@sjcrh/proteinpaint-client 2.184.0 → 2.185.0

package/dist/chunk-GCXNR5FP.js

@@ -1,229 +0,0 @@
-import {
-  keyupEnter
-} from "./chunk-KBYRXJ6Y.js";
-import {
-  get_bin_label,
-  get_bin_range_equation
-} from "./chunk-GXINX3WK.js";
-
-// termsetting/handlers/NumCustomBinEditor.ts
-var NumCustomBinEditor = class {
-  constructor(editHandler) {
-    this.dom = {};
-    this.editHandler = editHandler;
-    this.opts = editHandler.opts;
-    this.tw = editHandler.tw;
-    this.termsetting = editHandler.termsetting;
-  }
-  async render(div) {
-    if (this.q?.type != "custom-bin") this.q = this.getDefaultQ();
-    await this.editHandler.handler.density.setBinLines(this.getBoundaryOpts());
-    if (this.dom.inputsDiv) {
-      if (this.editHandler.dom.binsDiv?.node().contains(this.dom.inputsDiv.node())) return;
-      else {
-        this.dom.inputsDiv.remove();
-        delete this.dom.inputsDiv;
-      }
-    }
-    this.dom.inputsDiv = div.append("div").style("display", "flex").style("width", "100%");
-    this.renderCustomBinInputs();
-  }
-  getBoundaryOpts() {
-    return {
-      values: this.q.lst.slice(1).map((bin) => ({ x: bin.startunbounded ? bin.stop : bin.start, isDraggable: true })),
-      callback: (d, value) => {
-        const boundaryValues = this.q.lst.slice(1).map((d2) => "start" in d2 ? d2.start : "");
-        boundaryValues[d.index] = value;
-        this.dom.customBinBoundaryInput.text(boundaryValues.join(",\n"));
-        this.handleInputChange("drag");
-        return 0;
-      }
-    };
-  }
-  getDefaultQ() {
-    if (this.tw.q.mode == "discrete" && this.tw.q.type == "custom-bin") {
-      const copy = JSON.parse(JSON.stringify(this.tw.q));
-      copy.lst.forEach((bin) => {
-        if (!bin.label) bin.label = get_bin_label(bin, this.tw.q, this.tw.term.valueConversion);
-        bin.range = get_bin_range_equation(bin, this.tw.q);
-      });
-      return copy;
-    }
-    const { min, max } = this.editHandler.handler.density_data;
-    const defaultCustomBoundary = (
-      /* when no sample is annotated by this term,
-      minvalue and maxvalue are both null
-      setting defaultCustomBoundary to arbitrary "0" will allow existing UI to work
-      but remains to be evaluated if is really okay to use 0
-      */
-      !Number.isFinite(min) || !Number.isFinite(max) ? 0 : (
-        // minvalue and maxvalue is valid number
-        max != min ? min + (max - min) / 2 : max
-      )
-    );
-    const firstBin = {
-      startunbounded: true,
-      startinclusive: false,
-      stopinclusive: false,
-      stop: +defaultCustomBoundary.toFixed(this.tw.term.type == "integer" ? 0 : 2)
-    };
-    const lastBin = {
-      stopunbounded: true,
-      startinclusive: true,
-      stopinclusive: false,
-      start: +defaultCustomBoundary.toFixed(this.tw.term.type == "integer" ? 0 : 2)
-    };
-    return {
-      mode: "discrete",
-      type: "custom-bin",
-      lst: [
-        // Type '{ label: any; range: any; startunbounded: boolean; startinclusive: boolean; stopinclusive: boolean; stop: number; }' is not assignable to type 'StartUnboundedBin | FullyBoundedBin'.
-        // Property 'start' is missing in type '{ label: any; range: any; startunbounded: boolean; startinclusive: boolean; stopinclusive: boolean; stop: number; }' but required in type 'FullyBoundedBin'.
-        {
-          ...firstBin,
-          label: get_bin_label(firstBin, this.tw.q, this.tw.term.valueConversion),
-          range: get_bin_range_equation(firstBin, this.tw.q)
-        },
-        {
-          ...lastBin,
-          label: get_bin_label(lastBin, this.tw.q, this.tw.term.valueConversion),
-          range: get_bin_range_equation(lastBin, this.tw.q)
-        }
-        //satisfies StopUnboundedBin
-      ]
-    };
-  }
-  /******************* Functions for Numerical Custom size bins *******************/
-  renderCustomBinInputs() {
-    const q = this.q;
-    const boundaryDiv = this.dom.inputsDiv.append("div").style("margin-right", "20px");
-    this.dom.rangeAndLabelDiv = this.dom.inputsDiv.append("div");
-    boundaryDiv.append("div").style("margin-bottom", "5px").style("color", "rgb(136, 136, 136)").text("Bin boundaries");
-    this.dom.customBinBoundaryInput = boundaryDiv.append("textarea").style("width", "100px").style("height", "70px").text(
-      q.lst.slice(1).map((d) => "start" in d ? d.start : "").join("\n")
-    ).on("change", () => this.handleInputChange()).on("keyup", async (event) => {
-      if (!keyupEnter(event) && event.key != 8 && event.key != "Enter") return;
-      if (!this.dom.inputsDiv.selectAll("input").node().value) return;
-      this.handleInputChange();
-    });
-    boundaryDiv.append("div").style("font-size", ".6em").style("margin-left", "1px").style("color", "#858585").html("Enter numeric values </br>seperated by ENTER");
