@platforma-sdk/ui-vue 1.30.25 → 1.30.37

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

@@ -0,0 +1,134 @@
+import Aioli from '@biowasm/aioli';
+import {
+  type MaybeRefOrGetter,
+  onWatcherCleanup,
+  reactive,
+  toValue,
+  watchEffect,
+} from 'vue';
+import type { SequenceRow } from './types';
+
+export function useAlignedRows(sequenceRows: MaybeRefOrGetter<SequenceRow[]>) {
+  const alignment = reactive({
+    value: new Map<string, string>(),
+    loading: false,
+  });
+  watchEffect(async () => {
+    const inputRows = toValue(sequenceRows);
+    let aborted = false;
+    onWatcherCleanup(() => {
+      aborted = true;
+    });
+    try {
+      alignment.loading = true;
+      const value = await multiSequenceAlignment(inputRows);
+      if (aborted) return;
+      alignment.value = value;
+    } catch (error) {
+      console.error(error);
+      alignment.value.clear();
+    } finally {
+      alignment.loading = false;
+    }
+  });
+  return alignment;
+}
+
+const cache = new Map<string, Map<string, string>>();
+
+async function multiSequenceAlignment(
+  sequenceRows: SequenceRow[],
+): Promise<Map<string, string>> {
+  const inputHash = await hash(sequenceRows);
+  let result = cache.get(inputHash);
+  if (result) {
+    return result;
+  }
+  const CLI = await new Aioli(['kalign/3.3.1']);
+  const file = new File(
+    sequenceRows.map((row) => `>${row.header}\n${row.sequence}\n`),
+    'input',
+  );
+  await CLI.mount(file);
+  await CLI.exec('kalign -f fasta -i input -o output');
+  const output = await CLI.cat('output');
+  result = parseKalignOutput(output);
+  cache.set(inputHash, result);
+  return result;
+}
+
+function parseKalignOutput(output: string): Map<string, string> {
+  const result = new Map<string, string>();
+  let lastHeader = '';
+  for (let line of output.split('\n')) {
+    line = line.trim();
+    if (!line) {
+      continue;
+    }
+    if (line.startsWith('>')) {
+      const header = line.slice(1);
+      result.set(header, '');
+      lastHeader = header;
+      continue;
+    }
+    const sequence = result.get(lastHeader);
+    if (sequence === undefined) {
+      throw new Error('Malformed kalign output, aborting.');
+    }
+    result.set(lastHeader, sequence + line);
+  }
+  return result;
+}
+
+async function hash(rows: SequenceRow[]): Promise<string> {
+  const encoder = new TextEncoder();
+  const decoder = new TextDecoder();
+  const sha256 = (input: BufferSource) =>
+    crypto.subtle.digest('SHA-256', input);
+  const chunks = await Promise.all(rows.map(
+    ({ header, sequence }) => sha256(encoder.encode(`${header} ${sequence}`)),
+  ));
+  const data = chunks.reduce<Uint8Array>((acc, chunk, index) => {
+    acc.set(new Uint8Array(chunk), index * 32);
+    return acc;
+  }, new Uint8Array(chunks.length * 32));
+  return decoder.decode(await sha256(data));
+}
+
+if (import.meta.vitest) {
+  const { test, expect } = import.meta.vitest;
+
+  test('parseKalignOutput', () => {
+    const serialized = `>1aab_
+GKGDPKKPRG-KMSSYAFFVQTSREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKF
+EDMAKADKARYEREMKTY-IPPKGE---------
+>1j46_A
+-----MQDRV-KRPMNAFIVWSRDQRRKMALENPRMRNSEISKQLGYQWKMLTEAEKWPF
+FQEAQKLQAMHREKYPNYKYRPRRKAKMLPK---
+>1k99_A
+MKKLKKHPDFPKKPLTPYFRFFMEKRAKYAKLHPEMSNLDLTKILSKKYKELPEKKKMKY
+IQDFQREKQ-EFERNLARFREDHPDLIQNAKK--
+>2lef_A
+-----MHI---KKPLNAFMLYMKEMRANVVAESTLKESAAINQILGRRWHALSREEQAKY
+YELARKERQLHMQLYPGWSARDNYGKKKKRKREK`;
+    const parsed = new Map([
+      [
+        '1aab_',
+        'GKGDPKKPRG-KMSSYAFFVQTSREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKARYEREMKTY-IPPKGE---------',
+      ],
+      [
+        '1j46_A',
+        '-----MQDRV-KRPMNAFIVWSRDQRRKMALENPRMRNSEISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREKYPNYKYRPRRKAKMLPK---',
+      ],
+      [
+        '1k99_A',
+        'MKKLKKHPDFPKKPLTPYFRFFMEKRAKYAKLHPEMSNLDLTKILSKKYKELPEKKKMKYIQDFQREKQ-EFERNLARFREDHPDLIQNAKK--',
+      ],
+      [
+        '2lef_A',
+        '-----MHI---KKPLNAFMLYMKEMRANVVAESTLKESAAINQILGRRWHALSREEQAKYYELARKERQLHMQLYPGWSARDNYGKKKKRKREK',
+      ],
+    ]);
+    expect(parseKalignOutput(serialized)).toEqual(parsed);
+  });
+}

package/src/components/PlMultiSequenceAlignment/types.ts

@@ -0,0 +1,5 @@
+export type SequenceRow = {
+  labels: string[];
+  sequence: string;
+  header: string;
+};

package/src/lib.ts

@@ -28,6 +28,8 @@ export * from './components/PlAgGridColumnManager';
 
 export * from './components/PlTableFilters';
 
+export * from './components/PlMultiSequenceAlignment';
+
 export * from './defineApp';
 
 export * from './createModel';

package/src/vite-env.d.ts

@@ -6,3 +6,16 @@
 //   const component: DefineComponent<{}, {}, any>;
 //   export default component;
 // }
+
+type Mount = File | { name: string; data: Blob | string };
+
+declare module '@biowasm/aioli' {
+  class Aioli {
+    constructor(tools: string[]);
+    mount(mounts: Mount | Mount[]): Promise<void>;
+    exec(command: string): Promise<string>;
+    cat(filename: string): Promise<string>;
+    // Add any other methods used or known
+  }
+  export default Aioli;
+}

package/tsconfig.lib.json

@@ -21,7 +21,9 @@
     "noUnusedLocals": false,
     "noUnusedParameters": true,
     "noFallthroughCasesInSwitch": true,
-    "outDir": "dist"
+    "outDir": "dist",
+
+    "types": ["vitest/importMeta"]
   },
   "include": ["src/**/*.ts", "src/**/*.tsx", "src/**/*.vue"]
 }

package/vite.config.ts

@@ -1,7 +1,7 @@
-import { defineConfig } from 'vite';
 import vue from '@vitejs/plugin-vue';
-import sourcemaps from 'rollup-plugin-sourcemaps2';
 import { resolve } from 'path';
+import sourcemaps from 'rollup-plugin-sourcemaps2';
+import { defineConfig } from 'vite';
 
 // https://vitejs.dev/config/
 export default defineConfig({
@@ -37,4 +37,7 @@ export default defineConfig({
       },
     },
   },
+  define: {
+    'import.meta.vitest': 'undefined',
+  },
 });

package/vitest.config.ts

@@ -0,0 +1,7 @@
+import { defineConfig } from 'vitest/config';
+
+export default defineConfig({
+  test: {
+    includeSource: ['src/**/*.{js,ts}'],
+  },
+});