@datagrok/bio 2.11.28 → 2.11.30

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Files changed (58) hide show
  1. package/CHANGELOG.md +12 -1
  2. package/dist/23.js +2 -0
  3. package/dist/23.js.map +1 -0
  4. package/dist/282.js +2 -0
  5. package/dist/282.js.map +1 -0
  6. package/dist/36.js +2 -0
  7. package/dist/36.js.map +1 -0
  8. package/dist/40.js +2 -0
  9. package/dist/40.js.map +1 -0
  10. package/dist/413.js +2 -0
  11. package/dist/413.js.map +1 -0
  12. package/dist/42.js +1 -1
  13. package/dist/42.js.map +1 -1
  14. package/dist/427.js +2 -0
  15. package/dist/427.js.map +1 -0
  16. package/dist/65.js +2 -0
  17. package/dist/65.js.map +1 -0
  18. package/dist/709.js +3 -0
  19. package/dist/709.js.map +1 -0
  20. package/dist/package-test.js +1 -1
  21. package/dist/package-test.js.map +1 -1
  22. package/dist/package.js +1 -1
  23. package/dist/package.js.map +1 -1
  24. package/files/tests/to-atomic-level-msa-fasta-input.csv +10 -0
  25. package/files/tests/to-atomic-level-msa-fasta-output.csv +2178 -0
  26. package/package.json +9 -9
  27. package/src/package.ts +12 -10
  28. package/src/tests/msa-tests.ts +2 -2
  29. package/src/tests/pepsea-tests.ts +1 -1
  30. package/src/tests/renderers-test.ts +16 -16
  31. package/src/tests/splitters-test.ts +7 -12
  32. package/src/tests/substructure-filters-tests.ts +277 -55
  33. package/src/tests/to-atomic-level-tests.ts +32 -22
  34. package/src/tests/utils/sequences-generators.ts +6 -3
  35. package/src/tests/utils.ts +6 -6
  36. package/src/utils/cell-renderer.ts +2 -0
  37. package/src/utils/docker.ts +36 -0
  38. package/src/viewers/vd-regions-viewer.ts +4 -0
  39. package/src/viewers/web-logo-viewer.ts +4 -0
  40. package/src/widgets/bio-substructure-filter-helm.ts +168 -0
  41. package/src/widgets/bio-substructure-filter-types.ts +131 -0
  42. package/src/widgets/bio-substructure-filter.ts +215 -175
  43. package/src/widgets/composition-analysis-widget.ts +1 -1
  44. package/dist/100.js +0 -2
  45. package/dist/100.js.map +0 -1
  46. package/dist/118.js +0 -2
  47. package/dist/118.js.map +0 -1
  48. package/dist/361.js +0 -2
  49. package/dist/361.js.map +0 -1
  50. package/dist/471.js +0 -2
  51. package/dist/471.js.map +0 -1
  52. package/dist/649.js +0 -2
  53. package/dist/649.js.map +0 -1
  54. package/dist/664.js +0 -2
  55. package/dist/664.js.map +0 -1
  56. package/dist/886.js +0 -3
  57. package/dist/886.js.map +0 -1
  58. /package/dist/{886.js.LICENSE.txt → 709.js.LICENSE.txt} +0 -0
package/CHANGELOG.md CHANGED
@@ -1,6 +1,17 @@
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  # Bio changelog
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- ## 2.12.0 (WIP)
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+ ## 2.11.30 (2024-02-15)
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+
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+ ### Features
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+
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+ * GROK-14598: Bio: Substructure filter sync between cloned views, tests
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+
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+ ### Bug fixes
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+
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+ * GROK-14916: Bio: Fix biosubstructure filter for sequences of Helm
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+ * GROK-14913: Bio: Fix To Atomic Level for sequences with gaps, tests
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+
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+ ## 2.11.28 (2024-02-07)
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  ### Features
