@platforma-sdk/ui-vue 1.42.4 → 1.42.8

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Files changed (26) hide show
  1. package/.turbo/turbo-build.log +13 -13
  2. package/.turbo/turbo-type-check.log +1 -1
  3. package/CHANGELOG.md +13 -0
  4. package/dist/components/PlMultiSequenceAlignment/MultiSequenceAlignmentView.vue.d.ts.map +1 -1
  5. package/dist/components/PlMultiSequenceAlignment/MultiSequenceAlignmentView.vue2.js +37 -29
  6. package/dist/components/PlMultiSequenceAlignment/MultiSequenceAlignmentView.vue2.js.map +1 -1
  7. package/dist/components/PlMultiSequenceAlignment/MultiSequenceAlignmentView.vue3.js +18 -14
  8. package/dist/components/PlMultiSequenceAlignment/MultiSequenceAlignmentView.vue3.js.map +1 -1
  9. package/dist/components/PlMultiSequenceAlignment/PlMultiSequenceAlignment.vue.d.ts.map +1 -1
  10. package/dist/components/PlMultiSequenceAlignment/PlMultiSequenceAlignment.vue2.js +100 -98
  11. package/dist/components/PlMultiSequenceAlignment/PlMultiSequenceAlignment.vue2.js.map +1 -1
  12. package/dist/components/PlMultiSequenceAlignment/data.d.ts +1 -1
  13. package/dist/components/PlMultiSequenceAlignment/data.js +18 -18
  14. package/dist/components/PlMultiSequenceAlignment/data.js.map +1 -1
  15. package/dist/composition/fileContent.d.ts.map +1 -1
  16. package/dist/composition/fileContent.js +57 -54
  17. package/dist/composition/fileContent.js.map +1 -1
  18. package/dist/lib/model/common/dist/index.js.map +1 -1
  19. package/dist/lib/ui/uikit/dist/lib/model/common/dist/index.js.map +1 -1
  20. package/dist/lib/ui/uikit/dist/sdk/model/dist/index.js +1 -1
  21. package/dist/sdk/model/dist/index.js +1 -1
  22. package/package.json +6 -6
  23. package/src/components/PlMultiSequenceAlignment/MultiSequenceAlignmentView.vue +65 -18
  24. package/src/components/PlMultiSequenceAlignment/PlMultiSequenceAlignment.vue +16 -11
  25. package/src/components/PlMultiSequenceAlignment/data.ts +10 -10
  26. package/src/composition/fileContent.ts +21 -9
@@ -1,17 +1,17 @@
1
- import { defineComponent as L, mergeModels as U, useModel as J, onBeforeMount as G, reactive as g, computed as R, watchEffect as N, useTemplateRef as H, createElementBlock as T, openBlock as f, Fragment as V, createVNode as j, createBlock as S, unref as i, withCtx as b, createTextVNode as k, toDisplayString as q, createCommentVNode as A, normalizeClass as K } from "vue";
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- import { isJsonEqual as I } from "../../lib/util/helpers/dist/index.js";
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+ import { defineComponent as U, mergeModels as J, useModel as G, onBeforeMount as H, reactive as h, computed as R, watchEffect as L, useTemplateRef as K, createElementBlock as N, openBlock as p, Fragment as T, createVNode as V, createBlock as S, unref as m, withCtx as b, createTextVNode as w, toDisplayString as q, createCommentVNode as j, normalizeClass as Q } from "vue";
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+ import { isJsonEqual as v } from "../../lib/util/helpers/dist/index.js";
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  import "../../lib/ui/uikit/dist/index.js";
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- import { getRawPlatformaInstance as Q } from "../../sdk/model/dist/index.js";
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- import { useSequenceColumnsOptions as W, useLabelColumnsOptions as X, useMarkupColumnsOptions as Y, useMultipleAlignmentData as Z, sequenceLimit as B } from "./data.js";
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- import { runMigrations as ee } from "./migrations.js";
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- import te from "./MultiSequenceAlignmentView.vue.js";
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- import { defaultSettings as D } from "./settings.js";
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- import oe from "./Toolbar.vue.js";
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+ import { getRawPlatformaInstance as W } from "../../sdk/model/dist/index.js";
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+ import { useSequenceColumnsOptions as X, useLabelColumnsOptions as Y, useMarkupColumnsOptions as Z, useMultipleAlignmentData as ee, sequenceLimit as A } from "./data.js";
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+ import { runMigrations as te } from "./migrations.js";
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+ import oe from "./MultiSequenceAlignmentView.vue.js";
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+ import { defaultSettings as B } from "./settings.js";
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+ import ne from "./Toolbar.vue.js";
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  import P from "../../lib/ui/uikit/dist/components/PlAlert/PlAlert.vue.js";
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- import ne from "../../lib/ui/uikit/dist/components/PlSplash/PlSplash.vue.js";
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- const ge = /* @__PURE__ */ L({
