@sjcrh/proteinpaint-client 2.220.0 → 2.222.0

package/dist/chunk-4NQS45KH.js

@@ -1,302 +0,0 @@
-import {
-  appear2 as appear,
-  axisstyle,
-  bwSetting,
-  disappear2 as disappear,
-  makeNumericAxisConfig,
-  rgb2hex
-} from "./chunk-PEKCVKJK.js";
-import {
-  dofetch3
-} from "./chunk-4TJO2DGU.js";
-import {
-  axisLeft
-} from "./chunk-WJLRU5OF.js";
-import {
-  format,
-  linear
-} from "./chunk-4OLM3KSB.js";
-
-// src/block.tk.bigwig.js
-function bigwigfromtemplate(tk, template) {
-  tk.scale = {};
-  if (template.scale) {
-    for (const k in template.scale) {
-      tk.scale[k] = template.scale[k];
-    }
-  } else {
-    tk.scale.auto = 1;
-  }
-  if (tk.normalize) {
-  } else {
-    tk.normalize = {
-      dividefactor: 1,
-      disable: 1
-    };
-  }
-  tk.barheight = template.height || 50;
-  tk.height_main = tk.toppad + tk.barheight + tk.bottompad;
-  if (!tk.ncolor) tk.ncolor = "#BD005E";
-  if (!tk.ncolor2) tk.ncolor2 = "#5E00BD";
-  if (!tk.pcolor) tk.pcolor = "#005EBD";
-  if (!tk.pcolor2) tk.pcolor2 = "#FA7D00";
-}
-function bigwigmaketk(tk, block) {
-  tk.img = tk.glider.append("image");
-  tk.tklabel.attr("y", tk.barheight / 2);
-  tk.leftaxis = tk.gleft.append("g");
-  tk.config_handle = block.maketkconfighandle(tk).on("click", () => {
-    tk.tkconfigtip.clear().showunder(tk.config_handle.node());
-    bigwigconfigpanel(tk, block, tk.tkconfigtip.d, () => bigwigload(tk, block));
-  });
-}
-async function bigwigload(tk, block) {
-  block.tkcloakon(tk);
-  const par = block.tkarg_q(tk);
-  if (tk.dotplotfactor) par.dotplotfactor = tk.dotplotfactor;
-  if (tk.bgcolor) par.bgcolor = tk.bgcolor;
-  tk.height_main = tk.toppad + tk.barheight + tk.bottompad;
-  tk.img.attr("width", block.width).attr("height", tk.barheight);
-  let errtext;
-  try {
-    let data;
-    if (tk.imgData) {
-      data = tk.imgData;
-    } else {
-      data = await dofetch3("tkbigwig", { method: "POST", body: JSON.stringify(par) });
-    }
-    if (data.error) throw data.error;
-    if (!data.src) throw "data.src missing";
-    tk.tklabel.transition().attr("y", tk.barheight / 2);
-    tk.img.attr("xlink:href", data.src);
-    if (data.minv != void 0) {
-      tk.scale.min = data.minv;
-    }
-    if (data.maxv != void 0) {
-      tk.scale.max = data.maxv;
-    }
-    tk.leftaxis.selectAll("*").remove();
-    if (data.nodata) {
-      throw "No data in view range";
-    }
-    const scale = linear().domain([tk.scale.min, tk.scale.max]).range([tk.barheight, 0]);
-    const axis = axisLeft().scale(scale).tickValues([tk.scale.min, tk.scale.max]);
-    if (tk.integer4axis) {
-      axis.tickFormat(format("d"));
-    }
-    axisstyle({
-      axis: tk.leftaxis.call(axis),
-      color: "black",
-      showline: true
-    });
-  } catch (err) {
-    tk.img.attr("width", 0).attr("height", 0);
-    if (err.stack) {
-      console.log(err.stack);
-    }
-    errtext = typeof err == "string" ? err : err.message;
-  } finally {
-    block.tkcloakoff(tk, { error: errtext });
-    block.block_setheight();
-    for (const panel of tk.subpanels) {
-      bigwigloadsubpanel(tk, block, panel);
-    }
-  }
-}
-async function bigwigloadsubpanel(tk, block, panel) {
-  block.tkcloakon_subpanel(panel);
-  const par = block.tkarg_q(tk);
-  if (tk.dotplotfactor) {
-    par.dotplotfactor = tk.dotplotfactor;
-  }
-  par.width = panel.width;
-  par.rglst = [
-    {
-      chr: panel.chr,
-      start: panel.start,
-      stop: panel.stop,
-      width: panel.width
-    }
-  ];
-  delete par.percentile;
-  delete par.autoscale;
-  panel.img.attr("width", panel.width).attr("height", tk.barheight);
-  let errtext;
-  try {
-    if (tk.imgData) throw "subpanel not supported by imgData yet";
-    const data = await dofetch3("tkbigwig", { method: "POST", body: JSON.stringify(par) });
-    if (data.error) throw data.error;
-    panel.img.attr("xlink:href", data.src);
-  } catch (err) {
-    panel.img.attr("width", 0).attr("height", 0);
-    if (err.stack) {
-      console.log(err.stack);
-    }
-    errtext = typeof err == "string" ? err : err.message;
-  } finally {
-    block.tkcloakoff_subpanel(panel, { error: errtext });
-  }
-}
-function bigwigconfigpanel(tk, block, holder, loader) {
-  const config = {
-    pcolor: {},
-    ncolor: {},
