@platforma-sdk/ui-vue 1.45.35 → 1.45.36

package/src/components/PlMultiSequenceAlignment/Toolbar.vue

@@ -1,228 +0,0 @@
-<script setup lang="ts">
-import { isJsonEqual } from '@milaboratories/helpers';
-import {
-  type ListOptionNormalized,
-  PlBtnGhost,
-  PlBtnPrimary,
-  PlBtnSecondary,
-  PlCheckbox,
-  PlDropdown,
-  PlDropdownMulti,
-  PlNumberField,
-  PlSlideModal,
-} from '@milaboratories/uikit';
-import type {
-  PlMultiSequenceAlignmentColorSchemeOption as ColorSchemeOption,
-  PlMultiSequenceAlignmentSettings as Settings,
-  PlMultiSequenceAlignmentWidget,
-  PObjectId,
-  PTableColumnId,
-} from '@platforma-sdk/model';
-import { computed, ref, useCssModule, watchEffect } from 'vue';
-import { defaultSettings } from './settings';
-
-const props = defineProps<{
-  settings: Settings;
-  sequenceColumnOptions: ListOptionNormalized<PObjectId>[] | undefined;
-  labelColumnOptions: ListOptionNormalized<PTableColumnId>[] | undefined;
-  colorSchemeOptions: ListOptionNormalized<ColorSchemeOption>[];
-}>();
-
-const emit = defineEmits<{
-  updateSettings: [Partial<Settings>];
-  export: [];
-}>();
-
-const classes = useCssModule();
-
-const settingsOpen = ref(false);
-
-function updateSetting<K extends keyof Settings>(
-  key: K,
-  value: Settings[K] | undefined,
-) {
-  emit('updateSettings', { [key]: value });
-}
-
-function toggleWidget(
-  widget: PlMultiSequenceAlignmentWidget,
-  checked: boolean,
-) {
-  updateSetting(
-    'widgets',
-    checked
-      ? [...props.settings.widgets, widget]
-      : props.settings.widgets.filter((w) => widget !== w),
-  );
-}
-
-const alignmentParams = ref({ ...props.settings.alignmentParams });
-watchEffect(() => {
-  alignmentParams.value = { ...props.settings.alignmentParams };
-});
-
-const alignmentParamsChangesPending = computed(() =>
-  !isJsonEqual(props.settings.alignmentParams, alignmentParams.value),
-);
-
-const canResetAlignmentParams = computed(() =>
-  !isJsonEqual(props.settings.alignmentParams, defaultSettings.alignmentParams),
-);
-</script>
-
-<template>
-  <div :class="classes.container">
-    <div :class="classes.line">
-      <div :class="classes.section">
-        <PlDropdownMulti
-          label="Sequence Columns"
-          :model-value="props.settings.sequenceColumnIds ?? []"
-          :options="props.sequenceColumnOptions"
-          clearable
-          @update:model-value="event => updateSetting('sequenceColumnIds', event)"
-        />
-        <PlDropdownMulti
-          :model-value="props.settings.labelColumnIds ?? []"
-          label="Label Columns"
-          :options="props.labelColumnOptions"
-          clearable
-          @update:model-value="event => updateSetting('labelColumnIds', event)"
-        />
-        <PlDropdown
-          :model-value="props.settings.colorScheme"
-          label="Color Scheme"
-          :options="props.colorSchemeOptions"
-          @update:model-value="event => updateSetting('colorScheme', event)"
-        />
-      </div>
-      <div :class="classes.buttons">
-        <PlBtnGhost icon="settings" @click.stop="settingsOpen = true">
-          Settings
-        </PlBtnGhost>
-        <PlBtnGhost icon="export" @click.stop="emit('export')">
-          Export
-        </PlBtnGhost>
-      </div>
-    </div>
-    <div :class="classes.line">
-      <div :class="classes.section">
-        <PlCheckbox
