@sjcrh/proteinpaint-client 2.220.0 → 2.221.0

package/dist/matrix.interactivity-MGOYEKDN.js

@@ -1,33 +0,0 @@
-import {
-  getConfigForShowAll,
-  setInteractivity,
-  showAll
-} from "./chunk-GK5QS5BR.js";
-import "./chunk-PEKCVKJK.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-YR6EXI2K.js";
-import "./chunk-CNFTQSNE.js";
-import "./chunk-RIHO7ZD5.js";
-import "./chunk-TVJOSRCH.js";
-import "./chunk-3CIL7KH7.js";
-import "./chunk-T4XPCSLP.js";
-import "./chunk-4TJO2DGU.js";
-import "./chunk-W5J3LTYS.js";
-import "./chunk-MHWYRNGA.js";
-import "./chunk-JHLF2ZC2.js";
-import "./chunk-WJLRU5OF.js";
-import "./chunk-HBNB5TRH.js";
-import "./chunk-PF4DSFDR.js";
-import "./chunk-4OLM3KSB.js";
-import "./chunk-6XKAOSQE.js";
-import "./chunk-TLT4YIG3.js";
-import "./chunk-5R63Q5KH.js";
-import "./chunk-I6Y4O3RR.js";
-import "./chunk-Q5RDQNIT.js";
-import "./chunk-HS5PO5ZQ.js";
-export {
-  getConfigForShowAll,
-  setInteractivity,
-  showAll
-};
-//# sourceMappingURL=matrix.interactivity-MGOYEKDN.js.map

package/dist/matrix.layout-T7EC5ZC2.js

@@ -1,35 +0,0 @@
-import {
-  getMaxGrpLabelWidth,
-  setAutoDimensions,
-  setLabelsAndScales,
-  setLayout
-} from "./chunk-DZDK64XY.js";
-import "./chunk-PEKCVKJK.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-YR6EXI2K.js";
-import "./chunk-CNFTQSNE.js";
-import "./chunk-RIHO7ZD5.js";
-import "./chunk-TVJOSRCH.js";
-import "./chunk-3CIL7KH7.js";
-import "./chunk-T4XPCSLP.js";
-import "./chunk-4TJO2DGU.js";
-import "./chunk-W5J3LTYS.js";
-import "./chunk-MHWYRNGA.js";
-import "./chunk-JHLF2ZC2.js";
-import "./chunk-WJLRU5OF.js";
-import "./chunk-HBNB5TRH.js";
-import "./chunk-PF4DSFDR.js";
-import "./chunk-4OLM3KSB.js";
-import "./chunk-6XKAOSQE.js";
-import "./chunk-TLT4YIG3.js";
-import "./chunk-5R63Q5KH.js";
-import "./chunk-I6Y4O3RR.js";
-import "./chunk-Q5RDQNIT.js";
-import "./chunk-HS5PO5ZQ.js";
-export {
-  getMaxGrpLabelWidth,
-  setAutoDimensions,
-  setLabelsAndScales,
-  setLayout
-};
-//# sourceMappingURL=matrix.layout-T7EC5ZC2.js.map

package/dist/matrix.renderers-GR77V3RL.js

@@ -1,30 +0,0 @@
-import {
-  setRenderers
-} from "./chunk-HJKVYTYK.js";
-import "./chunk-C2MCQZWH.js";
-import "./chunk-PEKCVKJK.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-YR6EXI2K.js";
-import "./chunk-CNFTQSNE.js";
-import "./chunk-RIHO7ZD5.js";
-import "./chunk-TVJOSRCH.js";
-import "./chunk-3CIL7KH7.js";
-import "./chunk-T4XPCSLP.js";
-import "./chunk-4TJO2DGU.js";
-import "./chunk-W5J3LTYS.js";
-import "./chunk-MHWYRNGA.js";
-import "./chunk-JHLF2ZC2.js";
-import "./chunk-WJLRU5OF.js";
-import "./chunk-HBNB5TRH.js";
-import "./chunk-PF4DSFDR.js";
-import "./chunk-4OLM3KSB.js";
-import "./chunk-6XKAOSQE.js";
-import "./chunk-TLT4YIG3.js";
-import "./chunk-5R63Q5KH.js";
-import "./chunk-I6Y4O3RR.js";
-import "./chunk-Q5RDQNIT.js";
-import "./chunk-HS5PO5ZQ.js";
-export {
-  setRenderers
-};
-//# sourceMappingURL=matrix.renderers-GR77V3RL.js.map

package/dist/matrix.sort.unit.spec-YUCV7G5L.js

@@ -1,464 +0,0 @@
-import {
-  getPlotConfig
-} from "./chunk-Z53VY5JV.js";
-import {
-  getSampleSorter,
-  getSortOptions
-} from "./chunk-5DI4UNH5.js";
-import "./chunk-C2MCQZWH.js";
-import {
-  require_tape
-} from "./chunk-PJYCTAMC.js";
-import "./chunk-PEKCVKJK.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-YR6EXI2K.js";
-import "./chunk-CNFTQSNE.js";