-    pcolor2: {},
-    ncolor2: {},
-    // .row
-    // .lab
-    dotplot: {},
-    // .row
-    dividefactor: {}
-  };
-  {
-    const row = holder.append("div").style("margin-bottom", "15px");
-    row.append("span").html("Height  ");
-    row.append("input").attr("size", 5).property("value", tk.barheight).on("keyup", (event) => {
-      if (event.code != "Enter") return;
-      const s = event.target.value;
-      if (s == "") return;
-      const v = Number.parseInt(s);
-      if (Number.isNaN(v) || v <= 1) {
-        alert("track height must be positive integer");
-        return;
-      }
-      tk.barheight = v;
-      loader(bwSetting.height);
-    });
-  }
-  config.pcolor.row = holder.append("div").style("margin-bottom", "15px");
-  config.pcolor.lab = config.pcolor.row.append("span").text("Positive value color").style("padding-right", "10px");
-  config.pcolor.row.append("input").attr("type", "color").property("value", rgb2hex(tk.pcolor)).on("change", (event) => {
-    tk.pcolor = event.target.value;
-    loader(bwSetting.pcolor);
-  });
-  config.ncolor.row = holder.append("div").style("margin-bottom", "15px");
-  config.ncolor.lab = config.ncolor.row.append("span").text("Negative value color").style("padding-right", "10px");
-  config.ncolor.row.append("input").attr("type", "color").property("value", rgb2hex(tk.ncolor)).on("change", (event) => {
-    tk.ncolor = event.target.value;
-    loader(bwSetting.ncolor);
-  });
-  if (!tk.scale.auto) {
-    config.pcolor2.row = holder.append("div").style("margin-bottom", "15px");
-    config.pcolor2.lab = config.pcolor2.row.append("span").html("&ge;Max color").style("padding-right", "10px");
-    config.pcolor2.row.append("input").attr("type", "color").property("value", rgb2hex(tk.pcolor2)).on("change", (event) => {
-      tk.pcolor2 = event.target.value;
-      loader(bwSetting.pcolor2);
-    });
-    config.ncolor2.row = holder.append("div").style("margin-bottom", "15px");
-    config.ncolor2.lab = config.ncolor2.row.append("span").html("&le;Min color").style("padding-right", "10px");
-    config.ncolor2.row.append("input").attr("type", "color").property("value", rgb2hex(tk.ncolor2)).on("change", (event) => {
-      tk.ncolor2 = event.target.value;
-      loader(bwSetting.ncolor2);
-    });
-  }
-  {
-    const setting = {};
-    if (tk.scale.auto) {
-      setting.auto = 1;
-    } else if (tk.scale.percentile) {
-      setting.percentile = tk.scale.percentile;
-    } else {
-      setting.fixed = { min: tk.scale.min, max: tk.scale.max };
-    }
-    makeNumericAxisConfig({
-      holder: holder.append("div").style("margin-bottom", "15px"),
-      setting,
-      callback: (s) => {
-        if (s.auto) {
-          tk.scale.auto = 1;
-          loader(bwSetting.autoscale);
-          return;
-        }
-        if (s.fixed) {
-          delete tk.scale.auto;
-          delete tk.scale.percentile;
-          tk.scale.max = s.fixed.max;
-          tk.scale.min = s.fixed.min;
-          loader(bwSetting.fixedscale);
-          return;
-        }
-        delete tk.scale.auto;
-        tk.scale.percentile = s.percentile;
-        loader(bwSetting.percentilescale);
-      }
-    });
-  }
-  {
-    config.dotplot.row = holder.append("div").style("margin-bottom", "15px");
-    config.dotplot.row.append("span").html("Dot plot&nbsp;&nbsp;");
-    const s = config.dotplot.row.append("select").on("change", (event) => {
-      const i = event.target.selectedIndex;
-      if (i == 0) {
-        delete tk.dotplotfactor;
-      } else {
-        tk.dotplotfactor = Number.parseInt(event.target.options[i].innerHTML);
-      }
-      loader(i == 0 ? bwSetting.nodotplot : bwSetting.usedotplot);
-    });
-    let o = s.append("option").text("no");
-    if (!tk.dotplotfactor) {
-      o.property("selected", 1);
-    }
-    o = s.append("option").text("5");
-    if (tk.dotplotfactor == 5) {
-      o.property("selected", 1);
-    }
-    o = s.append("option").text("10");
-    if (tk.dotplotfactor == 10) {
-      o.property("selected", 1);
-    }
-    o = s.append("option").text("15");
-    if (tk.dotplotfactor == 15) {
-      o.property("selected", 1);
-    }
-    o = s.append("option").text("20");
-    if (tk.dotplotfactor == 20) {
-      o.property("selected", 1);