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+ import se from "../../lib/ui/uikit/dist/components/PlSplash/PlSplash.vue.js";
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+ const he = /* @__PURE__ */ U({
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  __name: "PlMultiSequenceAlignment",
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- props: /* @__PURE__ */ U({
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+ props: /* @__PURE__ */ J({
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  pFrame: {},
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- const o = g({
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- pFrame: c.pFrame,
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+ pFrame: u.pFrame,
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+ pFrame: u.pFrame,
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+ }))), l = h(ee(() => ({
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+ pFrame: u.pFrame,
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  sequenceColumnIds: o.sequenceColumnIds,
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  labelColumnIds: o.labelColumnIds,
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- selection: c.selection,
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+ selection: u.selection,
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  colorScheme: o.colorScheme,
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  alignmentParams: o.alignmentParams
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- }))), w = new Intl.NumberFormat("en").format, _ = R(
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+ }))), I = new Intl.NumberFormat("en").format, D = R(
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@@ -53,7 +53,7 @@ const ge = /* @__PURE__ */ L({
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+ ...(y.data ?? []).map(({ label: t, value: n }) => ({
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@@ -61,82 +61,84 @@ const ge = /* @__PURE__ */ L({
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- N(() => {
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+ L(() => {
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  var n, e;
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+ ([s, r]) => !v(
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+ o[s],
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- var e, a, r, m;
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+ }), L(() => {
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+ var e, s, r;
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- (e = o.sequenceColumnIds) != null && e.some(
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- return !((u = C.data) != null && u.options.some(
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- ({ value: d }) => I(d, s)
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+ !f.isLoading && ((e = o.sequenceColumnIds) != null && e.some(
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+ (a) => {
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+ var i;
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+ return (((i = f.data) == null ? void 0 : i.options) ?? []).every(
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+ ({ value: c }) => !v(c, a)
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+ );
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  }
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- ) && t.push("sequenceColumnIds"), (a = o.labelColumnIds) != null && a.some(
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- (s) => {
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- var u;
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- return !((u = y.data) != null && u.options.some(
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- ({ value: d }) => I(d, s)
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- ));
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+ )) && t.push("sequenceColumnIds"), !g.isLoading && ((s = o.labelColumnIds) != null && s.some(
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+ (a) => {
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+ var i;
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+ return (((i = g.data) == null ? void 0 : i.options) ?? []).every(
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+ ({ value: c }) => !v(c, a)
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+ );
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- ) && t.push("labelColumnIds");
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+ )) && t.push("labelColumnIds");
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- ({ value: s }) => I(s, n)
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- )) && t.push("colorScheme"), t.length && E(Object.fromEntries(
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- t.map((s) => [s, void 0])
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+ !y.isLoading && n && (y.data ?? []).every(
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+ ({ value: a }) => !v(a, n)
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+ ) && t.push("colorScheme"), t.length && F(Object.fromEntries(
