@datagrok/helm 2.1.25 → 2.1.27

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Files changed (14) hide show
  1. package/CHANGELOG.md +15 -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/package.json +6 -5
  7. package/src/cell-renderer.ts +0 -30
  8. package/src/helm-helper.ts +62 -0
  9. package/src/helm-web-editor.ts +1 -34
  10. package/src/package-test.ts +1 -0
  11. package/src/package.ts +64 -41
  12. package/src/tests/properties-widget-tests.ts +81 -0
  13. package/src/widgets/properties-widget.ts +43 -0
  14. package/tsconfig.json +6 -5
package/CHANGELOG.md CHANGED
@@ -1,6 +1,20 @@
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  # Helm changelog
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- ## 2.2.0 (WIP)
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+ ## 2.1.27 (2024-02-15)
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+
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+ ### Bug fixes
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+
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+ * Fix dojo patch dependency on package init
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+ * Fix getMolfiles without current table view
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+ * Fix initHelm/rewriteLibraries without current table view
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+
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+ ## 2.1.26 (2024-02-14)
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+
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+ ### Bug fixes
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+
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+ * Fix Properties panel of Context panel for sequences of MSA with gaps
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+
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+ ## 2.1.25 (2024-02-09)
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  ### Features
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package/dist/package-test.js CHANGED
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isNaN(parseInt(n))?[i,n]:[i,""]}static getColorAAPivot(t="",e="grok"){const n=this.getPalette(e);let[i,s]=this.getInnerOuter(t);if(i=i.length>6?`${i.slice(0,3)}...`:i,s=s.length>6?`${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,i,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,i,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,i,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,i,s,4]}return[this.undefinedColor,i,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 G{}G.SemType="Nucleotides",G.SemTypeMultipleAlignment="NucleotidesMultipleAlignment",G.Names={A:"Adenine",C:"Cytosine",G:"Guanine",T:"Thymine",U:"Uracil"};class U extends class{}{static buildPalette(){return[].concat(...Object.values(F.colourPalette))}get(e){const n=class{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}}.hashCode(e)%U.palette.length;return function(e){if(null==e)return"rgb(100,100,100)";const n=t.Color.fromHtml(e),i=t.Color.g(n),s=t.Color.r(n),r=t.Color.b(n),o=Math.sqrt(Math.pow(0-s,2)+Math.pow(0-i,2)+Math.pow(0-r,2));return o>210?`rgb(${s/o*210},${i/o*210},${r/o*210})`:t.Color.toRgb(n)}(U.palette[n])}}U.palette=U.buildPalette();new Uint32Array(65536);var W,K,Y,Q,z,j,J,q;(K=W||(W={})).HAMMING="Hamming",K.LEVENSHTEIN="Levenshtein",K.NEEDLEMANN_WUNSCH="Needlemann-Wunsch",K.MONOMER_CHEMICAL_DISTANCE="Monomer chemical distance",W.HAMMING,W.LEVENSHTEIN,W.NEEDLEMANN_WUNSCH,W.MONOMER_CHEMICAL_DISTANCE,new class{constructor(){this.uh=`units-handler.${t.SEMTYPE.MACROMOLECULE}`}},P.FASTA,P.SEPARATOR,P.HELM;class X{constructor(t,e=!1){if(this._length=0,this._version=0,this._updateLevel=0,this._selectedCount=0,this._selectedCountVersion=-1,this._selectedIndexesVersion=-1,this._versionedName="",this._versionedNameVersion=-1,this.SHRINK_THRESHOLD=256,"number"==typeof t){const n=t,i=X._createBuffer(n);if(e)for(let t=0;t<i.length;t++)i[t]=-1;this._data=i,this._length=n}else{if(!(t instanceof Uint32Array))throw new Error("Invalid constructor");this._data=t,this._length=e}}getRawData(){return this._data}assureGoez(t,e){if(t<0)throw new Error(`${e} should be greater than zero`)}assureInRange(t,e,n,i){if(t<e||t>n)throw new Error(`Argument ${i} (${t}) out of range (${e}, ${n})`)}copy(t,e,n){for(let i=0;i<n;i++)e[i]=t[i]}copyFrom(t){if(this._length!=t._length)throw new Error(`Lengths differ (${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} != ${e._length})`);const n=new X(t._length);n._length=t._length,n._data=X._createBuffer(n._length),n._version=0;const i=t.lengthInInts;for(let s=0;s<i;s++)n._data[s]=t._data[s]&e._data[s];return n}static _createBuffer(t){return new Uint32Array(Math.floor((t+31)/32))}static fromValues(t){const e=new X(t.length);e._version=0;for(let n=0;n<e._length;n++)t[n]&&(e._data[Math.floor(n/32)]|=1<<(n%32&31));return e}static fromSeq(t,e){const n=new X(t);for(let i=0;i<t;++i)n.setBit(i,e(i));return n._version=0,n}static fromString(t){return X.fromSeq(t.length,(e=>"1"==t.charAt(e)))}static fromUint32Array(t,e){const n=new X(t);return n._data=e,n}static fromBytes(t){const e=t.length,n=new X(8*e);n._data=new Uint32Array(Math.floor((e+3)/4)),n._length=8*e;let i=0,s=0;for(;e-s>=4;)n._data[i++]=255&t[s]|(255&t[s+1])<<8|(255&t[s+2])<<16|(255&t[s+3])<<24,s+=4;return e-s==3&&(n._data[i]=(255&t[s+2])<<16),e-s==2&&(n._data[i]|=(255&t[s+1])<<8),e-s==1&&(n._data[i]|=255&t[s]),n._version=0,n}toString(){return`${this._length} bits, ${this.countBits(!0)} set`}equals(t){if(this==t)return!0;if(null==t)return!1;if(this._length!=t._length)return!1;if(0==this._length)return!0;for(let e=0;e<this._data.length-1;e++)if(this._data[e]!=t._data[e])return!1;for(let e=8*(this._data.length-1);e<this._length;e++)if(this.getBit(e)!=t.getBit(e))return!1;return!0}clone(){const t=new X(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,i=this.lengthInInts;for(let 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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 i=this._length;this.setLength(this._length+e);for(let n=i-1;n>=t;n--)this.setBit(n+e,this.getBit(n));for(let i=t;i<t+e;i++)this.setBit(i,n)}removeAt(t,e=1){if(e<0)throw new Error("n cannot be negative");if(this.assureInRange(t,0,this._length-e,"pos"),this.contains(!0))for(let 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this.countBits(!1)>0}findNext(t,e=!0){if(this.assureInRange(t,-1,this._length,"index"),t>=this._length-1)return-1;let n=31&(t=t<0?0:t+1);const i=this.lengthInInts;for(let s=Math.floor(t/32);s<i;s++){let i=e?this._data[s]:~this._data[s];if(0!