-    }
-  }
-  config.dividefactor.row = holder.append("div");
-  {
-    const id = Math.random().toString();
-    const input = config.dividefactor.row.append("input").attr("type", "checkbox").attr("id", id);
-    if (!tk.normalize.disable) {
-      input.property("checked", 1);
-    }
-    config.dividefactor.row.append("label").html("&nbsp;Apply normalization").attr("for", id);
-    const folder = config.dividefactor.row.append("div").style("margin", "5px 10px 0px 20px").style("display", tk.normalize.disable ? "none" : "block");
-    folder.append("span").html("Divide raw value by&nbsp;");
-    const factorinput = folder.append("input").attr("type", "number").style("width", "60px").property("value", tk.normalize.dividefactor).on("keyup", (event) => {
-      if (event.code != "Enter" && event.code != "NumpadEnter") return;
-      const v = event.target.value;
-      if (v <= 0) {
-        return;
-      }
-      tk.normalize.dividefactor = v;
-      loader(bwSetting.usedividefactor);
-    });
-    folder.append("div").text("Enter a value above zero").style("font-size", ".7em").style("color", "#858585");
-    input.on("change", (event) => {
-      if (event.target.checked) {
-        appear(folder);
-        delete tk.normalize.disable;
-        factorinput.property("value", tk.normalize.dividefactor);
-        loader(bwSetting.usedividefactor);
-        return;
-      }
-      disappear(folder);
-      tk.normalize.disable = 1;
-      loader(bwSetting.nodividefactor);
-    });
-  }
-  return config;
-}
-
-export {
-  bigwigfromtemplate,
-  bigwigmaketk,
-  bigwigload,
-  bigwigloadsubpanel,
-  bigwigconfigpanel
-};
-//# sourceMappingURL=chunk-4NQS45KH.js.map

package/dist/chunk-4NQS45KH.js.map

@@ -1,7 +0,0 @@
-{
-  "version": 3,
-  "sources": ["../src/block.tk.bigwig.js"],
-  "sourcesContent": ["import { scaleLinear } from 'd3-scale'\nimport * as d3axis from 'd3-axis'\nimport * as client from './client'\nimport { dofetch3 } from '#common/dofetch'\nimport { format as d3format } from 'd3-format'\nimport { makeNumericAxisConfig } from '#dom/numericAxis'\n\n/*\nFIXME\nbigwigloadsubpanel should return promise and be tracked\n*/\n\nexport function bigwigfromtemplate(tk, template) {\n\ttk.scale = {}\n\tif (template.scale) {\n\t\tfor (const k in template.scale) {\n\t\t\ttk.scale[k] = template.scale[k]\n\t\t}\n\t} else {\n\t\ttk.scale.auto = 1\n\t}\n\n\tif (tk.normalize) {\n\t} else {\n\t\t// disable by default\n\t\ttk.normalize = {\n\t\t\tdividefactor: 1,\n\t\t\tdisable: 1\n\t\t}\n\t}\n\ttk.barheight = template.height || 50\n\ttk.height_main = tk.toppad + tk.barheight + tk.bottompad\n\tif (!tk.ncolor) tk.ncolor = '#BD005E'\n\tif (!tk.ncolor2) tk.ncolor2 = '#5E00BD'\n\tif (!tk.pcolor) tk.pcolor = '#005EBD'\n\tif (!tk.pcolor2) tk.pcolor2 = '#FA7D00'\n}\n\nexport function bigwigmaketk(tk, block) {\n\ttk.img = tk.glider.append('image')\n\ttk.tklabel.attr('y', tk.barheight / 2)\n\n\ttk.leftaxis = tk.gleft.append('g')\n\n\ttk.config_handle = block.maketkconfighandle(tk).on('click', () => {\n\t\ttk.tkconfigtip.clear().showunder(tk.config_handle.node())\n\t\tbigwigconfigpanel(tk, block, tk.tkconfigtip.d, () => bigwigload(tk, block))\n\t})\n}\n\nexport async function bigwigload(tk, block) {\n\t/*\n\tcalled by change view range\n\tor updating any rendering style, e.g. height\n\t*/\n\tblock.tkcloakon(tk)\n\tconst par = block.tkarg_q(tk)\n\tif (tk.dotplotfactor) par.dotplotfactor = tk.dotplotfactor\n\tif (tk.bgcolor) par.bgcolor = tk.bgcolor // bg colors for loci with a valid numerical value, useful when low values are cared about e.g. in dna methylation beta value\n\n\ttk.height_main = tk.toppad + tk.barheight + tk.bottompad\n\ttk.img.attr('width', block.width).attr('height', tk.barheight)\n\n\tlet errtext\n\ttry {\n\t\tlet data\n\t\tif (tk.imgData) {\n\t\t\tdata = tk.imgData // premade data; same structure as below\n\t\t} else {\n\t\t\tdata = await dofetch3('tkbigwig', { method: 'POST', body: JSON.stringify(par) })\n\t\t}\n\t\tif (data.error) throw data.error\n\t\tif (!data.src) throw 'data.src missing'\n\n\t\t// in case height changed\n\t\ttk.tklabel.transition().attr('y', tk.barheight / 2)\n\n\t\ttk.img.attr('xlink:href', data.src)\n\n\t\tif (data.minv != undefined) {\n\t\t\ttk.scale.min = data.minv\n\t\t}\n\t\tif (data.maxv != undefined) {\n\t\t\ttk.scale.max = data.maxv\n\t\t}\n\t\ttk.leftaxis.selectAll('*').remove()\n\n\t\tif (data.nodata) {\n\t\t\tthrow 'No data in view range'\n\t\t\t// won't update axis\n\t\t}\n\n\t\t// update axis\n\t\tconst scale = scaleLinear().domain([tk.scale.min, tk.scale.max]).range([tk.barheight, 0])\n\n\t\tconst axis = d3axis.axisLeft().scale(scale).tickValues([tk.scale.min, tk.scale.max])\n\n\t\tif (tk.integer4axis) {\n\t\t\taxis.tickFormat(d3format('d'))\n\t\t}\n\n\t\tclient.axisstyle({\n\t\t\taxis: tk.leftaxis.call(axis),\n\t\t\tcolor: 'black',\n\t\t\tshowline: true\n\t\t})\n\t} catch (err) {\n\t\ttk.img.attr('width', 0).attr('height', 0)\n\t\tif (err.stack) {\n\t\t\t// error\n\t\t\tconsole.log(err.stack)\n\t\t}\n\t\terrtext = typeof err == 'string' ? err : err.message\n\t} finally {\n\t\tblock.tkcloakoff(tk, { error: errtext })\n\t\tblock.block_setheight()\n\n\t\t// also load subpanels whenever main panel updates\n\t\tfor (const panel of tk.subpanels) {\n\t\t\tbigwigloadsubpanel(tk, block, panel)\n\t\t}\n\t}\n}\n\nexport async function bigwigloadsubpanel(tk, block, panel) {\n\tblock.tkcloakon_subpanel(panel)\n\tconst par = block.tkarg_q(tk)\n\tif (tk.dotplotfactor) {\n\t\tpar.dotplotfactor = tk.dotplotfactor\n\t}\n\tpar.width = panel.width\n\tpar.rglst = [\n\t\t{\n\t\t\tchr: panel.chr,\n\t\t\tstart: panel.start,\n\t\t\tstop: panel.stop,\n\t\t\twidth: panel.width\n\t\t}\n\t]\n\tdelete par.percentile\n\tdelete par.autoscale\n\n\tpanel.img.attr('width', panel.width).attr('height', tk.barheight)\n\n\tlet errtext\n\ttry {\n\t\tif (tk.imgData) throw 'subpanel not supported by imgData yet'\n\t\tconst data = await dofetch3('tkbigwig', { method: 'POST', body: JSON.stringify(par) })\n\t\tif (data.error) throw data.error\n\t\tpanel.img.attr('xlink:href', data.src)\n\t} catch (err) {\n\t\tpanel.img.attr('width', 0).attr('height', 0)\n\t\tif (err.stack) {\n\t\t\t// error\n\t\t\tconsole.log(err.stack)\n\t\t}\n\t\terrtext = typeof err == 'string' ? err : err.message\n\t} finally {\n\t\tblock.tkcloakoff_subpanel(panel, { error: errtext })\n\t}\n}\n\nexport function bigwigconfigpanel(tk, block, holder, loader) {\n\t// provide hooks to each component, so that caller can choose to hide certain ones\n\tconst config = {\n\t\tpcolor: {},\n\t\tncolor: {},\n\t\tpcolor2: {},\n\t\tncolor2: {},\n\t\t// .row\n\t\t// .lab\n\n\t\tdotplot: {},\n\t\t// .row\n\n\t\tdividefactor: {}\n\t}\n\n\t// height\n\t{\n\t\tconst row = holder.append('div').style('margin-bottom', '15px')\n\t\trow.append('span').html('Height&nbsp;&nbsp;')\n\t\trow\n\t\t\t.append('input')\n\t\t\t.attr('size', 5)\n\t\t\t.property('value', tk.barheight)\n\t\t\t.on('keyup', event => {\n\t\t\t\tif (event.code != 'Enter') return\n\t\t\t\tconst s = event.target.value\n\t\t\t\tif (s == '') return\n\t\t\t\tconst v = Number.parseInt(s)\n\t\t\t\tif (Number.isNaN(v) || v <= 1) {\n\t\t\t\t\talert('track height must be positive integer')\n\t\t\t\t\treturn\n\t\t\t\t}\n\t\t\t\ttk.barheight = v\n\t\t\t\tloader(client.bwSetting.height)\n\t\t\t})\n\t}\n\n\t// pcolor\n\tconfig.pcolor.row = holder.append('div').style('margin-bottom', '15px')\n\tconfig.pcolor.lab = config.pcolor.row.append('span').text('Positive value color').style('padding-right', '10px')\n\tconfig.pcolor.row\n\t\t.append('input')\n\t\t.attr('type', 'color')\n\t\t.property('value', client.rgb2hex(tk.pcolor))\n\t\t.on('change', event => {\n\t\t\ttk.pcolor = event.target.value\n\t\t\tloader(client.bwSetting.pcolor)\n\t\t})\n\n\t// ncolor\n\tconfig.ncolor.row = holder.append('div').style('margin-bottom', '15px')\n\tconfig.ncolor.lab = config.ncolor.row.append('span').text('Negative value color').style('padding-right', '10px')\n\tconfig.ncolor.row\n\t\t.append('input')\n\t\t.attr('type', 'color')\n\t\t.property('value', client.rgb2hex(tk.ncolor))\n\t\t.on('change', event => {\n\t\t\ttk.ncolor = event.target.value\n\t\t\tloader(client.bwSetting.ncolor)\n\t\t})\n\n\tif (!tk.scale.auto) {\n\t\t// pcolor2\n\t\tconfig.pcolor2.row = holder.append('div').style('margin-bottom', '15px')\n\t\tconfig.pcolor2.lab = config.pcolor2.row.append('span').html('&ge;Max color').style('padding-right', '10px')\n\t\tconfig.pcolor2.row\n\t\t\t.append('input')\n\t\t\t.attr('type', 