@sjcrh/proteinpaint-client 2.204.0 → 2.205.0

package/dist/block.tk.bedgraphdot-3F6AMWFD.js

@@ -1,379 +0,0 @@
-import {
-  appear2 as appear,
-  axisstyle,
-  bwSetting,
-  disappear2 as disappear,
-  rgb2hex
-} from "./chunk-7RX5UEF3.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-KV4W2ACA.js";
-import "./chunk-L42F5J5C.js";
-import "./chunk-HKQDZKSF.js";
-import "./chunk-ELJX3QIQ.js";
-import "./chunk-EEB5VE2A.js";
-import "./chunk-6RRZRISL.js";
-import "./chunk-2KM4PRQM.js";
-import {
-  dofetch
-} from "./chunk-FUSTNOQZ.js";
-import "./chunk-VSPUFGDX.js";
-import "./chunk-WVPFLPWB.js";
-import "./chunk-S5SOLLGM.js";
-import "./chunk-WINIL2KN.js";
-import "./chunk-PF4DSFDR.js";
-import "./chunk-D6G64XPJ.js";
-import "./chunk-W5J3LTYS.js";
-import {
-  axisLeft
-} from "./chunk-YLJOZP4P.js";
-import {
-  format,
-  linear
-} from "./chunk-HDTFYTEL.js";
-import "./chunk-FXQXCOII.js";
-import "./chunk-TLT4YIG3.js";
-import "./chunk-5R63Q5KH.js";
-import "./chunk-I6Y4O3RR.js";
-import "./chunk-Q5RDQNIT.js";
-import "./chunk-DQC5FFGV.js";
-import "./chunk-HS5PO5ZQ.js";
-
-// src/block.tk.bedgraphdot.js
-async function loadTk(tk, block) {
-  block.tkcloakon(tk);
-  block.block_setheight();
-  const _finish = loadTk_finish_closure(tk, block);
-  try {
-    if (tk.uninitialized) {
-      makeTk(tk, block);
-      delete tk.uninitialized;
-    }
-    await loadTk_do(tk, block);
-    _finish({});
-  } catch (e) {
-    tk.height_main = 50;
-    _finish({ error: e.message || e });
-    if (e.stack) console.log(e.stack);
-    return;
-  }
-}
-function loadTk_finish_closure(tk, block) {
-  return (data) => {
-    block.tkcloakoff(tk, { error: data.error });
-    block.block_setheight();
-    block.setllabel();
-  };
-}
-function makeTk(tk, block) {
-  if (!tk.scale) tk.scale = {};
-  if (Number.isFinite(tk.scale.min) && Number.isFinite(tk.scale.max)) {
-  } else {
-    tk.scale.auto = true;
-  }
-  if (!Number.isFinite(tk.barheight)) tk.barheight = 100;
-  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";
-  tk.leftaxis = tk.gleft.append("g");
-  tk.config_handle = block.maketkconfighandle(tk).on("click", () => {
-    tk.tkconfigtip.clear().showunder(tk.config_handle.node());
-  });
-}
-async function loadTk_do(tk, block) {
-  block.tkcloakon(tk);
-  const par = block.tkarg_q(tk);
-  par.rglst = rglst_quickfix(tk, block);
-  par.genome = block.genome.name;
-  tk.height_main = tk.toppad + tk.barheight + tk.bottompad;
-  tk.glider.selectAll("*").remove();
-  const data = await dofetch("tkbedgraphdot", par);
-  if (data.error) throw data.error;
-  tk.tklabel.transition().attr("y", tk.barheight / 2);
-  for (const r of data.rglst) {
-    const img = tk.glider.append("g").attr("transform", "translate(" + r.xoff + "," + tk.toppad + ")").append("image").attr("width", r.width).attr("height", tk.barheight).attr("xlink:href", r.img);
-  }
-  tk.leftaxis.selectAll("*").remove();
-  if (data.nodata) {
-    throw "no data in view range";
-  }
-  if (data.minv != void 0) {
-    tk.scale.min = data.minv;
-    tk.scale.max = data.maxv;
-  }
-  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
-  });
-}
-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 row = holder.append("div").style("margin-bottom", "15px");
-    row.append("span").html("Y scale&nbsp;&nbsp;");
-    const ss = row.append("select");
-    const ssop1 = ss.append("option").text("automatic");
-    const ssop2 = ss.append("option").text("fixed");
-    const ssop3 = ss.append("option").text("percentile");
-    ss.on("change", (event) => {
-      const si = event.target.selectedIndex;
-      if (si == 0) {
-        fixed.style("display", "none");
-        percentile.style("display", "none");
-        tk.scale.auto = 1;
-        loader(bwSetting.autoscale);
-        return;
-      }
-      if (si == 1) {
-        fixed.style("display", "block");
-        percentile.style("display", "none");
-        return;
-      }
