chromosomeList.forEach((chr, index) => {
+      const chrh = chr.width;
+      if (index % 2 === 0) {
+        this.layerMap.append("rect").attr("x", -Grid.defaultChrLabWidth).attr("width", Grid.defaultChrLabWidth).attr("height", chrh).attr("y", yoff).attr("fill", Grid.checkerFill);
+      }
+      this.layerMap.append("text").attr("font-family", Grid.font).attr("text-anchor", "end").attr("dominant-baseline", "central").attr("font-size", 12).attr("y", yoff + chrh / 2).text(chr.label);
+      yoff += chrh;
+      this.layerSv.append("line").attr("x2", grid.totalpx).attr("y1", yoff).attr("y2", yoff).attr("stroke", Grid.spaceColor).attr("shape-rendering", "crispEdges");
+      yoff += Grid.borderWidth;
+    });
+  }
+};
+
+// tracks/hic/genome/ChrsTooltips.ts
+var ChrsTooltips = class {
+  constructor() {
+    this.chrx_tip = new Menu({ border: "solid 1px #ccc", padding: "0px", offsetX: 0, offsetY: 0 });
+    this.chry_tip = new Menu({ border: "solid 1px #ccc", padding: "0px", offsetX: 0, offsetY: 0 });
+  }
+  render(img, chrx, chry) {
+    const p = img.node().getBoundingClientRect();
+    this.chrx_tip.clear().show(p.left, p.top).d.style("top", null).style("bottom", window.innerHeight - p.top - window.pageYOffset + "px").text(chrx);
+    this.chry_tip.clear().show(p.left, p.top).d.style("left", null).style("right", document.body.clientWidth - p.left - window.pageXOffset + "px").text(chry);
+  }
+};
+
+// tracks/hic/grid/GridElementRenderer.ts
+var GridElementRenderer = class {
+  constructor(layerMap, app) {
+    this.app = app;
+    this.layerMap = layerMap;
+    this.tooltips = new ChrsTooltips();
+  }
+  render(obj, lead, follow, holder) {
+    obj.canvas = holder.append("canvas").style("display", "none").node();
+    obj.ctx = obj.canvas.getContext("2d");
+    obj.canvas.width = obj.xbins;
+    obj.canvas.height = obj.ybins;
+    obj.img = this.layerMap.append("image").attr("width", obj.canvas.width).attr("height", obj.canvas.height).attr("x", obj.x).attr("y", obj.y).on("click", async () => {
+      await this.app.dispatch({
+        type: "view_create",
+        view: "chrpair",
+        config: {
+          x: {
+            chr: lead
+          },
+          y: {
+            chr: follow
+          }
+        }
+      });
+    }).on("mouseover", () => {
+      this.tooltips.render(obj.img, lead, follow);
+    });
+    if (lead != follow) {
+      obj.canvas2 = holder.append("canvas").style("display", "none").node();
+      obj.canvas2.width = obj.ybins;
+      obj.canvas2.height = obj.xbins;
+      obj.ctx2 = obj.canvas2.getContext("2d");
+      obj.img2 = this.layerMap.append("image").attr("width", obj.canvas2.width).attr("height", obj.canvas2.height).attr("x", obj.y).attr("y", obj.x).on("click", async () => {
+        await this.app.dispatch({
+          type: "view_create",
+          view: "chrpair",
+          config: {
+            x: {
+              chr: follow
+            },
+            y: {
+              chr: lead
+            }
+          }
+        });
+      }).on("mouseover", () => {
+        this.tooltips.render(obj.img2, follow, lead);
+      });
+    } else {
+      obj.ctx2 = obj.ctx;
+    }
+  }
+};
+
+// tracks/hic/grid/GridElementsRenderer.ts
+var GridElementsRenderer = class {
+  constructor(grid, layerMap, app) {
+    this.grid = grid;
+    this.gridElementRenderer = new GridElementRenderer(layerMap, app);
+  }
+  render(holder) {
+    for (const [chrx, chryMap] of this.grid.chromosomeMatrix) {
+      for (const [chry, gridElem] of chryMap) {
+        this.gridElementRenderer.render(gridElem, chrx, chry, holder);
+      }
+    }
+  }
+};
+
+// tracks/hic/genome/GenomeView.ts
+var GenomeView = class {
+  constructor(opts) {
+    /** Dom */
+    this.tip = new Menu();
+    this.pica_x = new Menu({ border: "solid 1px #ccc", padding: "0px", offsetX: 0, offsetY: 0 });
+    this.pica_y = new Menu({ border: "solid 1px #ccc", padding: "0px", offsetX: 0, offsetY: 0 });
+    /** Data */
+    /** px width for each chr */
+    this.chr2px = {};
+    this.lead2follow = /* @__PURE__ */ new Map();
+    this.values = [];
+    /** Defaults */
+    this.defaultChrLabWidth = 100;
+    this.borderwidth = 1;
+    this.default_maxVPerc = 5;
+    this.fontsize = 15;
+    this.xoff = 0;
+    this.yoff = 0;
+    this.binpx = 1;
+    this.atdev_chrnum = 8;
+    this.min = 0;
+    this.max = 0;
+    this.app = opts.app;
+    this.hic = opts.hic;
+    this.plotDiv = opts.plotDiv;
+    this.data = opts.data;
+    this.parent = opts.parent;
+    this.resolution = opts.resolution || opts.hic.bpresolution[0];
+    this.svg = this.plotDiv.plot.append("svg").attr("data-testid", "sjpp-hic-genome-svg");
+    this.layer_map = this.svg.append("g").attr("data-testid", "sjpp-hic-layerMap-g");
+    this.layer_sv = this.svg.append("g").attr("data-testid", "sjpp-hic-layerSv-g");
+    this.colorizeElement = new ColorizeElement();
+    this.viewModel = new GridViewModel(opts);
+    this.viewRender = new GridRenderer(this.svg, this.layer_map, this.layer_sv, this.viewModel.grid);
+    this.gridElementsRenderer = new GridElementsRenderer(this.viewModel.grid, this.layer_map, this.app);
+    this.gridFormattedData = new GridElementsFormattedData();
+  }
+  makeSv() {
+    const unknownchr = /* @__PURE__ */ new Set();
+    const radius = 8;
