jbrowse-plugin-protein3d 1.2.0 → 1.2.1

package/README.md

@@ -37,9 +37,11 @@ Using the plugin:
   gene, and reads the R248 hotspot back to its codon;
   [Proteins on genomes.jbrowse.org](https://jbrowse.org/jb2/docs/tutorials/genomes_proteins/)
   launches a structure and an MSA from any gene's right-click menu.
-- [Demos](docs/demos.md): structures that are easy to map wrong, each one link
-  away — a peptide bound to a larger partner, a protein bound to DNA, a receptor
-  with another protein fused into it, a phosphorylated residue, and a
+- [Demos](docs/demos.md): one link each. Genes opened by name alone in human,
+  mouse, yeast, bacteria, fungi and viruses (E. coli recA, M. tuberculosis katG,
+  the SARS-CoV-2 spike, the HIV-1 capsid), then the structures that are easy to
+  map wrong — a peptide bound to a larger partner, a protein bound to DNA, a
+  receptor with another protein fused into it, a phosphorylated residue, and a
   mitochondrial protein.
 - [Your own structures](docs/your-own-structures.md): opening a model you folded
   yourself (ColabFold, AlphaFold 3, Boltz…) instead of the AlphaFold DB one,

package/dist/LaunchProteinView/utils/util.js

@@ -122,6 +122,15 @@ export function findRecognizedDbIds(f) {
     }
     return [...new Set(recognizedIds)];
 }
+// `UniProtKB/Swiss-Prot:P0A7G6`, the reviewed entry before a TrEMBL one
+function dbxrefUniProtId(f) {
+    const entries = parseDbxref(f?.get('Dbxref') ?? f?.get('dbxref') ?? f?.get('db_xref'));
+    return ['UniProtKB/Swiss-Prot:', 'UniProtKB/TrEMBL:']
+        .flatMap(prefix => entries
+        .filter(e => e.startsWith(prefix))
+        .map(e => e.slice(prefix.length)))
+        .find(id => id.length > 0);
+}
 /**
  * Extract all useful identifiers from a feature for UniProt lookup.
  * If the feature is a gene, prioritizes identifiers from the preferred
@@ -140,13 +149,24 @@ export function extractFeatureIdentifiers(f, preferredTranscriptId) {
                 transcripts[0] ??
                 f;
     }
-    // --- Extracting Recognized IDs and UniProt ID from featureToProcess ---
-    const recognizedIds = findRecognizedDbIds(featureToProcess);
+    // NCBI's GFF3 puts the protein on the CDS record, not the transcript: its
+    // RefSeq accession always, and for a curated genome (E. coli K-12, yeast)
+    // the UniProt accession itself. A prokaryotic gene has no transcript record
+    // between, so the CDS is the only place either appears.
+    const cds = featureToProcess
+        .get('subfeatures')
+        ?.find(sub => sub.get('type')?.toLowerCase() === 'cds');
+    const recognizedIds = [
+        ...findRecognizedDbIds(featureToProcess),
+        ...findRecognizedDbIds(cds),
+    ];
     // Handle UniProt ID from feature attributes (trust that it's valid if present)
     const uniprotIdAttr = featureToProcess.get('uniprot') ??
         featureToProcess.get('uniprotId') ??
         featureToProcess.get('uniprotid') ??
-        featureToProcess.get('UniProt');
+        featureToProcess.get('UniProt') ??
+        dbxrefUniProtId(featureToProcess) ??
