@sjcrh/proteinpaint-client 2.190.2 → 2.191.2

package/dist/chunk-Y2Z4XDHA.js

@@ -1,170 +0,0 @@
-import {
-  getEmptyCell,
-  maySetEmptyCell,
-  setCellProps
-} from "./chunk-QWOZ2QDM.js";
-import {
-  TermTypeGroups
-} from "./chunk-EBKERML3.js";
-import {
-  __export
-} from "./chunk-HFNDKYVF.js";
-
-// plots/matrix/matrix.serieses.js
-var matrix_serieses_exports = {};
-__export(matrix_serieses_exports, {
-  getSerieses: () => getSerieses
-});
-function getSerieses(data) {
-  const s = this.settings.matrix;
-  const serieses = [];
-  const { colw, dx, dy, xMin, xMax } = this.dimensions;
-  const dvt = this.config.divideBy || {};
-  const divideByTermId = "id" in dvt ? dvt.id : dvt.name;
-  const legendGroups = {};
-  this.colorScaleByTermId = {};
-  for (const t of this.termOrder) {
-    const $id = t.tw.$id;
-    const termid = "id" in t.tw.term ? t.tw.term.id : t.tw.term.name;
-    const isDivideByTerm = termid === divideByTermId;
-    const emptyGridCells = [];
-    const cellht = t.grp.type == "hierCluster" ? s.clusterRowh : dy;
-    const htAdjust = t.grp.type == "hierCluster" ? 0 : t.totalHtAdjustments;
-    const y = s.transpose ? 0 : t.totalIndex * cellht + t.visibleGrpIndex * s.rowgspace + htAdjust;
-    const twSpecificSettings = this.config.settings.matrix.twSpecificSettings;
-    const hoverY0 = (twSpecificSettings[$id]?.contBarGap || 0) + y;
-    const series = {
-      t,
-      tw: t.tw,
-      cells: [],
-      y,
-      hoverY0,
-      hoverY1: hoverY0 + (twSpecificSettings[$id]?.contBarH || cellht)
-    };
-    for (const so of this.unfilteredSampleOrder) {
-      const { totalIndex, grpIndex, row } = so;
-      series.x = !s.transpose ? 0 : t.totalIndex * dx + t.visibleGrpIndex * s.colgspace;
-      const anno = row[$id];
-      const cellTemplate = {
-        s: so,
-        sample: row.sample,
-        tw: t.tw,
-        term: t.tw.term,
-        termid,
-        $id,
-        totalIndex,
-        grpIndex,
-        row,
-        t,
-        seriesY: y
-      };
-      if (!anno) {
-        if (!so.grp.isExcluded && (s.useCanvas || so.grp)) {
-          const cell = getEmptyCell(cellTemplate, s, this.dimensions);
-          series.cells.push(cell);
-        }
-        continue;
-      }
-      const key = anno.key;
-      const values = anno.filteredValues || anno.values || [anno.value];
-      const numRects = s.cellEncoding == "oncoprint" ? 1 : values.length;
-      const height = !s.transpose ? s.rowh / numRects : colw;
-      const width = !s.transpose ? colw : colw / values.length;
-      const siblingCells = [];
-      if (!anno || !anno.renderedValues?.length) {
-        if (!so.grp.isExcluded && (s.useCanvas || so.grp)) {
-          const cell = getEmptyCell(cellTemplate, s, this.dimensions);
-          series.cells.push(cell);
-        }
-        continue;
-      }
-      for (const [i, value] of values.entries()) {
-        const cell = Object.assign({ key, siblingCells }, cellTemplate);
-        cell.valueIndex = i;
-        let legend;
-        if (typeof t.tw.setCellProps == "function") {
-          legend = t.tw.setCellProps(cell, anno, value, s, t, this, width, height, dx, dy, i);
-        } else {
-          const cellProps = t.grp.type == "hierCluster" ? setCellProps["hierCluster"] : t.tw.term.type == "samplelst" ? setCellProps["categorical"] : setCellProps[t.tw.term.type];