=n)i&=4294967295<<n&4294967295,n=0;else if(!e&&-4294967296==i)continue;for(let e=0;0!=i;e+=8,i>>>=8){const n=X._firstOnBit[255&i];if(n>=0)return(t=n+32*s+e)>=this._length?-1:t}}return-1}findPrev(t,e=!0){if(0==t)return-1;this.assureInRange(t,-1,this._length,"index");let n=1+(t=t<0?this._length-1:t-1)&31;for(let i=Math.floor(t/32);i>=0;i--){let t=e?this._data[i]:~this._data[i];0!=n&&(t&=~(4294967295<<n),n=0);for(let e=24;0!=t;e-=8,t<<=8){const n=X._lastOnBit[t>>>24];if(n>=0)return n+32*i+e}}return-1}}async function Z(){const e=t.Func.find({package:"Bio",name:"getMonomerLibHelper"});if(0===e.length)throw new Error('Package "Bio" must be installed for MonomerLibHelper.');return(await e[0].prepare().call()).getOutputParamValue()}X._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]),X._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]),X._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"}(Y||(Y={})),function(t){t.Euclidean="Euclidean"}(Q||(Q={})),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"}(z||(z={})),function(t){t.TanimotoIntArray="TanimotoIntArray"}(j||(j={})),function(t){t.Vector="Vector",t.String="String",t.BitArray="BitArray",t.MacroMolecule="MacroMolecule",t.Number="Number",t.IntArray="IntArray"}(J||(J={})),function(t){t.NumericDistance="NumericDistance"}(q||(q={})),z.Tanimoto,z.Dice,z.Asymmetric,z.BraunBlanquet,z.Cosine,z.Kulczynski,z.McConnaughey,z.RogotGoldberg,z.Russel,z.Sokal,z.Hamming,z.Euclidean,z.Tanimoto,z.Dice,z.Asymmetric,z.BraunBlanquet,z.Cosine,z.Kulczynski,z.McConnaughey,z.RogotGoldberg,z.Russel,z.Sokal,z.Hamming,z.Euclidean,z.Tanimoto,z.Dice,z.Cosine,z.Tanimoto,z.Asymmetric,z.Cosine,z.Sokal,W.HAMMING,W.LEVENSHTEIN,W.MONOMER_CHEMICAL_DISTANCE;const tt="Libraries",et={explicit:["HELMCoreLibrary.json"],exclude:[]};let nt=Promise.resolve();async function it(){let t;return nt=nt.then((async()=>{const n=await e.dapi.userDataStorage.getValue(tt,"Settings",!0);t=n?JSON.parse(n):{exclude:[],explicit:[]},t.exclude=t.exclude instanceof Array?t.exclude:[],t.explicit=t.explicit instanceof Array?t.explicit:[],console.debug(`Bio: getUserLibSettings()\n${JSON.stringify(t,void 0,2)}`)})),await nt,t}async function st(t){nt=nt.then((async()=>{console.debug(`Bio: setUserLibSettings()\n${JSON.stringify(t,void 0,2)}`),await e.dapi.userDataStorage.postValue(tt,"Settings",JSON.stringify(t),!0)})),await nt}async function rt(){await st(et)}var ot=function(t,e,n,i){return new(n||(n=Promise))((function(s,r){function o(t){try{l(i.next(t))}catch(t){r(t)}}function a(t){try{l(i.throw(t))}catch(t){r(t)}}function l(t){var e;t.done?s(t.value):(e=t.value,e instanceof n?e:new n((function(t){t(e)}))).then(o,a)}l((i=i.apply(t,e||[])).next())}))};m("findMonomers",(()=>{let t,e;A((()=>ot(void 0,void 0,void 0,(function*(){t=yield Z(),e=yield it(),yield rt(),yield t.loadLibraries(!0)})))),_((()=>ot(void 0,void 0,void 0,(function*(){yield st(e),yield t.loadLibraries(!0)}))));const n={withoutMissed:{test:"PEPTIDE1{meI.hHis.Aca.N.T.dE.Thr_PO3H2.Aca.D-Tyr_Et}$$$$",tgt:new Set},withMissed:{test:"PEPTIDE1{meI.missed2.Aca.N.T.dE.Thr_PO3H2.Aca.D-Tyr_Et}$$$$",tgt:new Set(["missed2"])}};for(const[t,e]of Object.entries(n))g(t,(()=>ot(void 0,void 0,void 0,(function*(){i(e.test,e.tgt)}))));function i(t,e){p(function(t){const e=Object.keys(org.helm.webeditor.monomerTypeList()),n=[],i=[];for(let t=0;t<e.length;t++)n.push(new scil.helm.Monomers.getMonomerSet(e[t])),Object.keys(n[t]).forEach((e=>{i.push(n[t][e].id)}));return new Set(t.filter((t=>!i.includes(t))))}(O(t)),e)}}));const at=$;var lt,ht=n.n(at),ct=function(t,e,n,i){return new(n||(n=Promise))((function(s,r){function o(t){try{l(i.next(t))}catch(t){r(t)}}function a(t){try{l(i.throw(t))}catch(t){r(t)}}function l(t){var e;t.done?s(t.value):(e=t.value,e instanceof n?e:new n((function(t){t(e)}))).then(o,a)}l((i=i.apply(t,e||[])).next())}))};m("renderers",(()=>{g("missedInLib",(()=>ct(void 0,void 0,void 0,(function*(){yield function(){return ct(this,void 0,void 0,(function*(){const n=yield e.dapi.files.readCsv("System:AppData/Helm/tests/sample_HELM-missedInLib.csv"),i=n.getCol("HELM"),s=e.shell.addTableView(n);yield function(t,e="Timeout exceeded",n=500,i=50){return r(this,void 0,void 0,(function*(){return new Promise(((s,r)=>{setTimeout((()=>{clearInterval(o),r(new Error(e))}),n);const o=setInterval((()=>{t()&&(clearInterval(o),s())}),i)}))}))}((()=>ht()(s.root).find(".d4-grid canvas").length>0),"Table view canvas not found",100),y(i.semType,t.SEMTYPE.MACROMOLECULE),y(i.getTag(t.TAGS.UNITS),P.HELM),y(i.getTag(t.TAGS.CELL_RENDERER),"helm");const o=i.getTag(".cell-renderer.render.error");if(o){const t=JSON.parse(o),e=new Error(t.message);throw e.stack=t.stack,e}}))}()}))))}));class ut extends class{constructor(t){this.init(t)}init(t){this.fileContent=t.replace(/\r/g,""),this._atomCount=void 0,this._atomTypes=void 0,this._bondCount=void 0,this._bondTypes=void 0,this.xyzAtomCoordinates=void 0,this._pairsOfBondedAtoms=void 0}get atomCount(){return void 0===this._atomCount&&this.setAtomAndBondCounts(),this._atomCount}get bondCount(){return void 0===this._bondCount&&this.setAtomAndBondCounts(),this._bondCount}get x(){var t;return null!==(t=this.xyzAtomCoordinates)&&void 0!==t||(this.xyzAtomCoordinates=this.parseAtomCoordinates()),this.xyzAtomCoordinates.x}get y(){var t;return null!==(t=this.xyzAtomCoordinates)&&void 0!==t||(this.xyzAtomCoordinates=this.parseAtomCoordinates()),this.xyzAtomCoordinates.y}get z(){var t;return null!==(t=this.xyzAtomCoordinates)&&void 0!==t||(this.xyzAtomCoordinates=this.parseAtomCoordinates()),this.xyzAtomCoordinates.z}get atomTypes(){var t;return null!==(t=this._atomTypes)&&void 0!==t||(this._atomTypes=this.parseAtomTypes()),this._atomTypes}get pairsOfBondedAtoms(){var t;return null!==(t=this._pairsOfBondedAtoms)&&void 0!==t||(this._pairsOfBondedAtoms=this.parseBondedAtomPairs()),this._pairsOfBondedAtoms}get bondTypes(){var t;return null!==(t=this._bondTypes)&&void 0!