npm - jbrowse-plugin-protein3d - Versions diffs - 0.4.13 → 0.5.0 - Mend

jbrowse-plugin-protein3d 0.4.13 → 0.5.0

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 (53) hide show

package/dist/jbrowse-plugin-protein3d.umd.production.min.js CHANGED Viewed

@@ -1,30 +1,30 @@
-"use strict";var JBrowsePluginProtein3d=(()=>{var Wm=Object.create;var $o=Object.defineProperty;var _m=Object.getOwnPropertyDescriptor;var Rm=Object.getOwnPropertyNames;var Jm=Object.getPrototypeOf,Km=Object.prototype.hasOwnProperty;var S=(e,t)=>()=>(e&&(t=e(e=0)),t);var V=(e,t)=>()=>(t||e((t={exports:{}}).exports,t),t.exports),vt=(e,t)=>{for(var o in t)$o(e,o,{get:t[o],enumerable:!0})},ts=(e,t,o,n)=>{if(t&&typeof t=="object"||typeof t=="function")for(let r of Rm(t))!Km.call(e,r)&&r!==o&&$o(e,r,{get:()=>t[r],enumerable:!(n=_m(t,r))||n.enumerable});return e};var p=(e,t,o)=>(o=e!=null?Wm(Jm(e)):{},ts(t||!e||!e.__esModule?$o(o,"default",{value:e,enumerable:!0}):o,e)),Ym=e=>ts($o({},"__esModule",{value:!0}),e);var ns=V((Ig,os)=>{os.exports=JBrowseExports["@jbrowse/core/Plugin"]});var x=V((Fg,rs)=>{rs.exports=JBrowseExports.react});var _=V((Lg,is)=>{is.exports=JBrowseExports["mobx-react"]});var te=V((Eg,ss)=>{ss.exports=JBrowseExports["@jbrowse/core/util"]});var tt=V((qg,as)=>{as.exports=JBrowseExports["tss-react/mui"]});function ge(){return Xo||(Xo=import(Zm+"molstar-chunk.js").catch(function(e){throw Xo=void 0,e})),Xo}var ds,Zm,Xo,Ht=S(()=>{"use strict";ds=typeof document<"u"?document.currentScript?.src:void 0,Zm=ds?ds.replace(/\/[^/]*$/,"/"):""});function Pt(e){return!!e&&typeof e=="object"&&"hoverPosition"in e&&!!e.hoverPosition&&typeof e.hoverPosition=="object"&&"coord"in e.hoverPosition&&"refName"in e.hoverPosition}async function gs({structure:e,selectedResidue:t}){let{Script:o}=await ge();return o.getStructureSelection(n=>n.struct.generator.atomGroups({"residue-test":n.core.rel.eq([n.struct.atomProperty.macromolecular.label_seq_id(),t]),"group-by":n.struct.atomProperty.macromolecular.residueKey()}),e)}function cr(e){return Object.fromEntries(Object.entries(e).map(([t,o])=>[o,+t]))}var Ut=S(()=>{"use strict";Ht()});function ws(e){let t=e.strand,o=e.refName;if(t!==-1&&t!==1)throw new Error(`Invalid strand value: ${t}. Expected 1 or -1.`);if(!o)throw new Error("refName is required");let n=new Map;for(let a of e.subfeatures??[])if(a.type==="CDS"&&a.start<a.end){let u=`${a.start}-${a.end}`;n.has(u)||n.set(u,a)}let r=[...n.values()].sort((a,u)=>t*(a.start-u.start)),i={},s={},l={};if(r.length!==0){let u=(3-(r[0]?.phase??0))%3,m=-1;for(let d of r){let c=d.end-d.start;for(let y=0;y<c;y++){let w=t===1?d.start+y:d.end-1-y,h=Math.floor(u++/3);i[w]=h,h!==m?(s[h]=w,l[h]=[w],m=h):l[h].push(w)}}}return{g2p:i,p2g:s,p2gCodon:l,refName:o,strand:t}}function Qo(e,t,o){let n=e[t];if(n!==void 0)return o===1?[n,n+3]:[n-2,n+1]}var en=S(()=>{});var to=V((Wg,xs)=>{xs.exports=JBrowseExports.mobx});function Ss(e){let t=e.alns[1].seq,o=e.alns[0].seq;if(t.length!==o.length)throw new Error("mismatched length");let n=0,r=0,i={},s={};for(let l=0;l<t.length;l++){let a=t[l];o[l]==="-"?n++:a==="-"?r++:(i[n]=r,s[r]=n,r++,n++)}return{structureSeqToTranscriptSeqPosition:i,transcriptSeqToStructureSeqPosition:s}}function vs(e){let t={};for(let o=0,n=0;o<e.length;o++)e[o]!