@datagrok/bio 2.11.27 → 2.11.29

package/package.json

@@ -5,7 +5,7 @@
     "name": "Leonid Stolbov",
     "email": "lstolbov@datagrok.ai"
   },
-  "version": "2.11.27",
+  "version": "2.11.29",
   "description": "Bioinformatics support (import/export of sequences, conversion, visualization, analysis). [See more](https://github.com/datagrok-ai/public/blob/master/packages/Bio/README.md) for details.",
   "repository": {
     "type": "git",
@@ -34,9 +34,9 @@
   ],
   "dependencies": {
     "@biowasm/aioli": "^3.1.0",
-    "@datagrok-libraries/bio": "^5.39.18",
+    "@datagrok-libraries/bio": "^5.39.22",
     "@datagrok-libraries/chem-meta": "^1.2.1",
-    "@datagrok-libraries/ml": "^6.4.1",
+    "@datagrok-libraries/ml": "^6.4.7",
     "@datagrok-libraries/tutorials": "^1.3.11",
     "@datagrok-libraries/utils": "^4.1.36",
     "@datagrok-libraries/math": "^1.0.7",

package/src/package.ts

@@ -483,7 +483,7 @@ export async function activityCliffs(table: DG.DataFrame, molecules: DG.Column<s
 //input: double gapOpen = 1 {caption: Gap open penalty; default: 1; optional: true}
 //input: double gapExtend = 0.6 {caption: Gap extension penalty; default: 0.6; optional: true}
 // eslint-disable-next-line max-len
-//input: string fingerprintType = Morgan {caption: Fingerprint type; choices: ['Morgan', 'RDKit', 'Pattern']; default: Morgan; optional: true}
+//input: string fingerprintType = Morgan {caption: Fingerprint type; choices: ['Morgan', 'RDKit', 'Pattern', 'AtomPair', 'MACCS', 'TopologicalTorsion']; default: Morgan; optional: true}
 //output: object result
 export async function macromoleculePreprocessingFunction(
   col: DG.Column, metric: MmDistanceFunctionsNames, gapOpen: number = 1, gapExtend: number = 0.6,

package/src/utils/cell-renderer.ts

@@ -215,6 +215,8 @@ export class MacromoleculeSequenceCellRenderer extends DG.GridCellRenderer {
 
       const tempReferenceSequence: string | null = tableColTemp[tempTAGS.referenceSequence];
       const tempCurrentWord: string | null = tableColTemp[tempTAGS.currentWord];
+      if (tempCurrentWord && tableCol?.dataFrame?.currentRowIdx === -1)
+        tableColTemp[tempTAGS.currentWord] = null;
       const referenceSequence: ISeqSplitted = splitterFunc(
         ((tempReferenceSequence != null) && (tempReferenceSequence != '')) ?
           tempReferenceSequence : tempCurrentWord ?? '');

package/src/viewers/web-logo-viewer.ts

@@ -457,7 +457,7 @@ export class WebLogoViewer extends DG.JsViewer implements IWebLogoViewer {
   private static viewerCounter: number = -1;
   private readonly viewerId: number = ++WebLogoViewer.viewerCounter;
 
-  private viewerToLog(): string { return `MolstarViewer<${this.viewerId}>`; }
+  private viewerToLog(): string { return `WebLogoViewer<${this.viewerId}>`; }
 