==t||(this._bondTypes=this.parseBondTypes()),this._bondTypes}setAtomAndBondCounts(){const{atomCount:t,bondCount:e}=this.parseAtomAndBondCounts();this._atomCount=t,this._bondCount=e}getNextColumnIdx(t){for(;!this.isWhitespace(t);)++t;for(;this.isWhitespace(t);)++t;return t}shiftIdxToSpecifiedColumn(t,e){let n=t;const i=this.isWhitespace(n)?e:e-1;for(let t=0;t<i;t++)n=this.getNextColumnIdx(n);return n}parseAtomTypes(){const t=this.atomCount,e=new Array(t);let n=this.getAtomBlockIdx();for(let i=0;i<t;i++)n=this.shiftIdxToAtomType(n),e[i]=this.parseAtomType(n),n=this.getNextLineIdx(n);return e}parseAtomCoordinates(){const t=new Float32Array(this.atomCount),e=new Float32Array(this.atomCount),n=new Float32Array(this.atomCount);let i=this.getAtomBlockIdx();for(let s=0;s<this.atomCount;s++){i=this.shiftIdxToXColumn(i);for(const r of[t,e,n])r[s]=this.parseFloatValue(i),i=this.getNextColumnIdx(i);i=this.getNextLineIdx(i)}return{x:t,y:e,z:n}}parseBondedAtomPairs(){const t=new Array(this.bondCount);let e=this.getBondBlockIdx();for(let n=0;n<this.bondCount;n++){e=this.shiftIdxToBondedAtomsPair(e);const i=new Uint16Array(2);i[0]=this.parseIntValue(e),e=this.getNextColumnIdx(e),i[1]=this.parseIntValue(e),t[n]=i,e=this.getNextLineIdx(e)}return t}parseBondTypes(){const t=this.bondCount,e=new Uint16Array(t);let n=this.getBondBlockIdx();for(let i=0;i<t;i++)n=this.shiftIdxToBondType(n),e[i]=this.parseIntValue(n),n=this.getNextLineIdx(n);return e}isWhitespace(t){const e=this.fileContent[t];return" "===e||"\t"===e}getNextLineIdx(t){return"\n"!==this.fileContent[t]?this.fileContent.indexOf("\n",t)+1:t+1}parseFloatValue(t){return this.parseNumericValue(parseFloat,t)}parseIntValue(t){return this.parseNumericValue(parseInt,t)}parseNumericValue(t,e){let n=e+1;for(;!this.isWhitespace(n);)++n;return t(this.fileContent.substring(e,n))}}{constructor(t){super(t),this.init(t)}init(t){super.init(t)}parseAtomType(t){let e=t,n=e;return this.isQuote(e)?(n=this.getNextIdenticalChar(e),e++):n=this.fileContent.indexOf(" ",n),this.fileContent.substring(e,n)}isQuote(t){const e=this.fileContent[t].charCodeAt(0);return 39===e||34===e}getNextIdenticalChar(t){const e=this.fileContent[t];return e?this.fileContent.indexOf(e,t+1):-1}isQuery(){return this.isQueryOrFragment(((t,e)=>{return 39===t||34===t||76===t&&!((n=this.fileContent.charCodeAt(e+1))>64&&n<91||n>96&&n<123);var n}))}isFragment(){return this.isQueryOrFragment((t=>82===t||42===t))}isQueryOrFragment(t){const e=this.atomCount;let n=this.getAtomBlockIdx();for(let i=0;i<e;i++){if(n=this.shiftIdxToAtomType(n),t(this.fileContent.charCodeAt(n),n))return!0;n=this.getNextLineIdx(n)}return!1}}!function(t){t.HEADER="V2000",t[t.NUM_OF_HEADER_LINES=3]="NUM_OF_HEADER_LINES",t[t.NUM_OF_COUNTS_DIGITS=3]="NUM_OF_COUNTS_DIGITS",t[t.ATOM_TYPE_COL=4]="ATOM_TYPE_COL",t[t.FIRST_BONDED_ATOM_COL=1]="FIRST_BONDED_ATOM_COL",t[t.BOND_TYPE_COL=3]="BOND_TYPE_COL",t[t.RGP_SHIFT=8]="RGP_SHIFT",t.RGP_LINE="M RGP",t.A_LINE="A ",t.END="M END"}(lt||(lt={}));class ft extends ut{constructor(t){super(t)}static validate(t){return-1!==t.indexOf(lt.HEADER)&&-1!==t.indexOf(lt.END)}shiftIdxToAtomType(t){return this.shiftIdxToSpecifiedColumn(t,lt.ATOM_TYPE_COL)}getCountsLineIdx(){let t=0;for(let e=0;e<lt.NUM_OF_HEADER_LINES;++e)t=this.getNextLineIdx(t);return t}getAtomBlockIdx(){let t=this.getCountsLineIdx();return t=this.getNextLineIdx(t),t}shiftIdxToXColumn(t){return this.getNextColumnIdx(t)}shiftIdxToBondedAtomsPair(t){return this.shiftIdxToSpecifiedColumn(t,lt.FIRST_BONDED_ATOM_COL)}shiftIdxToBondType(t){return this.shiftIdxToSpecifiedColumn(t,lt.BOND_TYPE_COL)}getBondBlockIdx(){let t=this.getAtomBlockIdx();for(let e=0;e<this.atomCount;e++)t=this.getNextLineIdx(t);return t}parseAtomAndBondCounts(){let t=this.getCountsLineIdx(),e=t+lt.NUM_OF_COUNTS_DIGITS;const n=parseInt(this.fileContent.substring(t,e));return t=e,e+=lt.NUM_OF_COUNTS_DIGITS,{atomCount:n,bondCount:parseInt(this.fileContent.substring(t,e))}}}class dt extends ut{constructor(t){super(t),this.init(t)}shiftIdxToAtomType(t){return this.shiftIdxToSpecifiedColumn(t,4)}getCountsLineIdx(){return this.fileContent.indexOf("M V30 COUNTS ")}getAtomBlockIdx(){let t=this.fileContent.indexOf("M V30 BEGIN ATOM");return t=this.getNextLineIdx(t),t}shiftIdxToXColumn(t){let e=this.shiftIdxToAtomType(t);return this.isQuote(e)?(e=this.getNextIdenticalChar(e),e=this.getNextColumnIdx(e),e):this.shiftIdxToSpecifiedColumn(t,5)}shiftIdxToBondedAtomsPair(t){return this.shiftIdxToSpecifiedColumn(t,5)}shiftIdxToBondType(t){return this.shiftIdxToSpecifiedColumn(t,4)}getBondBlockIdx(){return this.getNextLineIdx(this.fileContent.indexOf("M V30 BEGIN BOND"))}static validate(t){return-1!==t.indexOf("V3000")&&-1!==t.indexOf("M END")}parseAtomAndBondCounts(){let t=this.fileContent.indexOf("M V30 COUNTS ")+14,e=this.fileContent.indexOf(" ",t+1);const n=parseInt(this.fileContent.substring(t,e));return t=e+1,e=this.fileContent.indexOf(" ",t+1),{atomCount:n,bondCount:parseInt(this.fileContent.substring(t,e))}}}function gt(t,e=5e3){return n=this,i=void 0,o=function*(){yield v(100),yield function(t,e,n,i=0){return r(this,void 0,void 0,(function*(){return new Promise(((s,r)=>{const o=t.subscribe((t=>{try{e(t),s("OK")}catch(t){r(t)}o.unsubscribe(),clearTimeout(a)})),a=setTimeout((()=>{o.unsubscribe(),r("timeout")}),i);n()}))}))}(t.onAfterDrawContent,(()=>{}),(()=>{t.invalidate()}),e)},new((s=void 0)||(s=Promise))((function(t,e){function 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Ct;!function(t){t.HAMMING="Hamming",t.LEVENSHTEIN="Levenshtein",t.NEEDLEMANN_WUNSCH="Needlemann-Wunsch",t.MONOMER_CHEMICAL_DISTANCE="Monomer chemical distance"}(Ct||(Ct={}));const yt={[Ct.HAMMING]:dt,[Ct.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,s=e.length,i=1<<n-1;let r=-1,o=0,a=n,l=n;for(;l--;)pt[t.charCodeAt(l)]|=1<<l;for(l=0;l<s;l++){let t=pt[e.charCodeAt(l)];const n=t|o;t|=(t&r)+r^r,o|=~(t|r),r&=t,o&i&&a++,r&i&&a--,o=o<<1|1,r=r<<1|~(n|o),o&=n}for(l=n;l--;)pt[t.charCodeAt(l)]=0;return a})(t,e):((t,e)=>{const n=e.length,s=t.length,i=[],r=[],o=Math.ceil(n/32),a=Math.ceil(s/32);for(let t=0;t<o;t++)r[t]=-1,i[t]=0;let l=0;for(;l<a-1;l++){let o=0,a=-1;const h=32*l,c=Math.min(32,s)+h;for(let e=h;e<c;e++)pt[t.charCodeAt(e)]|=1<<e;for(let t=0;t<n;t++){const n=pt[e.charCodeAt(t)],s=r[t/32|0]>>>t&1,l=i[t/32|0]>>>t&1,h=n|o,c=((n|l)&a)+a^a|n|l;let u=o|~(c|a),g=a&c;u>>>31^s&&(r[t/32|0]^=1<<t),g>>>31^l&&(i[t/32|0]^=1<<t),u=u<<1|s,g=g<<1|l,a=g|~(h|u),o=u&h}for(let e=h;e<c;e++)pt[t.charCodeAt(e)]=0}let h=0,c=-1;const u=32*l,g=Math.min(32,s-u)+u;for(let e=u;e<g;e++)pt[t.charCodeAt(e)]|=1<<e;let f=s;for(let t=0;t<n;t++){const n=pt[e.charCodeAt(t)],o=r[t/32|0]>>>t&1,a=i[t/32|0]>>>t&1,l=n|h,u=((n|a)&c)+c^c|n|a;let g=h|~(u|c),d=c&u;f+=g>>>s-1&1,f-=d>>>s-1&1,g>>>31^o&&(r[t/32|0]^=1<<t),d>>>31^a&&(i[t/32|0]^=1<<t),g=g<<1|o,d=d<<1|a,c=d|~(l|g),h=g&l}for(let e=u;e<g;e++)pt[t.charCodeAt(e)]=0;return f})(t,e)})(t,e)/Math.max(t.length,e.length)},[Ct.NEEDLEMANN_WUNSCH]:function(t){return(e,n)=>{const{gapOpen:s,gapExtend:i,scoringMatrix:r,alphabetIndexes:o}={...mt,...t},a=[new Array(e.length+1).fill(0),new Array(e.length+1).fill(0)],l=new Array(e.length+1).fill(!1),h=new Array(e.length+1).fill(!1);let c=0,u=1;for(let t=1;t<e.length+1;t++)a[0][t]=-s-(t-1)*i;for(let t=1;t<n.length+1;t++){a[u][0]=-s-(t-1)*i;for(let g=1;g<e.length+1;g++){const f=a[c][g-1]+r[o[e[g-1]]][o[n[t-1]]],d=a[c][g]-(l[g]?i:s),p=a[u][g-1]-(h[g-1]?i:s);a[u][g]=Math.max(f,p,d),a[u][g]===f?