=="-"&&(t[n]=o,n++);return t}function Ts(e){return vs(e.alns[1].seq)}function Ps(e){return vs(e.alns[0].seq)}function oo(e){return ws(e.toJSON())}var ko=S(()=>{"use strict";en()});var As,ot,dr,Gt,tn=S(()=>{"use strict";As=p(te());en();ot=p(to());ko();dr=class{views=ot.observable.map();constructor(){(0,ot.makeObservable)(this,{register:ot.action,unregister:ot.action,cleanupStaleViews:ot.action,entries:ot.computed})}register(t){this.views.set(t.viewId,t)}unregister(t){this.views.delete(t)}cleanupStaleViews(t){let o=new Set(t.views.map(n=>n.id));for(let n of this.views.keys())o.has(n)||this.views.delete(n)}get(t){return this.views.get(t)}getByUniprotId(t,o){o&&this.cleanupStaleViews(o);for(let n of this.views.values())if(n.uniprotId===t)return n}get entries(){return[...this.views.values()]}getGenomeHighlightForProteinPosition(t,o,n){let r=this.getByUniprotId(t,n);if(!r)return;let i=new As.SimpleFeature(r.feature),s=oo(i);if(!s)return;let{p2g:l,strand:a,refName:u}=s,m=Qo(l,o,a);if(!m)return;let[d,c]=m;return{refName:u,start:d,end:c}}},Gt=new dr});function oe(e){return e.replaceAll("*","")}function Ot(e){let o=(e.get("subfeatures")??[]).filter(n=>n.get("type")==="mRNA"||n.get("type")==="transcript");return o.length>0?o:[e]}function Co(e){return e?.replace(/\.[^./]+$/,"")}function Hs(e){return e===void 0?"":e.id()}function Ae(e){return e===void 0?"":e.get("name")??e.get("id")??""}function no(e){return e===void 0?"":e.get("gene_name")??e.get("name")??e.get("id")??""}function At(e){return Us.test(e)||Gs.test(e)||Os.test(e)||zs.test(e)||js.test(e)||Ws.test(e)||br.test(e)}function rn(e){if(Us.test(e)||Gs.test(e)||Os.test(e))return"ensembl";if(zs.test(e)||js.test(e))return"refseq";if(Ws.test(e))return"ccds";if(br.test(e))return"hgnc"}function nc(e){return e?Array.isArray(e)?e.flatMap(t=>typeof t=="string"?t.split(","):[]):typeof e=="string"?e.split(",").map(t=>t.trim()):[]:[]}function rc(e){let t=[];for(let o of e){let n=o.split(":"),r=n[n.length-1];r&&At(r)&&t.push(r),At(o)&&t.push(o),o.startsWith("HGNC:HGNC:")?t.push(o.replace("HGNC:HGNC:","HGNC:")):o.startsWith("HGNC:")&&/^HGNC:\d+$/.test(o)&&t.push(o)}return[...new Set(t)]}function ic(e){if(!e)return[];let t=[],o=[e.get("ID"),e.get("id"),e.get("name"),e.get("Name"),e.get("transcript_id"),e.get("protein_id"),e.get("protAcc"),e.get("mrnaAcc")];for(let s of o)if(typeof s=="string"){let l=s.replace(/\.[^./]+$/,"");At(l)&&t.push(l)}let n=e.get("hgnc")??e.get("HGNC");if(typeof n=="string"||typeof n=="number"){let s=String(n);/^\d+$/.test(s)?t.push(`HGNC:${s}`):br.test(s)&&t.push(s)}let r=e.get("Dbxref")??e.get("dbxref")??e.get("db_xref"),i=rc(nc(r));for(let s of i)t.push(s);return[...new Set(t)]}function _s(e){if(!e)return{recognizedIds:[]};let t=e;if(e.get("type")==="gene"){let l=Ot(e);l.length>0&&(t=l[0])}let 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t={};for(let o=0,n=0;o<e.length;o++)e[o]!