@datagrok/sequence-translator 1.1.0 → 1.1.4

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Files changed (27) hide show
  1. package/CHANGELOG.md +34 -1
  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/files/codes-to-symbols.json +1 -0
  7. package/files/formats-to-helm.json +4 -0
  8. package/files/monomer-lib.json +48 -0
  9. package/package.json +9 -12
  10. package/src/model/axolabs/const.ts +2 -2
  11. package/src/model/const.ts +0 -1
  12. package/src/model/format-translation/conversion-utils.ts +3 -2
  13. package/src/model/format-translation/format-converter.ts +3 -1
  14. package/src/model/monomer-lib/lib-wrapper.ts +13 -0
  15. package/src/model/sequence-to-structure-utils/sdf-tab.ts +4 -1
  16. package/src/package-test.ts +3 -1
  17. package/src/package.ts +12 -2
  18. package/src/tests/const.ts +18 -11
  19. package/src/tests/formats-support.ts +40 -0
  20. package/src/tests/formats-to-helm.ts +53 -0
  21. package/src/tests/helm-to-nucleotides.ts +28 -0
  22. package/src/view/const/view.ts +1 -1
  23. package/src/view/tabs/axolabs.ts +33 -34
  24. package/src/view/tabs/main.ts +4 -4
  25. package/src/view/tabs/sdf.ts +30 -10
  26. package/src/view/view.ts +0 -2
  27. package/src/tests/smiles-tests.ts +0 -33
package/CHANGELOG.md CHANGED
@@ -1,3 +1,36 @@
1
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  # Sequence Translator changelog
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- ## 1.0.17 (2023-07-24) (WIP)
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+ ## 1.1.4 (2023-09-07)
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+
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+ ### Bug fixes
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+
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+ * Fixed molfile direction for AS and AS2 on SDF tab
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+
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+ ## 1.1.3 (2023-09-07)
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+
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+ ### Bug fixes
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+
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+ * Fixed Direction of AS and AS2 for SDF tab
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+
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+ ## 1.1.2 (2023-08-16)
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+
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+ ### Bug fixes
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+
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+ * Fixed HELM generation for modifications
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+
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+ ## 1.1.1 (2023-08-10)
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+
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+ ### Features
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+
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+ * Updated dependencies
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+
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+ ## 1.1.0 (2023-07-26)
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+
