@datagrok/helm 2.1.30 → 2.1.31

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (9) hide show
  1. package/CHANGELOG.md +7 -0
  2. package/dist/package-test.js +1 -1
  3. package/dist/package-test.js.map +1 -1
  4. package/dist/package.js +1 -1
  5. package/dist/package.js.map +1 -1
  6. package/package.json +5 -5
  7. package/src/package.ts +17 -15
  8. package/src/tests/properties-widget-tests.ts +2 -2
  9. package/src/widgets/properties-widget.ts +5 -5
package/dist/package.js CHANGED
@@ -1,2 +1,2 @@
1
- var helm;(()=>{"use strict";var t={n:e=>{var n=e&&e.__esModule?()=>e.default:()=>e;return t.d(n,{a:n}),n},d:(e,n)=>{for(var r in n)t.o(n,r)&&!t.o(e,r)&&Object.defineProperty(e,r,{enumerable:!0,get:n[r]})},o:(t,e)=>Object.prototype.hasOwnProperty.call(t,e),r:t=>{"undefined"!=typeof Symbol&&Symbol.toStringTag&&Object.defineProperty(t,Symbol.toStringTag,{value:"Module"}),Object.defineProperty(t,"__esModule",{value:!0})}},e={};t.r(e),t.d(e,{_package:()=>yt,editMoleculeCell:()=>Ot,getHelmHelper:()=>Rt,getMolfiles:()=>It,getMonomerLib:()=>Mt,helmCellRenderer:()=>Nt,initHelm:()=>Tt,openEditor:()=>Lt,propertiesWidget:()=>xt});const n=grok,r=ui,s=DG,i=$;var o,l,a=t.n(i);function h(t){var e;return"string"==typeof t||t instanceof String?t:("object"==typeof t||t instanceof Object)&&"$thrownJsError"in t?h(t.$thrownJsError):t instanceof Error?null!==(e=t.stack)&&void 0!==e?e:t.message:t.toString()}class c{constructor(t,e,n){this.name=t,this.alphabet=e,this.cutoff=n}}class u extends c{constructor(t,e,n){super(t.name,t.alphabet,t.cutoff),this.freq=e,this.similarity=n}}(l=o||(o={})).FASTA="fasta",l.SEPARATOR="separator",l.HELM="helm";const g=/(?:\[([A-Za-z0-9_\-,()]+)\])|([A-Za-z\-])/g,m=new class{constructor(){this.fasta={peptide:new Set(["G","L","Y","S","E","Q","D","N","F","A","K","R","H","C","V","P","W","I","M","T"]),dna:new Set(["A","C","G","T"]),rna:new Set(["A","C","G","U"])}}},f=[new c("PT",m.fasta.peptide,.5),new c("DNA",m.fasta.dna,.55),new c("RNA",m.fasta.rna,.55)],d=wu;var p=t.n(d);function C(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,s=new Float32Array((n.length+r)*(n.length+r));return Object.entries(e).forEach((([t,r])=>{const i=n[r];Object.entries(e).forEach((([e,r])=>{s[t.charCodeAt(0)*n.length+e.charCodeAt(0)]=i[r]}))})),(t,e)=>s[t.charCodeAt(0)*n.length+e.charCodeAt(0)]}(),n=t?.threshold??0;return(t,r)=>{let s=0;const i=t.length,o=r.length,l=Math.max(i,o)*(1-n);i!==o&&(s=Math.abs(i-o));let a=0;for(let n=0;n<Math.min(i,o);n++)if(t[n]!==r[n]&&(a+=e(t[n],r[n]),a>l))return 1;return a+=s,a/=Math.max(i,o),a}}const A=new Uint32Array(65536),b={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 _;!function(t){t.HAMMING="Hamming",t.LEVENSHTEIN="Levenshtein",t.NEEDLEMANN_WUNSCH="Needlemann-Wunsch",t.MONOMER_CHEMICAL_DISTANCE="Monomer chemical distance"}(_||(_={}));const w={[_.HAMMING]:C,[_.LEVENSHTEIN]:function(){return(t,e)=>((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,r=e.length,s=1<<n-1;let i=-1,o=0,l=n,a=n;for(;a--;)A[t.charCodeAt(a)]|=1<<a;for(a=0;a<r;a++){let t=A[e.charCodeAt(a)];const n=t|o;t|=(t&i)+i^i,o|=~(t|i),i&=t,o&s&&l++,i&s&&l--,o=o<<1|1,i=i<<1|~(n|o),o&=n}for(a=n;a--;)A[t.charCodeAt(a)]=0;return l})(t,e):((t,e)=>{const n=e.length,r=t.length,s=[],i=[],o=Math.ceil(n/32),l=Math.ceil(r/32);for(let t=0;t<o;t++)i[t]=-1,s[t]=0;let a=0;for(;a<l-1;a++){let o=0,l=-1;const h=32*a,c=Math.min(32,r)+h;for(let e=h;e<c;e++)A[t.charCodeAt(e)]|=1<<e;for(let t=0;t<n;t++){const n=A[e.charCodeAt(t)],r=i[t/32|0]>>>t&1,a=s[t/32|0]>>>t&1,h=n|o,c=((n|a)&l)+l^l|n|a;let u=o|~(c|l),g=l&c;u>>>31^r&&(i[t/32|0]^=1<<t),g>>>31^a&&(s[t/32|0]^=1<<t),u=u<<1|r,g=g<<1|a,l=g|~(h|u),o=u&h}for(let e=h;e<c;e++)A[t.charCodeAt(e)]=0}let h=0,c=-1;const u=32*a,g=Math.min(32,r-u)+u;for(let e=u;e<g;e++)A[t.charCodeAt(e)]|=1<<e;let m=r;for(let t=0;t<n;t++){const n=A[e.charCodeAt(t)],o=i[t/32|0]>>>t&1,l=s[t/32|0]>>>t&1,a=n|h,u=((n|l)&c)+c^c|n|l;let g=h|~(u|c),f=c&u;m+=g>>>r-1&1,m-=f>>>r-1&1,g>>>31^o&&(i[t/32|0]^=1<<t),f>>>31^l&&(s[t/32|0]^=1<<t),g=g<<1|o,f=f<<1|l,c=f|~(a|g),h=g&a}for(let e=u;e<g;e++)A[t.charCodeAt(e)]=0;return m})(t,e)})(t,e)/Math.max(t.length,e.length)},[_.NEEDLEMANN_WUNSCH]:function(t){const e=new Uint16Array(65536),{gapOpen:n,gapExtend:r,scoringMatrix:s,alphabetIndexes:i}={...b,...t};Object.entries(i).forEach((([t,n])=>e[t.charCodeAt(0)]=n));const o=[new Float32Array(1e4),new Float32Array(1e4)];return(t,i)=>{const l=new Array(t.length+1).fill(!1),a=new Array(t.length+1).fill(!1);let h=0,c=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 u=1;u<i.length+1;u++){o[c][0]=-n-(u-1)*r;for(let g=1;g<t.length+1;g++){const m=o[h][g-1]+s[e[t.charCodeAt(g-1)]][e[i.charCodeAt(u-1)]],f=o[h][g]-(l[g]?r:n),d=o[c][g-1]-(a[g-1]?r:n);o[c][g]=Math.max(m,d,f),o[c][g]===m?(l[g]=!1,a[g]=!1):o[c][g]===d?(l[g]=!1,a[g]=!0):(l[g]=!0,a[g]=!1)}h=c,c=(c+1)%2}const u=Math.max(t.length,i.length);return(u-o[h][t.length])/u}},[_.MONOMER_CHEMICAL_DISTANCE]:C},E=new RegExp("[rd]\\((\\w)\\)p?","g");class y{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,r=y._createBuffer(n);if(e)for(let t=0;t<r.length;t++)r[t]=-1;this._data=r,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} != ${e._length})`);const n=new y(t._length);n._length=t._length,n._data=y._createBuffer(n._length),n._version=0;const r=t.lengthInInts;for(let s=0;s<r;s++)n._data[s]=t._data[s]&e._data[s];return n}static _createBuffer(t){return new Uint32Array(Math.floor((t+31)/32))}static fromValues(t){const e=new y(t.length);e._version=0;for(let n=0;n<e._length;n++)t[n]&&(e._data[Math.floor(n/32)]|=1<<(n%32&31));return e}static fromSeq(t,e){const n=new y(t);for(let r=0;r<t;++r)n.setBit(r,e(r));return n._version=0,n}static fromString(t){return y.fromSeq(t.length,(e=>"1"==t.charAt(e)))}static fromUint32Array(t,e){const n=new y(t);return n._data=e,n}static fromBytes(t){const e=t.length,n=new y(8*e);n._data=new Uint32Array(Math.floor((e+3)/4)),n._length=8*e;let r=0,s=0;for(;e-s>=4;)n._data[r++]=255&t[s]|(255&t[s+1])<<8|(255&t[s+2])<<16|(255&t[s+3])<<24,s+=4;return e-s==3&&(n._data[r]=(255&t[s+2])<<16),e-s==2&&(n._data[r]|=(255&t[s+1])<<8),e-s==1&&(n._data[r]|=255&t[s]),n._version=0,n}toString(){return`${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 y(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,s=!0){if(n&&s&&this.setAll(!e,!1),s)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 y.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 s=Math.min(t,e),i=Math.max(t,e);if(n)for(let t=s;t<=i;t++)this.setTrue(t);else for(let t=s;t<=i;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 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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+=y._onBitCount[255&t];let n=this._data[e];const r=31&this._length;for(0!=r&&(n&=~(4294967295<<r));0!=n;n>>>=8)this._selectedCount+=y._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 r=this.lengthInInts;let s=0;for(;s<r-1;s++)for(let e=this._data[s]&t._data[s];0!=e;e>>>=8)n+=y._onBitCount[255&e];let i=this._data[s]&t._data[s];const o=31&this._length;for(0!=o&&(i&=~(4294967295<<o));0!=i;i>>>=8)n+=y._onBitCount[255&i];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 r=this.lengthInInts;for(let s=Math.floor(t/32);s<r;s++){let r=e?this._data[s]:~this._data[s];if(0!=n)r&=4294967295<<n&4294967295,n=0;else if(!e&&-4294967296==r)continue;for(let e=0;0!=r;e+=8,r>>>=8){const n=y._firstOnBit[255&r];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 r=Math.floor(t/32);r>=0;r--){let t=e?this._data[r]:~this._data[r];0!=n&&(t&=~(4294967295<<n),n=0);for(let e=24;0!=t;e-=8,t<<=8){const n=y._lastOnBit[t>>>24];if(n>=0)return n+32*r+e}}return-1}}var T,M,S,N,v,O,L;y._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]),y._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]),y._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]),function(t){t.Levenshtein="Levenshtein",t.JaroWinkler="Jaro-Winkler",t.Manhattan="Manhattan",t.Onehot="One-Hot"}(T||(T={})),function(t){t.Euclidean="Euclidean"}(M||(M={})),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"}(N||(N={})),function(t){t.Vector="Vector",t.String="String",t.BitArray="BitArray",t.MacroMolecule="MacroMolecule",t.Number="Number",t.IntArray="IntArray",t.NumberArray="NumberArray"}(v||(v={})),function(t){t.Difference="Difference"}(O||(O={})),function(t){t.CommonItems="Common Items"}(L||(L={})),S.Tanimoto,S.Dice,S.Asymmetric,S.BraunBlanquet,S.Cosine,S.Kulczynski,S.McConnaughey,S.RogotGoldberg,S.Russel,S.Sokal,S.Hamming,S.Euclidean,S.Tanimoto,S.Dice,S.Asymmetric,S.BraunBlanquet,S.Cosine,S.Kulczynski,S.McConnaughey,S.RogotGoldberg,S.Russel,S.Sokal,S.Hamming,S.Euclidean,S.Tanimoto,S.Dice,S.Cosine,S.Tanimoto,S.Asymmetric,S.Cosine,S.Sokal,_.HAMMING,_.LEVENSHTEIN,_.MONOMER_CHEMICAL_DISTANCE,_.NEEDLEMANN_WUNSCH;const x=new class{constructor(){this.uh=`units-handler.${s.SEMTYPE.MACROMOLECULE}`}},H={[o.FASTA]:"-",[o.SEPARATOR]:"",[o.HELM]:"*"};class I{static setUnitsToFastaColumn(t){if(t.column.semType!==s.SEMTYPE.MACROMOLECULE||t.column.getTag(s.TAGS.UNITS)!==o.FASTA)throw new Error(`The column of notation '${o.FASTA}' must be '${s.SEMTYPE.MACROMOLECULE}'.`);t.column.setTag(s.TAGS.UNITS,o.FASTA),I.setTags(t)}static setUnitsToSeparatorColumn(t,e){if(t.column.semType!==s.SEMTYPE.MACROMOLECULE||t.column.getTag(s.TAGS.UNITS)!==o.SEPARATOR)throw new Error(`The column of notation '${o.SEPARATOR}' must be '${s.SEMTYPE.MACROMOLECULE}'.`);if(!e)throw new Error(`The column of notation '${o.SEPARATOR}' must have the separator tag.`);t.column.setTag(s.TAGS.UNITS,o.SEPARATOR),t.column.setTag("separator",e),I.setTags(t)}static setUnitsToHelmColumn(t){if(t.column.semType!==s.SEMTYPE.MACROMOLECULE)throw new Error(`The column of notation '${o.HELM}' must be '${s.SEMTYPE.MACROMOLECULE}'`);t.column.setTag(s.TAGS.UNITS,o.HELM),I.setTags(t)}static setTags(t){const e=t.column.getTag(s.TAGS.UNITS),n=t.stats;if(Object.keys(n.freq).some((t=>t.length>1)),[o.FASTA,o.SEPARATOR].includes(e)){if(!t.column.getTag("alphabet")&&0===Object.keys(n.freq).length)throw new Error("Alphabet is empty and not annotated.");let e=t.column.getTag("aligned");null===e&&(e=n.sameLength?"SEQ.MSA":"SEQ",t.column.setTag("aligned",e));let r=t.column.getTag("alphabet");if(null===r&&(r=function(t,e,n="-"){const r=e.map((e=>{const r=function(t,e,n="-"){const r=new Set([...new Set(Object.keys(t)),...e]);r.delete(n);const s=[],i=[];for(const n of r)s.push(n in t?t[n]:0),i.push(e.has(n)?1:0);const o=new k(s),l=new k(i);return function(t,e){if(t.length!