@datagrok/bio 1.8.2 → 1.10.2
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/detectors.js +37 -0
- package/dist/package-test.js +557 -5547
- package/dist/package.js +513 -5517
- package/package.json +7 -5
- package/src/package.ts +29 -14
- package/src/tests/WebLogo-positions-test.ts +17 -13
- package/src/tests/detectors-test.ts +35 -20
- package/src/tests/msa-tests.ts +2 -1
- package/src/tests/test-sequnces-generators.ts +45 -0
- package/src/utils/atomic-works.ts +2 -0
- package/src/utils/cell-renderer.ts +35 -96
- package/src/utils/sequence-activity-cliffs.ts +5 -21
- package/src/utils/sequence-space.ts +5 -3
- package/src/widgets/representations.ts +1 -1
- package/{test-Bio-dc07f068a0b2-3cd5a505.html → test-Bio-eb4783c07294-0aa1538b.html} +2 -2
- package/webpack.config.js +1 -0
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@@ -1,4 +1,4 @@
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import {
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import {ITooltipAndPanelParams} from '@datagrok-libraries/ml/src/viewers/activity-cliffs';
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import * as DG from 'datagrok-api/dg';
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import * as ui from 'datagrok-api/ui';
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import {getSimilarityFromDistance} from '@datagrok-libraries/utils/src/similarity-metrics';
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@@ -12,25 +12,9 @@ export async function sequenceGetSimilarities(col: DG.Column, seq: string): Prom
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return DG.Column.fromList(DG.COLUMN_TYPE.FLOAT, 'distances', distances);
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}
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export function
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params.
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ui.divText(
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ui.divText(params.activity.name),
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]);
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columnNames.style.fontWeight = 'bold';
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columnNames.style.display = 'flex';
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columnNames.style.justifyContent = 'space-between';
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params.tooltips[params.line.id].append(columnNames);
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params.line.mols.forEach((mol: number) => {
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const seq = ui.divText(params.df.get(params.seqCol.name, mol));
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const activity = ui.divText(params.df.get(params.activity.name, mol).toFixed(2));
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activity.style.display = 'flex';
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activity.style.justifyContent = 'left';
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activity.style.paddingLeft = '30px';
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params.tooltips[params.line.id].append(ui.divV([
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seq,
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activity,
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], {style: {paddingLeft: '5px'}}));
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export function drawSequences(params: ITooltipAndPanelParams) {
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params.line.mols.forEach((mol: number, index: number) => {
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ui.empty(params.hosts[index]);
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params.hosts[index].append(ui.divText(params.seqCol.get(mol)));
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});
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}
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@@ -12,7 +12,9 @@ export interface ISequenceSpaceResult {
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}
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export async function sequenceSpace(spaceParams: ISequenceSpaceParams): Promise<ISequenceSpaceResult> {
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// code deprecated since seqCol is encoded
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/* let preparedData: any;
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if (!(spaceParams.seqCol!.tags[DG.TAGS.UNITS] === 'HELM')) {
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const sep = spaceParams.seqCol.getTag('separator');
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const sepFinal = sep ? sep === '.' ? '\\\.' : sep : '-';
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@@ -23,10 +25,10 @@ export async function sequenceSpace(spaceParams: ISequenceSpaceParams): Promise<
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preparedData = spaceParams.seqCol.toList().map((v: string) => v.replace(regex, '')) as string[];
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} else {
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preparedData = spaceParams.seqCol.toList();
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}
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} */
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const sequenceSpaceResult = await reduceDimensinalityWithNormalization(
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spaceParams.seqCol.toList(),
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spaceParams.methodName,
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spaceParams.similarityMetric as StringMetrics | BitArrayMetrics,
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spaceParams.options);
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@@ -22,7 +22,7 @@ export async function representationsWidget(macroMolecule: DG.Cell, monomersLibO
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const atomicCodes = getMolfilesFromSingleSeq(macroMolecule, monomersLibObject);
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const result = await getMacroMol(atomicCodes!);
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const molBlock2D = result[0];
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molBlock3D = (await grok.functions.call('Bio:Embed', {molBlock2D})) as string;
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molBlock3D = (await grok.functions.call('Bio:Embed', {molBlock2D})) as unknown as string;
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} catch (e) {
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console.warn(e);
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}
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@@ -1,4 +1,4 @@
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<html><head><meta charset="utf-8"/><title>Bio Test Report. Datagrok version datagrok/datagrok:latest SHA=
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<html><head><meta charset="utf-8"/><title>Bio Test Report. Datagrok version datagrok/datagrok:latest SHA=eb4783c07294. Commit 0aa1538b.</title><style type="text/css">html,
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body {
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font-family: Arial, Helvetica, sans-serif;
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font-size: 1rem;
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@@ -229,7 +229,7 @@ header {
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font-size: 1rem;
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padding: 0 0.5rem;
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}
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</style></head><body><div id="jesthtml-content"><header><h1 id="title">Bio Test Report. Datagrok version datagrok/datagrok:latest SHA=
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</style></head><body><div id="jesthtml-content"><header><h1 id="title">Bio Test Report. Datagrok version datagrok/datagrok:latest SHA=eb4783c07294. Commit 0aa1538b.</h1></header><div id="metadata-container"><div id="timestamp">Started: 2022-09-02 13:13:34</div><div id="summary"><div id="suite-summary"><div class="summary-total">Suites (1)</div><div class="summary-passed">1 passed</div><div class="summary-failed summary-empty">0 failed</div><div class="summary-pending summary-empty">0 pending</div></div><div id="test-summary"><div class="summary-total">Tests (1)</div><div class="summary-passed">1 passed</div><div class="summary-failed summary-empty">0 failed</div><div class="summary-pending summary-empty">0 pending</div></div></div></div><div id="suite-1" class="suite-container"><div class="suite-info"><div class="suite-path">/home/runner/work/public/public/packages/Bio/src/__jest__/remote.test.ts</div><div class="suite-time warn">45.182s</div></div><div class="suite-tests"><div class="test-result passed"><div class="test-info"><div class="test-suitename"> </div><div class="test-title">TEST</div><div class="test-status">passed</div><div class="test-duration">30.315s</div></div></div></div><div class="suite-consolelog"><div class="suite-consolelog-header">Console Log</div><div class="suite-consolelog-item"><pre class="suite-consolelog-item-origin"> at Object.<anonymous> (/home/runner/work/public/public/packages/Bio/src/__jest__/test-node.ts:63:11)
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at Generator.next (<anonymous>)
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at fulfilled (/home/runner/work/public/public/packages/Bio/src/__jest__/test-node.ts:28:58)
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at processTicksAndRejections (internal/process/task_queues.js:97:5)</pre><pre class="suite-consolelog-item-message">Using web root: http://localhost:8080</pre></div><div class="suite-consolelog-item"><pre class="suite-consolelog-item-origin"> at /home/runner/work/public/public/packages/Bio/src/__jest__/remote.test.ts:40:11
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