@datagrok/bio - npm Package Compare versions

Comparing version 2.11.20 to 2.11.21

dist/23.js

@@ -1,2 +0,2 @@
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+var bio;(()=>{"use strict";var e,r,t={5023:(e,r,t)=>{const o=e=>null==e;var n=t(6361),a=t(9657);onmessage=async e=>{const{values:r,startIdx:t,endIdx:s,threshold:i,fnName:c,opts:l}=e.data;try{const e=[],p=[],h=[],f=s-t;if((0,n.sQ)(c))for(let e=0;e<r.length;++e)o(r[e])||(r[e]=new a.Z(r[e]._data,r[e]._length));let u=0;const g=new n.UH(c).getMeasure(l),v=r.length-2-Math.floor(Math.sqrt(-8*t+4*r.length*(r.length-1)-7)/2-.5),b=t-r.length*v+Math.floor((v+1)*(v+2)/2);let d=v,w=b;for(;u<f;){const t=o(r[d])||o(r[w])?1:g(r[d],r[w]);1-t>=i&&(e.push(d),p.push(w),h.push(t)),u++,w++,w===r.length&&(d++,w=d+1)}const y=new Int32Array(e),m=new Int32Array(p),x=new Float32Array(h);postMessage({i:y,j:m,distance:x})}catch(e){postMessage({error:e})}}}},o={};function n(e){var r=o[e];if(void 0!==r)return r.exports;var a=o[e]={exports:{}};return t[e](a,a.exports,n),a.exports}n.m=t,n.x=()=>{var e=n.O(void 0,[378,361],(()=>n(5023)));return n.O(e)},e=[],n.O=(r,t,o,a)=>{if(!t){var s=1/0;for(p=0;p<e.length;p++){for(var[t,o,a]=e[p],i=!0,c=0;c<t.length;c++)(!1&a||s>=a)&&Object.keys(n.O).every((e=>n.O[e](t[c])))?t.splice(c--,1):(i=!1,a<s&&(s=a));if(i){e.splice(p--,1);var l=o();void 0!==l&&(r=l)}}return r}a=a||0;for(var p=e.length;p>0&&e[p-1][2]>a;p--)e[p]=e[p-1];e[p]=[t,o,a]},n.d=(e,r)=>{for(var t in r)n.o(r,t)&&!n.o(e,t)&&Object.defineProperty(e,t,{enumerable:!0,get:r[t]})},n.f={},n.e=e=>Promise.all(Object.keys(n.f).reduce(((r,t)=>(n.f[t](e,r),r)),[])),n.u=e=>e+".js",n.g=function(){if("object"==typeof globalThis)return globalThis;try{return this||new Function("return this")()}catch(e){if("object"==typeof window)return window}}(),n.o=(e,r)=>Object.prototype.hasOwnProperty.call(e,r),(()=>{var e;n.g.importScripts&&(e=n.g.location+"");var r=n.g.document;if(!e&&r&&(r.currentScript&&(e=r.currentScript.src),!e)){var t=r.getElementsByTagName("script");if(t.length)for(var o=t.length-1;o>-1&&!e;)e=t[o--].src}if(!e)throw new Error("Automatic publicPath is not supported in this browser");e=e.replace(/#.*$/,"").replace(/\?.*$/,"").replace(/\/[^\/]+$/,"/"),n.p=e})(),(()=>{var e={23:1};n.f.i=(r,t)=>{e[r]||importScripts(n.p+n.u(r))};var r=self.webpackChunkbio=self.webpackChunkbio||[],t=r.push.bind(r);r.push=r=>{var[o,a,s]=r;for(var i in a)n.o(a,i)&&(n.m[i]=a[i]);for(s&&s(n);o.length;)e[o.pop()]=1;t(r)}})(),r=n.x,n.x=()=>Promise.all([n.e(378),n.e(361)]).then(r);var a=n.x();bio=a})();
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dist/282.js