(l[g]=!1,h[g]=!1):a[u][g]===p?(l[g]=!1,h[g]=!0):(l[g]=!0,h[g]=!1)}c=u,u=(u+1)%2}const g=e.split("").map((t=>r[o[t]][o[t]])).reduce(((t,e)=>t+e),0),f=n.split("").map((t=>r[o[t]][o[t]])).reduce(((t,e)=>t+e),0),d=Math.max(g,f);return(d-a[c][e.length])/d}},[Ct.MONOMER_CHEMICAL_DISTANCE]:dt},xt=new class{constructor(){this.uh=`units-handler.${t.SEMTYPE.MACROMOLECULE}`}},At={[W.FASTA]:"-",[W.SEPARATOR]:"",[W.HELM]:"*"};class Tt{static setUnitsToFastaColumn(e){if(e.column.semType!==t.SEMTYPE.MACROMOLECULE||e.column.getTag(t.TAGS.UNITS)!==W.FASTA)throw new Error(`The column of notation '${W.FASTA}' must be '${t.SEMTYPE.MACROMOLECULE}'.`);e.column.setTag(t.TAGS.UNITS,W.FASTA),Tt.setTags(e)}static setUnitsToSeparatorColumn(e,n){if(e.column.semType!==t.SEMTYPE.MACROMOLECULE||e.column.getTag(t.TAGS.UNITS)!==W.SEPARATOR)throw new Error(`The column of notation '${W.SEPARATOR}' must be '${t.SEMTYPE.MACROMOLECULE}'.`);if(!n)throw new Error(`The column of notation '${W.SEPARATOR}' must have the separator tag.`);e.column.setTag(t.TAGS.UNITS,W.SEPARATOR),e.column.setTag("separator",n),Tt.setTags(e)}static setUnitsToHelmColumn(e){if(e.column.semType!==t.SEMTYPE.MACROMOLECULE)throw new Error(`The column of notation '${W.HELM}' must be '${t.SEMTYPE.MACROMOLECULE}'`);e.column.setTag(t.TAGS.UNITS,W.HELM),Tt.setTags(e)}static setTags(e){const n=e.column.getTag(t.TAGS.UNITS),s=e.stats;if(Object.keys(s.freq).some((t=>t.length>1)),[W.FASTA,W.SEPARATOR].includes(n)){if(!e.column.getTag("alphabet")&&0===Object.keys(s.freq).length)throw new Error("Alphabet is empty and not annotated.");let t=e.column.getTag("aligned");null===t&&(t=s.sameLength?"SEQ.MSA":"SEQ",e.column.setTag("aligned",t));let n=e.column.getTag("alphabet");if(null===n&&(n=ft(s.freq,J),e.column.setTag("alphabet",n)),"UN"===n){const t=Object.keys(s.freq).length,n=Object.keys(s.freq).some((t=>t.length>1));e.column.setTag(".alphabetSize",t.toString()),e.column.setTag(".alphabetIsMultichar",n?"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===W.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==W.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===W.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(),s=this._column.categories;for(let i=0;i<e;i++){const e=s[n[i]];this._splitted[i]=t(e)}}return this._splitted}get stats(){if(null===this._stats){const t={};let e=!0,n=null;for(const s of this.splitted){null==n?n=s.length:s.length!==n&&(e=!1);for(const e of s)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())):j().count(1).take(this.maxLength).map((t=>t.toString())).toArray()}return this._posList}isFasta(){return this.notation===W.FASTA}isSeparator(){return this.notation===W.SEPARATOR}isHelm(){return this.notation===W.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===W.FASTA&&t===At[W.FASTA]||this.units===W.HELM&&t===At[W.HELM]}getNotation(){if(this.units.toLowerCase().startsWith(W.FASTA))return W.FASTA;if(this.units.toLowerCase().startsWith(W.SEPARATOR))return W.SEPARATOR;if(this.units.toLowerCase().startsWith(W.HELM))return W.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(e,n,s,i){const r=this.column,o=e.toLowerCase()+"("+r.name+")",a=s??r.dataFrame.columns.getUnusedName(o),l=t.Column.fromList("string",a,i??new Array(this.column.length).fill(""));if(l.semType=t.SEMTYPE.MACROMOLECULE,l.setTag(t.TAGS.UNITS,e),e===W.SEPARATOR){if(!n)throw new Error(`Notation '${W.SEPARATOR}' requires separator value.`);l.setTag("separator",n)}l.setTag(t.TAGS.CELL_RENDERER,"Macromolecule");const h=r.getTag("aligned");h&&l.setTag("aligned",h);const c=r.getTag("alphabet");null!=c&&l.setTag("alphabet",c);let u=r.getTag(".alphabetSize");null!=c&&u&&l.setTag(".alphabetSize",u);const g=r.getTag(".alphabetIsMultichar");return null!=c&&void 0!==g&&l.setTag(".alphabetIsMultichar",g),e==W.HELM&&(u=this.getAlphabetSize().toString(),l.setTag(".alphabetSize",u)),l}getNewColumnFromList(t,e){return this.getNewColumn(this.notation,this.separator,t,e)}static getNewColumn(t){const e=Tt.getOrCreate(t),n=e.notation;return e.getNewColumn(n)}static unitsStringIsValid(t){return t=t.toLowerCase(),[W.FASTA,W.SEPARATOR,W.HELM].some((e=>t.startsWith(e.toLowerCase())))}static getNewColumnFromParams(e,n,s){if(!Tt.unitsStringIsValid(s))throw new Error("Invalid format of 'units' parameter");const i=t.Column.fromList("string",n,new Array(e).fill(""));return i.semType=t.SEMTYPE.MACROMOLECULE,i.setTag(t.TAGS.UNITS,s),i}getSplitter(t){if(this.units.toLowerCase().startsWith(W.FASTA))return null===this.column.getTag("alphabet")||this.getAlphabetIsMultichar()?at:lt;if(this.units.toLowerCase().startsWith(W.SEPARATOR))return ht(this.separator,t);if(this.units.toLowerCase().startsWith(W.HELM))return gt;throw new Error(`Unexpected units ${this.units} .`)}getDistanceFunctionName(){if(!this.isFasta())throw new Error("Only FASTA notation is supported");return this.isMsa()?Ct.HAMMING:(this.alphabet,Ct.LEVENSHTEIN)}getDistanceFunction(){return yt[this.getDistanceFunctionName()]()}async checkHelmCompatibility(){if(this.column.tags.has(".isHelmCompatible"))return"true"===this.column.getTag(".isHelmCompatible");const t=(await Rt()).getBioLib().getMonomerSymbolsByType("PEPTIDE".toString()),e=new Set(t),n=ht(this.separator);for(const t of this.column.categories){const s=n(t);for(const t of s)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,Tt.getOrCreate(t).getSplitter())),this._splitter}toFasta(t){return t===W.FASTA}toSeparator(t){return t===W.SEPARATOR}toHelm(t){return t===W.HELM}convertHelmToFastaSeparator(t,e,n,s){s||(s=this.toFasta(e)?At[W.FASTA]:At[W.SEPARATOR]),n||(n=this.toFasta(e)?"":this.separator);const i=t.startsWith("RNA"),r=this.splitter(t),o=[];for(let t=0;t<r.length;t++){let n=r[t];if(i&&(n=n.replace(G,"")),n===At[W.HELM])o.push(s);else if(this.toFasta(e)&&n.length>1){const t="["+n+"]";o.push(t)}else o.push(n)}return o.join(n)}convert(t,e){const n=this.getConverter(t,e),s=this.getNewColumn(t,e);return s.init((t=>{const e=this.column.get(t);return e?n(e):e})),s}getRegion(t,e,n){const s=this.getNewColumn(this.notation,this.separator);s.name=n,Math.max(...this.splitted.map((t=>t.length)));const i=t??0,r=e??this.maxLength-1,o=this.getJoiner(),a=r-i+1;s.init((t=>{const e=this.splitted[t],n=new Array(a);for(let t=0;t<a;++t){const s=i+t;n[t]=s<e.length?e[s]:At[this.notation]}return o(n)}));const l=t=>{const e=t.split(",").map((t=>t.trim())),n=new Array(a);for(let t=0;t<a;++t){const s=i+t;n[t]=s<e.length?e[s]:"?"