-          legend = cellProps(cell, t.tw, anno, value, s, t, this, width, height, dx, dy, i);
-        }
-        if (!s.useCanvas && (cell.x + cell.width < xMin || cell.x - cell.width > xMax)) continue;
-        if (legend) {
-          for (const l of [legendGroups, so.grp.legendGroups]) {
-            if (!l) continue;
-            if (!l[legend.group]) {
-              l[legend.group] = {
-                ref: legend.ref,
-                values: {},
-                order: legend.order,
-                $id,
-                origin: legend.entry.origin
-              };
-              if (legend.entry.dt) l[legend.group].dt = [legend.entry.dt];
-            }
-            const lg = l[legend.group];
-            if (lg.dt && !lg.dt.includes(legend.entry.dt)) lg.dt.push(legend.entry.dt);
-            const legendK = legend.entry.origin ? legend.entry.origin + legend.value : legend.value;
-            if (!lg.values[legendK]) {
-              lg.values[legendK] = JSON.parse(JSON.stringify(legend.entry));
-              if (legend.entry.scale) lg.values[legendK].scale = legend.entry.scale;
-            }
-            if (!lg.values[legendK].samples) lg.values[legendK].samples = /* @__PURE__ */ new Set();
-            if (t.tw.term.name === TermTypeGroups.MUTATION_SIGNATURE) {
-              if (value?.value > 0) lg.values[legendK].samples.add(row.sample);
-            } else lg.values[legendK].samples.add(row.sample);
-            if (isDivideByTerm) {
-              lg.values[legend.value].isExcluded = so.grp.isExcluded;
-            }
-          }
-        }
-        if (!so.grp.isExcluded) {
-          if (anno.renderedValues.includes(value)) series.cells.push(cell);
-          siblingCells.push(cell);
-        }
-      }
-      if (s.showGrid == "rect" && !so.grp.isExcluded) {
-        const cell = t.grp.type == "hierCluster" ? getEmptyCell(cellTemplate, s, this.dimensions) : maySetEmptyCell[t.tw.term.type]?.(siblingCells, cellTemplate, s, this.dimensions, this);
-        if (cell) emptyGridCells.push(cell);
-      }
-    }
-    if (emptyGridCells.length) series.cells.unshift(...emptyGridCells);
-    if (series.cells.length) serieses.push(series);
-  }
-  addAllHiddenLegendGroups(legendGroups, this);
-  this.legendData = this.getLegendData(legendGroups, data.refs, this);
-  for (const grp of this.sampleGroups) {
-    grp.legendData = this.getLegendData(grp.legendGroups, data.refs, this);
-  }
-  return serieses;
-}
-function addAllHiddenLegendGroups(legendGroups, self) {
-  for (const valueFilter of self.config.legendValueFilter.lst) {
-    if (valueFilter.tvs.term.type == "categorical" && !legendGroups[valueFilter.tvs.term.$id]) {
-      legendGroups[valueFilter.tvs.term.$id] = {
-        ref: {},
-        values: {},
-        $id: valueFilter.tvs.term.$id
-      };
-    } else if (valueFilter.tvs.term.type == "geneVariant" && !legendGroups[valueFilter.legendGrpName]) {
-      legendGroups[valueFilter.legendGrpName] = {
-        ref: {},
-        values: {},
-        dt: [valueFilter.tvs.values[0].dt],
-        origin: valueFilter.tvs.values[0].origin
-      };
-    } else if ((valueFilter.tvs.term.type == "integer" || valueFilter.tvs.term.type == "float") && !legendGroups[valueFilter.tvs.term.$id]) {
