@datagrok/peptides 1.20.0 → 1.21.1

package/dist/603.js

@@ -1,2 +0,0 @@
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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, fnNames, opts, threshold, weights, aggregationMethod } = event.data;\n    try {\n        const knnIndexes = new Array(values[0].length).fill(null).map(() => new Array(0));\n        const knnDistances = new Array(values[0].length).fill(null).map(() => new Array(0));\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            if (1 - value > threshold) {\n                knnDistances[mi].push(value);\n                knnIndexes[mi].push(mj);\n                knnDistances[mj].push(value);\n                knnIndexes[mj].push(mi);\n            }\n            cnt++;\n            mj++;\n            if (mj === values[0].length) {\n                mi++;\n                mj = mi + 1;\n            }\n        }\n        postMessage({ knnDistances, knnIndexes });\n    }\n    catch (e) {\n        postMessage({ error: e });\n    }\n};\n//# 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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, sampleLength, fnNames, opts, weights, aggregationMethod } = event.data;\n    try {\n        let distances = new Float32Array(sampleLength);\n        const chunkSize = endIdx - startIdx;\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 increment = Math.floor(chunkSize / sampleLength);\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        let distanceArrayCounter = 0;\n        while (cnt < chunkSize && distanceArrayCounter < sampleLength) {\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            distances[distanceArrayCounter] = value;\n            distanceArrayCounter++;\n            // const currentIncrement = Math.floor(Math.random() * increment) + 1\n            cnt += increment;\n            mj += increment;\n            while (mj >= values[0].length && cnt < chunkSize) {\n                mi++;\n                mj = mi + 1 + (mj - values[0].length);\n            }\n        }\n        if (distanceArrayCounter < sampleLength)\n            distances = distances.slice(0, distanceArrayCounter);\n        postMessage({ distance: distances });\n    }\n    catch (e) {\n        postMessage({ error: e });\n    }\n};\n//# 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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, 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 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 = mi + 1;\n            }\n        }\n        postMessage({ knnDistances, knnIndexes });\n    }\n    catch (e) {\n        postMessage({ error: e });\n    }\n};\n//# 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