-          :model-value="props.settings.widgets.includes('seqLogo')"
-          @update:model-value="event => toggleWidget('seqLogo', event)"
-        >
-          Seq logo
-        </PlCheckbox>
-        <PlCheckbox
-          :model-value="props.settings.widgets.includes('consensus')"
-          @update:model-value="event => toggleWidget('consensus', event)"
-        >
-          Consensus
-        </PlCheckbox>
-        <PlCheckbox :model-value="false" disabled>Navigator</PlCheckbox>
-        <PlCheckbox
-          :model-value="props.settings.widgets.includes('tree')"
-          @update:model-value="event => toggleWidget('tree', event)"
-        >
-          Tree
-        </PlCheckbox>
-        <PlCheckbox
-          :model-value="props.settings.widgets.includes('legend')"
-          :disabled="props.settings.colorScheme.type === 'no-color'"
-          @update:model-value="event => toggleWidget('legend', event)"
-        >
-          Legend
-        </PlCheckbox>
-      </div>
-    </div>
-  </div>
-  <PlSlideModal v-model="settingsOpen">
-    <template #title>Settings</template>
-    <PlNumberField
-      v-model="alignmentParams.gpo"
-      label="Gap open penalty"
-      :step="0.1"
-      @keyup.enter="updateSetting('alignmentParams', alignmentParams)"
-    >
-      <template #tooltip>
-        Penalty score assigned to the introduction of a gap in the alignment
-      </template>
-    </PlNumberField>
-    <PlNumberField
-      v-model="alignmentParams.gpe"
-      label="Gap extension penalty"
-      :step="0.1"
-      @keyup.enter="updateSetting('alignmentParams', alignmentParams)"
-    >
-      <template #tooltip>
-        Penalty score assigned to each additional residue added to an existing
-        gap
-      </template>
-    </PlNumberField>
-    <PlNumberField
-      v-model="alignmentParams.tgpe"
-      label="Terminal gap extension penalty"
-      :step="0.1"
-      @keyup.enter="updateSetting('alignmentParams', alignmentParams)"
-    >
-      <template #tooltip>
-        Penalty score assigned to extending gaps at the ends of sequences
-      </template>
-    </PlNumberField>
-    <div
-      v-if="alignmentParamsChangesPending"
-      :class="classes.pendingChanges"
-    >
-      <PlBtnPrimary @click="updateSetting('alignmentParams', alignmentParams)">
-        Apply
-      </PlBtnPrimary>
-      <PlBtnGhost @click="alignmentParams = props.settings.alignmentParams">
-        Cancel
-      </PlBtnGhost>
-    </div>
-    <PlBtnSecondary
-      v-if="canResetAlignmentParams"
-      :class="classes.resetButton"
-      icon="reverse"
-      @click="updateSetting('alignmentParams', undefined)"
-    >
-      Reset to Default
-    </PlBtnSecondary>
-  </PlSlideModal>
-</template>
-
-<style module>
-.container {
-  display: flex;
-  flex-direction: column;
-  gap: 24px;
-}
-
-.line {
-  display: flex;
-  justify-content: space-between;
-}
-
-.section {
-  display: flex;
-  flex-wrap: wrap;
-  gap: 24px;
-}
-
-.buttons {
-  display: flex;
-}
-
-.pendingChanges {
-  display: flex;
-  button {
-    min-width: 160px;
-  }
-}
-
-.resetButton {
-  margin-block-start: auto;
-  span {
-    text-transform: none;
-  }
-}
-</style>

package/src/components/PlMultiSequenceAlignment/cell-size.ts

@@ -1,4 +0,0 @@
-export const cellSize = {
-  inline: 20,
-  block: 24,
-};

package/src/components/PlMultiSequenceAlignment/chemical-properties.ts