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+ * Dependency: datgarok-api >= 1.15.2
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+
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+ ### Features
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+
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+ * Option to add extra formats for translation in addition to `Axolabs`, `BioSpring` and `MerMade12`
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+ * Generation of HELM strings
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+ * Improved SMILES generation
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+ * UI/UX adjustments
package/dist/package-test.js CHANGED
@@ -1,2 +1,2 @@
1
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BOND");o+=t[e].substring(m+1,p);let O=t[e].indexOf("M V30 MDLV30/STEABS ATOMS=(");for(;-1!==O;){O+=28;const n=t[e].indexOf(")",O);t[e].substring(O,n).split(" ").slice(1).forEach((t=>{a.push(parseInt(t)+i)})),O=n,O=t[e].indexOf("M V30 MDLV30/STEABS ATOMS=(",O)}i+=u.natom-1,c+=u.nbond,l+=n?Math.max(...C.x):C.x[u.natom-1]-C.x[0]}const u=Math.ceil(a.length/4);s+="M V30 MDLV30/STEABS ATOMS=("+a.length+" -\n";for(let t=0;t<u;t++){s+="M V30 ";const e=t+1===u?a.length-4*(u-1):4;for(let n=0;n<e;n++)s+=n+1===e?t===u-1?a[4*t+n]+")\n":a[4*t+n]+" -\n":a[4*t+n]+" "}return i++,n+="M V30 COUNTS "+i+" "+c+" 0 0 0\n",n+="M V30 BEGIN ATOM\n",n+=r,n+="M V30 END ATOM\n",n+="M V30 BEGIN BOND\n",n+=o,n+="M V30 END BOND\n",e&&a.length>0?(n+="M V30 BEGIN COLLECTION\n",n+=s,n+="M V30 END COLLECTION\n"):n=n.replace(/ CFG=\d/g," "),n+="M V30 END CTAB\n",n+="M END",n}fix5Prime(t,e,n){const 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O,A,b=n(973),H={};H.styleTagTransform=g(),H.setAttributes=C(),H.insert=l().bind(null,"head"),H.domAPI=i(),H.insertStyleElement=d(),s()(b.Z,H),b.Z&&b.Z.locals&&b.Z.locals,n(402),(A=O||(O={})).HEADER="V2000",A[A.NUM_OF_HEADER_LINES=3]="NUM_OF_HEADER_LINES",A[A.NUM_OF_COUNTS_DIGITS=3]="NUM_OF_COUNTS_DIGITS",A[A.ATOM_TYPE_COL=4]="ATOM_TYPE_COL",A[A.FIRST_BONDED_ATOM_COL=1]="FIRST_BONDED_ATOM_COL",A[A.BOND_TYPE_COL=3]="BOND_TYPE_COL",A[A.RGP_SHIFT=8]="RGP_SHIFT",A.RGP_LINE="M RGP",A.A_LINE="A ",A.END="M END",Error;var w=n(865),E={};function x(t,e){const n=document.createElement("canvas").getContext("2d");return n.font=String(e),2*n.measureText(t).width}E.styleTagTransform=g(),E.setAttributes=C(),E.insert=l().bind(null,"head"),E.domAPI=i(),E.insertStyleElement=d(),s()(w.Z,E),w.Z&&w.Z.locals&&w.Z.locals;Math.max(x("SS: 5'",17),x("AS: 3'",17)),Math.max(x("3'",17),x("5'",17)),n(803);var y=n(895);wu;class v{constructor(t,e,n){this.name=t,this.alphabet=e,this.cutoff=n}}class S extends v{constructor(t,e,n){super(t.name,t.alphabet,t.cutoff),this.freq=e,this.similarity=n}}const M=/(\[[A-Za-z0-9-_]+\]|.)/g,N=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"])}}},T=[new v("PT",N.fasta.peptide,.5),new v("DNA",N.fasta.dna,.55),new v("RNA",N.fasta.rna,.55)],B=new Uint32Array(65536),P={gapOpen:8,gapExtend:2,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 I;!function(t){t.HAMMING="Hamming",t.LEVENSHTEIN="Levenshtein",t.NEEDLEMANN_WUNSCH="Needlemann-Wunsch"}(I||(I={}));const L={[I.HAMMING]:function(){return(t,e)=>{let n=0;t.length!