@datagrok/bio 2.22.4 → 2.22.5

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (10) hide show
  1. package/dist/455.js +1 -1
  2. package/dist/455.js.map +1 -1
  3. package/dist/package-test.js +1 -1
  4. package/dist/package-test.js.map +1 -1
  5. package/dist/package.js +3 -3
  6. package/dist/package.js.map +1 -1
  7. package/package.json +2 -2
  8. package/src/utils/monomer-cell-renderer.ts +52 -27
  9. package/test-console-output-1.log +391 -382
  10. package/test-record-1.mp4 +0 -0
package/dist/package-test.js CHANGED
@@ -1,4 +1,4 @@
1
- var bio_test;(()=>{var e={8924:(e,t,n)=>{"use strict";n.d(t,{X:()=>o});var r=n(7362);class o extends r.e{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,o)),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,o)),this.grokGroups}static get RasMol(){return void 0===this.rasMol&&(this.rasMol=new o({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(e){const t=e in o.aaSynonyms?o.aaSynonyms[e]:e;return super.get(t)}}o.aaSynonyms={MeNle:"L",MeA:"A",MeG:"G",MeF:"F"};class s{static getPalette(e="grok"){switch(e){case"grok":return o.GrokGroups;case"lesk":return o.Lesk;default:throw new Error(`ChemPalette: scheme \`${e}\` does not exist`)}}static getInnerOuter(e){let t=0,n="",r="";for(const o of e)"("==o?t++:")"==o?t--:t?n+=o:r+=o;return isNaN(parseInt(n))?[r,n]:[r,""]}static getColorAAPivot(e="",t="grok"){const n=this.getPalette(t);let[r,o]=this.getInnerOuter(e);if(r=r.length>6?`${r.slice(0,3)}...`:r,o=o.length>6?`${o.slice(0,3)}...`:o,1==e.length||"("==e[1]){const t=e[0]?.toUpperCase();return t in n?[n.get(t),t,o,1]:[this.undefinedColor,r,o,1]}if("d"==e[0]&&e[1]in n&&(2==e.length||"("==e[2])){const t=e[1]?.toUpperCase();return t in n?[n.get(t),t,o,2]:[this.undefinedColor,r,o,2]}if(e.substring(0,3)in this.AAFullNames&&(3==e.length||"("==e[3])){const t=this.AAFullNames[e.substring(0,3)];return t in n?[n.get(t),t,o,3]:[this.undefinedColor,r,o,3]}if(e[0]?.toLowerCase()==e[0]&&e.substring(1,3)in this.AAFullNames&&(4==e.length||"("==e[4])){const t=this.AAFullNames[e.substring(1,3)];return t in n?[n.get(t),t,o,4]:[this.undefinedColor,r,o,4]}return[this.undefinedColor,r,o,0]}}s.SemType="Aminoacids",s.SemTypeMultipleAlignment="AminoacidsMultipleAlignment",s.undefinedColor="rgb(100,100,100)",s.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"},s.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"},s.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(*)*"},s.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"}},6717:(e,t,n)=>{"use strict";n.d(t,{j:()=>o});var r=n(6082);async function o(){const e=r.Func.find({package:"Chem",name:"getRdKitModule"});if(0===e.length)throw new Error('Package "Chem" must be installed for getRdKitModule.');return(await e[0].prepare().call()).getOutputParamValue()}},3599:(e,t,n)=>{"use strict";n.d(t,{o:()=>r.o});var r=n(6869)},9124:(e,t,n)=>{"use strict";n.d(t,{b2:()=>s,fA:()=>i});var r=n(7389),o=n(6082);async function s(){const e="Helm",t=o.Func.find({package:e,name:"getHelmHelper"});if(0===t.length)throw new Error(`Package '${e}' must be installed for HelmHelper.`);return(await t[0].prepare().call()).getOutputParamValue()}function i(e,t){if(!e)throw new Error("Argument 'a' of type Atom or HelmType is mandatory.");let n,r;const o=e;return"ATOM"===o.T?(n=o.biotype(),r=o.elem):(n=e,r=t),[n,r]}o.JsInputBase,Error,r.input.helmAsync=async function(e,t){return(await s()).createHelmInput(e,t)}},8438:(e,t,n)=>{"use strict";function r(e){return e.startsWith("[")&&e.endsWith("]")?e.slice(1,-1):e}n.d(t,{D:()=>r})},8123:(e,t,n)=>{"use strict";n.d(t,{u:()=>r});const r={V2K_RGP_SHIFT:8,V2K_RGP_LINE:"M RGP",V2K_A_LINE:"A ",V3K_COUNTS_SHIFT:14,V3K_IDX_SHIFT:7,V3K_HEADER_FIRST_LINE:"\nDatagrok macromolecule handler\n\n",V3K_HEADER_SECOND_LINE:" 0 0 0 0 0 0 999 V3000\n",V3K_BEGIN_CTAB_BLOCK:"M V30 BEGIN CTAB\n",V3K_END_CTAB_BLOCK:"M V30 END CTAB\n",V3K_BEGIN_COUNTS_LINE:"M V30 COUNTS ",V3K_COUNTS_LINE_ENDING:" 0 0 0\n",V3K_BEGIN_ATOM_BLOCK:"M V30 BEGIN ATOM\n",V3K_END_ATOM_BLOCK:"M V30 END ATOM\n",V3K_BEGIN_BOND_BLOCK:"M V30 BEGIN BOND\n",V3K_END_BOND_BLOCK:"M V30 END BOND\n",V3K_BOND_CONFIG:" CFG=",V3K_BEGIN_DATA_LINE:"M V30 ",V3K_END:"M END",PRECISION_FACTOR:1e4,DEOXYRIBOSE:{polymerType:"RNA",symbol:"d"},RIBOSE:{polymerType:"RNA",symbol:"r"},PHOSPHATE:{polymerType:"RNA",symbol:"p"},OXYGEN:"O",HYDROGEN:"H"}},4356:(e,t,n)=>{"use strict";n.d(t,{Eu:()=>a,ub:()=>i});var r=n(4328);const o="Libraries";let s=Promise.resolve();async function i(){let e;return s=s.then((async()=>{const t=r.userSettings.getValue(o,"Settings",!0);e=t?JSON.parse(t):{exclude:[],explicit:[],duplicateMonomerPreferences:{}},e.exclude=e.exclude instanceof Array?e.exclude:[],e.explicit=e.explicit instanceof Array?e.explicit:[],e.duplicateMonomerPreferences=e.duplicateMonomerPreferences instanceof Object?e.duplicateMonomerPreferences:{},console.debug(`Bio: getUserLibSettings()\n${JSON.stringify(e,void 0,2)}`)})),await s,e}async function a(e){s=s.then((async()=>{console.debug(`Bio: setUserLibSettings()\n${JSON.stringify(e,void 0,2)}`),r.userSettings.add(o,"Settings",JSON.stringify(e),!0)})),await s}},5553:(e,t,n)=>{"use strict";n.d(t,{Qc:()=>E,WN:()=>C});var r=n(1991),o=n.n(r);const s="object"==typeof performance&&performance&&"function"==typeof performance.now?performance:Date,i=new Set,a="object"==typeof process&&process?process:{},c=(e,t,n,r)=>{"function"==typeof a.emitWarning?a.emitWarning(e,t,n,r):console.error(`[${n}] ${t}: ${e}`)};let l=globalThis.AbortController,u=globalThis.AbortSignal;if(void 0===l){u=class{onabort;_onabort=[];reason;aborted=!1;addEventListener(e,t){this._onabort.push(t)}},l=class{constructor(){t()}signal=new u;abort(e){if(!this.signal.aborted){this.signal.reason=e,this.signal.aborted=!0;for(const t of this.signal._onabort)t(e);this.signal.onabort?.(e)}}};let e="1"!==a.env?.LRU_CACHE_IGNORE_AC_WARNING;const t=()=>{e&&(e=!1,c("AbortController is not defined. If using lru-cache in node 14, load an AbortController polyfill from the `node-abort-controller` package. A minimal polyfill is provided for use by LRUCache.fetch(), but it should not be relied upon in other contexts (eg, passing it to other APIs that use AbortController/AbortSignal might have undesirable effects). You may disable this with LRU_CACHE_IGNORE_AC_WARNING=1 in the env.","NO_ABORT_CONTROLLER","ENOTSUP",t))}}Symbol("type");const d=e=>e&&e===Math.floor(e)&&e>0&&isFinite(e),h=e=>d(e)?e<=Math.pow(2,8)?Uint8Array:e<=Math.pow(2,16)?Uint16Array:e<=Math.pow(2,32)?Uint32Array:e<=Number.MAX_SAFE_INTEGER?p:null:null;class p extends Array{constructor(e){super(e),this.fill(0)}}class m{heap;length;static#e=!1;static create(e){const t=h(e);if(!t)return[];m.#e=!0;const n=new m(e,t);return m.#e=!1,n}constructor(e,t){if(!m.#e)throw new TypeError("instantiate Stack using Stack.create(n)");this.heap=new t(e),this.length=0}push(e){this.heap[this.length++]=e}pop(){return this.heap[--this.length]}}class 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r=n(6082),o=n(1991),s=n.n(o),i=n(330),a=n(3599);async function c(e,t,o,c,l,u,d){const h=e.length,p=e.dataFrame,m=Math.max(navigator.hardwareConcurrency-2,1),f=new Array(m).fill(null).map((()=>new Worker(new URL(n.p+n.u(455),n.b)))),g=h/m,y=new Array(m),b=u.getSeqHandler(e),w="RNA"==c?a.o.NUCLEOTIDE:a.o.AA,v=s().count(0).take(e.length).map((e=>{const t=b.getSplitted(e);return s().count(0).take(t.length).map((e=>({position:e,symbol:t.getCanonical(e),biotype:w}))).toArray()})).toArray();for(let e=0;e<m;e++){const n=f[e],r=Math.floor(e*g),s=e===m-1?h:Math.floor((e+1)*g);y[e]=new Promise((e=>{n.onmessage=t=>{e(t.data)}})),n.postMessage({seqList:v,monomersDict:t,alphabet:o,polymerType:c,start:r,end:s})}const A=[],E=[];await Promise.all(y).then((e=>{for(const t of e)A.push(...t.molfiles),E.push(...t.warnings)})),setTimeout((()=>{f.forEach((e=>{e.terminate()}))}),0);const C=(0,i.qj)(p,e.name),T=r.Column.fromType(r.COLUMN_TYPE.STRING,C,e.length).init((e=>A[e]?.molfile));return T.semType=r.SEMTYPE.MOLECULE,T.meta.units=r.UNITS.Molecule.MOLBLOCK,T.setTag(".sequence-src-col",e.name),{molCol:T,warnings:E}}function l(e,t){const n={},o={};for(const s of e){const e=t.getWebEditorMonomer(s.biotype,s.symbol).backgroundcolor,a=(0,i.vG)(e??r.Color.toRgb(r.Color.mouseOverRows))??