}return n.join(", ")},h=this.column.getTag(".positionNames");h&&s.setTag(".positionNames",l(h));const c=this.column.getTag(".positionLabels");return c&&s.setTag(".positionLabels",l(c)),s}getJoiner(){if(void 0===this._joiner){const t=this;if(this.notation===W.FASTA)this._joiner=function(e){return Et(t,e)};else if(this.notation===W.SEPARATOR)this._joiner=function(e){return bt(t,e,t.separator)};else{if(this.notation!==W.HELM)throw new Error;{const e="DNA"===t.alphabet||"RNA"===t.alphabet;this._joiner=function(n){return _t(t,n,e)}}}}return this._joiner}getConverter(t,e=void 0){if(t===W.SEPARATOR&&!e)throw new Error(`Target separator is not specified for target units '${W.SEPARATOR}'.`);const n=this;if(t===W.FASTA)return function(t){return function(t,e){const n=t.isHelm()?Nt(t,e):t.getSplitter()(e);return Et(t,n)}(n,t)};if(t===W.HELM)return function(t){return function(t,e){const n=e.startsWith("DNA")||e.startsWith("RNA"),s=t.getSplitter()(e);return _t(t,s,n)}(n,t)};if(t===W.SEPARATOR)return function(t){return function(t,e,n){const s=t.isHelm()?Nt(t,e):t.getSplitter()(e);return bt(t,s,n)}(n,t,e)};throw new Error}constructor(e){if(this._splitter=null,this._splitted=null,this._stats=null,this._maxLength=null,this._posList=null,this._joiner=void 0,e.type!==t.TYPE.STRING)throw new Error(`Unexpected column type '${e.type}', must be '${t.TYPE.STRING}'.`);this._column=e;const n=this._column.getTag(t.TAGS.UNITS);if(null==n)throw new Error("Units are not specified in column");if(this._units=n,this._notation=this.getNotation(),this._defaultGapSymbol=this.isFasta()?At[W.FASTA]:this.isHelm()?At[W.HELM]:At[W.SEPARATOR],!this.column.tags.has("aligned")||!this.column.tags.has("alphabet")||!this.column.tags.has(".alphabetIsMultichar")&&!this.isHelm()&&"UN"===this.alphabet)if(this.isFasta())Tt.setUnitsToFastaColumn(this);else if(this.isSeparator()){const t=e.getTag("separator");Tt.setUnitsToSeparatorColumn(this,t)}else{if(!this.isHelm())throw new Error(`Unexpected units '${this.column.getTag(t.TAGS.UNITS)}'.`);Tt.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[xt.uh];return e||(e=t.temp[xt.uh]=new Tt(t)),e}}function Et(t,e){const n=new Array(e.length);for(const[s,i]of j().enumerate(e)){let r=s;t.isHelm()&&(r=s.replace(G,"$1")),t.isGap(r)?r=At[W.FASTA]:r.length>1&&(r="["+e[i]+"]"),n[i]=r}return n.join("")}function bt(t,e,n){const s=new Array(e.length);for(const[n,i]of j().enumerate(e)){let e=n;t.isGap(e)&&(e=At[W.SEPARATOR]),s[i]=e}return s.map((t=>t??"")).join(n)}function _t(t,e,n){const[s,i,r,o]=t.getHelmWrappers();return`${s}${j()(e).map((e=>{let s=e;return s=t.isGap(s)?At[W.HELM]:n?s.replace(G,"$1"):1==e.length?`${i}${e}${r}`:`${i}[${e}]${r}`,s})).toArray().join(".")}${o}`}function Nt(t,e){const n=t.getSplitter()(e),s=new Array(n.length),i=e.startsWith("DNA"),r=e.startsWith("RNA");for(const[t,e]of j().enumerate(n)){let n=t;(i||r)&&(n=n.replace(G,"$1"),n="p"===n?null:n),s[e]=n}return s.filter((t=>null!==t))}class Ot{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,s=Ot._createBuffer(n);if(e)for(let t=0;t<s.length;t++)s[t]=-1;this._data=s,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,s){if(t<e||t>n)throw new Error(`Argument ${s} (${t}) out of range (${e}, ${n})`)}copy(t,e,n){for(let s=0;s<n;s++)e[s]=t[s]}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 Ot(t._length);n._length=t._length,n._data=Ot._createBuffer(n._length),n._version=0;const s=t.lengthInInts;for(let i=0;i<s;i++)n._data[i]=t._data[i]&e._data[i];return n}static _createBuffer(t){return new Uint32Array(Math.floor((t+31)/32))}static fromValues(t){const e=new Ot(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 Ot(t);for(let s=0;s<t;++s)n.setBit(s,e(s));return n._version=0,n}static fromString(t){return Ot.fromSeq(t.length,(e=>"1"==t.charAt(e)))}static fromUint32Array(t,e){const n=new Ot(t);return n._data=e,n}static fromBytes(t){const e=t.length,n=new Ot(8*e);n._data=new Uint32Array(Math.floor((e+3)/4)),n._length=8*e;let s=0,i=0;for(;e-i>=4;)n._data[s++]=255&t[i]|(255&t[i+1])<<8|(255&t[i+2])<<16|(255&t[i+3])<<24,i+=4;return e-i==3&&(n._data[s]=(255&t[i+2])<<16),e-i==2&&(n._data[s]|=(255&t[i+1])<<8),e-i==1&&(n._data[s]|=255&t[i]),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 Ot(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,s=this.lengthInInts;for(let t=0;t<s;t++)this._data[t]=n;this.incrementVersion(e)}setIndexes(t,e=!0,n=!0,s=!0){n&&this.setAll(!e,!1);for(const n of t)this.setFast(n,e);this.incrementVersion(s)}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,s=!0,i=!0){if(n&&i&&this.setAll(!e,!1),i)for(let n=0;n<this._length;n++)t(n)&&this.setFast(n,e);else for(let n=0;n<this._length;n++)this.setFast(n,t(n)?e:!e);this.incrementVersion(s)}getRange(t,e){this.assureInRange(t,0,this._length-1,"from"),this.assureInRange(e,0,this._length,"to");const n=[];for(let s=t;s<e;++s)n.push(this.getBit(s));return Ot.fromValues(n)}getRangeAsList(t,e){this.assureInRange(t,0,this._length-1,"from"),this.assureInRange(e,0,this._length,"to");const n=[];for(let s=t;s<e;++s)n.push(this.getBit(s));return n}setRange(t,e,n,s=!0){this.assureInRange(t,0,this._length-1,"from"),this.assureInRange(e,0,this._length-1,"to");const i=Math.min(t,e),r=Math.max(t,e);if(n)for(let t=i;t<=r;t++)this.setTrue(t);else for(let t=i;t<=r;t++)this.setFalse(t);return this.incrementVersion(s),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 s=this._length;this.setLength(this._length+e);for(let n=s-1;n>=t;n--)this.setBit(n+e,this.getBit(n));for(let s=t;s<t+e;s++)this.setBit(s,n)}removeAt(t,e=1){if(e<0)throw new Error("n cannot be negative");if(this.assureInRange(t,0,this._length-e,"pos"),this.contains(!0))for(let n=t;n<this._length-e;n++)this.setBit(n,this.getBit(n+e));this.setLength(this._length-e)}removeByMask(t,e=!0){if(this._length!=t.length)throw new Error("length != mask.length");if(t==this)this.setLength(t.countBits(!e)),this.setAll(!e);else{let n=0;for(let s=-1;-1!=(s=t.findNext(s,!e));)this.setFast(n++,this.getBit(s));this._length=n,this._version++}return this}getBit(t){return 0!