@datagrok/bio 2.0.13 → 2.0.17

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Files changed (35) hide show
  1. package/dist/package-test.js +2178 -1236
  2. package/dist/package.js +4196 -3513
  3. package/dist/vendors-node_modules_datagrok-libraries_ml_src_workers_dimensionality-reducer_js.js +135 -152
  4. package/files/data/sample_HELM_empty_vals.csv +537 -537
  5. package/files/samples/sample_HELM.csv +540 -540
  6. package/package.json +22 -15
  7. package/scripts/read-tree-pkl.py +215 -0
  8. package/src/__jest__/remote.test.ts +6 -4
  9. package/src/__jest__/test-node.ts +1 -1
  10. package/src/{utils → analysis}/sequence-activity-cliffs.ts +33 -30
  11. package/src/analysis/sequence-diversity-viewer.ts +48 -0
  12. package/src/analysis/sequence-search-base-viewer.ts +81 -0
  13. package/src/analysis/sequence-similarity-viewer.ts +107 -0
  14. package/src/{utils → analysis}/sequence-space.ts +0 -0
  15. package/src/calculations/monomerLevelMols.ts +64 -20
  16. package/src/package-test.ts +3 -1
  17. package/src/package.ts +64 -3
  18. package/src/substructure-search/substructure-search.ts +65 -0
  19. package/src/tests/WebLogo-positions-test.ts +5 -4
  20. package/src/tests/WebLogo-test.ts +6 -6
  21. package/src/tests/activity-cliffs-tests.ts +8 -16
  22. package/src/tests/activity-cliffs-utils.ts +3 -2
  23. package/src/tests/convert-test.ts +5 -3
  24. package/src/tests/fasta-export-tests.ts +110 -0
  25. package/src/tests/sequence-space-test.ts +7 -14
  26. package/src/tests/similarity-diversity-tests.ts +78 -0
  27. package/src/tests/splitters-test.ts +13 -0
  28. package/src/utils/cell-renderer.ts +81 -68
  29. package/src/utils/convert.ts +1 -1
  30. package/src/utils/multiple-sequence-alignment.ts +4 -5
  31. package/src/utils/save-as-fasta.ts +109 -0
  32. package/src/utils/ui-utils.ts +4 -0
  33. package/src/viewers/vd-regions-viewer.ts +6 -3
  34. package/src/widgets/representations.ts +58 -0
  35. package/test-Bio-7770371320b2-f8f97c6e.html +0 -374
package/test-Bio-7770371320b2-f8f97c6e.html DELETED
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- </style></head><body><div id="jesthtml-content"><header><h1 id="title">Bio Test Report. Datagrok version datagrok/datagrok:latest SHA=7770371320b2. Commit f8f97c6e.</h1></header><div id="metadata-container"><div id="timestamp">Started: 2022-09-20 10:00:38</div><div id="summary"><div id="suite-summary"><div class="summary-total">Suites (1)</div><div class="summary-passed summary-empty">0 passed</div><div class="summary-failed">1 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 summary-empty">0 passed</div><div class="summary-failed">1 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">42.219s</div></div><div class="suite-tests"><div class="test-result failed"><div class="test-info"><div class="test-suitename"> </div><div class="test-title">TEST</div><div class="test-status">failed</div><div class="test-duration">24.883s</div></div><div class="failureMessages"> <pre class="failureMsg">Error: Test result : Failed : 208 : Bio.renderers.setRendererManually : Error: Tag 'cell.renderer' has been manually set to 'MacromoleculeDifference' for column but after df was added as table, tag 'cell.renderer' has reset to 'sequence' instead of manual 'MacromoleculeDifference'.