'color')\n\t\t\t.property('value', client.rgb2hex(tk.pcolor2))\n\t\t\t.on('change', event => {\n\t\t\t\ttk.pcolor2 = event.target.value\n\t\t\t\tloader(client.bwSetting.pcolor2)\n\t\t\t})\n\t\t// ncolor2\n\t\tconfig.ncolor2.row = holder.append('div').style('margin-bottom', '15px')\n\t\tconfig.ncolor2.lab = config.ncolor2.row.append('span').html('&le;Min color').style('padding-right', '10px')\n\t\tconfig.ncolor2.row\n\t\t\t.append('input')\n\t\t\t.attr('type', 'color')\n\t\t\t.property('value', client.rgb2hex(tk.ncolor2))\n\t\t\t.on('change', event => {\n\t\t\t\ttk.ncolor2 = event.target.value\n\t\t\t\tloader(client.bwSetting.ncolor2)\n\t\t\t})\n\t}\n\n\t// y-scale\n\t{\n\t\tconst setting = {}\n\t\tif (tk.scale.auto) {\n\t\t\tsetting.auto = 1\n\t\t} else if (tk.scale.percentile) {\n\t\t\tsetting.percentile = tk.scale.percentile\n\t\t} else {\n\t\t\tsetting.fixed = { min: tk.scale.min, max: tk.scale.max }\n\t\t}\n\t\tmakeNumericAxisConfig({\n\t\t\tholder: holder.append('div').style('margin-bottom', '15px'),\n\t\t\tsetting,\n\t\t\tcallback: s => {\n\t\t\t\tif (s.auto) {\n\t\t\t\t\ttk.scale.auto = 1\n\t\t\t\t\tloader(client.bwSetting.autoscale)\n\t\t\t\t\treturn\n\t\t\t\t}\n\t\t\t\tif (s.fixed) {\n\t\t\t\t\tdelete tk.scale.auto\n\t\t\t\t\tdelete tk.scale.percentile\n\t\t\t\t\ttk.scale.max = s.fixed.max\n\t\t\t\t\ttk.scale.min = s.fixed.min\n\t\t\t\t\tloader(client.bwSetting.fixedscale)\n\t\t\t\t\treturn\n\t\t\t\t}\n\t\t\t\tdelete tk.scale.auto\n\t\t\t\ttk.scale.percentile = s.percentile\n\t\t\t\tloader(client.bwSetting.percentilescale)\n\t\t\t}\n\t\t})\n\t}\n\n\t// dot plot\n\t{\n\t\tconfig.dotplot.row = holder.append('div').style('margin-bottom', '15px')\n\t\tconfig.dotplot.row.append('span').html('Dot plot&nbsp;&nbsp;')\n\t\tconst s = config.dotplot.row.append('select').on('change', event => {\n\t\t\tconst i = event.target.selectedIndex\n\t\t\tif (i == 0) {\n\t\t\t\tdelete tk.dotplotfactor\n\t\t\t} else {\n\t\t\t\ttk.dotplotfactor = Number.parseInt(event.target.options[i].innerHTML)\n\t\t\t}\n\t\t\tloader(i == 0 ? client.bwSetting.nodotplot : client.bwSetting.usedotplot)\n\t\t})\n\t\tlet o = s.append('option').text('no')\n\t\tif (!tk.dotplotfactor) {\n\t\t\to.property('selected', 1)\n\t\t}\n\t\to = s.append('option').text('5')\n\t\tif (tk.dotplotfactor == 5) {\n\t\t\to.property('selected', 1)\n\t\t}\n\t\to = s.append('option').text('10')\n\t\tif (tk.dotplotfactor == 10) {\n\t\t\to.property('selected', 1)\n\t\t}\n\t\to = s.append('option').text('15')\n\t\tif (tk.dotplotfactor == 15) {\n\t\t\to.property('selected', 1)\n\t\t}\n\t\to = s.append('option').text('20')\n\t\tif (tk.dotplotfactor == 20) {\n\t\t\to.property('selected', 1)\n\t\t}\n\t}\n\n\t// normalization using a divide-by factor\n\tconfig.dividefactor.row = holder.append('div')\n\t//.style('margin-bottom','15px')\n\t{\n\t\tconst id = Math.random().toString()\n\t\tconst input = config.dividefactor.row.append('input').attr('type', 'checkbox').attr('id', id)\n\t\tif (!tk.normalize.disable) {\n\t\t\tinput.property('checked', 1)\n\t\t}\n\t\tconfig.dividefactor.row.append('label').html('&nbsp;Apply normalization').attr('for', id)\n\n\t\tconst folder = config.dividefactor.row\n\t\t\t.append('div')\n\t\t\t.style('margin', '5px 10px 0px 20px')\n\t\t\t.style('display', tk.normalize.disable ? 'none' : 'block')\n\t\tfolder.append('span').html('Divide raw value by&nbsp;')\n\t\tconst factorinput = folder\n\t\t\t.append('input')\n\t\t\t.attr('type', 'number')\n\t\t\t.style('width', '60px')\n\t\t\t.property('value', tk.normalize.dividefactor)\n\t\t\t.on('keyup', event => {\n\t\t\t\tif (event.code != 'Enter' && event.code != 'NumpadEnter') return\n\t\t\t\tconst v = event.target.value\n\t\t\t\tif (v <= 0) {\n\t\t\t\t\t// don't allow\n\t\t\t\t\treturn\n\t\t\t\t}\n\t\t\t\ttk.normalize.dividefactor = v\n\t\t\t\tloader(client.bwSetting.usedividefactor)\n\t\t\t})\n\t\tfolder.append('div').text('Enter a value above zero').style('font-size', '.7em').style('color', '#858585')\n\t\tinput.on('change', event => {\n\t\t\tif (event.target.checked) {\n\t\t\t\tclient.appear(folder)\n\t\t\t\tdelete tk.normalize.disable\n\t\t\t\tfactorinput.property('value', tk.normalize.dividefactor)\n\t\t\t\tloader(client.bwSetting.usedividefactor)\n\t\t\t\treturn\n\t\t\t}\n\t\t\tclient.disappear(folder)\n\t\t\ttk.normalize.disable = 1\n\t\t\tloader(client.bwSetting.nodividefactor)\n\t\t})\n\t}\n\treturn config\n}\n"],
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-  "names": []
-}

package/dist/chunk-4ZV6SE4B.js

@@ -1,240 +0,0 @@
-import {
-  make_radios
-} from "./chunk-PEKCVKJK.js";
-import {
-  initBinConfig
-} from "./chunk-4TJO2DGU.js";
-import {
-  toStoredUnit,
-  toUserUnit
-} from "./chunk-W5J3LTYS.js";
-import {
-  format
-} from "./chunk-4OLM3KSB.js";
-
-// termsetting/handlers/NumRegularBinEditor.ts
-var NumRegularBinEditor = class {
-  constructor(editHandler) {
-    this.dom = {};
-    this.editHandler = editHandler;
-    this.opts = editHandler.opts;
-    this.tw = editHandler.tw;
-    this.termsetting = editHandler.termsetting;
-  }
-  /* q holds bin boundaries in the unit the term's values are stored in, while the <input>s and the
-  density plot show them in the term's user-facing unit. toDisplay()/toStored() cross that boundary;
-  both are identity functions unless the term declares valueConversion{} */
-  toDisplay(v) {
-    return toUserUnit(v, this.tw.term);
-  }
-  toStored(v) {
-    return toStoredUnit(v, this.tw.term);
-  }
-  render(div) {
-    this.tw = this.editHandler.tw;
-    const isRemounting = !!this.dom.binsTable && this.editHandler.dom.binsDiv?.node().contains(this.dom.binsTable.node());
-    if (!isRemounting) this.q = this.getDefaultQ();
-    this.editHandler.handler.density.setBinLines(this.getBoundaryOpts());
-    if (isRemounting) return;
-    if (this.dom.binsTable) {
-      this.dom.binsTable.remove();
-      delete this.dom.binsTable;
-    }
-    const binsTable = div.append("table");
-    this.dom.binsTable = binsTable;
-    this.renderBinSizeInput(binsTable.append("tr"));
-    this.renderFirstBinInput(binsTable.append("tr"));
-    this.renderLastBinInputs(binsTable.append("tr"));
-  }
-  getDefaultQ() {
-    if (this.tw.q.type == "regular-bin") return JSON.parse(JSON.stringify(this.tw.q));
-    const t = this.tw.term;
-    const defaultQ = this.termsetting.opts.use_bins_less && t.bins?.less || t.bins?.default;
-    if (defaultQ) return JSON.parse(JSON.stringify(defaultQ));
-    const binConfig = initBinConfig(this.editHandler.handler.density_data);
-    return typeof binConfig == "string" ? JSON.parse(binConfig) : binConfig;
-  }
-  renderBinSizeInput(tr) {
-    const handler = this.editHandler.handler;
-    tr.append("td").style("margin", "5px").style("opacity", 0.5).text("Bin Size");
-    const { min, max } = handler.density_data;
-    const q = this.q;
-    const origBinSize = this.toDisplay(q.bin_size);
-    this.dom.bin_size_input = tr.append("td").append("input").attr("type", "number").attr(
-      "value",
-      handler.density.scaleFactor == 1 && "rounding" in q ? format(q.rounding || ".0f")(q.bin_size) : origBinSize
-    ).attr("data-testid", "sjpp-num-reg-bin-editor-size").style("margin-left", "15px").style("width", "100px").style("color", () => q.bin_size > Math.abs(max - min) ? "red" : "").on("change", (event) => {
-      const newValue = this.toStored(Number(event.target.value));
-      if (newValue <= 0) {
-        window.alert("Please enter non-negative bin size.");
-        event.target.value = origBinSize;
-        return;
-      }
-      if ((max - min) / newValue > 100) {
-        window.alert("Bin size too small. Try setting a bigger value.");
-        event.target.value = origBinSize;
-        return;
-      }
-      q.bin_size = newValue;
-      this.dom.bin_size_input.style(
-        "color",
-        q.bin_size > max - min ? "red" : this.toDisplay(newValue) != origBinSize ? "green" : ""
-      );
-      handler.density.setBinLines(this.getBoundaryOpts());
-    });
-  }
-  renderFirstBinInput(tr) {
-    const handler = this.editHandler.handler;
-    const q = this.q;
-    if (!q.first_bin) throw "missing q.first_bin";
-    tr.append("td").style("margin", "5px").style("opacity", 0.5).text("First Bin Stop");
-    const { min, max } = handler.density_data;
-    const origValue = this.toDisplay(q.first_bin.stop);
-    this.dom.first_stop_input = tr.append("td").append("input").attr("type", "number").property("value", origValue).style("width", "100px").style("margin-left", "15px").on("change", (event) => {