=="-"&&(t[n]=o,n++);return t}function ws(e){return ys(e.alns[1].seq)}function xs(e){return ys(e.alns[0].seq)}function eo(e){return fs(e.toJSON())}var Po=S(()=>{"use strict";Xo()});var Ss,ot,dr,Ut,Qo=S(()=>{"use strict";Ss=p($());Xo();ot=p(Qt());Po();dr=class{views=ot.observable.map();constructor(){(0,ot.makeObservable)(this,{register:ot.action,unregister:ot.action,cleanupStaleViews:ot.action,entries:ot.computed})}register(t){this.views.set(t.viewId,t)}unregister(t){this.views.delete(t)}cleanupStaleViews(t){let o=new Set(t.views.map(n=>n.id));for(let n of this.views.keys())o.has(n)||this.views.delete(n)}get(t){return this.views.get(t)}getByUniprotId(t,o){o&&this.cleanupStaleViews(o);for(let n of this.views.values())if(n.uniprotId===t)return n}get entries(){return[...this.views.values()]}getGenomeHighlightForProteinPosition(t,o,n){let r=this.getByUniprotId(t,n);if(!r)return;let i=new 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select:-moz-focusring,.msp-plugin select.msp-btn:-moz-focusring{color:transparent;text-shadow:0 0 0 #332b1f}.msp-plugin .msp-default-bg{background:#eeece7}.msp-plugin .msp-transparent-bg{background:transparent}.msp-plugin .msp-no-hover-outline:hover{color:#ae5d04;background-color:inherit;border:none;outline-offset:0!important;outline:none!important}.msp-plugin .msp-icon-inline{margin-right:8px}.msp-plugin .msp-control-row{position:relative;height:32px;background:#eeece7;margin-top:1px}.msp-plugin .msp-control-row>span.msp-control-row-label,.msp-plugin .msp-control-row>button.msp-control-button-label{line-height:32px;display:block;width:120px;text-align:right;padding:0 10px;color:#63533c;overflow:hidden;text-overflow:ellipsis;white-space:nowrap;position:relative;-webkit-user-select:none;-moz-user-select:none;-ms-user-select:none;-o-user-select:none;user-select:none;cursor:default}.msp-plugin .msp-control-row>button.msp-control-button-label{background:#eeece7;cursor:pointer}.msp-plugin 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rgb(200.993902439,194.6402439024,178.756097561)!important}.msp-plugin .msp-slider>div:first-child{position:absolute;inset:0 62px 0 18px;display:flex}.msp-plugin .msp-slider>div:last-child{position:absolute;height:32px;line-height:32px;text-align:center;right:0;width:50px;top:0;bottom:0}.msp-plugin .msp-slider-no-input>div:first-child{right:18px}.msp-plugin .msp-slider-no-input>div:last-child{visibility:hidden;width:0}.msp-plugin .msp-slider input[type=text]{padding-right:6px;padding-left:4px;font-size:80%;text-align:right}.msp-plugin .msp-slider2>div:first-child{position:absolute;height:32px;line-height:32px;text-align:center;left:0;width:25px;top:0;bottom:0;font-size:80%}.msp-plugin .msp-slider2>div:nth-child(2){position:absolute;inset:0 37px 0 35px;display:flex}.msp-plugin .msp-slider2>div:last-child{position:absolute;height:32px;line-height:32px;text-align:center;right:0;width:25px;top:0;bottom:0;font-size:80%}.msp-plugin .msp-slider2 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y==="Ix"?(c=e[w-1]+c,b="-"+b,l[w][h]===s[w-1][h]+o&&(y="M"),w--):(c="-"+c,b=t[h-1]+b,a[w][h]===s[w][h-1]+o&&(y="M"),h--);for(;w>0;)c=e[w-1]+c,b="-"+b,w--;for(;h>0;)c="-"+c,b=t[h-1]+b,h--;return{alignedSeq1:c,alignedSeq2:b,score:u}}function Hd(e,t){let o=[];for(let n=0;n<e.length;n++){let r=e[n],i=t[n];r!=="-"&&i!=="-"&&r.toUpperCase()===i.toUpperCase()?o.push("|"):r!=="-"&&i!