-import "./chunk-RIHO7ZD5.js";
-import "./chunk-TVJOSRCH.js";
-import "./chunk-3CIL7KH7.js";
-import "./chunk-T4XPCSLP.js";
-import "./chunk-4TJO2DGU.js";
-import "./chunk-W5J3LTYS.js";
-import "./chunk-MHWYRNGA.js";
-import "./chunk-JHLF2ZC2.js";
-import {
-  CNVClasses,
-  mutationClasses,
-  proteinChangingMutations,
-  synonymousMutations,
-  truncatingMutations
-} from "./chunk-WJLRU5OF.js";
-import "./chunk-HBNB5TRH.js";
-import "./chunk-PF4DSFDR.js";
-import "./chunk-4OLM3KSB.js";
-import "./chunk-6XKAOSQE.js";
-import "./chunk-TLT4YIG3.js";
-import "./chunk-5R63Q5KH.js";
-import "./chunk-I6Y4O3RR.js";
-import "./chunk-Q5RDQNIT.js";
-import {
-  __toESM
-} from "./chunk-HS5PO5ZQ.js";
-
-// plots/matrix/test/matrix.sort.unit.spec.js
-var import_tape = __toESM(require_tape(), 1);
-var terms = {
-  aaa: { name: "aaa", type: "geneVariant" },
-  bbb: { name: "bbb", type: "geneVariant" },
-  ccc: { name: "ccc", type: "geneVariant" }
-};
-async function getArgs(_settings = {}) {
-  const samples = {
-    1: {
-      sample: 1,
-      bbb: {
-        values: [{ dt: 1, class: "M" }]
-      },
-      ccc: {
-        values: [{ dt: 1, class: "M" }]
-      }
-    },
-    2: {
-      sample: 2,
-      aaa: {
-        values: [{ dt: 1, class: "M" }]
-      },
-      bbb: {
-        values: [{ dt: 1, class: "M" }]
-      }
-    },
-    3: {
-      sample: 3,
-      aaa: {
-        values: [
-          { dt: 1, class: "F" },
-          { dt: 4, class: "CNV_loss" }
-        ]
-      },
-      ccc: {
-        values: [{ dt: 1, class: "M" }]
-      }
-    },
-    4: {
-      sample: 4,
-      ccc: {
-        values: [{ dt: 1, class: "M" }]
-      }
-    },
-    5: {
-      sample: 5,
-      aaa: {
-        values: [{ dt: 1, class: "M" }]
-      },
-      bbb: {
-        values: [{ dt: 1, class: "M" }]
-      }
-    }
-  };
-  const sg = [
-    {
-      name: "Sample Group 1",
-      lst: [samples["1"], samples["2"], samples["3"]]
-    },
-    {
-      name: "Sample Group 2",
-      lst: [samples["4"], samples["5"]]
-    }
-  ];
-  const tg = [
-    {
-      name: "Term Group 1",
-      lst: [
-        { $id: "aaa", term: terms.aaa, q: { type: "values" } },
-        { $id: "bbb", term: terms.bbb, q: { type: "values" } },
-        { $id: "ccc", term: terms.ccc, q: { type: "values" } }
-      ]
-    }
-  ];
-  const app = { vocabApi: { termdbConfig: {} } };
-  const config = await getPlotConfig(
-    {
-      settings: {
-        matrix: {
-          sortSamplesTieBreakers: [{ $id: "sample", sortSamples: { by: "sample" } }],
-          sortByMutation: "presence",
-          sortByCNV: false,
-          hiddenVariants: [],
-          proteinChangingMutations,
-          truncatingMutations,
-          synonymousMutations,
-          mutationClasses,
-          CNVClasses,
-          ..._settings
-        }
-      }
-    },
-    app
-  );
-  const settings = config.settings;
-  config.sortOptions = getSortOptions(void 0, void 0, settings.matrix);
-  const rows = Object.values(samples);
-  return {
-    self: {
-      app,
-      config,
-      termGroups: tg,
-      sampleGroups: sg,
-      sampleOrder: [
-        {
-          grp: sg[0],
-          grpIndex: 0,
-          index: sg[0].lst.findIndex((s) => s.sample === 1),
-          row: samples["1"]
-        },
-        {
-          grp: sg[0],
-          grpIndex: 0,