+        dbxrefUniProtId(cds);
     const uniprotId = typeof uniprotIdAttr === 'string' && uniprotIdAttr.length > 0
         ? uniprotIdAttr
         : undefined;

package/dist/chunks/{ProteinView-B57QOH3K.js → ProteinView-MG7N24DJ.js}

@@ -1,4 +1,4 @@
-import{Aa as xe,Ba as Pt,Ca as Ct,E as tt,Fa as Tt,Ha as kt,M as rt,R as ye,U as ot,W as nt,a as k,b as xo,da as at,ea as ut,fa as dt,g as Ne,ga as ct,h as wo,ha as pt,ia as ve,k as _e,ka as Se,l as Ke,m as Ge,p as je,pa as mt,q as Ye,r as Qe,ra as ft,sa as gt,t as Xe,ta as ht,u as Ze,ua as yt,v as Re,va as bt,w as et,wa as vt,xa as St,ya as xt,za as wt}from"./chunk-UTUOAPWU.js";import{a as C}from"./chunk-X5RLRQSB.js";import{c as it,d as st,f as be,g as lt}from"./chunk-GQU3SL56.js";import{a as $}from"./chunk-533QNNGN.js";import{a as he,b as U}from"./chunk-J236G3A2.js";import{a as w}from"./chunk-GVEKA5YG.js";import{a as So}from"./chunk-B3HKXTGK.js";import{a as A,c as l}from"./chunk-KVMUXFPB.js";var Ot=A((Cn,Vt)=>{Vt.exports=JBrowseExports["@mui/material/Checkbox"]});var zt=A((Tn,Wt)=>{Wt.exports=JBrowseExports["@mui/material/Divider"]});var we=A((kn,qt)=>{qt.exports=JBrowseExports["@mui/material/IconButton"]});var _t=A((Mn,Nt)=>{Nt.exports=JBrowseExports["@mui/material/ListItemIcon"]});var Gt=A((In,Kt)=>{Kt.exports=JBrowseExports["@mui/material/ListItemText"]});var Yt=A((Ln,jt)=>{jt.exports=JBrowseExports["@mui/material/Menu"]});var Xt=A((En,Qt)=>{Qt.exports=JBrowseExports["@mui/material/MenuItem"]});var Pe=A((Bn,Zt)=>{Zt.exports=JBrowseExports["@mui/material/Tooltip"]});var Ce=A((Hn,rr)=>{rr.exports=JBrowseExports["@mui/material/Typography"]});var hr=A((_n,gr)=>{gr.exports=JBrowseExports["@mui/material/Chip"]});var br=A((Kn,yr)=>{yr.exports=JBrowseExports["@mui/material/Link"]});var P=l(w()),_=l(he());var Mt=l($(),1),X=(0,C.createSvgIcon)((0,Mt.jsx)("path",{d:"M19 6.41 17.59 5 12 10.59 6.41 5 5 6.41 10.59 12 5 17.59 6.41 19 12 13.41 17.59 19 19 17.59 13.41 12z"}),"Close");var bo=l(U()),se=l(k());var M=l(w()),T=l(U());function It(o){let e=o.next();for(;!e.done&&e.value.trim()==="";)e=o.next();return e.value}function Et(o){let e=o.trim();return e?e.split(/\s+/).every(n=>/^\d+$/.test(n)):!1}function Po(o){let e=o.trim();return/^\w+\s+/.test(e)&&!Et(o)}function Co(o){return o.length>=3&&/^\d+$/.test(o[1])}function To(o,e){let n=o.trim().split(/\s+/),r=n[e],i=o.indexOf(r,o.indexOf(n[0])+n[0].length);return[i,i+r.length]}function Lt(o){let e=It(o),t=[],n="";if(!e)return;for(;e;)Et(e)||(Po(e)?t.push(e):n=e),e=o.next().value;if(t.length===0)return;let r=t.map(S=>S.trim().split(/\s+/)),i=r[0];if(!i)return;let s=Co(i)?2:1,[a,u]=To(t[0],s),y=r.map(S=>S[0]),d=r.map(S=>S[s]),h=n.slice(a,u),v=d[0];if(v){let S=v.length-h.length;S>0&&(h+=" ".repeat(S))}return{ids:y,seqs:d,consensus:h}}function Bt(o){let e,t=Lt(o);if(t!==void 0)for(;e=Lt(o);){for(let n=0;n<e.seqs.length;n++)t.seqs[n]+=e.seqs[n];t.consensus+=e.consensus}return t}function At(o){let e=o.split(`