=(this._data[Math.floor(t/32)]&1<<(31&t))}setBit(t,e,n=!0){this.setFast(t,e),this._version++}setFast(t,e){e?this._data[Math.floor(t/32)]|=1<<(31&t):this._data[Math.floor(t/32)]&=~(1<<(31&t))}setTrue(t){this._data[Math.floor(t/32)]|=1<<(31&t)}setFalse(t){this._data[Math.floor(t/32)]&=~(1<<(31&t))}trueCount(){return this.countBits(!0)}falseCount(){return this.countBits(!1)}countBits(t){if(0==this._length)return 0;if(this._selectedCountVersion!=this._version){this._selectedCount=0;const t=this.lengthInInts;let e=0;for(;e<t-1;e++)for(let t=this._data[e];0!=t;t>>>=8)this._selectedCount+=Ot._onBitCount[255&t];let n=this._data[e];const s=31&this._length;for(0!=s&&(n&=~(4294967295<<s));0!=n;n>>>=8)this._selectedCount+=Ot._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 s=this.lengthInInts;let i=0;for(;i<s-1;i++)for(let e=this._data[i]&t._data[i];0!=e;e>>>=8)n+=Ot._onBitCount[255&e];let r=this._data[i]&t._data[i];const o=31&this._length;for(0!=o&&(r&=~(4294967295<<o));0!=r;r>>>=8)n+=Ot._onBitCount[255&r];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 s=this.lengthInInts;for(let i=Math.floor(t/32);i<s;i++){let s=e?this._data[i]:~this._data[i];if(0!=n)s&=4294967295<<n&4294967295,n=0;else if(!e&&-4294967296==s)continue;for(let e=0;0!=s;e+=8,s>>>=8){const n=Ot._firstOnBit[255&s];if(n>=0)return(t=n+32*i+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 s=Math.floor(t/32);s>=0;s--){let t=e?this._data[s]:~this._data[s];0!=n&&(t&=~(4294967295<<n),n=0);for(let e=24;0!=t;e-=8,t<<=8){const n=Ot._lastOnBit[t>>>24];if(n>=0)return n+32*s+e}}return-1}}var wt,It,St,Mt,Lt,vt;async function Rt(){const e=t.Func.find({package:"Bio",name:"getMonomerLibHelper"});if(0===e.length)throw new Error('Package "Bio" must be installed for MonomerLibHelper.');return(await e[0].prepare().call()).getOutputParamValue()}Ot._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]),Ot._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]),Ot._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"}(wt||(wt={})),function(t){t.Euclidean="Euclidean"}(It||(It={})),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"}(St||(St={})),function(t){t.TanimotoIntArray="TanimotoIntArray"}(Mt||(Mt={})),function(t){t.Vector="Vector",t.String="String",t.BitArray="BitArray",t.MacroMolecule="MacroMolecule",t.Number="Number",t.IntArray="IntArray"}(Lt||(Lt={})),function(t){t.NumericDistance="NumericDistance"}(vt||(vt={})),St.Tanimoto,St.Dice,St.Asymmetric,St.BraunBlanquet,St.Cosine,St.Kulczynski,St.McConnaughey,St.RogotGoldberg,St.Russel,St.Sokal,St.Hamming,St.Euclidean,St.Tanimoto,St.Dice,St.Asymmetric,St.BraunBlanquet,St.Cosine,St.Kulczynski,St.McConnaughey,St.RogotGoldberg,St.Russel,St.Sokal,St.Hamming,St.Euclidean,St.Tanimoto,St.Dice,St.Cosine,St.Tanimoto,St.Asymmetric,St.Cosine,St.Sokal,Ct.HAMMING,Ct.LEVENSHTEIN,Ct.MONOMER_CHEMICAL_DISTANCE;const Pt="Libraries",Ht={explicit:["HELMCoreLibrary.json"],exclude:[]};let Dt=Promise.resolve();async function Ft(){let t;return Dt=Dt.then((async()=>{const n=await e.dapi.userDataStorage.getValue(Pt,"Settings",!0);t=n?JSON.parse(n):{exclude:[],explicit:[]},t.exclude=t.exclude instanceof Array?t.exclude:[],t.explicit=t.explicit instanceof Array?t.explicit:[],console.debug(`Bio: getUserLibSettings()\n${JSON.stringify(t,void 0,2)}`)})),await Dt,t}async function $t(t){Dt=Dt.then((async()=>{console.debug(`Bio: setUserLibSettings()\n${JSON.stringify(t,void 0,2)}`),await e.dapi.userDataStorage.postValue(Pt,"Settings",JSON.stringify(t),!0)})),await Dt}async function kt(){await $t(Ht)}w("findMonomers",(()=>{let t,e;I((async()=>{t=await Rt(),e=await Ft(),await kt(),await t.loadLibraries(!0)})),S((async()=>{await $t(e),await t.loadLibraries(!0)}));const n={withoutMissed:{test:"PEPTIDE1{meI.hHis.Aca.N.T.dE.Thr_PO3H2.Aca.D-Tyr_Et}$$$$",tgt:new Set},withMissed:{test:"PEPTIDE1{meI.missed2.Aca.N.T.dE.Thr_PO3H2.Aca.D-Tyr_Et}$$$$",tgt:new Set(["missed2"])}};for(const[t,e]of Object.entries(n))E(t,(async()=>{s(e.test,e.tgt)}));function s(t,e){N(function(t){const e=Object.keys(org.helm.webeditor.monomerTypeList()),n=[],s=[];for(let t=0;t<e.length;t++)n.push(new scil.helm.Monomers.getMonomerSet(e[t])),Object.keys(n[t]).forEach((e=>{s.push(n[t][e].id)}));return new Set(t.filter((t=>!s.includes(t))))}(H(t)),e)}}));const Bt=$;var Ut,Gt=n.n(Bt);w("renderers",(()=>{E("missedInLib",(async()=>{await async function(){const n=await e.dapi.files.readCsv("System:AppData/Helm/tests/sample_HELM-missedInLib.csv"),s=n.getCol("HELM"),i=e.shell.addTableView(n);await function(t,e="Timeout exceeded",n=500,s=50){return r(this,void 0,void 0,(function*(){return new Promise(((i,r)=>{setTimeout((()=>{clearInterval(o),r(new Error(e))}),n);const o=setInterval((()=>{t()&&(clearInterval(o),i())}),s)}))}))}((()=>Gt()(i.root).find(".d4-grid canvas").length>0),"Table view canvas not found",100),b(s.semType,t.SEMTYPE.MACROMOLECULE),b(s.getTag(t.TAGS.UNITS),W.HELM),b(s.getTag(t.TAGS.CELL_RENDERER),"helm");const o=s.getTag(".cell-renderer.render.error");if(o){const t=JSON.parse(o),e=new Error(t.message);throw e.stack=t.stack,e}}()}))}));class Vt{constructor(t){this.init(t)}init(t){this.fileContent=t.replace(/\r/g,""),this._atomCount=void 0,this._atomTypes=void 0,this._bondCount=void 0,this._bondTypes=void 0,this.xyzAtomCoordinates=void 0,this._pairsOfBondedAtoms=void 0}get atomCount(){return void 0===this._atomCount&&this.setAtomAndBondCounts(),this._atomCount}get bondCount(){return void 0===this._bondCount&&this.setAtomAndBondCounts(),this._bondCount}get x(){var t;return null!==(t=this.xyzAtomCoordinates)&&void 0!==t||(this.xyzAtomCoordinates=this.parseAtomCoordinates()),this.xyzAtomCoordinates.x}get y(){var t;return null!==(t=this.xyzAtomCoordinates)&&void 0!==t||(this.xyzAtomCoordinates=this.parseAtomCoordinates()),this.xyzAtomCoordinates.y}get z(){var t;return null!==(t=this.xyzAtomCoordinates)&&void 0!==t||(this.xyzAtomCoordinates=this.parseAtomCoordinates()),this.xyzAtomCoordinates.z}get atomTypes(){var t;return null!==(t=this._atomTypes)&&void 0!==t||(this._atomTypes=this.parseAtomTypes()),this._atomTypes}get pairsOfBondedAtoms(){var t;return null!==(t=this._pairsOfBondedAtoms)&&void 0!==t||(this._pairsOfBondedAtoms=this.parseBondedAtomPairs()),this._pairsOfBondedAtoms}get bondTypes(){var t;return null!==(t=this._bondTypes)&&void 0!