-    this.renderBoundaryInputDivs();
-  }
-  renderBoundaryInputDivs() {
-    const data = this.q.lst;
-    const holder = this.dom.rangeAndLabelDiv;
-    holder.selectAll("*").remove();
-    const grid = holder.append("div").style("display", "grid").style("grid-template-columns", "auto auto").style("column-gap", "20px").style("align-items", "center");
-    grid.append("div").style("margin-bottom", "3px").style("color", "rgb(136, 136, 136)").text("Range");
-    grid.append("div").style("margin-bottom", "3px").style("color", "rgb(136, 136, 136)").text("Bin label");
-    for (const d of data) {
-      grid.append("div").attr("name", "range").html(d.range);
-      grid.append("div").append("input").attr("type", "text").style("margin", "2px 0px").property("value", d.label).on("change", function() {
-        d.label = this.value;
-      });
-    }
-    this.dom.customBinRanges = this.dom.inputsDiv.selectAll('div[name="range"]').data(data);
-    this.dom.customBinLabelInput = this.dom.inputsDiv.selectAll("input").data(data);
-  }
-  handleInputChange(eventType = "") {
-    const self = this.tw;
-    const inputs = this.dom.inputsDiv.selectAll("input");
-    inputs.property("value", "");
-    const data = this.processCustomBinInputs();
-    if (data == void 0) {
-      return;
-    }
-    if (self.q.hiddenValues) this.tw.q.hiddenValues = self.q.hiddenValues;
-    if (this.binsChanged(data, this.q.lst)) {
-      this.q.lst = data;
-    }
-    this.renderBoundaryInputDivs();
-    if (eventType != "drag") this.editHandler.handler.density.setBinLines(this.getBoundaryOpts());
-  }
-  binsChanged(data, qlst) {
-    if (data.length != qlst.length) return true;
-    if (Object.keys(data[0]).length !== Object.keys(qlst[0]).length) return true;
-    for (const [i, bin] of qlst.entries()) {
-      for (const k of Object.keys(bin)) {
-        if (bin[k] && bin[k] !== data[i][k]) {
-          return true;
-        }
-      }
-    }
-    return false;
-  }
-  processCustomBinInputs() {
-    const self = this.termsetting;
-    const startinclusive = this.editHandler.boundaryInclusion == "startinclusive";
-    const stopinclusive = this.editHandler.boundaryInclusion == "stopinclusive";
-    const inputs = this.dom.inputsDiv.node().querySelectorAll("input");
-    const inputData = this.dom.customBinBoundaryInput.property("value").split("\n").filter((d) => d != "" && !isNaN(d));
-    const trackBins = new Set(inputData);
-    if (!trackBins.size) return this.tw.q.lst;
-    const sortedBins = Array.from(trackBins).map(Number).sort((a, b) => a - b);
-    const data = [
-      // first bin: StartUnbounded type
-      {
-        startunbounded: true,
-        stop: sortedBins[0],
-        startinclusive: false,
-        stopinclusive,
-        label: inputs[0].value
-      }
-    ];
-    if (!data[0].label) data[0].label = get_bin_label(data[0], self.q, self.term.valueConversion);
-    if (!data[0].range) data[0].range = get_bin_range_equation(data[0], self.q);
-    for (const [i, d] of sortedBins.entries()) {
-      let bin;
-      const label = inputs[i + 1]?.value || "";
-      if (i !== trackBins.size - 1) {
-        bin = {
-          start: +d,
-          startinclusive,
-          stopinclusive,
-          stop: sortedBins[i + 1],
-          label
-          //range: ''
-        };
-      } else {
-        bin = {
-          start: +d,
-          startinclusive,
-          stopinclusive: false,
-          stopunbounded: true,
-          label
-          //range: ''
-        };
-      }
-      if (bin.label === "" || bin.label === void 0) bin.label = get_bin_label(bin, self.q, self.term.valueConversion);
-      if (bin.range === "" || bin.range === void 0) bin.range = get_bin_range_equation(bin, self.q);
-      data.push(bin);
-    }
-    return data;
-  }
-  getEditedQ(destroyDom = true) {
-    const lst = this.processCustomBinInputs();
-    if (destroyDom) {
-      for (const name of Object.keys(this.dom)) {
-        this.dom[name].remove();
-        delete this.dom[name];
-      }
-    }
-    return {
-      mode: "discrete",
-      type: "custom-bin",
-      lst
-    };
-  }
-  undoEdits() {
-    this.q = this.getDefaultQ();
-    this.dom.inputsDiv.selectAll("*").remove();
-    this.renderCustomBinInputs();
-    this.editHandler.handler.density.setBinLines(this.getBoundaryOpts());
-  }
-};
-
-export {
-  NumCustomBinEditor
-};
-//# sourceMappingURL=chunk-GCXNR5FP.js.map

package/dist/chunk-GMDQIP3M.js

@@ -1,31 +0,0 @@
-import {
-  IN_frame,
-  OUT_frame
-} from "./chunk-XRVBHNCW.js";
-
-// src/spliceevent.exonskip.getdefault.js
-function spliceevent_exonskip_getdefault_default(events) {
-  let evt2showidx = 0;
-  for (let i = 1; i < events.length; i++) {
-    const e = events[i];
-    const e2show = events[evt2showidx];