-      legendGroups[valueFilter.tvs.term.$id] = {
-        ref: {},
-        values: {},
-        $id: valueFilter.tvs.term.$id
-      };
-    }
-  }
-}
-
-export {
-  getSerieses,
-  matrix_serieses_exports
-};
-//# sourceMappingURL=chunk-Y2Z4XDHA.js.map

package/dist/chunk-YFKJ2TMX.js

@@ -1,194 +0,0 @@
-import {
-  sample_match_termvaluesetting
-} from "./chunk-X27TRPIZ.js";
-import {
-  isDictionaryType
-} from "./chunk-XOCO3LVN.js";
-import {
-  __export
-} from "./chunk-HFNDKYVF.js";
-
-// plots/matrix/matrix.data.js
-var matrix_data_exports = {};
-__export(matrix_data_exports, {
-  applyLegendValueFilter: () => applyLegendValueFilter,
-  getMatrixRequestOpts: () => getMatrixRequestOpts,
-  mayRequireToken: () => mayRequireToken,
-  setData: () => setData
-});
-function mayRequireToken(tokenMessage = "") {
-  const message = tokenMessage || this.state.tokenVerificationMessage;
-  if (!message && this.state.hasVerifiedToken) {
-    this.dom.errdiv.style("display", "none").html();
-    this.dom.controls.style("display", this.opts.controls ? "inline-block" : "");
-    this.dom.svg.style("display", "");
-    return false;
-  } else {
-    this.dom.errdiv.style("display", "").html(message || "Requires login");
-    this.dom.controls.style("display", "none");
-    this.dom.svg.style("display", "none");
-    return true;
-  }
-}
-function getMatrixRequestOpts(state, config) {
-  const terms = [];
-  const termgroups = this.chartType == "hierCluster" ? config.termgroups.filter((grp) => grp.type != "hierCluster") : config.termgroups;
-  for (const grp of termgroups) {
-    terms.push(...getNormalizedTwLstCopy(grp.lst));
-  }
-  if (config.divideBy) terms.push(normalizeTwForRequest(structuredClone(config.divideBy)));
-  const opts = {
-    terms,
-    filter: state.filter,
-    filter0: state.filter0,
-    maxGenes: state.config.settings.matrix.maxGenes,
-    /*********** quick fix
-    when the flag is true, set artificially large number to ensure all genes are sent in one query
-    this avoids changing getAnnotatedSampleData()
-    additional non-matrix app that calls getAnnotatedSampleData will NEED THE SAME FIX
-    */
-    termsPerRequest: this.app.vocabApi.termdbConfig.queries?.snvindel?.byisoform?.processTwsInOneQuery ? 1e3 : 1
-  };
-  if (this.chartType == "hierCluster") {
-    opts.isHierCluster = 1;
-  }
-  return opts;
-}
-function getNormalizedTwLstCopy(twlst) {
-  const lst = [];
-  for (const tw of twlst) {
-    if (tw.type && tw.constructor.name != "Object") lst.push(tw);
-    else lst.push(normalizeTwForRequest(tw));
-  }
-  lst.forEach(normalizeTwForRequest);
-  lst.sort(sortTwLst);
-  return lst;
-}
-function normalizeTwForRequest(_tw) {
-  const tw = structuredClone(_tw);
-  if (!tw?.term) return;
-  delete tw.term.category2samplecount;
-  if (isDictionaryType(tw.term.type) && tw.term.type !== "samplelst") delete tw.term.values;
-  return tw;
-}
-function sortTwLst(twa, twb) {
-  const a = twa?.$id || twa.term?.id || twa?.term?.name;
-  const b = twb?.$id || twb.term?.id || twb?.term?.name;
-  return a < b ? -1 : 1;
-}
-async function setData(_data) {
-  const opts = this.currRequestOpts?.matrix || this.getMatrixRequestOpts(this.state, this.config);
-  this.numTerms = opts.terms.length;
