@platforma-sdk/ui-vue 1.42.53 → 1.43.1

package/src/components/PlMultiSequenceAlignment/migrations.ts

@@ -6,7 +6,7 @@ import {
 } from '@platforma-sdk/model';
 import { type Ref } from 'vue';
 
-const latestVersion = 1;
+const latestVersion = 2;
 
 export function runMigrations(model: Ref<PlMultiSequenceAlignmentModel>) {
   const currentVersion = getCurrentVersion(model.value);
@@ -20,6 +20,11 @@ export function runMigrations(model: Ref<PlMultiSequenceAlignmentModel>) {
           .map((id) => parseJson(id));
       }
     }
+    if (currentVersion < 2) {
+      if (model.value.colorScheme?.type === 'markup') {
+        delete model.value.colorScheme;
+      }
+    }
   } catch (error) {
     console.error(error);
     model.value = {};

package/src/components/PlMultiSequenceAlignment/multi-sequence-alignment.worker.ts

@@ -0,0 +1,54 @@
+import kalign from '@milaboratories/biowasm-tools/kalign';
+import type { PlMultiSequenceAlignmentSettings } from '@platforma-sdk/model';
+
+addEventListener(
+  'message',
+  async ({ data }: MessageEvent<RequestMessage>) => {
+    try {
+      postMessage(await onMessage(data));
+    } catch (error) {
+      reportError(error);
+    }
+  },
+);
+
+export type RequestMessage = {
+  sequences: string[];
+  params: PlMultiSequenceAlignmentSettings['alignmentParams'];
+};
+
+export type ResponseMessage = string[];
+
+async function onMessage(
+  { sequences, params }: RequestMessage,
+): Promise<ResponseMessage> {
+  if (sequences.length < 2) {
+    throw new Error(
+      'Cannot run multiple sequences alignment on less than 2 sequences.',
+    );
+  }
+  const input = sequences
+    .map((sequence, index) => `>${index}\n${sequence}`)
+    .join('\n');
+  const output = await kalign(input, params);
+  return parseKalignOutput(output);
+}
+
+function parseKalignOutput(output: string): string[] {
+  const result: string[] = [];
+  let index = -1;
+  for (let line of output.split('\n')) {
+    line = line.trim();
+    if (!line) {
+      continue;
+    }
+    if (line.startsWith('>')) {
+      index += 1;
+      continue;
+    }
+    if (index >= 0) {
+      result[index] = (result[index] ?? '').concat(line);
+    }
+  }
+  return result;
+}

package/src/components/PlMultiSequenceAlignment/phylogenetic-tree.worker.ts

@@ -0,0 +1,89 @@
+import rapidnj from '@milaboratories/biowasm-tools/rapidnj';
+
+addEventListener(
+  'message',
+  async ({ data }: MessageEvent<RequestMessage>) => {
+    try {
+      postMessage(await onMessage(data));
+    } catch (error) {
+      reportError(error);
+    }
+  },
+);
+
+export type RequestMessage = string[];
+
+export type ResponseMessage = TreeNodeData[];
+
+async function onMessage(sequences: RequestMessage): Promise<ResponseMessage> {
+  if (sequences.length < 2) {
+    throw new Error(
+      'Cannot build phylogenetic tree for less than 2 sequences.',
+    );
+  }
+  const input = sequences
+    .map((sequence, index) => `>${index}\n${sequence}`)
+    .join('\n');
+  const output = await rapidnj(input);
+  return Array.from(parseRapidnjOutput(output));
+}
+
+function parseRapidnjOutput(input: string) {
+  let prevIndex = 0;
+  const root = new TreeNode();
+  let node = root;
+  let virtualId = -1;
+  for (const match of input.matchAll(/[(,);]/g)) {
+    const [token] = match;
+    const [id, length] = input.slice(prevIndex, match.index).split(':');
+    if (id) node.id = Number(id.slice(1, -1));
+    if (length) node.length = Number(length);
+    node.id ??= virtualId--;
+    switch (token) {
+      case '(':
+        node = node.newChild();
+        break;
+      case ',':
+        node = node.parent!.newChild();
+        break;
+      case ')':
+        node = node.parent!;
+        break;
+      case ';':
+        return root;
+    }
+    prevIndex = match.index + 1;
+  }
+  throw new Error('Missing semicolon.');
+}
+
+class TreeNode {
+  id?: number;
+  length?: number;
+  parent?: TreeNode;
+  children?: TreeNode[];
+
+  newChild(): TreeNode {
+    const node = new TreeNode();
+    node.parent = this;
+    (this.children ??= []).push(node);
+    return node;
+  }
+
+  *[Symbol.iterator](): Generator<TreeNodeData> {
+    if (this.id === undefined) {
+      throw new Error('Node ID cannot be undefined.');
+    }
+    const result: TreeNodeData = { id: this.id };
+    if (this.length !== undefined) result.length = this.length;
+    if (this.parent) result.parentId = this.parent.id;
+    yield result;
+    for (const child of this.children ?? []) yield * child;
+  }
+}
+
+export interface TreeNodeData {
+  id: number;
+  length?: number;
+  parentId?: number;
+}