=e.length)throw new Error("The dimensionality of the vectors must match");let n=0;for(let r=0;r<t.length;r++)n+=t[r]*e[r];return n}(o,l)/(G(o)*G(l))}(t,e.alphabet,n);return new u(e,t,r)}));let s;const i=Math.max(...r.map((t=>t.similarity>t.cutoff?t.similarity:-1)));s=i>0?r.find((t=>t.similarity===i)).name:"UN";return s}(n.freq,f),t.column.setTag("alphabet",r)),"UN"===r){const e=Object.keys(n.freq).length,r=Object.keys(n.freq).some((t=>t.length>1));t.column.setTag(".alphabetSize",e.toString()),t.column.setTag(".alphabetIsMultichar",r?"true":"false")}}}get column(){return this._column}get units(){return this._units}get notation(){return this._notation}get defaultGapSymbol(){return this._defaultGapSymbol}get separator(){const t=this.column.getTag("separator")??void 0;if(this.notation===o.SEPARATOR&&void 0===t)throw new Error(`Separator is mandatory for column '${this.column.name}' of notation '${this.notation}'.`);return t}get aligned(){const t=this.column.getTag("aligned");if(!t&&(this.isFasta()||this.isSeparator()))throw new Error("Tag aligned not set");return t}get alphabet(){const t=this.column.getTag("alphabet");if(!t&&(this.isFasta()||this.isSeparator()))throw new Error("Tag alphabet not set");return t}get helmCompatible(){return this.column.getTag(".isHelmCompatible")}getAlphabetSize(){if(this.notation==o.HELM||"UN"==this.alphabet){const t=this.column.getTag(".alphabetSize");let e;if(t)e=parseInt(t);else{const t=this.stats;e=Object.keys(t.freq).length}return e}switch(this.alphabet){case"PT":return 20;case"DNA":case"RNA":return 4;case"NT":return console.warn("Unexpected alphabet 'NT'."),4;default:throw new Error(`Unexpected alphabet '${this.alphabet}'.`)}}getAlphabetIsMultichar(){return this.notation===o.HELM||"UN"===this.alphabet&&"true"===this.column.getTag(".alphabetIsMultichar")}get splitted(){if(null===this._splitted){const t=this.getSplitter(),e=this._column.length;this._splitted=new Array(e);const n=this._column.getRawData(),r=this._column.categories;for(let s=0;s<e;s++){const e=r[n[s]];this._splitted[s]=t(e)}}return this._splitted}get stats(){if(null===this._stats){const t={};let e=!0,n=null;for(const r of this.splitted){null==n?n=r.length:r.length!==n&&(e=!1);for(const e of r)e in t||(t[e]=0),t[e]+=1}this._stats={freq:t,sameLength:e}}return this._stats}get maxLength(){return null===this._maxLength&&(this._maxLength=0===this.splitted.length?0:Math.max(...this.splitted.map((t=>t.length)))),this._maxLength}get posList(){if(null===this._posList){const t=this.column.getTag(".positionNames");this._posList=t?t.split(", ").map((t=>t.trim())):p().count(1).take(this.maxLength).map((t=>t.toString())).toArray()}return this._posList}isFasta(){return this.notation===o.FASTA}isSeparator(){return this.notation===o.SEPARATOR}isHelm(){return this.notation===o.HELM}isRna(){return"RNA"===this.alphabet}isDna(){return"DNA"===this.alphabet}isPeptide(){return"PT"===this.alphabet}isMsa(){return!!this.aligned&&this.aligned.toUpperCase().includes("MSA")}isHelmCompatible(){return"true"===this.helmCompatible}isGap(t){return!t||this.units===o.FASTA&&t===H[o.FASTA]||this.units===o.HELM&&t===H[o.HELM]}getNotation(){if(this.units.toLowerCase().startsWith(o.FASTA))return o.FASTA;if(this.units.toLowerCase().startsWith(o.SEPARATOR))return o.SEPARATOR;if(this.units.toLowerCase().startsWith(o.HELM))return o.HELM;throw new Error(`Column '${this.column.name}' has unexpected notation '${this.units}'.`)}getHelmWrappers(){return[this.isDna()||this.isRna()||this.isHelmCompatible()?"RNA1{":"PEPTIDE1{",this.isDna()?"d(":this.isRna()?"r(":"",this.isDna()||this.isRna()?")p":"","}$$$$"]}getNewColumn(t,e,n,r){const i=this.column,l=t.toLowerCase()+"("+i.name+")",a=n??i.dataFrame.columns.getUnusedName(l),h=s.Column.fromList("string",a,r??new Array(this.column.length).fill(""));if(h.semType=s.SEMTYPE.MACROMOLECULE,h.setTag(s.TAGS.UNITS,t),t===o.SEPARATOR){if(!e)throw new Error(`Notation '${o.SEPARATOR}' requires separator value.`);h.setTag("separator",e)}h.setTag(s.TAGS.CELL_RENDERER,"sequence");const c=i.getTag("aligned");c&&h.setTag("aligned",c);const u=i.getTag("alphabet");null!=u&&h.setTag("alphabet",u);let g=i.getTag(".alphabetSize");null!=u&&g&&h.setTag(".alphabetSize",g);const m=i.getTag(".alphabetIsMultichar");return null!=u&&void 0!==m&&h.setTag(".alphabetIsMultichar",m),t==o.HELM&&(g=this.getAlphabetSize().toString(),h.setTag(".alphabetSize",g)),h}getNewColumnFromList(t,e){return this.getNewColumn(this.notation,this.separator,t,e)}static getNewColumn(t){const e=I.getOrCreate(t),n=e.notation;return e.getNewColumn(n)}static unitsStringIsValid(t){return t=t.toLowerCase(),[o.FASTA,o.SEPARATOR,o.HELM].some((e=>t.startsWith(e.toLowerCase())))}static getNewColumnFromParams(t,e,n){if(!I.unitsStringIsValid(n))throw new Error("Invalid format of 'units' parameter");const r=s.Column.fromList("string",e,new Array(t).fill(""));return r.semType=s.SEMTYPE.MACROMOLECULE,r.setTag(s.TAGS.UNITS,n),r}getSplitter(t){if(this.units.toLowerCase().startsWith(o.FASTA))return null===this.column.getTag("alphabet")||this.getAlphabetIsMultichar()?Y:K;if(this.units.toLowerCase().startsWith(o.SEPARATOR))return Q(this.separator,t);if(this.units.toLowerCase().startsWith(o.HELM))return X;throw new Error(`Unexpected units ${this.units} .`)}getDistanceFunctionName(){if(!this.isFasta())throw new Error("Only FASTA notation is supported");return this.isMsa()?_.HAMMING:(this.alphabet,_.LEVENSHTEIN)}getDistanceFunction(){return w[this.getDistanceFunctionName()]()}async checkHelmCompatibility(){if(this.column.tags.has(".isHelmCompatible"))return"true"===this.column.getTag(".isHelmCompatible");const t=(await async function(){const t=s.Func.find({package:"Bio",name:"getMonomerLibHelper"});if(0===t.length)throw new Error('Package "Bio" must be installed for MonomerLibHelper.');return(await t[0].prepare().call()).getOutputParamValue()}()).getBioLib().getMonomerSymbolsByType("PEPTIDE".toString()),e=new Set(t),n=Q(this.separator);for(const t of this.column.categories){const r=n(t);for(const t of r)if(!e.has(t))return this.column.setTag(".isHelmCompatible","false"),!1}return this.column.setTag(".isHelmCompatible","true"),!0}get splitter(){var t;return null===this._splitter&&(this._splitter=(t=this.column,I.getOrCreate(t).getSplitter())),this._splitter}toFasta(t){return t===o.FASTA}toSeparator(t){return t===o.SEPARATOR}toHelm(t){return t===o.HELM}convertHelmToFastaSeparator(t,e,n,r){r||(r=this.toFasta(e)?H[o.FASTA]:H[o.SEPARATOR]),n||(n=this.toFasta(e)?"":this.separator);const s=t.startsWith("RNA"),i=this.splitter(t),l=[];for(let t=0;t<i.length;t++){let n=i[t];if(s&&(n=n.replace(E,"")),n===H[o.HELM])l.push(r);else if(this.toFasta(e)&&n.length>1){const t="["+n+"]";l.push(t)}else l.push(n)}return l.join(n)}convert(t,e){const n=this.getConverter(t,e),r=this.getNewColumn(t,e);return r.init((t=>{const e=this.column.get(t);return e?n(e):e})),r}getRegion(t,e,n){const r=this.getNewColumn(this.notation,this.separator);r.name=n,Math.max(...this.splitted.map((t=>t.length)));const s=t??0,i=e??this.maxLength-1,o=this.getJoiner(),l=i-s+1;r.init((t=>{const e=this.splitted[t],n=new Array(l);for(let t=0;t<l;++t){const r=s+t;n[t]=r<e.length?e[r]:H[this.notation]}return o(n)}));const a=t=>{const e=t.split(",").map((t=>t.trim())),n=new Array(l);for(let t=0;t<l;++t){const r=s+t;n[t]=r<e.length?e[r]:"?"}return n.join(", ")},h=this.column.getTag(".positionNames");h&&r.setTag(".positionNames",a(h));const c=this.column.getTag(".positionLabels");return c&&r.setTag(".positionLabels",a(c)),r}getJoiner(){if(void 0===this._joiner){const t=this;if(this.notation===o.FASTA)this._joiner=function(e){return R(t,e)};else if(this.notation===o.SEPARATOR)this._joiner=function(e){return P(t,e,t.separator)};else{if(this.notation!==o.HELM)throw new Error;{const e="DNA"===t.alphabet||"RNA"===t.alphabet;this._joiner=function(n){return F(t,n,e)}}}}return this._joiner}getConverter(t,e=void 0){if(t===o.SEPARATOR&&!e)throw new Error(`Target separator is not specified for target units '${o.SEPARATOR}'.`);const n=this;if(t===o.FASTA)return function(t){return function(t,e){const n=t.isHelm()?B(t,e):t.getSplitter()(e);return R(t,n)}(n,t)};if(t===o.HELM)return function(t){return function(t,e){const n=e.startsWith("DNA")||e.startsWith("RNA"),r=t.getSplitter()(e);return F(t,r,n)}(n,t)};if(t===o.SEPARATOR)return function(t){return function(t,e,n){const r=t.isHelm()?B(t,e):t.getSplitter()(e);return P(t,r,n)}(n,t,e)};throw new Error}constructor(t){if(this._splitter=null,this._splitted=null,this._stats=null,this._maxLength=null,this._posList=null,this._joiner=void 0,t.type!==s.TYPE.STRING)throw new Error(`Unexpected column type '${t.type}', must be '${s.TYPE.STRING}'.`);this._column=t;const e=this._column.getTag(s.TAGS.UNITS);if(null==e)throw new Error("Units are not specified in column");if(this._units=e,this._notation=this.getNotation(),this._defaultGapSymbol=this.isFasta()?H[o.FASTA]:this.isHelm()?H[o.HELM]:H[o.SEPARATOR],!this.column.tags.has("aligned")||!this.column.tags.has("alphabet")||!this.column.tags.has(".alphabetIsMultichar")&&!this.isHelm()&&"UN"===this.alphabet)if(this.isFasta())I.setUnitsToFastaColumn(this);else if(this.isSeparator()){const e=t.getTag("separator");I.setUnitsToSeparatorColumn(this,e)}else{if(!this.isHelm())throw new Error(`Unexpected units '${this.column.getTag(s.TAGS.UNITS)}'.`);I.setUnitsToHelmColumn(this)}if(!this.column.tags.has(".alphabetIsMultichar"))if(this.isHelm())this.column.setTag(".alphabetIsMultichar","true");else if(["UN"].includes(this.alphabet))throw new Error(`For column '${this.column.name}' of alphabet '${this.alphabet}' tag '.alphabetIsMultichar' is mandatory.