@platforma-sdk/ui-vue 1.45.35 → 1.45.36

package/src/components/PlMultiSequenceAlignment/markup.ts

@@ -1,141 +0,0 @@
-import type { HighlightLegend } from './types';
-
-export type Markup = { id: string; start: number; length: number }[];
-
-export function parseMarkup(row: string): Markup {
-  return Array.from(row.matchAll(
-    /(?<id>[^:]*):(?<start>[0-9A-Za-z]*)(?:\+(?<length>[0-9A-Za-z]*))?\|?/g,
-  )).map((match) => {
-    const matchGroups = match.groups as {
-      id: string;
-      start: string;
-      length: string | undefined;
-    };
-    const start = Number.parseInt(matchGroups.start, 36);
-    const length = matchGroups.length
-      ? Number.parseInt(matchGroups.length, 36)
-      : 0;
-    return {
-      id: matchGroups.id,
-      start,
-      length,
-    };
-  });
-}
-
-export function markupAlignedSequence(
-  alignedSequence: string,
-  markup: Markup,
-): Markup {
-  const indexMap = alignedSequence.split('').reduce<number[]>(
-    (acc, char, index) => {
-      if (char !== '-') acc.push(index);
-      return acc;
-    },
-    [],
-  );
-  const adjusted = markup.map((segment) => {
-    const start = indexMap[segment.start];
-    const end = indexMap[segment.start + segment.length - 1] + 1;
-    return {
-      id: segment.id,
-      start: start,
-      length: end - start,
-    };
-  });
-  return adjusted;
-}
-
-export function highlightByMarkup(
-  { markupRows, columnCount, labels }: {
-    markupRows: Markup[];
-    columnCount: number;
-    labels: Record<string, string>;
-  },
-): { blob: Blob; legend: HighlightLegend } {
-  const linesById: Map<string, {
-    row: number;
-    start: number;
-    length: number;
-  }[]> = new Map();
-  for (const [row, markup] of markupRows.entries()) {
-    for (const { id, start, length } of markup) {
-      let bucket = linesById.get(id);
-      if (!bucket) linesById.set(id, bucket = []);
-      bucket.push({ row, start, length });
-    }
-  }
-  const legend: HighlightLegend = Object.fromEntries(
-    Object.entries(labels)
-      .map(([id, label], index) =>
-        [
-          id,
-          {
-            label,
-            color: markupColors[index % markupColors.length],
-          },
-        ] as const,
-      )
-      .filter(([id]) => linesById.has(id)),
-  );
-  const blob = new Blob(
-    (function*() {
-      const viewBox = `0 0 ${columnCount} ${markupRows.length * 2}`;
-      yield `<svg xmlns="http://www.w3.org/2000/svg" viewBox="${viewBox}" stroke-width="2" preserveAspectRatio="none">`;
-      for (const [id, lines] of linesById) {
-        const { color } = legend[id];
-        yield `<path stroke="${color}" d="`;
-        let x = 0, y = 0;
-        for (const { row, start, length } of lines) {
-          yield `m${start - x},${row * 2 + 1 - y}h${length}`;
-          x = start + length;
-          y = row * 2 + 1;
-        }
-        yield '"/>';
-      }
-      yield '</svg>';
-    })().toArray(),
-    { type: 'image/svg+xml' },
-  );
-  return { blob, legend };
-}
-
-const markupColors = [
-  '#E5F2FF',
-  '#FFE8E8',
-  '#F0EBFF',
-  '#FFFFE3',
-  '#E5F7E5',
-  '#FEEAFE',
-  '#FDEED6',
-  '#E8FDFE',
-  '#CCDFF2',
-  '#F2CCCD',
-  '#D5CCF2',
-  '#F2F2CC',
-  '#CCF2CC',
-  '#F2CCF2',
-  '#EFDDBF',
-  '#DEEEEF',
-];
-
-if (import.meta.vitest) {
-  const { test, expect } = import.meta.vitest;
-  test('annotateAlignedRow', () => {
-    const alignedSequence
-      = 'EVRLVESGGALVQPGGSLRLSCVAASGFTFINNWVTWVRQAPGKGLEWVANIKEDGSQKYYVDSVKGRFTISRDNAEKSVYLQMSSLRVDDTAVYYCAR------------GRAV----D---QWGQGTLVTVSS';
-    //   0         10        20        30        40        50        60        70        80        90        100       110       120       130
-    //   EVRLVESGGALVQPGGSLRLSCVAASGFTFINNWVTWVRQAPGKGLEWVANIKEDGSQKYYVDSVKGRFTISRDNAEKSVYLQMSSLRVDDTAVYYCARGRAVDQWGQGTLVTVSS
-    const markup = [
-      { id: '1', start: 0, length: 99 },
-      { id: '2', start: 99, length: 3 },
-      { id: '3', start: 102, length: 14 },
-    ];
-    const alignedMarkup = markupAlignedSequence(alignedSequence, markup);
-    expect(alignedMarkup).toEqual([
-      { id: '1', start: 0, length: 99 },
-      { id: '2', start: 111, length: 3 },
-      { id: '3', start: 114, length: 21 },
-    ]);
-  });
-}