+    for (const item of this.hic.sv.items) {
+      const _o = this.lead2follow.get(item.chr1);
+      if (!_o) {
+        unknownchr.add(item.chr1);
+        continue;
+      }
+      const obj = _o.get(item.chr2);
+      if (!obj) {
+        unknownchr.add(item.chr2);
+        continue;
+      }
+      const p1 = item.position1 / this.resolution;
+      const p2 = item.position2 / this.resolution;
+      this.layer_sv.append("circle").attr("stroke", "black").attr("fill", "white").attr("fill-opacity", 0).attr("cx", obj.x + p1).attr("cy", obj.y + p2).attr("r", radius).on("mouseover", (event) => {
+        this.tooltipSv(event, item);
+      }).on("mouseout", () => {
+        this.tip.hide();
+      }).on("click", () => {
+        this.clickSv(item);
+      });
+      if (obj.img2) {
+        this.layer_sv.append("circle").attr("stroke", "black").attr("fill", "whilte").attr("fill-opacity", 0).attr("cy", obj.x + p1).attr("cx", obj.y + p2).attr("r", radius).on("mouseover", (event) => {
+          this.tooltipSv(event, item);
+        }).on("mouseout", () => {
+          this.tip.hide();
+        }).on("click", () => {
+          this.clickSv(item);
+        });
+      }
+    }
+  }
+  tooltipSv(event, item) {
+    this.tip.clear().show(event.clientX, event.clientY).d.append("div").text(
+      item.chr1 == item.chr2 ? `${item.chr1}:${item.position1}-${item.position2}` : `${item.chr1}:${item.position1}>${item.chr2}:${item.position2}`
+    );
+  }
+  clickSv(item) {
+    const default_svpointspan = 5e5;
+    const default_subpanelpxwidth = 600;
+    const subpanel_bordercolor = "rgba(200,0,0,.1)";
+    const pane = newpane({ x: 100, y: 100 });
+    pane.header.text(
+      this.hic.name + " " + (item.chr1 == item.chr2 ? `${item.chr1}:${item.position1}-${item.position2}` : `${item.chr1}:${item.position1}>${item.chr2}:${item.position2}`)
+    );
+    const tracks = [
+      {
+        type: tkt.hicstraw,
+        file: this.hic.file,
+        enzyme: this.hic.enzyme,
+        maxpercentage: this.default_maxVPerc,
+        pyramidup: 1,
+        name: this.hic.name
+      }
+    ];
+    if (this.hic.tklst) {
+      for (const t of this.hic.tklst) {
+        tracks.push(t);
+      }
+    }
+    first_genetrack_tolist(this.hic.genome, tracks);
+    const arg = {
+      holder: pane.body,
+      hostURL: this.hic.hostURL,
+      jwt: this.hic.jwt,
+      genome: this.hic.genome,
+      nobox: 1,
+      tklst: tracks
+    };
+    if (item.chr1 == item.chr2 && Math.abs(item.position2 - item.position1) < default_svpointspan * 2) {
+      arg.chr = item.chr1;
+      const w = Math.abs(item.position2 - item.position1);
+      arg.start = Math.max(1, Math.min(item.position1, item.position2) - w);
+      arg.stop = Math.min(
+        this.hic.genome.chrlookup[item.chr1.toUpperCase()].len,
+        Math.max(item.position1, item.position2) + w
+      );
+    } else {
+      arg.chr = item.chr1;
+      arg.start = Math.max(1, item.position1 - default_svpointspan / 2);
+      arg.stop = Math.min(
+        this.hic.genome.chrlookup[item.chr1.toUpperCase()].len,
+        item.position1 + default_svpointspan / 2
+      );
+      arg.width = default_subpanelpxwidth;
+      arg.subpanels = [
+        {
+          chr: item.chr2,
+          start: Math.max(1, item.position2 - default_svpointspan / 2),
+          stop: Math.min(
+            this.hic.genome.chrlookup[item.chr2.toUpperCase()].len,
+            item.position2 + default_svpointspan / 2
+          ),
+          width: default_subpanelpxwidth,
+          leftpad: 10,
+          leftborder: subpanel_bordercolor
+        }
+      ];
+    }
+    blocklazyload(arg);
+  }
+  render() {
+    this.viewRender.render();
+    this.gridElementsRenderer.render(this.hic.holder);
+    if (this.hic.sv && this.hic.sv.items) {
+      this.makeSv();
+    }
+    this.update(this.data);
+  }
+  update(data) {
+    this.data = data;
+    this.min = this.parent("min");
+    this.max = this.parent("max");
+    for (const data2 of this.data) {
+      if (!this.hic.chrlst.includes(data2.lead) || !this.hic.chrlst.includes(data2.follow)) continue;
+      const obj = this.viewModel.grid.chromosomeMatrix.get(data2.lead).get(data2.follow);
+      if (!obj) continue;
+      obj.ctx.clearRect(0, 0, obj.canvas.width, obj.canvas.height);
+      if (obj.canvas2) {
+        obj.ctx2.clearRect(0, 0, obj.canvas2.width, obj.canvas.height);
+      }
+      obj.data = this.gridFormattedData.formatData("genome", data2.items, this.binpx, this.resolution);
+      for (const [xPx, yPx, value] of obj.data) {
+        this.colorizeElement.colorizeElement(xPx, yPx, value, obj, this.binpx, this.binpx, this.min, this.max, "genome");
+      }
+      obj.img.attr("xlink:href", obj.canvas.toDataURL());
+      if (obj.canvas2) {
+        obj.img2.attr("xlink:href", obj.canvas2.toDataURL());
+      }
+    }
+    this.app.dispatch({ type: "loading_active", active: false });
+  }
+};
+
+// tracks/hic/controls/NormalizationMethodControl.ts
+var NormalizationMethodControl = class {
+  constructor(holder, normalization, defaultNmeth, callback) {
+    this.holder = holder;
+    this.normalization = normalization;
+    this.defaultNmeth = defaultNmeth;
+    this.callback = callback;
+  }
+  render() {
+    if (!this.normalization?.length) {
+      this.nmethSelect = this.holder.text(this.defaultNmeth);