`)}static getOrCreate(t){let e=t.temp[x.uh];return e||(e=t.temp[x.uh]=new I(t)),e}}function R(t,e){const n=new Array(e.length);for(const[r,s]of p().enumerate(e)){let i=r;t.isHelm()&&(i=r.replace(E,"$1")),t.isGap(i)?i=H[o.FASTA]:i.length>1&&(i="["+e[s]+"]"),n[s]=i}return n.join("")}function P(t,e,n){const r=new Array(e.length);for(const[n,s]of p().enumerate(e)){let e=n;t.isGap(e)&&(e=H[o.SEPARATOR]),r[s]=e}return r.map((t=>t??"")).join(n)}function F(t,e,n){const[r,s,i,l]=t.getHelmWrappers();return`${r}${p()(e).map((e=>{let r=e;return r=t.isGap(r)?H[o.HELM]:n?r.replace(E,"$1"):1==e.length?`${s}${e}${i}`:`${s}[${e}]${i}`,r})).toArray().join(".")}${l}`}function B(t,e){const n=t.getSplitter()(e),r=new Array(n.length),s=e.startsWith("DNA"),i=e.startsWith("RNA");for(const[t,e]of p().enumerate(n)){let n=t;(s||i)&&(n=n.replace(E,"$1"),n="p"===n?null:n),r[e]=n}return r.filter((t=>null!==t))}class k extends Float32Array{}function G(t){let e=0;for(let n=0;n<t.length;n++)e+=t[n]*t[n];return Math.sqrt(e)}class U{static makePalette(t,e=!1,n=U){const r={};return t.forEach((t=>{const n=t[0],s=t[1];n.forEach(((t,n)=>{r[t]=this.colourPalette[s][e?0:n]}))})),new n(r)}constructor(t){this._palette=t}get(t){return this._palette[t]}}U.undefinedColor="rgb(100,100,100)",U.colourPalette={orange:["rgb(255,187,120)","rgb(245,167,100)","rgb(235,137,70)","rgb(205, 111, 71)"],all_green:["rgb(44,160,44)","rgb(74,160,74)","rgb(23,103,57)","rgb(30,110,96)","rgb(60,131,95)","rgb(24,110,79)","rgb(152,223,138)","rgb(182, 223, 138)","rgb(152, 193, 138)"],all_blue:["rgb(31,119,180)","rgb(23,190,207)","rgb(122, 102, 189)","rgb(158,218,229)","rgb(141, 124, 217)","rgb(31, 120, 150)"],magenta:["rgb(162,106,192)","rgb(197,165,224)","rgb(208,113,218)"],red:["rgb(214,39,40)","rgb(255,152,150)"],st_blue:["rgb(23,190,207)","rgb(158,218,229)","rgb(31,119,180)"],dark_blue:["rgb(31,119,180)","rgb(31, 120, 150)"],light_blue:["rgb(23,190,207)","rgb(158,218,229)","rgb(108, 218, 229)","rgb(23,190,227)"],lilac_blue:["rgb(124,102,211)","rgb(149,134,217)","rgb(97, 81, 150)"],dark_green:["rgb(23,103,57)","rgb(30,110,96)","rgb(60,131,95)","rgb(24,110,79)"],green:["rgb(44,160,44)","rgb(74,160,74)"],light_green:["rgb(152,223,138)","rgb(182, 223, 138)","rgb(152, 193, 138)"],st_green:["rgb(44,160,44)","rgb(152,223,138)","rgb(39, 174, 96)","rgb(74,160,74)"],pink:["rgb(247,182,210)"],brown:["rgb(140,86,75)","rgb(102, 62, 54)"],gray:["rgb(127,127,127)","rgb(199,199,199)","rgb(196,156,148)","rgb(222, 222, 180)"],yellow:["rgb(188,189,34)"],white:["rgb(230,230,230)"]};class D extends U{static get Lesk(){return void 0===this.lesk&&(this.lesk=this.makePalette([[["G","A","S","T"],"orange"],[["C","V","I","L","P","F","Y","M","W"],"all_green"],[["N","Q","H"],"magenta"],[["D","E"],"red"],[["K","R"],"all_blue"]],!1,D)),this.lesk}static get GrokGroups(){return void 0===this.grokGroups&&(this.grokGroups=this.makePalette([[["C","U"],"yellow"],[["G","P"],"red"],[["A","V","I","L","M","F","Y","W"],"all_green"],[["R","H","K"],"light_blue"],[["D","E"],"dark_blue"],[["S","T","N","Q"],"orange"]],!1,D)),this.grokGroups}static get RasMol(){return void 0===this.rasMol&&(this.rasMol=new D({D:"#E60A0A",E:"#E60A0A",C:"#E6E600",M:"#E6E600",K:"#145AFF",R:"#145AFF",S:"#FA9600",T:"#FA9600",F:"#3232AA",Y:"#3232AA",N:"#00DCDC",Q:"#00DCDC",G:"#EBEBEB",L:"#0F820F",V:"#0F820F",I:"#0F820F",A:"#C8C8C8",W:"#B45AB4",H:"#8282D2",P:"#DC9682",others:"#BEA06E"})),this.rasMol}get(t){const e=t in D.aaSynonyms?D.aaSynonyms[t]:t;return super.get(e)}}D.aaSynonyms={MeNle:"L",MeA:"A",MeG:"G",MeF:"F"};class V{static getPalette(t="grok"){switch(t){case"grok":return D.GrokGroups;case"lesk":return D.Lesk;default:throw new Error(`ChemPalette: scheme \`${t}\` does not exist`)}}static getInnerOuter(t){let e=0,n="",r="";for(const s of t)"("==s?e++:")"==s?e--:e?n+=s:r+=s;return isNaN(parseInt(n))?[r,n]:[r,""]}static getColorAAPivot(t="",e="grok"){const n=this.getPalette(e);let[r,s]=this.getInnerOuter(t);if(r=r.length>6?`${r.slice(0,3)}...`:r,s=s.length>6?`${s.slice(0,3)}...`:s,1==t.length||"("==t[1]){const e=t[0]?.toUpperCase();return e in n?[n.get(e),e,s,1]:[this.undefinedColor,r,s,1]}if("d"==t[0]&&t[1]in n&&(2==t.length||"("==t[2])){const e=t[1]?.toUpperCase();return e in n?[n.get(e),e,s,2]:[this.undefinedColor,r,s,2]}if(t.substring(0,3)in this.AAFullNames&&(3==t.length||"("==t[3])){const e=this.AAFullNames[t.substring(0,3)];return e in n?[n.get(e),e,s,3]:[this.undefinedColor,r,s,3]}if(t[0]?.toLowerCase()==t[0]&&t.substring(1,3)in this.AAFullNames&&(4==t.length||"("==t[4])){const e=this.AAFullNames[t.substring(1,3)];return e in n?[n.get(e),e,s,4]:[this.undefinedColor,r,s,4]}return[this.undefinedColor,r,s,0]}}V.SemType="Aminoacids",V.SemTypeMultipleAlignment="AminoacidsMultipleAlignment",V.undefinedColor="rgb(100,100,100)",V.Names={G:"Glycine",L:"Leucine",Y:"Tyrosine",S:"Serine",E:"Glutamic acid",Q:"Glutamine",D:"Aspartic acid",N:"Asparagine",F:"Phenylalanine",A:"Alanine",K:"Lysine",R:"Arginine",H:"Histidine",C:"Cysteine",V:"Valine",P:"Proline",W:"Tryptophan",I:"Isoleucine",M:"Methionine",T:"Threonine"},V.AASmiles={G:"NCC(=O)O",L:"N[C@H](CC(C)C)C(=O)O",Y:"NC(CC1=CC=C(O)C=C1)C(=O)O",S:"NC(CO)C(=O)O",E:"N[C@@H](CCC(O)=O)C(=O)O",Q:"N[C@@H](CCC(N)=O)C(=O)O",D:"N[C@@H](CC(O)=O)C(=O)O",N:"N[C@@H](CC(N)=O)C(=O)O",F:"NC(CC1=CC=CC=C1)C(=O)O",A:"N[C@H](C)C(=O)O",K:"NC(CCCCN)C(=O)O",R:"N[C@H](CCCNC(=N)C)C(=O)O",H:"NC(CC1=CN=C[N]1)C(=O)O",C:"N[C@@H](CS)C(=O)O",V:"NC(C(C)C)C(=O)O",P:"N(CCC1)C1C(=O)O",W:"N[C@@H](Cc1c2ccccc2n([H])c1)C(=O)O",I:"N[C@H]([C@H](C)CC)C(=O)O",M:"NC(CCSC)C(=O)O",T:"NC(C(O)C)C(=O)O"},V.AASmilesTruncated={G:"*C*",L:"CC(C)C[C@H](*)*",Y:"C1=CC(=CC=C1CC(*)*)O",S:"OCC(*)C*",E:"*[C@@H](CCC(O)=O)*",Q:"*N[C@@H](CCC(N)=O)*",D:"*[C@@H](CC(O)=O)*",N:"*[C@@H](CC(N)=O)*",F:"C1=CC=C(C=C1)CC(*)*",A:"C[C@H](*)*",K:"C(CCN)CC(*)*",R:"*[C@H](CCCNC(=N)C)*",H:"C1=C(NC=N1)CC(*)*",C:"C([C@@H](*)*)S",V:"CC(C)C(*)*",P:"C1CCN(*)C1*",W:"*[C@@H](Cc1c2ccccc2n([H])c1)*",I:"CC[C@H](C)[C@H](*)*",M:"CSCCC(*)*",T:"CC(O)C(*)*"},V.AAFullNames={Ala:"A",Arg:"R",Asn:"N",Asp:"D",Cys:"C",Gln:"Q",Glu:"E",Gly:"G",His:"H",Ile:"I",Leu:"L",Lys:"K",Met:"M",Phe:"F",Pro:"P",Ser:"S",Thr:"T",Trp:"W",Tyr:"Y",Val:"V"};class W{}W.SemType="Nucleotides",W.SemTypeMultipleAlignment="NucleotidesMultipleAlignment",W.Names={A:"Adenine",C:"Cytosine",G:"Guanine",T:"Thymine",U:"Uracil"};class j{static hashCode(t){let e=0;if(0===t.length)return e;for(let n=0;n<t.length;n++)e=(e<<5)-e+t.charCodeAt(n),e|=0;return e}}class z{}class q extends z{static buildPalette(){return[].concat(...Object.values(U.colourPalette))}get(t){const e=j.hashCode(t)%q.palette.length;return function(t){if(null==t)return"rgb(100,100,100)";const e=s.Color.fromHtml(t),n=s.Color.g(e),r=s.Color.r(e),i=s.Color.b(e),o=Math.sqrt(Math.pow(0-r,2)+Math.pow(0-n,2)+Math.pow(0-i,2));return o>210?`rgb(${r/o*210},${n/o*210},${i/o*210})`:s.Color.toRgb(e)}(q.palette[e])}}function Y(t){return p()(t.toString().matchAll(g)).map((t=>t[2]??t[1])).toArray()}function K(t){return t||[]}function Q(t,e=void 0){return n=>n?n.replaceAll('"-"',"").replaceAll("'-'","").split(t,e):[]}q.palette=q.buildPalette();const J=/(PEPTIDE1|DNA1|RNA1)\{([^}]+)}/g,Z=/\[([^\[\]]+)]/g;function X(t){J.lastIndex=0;const e=J.exec(t.toString()),n=e?e[2]:null;return(n?n.split("."):[]).map((t=>{Z.lastIndex=0;const e=Z.exec(t);return e&&e.length>=2?e[1]:t}))}const tt=/([^\W_]+)/g;const et=/\{(\*\.)+/g,nt=/\.(\*\.)+/g,rt=/(\.\*)+\}/g;function st(t){return t.replaceAll(et,"{").replaceAll(nt,".").replaceAll(rt,"}").replace("{*}","{}")}function it(t){t=ht(t,"$")[0];const e=[];if(!scil.Utils.isNullOrEmpty(t)){const n=ht(t,"|");for(let r=0;r<n.length;++r){let s=(t=ct(n[r]).str).indexOf("{");s=(t=t.substring(s+1)).indexOf("}");const i=ht(t=t.substring(0,s),".");for(const t of i)if(t&&""!==t)if(t.startsWith("[")&&t.includes("]")){const n=lt(t,1,"[","]"),r=t.substring(1,n);e.push(r);const s=t.substring(n+1);i.push(s)}else if(t.includes("[")&&t.endsWith("]")){const n=at(t,t.length-2,"[","]"),r=t.substring(n+1,t.length-1);e.push(r);const s=t.substring(0,n);i.push(s)}else if(t.includes("(")&&t.includes(")")){const e=t.substring(0,t.indexOf("(")),n=t.substring(t.lastIndexOf(")")+1),r=[e,t.substring(e.length+1,t.length-n.length-1),n];for(const t of r)i.push(t)}else e.push(t)}}return e}function ot(t){const e=Object.keys(org.helm.webeditor.monomerTypeList()),n=[],r=[];for(let t=0;t<e.length;t++)n.push(new scil.helm.Monomers.getMonomerSet(e[t])),Object.keys(n[t]).forEach((e=>{r.push(n[t][e].id)}));return new Set(t.filter((t=>!r.includes(t))))}function lt(t,e,n,r){let s=e,i=0;for(;s<t.length;){if(t[s]===n&&i++,t[s]===r){if(0===i)return s;i--}s++}return-1}function at(t,e,n,r){let s=e,i=0;for(;s>=0;){if(t[s]===r&&i++,t[s]===n){if(0===i)return s;i--}s--}return-1}function ht(t,e){const n=[];let r="",s=0,i=0,o=0,l=0;for(let a=0;a<t.length;++a){let h=t.substring(a,a+1);if(h==e&&0==i&&0==s&&0==o&&0==l)n.push(r),r="";else{if(r+=h,l>0&&"\\"==h&&a+1<t.length){++a;const e=t.substring(a,a+1);r+=e,h+=e}'"'==h?a>0&&"\\"==t.substring(a-1,a)||(l=0==l?1:0):"["==h?++i:"]"==h?--i:"("==h?++s:")"==h?--s:"{"==h?++o:"}"==h&&--o}}return n.push(r),n}function ct(t){const e=ut(t,'"');if(null!=e.tag)return e;const n=ut(t,"'");return{tag:e.tag,repeat:n.tag,str:n.str}}function ut(t,e){let n=null;if(scil.Utils.endswith(t,e)){let r=t.length-1;for(;r>0&&(r=t.lastIndexOf(e,r-1),!(r<=0||"\\"!=t.substring(r-1,r))););r>0&&r<t.length-1&&(n=t.substring(r+1,t.length-1),t=t.substring(0,r))}return null!=n&&(n=function(t){return scil.Utils.isNullOrEmpty(t)?t:t.replace(/[\\]./g,(function(t){switch(t){case"\\r":return"\r";case"\\n":return"\n";case"\\t":return"\t";default:return t.substring(1)}}))}(n.replace(new RegExp("\\"+e,"g"),e))),{tag:n,str:t}}var gt,mt;function ft(t,e,n,r,s,i,o="rgb(100,100,100)",l=0,a=!1,h=1,c="",u=!1,g=mt.classic,m=[],f=0,d=null,p=[],C=null,A={}){s.textAlign="start";let b=i.substring(0),_=u?"":c;g===mt.MSA&&(_="");let w=!0,E=!0,y="difference";null!=d&&null!=d.cell.column&&(w=d.cell.column.temp["color-code"]??!0,E=d.cell.column.temp["compare-with-current"]??!0,y=d.cell.column.temp["highlight-difference"]??"difference");const T=p[f];E&&p.length>0&&"difference"===y&&(h=b==T?.3:h),E&&p.length>0&&"equal"===y&&(h=b!=T?.3:h),null!=C&&(b=function(t,e){if(t.length<=e)return t;const n=t.match(tt),r=t.length>e||(n?.length??0)>1,s=n?.[0]??" ";return r?s.substring(0,e-1)+"…":s}(b,C));const M=b+_;A[M]??