   // -- Data --
 

package/dist/100.js

@@ -1,2 +0,0 @@
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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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{ isNil } from './utils';\nimport { Measure, isBitArrayMetric } from '../typed-metrics';\nimport BitArray from '@datagrok-libraries/utils/src/bit-array';\nonmessage = (event) => {\n    const { values, fnName, startRow, startCol, chunckSize, opts } = event.data;\n    const data = {};\n    try {\n        // if (startRow != -1)\n        //   throw new Error('Error in distance matrix worker'); // TODO: remove this line\n        let i = startRow;\n        let j = startCol;\n        let cnt = 0;\n        let lmin = 0;\n        let lmax = Number.MIN_VALUE;\n        if (isBitArrayMetric(fnName)) {\n            for (let i = 0; i < values.length; ++i) {\n                if (isNil(values[i]))\n                    continue;\n                values[i] = new BitArray(values[i]._data, values[i]._length);\n            }\n        }\n        const retVal = new Float32Array(chunckSize);\n        const distanceFn = new Measure(fnName).getMeasure(opts);\n        while (cnt < chunckSize) {\n            const value = !isNil(values[i]) && !isNil(values[j]) ?\n                distanceFn(values[i], values[j]) : 1;\n            retVal[cnt] = value;\n            if (value < lmin)\n                lmin = value;\n            if (value > lmax)\n                lmax = value;\n            cnt++;\n            j++;\n            if (j === values.length) {\n                i++;\n                j = i + 1;\n            }\n        }\n        data.distanceMatrixData = retVal;\n        data.min = lmin;\n        data.max = lmax;\n    }\n    catch (e) {\n        data.error = e;\n    }\n    postMessage(data);\n};\n//# 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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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{ 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, fnName, opts } = event.data;\n    try {\n        // if (startIdx != -1)\n        //   throw new Error('Error in sparse threshold worker'); // TODO: remove this line\n        let distances = new Float32Array(sampleLength);\n        const chunkSize = endIdx - startIdx;\n        if (isBitArrayMetric(fnName)) {\n            for (let i = 0; i < values.length; ++i) {\n                if (isNil(values[i]))\n                    continue;\n                values[i] = new BitArray(values[i]._data, values[i]._length);\n            }\n        }\n        let cnt = 0;\n        const increment = Math.floor(chunkSize / sampleLength);\n        const distanceFn = new Measure(fnName).getMeasure(opts);\n        const startRow = values.length - 2 - Math.floor(Math.sqrt(-8 * startIdx + 4 * values.length * (values.length - 1) - 7) / 2 - 0.5);\n        const startCol = startIdx - values.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 value = !isNil(values[mi]) && !isNil(values[mj]) ?\n                distanceFn(values[mi], values[mj]) : 1;\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.length && cnt < chunkSize) {\n                mi++;\n                mj = mi + 1 + (mj - values.length);\n            }\n        }\n        if (distanceArrayCounter < sampleLength) {\n            distances = distances.slice(0, distanceArrayCounter);\n        }\n        postMessage({ distance: distances });\n    }\n    catch (e) {\n        postMessage({ error: e });\n    }\n};\n//# 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this.incrementVersion(e),this}xor(t,e=!0){if(this._length!=t._length)throw new Error("Array lengths differ.");for(let e=0,n=this.lengthInInts;e<n;e++)this._data[e]^=t._data[e];return this.incrementVersion(e),this}insertAt(t,e,n=!1){if(this.assureInRange(t,0,this._length,"pos"),0==e)return;const r=this._length;this.setLength(this._length+e);for(let n=r-1;n>=t;n--)this.setBit(n+e,this.getBit(n));for(let r=t;r<t+e;r++)this.setBit(r,n)}removeAt(t,e=1){if(e<0)throw new Error("n cannot be negative");if(this.assureInRange(t,0,this._length-e,"pos"),this.contains(!0))for(let n=t;n<this._length-e;n++)this.setBit(n,this.getBit(n+e));this.setLength(this._length-e)}removeByMask(t,e=!0){if(this._length!