==e.length&&(n=Math.abs(t.length-e.length));let r=0;for(let n=0;n<Math.min(t.length,e.length);n++)t[n]!==e[n]&&r++;return r+=n,r/=Math.max(t.length,e.length),r}},[I.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,o=1<<n-1;let s=-1,a=0,i=n,c=n;for(;c--;)B[t.charCodeAt(c)]|=1<<c;for(c=0;c<r;c++){let t=B[e.charCodeAt(c)];const n=t|a;t|=(t&s)+s^s,a|=~(t|s),s&=t,a&o&&i++,s&o&&i--,a=a<<1|1,s=s<<1|~(n|a),a&=n}for(c=n;c--;)B[t.charCodeAt(c)]=0;return i})(t,e):((t,e)=>{const n=e.length,r=t.length,o=[],s=[],a=Math.ceil(n/32),i=Math.ceil(r/32);for(let t=0;t<a;t++)s[t]=-1,o[t]=0;let c=0;for(;c<i-1;c++){let a=0,i=-1;const l=32*c,u=Math.min(32,r)+l;for(let e=l;e<u;e++)B[t.charCodeAt(e)]|=1<<e;for(let t=0;t<n;t++){const n=B[e.charCodeAt(t)],r=s[t/32|0]>>>t&1,c=o[t/32|0]>>>t&1,l=n|a,u=((n|c)&i)+i^i|n|c;let C=a|~(u|i),h=i&u;C>>>31^r&&(s[t/32|0]^=1<<t),h>>>31^c&&(o[t/32|0]^=1<<t),C=C<<1|r,h=h<<1|c,i=h|~(l|C),a=C&l}for(let e=l;e<u;e++)B[t.charCodeAt(e)]=0}let l=0,u=-1;const C=32*c,h=Math.min(32,r-C)+C;for(let e=C;e<h;e++)B[t.charCodeAt(e)]|=1<<e;let d=r;for(let t=0;t<n;t++){const n=B[e.charCodeAt(t)],a=s[t/32|0]>>>t&1,i=o[t/32|0]>>>t&1,c=n|l,C=((n|i)&u)+u^u|n|i;let h=l|~(C|u),f=u&C;d+=h>>>r-1&1,d-=f>>>r-1&1,h>>>31^a&&(s[t/32|0]^=1<<t),f>>>31^i&&(o[t/32|0]^=1<<t),h=h<<1|a,f=f<<1|i,u=f|~(c|h),l=h&c}for(let e=C;e<h;e++)B[t.charCodeAt(e)]=0;return d})(t,e)})(t,e)/Math.max(t.length,e.length)},[I.NEEDLEMANN_WUNSCH]:function(t){return(e,n)=>{const{gapOpen:r,gapExtend:o,scoringMatrix:s,alphabetIndexes:a}={...P,...t},i=[new Array(e.length+1).fill(0),new Array(e.length+1).fill(0)],c=new Array(e.length+1).fill(!1),l=new Array(e.length+1).fill(!1);let u=0,C=1;for(let t=1;t<e.length+1;t++)i[0][t]=-r-(t-1)*o;for(let t=1;t<n.length+1;t++){i[C][0]=-r-(t-1)*o;for(let h=1;h<e.length+1;h++){const d=i[u][h-1]+s[a[e[h-1]]][a[n[t-1]]],f=i[u][h]-(c[h]?o:r),g=i[C][h-1]-(l[h-1]?o:r);i[C][h]=Math.max(d,g,f),i[C][h]===d?(c[h]=!1,l[h]=!1):i[C][h]===g?(c[h]=!1,l[h]=!0):(c[h]=!0,l[h]=!1)}u=C,C=(C+1)%2}const h=e.split("").map((t=>s[a[t]][a[t]])).reduce(((t,e)=>t+e),0),d=n.split("").map((t=>s[a[t]][a[t]])).reduce(((t,e)=>t+e),0),f=Math.max(h,d);return(f-i[u][e.length])/f}}},k=new class{constructor(){this.uhTemp=`units-handler.${r.SEMTYPE.MACROMOLECULE}`}};class F{static setUnitsToFastaColumn(t){if(t.column.semType!==r.SEMTYPE.MACROMOLECULE||"fasta"!==t.column.getTag(r.TAGS.UNITS))throw new Error(`The column of notation 'fasta' must be '${r.SEMTYPE.MACROMOLECULE}'.`);t.column.setTag(r.TAGS.UNITS,"fasta"),F.setTags(t)}static setUnitsToSeparatorColumn(t,e){if(t.column.semType!==r.SEMTYPE.MACROMOLECULE||"separator"!==t.column.getTag(r.TAGS.UNITS))throw new Error(`The column of notation 'separator' must be '${r.SEMTYPE.MACROMOLECULE}'.`);if(!e)throw new Error("The column of notation 'separator' must have the separator tag.");t.column.setTag(r.TAGS.UNITS,"separator"),t.column.setTag("separator",e),F.setTags(t)}static setUnitsToHelmColumn(t){if(t.column.semType!