-  opts.loadingDiv = this.chartType != "hierCluster" && this.dom.loadingDiv;
-  opts.signal = this.api.getAbortSignal();
-  const data = await this.app.vocabApi.getAnnotatedSampleData(opts, _data);
-  this.data = data;
-  this.origData = structuredClone(this.data);
-  this.sampleIdMap = {};
-  for (const d of this.data.lst) {
-    this.sampleIdMap[d.sample] = d._ref_.label;
-  }
-}
-function applyLegendValueFilter() {
-  const self = this;
-  if (!self.config.legendValueFilter.lst.length && !self.config.legendGrpFilter.lst.length) return;
-  for (const grpFilter of self.config.legendGrpFilter.lst) {
-    if (grpFilter.dt) {
-      const filteredOutCats = /* @__PURE__ */ new Set();
-      for (const oneSampleData of self.origData.lst) {
-        for (const annoForOneTerm of Object.values(oneSampleData)) {
-          if (annoForOneTerm.values) {
-            const newValues = [];
-            for (const v of annoForOneTerm.values) {
-              if (!(grpFilter.dt.includes(v.dt) && (!grpFilter.origin || v.origin == grpFilter.origin))) {
-                newValues.push(v);
-              } else {
-                filteredOutCats.add(v.class);
-              }
-            }
-            annoForOneTerm.values = newValues;
-          }
-        }
-      }
-      grpFilter.filteredOutCats = [...filteredOutCats];
-      for (const oneSampleData of Object.values(self.origData.samples)) {
-        for (const annoForOneTerm of Object.values(oneSampleData)) {
-          if (annoForOneTerm.values)
-            annoForOneTerm.values = annoForOneTerm.values.filter(
-              (v) => !(grpFilter.dt.includes(v.dt) && (!grpFilter.origin || v.origin == grpFilter.origin))
-            );
-        }
-      }
-    }
-  }
-  const geneVariant$ids = Object.values(self.data.refs.byTermId).filter((v) => v.term?.type == "geneVariant").map((v) => v.$id);
-  const data = { samples: {}, lst: [], refs: self.data.refs };
-  const onlyHardFilter = structuredClone(self.config.legendValueFilter);
-  onlyHardFilter.lst = onlyHardFilter.lst.filter(
-    (l) => !l.tvs.legendFilterType || l.tvs.legendFilterType !== "geneVariant_soft"
-  );
-  for (const row of self.origData.lst) {
-    const include = sample_match_termvaluesetting(row, onlyHardFilter, geneVariant$ids);
-    if (include || self.chartType == "hierCluster") {
-      data.samples[row.sample] = row;
-      data.lst.push(row);
-    }
-  }
-  for (const valFilter of self.config.legendValueFilter.lst) {
-    if (valFilter.tvs.legendFilterType !== "geneVariant_soft") continue;
-    const tvsV = valFilter.tvs.values[0];
-    const filteredOutCats = /* @__PURE__ */ new Set();
-    for (const oneSampleData of data.lst) {
-      for (const annoForOneTerm of Object.values(oneSampleData)) {
-        if (annoForOneTerm.values) {
-          const newValues = [];
-          for (const v of annoForOneTerm.values) {
-            if (!(v.dt == tvsV.dt && (!tvsV.origin || v.origin == tvsV.origin) && tvsV.mclasslst.includes(v.class))) {
-              newValues.push(v);
-            } else {
-              filteredOutCats.add(v.class);
-            }
-          }
-          annoForOneTerm.values = newValues;
-        }
-      }
-    }
-    valFilter.filteredOutCats = [...filteredOutCats];
-    for (const oneSampleData of Object.values(data.samples)) {
