@sjcrh/proteinpaint-client 2.221.0 → 2.222.0

package/dist/chunk-IJSFSUI4.js

@@ -1,302 +0,0 @@
-import {
-  appear2 as appear,
-  axisstyle,
-  bwSetting,
-  disappear2 as disappear,
-  makeNumericAxisConfig,
-  rgb2hex
-} from "./chunk-WD7FZ5EE.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-IJSFSUI4.js.map

package/dist/chunk-IJSFSUI4.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-IRQKX6DL.js

@@ -1,263 +0,0 @@
-import {
-  hierCluster_renderers_exports
-} from "./chunk-GBKQHVKJ.js";
-import {
-  hierCluster_interactivity_exports
-} from "./chunk-WYSOOKFJ.js";
-import {
-  Matrix
-} from "./chunk-AJNFI6GA.js";
-import {
-  filterJoin,
-  getNormalRoot
-} from "./chunk-WD7FZ5EE.js";
-import {
-  clusterMethodLst,
-  distanceMethodLst,
-  dofetch3
-} from "./chunk-4TJO2DGU.js";
-import {
-  TermTypes2Dt,
-  dictionaryNumericTypes
-} from "./chunk-JHLF2ZC2.js";
-import {
-  colorScaleMap
-} from "./chunk-WJLRU5OF.js";
-import {
-  deepEqual,
-  getCompInit
-} from "./chunk-HBNB5TRH.js";
-import {
-  extent,
-  linear
-} from "./chunk-4OLM3KSB.js";
-
-// plots/matrix/hierCluster.js
-var HierCluster = class _HierCluster extends Matrix {
-  static type = "hierCluster";
-  constructor(opts) {
-    super(opts);
-    this.type = _HierCluster.type;
-    this.chartType = _HierCluster.type;
-  }
-  async init(appState) {
-    await super.init(appState);
-    this.maySetSandboxHeader(appState);
-    this.hcClipId = this.seriesClipId + "-hc";
-    this.dom.hcClipRect = this.dom.svg.select("defs").append("clipPath").attr("id", this.hcClipId).attr("clipPathUnits", "userSpaceOnUse").append("rect").attr("display", "block");
-    this.dom.topDendrogram = this.dom.svg.insert("g", "g").attr("clip-path", `url(#${this.hcClipId})`).append("g").attr("class", "sjpp-matrix-dendrogram").attr("data-testid", "hierCluster_top_dendrogram").on("click", (event) => {
-      const clickedClusterId = this.getClusterFromTopDendrogram(event);
-      if (clickedClusterId) {
-        this.clickedClusterIds = this.getAllChildrenClusterIds(clickedClusterId);
-        this.clickedClusterIds.push(clickedClusterId);
-        const clickedCluster = this.hierClusterData.clustering.col.mergedClusters.get(clickedClusterId);
-        const clickedClusterSampleNames = clickedCluster.children.map((c) => c.name);
-        this.addSelectedSamplesOptions(clickedClusterSampleNames, event);
-      } else {
-        delete this.clickedClusterIds;
-      }
-      if (this.clickedLeftClusterIds) {
-        delete this.clickedLeftClusterIds;
-        this.plotDendrogramHclust();
-      } else this.plotDendrogramHclust("top");
-    });
-    this.dom.leftDendrogram = this.dom.svg.insert("g", "g").attr("class", "sjpp-matrix-dendrogram").attr("data-testid", "hierCluster_left_dendrogram").on("click", (event) => {
-      const clickedLeftClusterId = this.getClusterFromLeftDendrogram(event);
-      if (clickedLeftClusterId) {
-        this.clickedLeftClusterIds = this.getAllChildrenClusterIds(clickedLeftClusterId, true);
-        this.clickedLeftClusterIds.push(clickedLeftClusterId);
-        const clickedLeftCluster = this.hierClusterData.clustering.row.mergedClusters.get(clickedLeftClusterId);
-        const clickedLeftClusterRowsNames = clickedLeftCluster.children.map((c) => c.name);
-        this.addSelectedRowsOptions(clickedLeftClusterRowsNames, event);
-      } else {
-        delete this.clickedLeftClusterIds;
-      }
-      if (this.clickedClusterIds) {
-        delete this.clickedClusterIds;
-        this.plotDendrogramHclust();
-      } else this.plotDendrogramHclust("left");
-    });
-  }
-  async setHierClusterData(_data = {}) {
-    this.prevServerData = this.currServerData;
-    const [d, twlst] = await this.requestData({});
-    if (d.error) throw d.error;
-    this.currServerData = structuredClone(d);
-    if (!deepEqual(this.prevServerData, this.currServerData)) {