@@ -1,2 +0,2 @@
-var bio;(()=>{"use strict";var e,r,t={1282:(e,r,t)=>{const n=e=>null==e;function o(e,r,t,n){if(t>e[e.length-1])return;const o=e.findIndex((e=>t>e))+1;e.pop(),e.splice(o,0,t),r.pop(),r.splice(o,0,n)}var a=t(6361),i=t(9657);onmessage=async e=>{const{values:r,startIdx:t,endIdx:l,fnName:s,opts:c,nNeighbours:p}=e.data;try{const e=new Array(r.length).fill(null).map((()=>new Array(p).fill(-1))),f=new Array(r.length).fill(null).map((()=>new Array(p).fill(999999))),h=l-t;if((0,a.sQ)(s))for(let e=0;e<r.length;++e)n(r[e])||(r[e]=new i.Z(r[e]._data,r[e]._length));let u=0;const g=new a.UH(s).getMeasure(c),v=r.length-2-Math.floor(Math.sqrt(-8*t+4*r.length*(r.length-1)-7)/2-.5),b=t-r.length*v+Math.floor((v+1)*(v+2)/2);let d=v,w=b;for(;u<h;){const t=n(r[d])||n(r[w])?1:g(r[d],r[w]);o(f[d],e[d],t,w),o(f[w],e[w],t,d),u++,w++,w===r.length&&(d++,w=d+1)}postMessage({knnDistances:f,knnIndexes:e})}catch(e){postMessage({error:e})}}}},n={};function o(e){var r=n[e];if(void 0!==r)return r.exports;var a=n[e]={exports:{}};return t[e](a,a.exports,o),a.exports}o.m=t,o.x=()=>{var e=o.O(void 0,[562,44,361],(()=>o(1282)));return o.O(e)},e=[],o.O=(r,t,n,a)=>{if(!t){var i=1/0;for(p=0;p<e.length;p++){for(var[t,n,a]=e[p],l=!0,s=0;s<t.length;s++)(!1&a||i>=a)&&Object.keys(o.O).every((e=>o.O[e](t[s])))?t.splice(s--,1):(l=!1,a<i&&(i=a));if(l){e.splice(p--,1);var c=n();void 0!==c&&(r=c)}}return r}a=a||0;for(var p=e.length;p>0&&e[p-1][2]>a;p--)e[p]=e[p-1];e[p]=[t,n,a]},o.d=(e,r)=>{for(var t in r)o.o(r,t)&&!o.o(e,t)&&Object.defineProperty(e,t,{enumerable:!0,get:r[t]})},o.f={},o.e=e=>Promise.all(Object.keys(o.f).reduce(((r,t)=>(o.f[t](e,r),r)),[])),o.u=e=>e+".js",o.g=function(){if("object"==typeof globalThis)return globalThis;try{return this||new Function("return this")()}catch(e){if("object"==typeof window)return window}}(),o.o=(e,r)=>Object.prototype.hasOwnProperty.call(e,r),(()=>{var e;o.g.importScripts&&(e=o.g.location+"");var r=o.g.document;if(!e&&r&&(r.currentScript&&(e=r.currentScript.src),!e)){var t=r.getElementsByTagName("script");if(t.length)for(var n=t.length-1;n>-1&&!e;)e=t[n--].src}if(!e)throw new Error("Automatic publicPath is not supported in this browser");e=e.replace(/#.*$/,"").replace(/\?.*$/,"").replace(/\/[^\/]+$/,"/"),o.p=e})(),(()=>{var e={282:1};o.f.i=(r,t)=>{e[r]||importScripts(o.p+o.u(r))};var r=self.webpackChunkbio=self.webpackChunkbio||[],t=r.push.bind(r);r.push=r=>{var[n,a,i]=r;for(var l in a)o.o(a,l)&&(o.m[l]=a[l]);for(i&&i(o);n.length;)e[n.pop()]=1;t(r)}})(),r=o.x,o.x=()=>Promise.all([562,44,361].map(o.e,o)).then(r);var a=o.x();bio=a})();