-    if (e.isskipexon && e2show.isaltexon) {
-      evt2showidx = i;
-      continue;
-    }
-    if (e.frame == OUT_frame && e2show.framenocheck) {
-      evt2showidx = i;
-      continue;
-    }
-    if (e.frame == IN_frame && e2show.frame != IN_frame) {
-      evt2showidx = i;
-      continue;
-    }
-  }
-  return evt2showidx;
-}
-
-export {
-  spliceevent_exonskip_getdefault_default
-};
-//# sourceMappingURL=chunk-GMDQIP3M.js.map

package/dist/chunk-GXINX3WK.js

@@ -1,281 +0,0 @@
-import {
-  getColors
-} from "./chunk-XRVBHNCW.js";
-import {
-  convertUnits,
-  isNumeric,
-  isStrictNumeric
-} from "./chunk-BEWDIM6H.js";
-import {
-  format
-} from "./chunk-OAWQ6LOO.js";
-
-// ../shared/utils/src/termdb.bins.js
-function validate_bins(binconfig) {
-  const bc = binconfig;
-  if (!bc || typeof bc !== "object") throw "bin schema must be an object";
-  if (!("type" in bc)) bc.type = "regular-bin";
-  if (bc.type == "custom-bin") {
-    if (!Array.isArray(bc.lst)) throw "binconfig.lst must be an array";
-    if (!bc.lst.length) throw "binconfig.lst must have entries";
-    const first_bin = bc.lst[0];
-    const last_bin = bc.lst[bc.lst.length - 1];
-    for (const bin of bc.lst) {
-      if (!("startinclusive" in bin) && !("stopinclusive" in bin)) {
-        throw "custom bin.startinclusive and/or bin.stopinclusive must be defined";
-      }
-      if (bin == first_bin) {
-        if ("startunbounded" in bin && !bin.startunbounded) {
-          throw `a custom first bin must not set bin.startunbounded to false`;
-        }
-        bin.startunbounded = true;
-        if ("start" in bin) {
-          throw "a custom first bin must not set a bin.start value";
-        }
-        if ("start_percentile" in bin) {
-          throw "the first bin must not set a bin.start_percentile value";
-        }
-        if (!("stop" in bin)) {
-          throw `a custom first bin must define a bin.stop value`;
-        }
-        if (!isStrictNumeric(bin.stop)) {
-          throw `a custom first bin.stop value should be numeric`;
-        }
-      } else if (bin == last_bin) {
-        if (!("start" in bin)) {
-          throw `a custom last bin must define a bin.start value`;
-        }
-        if (!isStrictNumeric(bin.start)) {
-          throw `a custom last bin.start must be numeric`;
-        }
-        if ("stopunbounded" in bin && !bin.stopunbounded) {
-          throw "a custom last bin must not set bin.stopunbounded to false";
-        }
-        bin.stopunbounded = true;
-        if ("stop" in bin) {
-          throw "a custom last bin must not set a bin.stop value";
-        }
-      } else {
-        if (bin.startunbounded || bin.stopunbounded) {
-          throw "bin.startunbounded and bin.stopunbounded must not be set for non-first/non-last bins";
-        }
-        if (!isStrictNumeric(bin.start)) throw "bin.start must be numeric for a non-first bin";
-        if (!isStrictNumeric(bin.stop)) throw "bin.stop must be numeric for a non-last bin";
-      }
-    }
-  } else if (bc.type == "regular-bin") {
-    if (!Number.isFinite(bc.bin_size)) throw "non-numeric bin_size";
-    if (bc.bin_size <= 0) throw "bin_size must be greater than 0";
-    if (!bc.startinclusive && !bc.stopinclusive) {
-      bc.startinclusive = 1;
-      bc.stopinclusive = 0;
-    }
-    if (!bc.first_bin) throw "first_bin{} missing";
-    if (typeof bc.first_bin != "object") throw "first_bin{} is not an object";
-    if (!Object.keys(bc.first_bin).length) throw "first_bin is an empty object";
-    {
-      const b = bc.first_bin;
-      b.startunbounded = true;
-      if (b.stop_percentile) {
-        if (!Number.isInteger(b.stop_percentile)) throw "first_bin.stop_percentile should be integer";
-        if (b.stop_percentile <= 0 || b.stop_percentile >= 100) throw "first_bin.stop_percentile out of bound (0-100)";
-      } else if (!Number.isFinite(b.stop)) {
-        throw "first_bin.stop not a number when stop_percentile is not set";
-      }
-    }
-    if (bc.last_bin) {
-      const b = bc.last_bin;
-      if (b.start_percentile) {
-        if (!Number.isInteger(b.start_percentile)) throw "last_bin.start_percentile should be integer";
-        if (b.start_percentile <= 0 || b.start_percentile >= 100) throw "last_bin.start_percentile out of bound (0-100)";
-      } else if (!Number.isFinite(b.start)) {
-        throw "last_bin.start not a number when start_percentile is not set";
-      }
-      b.stopunbounded = true;
-      if ("stop" in b) {
-        throw "a regular last bin must not set a bin.stop value";
-      }
-    }
-  } else {
-    throw `invalid binconfig.type="${bc.type}"`;
-  }
-}
-function compute_bins(binconfig, summaryfxn, valueConversion) {
-  const bc = binconfig;
-  validate_bins(bc);
-  if (bc.lst) {
-    const k2c2 = getColors(bc.lst.length);