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+ t.map((a) => [a, void 0])
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  });
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- const $ = H("msa");
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- async function z() {
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- var d, F, M;
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- const t = (F = (d = Q()) == null ? void 0 : d.lsDriver) == null ? void 0 : F.exportToPdf;
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+ const _ = K("msa");
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+ async function $() {
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+ var O, E, M;
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+ const t = (E = (O = W()) == null ? void 0 : O.lsDriver) == null ? void 0 : E.exportToPdf;
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  if (!t)
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  return console.error(
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  "API getPlatformaRawInstance().lsDriver.exportToPdf is not available"
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- const n = (M = $.value) == null ? void 0 : M.rootEl;
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+ const n = (M = _.value) == null ? void 0 : M.rootEl;
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  e.id = `print-target-${crypto.randomUUID()}`;
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- const a = new CSSStyleSheet();
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- a.insertRule(`
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+ }`);
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+ const r = n.cloneNode(!0);
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+ r.dataset.prePrint = "", e.replaceChildren(r), document.body.appendChild(e);
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+ s.insertRule(`
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- margin: ${s};
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+ size: ${z};
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+ margin: ${c};
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+ return p(), N(T, null, [
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- "color-scheme-options": _.value,
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- onExport: z
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+ "sequence-column-options": (e = f.data) == null ? void 0 : e.options,
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@@ -1 +1 @@
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- {"version":3,"file":"PlMultiSequenceAlignment.vue2.js","sources":["../../../src/components/PlMultiSequenceAlignment/PlMultiSequenceAlignment.vue"],"sourcesContent":["<script lang=\"ts\" setup>\nimport { isJsonEqual } from '@milaboratories/helpers';\nimport {\n type ListOptionNormalized,\n PlAlert,\n PlSplash,\n} from '@milaboratories/uikit';\nimport {\n getRawPlatformaInstance,\n type PColumnPredicate,\n type PFrameHandle,\n type PlMultiSequenceAlignmentColorSchemeOption,\n type PlMultiSequenceAlignmentModel,\n type PlMultiSequenceAlignmentSettings,\n type PlSelectionModel,\n} from '@platforma-sdk/model';\nimport {\n computed,\n onBeforeMount,\n reactive,\n useTemplateRef,\n watchEffect,\n} from 'vue';\nimport {\n sequenceLimit,\n useLabelColumnsOptions,\n useMarkupColumnsOptions,\n useMultipleAlignmentData,\n useSequenceColumnsOptions,\n} from './data';\nimport { runMigrations } from './migrations';\nimport MultiSequenceAlignmentView from './MultiSequenceAlignmentView.vue';\nimport { defaultSettings } from './settings';\nimport Toolbar from './Toolbar.vue';\n\nconst model = defineModel<PlMultiSequenceAlignmentModel>({ default: {} });\n\nonBeforeMount(() => {\n runMigrations(model);\n});\n\nconst settings = reactive<PlMultiSequenceAlignmentSettings>({\n ...defaultSettings,\n});\n\nconst props = defineProps<{\n /**\n * Handle to PFrame created using `createPFrameForGraphs`.\n * Should contain all desired sequence and label columns.\n */\n readonly pFrame: PFrameHandle | undefined;\n /**\n * Return true if column should be shown in sequence columns dropdown.\n * By default, all sequence columns are selected.\n */\n readonly sequenceColumnPredicate: PColumnPredicate;\n /**\n * Row selection model (from `PlAgDataTableV2` or `GraphMaker`).\n * If not provided or empty, all rows will be considered selected.\n * Warning: should be forwarded as a field of `reactive` object\n */\n readonly selection?: PlSelectionModel;\n}>();\n\nconst sequenceColumns = reactive(useSequenceColumnsOptions(() => ({\n pFrame: props.pFrame,\n sequenceColumnPredicate: props.sequenceColumnPredicate,\n})));\n\nconst labelColumns = reactive(useLabelColumnsOptions(() => ({\n pFrame: props.pFrame,\n sequenceColumnIds: settings.sequenceColumnIds,\n})));\n\nconst markupColumns = reactive(useMarkupColumnsOptions(() => ({\n pFrame: props.pFrame,\n sequenceColumnIds: settings.sequenceColumnIds,\n})));\n\nconst multipleAlignmentData = reactive(useMultipleAlignmentData(() => ({\n pframe: props.pFrame,\n sequenceColumnIds: settings.sequenceColumnIds,\n labelColumnIds: settings.labelColumnIds,\n selection: props.selection,\n colorScheme: settings.colorScheme,\n alignmentParams: settings.alignmentParams,\n})));\n\nconst formatNumber = new Intl.NumberFormat('en').format;\n\nconst colorSchemeOptions = computed<\n ListOptionNormalized<PlMultiSequenceAlignmentColorSchemeOption>[]\n>(\n () => [\n {\n label: 'Chemical Properties',\n value: { type: 'chemical-properties' },\n },\n {\n label: 'No Color',\n value: { type: 'no-color' },\n },\n ...