+var bio;(()=>{"use strict";var e,r,t={1282:(e,r,t)=>{const n=e=>null==e;function o(e,r,t,n){if(t>e[e.length-1])return;const o=e.findIndex((e=>t<e));e.pop(),e.splice(o,0,t),r.pop(),r.splice(o,0,n)}var a=t(6361),i=t(9657);onmessage=async e=>{const{values:r,startIdx:t,endIdx:l,fnName:s,opts:c,nNeighbours:p}=e.data;try{const e=new Array(r.length).fill(null).map((()=>new Array(p).fill(-1))),f=new Array(r.length).fill(null).map((()=>new Array(p).fill(999999))),h=l-t;if((0,a.sQ)(s))for(let e=0;e<r.length;++e)n(r[e])||(r[e]=new i.Z(r[e]._data,r[e]._length));let u=0;const g=new a.UH(s).getMeasure(c),v=r.length-2-Math.floor(Math.sqrt(-8*t+4*r.length*(r.length-1)-7)/2-.5),b=t-r.length*v+Math.floor((v+1)*(v+2)/2);let d=v,w=b;for(;u<h;){const t=n(r[d])||n(r[w])?1:g(r[d],r[w]);o(f[d],e[d],t,w),o(f[w],e[w],t,d),u++,w++,w===r.length&&(d++,w=d+1)}postMessage({knnDistances:f,knnIndexes:e})}catch(e){postMessage({error:e})}}}},n={};function o(e){var r=n[e];if(void 0!==r)return r.exports;var a=n[e]={exports:{}};return t[e](a,a.exports,o),a.exports}o.m=t,o.x=()=>{var e=o.O(void 0,[378,361],(()=>o(1282)));return o.O(e)},e=[],o.O=(r,t,n,a)=>{if(!t){var i=1/0;for(p=0;p<e.length;p++){for(var[t,n,a]=e[p],l=!0,s=0;s<t.length;s++)(!1&a||i>=a)&&Object.keys(o.O).every((e=>o.O[e](t[s])))?t.splice(s--,1):(l=!1,a<i&&(i=a));if(l){e.splice(p--,1);var c=n();void 0!==c&&(r=c)}}return r}a=a||0;for(var p=e.length;p>0&&e[p-1][2]>a;p--)e[p]=e[p-1];e[p]=[t,n,a]},o.d=(e,r)=>{for(var t in r)o.o(r,t)&&!o.o(e,t)&&Object.defineProperty(e,t,{enumerable:!0,get:r[t]})},o.f={},o.e=e=>Promise.all(Object.keys(o.f).reduce(((r,t)=>(o.f[t](e,r),r)),[])),o.u=e=>e+".js",o.g=function(){if("object"==typeof globalThis)return globalThis;try{return this||new Function("return this")()}catch(e){if("object"==typeof window)return window}}(),o.o=(e,r)=>Object.prototype.hasOwnProperty.call(e,r),(()=>{var e;o.g.importScripts&&(e=o.g.location+"");var r=o.g.document;if(!e&&r&&(r.currentScript&&(e=r.currentScript.src),!e)){var t=r.getElementsByTagName("script");if(t.length)for(var n=t.length-1;n>-1&&!e;)e=t[n--].src}if(!e)throw new Error("Automatic publicPath is not supported in this browser");e=e.replace(/#.*$/,"").replace(/\?.*$/,"").replace(/\/[^\/]+$/,"/"),o.p=e})(),(()=>{var e={282:1};o.f.i=(r,t)=>{e[r]||importScripts(o.p+o.u(r))};var r=self.webpackChunkbio=self.webpackChunkbio||[],t=r.push.bind(r);r.push=r=>{var[n,a,i]=r;for(var l in a)o.o(a,l)&&(o.m[l]=a[l]);for(i&&i(o);n.length;)e[n.pop()]=1;t(r)}})(),r=o.x,o.x=()=>Promise.all([o.e(378),o.e(361)]).then(r);var a=o.x();bio=a})();
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dist/361.js

