@datagrok/peptides 1.3.9 → 1.5.1
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/dist/package-test.js +1929 -1130
- package/dist/package.js +1701 -1045
- package/dist/vendors-node_modules_datagrok-libraries_ml_src_workers_dimensionality-reducer_js.js +3 -3
- package/files/tests/aligned_5k.d42 +0 -0
- package/package.json +3 -3
- package/src/__jest__/remote.test.ts +12 -5
- package/src/__jest__/test-node.ts +1 -1
- package/src/model.ts +481 -592
- package/src/package-test.ts +1 -0
- package/src/package.ts +15 -14
- package/src/tests/algorithms.ts +29 -20
- package/src/tests/core.ts +3 -6
- package/src/tests/utils.ts +4 -4
- package/src/utils/algorithms.ts +25 -22
- package/src/utils/cell-renderer.ts +34 -15
- package/src/utils/constants.ts +3 -36
- package/src/utils/misc.ts +26 -35
- package/src/utils/peptide-similarity-space.ts +4 -7
- package/src/utils/statistics.ts +20 -12
- package/src/utils/types.ts +8 -3
- package/src/viewers/logo-summary.ts +188 -7
- package/src/viewers/peptide-space-viewer.ts +5 -5
- package/src/viewers/sar-viewer.ts +230 -57
- package/src/widgets/distribution.ts +35 -10
- package/src/widgets/manual-alignment.ts +1 -1
- package/src/widgets/mutation-cliffs.ts +2 -3
- package/src/widgets/peptides.ts +67 -36
- package/src/widgets/settings.ts +20 -16
- package/{test-Peptides-62cc009524f3-0949dc07.html → test-Peptides-4775b69ad08a-1bc1a2b4.html} +33 -32
- package/tsconfig.json +3 -3
package/src/widgets/settings.ts
CHANGED
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@@ -1,12 +1,11 @@
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import * as ui from 'datagrok-api/ui';
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-
import * as grok from 'datagrok-api/grok';
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import * as DG from 'datagrok-api/dg';
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import * as type from '../utils/types';
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import * as C from '../utils/constants';
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import {PeptidesModel} from '../model';
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import $ from 'cash-dom';
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import wu from 'wu';
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//TODO: show sliderInput values
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export function getSettingsDialog(model: PeptidesModel): DG.Dialog {
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@@ -27,36 +26,41 @@ export function getSettingsDialog(model: PeptidesModel): DG.Dialog {
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});
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maxMutations.addPostfix((settings.maxMutations ?? 1).toString());
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const minActivityDelta = ui.sliderInput('Min activity delta', settings.minActivityDelta ?? 0, 0, 100, () => {
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const val =
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result.minActivityDelta = val;
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const val = minActivityDelta.value!.toFixed(3);
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result.minActivityDelta = parseFloat(val);
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$(minActivityDelta.root).find('label.ui-input-description').remove();
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minActivityDelta.addPostfix(val
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minActivityDelta.addPostfix(val);
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});
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minActivityDelta.addPostfix((settings.minActivityDelta ?? 0).toString());
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accordion.addPane('Mutation Cliffs', () => ui.inputs([maxMutations, minActivityDelta]), true);
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const inputsRows: HTMLElement[] = [];
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for (const col of model.df.columns.numerical) {
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const
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const colName = col.name;
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if (colName == settings.activityColumnName || colName == C.COLUMNS_NAMES.ACTIVITY_SCALED)
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continue;
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const isIncludedInput = ui.boolInput('', typeof (settings.columns ?? {})[colName] !== 'undefined',
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() => {
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if (
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result.columns![
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if (isIncludedInput.value)
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result.columns![colName] = aggregationInput.stringValue;
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else
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delete result.columns![
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delete result.columns![colName];
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}) as DG.InputBase<boolean>;
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const
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() => {
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if (
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const aggregationInput = ui.choiceInput('Aggregation', (settings.columns ?? {})[colName] ?? 'avg',
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Object.values(DG.STATS), () => {
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if (isIncludedInput.value)
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result.columns![colName] = aggregationInput.stringValue;
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else
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delete result.columns![col.name];