(markupColumns.data ?? 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+ {"version":3,"file":"PlMultiSequenceAlignment.vue2.js","sources":["../../../src/components/PlMultiSequenceAlignment/PlMultiSequenceAlignment.vue"],"sourcesContent":["<script lang=\"ts\" setup>\nimport { isJsonEqual } from '@milaboratories/helpers';\nimport {\n type ListOptionNormalized,\n PlAlert,\n PlSplash,\n} from '@milaboratories/uikit';\nimport {\n getRawPlatformaInstance,\n type PColumnPredicate,\n type PFrameHandle,\n type PlMultiSequenceAlignmentColorSchemeOption,\n type PlMultiSequenceAlignmentModel,\n type PlMultiSequenceAlignmentSettings,\n type PlSelectionModel,\n} from '@platforma-sdk/model';\nimport {\n computed,\n onBeforeMount,\n reactive,\n useTemplateRef,\n watchEffect,\n} from 'vue';\nimport {\n sequenceLimit,\n useLabelColumnsOptions,\n useMarkupColumnsOptions,\n useMultipleAlignmentData,\n useSequenceColumnsOptions,\n} from './data';\nimport { runMigrations } from './migrations';\nimport MultiSequenceAlignmentView from './MultiSequenceAlignmentView.vue';\nimport { defaultSettings } from './settings';\nimport Toolbar from './Toolbar.vue';\n\nconst model = defineModel<PlMultiSequenceAlignmentModel>({ default: {} });\n\nonBeforeMount(() => {\n runMigrations(model);\n});\n\nconst settings = reactive<PlMultiSequenceAlignmentSettings>({\n ...defaultSettings,\n});\n\nconst props = defineProps<{\n /**\n * Handle to PFrame created using `createPFrameForGraphs`.\n * Should contain all desired sequence and label columns.\n */\n readonly pFrame: PFrameHandle | undefined;\n /**\n * Return true if column should be shown in sequence columns dropdown.\n * By default, all sequence columns are selected.\n */\n readonly sequenceColumnPredicate: PColumnPredicate;\n /**\n * Row selection model (from `PlAgDataTableV2` or `GraphMaker`).\n * If not provided or empty, all rows will be considered selected.\n * Warning: should be forwarded as a field of `reactive` object\n */\n readonly selection?: PlSelectionModel;\n}>();\n\nconst sequenceColumns = reactive(useSequenceColumnsOptions(() => ({\n pFrame: props.pFrame,\n sequenceColumnPredicate: props.sequenceColumnPredicate,\n})));\n\nconst labelColumns = reactive(useLabelColumnsOptions(() => ({\n pFrame: props.pFrame,\n sequenceColumnIds: settings.sequenceColumnIds,\n})));\n\nconst markupColumns = reactive(useMarkupColumnsOptions(() => ({\n pFrame: props.pFrame,\n sequenceColumnIds: settings.sequenceColumnIds,\n})));\n\nconst multipleAlignmentData = reactive(useMultipleAlignmentData(() => ({\n pFrame: props.pFrame,\n sequenceColumnIds: settings.sequenceColumnIds,\n labelColumnIds: settings.labelColumnIds,\n selection: props.selection,\n colorScheme: settings.colorScheme,\n alignmentParams: settings.alignmentParams,\n})));\n\nconst formatNumber = new Intl.NumberFormat('en').format;\n\nconst colorSchemeOptions = computed<\n ListOptionNormalized<PlMultiSequenceAlignmentColorSchemeOption>[]\n>(\n () => [\n {\n label: 'Chemical Properties',\n value: { type: 'chemical-properties' },\n },\n {\n label: 'No Color',\n value: { type: 'no-color' },\n },\n ...(markupColumns.data ?? 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[]).every(\n ({ value }) => !isJsonEqual(value, markupColumnId),\n )\n ) {\n settingsToReset.push('colorScheme');\n }\n if (settingsToReset.length) {\n applySettings(Object.fromEntries(\n settingsToReset.map((key) => [key, undefined]),\n ));\n }\n});\n\nconst msaEl = useTemplateRef('msa');\n\nasync function exportPdf() {\n const exportToPdf = getRawPlatformaInstance()?.lsDriver\n ?.exportToPdf;\n if (!exportToPdf) {\n return console.error(\n 'API getPlatformaRawInstance().lsDriver.exportToPdf is not available',\n );\n }\n const msaRoot = msaEl.value?.rootEl;\n if (!msaRoot) {\n throw new Error('MSA element is not available.');\n }\n const printTarget = document.createElement('div');\n printTarget.id = `print-target-${crypto.randomUUID()}`;\n const printStyleSheet = new CSSStyleSheet();\n document.adoptedStyleSheets.push(printStyleSheet);\n printStyleSheet.insertRule(`\n@media screen {\n #${printTarget.id} {\n visibility: hidden;\n position: fixed;\n }\n}`);\n const msaClone = msaRoot.cloneNode(true) as HTMLElement;\n msaClone.dataset.prePrint = '';\n printTarget.replaceChildren(msaClone);\n document.body.appendChild(printTarget);\n const { height, width } = printTarget.getBoundingClientRect();\n const margin = CSS.cm(1);\n const pageSize = [width, height]\n .map((value) => CSS.px(value).add(margin.mul(2)))\n .join(' ');\n printStyleSheet.insertRule(`\n@media print {\n @page {\n size: ${pageSize};\n margin: ${margin};\n }\n body > :not(#${printTarget.id}) {\n display: none;\n }\n}`);\n try {\n await exportToPdf();\n } catch (error) {\n console.error(error);\n } finally {\n document.body.removeChild(printTarget);\n const index = document.adoptedStyleSheets.indexOf(printStyleSheet);\n if (index >= 0) {\n document.adoptedStyleSheets.splice(index, 1);\n }\n }\n}\n</script>\n\n<template>\n <Toolbar\n :settings=\"settings\"\n :sequence-column-options=\"sequenceColumns.data?.options\"\n :label-column-options=\"labelColumns.data?.options\"\n :color-scheme-options=\"colorSchemeOptions\"\n @update-settings=\"applySettings\"\n @export=\"exportPdf\"\n />\n <PlAlert v-if=\"error\" type=\"error\">\n {{ error }}\n </PlAlert>\n <PlAlert\n v-else-if=\"!multipleAlignmentData.isLoading\n && (multipleAlignmentData.data?.sequences ?? []).length < 2\"\n type=\"warn\"\n icon\n >\n Please select at least one sequence column and two or more rows to run\n alignment\n </PlAlert>\n <template v-else>\n <PlAlert\n v-if=\"multipleAlignmentData.data?.exceedsLimit\"\n type=\"warn\"\n icon\n label=\"Visualization is limited\"\n >\n MSA visualization supports {{ formatNumber(2) }} to\n {{ formatNumber(sequenceLimit) }} sequences. 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@@ -27,7 +27,7 @@ export declare const useMarkupColumnsOptions: (paramsGetter: () => {
27
27
  error: import('vue').Ref<Error | undefined, Error | undefined>;
28
28
  };
29
29
  export declare const useMultipleAlignmentData: (paramsGetter: () => {
30
- pframe: PFrameHandle | undefined;
30
+ pFrame: PFrameHandle | undefined;
31
31
  sequenceColumnIds: PObjectId[] | undefined;
32
32
  labelColumnIds: PTableColumnId[] | undefined;
33
33
  selection: PlSelectionModel | undefined;
@@ -1,5 +1,5 @@
1
1
  import { isJsonEqual as J } from "../../lib/util/helpers/dist/index.js";
2
- import { getRawPlatformaInstance as V, isLabelColumn as N, isLinkerColumn as W, createRowSelectionColumn as X } from "../../sdk/model/dist/index.js";
2
+ import { getRawPlatformaInstance as V, isLabelColumn as _, isLinkerColumn as W, createRowSelectionColumn as X } from "../../sdk/model/dist/index.js";
3
3
  import { ref as M, watch as G } from "vue";
4
4
  import { highlightByChemicalProperties as H } from "./chemical-properties.js";
5
5
  import { parseMarkup as K, markupAlignedSequence as Q, highlightByMarkup as Y } from "./markup.js";
@@ -23,7 +23,7 @@ async function an({
23
23
  const t = (await S().listColumns(c)).values().filter((o) => e(o)).map(({ spec: o, columnId: u }) => {
24
24
  var m;
25
25
  return {
26
- label: ((m = o.annotations) == null ? void 0 : m["pl7.app/label"]) ?? "Unlabelled column",
26
+ label: ((m = o.annotations) == null ? void 0 : m["pl7.app/label"]) ?? "Unlabeled column",
27
27
  value: u
28
28
  };
29
29
  }).toArray(), l = t.map(({ value: o }) => o);
@@ -45,11 +45,11 @@ async function on({
45
45
  );
46
46
  for (const [i, d] of l.entries()) {
47
47
  const a = D(i), g = p.find(
48
- ({ spec: v }) => N(v) && en(a, E(v.axesSpec[0]))
48
+ ({ spec: v }) => _(v) && en(a, E(v.axesSpec[0]))
49
49
  );
50
50
  t.set(
51
51
  g ? A({ type: "column", id: g.columnId }) : A({ type: "axis", id: a }),
52
- ((f = g == null ? void 0 : g.spec.annotations) == null ? void 0 : f["pl7.app/label"]) ?? ((h = d.annotations) == null ? void 0 : h["pl7.app/label"]) ?? "Unlabelled axis"
52
+ ((f = g == null ? void 0 : g.spec.annotations) == null ? void 0 : f["pl7.app/label"]) ?? ((h = d.annotations) == null ? void 0 : h["pl7.app/label"]) ?? "Unlabeled axis"
53
53
  );
54
54
  }
55
55
  const { hits: o } = await y.findColumns(c, {
@@ -61,13 +61,13 @@ async function on({
61
61
  const a = A({ type: "column", id: i });
62
62
  t.has(a) || t.set(
63
63
  a,
64
- ((b = d.annotations) == null ? void 0 : b["pl7.app/label"]) ?? "Unlabelled column"
64
+ ((b = d.annotations) == null ? void 0 : b["pl7.app/label"]) ?? "Unlabeled column"
65
65
  );
66
66
  }
67
67
  const u = t.entries().map(([i, d]) => ({ label: d, value: D(i) })).toArray(), m = u.values().filter(({ value: i }) => {
68
68
  if (i.type === "axis") return !0;
69
69
  const d = p.find(({ columnId: a }) => a === i.id);
70
- return d && N(d.spec);
70
+ return d && _(d.spec);
71
71
  }).map(({ value: i }) => i).toArray();
72
72
  return { options: u, defaults: m };
73
73
  }
@@ -95,19 +95,19 @@ async function rn({
95
95
  var u;
96
96
  return {
97
97
  value: l,
98
- label: ((u = o.annotations) == null ? void 0 : u["pl7.app/label"]) ?? "Unlabelled column"
98
+ label: ((u = o.annotations) == null ? void 0 : u["pl7.app/label"]) ?? "Unlabeled column"
99
99
  };
100
100
  }).toArray();
101
101
  }
102
102
  async function sn({
103
- pframe: c,
103
+ pFrame: c,
104
104
  sequenceColumnIds: e,
105
105
  labelColumnIds: y,
106
106
  selection: p,
107
107
  colorScheme: t,
108
108
  alignmentParams: l
109
109
  }) {
110
- var F, I;
110
+ var I, P;
111
111
  if (!c || !(e != null && e.length) || !y) return;
112
112
  const o = S(), u = await o.listColumns(c), m = u.filter((n) => W(n.spec)), f = X({ selection: p });
113
113
  let h = {
@@ -173,7 +173,7 @@ async function sn({
173
173
  if (!r)
174
174
  throw new Error(`Couldn't find sequence column (ID: \`${n}\`).`);
175
175
  return r;
176
- }), _ = y.map((n) => {
176
+ }), F = y.map((n) => {
177
177
  const r = a.find(({ spec: s }) => {
178
178
  if (n.type === "axis" && s.type === "axis")
179
179
  return J(n.id, s.id);
@@ -202,11 +202,11 @@ async function sn({
202
202
  ), z = L.map(
203
203
  (n) => {
204
204
  var r;
205
- return ((r = n.spec.spec.annotations) == null ? void 0 : r["pl7.app/label"]) ?? "Unlabelled column";
205
+ return ((r = n.spec.spec.annotations) == null ? void 0 : r["pl7.app/label"]) ?? "Unlabeled column";
206
206
  }
207
207
  ), B = Array.from(
208
208
  { length: g },
209
- (n, r) => _.map(
209
+ (n, r) => F.map(
210
210
  (s) => {
211
211
  var w;
212
212
  return ((w = O(s.data, r, { na: "", absent: "" })) == null ? void 0 : w.toString()) ?? "";
@@ -234,19 +234,19 @@ async function sn({
234
234
  );
235
235
  const r = Array.from(
236
236
  { length: g },
237
- (w, P) => {
238
- var U;
237
+ (w, U) => {
238
+ var N;
239
239
  const T = K(
240
- ((U = O(n.data, P, { na: "", absent: "" })) == null ? void 0 : U.toString()) ?? ""
240
+ ((N = O(n.data, U, { na: "", absent: "" })) == null ? void 0 : N.toString()) ?? ""
241
241
  );
242
- return Q($[P][0], T);
242
+ return Q($[U][0], T);
243
243
  }
244
244
  ), s = JSON.parse(
245
- ((F = n.spec.spec.annotations) == null ? void 0 : F["pl7.app/sequence/annotation/mapping"]) ?? "{}"
245
+ ((I = n.spec.spec.annotations) == null ? void 0 : I["pl7.app/sequence/annotation/mapping"]) ?? "{}"
246
246
  );
247
247
  k.highlightImage = Y({
248
248
  markupRows: r,
249
- columnCount: ((I = x.at(0)) == null ? void 0 : I.length) ?? 0,
249
+ columnCount: ((P = x.at(0)) == null ? void 0 : P.length) ?? 0,
250
250
  labels: s
251
251
  });
252
252
  }
@@ -1 +1 @@
1
- {"version":3,"file":"data.js","sources":["../../../src/components/PlMultiSequenceAlignment/data.ts"],"sourcesContent":["import { isJsonEqual } from '@milaboratories/helpers';\nimport type { ListOptionNormalized } from '@milaboratories/uikit';\nimport {\n type CalculateTableDataRequest,\n type CanonicalizedJson,\n canonicalizeJson,\n createRowSelectionColumn,\n ensureError,\n getAxisId,\n getRawPlatformaInstance,\n isLabelColumn,\n isLinkerColumn,\n type JoinEntry,\n matchAxisId,\n parseJson,\n type PColumnIdAndSpec,\n type PFrameHandle,\n type PlMultiSequenceAlignmentColorSchemeOption,\n type PlMultiSequenceAlignmentSettings,\n type PlSelectionModel,\n type PObjectId,\n type PTableColumnId,\n type PTableSorting,\n pTableValue,\n} from '@platforma-sdk/model';\nimport { ref, watch } from 'vue';\nimport { highlightByChemicalProperties } from './chemical-properties';\nimport {\n highlightByMarkup,\n markupAlignedSequence,\n parseMarkup,\n} from './markup';\nimport { multiSequenceAlignment } from './multi-sequence-alignment';\nimport { getResidueCounts } from './residue-counts';\nimport type { HighlightLegend, ResidueCounts } from './types';\n\nconst getPFrameDriver = () => getRawPlatformaInstance().pFrameDriver;\n\nexport const sequenceLimit = 1000;\n\nexport const useSequenceColumnsOptions = refreshOnDeepChange(\n getSequenceColumnsOptions,\n);\n\nexport const useLabelColumnsOptions = refreshOnDeepChange(\n getLabelColumnsOptions,\n);\n\nexport const useMarkupColumnsOptions = refreshOnDeepChange(\n getMarkupColumnsOptions,\n);\n\nexport const useMultipleAlignmentData = refreshOnDeepChange(\n getMultipleAlignmentData,\n);\n\nasync function getSequenceColumnsOptions({\n pFrame,\n sequenceColumnPredicate,\n}: {\n pFrame: PFrameHandle | undefined;\n sequenceColumnPredicate: (column: PColumnIdAndSpec) => boolean;\n}): Promise<OptionsWithDefaults<PObjectId> | undefined> {\n if (!pFrame) return;\n\n const pFrameDriver = getPFrameDriver();\n const columns = await pFrameDriver.listColumns(pFrame);\n const options = columns.values()\n .filter((column) => sequenceColumnPredicate(column))\n .map(({ spec, columnId }) => ({\n label: spec.annotations?.['pl7.app/label'] ?? 'Unlabelled column',\n value: columnId,\n }))\n .toArray();\n const defaults = options.map(({ value }) => value);\n return { options, defaults };\n}\n\nasync function getLabelColumnsOptions({\n pFrame,\n sequenceColumnIds,\n}: {\n pFrame: PFrameHandle | undefined;\n sequenceColumnIds: PObjectId[] | undefined;\n}): Promise<OptionsWithDefaults<PTableColumnId> | undefined> {\n if (!pFrame || !sequenceColumnIds) return;\n\n const pFrameDriver = getPFrameDriver();\n const columns = await pFrameDriver.listColumns(pFrame);\n const optionMap = new Map<CanonicalizedJson<PTableColumnId>, string>();\n\n const sequenceColumnsAxes = new Map(\n sequenceColumnIds.values().flatMap((id) => {\n const column = columns.find(({ columnId }) => columnId === id);\n if (!column) {\n throw new Error(`Couldn't find sequence column (ID: \\`${id}\\`).`);\n }\n return column.spec.axesSpec.values()\n .map((spec) => [canonicalizeJson(getAxisId(spec)), spec]);\n }),\n );\n\n for (const [axisIdJson, axisSpec] of sequenceColumnsAxes.entries()) {\n const axisId = parseJson(axisIdJson);\n const labelColumn = columns.find(({ spec }) =>\n isLabelColumn(spec) && matchAxisId(axisId, getAxisId(spec.axesSpec[0])),\n );\n optionMap.set(\n labelColumn\n ? canonicalizeJson({ type: 'column', id: labelColumn.columnId })\n : canonicalizeJson({ type: 'axis', id: axisId }),\n labelColumn?.spec.annotations?.['pl7.app/label']\n ?? axisSpec.annotations?.['pl7.app/label']\n ?? 'Unlabelled axis',\n );\n }\n\n const { hits: compatibleColumns } = await pFrameDriver.findColumns(pFrame, {\n columnFilter: {},\n compatibleWith: sequenceColumnsAxes.keys()\n .map((axisIdJson) => parseJson(axisIdJson))\n .toArray(),\n strictlyCompatible: false,\n });\n\n for (const { columnId, spec } of compatibleColumns) {\n const columnIdJson = canonicalizeJson({ type: 'column', id: columnId });\n if (optionMap.has(columnIdJson)) continue;\n optionMap.set(\n columnIdJson,\n spec.annotations?.['pl7.app/label'] ?? 'Unlabelled column',\n );\n }\n\n const options = optionMap.entries()\n .map(([value, label]) => ({ label, value: parseJson(value) }))\n .toArray();\n\n const defaults = options.values()\n .filter(({ value }) => {\n if (value.type === 'axis') return true;\n const column = columns.find(({ columnId }) => columnId === value.id);\n return column && isLabelColumn(column.spec);\n })\n .map(({ value }) => value)\n .toArray();\n return { options, defaults };\n}\n\nasync function getMarkupColumnsOptions({\n pFrame,\n sequenceColumnIds,\n}: {\n pFrame: PFrameHandle | undefined;\n sequenceColumnIds: PObjectId[] | undefined;\n}): Promise<ListOptionNormalized<PObjectId>[] | undefined> {\n if (!pFrame || sequenceColumnIds?.length !== 1) return;\n\n const pFrameDriver = getPFrameDriver();\n const columns = await pFrameDriver.listColumns(pFrame);\n const sequenceColumn = columns.find((column) =>\n column.columnId === sequenceColumnIds[0],\n );\n if (!sequenceColumn) {\n throw new Error(\n `Couldn't find sequence column (ID: \\`${sequenceColumnIds[0]}\\`).`,\n );\n }\n return columns.values()\n .filter((column) =>\n column.spec.annotations?.['pl7.app/sequence/isAnnotation'] === 'true'\n && isJsonEqual(sequenceColumn.spec.axesSpec, column.spec.axesSpec)\n && Object.entries(sequenceColumn.spec.domain ?? {}).every((\n [key, value],\n ) => column.spec.domain?.[key] === value),\n ).map(({ columnId, spec }) => ({\n value: columnId,\n label: spec.annotations?.['pl7.app/label'] ?? 'Unlabelled column',\n }))\n .toArray();\n}\n\nasync function getMultipleAlignmentData({\n pframe,\n sequenceColumnIds,\n labelColumnIds,\n selection,\n colorScheme,\n alignmentParams,\n}: {\n pframe: PFrameHandle | undefined;\n sequenceColumnIds: PObjectId[] | undefined;\n labelColumnIds: PTableColumnId[] | undefined;\n selection: PlSelectionModel | undefined;\n colorScheme: PlMultiSequenceAlignmentColorSchemeOption;\n alignmentParams: PlMultiSequenceAlignmentSettings['alignmentParams'];\n}): Promise<MultipleAlignmentData | undefined> {\n if (!pframe || !sequenceColumnIds?.length || !labelColumnIds) return;\n\n const pFrameDriver = getPFrameDriver();\n const columns = await pFrameDriver.listColumns(pframe);\n const linkerColumns = columns.filter((column) => isLinkerColumn(column.spec));\n\n const filterColumn = createRowSelectionColumn({ selection });\n\n // inner join of sequence columns\n let primaryEntry: JoinEntry<PObjectId> = {\n type: 'inner',\n entries: sequenceColumnIds.map((column) => ({\n type: 'column',\n column,\n })),\n };\n\n // if we have linkers, left join them\n if (linkerColumns.length > 0) {\n primaryEntry = {\n type: 'outer',\n primary: primaryEntry,\n secondary: linkerColumns.map(({ columnId }) => ({\n type: 'column',\n column: columnId,\n })),\n };\n }\n\n // inner join with filters\n if (filterColumn) {\n primaryEntry = {\n type: 'inner',\n entries: [\n primaryEntry,\n {\n type: 'inlineColumn',\n column: filterColumn,\n },\n ],\n };\n }\n\n // left join with labels\n const secondaryEntry: JoinEntry<PObjectId>[] = labelColumnIds\n .flatMap((column) => {\n if (column.type !== 'column') return [];\n return { type: 'column', column: column.id };\n });\n\n // and markup\n if (colorScheme.type === 'markup') {\n secondaryEntry.push({ type: 'column', column: colorScheme.columnId });\n }\n\n const sorting: PTableSorting[] = Array.from(\n new Set(\n sequenceColumnIds.values().flatMap((id) => {\n const column = columns.find(({ columnId }) => columnId === id);\n if (!column) {\n throw new Error(`Couldn't find sequence column (ID: ${id})`);\n }\n return column.spec.axesSpec\n .map((spec) => canonicalizeJson(getAxisId(spec)));\n }),\n ),\n )\n .sort()\n .map((id) => ({\n column: { type: 'axis', id: parseJson(id) },\n ascending: true,\n naAndAbsentAreLeastValues: true,\n }));\n\n const request: CalculateTableDataRequest<PObjectId> = {\n src: {\n type: 'outer',\n primary: primaryEntry,\n secondary: secondaryEntry,\n },\n filters: [],\n sorting,\n };\n\n const table = await pFrameDriver.calculateTableData(\n pframe,\n JSON.parse(JSON.stringify(request)),\n {\n offset: 0,\n // +1 is a hack to check whether the selection is over the limit\n length: sequenceLimit + 1,\n },\n );\n\n let rowCount = table?.