+    } else {
+      this.nmethSelect = this.holder.style("margin-right", "10px").append("select").on("change", async () => {
+        const nmeth = this.nmethSelect.node().value;
+        this.callback(nmeth, "nmeth");
+      });
+      for (const n of this.normalization) {
+        this.nmethSelect.append("option").text(n);
+      }
+    }
+  }
+  update(option) {
+    const options = this.nmethSelect.node().options;
+    if (!options) return;
+    const selectedNmeth = Array.from(options).find((o) => o.value === option);
+    if (!selectedNmeth) throw `Invalid normalization method: ${option}`;
+    selectedNmeth.selected = true;
+  }
+};
+
+// tracks/hic/controls/CutoffControl.ts
+var CutoffControl = class {
+  constructor(holder, value, callback) {
+    this.holder = holder;
+    this.value = value;
+    this.callback = callback;
+  }
+  render(opts) {
+    const cutoffDiv = this.holder.style("margin-right", "10px").append("input").attr("type", "number").style("width", opts && "width" in opts ? opts.width : "80px").style("margin-left", "0px").attr("type", "number").property("value", this.value).on("keyup", async (event) => {
+      if (event.code != "Enter") return;
+      const v = event.target.value;
+      this.callback(v);
+    });
+    return cutoffDiv;
+  }
+};
+
+// tracks/hic/controls/MatrixTypeControl.ts
+var MatrixTypeControl = class {
+  constructor(holder, callback) {
+    this.values = [
+      { label: "Observed", value: "observed" },
+      { label: "Expected", value: "expected" },
+      { label: "Observed/Expected", value: "oe" },
+      { label: "Log(Observed/Expected)", value: "log(oe)" }
+      // TODO: add server side logic to support these options
+      // { label: 'Log(Observed + 1)', value: 'log(obs+1)'},
+      // { label: 'Observed Pearson', value: 'op'}
+    ];
+    this.holder = holder;
+    this.callback = callback;
+  }
+  render() {
+    this.matrixSelect = this.holder.style("margin-right", "10px").append("select").on("change", async () => {
+      this.callback(this.matrixSelect.node().value, "matrixType");
+    });
+    for (const matrixType of this.values) {
+      this.matrixSelect.append("option").text(matrixType.label).attr("value", matrixType.value);
+    }
+  }
+  update(option) {
+    const options = this.matrixSelect.node().options;
+    if (!options) return;
+    const selectedNmeth = Array.from(options).find((o) => o.value === option);
+    if (!selectedNmeth) throw `Invalid normalization method: ${option}`;
+    selectedNmeth.selected = true;
+  }
+};
+
+// tracks/hic/controls/ControlPanel.ts
+var ControlPanel = class {
+  constructor(opts) {
+    this.zoomBlockCallback = (bool) => {
+      const detailView = this.parent("detail");
+      detailView.xBlock.block.zoomblock(2, bool);
+      detailView.yBlock.block.zoomblock(2, bool);
+    };
+    this.minCallback = (v) => {
+      if (Number(v) > Number(this.parent("max"))) {
+        this.error("Min cutoff cannot be greater than max cutoff");
+      } else {
+        this.parent("min", Number(v));
+        this.reColorHeatmap();
+        this.parent("infoBar").update();
+      }
+    };
+    this.maxCallback = (v) => {
+      if (Number(v) < Number(this.parent("min"))) {
+        this.error(`Max cutoff cannot be less than min cutoff`);
+      } else if (Number(v) < 0) {
+        this.error(`Max cutoff cannot be less than 0`);
+      } else {
+        this.parent("max", Number(v));
+        this.reColorHeatmap();
+        this.parent("infoBar").update();
+      }
+    };
+    this.reColorHeatmap = () => {
+      if (this.parent("activeView") == "genome") {
+        const genomeView = this.parent("genome");
+        const chrMatrix = genomeView.viewRender.grid.chromosomeMatrix;
+        if (!chrMatrix) return;
+        for (const map of chrMatrix) {
+          const yMap = map[1];
+          for (const obj of yMap) {
+            const canvasObj = obj[1];
+            if (!canvasObj) continue;
+            for (const [leadpx, followpx, val] of canvasObj.data) {
+              this.colorizeElement.colorizeElement(
+                leadpx,
+                followpx,
+                val,
+                canvasObj,
+                1,
+                1,
+                this.parent("min"),
+                this.parent("max"),
+                "genome"
+              );
+            }
+            canvasObj.img.attr("xlink:href", canvasObj.canvas.toDataURL());
+            if (canvasObj.canvas2) {
+              canvasObj.img2.attr("xlink:href", canvasObj.canvas2.toDataURL());
+            }
+          }
+        }
+      } else if (this.parent("activeView") == "chrpair") {
+        const view = this.parent("chrpair");
+        for (const [xCoord, yCoord, val] of view.data) {
+          this.colorizeElement.colorizeElement(
+            xCoord,
+            yCoord,
+            val,
+            view.ctx,
+            view.binpx,
+            view.binpx,
+            this.parent("min"),
+            this.parent("max"),
+            "chrpair"
+          );
+        }
+      } else if (this.parent("activeView") == "detail") {
+        const view = this.parent("detail");
+        for (const [xCoord, yCoord, width, height, value] of view.coords) {
+          this.colorizeElement.colorizeElement(
+            xCoord,
+            yCoord,
+            value,