==t||(this._bondTypes=this.parseBondTypes()),this._bondTypes}setAtomAndBondCounts(){const{atomCount:t,bondCount:e}=this.parseAtomAndBondCounts();this._atomCount=t,this._bondCount=e}getNextColumnIdx(t){for(;!this.isWhitespace(t);)++t;for(;this.isWhitespace(t);)++t;return t}shiftIdxToSpecifiedColumn(t,e){let n=t;const s=this.isWhitespace(n)?e:e-1;for(let t=0;t<s;t++)n=this.getNextColumnIdx(n);return n}parseAtomTypes(){const t=this.atomCount,e=new Array(t);let n=this.getAtomBlockIdx();for(let s=0;s<t;s++)n=this.shiftIdxToAtomType(n),e[s]=this.parseAtomType(n),n=this.getNextLineIdx(n);return e}parseAtomCoordinates(){const t=new Float32Array(this.atomCount),e=new Float32Array(this.atomCount),n=new Float32Array(this.atomCount);let s=this.getAtomBlockIdx();for(let i=0;i<this.atomCount;i++){s=this.shiftIdxToXColumn(s);for(const r of[t,e,n])r[i]=this.parseFloatValue(s),s=this.getNextColumnIdx(s);s=this.getNextLineIdx(s)}return{x:t,y:e,z:n}}parseBondedAtomPairs(){const t=new Array(this.bondCount);let e=this.getBondBlockIdx();for(let n=0;n<this.bondCount;n++){e=this.shiftIdxToBondedAtomsPair(e);const s=new Uint16Array(2);s[0]=this.parseIntValue(e),e=this.getNextColumnIdx(e),s[1]=this.parseIntValue(e),t[n]=s,e=this.getNextLineIdx(e)}return t}parseBondTypes(){const t=this.bondCount,e=new Uint16Array(t);let n=this.getBondBlockIdx();for(let s=0;s<t;s++)n=this.shiftIdxToBondType(n),e[s]=this.parseIntValue(n),n=this.getNextLineIdx(n);return e}isWhitespace(t){const e=this.fileContent[t];return" "===e||"\t"===e}getNextLineIdx(t){return"\n"!==this.fileContent[t]?this.fileContent.indexOf("\n",t)+1:t+1}parseFloatValue(t){return this.parseNumericValue(parseFloat,t)}parseIntValue(t){return this.parseNumericValue(parseInt,t)}parseNumericValue(t,e){let n=e+1;for(;!this.isWhitespace(n);)++n;return t(this.fileContent.substring(e,n))}}class Wt extends Vt{constructor(t){super(t),this.init(t)}init(t){super.init(t)}parseAtomType(t){let e=t,n=e;return this.isQuote(e)?(n=this.getNextIdenticalChar(e),e++):n=this.fileContent.indexOf(" ",n),this.fileContent.substring(e,n)}isQuote(t){const e=this.fileContent[t].charCodeAt(0);return 39===e||34===e}getNextIdenticalChar(t){const e=this.fileContent[t];return e?this.fileContent.indexOf(e,t+1):-1}isQuery(){return this.isQueryOrFragment(((t,e)=>{return 39===t||34===t||76===t&&!((n=this.fileContent.charCodeAt(e+1))>64&&n<91||n>96&&n<123);var n}))}isFragment(){return this.isQueryOrFragment((t=>82===t||42===t))}isQueryOrFragment(t){const e=this.atomCount;let n=this.getAtomBlockIdx();for(let s=0;s<e;s++){if(n=this.shiftIdxToAtomType(n),t(this.fileContent.charCodeAt(n),n))return!0;n=this.getNextLineIdx(n)}return!1}}!function(t){t.HEADER="V2000",t[t.NUM_OF_HEADER_LINES=3]="NUM_OF_HEADER_LINES",t[t.NUM_OF_COUNTS_DIGITS=3]="NUM_OF_COUNTS_DIGITS",t[t.ATOM_TYPE_COL=4]="ATOM_TYPE_COL",t[t.FIRST_BONDED_ATOM_COL=1]="FIRST_BONDED_ATOM_COL",t[t.BOND_TYPE_COL=3]="BOND_TYPE_COL",t[t.RGP_SHIFT=8]="RGP_SHIFT",t.RGP_LINE="M RGP",t.A_LINE="A ",t.END="M END"}(Ut||(Ut={}));class Yt extends Wt{constructor(t){super(t)}static validate(t){return-1!==t.indexOf(Ut.HEADER)&&-1!==t.indexOf(Ut.END)}shiftIdxToAtomType(t){return this.shiftIdxToSpecifiedColumn(t,Ut.ATOM_TYPE_COL)}getCountsLineIdx(){let t=0;for(let e=0;e<Ut.NUM_OF_HEADER_LINES;++e)t=this.getNextLineIdx(t);return t}getAtomBlockIdx(){let t=this.getCountsLineIdx();return t=this.getNextLineIdx(t),t}shiftIdxToXColumn(t){return this.getNextColumnIdx(t)}shiftIdxToBondedAtomsPair(t){return this.shiftIdxToSpecifiedColumn(t,Ut.FIRST_BONDED_ATOM_COL)}shiftIdxToBondType(t){return this.shiftIdxToSpecifiedColumn(t,Ut.BOND_TYPE_COL)}getBondBlockIdx(){let t=this.getAtomBlockIdx();for(let e=0;e<this.atomCount;e++)t=this.getNextLineIdx(t);return t}parseAtomAndBondCounts(){let t=this.getCountsLineIdx(),e=t+Ut.NUM_OF_COUNTS_DIGITS;const n=parseInt(this.fileContent.substring(t,e));return t=e,e+=Ut.NUM_OF_COUNTS_DIGITS,{atomCount:n,bondCount:parseInt(this.fileContent.substring(t,e))}}}class jt extends Wt{constructor(t){super(t),this.init(t)}shiftIdxToAtomType(t){return this.shiftIdxToSpecifiedColumn(t,4)}getCountsLineIdx(){return this.fileContent.indexOf("M V30 COUNTS ")}getAtomBlockIdx(){let t=this.fileContent.indexOf("M V30 BEGIN ATOM");return t=this.getNextLineIdx(t),t}shiftIdxToXColumn(t){let e=this.shiftIdxToAtomType(t);return this.isQuote(e)?(e=this.getNextIdenticalChar(e),e=this.getNextColumnIdx(e),e):this.shiftIdxToSpecifiedColumn(t,5)}shiftIdxToBondedAtomsPair(t){return this.shiftIdxToSpecifiedColumn(t,5)}shiftIdxToBondType(t){return this.shiftIdxToSpecifiedColumn(t,4)}getBondBlockIdx(){return this.getNextLineIdx(this.fileContent.indexOf("M V30 BEGIN BOND"))}static validate(t){return-1!==t.indexOf("V3000")&&-1!==t.indexOf("M END")}parseAtomAndBondCounts(){let t=this.fileContent.indexOf("M V30 COUNTS ")+14,e=this.fileContent.indexOf(" ",t+1);const n=parseInt(this.fileContent.substring(t,e));return t=e+1,e=this.fileContent.indexOf(" ",t+1),{atomCount:n,bondCount:parseInt(this.fileContent.substring(t,e))}}}class Kt{constructor(){}static getInstance(t){if(Yt.validate(t))return new Yt(t);if(jt.validate(t))return new jt(t);throw new Error("Malformed molfile")}}async function zt(t,e=5e3){await R(100),await function(t,e,n,s=0,i="timeout"){return r(this,void 0,void 0,(function*(){return new Promise(((r,o)=>{const a=t.subscribe((t=>{try{e(t),r("OK")}catch(t){o(t)}a.unsubscribe(),clearTimeout(l)})),l=setTimeout((()=>{a.unsubscribe(),o(i)}),s);n()}))}))}(t.onAfterDrawContent,(()=>{}),(()=>{t.invalidate()}),e)}w("getMolfiles",(()=>{let n,s;I((async()=>{n=await Rt(),s=await Ft(),await kt(),await n.loadLibraries(!0)})),S((async()=>{await $t(s),await n.loadLibraries(!0)})),E("linear1",(async()=>{const n=t.DataFrame.fromCsv("Helm, atoms, bonds\nPEPTIDE1{meI.hHis.Aca.N.T.dE.Thr_PO3H2.Aca.D-Tyr_Et.Tyr_ab-dehydroMe.dV}$$$$,11,10\nPEPTIDE1{meI.hHis.Aca.Cys_SEt.T.dK.Thr_PO3H2.Aca.Tyr_PO3H2.D-Chg.dV}$$$$,11,10\nPEPTIDE1{Lys_Boc.hHis.Aca.Cys_SEt.T.dK.Thr_PO3H2.Aca.Tyr_PO3H2}$$$$,9,8"),s=n.getCol("Helm"),i=e.shell.addTableView(n);Xt.logger.debug("Helm/getMolfiles/linear1, grid awaiting 1"),await zt(i.grid,5e3),Xt.logger.debug("Helm/getMolfiles/linear1, grid awaited 1");const r=await e.functions.call("Helm:getMolfiles",{col:s});b(r.length,s.length);const o=r.toList().map((t=>Kt.getInstance(t)));O(o.map((t=>t.atomCount)),n.getCol("atoms").toList()),O(o.map((t=>t.bondCount)),n.getCol("bonds").toList()),Xt.logger.debug("Helm/getMolfiles/linear1, grid awaiting 2"),await zt(i.grid,5e3),Xt.logger.debug("Helm/getMolfiles/linear1, grid awaited 2")}))}));const Qt=ui;const qt={Helm:{seq:"PEPTIDE1{I.H.A.C.T.[Thr_PO3H2].[Aca].[D-Tyr_Et]}|PEPTIDE2{E.A.