[1,0,0,.7];for(const e of s.atoms)n[e]=a;for(const e of s.bonds)o[e]=a}return{atoms:Object.keys(n).map((e=>parseInt(e))),bonds:Object.keys(o).map((e=>parseInt(e))),highlightAtomColors:n,highlightBondColors:o}}},3561:(e,t,n)=>{"use strict";n.d(t,{Hb:()=>c,YN:()=>f,gU:()=>l});var r=n(8123),o=n(294),s=n(3151),i=n(439),a=n(6197);function c(e,t,n){const o=new Map;for(const a of e.getMonomerSymbolsByType(t)){const c=e.getMonomer(t,a);if("RNA"===t&&("Branch"===c.monomerType||n===i.YI.DNA&&c.symbol===r.u.DEOXYRIBOSE.symbol||n===i.YI.RNA&&c.symbol===r.u.RIBOSE.symbol||c.symbol===r.u.PHOSPHATE.symbol)||"PEPTIDE"===t&&"Branch"!==c.monomerType){const e={};s.f6.forEach((t=>{e[t]=c[t]})),o.set(c.symbol,e)}}return o}function l(e,t,n,s){if(0===e.length)return o.vF.createEmpty();const c=m,{atomCount:l,bondCount:d,needsCapping:p}=c(e,t,n,s),g=new Array(l),y=new Array(d);let b,w=null,v=null;"PEPTIDE"===s?b=u:(b=h,w=n===i.YI.DNA?(0,o.xb)(t,r.u.DEOXYRIBOSE):(0,o.xb)(t,r.u.RIBOSE),v=(0,o.xb)(t,r.u.PHOSPHATE));const A={i:0,nodeShift:0,bondShift:0,backbonePositionShift:new Array(2).fill(0),branchPositionShift:new Array(2).fill(0),backboneAttachNode:0,branchAttachNode:0,flipFactor:1},E={sugar:w,phosphate:v,seqLength:e.length,atomCount:l,bondCount:d},C=new o.Cg,T=[];let S=0;for(A.i=0;A.i<E.seqLength;++A.i){const n=e[A.i];if(n.symbol===i._S)continue;const r=(0,o.xb)(t,{symbol:n.symbol,polymerType:(0,a.Y)(n.biotype)}),s=A.nodeShift,c=A.bondShift;b(r,g,y,A,E),r.stereoAtoms?.forEach((e=>T.push(e+S))),S+=r.atoms.x.length;const l=A.nodeShift-s,u=new Array(l);for(let e=0;e<l;++e)u[e]=s+e;const d=A.bondShift-c,h=new Array(d);for(let 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COLLECTION\n`}(T)),P+=r.u.V3K_END_CTAB_BLOCK,P+=r.u.V3K_END,{molfile:P,monomers:C}}function u(e,t,n,r){r.flipFactor=(-1)**(r.i%2),d(e,t,n,r)}function d(e,t,n,o){!function(e,t,n){for(let o=0;o<e.atoms.atomTypes.length;++o){const s=n.nodeShift+o+1;t[n.nodeShift+o]=r.u.V3K_BEGIN_DATA_LINE+s+" "+e.atoms.atomTypes[o]+" "+f(n.backbonePositionShift[0]+e.atoms.x[o])+" "+f(n.backbonePositionShift[1]+n.flipFactor*e.atoms.y[o])+" "+e.atoms.kwargs[o]}}(e,t,o),p(e,n,o),function(e,t,n){if(0!==n.backboneAttachNode){const o=n.bondShift,s=n.backboneAttachNode,i=e.meta.terminalNodes[0]+n.nodeShift;t[n.bondShift-1]=r.u.V3K_BEGIN_DATA_LINE+o+" 1 "+s+" "+i+"\n"}}(e,n,o),null!==e.meta.branchShift&&e.meta.terminalNodes.length>2&&function(e,t){t.branchAttachNode=t.nodeShift+e.meta.terminalNodes[2];for(let 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r=n(4328),o=n(6082),s=n(1991),i=n.n(s),a=n(439),c=n(3561),l=n(9235),u=n(294),d=n(9192),h=n(330),p=n(8123);async function m(e,t,n,s,c){if(t.semType!==o.SEMTYPE.MACROMOLECULE)return{molCol:null,warnings:[`Only the ${o.SEMTYPE.MACROMOLECULE} columns can be converted to atomic level, the chosen column has semType '${t.semType}'`]};let u=t;const p=s.getSeqHandler(t);let m,g;p.notation!==a.Hi.SEPARATOR&&(u=p.convert(a.Hi.SEPARATOR,"."),u.name=t.name);try{g=s.getSeqHandler(u).alphabet,m=(0,h.pz)(g)}catch(e){const[t,n]=(0,d.AP)(e);return{molCol:null,warnings:[t]}}const y=function(e,t){const n=e.length,o=new Array(n),s=t.getSeqHandler(e);let a=!1;const c=s.defaultBiotype;for(let e=0;e<n;++e){const t=s.getSplitted(e);a||(a=0===t.length),o[e]=i().count(0).take(t.length).filter((e=>!t.isGap(e))).map((e=>({position:e,biotype:c,symbol:t.getCanonical(e)}))).toArray()}return a&&r.shell.warning(`Some values in the "${e.name}" column are empty`),o}(u,s),b=f(y,m,g,n,c),w=u.length,v=await(0,l.R)(u,b,g,m,n,s,c);return v.warnings.length>.05*w&&r.shell.warning(`Molfile conversion resulted in ${v.warnings.length} errors`),v}function f(e,t,n,r,o){const s=(0,c.Hb)(r,t,n),i={},l={value:null};if("RNA"===t){const e=n===a.YI.RNA?[p.u.RIBOSE,p.u.PHOSPHATE]:[p.u.DEOXYRIBOSE,p.u.PHOSPHATE];for(const n of e)g(i,n.symbol,s,o,t,l)}for(let n=0;n<e.length;++n){const r=e[n];for(const e of r){const n=e.symbol;if(""!==n)try{if("RNA"===t&&3===n.split(/\(|\)/).filter((e=>!!e)).length){const e=n.split(/\(|\)/)[1];g(i,e,s,o,t,l),i[t]?.[e]&&(i[t][n]=i[t][e])}else g(i,n,s,o,t,l)}catch(e){const t=e instanceof Error?e.message:e.toString(),r=e instanceof Error?e.stack:void 0;throw console.error(`bio lib: getMonomersDictFromLib() sym='${n}', error:\n${t}\n${r}`),new Error(`Can't get monomer '${n}' from library: ${t}`)}}}return i}function g(e,t,n,r,o,s){const i={polymerType:o,symbol:t};if(!(0,u.bq)(e,i)){const a=function(e,t,n,r,o){if(t.has(e)){const 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e=0;e<s.terminalNodes.length;++e)s.terminalNodes[e]>t?--s.terminalNodes[e]:s.terminalNodes[e]===t&&(s.terminalNodes[e]=-1);for(let e=0;e<s.rNodes.length;++e)s.rNodes[e]>t?--s.rNodes[e]:s.rNodes[e]===t&&(s.rNodes[e]=-1);let i=0;for(;i<o.atomPairs.length;){const e=o.atomPairs[i][0],n=o.atomPairs[i][1];e===t||n===t?(o.atomPairs.splice(i,1),o.bondTypes=A(Uint32Array,o.bondTypes,i,1),o.bondConfiguration.has(i)&&o.bondConfiguration.delete(i),o.kwargs.has(i)&&o.kwargs.delete(i),--i):(o.atomPairs[i][0]=e>t?e-1:e,o.atomPairs[i][1]=n>t?n-1:n),++i}let a=Array.from(o.bondConfiguration.keys());a.forEach((e=>{if(o.bondConfiguration.has(e)&&e>n){const t=o.bondConfiguration.get(e);o.bondConfiguration.delete(e),o.bondConfiguration.set(e-1,t)}})),a=Array.from(o.kwargs.keys()),a.forEach((e=>{if(o.kwargs.has(e)&&e>n){const t=o.kwargs.get(e);o.kwargs.delete(e),o.kwargs.set(e-1,t)}}))}}function A(e,t,n,r){const o=new e(t.length-r);let s=0,i=0;for(;s<t.length;)s===n&&(s+=r),o[i]=t[s],++i,++s;return o}function E(e,t){let n;if(0===e)n=t>0?0:Math.PI;else if(0===t)n=e>0?-Math.PI/2:Math.PI/2;else{const r=t/e,o=Math.atan(r);n=e<0?Math.PI/2+o:-Math.PI/2+o}return n}function C(e,t){if(0!==t){const n=e.x,r=e.y,o=Math.cos(t),s=Math.sin(t);for(let e=0;e<n.length;++e){const t=n[e];n[e]=(0,c.YN)(t*o-r[e]*s),r[e]=(0,c.YN)(t*s+r[e]*o)}}}function T(e){S(e,!1)}function S(e,t){if(t){const t=e.atoms.y;for(let e=0;e<t.length;e++)t[e]=-t[e]}else{const t=e.atoms.x;for(let e=0;e<t.length;e++)t[e]=-t[e]}const n=e.bonds.bondConfiguration;for(const[e,t]of n){const r=1===t?3:1;n.set(e,r)}}function _(e,t,n){const r=e.atoms.x,o=e.atoms.y;for(let e=0;e<r.length;++e)r[e]=(0,c.YN)(r[e]+t),void 0!==n&&(o[e]=(0,c.YN)(o[e]+n))}},294:(e,t,n)=>{"use strict";function r(e,t){return e[t.polymerType]?.[t.symbol]}function o(e,t){return!!e[t.polymerType]?.[t.symbol]}function s(e,t,n){let r=e[t.polymerType];r||(r=e[t.polymerType]={}),r[t.symbol]=n}n.d(t,{Cg:()=>i,LQ:()=>s,bq:()=>o,vF:()=>a,xb:()=>r});class i extends Map{constructor(e){super(e)}}class a{constructor(e,t){this.molfile=e,this.monomers=t}static createEmpty(){return new a("",new i(null))}}},330:(e,t,n)=>{"use strict";n.d(t,{pz:()=>s,qj:()=>o,vG:()=>i});var r=n(2003);function o(e,t){return function(e,t){return e?e.columns.getUnusedName(t):t}(e,`molfile(${t})`)}function s(e){let t;if(e===r.YI.PT||e===r.YI.UN)t="PEPTIDE";else{if(e!==r.YI.RNA&&e!==r.YI.DNA)throw new Error(`Unexpected alphabet '${e}'.`);t="RNA"}return t}function i(e){const t=7===e.length?/^#?([a-f\d]{2})([a-f\d]{2})([a-f\d]{2})$/i.exec(e):/^#?([a-f\d]{2})([a-f\d]{2})([a-f\d]{2})([a-f\d]{2})$/i.exec(e);return t?[parseInt(t[1],16)/256,parseInt(t[2],16)/256,parseInt(t[3],16)/256,t.length>4?parseInt(t[4],16)/256:.3]:null}},1093:(e,t,n)=>{"use strict";n.d(t,{A:()=>o,Q:()=>s});var r=n(7362);class o extends r.e{static get Chromatogram(){return void 0===this.chromatogram&&(this.chromatogram=new o({A:"green",C:"blue",G:"black",T:"red",U:"red",others:"gray"})),this.chromatogram}}class s{}s.SemType="Nucleotides",s.SemTypeMultipleAlignment="NucleotidesMultipleAlignment",s.Names={A:"Adenine",C:"Cytosine",G:"Guanine",T:"Thymine",U:"Uracil"}},7362:(e,t,n)=>{"use strict";n.d(t,{e:()=>r});class r{static makePalette(e,t=!1,n=r){const o={};return e.forEach((e=>{const n=e[0],r=e[1];n.forEach(((e,n)=>{o[e]=this.colourPalette[r][t?0:n]}))})),new n(o)}constructor(e){this._palette=e}get(e,t){return this._palette[e]}}r.undefinedColor="rgb(100,100,100)",r.colourPalette={orange:["rgb(255,187,120)","rgb(245,167,100)","rgb(235,137,70)","rgb(205, 111, 71)"],all_green:["rgb(44,160,44)","rgb(74,160,74)","rgb(23,103,57)","rgb(30,110,96)","rgb(60,131,95)","rgb(24,110,79)","rgb(152,223,138)","rgb(182, 223, 138)","rgb(152, 193, 138)"],all_blue:["rgb(31,119,180)","rgb(23,190,207)","rgb(122, 102, 189)","rgb(158,218,229)","rgb(141, 124, 217)","rgb(31, 120, 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n=r.Color.fromHtml(e);if(t){const e=r.Color.g(n),t=r.Color.r(n),o=r.Color.b(n),s=Math.sqrt(Math.pow(0-t,2)+Math.pow(0-e,2)+Math.pow(0-o,2));if(s>210)return`rgb(${t/s*210},${e/s*210},${o/s*210})`}return r.Color.toRgb(n)}class