package/src/components/PlMultiSequenceAlignment/migrations.ts

@@ -1,46 +0,0 @@
-import {
-  type CanonicalizedJson,
-  parseJson,
-  type PlMultiSequenceAlignmentModel,
-  type PTableColumnId,
-} from '@platforma-sdk/model';
-import { type Ref } from 'vue';
-
-const latestVersion = 2;
-
-export function runMigrations(model: Ref<PlMultiSequenceAlignmentModel>) {
-  const currentVersion = getCurrentVersion(model.value);
-  try {
-    if (currentVersion < 1) {
-      const oldLabelColumnIds = model.value.labelColumnIds as unknown as
-        | CanonicalizedJson<PTableColumnId>[]
-        | undefined;
-      if (oldLabelColumnIds) {
-        model.value.labelColumnIds = oldLabelColumnIds
-          .map((id) => parseJson(id));
-      }
-    }
-    if (currentVersion < 2) {
-      if (model.value.colorScheme?.type === 'markup') {
-        delete model.value.colorScheme;
-      }
-    }
-  } catch (error) {
-    console.error(error);
-    model.value = {};
-  } finally {
-    model.value.version = latestVersion;
-  }
-}
-
-/**
- * If a model has a version, return it.
- * If it doesn't, but contains anything at all, that's version 0,
- * which is a pre-versioning version.
- * Otherwise, emtpy model is treated as the latest model.
- */
-function getCurrentVersion(model: PlMultiSequenceAlignmentModel) {
-  if (model.version !== undefined) return model.version;
-  if (Object.keys(model).length) return 0;
-  return latestVersion;
-}

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

@@ -1,54 +0,0 @@
-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

@@ -1,89 +0,0 @@
-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/residue-counts.ts