-      fixed.style("display", "none");
-      percentile.style("display", "block");
-    });
-    let usingfixed = false, usingperc = false;
-    if (tk.scale.auto) {
-      ssop1.property("selected", 1);
-    } else {
-      if (tk.scale.percentile) {
-        usingperc = true;
-        ssop3.property("selected", 1);
-      } else {
-        usingfixed = true;
-        ssop2.property("selected", 1);
-      }
-    }
-    const fixed = row.append("div").style("margin", "10px").style("display", usingfixed ? "block" : "none");
-    {
-      const row1 = fixed.append("div");
-      row1.append("span").html("Max&nbsp;").style("font-family", "Courier").style("font-size", ".9em");
-      const max = row1.append("input").attr("size", 5);
-      if (usingfixed) {
-        max.property("value", tk.scale.max);
-      }
-      const row2 = fixed.append("div");
-      row2.append("span").html("Min&nbsp;").style("font-family", "Courier").style("font-size", ".9em");
-      const min = row2.append("input").attr("size", 5);
-      if (usingfixed) {
-        min.property("value", tk.scale.min);
-      }
-      row2.append("button").text("Set").style("margin-left", "5px").on("click", () => {
-        const s1 = max.property("value");
-        if (s1 == "") {
-          return;
-        }
-        const v1 = Number.parseFloat(s1);
-        if (Number.isNaN(v1)) {
-          alert("invalid max value");
-          return;
-        }
-        const s2 = min.property("value");
-        if (s2 == "") {
-          return;
-        }
-        const v2 = Number.parseFloat(s2);
-        if (Number.isNaN(v2)) {
-          alert("invalid min value");
-          return;
-        }
-        delete tk.scale.auto;
-        delete tk.scale.percentile;
-        tk.scale.max = v1;
-        tk.scale.min = v2;
-        loader(bwSetting.fixedscale);
-      });
-    }
-    const percentile = row.append("div").style("margin-top", "6px").style("display", usingperc ? "block" : "none");
-    {
-      percentile.append("span").html("Percentile&nbsp;").style("font-family", "Courier").style("font-size", ".9em");
-      const input = percentile.append("input").attr("size", 5);
-      if (usingperc) {
-        input.property("value", tk.scale.percentile);
-      }
-      const setpercentile = (s) => {
-        if (s == "") return;
-        const v = Number.parseInt(s);
-        if (Number.isNaN(v) || v <= 0 || v > 100) {
-          alert("percentile should be integer within range 0-100");
-          return;
-        }
-        delete tk.scale.auto;
-        tk.scale.percentile = v;
-        loader(bwSetting.percentilescale);
-      };
-      input.on("keyup", (event) => {
-        if (event.code != "Enter") return;
-        setpercentile(input.property("value"));
-      });
-      percentile.append("button").text("Set").style("margin-left", "5px").on("click", () => {
-        setpercentile(input.property("value"));
-      });
-    }
-  }
-  {
-    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;
-}
-function rglst_quickfix(tk, block) {
-  let rglst = block.tkarg_rglst(tk);
-  if (block.usegm) {
-    const r = rglst[0];
-    r.usegm_isoform = block.usegm.isoform;
-    for (let i = 1; i < rglst.length; i++) {
-      const ri = rglst[i];
-      r.width += ri.width + block.regionspace;
-      r.start = Math.min(r.start, ri.start);
-      r.stop = Math.max(r.stop, ri.stop);
-    }
-    rglst = [r];
-  }
-  let xoff = 0;
-  for (const r of rglst) {
-    r.xoff = 0;
-    xoff += r.width + block.regionspace;
-  }
-  if (block.subpanels.length == tk.subpanels.length) {
-    for (const r of block.subpanels) {
-      rglst.push({
-        chr: r.chr,
-        start: r.start,
-        stop: r.stop,
-        width: r.width,
-        exonsf: r.exonsf,
-        xoff
-      });
-      xoff += r.width + r.leftpad;
-    }
-  }
-  return rglst;
-}
-export {
-  bigwigconfigpanel,
-  loadTk,
-  loadTk_do
-};
-//# sourceMappingURL=block.tk.bedgraphdot-3F6AMWFD.js.map