-      for (const annoForOneTerm of Object.values(oneSampleData)) {
-        if (annoForOneTerm.values)
-          annoForOneTerm.values = annoForOneTerm.values.filter(
-            (v) => !(v.dt == tvsV.dt && (!tvsV.origin || v.origin == tvsV.origin) && tvsV.mclasslst.includes(v.class))
-          );
-      }
-    }
-  }
-  if (self.chartType !== "hierCluster" && geneVariant$ids.length && self.app.vocabApi.vocab?.dslabel == "GDC")
-    remove_empty_sample(data, geneVariant$ids);
-  self.data = data;
-}
-function remove_empty_sample(data) {
-  for (const oneSampleData of data.lst) {
-    let removeSample = true;
-    for (const [key, annoForOneTerm] of Object.entries(oneSampleData)) {
-      if (!annoForOneTerm.values) continue;
-      const annoType = data.refs.byTermId[key].term.type;
-      if (annoType != "geneVariant") continue;
-      if (annoForOneTerm.values.length) removeSample = false;
-    }
-    if (removeSample) {
-      data.lst = data.lst.filter((dl) => dl.sample !== oneSampleData.sample);
-      delete data.samples[parseInt(oneSampleData.sample)];
-    }
-  }
-  return data;
-}
-
-export {
-  mayRequireToken,
-  getMatrixRequestOpts,
-  setData,
-  applyLegendValueFilter,
-  matrix_data_exports
-};
-//# sourceMappingURL=chunk-YFKJ2TMX.js.map

package/dist/chunk-YPVFTNLG.js

@@ -1,228 +0,0 @@
-import {
-  appInit
-} from "./chunk-TRY57CMI.js";
-import {
-  getDefaultViolinSettings
-} from "./chunk-XUFWJJM5.js";
-import {
-  select_default
-} from "./chunk-I6Y4O3RR.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-YPVFTNLG.js.map

package/dist/chunk-YPVFTNLG.js.map

@@ -1,7 +0,0 @@
-{
-  "version": 3,
-  "sources": ["../plots/regression.inputs.values.table.js"],
-  "sourcesContent": ["import { select } from 'd3-selection'\nimport { getDefaultViolinSettings } from './violin.js'\nimport { appInit } from './plot.app'\n\n/*\n\tdom elements for values table\n\tholder // main holder\n\t\tloading_div // loading message while updating term info\n\t\ttop_info_div // top info about scale + knots + promopt to select ref group\n\t\tviolin_div // violin plot of values (used when .mode=continuous)\n\t\ttable_div // tabular bar chart of values (used when .mode != continuous)\n\t\tbottom_info_div // total included and excluded samples\n\t\texcluded_div // excluded values with samplecount\n*/\n\nconst row_hover_bgcolor = '#fff6dc'\n\nexport class InputValuesTable {\n\tconstructor(opts) {\n\t\t// opts {holder, input, callback}\n\t\tthis.opts = opts\n\t\tthis.input = opts.input\n\t\tsetRenderers(this)\n\t\tthis.setDOM(opts.holder)\n\t}\n\n\tmain() {\n\t\ttry {\n\t\t\tconst term = this.input.term\n\t\t\t// may allow the values table even if there is a variable error,\n\t\t\t// in case it helps clarify the error message such as having\n\t\t\t// not exactly two samplecount bars available for a binary outcome term\n\n\t\t\tif (!term || !this.input.termStatus) {\n\t\t\t\tthis.dom.holder.style('display', 'none')\n\t\t\t\tthis.dom.loading_div.style('display', 'none')\n\t\t\t\treturn\n\t\t\t} else if (term) {\n\t\t\t\tthis.dom.holder.style('display', 'block')\n\t\t\t\tthis.dom.loading_div.style('display', 'block')\n\t\t\t\tthis.updateValueCount()\n\t\t\t\tthis.dom.loading_div.style('display', 'none')\n\t\t\t\tthis.render()\n\t\t\t\treturn\n\t\t\t}\n\t\t} catch (e) {\n\t\t\tthis.dom.loading_div.style('display', 'none')\n\t\t\tthrow e\n\t\t}\n\t}\n\n\tupdateValueCount() {\n\t\tconst i = this.input\n\t\ttry {\n\t\t\t/* TODO: may need to move validateQ out of a ts.pill */\n\t\t\tif (i.pill && i.pill.validateQ) {\n\t\t\t\ti.pill.validateQ({\n\t\t\t\t\tterm: i.term.term,\n\t\t\t\t\tq: i.term.q,\n\t\t\t\t\tsampleCounts: i.termStatus.sampleCounts\n\t\t\t\t})\n\t\t\t}\n\t\t} catch (e) {\n\t\t\ti.term.error = e\n\t\t}\n\t}\n}\n\nfunction setRenderers(self) {\n\tself.setDOM = holder => {\n\t\tself.dom = {\n\t\t\tholder: holder\n\t\t\t\t.style('margin', '10px')\n\t\t\t\t.style('font-size', '.8em')\n\t\t\t\t.style('text-align', 'left')\n\t\t\t\t.style('color', '#999'),\n\n\t\t\tloading_div: holder.append('div').text('Loading..').style('display', 'none'),\n\n\t\t\ttop_info_div: holder.append('div').style('padding-bottom', '5px'),\n\n\t\t\tviolin_div: holder.append('div').style('color', 'black').style('padding-top', '5px'),\n\n\t\t\ttable_div: holder\n\t\t\t\t.append('table')\n\t\t\t\t.style('margin', '5px 0px 15px 0px')\n\t\t\t\t.style('border-collapse', 'collapse')\n\t\t\t\t.style('color', 'black'),\n\n\t\t\tbottom_info_div: holder.append('div'),\n\n\t\t\texcluded_div: holder\n\t\t\t\t.append('table')\n\t\t\t\t.style('display', 'none')\n\t\t\t\t.style('margin', '5px 10px')\n\t\t\t\t.style('border-collapse', 'collapse')\n\t\t}\n\t}\n\n\tself.render = async () => {\n\t\tconst input = self.input\n\n\t\t// render top info\n\t\trenderTopInfo(input)\n\n\t\t// render included values\n\t\tawait renderValuesTable(input)\n\n\t\t// render bottom info\n\t\trenderBottomInfo(input)\n\n\t\t// render excluded values\n\t\trenderExcludedValues(input)\n\t}\n\n\tfunction renderTopInfo(input) {\n\t\tif (input.termStatus.topInfoStatus?.length) {\n\t\t\tself.dom.top_info_div.style('display', 'block').html(input.termStatus.topInfoStatus.join('<br>'))\n\t\t} else {\n\t\t\tself.dom.top_info_div.style('display', 'none')\n\t\t}\n\t}\n\n\tasync function renderValuesTable(input) {\n\t\tif (input.term.q.mode == 'continuous' || input.term.q.mode == 'spline') {\n\t\t\t// continuous or spline mode\n\t\t\t// render values as violin plot\n\t\t\tself.dom.violin_div.style('display', 'block')\n\t\t\tself.dom.table_div.style('display', 'none')\n\t\t\tif (self.plotAppApi) {\n\t\t\t\t// violin plot already created, refresh the plot\n\t\t\t\tconst action = {\n\t\t\t\t\ttype: 'app_refresh',\n\t\t\t\t\tstate: {\n\t\t\t\t\t\ttermfilter: {\n\t\t\t\t\t\t\tfilter: self.input.parent.parent.filter\n\t\t\t\t\t\t}\n\t\t\t\t\t},\n\t\t\t\t\tsubactions: [\n\t\t\t\t\t\t{\n\t\t\t\t\t\t\ttype: 'plot_edit',\n\t\t\t\t\t\t\tid: self.violinApi.id,\n\t\t\t\t\t\t\tconfig: {\n\t\t\t\t\t\t\t\tterm: input.term\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t}\n\t\t\t\t\t]\n\t\t\t\t}\n\t\t\t\tself.plotAppApi.dispatch(action)\n\t\t\t} else {\n\t\t\t\t// violin plot does not exist, create the plot\n\t\t\t\tconst opts = {\n\t\t\t\t\tholder: self.dom.violin_div,\n\t\t\t\t\tvocabApi: self.input.parent.app.vocabApi,\n\t\t\t\t\tstate: {\n\t\t\t\t\t\tvocab: {\n\t\t\t\t\t\t\tgenome: self.input.parent.app.vocabApi.genome,\n\t\t\t\t\t\t\tdslabel: self.input.parent.app.vocabApi.dslabel\n\t\t\t\t\t\t},\n\t\t\t\t\t\ttermfilter: {\n\t\t\t\t\t\t\tfilter: self.input.parent.parent.filter\n\t\t\t\t\t\t},\n\t\t\t\t\t\tplots: [\n\t\t\t\t\t\t\t{\n\t\t\t\t\t\t\t\tchartType: 'violin',\n\t\t\t\t\t\t\t\tterm: input.term,\n\t\t\t\t\t\t\t\tsettings: {\n\t\t\t\t\t\t\t\t\tviolin: getDefaultViolinSettings(null, {\n\t\t\t\t\t\t\t\t\t\tsvgw: 350,\n\t\t\t\t\t\t\t\t\t\taxisHeight: 25,\n\t\t\t\t\t\t\t\t\t\trightMargin: 10,\n\t\t\t\t\t\t\t\t\t\tdatasymbol: 'rug',\n\t\t\t\t\t\t\t\t\t\tradius: 8,\n\t\t\t\t\t\t\t\t\t\tplotThickness: 80\n\t\t\t\t\t\t\t\t\t})\n\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t]\n\t\t\t\t\t},\n\t\t\t\t\t// global options for plotAppApi\n\t\t\t\t\t// opts.violin will apply to all violin plots within the plotApp\n\t\t\t\t\t// rx will pass options by component type, which are not tracked in state\n\t\t\t\t\t// examples are callbacks, event listeners, etc\n\t\t\t\t\tviolin: {\n\t\t\t\t\t\tmode: 'minimal'\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t\tself.plotAppApi = await appInit(opts)\n\t\t\t\tconst plotId = self.plotAppApi.getState().plots[0].id\n\t\t\t\tself.violinApi = self.plotAppApi.getComponents(`plots.${plotId}`)\n\t\t\t}\n\t\t} else {\n\t\t\t// mode is neither continuous nor spline\n\t\t\t// render values as a tabular bar chart\n\t\t\tself.dom.violin_div.style('display', 'none')\n\t\t\tconst data = input.termStatus.sampleCounts\n\t\t\tif (!data || !data.length) {\n\t\t\t\tself.dom.table_div.style('display', 'none')\n\t\t\t\treturn\n\t\t\t}\n\t\t\tself.dom.table_div.style('display', 'block')\n\t\t\tconst l = self.input.orderedLabels\n\t\t\tconst sortFxn =\n\t\t\t\tl && l.length ? (a, b) => l.indexOf(a.label) - l.indexOf(b.label) : (a, b) => b.samplecount - a.samplecount\n\t\t\tconst tr_data = data.sort(sortFxn)\n\n\t\t\tconst maxCount = Math.max(...tr_data.map(v => v.samplecount), 0)\n\t\t\ttr_data.forEach(v => (v.bar_width_frac = Number((1 - (maxCount - v.samplecount) / maxCount).toFixed(4))))\n\n\t\t\tself.dom.table_div.selectAll('tr').remove()\n\t\t\tconst trs = self.dom.table_div.selectAll('tr').data(tr_data, b => b.key)\n\n\t\t\t//trs.exit().remove()\n\t\t\t//trs.each(trUpdate)\n\t\t\ttrs.enter().append('tr').each(trEnter)\n\t\t}\n\t}\n\n\tfunction renderBottomInfo(input) {\n\t\tif (input.termStatus.bottomSummaryStatus) {\n\t\t\tself.dom.bottom_info_div.style('display', 'block').html(input.termStatus.bottomSummaryStatus)\n\t\t} else {\n\t\t\tself.dom.bottom_info_div.style('display', 'none')\n\t\t}\n\t}\n\n\tfunction renderExcludedValues(input) {\n\t\tconst data = input.termStatus.excludeCounts\n\t\tif (!data || !data.length) {\n\t\t\tself.dom.excluded_div.style('display', 'none')\n\t\t\treturn\n\t\t}\n\t\tself.dom.excluded_div.style('display', 'block').selectAll('tr').remove()\n\t\tconst trs = self.dom.excluded_div.selectAll('tr').data(data, b => b.key)\n\n\t\t//trs.exit().remove()\n\t\t//trs.each(trUpdate)\n\t\ttrs.enter().append('tr').each(trEnter)\n\n\t\tself.dom.excluded_div.selectAll('td').style('color', '#999')\n\t}\n\n\tfunction trEnter(item) {\n\t\tconst tr = select(this)\n\t\tconst input = this.parentNode.__data__\n\t\tconst t = input.term\n\t\tconst maxBarWidth = 150\n\n\t\ttr.style('text-align', 'left').style('cursor', input.termStatus.allowToSelectRefGrp ? 