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@@ -1,2 +0,2 @@
-var bio;(()=>{"use strict";var r,e,t={3065:(r,e,t)=>{const o=r=>null==r;var a=t(6361),n=t(9657);onmessage=r=>{const{values:e,fnName:t,startRow:i,startCol:s,chunckSize:c,opts:l}=r.data,p={};try{let r=i,u=s,f=0,h=0,v=Number.MIN_VALUE;if((0,a.sQ)(t))for(let r=0;r<e.length;++r)o(e[r])||(e[r]=new n.Z(e[r]._data,e[r]._length));const g=new Float32Array(c),b=new a.UH(t).getMeasure(l);for(;f<c;){const t=o(e[r])||o(e[u])?1:b(e[r],e[u]);g[f]=t,t<h&&(h=t),t>v&&(v=t),f++,u++,u===e.length&&(r++,u=r+1)}p.distanceMatrixData=g,p.min=h,p.max=v}catch(r){p.error=r}postMessage(p)}}},o={};function a(r){var e=o[r];if(void 0!==e)return e.exports;var n=o[r]={exports:{}};return t[r](n,n.exports,a),n.exports}a.m=t,a.x=()=>{var r=a.O(void 0,[562,44,361],(()=>a(3065)));return a.O(r)},r=[],a.O=(e,t,o,n)=>{if(!t){var i=1/0;for(p=0;p<r.length;p++){for(var[t,o,n]=r[p],s=!0,c=0;c<t.length;c++)(!1&n||i>=n)&&Object.keys(a.O).every((r=>a.O[r](t[c])))?t.splice(c--,1):(s=!1,n<i&&(i=n));if(s){r.splice(p--,1);var l=o();void 0!==l&&(e=l)}}return e}n=n||0;for(var p=r.length;p>0&&r[p-1][2]>n;p--)r[p]=r[p-1];r[p]=[t,o,n]},a.d=(r,e)=>{for(var t in e)a.o(e,t)&&!a.o(r,t)&&Object.defineProperty(r,t,{enumerable:!0,get:e[t]})},a.f={},a.e=r=>Promise.all(Object.keys(a.f).reduce(((e,t)=>(a.f[t](r,e),e)),[])),a.u=r=>r+".js",a.g=function(){if("object"==typeof globalThis)return globalThis;try{return this||new Function("return this")()}catch(r){if("object"==typeof window)return window}}(),a.o=(r,e)=>Object.prototype.hasOwnProperty.call(r,e),(()=>{var r;a.g.importScripts&&(r=a.g.location+"");var e=a.g.document;if(!r&&e&&(e.currentScript&&(r=e.currentScript.src),!r)){var t=e.getElementsByTagName("script");if(t.length)for(var o=t.length-1;o>-1&&!r;)r=t[o--].src}if(!r)throw new Error("Automatic publicPath is not supported in this browser");r=r.replace(/#.*$/,"").replace(/\?.*$/,"").replace(/\/[^\/]+$/,"/"),a.p=r})(),(()=>{var r={65:1};a.f.i=(e,t)=>{r[e]||importScripts(a.p+a.u(e))};var e=self.webpackChunkbio=self.webpackChunkbio||[],t=e.push.bind(e);e.push=e=>{var[o,n,i]=e;for(var s in n)a.o(n,s)&&(a.m[s]=n[s]);for(i&&i(a);o.length;)r[o.pop()]=1;t(e)}})(),e=a.x,a.x=()=>Promise.all([562,44,361].map(a.e,a)).then(e);var n=a.x();bio=n})();
+var bio;(()=>{"use strict";var r,e,t={3065:(r,e,t)=>{const o=r=>null==r;var a=t(6361),n=t(9657);onmessage=r=>{const{values:e,fnName:t,startRow:i,startCol:s,chunckSize:c,opts:l}=r.data,p={};try{let r=i,u=s,f=0,h=0,v=Number.MIN_VALUE;if((0,a.sQ)(t))for(let r=0;r<e.length;++r)o(e[r])||(e[r]=new n.Z(e[r]._data,e[r]._length));const g=new Float32Array(c),b=new a.UH(t).getMeasure(l);for(;f<c;){const t=o(e[r])||o(e[u])?1:b(e[r],e[u]);g[f]=t,t<h&&(h=t),t>v&&(v=t),f++,u++,u===e.length&&(r++,u=r+1)}p.distanceMatrixData=g,p.min=h,p.max=v}catch(r){p.error=r}postMessage(p)}}},o={};function a(r){var e=o[r];if(void 0!==e)return e.exports;var n=o[r]={exports:{}};return t[r](n,n.exports,a),n.exports}a.m=t,a.x=()=>{var r=a.O(void 0,[378,361],(()=>a(3065)));return a.O(r)},r=[],a.O=(e,t,o,n)=>{if(!t){var i=1/0;for(p=0;p<r.length;p++){for(var[t,o,n]=r[p],s=!0,c=0;c<t.length;c++)(!1&n||i>=n)&&Object.keys(a.O).every((r=>a.O[r](t[c])))?t.splice(c--,1):(s=!1,n<i&&(i=n));if(s){r.splice(p--,1);var l=o();void 0!==l&&(e=l)}}return e}n=n||0;for(var p=r.length;p>0&&r[p-1][2]>n;p--)r[p]=r[p-1];r[p]=[t,o,n]},a.d=(r,e)=>{for(var t in e)a.o(e,t)&&!a.o(r,t)&&Object.defineProperty(r,t,{enumerable:!0,get:e[t]})},a.f={},a.e=r=>Promise.all(Object.keys(a.f).reduce(((e,t)=>(a.f[t](r,e),e)),[])),a.u=r=>r+".js",a.g=function(){if("object"==typeof globalThis)return globalThis;try{return this||new Function("return this")()}catch(r){if("object"==typeof window)return window}}(),a.o=(r,e)=>Object.prototype.hasOwnProperty.call(r,e),(()=>{var r;a.g.importScripts&&(r=a.g.location+"");var e=a.g.document;if(!r&&e&&(e.currentScript&&(r=e.currentScript.src),!r)){var t=e.getElementsByTagName("script");if(t.length)for(var o=t.length-1;o>-1&&!r;)r=t[o--].src}if(!r)throw new Error("Automatic publicPath is not supported in this browser");r=r.replace(/#.*$/,"").replace(/\?.*$/,"").replace(/\/[^\/]+$/,"/"),a.p=r})(),(()=>{var r={65:1};a.f.i=(e,t)=>{r[e]||importScripts(a.p+a.u(e))};var e=self.webpackChunkbio=self.webpackChunkbio||[],t=e.push.bind(e);e.push=e=>{var[o,n,i]=e;for(var s in n)a.o(n,s)&&(a.m[s]=n[s]);for(i&&i(a);o.length;)r[o.pop()]=1;t(e)}})(),e=a.x,a.x=()=>Promise.all([a.e(378),a.e(361)]).then(e);var n=a.x();bio=n})();
 //# sourceMappingURL=65.js.map