package/dist/block.tk.bigwig.ui-QO334QC3.js

@@ -1,206 +0,0 @@
-import {
-  isURL,
-  makeBtn,
-  makeGenomeDropDown,
-  makePrompt,
-  makeResetBtn,
-  makeTextAreaInput,
-  makeTextInput
-} from "./chunk-5EBRF6Z7.js";
-import {
-  Tabs,
-  appear,
-  first_genetrack_tolist
-} from "./chunk-7RX5UEF3.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-KV4W2ACA.js";
-import "./chunk-L42F5J5C.js";
-import "./chunk-HKQDZKSF.js";
-import "./chunk-ELJX3QIQ.js";
-import "./chunk-EEB5VE2A.js";
-import "./chunk-6RRZRISL.js";
-import "./chunk-2KM4PRQM.js";
-import "./chunk-FUSTNOQZ.js";
-import "./chunk-VSPUFGDX.js";
-import "./chunk-WVPFLPWB.js";
-import "./chunk-S5SOLLGM.js";
-import "./chunk-WINIL2KN.js";
-import "./chunk-PF4DSFDR.js";
-import "./chunk-D6G64XPJ.js";
-import "./chunk-W5J3LTYS.js";
-import "./chunk-YLJOZP4P.js";
-import "./chunk-HDTFYTEL.js";
-import "./chunk-FXQXCOII.js";
-import "./chunk-TLT4YIG3.js";
-import "./chunk-5R63Q5KH.js";
-import {
-  select_default
-} from "./chunk-I6Y4O3RR.js";
-import "./chunk-Q5RDQNIT.js";
-import "./chunk-DQC5FFGV.js";
-import "./chunk-HS5PO5ZQ.js";
-
-// src/block.tk.bigwig.ui.js
-async function bigwigUI(genomes, holder) {
-  const wrapper = holder.append("div").style("margin", "5px 5px 5px 20px").style(
-    "font-family",
-    "'Lucida Sans', 'Lucida Sans Regular', 'Lucida Grande', 'Lucida Sans Unicode', Geneva, Verdana, sans-serif"
-  ).classed("sjpp-bw-ui", true).style("overflow", "hidden");
-  const obj = {};
-  makePrompt(wrapper, "Select Genome").style("font-size", "1.15em").style("padding", "10px 0px").style("color", "#003366");
-  genomeSelection(wrapper, genomes, obj);
-  makePrompt(wrapper, "Provide Data").style("font-size", "1.15em").style("padding", "20px 0px 10px 0px").style("color", "#003366");
-  const tabs_div = wrapper.append("div").style("margin-left", "40px");
-  makeTrackEntryTabs(tabs_div, obj);
-  const controlBtnsDiv = wrapper.append("div").style("display", "flex").style("align-items", "center").style("margin", "40px 0px 40px 130px");
-  submitButton(controlBtnsDiv, obj, holder, genomes);
-  makeResetBtn(controlBtnsDiv, obj, ".sjpp_bigwigUI_input").style("margin", "0px 20px 20px 0px");
-  infoSection(wrapper, obj);
-}
-function makeTrackEntryTabs(tabs_div, obj) {
-  const tabs = [
-    {
-      label: "Single Track",
-      callback: async (event, tab) => {
-        tab.contentHolder.style("border", "none").style("display", "block");
-        const singlediv = tab.contentHolder.append("div").style("border", "none");
-        appear(tab.contentHolder);
-        makePrompt(singlediv, "Name");
-        trackNameInput(singlediv, obj);
-        makePrompt(singlediv, "File Path");
-        trackFilePathInput(singlediv, obj);
-        delete tab.callback;
-      }
-    },
-    {
-      label: "Multiple Tracks",
-      callback: async (event, tab) => {
-        tab.contentHolder.style("border", "none").style("display", "block");
-        appear(tab.contentHolder);
-        tab.contentHolder.append("div").html(
-          '<p style="margin-left: 10px;">Enter one track per line in the following format: [track name],[path/to/file.bw or URL]</p><p style="margin-left: 20px; color: #7d7c7c;">e.g. BigWig Track, proteinpaint_demo/hg19/bigwig/file.bw</p>'
-        );
-        multiTrackInput(tab.contentHolder, obj);
-        delete tab.callback;
-      }
-    }
-  ];
-  new Tabs({ holder: tabs_div, tabs }).main();
-}
-async function genomeSelection(div, genomes, obj) {
-  const genome_div = div.append("div").style("margin-left", "40px");
-  const g = makeGenomeDropDown(genome_div, genomes).style("border", "1px solid rgb(138, 177, 212)");
-  obj.genomeselect = g.node();
-}
-function trackNameInput(div, obj) {
-  const track_div = div.append("div").style("margin-left", "10px");
-  const name = makeTextInput(track_div, "BigWig track").style("border", "1px solid rgb(138, 177, 212)").classed("sjpp_bigwigUI_input", true).on("keyup", async () => {