=t.length)throw new Error("length != mask.length");if(t==this)this.setLength(t.countBits(!e)),this.setAll(!e);else{let n=0;for(let r=-1;-1!=(r=t.findNext(r,!e));)this.setFast(n++,this.getBit(r));this._length=n,this._version++}return this}getBit(t){return 0!=(this._data[Math.floor(t/32)]&1<<(31&t))}setBit(t,e,n=!0){this.setFast(t,e),this._version++}setFast(t,e){e?this._data[Math.floor(t/32)]|=1<<(31&t):this._data[Math.floor(t/32)]&=~(1<<(31&t))}setTrue(t){this._data[Math.floor(t/32)]|=1<<(31&t)}setFalse(t){this._data[Math.floor(t/32)]&=~(1<<(31&t))}trueCount(){return this.countBits(!0)}falseCount(){return this.countBits(!1)}countBits(t){if(0==this._length)return 0;if(this._selectedCountVersion!=this._version){this._selectedCount=0;const t=this.lengthInInts;let e=0;for(;e<t-1;e++)for(let t=this._data[e];0!=t;t>>>=8)this._selectedCount+=r._onBitCount[255&t];let n=this._data[e];const i=31&this._length;for(0!=i&&(n&=~(4294967295<<i));0!=n;n>>>=8)this._selectedCount+=r._onBitCount[255&n];this._selectedCountVersion=this._version}return t?this._selectedCount:this._length-this._selectedCount}countWhere(t){let e=0;if(this.trueCount()==this._length)for(let n=0;n<this._length;n++)e+=t(n)?1:0;else for(let n=-1;-1!=(n=this.findNext(n,!0));)e+=t(n)?1:0;return e}andWithCountBits(t,e){if(0==this._length)return 0;let n=0;const i=this.lengthInInts;let s=0;for(;s<i-1;s++)for(let e=this._data[s]&t._data[s];0!=e;e>>>=8)n+=r._onBitCount[255&e];let o=this._data[s]&t._data[s];const h=31&this._length;for(0!=h&&(o&=~(4294967295<<h));0!=o;o>>>=8)n+=r._onBitCount[255&o];return e?n:this._length-n}clear(){this.setLength(0)}contains(t){return this.findNext(-1,t)>=0}get allTrue(){return this.countBits(!0)==this._length}get allFalse(){return this.countBits(!1)==this._length}get anyTrue(){return this.countBits(!0)>0}get anyFalse(){return this.countBits(!1)>0}findNext(t,e=!0){if(this.assureInRange(t,-1,this._length,"index"),t>=this._length-1)return-1;let n=31&(t=t<0?0:t+1);const i=this.lengthInInts;for(let s=Math.floor(t/32);s<i;s++){let i=e?this._data[s]:~this._data[s];if(0!=n)i&=4294967295<<n&4294967295,n=0;else if(!e&&-4294967296==i)continue;for(let e=0;0!=i;e+=8,i>>>=8){const n=r._firstOnBit[255&i];if(n>=0)return(t=n+32*s+e)>=this._length?-1:t}}return-1}findPrev(t,e=!0){if(0==t)return-1;this.assureInRange(t,-1,this._length,"index");let n=1+(t=t<0?this._length-1:t-1)&31;for(let i=Math.floor(t/32);i>=0;i--){let t=e?this._data[i]:~this._data[i];0!=n&&(t&=~(4294967295<<n),n=0);for(let e=24;0!=t;e-=8,t<<=8){const n=r._lastOnBit[t>>>24];if(n>=0)return n+32*i+e}}return-1}}r._onBitCount=Int8Array.from([0,1,1,2,1,2,2,3,1,2,2,3,2,3,3,4,1,2,2,3,2,3,3,4,2,3,3,4,3,4,4,5,1,2,2,3,2,3,3,4,2,3,3,4,3,4,4,5,2,3,3,4,3,4,4,5,3,4,4,5,4,5,5,6,1,2,2,3,2,3,3,4,2,3,3,4,3,4,4,5,2,3,3,4,3,4,4,5,3,4,4,5,4,5,5,6,2,3,3,4,3,4,4,5,3,4,4,5,4,5,5,6,3,4,4,5,4,5,5,6,4,5,5,6,5,6,6,7,1,2,2,3,2,3,3,4,2,3,3,4,3,4,4,5,2,3,3,4,3,4,4,5,3,4,4,5,4,5,5,6,2,3,3,4,3,4,4,5,3,4,4,5,4,5,5,6,3,4,4,5,4,5,5,6,4,5,5,6,5,6,6,7,2,3,3,4,3,4,4,5,3,4,4,5,4,5,5,6,3,4,4,5,4,5,5,6,4,5,5,6,5,6,6,7,3,4,4,5,4,5,5,6,4,5,5,6,5,6,6,7,4,5,5,6,5,6,6,7,5,6,6,7,6,7,7,8]),r._firstOnBit=Int8Array.from([-1,0,1,0,2,0,1,0,3,0,1,0,2,0,1,0,4,0,1,0,2,0,1,0,3,0,1,0,2,0,1,0,5,0,1,0,2,0,1,0,3,0,1,0,2,0,1,0,4,0,1,0,2,0,1,0,3,0,1,0,2,0,1,0,6,0,1,0,2,0,1,0,3,0,1,0,2,0,1,0,4,0,1,0,2,0,1,0,3,0,1,0,2,0,1,0,5,0,1,0,2,0,1,0,3,0,1,0,2,0,1,0,4,0,1,0,2,0,1,0,3,0,1,0,2,0,1,0,7,0,1,0,2,0,1,0,3,0,1,0,2,0,1,0,4,0,1,0,2,0,1,0,3,0,1,0,2,0,1,0,5,0,1,0,2,0,1,0,3,0,1,0,2,0,1,0,4,0,1,0,2,0,1,0,3,0,1,0,2,0,1,0,6,0,1,0,2,0,1,0,3,0,1,0,2,0,1,0,4,0,1,0,2,0,1,0,3,0,1,0,2,0,1,0,5,0,1,0,2,0,1,0,3,0,1,0,2,0,1,0,4,0,1,0,2,0,1,0,3,0,1,0,2,0,1,0]),r._lastOnBit=Int8Array.from([-1,0,1,1,2,2,2,2,3,3,3,3,3,3,3,3,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,6,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7])},850:(t,e,n)=>{function r(t,e){let n=0;const r=t.length;if(r!==e.length)throw new Error("The dimensionality of the vectors must match");for(let i=0;i<r;++i)n+=Math.pow(t[i]-e[i],2);return Math.sqrt(n)}n.d(e,{dP:()=>r})}}]);
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