==r.SEMTYPE.MACROMOLECULE)throw new Error(`The column of notation 'helm' must be '${r.SEMTYPE.MACROMOLECULE}'`);t.column.setTag(r.TAGS.UNITS,"helm"),F.setTags(t)}static setTags(t){const e=t.column.getTag(r.TAGS.UNITS),n=t.stats;if(Object.keys(n.freq).some((t=>t.length>1)),["fasta","separator"].includes(e)){if(0===Object.keys(n.freq).length)throw new Error("Alphabet is empty");const e=n.sameLength?"SEQ.MSA":"SEQ";t.column.setTag("aligned",e);const 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 o=[],s=[];for(const n of r)o.push(n in t?t[n]:0),s.push(e.has(n)?1:0);const a=new U(o),i=new U(s);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}(a,i)/(D(a)*D(i))}(t,e.alphabet,n);return new S(e,t,r)}));let o;const s=Math.max(...r.map((t=>t.similarity>t.cutoff?t.similarity:-1)));o=s>0?r.find((t=>t.similarity===s)).name:"UN";return o}(n.freq,T);if(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 units(){return this._units}get column(){return this._column}get notation(){return this._notation}get defaultGapSymbol(){return this._defaultGapSymbol}get separator(){const t=this.column.getTag("separator")??void 0;if("separator"===this.notation&&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("helm"==this.notation||"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 '${this.alphabet}'.`)}}getAlphabetIsMultichar(){return"helm"===this.notation||"UN"===this.alphabet&&"true"===this.column.getTag(".alphabetIsMultichar")}get splitted(){if(null===this._splitted){const t=this.getSplitter(),e=this._column.length;this._splitted=new Array(e);const n=this._column.getRawData(),r=this._column.categories;for(let o=0;o<e;o++){const e=r[n[o]];this._splitted[o]=t(e)}}return this._splitted}get stats(){if(null===this._stats){const t={};let e=!0,n=null;for(const r of this.splitted){null==n?n=r.length:r.length!==n&&(e=!1);for(const e of r)e in t||(t[e]=0),t[e]+=1}this._stats={freq:t,sameLength:e}}return this._stats}isFasta(){return"fasta"===this.notation}isSeparator(){return"separator"===this.notation}isHelm(){return"helm"===this.notation}isRna(){return"RNA"===this.alphabet}isDna(){return"DNA"===this.alphabet}isPeptide(){return"PT"===this.alphabet}isMsa(){return!!this.aligned&&this.aligned.toUpperCase().includes("MSA")}isHelmCompatible(){return"true"===this.helmCompatible}getNotation(){if(this.units.toLowerCase().startsWith("fasta"))return"fasta";if(this.units.toLowerCase().startsWith("separator"))return"separator";if(this.units.toLowerCase().startsWith("helm"))return"helm";throw new Error(`Column '${this.column.name}' has unexpected notation '${this.units}'.`)}getNewColumn(t,e){const n=this.column,o=n.length,s=t.toLowerCase()+"("+n.name+")",a=n.dataFrame.columns.getUnusedName(s),i=r.Column.fromList("string",a,new Array(o).fill(""));if(i.semType=r.SEMTYPE.MACROMOLECULE,i.setTag(r.TAGS.UNITS,t),"separator"===t){if(!e)throw new Error("Notation 'separator' requires separator value.");i.setTag("separator",e)}i.setTag(r.TAGS.CELL_RENDERER,"Macromolecule");const c=n.getTag("aligned");c&&i.setTag("aligned",c);const l=n.getTag("alphabet");l&&i.setTag("alphabet",l);let u=n.getTag(".alphabetSize");u&&i.setTag(".alphabetSize",u);const C=n.getTag(".alphabetIsMultichar");return void 0!