@@ -1,124 +0,0 @@
-import type { ResidueCounts } from './types';
-
-export function getResidueCounts(
-  alignedSequences: string[],
-): ResidueCounts {
-  const columns: ResidueCounts = [];
-  for (const sequence of alignedSequences) {
-    for (const [columnIndex, residue] of sequence.split('').entries()) {
-      const column = columns[columnIndex] ??= {};
-      column[residue] = (column[residue] ?? 0) + 1;
-    }
-  }
-  return columns;
-}
-
-if (import.meta.vitest) {
-  const { test, expect } = import.meta.vitest;
-
-  test('getAlignmentStats', () => {
-    const alignedSequences = [
-      'GKGDPKKPRG-KMSSYAFFVQTSREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKARYEREMKTY-IPPKGE---------',
-      '-----MQDRV-KRPMNAFIVWSRDQRRKMALENPRMRNSEISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREKYPNYKYRPRRKAKMLPK---',
-      'MKKLKKHPDFPKKPLTPYFRFFMEKRAKYAKLHPEMSNLDLTKILSKKYKELPEKKKMKYIQDFQREKQ-EFERNLARFREDHPDLIQNAKK--',
-      '-----MHI---KKPLNAFMLYMKEMRANVVAESTLKESAAINQILGRRWHALSREEQAKYYELARKERQLHMQLYPGWSARDNYGKKKKRKREK',
-    ];
-
-    expect(getResidueCounts(alignedSequences)).toEqual([
-      { '-': 2, 'G': 1, 'M': 1 },
-      { '-': 2, 'K': 2 },
-      { '-': 2, 'G': 1, 'K': 1 },
-      { '-': 2, 'D': 1, 'L': 1 },
-      { '-': 2, 'K': 1, 'P': 1 },
-      { K: 2, M: 2 },
-      { H: 2, K: 1, Q: 1 },
-      { D: 1, I: 1, P: 2 },
-      { '-': 1, 'D': 1, 'R': 2 },
-      { '-': 1, 'F': 1, 'G': 1, 'V': 1 },
-      { '-': 3, 'P': 1 },
-      { K: 4 },
-      { K: 2, M: 1, R: 1 },
-      { P: 3, S: 1 },
-      { L: 2, M: 1, S: 1 },
-      { N: 2, T: 1, Y: 1 },
-      { A: 3, P: 1 },
-      { F: 3, Y: 1 },
-      { F: 2, I: 1, M: 1 },
-      { L: 1, R: 1, V: 2 },
-      { F: 1, Q: 1, W: 1, Y: 1 },
-      { F: 1, M: 1, S: 1, T: 1 },
-      { K: 1, M: 1, R: 1, S: 1 },
-      { D: 1, E: 2, R: 1 },
-      { E: 1, K: 1, M: 1, Q: 1 },
-      { E: 1, R: 3 },
-      { A: 2, H: 1, R: 1 },
-      { K: 3, N: 1 },
-      { K: 1, M: 1, V: 1, Y: 1 },
-      { A: 2, K: 1, V: 1 },
-      { A: 1, H: 1, K: 1, L: 1 },
-      { E: 2, L: 1, P: 1 },
-      { D: 1, H: 1, N: 1, S: 1 },
-      { A: 1, P: 2, T: 1 },
-      { E: 1, L: 1, R: 1, S: 1 },
-      { K: 1, M: 2, V: 1 },
-      { E: 1, N: 1, R: 1, S: 1 },
-      { F: 1, N: 2, S: 1 },
-      { A: 1, L: 1, S: 2 },
-      { A: 1, D: 1, E: 2 },
-      { F: 1, I: 2, L: 1 },
-      { N: 1, S: 2, T: 1 },
-      { K: 3, Q: 1 },
-      { I: 2, K: 1, Q: 1 },
-      { C: 1, L: 3 },
-      { G: 2, S: 2 },
-      { E: 1, K: 1, R: 1, Y: 1 },
-      { K: 1, Q: 1, R: 2 },
-      { W: 3, Y: 1 },
-      { H: 1, K: 3 },
-      { A: 1, E: 1, M: 1, T: 1 },
-      { L: 3, M: 1 },
-      { P: 1, S: 2, T: 1 },
-      { A: 1, E: 2, R: 1 },
-      { A: 1, E: 1, K: 2 },
-      { E: 3, K: 1 },
-      { K: 3, Q: 1 },
-      { A: 1, G: 1, M: 1, W: 1 },
-      { K: 3, P: 1 },
-      { F: 2, Y: 2 },
-      { E: 1, F: 1, I: 1, Y: 1 },
-      { D: 1, E: 1, Q: 2 },
-      { D: 1, E: 1, L: 1, M: 1 },
-      { A: 3, F: 1 },
-      { K: 1, Q: 2, R: 1 },
-      { A: 1, K: 2, R: 1 },
-      { D: 1, E: 2, L: 1 },
-      { K: 2, Q: 1, R: 1 },
-      { A: 2, Q: 2 },
-      { '-': 1, 'L': 1, 'M': 1, 'R': 1 },
-      { E: 1, H: 2, Y: 1 },
-      { E: 1, F: 1, M: 1, R: 1 },
-      { E: 2, Q: 1, R: 1 },
-      { E: 1, K: 1, L: 1, R: 1 },
-      { M: 1, N: 1, Y: 2 },
-      { K: 1, L: 1, P: 2 },
-      { A: 1, G: 1, N: 1, T: 1 },
-      { R: 1, W: 1, Y: 2 },
-      { '-': 1, 'F': 1, 'K': 1, 'S': 1 },
-      { A: 1, I: 1, R: 1, Y: 1 },
-      { E: 1, P: 1, R: 2 },
-      { D: 2, P: 2 },
-      { H: 1, K: 1, N: 1, R: 1 },
-      { G: 1, P: 1, R: 1, Y: 1 },
-      { D: 1, E: 1, G: 1, K: 1 },
-      { '-': 1, 'A': 1, 'K': 1, 'L': 1 },
-      { '-': 1, 'I': 1, 'K': 2 },
-      { '-': 1, 'K': 1, 'M': 1, 'Q': 1 },
-      { '-': 1, 'K': 1, 'L': 1, 'N': 1 },
-      { '-': 1, 'A': 1, 'P': 1, 'R': 1 },
-      { '-': 1, 'K': 3 },
-      { '-': 2, 'K': 1, 'R': 1 },
-      { '-': 3, 'E': 1 },
-      { '-': 3, 'K': 1 },
-    ]);
-  });
-}

package/src/components/PlMultiSequenceAlignment/settings.ts

@@ -1,7 +0,0 @@
-import type { PlMultiSequenceAlignmentSettings } from '@platforma-sdk/model';
-
-export const defaultSettings: PlMultiSequenceAlignmentSettings = {
-  colorScheme: { type: 'chemical-properties' },
-  widgets: ['seqLogo', 'consensus', 'legend'],
-  alignmentParams: { gpo: 5.5, gpe: 2.0, tgpe: 1.0 },
-};

package/src/components/PlMultiSequenceAlignment/types.ts

@@ -1,3 +0,0 @@
-export type HighlightLegend = Record<string, { label: string; color: string }>;
-
-export type ResidueCounts = Record<string, number>[];

package/src/components/PlMultiSequenceAlignment/useMiPlots.ts

@@ -1,23 +0,0 @@
-import { ensureError } from '@platforma-sdk/model';
-import { onMounted, shallowRef } from 'vue';
-
-export function useMiPlots() {
-  const load = async () => {
-    const { MiPlots } = await import('@milaboratories/miplots4');
-    return MiPlots;
-  };
-
-  const miplots = shallowRef<Awaited<ReturnType<typeof load>>>();
-
-  const error = shallowRef<Error>();
-
-  onMounted(async () => {
-    try {
-      miplots.value = await load();
-    } catch (err) {
-      error.value = ensureError(err);
-    }
-  });
-
-  return { miplots, error };
-}