+import{Aa as xe,Ba as Pt,Ca as Ct,E as tt,Fa as Tt,Ha as kt,M as rt,R as ye,U as ot,W as nt,a as k,b as xo,da as at,ea as ut,fa as dt,g as Ne,ga as ct,h as wo,ha as pt,ia as ve,k as _e,ka as Se,l as Ke,m as Ge,p as je,pa as mt,q as Ye,r as Qe,ra as ft,sa as gt,t as Xe,ta as ht,u as Ze,ua as yt,v as Re,va as bt,w as et,wa as vt,xa as St,ya as xt,za as wt}from"./chunk-252AFZJZ.js";import{a as C}from"./chunk-X5RLRQSB.js";import{c as it,d as st,f as be,g as lt}from"./chunk-GQU3SL56.js";import{a as $}from"./chunk-533QNNGN.js";import{a as he,b as U}from"./chunk-J236G3A2.js";import{a as w}from"./chunk-GVEKA5YG.js";import{a as So}from"./chunk-B3HKXTGK.js";import{a as A,c as l}from"./chunk-KVMUXFPB.js";var Ot=A((Cn,Vt)=>{Vt.exports=JBrowseExports["@mui/material/Checkbox"]});var zt=A((Tn,Wt)=>{Wt.exports=JBrowseExports["@mui/material/Divider"]});var we=A((kn,qt)=>{qt.exports=JBrowseExports["@mui/material/IconButton"]});var _t=A((Mn,Nt)=>{Nt.exports=JBrowseExports["@mui/material/ListItemIcon"]});var Gt=A((In,Kt)=>{Kt.exports=JBrowseExports["@mui/material/ListItemText"]});var Yt=A((Ln,jt)=>{jt.exports=JBrowseExports["@mui/material/Menu"]});var Xt=A((En,Qt)=>{Qt.exports=JBrowseExports["@mui/material/MenuItem"]});var Pe=A((Bn,Zt)=>{Zt.exports=JBrowseExports["@mui/material/Tooltip"]});var Ce=A((Hn,rr)=>{rr.exports=JBrowseExports["@mui/material/Typography"]});var hr=A((_n,gr)=>{gr.exports=JBrowseExports["@mui/material/Chip"]});var br=A((Kn,yr)=>{yr.exports=JBrowseExports["@mui/material/Link"]});var P=l(w()),_=l(he());var Mt=l($(),1),X=(0,C.createSvgIcon)((0,Mt.jsx)("path",{d:"M19 6.41 17.59 5 12 10.59 6.41 5 5 6.41 10.59 12 5 17.59 6.41 19 12 13.41 17.59 19 19 17.59 13.41 12z"}),"Close");var bo=l(U()),se=l(k());var M=l(w()),T=l(U());function It(o){let e=o.next();for(;!e.done&&e.value.trim()==="";)e=o.next();return e.value}function Et(o){let e=o.trim();return e?e.split(/\s+/).every(n=>/^\d+$/.test(n)):!1}function Po(o){let e=o.trim();return/^\w+\s+/.test(e)&&!Et(o)}function Co(o){return o.length>=3&&/^\d+$/.test(o[1])}function To(o,e){let n=o.trim().split(/\s+/),r=n[e],i=o.indexOf(r,o.indexOf(n[0])+n[0].length);return[i,i+r.length]}function Lt(o){let e=It(o),t=[],n="";if(!e)return;for(;e;)Et(e)||(Po(e)?t.push(e):n=e),e=o.next().value;if(t.length===0)return;let r=t.map(S=>S.trim().split(/\s+/)),i=r[0];if(!i)return;let s=Co(i)?2:1,[a,u]=To(t[0],s),y=r.map(S=>S[0]),d=r.map(S=>S[s]),h=n.slice(a,u),v=d[0];if(v){let S=v.length-h.length;S>0&&(h+=" ".repeat(S))}return{ids:y,seqs:d,consensus:h}}function Bt(o){let e,t=Lt(o);if(t!==void 0)for(;e=Lt(o);){for(let n=0;n<e.seqs.length;n++)t.seqs[n]+=e.seqs[n];t.consensus+=e.consensus}return t}function At(o){let e=o.split(`
 `).filter(s=>!s.startsWith("#")).join(`
 `),t=Bt(e.split(`