-    for (const bin of bc.lst) bin.color = k2c2(bin.label);
-  }
-  if (bc.type == "custom-bin") return JSON.parse(JSON.stringify(bc.lst));
-  if (typeof summaryfxn != "function") throw "summaryfxn required for modules/termdb.bins.js compute_bins()";
-  const percentiles = target_percentiles(bc);
-  const summary = summaryfxn(percentiles);
-  if (!summary || typeof summary !== "object") throw "invalid returned value by summaryfxn";
-  bc.results = { summary };
-  if (!bc.binLabelFormatter) bc.binLabelFormatter = getNumDecimalsFormatter(bc);
-  const minFloor = Math.floor(summary.min * 100) / 100;
-  const maxCeil = Math.ceil(summary.max * 100) / 100;
-  const min = bc.first_bin.startunbounded ? minFloor : bc.first_bin.start_percentile ? summary["p" + bc.first_bin.start_percentile] : bc.first_bin.start;
-  let max = maxCeil, last_start, last_stop;
-  if (bc.last_bin) {
-    max = bc.last_bin.stopunbounded ? maxCeil : bc.last_bin.stop_percentile ? summary["p" + bc.last_bin.stop_percentile] : isNumeric(bc.last_bin.stop) && bc.last_bin.stop <= summary.max ? bc.last_bin.stop : maxCeil;
-    last_start = isStrictNumeric(bc.last_bin.start_percentile) ? summary["p" + bc.last_bin.start_percentile] : isStrictNumeric(bc.last_bin.start) ? bc.last_bin.start : void 0;
-    last_stop = bc.last_bin.stopunbounded ? null : bc.last_bin.stop_percentile ? summary["p" + bc.last_bin.stop_percentile] : isStrictNumeric(bc.last_bin.stop) ? bc.last_bin.stop : null;
-  } else if (bc.lst) {
-    const last_bin = bc.lst[bc.lst.length - 1];
-    last_start = last_bin.start;
-    last_stop = "stop" in last_bin && !last_bin.stopunbounded ? last_bin.stop : maxCeil;
-    max = last_stop;
-  } else {
-    last_start = maxCeil;
-    last_stop = maxCeil;
-  }
-  const numericMax = isStrictNumeric(max);
-  const numericLastStart = isStrictNumeric(last_start);
-  const numericLastStop = isStrictNumeric(last_stop);
-  if (!numericMax && !numericLastStart) return [];
-  const bins = [];
-  let currBin = {
-    startunbounded: bc.first_bin.startunbounded,
-    start: bc.first_bin.startunbounded ? void 0 : min,
-    stop: isStrictNumeric(bc.first_bin.stop_percentile) ? +summary["p" + bc.first_bin.stop_percentile] : isStrictNumeric(bc.first_bin.stop) ? +bc.first_bin.stop : min + bc.bin_size,
-    startinclusive: bc.startinclusive,
-    stopinclusive: bc.stopinclusive
-  };
-  if (!isStrictNumeric(currBin.stop)) throw "the computed first_bin.stop is non-numeric" + currBin.stop;
-  const maxNumBins = 100;
-  while (numericMax && currBin.stop <= max || currBin.startunbounded && !bins.length || currBin.stopunbounded) {
-    bins.push(currBin);
-    if (currBin.stop >= max) {
-      currBin.stopunbounded = true;
-      if (bins.length > 1) {
-        delete currBin.stop;
-      }
-    }
-    currBin.label = get_bin_label(currBin, bc, valueConversion);
-    if (currBin.stopunbounded) break;
-    const upper = currBin.stop + bc.bin_size;
-    const previousStop = currBin.stop;
-    currBin = {
-      startinclusive: bc.startinclusive,
-      stopinclusive: bc.stopinclusive,
-      start: previousStop,
-      stop: numericLastStop && (previousStop == last_start || upper > last_stop) ? last_stop : numericLastStart && upper > last_start && previousStop != last_start ? last_start : upper
-    };
-    if (currBin.stop >= max) {
-      currBin.stop = max;
-      if (bc.last_bin && bc.last_bin.stopunbounded) currBin.stopunbounded = 1;
-      if (bc.last_bin && bc.last_bin.stopinclusive) currBin.stopinclusive = 1;
-    }
-    if (numericLastStart && currBin.start == last_start) {
-      if (bc.last_bin && bc.last_bin.stopunbounded) currBin.stopunbounded = 1;
-    }
-    if (currBin.start > currBin.stop) {
-      if (numericLastStart && currBin.stop == last_start && bc.last_bin && bc.last_bin.stopunbounded)
-        currBin.stopunbounded = true;
-      else break;
-    }
-    if (bins.length + 1 >= maxNumBins) {
-      bc.error = "max_num_bins_reached";
-      break;
-    }
-  }
-  delete bc.binLabelFormatter;
-  if (bins.length > 1) {
-    delete bins[bins.length - 1].stop;
-  }
-  const k2c = getColors(bins.length);
-  for (const bin of bins) bin.color = k2c(bin.label);
-  return bins;
-}
-function getNumDecimalsFormatter(bc) {
-  return "rounding" in bc ? format(bc.rounding) : (d) => d;
-}
-function get_bin_label(bin, binconfig, valueConversion) {
-  if (!bin) return "missing bin.label";
-  if (bin.label) return bin.label;
-  const bc = binconfig;
-  if (!bc.binLabelFormatter) bc.binLabelFormatter = getNumDecimalsFormatter(bc);
-  if (!bin.startunbounded && !bin.stopunbounded && !("startinclusive" in bin) && !("stopinclusive" in bin)) {
-    if (bc.startinclusive) bin.startinclusive = true;
-    else if (bc.stopinclusive) bin.stopinclusive = true;
-  }
-  const start = bc.use_as == "bins" || bin.start;