-      delete this.clickedClusterIds;
-      delete this.clickedLeftClusterIds;
-    }
-    const s = this.settings.hierCluster;
-    if (!d.clustering) {
-      if (d.gene) {
-        throw `Cannot do clustering: data is only available for 1 gene (${d.gene}). Try again by adding more genes.`;
-      }
-    }
-    this.hierClusterData = d;
-    const c = this.hierClusterData.clustering;
-    this.setHierColorScale(c);
-    const samples = {};
-    for (const [i, column] of c.col.order.entries()) {
-      samples[column.name] = { sample: column.name };
-      for (const [j, row] of c.row.order.entries()) {
-        const tw = twlst.find((tw2) => tw2.$id === row.name || tw2.id === row.name);
-        const value = c.matrix[j][i];
-        samples[column.name][tw.$id] = {
-          key: tw.term.name,
-          values: [
-            {
-              sample: column.name,
-              dt: TermTypes2Dt[this.state.config.dataType],
-              label: s.termGroupName,
-              // gene: tw.term.name,
-              // chr: tw.term.chr,
-              // pos: `${tw.term.start}-${tw.term.stop}`,
-              value
-              // the color will be computed in matrix.cells, so that
-              // it can get updated even when there are no nonsetting state diff
-            }
-          ]
-        };
-      }
-    }
-    this.hcTermNameOrder = this.settings.hierCluster.sortClusterRows == "asListed" ? twlst.map((t) => t.term.name) : this.settings.hierCluster.sortClusterRows == "byName" ? twlst.map((t) => t.term.name).sort() : dictionaryNumericTypes.has(this.config.dataType) ? c.row.order.map((row) => twlst.find((t) => t.$id == row.name || t.term.id == row.name)?.term.name) : c.row.order.map((row) => twlst.find((t) => t.$id == row.name)?.term.name);
-    if (this.hcTermNameOrder.includes(void 0)) throw `unable to map row.name to term.name`;
-    this.hcTermSorter = (a, b) => {
-      const i = this.hcTermNameOrder.indexOf(a.tw.term.name);
-      const j = this.hcTermNameOrder.indexOf(b.tw.term.name);
-      if (i == -1 && j == -1) return 0;
-      if (i == -1) return 1;
-      if (j == -1) return -1;
-      return i - j;
-    };
-    this.hcSampleNameOrder = c.col.order.map((col) => col.name);
-    this.hcSampleSorter = (a, b) => {
-      const i = this.hcSampleNameOrder.indexOf(a.sample);
-      const j = this.hcSampleNameOrder.indexOf(b.sample);
-      if (i == -1 && j == -1) return 0;
-      if (i == -1) return 1;
-      if (j == -1) return -1;
-      return i - j;
-    };
-    const byTermId = {};
-    for (const tw of twlst) {
-      if (d.byTermId?.[tw.term.name]) byTermId[tw.$id] = d.byTermId[tw.term.name];
-    }
-    this.hierClusterSamples = {
-      refs: { byTermId, bySampleId: d.bySampleId },
-      lst: c.col.order.map((c2) => samples[c2.name]),
-      samples,
-      removedHierClusterTerms: d.removedHierClusterTerms
-    };
-  }
-  async requestData() {
-    const body = this.currRequestOpts?.hierCluster || this.getHCRequestBody(this.state);
-    const twlst = this.hcTermGroup.lst;
-    const data = await dofetch3("termdb/cluster", { body, signal: this.api.getAbortSignal?.() });
-    return [data, twlst];
-  }
-  getHCRequestBody(state) {
-    this.hcTermGroup = this.config.termgroups.find((grp) => grp.type == "hierCluster") || this.termOrder?.find((t) => t.grp.type == "hierCluster")?.grp;
-    const s = state.config.settings.hierCluster;
-    const dictionaryLegendFilter = {
-      type: "tvslst",
-      in: true,
-      join: "and",
-      lst: state.config.legendValueFilter.lst.filter((f) => !f.tvs.legendFilterType)
-    };
-    const terms = this.getClusterRowTermsAsParameter();
-    if (!terms.length) throw "no data";
-    if (!clusterMethodLst.find((i) => i.value == s.clusterMethod)) throw "Invalid cluster method";
-    if (!distanceMethodLst.find((i) => i.value == s.distanceMethod)) throw "Invalid distance method";