(A[M]=s.measureText(M));let S=A[M];A[b]??(A[b]=s.measureText(b));let N=A[b].width;A[_]??(A[_]=s.measureText(_));const v=A[_].width,O=r/2-(S.fontBoundingBoxAscent+S.fontBoundingBoxDescent)/2+1;function L(n,r){const i=w?o:"rgb(0,0,0)";s.fillStyle=i,s.globalAlpha=h,g===mt.classic&&(s.fillText(b,t+n,e+O),s.fillStyle="#808080",s.fillText(_,t+r,e+O)),g===mt.MSA&&s.fillText(b,t+n,e+O)}S=S.width,g===mt.MSA&&(N=m[f],S=m[f]);const x=(m[f]??0)-(m[0]??0);if(a||S>n)return L(x,x+N),t+x+N+v;{const e=(n-S)/2;return L(e,e+N),t+x+e+N}}!function(t){t.maxMonomerLength=".mm.cellRenderer.maxMonomerLength"}(gt||(gt={})),function(t){t.MSA="MSA",t.classic="classic"}(mt||(mt={}));class dt{constructor(t){this.col=t,this.monomerCharWidth=7,this.leftPadding=5,this.monomerTextSizeMap={},this.col.dataFrame.onDataChanged.subscribe(),this.monomerLib=Mt(),this.monomerLib.onChanged.subscribe(this.monomerLibOnChanged.bind(this)),this._allPartsList=new Array(this.col.length).fill(null),this._lengthsList=new Array(this.col.length).fill(null),this._editorList=new Array(this.col.length).fill(null)}skipCell(t){this._allPartsList[t]=[],this._lengthsList[t]=[]}getCellAllPartsLengths(t){const[e,n]=this.getCellMonomerLengthsForSeq(t),r=new Array(n.length+1);r[0]=this.leftPadding;for(let t=1;t<r.length;t++)r[t]=r[t-1]+n[t-1];return[e,n,r]}getCellMonomerLengthsForSeq(t){let e=this._allPartsList[t];null===e&&(e=this._allPartsList[t]=this.getAllParts(t));let n=this._lengthsList[t];if(null===n){n=this._lengthsList[t]=new Array(e.length);for(const[t,r]of p().enumerate(e)){const e=t.length*this.monomerCharWidth;n[r]=e}}return[e,n]}getAllParts(t){const e=this.col.get(t),n=e?it(e):[];return e?function(t,e){const n=[];for(let r=0;r<t.length;++r){const s=e.indexOf(t[r]),i=e.slice(0,s);n.push(i),n.push(t[r]),e=e.substring(s+t[r].length)}return n.push(e),n}(n,e):[]}getMonomer(t){let e=null;if(t.polymerType)e=this.monomerLib.getMonomer(t.polymerType,t.symbol);else for(const n of this.monomerLib.getPolymerTypes())if(e=this.monomerLib.getMonomer(n,t.symbol),e)break;return e}monomerLibOnChanged(t){this._lengthsList.fill(null),this._allPartsList.fill(null),this._editorList.fill(null)}static getOrCreate(t){return"bio-helmMonomerPlacer"in t.temp||(t.temp["bio-helmMonomerPlacer"]=new dt(t)),t.temp["bio-helmMonomerPlacer"]}setEditor(t,e){this._editorList[t]=e}getEditor(t){return this._editorList[t]}}class pt extends s.GridCellRenderer{get name(){return"helm"}get cellType(){return"helm"}get defaultWidth(){return 400}get defaultHeight(){return 100}onMouseMove(t,e){try{let s=null;try{s=t.tableColumn}catch{}if(!s)return;const i=t.bounds,o=e.offsetX-i.x,l=e.offsetY-i.y,a=dt.getOrCreate(s),h=a.getEditor(t.tableRowIndex);let c,u=new Set;if(h)c=function(t,e,n,r){let s=null;function i(n){let s,i;for(let o=0;o<r.m.atoms.length;++o)if(!n.includes(o)){const n=r.m.atoms[o].p.x,l=r.m.atoms[o].p.y,a=Math.sqrt((t-n)**2+(e-l)**2);(void 0===i||i>a)&&(s=o,i=a)}return[s,i]}const[o,l]=i([]),[a,h]=i([o]);if(void 0!==o&&void 0!==l){const t=function(t){let e;switch(t.bio.type){case"HELM_BASE":case"HELM_SUGAR":case"HELM_LINKER":e="RNA";break;default:e="PEPTIDE"}return{symbol:t.elem,polymerType:e}}(r.m.atoms[o]);void 0!==a&&void 0!==h?l<.45*h&&(s=t):l<.35*n.bounds.height&&(s=t)}return s}(o,l,t,h);else{const e=it(t.cell.value?st(t.cell.value):"");u=ot(e);const n=new Set(e);if(c=function(t,e,n,r){let s=null;const[i,o,l]=r.getCellAllPartsLengths(n.tableRowIndex);let a=0,h=Object.values(o).length-1,c=!1,u=0,g=0;if(t>l[0])for(;!c&&u<l.length;)g=Math.floor((h+a)/2),t>=l[g]&&t<=l[g+1]?(a=g,c=!0):t<l[g]?h=g-1:t>l[g+1]&&(a=g+1),a==h&&(c=!0),u++;return a=t>=l[a]?a:a-1,a>=0&&(s=function(t,e,n){let r;for(const s of n.getPolymerTypes())t.startsWith(s)&&(r={symbol:e,polymerType:s});return r||(r={symbol:e}),r}(i[0],i[a],r.monomerLib)),s}(o,0,t,a),c&&!n.has(c.symbol)&&(c=null),c){const t=a.monomerTextSizeMap[c.symbol];if(t){const e=i.height/2-(t.fontBoundingBoxAscent+t.fontBoundingBoxDescent)/2+1,n=e-t.fontBoundingBoxAscent,r=e+t.fontBoundingBoxDescent;(l<n||r<l)&&(c=null)}}}if(c)if(u.has(c.symbol))r.tooltip.show(r.divV([r.divText(`Monomer '${c.symbol}' not found.`),r.divText("Open the Context Panel, then expand Manage Libraries")]),e.x+16,e.y+16);else{const t=a.getMonomer(c);if(t){const s={autoCrop:!0,autoCropMargin:0,suppressChiralText:!0},i=n.chem.svgMol(t.smiles,void 0,void 0,s);r.tooltip.show(r.divV([r.divText(c.symbol),i]),e.x+16,e.y+16)}}else{if(0==u.size)return void r.tooltip.hide();{const t=p()(u.keys()).toArray().sort().filter(((t,e)=>e<3)).join(", ")+(u.size>3?", ...":"");r.tooltip.show(r.divV([r.divText("Monomers missed in monomer libraries:"),r.divText(t)]),e.x+16,e.y+16)}}}catch(t){const e=h(t);console.error("Helm: HelmCellRenderer.onMouseMove() error:\n"+e)}finally{e.preventDefault(),e.stopPropagation()}}render(t,e,n,s,i,o,l){t.save();try{let l=null;try{l=o.tableColumn}catch{}if(!l)return;const a=-1!==o.gridRow?o.grid:void 0,h="red",c="#404040",u="#C0C0C0",g=o.cell.value?st(o.cell.value):"",m=it(g),f=new Set(m),d=ot(m),p=dt.getOrCreate(l);if(0==d.size){const t=o.element=r.div([],{style:{width:s-2+"px",height:i-2+"px",margin:"1px",backgroundColor:"#FFE0E0"}});t.setAttribute("dataformat","helm"),t.setAttribute("data",g),t.parentElement&&(o.grid?.canvas?.offsetLeft??0)>0&&(t.parentElement.style.left=`${(o.grid?.canvas?.offsetLeft??0)+t.parentElement.offsetLeft}px`);const e=new JSDraw2.Editor(t,{width:s,height:i,skin:"w8",viewonly:!0});return p.setEditor(o.tableRowIndex,e),void p.skipCell(o.tableRowIndex)}if(d.size>0){if(!a){const e=window.devicePixelRatio;i=28,t.canvas.height=i*e,t.canvas.style.height=`${i}px`}s=a?Math.min(a.canvas.width-e,s):t.canvas.width-e,t.beginPath(),t.rect(e,n,s,i),t.clip(),t.transform(1,0,0,1,e,n),t.font="12px monospace",t.textBaseline="top";const[r,l,g]=p.getCellAllPartsLengths(o.tableRowIndex);for(let e=0;e<r.length;++e){const n=r[e],o="."===n||n.endsWith("{")||n.startsWith("}")?u:d.has(n)?h:f.has(n)?c:u;t.fillStyle=o,ft(g[e],0,s,i,t,r[e],o,0,!0,1,void 0,void 0,void 0,void 0,void 0,void 0,void 0,void 0,p.monomerTextSizeMap)}}}finally{t.restore()}}}class Ct{constructor(){this.w=200,this.h=100,this.host=r.div([],{style:{width:`${this.w}px`,height:`${this.h}px`}}),this.editor=new JSDraw2.Editor(this.host,{width:this.w,height:this.h,viewonly:!0})}resizeEditor(t,e){this.editor.setSize(t,e)}}class At{createHelmWebEditor(){return new Ct}createWebEditorApp(t,e){org.helm.webeditor.MolViewer.molscale=.8;const n=new scil.helm.App(t,{showabout:!1,mexfontsize:"90%",mexrnapinontab:!0,topmargin:20,mexmonomerstab:!0,sequenceviewonly:!1,mexfavoritefirst:!0,mexfilter:!0}),r=n.calculateSizes();n.canvas.resize(r.rightwidth-100,r.topheight-210);let s={width:r.rightwidth-100+"px",height:r.bottomheight+"px"};return scil.apply(n.sequence.style,s),scil.apply(n.notation.style,s),s={width:r.rightwidth+"px",height:r.bottomheight+n.toolbarheight+"px"},scil.apply(n.properties.parent.style,s),n.structureview.resize(r.rightwidth,r.bottomheight+n.toolbarheight),n.mex.resize(r.topheight-80),setTimeout((()=>{n.canvas.helm.setSequence(e,"HELM")}),200),n}static async getInstance(){let t=window.$helmHelper;return t||(window.$helmHelper=t=new At),t}}const bt="smiles",_t="capGroupName",wt="label";let Et=null;const yt=new s.Package;async function Tt(){return org.helm.webeditor.kCaseSensitive=!0,Promise.all([new Promise(((t,e)=>{dojo.ready((function(){t(null)}))})).then((()=>{window.dojox.gfx.svg.Text.prototype.getTextWidth=function(){const t=this.rawNode,e=t.parentNode,n=t.cloneNode(!0);n.style.visibility="hidden";let r=0;const s=n.firstChild.nodeValue;if(e.appendChild(n),""!=s){let t=100;for(;!r&&--t>0;)r=n.getBBox?parseInt(n.getBBox().width):68}return e.removeChild(n),r}})),n.functions.call("Bio:getBioLib")]).then((([t,e])=>{Et=e,St(),Et.onChanged.subscribe((t=>{try{St();const t=Et.getPolymerTypes(),e="Monomer lib updated:<br />"+(0==t.length?"empty":t.map((t=>`${t} ${Et.getMonomerSymbolsByType(t).length}`)).join("<br />"));n.shell.info(e)}catch(t){const e=h(t);console.error("Helm: initHelm monomerLib.onChanged() error:\n"+e)}}))})).catch((t=>{const e=t instanceof Error?t.message:t?t.toString():"Exception 'undefined'";n.shell.error(`Package 'Helm' init initHelm() error: ${e}`);const r=new Error(e);throw r.stack=t.stack,r}))}function Mt(){return Et}function St(){org.helm.webeditor.Monomers.clear(),Et.getPolymerTypes().forEach((t=>{Et.getMonomerSymbolsByType(t).forEach((e=>{let n=!1;const r=Et.getMonomer(t,e),s={id:e,m:r.molfile,n:r.name,na:r.naturalAnalog,rs:r.rgroups.length,type:r.polymerType,mt:r.monomerType,at:{}};if(r.rgroups.length>0){s.rs=r.rgroups.length;const t={};r.rgroups.forEach((e=>{t[e[wt]]=e[_t]})),s.at=t}else null!=r[bt]?(s.rs=Object.keys(Ht(r[bt].toString())).length,s.at=Ht(r[bt].toString())):n=!0;n||org.helm.webeditor.Monomers.addOneMonomer(s)}))}));const t=n.shell.tv?.grid;t&&t.invalidate()}function Nt(){return new pt}function vt(t,e,s){const i=ot(it(t&&void 0===s?t.value:e));0===i.size?function(t,e,s){const i=r.div(),o=n.shell.tv.grid.dataFrame.columns.bySemType("Macromolecule"),l=I.getOrCreate(o);org.helm.webeditor.MolViewer.molscale=.8;const a=new scil.helm.App(i,{showabout:!1,mexfontsize:"90%",mexrnapinontab:!0,topmargin:20,mexmonomerstab:!0,sequenceviewonly:!1,mexfavoritefirst:!0,mexfilter:!0}),h=a.calculateSizes();a.canvas.resize(h.rightwidth-100,h.topheight-210);let c={width:h.rightwidth-100+"px",height:h.bottomheight+"px"};scil.apply(a.sequence.style,c),scil.apply(a.notation.style,c),c={width:h.rightwidth+"px",height:h.bottomheight+a.toolbarheight+"px"},scil.apply(a.properties.parent.style,c),a.structureview.resize(h.rightwidth,h.bottomheight+a.toolbarheight),a.mex.resize(h.topheight-80),setTimeout((()=>{t&&void 0===s?a.canvas.helm.setSequence(t.value,"HELM"):a.canvas.helm.setSequence(e,"HELM")}),200),r.dialog({showHeader:!1,showFooter:!0}).add(i).onOK((()=>{const e=a.canvas.getHelm(!0).replace(/<\/span>/g,"").replace(/<span style='background:#bbf;'>/g,"");if(t)if(void 0===s)t.value=e;else{const n=l.convertHelmToFastaSeparator(e,s);t.value=n}})).show({modal:!0,fullScreen:!0})}(t,e,s):1===i.size&&i.has(H[o.HELM])?n.shell.warning(`WebEditor doesn't support Helm with gaps '${H[o.HELM]}'.