[meG]}$PEPTIDE1,PEPTIDE2,4:R3-1:R1$$$V2.0",units:W.HELM,res:{formula:"C58H94N13O21SP","molecular weight":1372.48,"extinction coefficient":1.55}},separator:{seq:"I/H/A/C/T/Thr_PO3H2/Aca/D-Tyr_Et",units:W.SEPARATOR,separator:"/",alphabet:"UN",res:{formula:"C47H77N10O15SP","molecular weight":1085.21,"extinction coefficient":1.55}},separator2:{seq:"meI/hHis/Aca/N/T/dK/Thr_PO3H2/Aca/D-Tyr_Et/Aze/dV/E/N////Phe_4Me",units:W.SEPARATOR,separator:"/",alphabet:"UN",res:{formula:"C91H146N19O25P","molecular weight":1937.21,"extinction coefficient":1.49}},"separator-gaps":{seq:"I/H/A//T/Thr_PO3H2/Aca/D-Tyr_Et",units:W.SEPARATOR,separator:"/",alphabet:"UN",res:{formula:"C44H72N9O14P","molecular weight":982.07,"extinction coefficient":1.49}},"fasta-PT":{seq:"IHACTTAY",units:W.FASTA,alphabet:"PT",res:{formula:"C38H58N10O12S","molecular weight":878.99,"extinction coefficient":1.55}},"fasta-DNA":{seq:"ACGTATTCC",units:W.FASTA,alphabet:"DNA",res:{formula:"C87H113N30O56P9","molecular weight":2753.76,"extinction coefficient":91.74}}};function Jt(e,n,s,i,r){const o=t.Column.fromList(t.COLUMN_TYPE.STRING,"seq",[e]);o.semType=t.SEMTYPE.MACROMOLECULE,o.setTag(t.TAGS.UNITS,n),s&&o.setTag("separator",s),i&&o.setTag("alphabet",i),N(function(t,e){const n=(e.isHelm()?t:e.getConverter(W.HELM)(t)).replaceAll(/\.(\*\.)+/g,".").replaceAll(/\{(\*\.)+/g,"{").replaceAll(/(\.\*)+}/g,"}"),s=Qt.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),i=Math.round(100*t.getMolWeight())/100,r=Math.round(100*t.getExtinctionCoefficient(!0))/100;return{formula:e.replace(/<sub>/g,"").replace(/<\/sub>/g,""),"molecular weight":i,"extinction coefficient":r}}finally{Gt()(s).empty(),s.remove()}}(e,Tt.getOrCreate(o)),r)}w("properties-widget",(()=>{for(const[t,e]of Object.entries(qt))E(t,(async()=>{Jt(e.seq,e.units,e.separator,e.alphabet,e.res)}))}));const Xt=new t.Package;async function Zt(n,s,o){const a=await function(n){var s,o,a,y,x,E,_;return r(this,void 0,void 0,(function*(){const N=null===(o=null===(s=e.functions.getCurrentCall())||void 0===s?void 0:s.func)||void 0===o?void 0:o.package;yield function(n,s){return r(this,void 0,void 0,(function*(){const s=n.id;if(C[s])return;const o=g;if(void 0!==o[f]||void 0!==o[d]||Object.keys(o).find((t=>t.startsWith(f))))return void(C[s]=!0);if("DevTools"===n.name){o[m]={tests:[],clear:!0};const e=t.Func.find({tags:["dartTest"]});for(const t of e)o[m].tests.push(new T(m,t.name,(()=>r(this,void 0,void 0,(function*(){return yield t.apply()}))),{isAggregated:t.outputs.length>0,timeout:3e5}))}const a=[],l=[],h=[],c=yield e.dapi.functions.filter(`package.id = "${s}"`).list(),u=new RegExp(/skip:\s*([^,\s]+)|wait:\s*(\d+)|cat:\s*([^,\s]+)|timeout:\s*(\d+)/g);for(const t of c){const n=t.options.test,s=t.options.demoPath;if(n&&Array.isArray(n)&&n.length)for(let s=0;s<n.length;s++){const i=n[s].matchAll(u),l={};Array.from(i).forEach((t=>{t[0].startsWith("skip")?l.skip=t[1]:t[0].startsWith("wait")?l.wait=parseInt(t[2]):t[0].startsWith("cat")?l.cat=t[3]:t[0].startsWith("timeout")&&(l.timeout=parseInt(t[4]))}));const h=new T(f,1===n.length?t.name:`${t.name} ${s+1}`,(()=>r(this,void 0,void 0,(function*(){const i=yield e.functions.eval(M(n[s],t));if(l.wait&&(yield R(l.wait)),"boolean"==typeof i&&!i)throw`Failed: ${n[s]}, expected true, got ${i}`}))),{skipReason:l.skip,timeout:l.timeout});if(l.cat){const t=f+": "+l.cat;h.category=t,void 0===o[t]&&(o[t]={tests:[],clear:!0}),o[t].tests.push(h)}else a.push(h)}if(s){const n=t.options.demoWait?parseInt(t.options.demoWait):void 0,s=new T(d,t.friendlyName,(()=>r(this,void 0,void 0,(function*(){if(e.shell.lastError="",yield t.apply(),yield R(n||2e3),e.shell.lastError)throw new Error(e.shell.lastError)}))),{skipReason:t.options.demoSkip});l.push(s)}if(t.hasTag("semTypeDetector")){const e=new T(p,t.friendlyName,(()=>r(this,void 0,void 0,(function*(){const e=[];for(const n of i.clone().columns){const s=yield t.apply([n]);e.push(s||n.semType)}b(e.filter((t=>t)).length,1)}))),{skipReason:t.options.skipTest});h.push(e)}}C[s]=!0,a.length&&(o[f]={tests:a,clear:!0}),l.length&&(o[d]={tests:l,clear:!0}),h.length&&(o[p]={tests:h,clear:!1})}))}(N);const O=[];console.log("Running tests"),null!=n||(n={}),null!==(a=(_=n).testContext)&&void 0!==a||(_.testContext=new A),e.shell.lastError="";const w=[],I=function(){const t=[];return console.log=(...e)=>{t.push(...e),l(...e)},console.info=(...e)=>{t.push(...e),h(...e)},console.warn=(...e)=>{t.push(...e),c(...e)},console.error=(...e)=>{t.push(...e),u(...e)},t}();for(const[s,i]of Object.entries(g)){if((null==n?void 0:n.category)&&!s.toLowerCase().startsWith(null==n?void 0:n.category.toLowerCase())||(null===(y=n.exclude)||void 0===y?void 0:y.some((t=>s.startsWith(t)))))continue;l(`Started ${s} category`),w.push(s);const r=null===(x=i.tests)||void 0===x?void 0:x.every((t=>{var e;return null===(e=t.options)||void 0===e?void 0:e.skipReason}));try{i.before&&!r&&(yield i.before())}catch(t){i.beforeStatus=L(t)}const o=null!==(E=i.tests)&&void 0!==E?E:[],a=[];if(i.clear)for(let s=0;s<o.length;s++)a.push(yield v(o[s],null==n?void 0:n.test,I,i.timeout,N.name,n.verbose)),console.log("CLEARING"),e.shell.closeAll(),t.Balloon.closeAll();else for(let t=0;t<o.length;t++)a.push(yield v(o[t],null==n?void 0:n.test,I,i.timeout,N.name,n.verbose));const h=a.filter((t=>"skipped"!=t.result));try{i.after&&!r&&(yield i.after())}catch(t){i.afterStatus=L(t)}i.afterStatus&&h.push({category:s,name:"after",result:i.afterStatus,success:!1,ms:0,skipped:!1}),i.beforeStatus&&h.push({category:s,name:"before",result:i.beforeStatus,success:!1,ms:0,skipped:!1}),O.push(...h)}if(console.log=l,console.info=h,console.warn=c,console.error=u,n.testContext.catchUnhandled&&(yield R(1e3),e.shell.lastError.length>0&&O.push({category:"Unhandled exceptions",name:"exceptions",result:e.shell.lastError,success:!1,ms:0,skipped:!1})),!n.test&&O.length){const s=O.filter((t=>t.success)).length,i=O.filter((t=>t.skipped)).length,r=O.filter((t=>!t.success)),o=N.name;for(const t of w){const n=O.filter((e=>e.category===t)),s=n.filter((t=>!t.success)).length,i={success:0===s,passed:n.filter((t=>t.success)).length,skipped:n.filter((t=>t.skipped)).length,failed:s,type:"package",packageName:o,category:t};e.log.usage(`${o}: ${t}`,i,`category-package ${o}: ${t}`)}if(!n.category){const t={success:0===r.length,passed:s,skipped:i,failed:r.length,type:"package",packageName:o};e.log.usage(o,t,`package-package ${o}`)}if(n.testContext.report){const e=new t.Logger,n="Package @package tested: @successful successful, @skipped skipped, @failed failed tests",o={successful:s,skipped:i,failed:r.length,package:N};for(const t of r)Object.assign(o,{[`${t.category} | ${t.name}`]:t.result});e.log(n,o,"package-tested")}}return O}))}({category:n,test:s,testContext:o});return t.DataFrame.fromObjects(a)}})(),helm_test=s})();
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