@@ -1,199 +0,0 @@
-import type { HighlightLegend, ResidueCounts } from './types';
-
-export function highlightByChemicalProperties(
-  { sequences, residueCounts }: {
-    sequences: string[];
-    residueCounts: ResidueCounts;
-  },
-): { blob: Blob; legend: HighlightLegend } {
-  const lines: {
-    category: ChemicalCategory;
-    column: number;
-    start: number;
-    length: number;
-  }[] = [];
-  const chemicalProperties = getAlignmentChemicalProperties({
-    residueCounts,
-    rowCount: sequences.length,
-  });
-  const width = sequences.at(0)?.length ?? 0;
-  const height = sequences.length;
-  for (let column = 0; column < width; column += 1) {
-    for (let row = 0; row < height; row += 1) {
-      const residue = sequences[row][column];
-      const category = chemicalProperties
-        .at(column)
-        ?.find(({ residues }) => residues.includes(residue))
-        ?.category;
-      if (!category) continue;
-      const lastLine = lines.at(-1);
-      if (
-        lastLine
-        && lastLine.category === category
-        && lastLine.column === column
-        && lastLine.start + lastLine.length === row
-      ) {
-        lastLine.length += 1;
-      } else {
-        lines.push({ category, column, start: row, length: 1 });
-      }
-    }
-  }
-  const linesByCategory = Map.groupBy(lines, ({ category }) => category);
-  const blob = new Blob(
-    (function*() {
-      const viewBox = `0 0 ${width * 2} ${height}`;
-      yield `<svg xmlns="http://www.w3.org/2000/svg" viewBox="${viewBox}" stroke-width="2" preserveAspectRatio="none">`;
-      for (const [category, lines] of linesByCategory) {
-        const color = chemicalPropertiesColorScheme[category]?.color;
-        if (!color) continue;
-        yield `<path stroke="${color}" d="`;
-        let x = 0, y = 0;
-        for (const { column, start, length } of lines) {
-          yield `m${column * 2 + 1 - x},${start - y}v${length}`;
-          x = column * 2 + 1;
-          y = start + length;
-        }
-        yield '"/>';
-      }
-      yield '</svg>';
-    })().toArray(),
-    { type: 'image/svg+xml' },
-  );
-  const legend = Object.fromEntries(
-    Object.entries(chemicalPropertiesColorScheme)
-      .filter(([color]) => linesByCategory.has(color as ChemicalCategory)),
-  );
-  return { blob, legend };
-}
-
-const getAlignmentChemicalProperties = (
-  { residueCounts, rowCount }: {
-    residueCounts: ResidueCounts;
-    rowCount: number;
-  },
-): ColumnChemicalProperties[] =>
-  residueCounts.map((column) => {
-    const matchedRules = new Set<string>();
-    return categoryCriterion.filter(({ residues, rules }) =>
-      residues.split('').some((residue) => residue in column)
-      && (!rules || rules.split('').map((ruleName) =>
-        [ruleName, ruleDefinitions[ruleName as RuleName]] as const,
-      ).some(([ruleName, { residues, threshold }]) => {
-        if (matchedRules.has(ruleName)) return true;
-        const groupCount = residues.split('')
-          .reduce((acc, residue) => acc + (column[residue] ?? 0), 0);
-        const matches = groupCount >= rowCount * threshold;
-        if (matches) matchedRules.add(ruleName);
-        return matches;
-      })),
-    );
-  });
-
-type ColumnChemicalProperties = {
-  residues: string;
-  category: ChemicalCategory;
-}[];
-
-const chemicalPropertiesColorScheme = {
-  hydrophobic: {