+            view.ctx,
+            width,
+            height,
+            this.parent("min"),
+            this.parent("max"),
+            "detail"
+          );
+        }
+      }
+    };
+    this.dropdownCallback = (v, prop) => {
+      const state = this.app.getState();
+      this.app.dispatch({
+        type: "view_update",
+        view: state.currView,
+        config: { [prop]: v }
+      });
+    };
+    this.type = "controlPanel";
+    this.controls = {};
+    this.app = opts.app;
+    this.controlsDiv = opts.controlsDiv;
+    this.hic = opts.hic;
+    this.colorizeElement = new ColorizeElement();
+    this.parent = opts.parent;
+    this.error = opts.error;
+  }
+  getState(appState) {
+    return appState;
+  }
+  addLabel(tr, text) {
+    return tr.append("td").style("color", "#858585").style("font-size", ".8em").style("vertical-align", text.toUpperCase() == "VIEW" ? "top" : "middle").text(text.toUpperCase());
+  }
+  init() {
+    const state = this.app.getState();
+    const menuWrapper = this.controlsDiv.style("background", "rgb(253, 250, 244)").style("vertical-align", "top").style("padding", "5px").style("border", "solid 0.5px #ccc");
+    let menuVisible = true;
+    this.controlsDiv.append("button").style("display", "block").style("border", "none").style("font-size", "1.5em").style("background", "none").html("&#8801;").on("click", () => {
+      menuVisible = !menuVisible;
+      menu.style("display", menuVisible ? "block" : "none");
+    });
+    const menu = menuWrapper.append("div").attr("class", "sjpp-hic-menu").style("display", menuVisible ? "block" : "none");
+    const menuTable = menu.append("table").style("border-spacing", "3px");
+    this.controls.normalizationRow = menuTable.append("tr");
+    this.addLabel(this.controls.normalizationRow, "NORMALIZATION");
+    this.controls.nmeth = new NormalizationMethodControl(
+      this.controls.normalizationRow.append("td").attr("class", "sjpp-nmeth-select"),
+      this.hic.normalization,
+      state.defaultNmeth,
+      this.dropdownCallback
+    );
+    this.controls.nmeth.render();
+    this.controls.minCutoffRow = menuTable.append("tr");
+    this.controls.minCutoffLabel = this.addLabel(this.controls.minCutoffRow, "");
+    this.controls.inputBpMinV = new CutoffControl(
+      this.controls.minCutoffRow.append("td"),
+      this.parent("min"),
+      this.minCallback
+    ).render({ width: "120px" });
+    this.controls.maxCutoffRow = menuTable.append("tr");
+    this.controls.maxCutoffLabel = this.addLabel(this.controls.maxCutoffRow, "");
+    this.controls.inputBpMaxV = new CutoffControl(
+      this.controls.maxCutoffRow.append("td"),
+      this.parent("max"),
+      this.maxCallback
+    ).render({ width: "120px" });
+    this.controls.matrixTypeRow = menuTable.append("tr");
+    this.addLabel(this.controls.matrixTypeRow, "matrix type");
+    this.controls.matrixType = new MatrixTypeControl(this.controls.matrixTypeRow.append("td"), this.dropdownCallback);
+    this.controls.matrixType.render();
+    this.controls.widthRow = menuTable.append("tr");
+    this.addLabel(this.controls.widthRow, "WIDTH / height");
+    this.controls.width = this.controls.widthRow.append("td");
+    this.controls.width.style("margin-right", "10px").append("input").attr("type", "number").style("width", "80px").style("margin-left", "0px").attr("type", "number").property("value", state.width).on("keyup", async (event) => {
+      if (event.code != "Enter") return;
+      const v = event.target.value;
+      this.app.dispatch({
+        type: "view_update",
+        config: {
+          settings: { widthHeightPx: Number.parseInt(v) }
+        }
+      });
+    });
+    const viewRow = menuTable.append("tr");
+    this.addLabel(viewRow, "VIEW");
+    const viewBtnDiv = viewRow.append("td");
+    this.controls.view = viewBtnDiv.append("span").style("padding-right", "5px").style("display", "block");
+    this.controls.genomeViewBtn = viewBtnDiv.append("button").style("display", "none").style("padding", "2px").style("margin-top", "4px").html("&#8810; Genome").on("click", async () => {
+      await this.app.dispatch({
+        type: "view_create",
+        view: "genome",
+        config: {
+          x: {},
+          y: {}
+        }
+      });
+    });
+    this.controls.chrpairViewBtn = viewBtnDiv.append("button").style("display", "none").style("padding", "2px").style("margin", "4px 0px").on("click", async () => {
+      const currState = this.app.getState();
+      await this.app.dispatch({
+        type: "view_create",
+        view: "chrpair",
+        config: {
+          x: {
+            chr: currState.x.chr
+          },
+          y: {
+            chr: currState.y.chr
+          }
+        }
+      });
+    });
+    this.controls.horizontalViewBtn = viewBtnDiv.append("button").style("display", "none").style("padding", "2px").style("margin", "4px 0px").html("Horizontal View &#8811;").on("click", async () => {
+      await this.app.dispatch({
+        type: "view_create",
+        view: "horizontal"
+      });
+    });
+    this.controls.detailViewBtn = viewBtnDiv.append("button").style("display", "none").style("padding", "2px").style("margin", "4px 0px").html("&#8810; Detailed View").on("click", async () => {
+      await this.app.dispatch({
+        type: "view_create",
