@sjcrh/proteinpaint-client 2.181.0 → 2.183.0

package/dist/chunk-A2Y3GEUH.js

@@ -1,228 +0,0 @@
-import {
-  appInit
-} from "./chunk-SK7YVOQN.js";
-import {
-  getDefaultViolinSettings
-} from "./chunk-TVXESYIR.js";
-import {
-  select_default
-} from "./chunk-NDWTN4U5.js";
-
-// plots/regression.inputs.values.table.js
-var row_hover_bgcolor = "#fff6dc";
-var InputValuesTable = class {
-  constructor(opts) {
-    this.opts = opts;
-    this.input = opts.input;
-    setRenderers(this);
-    this.setDOM(opts.holder);
-  }
-  main() {
-    try {
-      const term = this.input.term;
-      if (!term || !this.input.termStatus) {
-        this.dom.holder.style("display", "none");
-        this.dom.loading_div.style("display", "none");
-        return;
-      } else if (term) {
-        this.dom.holder.style("display", "block");
-        this.dom.loading_div.style("display", "block");
-        this.updateValueCount();
-        this.dom.loading_div.style("display", "none");
-        this.render();
-        return;
-      }
-    } catch (e) {
-      this.dom.loading_div.style("display", "none");
-      throw e;
-    }
-  }
-  updateValueCount() {
-    const i = this.input;
-    try {
-      if (i.pill && i.pill.validateQ) {
-        i.pill.validateQ({
-          term: i.term.term,
-          q: i.term.q,
-          sampleCounts: i.termStatus.sampleCounts
-        });
-      }
-    } catch (e) {
-      i.term.error = e;
-    }
-  }
-};
-function setRenderers(self) {
-  self.setDOM = (holder) => {
-    self.dom = {
-      holder: holder.style("margin", "10px").style("font-size", ".8em").style("text-align", "left").style("color", "#999"),
-      loading_div: holder.append("div").text("Loading..").style("display", "none"),
-      top_info_div: holder.append("div").style("padding-bottom", "5px"),
-      violin_div: holder.append("div").style("color", "black").style("padding-top", "5px"),
-      table_div: holder.append("table").style("margin", "5px 0px 15px 0px").style("border-collapse", "collapse").style("color", "black"),
-      bottom_info_div: holder.append("div"),
-      excluded_div: holder.append("table").style("display", "none").style("margin", "5px 10px").style("border-collapse", "collapse")
-    };
-  };
-  self.render = async () => {
-    const input = self.input;
-    renderTopInfo(input);
-    await renderValuesTable(input);
-    renderBottomInfo(input);
-    renderExcludedValues(input);
-  };
-  function renderTopInfo(input) {
-    if (input.termStatus.topInfoStatus?.length) {
-      self.dom.top_info_div.style("display", "block").html(input.termStatus.topInfoStatus.join("<br>"));
-    } else {
-      self.dom.top_info_div.style("display", "none");
-    }
-  }
-  async function renderValuesTable(input) {
-    if (input.term.q.mode == "continuous" || input.term.q.mode == "spline") {
-      self.dom.violin_div.style("display", "block");
-      self.dom.table_div.style("display", "none");
-      if (self.plotAppApi) {
-        const action = {
-          type: "app_refresh",
-          state: {
-            termfilter: {
-              filter: self.input.parent.parent.filter
-            }
-          },
-          subactions: [
-            {
-              type: "plot_edit",
-              id: self.violinApi.id,
-              config: {
-                term: input.term
-              }
-            }
-          ]
-        };
-        self.plotAppApi.dispatch(action);
-      } else {
-        const opts = {
-          holder: self.dom.violin_div,
-          vocabApi: self.input.parent.app.vocabApi,
-          state: {
-            vocab: {
-              genome: self.input.parent.app.vocabApi.genome,
-              dslabel: self.input.parent.app.vocabApi.dslabel
-            },
-            termfilter: {
-              filter: self.input.parent.parent.filter
-            },
-            plots: [
-              {
-                chartType: "violin",
-                term: input.term,
-                settings: {
-                  violin: getDefaultViolinSettings(null, {
-                    svgw: 350,
-                    axisHeight: 25,
-                    rightMargin: 10,
-                    datasymbol: "rug",
-                    radius: 8,
-                    plotThickness: 80
-                  })
-                }
-              }
-            ]
-          },
-          // global options for plotAppApi
-          // opts.violin will apply to all violin plots within the plotApp
-          // rx will pass options by component type, which are not tracked in state
-          // examples are callbacks, event listeners, etc
-          violin: {
-            mode: "minimal"
-          }
-        };
-        self.plotAppApi = await appInit(opts);