==C&&i.setTag(".alphabetIsMultichar",C),"helm"==t&&(u=this.getAlphabetSize().toString(),i.setTag(".alphabetSize",u)),i}static getNewColumn(t){const e=F.getOrCreate(t),n=e.notation;return e.getNewColumn(n)}static unitsStringIsValid(t){return t=t.toLowerCase(),["fasta","separator","helm"].some((e=>t.startsWith(e.toLowerCase())))}static getNewColumnFromParams(t,e,n){if(!F.unitsStringIsValid(n))throw new Error("Invalid format of 'units' parameter");const o=r.Column.fromList("string",e,new Array(t).fill(""));return o.semType=r.SEMTYPE.MACROMOLECULE,o.setTag(r.TAGS.UNITS,n),o}getSplitter(){return function(t){if(t.semType!==r.SEMTYPE.MACROMOLECULE)throw new Error(`Get splitter for semType "${r.SEMTYPE.MACROMOLECULE}" only.`);return function(t,e,n){if(t.toLowerCase().startsWith("fasta"))return Y;if(t.toLowerCase().startsWith("separator"))return z(e,void 0);if(t.toLowerCase().startsWith("helm"))return Q;throw new Error(`Unexpected units ${t} .`)}(t.getTag(r.TAGS.UNITS),t.getTag("separator"))}(this._column)}getDistanceFunctionName(){if(!this.isFasta())throw new Error("Only FASTA notation is supported");if(this.isMsa())return I.HAMMING;switch(this.alphabet){case"DNA":case"RNA":default:return I.LEVENSHTEIN;case"PT":return I.NEEDLEMANN_WUNSCH}}getDistanceFunction(){return L[this.getDistanceFunctionName()]()}async checkHelmCompatibility(){if(this.column.tags.has(".isHelmCompatible"))return"true"===this.column.getTag(".isHelmCompatible");const t=(await X()).getBioLib().getMonomerSymbolsByType("PEPTIDE".toString()),e=new Set(t),n=z(this.separator);for(const t of this.column.categories){const r=n(t);for(const t of r)if(!e.has(t))return this.column.setTag(".isHelmCompatible","false"),!1}return this.column.setTag(".isHelmCompatible","true"),!0}constructor(t){this._splitted=null,this._stats=null,this._column=t;const e=this._column.getTag(r.TAGS.UNITS);if(null==e)throw new Error("Units are not specified in column");if(this._units=e,this._notation=this.getNotation(),this._defaultGapSymbol=this.isFasta()?F._defaultGapSymbolsDict.FASTA:this.isHelm()?F._defaultGapSymbolsDict.HELM:F._defaultGapSymbolsDict.SEPARATOR,!this.column.tags.has("aligned")||!this.column.tags.has("alphabet")||!this.column.tags.has(".alphabetIsMultichar")&&!this.isHelm()&&"UN"===this.alphabet)if(this.isFasta())F.setUnitsToFastaColumn(this);else if(this.isSeparator()){const e=t.getTag("separator");F.setUnitsToSeparatorColumn(this,e)}else{if(!this.isHelm())throw new Error(`Unexpected units '${this.column.getTag(r.TAGS.UNITS)}'.`);F.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){return k.uhTemp in t.temp||(t.temp[k.uhTemp]=new F(t)),t.temp[k.uhTemp]}}F._defaultGapSymbolsDict={HELM:"*",SEPARATOR:"",FASTA:"-"};class U extends Float32Array{}function D(t){let e=0;for(let n=0;n<t.length;n++)e+=t[n]*t[n];return Math.sqrt(e)}class _{static makePalette(t,e=!1,n=_){const r={};return t.forEach((t=>{const n=t[0],o=t[1];n.forEach(((t,n)=>{r[t]=this.colourPalette[o][e?0:n]}))})),new n(r)}constructor(t){this._palette=t}get(t){return this._palette[t]}}_.undefinedColor="rgb(100,100,100)",_.