=="-"&&jo(r,i)>0?o.push(":"):o.push(" ")}return o.join("")}function Op(e,t,o){let{alignedSeq1:n,alignedSeq2:r}=o==="smith_waterman"?Bd(e,t):Vd(e,t);return{consensus:Hd(n,r),alns:[{id:"a",seq:n},{id:"b",seq:r}]}}var Gp=Object.fromEntries([{name:"alanine",abbreviation:"Ala",singleLetterCode:"A"},{name:"arginine",abbreviation:"Arg",singleLetterCode:"R"},{name:"asparagine",abbreviation:"Asn",singleLetterCode:"N"},{name:"aspartic acid",abbreviation:"Asp",singleLetterCode:"D"},{name:"cysteine",abbreviation:"Cys",singleLetterCode:"C"},{name:"glutamic acid",abbreviation:"Glu",singleLetterCode:"E"},{name:"glutamine",abbreviation:"Gln",singleLetterCode:"Q"},{name:"glycine",abbreviation:"Gly",singleLetterCode:"G"},{name:"histidine",abbreviation:"His",singleLetterCode:"H"},{name:"isoleucine",abbreviation:"Ile",singleLetterCode:"I"},{name:"leucine",abbreviation:"Leu",singleLetterCode:"L"},{name:"lysine",abbreviation:"Lys",singleLetterCode:"K"},{name:"methionine",abbreviation:"Met",singleLetterCode:"M"},{name:"phenylalanine",abbreviation:"Phe",singleLetterCode:"F"},{name:"proline",abbreviation:"Pro",singleLetterCode:"P"},{name:"serine",abbreviation:"Ser",singleLetterCode:"S"},{name:"threonine",abbreviation:"Thr",singleLetterCode:"T"},{name:"tryptophan",abbreviation:"Trp",singleLetterCode:"W"},{name:"tyrosine",abbreviation:"Tyr",singleLetterCode:"Y"},{name:"valine",abbreviation:"Val",singleLetterCode:"V"}].map(e=>[e.abbreviation.toUpperCase(),e]));Di();Vi();fo();function zd(e,t){return{structureSeqPos:e.StructureProperties.residue.label_seq_id(t)-1,code:e.StructureProperties.atom.label_comp_id(t),chain:e.StructureProperties.chain.auth_asym_id(t)}}async function Bi({plugin:e,kind:t,onUpdate:o}){let n=await qe(),r=e.behaviors.interaction[t].subscribe(i=>{if(n.StructureElement.Loci.is(i.current.loci)){let s=n.StructureElement.Loci.getFirstLocation(i.current.loci);o(s?zd(n,s):void 0)}else o(void 0)});return()=>{r.unsubscribe()}}Re();ce();Po();var Rd=re.types.model({url:re.types.maybe(re.types.string),data:re.types.maybe(re.types.string),connectedViewId:re.types.maybe(re.types.string),pairwiseAlignment:re.types.frozen(),feature:re.types.frozen(),userProvidedTranscriptSequence:re.types.string}).volatile(()=>({clickedStructureRange:void 0,hoverPosition:void 0,structureSequences:void 0,structureConfidence:void 0,isMouseInAlignment:!1,loadedToMolstar:!1,alignmentHoverRange:void 0,selectedFeatureId:void 0,hiddenFeatureTypes:new Set})).actions(e=>({setStructureData(t){e.structureSequences=t.sequences,e.structureConfidence=t.confidence},hideFeatureType(t){e.hiddenFeatureTypes=new Set([...e.hiddenFeatureTypes,t])},showFeatureType(t){let o=new Set(e.hiddenFeatureTypes);o.delete(t),e.hiddenFeatureTypes=o},showAllFeatureTypes(){e.hiddenFeatureTypes=new Set},setLoadedToMolstar(t){e.loadedToMolstar=t}})).views(e=>({get connectedView(){let{views:t}=(0,_o.getSession)(e);return t.find(o=>o.id===e.connectedViewId)}})).actions(e=>({setClickedStructureRange(t){e.clickedStructureRange=t},setAlignmentHoverRange(t){e.alignmentHoverRange=t},setSelectedFeatureId(t){e.selectedFeatureId=t},setHoveredPosition(t){e.hoverPosition=t?{...t,source:"structure"}:void 0},setGenomeHoveredPosition(t){e.hoverPosition=t===void 0?void 0:{structureSeqPos:t,source:"genome"}},setAlignment(t){e.pairwiseAlignment=t},setIsMouseInAlignment(t){e.isMouseInAlignment=t}})).views(e=>({get uniprotId(){let{url:t}=e;if(t)return yn(t)},get coordinateMapper(){return e.pairwiseAlignment?Vp(e.pairwiseAlignment):void 0},get structureSeqToTranscriptSeqPosition(){return this.coordinateMapper?.maps.structureSeqToTranscriptSeqPosition},get transcriptSeqToStructureSeqPosition(){return this.coordinateMapper?.maps.transcriptSeqToStructureSeqPosition},get structurePositionToAlignmentMap(){return this.coordinateMapper?.maps.structurePositionToAlignmentMap},get transcriptPositionToAlignmentMap(){return this.coordinateMapper?.maps.transcriptPositionToAlignmentMap},get confidenceCells(){let t=e.structureConfidence;return Ip(t)?Ni(t,this.structurePositionToAlignmentMap):[]},get hydrophobicityCells(){let t=e.structureSequences?.