`):n.shell.warning(`Monomers ${Array.from(i).map((t=>`'${t}'`)).join(", ")} are absent! <br/>Please, upload the monomer library! <br/><a href="https://datagrok.ai/help/domains/bio/macromolecules" target="_blank">Learn more</a>`)}function Ot(t){vt(t.cell,void 0,void 0)}function Lt(t){const e=n.shell.tv.grid.dataFrame,r=e.columns.bySemType("Macromolecule"),i=I.getOrCreate(r);r.getTag(s.TAGS.UNITS)===o.HELM&&vt(e.currentCell,void 0,void 0);const l=i.getConverter(o.HELM)(t);vt(e.currentCell,l,r.getTag(s.TAGS.UNITS))}function xt(t){return function(t){const e=I.getOrCreate(t.cell.column),n=function(t,e){const n=st(e.isHelm()?t:e.getConverter(o.HELM)(t)),s=r.div([],{style:{width:"0",height:"0"}});document.documentElement.appendChild(s);try{const t=new JSDraw2.Editor(s,{viewonly:!0});t.setHelm(n);const e=t.getFormula(!0),r=Math.round(100*t.getMolWeight())/100,i=Math.round(100*t.getExtinctionCoefficient(!0))/100;return{formula:e.replace(/<sub>/g,"").replace(/<\/sub>/g,""),"molecular weight":r,"extinction coefficient":i}}finally{a()(s).empty(),s.remove()}}(t.value,e);return new s.Widget(r.tableFromMap(n))}(t)}function Ht(t){const e=t.match(/(?<=\[)[^\][]*(?=])/gm),n={};let r,s="";if(e)for(let t=0;t<e.length;t++)if(null!=e[t]&&/\d/.test(e[t])){r=e[t][e[t].length-1],e[t]=e[t].replace(/[0-9]/g,"");for(let n=0;n<e[t].length;n++)":"!=e[t][n]&&(s+=e[t][n]);n["R"+r]=s,s=""}return n}function It(t){const e=s.Column.string("mols",t.length),n=r.div([],{style:{width:"0",height:"0"}});document.documentElement.appendChild(n);try{const r=new JSDraw2.Editor(n,{viewonly:!0});return e.init((e=>(r.setHelm(t.get(e)),r.getMolfile()))),e}finally{a()(n).empty(),n.remove()}}async function Rt(){return At.getInstance()}helm=e})();
1
+ var helm;(()=>{"use strict";var t={n:e=>{var n=e&&e.__esModule?()=>e.default:()=>e;return t.d(n,{a:n}),n},d:(e,n)=>{for(var r in n)t.o(n,r)&&!t.o(e,r)&&Object.defineProperty(e,r,{enumerable:!0,get:n[r]})},o:(t,e)=>Object.prototype.hasOwnProperty.call(t,e),r:t=>{"undefined"!=typeof Symbol&&Symbol.toStringTag&&Object.defineProperty(t,Symbol.toStringTag,{value:"Module"}),Object.defineProperty(t,"__esModule",{value:!0})}},e={};t.r(e),t.d(e,{_package:()=>yt,editMoleculeCell:()=>Lt,getHelmHelper:()=>Pt,getMolfiles:()=>It,getMonomerLib:()=>Mt,helmCellRenderer:()=>Nt,initHelm:()=>St,openEditor:()=>Ht,propertiesWidget:()=>xt});const n=grok,r=ui,s=DG,i=$;var o,l,a=t.n(i);function h(t){var e;return"string"==typeof t||t instanceof String?t:("object"==typeof t||t instanceof Object)&&"$thrownJsError"in t?h(t.$thrownJsError):t instanceof Error?null!==(e=t.stack)&&void 0!==e?e:t.message:t.toString()}class c{constructor(t,e,n){this.name=t,this.alphabet=e,this.cutoff=n}}class g extends c{constructor(t,e,n){super(t.name,t.alphabet,t.cutoff),this.freq=e,this.similarity=n}}(l=o||(o={})).FASTA="fasta",l.SEPARATOR="separator",l.HELM="helm";const u=/(?:\[([A-Za-z0-9_\-,()]+)\])|([A-Za-z\-])/g,m=new class{constructor(){this.fasta={peptide:new Set(["G","L","Y","S","E","Q","D","N","F","A","K","R","H","C","V","P","W","I","M","T"]),dna:new Set(["A","C","G","T"]),rna:new Set(["A","C","G","U"])}}},f=[new c("PT",m.fasta.peptide,.5),new c("DNA",m.fasta.dna,.55),new c("RNA",m.fasta.rna,.55)],d=wu;var p=t.n(d);function C(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,s=new Float32Array((n.length+r)*(n.length+r));return Object.entries(e).forEach((([t,r])=>{const i=n[r];Object.entries(e).forEach((([e,r])=>{s[t.charCodeAt(0)*n.length+e.charCodeAt(0)]=i[r]}))})),(t,e)=>s[t.charCodeAt(0)*n.length+e.charCodeAt(0)]}(),n=t?.threshold??0;return(t,r)=>{let s=0;const i=t.length,o=r.length,l=Math.max(i,o)*(1-n);i!==o&&(s=Math.abs(i-o));let a=0;for(let n=0;n<Math.min(i,o);n++)if(t[n]!==r[n]&&(a+=e(t[n],r[n]),a>l))return 1;return a+=s,a/=Math.max(i,o),a}}const A=new Uint32Array(65536),b={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 _;!function(t){t.HAMMING="Hamming",t.LEVENSHTEIN="Levenshtein",t.NEEDLEMANN_WUNSCH="Needlemann-Wunsch",t.MONOMER_CHEMICAL_DISTANCE="Monomer chemical distance"}(_||(_={}));const w={[_.HAMMING]:C,[_.LEVENSHTEIN]:function(){return(t,e)=>((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,r=e.length,s=1<<n-1;let i=-1,o=0,l=n,a=n;for(;a--;)A[t.charCodeAt(a)]|=1<<a;for(a=0;a<r;a++){let t=A[e.charCodeAt(a)];const n=t|o;t|=(t&i)+i^i,o|=~(t|i),i&=t,o&s&&l++,i&s&&l--,o=o<<1|1,i=i<<1|~(n|o),o&=n}for(a=n;a--;)A[t.charCodeAt(a)]=0;return l})(t,e):((t,e)=>{const n=e.length,r=t.length,s=[],i=[],o=Math.ceil(n/32),l=Math.ceil(r/32);for(let t=0;t<o;t++)i[t]=-1,s[t]=0;let a=0;for(;a<l-1;a++){let o=0,l=-1;const h=32*a,c=Math.min(32,r)+h;for(let e=h;e<c;e++)A[t.charCodeAt(e)]|=1<<e;for(let t=0;t<n;t++){const n=A[e.charCodeAt(t)],r=i[t/32|0]>>>t&1,a=s[t/32|0]>>>t&1,h=n|o,c=((n|a)&l)+l^l|n|a;let 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Items"}(H||(H={})),O.Tanimoto,O.Dice,O.Asymmetric,O.BraunBlanquet,O.Cosine,O.Kulczynski,O.McConnaughey,O.RogotGoldberg,O.Russel,O.Sokal,O.Hamming,O.Euclidean,O.Tanimoto,O.Dice,O.Asymmetric,O.BraunBlanquet,O.Cosine,O.Kulczynski,O.McConnaughey,O.RogotGoldberg,O.Russel,O.Sokal,O.Hamming,O.Euclidean,O.Tanimoto,O.Dice,O.Cosine,O.Tanimoto,O.Asymmetric,O.Cosine,O.Sokal,_.HAMMING,_.LEVENSHTEIN,_.MONOMER_CHEMICAL_DISTANCE,_.NEEDLEMANN_WUNSCH;const x=new class{constructor(){this.uh=`units-handler.${s.SEMTYPE.MACROMOLECULE}`}},R={[o.FASTA]:"-",[o.SEPARATOR]:"",[o.HELM]:"*"};class I{constructor(t){if(this._splitter=null,this.cached=!0,this._splitted=null,this.columnVersion=null,this._stats=null,this._maxLength=null,this._posList=null,this._joiner=void 0,t.type!==s.TYPE.STRING)throw new Error(`Unexpected column type '${t.type}', must be '${s.TYPE.STRING}'.`);this._column=t,this._columnVersion=t.version;const e=this._column.getTag(s.TAGS.UNITS);if(null==e)throw new Error("Units are not specified in column");if(this._units=e,this._notation=this.getNotation(),this._defaultGapOriginal=this.isFasta()?R[o.FASTA]:this.isHelm()?R[o.HELM]:R[o.SEPARATOR],!this.column.tags.has("aligned")||!this.column.tags.has("alphabet")||!this.column.tags.has(".alphabetIsMultichar")&&!this.isHelm()&&"UN"===this.alphabet)if(this.isFasta())I.setUnitsToFastaColumn(this);else if(this.isSeparator()){const e=t.getTag("separator");I.setUnitsToSeparatorColumn(this,e)}else{if(!this.isHelm())throw new Error(`Unexpected units '${this.column.getTag(s.TAGS.UNITS)}'.`);I.setUnitsToHelmColumn(this)}if(!this.column.tags.has(".alphabetIsMultichar"))if(this.isHelm())this.column.setTag(".alphabetIsMultichar","true");else if(["UN"].includes(this.alphabet))throw new Error(`For column '${this.column.name}' of alphabet '${this.alphabet}' tag '.alphabetIsMultichar' is mandatory.`)}static setUnitsToFastaColumn(t){if(t.column.semType!==s.SEMTYPE.MACROMOLECULE||t.column.getTag(s.TAGS.UNITS)!==o.FASTA)throw new Error(`The column of notation '${o.FASTA}' must be '${s.SEMTYPE.MACROMOLECULE}'.`);t.column.setTag(s.TAGS.UNITS,o.FASTA),I.setTags(t)}static setUnitsToSeparatorColumn(t,e){if(t.column.semType!==s.SEMTYPE.MACROMOLECULE||t.column.getTag(s.TAGS.UNITS)!==o.SEPARATOR)throw new Error(`The column of notation '${o.SEPARATOR}' must be '${s.SEMTYPE.MACROMOLECULE}'.`);if(!e)throw new Error(`The column of notation '${o.SEPARATOR}' must have the separator tag.`);t.column.setTag(s.TAGS.UNITS,o.SEPARATOR),t.column.setTag("separator",e),I.setTags(t)}static setUnitsToHelmColumn(t){if(t.column.semType!==s.SEMTYPE.MACROMOLECULE)throw new Error(`The column of notation '${o.HELM}' must be '${s.SEMTYPE.MACROMOLECULE}'`);t.column.setTag(s.TAGS.UNITS,o.HELM),I.setTags(t)}static setTags(t){const e=t.column.getTag(s.TAGS.UNITS),n=t.stats;if(Object.keys(n.freq).some((t=>t.length>1)),[o.FASTA,o.SEPARATOR].includes(e)){if(!t.column.getTag("alphabet")&&0===Object.keys(n.freq).length)throw new Error("Alphabet is empty and not annotated.");let e=t.column.getTag("aligned");null===e&&(e=n.sameLength?"SEQ.MSA":"SEQ",t.column.setTag("aligned",e));let r=t.column.getTag("alphabet");if(null===r&&(r=function(t,e,n="-"){const r=e.map((e=>{const r=function(t,e,n="-"){const r=new Set([...new Set(Object.keys(t)),...e]);r.delete(n);const s=[],i=[];for(const n of r)s.push(n in t?t[n]:0),i.push(e.has(n)?1:0);const o=new B(s),l=new B(i);return function(t,e){if(t.length!=e.length)throw new Error("The dimensionality of the vectors must match");let n=0;for(let r=0;r<t.length;r++)n+=t[r]*e[r];return n}(o,l)/(k(o)*k(l))}(t,e.alphabet,n);return new g(e,t,r)}));let s;const i=Math.max(...r.map((t=>t.similarity>t.cutoff?t.similarity:-1)));s=i>0?r.find((t=>t.similarity===i)).name:"UN";return s}(n.freq,f),t.column.setTag("alphabet",r)),"UN"===r){const e=Object.keys(n.freq).length,r=Object.keys(n.freq).some((t=>t.length>1));t.column.setTag(".alphabetSize",e.toString()),t.column.setTag(".alphabetIsMultichar",r?"true":"false")}}}get column(){return this._column}get length(){return this._column.length}get units(){return this._units}get notation(){return this._notation}get defaultGapOriginal(){return this._defaultGapOriginal}get separator(){const t=this.column.getTag("separator")??void 0;if(this.notation===o.SEPARATOR&&void 0===t)throw new Error(`Separator is mandatory for column '${this.column.name}' of notation '${this.notation}'.`);return t}get aligned(){const t=this.column.getTag("aligned");if(!t&&(this.isFasta()||this.isSeparator()))throw new Error("Tag aligned not set");return t}get alphabet(){const t=this.column.getTag("alphabet");if(!t&&(this.isFasta()||this.isSeparator()))throw new Error("Tag alphabet not set");return t}get helmCompatible(){return this.column.getTag(".isHelmCompatible")}getAlphabetSize(){if(this.notation==o.HELM||"UN"==this.alphabet){const t=this.column.getTag(".alphabetSize");let e;if(t)e=parseInt(t);else{const t=this.stats;e=Object.keys(t.freq).length}return e}switch(this.alphabet){case"PT":return 20;case"DNA":case"RNA":return 4;case"NT":return console.warn("Unexpected alphabet 'NT'."),4;default:throw new Error(`Unexpected alphabet '${this.alphabet}'.`)}}getAlphabetIsMultichar(){return this.notation===o.HELM||"UN"===this.alphabet&&"true"===this.column.getTag(".alphabetIsMultichar")}getSplitted(t){if(this.cached){this.column.version===this.columnVersion&&null!