a{static hashCode(e){let t=0;if(0===e.length)return t;for(let n=0;n<e.length;n++)t=(t<<5)-t+e.charCodeAt(n),t|=0;return t}}class c{}class l extends c{get(e,t){return"#666666"}}class u extends c{static get palette(){return u._pallete||(u._pallete=u.buildPalette()),u._pallete}static buildPalette(){return(0,s.pj)().then((e=>{e.awaitLoaded(1/0).then((()=>{const t=e.getMonomerLib();t.onChanged.subscribe((()=>{u.customMonomerColors={},u.polymerTypes=t.getPolymerTypes();for(const e of this.polymerTypes){const n=t.getMonomerSymbolsByType(e);for(const r of n){const n=t.getMonomer(e,r);n?.meta?.colors?.default?.background&&(this.customMonomerColors[r]||(this.customMonomerColors[r]={}),this.customMonomerColors[r][e]=i(n.meta.colors.default.background))}}}))}))})),[].concat(...Object.values(o.e.colourPalette))}get(e,t){const n=u.palette.length,r=u.customMonomerColors[e],o=t??"PEPTIDE";if(r&&r[o])return r[o];const s=a.hashCode(e)%n;return i(u.palette[s])}}u._pallete=null,u.customMonomerColors={},u.polymerTypes=[];class d extends o.e{static get Gray(){return void 0===this.gray&&(this.gray=new l),this.gray}static get Color(){return void 0===this.color&&(this.color=new u),this.color}}},6642:(e,t,n)=>{"use strict";n.d(t,{BG:()=>i,sD:()=>c});var r=n(4328),o=n(1858),s=n(8070);function i(e){let t=null,n=null;try{n=e.dart?e.gridColumn:null,t=n?n.temp:null}catch{[n,t]=[null,null]}const r=e.cell.column;if(t=t??(r?r.temp:null),!t)throw new Error("Grid cell renderer back store (GridColumn or Column) not found.");return[n,r,t]}class a{onKeyDown(e,t){}onKeyPress(e,t){}onMouseEnter(e,t){}onMouseLeave(e,t){}onMouseDown(e,t){}onMouseUp(e,t){}onMouseMove(e,t){}onClick(e,t){}onDoubleClick(e,t){}}class c extends a{constructor(e,t,n){super(),this.gridCol=e,this.tableCol=t,this.logger=n,this.subs=[],this.dirty=!0,this.destroyed=!1,this.viewerId=++c.viewerCounter,this.errors=[],this._onRendered=new o.Subject,this.tableCol&&this.tableCol.dataFrame&&(this.subs.push(this.tableCol.dataFrame.onDataChanged.subscribe((()=>{this.dirty=!0}))),this.subs.push(this.tableCol.dataFrame.onColumnsRemoved.subscribe((e=>{try{this.destroyed||!this.tableCol||this.tableCol.dataFrame||this.destroy()}catch(e){this.logger.error(e)}})))),this.tableCol&&this.subs.push(r.events.onTableRemoved.subscribe((e=>{try{const t=e.args.dataFrame;this.tableCol?.dataFrame.id!==t.id||this.destroyed||this.destroy()}catch(e){this.logger.error(e)}}))),this.gridCol&&this.subs.push(r.events.onViewRemoving.subscribe((e=>{try{const t=e.args.view;this.gridCol?.dart&&this.gridCol.grid&&this.gridCol?.grid?.dart&&this.gridCol?.grid?.view?.id===t.id&&!this.destroyed&&this.destroy()}catch(e){this.logger.error(e)}})))}toLog(){return`${this.constructor.name}<${this.viewerId}>`}destroy(){for(const e of this.subs)e.unsubscribe();this.destroyed=!0}invalidateGrid(){this.gridCol&&this.gridCol.dart&&this.gridCol.grid?.invalidate()}reset(){this.dirty=!1}get onRendered(){return this._onRendered}invalidate(e){this.invalidateGrid()}async awaitRendered(e=1e4,t=`${e} timeout`){const n=`${this.toLog()}.awaitRendered()`;if(this.logger.debug(`${n}, start, testEvent before`),await(0,s.PE)(this._onRendered,(()=>{}),(()=>{this.invalidate()}),e,`${n}, ${t}`),this.errors.length>0){const e=this.errors[0];throw this.errors=[],e}this.logger.debug(`${n}, end`)}}c.viewerCounter=-1},673:(e,t,n)=>{"use strict";n.d(t,{s:()=>r});const r={true:"1",false:"0"}},6882:(e,t,n)=>{"use strict";n.d(t,{Bb:()=>b,Jy:()=>w,S$:()=>y,U0:()=>v});var r=n(7389),o=n(6082),s=n(1991),i=n.n(s),a=n(8312),c=n(2003),l=n(6642),u=n(6718),d=n(9192),h=n(3856),p=n(673),m=n(3599),f=n(5553),g=n(9713);const y="rgb(100,100,100)";function b(e,t,n){if((n??0)>0&&t<(e[0]??0)+n)return-1;t-=n??0;let r,o=100,s=0,i=e.length-1;for(;s<=i;){if(r=Math.floor((i+s)/2),e[r]<=t&&t<e[r+1])return r;if(t<e[r]?i=r-1:s=r+1,--o<=0)throw new Error(`Get position for pointer x = ${t} searching has not converged on ${JSON.stringify(e)}. `)}return null}class w extends l.sD{get separatorWidth(){return this.props?.fontCharWidth?this.props?.fontCharWidth:5}constructor(e,t,n,r,s){if(super(e,t,n),this.monomerLengthLimit=r,this.propsProvider=s,this.colWidth=0,this._monomerLengthList=null,this._processedMaxVisibleSeqLength=0,this._monomerLengthMap={},this._monomerStructureMap={},this._ellipsisBounds=void 0,this._totalLinesNeeded=0,this._lineHeight=20,this._cellBounds=new Map,this.sysMonomerLib=null,this.padding=5,this._leftThreeDotsPadding=0,this.props=this.propsProvider(),this._processedRows=o.BitSet.create(this.tableCol.length),this.gridCol&&this.subs.push(this.gridCol.grid.onAfterDrawContent.subscribe((()=>{this._onRendered.next()}))),this.tableCol&&this.gridCol){this.subs.push(this.tableCol.dataFrame.onCurrentRowChanged.subscribe((()=>{-1===this.tableCol.dataFrame.currentRowIdx&&(this.tableCol.temp["reference-sequence"]=null,this.tableCol.temp["current-word"]=null,this.invalidateGrid())})));const e=[c.gp.positionShift,"renderMultiline"];this.subs.push(o.debounce(this.tableCol.dataFrame.onMetadataChanged.pipe(g.filter((t=>t.args.source===this.tableCol&&e.includes(t.args.key)))),200).subscribe((e=>{this.reset()}))),this.subs.push(o.debounce(this.tableCol.dataFrame.onMetadataChanged.pipe(g.filter((e=>e.args.source===this.tableCol&&e.args.key===c.gp.positionShift))),200).subscribe((e=>{this.reset()})))}}calculateFontBasedSpacing(e){const t=e.measureText("M");let n=12;if(this.tableCol?.temp[".mm.cellRenderer.fontSize"]){const e=this.tableCol.temp[".mm.cellRenderer.fontSize"];"number"!=typeof e||isNaN(e)||(n=Math.max(e,1))}return{lineHeight:Math.max(1.4*n,t.fontBoundingBoxAscent+t.fontBoundingBoxDescent+4),monomerSpacing:Math.max(2,.2*this.props.fontCharWidth)}}shouldUseMultilineRendering(e){return"true"===e.getTag("renderMultiline")}calculateMultiLineLayoutDynamic(e,t,n,r,o,s){if(this.dirty)try{this.reset()}catch(e){const[t,n]=(0,d.AP)(e);this.logger.error(t,void 0,n)}const{lineHeight:i,monomerSpacing:a}=this.calculateFontBasedSpacing(e),c=t-2*this.padding;let l=0;const u=[];if(r.length>0)for(let t=o;t<r.length;t++){const n=r.getOriginal(t),o=this.props.monomerToShort(n,s);u.push({text:o,posIdx:t}),l=Math.max(l,e.measureText(o).width)}if(0===u.length)return{lineLayouts:[],lineHeight:i};const h=l;let p=Math.floor((c+a)/(h+a));p=Math.max(1,p);const m=n-2*this.padding,f=Math.max(0,Math.floor(m/i)),g=[];let y=0;for(let e=0;e<f&&y<u.length;e++){const t=[];for(let e=0;e<p&&y<u.length;e++){const n=u[y],r=this.padding+e*(h+a);t.push({posIdx:n.posIdx,x:r,width:h,om:n.text,isSeparator:!1}),y++}g.push({lineIdx:e,elements:t})}return{lineLayouts:g,lineHeight:i}}async init(){await Promise.all([(async()=>{this.seqHelper=await(0,a.Q)(),this.invalidateGrid()})(),(async()=>{const e=await(0,u.pj)();this.sysMonomerLib=e.getMonomerLib()})()]),this.subs.push(this.sysMonomerLib.onChanged.subscribe((()=>{this.reset()}))),this.reset()}static getFontSettings(e){let t=12;return e&&e.temp[".mm.cellRenderer.fontSize"]&&"number"==typeof e.temp[".mm.cellRenderer.fontSize"]&&!isNaN(e.temp[".mm.cellRenderer.fontSize"])&&(t=Math.max(e.temp[".mm.cellRenderer.fontSize"],1)),{font:`${t}px monospace`,fontWidth:.6*t}}toLog(){return`MonomerPlacer<${this.viewerId}>`}getMonomerLib(){return this.tableCol.temp[".mm.cellRenderer.overriddenLibrary"]??this.sysMonomerLib}reset(){this.propsProvider&&(this.props=this.propsProvider()),this._processedRows=o.BitSet.create(this.tableCol.length),this._monomerLengthList=null,this._monomerLengthMap={},this._monomerStructureMap={},this._cellBounds.clear(),super.reset(),this.invalidateGrid()}invalidateGrid(){this.gridCol&&this.gridCol.dart&&this.gridCol.grid?.invalidate()}getCellMonomerLengths(e,t){const n=this.seqHelper.getSeqHandler(this.tableCol);if(this.colWidth<t&&(this.colWidth=t,this.dirty=!0),this.dirty)try{this.reset()}catch(e){const[t,n]=(0,d.AP)(e);this.logger.error(t,void 0,n)}const r=n.isMsa()?this.getCellMonomerLengthsForSeqMsa():this.getCellMonomerLengthsForSeq(e);return[r,this.getSummedMonomerLengths(r)]}getSummedMonomerLengths(e){const t=new Array(e.length+1);t[0]=this.padding;for(let n=1;n<t.length;n++)t[n]=t[n-1]+e[n-1];let n=t[0];for(let e=1;e<t.length;e++)t[e]?n=t[e]:t[e]=n;return t}getCellMonomerLengthsForSeqValue(e,t){const n=this.seqHelper.getSeqHandler(this.tableCol),r=this.props.separatorWidth+1*this.props.fontCharWidth,o=this.positionShift,s=Math.ceil(t/r)+o,i=n.splitter(e),a=Math.min(s,i.length),c=new Array(a-o);let l=0;for(let e=o;e<a;++e){const r=i.getOriginal(e),s=this.props.monomerToShort(r,this.monomerLengthLimit),a=(n.isSeparator()?this.separatorWidth:this.props.separatorWidth)+s.length*this.props.fontCharWidth;if(c[e-o]=a,l+=a,l>t)break}return c}getCellMonomerLengthsForSeq(e){this.toLog(),null===this._monomerLengthList&&(this._monomerLengthList=new Array(this.tableCol.length).fill(null));const t=this.positionShift,n=this.seqHelper.getSeqHandler(this.tableCol),r=this.props.separatorWidth+1*this.props.fontCharWidth,o=Math.ceil(this.colWidth/r)+t,s=n.getSplitted(e),i=Math.min(o,s.length);let a=this._monomerLengthList[e];if(null===a||a.length!