-    label: 'Hydrophobic',
-    color: '#99CCFF',
-  },
-  positiveCharge: {
-    label: 'Positive Charged',
-    color: '#FFA2A3',
-  },
-  negativeCharge: {
-    label: 'Negative Charged',
-    color: '#C1ADFF',
-  },
-  polar: {
-    label: 'Polar',
-    color: '#99E099',
-  },
-  cysteine: {
-    label: 'Cysteines',
-    color: '#FAAAFA',
-  },
-  glycine: {
-    label: 'Glycines',
-    color: '#F7BC5D',
-  },
-  proline: {
-    label: 'Prolines',
-    color: '#FFFF8F',
-  },
-  aromatic: {
-    label: 'Aromatic',
-    color: '#A2F5FA',
-  },
-} satisfies HighlightLegend;
-
-export type ChemicalCategory = keyof typeof chemicalPropertiesColorScheme;
-
-/*
- * Below taken mostly from
- * https://www.rbvi.ucsf.edu/chimera/1.2065/docs/ContributedSoftware/multalignviewer/colprot.par}
- */
-
-const ruleDefinitions = {
-  '%': { residues: 'WLVIMAFCYHP', threshold: 0.6 },
-  '#': { residues: 'WLVIMAFCYHP', threshold: 0.8 },
-  '-': { residues: 'ED', threshold: 0.5 },
-  '+': { residues: 'KR', threshold: 0.6 },
-  'g': { residues: 'G', threshold: 0.5 },
-  'n': { residues: 'N', threshold: 0.5 },
-  'q': { residues: 'QE', threshold: 0.5 },
-  'p': { residues: 'P', threshold: 0.5 },
-  't': { residues: 'TS', threshold: 0.5 },
-  'A': { residues: 'A', threshold: 0.85 },
-  'C': { residues: 'C', threshold: 0.85 },
-  'D': { residues: 'D', threshold: 0.85 },
-  'E': { residues: 'E', threshold: 0.85 },
-  'F': { residues: 'F', threshold: 0.85 },
-  'G': { residues: 'G', threshold: 0.85 },
-  'H': { residues: 'H', threshold: 0.85 },
-  'I': { residues: 'I', threshold: 0.85 },
-  'K': { residues: 'K', threshold: 0.85 },
-  'L': { residues: 'L', threshold: 0.85 },
-  'M': { residues: 'M', threshold: 0.85 },
-  'N': { residues: 'N', threshold: 0.85 },
-  'P': { residues: 'P', threshold: 0.85 },
-  'Q': { residues: 'Q', threshold: 0.85 },
-  'R': { residues: 'R', threshold: 0.85 },
-  'S': { residues: 'S', threshold: 0.85 },
-  'T': { residues: 'T', threshold: 0.85 },
-  'V': { residues: 'V', threshold: 0.85 },
-  'W': { residues: 'W', threshold: 0.85 },
-  'Y': { residues: 'Y', threshold: 0.85 },
-};
-
-type RuleName = keyof typeof ruleDefinitions;
-
-const categoryCriterion: Criteria[] = [
-  { residues: 'G', category: 'glycine', rules: '' },
-  { residues: 'P', category: 'proline', rules: '' },
-  { residues: 'T', category: 'polar', rules: 'tST%#' },
-  { residues: 'S', category: 'polar', rules: 'tST#' },
-  { residues: 'N', category: 'polar', rules: 'nND' },
-  { residues: 'Q', category: 'polar', rules: 'qQE+KR' },
-  // criteria below has to go before the other criteria for C,
-  // otherwise it will never match
-  { residues: 'C', category: 'cysteine', rules: 'C' },
-  { residues: 'WLVIMF', category: 'hydrophobic', rules: '%#ACFHILMVWYPp' },
-  // below there was an 's' rule too,
-  // but no definition of such rule was provided
-  { residues: 'A', category: 'hydrophobic', rules: '%#ACFHILMVWYPpTSG' },
-  { residues: 'C', category: 'hydrophobic', rules: '%#AFHILMVWYSPp' },
-  { residues: 'HY', category: 'aromatic', rules: '%#ACFHILMVWYPp' },
-  { residues: 'E', category: 'negativeCharge', rules: '-DEqQ' },
-  { residues: 'D', category: 'negativeCharge', rules: '-DEnN' },
-  { residues: 'KR', category: 'positiveCharge', rules: '+KRQ' },
-];
-
-type Criteria = {
-  residues: string;
-  category: ChemicalCategory;
-  rules: string;
-};