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}) as DG.InputBase<string>;
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$(
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const inputsRow = ui.inputsRow(col.name, [
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$(aggregationInput.root).find('label').css('width', 'auto');
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const inputsRow = ui.inputsRow(col.name, [isIncludedInput, aggregationInput]);
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$(inputsRow).find('div.ui-div').css('display', 'inline-flex');
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inputsRows.push(inputsRow);
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}
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if (inputsRows.length != 0)
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accordion.addPane('Columns to include', () => ui.divV(inputsRows), false);
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const dialog = ui.dialog('Peptides settings').add(accordion);
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dialog.root.style.width = '400px';
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package/{test-Peptides-62cc009524f3-0949dc07.html → test-Peptides-4775b69ad08a-1bc1a2b4.html}
RENAMED
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@@ -1,4 +1,4 @@
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<html><head><meta charset="utf-8"/><title>Peptides Test Report. Datagrok version datagrok/datagrok:
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<html><head><meta charset="utf-8"/><title>Peptides Test Report. Datagrok version datagrok/datagrok:bleeding-edge SHA=4775b69ad08a. Commit 1bc1a2b4.</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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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">Peptides Test Report. Datagrok version datagrok/datagrok:
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at /home/runner/work/public/public/packages/Peptides/src/__jest__/remote.test.ts:68:20
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at Generator.next (<anonymous>)
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at fulfilled (/home/runner/work/public/public/packages/Peptides/src/__jest__/remote.test.ts:31:58)
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at processTicksAndRejections (internal/process/task_queues.js:97:5)</pre></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/Peptides/src/__jest__/test-node.ts:62:11)
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</style></head><body><div id="jesthtml-content"><header><h1 id="title">Peptides Test Report. Datagrok version datagrok/datagrok:bleeding-edge SHA=4775b69ad08a. Commit 1bc1a2b4.</h1></header><div id="metadata-container"><div id="timestamp">Started: 2022-12-22 14:26:33</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/Peptides/src/__jest__/remote.test.ts</div><div class="suite-time warn">65.742s</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">56.156s</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/Peptides/src/__jest__/test-node.ts:62:11)
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at Generator.next (<anonymous>)
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at fulfilled (/home/runner/work/public/public/packages/Peptides/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/Peptides/src/__jest__/remote.test.ts:40:11
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at Object.<anonymous>.__awaiter (/home/runner/work/public/public/packages/Peptides/src/__jest__/remote.test.ts:30:12)
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at Object.<anonymous> (/home/runner/work/public/public/packages/Peptides/src/__jest__/remote.test.ts:38:23)
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at Promise.then.completed (/home/runner/work/public/public/packages/Peptides/node_modules/jest-circus/build/utils.js:391:28)
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at new Promise (<anonymous>)</pre><pre class="suite-consolelog-item-message">Testing Peptides package</pre></div><div class="suite-consolelog-item"><pre class="suite-consolelog-item-origin"> at /home/runner/work/public/public/packages/Peptides/src/__jest__/remote.test.ts:
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at new Promise (<anonymous>)</pre><pre class="suite-consolelog-item-message">Testing Peptides package</pre></div><div class="suite-consolelog-item"><pre class="suite-consolelog-item-origin"> at /home/runner/work/public/public/packages/Peptides/src/__jest__/remote.test.ts:71:11
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at Generator.next (<anonymous>)
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at fulfilled (/home/runner/work/public/public/packages/Peptides/src/__jest__/remote.test.ts:31:58)
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at processTicksAndRejections (internal/process/task_queues.js:97:5)</pre><pre class="suite-consolelog-item-message">Test result : Success :
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Test result : Success :
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at processTicksAndRejections (internal/process/task_queues.js:97:5)</pre><pre class="suite-consolelog-item-message">Test result : Success : 1783 : Peptides.Core.Start analysis: simple : OK
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Test result : Success : 1047 : Peptides.Core.Start analysis: сomplex : OK
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Test result : Success : 3669 : Peptides.Core.Save and load project : OK
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Test result : Success : 1 : Peptides.Peptide space.test_table.is_not_empty : OK
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Test result : Success : 2129 : Peptides.Peptide space.PeptideSimilaritySpaceWidget.is_drawing : OK
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Test result : Success : 2 : Peptides.Peptide space.test_deminsionality_reducer : OK