[0];return t?Ni(Wp(ee(t)),this.structurePositionToAlignmentMap):[]},get pairwiseAlignmentToTranscriptPosition(){return this.coordinateMapper?.maps.alignmentToTranscriptPosition},get pairwiseAlignmentToStructurePosition(){return this.coordinateMapper?.maps.alignmentToStructurePosition},get hoverString(){let t=e.hoverPosition;if(t===void 0)return"";let o=this.hoverStructureLetter,n=this.hoverGenomeLetter,r=[];return t.structureSeqPos!==void 0&&r.push(`${t.structureSeqPos+1}`),o&&r.push(`Structure: ${o}`),n&&o&&n!==o&&r.push(`Genome: ${n}`),t.chain&&r.push(`Chain: ${t.chain}`),r.join(", ")},get genomeToTranscriptSeqMapping(){return e.feature?eo(new _o.SimpleFeature(e.feature)):void 0},get structureSeqHoverPos(){return e.hoverPosition?.structureSeqPos},get alignmentHoverPos(){let t=this.structureSeqHoverPos;return t===void 0?void 0:this.coordinateMapper?.structureToAlignment(Np(t))},get hoverStructureRange(){let{alignmentHoverRange:t}=e,o=this.pairwiseAlignmentToStructurePosition;if(!t||!o)return;let n=o[t.start],r=o[t.end];return n===void 0||r===void 0?void 0:{start:n,end:r+1}},get hoverHighlightRange(){let t=this.structureSeqHoverPos;return this.hoverStructureRange??(t===void 0?void 0:{start:t,end:t+1})},get clickAlignmentRange(){let t=e.clickedStructureRange,o=this.structurePositionToAlignmentMap;if(!t||!o)return;let n=o[t.start],r=o[t.end-1];return n===void 0||r===void 0?void 0:{start:n,end:r}},structureRangeToGenomeHighlight(t){let o=e.connectedView?.assemblyNames[0],n=this.genomeToTranscriptSeqMapping;if(!t||!o||!n)return[];let r={genomeToTranscriptSeqMapping:n,pairwiseAlignment:e.pairwiseAlignment,structureSeqToTranscriptSeqPosition:this.structureSeqToTranscriptSeqPosition},i=t.end>t.start+1?qi({model:r,structureSeqPos:t.start,structureSeqEndPos:t.end}):$n({model:r,structureSeqPos:t.start});if(!i)return[];let[s,l]=i;return[{assemblyName:o,refName:n.refName,start:s,end:l}]},get hoverGenomeHighlights(){return e.hoverPosition?.source==="genome"?[]:this.structureRangeToGenomeHighlight(this.hoverHighlightRange)},get clickGenomeHighlights(){return this.structureRangeToGenomeHighlight(e.clickedStructureRange)},get hoverStructureLetter(){let t=e.hoverPosition?.code;if(t)return Gp[t]?.singleLetterCode;let o=this.structureSeqHoverPos;if(o!==void 0&&e.structureSequences?.[0])return e.structureSequences[0][o]},get hoverGenomeLetter(){let t=this.structureSeqHoverPos;if(t===void 0)return;let o=this.structureSeqToTranscriptSeqPosition?.[t];if(o!==void 0)return e.userProvidedTranscriptSequence[o]},get alignmentMatchSet(){let t=e.pairwiseAlignment?.consensus;if(!t)return;let o=new Set;for(let n=0;n<t.length;n++)(t[n]==="|"||t[n]===":")&&o.add(n);return o},get alignmentPending(){return!e.pairwiseAlignment&&!!e.userProvidedTranscriptSequence&&!!e.structureSequences?.[0]},get exactMatch(){let t=ee(e.userProvidedTranscriptSequence),o=e.structureSequences?.