=i-t){a=this._monomerLengthList[e]=new Array(s.length);let r=0;for(let e=t;e<i;++e){const o=s.getOriginal(e),i=this.props.monomerToShort(o,this.monomerLengthLimit),c=(n.isSeparator()?this.separatorWidth:this.props.separatorWidth)+i.length*this.props.fontCharWidth;if(a[e-t]=c,r+=c,r>this.colWidth)break}}return a}getCellMonomerLengthsForSeqMsa(){var e;this.toLog(),null===this._monomerLengthList&&(this._monomerLengthList=new Array(1).fill(null)),(e=this._monomerLengthList)[0]??(e[0]=new Array(0));const t=this._monomerLengthList[0],{startIdx:n,endIdx:r}=(()=>{try{const e=this.gridCol&&this.gridCol.dart?this.gridCol.grid:null;return e&&e.dart?{startIdx:Math.max(Math.floor((e?.vertScroll.min??0)-10),0),endIdx:Math.min(Math.ceil((e?.vertScroll.max??0)+10),this.tableCol.length)}:{startIdx:0,endIdx:Math.min(this.tableCol.length,10)}}catch(e){return{startIdx:0,endIdx:Math.min(this.tableCol.length,10)}}})(),o=this.props.separatorWidth+1*this.props.fontCharWidth,s=this.positionShift,i=Math.ceil(this.colWidth/o)+s;for(let e=n;e<r;e++){if(this._processedRows.get(e)&&i<=this._processedMaxVisibleSeqLength)continue;const n=this.seqHelper.getSeqHandler(this.tableCol).getSplitted(e,i),r=Math.min(i,n.length);r-s>t.length&&t.push(...new Array(r-s-t.length).fill(o));let a=0;for(let e=s;e<r;++e){const r=n.getOriginal(e),o=this.props.monomerToShort(r,this.monomerLengthLimit),i=this.props.separatorWidth+o.length*this.props.fontCharWidth;if(t[e-s]=Math.max(t[e-s]??0,i),a+=i,a>=this.colWidth)break}this._processedMaxVisibleSeqLength=Math.max(this._processedMaxVisibleSeqLength,i),this._processedRows.set(e,!0)}return t}getPosition(e,t,n,r){const[o,s]=this.getCellMonomerLengths(e,n);return 0===this.seqHelper.getSeqHandler(this.tableCol).getSplitted(e).length?null:b(s,t,r)}setMonomerLengthLimit(e){this.monomerLengthLimit!=e&&(this.monomerLengthLimit=e,this.dirty=!0)}setSeparatorWidth(e){this.separatorWidth!=e&&(this.props.separatorWidth=e,this.dirty=!0)}get positionShift(){const e=Number.parseInt(this.tableCol?.tags[c.gp.positionShift]??"0")??0;return isNaN(e)?0:Math.max(e,0)}render(e,t,n,r,s,a,l){const u=a.grid?.canvas===e.canvas;if(!this.seqHelper)return;const m=this.tableCol,f=this.positionShift;e.save();try{const l=this.seqHelper.getSeqHandler(m);let d=this.monomerLengthLimit;if(h.gp.maxMonomerLength in m.tags){const e=parseInt(m.getTag(h.gp.maxMonomerLength));d=!isNaN(e)&&e?e:50}if(m.temp[".mm.cellRenderer.settingsChanged"]===p.s.true||this.monomerLengthLimit!=d){let e=0;const t=8;e=m.temp[".mm.cellRenderer.gapLength"]??e,this.setMonomerLengthLimit(d),this.setSeparatorWidth(l.isMsa()?t:e),m.temp[".mm.cellRenderer.settingsChanged"]=p.s.false,this.dirty=!0}const g=a.cell.rowIndex,b=a.cell.value;u&&(r=v(a.grid,e,t,r,window.devicePixelRatio)),e.beginPath(),e.rect(t,n,r,s),e.clip(),e.font=this.props?.font??"12px monospace",e.textBaseline="top";const w=m.meta.units,A=m.getTag(c.gp.aligned),E=m.getTag(c.gp.separator)??"",C=u?l.getSplitted(g):l.splitter(b);let T=h.yg.classic;A?.includes("MSA")&&w===c.Hi.SEPARATOR&&(T=h.yg.MSA);const S=m.temp["reference-sequence"],_=this.tableCol.temp["current-word"],P=(()=>{const e=(0,l.splitter)(null!=S&&""!==S?S:_??"");return i().count(0).take(e.length).slice(f).map((t=>e.getCanonical(t))).toArray()})(),M=Number.parseInt(m.getTag(c.gp.selectedPosition)??"-200");if(this.shouldUseMultilineRendering(m)){const i=[],c=this.calculateMultiLineLayoutDynamic(e,r,s,C,f,d);let u=n+this.padding;1===c.lineLayouts.length&&(u=n+(s-c.lineHeight)/2);for(const r of c.lineLayouts){const s=u+r.lineIdx*c.lineHeight;for(const u of r.elements){const d=t+u.x,p=u,g=p.posIdx,b=C.getCanonical(g);let w=y;const v=this.getMonomerLib();v&&(w=v.getMonomerTextColor(l.defaultBiotype,b));let A=0;if(a.tableRowIndex!==m.dataFrame.currentRowIdx&&P.length>0){const e=g-f;e>=0&&e<P.length&&b===P[e]&&(A=.7)}i.push({lineIdx:r.lineIdx,monomerIdx:g-f,bounds:new o.Rect(u.x,s-n,u.width,c.lineHeight),sequencePosition:g}),(0,h.oZ)(e,p.om,d,s,u.width,c.lineHeight,{color:w,isMultiLineContext:!0,transparencyRate:A,selectedPosition:isNaN(M)||M<1?void 0:M,wordIdx:g})}}null!==a.tableRowIndex&&this._cellBounds.set(a.tableRowIndex,i)}else{this._leftThreeDotsPadding=this.shouldRenderShiftedThreeDots(f)?e.measureText("...").width:0;let[,o]=this.getCellMonomerLengths(a.tableRowIndex,r);u||(o=this.getSummedMonomerLengths(this.getCellMonomerLengthsForSeqValue(b,r)));const i=this.props.separatorWidth+1*this.props.fontCharWidth,c=Math.min(C.length,Math.ceil(r/i)+f);for(let i=f;i<c;++i){const c=i<C.length?C.getOriginal(i):l.defaultGapOriginal,u=i<C.length?C.getCanonical(i):l.defaultGapOriginal;let p=y;this.getMonomerLib()&&(p=this.getMonomerLib().getMonomerTextColor(l.defaultBiotype,u));const m={color:p,pivot:0,left:!0,transparencyRate:0,separator:E,last:i===C.length-1,drawStyle:T,maxWord:o,wordIdx:i-f,gridCell:a,referenceSequence:P,maxLengthOfMonomer:d,monomerTextSizeMap:this._monomerLengthMap,logger:this.logger,selectedPosition:isNaN(M)||M<1?void 0:M-f};(0,h.oZ)(e,c,t+this.padding+this._leftThreeDotsPadding,n,r,s,m)}if(this.shouldRenderShiftedThreeDots(f)){const i={color:y,pivot:0,left:!0,transparencyRate:0,separator:E,last:!1,drawStyle:T,maxWord:o,wordIdx:0,gridCell:a,maxLengthOfMonomer:d,monomerTextSizeMap:this._monomerLengthMap,logger:this.logger};(0,h.oZ)(e,"...",t+this.padding,n,r,s,i)}}}catch(e){const[t,n]=(0,d.AP)(e);this.logger.error(t,void 0,n),this.errors.push(e)}finally{e.restore()}}shouldRenderShiftedThreeDots(e){return e>0&&(!this.gridCol||!this.gridCol.dart||!this.gridCol.grid||!this.gridCol.grid.dart||(this.gridCol.grid.props.colHeaderHeight??0)<=50)}onMouseMove(e,t){const n=`${this.toLog()}.onMouseMove()`;if(!this.seqHelper||null==e.tableRowIndex)return;const o=this.positionShift,s=e.bounds,i=t.offsetX-e.gridColumn.left+(e.gridColumn.left-s.x),a=t.offsetY-s.y;this.gridCol?.grid?.canvas&&(this.gridCol.grid.canvas.style.cursor="default");let l=null;const u=this._cellBounds.get(e.tableRowIndex);if(u){for(const e of u)if(e.bounds.contains(i,a)){l=e.monomerIdx;break}}else{const t=this.shouldRenderShiftedThreeDots(o)&&(this._leftThreeDotsPadding??0)>0?this._leftThreeDotsPadding:0;l=this.getPosition(e.tableRowIndex,i,s.width,t)}this.logger.debug(`${n}, argsX: ${i}, argsY: ${a}, left: ${l}`);const d=this.seqHelper.getSeqHandler(this.tableCol),h=d.getSplitted(e.tableRowIndex);if(null!==l&&l>=0&&l+o<h.length){const n=d.alphabet??c.YI.UN,s={position:l,biotype:n===c.YI.RNA||n===c.YI.DNA?m.o.NUCLEOTIDE:m.o.AA,symbol:h.getCanonical(l+o)},i=[];let a=this._monomerStructureMap[s.symbol];if(!a){const e=this.getMonomerLib();a=this._monomerStructureMap[s.symbol]=e?e.getTooltip(s.biotype,s.symbol):r.divText("Monomer library is not available")}i.push(a),r.tooltip.show(r.divV(i),t.x+16,t.y+16),(0,f.WN)(e,s)}else-1===l?r.tooltip.show(r.divText(`${Math.min(o,h.length)} hidden monomers`),t.x+16,t.y+16):r.tooltip.hide(),(0,f.WN)(e,null)}}function v(e,t,n,r,o){return e?Math.max(Math.min(e.canvas.width/o-n,r)):Math.max(t.canvas.width/o-n,0)}},3856:(e,t,n)=>{"use strict";n.d(t,{Mn:()=>u,gp:()=>l,oZ:()=>p,yg:()=>d});var r=n(6082),o=n(7278);const s="rgb(100,100,100)",i="#808080",a="rgb(0,0,0)",c=o.zS;var l,u,d;!function(e){e.maxMonomerLength=".mm.cellRenderer.maxMonomerLength"}(l||(l={})),function(e){e.applyToBackground=".m.cellRenderer.applyToBackground"}(u||(u={})),function(e){e.MSA="MSA",e.classic="classic"}(d||(d={}));const h=new class{constructor(){this.color=s,this.pivot=0,this.left=!1,this.transparencyRate=0,this.separator="",this.last=!1,this.drawStyle=d.classic,this.maxWord=[],this.wordIdx=0,this.gridCell=null,this.referenceSequence=null,this.maxLengthOfMonomer=null,this.monomerTextSizeMap={},this.logger=void 0,this.selectedPosition=void 0,this.isMultiLineContext=!1,this.lineNumber=0}};function p(e,t,n,o,l,u,p){var m,f,g;const y={...h,...p};if(y.isMultiLineContext){e.textBaseline="middle",e.textAlign="center";let r=t;null!