package.json

@@ -8,3 +8,3 @@ {
   },
-  "version": "2.11.20",
+  "version": "2.11.21",
   "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.",
@@ -38,5 +38,5 @@ "repository": {
     "@biowasm/aioli": "^3.1.0",
-    "@datagrok-libraries/bio": "^5.39.14",
+    "@datagrok-libraries/bio": "^5.39.16",
     "@datagrok-libraries/chem-meta": "^1.2.1",
-    "@datagrok-libraries/ml": "^6.3.67",
+    "@datagrok-libraries/ml": "^6.3.68",
     "@datagrok-libraries/tutorials": "^1.3.11",
@@ -43,0 +43,0 @@ "@datagrok-libraries/utils": "^4.1.36",

src/analysis/sequence-diversity-viewer.ts

@@ -10,4 +10,6 @@ import * as ui from 'datagrok-api/ui';
 import {Subject} from 'rxjs';
-import {calcMmDistanceMatrix, dmLinearIndex} from './workers/mm-distance-worker-creator';
 import {UnitsHandler} from '@datagrok-libraries/bio/src/utils/units-handler';
+import {getEncodedSeqSpaceCol} from './sequence-space';
+import {MmDistanceFunctionsNames} from '@datagrok-libraries/ml/src/macromolecule-distance-functions';
+import {DistanceMatrixService, dmLinearIndex} from '@datagrok-libraries/ml/src/distance-matrix';
 