-    const body = {
-      genome: state.vocab.genome,
-      dslabel: state.vocab.dslabel,
-      dataType: state.config.dataType,
-      clusterMethod: s.clusterMethod,
-      distanceMethod: s.distanceMethod,
-      zScoreTransformation: s.zScoreTransformation,
-      terms,
-      filter: getNormalRoot(filterJoin([state.filter, dictionaryLegendFilter])),
-      filter0: state.filter0
-    };
-    if (state.config.dataType == "proteomeAbundance") {
-      body.proteomeDetails = {
-        organism: state.config.proteomeDetails?.organism,
-        assay: state.config.proteomeDetails?.assay,
-        cohort: state.config.proteomeDetails?.cohort
-      };
-    }
-    return body;
-  }
-  combineData() {
-    if (!this.hierClusterSamples) return;
-    const d = this.data;
-    const removedHierClusterTerms = this.hierClusterSamples.removedHierClusterTerms;
-    const samples = {};
-    const lst = [];
-    for (const sampleId in this.hierClusterSamples.samples) {
-      const s = this.hierClusterSamples.samples[sampleId];
-      samples[sampleId] = s;
-      lst.push(s);
-      if (sampleId in d.samples) Object.assign(s, d.samples[sampleId]);
-      const _ref_ = this.hierClusterSamples.refs.bySampleId[sampleId] || {};
-      if (!s._ref_) s._ref_ = _ref_;
-      else Object.assign(s._ref_, _ref_);
-    }
-    const t = this.hierClusterSamples.refs.byTermId;
-    for (const $id of Object.keys(t)) {
-      d.refs.byTermId[$id] = Object.assign({}, d.refs.byTermId[$id] || {}, t[$id]);
-    }
-    this.data = { samples, lst, refs: d.refs, removedHierClusterTerms };
-  }
-  setHierColorScale(c) {
-    const hc = this.settings.hierCluster;
-    const scale = linear(colorScaleMap[hc.colorScale].domain, colorScaleMap[hc.colorScale].range).clamp(true);
-    const globalMinMaxes = [];
-    for (const row of c.matrix) {
-      globalMinMaxes.push(...extent(row));
-    }
-    const absMax = Math.min(hc.zScoreCap, Math.max(...extent(globalMinMaxes).map(Math.abs)));
-    const [min, max] = hc.zScoreTransformation ? [-absMax, absMax] : [Math.min(...globalMinMaxes), Math.max(...globalMinMaxes)];
-    this.hierClusterValues = { scale, min, max };
-  }
-  getValueColor(value) {
-    const hc = this.settings.hierCluster;
-    if (hc.zScoreTransformation) {
-      const zScoreCap = this.settings.hierCluster.zScoreCap;
-      return this.hierClusterValues.scale((value - -zScoreCap) / (zScoreCap * 2));
-    } else {
-      return this.hierClusterValues.scale(value / this.hierClusterValues.max);
-    }
-  }
-  /* returns list of gene terms as request parameter, e.g. {gene,chr,start,stop}
-  	request parameter only need term but not tw, as it will simply fetch continuous sample values on terms without transform
-  
-  	use of this function is unfortunate because:
-  		the incomplete migration of {name} to {gene} for gene-based term
-  		geneset edit ui is hardcoded to return {name}
-  		existing plot states contain {name}
-  
-  	!!! migration instruction !!!
-  	- term.name is for display only, if a term is gene-based, it has term.gene=str
-  	- a geneVariant term can be based on a genomic range (and not a gene), in that case it won't have term.gene and cannot be used where gene is expected, e.g. gene-based clustering analysis
-  
-  	*/
-  getClusterRowTermsAsParameter() {
-    const lst = this.hcTermGroup.lst.map(this.opts.app.vocabApi.getTwMinCopy);
-    lst.sort((a, b) => a.term.name < b.term.name ? -1 : 1);
-    return lst;
-  }
-};
-for (const methods of [hierCluster_renderers_exports, hierCluster_interactivity_exports]) {
-  for (const methodName in methods) HierCluster.prototype[methodName] = methods[methodName];
-}
-var hierClusterInit = getCompInit(HierCluster);
-var componentInit = hierClusterInit;
-
-export {
-  HierCluster,
-  hierClusterInit,
-  componentInit
-};
-//# sourceMappingURL=chunk-IRQKX6DL.js.map