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Test result : Success : 0 : Peptides.Peptide space.test_peptide_similarity_space_viewer : OK
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Test result : Success : 0 : Peptides.Algorithms.MutationCliffs : OK
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Test result : Success : 2002 : Peptides.Algorithms.peptide_space.DimensinalityReducer.UMAP.Levenshtein.is_numeric : OK
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Test result : Success : 2342 : Peptides.Algorithms.peptide_space.DimensinalityReducer.UMAP.Jaro-Winkler.is_numeric : OK
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Test result : Success : 2307 : Peptides.Algorithms.peptide_space.DimensinalityReducer.t-SNE.Levenshtein.is_numeric : OK
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Test result : Success : 2655 : Peptides.Algorithms.peptide_space.DimensinalityReducer.t-SNE.Jaro-Winkler.is_numeric : OK
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Test result : Success : 150 : Peptides.Algorithms.peptide_space.DimensinalityReducer.SPE.Levenshtein.is_numeric : OK
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Test result : Success : 445 : Peptides.Algorithms.peptide_space.DimensinalityReducer.SPE.Jaro-Winkler.is_numeric : OK
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Test result : Success : 131 : Peptides.Algorithms.peptide_space.DimensinalityReducer.pSPE.Levenshtein.is_numeric : OK
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Test result : Success : 419 : Peptides.Algorithms.peptide_space.DimensinalityReducer.pSPE.Jaro-Winkler.is_numeric : OK
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Test result : Success : 5686 : Peptides.Algorithms.peptide_space.DimensinalityReducer.OriginalSPE.Levenshtein.is_numeric : OK
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Test result : Success : 5437 : Peptides.Algorithms.peptide_space.DimensinalityReducer.OriginalSPE.Jaro-Winkler.is_numeric : OK
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Test result : Success : 1712 : Peptides.Algorithms.peptide_space.PeptideSimilaritySpaceViewer.UMAP.Levenshtein.is_proper : OK
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Test result : Success : 2131 : Peptides.Algorithms.peptide_space.PeptideSimilaritySpaceViewer.UMAP.Jaro-Winkler.is_proper : OK
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Test result : Success : 2631 : Peptides.Algorithms.peptide_space.PeptideSimilaritySpaceViewer.t-SNE.Levenshtein.is_proper : OK
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Test result : Success : 3008 : Peptides.Algorithms.peptide_space.PeptideSimilaritySpaceViewer.t-SNE.Jaro-Winkler.is_proper : OK
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Test result : Success : 343 : Peptides.Algorithms.peptide_space.PeptideSimilaritySpaceViewer.SPE.Levenshtein.is_proper : OK
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Test result : Success : 471 : Peptides.Algorithms.peptide_space.PeptideSimilaritySpaceViewer.SPE.Jaro-Winkler.is_proper : OK
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Test result : Success : 162 : Peptides.Algorithms.peptide_space.PeptideSimilaritySpaceViewer.pSPE.Levenshtein.is_proper : OK
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Test result : Success : 497 : Peptides.Algorithms.peptide_space.PeptideSimilaritySpaceViewer.pSPE.Jaro-Winkler.is_proper : OK
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Test result : Success : 5454 : Peptides.Algorithms.peptide_space.PeptideSimilaritySpaceViewer.OriginalSPE.Levenshtein.is_proper : OK
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Test result : Success : 6105 : Peptides.Algorithms.peptide_space.PeptideSimilaritySpaceViewer.OriginalSPE.Jaro-Winkler.is_proper : OK
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</pre></div><div class="suite-consolelog-item"><pre class="suite-consolelog-item-origin"> at /home/runner/work/public/public/packages/Peptides/src/__jest__/remote.test.ts:73:11
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at Generator.next (<anonymous>)
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at fulfilled (/home/runner/work/public/public/packages/Peptides/src/__jest__/remote.test.ts:31:58)
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at processTicksAndRejections (internal/process/task_queues.js:97:5)</pre><pre class="suite-consolelog-item-message">Test result : Skipped : 0 : Peptides.Algorithms.MutationCliffs - Benchmark 5k : Benchmark
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</pre></div></div></div></div></body></html>
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package/tsconfig.json
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/* Basic Options */
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// "incremental": true, /* Enable incremental compilation */
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"target": "
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"module": "
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"lib": ["
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"target": "ES6", /* Specify ECMAScript target version: 'ES3' (default), 'ES5', 'ES2015', 'ES2016', 'ES2017', 'ES2018', 'ES2019', 'ES2020', or 'ESNEXT'. */
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"module": "ES2022", /* Specify module code generation: 'none', 'commonjs', 'amd', 'system', 'umd', 'es2015', 'es2020', or 'ESNext'. */
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"lib": ["ES2022", "dom"], /* Specify library files to be included in the compilation. */
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// "allowJs": true, /* Allow javascript files to be compiled. */
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// "checkJs": true, /* Report errors in .js files. */
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// "jsx": "preserve", /* Specify JSX code generation: 'preserve', 'react-native', 'react', 'react-jsx' or 'react-jsxdev'. */
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