==this._splitted||(this.columnVersion=this.column.version,this._splitted=new Array(this.column.length));let e=this._splitted[t]?this._splitted[t].deref():void 0;if(!e){const n=this.column.get(t);e=this.splitter(n),this._splitted[t]=new WeakRef(e)}return e}{const e=this.column.get(t);return this.splitter(e)}}get stats(){if(null===this._stats){const t={};let e=!0,n=null;const r=this.column.length;for(let s=0;s<r;++s){const r=this.getSplitted(s);null==n?n=r.length:r.length!==n&&(e=!1);for(const e of r.canonicals)e in t||(t[e]=0),t[e]+=1}this._stats={freq:t,sameLength:e}}return this._stats}get maxLength(){return null===this._maxLength&&(this._maxLength=0===this.column.length?0:Math.max(...p().count(0).take(this.column.length).map((t=>this.getSplitted(t).length)))),this._maxLength}get posList(){if(null===this._posList){const t=this.column.getTag(".positionNames");this._posList=t?t.split(", ").map((t=>t.trim())):p().count(1).take(this.maxLength).map((t=>t.toString())).toArray()}return this._posList}isFasta(){return this.notation===o.FASTA}isSeparator(){return this.notation===o.SEPARATOR}isHelm(){return this.notation===o.HELM}isRna(){return"RNA"===this.alphabet}isDna(){return"DNA"===this.alphabet}isPeptide(){return"PT"===this.alphabet}isMsa(){return!!this.aligned&&this.aligned.toUpperCase().includes("MSA")}isHelmCompatible(){return"true"===this.helmCompatible}isGap(t){return!t||t===this._defaultGapOriginal}getNotation(){if(this.units.toLowerCase().startsWith(o.FASTA))return o.FASTA;if(this.units.toLowerCase().startsWith(o.SEPARATOR))return o.SEPARATOR;if(this.units.toLowerCase().startsWith(o.HELM))return o.HELM;throw new Error(`Column '${this.column.name}' has unexpected notation '${this.units}'.`)}getHelmWrappers(){return[this.isDna()||this.isRna()||this.isHelmCompatible()?"RNA1{":"PEPTIDE1{",this.isDna()?"d(":this.isRna()?"r(":"",this.isDna()||this.isRna()?")p":"","}$$$$"]}getNewColumn(t,e,n,r){const i=this.column,l=t.toLowerCase()+"("+i.name+")",a=n??i.dataFrame.columns.getUnusedName(l),h=s.Column.fromList("string",a,r??new Array(this.column.length).fill(""));if(h.semType=s.SEMTYPE.MACROMOLECULE,h.setTag(s.TAGS.UNITS,t),t===o.SEPARATOR){if(!e)throw new Error(`Notation '${o.SEPARATOR}' requires separator value.`);h.setTag("separator",e)}h.setTag(s.TAGS.CELL_RENDERER,"sequence");const c=i.getTag("aligned");c&&h.setTag("aligned",c);let g=i.getTag("alphabet");g||this.notation!==o.HELM||t===o.HELM||(g="UN"),null!=g&&h.setTag("alphabet",g);let u=i.getTag(".alphabetSize");null!=g&&u&&h.setTag(".alphabetSize",u);const m=i.getTag(".alphabetIsMultichar");return null!=g&&void 0!==m&&h.setTag(".alphabetIsMultichar",m),t==o.HELM&&(u=this.getAlphabetSize().toString(),h.setTag(".alphabetSize",u)),h}getNewColumnFromList(t,e){return this.getNewColumn(this.notation,this.separator,t,e)}static getNewColumn(t){const e=I.forColumn(t),n=e.notation;return e.getNewColumn(n)}static unitsStringIsValid(t){return t=t.toLowerCase(),[o.FASTA,o.SEPARATOR,o.HELM].some((e=>t.startsWith(e.toLowerCase())))}static getNewColumnFromParams(t,e,n){if(!I.unitsStringIsValid(n))throw new Error("Invalid format of 'units' parameter");const r=s.Column.fromList("string",e,new Array(t).fill(""));return r.semType=s.SEMTYPE.MACROMOLECULE,r.setTag(s.TAGS.UNITS,n),r}getSplitter(t){if(this.units.toLowerCase().startsWith(o.FASTA))return null===this.column.getTag("alphabet")||this.getAlphabetIsMultichar()?K:J;if(this.units.toLowerCase().startsWith(o.SEPARATOR))return Q(this.separator,t);if(this.units.toLowerCase().startsWith(o.HELM))return tt;throw new Error(`Unexpected units ${this.units} .`)}split(t){return this.splitter(t)}getDistanceFunctionName(){if(!this.isFasta())throw new Error("Only FASTA notation is supported");return this.isMsa()?_.HAMMING:(this.alphabet,_.LEVENSHTEIN)}getDistanceFunction(){return w[this.getDistanceFunctionName()]()}async checkHelmCompatibility(){if(this.column.tags.has(".isHelmCompatible"))return"true"===this.column.getTag(".isHelmCompatible");const t=(await async function(){const t=s.Func.find({package:"Bio",name:"getMonomerLibHelper"});if(0===t.length)throw new Error('Package "Bio" must be installed for MonomerLibHelper.');return(await t[0].prepare().call()).getOutputParamValue()}()).getBioLib().getMonomerSymbolsByType("PEPTIDE".toString()),e=new Set(t),n=(Q(this.separator),new Set),r=this.column.length,i=this.column.getRawData();for(let t=0;t<r;++t){const r=i[t];if(!(r in n)){n.add(r);const s=this.getSplitted(t);for(const t of s.canonicals)if(!e.has(t))return this.column.setTag(".isHelmCompatible","false"),!1}}return this.column.setTag(".isHelmCompatible","true"),!0}get splitter(){return null===this._splitter&&(this._splitter=this.getSplitter()),this._splitter}toFasta(t){return t===o.FASTA}toSeparator(t){return t===o.SEPARATOR}toHelm(t){return t===o.HELM}convertHelmToFastaSeparator(t,e,n,r){r||(r=this.toFasta(e)?R[o.FASTA]:R[o.SEPARATOR]),n||(n=this.toFasta(e)?"":this.separator);const s=t.startsWith("RNA"),i=this.splitter(t),l=[];for(let t=0;t<i.length;++t){let n=i.getOriginal(t);if(s&&(n=n.replace(E,"")),n===R[o.HELM])l.push(r);else if(this.toFasta(e)&&n.length>1){const t="["+n+"]";l.push(t)}else l.push(n)}return l.join(n)}convert(t,e){const n=this.getJoiner({notation:t,separator:e}),r=this.getNewColumn(t,e);return r.init((t=>{const e=this.getSplitted(t);return n(e)})),r}getRegion(t,e,n){const r=this.getNewColumn(this.notation,this.separator);r.name=n;const s=t??0,i=e??this.maxLength-1,o=this.getJoiner(),l=i-s+1;r.init((t=>{const e=this.getSplitted(t),n=new Array(l);for(let t=0;t<l;++t){const r=s+t,i=e.getOriginal(r);n[t]=r<e.length?i:R[this.notation]}return o(new z(n,R[this.notation]))}));const a=t=>{const e=t.split(",").map((t=>t.trim())),n=new Array(l);for(let t=0;t<l;++t){const r=s+t;n[t]=r<e.length?e[r]:"?"}return n.join(", ")},h=this.column.getTag(".positionNames");h&&r.setTag(".positionNames",a(h));const c=this.column.getTag(".positionLabels");return c&&r.setTag(".positionLabels",a(c)),r}get joiner(){return this._joiner||(this._joiner=this.getJoiner()),this._joiner}getJoiner(t){const e=t?t.notation:this.notation,n=t?t.separator:this.separator;let r;const s=this;switch(e){case o.FASTA:r=function(t){return s.joinToFasta(t,s.isHelm())};break;case o.SEPARATOR:if(!n)throw new Error(`Separator is mandatory for notation '${e}'.`);r=function(t){return P(t,n,s.isHelm())};break;case o.HELM:{const t="DNA"===s.alphabet||"RNA"===s.alphabet,e=s.getHelmWrappers();r=function(n){return F(n,e,t)};break}default:throw new Error(`Unexpected notation '${e}'.`)}return r}getConverter(t,e=void 0){if(t===o.SEPARATOR&&!e)throw new Error(`Target separator is not specified for target units '${o.SEPARATOR}'.`);const n=this;if(t===o.FASTA)return function(t){return n.convertToFasta(t)};if(t===o.HELM)return function(t){return n.convertToHelm(t)};if(t===o.SEPARATOR)return function(t){return n.convertToSeparator(t,e)};throw new Error}static forColumn(t){let e=t.temp[x.uh];return e&&e.columnVersion===t.version||(e=t.temp[x.uh]=new I(t)),e}joinToFasta(t,e){const n=new Array(t.length);for(let r=0;r<t.length;++r){const s=t.getOriginal(r);let i=t.getOriginal(r);e&&(i=i.replace(E,"$1")),""===s?i=R[o.FASTA]:s===T?i="":i.length>1&&(i="["+i+"]"),n[r]=i}return n.join("")}convertToFasta(t){const e=this.splitter,n=this.isHelm()?this.splitterAsHelmNucl(t):e(t);return this.joinToFasta(n,this.isHelm())}convertToSeparator(t,e){return P(this.isHelm()?this.splitterAsHelmNucl(t):this.splitter(t),e,this.isHelm())}convertToHelm(t){const e=this.getHelmWrappers(),n=t.startsWith("DNA")||t.startsWith("RNA");return F(this.splitter(t),e,n)}splitterAsHelmNucl(t){const e=this.splitter(t),n=new Array(e.length),r=t.startsWith("DNA"),s=t.startsWith("RNA");for(let t=0;t<e.length;++t){let i=e.getOriginal(t);(r||s)&&(i=i.replace(E,"$1"),i=i===T?null:i),n[t]=i||null}return new z(n.filter((t=>!!t)),R[o.HELM])}}function P(t,e,n){const r=new Array(t.length);for(let e=0;e<t.length;++e){const s=t.getCanonical(e);let i=t.getOriginal(e);n&&(i=i.replace(E,"$1")),""===s?i=R[o.SEPARATOR]:s===T&&(i=""),r[e]=i}return r.join(e)}function F(t,e,n){const[r,s,i,l]=e,a=new Array(t.length);for(let e=0;e<t.length;++e){const r=t.getCanonical(e);let l=t.getOriginal(e);""===r?l=R[o.HELM]:(n&&(l=l.replace(E,"$1")),l=1===l.length?`${s}${l}${i}`:`${s}[${l}]${i}`),a[e]=l}return`${r}${a.join(".")}${l}`}class B extends Float32Array{}function k(t){let e=0;for(let n=0;n<t.length;n++)e+=t[n]*t[n];return Math.sqrt(e)}class G{static makePalette(t,e=!1,n=G){const r={};return t.forEach((t=>{const n=t[0],s=t[1];n.forEach(((t,n)=>{r[t]=this.colourPalette[s][e?0:n]}))})),new n(r)}constructor(t){this._palette=t}get(t){return this._palette[t]}}G.undefinedColor="rgb(100,100,100)",G.colourPalette={orange:["rgb(255,187,120)","rgb(245,167,100)","rgb(235,137,70)","rgb(205, 111, 71)"],all_green:["rgb(44,160,44)","rgb(74,160,74)","rgb(23,103,57)","rgb(30,110,96)","rgb(60,131,95)","rgb(24,110,79)","rgb(152,223,138)","rgb(182, 223, 138)","rgb(152, 193, 138)"],all_blue:["rgb(31,119,180)","rgb(23,190,207)","rgb(122, 102, 189)","rgb(158,218,229)","rgb(141, 124, 217)","rgb(31, 120, 150)"],magenta:["rgb(162,106,192)","rgb(197,165,224)","rgb(208,113,218)"],red:["rgb(214,39,40)","rgb(255,152,150)"],st_blue:["rgb(23,190,207)","rgb(158,218,229)","rgb(31,119,180)"],dark_blue:["rgb(31,119,180)","rgb(31, 120, 150)"],light_blue:["rgb(23,190,207)","rgb(158,218,229)","rgb(108, 218, 229)","rgb(23,190,227)"],lilac_blue:["rgb(124,102,211)","rgb(149,134,217)","rgb(97, 81, 150)"],dark_green:["rgb(23,103,57)","rgb(30,110,96)","rgb(60,131,95)","rgb(24,110,79)"],green:["rgb(44,160,44)","rgb(74,160,74)"],light_green:["rgb(152,223,138)","rgb(182, 223, 138)","rgb(152, 193, 138)"],st_green:["rgb(44,160,44)","rgb(152,223,138)","rgb(39, 174, 96)","rgb(74,160,74)"],pink:["rgb(247,182,210)"],brown:["rgb(140,86,75)","rgb(102, 62, 54)"],gray:["rgb(127,127,127)","rgb(199,199,199)","rgb(196,156,148)","rgb(222, 222, 180)"],yellow:["rgb(188,189,34)"],white:["rgb(230,230,230)"]};class U extends G{static get Lesk(){return void 0===this.lesk&&(this.lesk=this.makePalette([[["G","A","S","T"],"orange"],[["C","V","I","L","P","F","Y","M","W"],"all_green"],[["N","Q","H"],"magenta"],[["D","E"],"red"],[["K","R"],"all_blue"]],!1,U)),this.lesk}static get GrokGroups(){return void 0===this.grokGroups&&(this.grokGroups=this.makePalette([[["C","U"],"yellow"],[["G","P"],"red"],[["A","V","I","L","M","F","Y","W"],"all_green"],[["R","H","K"],"light_blue"],[["D","E"],"dark_blue"],[["S","T","N","Q"],"orange"]],!1,U)),this.grokGroups}static get RasMol(){return void 0===this.rasMol&&(this.rasMol=new U({D:"#E60A0A",E:"#E60A0A",C:"#E6E600",M:"#E6E600",K:"#145AFF",R:"#145AFF",S:"#FA9600",T:"#FA9600",F:"#3232AA",Y:"#3232AA",N:"#00DCDC",Q:"#00DCDC",G:"#EBEBEB",L:"#0F820F",V:"#0F820F",I:"#0F820F",A:"#C8C8C8",W:"#B45AB4",H:"#8282D2",P:"#DC9682",others:"#BEA06E"})),this.rasMol}get(t){const e=t in U.aaSynonyms?U.aaSynonyms[t]:t;return super.get(e)}}U.aaSynonyms={MeNle:"L",MeA:"A",MeG:"G",MeF:"F"};class D{static getPalette(t="grok"){switch(t){case"grok":return U.GrokGroups;case"lesk":return U.Lesk;default:throw new Error(`ChemPalette: scheme \`${t}\` does not exist`)}}static getInnerOuter(t){let e=0,n="",r="";for(const s of t)"("==s?e++:")"==s?e--:e?n+=s:r+=s;return isNaN(parseInt(n))?