-          index: sg[0].lst.findIndex((s) => s.sample === 2),
-          row: samples["2"]
-        },
-        {
-          grp: sg[0],
-          grpIndex: 0,
-          index: sg[0].lst.findIndex((s) => s.sample === 3),
-          row: samples["3"]
-        },
-        {
-          grp: sg[1],
-          grpIndex: 1,
-          index: sg[1].lst.findIndex((s) => s.sample === 4),
-          row: samples["4"]
-        },
-        {
-          grp: sg[1],
-          grpIndex: 1,
-          index: sg[1].lst.findIndex((s) => s.sample === 5),
-          row: samples["5"]
-        }
-      ],
-      termOrder: [
-        {
-          grp: tg[0],
-          grpIndex: 0,
-          counts: rows.filter((r) => "aaa" in r).length,
-          index: tg[0].lst.findIndex((tw) => tw.term.name == "aaa"),
-          tw: tg[0].lst.find((tw) => tw.term.name == "aaa")
-        },
-        {
-          grp: tg[0],
-          grpIndex: 0,
-          counts: rows.filter((r) => "bbb" in r).length,
-          index: tg[0].lst.findIndex((tw) => tw.term.name == "bbb"),
-          tw: tg[0].lst.find((tw) => tw.term.name == "bbb")
-        },
-        {
-          grp: tg[0],
-          grpIndex: 0,
-          counts: rows.filter((r) => "ccc" in r).length,
-          index: tg[0].lst.findIndex((tw) => tw.term.name == "ccc"),
-          tw: tg[0].lst.find((tw) => tw.term.name == "ccc")
-        }
-      ]
-    },
-    settings: settings.matrix,
-    rows: Object.values(samples)
-  };
-}
-function simpleMatrix(sampleNames, termOrder, rows) {
-  const lst = [];
-  for (const sn of sampleNames) lst.push(...sn);
-  rows.sort((a, b) => lst.indexOf(a.sample) - lst.indexOf(b.sample));
-  const matrix = termOrder.map(() => []);
-  for (const r of rows) {
-    for (const [i, m] of matrix.entries()) {
-      m.push(termOrder[i].tw.$id in r ? `${r.sample}` : " ");
-    }
-  }
-  return matrix;
-}
-(0, import_tape.default)("\n", function(test) {
-  test.comment("-***- plots/matrix.sort -***-");
-  test.end();
-});
-(0, import_tape.default)("sortSamplesBy = asListed", async (test) => {
-  test.timeoutAfter(1e3);
-  test.plan(2);
-  const { self, settings, rows } = await getArgs({ sortSamplesBy: "asListed" });
-  self.asListedSampleOrder = [1, 2, 3, 4, 5];
-  const sorter = getSampleSorter(self, settings, rows);
-  const sampleNames = self.sampleGroups.map((g) => g.lst.sort(sorter).map((s) => s.sample));
-  test.deepEqual(
-    sampleNames,
-    [
-      [1, 2, 3],
-      [4, 5]
-    ],
-    "should sort the samples as listed"
-  );
-  test.deepEqual(
-    simpleMatrix(sampleNames, self.termOrder, rows),
-    // prettier-ignore
-    [
-      [" ", "2", "3", " ", "5"],
-      ["1", "2", " ", " ", "5"],
-      ["1", " ", "3", "4", " "]
-    ],
-    "should sort sample and rows in the expected order"
-  );
-  test.end();
-});
-(0, import_tape.default)("sortPriority by Mutation categories, default no value sorting, that uses a filter", async (test) => {
-  test.timeoutAfter(1e3);
-  test.plan(2);
-  const { self, settings, rows } = await getArgs({
-    sortSamplesBy: "a"
-  });
-  const sorter = getSampleSorter(self, settings, rows);
-  const sampleNames = self.sampleGroups.map((g) => g.lst.sort(sorter).map((s) => s.sample));
-  test.deepEqual(
-    sampleNames,
-    [
-      // NOTE on 5/29/2024:
-      // When prioritizing truncating mutations, samples with F (truncating)