+        view: "detail"
+      });
+    });
+    this.controls.zoomDiv = menuTable.append("tr").style("display", state.currView == "detail" ? "contents" : "none");
+    this.addLabel(this.controls.zoomDiv, "ZOOM");
+    const zoomDiv = this.controls.zoomDiv.append("td");
+    this.controls.zoomIn = zoomDiv.append("button").style("margin-right", "10px").text("In").on("click", () => {
+      this.zoomBlockCallback(false);
+    });
+    this.controls.zoomOut = zoomDiv.append("button").style("margin-right", "10px").text("Out").on("click", () => {
+      this.zoomBlockCallback(true);
+    });
+  }
+  showBtns() {
+    const state = this.app.getState();
+    this.controls.genomeViewBtn.style("display", state.currView === "genome" ? "none" : "inline-block");
+    if (state.currView === "detail") {
+      this.controls.chrpairViewBtn.html(`&#8810; Entire ${state.x.chr}-${state.y.chr}`).style("display", "block");
+      this.controls.horizontalViewBtn.style("display", "block");
+      this.controls.zoomDiv.style("display", "contents");
+      this.controls.detailViewBtn.style("display", "none");
+    } else if (state.currView === "horizontal") {
+      this.controls.chrpairViewBtn.html(`&#8810; Entire ${state.x.chr}-${state.y.chr}`).style("display", "block");
+      this.controls.detailViewBtn.style("display", "block");
+      this.controls.horizontalViewBtn.style("display", "none");
+      this.controls.zoomDiv.style("display", "none");
+    } else {
+      this.controls.chrpairViewBtn.style("display", "none");
+      this.controls.horizontalViewBtn.style("display", "none");
+      this.controls.detailViewBtn.style("display", "none");
+      this.controls.zoomDiv.style("display", "none");
+      this.controls.widthRow.style("display", "none");
+    }
+  }
+  showHideControls() {
+    const state = this.app.getState();
+    this.controls.normalizationRow.style("display", state.currView == "horizontal" ? "none" : "");
+    this.controls.minCutoffRow.style("display", state.currView == "horizontal" ? "none" : "");
+    this.controls.maxCutoffRow.style("display", state.currView == "horizontal" ? "none" : "");
+    this.controls.matrixTypeRow.style("display", state.currView == "horizontal" ? "none" : "");
+    this.controls.widthRow.style("display", state.currView == "detail" ? "contents" : "none");
+  }
+  main(appState) {
+    const state = this.app.getState(appState);
+    this.controls.nmeth.update(state[state.currView].nmeth);
+    this.controls.matrixType.update(state[state.currView].matrixType);
+    this.controls.zoomDiv.style("display", state.currView == "detail" ? "contents" : "none");
+    if (state.currView == "chrpair") {
+      this.controls.view.text(`${state.x.chr}-${state.y.chr} Pair`);
+    } else {
+      this.controls.view.text(state.currView.charAt(0).toUpperCase() + state.currView.slice(1));
+    }
+    const formatAbsMin = this.parent("absMin") < 1e-5 ? Number(this.parent("absMin")).toExponential(1) : Number(this.parent("absMin").toFixed(6));
+    const formatAbsMax = this.parent("absMax") < 1e-5 ? Number(this.parent("absMax")).toExponential(1) : Number(this.parent("absMax").toFixed(6));
+    this.controls.width.select("input").property("value", state.settings.widthHeightPx);
+    this.controls.inputBpMinV.property("value", this.parent("min"));
+    this.controls.inputBpMaxV.property("value", this.parent("max"));
+    this.controls.minCutoffLabel.html(`MIN CUTOFF <br>(>= ${formatAbsMin})`);
+    this.controls.maxCutoffLabel.html(`MAX CUTOFF <br>(<= ${formatAbsMax})`);
+    this.showBtns();
+    this.showHideControls();
+  }
+};
+var controlPanelInit = getCompInit(ControlPanel);
+
+// tracks/hic/dom/InfoBar.ts
+var InfoBar = class {
+  constructor(opts) {
+    /** Defaults **/
+    //Color shown on the left of the color scale
+    this.startColor = "white";
+    //Color shown on the right of the color scale
+    this.endColor = "red";
+    this.addLabel = (text) => {
+      return this.labelRow.append("td").style("color", "#858585").style("font-size", ".8em").style("text-align", "center").style("vertical-align", "middle").text(text.toUpperCase());
+    };
+    this.addValue = (text) => {
+      return this.valueRow.append("td").style("font-size", "1em").style("text-align", "center").style("vertical-align", "middle").text(text);
+    };
+    this.type = "infoBar";
+    this.app = opts.app;
+    this.hic = opts.hic;
+    const table = opts.infoBarDiv;
+    this.labelRow = table.append("tr");
+    this.valueRow = table.append("tr");
+    this.parent = opts.parent;
+  }
+  async render() {
+    this.addLabel("Version");
+    this.addValue(this.hic.version);
+    this.addLabel("Enzyme");
+    this.addValue(this.hic.enzyme || "N/A");
+    this.addLabel("Resolution");
+    this.resolutionDiv = this.addValue("");
+    this.colorScaleLabel = this.addLabel("Scale");
+    this.colorScaleDiv = this.valueRow.append("td");
+    this.colorScale = new ColorScale({
+      barheight: 20,
+      barwidth: 100,
+      domain: [this.parent("min"), this.parent("max")],
+      fontSize: 12,
+      height: 40,
+      width: 150,
+      holder: this.colorScaleDiv,
+      colors: [this.startColor, this.endColor],
+      position: "20,0",
+      ticks: 3,
+      tickSize: 5,
+      //Do not use min value here on initialization. It's 0 and will not update later.