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-
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- at /home/runner/work/public/public/packages/Bio/src/__jest__/remote.test.ts:68:20
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- at Generator.next (&lt;anonymous&gt;)
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- at fulfilled (/home/runner/work/public/public/packages/Bio/src/__jest__/remote.test.ts:31:58)
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- at runMicrotasks (&lt;anonymous&gt;)
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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.&lt;anonymous&gt; (/home/runner/work/public/public/packages/Bio/src/__jest__/test-node.ts:63:11)
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- at Generator.next (&lt;anonymous&gt;)
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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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- at Generator.next (&lt;anonymous&gt;)
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- at /home/runner/work/public/public/packages/Bio/src/__jest__/remote.test.ts:34:71
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- at new Promise (&lt;anonymous&gt;)
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- at Object.&lt;anonymous&gt;.__awaiter (/home/runner/work/public/public/packages/Bio/src/__jest__/remote.test.ts:30:12)
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- at Object.&lt;anonymous&gt; (/home/runner/work/public/public/packages/Bio/src/__jest__/remote.test.ts:38:23)
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- at Promise.then.completed (/home/runner/work/public/public/packages/Bio/node_modules/jest-circus/build/utils.js:391:28)
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- at new Promise (&lt;anonymous&gt;)</pre><pre class="suite-consolelog-item-message">Testing Bio package</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:66:11
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- at Generator.next (&lt;anonymous&gt;)
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- at fulfilled (/home/runner/work/public/public/packages/Bio/src/__jest__/remote.test.ts:31:58)
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- at runMicrotasks (&lt;anonymous&gt;)
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- at processTicksAndRejections (internal/process/task_queues.js:97:5)</pre><pre class="suite-consolelog-item-message">Test result : Success : 13 : Bio.WebLogo.testGetStats : OK
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- Test result : Success : 1 : Bio.WebLogo.testGetAlphabetSimilarity : OK
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- Test result : Success : 2 : Bio.WebLogo.testPickupPaletteN1 : OK
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- Test result : Success : 4 : Bio.WebLogo.testPickupPaletteN1e : OK
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- Test result : Success : 1 : Bio.WebLogo.testPickupPaletteAA1 : OK
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- Test result : Success : 2 : Bio.WebLogo.testPickupPaletteX : OK
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- Test result : Success : 0 : Bio.WebLogo.monomerToText.longMonomerSingle : OK
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- Test result : Success : 1 : Bio.WebLogo.monomerToText.longMonomerShort : OK
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- Test result : Success : 0 : Bio.WebLogo.monomerToText.longMonomerLong56 : OK
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- Test result : Success : 0 : Bio.WebLogo.monomerToText.longMonomerComplexFirstPartShort : OK
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- Test result : Success : 1 : Bio.WebLogo.monomerToText.longMonomerComplexFirstPartLong56 : OK
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- Test result : Success : 0 : Bio.Palettes.testPaletteN : OK
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- Test result : Success : 0 : Bio.Palettes.testPaletteAA : OK
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- Test result : Success : 1 : Bio.Palettes.testPalettePtMe : OK
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- Test result : Success : 100 : Bio.detectors.NegativeEmpty : OK
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- Test result : Success : 19 : Bio.detectors.Negative1 : OK
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- Test result : Success : 20 : Bio.detectors.Negative2 : OK
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- Test result : Success : 27 : Bio.detectors.Negative3 : OK
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- Test result : Success : 23 : Bio.detectors.NegativeSmiles : OK
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- Test result : Success : 15 : Bio.detectors.Dna1 : OK
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- Test result : Success : 31 : Bio.detectors.Rna1 : OK
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- Test result : Success : 49 : Bio.detectors.AA1 : OK
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- Test result : Success : 24 : Bio.detectors.MsaDna1 : OK
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- Test result : Success : 24 : Bio.detectors.MsaAA1 : OK
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- Test result : Success : 36 : Bio.detectors.SepDna : OK
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- Test result : Success : 24 : Bio.detectors.SepRna : OK
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- Test result : Success : 22 : Bio.detectors.SepPt : OK
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- Test result : Success : 6 : Bio.detectors.SepUn1 : OK
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- Test result : Success : 20 : Bio.detectors.SepUn2 : OK
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- Test result : Success : 12 : Bio.detectors.SepMsaN1 : OK