-      // will be sorted before samples with only M (non-truncating)
-      // for a given gene row
-      [3, 2, 1],
-      [5, 4]
-    ],
-    "should sort the samples by dt then value"
-  );
-  test.deepEqual(
-    simpleMatrix(sampleNames, self.termOrder, rows),
-    // prettier-ignore
-    [
-      ["3", "2", " ", "5", " "],
-      [" ", "2", "1", "5", " "],
-      ["3", " ", "1", " ", "4"]
-    ],
-    "should sort sample and rows in the expected order"
-  );
-  test.end();
-});
-(0, import_tape.default)("sortPriority by Mutation categories with value sorting, that uses a filter", async (test) => {
-  test.timeoutAfter(1e3);
-  test.plan(2);
-  const { self, settings, rows } = await getArgs({
-    sortSamplesBy: "a",
-    showMatrixMutation: "onlyPC",
-    showMatrixCNV: "all"
-  });
-  const tb = settings.sortOptions.a.sortPriority[0].tiebreakers[2];
-  tb.disabled = false;
-  tb.isOrdered = true;
-  const sorter = getSampleSorter(self, settings, rows);
-  const sampleNames = self.sampleGroups.map((g) => g.lst.sort(sorter).map((s) => s.sample));
-  test.deepEqual(
-    sampleNames,
-    [
-      [3, 2, 1],
-      [5, 4]
-    ],
-    "should sort the samples by dt then value"
-  );
-  test.deepEqual(
-    simpleMatrix(sampleNames, self.termOrder, rows),
-    // prettier-ignore
-    [
-      ["3", "2", " ", "5", " "],
-      [" ", "2", "1", "5", " "],
-      ["3", " ", "1", " ", "4"]
-    ],
-    "should sort sample and rows in the expected order"
-  );
-  test.end();
-});
-(0, import_tape.default)("custom sortPriority, without filter", async (test) => {
-  test.timeoutAfter(1e3);
-  test.plan(2);
-  const { self, settings, rows } = await getArgs({
-    sortSamplesBy: "custom",
-    sortOptions: {
-      custom: {
-        value: "custom",
-        sortPriority: [
-          {
-            types: ["geneVariant"],
-            tiebreakers: [
-              {
-                by: "dt",
-                order: [1]
-                // snvindel, cnv,
-                // other dt values will be ordered last
-                // for the sorter to not consider certain dt values,
-                // need to explicitly not use such values for sorting
-                // ignore: [4]
-              },
-              {
-                by: "class",
-                order: [
-                  // truncating
-                  "F",
-                  "N",
-                  // indel
-                  "D",
-                  "I",
-                  // point
-                  "M",
-                  "P",
-                  "L",
-                  // noncoding
-                  "Utr3",
-                  "Utr5",
-                  "S",
-                  "Intron"
-                ]
-              }
-            ]
-          },
-          {
-            types: ["geneVariant"],
-            tiebreakers: [
-              {
-                by: "dt",
-                order: [4]
-                // snvindel, cnv,
-                // other dt values will be ordered last
-                // for the sorter to not consider certain dt values,
-                // need to explicitly not use such values for sorting
-                // ignore: [4]
-              },
-              {
-                by: "class",
-                order: [
-                  // Lou and JZ wanted samples with CNV to be sorted first??