+      markedValue: 1
+    });
+  }
+  update() {
+    const res = this.parent("calcResolution");
+    let resolutionText;
+    if (res < this.hic.bpresolution[this.hic.bpresolution.length - 1]) {
+      resolutionText = `${res} fragment${res > 1 ? "s" : ""}`;
+    } else {
+      resolutionText = bplen(res);
+    }
+    this.resolutionDiv.text(resolutionText);
+    if (this.parent("state").currView == "horizontal") {
+      this.colorScaleLabel.style("display", "none");
+      this.colorScaleDiv.style("display", "none");
+    } else {
+      this.colorScaleLabel.style("display", "");
+      this.colorScaleDiv.style("display", "");
+      const min = this.parent("min");
+      const max = this.parent("max");
+      if (min < 0) {
+        this.colorScale.colors = ["blue", "white", "red"];
+        this.colorScale.domain = [min, 0, max];
+      } else {
+        this.colorScale.colors = ["white", "red"];
+        this.colorScale.domain = [0, max];
+      }
+      this.colorScale.markedValue = min;
+      this.colorScale.updateScale();
+    }
+  }
+};
+
+// tracks/hic/data/DataMapper.ts
+var DataMapper = class {
+  constructor(hic, percentile) {
+    this.hic = hic;
+    this.percentile = percentile ? percentile / 100 : 0.99;
+  }
+  sortData(data) {
+    const vlst = [];
+    if (data?.items && data?.items.length) {
+      for (const i of data.items) {
+        vlst.push(i[2]);
+      }
+    } else {
+      const blankChrs = /* @__PURE__ */ new Set();
+      for (const d of data) {
+        if (d.lead == "chrM" && !d.items.length || d.lead == "chrY" && !d.items.length) {
+          blankChrs.add(d.lead);
+          continue;
+        }
+        for (const i of d.items) {
+          vlst.push(i[2]);
+        }
+      }
+      if (blankChrs.size) {
+        for (const c of blankChrs) {
+          const idx = this.hic.chrlst.indexOf(c);
+          this.hic.chrlst.splice(idx, 1);
+        }
+      }
+    }
+    const sortedVlst = vlst.sort((a, b) => a - b);
+    const max = sortedVlst[Math.floor(sortedVlst.length * this.percentile)];
+    const min = sortedVlst[0];
+    return [min, max, sortedVlst[sortedVlst.length - 1]];
+  }
+};
+
+// tracks/hic/data/GenomeDataFetcher.ts
+var GenomeDataFetcher = class {
+  constructor(hic, debugmode, errList = []) {
+    this.data = [];
+    this.hic = hic;
+    this.debugmode = debugmode;
+    this.errList = errList || [];
+  }
+  async getData(obj) {
+    if (this.data.length) this.data = [];
+    if (!obj?.matrixType) obj.matrixType = "observed";
+    try {
+      const res = await dofetch3("hicgenome?", {
+        method: "POST",
+        body: JSON.stringify({
+          chrlst: this.hic.chrlst,
+          nmeth: obj.nmeth,
+          resolution: obj.resolution,
+          matrixType: obj.matrixType,
+          file: this.hic.file,
+          url: this.hic.url,
+          nochr: this.hic.nochr
+        })
+      });
+      if (res.error) {
+        const errs = res.error.split("\n");
+        for (const e of errs) {
+          this.errList.push(e);
+        }
+      }
+      return res.data;
+    } catch (e) {
+      this.errList.push(e.message || e);
+      if (e.stack) console.error(e.stack);
+    }
+  }
+};
+
+// tracks/hic/data/DataFetcher.ts
+var DataFetcher = class {
+  constructor(hic, debugmode, errList = []) {
+    this.hic = hic;
+    this.debugmode = debugmode;
+    this.errList = errList || [];
+  }
+  async getData(obj) {
+    if (!obj?.matrixType) obj.matrixType = "observed";
+    const arg = {
+      matrixType: obj.matrixType,
+      file: this.hic.file,
+      url: this.hic.url,
+      pos1: this.hic.nochr ? obj.lead.replace("chr", "") : obj.lead,
+      pos2: this.hic.nochr ? obj.follow.replace("chr", "") : obj.follow,
+      nmeth: obj.nmeth,
+      resolution: obj.resolution
+    };
+    try {
+      const data = await dofetch3("hicdata?", {
+        method: "POST",
+        body: JSON.stringify(arg)
+      });
+      if (data.error) {
+        throw Error(`${obj.lead} - ${obj.follow}: ${data.error.error}`);
+      }
+      if (!data.items || data.items.length == 0) return;
+      return data;
+    } catch (e) {
+      this.errList.push(e.message || e);
+      if (e.stack) console.error(e.stack);
+    }
+  }
+};
+
+// tracks/hic/HicComponent.ts
+var HicComponent = class {
+  constructor(opts) {
+    this.components = {
+      controls: []
+    };
+    this.genomeData = [];
+    this.calcResolution = null;
+    this.firstRender = true;
+    this.min = 0;
+    this.absMin = 0;
+    this.max = 0;
+    this.absMax = 0;
+    this.hasStatePreMain = true;
+    this.type = "view";
+    this.hic = opts.hic;
+    this.state = opts.state;
+    this.dom = opts.dom;
+    this.errList = opts.errList;
+    this.plotDiv = this.dom.plotDiv.append("table").classed("sjpp-hic-plot-main", true);
+    const tr1 = this.plotDiv.append("tr");
+    const tr2 = this.plotDiv.append("tr");
+    this.plotDiv = {
+      plot: tr1.append("td").classed("sjpp-hic-plot", true).attr("data-testid", "sjpp-hic-plot"),
+      yAxis: tr1.append("td").classed("sjpp-hic-plot-yaxis", true).attr("data-testid", "sjpp-hic-yaxis"),
+      xAxis: tr2.append("td").classed("sjpp-hic-plot-xaxis", true).attr("data-testid", "sjpp-hic-xaxis"),
+      blank: tr2.append("td")
+    };
+    this.app = opts.app;
+    this.dataMapper = new DataMapper(this.hic, opts.state.maxCutoffPercentile);
+    this.activeView = this.state.currView;