[0]?ee(e.structureSequences[0]):void 0;return t===o},get parentView(){return(0,re.getParent)(e,2)},get zoomToBaseLevel(){return this.parentView.zoomToBaseLevel},get autoScrollAlignment(){return this.parentView.autoScrollAlignment},get showHighlight(){return this.parentView.showHighlight},get showProteinTracks(){return this.parentView.showProteinTracks},get trackHeight(){return this.parentView.compactTracks?8:12},get trackGap(){return this.parentView.compactTracks?1:2},get alignmentAlgorithm(){return za(this.parentView.alignmentAlgorithm)},get molstarPluginContext(){return this.parentView.molstarPluginContext},get structureIndex(){return this.parentView.structures.indexOf(e)},get molstarStructure(){let t=this.structureIndex;return e.loadedToMolstar&&t>=0?this.molstarPluginContext?.managers.structure.hierarchy.current.structures[t]?.cell.obj?.data:void 0}})).actions(e=>({setError(t){e.parentView.setError(t)},hoverAlignmentPosition(t){if(!e.alignmentHoverRange){let o=e.coordinateMapper?.alignmentToStructure(Ei(t));e.setHoveredPosition(o!==void 0?{structureSeqPos:o}:void 0)}},clickAlignmentPosition(t){let o=e.coordinateMapper?.alignmentToStructure(Ei(t));e.setSelectedFeatureId(void 0),o!==void 0?Wo({model:e,structureSeqPos:o}).catch(n=>{console.error(n),e.parentView.setError(n)}):e.setClickedStructureRange(void 0)}})).actions(e=>({afterAttach(){let t=(o,n)=>{(0,re.addDisposer)(e,(0,So.autorun)(async()=>{let{molstarPluginContext:r}=e;r&&(0,re.addDisposer)(e,await Bi({plugin:r,kind:o,onUpdate:n}))}))};(0,re.addDisposer)(e,(0,So.autorun)(async()=>{try{let{userProvidedTranscriptSequence:o,structureSequences:n,exactMatch:r,alignmentAlgorithm:i}=e,s=o,l=n?.[0];if(e.pairwiseAlignment||!s||!l)return;let a=ee(s),u=ee(l);if(r)e.setAlignment({consensus:"|".repeat(a.length),alns:[{id:"seq1",seq:a},{id:"seq2",seq:u}]});else{let m=Op(a,u,i);e.setAlignment(m),e.parentView.setShowAlignment(!0)}}catch(o){console.error(o),e.parentView.setError(o)}})),(0,re.addDisposer)(e,(0,So.autorun)(()=>{let{hovered:o}=(0,_o.getSession)(e),{transcriptSeqToStructureSeqPosition:n,genomeToTranscriptSeqMapping:r,connectedView:i}=e;if(i?.initialized&&r&&kt(o)){let{hoverPosition:s}=o,l=r.g2p[s.coord-1],a=l===void 0?void 0:n?.[l];e.setGenomeHoveredPosition(a)}else e.hoverPosition?.source==="genome"&&e.setGenomeHoveredPosition(void 0)})),t("click",o=>{o&&(e.setHoveredPosition(o),e.setSelectedFeatureId(void 0),Wo({model:e,structureSeqPos:o.structureSeqPos}).catch(n=>{console.error(n),e.parentView.setError(n)}))}),t("hover",o=>{e.setHoveredPosition(o)}),(0,re.addDisposer)(e,(0,So.autorun)(async()=>{let{showHighlight:o,structureSeqToTranscriptSeqPosition:n,molstarPluginContext:r,molstarStructure:i}=e;i&&r&&n&&await zo({structure:i,plugin:r,channel:"select",spec:o?{kind:"list",residues:Object.keys(n).map(s=>+s)}:void 0})})),(0,re.addDisposer)(e,(0,So.autorun)(async()=>{let{molstarStructure:o,molstarPluginContext:n,hoverHighlightRange:r}=e;o&&n&&await zo({structure:o,plugin:n,channel:"highlight",spec:r?