-                  "CNV_loss",
-                  "CNV_amp"
-                ]
-              }
-            ]
-          }
-        ]
-      }
-    }
-  });
-  const sorter = getSampleSorter(self, settings, rows);
-  const sampleNames = self.sampleGroups.map((g) => g.lst.sort(sorter).map((s) => s.sample));
-  test.deepEqual(
-    sampleNames,
-    [
-      [3, 2, 1],
-      [5, 4]
-    ],
-    "should sort the samples by dt then value"
-  );
-  test.deepEqual(
-    simpleMatrix(sampleNames, self.termOrder, rows),
-    // prettier-ignore
-    [
-      ["3", "2", " ", "5", " "],
-      [" ", "2", "1", "5", " "],
-      ["3", " ", "1", " ", "4"]
-    ],
-    "should sort sample and rows in the expected order"
-  );
-  test.end();
-});
-(0, import_tape.default)("sort against selectedTerms", async (test) => {
-  test.timeoutAfter(1e3);
-  test.plan(2);
-  const { self, settings, rows } = await getArgs({ sortSamplesBy: "dt" });
-  self.termGroups[0].lst[1].sortSamples = {};
-  settings.sortSamplesBy = "a";
-  const sorter = getSampleSorter(self, settings, rows);
-  const sampleNames = self.sampleGroups.map((g) => g.lst.sort(sorter).map((s) => s.sample));
-  test.deepEqual(
-    sampleNames,
-    [
-      [2, 1, 3],
-      [5, 4]
-    ],
-    "should sort the samples by dt-only"
-  );
-  test.deepEqual(
-    simpleMatrix(sampleNames, self.termOrder, rows),
-    // prettier-ignore
-    [
-      ["2", " ", "3", "5", " "],
-      ["2", "1", " ", "5", " "],
-      [" ", "1", "3", " ", "4"]
-    ],
-    "should sort sample and rows in the expected order"
-  );
-  test.end();
-});
-(0, import_tape.default)("getSampleSorter() should apply an opts.skipSorter() argument", async (test) => {
-  test.timeoutAfter(1e3);
-  test.plan(2);
-  const { self, settings, rows } = await getArgs({
-    sortSamplesBy: "a"
-  });
-  const sorter = getSampleSorter(self, settings, rows, {
-    skipSorter: (p, tw) => tw.term.name == "aaa"
-  });
-  const sampleNames = self.sampleGroups.map((g) => g.lst.sort(sorter).map((s) => s.sample));
-  test.deepEqual(
-    sampleNames,
-    [
-      [1, 2, 3],
-      [5, 4]
-    ],
-    "should sort the samples by dt then value"
-  );
-  test.deepEqual(
-    simpleMatrix(sampleNames, self.termOrder, rows),
-    // prettier-ignore
-    [
-      [" ", "2", "3", "5", " "],
-      ["1", "2", " ", "5", " "],
-      ["1", " ", "3", " ", "4"]
-    ],
-    "should sort sample and rows in the expected order"
-  );
-  test.end();
-});
-//# sourceMappingURL=matrix.sort.unit.spec-YUCV7G5L.js.map