-    obj.trackname = name.property("value").trim();
-  });
-}
-function trackFilePathInput(div, obj) {
-  const track_div = div.append("div").style("margin-left", "10px");
-  const filepath = makeTextInput(track_div).style("border", "1px solid rgb(138, 177, 212)").classed("sjpp_bigwigUI_input", true).on("keyup", async () => {
-    obj.filepath = filepath.property("value").trim();
-    obj.tabInUse = "single";
-  });
-}
-function multiTrackInput(div, obj) {
-  const pasteTrack_div = div.append("div").style("display", "block");
-  const multi = makeTextAreaInput({ div: pasteTrack_div }).style("border", "1px solid rgb(138, 177, 212)").style("margin", "0px 0px 0px 20px").classed("sjpp_bigwigUI_input", true).on("keyup", async () => {
-    obj.multitrackdata = multi.property("value").trim();
-    obj.tabInUse = "multi";
-  });
-}
-function submitButton(div, obj, holder, genomes) {
-  const submit = makeBtn({
-    div,
-    text: "Submit"
-  });
-  submit.style("margin", "0px 20px 20px 60px").style("font-size", "16px").on("click", () => {
-    const runpp_arg = {
-      holder: holder.append("div").style("margin", "20px").node(),
-      /** Do not use window.location.origin. See comment: line 180, renderContent(), client/appdrawer/adSandbox.js*/
-      host: sessionStorage.getItem("hostURL")
-    };
-    const bigwig_arg = validateInput(obj, genomes);
-    if (!bigwig_arg) return;
-    select_default(".sjpp-bw-ui").remove();
-    runproteinpaint(Object.assign(runpp_arg, bigwig_arg));
-  });
-}
-function validateInput(obj, genomes) {
-  if (!obj.filepath && !obj.multitrackdata) {
-    alert("Provide data for either a single track or multiple tracks.");
-    return;
-  }
-  let genome = obj.genomeselect.options[obj.genomeselect.selectedIndex].text;
-  const runpp_args = {
-    block: true,
-    nobox: 1,
-    noheader: true,
-    genome,
-    tracks: []
-  };
-  const g = genomes[genome];
-  if (obj.tabInUse == "single") {
-    let file, url;
-    if (isURL(obj.filepath)) url = obj.filepath;
-    else file = obj.filepath;
-    const tk = {
-      type: "bigwig",
-      name: obj.trackname || "BigWig track",
-      file,
-      url,
-      scale: {
-        auto: 1
-      }
-    };
-    runpp_args.tracks.push(tk);
-    first_genetrack_tolist(g, runpp_args.tracks);
-    return runpp_args;
-  }
-  if (obj.tabInUse == "multi") {
-    for (const data of obj.multitrackdata.split(/[\r\n]/)) {
-      const line = data.split(",");
-      if (line[0] && !line[1]) alert("Problem with submission. Are commas between the track names and filepaths?");
-      if (line[0] && line[1]) {
-        let file, url;
-        const tmp = line[1].trim();
-        if (isURL(tmp)) url = tmp;
-        else file = tmp;
-        const tk = {
-          type: "bigwig",
-          name: line[0].trim(),
-          file,
-          url,
-          scale: {
-            auto: 1
-          },
-          iscustom: true
-        };
-        runpp_args.tracks.push(tk);
-      }
-    }
-    first_genetrack_tolist(g, runpp_args.tracks);
-    return runpp_args;
-  }
-  throw "unknown option";
-}
-function infoSection(div) {
-  div.append("div").style("margin", "10px").style("opacity", "0.65").style("line-height", "1.5").html(`<ul>
-                <li>
-                    <a href=https://docs.google.com/document/d/1ZnPZKSSajWyNISSLELMozKxrZHQbdxQkkkQFnxw6zTs/edit#heading=h.6spyog171fm9 target=_blank>BigWig track documentation</a>
-                </li>
-                <li>
-                    <a href=https://proteinpaint.stjude.org/ppdemo/hg19/bigwig/file.bw target=_blank>Example file</a>
-                </li>
-                <li>
-                    Please see the <a href=https://genome.ucsc.edu/goldenpath/help/bigWig.html target=_blank>UCSC documention</a> for information on bigWig file formatting.
-                </li>
-            </ul>`);
-}
-export {
-  bigwigUI
-};
-//# sourceMappingURL=block.tk.bigwig.ui-QO334QC3.js.map