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 V extends _{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,V)),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,V)),this.grokGroups}static get RasMol(){return void 0===this.rasMol&&(this.rasMol=new V({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 V.aaSynonyms?V.aaSynonyms[t]:t;return super.get(e)}}V.aaSynonyms={MeNle:"L",MeA:"A",MeG:"G",MeF:"F"};class G{static getPalette(t="grok"){switch(t){case"grok":return V.GrokGroups;case"lesk":return V.Lesk;default:throw new Error(`ChemPalette: scheme \`${t}\` does not exist`)}}static getInnerOuter(t){let e=0,n="",r="";for(const o of t)"("==o?e++:")"==o?e--:e?n+=o:r+=o;return isNaN(parseInt(n))?[r,n]:[r,""]}static getColorAAPivot(t="",e="grok"){const n=this.getPalette(e);let[r,o]=this.getInnerOuter(t);if(r=r.length>6?`${r.slice(0,3)}...`:r,o=o.length>6?`${o.slice(0,3)}...`:o,1==t.length||"("==t[1]){const e=t[0]?.toUpperCase();return e in n?[n.get(e),e,o,1]:[this.undefinedColor,r,o,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,o,2]:[this.undefinedColor,r,o,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,o,3]:[this.undefinedColor,r,o,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,o,4]:[this.undefinedColor,r,o,4]}return[this.undefinedColor,r,o,0]}}G.SemType="Aminoacids",G.SemTypeMultipleAlignment="AminoacidsMultipleAlignment",G.undefinedColor="rgb(100,100,100)",G.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"},G.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"},G.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(*)*"},G.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 R{}R.SemType="Nucleotides",R.SemTypeMultipleAlignment="NucleotidesMultipleAlignment",R.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 q{}class W extends q{static buildPalette(){return[].concat(...Object.values(_.colourPalette))}get(t){const e=j.hashCode(t)%W.palette.length;return function(t){if(null==t)return"rgb(100,100,100)";const e=r.Color.fromHtml(t),n=r.Color.g(e),o=r.Color.r(e),s=r.Color.b(e),a=Math.sqrt(Math.pow(0-o,2)+Math.pow(0-n,2)+Math.pow(0-s,2));return a>210?`rgb(${o/a*210},${n/a*210},${s/a*210})`:r.Color.toRgb(e)}(W.palette[e])}}function Y(t){return t.toString().replace(M,".$1").slice(1).split(".").map((t=>t.startsWith("[")&&t.endsWith("]")?t.slice(1,-1):"-"===t?"":t))}function z(t,e){return n=>n.split(t,e)}W.palette=W.buildPalette();const Z=/(PEPTIDE1|DNA1|RNA1)\{([^}]+)}/g,K=/\[([^\[\]]+)]/g;function Q(t){Z.lastIndex=0;const e=Z.exec(t.toString()),n=e?e[2]:null;return(n?n.split("."):[]).map((t=>{K.lastIndex=0;const e=K.exec(t);return e&&e.length>=2?e[1]:t}))}async function X(){const t=r.Func.find({package:"Bio",name:"getMonomerLibHelper"});if(0===t.length)throw new Error('Package "Bio" must be installer for MonomerLibraryHelper.');return(await t[0].prepare().call()).getOutputParamValue()}n(61);class J extends r.Package{_monomerLib;get monomerLib(){if(!this._monomerLib)throw new Error("ST: monomer lib not loaded");return this._monomerLib}async initMonomerLib(){if(void 0!==this._monomerLib)return;const t=r.TaskBarProgressIndicator.create("Initializing Sequence Translator monomer library ...");try{const e=await X();this._monomerLib=await e.readLibrary(y.BX,y.a_)}catch(t){const e=t.hasOwnProperty("message")?t.message:t.toString();throw new Error("Sequence Translator: Loading monomer library error: "+e)}finally{t.close()}}}const tt=new J},976:t=>{t.exports=DG},469:t=>{t.exports=grok}},e={};function n(r){var o=e[r];if(void 0!