+    this.error = opts.error;
+    this.resolution = new Resolution(this.error);
+    this.parent = (prop) => {
+      return this[prop];
+    };
+    this.detailDataMapper = new DetailDataMapper(this.hic, this.errList, this.parent);
+  }
+  getState(appState) {
+    return appState;
+  }
+  reactsTo(action) {
+    if (action.type.startsWith("view")) return true;
+    else return false;
+  }
+  initView() {
+    const opts = {
+      plotDiv: this.plotDiv,
+      hic: this.hic,
+      app: this.app,
+      parent: (prop) => {
+        return this[prop];
+      }
+    };
+    if (this.state.currView == "genome") {
+      opts["data"] = this.data;
+      this.genome = new GenomeView(opts);
+      this.genome.render();
+    } else if (this.state.currView === "chrpair") {
+      opts["items"] = this.data;
+      this.chrpair = new ChrPairView(opts);
+      this.chrpair.render();
+    } else if (this.state.currView === "detail") {
+      opts["data"] = this.data;
+      this.detail = new DetailView(opts);
+      this.detail.render();
+    } else if (this.state.currView === "horizontal") {
+      this.horizontal = new HorizontalView(opts);
+      this.horizontal.render();
+    } else {
+      throw Error(`Unknown view: ${this.state.currView}`);
+    }
+  }
+  async fetchData(obj) {
+    if (this.data?.length) this.data = [];
+    if (this.state.currView == "genome") {
+      if (this.activeView != "genome" && this.genomeData?.length) this.data = this.genomeData;
+      else {
+        const genomeFetcher = new GenomeDataFetcher(this.hic, true, this.errList);
+        this.genomeData = await genomeFetcher.getData(obj);
+        this.data = this.genomeData;
+      }
+    } else if (this.state.currView == "detail") {
+      this.data = await this.detailDataMapper.getData(this.state.x, this.state.y, this.fragData);
+    } else {
+      if (!this.state?.x?.chr || !this.state?.y?.chr) {
+        this.errList.push(`No positions provided for ${this.activeView} view.`);
+        return;
+      } else {
+        const chrx = this.state.x;
+        const chry = this.state.y;
+        obj["lead"] = `${chrx.start && chrx.stop ? `${chrx.chr}:${chrx.start}-${chrx.stop}` : chrx.chr}`;
+        obj["follow"] = `${chry.start && chry.stop ? `${chry.chr}:${chry.start}-${chry.stop}` : chry.chr}`;
+      }
+      const dataFetcher = new DataFetcher(this.hic, true, this.errList);
+      this.data = await dataFetcher.getData(obj);
+    }
+  }
+  async setResolution(appState) {
+    const state = this.app.getState(appState);
+    this.calcResolution = this.resolution.getResolution(state, this.hic);
+    if (state.currView == "detail" && this.calcResolution == null) {
+      await this.detailDataMapper.getFragData(state.x, state.y);
+      this.fragData = this.detailDataMapper.frag;
+      const maxFragSpan = Math.min(
+        this.fragData.x.stop - this.fragData.x.start,
+        this.fragData.y.stop - this.fragData.y.start
+      );
+      this.calcResolution = this.resolution.findResFromArray(
+        maxFragSpan,
+        state.minFragSpan,
+        this.hic.fragresolution,
+        true
+      );
+    } else {
+      this.fragData = null;
+    }
+    return this.calcResolution;
+  }
+  async setDataArgs(appState) {
+    const state = this.app.getState(appState);
+    const currView = state[state.currView];
+    const args = {
+      nmeth: currView.nmeth,
+      resolution: await this.setResolution(appState),
+      matrixType: currView.matrixType
+    };
+    if (state.currView == "chrpair") {
+      args["lead"] = state.x.chr;
+      args["follow"] = state.y.chr;
+    }
+    return args;
+  }
+  async getViewData(appState) {
+    const args = await this.setDataArgs(appState);
+    await this.fetchData(args);
+    if (this.data?.length > 0 || this.data?.items?.length > 0) {
+      const [min, max, absMax] = this.dataMapper.sortData(this.data);
+      this.min = this.absMin = min;
+      this.max = max;
+      this.absMax = absMax;
+    } else {
+      if (this.state.currView != "genome") {
+        const state = this.app.getState(appState);
+        const xPosMessage = state.x?.start ? `${state.x.chr}:${state.x.start}-${state.x.stop}` : state.x.chr;
+        const yPosMessage = state.y?.start ? `${state.y.chr}:${state.y.start}-${state.y.stop}` : state.y.chr;
+        this.errList.push(`No data returned for ${xPosMessage} and ${yPosMessage}`);
+      }
+    }
+  }
+  async init() {
+    this.components = {
+      controls: await controlPanelInit({
+        app: this.app,
+        controlsDiv: this.dom.controlsDiv,
+        hic: this.hic,
+        parent: (prop, value) => {
+          if (value) this[prop] = value;
+          return this[prop];
+        },
+        error: this.error.bind(this)
+      })
+    };
+    this.infoBar = new InfoBar({
+      app: this.app,
+      infoBarDiv: this.dom.infoBarDiv.append("table").style("border-spacing", "3px"),
+      hic: this.hic,
+      parent: (prop) => {
+        return this[prop];
+      }
+    });
+    this.infoBar.render();
+  }
+  async main(appState) {
+    if (this.errList.length) {
+      this.app.dispatch({ type: "loading_active", active: false });
+      return;
+    }
+    const state = this.app.getState(appState);
+    if (this.firstRender == true) {
+      this.firstRender = false;
+      await this.getViewData(appState);
+      this.initView();
+    } else {
+      if (state.currView != "horizontal") {