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- Test result : Success : 546 : Bio.detectors.SamplesFastaCsvPt : OK
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- Test result : Success : 15 : Bio.detectors.SamplesFastaCsvNegativeEntry : OK
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- Test result : Success : 19 : Bio.detectors.SamplesFastaCsvNegativeLength : OK
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- Test result : Success : 72 : Bio.detectors.SamplesFastaCsvNegativeUniProtKB : OK
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- Test result : Success : 332 : Bio.detectors.SamplesFastaFastaPt : OK
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- Test result : Success : 1001 : Bio.detectors.samplesPeptidesComplexNegativeID : OK
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- Test result : Success : 25 : Bio.detectors.SamplesPeptidesComplexNegativeMeasured : OK
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- Test result : Success : 179 : Bio.detectors.SamplesPeptidesComplexNegativeValue : OK
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- Test result : Success : 266 : Bio.detectors.samplesMsaComplexUn : OK
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- Test result : Success : 35 : Bio.detectors.samplesMsaComplexNegativeActivity : OK
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- Test result : Success : 186 : Bio.detectors.samplesIdCsvNegativeID : OK
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- Test result : Success : 199 : Bio.detectors.samplesSarSmallCsvNegativeSmiles : OK
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- Test result : Success : 199 : Bio.detectors.samplesHelmCsvHELM : OK
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- Test result : Success : 24 : Bio.detectors.samplesHelmCsvNegativeActivity : OK
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- Test result : Success : 183 : Bio.detectors.samplesTestHelmNegativeID : OK
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- Test result : Success : 14 : Bio.detectors.samplesTestHelmNegativeTestType : OK
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- Test result : Success : 9 : Bio.detectors.samplesTestHelmPositiveHelmString : OK
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- Test result : Success : 7 : Bio.detectors.samplesTestHelmNegativeValid : OK
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- Test result : Success : 4 : Bio.detectors.samplesTestHelmNegativeMolWeight : OK
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- Test result : Success : 13 : Bio.detectors.samplesTestHelmNegativeMolFormula : OK
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- Test result : Success : 9 : Bio.detectors.samplesTestHelmNegativeSmiles : OK
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- Test result : Success : 1031 : Bio.detectors.samplesTestDemogNegativeAll : OK
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- Test result : Success : 554 : Bio.detectors.samplesTestSmiles2NegativeSmiles : OK
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- Test result : Success : 176 : Bio.detectors.samplesTestActivityCliffsNegativeSmiles : OK
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- Test result : Success : 177 : Bio.detectors.samplesFastaPtPosSequence : OK
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- Test result : Success : 169 : Bio.detectors.samplesTestCerealNegativeCerealName : OK
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- Test result : Success : 680 : Bio.detectors.samplesTestSpgi100NegativeStereoCategory : OK
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- Test result : Success : 4 : Bio.detectors.samplesTestSpgi100NegativeScaffoldNames : OK
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- Test result : Success : 11 : Bio.detectors.samplesTestSpgi100NegativePrimaryScaffoldName : OK
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- Test result : Success : 4 : Bio.detectors.samplesTestSpgi100NegativeSampleName : OK
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- Test result : Success : 216 : Bio.detectors.samplesTestUnichemSourcesNegativeSrcUrl : OK
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- Test result : Success : 3 : Bio.detectors.samplesTestUnichemSourcesNegativeBaseIdUrl : OK
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- Test result : Success : 213 : Bio.detectors.samplesTestDmvOfficesNegativeOfficeName : OK
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- Test result : Success : 5 : Bio.detectors.samplesTestDmvOfficesNegativeCity : OK
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- Test result : Success : 237 : Bio.detectors.samplesTestAlertCollectionNegativeSmarts : OK
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- Test result : Success : 1083 : Bio.MSA.isCorrect : OK
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- Test result : Success : 257 : Bio.MSA.isCorrectLong : OK
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- Test result : Success : 1244 : Bio.sequenceSpace.sequenceSpaceOpens : OK
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- Test result : Success : 6056 : Bio.sequenceSpace.sequenceSpaceOpensWithEmptyRows : OK
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- Test result : Success : 941 : Bio.activityCliffs.activityCliffsOpen : OK
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- Test result : Success : 857 : Bio.activityCliffs.activityCliffsOpenWithEmptyRows : OK
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- Test result : Success : 2 : Bio.splitters.helm1 : OK
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- Test result : Success : 1 : Bio.splitters.helm2 : OK
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- Test result : Success : 1 : Bio.splitters.helm3-multichar : OK
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- Test result : Success : 1 : Bio.splitters.testHelm1 : OK