package/src/components/PlMultiSequenceAlignment/settings.ts

@@ -1,8 +1,7 @@
 import type { PlMultiSequenceAlignmentSettings } from '@platforma-sdk/model';
-import { defaultAlignmentParams } from './multi-sequence-alignment';
 
 export const defaultSettings: PlMultiSequenceAlignmentSettings = {
   colorScheme: { type: 'chemical-properties' },
   widgets: ['seqLogo', 'consensus', 'legend'],
-  alignmentParams: defaultAlignmentParams,
+  alignmentParams: { gpo: 5.5, gpe: 2.0, tgpe: 1.0 },
 };

package/src/lib.ts

@@ -15,8 +15,8 @@ export * from './components/PlAgColumnHeader';
 export * from './components/PlAgCellFile';
 export * from './components/PlAgCellProgress';
 export * from './components/PlAgCellStatusTag';
-export * from './components/PlAgChartStackedBarCell';
 export * from './components/PlAgChartHistogramCell';
+export * from './components/PlAgChartStackedBarCell';
 
 export * from './components/PlAgDataTable';
 
@@ -50,8 +50,6 @@ export * from './computedResult';
 
 export * from './composition/fileContent';
 
-export { multiSequenceAlignment } from './components/PlMultiSequenceAlignment/multi-sequence-alignment';
-
 export * from '@milaboratories/uikit';
 
 export type * from '@milaboratories/uikit';

package/dist/components/PlMultiSequenceAlignment/multi-sequence-alignment.d.ts

@@ -1,7 +0,0 @@
-import { PlMultiSequenceAlignmentModel } from '@platforma-sdk/model';
-export declare const defaultAlignmentParams: {
-    gpo: number;
-    gpe: number;
-    tgpe: number;
-};
-export declare function multiSequenceAlignment(sequences: string[], alignmentParams?: PlMultiSequenceAlignmentModel['alignmentParams']): Promise<string[]>;

package/dist/components/PlMultiSequenceAlignment/multi-sequence-alignment.js

@@ -1,51 +0,0 @@
-import l from "@milaboratories/biowasm-tools";
-import { objectHash as s } from "../../objectHash.js";
-const c = /* @__PURE__ */ new Map(), f = {
-  gpo: 5.5,
-  gpe: 2,
-  tgpe: 1
-}, m = /* @__PURE__ */ (() => {
-  let n;
-  return async () => (n || (n = await new l(["kalign"])), n);
-})();
-async function $(n, a = f) {
-  if (n.length < 2) return n;
-  const i = await s([n, a]);
-  let t = c.get(i);
-  if (t) return t;
-  const e = await m(), o = {
-    input: `/shared/data/input-${i}`,
-    output: `/shared/data/output-${i}`,
-    ...a
-  };
-  e.mount(
-    new File(
-      n.map((r, u) => `>${u}
-${r}
-`),
-      // HACK: remove when mount will handle mounts properly
-      o.input.split("/").at(-1)
-    )
-  ), await e.exec(`kalign ${Object.entries(o).map(([r, u]) => `--${r} ${u}`).join(" ")}`);
-  const p = await e.cat(o.output);
-  return t = g(p), c.set(i, t), t;
-}
-function g(n) {
-  const a = [];
-  let i = -1;
-  for (let t of n.split(`
-`))
-    if (t = t.trim(), !!t) {
-      if (t.startsWith(">")) {
-        i += 1;
-        continue;
-      }
-      i >= 0 && (a[i] = (a[i] ?? "").concat(t));
-    }
-  return a;
-}
-export {
-  f as defaultAlignmentParams,
-  $ as multiSequenceAlignment
-};
-//# sourceMappingURL=multi-sequence-alignment.js.map