=y.maxLengthOfMonomer&&(r=c(r,y.maxLengthOfMonomer));const i=Math.max(.1,1-(y.transparencyRate??0));e.globalAlpha=i;const d=e.measureText(r),h=d.fontBoundingBoxAscent+d.fontBoundingBoxDescent,p=o+(u-h)/2+d.fontBoundingBoxAscent;let m=y.color??s;return m&&m!==s||(m=a),e.fillStyle=m,y.selectedPosition===y.wordIdx+1&&(e.save(),e.fillStyle="rgba(60, 177, 115, 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S=y.monomerTextSizeMap[b].width;const _=u/2-(T.fontBoundingBoxAscent+T.fontBoundingBoxDescent)/2+1;(g=y.monomerTextSizeMap)[w]??(g[w]=e.measureText(w));const P=y.monomerTextSizeMap[w].width;function M(t,s){let c=v?y.color:a;y.selectedPosition===y.wordIdx+1&&(e.fillStyle="rgba(60, 177, 115, 0.2)",e.fillRect(n+t-4,o-5,y.monomerTextSizeMap[b].width+8,u+10),c=r.Color.toHtml(r.Color.setAlpha(r.Color.fromHtml(c),255))),e.fillStyle=c,e.globalAlpha=1-y.transparencyRate,y.drawStyle===d.classic&&(e.fillText(b,n+t,o+_),e.fillStyle=i,e.fillText(w,n+s,o+_)),y.drawStyle===d.MSA&&e.fillText(b,n+t,o+_),e.globalAlpha=1}T=T.width,y.drawStyle===d.MSA&&(S=y.maxWord[y.wordIdx],T=y.maxWord[y.wordIdx]);const x=(y.maxWord[y.wordIdx]??0)-(y.maxWord[0]??0);if(y.left||T>l)return M(x,x+S),n+x+S+P;{const e=(l-T)/2;return M(e,e+S),n+x+e+S}}},6307:(e,t,n)=>{"use strict";n.d(t,{F:()=>i});var r=n(7389),o=n(6082),s=n(439);function i(e,t,n){let i=0,a=null;for(const t of Object.values(e))i+=t,a=null===a?t:Math.max(a,t);const c=a/i,l=Object.assign({},...Array.from(Object.entries(e)).sort(((e,t)=>t[1]-e[1])).map((([e,a])=>{const l=a/i;let u;try{const r=n.getMonomerColors(t,e);u=r?.backgroundcolor||"#CCCCCC"}catch(t){console.warn(`Failed to get colors for monomer ${e}:`,t),u="#CCCCCC"}const d=r.div("",{classes:"macromolecule-cell-comp-analysis-bar"});d.style.width=50*l/c+"px",d.style.backgroundColor=u,s._S===e&&(d.style.borderWidth="1px",d.style.borderStyle="solid",d.style.borderColor=o.Color.toHtml(o.Color.lightGray));const h=s._S===e?"-":e,p=r.div(`${(100*l).toFixed(2)}%`),m=r.div([d,p],{classes:"macromolecule-cell-comp-analysis-value"});return{[h]:m}}))),u=r.tableFromMap(l);return Array.from(u.rows).forEach((e=>{const t=e.getElementsByClassName("macromolecule-cell-comp-analysis-bar")[0].style.backgroundColor;e.cells[0].style.color=t})),u}},3151:(e,t,n)=>{"use strict";n.d(t,{f6:()=>r});const r=["symbol","molfile","rgroups","name"];new RegExp("[rd]\\((\\w)\\)p?","g")},9192:(e,t,n)=>{"use strict";function r(e){return"string"==typeof e||e instanceof String?e:"StateError"===e.constructor.name?e.message:"StateError"===e.constructor.name&&"$thrownJsError"in e?r(e.$thrownJsError):e instanceof Error?e.message:e.toString()}function o(e){return e instanceof Error?e.stack:"StateError"===e.constructor.name&&"$thrownJsError"in e?o(e.$thrownJsError):void 0}function s(e){return[r(e),o(e)]}n.d(t,{AP:()=>s})},3516:(e,t,n)=>{"use strict";n.d(t,{m:()=>s});var r=n(6082),o=n(439);class s{get descriptionsArray(){return this._descriptionsArray}get sequencesArray(){return this._sequencesArray}parseMacromolecule(e,t){return this._fileContent.slice(e,t).split(/\s/).join("")}parseColumns(){const e=/^>(.*)$/gm;let t,n=0;for(;t=e.exec(this._fileContent);){const r=this._fileContent.substring(t.index+1,e.lastIndex);this._descriptionsArray.push(r),0!==n&&this._sequencesArray.push(this.parseMacromolecule(n,t.index)),n=e.lastIndex+1}this._sequencesArray.push(this.parseMacromolecule(n,-1))}importFasta(){const e=r.Column.fromStrings("description",this.descriptionsArray),t=r.Column.fromStrings("sequence",this.sequencesArray);return t.semType=r.SEMTYPE.MACROMOLECULE,t.meta.units=o.Hi.FASTA,[r.DataFrame.fromColumns([e,t])]}constructor(e){this._descriptionsArray=[],this._sequencesArray=[],this._fileContent=e,this.parseColumns()}}},6873:(e,t,n)=>{"use strict";n.d(t,{dW:()=>i,fD:()=>s});var r=n(6082),o=(n(1991),n(2003));function s(){const e=[];return e.push(r.Column.fromList("string","MSA",new Array(10**6).fill("meI/hHis/Aca/N/T/dE/Thr_PO3H2/Aca/D-Tyr_Et/Tyr_ab-dehydroMe/dV/E/N/D-Orn/D-aThr//Phe_4Me"))),e.push(r.Column.fromList(r.COLUMN_TYPE.FLOAT,"Activity",new Array(10**6).fill(5.30751))),e}function i(e=10**5){const 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r,o,s,i=n(2738);!function(e){e.FASTA="fasta",e.SEPARATOR="separator",e.HELM="helm",e.CUSTOM="custom"}(r||(r={})),function(e){e.DNA="DNA",e.RNA="RNA",e.PT="PT",e.UN="UN"}(o||(o={})),function(e){e.aligned="aligned",e.alphabet="alphabet",e.alphabetSize=".alphabetSize",e.alphabetIsMultichar=".alphabetIsMultichar",e.separator="separator",e.isHelmCompatible=".isHelmCompatible",e.positionNames=".positionNames",e.positionLabels=".positionLabels",e.regions=".regions",e.positionShift=".positionShift",e.selectedPosition=".selectedPosition"}(s||(s={}));const a=", ",c=/(?:\[([A-Za-z0-9_\-,()]+)\])|([A-Za-z\-])/g,l=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"])}}},u=[new i.a(o.PT,l.fasta.peptide,.5),new i.a(o.DNA,l.fasta.dna,.55),new i.a(o.RNA,l.fasta.rna,.55)],d="",h={[r.FASTA]:"-",[r.SEPARATOR]:"",[r.HELM]:"*"}},2003:(e,t,n)=>{"use 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r=n(6082),o=n(1991),s=n.n(o),i=n(330),a=n(3599);async function c(e,t,o,c,l,u,d){const h=e.length,p=e.dataFrame,m=Math.max(navigator.hardwareConcurrency-2,1),f=new Array(m).fill(null).map((()=>new Worker(new URL(n.p+n.u(455),n.b)))),g=h/m,y=new Array(m),b=u.getSeqHandler(e),w="RNA"==c?a.o.NUCLEOTIDE:a.o.AA,v=s().count(0).take(e.length).map((e=>{const t=b.getSplitted(e);return s().count(0).take(t.length).map((e=>({position:e,symbol:t.getCanonical(e),biotype:w}))).toArray()})).toArray();for(let e=0;e<m;e++){const n=f[e],r=Math.floor(e*g),s=e===m-1?h:Math.floor((e+1)*g);y[e]=new Promise((e=>{n.onmessage=t=>{e(t.data)}})),n.postMessage({seqList:v,monomersDict:t,alphabet:o,polymerType:c,start:r,end:s})}const A=[],E=[];await Promise.all(y).then((e=>{for(const t of e)A.push(...t.molfiles),E.push(...t.warnings)})),setTimeout((()=>{f.forEach((e=>{e.terminate()}))}),0);const C=(0,i.qj)(p,e.name),T=r.Column.fromType(r.COLUMN_TYPE.STRING,C,e.length).init((e=>A[e]?.molfile));return T.semType=r.SEMTYPE.MOLECULE,T.meta.units=r.UNITS.Molecule.MOLBLOCK,T.setTag(".sequence-src-col",e.name),{molCol:T,warnings:E}}function l(e,t){const n={},o={};for(const s of e){const e=t.getWebEditorMonomer(s.biotype,s.symbol).backgroundcolor,a=(0,i.vG)(e??r.Color.toRgb(r.Color.mouseOverRows))??[1,0,0,.7];for(const e of s.atoms)n[e]=a;for(const e of s.bonds)o[e]=a}return{atoms:Object.keys(n).map((e=>parseInt(e))),bonds:Object.keys(o).map((e=>parseInt(e))),highlightAtomColors:n,highlightBondColors:o}}},3561:(e,t,n)=>{"use strict";n.d(t,{Hb:()=>c,YN:()=>f,gU:()=>l});var r=n(8123),o=n(294),s=n(3151),i=n(439),a=n(6197);function c(e,t,n){const o=new Map;for(const a of e.getMonomerSymbolsByType(t)){const c=e.getMonomer(t,a);if("RNA"===t&&("Branch"===c.monomerType||n===i.YI.DNA&&c.symbol===r.u.DEOXYRIBOSE.symbol||n===i.YI.RNA&&c.symbol===r.u.RIBOSE.symbol||c.symbol===r.u.PHOSPHATE.symbol)||"PEPTIDE"===t&&"Branch"!==c.monomerType){const e={};s.f6.forEach((t=>{e[t]=c[t]})),o.set(c.symbol,e)}}return o}function l(e,t,n,s){if(0===e.length)return o.vF.createEmpty();const c=m,{atomCount:l,bondCount:d,needsCapping:p}=c(e,t,n,s),g=new Array(l),y=new Array(d);let b,w=null,v=null;"PEPTIDE"===s?b=u:(b=h,w=n===i.YI.DNA?(0,o.xb)(t,r.u.DEOXYRIBOSE):(0,o.xb)(t,r.u.RIBOSE),v=(0,o.xb)(t,r.u.PHOSPHATE));const A={i:0,nodeShift:0,bondShift:0,backbonePositionShift:new Array(2).fill(0),branchPositionShift:new Array(2).fill(0),backboneAttachNode:0,branchAttachNode:0,flipFactor:1},E={sugar:w,phosphate:v,seqLength:e.length,atomCount:l,bondCount:d},C=new o.Cg,T=[];let S,_=0;for(A.i=0;A.i<E.seqLength;++A.i){const n=e[A.i];if(n.symbol===i._S)continue;const r=(0,o.xb)(t,{symbol:n.symbol,polymerType:(0,a.Y)(n.biotype)});S=r.terminalR2Atom;const s=A.nodeShift,c=A.bondShift;b(r,g,y,A,E),r.stereoAtoms?.forEach((e=>T.push(e+_))),_+=r.atoms.x.length;const l=A.nodeShift-s,u=new Array(l);for(let e=0;e<l;++e)u[e]=s+e;const d=A.bondShift-c,h=new 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r=n(4328),o=n(6082),s=n(1991),i=n.n(s),a=n(439),c=n(3561),l=n(9235),u=n(294),d=n(9192),h=n(330),p=n(8123);async function m(e,t,n,s,c){if(t.semType!==o.SEMTYPE.MACROMOLECULE)return{molCol:null,warnings:[`Only the ${o.SEMTYPE.MACROMOLECULE} columns can be converted to atomic level, the chosen column has semType '${t.semType}'`]};let u=t;const p=s.getSeqHandler(t);let m,g;p.notation!