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- Test result : Success : 2 : Bio.splitters.testHelm2 : OK
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- Test result : Success : 1 : Bio.splitters.testHelm3 : OK
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- Test result : Success : 263 : Bio.splitters.splitToMonomers : OK
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- Test result : Success : 1 : Bio.splitters.getHelmMonomers : OK
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- Test result : Success : 75 : Bio.renderers.long sequence performance : OK
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- Test result : Success : 573 : Bio.renderers.many sequence performance : OK
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- Test result : Success : 238 : Bio.renderers.rendererMacromoleculeFasta : OK
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- Test result : Success : 246 : Bio.renderers.rendererMacromoleculeSeparator : OK
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- Test result : Success : 70 : Bio.renderers.rendererMacromoleculeDifference : OK
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- Test result : Success : 440 : Bio.renderers.afterMsa : OK
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- Test result : Success : 281 : Bio.renderers.afterConvert : OK
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- Test result : Success : 185 : Bio.renderers.selectRendererBySemType : OK
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- Test result : Success : 4 : Bio.converters.testFastaPtToSeparator : OK
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- Test result : Success : 3 : Bio.converters.testFastaDnaToSeparator : OK
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- Test result : Success : 3 : Bio.converters.testFastaRnaToSeparator : OK
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- Test result : Success : 20 : Bio.converters.testFastaGapsToSeparator : OK
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- Test result : Success : 2 : Bio.converters.testFastaPtToHelm : OK
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- Test result : Success : 2 : Bio.converters.testFastaDnaToHelm : OK
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- Test result : Success : 1 : Bio.converters.testFastaRnaToHelm : OK
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- Test result : Success : 1 : Bio.converters.testFastaGapsToHelm : OK
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- Test result : Success : 1 : Bio.converters.testSeparatorPtToFasta : OK
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- Test result : Success : 0 : Bio.converters.testSeparatorDnaToFasta : OK
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- Test result : Success : 0 : Bio.converters.testSeparatorRnaToFasta : OK
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- Test result : Success : 0 : Bio.converters.testSeparatorGapsToFasta : OK
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- Test result : Success : 1 : Bio.converters.testSeparatorPtToHelm : OK
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- Test result : Success : 0 : Bio.converters.testSeparatorDnaToHelm : OK
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- Test result : Success : 0 : Bio.converters.testSeparatorRnaToHelm : OK
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- Test result : Success : 1 : Bio.converters.testSeparatorGapsToHelm : OK
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- Test result : Success : 1 : Bio.converters.testHelmDnaToFasta : OK
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- Test result : Success : 1 : Bio.converters.testHelmRnaToFasta : OK
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- Test result : Success : 0 : Bio.converters.testHelmPtToFasta : OK
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- Test result : Success : 0 : Bio.converters.testHelmDnaToSeparator : OK
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- Test result : Success : 1 : Bio.converters.testHelmRnaToSeparator : OK
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- Test result : Success : 0 : Bio.converters.testHelmPtToSeparator : OK
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- Test result : Success : 1 : Bio.converters.testHelmLoneRibose : OK
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- Test result : Success : 2 : Bio.converters.testHelmLoneDeoxyribose : OK
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- Test result : Success : 2 : Bio.converters.testHelmLonePhosphorus : OK
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- Test result : Success : 0 : Bio.fastaFileHandler.testNormalFormatting : OK
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- Test result : Success : 0 : Bio.fastaFileHandler.testExtraSpaces : OK
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- Test result : Success : 0 : Bio.fastaFileHandler.testExtraNewlines : OK
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- Test result : Success : 94 : Bio.WebLogo-positions.allPositions : OK
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- Test result : Success : 151 : Bio.WebLogo-positions.positions with shrinkEmptyTail option true (filterd) : OK
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- Test result : Success : 104 : Bio.WebLogo-positions.positions with skipEmptyPositions option : OK
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- Test result : Success : 14 : Bio.checkInputColumn.testMsaPos : OK
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- Test result : Success : 4 : Bio.checkInputColumn.testMsaNegHelm : OK
372
- Test result : Success : 3 : Bio.checkInputColumn.testMsaNegUN : OK
373
- Test result : Success : 1 : Bio.checkInputColumn.testGetActionFunctionMeta : OK
374
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