[r,n]:[r,""]}static getColorAAPivot(t="",e="grok"){const n=this.getPalette(e);let[r,s]=this.getInnerOuter(t);if(r=r.length>6?`${r.slice(0,3)}...`:r,s=s.length>6?`${s.slice(0,3)}...`:s,1==t.length||"("==t[1]){const e=t[0]?.toUpperCase();return e in n?[n.get(e),e,s,1]:[this.undefinedColor,r,s,1]}if("d"==t[0]&&t[1]in n&&(2==t.length||"("==t[2])){const e=t[1]?.toUpperCase();return e in n?[n.get(e),e,s,2]:[this.undefinedColor,r,s,2]}if(t.substring(0,3)in this.AAFullNames&&(3==t.length||"("==t[3])){const e=this.AAFullNames[t.substring(0,3)];return e in n?[n.get(e),e,s,3]:[this.undefinedColor,r,s,3]}if(t[0]?.toLowerCase()==t[0]&&t.substring(1,3)in this.AAFullNames&&(4==t.length||"("==t[4])){const e=this.AAFullNames[t.substring(1,3)];return e in n?[n.get(e),e,s,4]:[this.undefinedColor,r,s,4]}return[this.undefinedColor,r,s,0]}}D.SemType="Aminoacids",D.SemTypeMultipleAlignment="AminoacidsMultipleAlignment",D.undefinedColor="rgb(100,100,100)",D.Names={G:"Glycine",L:"Leucine",Y:"Tyrosine",S:"Serine",E:"Glutamic acid",Q:"Glutamine",D:"Aspartic acid",N:"Asparagine",F:"Phenylalanine",A:"Alanine",K:"Lysine",R:"Arginine",H:"Histidine",C:"Cysteine",V:"Valine",P:"Proline",W:"Tryptophan",I:"Isoleucine",M:"Methionine",T:"Threonine"},D.AASmiles={G:"NCC(=O)O",L:"N[C@H](CC(C)C)C(=O)O",Y:"NC(CC1=CC=C(O)C=C1)C(=O)O",S:"NC(CO)C(=O)O",E:"N[C@@H](CCC(O)=O)C(=O)O",Q:"N[C@@H](CCC(N)=O)C(=O)O",D:"N[C@@H](CC(O)=O)C(=O)O",N:"N[C@@H](CC(N)=O)C(=O)O",F:"NC(CC1=CC=CC=C1)C(=O)O",A:"N[C@H](C)C(=O)O",K:"NC(CCCCN)C(=O)O",R:"N[C@H](CCCNC(=N)C)C(=O)O",H:"NC(CC1=CN=C[N]1)C(=O)O",C:"N[C@@H](CS)C(=O)O",V:"NC(C(C)C)C(=O)O",P:"N(CCC1)C1C(=O)O",W:"N[C@@H](Cc1c2ccccc2n([H])c1)C(=O)O",I:"N[C@H]([C@H](C)CC)C(=O)O",M:"NC(CCSC)C(=O)O",T:"NC(C(O)C)C(=O)O"},D.AASmilesTruncated={G:"*C*",L:"CC(C)C[C@H](*)*",Y:"C1=CC(=CC=C1CC(*)*)O",S:"OCC(*)C*",E:"*[C@@H](CCC(O)=O)*",Q:"*N[C@@H](CCC(N)=O)*",D:"*[C@@H](CC(O)=O)*",N:"*[C@@H](CC(N)=O)*",F:"C1=CC=C(C=C1)CC(*)*",A:"C[C@H](*)*",K:"C(CCN)CC(*)*",R:"*[C@H](CCCNC(=N)C)*",H:"C1=C(NC=N1)CC(*)*",C:"C([C@@H](*)*)S",V:"CC(C)C(*)*",P:"C1CCN(*)C1*",W:"*[C@@H](Cc1c2ccccc2n([H])c1)*",I:"CC[C@H](C)[C@H](*)*",M:"CSCCC(*)*",T:"CC(O)C(*)*"},D.AAFullNames={Ala:"A",Arg:"R",Asn:"N",Asp:"D",Cys:"C",Gln:"Q",Glu:"E",Gly:"G",His:"H",Ile:"I",Leu:"L",Lys:"K",Met:"M",Phe:"F",Pro:"P",Ser:"S",Thr:"T",Trp:"W",Tyr:"Y",Val:"V"};class V{}V.SemType="Nucleotides",V.SemTypeMultipleAlignment="NucleotidesMultipleAlignment",V.Names={A:"Adenine",C:"Cytosine",G:"Guanine",T:"Thymine",U:"Uracil"};class W{static hashCode(t){let e=0;if(0===t.length)return e;for(let n=0;n<t.length;n++)e=(e<<5)-e+t.charCodeAt(n),e|=0;return e}}class j{}class q extends j{static buildPalette(){return[].concat(...Object.values(G.colourPalette))}get(t){const e=W.hashCode(t)%q.palette.length;return function(t){if(null==t)return"rgb(100,100,100)";const e=s.Color.fromHtml(t),n=s.Color.g(e),r=s.Color.r(e),i=s.Color.b(e),o=Math.sqrt(Math.pow(0-r,2)+Math.pow(0-n,2)+Math.pow(0-i,2));return o>210?`rgb(${r/o*210},${n/o*210},${i/o*210})`:s.Color.toRgb(e)}(q.palette[e])}}q.palette=q.buildPalette();class z{get length(){return this.mList.length}get canonicals(){return this.mList}get originals(){return this.mList}isGap(t){return this.getOriginal(t)===this.gapOriginalMonomer}getCanonical(t){return this.mList[t]}getOriginal(t){return this.mList[t]}constructor(t,e){this.mList=t,this.gapOriginalMonomer=e}}class Y{get length(){return this.seqS.length}get canonicals(){return this.seqS}get originals(){return this.seqS}isGap(t){return this.getOriginal(t)===R[o.FASTA]}getCanonical(t){return this.isGap(t)?"":this.seqS[t]}getOriginal(t){return this.seqS[t]}constructor(t){this.seqS=t}}const K=t=>{const e=p()(t.toString().matchAll(u)).map((t=>t[2]??t[1])).toArray();return new z(e,R[o.FASTA])},J=t=>t?new Y(t):new z([],R[o.FASTA]);function Q(t,e=void 0){return n=>{if(n){const r=n.replaceAll('"-"',"").replaceAll("'-'","").split(t,e);return new z(r,R[o.SEPARATOR])}return new z([],R[o.SEPARATOR])}}const Z=/(PEPTIDE1|DNA1|RNA1)\{([^}]+)}/g,X=/\[([^\[\]]+)]/g,tt=t=>{Z.lastIndex=0;const e=Z.exec(t.toString()),n=e?e[2]:null,r=n?n.split("."):[];return new z(r.map((t=>{X.lastIndex=0;const e=X.exec(t);return e&&e.length>=2?e[1]:t})),R[o.HELM])},et=/([^\W_]+)/g;const nt=/\{(\*\.)+/g,rt=/\.(\*\.)+/g,st=/(\.\*)+\}/g;function it(t){return t.replaceAll(nt,"{").replaceAll(rt,".").replaceAll(st,"}").replace("{*}","{}")}function ot(t){t=ct(t,"$")[0];const e=[];if(!scil.Utils.isNullOrEmpty(t)){const n=ct(t,"|");for(let r=0;r<n.length;++r){let s=(t=gt(n[r]).str).indexOf("{");s=(t=t.substring(s+1)).indexOf("}");const i=ct(t=t.substring(0,s),".");for(const t of i)if(t&&""!==t)if(t.startsWith("[")&&t.includes("]")){const n=at(t,1,"[","]"),r=t.substring(1,n);e.push(r);const s=t.substring(n+1);i.push(s)}else if(t.includes("[")&&t.endsWith("]")){const n=ht(t,t.length-2,"[","]"),r=t.substring(n+1,t.length-1);e.push(r);const s=t.substring(0,n);i.push(s)}else if(t.includes("(")&&t.includes(")")){const e=t.substring(0,t.indexOf("(")),n=t.substring(t.lastIndexOf(")")+1),r=[e,t.substring(e.length+1,t.length-n.length-1),n];for(const t of r)i.push(t)}else e.push(t)}}return e}function lt(t){const e=Object.keys(org.helm.webeditor.monomerTypeList()),n=[],r=[];for(let t=0;t<e.length;t++)n.push(new scil.helm.Monomers.getMonomerSet(e[t])),Object.keys(n[t]).forEach((e=>{r.push(n[t][e].id)}));return new Set(t.filter((t=>!r.includes(t))))}function at(t,e,n,r){let s=e,i=0;for(;s<t.length;){if(t[s]===n&&i++,t[s]===r){if(0===i)return s;i--}s++}return-1}function ht(t,e,n,r){let s=e,i=0;for(;s>=0;){if(t[s]===r&&i++,t[s]===n){if(0===i)return s;i--}s--}return-1}function ct(t,e){const n=[];let r="",s=0,i=0,o=0,l=0;for(let a=0;a<t.length;++a){let h=t.substring(a,a+1);if(h==e&&0==i&&0==s&&0==o&&0==l)n.push(r),r="";else{if(r+=h,l>0&&"\\"==h&&a+1<t.length){++a;const e=t.substring(a,a+1);r+=e,h+=e}'"'==h?a>0&&"\\"==t.substring(a-1,a)||(l=0==l?1:0):"["==h?++i:"]"==h?--i:"("==h?++s:")"==h?--s:"{"==h?++o:"}"==h&&--o}}return n.push(r),n}function gt(t){const e=ut(t,'"');if(null!=e.tag)return e;const n=ut(t,"'");return{tag:e.tag,repeat:n.tag,str:n.str}}function ut(t,e){let n=null;if(scil.Utils.endswith(t,e)){let r=t.length-1;for(;r>0&&(r=t.lastIndexOf(e,r-1),!(r<=0||"\\"!=t.substring(r-1,r))););r>0&&r<t.length-1&&(n=t.substring(r+1,t.length-1),t=t.substring(0,r))}return null!=n&&(n=function(t){return scil.Utils.isNullOrEmpty(t)?t:t.replace(/[\\]./g,(function(t){switch(t){case"\\r":return"\r";case"\\n":return"\n";case"\\t":return"\t";default:return t.substring(1)}}))}(n.replace(new RegExp("\\"+e,"g"),e))),{tag:n,str:t}}var mt,ft;function dt(t,e,n,r,s,i,o="rgb(100,100,100)",l=0,a=!1,h=1,c="",g=!1,u=ft.classic,m=[],f=0,d=null,p=null,C=null,A={}){s.textAlign="start";let b=i.substring(0),_=g?"":c;u===ft.MSA&&(_="");let w=!0,T=!0,E="difference";if(null!=d&&null!=d.cell.column&&(w=d.cell.column.temp["color-code"]??!0,T=d.cell.column.temp["compare-with-current"]??!0,E=d.cell.column.temp["highlight-difference"]??"difference"),p){const t=p[f];T&&p.length>0&&"difference"===E&&(h=b==t?.3:h),T&&p.length>0&&"equal"===E&&(h=b!=t?.3:h)}null!=C&&(b=function(t,e){if(t.length<=e)return t;const n=t.match(et),r=t.length>e||(n?.length??0)>1,s=n?.[0]??" ";return r?s.substring(0,e-1)+"…":s}(b,C));const y=b+_;A[y]??(A[y]=s.measureText(y));let S=A[y];A[b]??(A[b]=s.measureText(b));let M=A[b].width;A[_]??(A[_]=s.measureText(_));const O=A[_].width,N=r/2-(S.fontBoundingBoxAscent+S.fontBoundingBoxDescent)/2+1;function v(n,r){const i=w?o:"rgb(0,0,0)";s.fillStyle=i,s.globalAlpha=h,u===ft.classic&&(s.fillText(b,t+n,e+N),s.fillStyle="#808080",s.fillText(_,t+r,e+N)),u===ft.MSA&&s.fillText(b,t+n,e+N)}S=S.width,u===ft.MSA&&(M=m[f],S=m[f]);const L=(m[f]??0)-(m[0]??0);if(a||S>n)return v(L,L+M),t+L+M+O;{const e=(n-S)/2;return v(e,e+M),t+L+e+M}}!function(t){t.maxMonomerLength=".mm.cellRenderer.maxMonomerLength"}(mt||(mt={})),function(t){t.MSA="MSA",t.classic="classic"}(ft||(ft={}));class pt{constructor(t){this.col=t,this.monomerCharWidth=7,this.leftPadding=5,this.monomerTextSizeMap={},this.col.dataFrame.onDataChanged.subscribe(),this.monomerLib=Mt(),this.monomerLib.onChanged.subscribe(this.monomerLibOnChanged.bind(this)),this._allPartsList=new Array(this.col.length).fill(null),this._lengthsList=new Array(this.col.length).fill(null),this._editorList=new Array(this.col.length).fill(null)}skipCell(t){this._allPartsList[t]=[],this._lengthsList[t]=[]}getCellAllPartsLengths(t){const[e,n]=this.getCellMonomerLengthsForSeq(t),r=new Array(n.length+1);r[0]=this.leftPadding;for(let t=1;t<r.length;t++)r[t]=r[t-1]+n[t-1];return[e,n,r]}getCellMonomerLengthsForSeq(t){let e=this._allPartsList[t];null===e&&(e=this._allPartsList[t]=this.getAllParts(t));let n=this._lengthsList[t];if(null===n){n=this._lengthsList[t]=new Array(e.length);for(const[t,r]of p().enumerate(e)){const e=t.length*this.monomerCharWidth;n[r]=e}}return[e,n]}getAllParts(t){const e=this.col.get(t),n=e?ot(e):[];return e?function(t,e){const n=[];for(let r=0;r<t.length;++r){const s=e.indexOf(t[r]),i=e.slice(0,s);n.push(i),n.push(t[r]),e=e.substring(s+t[r].length)}return n.push(e),n}(n,e):[]}getMonomer(t){let e=null;if(t.polymerType)e=this.monomerLib.getMonomer(t.polymerType,t.symbol);else for(const n of this.monomerLib.getPolymerTypes())if(e=this.monomerLib.getMonomer(n,t.symbol),e)break;return e}monomerLibOnChanged(t){this._lengthsList.fill(null),this._allPartsList.fill(null),this._editorList.fill(null)}static getOrCreate(t){return"bio-helmMonomerPlacer"in t.temp||(t.temp["bio-helmMonomerPlacer"]=new pt(t)),t.temp["bio-helmMonomerPlacer"]}setEditor(t,e){this._editorList[t]=e}getEditor(t){return this._editorList[t]}}class Ct extends s.GridCellRenderer{get name(){return"helm"}get cellType(){return"helm"}get defaultWidth(){return 400}get defaultHeight(){return 100}onMouseMove(t,e){try{let s=null;try{s=t.tableColumn}catch{}if(!s)return;const i=t.bounds,o=e.offsetX-i.x,l=e.offsetY-i.y,a=pt.getOrCreate(s),h=a.getEditor(t.tableRowIndex);let c,g=new Set;if(h)c=function(t,e,n,r){let s=null;function i(n){let s,i;for(let o=0;o<r.m.atoms.length;++o)if(!n.includes(o)){const n=r.m.atoms[o].p.x,l=r.m.atoms[o].p.y,a=Math.sqrt((t-n)**2+(e-l)**2);(void 0===i||i>a)&&(s=o,i=a)}return[s,i]}const[o,l]=i([]),[a,h]=i([o]);if(void 0!