@@ -62,3 +64,7 @@ export class SequenceDiversityViewer extends SequenceSearchBaseViewer {
   private async computeByMM() {
-    const distanceMatrixData = await calcMmDistanceMatrix(this.moleculeColumn!);
+    const encodedSequences =
+        (await getEncodedSeqSpaceCol(this.moleculeColumn!, MmDistanceFunctionsNames.LEVENSHTEIN)).seqList;
+    const distanceMatrixService = new DistanceMatrixService(true, false);
+    const distanceMatrixData = await distanceMatrixService.calc(encodedSequences, MmDistanceFunctionsNames.LEVENSHTEIN);
+    distanceMatrixService.terminate();
     const len = this.moleculeColumn!.length;
@@ -65,0 +71,0 @@ const linearizeFunc = dmLinearIndex(len);

src/analysis/sequence-similarity-viewer.ts

@@ -11,4 +11,6 @@ import * as grok from 'datagrok-api/grok';
 import {UnitsHandler} from '@datagrok-libraries/bio/src/utils/units-handler';
-import {calcMmDistanceMatrix, dmLinearIndex} from './workers/mm-distance-worker-creator';
-import {calculateMMDistancesArray} from './workers/mm-distance-array-service';
+import {alignSequencePair} from '@datagrok-libraries/bio/src/utils/macromolecule/alignment';
+import {KnnResult, SparseMatrixService} from '@datagrok-libraries/ml/src/distance-matrix/sparse-matrix-service';
+import {getEncodedSeqSpaceCol} from './sequence-space';
+import {MmDistanceFunctionsNames} from '@datagrok-libraries/ml/src/macromolecule-distance-functions';
 
@@ -30,2 +32,4 @@ export class SequenceSimilarityViewer extends SequenceSearchBaseViewer {
   mmDistanceMatrix: Float32Array;
+  knn?: KnnResult;
+  kPrevNeighbors: number = 0;
 
@@ -53,3 +57,3 @@ constructor() {
 
-        await (uh.isFasta() ? this.computeByMM() : this.computeByChem());
+        await (!uh.isHelm() ? this.computeByMM() : this.computeByChem());
         const similarColumnName: string = this.similarColumnLabel != null ? this.similarColumnLabel :
@@ -99,25 +103,20 @@ `similar (${this.moleculeColumnName})`;
   private async computeByMM() {
-    let distanceArray = new Float32Array();
-    if (!this.distanceMatrixComputed && this.preComputeDistanceMatrix) {
-      this.mmDistanceMatrix = await calcMmDistanceMatrix(this.moleculeColumn!);
-      this.distanceMatrixComputed = true;
-    } else if (!this.preComputeDistanceMatrix) {
-      // use fast distance array calculation if matrix will take too much space
-      distanceArray = await calculateMMDistancesArray(this.moleculeColumn!, this.targetMoleculeIdx);
+    const len = this.moleculeColumn!.length;
+    const actualLimit = Math.min(this.limit, len - 1);
+    if (!this.knn || this.kPrevNeighbors !== actualLimit) {
+      const encodedSequences =
+        (await getEncodedSeqSpaceCol(this.moleculeColumn!, MmDistanceFunctionsNames.LEVENSHTEIN)).seqList;
+
+      this.kPrevNeighbors = actualLimit;
+      this.knn = await (new SparseMatrixService()
+        .getKNN(encodedSequences, MmDistanceFunctionsNames.LEVENSHTEIN, Math.min(this.limit, len - 1)));
     }
-    const len = this.moleculeColumn!.length;
-    const linearizeFunc = dmLinearIndex(len);
-    // array that keeps track of the indexes and scores together
-    const indexWScore = Array(len).fill(0)
-      .map((_, i) => ({
-        idx: i, score: i === this.targetMoleculeIdx ? 1 :
-          this.preComputeDistanceMatrix ? 1 - this.mmDistanceMatrix[linearizeFunc(this.targetMoleculeIdx, i)] :
-            1 - distanceArray[i]
-      }));
+    const indexWScore = new Array(actualLimit).fill(0).map((_, i) => ({
+      idx: this.knn!.knnIndexes[this.targetMoleculeIdx][i],
+      score: 1 - this.knn!.knnDistances[this.targetMoleculeIdx][i],
+    }));
     indexWScore.sort((a, b) => b.score - a.score);
-    // get the most similar molecules
-    const actualLimit = Math.min(this.limit, len);
-    const mostSimilar = indexWScore.slice(0, actualLimit);
-    this.idxs = DG.Column.int('indexes', actualLimit).init((i) => mostSimilar[i].idx);
-    this.scores = DG.Column.float('score', actualLimit).init((i) => mostSimilar[i].score);
+    indexWScore.unshift({idx: this.targetMoleculeIdx, score: DG.FLOAT_NULL});
+    this.idxs = DG.Column.int('indexes', actualLimit + 1).init((i) => indexWScore[i].idx);
+    this.scores = DG.Column.float('score', actualLimit + 1).init((i) => indexWScore[i].score);
   }
@@ -134,3 +133,4 @@
     const subParts2 = splitter(resDf.get(molColName, resDf.currentRowIdx));
-    const canvas = createDifferenceCanvas(subParts1, subParts2, uh.units, molDifferences);
+    const alignment = alignSequencePair(Array.from(subParts1), Array.from(subParts2));
+    const canvas = createDifferenceCanvas(alignment.seq1Splitted, alignment.seq2Splitted, uh.units, molDifferences);
     propPanel.append(ui.div(canvas, {style: {width: '300px', overflow: 'scroll'}}));
@@ -137,0 +137,0 @@ if (subParts1.length !== subParts2.length) {

src/tests/similarity-diversity-tests.ts

@@ -51,3 +51,3 @@ import * as DG from 'datagrok-api/dg';
   const str0: string = 'D-Tyr_Et/Tyr_ab-dehydroMe/dV/E/N/D-Orn/D-aThr//Phe_4Me';
-  const str1: string = 'meI/hHis//Aca/meM/Tyr_ab-dehydroMe/dV/E/N/D-Orn/D-aThr//Phe_4Me';
+  const str1: string = 'Thr_PO3H2/Aca/D-Tyr_Et/Tyr_ab-dehydroMe/dV/Chg/N/D-Orn/D-aThr//Phe_4Me';
   const simStr1: string = 'meI/hHis/Aca/Cys_SEt/T/dK/Thr_PO3H2/Aca/Tyr_PO3H2/D-Chg/dV/Phe_ab-dehydro/N/D-Orn/D-aThr//Phe_4Me';
@@ -61,4 +61,4 @@ /* eslint-enable max-len */
   expect(similaritySearchViewer.molCol!.get(0), str0);
-  expect(similaritySearchViewer.scores!.get(1), 0.4722222089767456);
-  expect(similaritySearchViewer.idxs!.get(1), 11);
+  expect((similaritySearchViewer.scores!.get(1) as number).toFixed(2), '0.73');
+  expect(similaritySearchViewer.idxs!.get(1), 4);
   expect(similaritySearchViewer.molCol!.get(1), str1);
@@ -65,0 +65,0 @@ moleculesView.dataFrame.currentRowIdx = 1;

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Worsened metrics

Total package byte prevSize

22330108

decreased by-0.05%

Number of package files

205

decreased by-3.3%

Lines of code

56628

decreased by-0.18%

Dependency changes

• Updated@datagrok-libraries/bio@^5.39.16

• Updated@datagrok-libraries/ml@^6.3.68