-  const stop = bc.use_as == "bins" || bin.stop;
-  let label_offset = 0;
-  if ("label_offset" in bc) {
-    bc.label_offset_ignored = "bin_size" in bc && bc.bin_size < bc.label_offset;
-    if (!bc.label_offset_ignored) label_offset = bc.label_offset;
-  } else if (bc.bin_size === 1 && bc.termtype == "integer") {
-    label_offset = 1;
-  }
-  if (bin.startunbounded) {
-    const oper = bin.stopinclusive ? "\u2264" : "<";
-    const v1 = valueConversion ? convertUnits(stop, valueConversion.fromUnit, valueConversion.toUnit, valueConversion.scaleFactor, true) : bc.binLabelFormatter(stop);
-    return oper + v1;
-  }
-  if (bin.stopunbounded || start === stop) {
-    const oper = bin.startinclusive ? "\u2265" : ">";
-    const v0 = valueConversion ? convertUnits(start, valueConversion.fromUnit, valueConversion.toUnit, valueConversion.scaleFactor, true) : bc.binLabelFormatter(start);
-    return oper + v0;
-  }
-  if (label_offset && bin.startinclusive && !bin.stopinclusive) {
-    if (Number.isInteger(bc.bin_size) && Math.abs(start - stop) === label_offset) {
-      return "" + (valueConversion ? convertUnits(start, valueConversion.fromUnit, valueConversion.toUnit, valueConversion.scaleFactor, true) : bc.binLabelFormatter(start));
-    } else {
-      const v0 = valueConversion ? convertUnits(start, valueConversion.fromUnit, valueConversion.toUnit, valueConversion.scaleFactor, true) : bc.binLabelFormatter(start);
-      const v1 = valueConversion ? convertUnits(
-        stop - label_offset,
-        valueConversion.fromUnit,
-        valueConversion.toUnit,
-        valueConversion.scaleFactor,
-        true
-      ) : bc.binLabelFormatter(stop - label_offset);
-      return +v0 >= +v1 ? v0.toString() : v0 + " to " + v1;
-    }
-  } else {
-    const oper0 = bin.startinclusive ? "" : ">";
-    const oper1 = bin.stopinclusive ? "" : "<";
-    const v0 = valueConversion ? convertUnits(start, valueConversion.fromUnit, valueConversion.toUnit, valueConversion.scaleFactor, true) : Number.isInteger(start) ? start : bc.binLabelFormatter(start);
-    const v1 = valueConversion ? convertUnits(stop, valueConversion.fromUnit, valueConversion.toUnit, valueConversion.scaleFactor, true) : Number.isInteger(stop) ? stop : bc.binLabelFormatter(stop);
-    if (+v0 >= +v1) {
-      const oper = bin.startinclusive ? "\u2265" : ">";
-      return oper + v0;
-    } else {
-      return oper0 + v0 + " to " + oper1 + v1;
-    }
-  }
-}
-function get_bin_range_equation(bin, binconfig) {
-  const x = '<span style="font-family:Times;font-style:italic;">x</span>';
-  let range_eq;
-  const copy = structuredClone(bin);
-  copy.label = "";
-  const bin_label = get_bin_label(copy, binconfig);
-  if (bin.startunbounded || bin.stopunbounded) {
-    range_eq = x + " " + bin_label;
-  } else if (bin.startinclusive) {
-    range_eq = bin_label.replace("to <", "\u2264 " + x + " <");
-  } else if (bin.stopinclusive) {
-    range_eq = bin_label.replace(">", "").replace("to", "< " + x + " \u2264");
-  }
-  return range_eq;
-}
-function target_percentiles(binconfig) {
-  const percentiles = [];
-  const f = binconfig.first_bin;
-  if (f && isStrictNumeric(f.start_percentile)) percentiles.push(f.start_percentile);
-  if (f && isStrictNumeric(f.stop_percentile)) percentiles.push(f.stop_percentile);
-  const l = binconfig.last_bin;
-  if (l && isStrictNumeric(l.start_percentile)) percentiles.push(l.start_percentile);
-  if (l && isStrictNumeric(l.stop_percentile)) percentiles.push(l.stop_percentile);
-  return percentiles;
-}
-
-export {
-  compute_bins,
-  get_bin_label,
-  get_bin_range_equation
-};
-//# sourceMappingURL=chunk-GXINX3WK.js.map

package/dist/chunk-GXINX3WK.js.map

@@ -1,7 +0,0 @@
-{
-  "version": 3,
-  "sources": ["../../shared/utils/src/termdb.bins.js"],
-  "sourcesContent": ["import { format } from 'd3-format'\nimport { getColors } from './common.js'\nimport { isNumeric, isStrictNumeric, convertUnits } from './helpers.js'\n\nexport default function validate_bins(binconfig) {\n\t// Number.isFinite('1') returns false, which is desired\n\n\tconst bc = binconfig\n\tif (!bc || typeof bc !== 'object') throw 'bin schema must be an object'\n\t// assign default type\n\tif (!('type' in bc)) bc.type = 'regular-bin'\n\n\tif (bc.type == 'custom-bin') {\n\t\tif (!Array.isArray(bc.lst)) throw 'binconfig.lst must be an array'\n\t\tif (!bc.lst.length) throw 'binconfig.lst must have entries'\n\t\tconst first_bin = bc.lst[0]\n\t\tconst last_bin = bc.lst[bc.lst.length - 1]\n\n\t\tfor (const bin of bc.lst) {\n\t\t\tif (!('startinclusive' in bin) && !