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package/dist/23.js ADDED
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function insertSmaller(distancesAr, indexes, num, index) {\n if (num > distancesAr[distancesAr.length - 1])\n return;\n const newPosition = distancesAr.findIndex((v) => num < v);\n distancesAr.pop();\n distancesAr.splice(newPosition, 0, num);\n indexes.pop();\n indexes.splice(newPosition, 0, index);\n}\nexport function insertLarger(distancesAr, indexes, num, index) {\n if (num < distancesAr[distancesAr.length - 1])\n return;\n const newPosition = distancesAr.findIndex((v) => num > v);\n distancesAr.pop();\n distancesAr.splice(newPosition, 0, num);\n indexes.pop();\n indexes.splice(newPosition, 0, index);\n}\nexport function getAggregationFunction(aggregationMethod, weights) {\n switch (aggregationMethod) {\n case DistanceAggregationMethods.MANHATTAN:\n return (vs) => vs.reduce((acc, val, idx) => acc + val * weights[idx], 0);\n default:\n return (vs) => {\n // euclidean\n const sum = vs.reduce((acc, val, idx) => acc + (val * weights[idx]) ** 2, 0);\n return Math.sqrt(sum);\n };\n }\n}\n//# 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{ getAggregationFunction, isNil } from './utils';\nimport { Measure, isBitArrayMetric } from '../typed-metrics';\nimport BitArray from '@datagrok-libraries/utils/src/bit-array';\nonmessage = async (event) => {\n const { values, startIdx, endIdx, threshold, fnNames, opts, aggregationMethod, weights } = event.data;\n try {\n // if (startIdx != -1)\n // throw new Error('Error in sparse matrix worker'); // TODO: remove this line\n const i = [];\n const j = [];\n const distances = [];\n const chunkSize = endIdx - startIdx;\n //const mi = startRow;\n //const mj = startCol;\n const aggregate = getAggregationFunction(aggregationMethod, weights);\n values.forEach((v, colIdx) => {\n if (isBitArrayMetric(fnNames[colIdx])) {\n for (let i = 0; i < v.length; ++i) {\n if (isNil(v[i]))\n continue;\n values[colIdx][i] = new BitArray(values[colIdx][i]._data, values[colIdx][i]._length);\n }\n }\n });\n let cnt = 0;\n const distanceFns = new Array(fnNames.length).fill(null).map((_, i) => new Measure(fnNames[i]).getMeasure(opts[i]));\n const startRow = values[0].length - 2 - Math.floor(Math.sqrt(-8 * startIdx + 4 * values[0].length * (values[0].length - 1) - 7) / 2 - 0.5);\n const startCol = startIdx - values[0].length * startRow + Math.floor((startRow + 1) * (startRow + 2) / 2);\n let mi = startRow;\n let mj = startCol;\n while (cnt < chunkSize) {\n //const value = seq1List[mi] && seq1List[mj] ? hamming(seq1List[mi], seq1List[mj]) : 0;\n const distanceValues = distanceFns.map((fn, idx) => !isNil(values[idx][mi]) && !isNil(values[idx][mj]) ?\n fn(values[idx][mi], values[idx][mj]) : 1);\n const value = distanceValues.length === 1 ? distanceValues[0] : aggregate(distanceValues);\n if (1 - value >= threshold) {\n i.push(mi);\n j.push(mj);\n distances.push(value);\n }\n cnt++;\n mj++;\n if (mj === values[0].length) {\n mi++;\n mj = mi + 1;\n }\n }\n const iArray = new Int32Array(i);\n const jArray = new Int32Array(j);\n const distanceArray = new Float32Array(distances);\n postMessage({ i: iArray, j: jArray, distance: distanceArray });\n }\n catch (e) {\n postMessage({ error: e });\n }\n};\n//# 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notFulfilled = Infinity;\n\tfor (var i = 0; i < deferred.length; i++) {\n\t\tvar [chunkIds, fn, priority] = deferred[i];\n\t\tvar fulfilled = true;\n\t\tfor (var j = 0; j < chunkIds.length; j++) {\n\t\t\tif ((priority & 1 === 0 || notFulfilled >= priority) && Object.keys(__webpack_require__.O).every((key) => (__webpack_require__.O[key](chunkIds[j])))) {\n\t\t\t\tchunkIds.splice(j--, 1);\n\t\t\t} else {\n\t\t\t\tfulfilled = false;\n\t\t\t\tif(priority < notFulfilled) notFulfilled = priority;\n\t\t\t}\n\t\t}\n\t\tif(fulfilled) {\n\t\t\tdeferred.splice(i--, 1)\n\t\t\tvar r = fn();\n\t\t\tif (r !