{kind:"range",...r}:void 0})}))}})),Zn=Rd;fo();var Kd="SuperpositionTransform";async function Hi(e){let{QueryContext:t,StructureElement:o,StructureSelection:n,StructureSelectionQueries:r,PluginCommands:i,PluginStateObject:s,tmAlign:l}=await qe(),a=e.managers.structure.hierarchy.current.structures;if(a.length<2)return;let{query:u}=r.trace,d=a.map(w=>{let h=w.cell.obj?.data;if(!h)return;let y=e.helpers.substructureParent.get(h);if(!y)return;let f=e.state.data.selectQ(v=>v.byValue(y).rootOfType(s.Molecule.Structure))[0]?.obj?.data;if(!f)return;let g=n.toLociWithSourceUnits(u(new t(h)));return o.Loci.remap(g,f)}).filter(w=>w!==void 0);if(d.length<2)return;let b=e.managers.structure.hierarchy.findStructure(d[0]?.structure)?.transform?.cell.obj?.data.coordinateSystem;for(let w=1;w<d.length;w++){let h=l(d[0],d[w]),{bTransform:y,tmScoreA:f,tmScoreB:g,rmsd:v,alignedLength:E}=h;await Yd(e,a[w].cell,y,b),e.log.info(`TM-align: TM-score=${f.toFixed(4)}/${g.toFixed(4)}, RMSD=${v.toFixed(2)} \xC5, aligned ${E} residues.`)}await new Promise(w=>requestAnimationFrame(w)),await i.Camera.Reset(e)}async function Yd(e,t,o,n){let{Mat4:r,StateObjectRef:i,StateTransforms:s}=await qe(),l=i.resolveAndCheck(e.state.data,t);if(!l)return;let a=e.state.data.selectQ(c=>c.byRef(l.transform.ref).subtree().withTransformer(s.Model.TransformStructureConformation))[0],m={transform:{name:"matrix",params:{data:n&&!r.isIdentity(n.matrix)?r.mul(r(),n.matrix,o):o,transpose:!1}}},d=a?e.state.data.build().to(a).update(m):e.state.data.build().to(t).insert(s.Model.TransformStructureConformation,m,{tags:Kd});await e.runTask(e.state.data.updateTree(d))}var Rp="proteinView-settings",Kp=["showAlignment","showProteinTracks","showHighlight","zoomToBaseLevel","autoScrollAlignment","compactTracks"];function $d(){return ue.types.compose("ProteinView",Yp.BaseViewModel,ue.types.model({id:$p.ElementId,type:ue.types.literal("ProteinView"),structures:ue.types.array(Zn),showControls:!1,height:ue.types.optional(ue.types.number,650),showHighlight:!1,zoomToBaseLevel:!0,autoScrollAlignment:!1,colorScheme:ue.types.optional(ue.types.enumeration("ColorScheme",kp),"default"),showAlignment:!0,showProteinTracks:!0,compactTracks:!0,alignmentAlgorithm:ue.types.optional(ue.types.string,Io),connectedMsaViewId:ue.types.maybe(ue.types.string),init:ue.types.frozen()})).volatile(()=>({error:void 0,molstarPluginContext:void 0,showManualAlignmentDialog:!1,showAddStructureDialog:!1})).actions(e=>({setHeight(t){return e.height=t,t},setShowAlignment(t){e.showAlignment=t},setShowControls(t){e.showControls=t},setError(t){e.error=t},setShowHighlight(t){e.showHighlight=t},setShowProteinTracks(t){e.showProteinTracks=t},setCompactTracks(t){e.compactTracks=t},setZoomToBaseLevel(t){e.zoomToBaseLevel=t},setAutoScrollAlignment(t){e.autoScrollAlignment=t},setAlignmentAlgorithm(t){e.alignmentAlgorithm=t},setColorScheme(t){e.colorScheme=t},setMolstarPluginContext(t){if(t!==e.molstarPluginContext)for(let o of e.structures)o.setLoadedToMolstar(!1);e.molstarPluginContext=t},setShowManualAlignmentDialog(t){e.showManualAlignmentDialog=t},setShowAddStructureDialog(t){e.showAddStructureDialog=t},setInit(t){e.init=t},setConnectedMsaViewId(t){e.connectedMsaViewId=t},addStructure(t){e.structures.push(Zn.create({url:t.url,data:t.data,userProvidedTranscriptSequence:""}))}})).actions(e=>({async addStructureAndSuperpose(t){let{molstarPluginContext:o}=e;if(!o)return;let n=Zn.create({url:t.url,data:t.data,userProvidedTranscriptSequence:""});n.setLoadedToMolstar(!0),e.structures.push(n);try{n.setStructureData(await Kn({structure:t,plugin:o})),e.structures.length>1&&await Hi(o)}catch(r){e.setError(r),console.error(r)}}})).actions(e=>({afterAttach(){try{let t=localStorage.getItem(Rp);if(t){let o=JSON.parse(t);for(let n of Kp)o[n]!