==a.Hi.SEPARATOR&&(u=p.convert(a.Hi.SEPARATOR,"."),u.name=t.name);try{g=s.getSeqHandler(u).alphabet,m=(0,h.pz)(g)}catch(e){const[t,n]=(0,d.AP)(e);return{molCol:null,warnings:[t]}}const y=function(e,t){const n=e.length,o=new Array(n),s=t.getSeqHandler(e);let a=!1;const c=s.defaultBiotype;for(let e=0;e<n;++e){const t=s.getSplitted(e);a||(a=0===t.length),o[e]=i().count(0).take(t.length).filter((e=>!t.isGap(e))).map((e=>({position:e,biotype:c,symbol:t.getCanonical(e)}))).toArray()}return a&&r.shell.warning(`Some values in the "${e.name}" column are 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w(e,t,n){return[(0,c.YN)(e.atoms.x[t]-e.atoms.x[n]),(0,c.YN)(e.atoms.y[t]-e.atoms.y[n])]}function v(e,t){if(void 0!==t){const n=t-1,r=e.atoms,o=e.bonds,s=e.meta,i=r.atomTypes.splice(n,1)[0];r.x=A(Float32Array,r.x,n,1),r.y=A(Float32Array,r.y,n,1),r.kwargs.splice(n,1);for(let e=0;e<s.terminalNodes.length;++e)s.terminalNodes[e]>t?--s.terminalNodes[e]:s.terminalNodes[e]===t&&(s.terminalNodes[e]=-1);for(let e=0;e<s.rNodes.length;++e)s.rNodes[e]>t?--s.rNodes[e]:s.rNodes[e]===t&&(s.rNodes[e]=-1);let a=0;for(;a<o.atomPairs.length;){const e=o.atomPairs[a][0],n=o.atomPairs[a][1];e===t||n===t?(o.atomPairs.splice(a,1),o.bondTypes=A(Uint32Array,o.bondTypes,a,1),o.bondConfiguration.has(a)&&o.bondConfiguration.delete(a),o.kwargs.has(a)&&o.kwargs.delete(a),--a):(o.atomPairs[a][0]=e>t?e-1:e,o.atomPairs[a][1]=n>t?n-1:n),++a}let c=Array.from(o.bondConfiguration.keys());return c.forEach((e=>{if(o.bondConfiguration.has(e)&&e>n){const 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e=0;e<r.length;++e)r[e]=(0,c.YN)(r[e]+t),void 0!==n&&(o[e]=(0,c.YN)(o[e]+n))}},294:(e,t,n)=>{"use strict";function r(e,t){return e[t.polymerType]?.[t.symbol]}function o(e,t){return!!e[t.polymerType]?.[t.symbol]}function s(e,t,n){let r=e[t.polymerType];r||(r=e[t.polymerType]={}),r[t.symbol]=n}n.d(t,{Cg:()=>i,LQ:()=>s,bq:()=>o,vF:()=>a,xb:()=>r});class i extends Map{constructor(e){super(e)}}class a{constructor(e,t){this.molfile=e,this.monomers=t}static createEmpty(){return new a("",new i(null))}}},330:(e,t,n)=>{"use strict";n.d(t,{pz:()=>s,qj:()=>o,vG:()=>i});var r=n(2003);function o(e,t){return function(e,t){return e?e.columns.getUnusedName(t):t}(e,`molfile(${t})`)}function s(e){let t;if(e===r.YI.PT||e===r.YI.UN)t="PEPTIDE";else{if(e!==r.YI.RNA&&e!==r.YI.DNA)throw new Error(`Unexpected alphabet '${e}'.`);t="RNA"}return t}function i(e){const t=7===e.length?/^#?([a-f\d]{2})([a-f\d]{2})([a-f\d]{2})$/i.exec(e):/^#?([a-f\d]{2})([a-f\d]{2})([a-f\d]{2})([a-f\d]{2})$/i.exec(e);return t?[parseInt(t[1],16)/256,parseInt(t[2],16)/256,parseInt(t[3],16)/256,t.length>4?parseInt(t[4],16)/256:.3]:null}},1093:(e,t,n)=>{"use strict";n.d(t,{A:()=>o,Q:()=>s});var r=n(7362);class o extends r.e{static get Chromatogram(){return void 0===this.chromatogram&&(this.chromatogram=new o({A:"green",C:"blue",G:"black",T:"red",U:"red",others:"gray"})),this.chromatogram}}class s{}s.SemType="Nucleotides",s.SemTypeMultipleAlignment="NucleotidesMultipleAlignment",s.Names={A:"Adenine",C:"Cytosine",G:"Guanine",T:"Thymine",U:"Uracil"}},7362:(e,t,n)=>{"use strict";n.d(t,{e:()=>r});class r{static makePalette(e,t=!1,n=r){const o={};return e.forEach((e=>{const n=e[0],r=e[1];n.forEach(((e,n)=>{o[e]=this.colourPalette[r][t?0:n]}))})),new n(o)}constructor(e){this._palette=e}get(e,t){return this._palette[e]}}r.undefinedColor="rgb(100,100,100)",r.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)"]}},4574:(e,t,n)=>{"use strict";n.d(t,{O:()=>s,n:()=>o});var r=n(1858);class o{constructor(e,t=!0,n){return this.substructure=e,this.readOnly=t,this.logger=n,new Proxy(this,{set:(e,t,n)=>{if(this.logger?.debug(`BioFilterProps.set ${t.toString()}( '${n}' )`),this.readOnly)throw new Error("Properties are immutable.");return e[t]=n,!0}})}}class s{constructor(){this.onChanged=new r.Subject,this._props=null,this._propsChanging=!1}get props(){return this._props||(this._props=this.emptyProps),this._props}set props(e){this._propsChanging=!0;try{this._props=e,this.applyProps(),this.onChanged.next()}finally{this._propsChanging=!1}}saveProps(){const e={};for(const[t,n]of Object.entries(this.props))"_onChanged"!==t&&"logger"!==t&&(e[t]=this.props[t]);return e}async detach(){}get filterSummary(){return this.props.substructure}get isFiltering(){return""!==this.props.substructure}resetFilter(){this.props=this.emptyProps,this.onChanged.next()}}},4152:(e,t,n)=>{"use strict";n.d(t,{$u:()=>c,oT:()=>d});var r=n(6082),o=n(7362),s=n(6718);function i(e,t=!0){if(null==e)return"rgb(100,100,100)";const n=r.Color.fromHtml(e);if(t){const e=r.Color.g(n),t=r.Color.r(n),o=r.Color.b(n),s=Math.sqrt(Math.pow(0-t,2)+Math.pow(0-e,2)+Math.pow(0-o,2));if(s>210)return`rgb(${t/s*210},${e/s*210},${o/s*210})`}return r.Color.toRgb(n)}class a{static hashCode(e){let t=0;if(0===e.length)return t;for(let n=0;n<e.length;n++)t=(t<<5)-t+e.charCodeAt(n),t|=0;return t}}class c{}class l extends c{get(e,t){return"#666666"}}class u extends c{static get palette(){return u._pallete||(u._pallete=u.buildPalette()),u._pallete}static buildPalette(){return(0,s.pj)().then((e=>{e.awaitLoaded(1/0).then((()=>{const t=e.getMonomerLib();t.onChanged.subscribe((()=>{u.customMonomerColors={},u.polymerTypes=t.getPolymerTypes();for(const e of this.polymerTypes){const n=t.getMonomerSymbolsByType(e);for(const r of n){const n=t.getMonomer(e,r);n?.meta?.colors?.default?.background&&(this.customMonomerColors[r]||(this.customMonomerColors[r]={}),this.customMonomerColors[r][e]=i(n.meta.colors.default.background))}}}))}))})),[].concat(...Object.values(o.e.colourPalette))}get(e,t){const n=u.palette.length,r=u.customMonomerColors[e],o=t??"PEPTIDE";if(r&&r[o])return r[o];const s=a.hashCode(e)%n;return i(u.palette[s])}}u._pallete=null,u.customMonomerColors={},u.polymerTypes=[];class d extends o.e{static get Gray(){return void 0===this.gray&&(this.gray=new l),this.gray}static get Color(){return void 0===this.color&&(this.color=new u),this.color}}},6642:(e,t,n)=>{"use strict";n.d(t,{BG:()=>i,sD:()=>c});var r=n(4328),o=n(1858),s=n(8070);function i(e){let t=null,n=null;try{n=e.dart?e.gridColumn:null,t=n?n.temp:null}catch{[n,t]=[null,null]}const r=e.cell.column;if(t=t??(r?r.temp:null),!t)throw new Error("Grid cell renderer back store (GridColumn or Column) not found.");return[n,r,t]}class a{onKeyDown(e,t){}onKeyPress(e,t){}onMouseEnter(e,t){}onMouseLeave(e,t){}onMouseDown(e,t){}onMouseUp(e,t){}onMouseMove(e,t){}onClick(e,t){}onDoubleClick(e,t){}}class c extends a{constructor(e,t,n){super(),this.gridCol=e,this.tableCol=t,this.logger=n,this.subs=[],this.dirty=!0,this.destroyed=!1,this.viewerId=++c.viewerCounter,this.errors=[],this._onRendered=new o.Subject,this.tableCol&&this.tableCol.dataFrame&&(this.subs.push(this.tableCol.dataFrame.onDataChanged.subscribe((()=>{this.dirty=!0}))),this.subs.push(this.tableCol.dataFrame.onColumnsRemoved.subscribe((e=>{try{this.destroyed||!this.tableCol||this.tableCol.dataFrame||this.destroy()}catch(e){this.logger.error(e)}})))),this.tableCol&&this.subs.push(r.events.onTableRemoved.subscribe((e=>{try{const t=e.args.dataFrame;this.tableCol?.dataFrame.id!==t.id||this.destroyed||this.destroy()}catch(e){this.logger.error(e)}}))),this.gridCol&&this.subs.push(r.events.onViewRemoving.subscribe((e=>{try{const t=e.args.view;this.gridCol?.dart&&this.gridCol.grid&&this.gridCol?.grid?.dart&&this.gridCol?.grid?.view?.id===t.id&&!this.destroyed&&this.destroy()}catch(e){this.logger.error(e)}})))}toLog(){return`${this.constructor.name}<${this.viewerId}>`}destroy(){for(const e of this.subs)e.unsubscribe();this.destroyed=!0}invalidateGrid(){this.gridCol&&this.gridCol.dart&&this.gridCol.grid?.invalidate()}reset(){this.dirty=!1}get onRendered(){return this._onRendered}invalidate(e){this.invalidateGrid()}async awaitRendered(e=1e4,t=`${e} timeout`){const n=`${this.toLog()}.awaitRendered()`;if(this.logger.debug(`${n}, start, testEvent before`),await(0,s.PE)(this._onRendered,(()=>{}),(()=>{this.invalidate()}),e,`${n}, ${t}`),this.errors.length>0){const e=this.errors[0];throw this.errors=[],e}this.logger.debug(`${n}, end`)}}c.viewerCounter=-1},673:(e,t,n)=>{"use strict";n.d(t,{s:()=>r});const r={true:"1",false:"0"}},6882:(e,t,n)=>{"use strict";n.d(t,{Bb:()=>b,Jy:()=>w,S$:()=>y,U0:()=>v});var r=n(7389),o=n(6082),s=n(1991),i=n.n(s),a=n(8312),c=n(2003),l=n(6642),u=n(6718),d=n(9192),h=n(3856),p=n(673),m=n(3599),f=n(5553),g=n(9713);const y="rgb(100,100,100)";function b(e,t,n){if((n??0)>0&&t<(e[0]??0)+n)return-1;t-=n??0;let r,o=100,s=0,i=e.length-1;for(;s<=i;){if(r=Math.floor((i+s)/2),e[r]<=t&&t<e[r+1])return r;if(t<e[r]?i=r-1:s=r+1,--o<=0)throw new Error(`Get position for pointer x = ${t} searching has not converged on ${JSON.stringify(e)}. `)}return null}class w extends l.sD{get separatorWidth(){return this.props?.fontCharWidth?this.props?.fontCharWidth:5}constructor(e,t,n,r,s){if(super(e,t,n),this.monomerLengthLimit=r,this.propsProvider=s,this.colWidth=0,this._monomerLengthList=null,this._processedMaxVisibleSeqLength=0,this._monomerLengthMap={},this._monomerStructureMap={},this._ellipsisBounds=void 0,this._totalLinesNeeded=0,this._lineHeight=20,this._cellBounds=new Map,this.sysMonomerLib=null,this.padding=5,this._leftThreeDotsPadding=0,this.props=this.propsProvider(),this._processedRows=o.BitSet.create(this.tableCol.length),this.gridCol&&this.subs.push(this.gridCol.grid.onAfterDrawContent.subscribe((()=>{this._onRendered.next()}))),this.tableCol&&this.gridCol){this.subs.push(this.tableCol.dataFrame.onCurrentRowChanged.subscribe((()=>{-1===this.tableCol.dataFrame.currentRowIdx&&(this.tableCol.temp["reference-sequence"]=null,this.tableCol.temp["current-word"]=null,this.invalidateGrid())})));const e=[c.gp.positionShift,"renderMultiline"];this.subs.push(o.debounce(this.tableCol.dataFrame.onMetadataChanged.pipe(g.filter((t=>t.args.source===this.tableCol&&e.includes(t.args.key)))),200).subscribe((e=>{this.reset()}))),this.subs.push(o.debounce(this.tableCol.dataFrame.onMetadataChanged.pipe(g.filter((e=>e.args.source===this.tableCol&&e.args.key===c.gp.positionShift))),200).subscribe((e=>{this.reset()})))}}calculateFontBasedSpacing(e){const t=e.measureText("M");let n=12;if(this.tableCol?.temp[".mm.cellRenderer.fontSize"]){const e=this.tableCol.temp[".mm.cellRenderer.fontSize"];"number"!=typeof e||isNaN(e)||(n=Math.max(e,1))}return{lineHeight:Math.max(1.4*n,t.fontBoundingBoxAscent+t.fontBoundingBoxDescent+4),monomerSpacing:Math.max(2,.2*this.props.fontCharWidth)}}shouldUseMultilineRendering(e){return"true"===e.getTag("renderMultiline")}calculateMultiLineLayoutDynamic(e,t,n,r,o,s){if(this.dirty)try{this.reset()}catch(e){const[t,n]=(0,d.AP)(e);this.logger.error(t,void 0,n)}const{lineHeight:i,monomerSpacing:a}=this.calculateFontBasedSpacing(e),c=t-2*this.padding;let l=0;const u=[];if(r.length>0)for(let t=o;t<r.length;t++){const n=r.getOriginal(t),o=this.props.monomerToShort(n,s);u.push({text:o,posIdx:t}),l=Math.max(l,e.measureText(o).width)}if(0===u.length)return{lineLayouts:[],lineHeight:i};const h=l;let p=Math.floor((c+a)/(h+a));p=Math.max(1,p);const m=n-2*this.padding,f=Math.max(0,Math.floor(m/i)),g=[];let y=0;for(let e=0;e<f&&y<u.length;e++){const t=[];for(let e=0;e<p&&y<u.length;e++){const n=u[y],r=this.padding+e*(h+a);t.push({posIdx:n.posIdx,x:r,width:h,om:n.text,isSeparator:!1}),y++}g.push({lineIdx:e,elements:t})}return{lineLayouts:g,lineHeight:i}}async init(){await Promise.all([(async()=>{this.seqHelper=await(0,a.Q)(),this.invalidateGrid()})(),(async()=>{const e=await(0,u.pj)();this.sysMonomerLib=e.getMonomerLib()})()]),this.subs.push(this.sysMonomerLib.onChanged.subscribe((()=>{this.reset()}))),this.reset()}static getFontSettings(e){let t=12;return e&&e.temp[".mm.cellRenderer.fontSize"]&&"number"==typeof e.temp[".mm.cellRenderer.fontSize"]&&!isNaN(e.temp[".mm.cellRenderer.fontSize"])&&(t=Math.max(e.temp[".mm.cellRenderer.fontSize"],1)),{font:`${t}px monospace`,fontWidth:.6*t}}toLog(){return`MonomerPlacer<${this.viewerId}>`}getMonomerLib(){return this.tableCol.temp[".mm.cellRenderer.overriddenLibrary"]??this.sysMonomerLib}reset(){this.propsProvider&&(this.props=this.propsProvider()),this._processedRows=o.BitSet.create(this.tableCol.length),this._monomerLengthList=null,this._monomerLengthMap={},this._monomerStructureMap={},this._cellBounds.clear(),super.reset(),this.invalidateGrid()}invalidateGrid(){this.gridCol&&this.gridCol.dart&&this.gridCol.grid?.invalidate()}getCellMonomerLengths(e,t){const n=this.seqHelper.getSeqHandler(this.tableCol);if(this.colWidth<t&&(this.colWidth=t,this.dirty=!0),this.dirty)try{this.reset()}catch(e){const[t,n]=(0,d.AP)(e);this.logger.error(t,void 0,n)}const r=n.isMsa()?this.getCellMonomerLengthsForSeqMsa():this.getCellMonomerLengthsForSeq(e);return[r,this.getSummedMonomerLengths(r)]}getSummedMonomerLengths(e){const t=new Array(e.length+1);t[0]=this.padding;for(let n=1;n<t.length;n++)t[n]=t[n-1]+e[n-1];let n=t[0];for(let e=1;e<t.length;e++)t[e]?n=t[e]:t[e]=n;return t}getCellMonomerLengthsForSeqValue(e,t){const n=this.seqHelper.getSeqHandler(this.tableCol),r=this.props.separatorWidth+1*this.props.fontCharWidth,o=this.positionShift,s=Math.ceil(t/r)+o,i=n.splitter(e),a=Math.min(s,i.length),c=new Array(a-o);let l=0;for(let e=o;e<a;++e){const r=i.getOriginal(e),s=this.props.monomerToShort(r,this.monomerLengthLimit),a=(n.isSeparator()?this.separatorWidth:this.props.separatorWidth)+s.length*this.props.fontCharWidth;if(c[e-o]=a,l+=a,l>t)break}return c}getCellMonomerLengthsForSeq(e){this.toLog(),null===this._monomerLengthList&&(this._monomerLengthList=new Array(this.tableCol.length).fill(null));const t=this.positionShift,n=this.seqHelper.getSeqHandler(this.tableCol),r=this.props.separatorWidth+1*this.props.fontCharWidth,o=Math.ceil(this.colWidth/r)+t,s=n.getSplitted(e),i=Math.min(o,s.length);let a=this._monomerLengthList[e];if(null===a||a.length!=i-t){a=this._monomerLengthList[e]=new Array(s.length);let r=0;for(let e=t;e<i;++e){const o=s.getOriginal(e),i=this.props.monomerToShort(o,this.monomerLengthLimit),c=(n.isSeparator()?this.separatorWidth:this.props.separatorWidth)+i.length*this.props.fontCharWidth;if(a[e-t]=c,r+=c,r>this.colWidth)break}}return a}getCellMonomerLengthsForSeqMsa(){var e;this.toLog(),null===this._monomerLengthList&&(this._monomerLengthList=new Array(1).fill(null)),(e=this._monomerLengthList)[0]??(e[0]=new Array(0));const t=this._monomerLengthList[0],{startIdx:n,endIdx:r}=(()=>{try{const e=this.gridCol&&this.gridCol.dart?this.gridCol.grid:null;return e&&e.dart?{startIdx:Math.max(Math.floor((e?.vertScroll.min??0)-10),0),endIdx:Math.min(Math.ceil((e?.vertScroll.max??0)+10),this.tableCol.length)}:{startIdx:0,endIdx:Math.min(this.tableCol.length,10)}}catch(e){return{startIdx:0,endIdx:Math.min(this.tableCol.length,10)}}})(),o=this.props.separatorWidth+1*this.props.fontCharWidth,s=this.positionShift,i=Math.ceil(this.colWidth/o)+s;for(let e=n;e<r;e++){if(this._processedRows.get(e)&&i<=this._processedMaxVisibleSeqLength)continue;const n=this.seqHelper.getSeqHandler(this.tableCol).getSplitted(e,i),r=Math.min(i,n.length);r-s>t.length&&t.push(...new Array(r-s-t.length).fill(o));let a=0;for(let e=s;e<r;++e){const r=n.getOriginal(e),o=this.props.monomerToShort(r,this.monomerLengthLimit),i=this.props.separatorWidth+o.length*this.props.fontCharWidth;if(t[e-s]=Math.max(t[e-s]??0,i),a+=i,a>=this.colWidth)break}this._processedMaxVisibleSeqLength=Math.max(this._processedMaxVisibleSeqLength,i),this._processedRows.set(e,!0)}return t}getPosition(e,t,n,r){const[o,s]=this.getCellMonomerLengths(e,n);return 0===this.seqHelper.getSeqHandler(this.tableCol).getSplitted(e).length?null:b(s,t,r)}setMonomerLengthLimit(e){this.monomerLengthLimit!=e&&(this.monomerLengthLimit=e,this.dirty=!0)}setSeparatorWidth(e){this.separatorWidth!=e&&(this.props.separatorWidth=e,this.dirty=!0)}get positionShift(){const e=Number.parseInt(this.tableCol?.tags[c.gp.positionShift]??"0")??0;return isNaN(e)?0:Math.max(e,0)}render(e,t,n,r,s,a,l){const u=a.grid?.canvas===e.canvas;if(!this.seqHelper)return;const m=this.tableCol,f=this.positionShift;e.save();try{const l=this.seqHelper.getSeqHandler(m);let d=this.monomerLengthLimit;if(h.gp.maxMonomerLength in m.tags){const e=parseInt(m.getTag(h.gp.maxMonomerLength));d=!isNaN(e)&&e?e:50}if(m.temp[".mm.cellRenderer.settingsChanged"]===p.s.true||this.monomerLengthLimit!=d){let e=0;const t=8;e=m.temp[".mm.cellRenderer.gapLength"]??e,this.setMonomerLengthLimit(d),this.setSeparatorWidth(l.isMsa()?t:e),m.temp[".mm.cellRenderer.settingsChanged"]=p.s.false,this.dirty=!0}const g=a.cell.rowIndex,b=a.cell.value;u&&(r=v(a.grid,e,t,r,window.devicePixelRatio)),e.beginPath(),e.rect(t,n,r,s),e.clip(),e.font=this.props?.font??"12px monospace",e.textBaseline="top";const w=m.meta.units,A=m.getTag(c.gp.aligned),E=m.getTag(c.gp.separator)??"",C=u?l.getSplitted(g):l.splitter(b);let T=h.yg.classic;A?.includes("MSA")&&w===c.Hi.SEPARATOR&&(T=h.yg.MSA);const S=m.temp["reference-sequence"],_=this.tableCol.temp["current-word"],P=(()=>{const e=(0,l.splitter)(null!=S&&""!==S?S:_??"");return i().count(0).take(e.length).slice(f).map((t=>e.getCanonical(t))).toArray()})(),M=Number.parseInt(m.getTag(c.gp.selectedPosition)??"-200");if(this.shouldUseMultilineRendering(m)){const i=[],c=this.calculateMultiLineLayoutDynamic(e,r,s,C,f,d);let u=n+this.padding;1===c.lineLayouts.length&&(u=n+(s-c.lineHeight)/2);for(const r of c.lineLayouts){const s=u+r.lineIdx*c.lineHeight;for(const u of r.elements){const d=t+u.x,p=u,g=p.posIdx,b=C.getCanonical(g);let w=y;const v=this.getMonomerLib();v&&(w=v.getMonomerTextColor(l.defaultBiotype,b));let A=0;if(a.tableRowIndex!==m.dataFrame.currentRowIdx&&P.length>0){const e=g-f;e>=0&&e<P.length&&b===P[e]&&(A=.7)}i.push({lineIdx:r.lineIdx,monomerIdx:g-f,bounds:new o.Rect(u.x,s-n,u.width,c.lineHeight),sequencePosition:g}),(0,h.oZ)(e,p.om,d,s,u.width,c.lineHeight,{color:w,isMultiLineContext:!0,transparencyRate:A,selectedPosition:isNaN(M)||M<1?void 0:M,wordIdx:g})}}null!==a.tableRowIndex&&this._cellBounds.set(a.tableRowIndex,i)}else{this._leftThreeDotsPadding=this.shouldRenderShiftedThreeDots(f)?e.measureText("...").width:0;let[,o]=this.getCellMonomerLengths(a.tableRowIndex,r);u||(o=this.getSummedMonomerLengths(this.getCellMonomerLengthsForSeqValue(b,r)));const i=this.props.separatorWidth+1*this.props.fontCharWidth,c=Math.min(C.length,Math.ceil(r/i)+f);for(let i=f;i<c;++i){const c=i<C.length?C.getOriginal(i):l.defaultGapOriginal,u=i<C.length?C.getCanonical(i):l.defaultGapOriginal;let p=y;this.getMonomerLib()&&(p=this.getMonomerLib().getMonomerTextColor(l.defaultBiotype,u));const m={color:p,pivot:0,left:!0,transparencyRate:0,separator:E,last:i===C.length-1,drawStyle:T,maxWord:o,wordIdx:i-f,gridCell:a,referenceSequence:P,maxLengthOfMonomer:d,monomerTextSizeMap:this._monomerLengthMap,logger:this.logger,selectedPosition:isNaN(M)||M<1?void 0:M-f};(0,h.oZ)(e,c,t+this.padding+this._leftThreeDotsPadding,n,r,s,m)}if(this.shouldRenderShiftedThreeDots(f)){const i={color:y,pivot:0,left:!0,transparencyRate:0,separator:E,last:!1,drawStyle:T,maxWord:o,wordIdx:0,gridCell:a,maxLengthOfMonomer:d,monomerTextSizeMap:this._monomerLengthMap,logger:this.logger};(0,h.oZ)(e,"...",t+this.padding,n,r,s,i)}}}catch(e){const[t,n]=(0,d.AP)(e);this.logger.error(t,void 0,n),this.errors.push(e)}finally{e.restore()}}shouldRenderShiftedThreeDots(e){return e>0&&(!this.gridCol||!this.gridCol.dart||!this.gridCol.grid||!this.gridCol.grid.dart||(this.gridCol.grid.props.colHeaderHeight??0)<=50)}onMouseMove(e,t){const n=`${this.toLog()}.onMouseMove()`;if(!this.seqHelper||null==e.tableRowIndex)return;const o=this.positionShift,s=e.bounds,i=t.offsetX-e.gridColumn.left+(e.gridColumn.left-s.x),a=t.offsetY-s.y;this.gridCol?.grid?.canvas&&(this.gridCol.grid.canvas.style.cursor="default");let l=null;const u=this._cellBounds.get(e.tableRowIndex);if(u){for(const e of u)if(e.bounds.contains(i,a)){l=e.monomerIdx;break}}else{const t=this.shouldRenderShiftedThreeDots(o)&&(this._leftThreeDotsPadding??0)>0?this._leftThreeDotsPadding:0;l=this.getPosition(e.tableRowIndex,i,s.width,t)}this.logger.debug(`${n}, argsX: ${i}, argsY: ${a}, left: ${l}`);const d=this.seqHelper.getSeqHandler(this.tableCol),h=d.getSplitted(e.tableRowIndex);if(null!==l&&l>=0&&l+o<h.length){const 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l,u,d;!function(e){e.maxMonomerLength=".mm.cellRenderer.maxMonomerLength"}(l||(l={})),function(e){e.applyToBackground=".m.cellRenderer.applyToBackground"}(u||(u={})),function(e){e.MSA="MSA",e.classic="classic"}(d||(d={}));const h=new class{constructor(){this.color=s,this.pivot=0,this.left=!1,this.transparencyRate=0,this.separator="",this.last=!1,this.drawStyle=d.classic,this.maxWord=[],this.wordIdx=0,this.gridCell=null,this.referenceSequence=null,this.maxLengthOfMonomer=null,this.monomerTextSizeMap={},this.logger=void 0,this.selectedPosition=void 0,this.isMultiLineContext=!1,this.lineNumber=0}};function p(e,t,n,o,l,u,p){var m,f,g;const y={...h,...p};if(y.isMultiLineContext){e.textBaseline="middle",e.textAlign="center";let r=t;null!=y.maxLengthOfMonomer&&(r=c(r,y.maxLengthOfMonomer));const i=Math.max(.1,1-(y.transparencyRate??0));e.globalAlpha=i;const d=e.measureText(r),h=d.fontBoundingBoxAscent+d.fontBoundingBoxDescent,p=o+(u-h)/2+d.fontBoundingBoxAscent;let m=y.color??s;return m&&m!==s||(m=a),e.fillStyle=m,y.selectedPosition===y.wordIdx+1&&(e.save(),e.fillStyle="rgba(60, 177, 115, 0.2)",e.fillRect(n,o,l,u),e.restore(),e.fillStyle=m),e.fillText(r,n+l/2,p),e.globalAlpha=1,e.textBaseline="top",e.textAlign="start",n+l}p.logger?.debug("Bio: printLeftOrCentered(), start"),e.textAlign="start";let b=t.substring(0),w=y.last?"":y.separator;y.drawStyle===d.MSA&&(w="");let v=!0,A=!0,E="difference";if(null!=y.gridCell&&null!=y.gridCell.cell.column&&(v=y.gridCell.cell.column.temp["color-code"]??!0,A=y.gridCell.cell.column.temp["compare-with-current"]??!0,E=y.gridCell.cell.column.temp["highlight-difference"]??"difference"),y.referenceSequence){const e=y.referenceSequence[y.wordIdx];A&&y.referenceSequence.length>0&&"difference"===E&&(y.transparencyRate=b==e?.7:y.transparencyRate),A&&y.referenceSequence.length>0&&"equal"===E&&(y.transparencyRate=b!=e?.7:y.transparencyRate)}null!=y.maxLengthOfMonomer&&(b=c(b,y.maxLengthOfMonomer));const C=b+w;(m=y.monomerTextSizeMap)[C]??(m[C]=e.measureText(C));let T=y.monomerTextSizeMap[C];(f=y.monomerTextSizeMap)[b]??(f[b]=e.measureText(b));let S=y.monomerTextSizeMap[b].width;const _=u/2-(T.fontBoundingBoxAscent+T.fontBoundingBoxDescent)/2+1;(g=y.monomerTextSizeMap)[w]??(g[w]=e.measureText(w));const P=y.monomerTextSizeMap[w].width;function M(t,s){let c=v?y.color:a;y.selectedPosition===y.wordIdx+1&&(e.fillStyle="rgba(60, 177, 115, 0.2)",e.fillRect(n+t-4,o-5,y.monomerTextSizeMap[b].width+8,u+10),c=r.Color.toHtml(r.Color.setAlpha(r.Color.fromHtml(c),255))),e.fillStyle=c,e.globalAlpha=1-y.transparencyRate,y.drawStyle===d.classic&&(e.fillText(b,n+t,o+_),e.fillStyle=i,e.fillText(w,n+s,o+_)),y.drawStyle===d.MSA&&e.fillText(b,n+t,o+_),e.globalAlpha=1}T=T.width,y.drawStyle===d.MSA&&(S=y.maxWord[y.wordIdx],T=y.maxWord[y.wordIdx]);const x=(y.maxWord[y.wordIdx]??0)-(y.maxWord[0]??0);if(y.left||T>l)return M(x,x+S),n+x+S+P;{const e=(l-T)/2;return M(e,e+S),n+x+e+S}}},6307:(e,t,n)=>{"use 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t=e.getElementsByClassName("macromolecule-cell-comp-analysis-bar")[0].style.backgroundColor;e.cells[0].style.color=t})),u}},3151:(e,t,n)=>{"use strict";n.d(t,{f6:()=>r});const r=["symbol","molfile","rgroups","name"];new RegExp("[rd]\\((\\w)\\)p?","g")},9192:(e,t,n)=>{"use strict";function r(e){return"string"==typeof e||e instanceof String?e:"StateError"===e.constructor.name?e.message:"StateError"===e.constructor.name&&"$thrownJsError"in e?r(e.$thrownJsError):e instanceof Error?e.message:e.toString()}function o(e){return e instanceof Error?e.stack:"StateError"===e.constructor.name&&"$thrownJsError"in e?o(e.$thrownJsError):void 0}function s(e){return[r(e),o(e)]}n.d(t,{AP:()=>s})},3516:(e,t,n)=>{"use strict";n.d(t,{m:()=>s});var r=n(6082),o=n(439);class s{get descriptionsArray(){return this._descriptionsArray}get sequencesArray(){return this._sequencesArray}parseMacromolecule(e,t){return this._fileContent.slice(e,t).split(/\s/).join("")}parseColumns(){const e=/^>(.*)$/gm;let t,n=0;for(;t=e.exec(this._fileContent);){const r=this._fileContent.substring(t.index+1,e.lastIndex);this._descriptionsArray.push(r),0!==n&&this._sequencesArray.push(this.parseMacromolecule(n,t.index)),n=e.lastIndex+1}this._sequencesArray.push(this.parseMacromolecule(n,-1))}importFasta(){const e=r.Column.fromStrings("description",this.descriptionsArray),t=r.Column.fromStrings("sequence",this.sequencesArray);return t.semType=r.SEMTYPE.MACROMOLECULE,t.meta.units=o.Hi.FASTA,[r.DataFrame.fromColumns([e,t])]}constructor(e){this._descriptionsArray=[],this._sequencesArray=[],this._fileContent=e,this.parseColumns()}}},6873:(e,t,n)=>{"use strict";n.d(t,{dW:()=>i,fD:()=>s});var r=n(6082),o=(n(1991),n(2003));function s(){const e=[];return e.push(r.Column.fromList("string","MSA",new Array(10**6).fill("meI/hHis/Aca/N/T/dE/Thr_PO3H2/Aca/D-Tyr_Et/Tyr_ab-dehydroMe/dV/E/N/D-Orn/D-aThr//Phe_4Me"))),e.push(r.Column.fromList(r.COLUMN_TYPE.FLOAT,"Activity",new Array(10**6).fill(5.30751))),e}function 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