-        const plotId = self.plotAppApi.getState().plots[0].id;
-        self.violinApi = self.plotAppApi.getComponents(`plots.${plotId}`);
-      }
-    } else {
-      self.dom.violin_div.style("display", "none");
-      const data = input.termStatus.sampleCounts;
-      if (!data || !data.length) {
-        self.dom.table_div.style("display", "none");
-        return;
-      }
-      self.dom.table_div.style("display", "block");
-      const l = self.input.orderedLabels;
-      const sortFxn = l && l.length ? (a, b) => l.indexOf(a.label) - l.indexOf(b.label) : (a, b) => b.samplecount - a.samplecount;
-      const tr_data = data.sort(sortFxn);
-      const maxCount = Math.max(...tr_data.map((v) => v.samplecount), 0);
-      tr_data.forEach((v) => v.bar_width_frac = Number((1 - (maxCount - v.samplecount) / maxCount).toFixed(4)));
-      self.dom.table_div.selectAll("tr").remove();
-      const trs = self.dom.table_div.selectAll("tr").data(tr_data, (b) => b.key);
-      trs.enter().append("tr").each(trEnter);
-    }
-  }
-  function renderBottomInfo(input) {
-    if (input.termStatus.bottomSummaryStatus) {
-      self.dom.bottom_info_div.style("display", "block").html(input.termStatus.bottomSummaryStatus);
-    } else {
-      self.dom.bottom_info_div.style("display", "none");
-    }
-  }
-  function renderExcludedValues(input) {
-    const data = input.termStatus.excludeCounts;
-    if (!data || !data.length) {
-      self.dom.excluded_div.style("display", "none");
-      return;
-    }
-    self.dom.excluded_div.style("display", "block").selectAll("tr").remove();
-    const trs = self.dom.excluded_div.selectAll("tr").data(data, (b) => b.key);
-    trs.enter().append("tr").each(trEnter);
-    self.dom.excluded_div.selectAll("td").style("color", "#999");
-  }
-  function trEnter(item) {
-    const tr = select_default(this);
-    const input = this.parentNode.__data__;
-    const t = input.term;
-    const maxBarWidth = 150;
-    tr.style("text-align", "left").style("cursor", input.termStatus.allowToSelectRefGrp ? "pointer" : "default");
-    const tdSpacing = "1px 10px 1px 0px";
-    tr.append("td").style("padding", tdSpacing).style("text-align", "left").style("color", "black").text(item.samplecount !== void 0 ? "n=" + item.samplecount : "");
-    tr.append("td").style("padding", tdSpacing).style("text-align", "left").style("color", "black").text(item.label);
-    const bar_td = tr.append("td").style("padding", tdSpacing);
-    const barWidth = maxBarWidth * item.bar_width_frac;
-    bar_td.append("div").style("margin", tdSpacing).style("width", barWidth + "px").style("height", "15px").style("background-color", "#ddd");
-    addTrBehavior({ input, item, tr, rendered: false });
-  }
-  function addTrBehavior({ input, item, tr, rendered }) {
-    if (!item.bar_width_frac) return;
-    const t = input.term;
-    const hover_flag = input.termStatus.allowToSelectRefGrp;
-    let ref_text;
-    if (rendered) {
-      tr.style("background", "white");
-      ref_text = select_default(tr.node().lastChild).select("div").style("display", item.key === t.refGrp && hover_flag ? "inline-block" : "none").style("border", item.key === t.refGrp && hover_flag ? "1px solid #bbb" : "");
-    } else if (input.term.q.mode != "cutoff") {
-      const reference_td = tr.append("td").style("padding", "1px 5px").style("text-align", "left");
-      ref_text = reference_td.append("div").style("display", item.key === t.refGrp && hover_flag ? "inline-block" : "none").style("padding", "2px 10px").style("border", item.key === t.refGrp && hover_flag ? "1px solid #bbb" : "").style("border-radius", "10px").style("color", "#999").style("font-size", ".7em").text("REFERENCE");
-      if (hover_flag) {
-        tr.on("mouseover", () => {
-          if (t.refGrp !== item.key) {
-            tr.style("background", row_hover_bgcolor);
-            ref_text.style("display", "inline-block").style("border", "").text("Set as reference");
-          } else tr.style("background", "white");
-        }).on("mouseout", () => {
-          tr.style("background", "white");
-          if (t.refGrp !== item.key) ref_text.style("display", "none");
-        }).on("click", () => {
-          t.refGrp = item.key;
-          ref_text.style("border", "1px solid #bbb").text("REFERENCE");
-          self.opts.callback(t);
-        });
-      }
-    }
-  }
-}
-
-export {
-  InputValuesTable
-};
-//# sourceMappingURL=chunk-A2Y3GEUH.js.map

package/dist/chunk-AAEXTQT3.js

@@ -1,330 +0,0 @@
-import {
-  getColors
-} from "./chunk-ZLH4PJKX.js";
-import {
-  convertUnits,
-  isNumeric,
-  isStrictNumeric
-} from "./chunk-TV74I3Y5.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-AAEXTQT3.js.map