==void 0&&(e[n]=o[n])}}catch(t){console.error("Failed to restore protein view settings",t)}(0,ue.addDisposer)(e,(0,Jo.autorun)(()=>{try{let t={};for(let o of Kp)t[o]=e[o];localStorage.setItem(Rp,JSON.stringify(t))}catch(t){console.error("Failed to save protein view settings",t)}})),(0,ue.addDisposer)(e,(0,Jo.autorun)(()=>{let{init:t}=e;if(t){let{structures:o,showControls:n,showAlignment:r}=t;if(o)for(let i of o)e.addStructure(i);n!==void 0&&e.setShowControls(n),r!==void 0&&e.setShowAlignment(r),e.setInit(void 0)}})),(0,ue.addDisposer)(e,(0,Jo.autorun)(()=>{let{molstarPluginContext:t,colorScheme:o}=e,n=e.structures.filter(r=>r.structureSequences!==void 0).length;t&&n>0&&Cp({plugin:t,colorScheme:o}).catch(r=>{console.error(r),e.setError(r)})})),(0,ue.addDisposer)(e,(0,Jo.autorun)(Fp(e)))}})).views(e=>({get primaryStructure(){return e.structures[0]},menuItems(){return[{label:"Pairwise alignment",icon:Ci,type:"checkbox",checked:e.showAlignment,onClick:()=>{e.setShowAlignment(!e.showAlignment)}},{label:"Protein feature tracks",icon:Ci,type:"checkbox",checked:e.showProteinTracks,onClick:()=>{e.setShowProteinTracks(!e.showProteinTracks)}},{label:"Color scheme...",subMenu:xo.map(t=>({label:t.label,type:"radio",checked:e.colorScheme===t.value,onClick:()=>{e.setColorScheme(t.value)}}))},{label:"Add structure...",onClick:()=>{e.setShowAddStructureDialog(!0)}},{label:"Advanced...",icon:ro,subMenu:[{label:"Pairwise alignment as green highlight",type:"checkbox",checked:e.showHighlight,onClick:()=>{e.setShowHighlight(!e.showHighlight)}},{label:"Show all protein feature tracks",onClick:()=>{for(let t of e.structures)t.showAllFeatureTypes()}},{label:"Import manual alignment...",onClick:()=>{e.setShowManualAlignmentDialog(!0)}},{label:"Re-align structures (TM-align)",onClick:()=>{e.molstarPluginContext&&Hi(e.molstarPluginContext).catch(t=>{console.error(t),e.setError(t)})}},{label:"Zoom to base level on click",type:"checkbox",checked:e.zoomToBaseLevel,onClick:()=>{e.setZoomToBaseLevel(!e.zoomToBaseLevel)}},{label:"Auto-scroll protein feature view on hover",type:"checkbox",checked:e.autoScrollAlignment,onClick:()=>{e.setAutoScrollAlignment(!e.autoScrollAlignment)}}]}]}}))}var Zp=$d;var Ag=(0,Mm.lazy)(()=>Promise.resolve().then(()=>(Cm(),km)));function Ki(e){e.addViewType(()=>new Im.ViewType({name:"ProteinView",displayName:"Protein view",stateModel:Zp(),ReactComponent:Ag}))}var Bm=p(rn());var Fm=p(oo());var Pg=(0,Fm.ConfigurationSchema)("UniProtVariationAdapter",{location:{type:"fileLocation",defaultValue:{uri:"/path/to/my.bed.gz",locationType:"UriLocation"}},scoreField:{type:"string",defaultValue:""}},{explicitlyTyped:!0}),Lm=Pg;function Yi(e){e.addAdapterType(()=>new Bm.default({name:"UniProtVariationAdapter",displayName:"UniProtVariation adapter",configSchema:Lm,getAdapterClass:()=>Promise.resolve().then(()=>(Vm(),Nm)).then(t=>t.default)}))}var Hm="0.5.0";var ir=class extends Um.default{name="ProteinViewer";version=Hm;install(t){Ki(t),Ai(t),Pi(t),yr(t),wr(t),xr(t),Yi(t)}configure(t){}};return Jm(kg);})();
 /*! Bundled license information:
 use-sync-external-store/cjs/use-sync-external-store-shim.production.js: