@datagrok/bio - npm Package Compare versions

Comparing version 2.11.42 to 2.12.0

CHANGELOG.md

 # Bio changelog
 
+## 2.12.0 (WIP)
+
+### Features
+
+* #2707: Add original and canonical to monomer
+
 ## 2.11.42 (2024-03-27)
@@ -4,0 +10,0 @@

detectors.js

@@ -34,3 +34,3 @@ /**
 /** Class for handling notation units in Macromolecule columns */
-const UnitsHandler = {
+const SeqHandler = {
   TAGS: {
@@ -167,4 +167,4 @@ aligned: 'aligned',
         const alphabetIsMultichar = Object.keys(statsAsHelm.freq).some((m) => m.length > 1);
-        // col.setTag(UnitsHandler.TAGS.alphabetSize, alphabetSize.toString());
-        col.setTag(UnitsHandler.TAGS.alphabetIsMultichar, alphabetIsMultichar ? 'true' : 'false');
+        // col.setTag(SeqHandler.TAGS.alphabetSize, alphabetSize.toString());
+        col.setTag(SeqHandler.TAGS.alphabetIsMultichar, alphabetIsMultichar ? 'true' : 'false');
 
@@ -241,8 +241,8 @@ return DG.SEMTYPE.MACROMOLECULE;
         col.setTag(DG.TAGS.UNITS, units);
-        if (separator) col.setTag(UnitsHandler.TAGS.separator, separator);
-        col.setTag(UnitsHandler.TAGS.aligned, ALIGNMENT.SEQ_MSA);
-        col.setTag(UnitsHandler.TAGS.alphabet, alphabet);
+        if (separator) col.setTag(SeqHandler.TAGS.separator, separator);
+        col.setTag(SeqHandler.TAGS.aligned, ALIGNMENT.SEQ_MSA);
+        col.setTag(SeqHandler.TAGS.alphabet, alphabet);
         if (alphabet === ALPHABET.UN) {
           const alphabetIsMultichar = Object.keys(stats.freq).some((m) => m.length > 1);
-          col.setTag(UnitsHandler.TAGS.alphabetIsMultichar, alphabetIsMultichar ? 'true' : 'false');
+          col.setTag(SeqHandler.TAGS.alphabetIsMultichar, alphabetIsMultichar ? 'true' : 'false');
         }
@@ -289,9 +289,9 @@ return DG.SEMTYPE.MACROMOLECULE;
         col.setTag(DG.TAGS.UNITS, units);
-        if (separator) col.setTag(UnitsHandler.TAGS.separator, separator);
-        col.setTag(UnitsHandler.TAGS.aligned, aligned);
-        col.setTag(UnitsHandler.TAGS.alphabet, alphabet);
+        if (separator) col.setTag(SeqHandler.TAGS.separator, separator);
+        col.setTag(SeqHandler.TAGS.aligned, aligned);
+        col.setTag(SeqHandler.TAGS.alphabet, alphabet);
         if (alphabet === ALPHABET.UN) {
           // alphabetSize calculated on (sub)sample of data is incorrect
           const alphabetIsMultichar = Object.keys(stats.freq).some((m) => m.length > 1);
-          col.setTag(UnitsHandler.TAGS.alphabetIsMultichar, alphabetIsMultichar ? 'true' : 'false');
+          col.setTag(SeqHandler.TAGS.alphabetIsMultichar, alphabetIsMultichar ? 'true' : 'false');
         }
@@ -298,0 +298,0 @@ return DG.SEMTYPE.MACROMOLECULE;

dist/36.js

@@ -1,2 +0,2 @@
-"use strict";(self.webpackChunkbio=self.webpackChunkbio||[]).push([[36],{5697:(t,e,n)=>{n.d(e,{Dz:()=>C,FV:()=>a,KR:()=>o,MI:()=>M,NB:()=>c,UX:()=>f,WI:()=>g,Zd:()=>u,_h:()=>l,aW:()=>d,bX:()=>B,fX:()=>A,s:()=>_,yU:()=>m});var r=n(9657),i=n(1040),s=n(708);function h(t,e){const n=t.trueCount()+e.trueCount();if(0==n)return 1;const r=t.andWithCountBits(e,!0);return r/(n-r)}function o(t,e){return 1-h(t,e)}function a(t,e){return I(h(new r.Z(t,32*t.length),new r.Z(e,32*e.length)))}function l(t,e){return 1-function(t,e){const n=t.trueCount()+e.trueCount();return 0==n?0:2*t.andWithCountBits(e,!0)/n}(t,e)}function u(t,e){return 1-function(t,e){const n=t.trueCount()*e.trueCount();return 0==n?0:t.andWithCountBits(e,!0)/Math.sqrt(n)}(t,e)}function g(t,e){return Math.sqrt(t.trueCount()+e.trueCount()-2*t.andWithCountBits(e,!0))}function f(t,e){return t.trueCount()+e.trueCount()-2*t.andWithCountBits(e,!0)}function c(t,e){return 1-function(t,e){const n=t.trueCount()+e.trueCount(),r=t.andWithCountBits(e,!0);return r/(2*n-3*r)}(t,e)}function _(t,e){return I(function(t,e){const n=t.trueCount()+e.trueCount(),r=t.trueCount()*e.trueCount();return 0==r?0:t.andWithCountBits(e,!0)*n/(2*r)}(t,e))}function d(t,e){return I(function(t,e){const n=t.trueCount()+e.trueCount(),r=t.trueCount()*e.trueCount();return 0==r?0:(t.andWithCountBits(e,!0)*n-r)/r}(t,e))}function m(t,e){return 1-function(t,e){const n=Math.min(t.trueCount(),e.trueCount());return 0==n?0:t.andWithCountBits(e,!0)/n}(t,e)}function C(t,e){return I(function(t,e){const n=Math.max(t.trueCount(),e.trueCount());return 0==n?0:t.andWithCountBits(e,!0)/n}(t,e))}function A(t,e){return I(function(t,e){return 0==t.length?0:t.andWithCountBits(e,!0)/t.length}(t,e))}function M(t,e){return I(function(t,e){const n=t.andWithCountBits(e,!0),r=t.countBits(!0)+e.countBits(!0),i=t.length,s=i-r+n;return n==i||s==i?1:n/r+s/(2*i-r)}(t,e))}function I(t){return 0===t?3402823e32:1/t-1}function B(t){if(t&&null!=t.range&&t.range>0){const e=t.range;return(t,n)=>Math.abs(t-n)/e}return(t,e)=>Math.abs(t-e)}i.gk.Tanimoto,i.gk.Dice,i.gk.Asymmetric,i.gk.BraunBlanquet,i.gk.Cosine,i.gk.Kulczynski,i.gk.McConnaughey,i.gk.RogotGoldberg,i.gk.Russel,i.gk.Sokal,i.gk.Hamming,i.gk.Euclidean,i.gk.Tanimoto,i.gk.Dice,i.gk.Asymmetric,i.gk.BraunBlanquet,i.gk.Cosine,i.gk.Kulczynski,i.gk.McConnaughey,i.gk.RogotGoldberg,i.gk.Russel,i.gk.Sokal,i.gk.Hamming,i.gk.Euclidean,i.gk.Tanimoto,i.gk.Dice,i.gk.Cosine,i.gk.Tanimoto,i.gk.Asymmetric,i.gk.Cosine,i.gk.Sokal,s.U.HAMMING,s.U.LEVENSHTEIN,s.U.MONOMER_CHEMICAL_DISTANCE,s.U.NEEDLEMANN_WUNSCH},708:(t,e,n)=>{function r(t={}){const e=function(){if(!t||!t.scoringMatrix||!t.alphabetIndexes)return(t,e)=>t===e?0:1;if(t.scoringMatrix.length!==Object.keys(t.alphabetIndexes).length)throw new Error("Scoring matrix and alphabet indexes should have the same length");const e=t.alphabetIndexes,n=t.scoringMatrix,r=Math.min(...Object.keys(e).map((t=>t.charCodeAt(0))))+1,i=new Float32Array((n.length+r)*(n.length+r));return Object.entries(e).forEach((([t,r])=>{const s=n[r];Object.entries(e).forEach((([e,r])=>{i[t.charCodeAt(0)*n.length+e.charCodeAt(0)]=s[r]}))})),(t,e)=>i[t.charCodeAt(0)*n.length+e.charCodeAt(0)]}(),n=t?.threshold??0;return(t,r)=>{let i=0;const s=t.length,h=r.length,o=Math.max(s,h)*(1-n);s!==h&&(i=Math.abs(s-h));let a=0;for(let n=0;n<Math.min(s,h);n++)if(t[n]!==r[n]&&(a+=e(t[n],r[n]),a>o))return 1;return a+=i,a/=Math.max(s,h),a}}n.d(e,{U:()=>h,o:()=>o});var i=n(1811);const s={gapOpen:1,gapExtend:.6,scoringMatrix:[[4,-1,-2,-2,0,-1,-1,0,-2,-1,-1,-1,-1,-2,-1,1,0,-3,-2,0,-2,-1,0,-4],[-1,5,0,-2,-3,1,0,-2,0,-3,-2,2,-1,-3,-2,-1,-1,-3,-2,-3,-1,0,-1,-4],[-2,0,6,1,-3,0,0,0,1,-3,-3,0,-2,-3,-2,1,0,-4,-2,-3,3,0,-1,-4],[-2,-2,1,6,-3,0,2,-1,-1,-3,-4,-1,-3,-3,-1,0,-1,-4,-3,-3,4,1,-1,-4],[0,-3,-3,-3,9,-3,-4,-3,-3,-1,-1,-3,-1,-2,-3,-1,-1,-2,-2,-1,-3,-3,-2,-4],[-1,1,0,0,-3,5,2,-2,0,-3,-2,1,0,-3,-1,0,-1,-2,-1,-2,0,3,-1,-4],[-1,0,0,2,-4,2,5,-2,0,-3,-3,1,-2,-3,-1,0,-1,-3,-2,-2,1,4,-1,-4],[0,-2,0,-1,-3,-2,-2,6,-2,-4,-4,-2,-3,-3,-2,0,-2,-2,-3,-3,-1,-2,-1,-4],[-2,0,1,-1,-3,0,0,-2,8,-3,-3,-1,-2,-1,-2,-1,-2,-2,2,-3,0,0,-1,-4],[-1,-3,-3,-3,-1,-3,-3,-4,-3,4,2,-3,1,0,-3,-2,-1,-3,-1,3,-3,-3,-1,-4],[-1,-2,-3,-4,-1,-2,-3,-4,-3,2,4,-2,2,0,-3,-2,-1,-2,-1,1,-4,-3,-1,-4],[-1,2,0,-1,-3,1,1,-2,-1,-3,-2,5,-1,-3,-1,0,-1,-3,-2,-2,0,1,-1,-4],[-1,-1,-2,-3,-1,0,-2,-3,-2,1,2,-1,5,0,-2,-1,-1,-1,-1,1,-3,-1,-1,-4],[-2,-3,-3,-3,-2,-3,-3,-3,-1,0,0,-3,0,6,-4,-2,-2,1,3,-1,-3,-3,-1,-4],[-1,-2,-2,-1,-3,-1,-1,-2,-2,-3,-3,-1,-2,-4,7,-1,-1,-4,-3,-2,-2,-1,-2,-4],[1,-1,1,0,-1,0,0,0,-1,-2,-2,0,-1,-2,-1,4,1,-3,-2,-2,0,0,0,-4],[0,-1,0,-1,-1,-1,-1,-2,-2,-1,-1,-1,-1,-2,-1,1,5,-2,-2,0,-1,-1,0,-4],[-3,-3,-4,-4,-2,-2,-3,-2,-2,-3,-2,-3,-1,1,-4,-3,-2,11,2,-3,-4,-3,-2,-4],[-2,-2,-2,-3,-2,-1,-2,-3,2,-1,-1,-2,-1,3,-3,-2,-2,2,7,-1,-3,-2,-1,-4],[0,-3,-3,-3,-1,-2,-2,-3,-3,3,1,-2,1,-1,-2,-2,0,-3,-1,4,-3,-2,-1,-4],[-2,-1,3,4,-3,0,1,-1,0,-3,-4,0,-3,-3,-2,0,-1,-4,-3,-3,4,1,-1,-4],[-1,0,0,1,-3,3,4,-2,0,-3,-3,1,-1,-3,-1,0,-1,-3,-2,-2,1,4,-1,-4],[0,-1,-1,-1,-2,-1,-1,-1,-1,-1,-1,-1,-1,-1,-2,0,0,-2,-1,-1,-1,-1,-1,-4],[-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,1]],alphabetIndexes:{A:0,R:1,N:2,D:3,C:4,Q:5,E:6,G:7,H:8,I:9,L:10,K:11,M:12,F:13,P:14,S:15,T:16,W:17,Y:18,V:19,B:20,Z:21,X:22,"*":23}};var h;!function(t){t.HAMMING="Hamming",t.LEVENSHTEIN="Levenshtein",t.NEEDLEMANN_WUNSCH="Needlemann-Wunsch",t.MONOMER_CHEMICAL_DISTANCE="Monomer chemical distance"}(h||(h={}));const o={[h.HAMMING]:r,[h.LEVENSHTEIN]:function(){return(t,e)=>(0,i.T)(t,e)/Math.max(t.length,e.length)},[h.NEEDLEMANN_WUNSCH]:function(t){const e=new Uint16Array(65536),{gapOpen:n,gapExtend:r,scoringMatrix:i,alphabetIndexes:h}={...s,...t};Object.entries(h).forEach((([t,n])=>e[t.charCodeAt(0)]=n));const o=[new Float32Array(1e4),new Float32Array(1e4)];return(t,s)=>{const h=new Array(t.length+1).fill(!1),a=new Array(t.length+1).fill(!1);let l=0,u=1;for(let e=1;e<t.length+1;e++)o[0][e]=-n-(e-1)*r,o[1][e]=0;o[0][0]=0;for(let g=1;g<s.length+1;g++){o[u][0]=-n-(g-1)*r;for(let f=1;f<t.length+1;f++){const c=o[l][f-1]+i[e[t.charCodeAt(f-1)]][e[s.charCodeAt(g-1)]],_=o[l][f]-(h[f]?r:n),d=o[u][f-1]-(a[f-1]?r:n);o[u][f]=Math.max(c,d,_),o[u][f]===c?(h[f]=!1,a[f]=!1):o[u][f]===d?(h[f]=!1,a[f]=!0):(h[f]=!0,a[f]=!1)}l=u,u=(u+1)%2}const g=Math.max(t.length,s.length);return(g-o[l][t.length])/g}},[h.MONOMER_CHEMICAL_DISTANCE]:r}},1040:(t,e,n)=>{var r,i,s,h,o,a;n.d(e,{CF:()=>i,Qe:()=>o,W:()=>r,Yc:()=>a,gd:()=>h,gk:()=>s}),function(t){t.Levenshtein="Levenshtein",t.JaroWinkler="Jaro-Winkler",t.Manhattan="Manhattan",t.Onehot="One-Hot"}(r||(r={})),function(t){t.Euclidean="Euclidean"}(i||(i={})),function(t){t.Tanimoto="Tanimoto",t.Dice="Dice",t.Asymmetric="Asymmetric",t.BraunBlanquet="Braun-Blanquet",t.Cosine="Cosine",t.Kulczynski="Kulczynski",t.McConnaughey="Mc-Connaughey",t.RogotGoldberg="Rogot-Goldberg",t.Russel="Russel",t.Sokal="Sokal",t.Hamming="Hamming",t.Euclidean="Euclidean"}(s||(s={})),function(t){t.TanimotoIntArray="TanimotoIntArray"}(h||(h={})),function(t){t.Vector="Vector",t.String="String",t.BitArray="BitArray",t.MacroMolecule="MacroMolecule",t.Number="Number",t.IntArray="IntArray"}(o||(o={})),function(t){t.Difference="Difference"}(a||(a={}))},9657:(t,e,n)=>{n.d(e,{Z:()=>r});class r{constructor(t,e=!1){if(this._length=0,this._version=0,this._updateLevel=0,this._selectedCount=0,this._selectedCountVersion=-1,this._selectedIndexesVersion=-1,this._versionedName="",this._versionedNameVersion=-1,this.SHRINK_THRESHOLD=256,"number"==typeof t){const n=t,i=r._createBuffer(n);if(e)for(let t=0;t<i.length;t++)i[t]=-1;this._data=i,this._length=n}else{if(!(t instanceof Uint32Array))throw new Error("Invalid constructor");this._data=t,this._length=e}}getRawData(){return this._data}assureGoez(t,e){if(t<0)throw new Error(`${e} should be greater than zero`)}assureInRange(t,e,n,r){if(t<e||t>n)throw new Error(`Argument ${r} (${t}) out of range (${e}, ${n})`)}copy(t,e,n){for(let r=0;r<n;r++)e[r]=t[r]}copyFrom(t){if(this._length!=t._length)throw new Error(`Lengths differ (${this._length} != ${t._length})`);this.copy(t._data,this._data,this.lengthInInts),this._version++}get length(){return this._length}get buffer(){return this._data}set buffer(t){this._data=t,this._version++}get version(){return this._version}set version(t){this._version=t}incrementVersion(t=!0){this._version++}get lengthInInts(){return Math.floor((this._length+31)/32)}get versionedName(){return this._version==this._versionedNameVersion?this._versionedName:""}set versionedName(t){this._versionedName=t,this._versionedNameVersion=this._version}get self(){return this}setLength(t){if(t<0)throw new Error("should be >= 0");if(t==this._length)return;const e=Math.floor((t+31)/32);if(e>this._data.length||e+this.SHRINK_THRESHOLD<this._data.length){const t=new Uint32Array(e);this.copy(this._data,t,e>this._data.length?this._data.length:e),this._data=t}t>this._length&&(this._length%32>0&&(this._data[this.lengthInInts-1]&=(1<<(this._length%32&31))-1),this._data.fill(0,this.lengthInInts,e)),this._length=t,this._version++}static fromAnd(t,e){if(t._length!=e._length)throw new Error(`Lengths differ (${t._length} != ${e._length})`);const n=new r(t._length);n._length=t._length,n._data=r._createBuffer(n._length),n._version=0;const i=t.lengthInInts;for(let r=0;r<i;r++)n._data[r]=t._data[r]&e._data[r];return n}static _createBuffer(t){return new Uint32Array(Math.floor((t+31)/32))}static fromValues(t){const e=new r(t.length);e._version=0;for(let n=0;n<e._length;n++)t[n]&&(e._data[Math.floor(n/32)]|=1<<(n%32&31));return e}static fromSeq(t,e){const n=new r(t);for(let r=0;r<t;++r)n.setBit(r,e(r));return n._version=0,n}static fromString(t){return r.fromSeq(t.length,(e=>"1"==t.charAt(e)))}static fromUint32Array(t,e){const n=new r(t);return n._data=e,n}static fromBytes(t){const e=t.length,n=new r(8*e);n._data=new Uint32Array(Math.floor((e+3)/4)),n._length=8*e;let i=0,s=0;for(;e-s>=4;)n._data[i++]=255&t[s]|(255&t[s+1])<<8|(255&t[s+2])<<16|(255&t[s+3])<<24,s+=4;return e-s==3&&(n._data[i]=(255&t[s+2])<<16),e-s==2&&(n._data[i]|=(255&t[s+1])<<8),e-s==1&&(n._data[i]|=255&t[s]),n._version=0,n}toString(){return`${this._length} bits, ${this.countBits(!0)} set`}equals(t){if(this==t)return!0;if(null==t)return!1;if(this._length!=t._length)return!1;if(0==this._length)return!0;for(let e=0;e<this._data.length-1;e++)if(this._data[e]!=t._data[e])return!1;for(let e=8*(this._data.length-1);e<this._length;e++)if(this.getBit(e)!=t.getBit(e))return!1;return!0}clone(){const t=new r(0,!1);return t._data=Uint32Array.from(this._data),t._length=this._length,t._version=this._version,t}init(t,e){this.setAll(!1,!1);for(let e=0;e<this._length;e++)t(e)&&(this._data[Math.floor(e/32)]|=1<<(e%32&31));return this.incrementVersion(e),this}invert(t=!0){for(let t=0;t<this._data.length;t++)this._data[t]^=-1;this.incrementVersion(t)}setAll(t,e=!1){const n=t?-1:0,r=this.lengthInInts;for(let t=0;t<r;t++)this._data[t]=n;this.incrementVersion(e)}setIndexes(t,e=!0,n=!0,r=!0){n&&this.setAll(!e,!1);for(const n of t)this.setFast(n,e);this.incrementVersion(r)}everyIndex(t,e=!0){for(const n of t)if(this.getBit(n)!=e)return!1;return!0}anyIndex(t,e=!0){for(const n of t)if(this.getBit(n)==e)return!0;return!1}setWhere(t,e=!0,n=!0,r=!0,i=!0){if(n&&i&&this.setAll(!e,!1),i)for(let n=0;n<this._length;n++)t(n)&&this.setFast(n,e);else for(let n=0;n<this._length;n++)this.setFast(n,t(n)?e:!e);this.incrementVersion(r)}getRange(t,e){this.assureInRange(t,0,this._length-1,"from"),this.assureInRange(e,0,this._length,"to");const n=[];for(let r=t;r<e;++r)n.push(this.getBit(r));return r.fromValues(n)}getRangeAsList(t,e){this.assureInRange(t,0,this._length-1,"from"),this.assureInRange(e,0,this._length,"to");const n=[];for(let r=t;r<e;++r)n.push(this.getBit(r));return n}setRange(t,e,n,r=!0){this.assureInRange(t,0,this._length-1,"from"),this.assureInRange(e,0,this._length-1,"to");const i=Math.min(t,e),s=Math.max(t,e);if(n)for(let t=i;t<=s;t++)this.setTrue(t);else for(let t=i;t<=s;t++)this.setFalse(t);return this.incrementVersion(r),this}setRandom(t,e,n=!0){if(t<0||t>this._length)throw new Error("n must be >= 0 && <= Count");t>this._length/2&&this.setRandom(this._length-t,!e),this.setAll(!e);for(let n=0;n<t;){const t=Math.floor(Math.random()*this._length);this.getBit(t)!=e&&(this.setFast(t,e),n++)}this.incrementVersion(n)}and(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}andNot(t,e=!0){if(this._length!=t._length)throw new Error("Array lengths differ.");const n=this.lengthInInts;for(let e=0;e<n;e++)this._data[e]&=~t._data[e];return this.incrementVersion(e),this}notAnd(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]=~this._data[e]&t._data[e];return this.incrementVersion(e),this}not(t=!0){for(let t=0,e=this.lengthInInts;t<e;t++)this._data[t]=~this._data[t];return this.incrementVersion(t),this}or(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}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 h=this._data[s]&t._data[s];const o=31&this._length;for(0!=o&&(h&=~(4294967295<<o));0!=h;h>>>=8)n+=r._onBitCount[255&h];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])},1811:(t,e,n)=>{n.d(e,{T:()=>i});const r=new Uint32Array(65536),i=(t,e)=>{if(t.length<e.length){const n=e;e=t,t=n}return 0===e.length?t.length:t.length<=32?((t,e)=>{const n=t.length,i=e.length,s=1<<n-1;let h=-1,o=0,a=n,l=n;for(;l--;)r[t.charCodeAt(l)]|=1<<l;for(l=0;l<i;l++){let t=r[e.charCodeAt(l)];const n=t|o;t|=(t&h)+h^h,o|=~(t|h),h&=t,o&s&&a++,h&s&&a--,o=o<<1|1,h=h<<1|~(n|o),o&=n}for(l=n;l--;)r[t.charCodeAt(l)]=0;return a})(t,e):((t,e)=>{const n=e.length,i=t.length,s=[],h=[],o=Math.ceil(n/32),a=Math.ceil(i/32);for(let t=0;t<o;t++)h[t]=-1,s[t]=0;let l=0;for(;l<a-1;l++){let o=0,a=-1;const u=32*l,g=Math.min(32,i)+u;for(let e=u;e<g;e++)r[t.charCodeAt(e)]|=1<<e;for(let t=0;t<n;t++){const n=r[e.charCodeAt(t)],i=h[t/32|0]>>>t&1,l=s[t/32|0]>>>t&1,u=n|o,g=((n|l)&a)+a^a|n|l;let f=o|~(g|a),c=a&g;f>>>31^i&&(h[t/32|0]^=1<<t),c>>>31^l&&(s[t/32|0]^=1<<t),f=f<<1|i,c=c<<1|l,a=c|~(u|f),o=f&u}for(let e=u;e<g;e++)r[t.charCodeAt(e)]=0}let u=0,g=-1;const f=32*l,c=Math.min(32,i-f)+f;for(let e=f;e<c;e++)r[t.charCodeAt(e)]|=1<<e;let _=i;for(let t=0;t<n;t++){const n=r[e.charCodeAt(t)],o=h[t/32|0]>>>t&1,a=s[t/32|0]>>>t&1,l=n|u,f=((n|a)&g)+g^g|n|a;let c=u|~(f|g),d=g&f;_+=c>>>i-1&1,_-=d>>>i-1&1,c>>>31^o&&(h[t/32|0]^=1<<t),d>>>31^a&&(s[t/32|0]^=1<<t),c=c<<1|o,d=d<<1|a,g=d|~(l|c),u=c&l}for(let e=f;e<c;e++)r[t.charCodeAt(e)]=0;return _})(t,e)}},3979:(t,e)=>{e.H$=void 0,e.H$=function(t,e,n){var r=function(t,e,n){if(0===t.length||0===e.length)return 0;if(n&&!n.caseSensitive&&(t=t.toUpperCase(),e=e.toUpperCase()),t===e)return 1;for(var r=0,i=t.length,s=e.length,h=Math.floor(Math.max(i,s)/2)-1,o=new Array(i),a=new Array(s),l=0;l<i;l++)for(var u=Math.max(0,l-h);u<=Math.min(s,l+h+1);u++)if(!o[l]&&!a[u]&&t[l]===e[u]){++r,o[l]=a[u]=!0;break}if(0===r)return 0;var g=0,f=0;for(l=0;l<i;l++)if(o[l]){for(;!a[f];)f++;t.charAt(l)!==e.charAt(f++)&&g++}return(r/i+r/s+(r-(g/=2))/r)/3}(t,e,n),i=0;if(r>.7){for(var s=Math.min(t.length,e.length),h=0;t[h]===e[h]&&h<4&&h<s;)++i,h++;r+=.1*i*(1-r)}return r}}}]);
+"use strict";(self.webpackChunkbio=self.webpackChunkbio||[]).push([[36],{5697:(t,e,n)=>{n.d(e,{Dz:()=>C,FV:()=>a,Jv:()=>y,KR:()=>o,MI:()=>M,NB:()=>f,UX:()=>c,WI:()=>g,Zd:()=>u,_h:()=>l,aW:()=>d,bX:()=>B,fX:()=>A,s:()=>_,yU:()=>m});var r=n(9657),i=n(1040),s=n(708);function h(t,e){const n=t.trueCount()+e.trueCount();if(0==n)return 1;const r=t.andWithCountBits(e,!0);return r/(n-r)}function o(t,e){return 1-h(t,e)}function a(t,e){return I(h(new r.Z(t,32*t.length),new r.Z(e,32*e.length)))}function l(t,e){return 1-function(t,e){const n=t.trueCount()+e.trueCount();return 0==n?0:2*t.andWithCountBits(e,!0)/n}(t,e)}function u(t,e){return 1-function(t,e){const n=t.trueCount()*e.trueCount();return 0==n?0:t.andWithCountBits(e,!0)/Math.sqrt(n)}(t,e)}function g(t,e){return Math.sqrt(t.trueCount()+e.trueCount()-2*t.andWithCountBits(e,!0))}function c(t,e){return t.trueCount()+e.trueCount()-2*t.andWithCountBits(e,!0)}function f(t,e){return 1-function(t,e){const n=t.trueCount()+e.trueCount(),r=t.andWithCountBits(e,!0);return r/(2*n-3*r)}(t,e)}function _(t,e){return I(function(t,e){const n=t.trueCount()+e.trueCount(),r=t.trueCount()*e.trueCount();return 0==r?0:t.andWithCountBits(e,!0)*n/(2*r)}(t,e))}function d(t,e){return I(function(t,e){const n=t.trueCount()+e.trueCount(),r=t.trueCount()*e.trueCount();return 0==r?0:(t.andWithCountBits(e,!0)*n-r)/r}(t,e))}function m(t,e){return 1-function(t,e){const n=Math.min(t.trueCount(),e.trueCount());return 0==n?0:t.andWithCountBits(e,!0)/n}(t,e)}function C(t,e){return I(function(t,e){const n=Math.max(t.trueCount(),e.trueCount());return 0==n?0:t.andWithCountBits(e,!0)/n}(t,e))}function A(t,e){return I(function(t,e){return 0==t.length?0:t.andWithCountBits(e,!0)/t.length}(t,e))}function M(t,e){return I(function(t,e){const n=t.andWithCountBits(e,!0),r=t.countBits(!0)+e.countBits(!0),i=t.length,s=i-r+n;return n==i||s==i?1:n/r+s/(2*i-r)}(t,e))}function I(t){return 0===t?3402823e32:1/t-1}function B(t){if(t&&null!=t.range&&t.range>0){const e=t.range;return(t,n)=>Math.abs(t-n)/e}return(t,e)=>Math.abs(t-e)}function y(t){const e=function(t){const e=t?.mostCommon??new Set;return(t,n)=>{const r=t.length,i=n.length;let s=0,h=0,o=0;for(;h<r&&o<i;)t[h]===n[o]?(e?.has(t[h])||++s,++h,++o):t[h]<n[o]?++h:++o;return s}}(t);return(t,n)=>0===n.length||0===t.length?1e4:Math.min(t.length,n.length)/(e(t,n)+1e-4)}i.gk.Tanimoto,i.gk.Dice,i.gk.Asymmetric,i.gk.BraunBlanquet,i.gk.Cosine,i.gk.Kulczynski,i.gk.McConnaughey,i.gk.RogotGoldberg,i.gk.Russel,i.gk.Sokal,i.gk.Hamming,i.gk.Euclidean,i.gk.Tanimoto,i.gk.Dice,i.gk.Asymmetric,i.gk.BraunBlanquet,i.gk.Cosine,i.gk.Kulczynski,i.gk.McConnaughey,i.gk.RogotGoldberg,i.gk.Russel,i.gk.Sokal,i.gk.Hamming,i.gk.Euclidean,i.gk.Tanimoto,i.gk.Dice,i.gk.Cosine,i.gk.Tanimoto,i.gk.Asymmetric,i.gk.Cosine,i.gk.Sokal,s.U.HAMMING,s.U.LEVENSHTEIN,s.U.MONOMER_CHEMICAL_DISTANCE,s.U.NEEDLEMANN_WUNSCH},708:(t,e,n)=>{function r(t={}){const e=function(){if(!t||!t.scoringMatrix||!t.alphabetIndexes)return(t,e)=>t===e?0:1;if(t.scoringMatrix.length!==Object.keys(t.alphabetIndexes).length)throw new Error("Scoring matrix and alphabet indexes should have the same length");const e=t.alphabetIndexes,n=t.scoringMatrix,r=Math.min(...Object.keys(e).map((t=>t.charCodeAt(0))))+1,i=new Float32Array((n.length+r)*(n.length+r));return Object.entries(e).forEach((([t,r])=>{const s=n[r];Object.entries(e).forEach((([e,r])=>{i[t.charCodeAt(0)*n.length+e.charCodeAt(0)]=s[r]}))})),(t,e)=>i[t.charCodeAt(0)*n.length+e.charCodeAt(0)]}(),n=t?.threshold??0;return(t,r)=>{let i=0;const s=t.length,h=r.length,o=Math.max(s,h)*(1-n);s!==h&&(i=Math.abs(s-h));let a=0;for(let n=0;n<Math.min(s,h);n++)if(t[n]!==r[n]&&(a+=e(t[n],r[n]),a>o))return 1;return a+=i,a/=Math.max(s,h),a}}n.d(e,{U:()=>h,o:()=>o});var i=n(1811);const s={gapOpen:1,gapExtend:.6,scoringMatrix:[[4,-1,-2,-2,0,-1,-1,0,-2,-1,-1,-1,-1,-2,-1,1,0,-3,-2,0,-2,-1,0,-4],[-1,5,0,-2,-3,1,0,-2,0,-3,-2,2,-1,-3,-2,-1,-1,-3,-2,-3,-1,0,-1,-4],[-2,0,6,1,-3,0,0,0,1,-3,-3,0,-2,-3,-2,1,0,-4,-2,-3,3,0,-1,-4],[-2,-2,1,6,-3,0,2,-1,-1,-3,-4,-1,-3,-3,-1,0,-1,-4,-3,-3,4,1,-1,-4],[0,-3,-3,-3,9,-3,-4,-3,-3,-1,-1,-3,-1,-2,-3,-1,-1,-2,-2,-1,-3,-3,-2,-4],[-1,1,0,0,-3,5,2,-2,0,-3,-2,1,0,-3,-1,0,-1,-2,-1,-2,0,3,-1,-4],[-1,0,0,2,-4,2,5,-2,0,-3,-3,1,-2,-3,-1,0,-1,-3,-2,-2,1,4,-1,-4],[0,-2,0,-1,-3,-2,-2,6,-2,-4,-4,-2,-3,-3,-2,0,-2,-2,-3,-3,-1,-2,-1,-4],[-2,0,1,-1,-3,0,0,-2,8,-3,-3,-1,-2,-1,-2,-1,-2,-2,2,-3,0,0,-1,-4],[-1,-3,-3,-3,-1,-3,-3,-4,-3,4,2,-3,1,0,-3,-2,-1,-3,-1,3,-3,-3,-1,-4],[-1,-2,-3,-4,-1,-2,-3,-4,-3,2,4,-2,2,0,-3,-2,-1,-2,-1,1,-4,-3,-1,-4],[-1,2,0,-1,-3,1,1,-2,-1,-3,-2,5,-1,-3,-1,0,-1,-3,-2,-2,0,1,-1,-4],[-1,-1,-2,-3,-1,0,-2,-3,-2,1,2,-1,5,0,-2,-1,-1,-1,-1,1,-3,-1,-1,-4],[-2,-3,-3,-3,-2,-3,-3,-3,-1,0,0,-3,0,6,-4,-2,-2,1,3,-1,-3,-3,-1,-4],[-1,-2,-2,-1,-3,-1,-1,-2,-2,-3,-3,-1,-2,-4,7,-1,-1,-4,-3,-2,-2,-1,-2,-4],[1,-1,1,0,-1,0,0,0,-1,-2,-2,0,-1,-2,-1,4,1,-3,-2,-2,0,0,0,-4],[0,-1,0,-1,-1,-1,-1,-2,-2,-1,-1,-1,-1,-2,-1,1,5,-2,-2,0,-1,-1,0,-4],[-3,-3,-4,-4,-2,-2,-3,-2,-2,-3,-2,-3,-1,1,-4,-3,-2,11,2,-3,-4,-3,-2,-4],[-2,-2,-2,-3,-2,-1,-2,-3,2,-1,-1,-2,-1,3,-3,-2,-2,2,7,-1,-3,-2,-1,-4],[0,-3,-3,-3,-1,-2,-2,-3,-3,3,1,-2,1,-1,-2,-2,0,-3,-1,4,-3,-2,-1,-4],[-2,-1,3,4,-3,0,1,-1,0,-3,-4,0,-3,-3,-2,0,-1,-4,-3,-3,4,1,-1,-4],[-1,0,0,1,-3,3,4,-2,0,-3,-3,1,-1,-3,-1,0,-1,-3,-2,-2,1,4,-1,-4],[0,-1,-1,-1,-2,-1,-1,-1,-1,-1,-1,-1,-1,-1,-2,0,0,-2,-1,-1,-1,-1,-1,-4],[-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,1]],alphabetIndexes:{A:0,R:1,N:2,D:3,C:4,Q:5,E:6,G:7,H:8,I:9,L:10,K:11,M:12,F:13,P:14,S:15,T:16,W:17,Y:18,V:19,B:20,Z:21,X:22,"*":23}};var h;!function(t){t.HAMMING="Hamming",t.LEVENSHTEIN="Levenshtein",t.NEEDLEMANN_WUNSCH="Needlemann-Wunsch",t.MONOMER_CHEMICAL_DISTANCE="Monomer chemical distance"}(h||(h={}));const o={[h.HAMMING]:r,[h.LEVENSHTEIN]:function(){return(t,e)=>(0,i.T)(t,e)/Math.max(t.length,e.length)},[h.NEEDLEMANN_WUNSCH]:function(t){const e=new Uint16Array(65536),{gapOpen:n,gapExtend:r,scoringMatrix:i,alphabetIndexes:h}={...s,...t};Object.entries(h).forEach((([t,n])=>e[t.charCodeAt(0)]=n));const o=[new Float32Array(1e4),new Float32Array(1e4)];return(t,s)=>{const h=new Array(t.length+1).fill(!1),a=new Array(t.length+1).fill(!1);let l=0,u=1;for(let e=1;e<t.length+1;e++)o[0][e]=-n-(e-1)*r,o[1][e]=0;o[0][0]=0;for(let g=1;g<s.length+1;g++){o[u][0]=-n-(g-1)*r;for(let c=1;c<t.length+1;c++){const f=o[l][c-1]+i[e[t.charCodeAt(c-1)]][e[s.charCodeAt(g-1)]],_=o[l][c]-(h[c]?r:n),d=o[u][c-1]-(a[c-1]?r:n);o[u][c]=Math.max(f,d,_),o[u][c]===f?(h[c]=!1,a[c]=!1):o[u][c]===d?(h[c]=!1,a[c]=!0):(h[c]=!0,a[c]=!1)}l=u,u=(u+1)%2}const g=Math.max(t.length,s.length);return(g-o[l][t.length])/g}},[h.MONOMER_CHEMICAL_DISTANCE]:r}},1040:(t,e,n)=>{var r,i,s,h,o,a,l;n.d(e,{CF:()=>i,Qe:()=>o,W:()=>r,Yc:()=>a,gd:()=>h,gj:()=>l,gk:()=>s}),function(t){t.Levenshtein="Levenshtein",t.JaroWinkler="Jaro-Winkler",t.Manhattan="Manhattan",t.Onehot="One-Hot"}(r||(r={})),function(t){t.Euclidean="Euclidean"}(i||(i={})),function(t){t.Tanimoto="Tanimoto",t.Dice="Dice",t.Asymmetric="Asymmetric",t.BraunBlanquet="Braun-Blanquet",t.Cosine="Cosine",t.Kulczynski="Kulczynski",t.McConnaughey="Mc-Connaughey",t.RogotGoldberg="Rogot-Goldberg",t.Russel="Russel",t.Sokal="Sokal",t.Hamming="Hamming",t.Euclidean="Euclidean"}(s||(s={})),function(t){t.TanimotoIntArray="TanimotoIntArray"}(h||(h={})),function(t){t.Vector="Vector",t.String="String",t.BitArray="BitArray",t.MacroMolecule="MacroMolecule",t.Number="Number",t.IntArray="IntArray",t.NumberArray="NumberArray"}(o||(o={})),function(t){t.Difference="Difference"}(a||(a={})),function(t){t.CommonItems="Common Items"}(l||(l={}))},9657:(t,e,n)=>{n.d(e,{Z:()=>r});class r{constructor(t,e=!1){if(this._length=0,this._version=0,this._updateLevel=0,this._selectedCount=0,this._selectedCountVersion=-1,this._selectedIndexesVersion=-1,this._versionedName="",this._versionedNameVersion=-1,this.SHRINK_THRESHOLD=256,"number"==typeof t){const n=t,i=r._createBuffer(n);if(e)for(let t=0;t<i.length;t++)i[t]=-1;this._data=i,this._length=n}else{if(!(t instanceof Uint32Array))throw new Error("Invalid constructor");this._data=t,this._length=e}}getRawData(){return this._data}assureGoez(t,e){if(t<0)throw new Error(`${e} should be greater than zero`)}assureInRange(t,e,n,r){if(t<e||t>n)throw new Error(`Argument ${r} (${t}) out of range (${e}, ${n})`)}copy(t,e,n){for(let r=0;r<n;r++)e[r]=t[r]}copyFrom(t){if(this._length!=t._length)throw new Error(`Lengths differ (${this._length} != ${t._length})`);this.copy(t._data,this._data,this.lengthInInts),this._version++}get length(){return this._length}get buffer(){return this._data}set buffer(t){this._data=t,this._version++}get version(){return this._version}set version(t){this._version=t}incrementVersion(t=!0){this._version++}get lengthInInts(){return Math.floor((this._length+31)/32)}get versionedName(){return this._version==this._versionedNameVersion?this._versionedName:""}set versionedName(t){this._versionedName=t,this._versionedNameVersion=this._version}get self(){return this}setLength(t){if(t<0)throw new Error("should be >= 0");if(t==this._length)return;const e=Math.floor((t+31)/32);if(e>this._data.length||e+this.SHRINK_THRESHOLD<this._data.length){const t=new Uint32Array(e);this.copy(this._data,t,e>this._data.length?this._data.length:e),this._data=t}t>this._length&&(this._length%32>0&&(this._data[this.lengthInInts-1]&=(1<<(this._length%32&31))-1),this._data.fill(0,this.lengthInInts,e)),this._length=t,this._version++}static fromAnd(t,e){if(t._length!=e._length)throw new Error(`Lengths differ (${t._length} != ${e._length})`);const n=new r(t._length);n._length=t._length,n._data=r._createBuffer(n._length),n._version=0;const i=t.lengthInInts;for(let r=0;r<i;r++)n._data[r]=t._data[r]&e._data[r];return n}static _createBuffer(t){return new Uint32Array(Math.floor((t+31)/32))}static fromValues(t){const e=new r(t.length);e._version=0;for(let n=0;n<e._length;n++)t[n]&&(e._data[Math.floor(n/32)]|=1<<(n%32&31));return e}static fromSeq(t,e){const n=new r(t);for(let r=0;r<t;++r)n.setBit(r,e(r));return n._version=0,n}static fromString(t){return r.fromSeq(t.length,(e=>"1"==t.charAt(e)))}static fromUint32Array(t,e){const n=new r(t);return n._data=e,n}static fromBytes(t){const e=t.length,n=new r(8*e);n._data=new Uint32Array(Math.floor((e+3)/4)),n._length=8*e;let i=0,s=0;for(;e-s>=4;)n._data[i++]=255&t[s]|(255&t[s+1])<<8|(255&t[s+2])<<16|(255&t[s+3])<<24,s+=4;return e-s==3&&(n._data[i]=(255&t[s+2])<<16),e-s==2&&(n._data[i]|=(255&t[s+1])<<8),e-s==1&&(n._data[i]|=255&t[s]),n._version=0,n}toString(){return`${this._length} bits, ${this.countBits(!0)} set`}equals(t){if(this==t)return!0;if(null==t)return!1;if(this._length!=t._length)return!1;if(0==this._length)return!0;for(let e=0;e<this._data.length-1;e++)if(this._data[e]!=t._data[e])return!1;for(let e=8*(this._data.length-1);e<this._length;e++)if(this.getBit(e)!=t.getBit(e))return!1;return!0}clone(){const t=new r(0,!1);return t._data=Uint32Array.from(this._data),t._length=this._length,t._version=this._version,t}init(t,e){this.setAll(!1,!1);for(let e=0;e<this._length;e++)t(e)&&(this._data[Math.floor(e/32)]|=1<<(e%32&31));return this.incrementVersion(e),this}invert(t=!0){for(let t=0;t<this._data.length;t++)this._data[t]^=-1;this.incrementVersion(t)}setAll(t,e=!1){const n=t?-1:0,r=this.lengthInInts;for(let t=0;t<r;t++)this._data[t]=n;this.incrementVersion(e)}setIndexes(t,e=!0,n=!0,r=!0){n&&this.setAll(!e,!1);for(const n of t)this.setFast(n,e);this.incrementVersion(r)}everyIndex(t,e=!0){for(const n of t)if(this.getBit(n)!=e)return!1;return!0}anyIndex(t,e=!0){for(const n of t)if(this.getBit(n)==e)return!0;return!1}setWhere(t,e=!0,n=!0,r=!0,i=!0){if(n&&i&&this.setAll(!e,!1),i)for(let n=0;n<this._length;n++)t(n)&&this.setFast(n,e);else for(let n=0;n<this._length;n++)this.setFast(n,t(n)?e:!e);this.incrementVersion(r)}getRange(t,e){this.assureInRange(t,0,this._length-1,"from"),this.assureInRange(e,0,this._length,"to");const n=[];for(let r=t;r<e;++r)n.push(this.getBit(r));return r.fromValues(n)}getRangeAsList(t,e){this.assureInRange(t,0,this._length-1,"from"),this.assureInRange(e,0,this._length,"to");const n=[];for(let r=t;r<e;++r)n.push(this.getBit(r));return n}setRange(t,e,n,r=!0){this.assureInRange(t,0,this._length-1,"from"),this.assureInRange(e,0,this._length-1,"to");const i=Math.min(t,e),s=Math.max(t,e);if(n)for(let t=i;t<=s;t++)this.setTrue(t);else for(let t=i;t<=s;t++)this.setFalse(t);return this.incrementVersion(r),this}setRandom(t,e,n=!0){if(t<0||t>this._length)throw new Error("n must be >= 0 && <= Count");t>this._length/2&&this.setRandom(this._length-t,!e),this.setAll(!e);for(let n=0;n<t;){const t=Math.floor(Math.random()*this._length);this.getBit(t)!=e&&(this.setFast(t,e),n++)}this.incrementVersion(n)}and(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}andNot(t,e=!0){if(this._length!=t._length)throw new Error("Array lengths differ.");const n=this.lengthInInts;for(let e=0;e<n;e++)this._data[e]&=~t._data[e];return this.incrementVersion(e),this}notAnd(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]=~this._data[e]&t._data[e];return this.incrementVersion(e),this}not(t=!0){for(let t=0,e=this.lengthInInts;t<e;t++)this._data[t]=~this._data[t];return this.incrementVersion(t),this}or(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}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 h=this._data[s]&t._data[s];const o=31&this._length;for(0!=o&&(h&=~(4294967295<<o));0!=h;h>>>=8)n+=r._onBitCount[255&h];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])},1811:(t,e,n)=>{n.d(e,{T:()=>i});const r=new Uint32Array(65536),i=(t,e)=>{if(t.length<e.length){const n=e;e=t,t=n}return 0===e.length?t.length:t.length<=32?((t,e)=>{const n=t.length,i=e.length,s=1<<n-1;let h=-1,o=0,a=n,l=n;for(;l--;)r[t.charCodeAt(l)]|=1<<l;for(l=0;l<i;l++){let t=r[e.charCodeAt(l)];const n=t|o;t|=(t&h)+h^h,o|=~(t|h),h&=t,o&s&&a++,h&s&&a--,o=o<<1|1,h=h<<1|~(n|o),o&=n}for(l=n;l--;)r[t.charCodeAt(l)]=0;return a})(t,e):((t,e)=>{const n=e.length,i=t.length,s=[],h=[],o=Math.ceil(n/32),a=Math.ceil(i/32);for(let t=0;t<o;t++)h[t]=-1,s[t]=0;let l=0;for(;l<a-1;l++){let o=0,a=-1;const u=32*l,g=Math.min(32,i)+u;for(let e=u;e<g;e++)r[t.charCodeAt(e)]|=1<<e;for(let t=0;t<n;t++){const n=r[e.charCodeAt(t)],i=h[t/32|0]>>>t&1,l=s[t/32|0]>>>t&1,u=n|o,g=((n|l)&a)+a^a|n|l;let c=o|~(g|a),f=a&g;c>>>31^i&&(h[t/32|0]^=1<<t),f>>>31^l&&(s[t/32|0]^=1<<t),c=c<<1|i,f=f<<1|l,a=f|~(u|c),o=c&u}for(let e=u;e<g;e++)r[t.charCodeAt(e)]=0}let u=0,g=-1;const c=32*l,f=Math.min(32,i-c)+c;for(let e=c;e<f;e++)r[t.charCodeAt(e)]|=1<<e;let _=i;for(let t=0;t<n;t++){const n=r[e.charCodeAt(t)],o=h[t/32|0]>>>t&1,a=s[t/32|0]>>>t&1,l=n|u,c=((n|a)&g)+g^g|n|a;let f=u|~(c|g),d=g&c;_+=f>>>i-1&1,_-=d>>>i-1&1,f>>>31^o&&(h[t/32|0]^=1<<t),d>>>31^a&&(s[t/32|0]^=1<<t),f=f<<1|o,d=d<<1|a,g=d|~(l|f),u=f&l}for(let e=c;e<f;e++)r[t.charCodeAt(e)]=0;return _})(t,e)}},3979:(t,e)=>{e.H$=void 0,e.H$=function(t,e,n){var r=function(t,e,n){if(0===t.length||0===e.length)return 0;if(n&&!n.caseSensitive&&(t=t.toUpperCase(),e=e.toUpperCase()),t===e)return 1;for(var r=0,i=t.length,s=e.length,h=Math.floor(Math.max(i,s)/2)-1,o=new Array(i),a=new Array(s),l=0;l<i;l++)for(var u=Math.max(0,l-h);u<=Math.min(s,l+h+1);u++)if(!o[l]&&!a[u]&&t[l]===e[u]){++r,o[l]=a[u]=!0;break}if(0===r)return 0;var g=0,c=0;for(l=0;l<i;l++)if(o[l]){for(;!a[c];)c++;t.charAt(l)!==e.charAt(c++)&&g++}return(r/i+r/s+(r-(g/=2))/r)/3}(t,e,n),i=0;if(r>.7){for(var s=Math.min(t.length,e.length),h=0;t[h]===e[h]&&h<4&&h<s;)++i,h++;r+=.1*i*(1-r)}return r}}}]);
 //# sourceMappingURL=36.js.map

dist/413.js

@@ -1,2 +0,2 @@
-"use strict";(self.webpackChunkbio=self.webpackChunkbio||[]).push([[413],{7862:(e,t,n)=>{var r;n.d(t,{y:()=>r}),function(e){e.EUCLIDEAN="EUCLIDEAN",e.MANHATTAN="MANHATTAN"}(r||(r={}))},6361:(e,t,n)=>{n.d(t,{UH:()=>r.UH,sQ:()=>r.sQ}),n(1040);var r=n(7861)},7861:(e,t,n)=>{n.d(t,{UH:()=>m,sQ:()=>M});var r=n(1811),o=n(3979),a=n(5697),i=n(850),s=n(708),g=n(1040);const c={[g.CF.Euclidean]:i.dP},h={[g.W.Levenshtein]:r.T,[g.W.JaroWinkler]:o.H$,[g.W.Manhattan]:function(e,t){if(e.length!==t.length)return 1;{let n=0;for(let r=1;r<e.length;r++)n+=e[r]==t[r]?0:1;return n/e.length}},[g.W.Onehot]:function(e,t){return e===t?0:1}},k={[g.gk.Tanimoto]:a.KR,[g.gk.Dice]:a._h,[g.gk.Asymmetric]:a.yU,[g.gk.BraunBlanquet]:a.Dz,[g.gk.Cosine]:a.Zd,[g.gk.Kulczynski]:a.s,[g.gk.McConnaughey]:a.aW,[g.gk.RogotGoldberg]:a.MI,[g.gk.Russel]:a.fX,[g.gk.Sokal]:a.NB,[g.gk.Hamming]:a.UX,[g.gk.Euclidean]:a.WI},u={[g.gd.TanimotoIntArray]:a.FV},l={[g.Yc.Difference]:a.bX},d={[g.Qe.Vector]:{[g.CF.Euclidean]:c[g.CF.Euclidean]},[g.Qe.String]:{[g.W.Levenshtein]:h[g.W.Levenshtein],[g.W.JaroWinkler]:h[g.W.JaroWinkler],[g.W.Manhattan]:h[g.W.Manhattan],[g.W.Onehot]:h[g.W.Onehot]},[g.Qe.BitArray]:{[g.gk.Tanimoto]:k[g.gk.Tanimoto],[g.gk.Dice]:k[g.gk.Dice],[g.gk.Asymmetric]:k[g.gk.Asymmetric],[g.gk.BraunBlanquet]:k[g.gk.BraunBlanquet],[g.gk.Cosine]:k[g.gk.Cosine],[g.gk.Kulczynski]:k[g.gk.Kulczynski],[g.gk.McConnaughey]:k[g.gk.McConnaughey],[g.gk.RogotGoldberg]:k[g.gk.RogotGoldberg],[g.gk.Russel]:k[g.gk.Russel],[g.gk.Sokal]:k[g.gk.Sokal]},[g.Qe.MacroMolecule]:{[s.U.HAMMING]:s.o[s.U.HAMMING],[s.U.LEVENSHTEIN]:s.o[s.U.LEVENSHTEIN],[s.U.NEEDLEMANN_WUNSCH]:s.o[s.U.NEEDLEMANN_WUNSCH],[s.U.MONOMER_CHEMICAL_DISTANCE]:s.o[s.U.MONOMER_CHEMICAL_DISTANCE]},[g.Qe.Number]:{[g.Yc.Difference]:l[g.Yc.Difference]},[g.Qe.IntArray]:{[g.gd.TanimotoIntArray]:u[g.gd.TanimotoIntArray]}},y=Object.keys(d).reduce(((e,t)=>{for(const n of Object.keys(d[t]))e[n]=t;return e}),{});function M(e){return"BitArray"==y[e]}class m{method;dataType;constructor(e){this.method=e,this.dataType=y[e]}getMeasure(e){const t=d;if(!t.hasOwnProperty(this.dataType)||!t[this.dataType].hasOwnProperty(this.method))throw new Error(`Unknown measure ${this.method} for data type ${this.dataType}`);return n=this.method,y[n]==g.Qe.MacroMolecule.toString()||function(e){return y[e]==g.Qe.Number.toString()}(this.method)?t[this.dataType][this.method](e):t[this.dataType][this.method];var n}static getMetricByDataType(e){return Object.keys(d[e])}static get availableMeasures(){return Object.keys(d)}}},850:(e,t,n)=>{function r(e,t){let n=0;const r=e.length;if(r!==t.length)throw new Error("The dimensionality of the vectors must match");for(let o=0;o<r;++o)n+=Math.pow(e[o]-t[o],2);return Math.sqrt(n)}n.d(t,{dP:()=>r})}}]);
+"use strict";(self.webpackChunkbio=self.webpackChunkbio||[]).push([[413],{7862:(e,t,n)=>{var r;n.d(t,{y:()=>r}),function(e){e.EUCLIDEAN="EUCLIDEAN",e.MANHATTAN="MANHATTAN"}(r||(r={}))},6361:(e,t,n)=>{n.d(t,{UH:()=>r.UH,sQ:()=>r.sQ}),n(1040);var r=n(7861)},7861:(e,t,n)=>{n.d(t,{UH:()=>M,sQ:()=>N});var r=n(1811),o=n(3979),a=n(5697),i=n(850),s=n(708),g=n(1040);const c={[g.CF.Euclidean]:i.dP},u={[g.W.Levenshtein]:r.T,[g.W.JaroWinkler]:o.H$,[g.W.Manhattan]:function(e,t){if(e.length!==t.length)return 1;{let n=0;for(let r=1;r<e.length;r++)n+=e[r]==t[r]?0:1;return n/e.length}},[g.W.Onehot]:function(e,t){return e===t?0:1}},h={[g.gk.Tanimoto]:a.KR,[g.gk.Dice]:a._h,[g.gk.Asymmetric]:a.yU,[g.gk.BraunBlanquet]:a.Dz,[g.gk.Cosine]:a.Zd,[g.gk.Kulczynski]:a.s,[g.gk.McConnaughey]:a.aW,[g.gk.RogotGoldberg]:a.MI,[g.gk.Russel]:a.fX,[g.gk.Sokal]:a.NB,[g.gk.Hamming]:a.UX,[g.gk.Euclidean]:a.WI},k={[g.gd.TanimotoIntArray]:a.FV},l={[g.Yc.Difference]:a.bX},m={[g.gj.CommonItems]:a.Jv},y={[g.Qe.Vector]:{[g.CF.Euclidean]:c[g.CF.Euclidean]},[g.Qe.String]:{[g.W.Levenshtein]:u[g.W.Levenshtein],[g.W.JaroWinkler]:u[g.W.JaroWinkler],[g.W.Manhattan]:u[g.W.Manhattan],[g.W.Onehot]:u[g.W.Onehot]},[g.Qe.BitArray]:{[g.gk.Tanimoto]:h[g.gk.Tanimoto],[g.gk.Dice]:h[g.gk.Dice],[g.gk.Asymmetric]:h[g.gk.Asymmetric],[g.gk.BraunBlanquet]:h[g.gk.BraunBlanquet],[g.gk.Cosine]:h[g.gk.Cosine],[g.gk.Kulczynski]:h[g.gk.Kulczynski],[g.gk.McConnaughey]:h[g.gk.McConnaughey],[g.gk.RogotGoldberg]:h[g.gk.RogotGoldberg],[g.gk.Russel]:h[g.gk.Russel],[g.gk.Sokal]:h[g.gk.Sokal]},[g.Qe.MacroMolecule]:{[s.U.HAMMING]:s.o[s.U.HAMMING],[s.U.LEVENSHTEIN]:s.o[s.U.LEVENSHTEIN],[s.U.NEEDLEMANN_WUNSCH]:s.o[s.U.NEEDLEMANN_WUNSCH],[s.U.MONOMER_CHEMICAL_DISTANCE]:s.o[s.U.MONOMER_CHEMICAL_DISTANCE]},[g.Qe.Number]:{[g.Yc.Difference]:l[g.Yc.Difference]},[g.Qe.IntArray]:{[g.gd.TanimotoIntArray]:k[g.gd.TanimotoIntArray]},[g.Qe.NumberArray]:{[g.gj.CommonItems]:m[g.gj.CommonItems]}},d=Object.keys(y).reduce(((e,t)=>{for(const n of Object.keys(y[t]))e[n]=t;return e}),{});function N(e){return"BitArray"==d[e]}class M{constructor(e){this.method=e,this.dataType=d[e]}metricNeedsArgs(e){return d[e]==g.Qe.MacroMolecule.toString()||d[e]==g.Qe.Number.toString()||function(e){return d[e]==g.Qe.NumberArray.toString()}(e)}getMeasure(e){const t=y;if(!t.hasOwnProperty(this.dataType)||!t[this.dataType].hasOwnProperty(this.method))throw new Error(`Unknown measure ${this.method} for data type ${this.dataType}`);return this.metricNeedsArgs(this.method)?t[this.dataType][this.method](e):t[this.dataType][this.method]}static getMetricByDataType(e){return Object.keys(y[e])}static get availableMeasures(){return Object.keys(y)}}},850:(e,t,n)=>{function r(e,t){let n=0;const r=e.length;if(r!==t.length)throw new Error("The dimensionality of the vectors must match");for(let o=0;o<r;++o)n+=Math.pow(e[o]-t[o],2);return Math.sqrt(n)}n.d(t,{dP:()=>r})}}]);
 //# sourceMappingURL=413.js.map

dist/590.js

@@ -1,2 +0,2 @@
-"use strict";(self.webpackChunkbio=self.webpackChunkbio||[]).push([[590],{2590:(n,e,t)=>{t.d(e,{_:()=>a});var r=t(7862),s=t(6814);class a{_workerCount;constructor(){this._workerCount=Math.max(navigator.hardwareConcurrency-2,1)}async calcMultiColumn(n,e,s,a=[{}],o=[1],l=r.y.EUCLIDEAN){const h=n[0].length*(n[0].length-1)/2,i=Math.floor(h/this._workerCount),c=n[0].length>2e4?await this.getMinimalThreshold(n,e,a,o,l):0;s<c&&(console.log(`using threshold ${c}`),s=c),a.forEach(((n,e)=>a[e].threshold=s));const w=new Array(this._workerCount),g=new Array(this._workerCount).fill(null).map((()=>new Worker(new URL(t.p+t.u(23),t.b))));for(let t=0;t<this._workerCount;t++)w[t]=new Promise(((r,c)=>{const w=t*i,u=t===this._workerCount-1?h:(t+1)*i;u<=w&&r({i:new Int32Array(0),j:new Int32Array(0),distance:new Float32Array(0),idx:t}),g[t].postMessage({values:n,startIdx:w,endIdx:u,threshold:s,fnNames:e,opts:a,weights:o,aggregationMethod:l}),g[t].onmessage=({data:{error:n,i:e,j:s,distance:a}})=>{n?(g[t].terminate(),c(n)):(g[t].terminate(),r({i:e,j:s,distance:a,idx:t}))}}));const u=await Promise.all(w),d=u.reduce(((n,e)=>n+e.i.length),0),k=new Int32Array(d),m=new Int32Array(d),y=new Float32Array(d);let f=0;for(const n of u)k.set(n.i,f),m.set(n.j,f),y.set(n.distance,f),f+=n.i.length;return{i:k,j:m,distance:y}}async calc(n,e,t,r={}){return await this.calcMultiColumn([n],[e],t,[r],[1])}async getKNN(n,e,t=15,r={}){return await this.multiColumnKNN([n],[e],t,[r],[1])}async getThresholdKNN(n,e,t=.8,r={}){return await this.multiColumnThresholdKnn([n],[e],t,[r],[1])}async multiColumnThresholdKnn(n,e,s=.8,a,o,l=r.y.EUCLIDEAN){if(n.length!==e.length||n.length!==a.length||n.length!==o.length)throw new Error("values, distance functions, options and weights arrays should have the same length");if(n.some((e=>e.length!==n[0].length)))throw new Error("all values arrays should have the same length");const h=n[0].length*(n[0].length-1)/2,i=Math.floor(h/this._workerCount),c=new Array(this._workerCount),w=new Array(this._workerCount).fill(null).map((()=>new Worker(new URL(t.p+t.u(427),t.b))));for(let t=0;t<this._workerCount;t++)c[t]=new Promise(((r,c)=>{const g=t*i,u=t===this._workerCount-1?h:(t+1)*i;u<=g&&r({knnDistances:new Array(0),knnIndexes:new Array(0)}),w[t].postMessage({values:n,startIdx:g,endIdx:u,fnNames:e,opts:a,threshold:s,weights:o,aggregationMethod:l}),w[t].onmessage=({data:{error:n,knnDistances:e,knnIndexes:s}})=>{n?(w[t].terminate(),c(n)):(w[t].terminate(),r({knnDistances:e,knnIndexes:s}))}}));const g=await Promise.all(c),u=new Int32Array(n[0].length);for(const e of g)for(let t=0;t<n[0].length;++t)u[t]+=e.knnIndexes[t]?.length??0;const d={knnDistances:new Array(n[0].length).fill(null).map(((n,e)=>new Array(u[e]))),knnIndexes:new Array(n[0].length).fill(null).map(((n,e)=>new Array(u[e])))};for(const e of g)for(let t=0;t<n[0].length;++t)for(let n=0;n<e.knnDistances[t]?.length;++n)d.knnDistances[t][u[t]-1]=e.knnDistances[t][n],d.knnIndexes[t][u[t]-1]=e.knnIndexes[t][n],u[t]-=1;return d}async multiColumnKNN(n,e,a=15,o,l,h=r.y.EUCLIDEAN){if(n.length!==e.length||n.length!==o.length||n.length!==l.length)throw new Error("values, distance functions, options and weights arrays should have the same length");if(n.some((e=>e.length!==n[0].length)))throw new Error("all values arrays should have the same length");const i=n[0].length*(n[0].length-1)/2,c=Math.floor(i/this._workerCount),w=new Array(this._workerCount),g=new Array(this._workerCount).fill(null).map((()=>new Worker(new URL(t.p+t.u(282),t.b))));for(let t=0;t<this._workerCount;t++)w[t]=new Promise(((r,s)=>{const w=t*c,u=t===this._workerCount-1?i:(t+1)*c;u<=w&&r({knnDistances:new Array(0),knnIndexes:new Array(0)}),g[t].postMessage({values:n,startIdx:w,endIdx:u,fnNames:e,opts:o,nNeighbours:a,weights:l,aggregationMethod:h}),g[t].onmessage=({data:{error:n,knnDistances:e,knnIndexes:a}})=>{n?(g[t].terminate(),s(n)):(g[t].terminate(),r({knnDistances:e,knnIndexes:a}))}}));const u=await Promise.all(w),d={knnDistances:new Array(n[0].length).fill(null).map((()=>new Array(a).fill(99999))),knnIndexes:new Array(n[0].length).fill(null).map((()=>new Array(a).fill(-1)))};for(const e of u)for(let t=0;t<n[0].length;++t)for(let n=0;n<e.knnDistances[t]?.length;++n)(0,s.cZ)(d.knnDistances[t],d.knnIndexes[t],e.knnDistances[t][n],e.knnIndexes[t][n]);return d}async getSampleDistances(n,e,s=[],a,o=r.y.EUCLIDEAN){const l=new Array(this._workerCount).fill(null).map((()=>new Worker(new URL(t.p+t.u(40),t.b))));try{const t=n[0].length*(n[0].length-1)/2,r=Math.floor(t/this._workerCount),h=1e6,i=Math.max(Math.min(t/1e3,h),Math.min(t,h)),c=Math.floor(i/this._workerCount),w=new Array(this._workerCount);for(let h=0;h<this._workerCount;h++)w[h]=new Promise(((i,w)=>{const g=h*r,u=h===this._workerCount-1?t:(h+1)*r;l[h].postMessage({values:n,startIdx:g,endIdx:u,sampleLength:c,fnNames:e,opts:s,weights:a,aggregationMethod:o}),l[h].onmessage=({data:{error:n,distance:e}})=>{l[h].terminate(),n?w(n):i({distance:e})}}));const g=await Promise.all(w),u=g.reduce(((n,e)=>n+e.distance.length),0),d=new Float32Array(u);let k=0;for(const n of g)d.set(n.distance,k),k+=n.distance.length;return d.sort(),d}catch(n){return l?.forEach((n=>n?.terminate())),console.error(n),new Float32Array(1).fill(.5)}}async getMinimalThreshold(n,e,t=[],s,a=r.y.EUCLIDEAN){try{const r=n.length*(n.length-1)/2,o=await this.getSampleDistances(n,e,t,s,a);return 1-o[Math.floor(7e7/r*o.length)]}catch(n){return console.error(n),.5}}static calcSync(n,e,t,r){const a=[],o=[],l=[];let h=0,i=0,c=0;const w=n.length*(n.length-1)/2;for(;h<w;){const e=(0,s.kK)(n[i])||(0,s.kK)(n[c])?1:t(n[i],n[c]);1-e>=r&&(a.push(i),o.push(c),l.push(e)),h++,c++,c===n.length&&(i++,c=i+1)}return{i:new Int32Array(a),j:new Int32Array(o),distance:new Float32Array(l)}}}},7862:(n,e,t)=>{var r;t.d(e,{y:()=>r}),function(n){n.EUCLIDEAN="EUCLIDEAN",n.MANHATTAN="MANHATTAN"}(r||(r={}))}}]);
+"use strict";(self.webpackChunkbio=self.webpackChunkbio||[]).push([[590],{2590:(n,e,t)=>{t.d(e,{_:()=>a});var r=t(7862),s=t(6814);class a{constructor(){this._workerCount=Math.max(navigator.hardwareConcurrency-2,1)}async calcMultiColumn(n,e,s,a=[{}],o=[1],l=r.y.EUCLIDEAN){const h=n[0].length*(n[0].length-1)/2,i=Math.floor(h/this._workerCount),c=n[0].length>2e4?await this.getMinimalThreshold(n,e,a,o,l):0;s<c&&(console.log(`using threshold ${c}`),s=c),a.forEach(((n,e)=>a[e].threshold=s));const w=new Array(this._workerCount),g=new Array(this._workerCount).fill(null).map((()=>new Worker(new URL(t.p+t.u(23),t.b))));for(let t=0;t<this._workerCount;t++)w[t]=new Promise(((r,c)=>{const w=t*i,u=t===this._workerCount-1?h:(t+1)*i;u<=w&&r({i:new Int32Array(0),j:new Int32Array(0),distance:new Float32Array(0),idx:t}),g[t].postMessage({values:n,startIdx:w,endIdx:u,threshold:s,fnNames:e,opts:a,weights:o,aggregationMethod:l}),g[t].onmessage=({data:{error:n,i:e,j:s,distance:a}})=>{n?(g[t].terminate(),c(n)):(g[t].terminate(),r({i:e,j:s,distance:a,idx:t}))}}));const u=await Promise.all(w),d=u.reduce(((n,e)=>n+e.i.length),0),k=new Int32Array(d),m=new Int32Array(d),y=new Float32Array(d);let f=0;for(const n of u)k.set(n.i,f),m.set(n.j,f),y.set(n.distance,f),f+=n.i.length;return{i:k,j:m,distance:y}}async calc(n,e,t,r={}){return await this.calcMultiColumn([n],[e],t,[r],[1])}async getKNN(n,e,t=15,r={}){return await this.multiColumnKNN([n],[e],t,[r],[1])}async getThresholdKNN(n,e,t=.8,r={}){return await this.multiColumnThresholdKnn([n],[e],t,[r],[1])}async multiColumnThresholdKnn(n,e,s=.8,a,o,l=r.y.EUCLIDEAN){if(n.length!==e.length||n.length!==a.length||n.length!==o.length)throw new Error("values, distance functions, options and weights arrays should have the same length");if(n.some((e=>e.length!==n[0].length)))throw new Error("all values arrays should have the same length");const h=n[0].length*(n[0].length-1)/2,i=Math.floor(h/this._workerCount),c=new Array(this._workerCount),w=new Array(this._workerCount).fill(null).map((()=>new Worker(new URL(t.p+t.u(427),t.b))));for(let t=0;t<this._workerCount;t++)c[t]=new Promise(((r,c)=>{const g=t*i,u=t===this._workerCount-1?h:(t+1)*i;u<=g&&r({knnDistances:new Array(0),knnIndexes:new Array(0)}),w[t].postMessage({values:n,startIdx:g,endIdx:u,fnNames:e,opts:a,threshold:s,weights:o,aggregationMethod:l}),w[t].onmessage=({data:{error:n,knnDistances:e,knnIndexes:s}})=>{n?(w[t].terminate(),c(n)):(w[t].terminate(),r({knnDistances:e,knnIndexes:s}))}}));const g=await Promise.all(c),u=new Int32Array(n[0].length);for(const e of g)for(let t=0;t<n[0].length;++t)u[t]+=e.knnIndexes[t]?.length??0;const d={knnDistances:new Array(n[0].length).fill(null).map(((n,e)=>new Array(u[e]))),knnIndexes:new Array(n[0].length).fill(null).map(((n,e)=>new Array(u[e])))};for(const e of g)for(let t=0;t<n[0].length;++t)for(let n=0;n<e.knnDistances[t]?.length;++n)d.knnDistances[t][u[t]-1]=e.knnDistances[t][n],d.knnIndexes[t][u[t]-1]=e.knnIndexes[t][n],u[t]-=1;return d}async multiColumnKNN(n,e,a=15,o,l,h=r.y.EUCLIDEAN){if(n.length!==e.length||n.length!==o.length||n.length!==l.length)throw new Error("values, distance functions, options and weights arrays should have the same length");if(n.some((e=>e.length!==n[0].length)))throw new Error("all values arrays should have the same length");const i=n[0].length*(n[0].length-1)/2,c=Math.floor(i/this._workerCount),w=new Array(this._workerCount),g=new Array(this._workerCount).fill(null).map((()=>new Worker(new URL(t.p+t.u(282),t.b))));for(let t=0;t<this._workerCount;t++)w[t]=new Promise(((r,s)=>{const w=t*c,u=t===this._workerCount-1?i:(t+1)*c;u<=w&&r({knnDistances:new Array(0),knnIndexes:new Array(0)}),g[t].postMessage({values:n,startIdx:w,endIdx:u,fnNames:e,opts:o,nNeighbours:a,weights:l,aggregationMethod:h}),g[t].onmessage=({data:{error:n,knnDistances:e,knnIndexes:a}})=>{n?(g[t].terminate(),s(n)):(g[t].terminate(),r({knnDistances:e,knnIndexes:a}))}}));const u=await Promise.all(w),d={knnDistances:new Array(n[0].length).fill(null).map((()=>new Array(a).fill(99999))),knnIndexes:new Array(n[0].length).fill(null).map((()=>new Array(a).fill(-1)))};for(const e of u)for(let t=0;t<n[0].length;++t)for(let n=0;n<e.knnDistances[t]?.length;++n)(0,s.cZ)(d.knnDistances[t],d.knnIndexes[t],e.knnDistances[t][n],e.knnIndexes[t][n]);return d}async getSampleDistances(n,e,s=[],a,o=r.y.EUCLIDEAN){const l=new Array(this._workerCount).fill(null).map((()=>new Worker(new URL(t.p+t.u(40),t.b))));try{const t=n[0].length*(n[0].length-1)/2,r=Math.floor(t/this._workerCount),h=1e6,i=Math.max(Math.min(t/1e3,h),Math.min(t,h)),c=Math.floor(i/this._workerCount),w=new Array(this._workerCount);for(let h=0;h<this._workerCount;h++)w[h]=new Promise(((i,w)=>{const g=h*r,u=h===this._workerCount-1?t:(h+1)*r;l[h].postMessage({values:n,startIdx:g,endIdx:u,sampleLength:c,fnNames:e,opts:s,weights:a,aggregationMethod:o}),l[h].onmessage=({data:{error:n,distance:e}})=>{l[h].terminate(),n?w(n):i({distance:e})}}));const g=await Promise.all(w),u=g.reduce(((n,e)=>n+e.distance.length),0),d=new Float32Array(u);let k=0;for(const n of g)d.set(n.distance,k),k+=n.distance.length;return d.sort(),d}catch(n){return l?.forEach((n=>n?.terminate())),console.error(n),new Float32Array(1).fill(.5)}}async getMinimalThreshold(n,e,t=[],s,a=r.y.EUCLIDEAN){try{const r=n.length*(n.length-1)/2,o=await this.getSampleDistances(n,e,t,s,a);return 1-o[Math.floor(7e7/r*o.length)]}catch(n){return console.error(n),.5}}static calcSync(n,e,t,r){const a=[],o=[],l=[];let h=0,i=0,c=0;const w=n.length*(n.length-1)/2;for(;h<w;){const e=(0,s.kK)(n[i])||(0,s.kK)(n[c])?1:t(n[i],n[c]);1-e>=r&&(a.push(i),o.push(c),l.push(e)),h++,c++,c===n.length&&(i++,c=i+1)}return{i:new Int32Array(a),j:new Int32Array(o),distance:new Float32Array(l)}}}},7862:(n,e,t)=>{var r;t.d(e,{y:()=>r}),function(n){n.EUCLIDEAN="EUCLIDEAN",n.MANHATTAN="MANHATTAN"}(r||(r={}))}}]);
 //# sourceMappingURL=590.js.map

dist/709.js

@@ -1,2 +0,2 @@
-var bio;(()=>{"use strict";var t,e,r={2357:(t,e,r)=>{var o=r(2590);async function n(t,e,r){const o=t.length,n=[],s=[];for(let a=0;a<o;a++)for(let l=a+1;l<o;l++){const o=t[a],i=t[l];e[o]?.[i]>=r&&(n.push(a),s.push(l))}return function(t,e,r){const o=new Float32Array(r.length).fill(0).map((()=>10*Math.random())),n=new Float32Array(r.length).fill(0).map((()=>10*Math.random())),s=new Float32Array(r.length).fill(0),a=new Float32Array(r.length).fill(0);for(let l=0;l<100;l++){const i=1-l/100;s.fill(0),a.fill(0);for(let r=0;r<t.length;r++){const l=t[r],c=e[r],f=o[l]-o[c],h=n[l]-n[c];Math.abs(f)>=1&&(s[l]-=i*f,s[c]+=i*f),Math.abs(h)>=1&&(a[l]-=i*h,a[c]+=i*h)}for(let t=0;t<r.length;t++){const e=Math.sqrt(s[t]*s[t]+a[t]*a[t]);e>0&&(o[t]+=s[t]/e*i,n[t]+=a[t]/e*i)}}let l=o[0],i=n[0],c=o[0],f=n[0];for(let t=1;t<r.length;t++)l=Math.min(l,o[t]),i=Math.min(i,n[t]),c=Math.max(c,o[t]),f=Math.max(f,n[t]);let h=c-l,u=f-i;0===h&&(h=c);for(let t=0;t<r.length;t++)o[t]=(o[t]-l)/h/2+.5;0===u&&(u=f);for(let t=0;t<r.length;t++)n[t]=(n[t]-i)/u/2+.5;return{embedX:o,embedY:n}}(n,s,t)}const s={expandFactor:2,maxIterations:5,inflateFactor:2,multFactor:1};class a{_options;constructor(t={}){this._options={...s,...t}}async transform(t,e){let r=this.toObjectForm(t);if(this._options.maxIterations>0){this.addLoops(r,e),this.normalize(r);for(let t=0;t<this._options.maxIterations;t++)r=this.expand(r,e),this.inflate(r),this.normalize(r)}const{clusters:o,is:n,js:s}=this.assignClusters(r,e);this.correctClusters(o);const a=await this.layout(o,r,e);return{clusters:o,embedX:a.embedX,embedY:a.embedY,is:n,js:s}}correctClusters(t){const e={};for(const r of t)e[r]||(e[r]=0),e[r]++;const r=Object.keys(e).map(Number).sort(((t,r)=>e[t]-e[r])),o={};r.forEach(((t,e)=>o[t]=e+1));for(let e=0;e<t.length;e++)t[e]=o[t[e]]}async layout(t,e,r){const o=new Float32Array(r).fill(0),s=new Float32Array(r).fill(0),a={};t.forEach(((t,e)=>{a[t]||(a[t]=[]),a[t].push(e)}));let l=0;const i=Object.keys(a);i.sort(((t,e)=>a[e].length-a[t].length));let c=6,f=0;for(const t of i){const r=a[t],i=await n(r,e,.001);l===Math.ceil(c/1.5)&&(l=0,f+=5/c,c=Math.ceil(1.5*c));const h=l%c*5/c*1.5;for(let t=0;t<i.embedX.length;t++)o[r[t]]=5*i.embedX[t]/c+h,s[r[t]]=5*i.embedY[t]/c+f;l++}return{embedX:o,embedY:s}}mergeClusters(t,e,r){const o=t[e],n=t[r];for(let e=0;e<t.length;e++)t[e]===n&&(t[e]=o)}assignClusters(t,e){let r=0;const o=[],n=[],s=Math.floor(Math.max(Math.log10(e),2))+1,a=Math.pow(10,s),l=new Array(e).fill(-1);for(const e of Object.keys(t))for(const s of Object.keys(t[e]))Math.round(t[e][s]*a)/a>0&&t[e][s]!==Number(e)&&Number(s)>Number(e)&&(o.push(Number(e)),n.push(Number(s)),-1!==l[Number(e)]&&-1!==l[Number(s)]?l[Number(e)]!==l[Number(s)]&&this.mergeClusters(l,Number(e),Number(s)):-1!==l[Number(e)]?l[Number(s)]=l[Number(e)]:-1!==l[Number(s)]?l[Number(e)]=l[Number(s)]:(r++,l[Number(e)]=r,l[Number(s)]=r));for(let t=0;t<l.length;t++)-1===l[t]&&(r++,l[t]=r);return{clusters:l,is:o,js:n}}toObjectForm(t){const e={};for(let r=0;r<t.i.length;r++)e[t.i[r]]||(e[t.i[r]]={}),e[t.i[r]][t.j[r]]=1-t.distance[r],e[t.j[r]]||(e[t.j[r]]={}),e[t.j[r]][t.i[r]]=1-t.distance[r];return e}addLoops(t,e){for(let r=0;r<e;r++)t[r]||(t[r]={}),t[r][r]=this._options.multFactor}normalize(t){for(const e of Object.keys(t)){const r=t[e];let o=0;for(const t of Object.keys(r))o+=r[t];if(0!==o)for(const n of Object.keys(r))t[e][n]/=o}}expand(t,e){const r={},o=Math.floor(Math.max(Math.log10(e),2))+1,n=Math.pow(10,o);for(let o=0;o<e;o++)if(t[o]){r[o]={};for(let s=o;s<e;s++){if(!t[o]?.[s])continue;const e=this.getExpandValue(t,o,s);Math.round(e*n)/n>0&&(r[o][s]=e,r[s]||(r[s]={}),r[s][o]=e)}}return r}inflate(t){for(const e of Object.keys(t)){const r=t[e];for(const o of Object.keys(r))t[e][o]=Math.pow(t[e][o],this._options.inflateFactor)}}getExpandValue(t,e,r){let o=0;const n=Object.keys(t[e]??{}),s=Object.keys(t[r]??{});for(const a of n)s.includes(a)&&(o+=t[e][a]*t[r][a]);return o}}onmessage=async t=>{const{data:e,threshold:r,weights:n,aggregationMethod:s,distanceFnArgs:l,distanceFns:i,maxIterations:c}=t.data,f=await(new o._).calcMultiColumn(e,i,r/100,l,n,s),h=await new a({maxIterations:c??5}).transform(f,e[0].length);postMessage({res:h})}},6814:(t,e,r)=>{r.d(e,{cZ:()=>n,kK:()=>o}),r(7862);const o=t=>null==t;function n(t,e,r,o){if(r>t[t.length-1])return;const n=t.findIndex((t=>r<t));t.pop(),t.splice(n,0,r),e.pop(),e.splice(n,0,o)}}},o={};function n(t){var e=o[t];if(void 0!==e)return e.exports;var s=o[t]={exports:{}};return r[t](s,s.exports,n),s.exports}n.m=r,n.x=()=>{var t=n.O(void 0,[590],(()=>n(2357)));return n.O(t)},t=[],n.O=(e,r,o,s)=>{if(!r){var a=1/0;for(f=0;f<t.length;f++){for(var[r,o,s]=t[f],l=!0,i=0;i<r.length;i++)(!1&s||a>=s)&&Object.keys(n.O).every((t=>n.O[t](r[i])))?r.splice(i--,1):(l=!1,s<a&&(a=s));if(l){t.splice(f--,1);var c=o();void 0!==c&&(e=c)}}return e}s=s||0;for(var f=t.length;f>0&&t[f-1][2]>s;f--)t[f]=t[f-1];t[f]=[r,o,s]},n.d=(t,e)=>{for(var r in e)n.o(e,r)&&!n.o(t,r)&&Object.defineProperty(t,r,{enumerable:!0,get:e[r]})},n.f={},n.e=t=>Promise.all(Object.keys(n.f).reduce(((e,r)=>(n.f[r](t,e),e)),[])),n.u=t=>t+".js",n.g=function(){if("object"==typeof globalThis)return globalThis;try{return this||new Function("return this")()}catch(t){if("object"==typeof window)return window}}(),n.o=(t,e)=>Object.prototype.hasOwnProperty.call(t,e),(()=>{var t;n.g.importScripts&&(t=n.g.location+"");var e=n.g.document;if(!t&&e&&(e.currentScript&&(t=e.currentScript.src),!t)){var r=e.getElementsByTagName("script");if(r.length)for(var o=r.length-1;o>-1&&!t;)t=r[o--].src}if(!t)throw new Error("Automatic publicPath is not supported in this browser");t=t.replace(/#.*$/,"").replace(/\?.*$/,"").replace(/\/[^\/]+$/,"/"),n.p=t})(),(()=>{n.b=self.location+"";var t={709:1};n.f.i=(e,r)=>{t[e]||importScripts(n.p+n.u(e))};var e=self.webpackChunkbio=self.webpackChunkbio||[],r=e.push.bind(e);e.push=e=>{var[o,s,a]=e;for(var l in s)n.o(s,l)&&(n.m[l]=s[l]);for(a&&a(n);o.length;)t[o.pop()]=1;r(e)}})(),e=n.x,n.x=()=>n.e(590).then(e);var s=n.x();bio=s})();
+var bio;(()=>{"use strict";var t,e,r={2357:(t,e,r)=>{var o=r(2590);async function n(t,e,r){const o=t.length,n=[],s=[];for(let a=0;a<o;a++)for(let l=a+1;l<o;l++){const o=t[a],i=t[l];e[o]?.[i]>=r&&(n.push(a),s.push(l))}return function(t,e,r){const o=new Float32Array(r.length).fill(0).map((()=>10*Math.random())),n=new Float32Array(r.length).fill(0).map((()=>10*Math.random())),s=new Float32Array(r.length).fill(0),a=new Float32Array(r.length).fill(0);for(let l=0;l<100;l++){const i=1-l/100;s.fill(0),a.fill(0);for(let r=0;r<t.length;r++){const l=t[r],c=e[r],f=o[l]-o[c],h=n[l]-n[c];Math.abs(f)>=1&&(s[l]-=i*f,s[c]+=i*f),Math.abs(h)>=1&&(a[l]-=i*h,a[c]+=i*h)}for(let t=0;t<r.length;t++){const e=Math.sqrt(s[t]*s[t]+a[t]*a[t]);e>0&&(o[t]+=s[t]/e*i,n[t]+=a[t]/e*i)}}let l=o[0],i=n[0],c=o[0],f=n[0];for(let t=1;t<r.length;t++)l=Math.min(l,o[t]),i=Math.min(i,n[t]),c=Math.max(c,o[t]),f=Math.max(f,n[t]);let h=c-l,u=f-i;0===h&&(h=c);for(let t=0;t<r.length;t++)o[t]=(o[t]-l)/h/2+.5;0===u&&(u=f);for(let t=0;t<r.length;t++)n[t]=(n[t]-i)/u/2+.5;return{embedX:o,embedY:n}}(n,s,t)}const s={expandFactor:2,maxIterations:5,inflateFactor:2,multFactor:1};class a{constructor(t={}){this._options={...s,...t}}async transform(t,e){let r=this.toObjectForm(t);if(this._options.maxIterations>0){this.addLoops(r,e),this.normalize(r);for(let t=0;t<this._options.maxIterations;t++)r=this.expand(r,e),this.inflate(r),this.normalize(r)}const{clusters:o,is:n,js:s}=this.assignClusters(r,e);this.correctClusters(o);const a=await this.layout(o,r,e);return{clusters:o,embedX:a.embedX,embedY:a.embedY,is:n,js:s}}correctClusters(t){const e={};for(const r of t)e[r]||(e[r]=0),e[r]++;const r=Object.keys(e).map(Number).sort(((t,r)=>e[t]-e[r])),o={};r.forEach(((t,e)=>o[t]=e+1));for(let e=0;e<t.length;e++)t[e]=o[t[e]]}async layout(t,e,r){const o=new Float32Array(r).fill(0),s=new Float32Array(r).fill(0),a={};t.forEach(((t,e)=>{a[t]||(a[t]=[]),a[t].push(e)}));let l=0;const i=Object.keys(a);i.sort(((t,e)=>a[e].length-a[t].length));let c=6,f=0;for(const t of i){const r=a[t],i=await n(r,e,.001);l===Math.ceil(c/1.5)&&(l=0,f+=5/c,c=Math.ceil(1.5*c));const h=l%c*5/c*1.5;for(let t=0;t<i.embedX.length;t++)o[r[t]]=5*i.embedX[t]/c+h,s[r[t]]=5*i.embedY[t]/c+f;l++}return{embedX:o,embedY:s}}mergeClusters(t,e,r){const o=t[e],n=t[r];for(let e=0;e<t.length;e++)t[e]===n&&(t[e]=o)}assignClusters(t,e){let r=0;const o=[],n=[],s=Math.floor(Math.max(Math.log10(e),2))+1,a=Math.pow(10,s),l=new Array(e).fill(-1);for(const e of Object.keys(t))for(const s of Object.keys(t[e]))Math.round(t[e][s]*a)/a>0&&t[e][s]!==Number(e)&&Number(s)>Number(e)&&(o.push(Number(e)),n.push(Number(s)),-1!==l[Number(e)]&&-1!==l[Number(s)]?l[Number(e)]!==l[Number(s)]&&this.mergeClusters(l,Number(e),Number(s)):-1!==l[Number(e)]?l[Number(s)]=l[Number(e)]:-1!==l[Number(s)]?l[Number(e)]=l[Number(s)]:(r++,l[Number(e)]=r,l[Number(s)]=r));for(let t=0;t<l.length;t++)-1===l[t]&&(r++,l[t]=r);return{clusters:l,is:o,js:n}}toObjectForm(t){const e={};for(let r=0;r<t.i.length;r++)e[t.i[r]]||(e[t.i[r]]={}),e[t.i[r]][t.j[r]]=1-t.distance[r],e[t.j[r]]||(e[t.j[r]]={}),e[t.j[r]][t.i[r]]=1-t.distance[r];return e}addLoops(t,e){for(let r=0;r<e;r++)t[r]||(t[r]={}),t[r][r]=this._options.multFactor}normalize(t){for(const e of Object.keys(t)){const r=t[e];let o=0;for(const t of Object.keys(r))o+=r[t];if(0!==o)for(const n of Object.keys(r))t[e][n]/=o}}expand(t,e){const r={},o=Math.floor(Math.max(Math.log10(e),2))+1,n=Math.pow(10,o);for(let o=0;o<e;o++)if(t[o]){r[o]={};for(let s=o;s<e;s++){if(!t[o]?.[s])continue;const e=this.getExpandValue(t,o,s);Math.round(e*n)/n>0&&(r[o][s]=e,r[s]||(r[s]={}),r[s][o]=e)}}return r}inflate(t){for(const e of Object.keys(t)){const r=t[e];for(const o of Object.keys(r))t[e][o]=Math.pow(t[e][o],this._options.inflateFactor)}}getExpandValue(t,e,r){let o=0;const n=Object.keys(t[e]??{}),s=Object.keys(t[r]??{});for(const a of n)s.includes(a)&&(o+=t[e][a]*t[r][a]);return o}}onmessage=async t=>{const{data:e,threshold:r,weights:n,aggregationMethod:s,distanceFnArgs:l,distanceFns:i,maxIterations:c}=t.data,f=await(new o._).calcMultiColumn(e,i,r/100,l,n,s),h=await new a({maxIterations:c??5}).transform(f,e[0].length);postMessage({res:h})}},6814:(t,e,r)=>{r.d(e,{cZ:()=>n,kK:()=>o}),r(7862);const o=t=>null==t;function n(t,e,r,o){if(r>t[t.length-1])return;const n=t.findIndex((t=>r<t));t.pop(),t.splice(n,0,r),e.pop(),e.splice(n,0,o)}}},o={};function n(t){var e=o[t];if(void 0!==e)return e.exports;var s=o[t]={exports:{}};return r[t](s,s.exports,n),s.exports}n.m=r,n.x=()=>{var t=n.O(void 0,[590],(()=>n(2357)));return n.O(t)},t=[],n.O=(e,r,o,s)=>{if(!r){var a=1/0;for(f=0;f<t.length;f++){for(var[r,o,s]=t[f],l=!0,i=0;i<r.length;i++)(!1&s||a>=s)&&Object.keys(n.O).every((t=>n.O[t](r[i])))?r.splice(i--,1):(l=!1,s<a&&(a=s));if(l){t.splice(f--,1);var c=o();void 0!==c&&(e=c)}}return e}s=s||0;for(var f=t.length;f>0&&t[f-1][2]>s;f--)t[f]=t[f-1];t[f]=[r,o,s]},n.d=(t,e)=>{for(var r in e)n.o(e,r)&&!n.o(t,r)&&Object.defineProperty(t,r,{enumerable:!0,get:e[r]})},n.f={},n.e=t=>Promise.all(Object.keys(n.f).reduce(((e,r)=>(n.f[r](t,e),e)),[])),n.u=t=>t+".js",n.g=function(){if("object"==typeof globalThis)return globalThis;try{return this||new Function("return this")()}catch(t){if("object"==typeof window)return window}}(),n.o=(t,e)=>Object.prototype.hasOwnProperty.call(t,e),(()=>{var t;n.g.importScripts&&(t=n.g.location+"");var e=n.g.document;if(!t&&e&&(e.currentScript&&(t=e.currentScript.src),!t)){var r=e.getElementsByTagName("script");if(r.length)for(var o=r.length-1;o>-1&&!t;)t=r[o--].src}if(!t)throw new Error("Automatic publicPath is not supported in this browser");t=t.replace(/#.*$/,"").replace(/\?.*$/,"").replace(/\/[^\/]+$/,"/"),n.p=t})(),(()=>{n.b=self.location+"";var t={709:1};n.f.i=(e,r)=>{t[e]||importScripts(n.p+n.u(e))};var e=self.webpackChunkbio=self.webpackChunkbio||[],r=e.push.bind(e);e.push=e=>{var[o,s,a]=e;for(var l in s)n.o(s,l)&&(n.m[l]=s[l]);for(a&&a(n);o.length;)t[o.pop()]=1;r(e)}})(),e=n.x,n.x=()=>n.e(590).then(e);var s=n.x();bio=s})();
 //# sourceMappingURL=709.js.map

package.json

@@ -5,6 +5,6 @@ {
   "author": {
-    "name": "Leonid Stolbov",
-    "email": "[e-mail]"
+    "name": "Aleksandr Tanas",
+    "email": "[e-mail]"
   },
-  "version": "2.11.42",
+  "version": "2.12.0",
   "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.",
@@ -38,6 +38,6 @@ "repository": {
     "@biowasm/aioli": "^3.1.0",
-    "@datagrok-libraries/bio": "5.39.29",
-    "@datagrok-libraries/chem-meta": "^1.2.1",
-    "@datagrok-libraries/ml": "^6.4.10",
-    "@datagrok-libraries/tutorials": "^1.3.11",
+    "@datagrok-libraries/bio": "5.40.0",
+    "@datagrok-libraries/chem-meta": "^1.2.3",
+    "@datagrok-libraries/ml": "^6.4.12",
+    "@datagrok-libraries/tutorials": "^1.3.12",
     "ajv": "^8.12.0",
@@ -59,5 +59,5 @@ "ajv-errors": "^3.0.0",
   "devDependencies": {
-    "@datagrok/chem": "^1.8.11",
-    "@datagrok/dendrogram": "^1.2.22",
-    "@datagrok/helm": "^2.1.27",
+    "@datagrok/chem": "^1.9.0",
+    "@datagrok/dendrogram": "^1.2.27",
+    "@datagrok/helm": "^2.1.30",
     "@types/node": "^17.0.24",
@@ -64,0 +64,0 @@ "@types/wu": "latest",

README.md

@@ -19,3 +19,3 @@ # Bio
 * [detectMacromolecule()](../Bio/detectors.js)
-* [class UnitsHandler](../../libraries/bio/src/utils/units-handler.ts)
+* [class SeqHandler](../../libraries/bio/src/utils/seq-handler.ts)
 
@@ -22,0 +22,0 @@ ## Atomic-Level structures from sequences

src/analysis/sequence-activity-cliffs.ts

@@ -5,2 +5,4 @@ import * as grok from 'datagrok-api/grok';
 
+import wu from 'wu';
+
 import {ITooltipAndPanelParams} from '@datagrok-libraries/ml/src/viewers/activity-cliffs';
@@ -12,3 +14,3 @@ import {getSimilarityFromDistance} from '@datagrok-libraries/ml/src/distance-metrics-methods';
 import {TAGS as bioTAGS} from '@datagrok-libraries/bio/src/utils/macromolecule';
-import {UnitsHandler} from '@datagrok-libraries/bio/src/utils/units-handler';
+import {SeqHandler} from '@datagrok-libraries/bio/src/utils/seq-handler';
 import {ISeqSplitted} from '@datagrok-libraries/bio/src/utils/macromolecule/types';
@@ -102,6 +104,4 @@
 
-  const sequencesArray = new Array<string>(2);
   const activitiesArray = new Array<number>(2);
   params.points.forEach((molIdx, idx) => {
-    sequencesArray[idx] = params.seqCol.get(molIdx);
     activitiesArray[idx] = params.activityCol.get(molIdx);
@@ -111,7 +111,6 @@ });
   const molDifferences: { [key: number]: HTMLCanvasElement } = {};
-  const uh = UnitsHandler.getOrCreate(params.seqCol);
-  const splitter = uh.getSplitter();
-  const subParts1 = splitter(sequencesArray[0]);
-  const subParts2 = splitter(sequencesArray[1]);
-  const canvas = createDifferenceCanvas(subParts1, subParts2, uh.units, molDifferences);
+  const sh = SeqHandler.forColumn(params.seqCol);
+  const subParts1 = sh.getSplitted(params.points[0]); // splitter(sequencesArray[0], {uh, rowIdx: -1});
+  const subParts2 = sh.getSplitted(params.points[1]); // splitter(sequencesArray[1], {uh, rowIdx: -1});
+  const canvas = createDifferenceCanvas(subParts1, subParts2, sh.units, molDifferences);
   propPanel.append(ui.div(canvas, {style: {width: '300px', overflow: 'scroll'}}));
@@ -142,3 +141,4 @@
   canvas.height = 30;
-  drawMoleculeDifferenceOnCanvas(context!, 0, 0, 0, 30, subParts1, subParts2, units, true, molDifferences);
+  drawMoleculeDifferenceOnCanvas(context!, 0, 0, 0, 30,
+    wu(subParts1.canonicals).toArray(), wu(subParts2.canonicals).toArray(), units, true, molDifferences);
   return canvas;
@@ -145,0 +145,0 @@ }

src/analysis/sequence-diversity-viewer.ts

@@ -10,3 +10,3 @@ import * as ui from 'datagrok-api/ui';
 import {Subject} from 'rxjs';
-import {UnitsHandler} from '@datagrok-libraries/bio/src/utils/units-handler';
+import {SeqHandler} from '@datagrok-libraries/bio/src/utils/seq-handler';
 import {getEncodedSeqSpaceCol} from './sequence-space';
@@ -33,4 +33,4 @@ import {MmDistanceFunctionsNames} from '@datagrok-libraries/ml/src/macromolecule-distance-functions';
       if (computeData && this.moleculeColumn) {
-        const uh = UnitsHandler.getOrCreate(this.moleculeColumn);
-        await (uh.isFasta() ? this.computeByMM() : this.computeByChem());
+        const sh = SeqHandler.forColumn(this.moleculeColumn);
+        await (sh.isFasta() ? this.computeByMM() : this.computeByChem());
 
@@ -37,0 +37,0 @@ const diverseColumnName: string = this.diverseColumnLabel != null ? this.diverseColumnLabel :

src/analysis/sequence-search-base-viewer.ts

@@ -17,3 +17,3 @@ import * as ui from 'datagrok-api/ui';
   fingerprintChoices = ['Morgan', 'Pattern'];
-  moleculeColumn?: DG.Column | null;
+  moleculeColumn?: DG.Column<string>;
   moleculeColumnName: string;
@@ -55,3 +55,3 @@ initialized: boolean = false;
         .subscribe((_: any) => this.render(false)));
-      this.moleculeColumn = this.dataFrame.columns.bySemType(DG.SEMTYPE.MACROMOLECULE);
+      this.moleculeColumn = this.dataFrame.columns.bySemType(DG.SEMTYPE.MACROMOLECULE) as DG.Column<string>;
       this.moleculeColumnName = this.moleculeColumn?.name!;
@@ -58,0 +58,0 @@ this.getProperty('limit')!.fromOptions({min: 1, max: this.dataFrame.rowCount});

src/analysis/sequence-similarity-viewer.ts

@@ -10,3 +10,3 @@ import * as grok from 'datagrok-api/grok';
 import {Subject} from 'rxjs';
-import {UnitsHandler} from '@datagrok-libraries/bio/src/utils/units-handler';
+import {SeqHandler} from '@datagrok-libraries/bio/src/utils/seq-handler';
 import {alignSequencePair} from '@datagrok-libraries/bio/src/utils/macromolecule/alignment';
@@ -54,5 +54,5 @@ import {KnnResult, SparseMatrixService} from '@datagrok-libraries/ml/src/distance-matrix/sparse-matrix-service';
         this.targetMoleculeIdx = this.dataFrame!.currentRowIdx == -1 ? 0 : this.dataFrame!.currentRowIdx;
-        const uh = UnitsHandler.getOrCreate(this.moleculeColumn!);
+        const sh = SeqHandler.forColumn(this.moleculeColumn!);
 
-        await (!uh.isHelm() ? this.computeByMM() : this.computeByChem());
+        await (!sh.isHelm() ? this.computeByMM() : this.computeByChem());
         const similarColumnName: string = this.similarColumnLabel != null ? this.similarColumnLabel :
@@ -126,9 +126,9 @@ `similar (${this.moleculeColumnName})`;
     const molColName = this.molCol?.name!;
-    const col = resDf.col(molColName)!;
-    const uh = UnitsHandler.getOrCreate(col);
-    const splitter = uh.getSplitter();
-    const subParts1 = splitter(this.moleculeColumn!.get(this.targetMoleculeIdx));
-    const subParts2 = splitter(resDf.get(molColName, resDf.currentRowIdx));
-    const alignment = alignSequencePair(Array.from(subParts1), Array.from(subParts2));
-    const canvas = createDifferenceCanvas(alignment.seq1Splitted, alignment.seq2Splitted, uh.units, molDifferences);
+    const resCol: DG.Column<string> = resDf.col(molColName)!;
+    const molColSh = SeqHandler.forColumn(this.moleculeColumn!);
+    const resSh = SeqHandler.forColumn(resCol);
+    const subParts1 = molColSh.getSplitted(this.targetMoleculeIdx);
+    const subParts2 = resSh.getSplitted(resDf.currentRowIdx);
+    const alignment = alignSequencePair(subParts1, subParts2);
+    const canvas = createDifferenceCanvas(alignment.seq1Splitted, alignment.seq2Splitted, resSh.units, molDifferences);
     propPanel.append(ui.div(canvas, {style: {width: '300px', overflow: 'scroll'}}));
@@ -135,0 +135,0 @@ if (subParts1.length !== subParts2.length) {

src/analysis/sequence-space.ts

@@ -0,6 +1,8 @@
+import * as ui from 'datagrok-api/ui';
 import * as DG from 'datagrok-api/dg';
 import * as grok from 'datagrok-api/grok';
+
 import {BitArrayMetrics} from '@datagrok-libraries/ml/src/typed-metrics';
 import {mmDistanceFunctionArgs} from '@datagrok-libraries/ml/src/macromolecule-distance-functions/types';
-import {UnitsHandler} from '@datagrok-libraries/bio/src/utils/units-handler';
+import {SeqHandler} from '@datagrok-libraries/bio/src/utils/seq-handler';
 import {getMonomerSubstitutionMatrix} from '@datagrok-libraries/bio/src/monomer-works/monomer-utils';
@@ -16,20 +18,23 @@ import {MmDistanceFunctionsNames} from '@datagrok-libraries/ml/src/macromolecule-distance-functions';
   seqCol: DG.Column, similarityMetric: BitArrayMetrics | MmDistanceFunctionsNames, fingerprintType: string = 'Morgan'
-): Promise<{seqList:string[], options: {[_:string]: any}}> {
-// encodes sequences using utf charachters to also support multichar and non fasta sequences
-  const ncUH = UnitsHandler.getOrCreate(seqCol);
-  const seqList = seqCol.toList();
-  const splitter = ncUH.getSplitter();
-  const seqColLength = seqList.length;
+): Promise<{ seqList: string[], options: { [_: string]: any } }> {
+// encodes sequences using utf characters to also support multichar and non fasta sequences
+  const rowCount = seqCol.length;
+  const sh = SeqHandler.forColumn(seqCol);
+  const encList = Array<string>(rowCount);
   let charCodeCounter = 36;
   const charCodeMap = new Map<string, string>();
-  for (let i = 0; i < seqColLength; i++) {
-    const seq = seqList[i];
-    if (seqList[i] === null || seqCol.isNone(i)) {
-      seqList[i] = null;
+  const seqColCats = seqCol.categories;
+  const seqColRawData = seqCol.getRawData();
+  for (let rowIdx = 0; rowIdx < rowCount; rowIdx++) {
+    const catI = seqColRawData[rowIdx];
+    const seq = seqColCats[catI];
+    if (seq === null || seqCol.isNone(rowIdx)) {
+      // @ts-ignore
+      encList[rowIdx] = null;
       continue;
     }
-    seqList[i] = '';
-    const splittedSeq = splitter(seq);
+    encList[rowIdx] = '';
+    const splittedSeq = sh.getSplitted(rowIdx);
     for (let j = 0; j < splittedSeq.length; j++) {
-      const char = splittedSeq[j];
+      const char = splittedSeq.getCanonical(j);
       if (!charCodeMap.has(char)) {
@@ -39,6 +44,6 @@ charCodeMap.set(char, String.fromCharCode(charCodeCounter));
       }
-      seqList[i] += charCodeMap.get(char)!;
+      encList[rowIdx] += charCodeMap.get(char)!;
     }
   }
-  let options = {};
+  let options = {} as mmDistanceFunctionArgs;
   if (similarityMetric === MmDistanceFunctionsNames.MONOMER_CHEMICAL_DISTANCE) {
@@ -53,3 +58,3 @@ const monomers = Array.from(charCodeMap.keys());
     });
-    const monomerHashToMatrixMap: {[_: string]: number} = {};
+    const monomerHashToMatrixMap: { [_: string]: number } = {};
     Object.entries(monomerRes.alphabetIndexes).forEach(([key, value]) => {
@@ -59,4 +64,3 @@ monomerHashToMatrixMap[charCodeMap.get(key)!] = value;
     // sets distance function args in place.
-    options = {scoringMatrix: monomerRes.scoringMatrix,
-      alphabetIndexes: monomerHashToMatrixMap} satisfies mmDistanceFunctionArgs;
+    options = {scoringMatrix: monomerRes.scoringMatrix, alphabetIndexes: monomerHashToMatrixMap};
   } else if (similarityMetric === MmDistanceFunctionsNames.NEEDLEMANN_WUNSCH) {
@@ -71,3 +75,3 @@ const monomers = Array.from(charCodeMap.keys());
     // });
-    const monomerHashToMatrixMap: {[_: string]: number} = {};
+    const monomerHashToMatrixMap: { [_: string]: number } = {};
     Object.entries(monomerRes.alphabetIndexes).forEach(([key, value]) => {
@@ -77,6 +81,5 @@ monomerHashToMatrixMap[charCodeMap.get(key)!] = value;
     // sets distance function args in place.
-    options = {scoringMatrix: monomerRes.scoringMatrix,
-      alphabetIndexes: monomerHashToMatrixMap} satisfies mmDistanceFunctionArgs;
+    options = {scoringMatrix: monomerRes.scoringMatrix, alphabetIndexes: monomerHashToMatrixMap};
   }
-  return {seqList, options};
+  return {seqList: encList, options};
 }

src/calculations/monomerLevelMols.ts

@@ -8,4 +8,4 @@ import * as grok from 'datagrok-api/grok';
 import {getHelmMonomers} from '../package';
-import {UnitsHandler} from '@datagrok-libraries/bio/src/utils/units-handler';
-import {ISeqSplitted} from '@datagrok-libraries/bio/src/utils/macromolecule/types';
+import {SeqHandler} from '@datagrok-libraries/bio/src/utils/seq-handler';
+import {GAP_SYMBOL, ISeqSplitted} from '@datagrok-libraries/bio/src/utils/macromolecule/types';
 
@@ -17,7 +17,7 @@ const V2000_ATOM_NAME_POS = 31;
 ): Promise<DG.Column> {
-  const uh = UnitsHandler.getOrCreate(mcol);
+  const sh = SeqHandler.forColumn(mcol);
   let molV3000Array;
   monomersDict ??= new Map();
-  const monomers = uh.isHelm() ?
-    getHelmMonomers(mcol) : Object.keys(uh.stats.freq).filter((it) => it !== '');
+  const monomers = sh.isHelm() ?
+    getHelmMonomers(mcol) : Object.keys(sh.stats.freq).filter((it) => it !== '');
 
@@ -29,3 +29,3 @@ for (let i = 0; i < monomers.length; i++) {
 
-  if (uh.isHelm()) {
+  if (sh.isHelm()) {
     molV3000Array = await grok.functions.call('HELM:getMolFiles', {col: mcol});
@@ -36,4 +36,3 @@ molV3000Array = changeV2000ToV3000(molV3000Array, monomersDict, pattern);
     for (let i = 0; i < mcol.length; i++) {
-      const sequenceMonomers = wu(uh.splitted[i]).filter((it) => it !== '').toArray();
-      const molV3000 = molV3000FromNonHelmSequence(sequenceMonomers, monomersDict, pattern);
+      const molV3000 = molV3000FromNonHelmSequence(sh.getSplitted(i), monomersDict, pattern);
       molV3000Array[i] = molV3000;
@@ -58,5 +57,8 @@ }
   for (let atomRowI = 0; atomRowI < monomers.length; atomRowI++) {
-    molV3000 += pattern ?
-      `M  V30 ${atomRowI + 1} R${monomersDict.get(monomers[atomRowI])} 0.000 0.000 0 0\n` :
-      `M  V30 ${atomRowI + 1} At 0.000 0.000 0 0 MASS=${monomersDict.get(monomers[atomRowI])}\n`;
+    const cm: string = monomers.getCanonical(atomRowI);
+    if (cm !== GAP_SYMBOL) {
+      molV3000 += pattern ?
+        `M  V30 ${atomRowI + 1} R${monomersDict.get(cm)} 0.000 0.000 0 0\n` :
+        `M  V30 ${atomRowI + 1} At 0.000 0.000 0 0 MASS=${monomersDict.get(cm)}\n`;
+    }
   }
@@ -63,0 +65,0 @@

src/package.ts

@@ -15,3 +15,3 @@ /* Do not change these import lines to match external modules in webpack configuration */
 } from '@datagrok-libraries/bio/src/utils/macromolecule';
-import {UnitsHandler} from '@datagrok-libraries/bio/src/utils/units-handler';
+import {SeqHandler} from '@datagrok-libraries/bio/src/utils/seq-handler';
 import {IMonomerLib} from '@datagrok-libraries/bio/src/types';
@@ -169,7 +169,7 @@ import {SeqPalette} from '@datagrok-libraries/bio/src/seq-palettes';
 
-//name: getUnitsHandler
+//name: getSeqHandler
 //input: column sequence { semType: Macromolecule }
 //output: object result
-export function getUnitsHandler(sequence: DG.Column<string>): UnitsHandler {
-  return UnitsHandler.getOrCreate(sequence);
+export function getSeqHandler(sequence: DG.Column<string>): SeqHandler {
+  return SeqHandler.forColumn(sequence);
 }
@@ -616,3 +616,3 @@
 
-    const _colUH = UnitsHandler.getOrCreate(col);
+    const _colSh = SeqHandler.forColumn(col);
     // TODO: prevent for cyclic, branched or multiple chains in Helm
@@ -636,3 +636,3 @@ return true;
     const colListNames: string [] = colList.map((col) => col.name);
-    const selectedCol = colList.find((c) => { return UnitsHandler.getOrCreate(c).isMsa(); });
+    const selectedCol = colList.find((c) => { return SeqHandler.forColumn(c).isMsa(); });
     const colInput: DG.InputBase = ui.choiceInput(
@@ -780,4 +780,4 @@ 'Column', selectedCol ? selectedCol.name : colListNames[0], colListNames);
 export function getHelmMonomers(sequence: DG.Column<string>): string[] {
-  const uh = UnitsHandler.getOrCreate(sequence);
-  const stats = uh.stats;
+  const sh = SeqHandler.forColumn(sequence);
+  const stats = sh.stats;
   return Object.keys(stats.freq);
@@ -784,0 +784,0 @@ }

src/tests/bio-tests.ts

@@ -7,7 +7,3 @@ import * as grok from 'datagrok-api/grok';
 import {
-  getAlphabetSimilarity,
-  monomerToShort,
-  pickUpPalette,
-  splitterAsFasta,
-  splitterAsHelm,
+  NOTATION, getAlphabetSimilarity, monomerToShort, pickUpPalette, splitterAsFasta, splitterAsHelm,
 } from '@datagrok-libraries/bio/src/utils/macromolecule';
@@ -17,3 +13,2 @@ import {Nucleotides, NucleotidesPalettes} from '@datagrok-libraries/bio/src/nucleotides';
 import {UnknownSeqPalette} from '@datagrok-libraries/bio/src/unknown';
-import {UnitsHandler} from '@datagrok-libraries/bio/src/utils/units-handler';
 import {getStatsForCol} from '@datagrok-libraries/bio/src/utils/macromolecule/utils';
@@ -68,2 +63,4 @@
     const seqCol: DG.Column = df.getCol('seq')!;
+    seqCol.semType = DG.SEMTYPE.MACROMOLECULE;
+    seqCol.setTag(DG.TAGS.UNITS, NOTATION.HELM);
     const stats = getStatsForCol(seqCol, 1, splitterAsHelm);
@@ -138,2 +135,4 @@
   const seqCol: DG.Column = dfN1.col('seq')!;
+  seqCol.semType = DG.SEMTYPE.MACROMOLECULE;
+  seqCol.setTag(DG.TAGS.UNITS, NOTATION.FASTA);
   const stats = getStatsForCol(seqCol, 5, splitterAsFasta);
@@ -167,2 +166,4 @@
   const col: DG.Column = df.col('seq')!;
+  col.semType = DG.SEMTYPE.MACROMOLECULE;
+  col.setTag(DG.TAGS.UNITS, NOTATION.FASTA);
   const cp = pickUpPalette(col);
@@ -176,2 +177,4 @@
   const col: DG.Column = df.col('seq')!;
+  col.semType = DG.SEMTYPE.MACROMOLECULE;
+  col.setTag(DG.TAGS.UNITS, NOTATION.FASTA);
   const cp = pickUpPalette(col);
@@ -185,2 +188,4 @@
   const col: DG.Column = df.col('seq')!;
+  col.semType = DG.SEMTYPE.MACROMOLECULE;
+  col.setTag(DG.TAGS.UNITS, NOTATION.FASTA);
   const cp = pickUpPalette(col);
@@ -194,2 +199,4 @@
   const col: DG.Column = df.col('seq')!;
+  col.semType = DG.SEMTYPE.MACROMOLECULE;
+  col.setTag(DG.TAGS.UNITS, NOTATION.FASTA);
   const cp = pickUpPalette(col);
@@ -196,0 +203,0 @@

src/tests/converters-test.ts

@@ -8,3 +8,3 @@ import * as DG from 'datagrok-api/dg';
 import {NOTATION} from '@datagrok-libraries/bio/src/utils/macromolecule';
-import {UnitsHandler} from '@datagrok-libraries/bio/src/utils/units-handler';
+import {SeqHandler} from '@datagrok-libraries/bio/src/utils/seq-handler';
 
@@ -137,4 +137,4 @@ // import {mmSemType} from '../const';
     return function(srcCol: DG.Column): DG.Column {
-      const converterUH = UnitsHandler.getOrCreate(srcCol);
-      const resCol = converterUH.convert(tgtNotation, tgtSeparator);
+      const converterSh = SeqHandler.forColumn(srcCol);
+      const resCol = converterSh.convert(tgtNotation, tgtSeparator);
       expect(resCol.getTag(DG.TAGS.UNITS), tgtNotation);
@@ -157,3 +157,3 @@ return resCol;
     expectArray(resCol.toList(), tgtCol.toList());
-    const _uh: UnitsHandler = UnitsHandler.getOrCreate(resCol);
+    const _sh: SeqHandler = SeqHandler.forColumn(resCol);
   }
@@ -160,0 +160,0 @@

src/tests/detectors-benchmark-tests.ts

@@ -7,3 +7,3 @@ import * as grok from 'datagrok-api/grok';
 import {ALPHABET, getAlphabet, NOTATION} from '@datagrok-libraries/bio/src/utils/macromolecule';
-import {UnitsHandler} from '@datagrok-libraries/bio/src/utils/units-handler';
+import {SeqHandler} from '@datagrok-libraries/bio/src/utils/seq-handler';
 
@@ -128,7 +128,7 @@ category('detectorsBenchmark', () => {
   function checkDetectorRes(col: DG.Column, tgt: TgtType): void {
-    const uh = UnitsHandler.getOrCreate(col);
+    const sh = SeqHandler.forColumn(col);
     expect(col.semType === tgt.semType, true);
-    expect(uh.notation === tgt.notation, true);
-    expect(uh.alphabet === tgt.alphabet, true);
-    expect(uh.separator === tgt.separator, true);
+    expect(sh.notation === tgt.notation, true);
+    expect(sh.alphabet === tgt.alphabet, true);
+    expect(sh.separator === tgt.separator, true);
   }
@@ -135,0 +135,0 @@ });

src/tests/detectors-tests.ts

@@ -9,3 +9,3 @@ import * as grok from 'datagrok-api/grok';
 import {ALIGNMENT, ALPHABET, NOTATION, TAGS as bioTAGS} from '@datagrok-libraries/bio/src/utils/macromolecule';
-import {UnitsHandler} from '@datagrok-libraries/bio/src/utils/units-handler';
+import {SeqHandler} from '@datagrok-libraries/bio/src/utils/seq-handler';
 
@@ -437,8 +437,8 @@ /*
 
-  const uh = UnitsHandler.getOrCreate(col);
-  expect(uh.getAlphabetSize(), alphabetSize);
-  expect(uh.getAlphabetIsMultichar(), alphabetIsMultichar);
-  if (!uh.isHelm()) {
-    expect(uh.aligned, aligned);
-    expect(uh.alphabet, alphabet);
+  const sh = SeqHandler.forColumn(col);
+  expect(sh.getAlphabetSize(), alphabetSize);
+  expect(sh.getAlphabetIsMultichar(), alphabetIsMultichar);
+  if (!sh.isHelm()) {
+    expect(sh.aligned, aligned);
+    expect(sh.alphabet, alphabet);
   }
@@ -466,8 +466,8 @@ }
 
-  const uh = UnitsHandler.getOrCreate(col);
-  expect(uh.getAlphabetSize(), alphabetSize);
-  expect(uh.getAlphabetIsMultichar(), alphabetIsMultichar);
-  if (!uh.isHelm()) {
-    expect(uh.aligned, aligned);
-    expect(uh.alphabet, alphabet);
+  const sh = SeqHandler.forColumn(col);
+  expect(sh.getAlphabetSize(), alphabetSize);
+  expect(sh.getAlphabetIsMultichar(), alphabetIsMultichar);
+  if (!sh.isHelm()) {
+    expect(sh.aligned, aligned);
+    expect(sh.alphabet, alphabet);
   }
@@ -474,0 +474,0 @@ }

src/tests/fasta-export-tests.ts

@@ -7,3 +7,4 @@ import * as DG from 'datagrok-api/dg';
 import {saveAsFastaDo, wrapSequence} from '../utils/save-as-fasta';
-import {splitterAsFasta} from '@datagrok-libraries/bio/src/utils/macromolecule';
+import {NOTATION, splitterAsFasta} from '@datagrok-libraries/bio/src/utils/macromolecule';
+import {SeqHandler} from '@datagrok-libraries/bio/src/utils/seq-handler';
 
@@ -91,6 +92,9 @@ type SaveAsFastaTestArgs = { srcCsv: string, idCols: string [], seqCol: string, lineWidth: number, tgtFasta: string };
   function _testWrapSequence(testKey: string, lineWidth: number = 10) {
-    const splitter = splitterAsFasta;
-
     const srcSeq: string = wrapData[testKey].src;
-    const wrapRes: string[] = wrapSequence(srcSeq, splitter, lineWidth);
+    const col = DG.Column.fromStrings('src', [srcSeq]);
+    col.semType = DG.SEMTYPE.MACROMOLECULE;
+    col.setTag(DG.TAGS.UNITS, NOTATION.FASTA);
+    const sh = SeqHandler.forColumn(col);
+    const srcSS = sh.getSplitted(0);
+    const wrapRes: string[] = wrapSequence(srcSS, lineWidth);
     const wrapTgt: string[] = wrapData[testKey].tgt;
@@ -105,2 +109,4 @@
     const seqCol: DG.Column = df.getCol(args.seqCol);
+    seqCol.semType = DG.SEMTYPE.MACROMOLECULE;
+    seqCol.setTag(DG.TAGS.UNITS, NOTATION.FASTA);
     const idCols: DG.Column[] = args.idCols.map((colName) => df.getCol(colName));
@@ -107,0 +113,0 @@

src/tests/mm-distance-tests.ts

@@ -6,3 +6,3 @@ import * as grok from 'datagrok-api/grok';
 import {category, expect, test} from '@datagrok-libraries/utils/src/test';
-import {UnitsHandler} from '@datagrok-libraries/bio/src/utils/units-handler';
+import {SeqHandler} from '@datagrok-libraries/bio/src/utils/seq-handler';
 import {MmDistanceFunctionsNames, mmDistanceFunctions}
@@ -46,4 +46,4 @@ from '@datagrok-libraries/ml/src/macromolecule-distance-functions';
   test('protein-distance-function', async () => {
-    const uh = await _initMacromoleculeColumn(protTable);
-    const distFunc = uh.getDistanceFunctionName();
+    const sh = await _initMacromoleculeColumn(protTable);
+    const distFunc = sh.getDistanceFunctionName();
     expect(distFunc, MmDistanceFunctionsNames.LEVENSHTEIN);
@@ -53,4 +53,4 @@ });
   test('DNA-distance-function', async () => {
-    const uh = await _initMacromoleculeColumn(DNATable);
-    const distFunc = uh.getDistanceFunctionName();
+    const sh = await _initMacromoleculeColumn(DNATable);
+    const distFunc = sh.getDistanceFunctionName();
     expect(distFunc, MmDistanceFunctionsNames.LEVENSHTEIN);
@@ -60,4 +60,4 @@ });
   test('MSA-distance-function', async () => {
-    const uh = await _initMacromoleculeColumn(MSATable);
-    const distFunc = uh.getDistanceFunctionName();
+    const sh = await _initMacromoleculeColumn(MSATable);
+    const distFunc = sh.getDistanceFunctionName();
     expect(distFunc, MmDistanceFunctionsNames.HAMMING);
@@ -132,3 +132,3 @@ });
 
-async function _initMacromoleculeColumn(csv: string): Promise<UnitsHandler> {
+async function _initMacromoleculeColumn(csv: string): Promise<SeqHandler> {
   const srcDf: DG.DataFrame = DG.DataFrame.fromCsv(csv);
@@ -141,4 +141,4 @@ const seqCol = srcDf.col('seq')!;
   await grok.data.detectSemanticTypes(srcDf);
-  const uh = UnitsHandler.getOrCreate(seqCol);
-  return uh;
+  const sh = SeqHandler.forColumn(seqCol);
+  return sh;
 }
@@ -145,0 +145,0 @@

src/tests/msa-tests.ts

@@ -106,9 +106,7 @@ import * as grok from 'datagrok-api/grok';
   const srcDf: DG.DataFrame = DG.DataFrame.fromCsv(srcCsv);
+  await grok.data.detectSemanticTypes(srcDf);
   const tgtDf: DG.DataFrame = DG.DataFrame.fromCsv(tgtCsv);
 
   const srcCol: DG.Column = srcDf.getCol('seq')!;
-  const semType: string = await grok.functions
-    .call('Bio:detectMacromolecule', {col: srcCol}) as unknown as string;
-  if (semType)
-    srcCol.semType = semType;
+  expect(srcCol.semType, DG.SEMTYPE.MACROMOLECULE);
 
@@ -125,20 +123,15 @@ const tgtCol: DG.Column = tgtDf.getCol('seq')!;
   const srcDf: DG.DataFrame = DG.DataFrame.fromCsv(srcCsv);
+  await grok.data.detectSemanticTypes(srcDf);
   const tgtDf: DG.DataFrame = DG.DataFrame.fromCsv(tgtCsv);
 
-  const srcSeqCol = srcDf.getCol('seq')!;
   const tgtCol = tgtDf.getCol('seq')!;
   const srcCol: DG.Column = srcDf.getCol('seq')!;
-  const semType: string = await grok.functions
-    .call('Bio:detectMacromolecule', {col: srcCol}) as unknown as string;
-  if (semType)
-    srcCol.semType = semType;
-
-  await grok.data.detectSemanticTypes(srcDf);
-  expect(srcSeqCol.semType, DG.SEMTYPE.MACROMOLECULE);
-  expect(srcSeqCol.getTag(DG.TAGS.UNITS), srcNotation);
+  expect(srcCol.semType, DG.SEMTYPE.MACROMOLECULE);
+  expect(srcCol.getTag(DG.TAGS.UNITS), srcNotation);
   if (alphabet)
-    expect(srcSeqCol.getTag(bioTAGS.alphabet), alphabet);
+    expect(srcCol.getTag(bioTAGS.alphabet), alphabet);
 
-  const msaSeqCol = await multipleSequenceAlignmentUI({col: srcSeqCol, pepsea: {method: pepseaMethod}});
+  const msaSeqCol = await multipleSequenceAlignmentUI({col: srcCol, pepsea: {method: pepseaMethod}});
   expect(msaSeqCol.semType, DG.SEMTYPE.MACROMOLECULE);
+  expect(msaSeqCol.semType, DG.SEMTYPE.MACROMOLECULE);
   expect(msaSeqCol.getTag(DG.TAGS.UNITS), tgtNotation);
@@ -145,0 +138,0 @@ expect(msaSeqCol.getTag(bioTAGS.aligned), ALIGNMENT.SEQ_MSA);

src/tests/renderers-monomer-placer.ts

@@ -9,3 +9,3 @@ import * as grok from 'datagrok-api/grok';
 import {monomerToShort} from '@datagrok-libraries/bio/src/utils/macromolecule';
-import {UnitsHandler} from '@datagrok-libraries/bio/src/utils/units-handler';
+import {SeqHandler} from '@datagrok-libraries/bio/src/utils/seq-handler';
 
@@ -97,5 +97,5 @@ import {_package} from '../package-test';
       const colTemp: MonomerPlacer = new MonomerPlacer(null, seqCol, () => {
-        const uh = UnitsHandler.getOrCreate(seqCol);
+        const sh = SeqHandler.forColumn(seqCol);
         return {
-          unitsHandler: uh,
+          seqHandler: sh,
           monomerCharWidth: charWidth,
@@ -102,0 +102,0 @@ separatorWidth: sepWidth,

src/tests/renderers-test.ts

 import * as grok from 'datagrok-api/grok';
 import * as DG from 'datagrok-api/dg';
 
-import $ from 'cash-dom';
-
-import {category, expect, test, awaitCheck, delay} from '@datagrok-libraries/utils/src/test';
+import {category, expect, test, delay} from '@datagrok-libraries/utils/src/test';
 import {ALIGNMENT, ALPHABET, NOTATION, TAGS as bioTAGS} from '@datagrok-libraries/bio/src/utils/macromolecule';
-import {UnitsHandler} from '@datagrok-libraries/bio/src/utils/units-handler';
+import {SeqHandler} from '@datagrok-libraries/bio/src/utils/seq-handler';
 
@@ -151,4 +149,4 @@ import {importFasta} from '../package';
 
-    // check newColumn with UnitsHandler constructor
-    const _uh: UnitsHandler = UnitsHandler.getOrCreate(msaSeqCol);
+    // check newColumn with SeqHandler constructor
+    const _sh: SeqHandler = SeqHandler.forColumn(msaSeqCol);
   }
@@ -176,4 +174,4 @@
 
-    // check tgtCol with UnitsHandler constructor
-    const _uh: UnitsHandler = UnitsHandler.getOrCreate(tgtCol);
+    // check tgtCol with SeqHandler constructor
+    const _sh: SeqHandler = SeqHandler.forColumn(tgtCol);
   }
@@ -180,0 +178,0 @@

src/tests/splitters-test.ts

@@ -5,11 +5,8 @@ import * as grok from 'datagrok-api/grok';
 
+import wu from 'wu';
+
 import {
-  after, before, category, test, expect, expectArray, delay, awaitCheck
+  after, before, category, test, expect, expectArray
 } from '@datagrok-libraries/utils/src/test';
-import {
-  TAGS as bioTAGS,
-  splitterAsFasta,
-  splitterAsHelm,
-  NOTATION
-} from '@datagrok-libraries/bio/src/utils/macromolecule';
+import {TAGS as bioTAGS, splitterAsFasta} from '@datagrok-libraries/bio/src/utils/macromolecule';
 
@@ -19,5 +16,9 @@ import {splitToMonomersUI} from '../utils/split-to-monomers';
 import * as C from '../utils/constants';
-
 import {getHelmMonomers} from '../package';
 
+import {splitterAsHelm} from '@datagrok-libraries/bio/src/utils/macromolecule/utils';
+import {ISeqSplitted} from '@datagrok-libraries/bio/src/utils/macromolecule/types';
+
+import {_package} from '../package-test';
+
 category('splitters', async () => {
@@ -137,3 +138,3 @@ before(async () => {
   // test('helmAsFasta', async () => {
-  //   // The columns can't be empty for UnitsHandler
+  //   // The columns can't be empty for SeqHandler
   //   /* eslint-disable max-len */
@@ -149,11 +150,11 @@ //   const srcSeq = '[meI][Pip][dK][Thr_PO3H2][L-hArg(Et,Et)][D-Tyr_Et][Tyr_ab-dehydroMe][dV]EN[D-Orn][D-aThr][Phe_4Me]';
 export async function _testFastaSplitter(src: string, tgt: string[]) {
-  const res: string[] = splitterAsFasta(src);
+  const res: ISeqSplitted = splitterAsFasta(src);
   console.debug(`Bio: tests: splitters: src=${JSON.stringify(src)}, res=${JSON.stringify(res)} .`);
-  expectArray(res, tgt);
+  expectArray(wu(res.originals).toArray(), tgt);
 }
 
 export async function _testHelmSplitter(src: string, tgt: string[]) {
-  const res: string[] = splitterAsHelm(src);
+  const res: ISeqSplitted = splitterAsHelm(src);
   console.debug(`Bio: tests: splitters: src=${JSON.stringify(src)}, res=${JSON.stringify(res)} .`);
-  expectArray(res, tgt);
+  expectArray(wu(res.originals).toArray(), tgt);
 }

src/tests/to-atomic-level-tests.ts

@@ -17,3 +17,3 @@ /* Do not change these import lines to match external modules in webpack configuration */
 import {UserLibSettings} from '@datagrok-libraries/bio/src/monomer-works/types';
-import {UnitsHandler} from '@datagrok-libraries/bio/src/utils/units-handler';
+import {SeqHandler} from '@datagrok-libraries/bio/src/utils/seq-handler';
 
@@ -202,3 +202,3 @@ import {toAtomicLevel} from '../package';
     seqCol.setTag(bioTAGS.alphabet, ALPHABET.PT);
-    const uh = UnitsHandler.getOrCreate(seqCol);
+    const sh = SeqHandler.forColumn(seqCol);
     const resCol = (await _testToAtomicLevel(srcDf, 'seq', monomerLibHelper))!;
@@ -205,0 +205,0 @@ expect(polishMolfile(resCol.get(0)), polishMolfile(tgtMol));

src/tests/units-handler-get-region.ts

@@ -5,6 +5,6 @@ import * as grok from 'datagrok-api/grok';
 import {category, expect, expectArray, test} from '@datagrok-libraries/utils/src/test';
-import {UnitsHandler} from '@datagrok-libraries/bio/src/utils/units-handler';
+import {SeqHandler} from '@datagrok-libraries/bio/src/utils/seq-handler';
 import {ALPHABET, NOTATION, TAGS} from '@datagrok-libraries/bio/src/utils/macromolecule';
 
-category('UnitsHandler: getRegion', () => {
+category('SeqHandler: getRegion', () => {
   const data: {
@@ -80,4 +80,4 @@ [testName: string]: {
 
-      const srcUh = UnitsHandler.getOrCreate(srcSeqCol);
-      const resSeqCol = srcUh.getRegion(testData.startIdx, testData.endIdx, 'regSeq');
+      const srcSh = SeqHandler.forColumn(srcSeqCol);
+      const resSeqCol = srcSh.getRegion(testData.startIdx, testData.endIdx, 'regSeq');
 
@@ -84,0 +84,0 @@ const tgtDf = DG.DataFrame.fromCsv(testData.tgtCsv);

src/tests/units-handler-splitted-tests.ts

 import * as grok from 'datagrok-api/grok';
 import * as DG from 'datagrok-api/dg';
 
+import wu from 'wu';
+
 import {category, expect, expectArray, test} from '@datagrok-libraries/utils/src/test';
-import {GapSymbols, UnitsHandler} from '@datagrok-libraries/bio/src/utils/units-handler';
+import {GapOriginals, SeqHandler} from '@datagrok-libraries/bio/src/utils/seq-handler';
 import {NOTATION} from '@datagrok-libraries/bio/src/utils/macromolecule';
-import {ISeqSplitted} from '@datagrok-libraries/bio/src/utils/macromolecule/types';
 
@@ -17,6 +18,6 @@ enum Tests {
 
-category('UnitsHandler', () => {
-  const fG = GapSymbols[NOTATION.FASTA];
-  const hG = GapSymbols[NOTATION.HELM];
-  const sG = GapSymbols[NOTATION.SEPARATOR];
+category('SeqHandler', () => {
+  const fG = GapOriginals[NOTATION.FASTA];
+  const hG = GapOriginals[NOTATION.HELM];
+  const sG = GapOriginals[NOTATION.SEPARATOR];
   const data: {
@@ -38,5 +39,5 @@ [testName: string]: {
         splitted: [
-          'ACGTCACGTC',
-          'CAGTGTCAGTGT',
-          'TTCAACTTCAAC',
+          ['A', 'C', 'G', 'T', 'C', 'A', 'C', 'G', 'T', 'C'],
+          ['C', 'A', 'G', 'T', 'G', 'T', 'C', 'A', 'G', 'T', 'G', 'T'],
+          ['T', 'T', 'C', 'A', 'A', 'C', 'T', 'T', 'C', 'A', 'A', 'C'],
         ]
@@ -56,5 +57,5 @@ }
           //@formatter:off
-          'AC-GT-CTAC-GT-CT',
-          'CAC-T-GTCAC-T-GT',
-          'ACCGTACTACCGTACT',
+          ['A', 'C', '-', 'G', 'T', '-', 'C', 'T', 'A', 'C', '-', 'G', 'T', '-', 'C', 'T'],
+          ['C', 'A', 'C', '-', 'T', '-', 'G', 'T', 'C', 'A', 'C', '-', 'T', '-', 'G', 'T'],
+          ['A', 'C', 'C', 'G', 'T', 'A', 'C', 'T', 'A', 'C', 'C', 'G', 'T', 'A', 'C', 'T'],
           //@formatter:on
@@ -135,10 +136,11 @@ ]
 
-      const uh = UnitsHandler.getOrCreate(col);
-      expect(uh.notation, testData.tgt.notation);
-      expect(uh.separator === testData.tgt.separator, true);
+      const sh = SeqHandler.forColumn(col);
+      expect(sh.notation, testData.tgt.notation);
+      expect(sh.separator === testData.tgt.separator, true);
 
-      const resSplitted: ISeqSplitted[] = uh.splitted;
+      const resSplitted: string[][] = wu.count(0).take(sh.length)
+        .map((rowIdx) => wu(sh.getSplitted(rowIdx).originals).toArray()).toArray();
       expectArray(resSplitted, testData.tgt.splitted);
-    }, testName == Tests.separatorMsa ? {skipReason: '#2468 CSV row starting with the quote character'} : undefined);
+    });
   }
 });

src/tests/units-handler-tests.ts

@@ -6,4 +6,4 @@ import * as grok from 'datagrok-api/grok';
 import {category, test, expect} from '@datagrok-libraries/utils/src/test';
-import {UnitsHandler} from '@datagrok-libraries/bio/src/utils/units-handler';
-import {ALPHABET, NOTATION, TAGS} from '@datagrok-libraries/bio/src/utils/macromolecule';
+import {SeqHandler} from '@datagrok-libraries/bio/src/utils/seq-handler';
+import {ALPHABET, NOTATION} from '@datagrok-libraries/bio/src/utils/macromolecule';
 
@@ -31,56 +31,56 @@ const seqDna = `seq
 
-category('UnitsHandler', () => {
+category('SeqHandler', () => {
   test('Seq-Fasta', async () => {
-    const [_df, uh] = await loadCsvWithDetection(seqDna);
-    expect(uh.notation, NOTATION.FASTA);
-    expect(uh.isMsa(), false);
+    const [_df, sh] = await loadCsvWithDetection(seqDna);
+    expect(sh.notation, NOTATION.FASTA);
+    expect(sh.isMsa(), false);
   });
 
   test('Seq-Fasta-MSA', async () => {
-    const [_df, uh] = await loadCsvWithDetection(seqDnaMsa);
-    expect(uh.notation, NOTATION.FASTA);
-    expect(uh.isMsa(), true);
+    const [_df, sh] = await loadCsvWithDetection(seqDnaMsa);
+    expect(sh.notation, NOTATION.FASTA);
+    expect(sh.isMsa(), true);
   });
 
   test('Seq-Fasta-units', async () => {
-    const [_df, uh] = await loadCsvWithDetection(seqDna);
-    expect(uh.notation, NOTATION.FASTA);
-    expect(uh.isMsa(), false);
+    const [_df, sh] = await loadCsvWithDetection(seqDna);
+    expect(sh.notation, NOTATION.FASTA);
+    expect(sh.isMsa(), false);
   });
 
   test('Seq-Fasta-MSA-units', async () => {
-    const [_df, uh] = await loadCsvWithDetection(seqDnaMsa);
-    expect(uh.notation, NOTATION.FASTA);
-    expect(uh.isMsa(), true);
+    const [_df, sh] = await loadCsvWithDetection(seqDnaMsa);
+    expect(sh.notation, NOTATION.FASTA);
+    expect(sh.isMsa(), true);
   });
 
   test('Seq-Helm', async () => {
-    const [_df, uh] = await loadCsvWithDetection(seqHelm);
-    expect(uh.notation, NOTATION.HELM);
-    expect(uh.isHelm(), true);
+    const [_df, sh] = await loadCsvWithDetection(seqHelm);
+    expect(sh.notation, NOTATION.HELM);
+    expect(sh.isHelm(), true);
   });
 
   test('Seq-UN', async () => {
-    const [_df, uh] = await loadCsvWithDetection(seqUn);
-    expect(uh.notation, NOTATION.SEPARATOR);
-    expect(uh.separator, '-');
-    expect(uh.alphabet, ALPHABET.UN);
+    const [_df, sh] = await loadCsvWithDetection(seqUn);
+    expect(sh.notation, NOTATION.SEPARATOR);
+    expect(sh.separator, '-');
+    expect(sh.alphabet, ALPHABET.UN);
   });
 
   test('Seq-UN-auto', async () => {
-    const [_df, uh] = await loadCsvWithDetection(seqUn);
-    expect(uh.notation, NOTATION.SEPARATOR);
-    expect(uh.separator, '-');
-    expect(uh.alphabet, ALPHABET.UN);
+    const [_df, sh] = await loadCsvWithDetection(seqUn);
+    expect(sh.notation, NOTATION.SEPARATOR);
+    expect(sh.separator, '-');
+    expect(sh.alphabet, ALPHABET.UN);
   });
 
-  async function loadCsvWithDetection(csv: string): Promise<[df: DG.DataFrame, uh: UnitsHandler]> {
+  async function loadCsvWithDetection(csv: string): Promise<[df: DG.DataFrame, sh: SeqHandler]> {
     const df = DG.DataFrame.fromCsv(csv);
     await grok.data.detectSemanticTypes(df);
-    const uh = UnitsHandler.getOrCreate(df.getCol('seq'));
-    return [df, uh];
+    const sh = SeqHandler.forColumn(df.getCol('seq'));
+    return [df, sh];
   }
 
   // async function loadCsvWithTag(csv: string, tag: string, value: string):
-  //   Promise<[df: DG.DataFrame, uh: UnitsHandler]> {
+  //   Promise<[df: DG.DataFrame, uh: SeqHandler]> {
   //   const df = DG.DataFrame.fromCsv(csv);
@@ -92,5 +92,5 @@ //   const col = df.getCol('seq');
   //     col.setTag(TAGS.separator, '-');
-  //   const uh = UnitsHandler.getOrCreate(df.getCol('seq'));
-  //   return [df, uh];
+  //   const sh = SeqHandler.forColumn(df.getCol('seq'));
+  //   return [df, sh];
   // }
 });

src/tests/WebLogo-layout-tests.ts

@@ -7,6 +7,6 @@ import * as DG from 'datagrok-api/dg';
 
-import {category, expect, test, testViewer} from '@datagrok-libraries/utils/src/test';
+import {category, delay, expect, test} from '@datagrok-libraries/utils/src/test';
 
 import {awaitGrid} from './utils';
-import {WebLogoViewer} from '../viewers/web-logo-viewer';
+import {Debounces, WebLogoViewer} from '../viewers/web-logo-viewer';
 
@@ -24,2 +24,4 @@ import {_package} from '../package-test';
     view.dockManager.dock(wlViewer);
+
+    await delay(Debounces.render * 2);
     await wlViewer.awaitRendered();
@@ -31,2 +33,3 @@ await awaitGrid(view.grid);
     view.loadLayout(viewLayout);
+    await delay(Debounces.render * 2);
     await wlViewer.awaitRendered();
@@ -33,0 +36,0 @@ await awaitGrid(view.grid);

src/tests/WebLogo-positions-test.ts

@@ -6,2 +6,5 @@ import * as grok from 'datagrok-api/grok';
 import {ALPHABET, NOTATION, TAGS as bioTAGS} from '@datagrok-libraries/bio/src/utils/macromolecule';
+import {SeqHandler} from '@datagrok-libraries/bio/src/utils/seq-handler';
+import {GAP_SYMBOL} from '@datagrok-libraries/bio/src/utils/macromolecule/types';
+
 import {
@@ -13,6 +16,3 @@ countForMonomerAtPosition,
 } from '../viewers/web-logo-viewer';
-import {UnitsHandler} from '@datagrok-libraries/bio/src/utils/units-handler';
 
-import {GAP_SYMBOL} from '../const';
-
 const g: string = GAP_SYMBOL;
@@ -187,4 +187,4 @@
     const atPI1: PI = resPosList[1];
-    const uh = UnitsHandler.getOrCreate(seqCol);
-    const countAt1 = countForMonomerAtPosition(df, uh, df.filter, 'G', atPI1);
+    const sh = SeqHandler.forColumn(seqCol);
+    const countAt1 = countForMonomerAtPosition(df, sh, df.filter, 'G', atPI1);
     expect(countAt1, 5);
@@ -191,0 +191,0 @@ await wlViewer.awaitRendered();

src/utils/cell-renderer.ts

@@ -19,3 +19,6 @@ import * as grok from 'datagrok-api/grok';
 import {UnknownSeqPalettes} from '@datagrok-libraries/bio/src/unknown';
-import {UnitsHandler} from '@datagrok-libraries/bio/src/utils/units-handler';
+import {GapOriginals, SeqHandler} from '@datagrok-libraries/bio/src/utils/seq-handler';
+import {ISeqSplitted} from '@datagrok-libraries/bio/src/utils/macromolecule/types';
+import {getSplitter} from '@datagrok-libraries/bio/src/utils/macromolecule/utils';
+import {errInfo} from '@datagrok-libraries/bio/src/utils/err-info';
 
@@ -29,7 +32,3 @@ import {
 import {_package, getBioLib} from '../package';
-import {ISeqSplitted} from '@datagrok-libraries/bio/src/utils/macromolecule/types';
-import {getSplitter} from '@datagrok-libraries/bio/src/utils/macromolecule/utils';
-import {errInfo} from '@datagrok-libraries/bio/src/utils/err-info';
 
-
 type TempType = { [tagName: string]: any };
@@ -44,3 +43,3 @@
 
-export function processSequence(subParts: ISeqSplitted): [string[], boolean] {
+export function processSequence(subParts: string[]): [string[], boolean] {
   const simplified = !wu.enumerate(subParts).some(([amino, index]) =>
@@ -105,2 +104,3 @@ amino.length > 1 &&
       if (seqColTemp._monomerStructureMap[monomerSymbol]) {
+        //
         tooltipElements.push(seqColTemp._monomerStructureMap[monomerSymbol]);
@@ -118,2 +118,3 @@ } else {
     } else {
+      //
       ui.tooltip.hide();
@@ -171,6 +172,6 @@ }
         () => {
-          const uh = UnitsHandler.getOrCreate(tableCol);
+          const sh = SeqHandler.forColumn(tableCol);
           return {
-            unitsHandler: uh,
-            monomerCharWidth: 7, separatorWidth: !uh.isMsa() ? gapLength : msaGapLength,
+            seqHandler: sh,
+            monomerCharWidth: 7, separatorWidth: !sh.isMsa() ? gapLength : msaGapLength,
             monomerToShort: monomerToShortFunction, monomerLengthLimit: maxLengthOfMonomer,
@@ -202,2 +203,3 @@ monomerLib: getBioLib()
       const value: any = gridCell.cell.value;
+      const rowIdx = gridCell.cell.rowIndex;
       const paletteType = tableCol.getTag(bioTAGS.alphabet);
@@ -220,4 +222,3 @@ const minDistanceRenderer = 50;
       const splitLimit = w / 5;
-      const uh = UnitsHandler.getOrCreate(tableCol);
-      const splitterFunc: SplitterFunc = uh.getSplitter(splitLimit);
+      const sh = SeqHandler.forColumn(tableCol);
 
@@ -228,7 +229,12 @@ const tempReferenceSequence: string | null = tableColTemp[tempTAGS.referenceSequence];
         tableColTemp[tempTAGS.currentWord] = null;
-      const referenceSequence: ISeqSplitted = splitterFunc(
-        ((tempReferenceSequence != null) && (tempReferenceSequence != '')) ?
-          tempReferenceSequence : tempCurrentWord ?? '');
 
-      const subParts: ISeqSplitted = splitterFunc(value);
+      const referenceSequence: string[] = (() => {
+        // @ts-ignore
+        const splitterFunc: SplitterFunc = sh.getSplitter(splitLimit);
+        return wu(splitterFunc(
+          ((tempReferenceSequence != null) && (tempReferenceSequence != '')) ?
+            tempReferenceSequence : tempCurrentWord ?? '').originals).toArray();
+      })();
+
+      const subParts: ISeqSplitted = sh.getSplitted(rowIdx);
       /* let x1 = x; */
@@ -241,10 +247,11 @@ let color = undefinedColor;
 
-      for (const [amino, index] of wu.enumerate(subParts)) {
+      for (let posIdx: number = 0; posIdx < subParts.length; ++posIdx) {
+        const amino: string = subParts.getOriginal(posIdx);
         color = palette.get(amino);
         g.fillStyle = undefinedColor;
-        const last = index === subParts.length - 1;
+        const last = posIdx === subParts.length - 1;
         /*x1 = */
         printLeftOrCentered(x + this.padding, y, w, h,
           g, amino, color, 0, true, 1.0, separator, last, drawStyle,
-          maxLengthWordsSum, index, gridCell, referenceSequence, maxLengthOfMonomer, seqColTemp._monomerLengthMap);
+          maxLengthWordsSum, posIdx, gridCell, referenceSequence, maxLengthOfMonomer, seqColTemp._monomerLengthMap);
         if (minDistanceRenderer > w) break;
@@ -298,4 +305,4 @@ }
     const splitter = getSplitter(units, separator);
-    const subParts1 = splitter(s1);
-    const subParts2 = splitter(s2);
+    const subParts1 = wu(splitter(s1).canonicals).toArray();
+    const subParts2 = wu(splitter(s2).canonicals).toArray();
     drawMoleculeDifferenceOnCanvas(g, x, y, w, h, subParts1, subParts2, units);
@@ -311,4 +318,4 @@ }
   h: number,
-  subParts1: ISeqSplitted,
-  subParts2: ISeqSplitted,
+  subParts1: string[],
+  subParts2: string[],
   units: string,
@@ -319,3 +326,3 @@ fullStringLength?: boolean,
   if (subParts1.length !== subParts2.length) {
-    const sequences: IComparedSequences = fillShorterSequence(wu(subParts1).toArray(), wu(subParts2).toArray());
+    const sequences: IComparedSequences = fillShorterSequence(subParts1, subParts2);
     subParts1 = sequences.subParts1;
@@ -359,3 +366,6 @@ subParts2 = sequences.subParts2;
         molDifferences[i] = createDifferenceCanvas(amino1, amino2, color1, color2, updatedY, vShift, h);
-    } else { updatedX = printLeftOrCentered(updatedX, updatedY, w, h, g, amino1, color1, 0, true, 0.5); }
+    } else {
+      //
+      updatedX = printLeftOrCentered(updatedX, updatedY, w, h, g, amino1, color1, 0, true, 0.5);
+    }
     updatedX += 4;
@@ -371,10 +381,5 @@ }
 
-function createDifferenceCanvas(
-  amino1: string,
-  amino2: string,
-  color1: string,
-  color2: string,
-  y: number,
-  shift: number,
-  h: number): HTMLCanvasElement {
+function createDifferenceCanvas(amino1: string, amino2: string, color1: string, color2: string,
+  y: number, shift: number, h: number
+): HTMLCanvasElement {
   const canvas = document.createElement('canvas');
@@ -412,3 +417,4 @@ const context = canvas.getContext('2d')!;
 
-  const emptyMonomersArray = new Array<string>(Math.abs(subParts1.length - subParts2.length)).fill('');
+  const emptyMonomersArray = new Array<string>(Math.abs(subParts1.length - subParts2.length))
+    .fill(GapOriginals[NOTATION.FASTA]);
 
@@ -421,4 +427,4 @@ function concatWithEmptyVals(subparts: string[]): string[] {
   subParts1.length > subParts2.length ?
-    subParts2 = concatWithEmptyVals(subParts2) : subParts1 = concatWithEmptyVals(subParts1);
+    subParts2 = concatWithEmptyVals(wu(subParts2).toArray()) : subParts1 = concatWithEmptyVals(wu(subParts1).toArray());
   return {subParts1: subParts1, subParts2: subParts2};
 }

src/utils/check-input-column.ts

@@ -5,3 +5,3 @@ import * as grok from 'datagrok-api/grok';
 
-import {UnitsHandler} from '@datagrok-libraries/bio/src/utils/units-handler';
+import {SeqHandler} from '@datagrok-libraries/bio/src/utils/seq-handler';
 
@@ -39,3 +39,3 @@ /**
 
-  const uh = UnitsHandler.getOrCreate(col);
+  const sh = SeqHandler.forColumn(col);
   if (col.semType !== DG.SEMTYPE.MACROMOLECULE) {
@@ -45,3 +45,3 @@ grok.shell.warning(name + ' analysis is allowed for Macromolecules semantic type');
   } else {
-    const notation: string = uh.notation;
+    const notation: string = sh.notation;
     if (allowedNotations.length > 0 &&
@@ -54,5 +54,5 @@ !allowedNotations.some((n) => notation.toUpperCase() == (n.toUpperCase()))
       res = false;
-    } else if (!uh.isHelm()) {
+    } else if (!sh.isHelm()) {
       // alphabet is not specified for 'helm' notation
-      const alphabet: string = uh.alphabet;
+      const alphabet: string = sh.alphabet;
       if (
@@ -59,0 +59,0 @@ allowedAlphabets.length > 0 &&

src/utils/context-menu.ts

@@ -5,3 +5,3 @@ import * as grok from 'datagrok-api/grok';
 
-import {UnitsHandler} from '@datagrok-libraries/bio/src/utils/units-handler';
+import {SeqHandler} from '@datagrok-libraries/bio/src/utils/seq-handler';
 import {NOTATION} from '@datagrok-libraries/bio/src/utils/macromolecule';
@@ -13,11 +13,14 @@
 export function addCopyMenuUI(cell: DG.Cell, menu: DG.Menu): void {
-  const uh = UnitsHandler.getOrCreate(cell.column);
-  const tgtNotationList: string[] = Object.values(NOTATION).filter((v) => v !== uh.units);
+  const sh = SeqHandler.forColumn(cell.column);
+  const tgtNotationList: string[] = Object.values(NOTATION).filter((v) => v !== sh.units);
 
   menu.group('Copy')
     .items(tgtNotationList, (tgtNotation) => {
-      const ncUH = UnitsHandler.getOrCreate(cell.column);
+      const srcCol = cell.column;
+      const srcRowIdx = cell.rowIndex;
+      const srcSh = SeqHandler.forColumn(srcCol);
       const separator = tgtNotation === NOTATION.SEPARATOR ? _package.properties.DefaultSeparator : undefined;
-      const converter = ncUH.getConverter(tgtNotation as NOTATION, separator);
-      const tgtSeq = converter(cell.value);
+      const joiner = srcSh.getJoiner({notation: tgtNotation as NOTATION, separator});
+      const srcSS = srcSh.getSplitted(srcRowIdx);
+      const tgtSeq = joiner(srcSS);
 
@@ -24,0 +27,0 @@ if (!navigator.clipboard) {

src/utils/convert.ts

@@ -7,7 +7,7 @@ import * as DG from 'datagrok-api/dg';
 import {Subscription} from 'rxjs';
-import {NOTATION, TAGS as bioTAGS} from '@datagrok-libraries/bio/src/utils/macromolecule';
-import {UnitsHandler} from '@datagrok-libraries/bio/src/utils/units-handler';
-import {expect} from '@datagrok-libraries/utils/src/test';
 
+import {NOTATION} from '@datagrok-libraries/bio/src/utils/macromolecule';
+import {SeqHandler} from '@datagrok-libraries/bio/src/utils/seq-handler';
 
+
 let convertDialog: DG.Dialog | null = null;
@@ -25,4 +25,4 @@ let convertDialogSubs: Subscription[] = [];
     throw new Error('No column with Macromolecule semantic type found');
-  let converterUH = UnitsHandler.getOrCreate(tgtCol);
-  let currentNotation: NOTATION = converterUH.notation;
+  let converterSh = SeqHandler.forColumn(tgtCol);
+  let currentNotation: NOTATION = converterSh.notation;
   const dialogHeader = ui.divText(
@@ -51,4 +51,4 @@ 'Current notation: ' + currentNotation,
     tgtCol = newCol;
-    converterUH = UnitsHandler.getOrCreate(tgtCol);
-    currentNotation = converterUH.notation;
+    converterSh = SeqHandler.forColumn(tgtCol);
+    currentNotation = converterSh.notation;
     if (currentNotation === NOTATION.HELM)
@@ -122,4 +122,4 @@ separatorInput.value = '/'; // helm monomers can have - in the name like D-aThr;
 export async function convertDo(srcCol: DG.Column, targetNotation: NOTATION, separator?: string): Promise<DG.Column> {
-  const converterUH = UnitsHandler.getOrCreate(srcCol);
-  const newColumn = converterUH.convert(targetNotation, separator);
+  const converterSh = SeqHandler.forColumn(srcCol);
+  const newColumn = converterSh.convert(targetNotation, separator);
   srcCol.dataFrame.columns.add(newColumn);
@@ -126,0 +126,0 @@

src/utils/get-region-func-editor.ts

@@ -6,3 +6,6 @@ import * as grok from 'datagrok-api/grok';
 import {TAGS as bioTAGS} from '@datagrok-libraries/bio/src/utils/macromolecule';
+import {SeqHandler} from '@datagrok-libraries/bio/src/utils/seq-handler';
 
+import {_package} from '../package';
+
 export interface GetRegionParams {
@@ -16,5 +19,2 @@ table: DG.DataFrame,
 
-import {UnitsHandler} from '@datagrok-libraries/bio/src/utils/units-handler';
-import {_package} from '../package';
-
 export interface SeqRegion {
@@ -75,3 +75,3 @@ name: string,
     const seqCol = this.inputs.sequence.value;
-    const uh = seqCol ? UnitsHandler.getOrCreate(seqCol) : null;
+    const sh = seqCol ? SeqHandler.forColumn(seqCol) : null;
     this.updateRegionItems();
@@ -95,5 +95,5 @@ this.updateStartEndInputItems();
       } else {
-        const uh = UnitsHandler.getOrCreate(this.inputs.sequence.value!);
-        this.inputs.start.value = uh.posList[0];
-        this.inputs.end.value = uh.posList[uh.posList.length - 1];
+        const sh = SeqHandler.forColumn(this.inputs.sequence.value!);
+        this.inputs.start.value = sh.posList[0];
+        this.inputs.end.value = sh.posList[sh.posList.length - 1];
       }
@@ -129,3 +129,3 @@ } finally {
     const seqCol = this.inputs.sequence.value;
-    const uh = seqCol ? UnitsHandler.getOrCreate(seqCol) : null;
+    const sh = seqCol ? SeqHandler.forColumn(seqCol) : null;
 
@@ -136,3 +136,3 @@ const startSE = (this.inputs.start.input as HTMLSelectElement);
     for (let i = endSE.options.length - 1; i >= 0; --i) endSE.options.remove(i);
-    for (const pos of uh?.posList ?? []) {
+    for (const pos of sh?.posList ?? []) {
       const startPosOE = document.createElement('option');
@@ -145,4 +145,4 @@ const endPosOE = document.createElement('option');
     }
-    startSE.value = uh?.posList[0] ?? '';
-    endSE.value = uh?.posList[uh?.posList.length - 1] ?? '';
+    startSE.value = sh?.posList[0] ?? '';
+    endSE.value = sh?.posList[sh?.posList.length - 1] ?? '';
   }
@@ -149,0 +149,0 @@

src/utils/get-region.ts

@@ -5,14 +5,12 @@ import * as grok from 'datagrok-api/grok';
 
-import {TAGS as bioTAGS} from '@datagrok-libraries/bio/src/utils/macromolecule';
-import {UnitsHandler} from '@datagrok-libraries/bio/src/utils/units-handler';
-import {getRegion} from '../package';
+import {SeqHandler} from '@datagrok-libraries/bio/src/utils/seq-handler';
 import {TaskBarProgressIndicator} from 'datagrok-api/dg';
 
 export function getRegionUI(col: DG.Column<string>): void {
-  const uh = UnitsHandler.getOrCreate(col);
+  const sh = SeqHandler.forColumn(col);
 
   const nameInput = ui.stringInput('Name', '');
-  const startPositionInput = ui.choiceInput('Start Position', uh.posList[0], uh.posList,
+  const startPositionInput = ui.choiceInput('Start Position', sh.posList[0], sh.posList,
     () => { /* TODO: update name placeholder with getDefaultName() */ });
-  const endPositionInput = ui.choiceInput('End Position', uh.posList[uh.posList.length], uh.posList,
+  const endPositionInput = ui.choiceInput('End Position', sh.posList[sh.posList.length], sh.posList,
     () => { /* TODO: update name placeholder with getDefaultName() */ });
@@ -45,3 +43,3 @@
 ): DG.Column<string> {
-  const uh = UnitsHandler.getOrCreate(col);
+  const sh = SeqHandler.forColumn(col);
 
@@ -51,5 +49,5 @@ let startPosIdx: number | null = null;
 
-  for (let posJ: number = 0; posJ < uh.posList.length; ++posJ) {
-    if (uh.posList[posJ] == startPosName) startPosIdx = posJ;
-    if (uh.posList[posJ] == endPosName) endPosIdx = posJ;
+  for (let posJ: number = 0; posJ < sh.posList.length; ++posJ) {
+    if (sh.posList[posJ] == startPosName) startPosIdx = posJ;
+    if (sh.posList[posJ] == endPosName) endPosIdx = posJ;
   }
@@ -61,3 +59,3 @@ if (startPosIdx === null && startPosName !== null)
 
-  if (uh.posList.length < endPosIdx!)
+  if (sh.posList.length < endPosIdx!)
     throw new Error(`End position ${endPosIdx} exceeds positions length`);
@@ -67,4 +65,4 @@
 
-  const regCol = uh.getRegion(startPosIdx, endPosIdx, regColName);
+  const regCol = sh.getRegion(startPosIdx, endPosIdx, regColName);
   return regCol;
 }

src/utils/macromolecule-column-widget.ts

@@ -6,6 +6,7 @@ import * as grok from 'datagrok-api/grok';
 import {TAGS as wlTAGS} from '@datagrok-libraries/bio/src/viewers/web-logo';
+import {SeqHandler} from '@datagrok-libraries/bio/src/utils/seq-handler';
+
 import {WebLogoViewer} from '../viewers/web-logo-viewer';
 
 import {_package} from '../package';
-import {UnitsHandler} from '@datagrok-libraries/bio/src/utils/units-handler';
 
@@ -27,3 +28,3 @@ /** Used in Macromolecule column tooltip */
   async init(): Promise<void> {
-    const uh = UnitsHandler.getOrCreate(this.seqCol);
+    const sh = SeqHandler.forColumn(this.seqCol);
     const pkgTooltipWebLogo = _package.properties.TooltipWebLogo;
@@ -37,3 +38,3 @@ const colTooltipWebLogo = this.seqCol.getTag(wlTAGS.tooltipWebLogo);
         positionHeight: 'Entropy',
-        positionWidth: (uh.getAlphabetIsMultichar() ? 24 : 16),
+        positionWidth: (sh.getAlphabetIsMultichar() ? 24 : 16),
         fixWidth: true,
@@ -40,0 +41,0 @@ fitArea: false,

src/utils/monomer-lib/library-file-manager/event-manager.ts

@@ -29,3 +29,3 @@ import * as rxjs from 'rxjs';
     return new Promise((resolve) => {
-      this._libraryFilesUpdateSubject$.pipe(
+      this._libraryFilesUpdateSubject$.pipe<string[]>(
         skip(1)
@@ -32,0 +32,0 @@ ).subscribe((fileNames) => {

src/utils/multiple-sequence-alignment-ui.ts

@@ -6,3 +6,3 @@ import * as grok from 'datagrok-api/grok';
 import {ALPHABET, NOTATION} from '@datagrok-libraries/bio/src/utils/macromolecule';
-import {UnitsHandler} from '@datagrok-libraries/bio/src/utils/units-handler';
+import {SeqHandler} from '@datagrok-libraries/bio/src/utils/seq-handler';
 import {ColumnInputOptions} from '@datagrok-libraries/utils/src/type-declarations';
@@ -164,5 +164,5 @@
       terminalGapInput.value = null;
-      const potentialColUH = UnitsHandler.getOrCreate(col);
-      const performCol: DG.Column<string> = potentialColUH.isFasta() ? col :
-        potentialColUH.convert(NOTATION.FASTA);
+      const potentialColSh = SeqHandler.forColumn(col);
+      const performCol: DG.Column<string> = potentialColSh.isFasta() ? col :
+        potentialColSh.convert(NOTATION.FASTA);
       return async () => await runKalign(performCol, false, unusedName, clustersColInput.value);
@@ -183,4 +183,4 @@ } else if (checkInputColumnUI(col, col.name,
       //if the column is separator with unknown alphabet, it might be helm. check if it can be converted to helm
-      const potentialColUH = UnitsHandler.getOrCreate(col);
-      const helmCol = potentialColUH.convert(NOTATION.HELM);
+      const potentialColSh = SeqHandler.forColumn(col);
+      const helmCol = potentialColSh.convert(NOTATION.HELM);
       switchDialog(pepseaInputRootStyles, kalignInputRootStyles, 'pepsea');
@@ -187,0 +187,0 @@ gapOpenInput.value ??= msaDefaultOptions.pepsea.gapOpen;

src/utils/pepsea.ts

@@ -135,2 +135,3 @@ /* Do not change these import lines to match external modules in webpack configuration */
   } else {
+    // @ts-ignore
     const responseStr = await grok.dapi.docker.dockerContainers.request(dockerfileId, path, params)!;
@@ -137,0 +138,0 @@ if (!responseStr)

src/utils/poly-tool/transformation.ts

@@ -6,3 +6,3 @@ import * as grok from 'datagrok-api/grok';
 import {NOTATION} from '@datagrok-libraries/bio/src/utils/macromolecule';
-import {UnitsHandler} from '@datagrok-libraries/bio/src/utils/units-handler';
+import {SeqHandler} from '@datagrok-libraries/bio/src/utils/seq-handler';
 import {ALIGNMENT, ALPHABET} from '@datagrok-libraries/bio/src/utils/macromolecule';
@@ -228,4 +228,4 @@
   const df = molColumn.dataFrame;
-  const uh = UnitsHandler.getOrCreate(molColumn);
-  const sourceHelmCol = uh.convert(NOTATION.HELM);
+  const sh = SeqHandler.forColumn(molColumn);
+  const sourceHelmCol = sh.convert(NOTATION.HELM);
   const pt = PolymerTransformation.getInstance(sourceHelmCol);
@@ -232,0 +232,0 @@ const fileSource = new DG.FileSource(RULES_PATH);

src/utils/save-as-fasta.ts

@@ -6,4 +6,4 @@ import * as DG from 'datagrok-api/dg';
 import wu from 'wu';
-import {splitterAsFasta, SplitterFunc} from '@datagrok-libraries/bio/src/utils/macromolecule';
-import {UnitsHandler} from '@datagrok-libraries/bio/src/utils/units-handler';
+import {SeqHandler} from '@datagrok-libraries/bio/src/utils/seq-handler';
+import {ISeqSplitted} from '@datagrok-libraries/bio/src/utils/macromolecule/types';
 
@@ -32,4 +32,4 @@ const FASTA_LINE_WIDTH = 60;
       if (col && col.semType === DG.SEMTYPE.MACROMOLECULE) {
-        const uh = UnitsHandler.getOrCreate(col);
-        return uh.isFasta();
+        const sh = SeqHandler.forColumn(col);
+        return sh.isFasta();
       }
@@ -82,13 +82,12 @@ return false;
 ): string {
-  const splitter: SplitterFunc = splitterAsFasta;
-
+  const sh = SeqHandler.forColumn(seqCol);
   const fastaLines: string[] = [];
 
-  for (let rowI: number = 0; rowI < seqCol.length; rowI++) {
+  for (let rowIdx: number = 0; rowIdx < seqCol.length; rowIdx++) {
     // multiple identifiers separated by vertical bars
     // https://en.wikipedia.org/wiki/FASTA_format
 
-    const seqId: string = idColList.map((col) => col.get(rowI).toString()).join('|');
-    const seq: string = seqCol.get(rowI);
-    const seqLineList: string[] = wrapSequence(seq, splitter, lineWidth);
+    const seqId: string = idColList.map((col) => col.get(rowIdx).toString()).join('|');
+    const srcSS = sh.getSplitted(rowIdx);
+    const seqLineList: string[] = wrapSequence(srcSS, lineWidth);
 
@@ -105,6 +104,5 @@ fastaLines.push(`>${seqId}${lineSeparator}`);
 /* split sequence for monomers to prevent wrapping monomer partially */
-export function wrapSequence(seq: string, splitter: SplitterFunc, lineWidth: number = FASTA_LINE_WIDTH): string[] {
-  const seqMonomerList = splitter(seq);
+export function wrapSequence(srcSS: ISeqSplitted, lineWidth: number = FASTA_LINE_WIDTH): string[] {
   let seqPos: number = 0;
-  const seqLength: number = seqMonomerList.length;
+  const seqLength: number = srcSS.length;
 
@@ -114,4 +112,5 @@ const seqLineList: string[] = [];
     /* join sliced monomer into line */
-    const seqLine: string[] = wu(seqMonomerList).slice(seqPos, seqPos + lineWidth).toArray();
-    const seqLineTxt: string = seqLine.map((m) => m.length > 1 ? `[${m}]` : m).join('');
+    const seqLine = wu(srcSS.originals).slice(seqPos, seqPos + lineWidth).toArray();
+    const seqLineTxt: string = seqLine.map((om) => om.length > 1 ? `[${om}]` : om)
+      .reduce((a, b) => a + b, '');
     seqLineList.push(seqLineTxt);
@@ -118,0 +117,0 @@ seqPos += seqLine.length;

src/utils/sequence-to-mol.ts

@@ -11,3 +11,3 @@ /* Do not change these import lines to match external modules in webpack configuration */
 import {getMonomerLibHelper} from '../package';
-import {UnitsHandler} from '@datagrok-libraries/bio/src/utils/units-handler';
+import {SeqHandler} from '@datagrok-libraries/bio/src/utils/seq-handler';
 import {NOTATION} from '@datagrok-libraries/bio/src/utils/macromolecule';
@@ -21,5 +21,5 @@
   if (nonlinear) {
-    const seqUh = UnitsHandler.getOrCreate(macroMolecule);
-    if (!seqUh.isHelm())
-      macroMolecule = seqUh.convert(NOTATION.HELM);
+    const seqSh = SeqHandler.forColumn(macroMolecule);
+    if (!seqSh.isHelm())
+      macroMolecule = seqSh.convert(NOTATION.HELM);
     helm2mol(df, macroMolecule);
@@ -26,0 +26,0 @@ return;

src/viewers/web-logo-viewer.ts

@@ -9,3 +9,3 @@ import * as grok from 'datagrok-api/grok';
 
-import {UnitsHandler} from '@datagrok-libraries/bio/src/utils/units-handler';
+import {SeqHandler} from '@datagrok-libraries/bio/src/utils/seq-handler';
 import {SeqPalette} from '@datagrok-libraries/bio/src/seq-palettes';
@@ -21,4 +21,3 @@ import {
 import {intToHtmlA} from '@datagrok-libraries/utils/src/color';
-import {ISeqSplitted} from '@datagrok-libraries/bio/src/utils/macromolecule/types';
-import {errInfo} from '@datagrok-libraries/bio/src/utils/err-info';
+import {GAP_SYMBOL, ISeqSplitted} from '@datagrok-libraries/bio/src/utils/macromolecule/types';
 import {testEvent} from '@datagrok-libraries/utils/src/test';
@@ -31,3 +30,2 @@ import {PromiseSyncer} from '@datagrok-libraries/bio/src/utils/syncer';
 import {_package} from '../package';
-import {GAP_SYMBOL} from '../const';
 
@@ -174,4 +172,3 @@ declare global {
 
-  calcScreen(
-    isGap: (m: string) => boolean, posIdx: number, firstVisiblePosIdx: number,
+  calcScreen(posIdx: number, firstVisiblePosIdx: number,
     absoluteMaxHeight: number, heightMode: PositionHeight, alphabetSizeLog: number,
@@ -187,9 +184,9 @@ positionWidthWithMargin: number, positionWidth: number, dpr: number, positionLabelsHeight: number
       .sort((a, b) => {
-        if (!isGap(a[0]) && !isGap(b[0]))
+        if (a[0] !== GAP_SYMBOL && b[0] !== GAP_SYMBOL)
           return b[1].value - a[1].value;
-        else if (isGap(a[0]) && isGap(b[0]))
+        else if (a[0] === GAP_SYMBOL && b[0] === GAP_SYMBOL)
           return 0;
-        else if (isGap(a[0]))
+        else if (a[0] === GAP_SYMBOL)
           return -1;
-        else /* (isGap(b[0])) */
+        else /* (b[0] === GAP_SYMBOL) */
           return +1;
@@ -208,7 +205,6 @@ });
   render(g: CanvasRenderingContext2D,
-    isGap: (m: string) => boolean,
     fontStyle: string, uppercaseLetterAscent: number, uppercaseLetterHeight: number, cp: SeqPalette
   ) {
     for (const [monomer, pmInfo] of Object.entries(this._freqs)) {
-      if (!isGap(monomer)) {
+      if (monomer !== GAP_SYMBOL) {
         const monomerTxt = monomerToShort(monomer, 5);
@@ -312,3 +308,3 @@ const b = pmInfo.bounds!;
 
-  private unitsHandler: UnitsHandler | null;
+  private seqHandler: SeqHandler | null;
   private initialized: boolean = false;
@@ -383,3 +379,3 @@
   public get positionMarginValue(): number {
-    if (this.positionMarginState === PositionMarginStates.AUTO && this.unitsHandler!.getAlphabetIsMultichar() === true)
+    if (this.positionMarginState === PositionMarginStates.AUTO && this.seqHandler!.getAlphabetIsMultichar() === true)
       return this.positionMargin;
@@ -396,3 +392,3 @@ else if (this.positionMarginState === PositionMarginStates.ON)
     this.textBaseline = 'top';
-    this.unitsHandler = null;
+    this.seqHandler = null;
 
@@ -601,3 +597,3 @@ // -- Data --
         try {
-          this.unitsHandler = UnitsHandler.getOrCreate(this.seqCol);
+          this.seqHandler = SeqHandler.forColumn(this.seqCol);
 
@@ -613,3 +609,3 @@ this.palette = pickUpPalette(this.seqCol);
         if (!this.seqCol) {
-          this.unitsHandler = null;
+          this.seqHandler = null;
           this.positionNames = [];
@@ -831,2 +827,3 @@ this.positionLabels = [];
       break;
+    case PROPS.sequenceColumnName:
     case PROPS.startPositionName:
@@ -971,5 +968,6 @@ case PROPS.endPositionName:
       const dfFilter = this.getFilter();
-      const maxLength: number = dfFilter.trueCount === 0 ? this.unitsHandler!.maxLength :
-        wu.enumerate(this.unitsHandler!.splitted).map(([mList, rowI]) => {
-          return dfFilter.get(rowI) && !!mList ? mList.length : 0;
+      const maxLength: number = dfFilter.trueCount === 0 ? this.seqHandler!.maxLength :
+        wu.count(0).take(this.seqHandler!.length).map((rowIdx) => {
+          const mList = this.seqHandler!.getSplitted(rowIdx);
+          return dfFilter.get(rowIdx) && !!mList ? mList.length : 0;
         }).reduce((max, l) => Math.max(max, l), 0);
@@ -995,3 +993,3 @@
       const length: number = this.startPosition <= this.endPosition ? this.endPosition - this.startPosition + 1 : 0;
-      this.unitsHandler = UnitsHandler.getOrCreate(this.seqCol);
+      this.seqHandler = SeqHandler.forColumn(this.seqCol);
       const posCount: number = this.startPosition <= this.endPosition ? this.endPosition - this.startPosition + 1 : 0;
@@ -1008,14 +1006,12 @@ this.positions = new Array(posCount);
       const dfRowCount = this.dataFrame.rowCount;
-      const splitted = this.unitsHandler.splitted;
 
       for (let jPos = 0; jPos < length; ++jPos) {
+        const pi = this.positions[jPos];
         // Here we want to build lists of values for every monomer in position jPos
         for (let rowI = 0; rowI < dfRowCount; ++rowI) {
           if (dfFilter.get(rowI)) {
-            const seqMList: ISeqSplitted = splitted[rowI];
-            const om: string = seqMList[this.startPosition + jPos] || this.unitsHandler.defaultGapSymbol;
-            const cm: string = this.unitsHandler?.defaultGapSymbol === om ? GAP_SYMBOL : om;
-            const pi = this.positions[jPos];
+            ++pi.sumRowCount;
+            const seqMList: ISeqSplitted = this.seqHandler.getSplitted(rowI);
+            const cm: string = seqMList.getCanonical(this.startPosition + jPos);
             const pmi = pi.getFreq(cm);
-            ++pi.sumRowCount;
             pmi.value = ++pmi.rowCount;
@@ -1037,6 +1033,6 @@ }
           if (dfFilter.get(rowI)) { // respect the filter
-            const seqMList: ISeqSplitted = splitted[rowI];
-            const m: string = seqMList[this.startPosition + jPos] || this.unitsHandler.defaultGapSymbol;
+            const seqMList: ISeqSplitted = this.seqHandler.getSplitted(rowI);
+            const cm: string = seqMList.getCanonical(this.startPosition + jPos);
             const value: number | null = valueCol.get(rowI);
-            this.positions[jPos].getFreq(m).push(value);
+            this.positions[jPos].getFreq(cm).push(value);
           }
@@ -1080,3 +1076,3 @@ }
         }
-        this.positions[jPos].calcScreen((m) => { return this.unitsHandler!.isGap(m); },
+        this.positions[jPos].calcScreen(
           jPos, this.slider.min, absoluteMaxHeight, this.positionHeight,
@@ -1137,6 +1133,4 @@ alphabetSizeLog, this._positionWidthWithMargin, this._positionWidth, dpr, positionLabelsHeight);
       const uppercaseLetterHeight = 12.2;
-      for (let jPos = firstPos; jPos <= lastPos; jPos++) {
-        this.positions[jPos].render(g, (m) => { return this.unitsHandler!.isGap(m); },
-          fontStyle, uppercaseLetterAscent, uppercaseLetterHeight, this.palette);
-      }
+      for (let jPos = firstPos; jPos <= lastPos; jPos++)
+        this.positions[jPos].render(g, fontStyle, uppercaseLetterAscent, uppercaseLetterHeight, this.palette);
     } finally {
@@ -1156,7 +1150,5 @@ g.restore();
     this.requestedRenderLevel = WlRenderLevel.None;
-    this.renderInt(renderLevel)
-      .catch((err: any) => {
-        const [errMsg, errStack] = errInfo(err);
-        _package.logger.error(errMsg, undefined, errStack);
-      });
+    this.viewSyncer.sync(logPrefix, async () => {
+      await this.renderInt(renderLevel);
+    });
   }
@@ -1168,3 +1160,3 @@
   public getAlphabetSize(): number {
-    return this.unitsHandler?.getAlphabetSize() ?? 0;
+    return this.seqHandler?.getAlphabetSize() ?? 0;
   }
@@ -1235,6 +1227,6 @@
         ui.tooltip.show(tooltipEl, args.x + 16, args.y + 16);
-      } else if (pi !== null && monomer && this.dataFrame && this.seqCol && this.unitsHandler) {
+      } else if (pi !== null && monomer && this.dataFrame && this.seqCol && this.seqHandler) {
         // Monomer at position tooltip
         // const monomerAtPosSeqCount = countForMonomerAtPosition(
-        //   this.dataFrame, this.unitsHandler!, this.getFilter(), monomer, atPI);
+        //   this.dataFrame, this.seqHandler!, this.getFilter(), monomer, atPI);
         const pmi = pi.getFreq(monomer);
@@ -1267,6 +1259,6 @@
       // prevents deselect all rows if we miss monomer bounds
-      if (pi !== null && monomer !== null && this.dataFrame && this.seqCol && this.unitsHandler) {
+      if (pi !== null && monomer !== null && this.dataFrame && this.seqCol && this.seqHandler) {
         // Calculate a new BitSet object for selection to prevent interfering with existing
         const selBS: DG.BitSet = DG.BitSet.create(this.dataFrame.selection.length, (rowI: number) => {
-          return checkSeqForMonomerAtPos(this.dataFrame, this.unitsHandler!, this.getFilter(), rowI, monomer, pi);
+          return checkSeqForMonomerAtPos(this.dataFrame, this.seqHandler!, this.getFilter(), rowI, monomer, pi);
         });
@@ -1306,4 +1298,4 @@ this.dataFrame.selection.init((i) => selBS.get(i));
     // Put the event trigger in the tail of the synced calls queue.
+    this.render(WlRenderLevel.None, callLog); // Put render request to the syncer
     this.viewSyncer.sync(`${logPrefix}`, async () => {
-      this.render(WlRenderLevel.None, callLog);
       this._onRendered.next();
@@ -1359,11 +1351,11 @@ });
 export function checkSeqForMonomerAtPos(
-  df: DG.DataFrame, unitsHandler: UnitsHandler, filter: DG.BitSet, rowI: number, monomer: string, at: PositionInfo,
+  df: DG.DataFrame, sh: SeqHandler, filter: DG.BitSet, rowI: number, monomer: string, at: PositionInfo,
 ): boolean {
-  const seqMList: ISeqSplitted = unitsHandler.splitted[rowI];
-  const seqM = at.pos < seqMList.length ? seqMList[at.pos] : null;
-  return ((seqM === monomer) || (seqM === '' && monomer === unitsHandler.defaultGapSymbol));
+  const seqMList: ISeqSplitted = sh.getSplitted(rowI);
+  const seqCM: string | null = at.pos < seqMList.length ? seqMList.getCanonical(at.pos) : null;
+  return seqCM !== null && seqCM === monomer;
 }
 
 export function countForMonomerAtPosition(
-  df: DG.DataFrame, uh: UnitsHandler, filter: DG.BitSet, monomer: string, at: PositionInfo
+  df: DG.DataFrame, sh: SeqHandler, filter: DG.BitSet, monomer: string, at: PositionInfo
 ): number {
@@ -1373,8 +1365,8 @@ let count = 0;
   while ((rowI = filter.findNext(rowI, true)) != -1) {
-    const seqMList: ISeqSplitted = uh.splitted[rowI];
+    const seqMList: ISeqSplitted = sh.getSplitted(rowI);
     const seqMPos: number = at.pos;
-    const seqM: string | null = seqMPos < seqMList.length ? seqMList[seqMPos] : null;
-    if (seqM === monomer) count++;
+    const seqCM: string | null = seqMPos < seqMList.length ? seqMList.getCanonical(seqMPos) : null;
+    if (seqCM !== null && seqCM === monomer) count++;
   }
   return count;
 }

src/widgets/bio-substructure-filter.ts

@@ -13,3 +13,3 @@ /**
 import $ from 'cash-dom';
-import {fromEvent, Observable, Subject, Subscription, Unsubscribable} from 'rxjs';
+import {fromEvent, Observable, Subject, Unsubscribable} from 'rxjs';
 
@@ -21,3 +21,3 @@ import {TAGS as bioTAGS, NOTATION} from '@datagrok-libraries/bio/src/utils/macromolecule';
 import {IHelmWebEditor, IWebEditorApp} from '@datagrok-libraries/bio/src/helm/types';
-import {UnitsHandler} from '@datagrok-libraries/bio/src/utils/units-handler';
+import {SeqHandler} from '@datagrok-libraries/bio/src/utils/seq-handler';
 import {IRenderer} from '@datagrok-libraries/bio/src/types/renderer';
@@ -125,3 +125,3 @@ import {ILogger} from '@datagrok-libraries/bio/src/utils/logger';
       this.column = dataFrame.columns.bySemType(DG.SEMTYPE.MACROMOLECULE);
-      const uh = UnitsHandler.getOrCreate(this.column!);
+      const sh = SeqHandler.forColumn(this.column!);
       this.columnName ??= this.column?.name;
@@ -128,0 +128,0 @@ this.notation ??= this.column?.getTag(DG.TAGS.UNITS);

src/widgets/composition-analysis-widget.ts

@@ -11,4 +11,4 @@ import * as grok from 'datagrok-api/grok';
 import '../../css/composition-analysis.css';
-import {UnitsHandler} from '@datagrok-libraries/bio/src/utils/units-handler';
-import {GAP_SYMBOL} from '../const';
+import {SeqHandler} from '@datagrok-libraries/bio/src/utils/seq-handler';
+import {GAP_SYMBOL} from '@datagrok-libraries/bio/src/utils/macromolecule/types';
 
@@ -34,8 +34,8 @@
   const counts: { [m: string]: number } = {};
-  const uh = UnitsHandler.getOrCreate(val.cell.column);
-  const splitter = uh.getSplitter();
-  const parts = splitter(val.value);
-  wu(parts).filter((p) => !!p && p !== '').forEach((m: string) => {
-    const count = counts[m] || 0;
-    counts[m] = count + 1;
+  const sh = SeqHandler.forColumn(val.cell.column as DG.Column<string>);
+  const rowIdx = val.cell.rowIndex;
+  const parts = sh.getSplitted(rowIdx);
+  wu(parts.canonicals).filter((cm) => cm !== GAP_SYMBOL).forEach((cm) => {
+    const count = counts[cm] || 0;
+    counts[cm] = count + 1;
   });
@@ -42,0 +42,0 @@ const table = buildCompositionTable(palette, counts);

New alerts

License Policy Violation

License

This package is not allowed per your license policy. Review the package's license to ensure compliance.

Found 1 instance in 1 package

Fixed alerts

License Policy Violation

License

This package is not allowed per your license policy. Review the package's license to ensure compliance.

Found 1 instance in 1 package

Improved metrics

Total package byte prevSize

28340363

increased by0.25%

Lines of code

48022

increased by0.08%

Dependency changes

• + Added@datagrok-libraries/bio@5.40.0(transitive)

• - Removed@datagrok-libraries/bio@5.39.29(transitive)

• Updated@datagrok-libraries/bio@5.40.0

• Updated@datagrok-libraries/chem-meta@^1.2.3

• Updated@datagrok-libraries/ml@^6.4.12

• Updated@datagrok-libraries/tutorials@^1.3.12