+        this.app.dispatch({ type: "loading_active", active: true });
+        await this.getViewData(appState);
+      }
+      if (this.activeView != state.currView) {
+        if (this.activeView == "genome") {
+          this.genome.svg.remove();
+        } else {
+          this.plotDiv.xAxis.selectAll("*").remove();
+          this.plotDiv.yAxis.selectAll("*").remove();
+          this.plotDiv.plot.selectAll("*").remove();
+        }
+        this.activeView = state.currView;
+        this.initView();
+      } else {
+        this[state.currView].update(this.data);
+      }
+    }
+    this.infoBar.update();
+    if (this.errList.length) {
+      this.error(this.errList);
+      this.app.dispatch({ type: "loading_active", active: false });
+    }
+  }
+};
+var viewCompInit = getCompInit(HicComponent);
+
+// tracks/hic/HicApp.ts
+var HicApp = class {
+  constructor(opts) {
+    this.views = ["genome", "chrpair", "detail", "horizontal"];
+    this.errList = [];
+    this.type = "app";
+    this.hic = {
+      enzyme: opts.enzyme,
+      file: opts.file,
+      url: opts.url,
+      genome: opts.genome,
+      holder: opts.holder,
+      hostUrl: opts.hostUrl,
+      jwt: opts.jwt,
+      position1: opts.position1,
+      position2: opts.position2,
+      maxCutoffPercentile: opts.maxCutoffPercentile,
+      name: "name" in opts ? opts.name : "Hi-C",
+      tklist: "tklst" in opts ? opts.tklst : [],
+      state: "state" in opts ? opts.state : {}
+    };
+    this.dom = {
+      errorDiv: opts.holder.append("div").classed("sjpp-hic-error", true),
+      controlsDiv: opts.holder.append("div").classed("sjpp-hic-controls", true).style("display", "inline-block"),
+      infoBarDiv: opts.holder.append("div").classed("sjpp-hic-infobar", true).style("display", "inline-block").style("vertical-align", "top").style("padding", "5px").style("border", "solid 0.5px #ccc"),
+      loadingDiv: select_default("body").append("div").attr("id", "sjpp-loading-overlay"),
+      plotDiv: opts.holder.append("div").classed("sjpp-hic-main", true).style("display", "inline-block"),
+      tip: new Menu()
+    };
+  }
+  async error(err) {
+    if (err && typeof err == "string") this.errList.push(err);
+    showErrorsWithCounter(this.errList, this.dom.errorDiv);
+    this.errList = [];
+  }
+  determineView() {
+    if (!this.hic.position1 && !this.hic.position2 && !this.hic.state.currView) this.hic.state.currView = "genome";
+    if (!this.hic.position1 && this.hic.position2) this.errList.push("Missing first position");
+    if (this.hic.position1 && !this.hic.position2) this.errList.push("Missing second position");
+    if (this.hic.position1 && this.hic.position2) {
+      const pos1 = this.hic.position1.split(/[:-]/);
+      const pos2 = this.hic.position2.split(/[:-]/);
+      this.hic.state.x = { chr: pos1[0] };
+      this.hic.state.y = { chr: pos2[0] };
+      if (!Number.isNaN(+pos1[1]) && !Number.isNaN(+pos1[2])) {
+        this.hic.state.x.start = +pos1[1];
+        this.hic.state.x.stop = +pos1[2];
+        this.hic.state.y.start = +pos2[1];
+        this.hic.state.y.stop = +pos2[2];
+        this.hic.state.currView = "detail";
+      } else {
+        this.hic.state.currView = "chrpair";
+      }
+    } else {
+      if (!this.views.some((v) => v === this.hic.state.currView)) this.error(`Unknown view: ${this.hic.state.currView}`);
+      else return this.hic.state.currView;
+    }
+  }
+  getViewsConfig() {
+    if (this.hic.maxCutoffPercentile) this.hic.state.maxCutoffPercentile = this.hic.maxCutoffPercentile;
+    let nmeth;
+    if (this.hic["normalization"]?.length > 0) {
+      if (!this.hic["normalization"].includes("NONE")) this.hic["normalization"].unshift("NONE");
+      nmeth = this.hic["normalization"][0];
+    } else {
+      nmeth = "NONE";
+    }
+    if (this.hic.state.currView) {
+      if (!this.hic.state[this.hic.state.currView]) this.hic.state[this.hic.state.currView] = {};
+      if (!this.hic.state[this.hic.state.currView]?.matrixType) {
+        this.hic.state[this.hic.state.currView].matrixType = "observed";
+      }
+      if (!this.hic.state[this.hic.state.currView]?.nmeth) {
+        this.hic.state[this.hic.state.currView].nmeth = nmeth;
+      }
+    }
+    for (const v of this.views) {
+      if (!this.hic.state[v]) {
+        this.hic.state[v] = {
+          matrixType: "observed",
+          nmeth
+        };
+      }
+    }
+  }
+  async init() {
+    this.determineView();
+    try {
+      await hicParseFile(this.hic, true, this.errList);
+      this.getViewsConfig();
+      this.store = await hicStoreInit({ app: this.api, state: this.hic.state });
+      this.state = await this.store.copyState();
+      this.components = {
+        loadingOverlay: await loadingInit({
+          app: this.api,
+          loadingDiv: this.dom.loadingDiv
+        }),
+        view: await viewCompInit({
+          app: this.api,
+          state: this.state,
+          dom: this.dom,
+          hic: this.hic,
+          errList: this.errList,
+          error: this.error
+        })
+      };
+      await this.api.dispatch();
+    } catch (e) {
+      console.error(e.stack || e);
+    }
+  }
+  main() {
+    if (this.errList.length) {
+      this.error(this.errList);
+      this.dom.loadingDiv.style("display", "none");
+      return;
+    }
+  }
+};
+var hicInit = getAppInit(HicApp);
+export {
+  hicInit
+};
+//# sourceMappingURL=HicApp-6AYCPCW6.js.map