==o&&void 0!==l){const t=function(t){let e;switch(t.bio.type){case"HELM_BASE":case"HELM_SUGAR":case"HELM_LINKER":e="RNA";break;default:e="PEPTIDE"}return{symbol:t.elem,polymerType:e}}(r.m.atoms[o]);void 0!==a&&void 0!==h?l<.45*h&&(s=t):l<.35*n.bounds.height&&(s=t)}return s}(o,l,t,h);else{const e=ot(t.cell.value?it(t.cell.value):"");g=lt(e);const n=new Set(e);if(c=function(t,e,n,r){let s=null;const[i,o,l]=r.getCellAllPartsLengths(n.tableRowIndex);let a=0,h=Object.values(o).length-1,c=!1,g=0,u=0;if(t>l[0])for(;!c&&g<l.length;)u=Math.floor((h+a)/2),t>=l[u]&&t<=l[u+1]?(a=u,c=!0):t<l[u]?h=u-1:t>l[u+1]&&(a=u+1),a==h&&(c=!0),g++;return a=t>=l[a]?a:a-1,a>=0&&(s=function(t,e,n){let r;for(const s of n.getPolymerTypes())t.startsWith(s)&&(r={symbol:e,polymerType:s});return r||(r={symbol:e}),r}(i[0],i[a],r.monomerLib)),s}(o,0,t,a),c&&!n.has(c.symbol)&&(c=null),c){const t=a.monomerTextSizeMap[c.symbol];if(t){const e=i.height/2-(t.fontBoundingBoxAscent+t.fontBoundingBoxDescent)/2+1,n=e-t.fontBoundingBoxAscent,r=e+t.fontBoundingBoxDescent;(l<n||r<l)&&(c=null)}}}if(c)if(g.has(c.symbol))r.tooltip.show(r.divV([r.divText(`Monomer '${c.symbol}' not found.`),r.divText("Open the Context Panel, then expand Manage Libraries")]),e.x+16,e.y+16);else{const t=a.getMonomer(c);if(t){const s={autoCrop:!0,autoCropMargin:0,suppressChiralText:!0},i=n.chem.svgMol(t.smiles,void 0,void 0,s);r.tooltip.show(r.divV([r.divText(c.symbol),i]),e.x+16,e.y+16)}}else{if(0==g.size)return void r.tooltip.hide();{const t=p()(g.keys()).toArray().sort().filter(((t,e)=>e<3)).join(", ")+(g.size>3?", ...":"");r.tooltip.show(r.divV([r.divText("Monomers missed in monomer libraries:"),r.divText(t)]),e.x+16,e.y+16)}}}catch(t){const e=h(t);console.error("Helm: HelmCellRenderer.onMouseMove() error:\n"+e)}finally{e.preventDefault(),e.stopPropagation()}}render(t,e,n,s,i,o,l){t.save();try{let l=null;try{l=o.tableColumn}catch{}if(!l)return;const a=-1!==o.gridRow?o.grid:void 0,h="red",c="#404040",g="#C0C0C0",u=o.cell.value?it(o.cell.value):"",m=ot(u),f=new Set(m),d=lt(m),p=pt.getOrCreate(l);if(0==d.size){const t=o.element=r.div([],{style:{width:s-2+"px",height:i-2+"px",margin:"1px",backgroundColor:"#FFE0E0"}});t.setAttribute("dataformat","helm"),t.setAttribute("data",u),t.parentElement&&(o.grid?.canvas?.offsetLeft??0)>0&&(t.parentElement.style.left=`${(o.grid?.canvas?.offsetLeft??0)+t.parentElement.offsetLeft}px`);const e=new JSDraw2.Editor(t,{width:s,height:i,skin:"w8",viewonly:!0});return p.setEditor(o.tableRowIndex,e),void p.skipCell(o.tableRowIndex)}if(d.size>0){if(!a){const e=window.devicePixelRatio;i=28,t.canvas.height=i*e,t.canvas.style.height=`${i}px`}s=a?Math.min(a.canvas.width-e,s):t.canvas.width-e,t.beginPath(),t.rect(e,n,s,i),t.clip(),t.transform(1,0,0,1,e,n),t.font="12px monospace",t.textBaseline="top";const[r,l,u]=p.getCellAllPartsLengths(o.tableRowIndex);for(let e=0;e<r.length;++e){const n=r[e],o="."===n||n.endsWith("{")||n.startsWith("}")?g:d.has(n)?h:f.has(n)?c:g;t.fillStyle=o,dt(u[e],0,s,i,t,r[e],o,0,!0,1,void 0,void 0,void 0,void 0,void 0,void 0,void 0,void 0,p.monomerTextSizeMap)}}}finally{t.restore()}}}class At{constructor(){this.w=200,this.h=100,this.host=r.div([],{style:{width:`${this.w}px`,height:`${this.h}px`}}),this.editor=new JSDraw2.Editor(this.host,{width:this.w,height:this.h,viewonly:!0})}resizeEditor(t,e){this.editor.setSize(t,e)}}class bt{createHelmWebEditor(){return new At}createWebEditorApp(t,e){org.helm.webeditor.MolViewer.molscale=.8;const n=new scil.helm.App(t,{showabout:!1,mexfontsize:"90%",mexrnapinontab:!0,topmargin:20,mexmonomerstab:!0,sequenceviewonly:!1,mexfavoritefirst:!0,mexfilter:!0}),r=n.calculateSizes();n.canvas.resize(r.rightwidth-100,r.topheight-210);let s={width:r.rightwidth-100+"px",height:r.bottomheight+"px"};return scil.apply(n.sequence.style,s),scil.apply(n.notation.style,s),s={width:r.rightwidth+"px",height:r.bottomheight+n.toolbarheight+"px"},scil.apply(n.properties.parent.style,s),n.structureview.resize(r.rightwidth,r.bottomheight+n.toolbarheight),n.mex.resize(r.topheight-80),setTimeout((()=>{n.canvas.helm.setSequence(e,"HELM")}),200),n}static async getInstance(){let t=window.$helmHelper;return t||(window.$helmHelper=t=new bt),t}}const _t="smiles",wt="capGroupName",Tt="label";let Et=null;const yt=new s.Package;async function St(){return org.helm.webeditor.kCaseSensitive=!0,Promise.all([new Promise(((t,e)=>{dojo.ready((function(){t(null)}))})).then((()=>{window.dojox.gfx.svg.Text.prototype.getTextWidth=function(){const t=this.rawNode,e=t.parentNode,n=t.cloneNode(!0);n.style.visibility="hidden";let r=0;const s=n.firstChild.nodeValue;if(e.appendChild(n),""!=s){let t=100;for(;!r&&--t>0;)r=n.getBBox?parseInt(n.getBBox().width):68}return e.removeChild(n),r}})),n.functions.call("Bio:getBioLib")]).then((([t,e])=>{Et=e,Ot(),Et.onChanged.subscribe((t=>{try{Ot();const t=Et.getPolymerTypes(),e="Monomer lib updated:<br />"+(0==t.length?"empty":t.map((t=>`${t} ${Et.getMonomerSymbolsByType(t).length}`)).join("<br />"));n.shell.info(e)}catch(t){const e=h(t);console.error("Helm: initHelm monomerLib.onChanged() error:\n"+e)}}))})).catch((t=>{const e=t instanceof Error?t.message:t?t.toString():"Exception 'undefined'";n.shell.error(`Package 'Helm' init initHelm() error: ${e}`);const r=new Error(e);throw r.stack=t.stack,r}))}function Mt(){return Et}function Ot(){org.helm.webeditor.Monomers.clear(),Et.getPolymerTypes().forEach((t=>{Et.getMonomerSymbolsByType(t).forEach((e=>{let n=!1;const r=Et.getMonomer(t,e),s={id:e,m:r.molfile,n:r.name,na:r.naturalAnalog,rs:r.rgroups.length,type:r.polymerType,mt:r.monomerType,at:{}};if(r.rgroups.length>0){s.rs=r.rgroups.length;const t={};r.rgroups.forEach((e=>{t[e[Tt]]=e[wt]})),s.at=t}else null!=r[_t]?(s.rs=Object.keys(Rt(r[_t].toString())).length,s.at=Rt(r[_t].toString())):n=!0;n||org.helm.webeditor.Monomers.addOneMonomer(s)}))}));const t=n.shell.tv?.grid;t&&t.invalidate()}function Nt(){return new Ct}function vt(t,e,s){const i=lt(ot(t&&void 0===s?t.value:e));0===i.size?function(t,e,n){const s=r.div(),i=t.column,o=I.forColumn(i);t.rowIndex,org.helm.webeditor.MolViewer.molscale=.8;const l=new scil.helm.App(s,{showabout:!1,mexfontsize:"90%",mexrnapinontab:!0,topmargin:20,mexmonomerstab:!0,sequenceviewonly:!1,mexfavoritefirst:!0,mexfilter:!0}),a=l.calculateSizes();l.canvas.resize(a.rightwidth-100,a.topheight-210);let h={width:a.rightwidth-100+"px",height:a.bottomheight+"px"};scil.apply(l.sequence.style,h),scil.apply(l.notation.style,h),h={width:a.rightwidth+"px",height:a.bottomheight+l.toolbarheight+"px"},scil.apply(l.properties.parent.style,h),l.structureview.resize(a.rightwidth,a.bottomheight+l.toolbarheight),l.mex.resize(a.topheight-80),setTimeout((()=>{t&&void 0===n?l.canvas.helm.setSequence(t.value,"HELM"):l.canvas.helm.setSequence(e,"HELM")}),200),r.dialog({showHeader:!1,showFooter:!0}).add(s).onOK((()=>{const e=l.canvas.getHelm(!0).replace(/<\/span>/g,"").replace(/<span style='background:#bbf;'>/g,"");if(t)if(void 0===n)t.value=e;else{const r=o.convertHelmToFastaSeparator(e,n,o.separator);t.value=r}})).show({modal:!0,fullScreen:!0})}(t,e,s):1===i.size&&i.has(R[o.HELM])?n.shell.warning(`WebEditor doesn't support Helm with gaps '${R[o.HELM]}'.`):n.shell.warning(`Monomers ${Array.from(i).map((t=>`'${t}'`)).join(", ")} are absent! <br/>Please, upload the monomer library! <br/><a href="https://datagrok.ai/help/domains/bio/macromolecules" target="_blank">Learn more</a>`)}function Lt(t){vt(t.cell,void 0,void 0)}function Ht(t){const e=n.shell.tv.grid.dataFrame,r=e.columns.bySemType("Macromolecule"),i=I.forColumn(r);r.getTag(s.TAGS.UNITS)===o.HELM&&vt(e.currentCell,void 0,void 0);const l=i.getConverter(o.HELM)(t);vt(e.currentCell,l,r.getTag(s.TAGS.UNITS))}function xt(t){return function(t){const e=I.forColumn(t.cell.column),n=function(t,e){const n=it(e.isHelm()?t:e.getConverter(o.HELM)(t)),s=r.div([],{style:{width:"0",height:"0"}});document.documentElement.appendChild(s);try{const t=new JSDraw2.Editor(s,{viewonly:!0});t.setHelm(n);const e=t.getFormula(!0),r=Math.round(100*t.getMolWeight())/100,i=Math.round(100*t.getExtinctionCoefficient(!0))/100;return{formula:e.replace(/<sub>/g,"").replace(/<\/sub>/g,""),"molecular weight":r,"extinction coefficient":i}}finally{a()(s).empty(),s.remove()}}(t.value,e);return new s.Widget(r.tableFromMap(n))}(t)}function Rt(t){const e=t.match(/(?<=\[)[^\][]*(?=])/gm),n={};let r,s="";if(e)for(let t=0;t<e.length;t++)if(null!=e[t]&&/\d/.test(e[t])){r=e[t][e[t].length-1],e[t]=e[t].replace(/[0-9]/g,"");for(let n=0;n<e[t].length;n++)":"!=e[t][n]&&(s+=e[t][n]);n["R"+r]=s,s=""}return n}function It(t){const e=s.Column.string("mols",t.length),n=r.div([],{style:{width:"0",height:"0"}});document.documentElement.appendChild(n);try{const r=new JSDraw2.Editor(n,{viewonly:!0});return e.init((e=>(r.setHelm(t.get(e)),r.getMolfile()))),e}finally{a()(n).empty(),n.remove()}}async function Pt(){return bt.getInstance()}helm=e})();
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