[0].data.data.length ?? 0;\n let exceedsLimit = false;\n if (rowCount > sequenceLimit) {\n rowCount = sequenceLimit;\n exceedsLimit = true;\n }\n\n const sequenceColumns = sequenceColumnIds.map((columnId) => {\n const column = table.find(({ spec }) => spec.id === columnId);\n if (!column) {\n throw new Error(`Couldn't find sequence column (ID: \\`${columnId}\\`).`);\n }\n return column;\n });\n\n const labelColumns = labelColumnIds.map((labelColumn) => {\n const column = table.find(({ spec }) => {\n if (labelColumn.type === 'axis' && spec.type === 'axis') {\n return isJsonEqual(labelColumn.id, spec.id);\n }\n if (labelColumn.type === 'column' && spec.type === 'column') {\n return labelColumn.id === spec.id;\n }\n });\n if (!column) {\n throw new Error(`Couldn't find label column (ID: \\`${labelColumn}\\`).`);\n }\n return column;\n });\n\n const alignedSequences = await Promise.all(\n sequenceColumns.map((column) =>\n multiSequenceAlignment(\n Array.from(\n { length: rowCount },\n (_, row) =>\n pTableValue(column.data, row, { na: '', absent: '' })?.toString()\n ?? 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'Unlabeled column',\n }))\n .toArray();\n}\n\nasync function getMultipleAlignmentData({\n pFrame,\n sequenceColumnIds,\n labelColumnIds,\n selection,\n colorScheme,\n alignmentParams,\n}: {\n pFrame: PFrameHandle | undefined;\n sequenceColumnIds: PObjectId[] | undefined;\n labelColumnIds: PTableColumnId[] | undefined;\n selection: PlSelectionModel | undefined;\n colorScheme: PlMultiSequenceAlignmentColorSchemeOption;\n alignmentParams: PlMultiSequenceAlignmentSettings['alignmentParams'];\n}): Promise<MultipleAlignmentData | undefined> {\n if (!pFrame || !sequenceColumnIds?.length || !labelColumnIds) return;\n\n const pFrameDriver = getPFrameDriver();\n const columns = await pFrameDriver.listColumns(pFrame);\n const linkerColumns = columns.filter((column) => isLinkerColumn(column.spec));\n\n const filterColumn = createRowSelectionColumn({ selection });\n\n // inner join of sequence columns\n let primaryEntry: JoinEntry<PObjectId> = {\n type: 'inner',\n entries: sequenceColumnIds.map((column) => ({\n type: 'column',\n column,\n })),\n };\n\n // if we have linkers, left join them\n if (linkerColumns.length > 0) {\n primaryEntry = {\n type: 'outer',\n primary: primaryEntry,\n secondary: linkerColumns.map(({ columnId }) => ({\n type: 'column',\n column: columnId,\n })),\n };\n }\n\n // inner join with filters\n if (filterColumn) {\n primaryEntry = {\n type: 'inner',\n entries: [\n primaryEntry,\n {\n type: 'inlineColumn',\n column: filterColumn,\n },\n ],\n };\n }\n\n // left join with labels\n const secondaryEntry: JoinEntry<PObjectId>[] = labelColumnIds\n .flatMap((column) => {\n if (column.type !== 'column') return [];\n return { type: 'column', column: column.id };\n });\n\n // and markup\n if (colorScheme.type === 'markup') {\n secondaryEntry.push({ type: 'column', column: colorScheme.columnId });\n }\n\n const sorting: PTableSorting[] = Array.from(\n new Set(\n sequenceColumnIds.values().flatMap((id) => {\n const column = columns.find(({ columnId }) => columnId === id);\n if (!column) {\n throw new Error(`Couldn't find sequence column (ID: ${id})`);\n }\n return column.spec.axesSpec\n .map((spec) => canonicalizeJson(getAxisId(spec)));\n }),\n ),\n )\n .sort()\n .map((id) => ({\n column: { type: 'axis', id: parseJson(id) },\n ascending: true,\n naAndAbsentAreLeastValues: true,\n }));\n\n const request: CalculateTableDataRequest<PObjectId> = {\n src: {\n type: 'outer',\n primary: primaryEntry,\n secondary: secondaryEntry,\n },\n filters: [],\n sorting,\n };\n\n const table = await pFrameDriver.calculateTableData(\n pFrame,\n JSON.parse(JSON.stringify(request)),\n {\n offset: 0,\n // +1 is a hack to check whether the selection is over the limit\n length: sequenceLimit + 1,\n },\n );\n\n let rowCount = table?.[0].data.data.length ?? 0;\n let exceedsLimit = false;\n if (rowCount > sequenceLimit) {\n rowCount = sequenceLimit;\n exceedsLimit = true;\n }\n\n const sequenceColumns = sequenceColumnIds.map((columnId) => {\n const column = table.find(({ spec }) => spec.id === columnId);\n if (!column) {\n throw new Error(`Couldn't find sequence column (ID: \\`${columnId}\\`).`);\n }\n return column;\n });\n\n const labelColumns = labelColumnIds.map((labelColumn) => {\n const column = table.find(({ spec }) => {\n if (labelColumn.type === 'axis' && spec.type === 'axis') {\n return isJsonEqual(labelColumn.id, spec.id);\n }\n if (labelColumn.type === 'column' && spec.type === 'column') {\n return labelColumn.id === spec.id;\n }\n });\n if (!column) {\n throw new Error(`Couldn't find label column (ID: \\`${labelColumn}\\`).`);\n }\n return column;\n });\n\n const alignedSequences = await Promise.all(\n sequenceColumns.map((column) =>\n multiSequenceAlignment(\n Array.from(\n { length: rowCount },\n (_, row) =>\n pTableValue(column.data, row, { na: '', absent: '' })?.toString()\n ?? 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