== undefined) result = r;\n\t\t}\n\t}\n\treturn result;\n};","var next = __webpack_require__.x;\n__webpack_require__.x = () => {\n\treturn Promise.all([\n\t\t__webpack_require__.e(36),\n\t\t__webpack_require__.e(413)\n\t]).then(next);\n};","import { DistanceAggregationMethods } from './types';\nexport const isNil = (x) => x === null || x === undefined;\nexport function insertSmaller(distancesAr, indexes, num, index) {\n if (num > distancesAr[distancesAr.length - 1])\n return;\n const newPosition = distancesAr.findIndex((v) => num < v);\n distancesAr.pop();\n distancesAr.splice(newPosition, 0, num);\n indexes.pop();\n indexes.splice(newPosition, 0, index);\n}\nexport function insertLarger(distancesAr, indexes, num, index) {\n if (num < distancesAr[distancesAr.length - 1])\n return;\n const newPosition = distancesAr.findIndex((v) => num > v);\n distancesAr.pop();\n distancesAr.splice(newPosition, 0, num);\n indexes.pop();\n indexes.splice(newPosition, 0, index);\n}\nexport function getAggregationFunction(aggregationMethod, weights) {\n switch (aggregationMethod) {\n case DistanceAggregationMethods.MANHATTAN:\n return (vs) => vs.reduce((acc, val, idx) => acc + val * weights[idx], 0);\n default:\n return (vs) => {\n // euclidean\n const sum = vs.reduce((acc, val, idx) => acc + (val * weights[idx]) ** 2, 0);\n return Math.sqrt(sum);\n };\n }\n}\n//# 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{ getAggregationFunction, insertSmaller, isNil } from './utils';\nimport { Measure, isBitArrayMetric } from '../typed-metrics';\nimport BitArray from '@datagrok-libraries/utils/src/bit-array';\nonmessage = async (event) => {\n const { values, startIdx, endIdx, fnNames, opts, nNeighbours, weights, aggregationMethod } = event.data;\n try {\n const knnIndexes = new Array(values[0].length).fill(null).map(() => new Array(nNeighbours).fill(-1));\n const knnDistances = new Array(values[0].length).fill(null).map(() => new Array(nNeighbours).fill(999999));\n const aggregate = getAggregationFunction(aggregationMethod, weights);\n const chunkSize = endIdx - startIdx;\n values.forEach((v, colIdx) => {\n if (isBitArrayMetric(fnNames[colIdx])) {\n for (let i = 0; i < v.length; ++i) {\n if (isNil(v[i]))\n continue;\n values[colIdx][i] = new BitArray(values[colIdx][i]._data, values[colIdx][i]._length);\n }\n }\n });\n let cnt = 0;\n const distanceFns = new Array(fnNames.length).fill(null).map((_, i) => new Measure(fnNames[i]).getMeasure(opts[i]));\n const startRow = values[0].length - 2 - Math.floor(Math.sqrt(-8 * startIdx + 4 * values[0].length * (values[0].length - 1) - 7) / 2 - 0.5);\n const startCol = startIdx - values[0].length * startRow + Math.floor((startRow + 1) * (startRow + 2) / 2);\n let mi = startRow;\n let mj = startCol;\n while (cnt < chunkSize) {\n //const value = seq1List[mi] && seq1List[mj] ? hamming(seq1List[mi], seq1List[mj]) : 0;\n const distanceValues = distanceFns.map((fn, idx) => !isNil(values[idx][mi]) && !isNil(values[idx][mj]) ?\n fn(values[idx][mi], values[idx][mj]) : 1);\n // const value = !isNil(values[mi]) && !isNil(values[mj]) ?\n // distanceFn(values[mi], values[mj]) : 1;\n const value = distanceValues.length === 1 ? distanceValues[0] : aggregate(distanceValues);\n insertSmaller(knnDistances[mi], knnIndexes[mi], value, mj);\n insertSmaller(knnDistances[mj], knnIndexes[mj], value, mi);\n cnt++;\n mj++;\n if (mj === values[0].length) {\n mi++;\n mj = 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