==o)return o.exports;var s=e[r]={id:r,exports:{}};return t[r](s,s.exports,n),s.exports}n.n=t=>{var e=t&&t.__esModule?()=>t.default:()=>t;return n.d(e,{a:e}),e},n.d=(t,e)=>{for(var r in e)n.o(e,r)&&!n.o(t,r)&&Object.defineProperty(t,r,{enumerable:!0,get:e[r]})},n.o=(t,e)=>Object.prototype.hasOwnProperty.call(t,e),n.r=t=>{"undefined"!=typeof Symbol&&Symbol.toStringTag&&Object.defineProperty(t,Symbol.toStringTag,{value:"Module"}),Object.defineProperty(t,"__esModule",{value:!0})},n.nc=void 0;var r={};(()=>{n.r(r),n.d(r,{_package:()=>C,test:()=>h,tests:()=>e.QK});var t=n(976),e=n(61),o=n(29),s=n(996);const 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isNaN(parseInt(n))?[r,n]:[r,""]}static getColorAAPivot(t="",e="grok"){const n=this.getPalette(e);let[r,o]=this.getInnerOuter(t);if(r=r.length>6?`${r.slice(0,3)}...`:r,o=o.length>6?`${o.slice(0,3)}...`:o,1==t.length||"("==t[1]){const e=t[0]?.toUpperCase();return e in n?[n.get(e),e,o,1]:[this.undefinedColor,r,o,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,o,2]:[this.undefinedColor,r,o,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,o,3]:[this.undefinedColor,r,o,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,o,4]:[this.undefinedColor,r,o,4]}return[this.undefinedColor,r,o,0]}}L.SemType="Aminoacids",L.SemTypeMultipleAlignment="AminoacidsMultipleAlignment",L.undefinedColor="rgb(100,100,100)",L.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"},L.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"},L.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(*)*"},L.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 I{}I.SemType="Nucleotides",I.SemTypeMultipleAlignment="NucleotidesMultipleAlignment",I.Names={A:"Adenine",C:"Cytosine",G:"Guanine",T:"Thymine",U:"Uracil"};class H{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 F{}class G extends F{static buildPalette(){return[].concat(...Object.values(k.colourPalette))}get(t){const e=H.hashCode(t)%G.palette.length;return function(t){if(null==t)return"rgb(100,100,100)";const e=r.Color.fromHtml(t),n=r.Color.g(e),o=r.Color.r(e),i=r.Color.b(e),s=Math.sqrt(Math.pow(0-o,2)+Math.pow(0-n,2)+Math.pow(0-i,2));return s>210?`rgb(${o/s*210},${n/s*210},${i/s*210})`:r.Color.toRgb(e)}(G.palette[e])}}G.palette=G.buildPalette();new Uint32Array(65536);var U,_;(_=U||(U={})).HAMMING="Hamming",_.LEVENSHTEIN="Levenshtein",_.NEEDLEMANN_WUNSCH="Needlemann-Wunsch",U.HAMMING,U.LEVENSHTEIN,U.NEEDLEMANN_WUNSCH,new class{constructor(){this.uhTemp=`units-handler.${r.SEMTYPE.MACROMOLECULE}`}},O.FASTA,O.SEPARATOR,O.HELM,n(61);class P extends r.Package{_monomerLib;get monomerLib(){if(!this._monomerLib)throw new Error("ST: monomer lib not loaded");return this._monomerLib}async initMonomerLib(){if(void 0!==this._monomerLib)return;const t=r.TaskBarProgressIndicator.create("Initializing Sequence Translator monomer library ...");try{const e=await async function(){const t=r.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()}();this._monomerLib=await e.readLibrary(N.BX,N.a_)}catch(t){const e=t.hasOwnProperty("message")?t.message:t.toString();throw new Error("Loading monomer library: "+e)}finally{t.close()}}}const j=new P},976:t=>{t.exports=DG},469:t=>{t.exports=grok}},e={};function n(r){var o=e[r];if(void 0!