package/dist/components/PlMultiSequenceAlignment/multi-sequence-alignment.js.map

@@ -1 +0,0 @@
-{"version":3,"file":"multi-sequence-alignment.js","sources":["../../../src/components/PlMultiSequenceAlignment/multi-sequence-alignment.ts"],"sourcesContent":["import Aioli from '@milaboratories/biowasm-tools';\nimport type { PlMultiSequenceAlignmentModel } from '@platforma-sdk/model';\nimport { objectHash } from '../../objectHash';\n\nconst cache = new Map<string, string[]>();\n\nexport const defaultAlignmentParams = {\n  gpo: 5.5,\n  gpe: 2.0,\n  tgpe: 1.0,\n} satisfies PlMultiSequenceAlignmentModel['alignmentParams'];\n\nconst getCli = (() => {\n  let cli: Aioli;\n  return async () => {\n    if (!cli) {\n      cli = await new Aioli(['kalign']);\n    }\n    return cli;\n  };\n})();\n\nexport async function multiSequenceAlignment(\n  sequences: string[],\n  alignmentParams: PlMultiSequenceAlignmentModel['alignmentParams'] =\n  defaultAlignmentParams,\n): Promise<string[]> {\n  if (sequences.length < 2) return sequences;\n  const hash = await objectHash([sequences, alignmentParams]);\n  let result = cache.get(hash);\n  if (result) return result;\n  const CLI = await getCli();\n  const params = {\n    input: `/shared/data/input-${hash}`,\n    output: `/shared/data/output-${hash}`,\n    ...alignmentParams,\n  };\n  CLI.mount(\n    new File(\n      sequences.map((sequence, index) => `>${index}\\n${sequence}\\n`),\n      // HACK: remove when mount will handle mounts properly\n      params.input.split('/').at(-1)!,\n    ),\n  );\n  await CLI.exec(`kalign ${\n    Object.entries(params)\n      .map(([key, value]) => `--${key} ${value}`)\n      .join(' ')\n  }`);\n  const output = await CLI.cat(params.output);\n  result = parseKalignOutput(output);\n  cache.set(hash, result);\n  return result;\n}\n\nfunction parseKalignOutput(output: string): string[] {\n  const result: string[] = [];\n  let index = -1;\n  for (let line of output.split('\\n')) {\n    line = line.trim();\n    if (!line) {\n      continue;\n    }\n    if (line.startsWith('>')) {\n      index += 1;\n      continue;\n    }\n    if (index >= 0) {\n      result[index] = (result[index] ?? '').concat(line);\n    }\n  }\n  return result;\n}\n\nif (import.meta.vitest) {\n  const { test, expect } = import.meta.vitest;\n\n  test('parseKalignOutput', () => {\n    const serialized = `some garbage\n[some more garbage]\n>1aab_\nGKGDPKKPRG-KMSSYAFFVQTSREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKF\nEDMAKADKARYEREMKTY-IPPKGE---------\n>1j46_A\n-----MQDRV-KRPMNAFIVWSRDQRRKMALENPRMRNSEISKQLGYQWKMLTEAEKWPF\nFQEAQKLQAMHREKYPNYKYRPRRKAKMLPK---\n>1k99_A\nMKKLKKHPDFPKKPLTPYFRFFMEKRAKYAKLHPEMSNLDLTKILSKKYKELPEKKKMKY\nIQDFQREKQ-EFERNLARFREDHPDLIQNAKK--\n>2lef_A\n-----MHI---KKPLNAFMLYMKEMRANVVAESTLKESAAINQILGRRWHALSREEQAKY\nYELARKERQLHMQLYPGWSARDNYGKKKKRKREK`;\n\n    expect(parseKalignOutput(serialized)).toEqual([\n      'GKGDPKKPRG-KMSSYAFFVQTSREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKARYEREMKTY-IPPKGE---------',\n      '-----MQDRV-KRPMNAFIVWSRDQRRKMALENPRMRNSEISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREKYPNYKYRPRRKAKMLPK---',\n      'MKKLKKHPDFPKKPLTPYFRFFMEKRAKYAKLHPEMSNLDLTKILSKKYKELPEKKKMKYIQDFQREKQ-EFERNLARFREDHPDLIQNAKK--',\n      '-----MHI---KKPLNAFMLYMKEMRANVVAESTLKESAAINQILGRRWHALSREEQAKYYELARKERQLHMQLYPGWSARDNYGKKKKRKREK',\n    ]);\n  });\n}\n"],"names":["cache","defaultAlignmentParams","getCli","cli","Aioli","multiSequenceAlignment","sequences","alignmentParams","hash","objectHash","result","CLI","params","sequence","index","key","value","output","parseKalignOutput","line"],"mappings":";;AAIA,MAAMA,wBAAY,IAAA,GAELC,IAAyB;AAAA,EACpC,KAAK;AAAA,EACL,KAAK;AAAA,EACL,MAAM;AACR,GAEMC,IAAU,uBAAM;AACpB,MAAIC;AACJ,SAAO,aACAA,MACHA,IAAM,MAAM,IAAIC,EAAM,CAAC,QAAQ,CAAC,IAE3BD;AAEX,GAAA;AAEA,eAAsBE,EACpBC,GACAC,IACAN,GACmB;AACnB,MAAIK,EAAU,SAAS,EAAG,QAAOA;AACjC,QAAME,IAAO,MAAMC,EAAW,CAACH,GAAWC,CAAe,CAAC;AAC1D,MAAIG,IAASV,EAAM,IAAIQ,CAAI;AAC3B,MAAIE,EAAQ,QAAOA;AACnB,QAAMC,IAAM,MAAMT,EAAA,GACZU,IAAS;AAAA,IACb,OAAO,sBAAsBJ,CAAI;AAAA,IACjC,QAAQ,uBAAuBA,CAAI;AAAA,IACnC,GAAGD;AAAA,EAAA;AAEL,EAAAI,EAAI;AAAA,IACF,IAAI;AAAA,MACFL,EAAU,IAAI,CAACO,GAAUC,MAAU,IAAIA,CAAK;AAAA,EAAKD,CAAQ;AAAA,CAAI;AAAA;AAAA,MAE7DD,EAAO,MAAM,MAAM,GAAG,EAAE,GAAG,EAAE;AAAA,IAAA;AAAA,EAC/B,GAEF,MAAMD,EAAI,KAAK,UACb,OAAO,QAAQC,CAAM,EAClB,IAAI,CAAC,CAACG,GAAKC,CAAK,MAAM,KAAKD,CAAG,IAAIC,CAAK,EAAE,EACzC,KAAK,GAAG,CACb,EAAE;AACF,QAAMC,IAAS,MAAMN,EAAI,IAAIC,EAAO,MAAM;AAC1C,SAAAF,IAASQ,EAAkBD,CAAM,GACjCjB,EAAM,IAAIQ,GAAME,CAAM,GACfA;AACT;AAEA,SAASQ,EAAkBD,GAA0B;AACnD,QAAMP,IAAmB,CAAA;AACzB,MAAII,IAAQ;AACZ,WAASK,KAAQF,EAAO,MAAM;AAAA,CAAI;AAEhC,QADAE,IAAOA,EAAK,KAAA,GACR,EAACA,GAGL;AAAA,UAAIA,EAAK,WAAW,GAAG,GAAG;AACxB,QAAAL,KAAS;AACT;AAAA,MACF;AACA,MAAIA,KAAS,MACXJ,EAAOI,CAAK,KAAKJ,EAAOI,CAAK,KAAK,IAAI,OAAOK,CAAI;AAAA;AAGrD,SAAOT;AACT;"}

package/src/components/PlMultiSequenceAlignment/multi-sequence-alignment.ts

@@ -1,101 +0,0 @@
-import Aioli from '@milaboratories/biowasm-tools';
-import type { PlMultiSequenceAlignmentModel } from '@platforma-sdk/model';
-import { objectHash } from '../../objectHash';
-
-const cache = new Map<string, string[]>();
-
-export const defaultAlignmentParams = {
-  gpo: 5.5,
-  gpe: 2.0,
-  tgpe: 1.0,
-} satisfies PlMultiSequenceAlignmentModel['alignmentParams'];
-
-const getCli = (() => {
-  let cli: Aioli;
-  return async () => {
-    if (!cli) {
-      cli = await new Aioli(['kalign']);
-    }
-    return cli;
-  };
-})();
-
-export async function multiSequenceAlignment(
-  sequences: string[],
-  alignmentParams: PlMultiSequenceAlignmentModel['alignmentParams'] =
-  defaultAlignmentParams,
-): Promise<string[]> {
-  if (sequences.length < 2) return sequences;
-  const hash = await objectHash([sequences, alignmentParams]);
-  let result = cache.get(hash);
-  if (result) return result;
-  const CLI = await getCli();
-  const params = {
-    input: `/shared/data/input-${hash}`,
-    output: `/shared/data/output-${hash}`,
-    ...alignmentParams,
-  };
-  CLI.mount(
-    new File(
-      sequences.map((sequence, index) => `>${index}\n${sequence}\n`),
-      // HACK: remove when mount will handle mounts properly
-      params.input.split('/').at(-1)!,
-    ),
-  );
-  await CLI.exec(`kalign ${
-    Object.entries(params)
-      .map(([key, value]) => `--${key} ${value}`)
-      .join(' ')
-  }`);
-  const output = await CLI.cat(params.output);
-  result = parseKalignOutput(output);
-  cache.set(hash, result);
-  return result;
-}
-
-function parseKalignOutput(output: string): string[] {
-  const result: string[] = [];
-  let index = -1;
-  for (let line of output.split('\n')) {
-    line = line.trim();
-    if (!line) {
-      continue;
-    }
-    if (line.startsWith('>')) {
-      index += 1;
-      continue;
-    }
-    if (index >= 0) {
-      result[index] = (result[index] ?? '').concat(line);
-    }
-  }
-  return result;
-}
-
-if (import.meta.vitest) {
-  const { test, expect } = import.meta.vitest;
-
-  test('parseKalignOutput', () => {
-    const serialized = `some garbage
-[some more garbage]
->1aab_
-GKGDPKKPRG-KMSSYAFFVQTSREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKF
-EDMAKADKARYEREMKTY-IPPKGE---------
->1j46_A
------MQDRV-KRPMNAFIVWSRDQRRKMALENPRMRNSEISKQLGYQWKMLTEAEKWPF
-FQEAQKLQAMHREKYPNYKYRPRRKAKMLPK---
->1k99_A
-MKKLKKHPDFPKKPLTPYFRFFMEKRAKYAKLHPEMSNLDLTKILSKKYKELPEKKKMKY
-IQDFQREKQ-EFERNLARFREDHPDLIQNAKK--
->2lef_A
------MHI---KKPLNAFMLYMKEMRANVVAESTLKESAAINQILGRRWHALSREEQAKY
-YELARKERQLHMQLYPGWSARDNYGKKKKRKREK`;
-
-    expect(parseKalignOutput(serialized)).toEqual([
-      'GKGDPKKPRG-KMSSYAFFVQTSREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKARYEREMKTY-IPPKGE---------',
-      '-----MQDRV-KRPMNAFIVWSRDQRRKMALENPRMRNSEISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREKYPNYKYRPRRKAKMLPK---',
-      'MKKLKKHPDFPKKPLTPYFRFFMEKRAKYAKLHPEMSNLDLTKILSKKYKELPEKKKMKYIQDFQREKQ-EFERNLARFREDHPDLIQNAKK--',
-      '-----MHI---KKPLNAFMLYMKEMRANVVAESTLKESAAINQILGRRWHALSREEQAKYYELARKERQLHMQLYPGWSARDNYGKKKKRKREK',
-    ]);
-  });
-}