-      const newValue = this.toStored(Number(event.target.value));
-      if (Number(event.target.value) < this.toDisplay(min) || Number(event.target.value) > this.toDisplay(max)) {
-        window.alert("First bin stop value out of bound.");
-        event.target.value = origValue;
-        return;
-      }
-      this.q.first_bin.stop = newValue;
-      handler.density.setBinLines(this.getBoundaryOpts());
-    });
-    tr.append("td").append("div").style("font-size", ".6em").style("opacity", 0.5).style("display", handler.density.no_density_data ? "none" : "block").text("Indicated by left-most red line. Drag to change.");
-  }
-  renderLastBinInputs(tr) {
-    const handler = this.editHandler.handler;
-    const q = this.q;
-    const isAuto = !q.last_bin || !Number.isFinite(q.last_bin.start);
-    tr.append("td").style("padding-top", "4px").style("opacity", 0.5).style("vertical-align", "top").text("Last Bin Start");
-    const td1 = tr.append("td").style("padding-left", "15px").style("vertical-align", "top");
-    const radio_div = td1.append("div");
-    const radios = make_radios({
-      holder: radio_div,
-      options: [
-        { label: "Automatic", value: "auto", checked: isAuto },
-        { label: "Fixed", value: "fixed", checked: !isAuto }
-      ],
-      callback: (v) => {
-        if (v == "auto") {
-          delete q.last_bin;
-          edit_div.style("display", "none");
-          handler.density.setBinLines(this.getBoundaryOpts());
-          return;
-        }
-        edit_div.style("display", "inline-block");
-        if (this.dom.last_start_input.property("value") == "") {
-          this.dom.last_start_input.property(
-            "value",
-            this.toDisplay(this.tw.q.last_bin?.start || handler.density_data.max)
-          );
-        }
-        this.setLastBinStart();
-      }
-    });
-    this.dom.fixed_radio = radios.inputs.filter((_, i) => i === 1);
-    const edit_div = tr.append("td").append("div").style("display", isAuto ? "none" : "inline-block");
-    this.dom.last_start_input = edit_div.append("input").attr("type", "number").property("value", Number.isFinite(q.last_bin?.start) ? this.toDisplay(q.last_bin.start) : "").style("width", "100px").on("change", () => this.setLastBinStart());
-    edit_div.append("div").style("font-size", ".6em").style("opacity", 0.5).style("display", handler.density.no_density_data ? "none" : "block").text("Indicated by right-most red line. Drag to change.");
-  }
-  setLastBinStart() {
-    const q = this.q;
-    const { max } = this.editHandler.handler.density_data;
-    const strInput = this.dom.last_start_input.property("value");
-    if (strInput === "") return;
-    const inputValue = this.toStored(Number(strInput));
-    if (q.first_bin && Number(strInput) <= this.toDisplay(q.first_bin.stop)) {
-      window.alert("Last bin start cannot be smaller than first bin stop.");
-      this.dom.last_start_input.property("value", this.toDisplay(max));
-      return;
-    }
-    if (Number(strInput) > this.toDisplay(max)) {
-      window.alert("Last bin start value out of bound.");
-      this.dom.last_start_input.property("value", this.toDisplay(max));
-      return;
-    }
-    if (q.last_bin) q.last_bin.start = inputValue;
-    else
-      q.last_bin = {
-        start: inputValue,
-        stopunbounded: true,
-        stopinclusive: false
-      };
-    this.editHandler.handler.density.setBinLines(this.getBoundaryOpts());
-  }
-  getBoundaryOpts() {
-    const { min, max } = this.editHandler.handler.density_data;
-    const binLinesStop = this.q.last_bin?.start ?? max + Math.abs(this.q.first_bin.stop) - Math.min(min, 0);
-    const boundaryValues = [];
-    for (let i = this.q.first_bin.stop; i <= binLinesStop; i = i + this.q.bin_size) {
-      if (this.q.last_bin?.start === i) break;
-      if (i > binLinesStop) boundaryValues[boundaryValues.length - 1].isLastVisibleLine = true;
-      const isDraggable = i === this.q.first_bin.stop || i === this.q.bin_size - 1;
-      boundaryValues.push({ x: this.toDisplay(i), isDraggable, movesWithLineIndex: !isDraggable ? 0 : -1 });
-    }
-    if (this.q.last_bin) {
-      boundaryValues.push({
-        x: this.toDisplay(this.q.last_bin.start),
-        isDraggable: true,
-        isLastVisibleLine: true,
-        movesWithLineIndex: -1
-      });
-    }
-    return {
-      values: boundaryValues,
-      // the dragged value arrives in display units, matching what the <input>s show
-      callback: (d, value) => {
-        if (d.index === 0) {
-          this.dom.first_stop_input.property("value", value);
-          this.q.first_bin.stop = this.toStored(value);
-        } else {
-          this.dom.last_start_input.property("value", value);
-          if (this.q.last_bin) this.q.last_bin.start = this.toStored(value);
-        }
-      }
-    };
-  }
-  getEditedQ(destroyDom = true) {
-    const bin_size = this.dom.bin_size_input.property("value");
-    const config = {
-      mode: "discrete",
-      type: "regular-bin",
-      startinclusive: this.editHandler.boundaryInclusion == "startinclusive",
-      stopinclusive: this.editHandler.boundaryInclusion == "stopinclusive",
-      bin_size: this.toStored(Number(bin_size)),
-      first_bin: {
-        startunbounded: true,
-        stop: this.toStored(Number(this.dom.first_stop_input.property("value")))
-      },
-      /* rounding formats the stored bin size, so it cannot be derived from the decimals of a
-      converted input. a converted term labels its bins through valueConversion instead */
-      rounding: this.editHandler.handler.density.scaleFactor != 1 ? ".0f" : bin_size.includes(".") && !bin_size.endsWith(".") ? `.${bin_size.split(".")[1].length}f` : ".0f"
-    };
-    if (this.dom.fixed_radio.property("checked")) {
-      config.last_bin = {
-        start: this.toStored(Number(this.dom.last_start_input.property("value"))),
-        stopunbounded: true
-      };
-    }
-    if (destroyDom) {
-      for (const name of Object.keys(this.dom)) {
-        this.dom[name].remove();
-        delete this.dom[name];
-      }
-    }
-    return config;
-  }
-  undoEdits() {
-    this.q = this.getDefaultQ();
-    this.dom.binsTable.selectAll("*").remove();
-    this.renderBinSizeInput(this.dom.binsTable.append("tr"));
-    this.renderFirstBinInput(this.dom.binsTable.append("tr"));
-    this.renderLastBinInputs(this.dom.binsTable.append("tr"));
-    this.editHandler.handler.density.setBinLines(this.getBoundaryOpts());
-  }
-};
-
-export {
-  NumRegularBinEditor
-};
-//# sourceMappingURL=chunk-4ZV6SE4B.js.map

package/dist/chunk-5TA5LHPW.js

@@ -1,54 +0,0 @@
-import {
-  addGeneSearchbox,
-  getSCGEunit,
-  getSampleAssayInfo
-} from "./chunk-PEKCVKJK.js";
-import {
-  Menu
-} from "./chunk-CNFTQSNE.js";
-import {
-  SINGLECELL_GENE_EXPRESSION
-} from "./chunk-WJLRU5OF.js";
-
-// termdb/handlers/singleCellGeneExpression.ts
-var SearchHandler = class {
-  async init(opts) {
-    this.validateOpts(opts);
-    this.callback = opts.callback;
-    this.app = opts.app;
-    const sample = opts.usecase?.specialCase?.config?.sample;
-    const { genes: geneList } = await getSampleAssayInfo(this.app.vocabApi, sample);
-    const holder = opts.holder.append("div").style("padding", "10px 0px");
-    const geneSearch = addGeneSearchbox({
-      tip: new Menu({ padding: "0px" }),
-      genome: opts.genomeObj,
-      geneList,
-      row: holder,
-      searchOnly: "gene",
-      callback: () => this.selectGene(geneSearch.geneSymbol, sample)
-    });
-  }
-  /**TODO: scge tw handler will validate that a sample is included. Need to resolve issue
-   * with sample info not included.*/
-  async selectGene(gene, sample) {
-    if (!gene) throw new Error("No gene selected");
-    const unit = getSCGEunit(this.app.vocabApi);
-    const name = `${gene} ${unit}`;
-    this.callback({ gene, name, type: SINGLECELL_GENE_EXPRESSION, sample });
-  }
-  validateOpts(opts) {
-    if (opts.callback == null) throw new Error("callback is required");
-    if (opts.app == null) throw new Error("app is required");
-    if (opts.holder == null) throw new Error("holder is required");
-    if (opts.genomeObj == null) throw new Error("genomeObj is required");
-    if (opts.usecase == null) throw new Error("usecase is required");
-    if (!opts.usecase?.specialCase?.config?.sample) {
-      throw new Error("usecase.specialCase.config.sample is required for singleCellGeneExpression handler");
-    }
-  }
-};
-
-export {
-  SearchHandler
-};
-//# sourceMappingURL=chunk-5TA5LHPW.js.map