('stopinclusive' in bin)) {\n\t\t\t\tthrow 'custom bin.startinclusive and/or bin.stopinclusive must be defined'\n\t\t\t}\n\n\t\t\tif (bin == first_bin) {\n\t\t\t\tif ('startunbounded' in bin && !bin.startunbounded) {\n\t\t\t\t\tthrow `a custom first bin must not set bin.startunbounded to false`\n\t\t\t\t}\n\t\t\t\tbin.startunbounded = true\n\t\t\t\tif ('start' in bin) {\n\t\t\t\t\tthrow 'a custom first bin must not set a bin.start value'\n\t\t\t\t}\n\t\t\t\tif ('start_percentile' in bin) {\n\t\t\t\t\tthrow 'the first bin must not set a bin.start_percentile value'\n\t\t\t\t}\n\t\t\t\tif (!('stop' in bin)) {\n\t\t\t\t\tthrow `a custom first bin must define a bin.stop value`\n\t\t\t\t}\n\t\t\t\tif (!isStrictNumeric(bin.stop)) {\n\t\t\t\t\tthrow `a custom first bin.stop value should be numeric`\n\t\t\t\t}\n\t\t\t} else if (bin == last_bin) {\n\t\t\t\tif (!('start' in bin)) {\n\t\t\t\t\tthrow `a custom last bin must define a bin.start value`\n\t\t\t\t}\n\t\t\t\tif (!isStrictNumeric(bin.start)) {\n\t\t\t\t\tthrow `a custom last bin.start must be numeric`\n\t\t\t\t}\n\t\t\t\tif ('stopunbounded' in bin && !bin.stopunbounded) {\n\t\t\t\t\tthrow 'a custom last bin must not set bin.stopunbounded to false'\n\t\t\t\t}\n\t\t\t\tbin.stopunbounded = true\n\t\t\t\tif ('stop' in bin) {\n\t\t\t\t\tthrow 'a custom last bin must not set a bin.stop value'\n\t\t\t\t}\n\t\t\t} else {\n\t\t\t\tif (bin.startunbounded || bin.stopunbounded) {\n\t\t\t\t\tthrow 'bin.startunbounded and bin.stopunbounded must not be set for non-first/non-last bins'\n\t\t\t\t}\n\t\t\t\tif (!isStrictNumeric(bin.start)) throw 'bin.start must be numeric for a non-first bin'\n\t\t\t\tif (!isStrictNumeric(bin.stop)) throw 'bin.stop must be numeric for a non-last bin'\n\t\t\t}\n\t\t}\n\t} else if (bc.type == 'regular-bin') {\n\t\t// required custom_bin parameter\n\t\tif (!Number.isFinite(bc.bin_size)) throw 'non-numeric bin_size'\n\t\tif (bc.bin_size <= 0) throw 'bin_size must be greater than 0'\n\n\t\tif (!bc.startinclusive && !bc.stopinclusive) {\n\t\t\tbc.startinclusive = 1\n\t\t\tbc.stopinclusive = 0\n\t\t}\n\n\t\tif (!bc.first_bin) throw 'first_bin{} missing'\n\t\tif (typeof bc.first_bin != 'object') throw 'first_bin{} is not an object'\n\t\tif (!Object.keys(bc.first_bin).length) throw 'first_bin is an empty object'\n\n\t\t{\n\t\t\tconst b = bc.first_bin\n\t\t\tb.startunbounded = true\n\t\t\t// requires stop_percentile, or stop\n\t\t\tif (b.stop_percentile) {\n\t\t\t\tif (!Number.isInteger(b.stop_percentile)) throw 'first_bin.stop_percentile should be integer'\n\t\t\t\tif (b.stop_percentile <= 0 || b.stop_percentile >= 100) throw 'first_bin.stop_percentile out of bound (0-100)'\n\t\t\t} else if (!Number.isFinite(b.stop)) {\n\t\t\t\tthrow 'first_bin.stop not a number when stop_percentile is not set'\n\t\t\t}\n\t\t}\n\n\t\tif (bc.last_bin) {\n\t\t\tconst b = bc.last_bin\n\t\t\t// requires start_percentile or start\n\t\t\tif (b.start_percentile) {\n\t\t\t\tif (!Number.isInteger(b.start_percentile)) throw 'last_bin.start_percentile should be integer'\n\t\t\t\tif (b.start_percentile <= 0 || b.start_percentile >= 100) throw 'last_bin.start_percentile out of bound (0-100)'\n\t\t\t} else if (!Number.isFinite(b.start)) {\n\t\t\t\tthrow 'last_bin.start not a number when start_percentile is not set'\n\t\t\t}\n\n\t\t\tb.stopunbounded = true\n\t\t\tif ('stop' in b) {\n\t\t\t\tthrow 'a regular last bin must not set a bin.stop value'\n\t\t\t}\n\t\t}\n\t} else {\n\t\tthrow `invalid binconfig.type=\"${bc.type}\"`\n\t}\n}\n\nexport function compute_bins(binconfig, summaryfxn, valueConversion) {\n\t/*\n  Bins generator\n  \nbinconfig   \n  configuration of bins per the Numerical Binning Scheme\n\nsummaryfxn (percentiles)=> return {min, max, pX, pY, ...}\n  - required function\n\n  - must accept an array of desired percentile values\n  and returns an object of computed properties\n  {\n    min: minimum value\n    max: maximum value\n    pX: percentile at X value, so p10 will be 10th percentile value\n    pY: .. corresponding to the desired percentile values \n  }\n*/\n\tconst bc = binconfig\n\n\tvalidate_bins(bc)\n\tif (bc.lst) {\n\t\tconst k2c = getColors(bc.lst.length) //to color bins\n\t\tfor (const bin of bc.lst) bin.color = k2c(bin.label)\n\t}\n\tif (bc.type == 'custom-bin') return JSON.parse(JSON.stringify(bc.lst))\n\tif (typeof summaryfxn != 'function') throw 'summaryfxn required for modules/termdb.bins.js compute_bins()'\n\tconst percentiles = target_percentiles(bc)\n\tconst summary = summaryfxn(percentiles)\n\tif (!summary || typeof summary !