==o)return o.exports;var i=e[r]={id:r,exports:{}};return t[r](i,i.exports,n),i.exports}n.n=t=>{var e=t&&t.__esModule?()=>t.default:()=>t;return n.d(e,{a:e}),e},n.d=(t,e)=>{for(var r in e)n.o(e,r)&&!n.o(t,r)&&Object.defineProperty(t,r,{enumerable:!0,get:e[r]})},n.o=(t,e)=>Object.prototype.hasOwnProperty.call(t,e),n.r=t=>{"undefined"!=typeof Symbol&&Symbol.toStringTag&&Object.defineProperty(t,Symbol.toStringTag,{value:"Module"}),Object.defineProperty(t,"__esModule",{value:!0})},n.nc=void 0;var r={};(()=>{n.r(r),n.d(r,{_package:()=>h,test:()=>m,tests:()=>e.QK});var t=n(976),e=n(61),o=n(29),i=n(893),s=n(996);const a={Axolabs:{UfAfsCfsGfuacg:"RNA1{[fR](U)p.[fR](A)[sp].[fR](C)[sp].[fR](G)p.[25r](U)p.[25r](A)p.[25r](C)p.[25r](G)}$$$$"},BioSpring:{"AT*GC*123456789":"RNA1{r(A)p.r(T)[sp].r(G)p.r(C)[sp].[fR](U)p.[fR](A)p.[fR](C)p.[fR](G)p.[25r](U)p.[25r](A)p.[25r](C)p.[25r](G)p.d([m5C])}$$$$"},Mermade12:{hefglijkLIJKHEFG:"RNA1{[25r](U)[sp].[25r](A)[sp].[25r](C)[sp].[25r](G)[sp].[fR](U)[sp].[fR](A)[sp].[fR](C)[sp].[fR](G)[sp].[fR](U)p.[fR](A)p.[fR](C)p.[fR](G)p.[25r](U)p.[25r](A)p.[25r](C)p.[25r](G)}$$$$"}},l={"RNA1{[fR](U)p.[fR](A)[sp].[fR](C)[sp].[fR](G)p.[25r](U)p.[25r](A)p.[25r](C)p.[25r](G)}$$$$":"UACGUACG","RNA1{r(A)p.r(T)[sp].r(G)p.r(C)[sp].[fR](U)p.[fR](A)p.[fR](C)p.[fR](G)p.[25r](U)p.[25r](A)p.[25r](C)p.[25r](G)p.d([m5C])}$$$$":"ATGCUACGUACGC","RNA1{[25r](U)[sp].[25r](A)[sp].[25r](C)[sp].[25r](G)[sp].[fR](U)[sp].[fR](A)[sp].[fR](C)[sp].[fR](G)[sp].[fR](U)p.[fR](A)p.[fR](C)p.[fR](G)p.[25r](U)p.[25r](A)p.[25r](C)p.[25r](G)}$$$$":"UACGUACGUACGUACG"};var c=n(563);function u(t,e){return new i.I(t,e).convertTo(o.NI.HELM)}function d(t,e){return new i.I(t,o.NI.HELM).convertTo(e)}(0,e.W3)("Formats to HELM",(()=>{(0,e.bb)((async()=>{await(0,s.VO)(),await c._package.initMonomerLib()}));for(const t of Object.keys(a))for(const[n,r]of Object.entries(a[t]))(0,e.Bu)(`${t} to HELM`,(async()=>{const o=r,i=u(n,t);(0,e.l_)(i,o)}))})),(0,e.W3)("HELM to Formats",(()=>{(0,e.bb)((async()=>{await(0,s.VO)(),await c._package.initMonomerLib()}));for(const t of Object.keys(a))for(const[n,r]of Object.entries(a[t]))(0,e.Bu)(`${t} to HELM`,(async()=>{const o=n,i=d(r,t);(0,e.l_)(i,o)}))}));var p=n(112),f=n(559);(0,e.W3)("HELM to Nucleotides",(()=>{(0,e.bb)((async()=>{await(0,s.VO)(),await c._package.initMonomerLib()})),Object.entries(l).forEach((([t,n],r)=>{(0,e.Bu)(`Sequence ${r+1} to nucleotides`,(async()=>{const r=n,o=(0,p.C)(t,f.A.getInstance());(0,e.l_)(o,r)}))}))}));var g=n(947);const A={[o.NI.AXOLABS]:"Afcgacsu",[o.NI.HELM]:"RNA1{[fR](A)p.[25r](C)p.[25r](G)p.[25r](A)p.[25r](C)[sp].[25r](U)}$$$$"};(0,e.W3)("Formats support",(()=>{(0,e.bb)((async()=>{await(0,s.VO)(),await c._package.initMonomerLib()})),Object.entries(A).forEach((([t,n])=>{(0,e.Bu)(`All formats for ${t}`,(async()=>{const r=function(t,e){const n=new g.b(t).getInvalidCodeIndex(e);return(0,p.D)(t,n,e)}(n,t),o=Object.keys(r).length,i=Object.keys(a).length+1;(0,e.l_)(o,i)}))}))}));const h=new t.Package;async function m(n,r,o){const i=await(0,e.ci)({category:n,test:r,testContext:o});return t.DataFrame.fromObjects(i)}})(),sequencetranslator_test=r})();
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