'pointer' : 'default')\n\n\t\tconst tdSpacing = '1px 10px 1px 0px'\n\t\t// sample count td\n\t\ttr.append('td')\n\t\t\t.style('padding', tdSpacing)\n\t\t\t.style('text-align', 'left')\n\t\t\t.style('color', 'black')\n\t\t\t.text(item.samplecount !== undefined ? 'n=' + item.samplecount : '')\n\n\t\t// label td\n\t\ttr.append('td').style('padding', tdSpacing).style('text-align', 'left').style('color', 'black').text(item.label)\n\n\t\t// sample count bar td\n\t\tconst bar_td = tr.append('td').style('padding', tdSpacing)\n\n\t\t// bar_width\n\t\tconst barWidth = maxBarWidth * item.bar_width_frac\n\t\tbar_td\n\t\t\t.append('div')\n\t\t\t.style('margin', tdSpacing)\n\t\t\t.style('width', barWidth + 'px')\n\t\t\t.style('height', '15px')\n\t\t\t.style('background-color', '#ddd')\n\n\t\taddTrBehavior({ input, item, tr, rendered: false })\n\t}\n\n\t/*\n\t// TODO: to use this function, need to add code that will take into account the order of the rows\n\tfunction trUpdate(item) {\n\t\tselect(this.firstChild).text(item.samplecount !== undefined ? 'n=' + item.samplecount : '')\n\t\tselect(this.firstChild.nextSibling).text(item.label)\n\n\t\tconst input = this.parentNode.__data__\n\t\tconst t = input.term\n\t\tlet rendered = true\n\t\tif ((t.q.mode == 'discrete' || t.q.mode == 'binary') && this.childNodes.length < 4) rendered = false\n\t\taddTrBehavior({ input, item, tr: select(this), rendered })\n\t}\n\t*/\n\n\tfunction addTrBehavior({ input, item, tr, rendered }) {\n\t\t// don't add tr effects for excluded values\n\t\tif (!item.bar_width_frac) return\n\n\t\tconst t = input.term\n\t\tconst hover_flag = input.termStatus.allowToSelectRefGrp\n\t\tlet ref_text\n\n\t\tif (rendered) {\n\t\t\ttr.style('background', 'white')\n\t\t\tref_text = select(tr.node().lastChild)\n\t\t\t\t.select('div')\n\t\t\t\t.style('display', item.key === t.refGrp && hover_flag ? 'inline-block' : 'none')\n\t\t\t\t.style('border', item.key === t.refGrp && hover_flag ? '1px solid #bbb' : '')\n\t\t} else if (input.term.q.mode != 'cutoff') {\n\t\t\tconst reference_td = tr.append('td').style('padding', '1px 5px').style('text-align', 'left')\n\n\t\t\tref_text = reference_td\n\t\t\t\t.append('div')\n\t\t\t\t.style('display', item.key === t.refGrp && hover_flag ? 'inline-block' : 'none')\n\t\t\t\t.style('padding', '2px 10px')\n\t\t\t\t.style('border', item.key === t.refGrp && hover_flag ? '1px solid #bbb' : '')\n\t\t\t\t.style('border-radius', '10px')\n\t\t\t\t.style('color', '#999')\n\t\t\t\t.style('font-size', '.7em')\n\t\t\t\t.text('REFERENCE')\n\n\t\t\tif (hover_flag) {\n\t\t\t\ttr.on('mouseover', () => {\n\t\t\t\t\tif (t.refGrp !== item.key) {\n\t\t\t\t\t\ttr.style('background', row_hover_bgcolor)\n\t\t\t\t\t\tref_text.style('display', 'inline-block').style('border', '').text('Set as reference')\n\t\t\t\t\t} else tr.style('background', 'white')\n\t\t\t\t})\n\t\t\t\t\t.on('mouseout', () => {\n\t\t\t\t\t\ttr.style('background', 'white')\n\t\t\t\t\t\tif (t.refGrp !== item.key) ref_text.style('display', 'none')\n\t\t\t\t\t})\n\t\t\t\t\t.on('click', () => {\n\t\t\t\t\t\tt.refGrp = item.key\n\t\t\t\t\t\tref_text.style('border', '1px solid #bbb').text('REFERENCE')\n\t\t\t\t\t\t// below will save to state, ui code should react to it\n\t\t\t\t\t\tself.opts.callback(t)\n\t\t\t\t\t})\n\t\t\t}\n\t\t}\n\t}\n}\n"],
-  "mappings": 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