== 'object') throw 'invalid returned value by summaryfxn'\n\tbc.results = { summary }\n\tif (!bc.binLabelFormatter) bc.binLabelFormatter = getNumDecimalsFormatter(bc)\n\n\t// round the min and max values for use as bin start and stop\n\t// in the first and last bins, respectively\n\tconst minFloor = Math.floor(summary.min * 100) / 100\n\tconst maxCeil = Math.ceil(summary.max * 100) / 100\n\tconst min = bc.first_bin.startunbounded\n\t\t? minFloor\n\t\t: bc.first_bin.start_percentile\n\t\t? summary['p' + bc.first_bin.start_percentile]\n\t\t: bc.first_bin.start\n\tlet max = maxCeil, // in order to include the max value in the last bin\n\t\tlast_start,\n\t\tlast_stop\n\n\tif (bc.last_bin) {\n\t\tmax = bc.last_bin.stopunbounded\n\t\t\t? maxCeil // in order to include the max value in the last bin\n\t\t\t: bc.last_bin.stop_percentile\n\t\t\t? summary['p' + bc.last_bin.stop_percentile]\n\t\t\t: isNumeric(bc.last_bin.stop) && bc.last_bin.stop <= summary.max // '0.0088' < 0.0088\n\t\t\t? bc.last_bin.stop\n\t\t\t: maxCeil // in order to include the max value in the last bin\n\t\tlast_start = isStrictNumeric(bc.last_bin.start_percentile)\n\t\t\t? summary['p' + bc.last_bin.start_percentile]\n\t\t\t: isStrictNumeric(bc.last_bin.start)\n\t\t\t? bc.last_bin.start\n\t\t\t: undefined\n\t\tlast_stop = bc.last_bin.stopunbounded\n\t\t\t? null\n\t\t\t: bc.last_bin.stop_percentile\n\t\t\t? summary['p' + bc.last_bin.stop_percentile]\n\t\t\t: isStrictNumeric(bc.last_bin.stop)\n\t\t\t? bc.last_bin.stop\n\t\t\t: null\n\t} else if (bc.lst) {\n\t\tconst last_bin = bc.lst[bc.lst.length - 1]\n\t\tlast_start = last_bin.start\n\t\tlast_stop = 'stop' in last_bin && !last_bin.stopunbounded ? last_bin.stop : maxCeil\n\t\tmax = last_stop\n\t} else {\n\t\tlast_start = maxCeil\n\t\tlast_stop = maxCeil\n\t}\n\n\tconst numericMax = isStrictNumeric(max)\n\tconst numericLastStart = isStrictNumeric(last_start)\n\tconst numericLastStop = isStrictNumeric(last_stop)\n\n\tif (!numericMax && !numericLastStart) return [] //throw 'unable to compute the last bin start or stop'\n\n\tconst bins = []\n\tlet currBin = {\n\t\tstartunbounded: bc.first_bin.startunbounded,\n\t\tstart: bc.first_bin.startunbounded ? undefined : min,\n\t\tstop: isStrictNumeric(bc.first_bin.stop_percentile)\n\t\t\t? +summary['p' + bc.first_bin.stop_percentile]\n\t\t\t: isStrictNumeric(bc.first_bin.stop)\n\t\t\t? +bc.first_bin.stop\n\t\t\t: min + bc.bin_size,\n\t\tstartinclusive: bc.startinclusive,\n\t\tstopinclusive: bc.stopinclusive\n\t}\n\n\tif (!isStrictNumeric(currBin.stop)) throw 'the computed first_bin.stop is non-numeric' + currBin.stop\n\tconst maxNumBins = 100 // harcoded limit for now to not stress sqlite\n\n\twhile ((numericMax && currBin.stop <= max) || (currBin.startunbounded && !bins.length) || currBin.stopunbounded) {\n\t\tbins.push(currBin)\n\t\t// force a computed last bin to have stopunbounded true\n\t\tif (currBin.stop >= max) {\n\t\t\tcurrBin.stopunbounded = true\n\t\t\tif (bins.length > 1) {\n\t\t\t\tdelete currBin.stop\n\t\t\t}\n\t\t}\n\t\tcurrBin.label = get_bin_label(currBin, bc, valueConversion)\n\t\tif (currBin.stopunbounded) break\n\n\t\tconst upper = currBin.stop + bc.bin_size\n\t\tconst previousStop = currBin.stop\n\t\tcurrBin = {\n\t\t\tstartinclusive: bc.startinclusive,\n\t\t\tstopinclusive: bc.stopinclusive,\n\t\t\tstart: previousStop,\n\t\t\tstop:\n\t\t\t\tnumericLastStop && (previousStop == last_start || upper > last_stop)\n\t\t\t\t\t? last_stop\n\t\t\t\t\t: numericLastStart && upper > last_start && previousStop != last_start\n\t\t\t\t\t? last_start\n\t\t\t\t\t: upper\n\t\t}\n\n\t\tif (currBin.stop >= max) {\n\t\t\tcurrBin.stop = max\n\t\t\tif (bc.last_bin && bc.last_bin.stopunbounded) currBin.stopunbounded = 1\n\t\t\tif (bc.last_bin && bc.last_bin.stopinclusive) currBin.stopinclusive = 1\n\t\t}\n\t\tif (numericLastStart && currBin.start == last_start) {\n\t\t\tif (bc.last_bin && bc.last_bin.stopunbounded) currBin.stopunbounded = 1\n\t\t}\n\t\tif (currBin.start > currBin.stop) {\n\t\t\tif (numericLastStart && currBin.stop == last_start && bc.last_bin && bc.last_bin.stopunbounded)\n\t\t\t\tcurrBin.stopunbounded = true\n\t\t\telse break\n\t\t}\n\t\tif (bins.length + 1 >= maxNumBins) {\n\t\t\tbc.error = 'max_num_bins_reached'\n\t\t\tbreak\n\t\t}\n\t}\n\tdelete bc.binLabelFormatter\n\tif (bins.length > 1) {\n\t\tdelete bins[bins.length - 1].stop\n\t}\n\tconst k2c = getColors(bins.length) //to color bins\n\tfor (const bin of bins) bin.color = k2c(bin.label)\n\treturn bins\n}\n\nfunction getNumDecimalsFormatter(bc) {\n\t//return format('rounding' in bc ? bc.rounding : '')\n\treturn 'rounding' in bc ? format(bc.rounding) : d => d // default to labeling using the start/stop value as-is\n}\n\nexport function get_bin_label(bin, binconfig, valueConversion) {\n\t/*\n  Generate a numeric bin label given a bin configuration and an optional term valueConversion object\n*/\n\tif (!bin) return 'missing bin.label'\n\tif (bin.label) return bin.label\n\n\tconst bc = binconfig\n\tif (!bc.binLabelFormatter) bc.binLabelFormatter = getNumDecimalsFormatter(bc)\n\tif (!bin.startunbounded && !bin.stopunbounded && !('startinclusive' in bin) && !('stopinclusive' in bin)) {\n\t\tif (bc.startinclusive) bin.startinclusive = true\n\t\telse if (bc.stopinclusive) bin.stopinclusive = true\n\t}\n\n\tconst start = bc.use_as == 'bins' || bin.start\n\tconst stop = bc.use_as == 'bins' || bin.stop\n\n\tlet label_offset = 0\n\tif ('label_offset' in bc) {\n\t\tbc.label_offset_ignored = 'bin_size' in bc && bc.bin_size < bc.label_offset\n\t\tif (!bc.label_offset_ignored) label_offset = bc.label_offset\n\t} else if (bc.bin_size === 1 && bc.termtype == 'integer') {\n\t\tlabel_offset = 1\n\t}\n\n\t// one side-unbounded bins\n\t// label will be \">v\" or \"<v\"\n\tif (bin.startunbounded) {\n\t\tconst oper = bin.stopinclusive ? '\u2264' : '<' // \\u2264\n\t\tconst v1 = valueConversion\n\t\t\t? convertUnits(stop, valueConversion.fromUnit, valueConversion.toUnit, valueConversion.scaleFactor, true)\n\t\t\t: bc.binLabelFormatter(stop) //bin.startinclusive && label_offset ? stop - label_offset : stop)\n\t\treturn oper + v1\n\t}\n\t// a data value may coincide with the last bin's start\n\tif (bin.stopunbounded || start === stop) {\n\t\tconst oper = bin.startinclusive /*|| label_offset*/ ? '\u2265' : '>' // \\u2265\n\t\tconst v0 = valueConversion\n\t\t\t? convertUnits(start, valueConversion.fromUnit, valueConversion.toUnit, valueConversion.scaleFactor, true)\n\t\t\t: bc.binLabelFormatter(start) //bin.startinclusive || start == min ? start : start + label_offset)\n\t\treturn oper + v0\n\t}\n\n\t// two-sided bins\n\tif (label_offset && bin.startinclusive && !bin.stopinclusive) {\n\t\tif (Number.isInteger(bc.bin_size) && Math.abs(start - stop) === label_offset) {\n\t\t\t// make a simpler label when the range simply spans the bin_size\n\t\t\treturn (\n\t\t\t\t'' +\n\t\t\t\t(valueConversion\n\t\t\t\t\t? convertUnits(start, valueConversion.fromUnit, valueConversion.toUnit, valueConversion.scaleFactor, true)\n\t\t\t\t\t: bc.binLabelFormatter(start))\n\t\t\t)\n\t\t} else {\n\t\t\tconst v0 = valueConversion\n\t\t\t\t? convertUnits(start, valueConversion.fromUnit, valueConversion.toUnit, valueConversion.scaleFactor, true)\n\t\t\t\t: bc.binLabelFormatter(start)\n\t\t\tconst v1 = valueConversion\n\t\t\t\t? convertUnits(\n\t\t\t\t\t\tstop - label_offset,\n\t\t\t\t\t\tvalueConversion.fromUnit,\n\t\t\t\t\t\tvalueConversion.toUnit,\n\t\t\t\t\t\tvalueConversion.scaleFactor,\n\t\t\t\t\t\ttrue\n\t\t\t\t  )\n\t\t\t\t: bc.binLabelFormatter(stop - label_offset)\n\t\t\t// ensure that last two bin labels make sense (the last is stopunbounded)\n\t\t\treturn +v0 >= +v1 ? v0.toString() : v0 + ' to ' + v1\n\t\t}\n\t} else {\n\t\t// stop_inclusive || label_offset == 0\n\t\tconst oper0 = bin.startinclusive ? '' : '>'\n\t\tconst oper1 = bin.stopinclusive ? '' : '<'\n\t\tconst v0 = valueConversion\n\t\t\t? convertUnits(start, valueConversion.fromUnit, valueConversion.toUnit, valueConversion.scaleFactor, true)\n\t\t\t: Number.isInteger(start)\n\t\t\t? start\n\t\t\t: bc.binLabelFormatter(start)\n\t\tconst v1 = valueConversion\n\t\t\t? convertUnits(stop, valueConversion.fromUnit, valueConversion.toUnit, valueConversion.scaleFactor, true)\n\t\t\t: Number.isInteger(stop)\n\t\t\t? stop\n\t\t\t: bc.binLabelFormatter(stop)\n\t\t// after rounding the bin labels, the bin start may equal the last bin stop as derived from actual data\n\t\tif (+v0 >= +v1) {\n\t\t\tconst oper = bin.startinclusive ? '\u2265' : '>' // \\u2265\n\t\t\treturn oper + v0\n\t\t} else {\n\t\t\treturn oper0 + v0 + ' to ' + oper1 + v1\n\t\t}\n\t}\n}\n\n// get bin range equation from bin label and bin properties\nexport function get_bin_range_equation(bin, binconfig) {\n\tconst x = '<span style=\"font-family:Times;font-style:italic;\">x</span>'\n\tlet range_eq\n\t// should always use computed (not user-customized) bin label to determine bin range text\n\tconst copy = structuredClone(bin)\n\tcopy.label = '' // mutate only the copy, and not the original bin argument\n\tconst bin_label = get_bin_label(copy, binconfig)\n\tif (bin.startunbounded || bin.stopunbounded) {\n\t\t// first or last bins, e.g. x \u2264 14 and x > 16\n\t\trange_eq = x + ' ' + bin_label\n\t} else if (bin.startinclusive) {\n\t\t// bins with startinclusive, e.g. 14 \u2264 x < 16\n\t\trange_eq = bin_label.replace('to <', '\u2264 ' + x + ' <')\n\t} else if (bin.stopinclusive) {\n\t\t// bins with stopinclusive, e.g. 14 < x \u2264 16\n\t\trange_eq = bin_label.replace('>', '').replace('to', '< ' + x + ' \u2264')\n\t}\n\treturn range_eq\n}\n\nexport function target_percentiles(binconfig) {\n\tconst percentiles = []\n\tconst f = binconfig.first_bin\n\tif (f && isStrictNumeric(f.start_percentile)) percentiles.push(f.start_percentile)\n\tif (f && isStrictNumeric(f.stop_percentile)) percentiles.push(f.stop_percentile)\n\tconst l = binconfig.last_bin\n\tif (l && isStrictNumeric(l.start_percentile)) percentiles.push(l.start_percentile)\n\tif (l && isStrictNumeric(l.stop_percentile)) percentiles.push(l.stop_percentile)\n\treturn percentiles\n}\n"],
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