 `)[Symbol.iterator]());if(t===void 0)throw new Error("No blocks parsed");let n=t.seqs.map((s,a)=>({id:t.ids[a],seq:s})),{consensus:r}=t,i=n[0];if(!i)throw new Error("No alignments found");if(r.length!==i.seq.length)throw new Error(`Consensus length !== sequence length. Con ${r.length} seq ${i.seq.length}`);if(n.length!==2)throw new Error(`Expected exactly 2 sequences in pairwise alignment, got ${n.length}`);return{consensus:r,alns:n}}var Ft=l(k());var ko=(0,Ft.observer)(function({model:e}){let[t,n]=(0,M.useState)(""),[r,i]=(0,M.useState)(),{showManualAlignmentDialog:s,alignmentStructure:a}=e,u=()=>{n(""),i(void 0),e.setShowManualAlignmentDialog(!1)},y=()=>{if(t.trim())try{let d=At(t.trim()),h=a?.entities,v=a&&h?Ct(d,a.userProvidedTranscriptSequence,h,a.mappedEntityId):void 0;!a||!v?i("No structure loaded to apply alignment to"):"problem"in v?i(v.problem):(a.importAlignment(Pt(d)),u())}catch(d){i(`Failed to parse alignment: ${d}`)}};return s?M.default.createElement(T.Dialog,{open:!0,onClose:u,maxWidth:"md",fullWidth:!0},M.default.createElement(T.DialogTitle,null,"Import manual alignment"),M.default.createElement(T.DialogContent,null,M.default.createElement(T.Typography,{variant:"body2",color:"text.secondary",sx:{mb:2}},"Paste a pre-computed alignment in Clustal format. The first sequence should be the transcript and the second should be the structure."),M.default.createElement(T.TextField,{multiline:!0,rows:12,fullWidth:!0,placeholder:`Example:
@@ -6,4 +6,4 @@ transcript  MKAAYLSMFGKEDHKPFGDDEVELFRAVPGLKLKIAG
             |||||||||||||||||||||||||||||||||||||
 structure   MKAAYLSMFGKEDHKPFGDDEVELFRAVPGLKLKIAG`,value:t,onChange:d=>{n(d.target.value),i(void 0)},slotProps:{htmlInput:{style:{fontFamily:"monospace",fontSize:12}}}}),r?M.default.createElement(T.Typography,{color:"error",variant:"body2",sx:{mt:1}},r):null),M.default.createElement(T.DialogActions,null,M.default.createElement(T.Button,{onClick:()=>{u()}},"Cancel"),M.default.createElement(T.Button,{onClick:()=>{y()},variant:"contained",color:"primary",disabled:!t.trim()},"Apply alignment"))):null}),Dt=ko;var f=l(w()),uo=l(he());var Ht=l($(),1),$t=(0,C.createSvgIcon)((0,Ht.jsx)("path",{d:"M12 2C6.49 2 2 6.49 2 12s4.49 10 10 10c1.38 0 2.5-1.12 2.5-2.5 0-.61-.23-1.2-.64-1.67-.08-.1-.13-.21-.13-.33 0-.28.22-.5.5-.5H16c3.31 0 6-2.69 6-6 0-4.96-4.49-9-10-9m5.5 11c-.83 0-1.5-.67-1.5-1.5s.67-1.5 1.5-1.5 1.5.67 1.5 1.5-.67 1.5-1.5 1.5m-3-4c-.83 0-1.5-.67-1.5-1.5S13.67 6 14.5 6s1.5.67 1.5 1.5S15.33 9 14.5 9M5 11.5c0-.83.67-1.5 1.5-1.5s1.5.67 1.5 1.5S7.33 13 6.5 13 5 12.33 5 11.5m6-4c0 .83-.67 1.5-1.5 1.5S8 8.33 8 7.5 8.67 6 9.5 6s1.5.67 1.5 1.5"}),"Palette");var Ut=l($(),1),Jt=(0,C.createSvgIcon)((0,Ut.jsx)("path",{d:"M3 17v2h6v-2zM3 5v2h10V5zm10 16v-2h8v-2h-8v-2h-2v6zM7 9v2H3v2h4v2h2V9zm14 4v-2H11v2zm-6-4h2V7h4V5h-4V3h-2z"}),"Tune");var co=l(Ot()),po=l(zt()),He=l(we()),mo=l(_t()),fo=l(Gt()),$e=l(Yt()),Ue=l(Xt()),Je=l(Pe()),me=l(k());var c=l(w()),Rt=l(he()),p=l(U()),er=l(k());var Mo=(0,er.observer)(function({model:e}){let[t,n]=(0,c.useState)(),[r,i]=(0,c.useState)(""),[s,a]=(0,c.useState)(""),[u,y]=(0,c.useState)("pdb"),[d,h]=(0,c.useState)(""),[v,S]=(0,c.useState)(),[O,Y]=(0,c.useState)(!0),{showAddStructureDialog:ee}=e,te=!!e.primaryStructure?.userProvidedTranscriptSequence,W=()=>{n(void 0),i(""),a(""),h(""),S(void 0),e.setShowAddStructureDialog(!1)},z=async()=>{try{let x=u==="pdb"&&r?{pdbId:r}:u==="uniprot"&&s?{uniprotId:s}:u==="url"&&d?{url:d}:u==="file"&&t?{data:await ct(t)}:void 0;if(x){let D=e.primaryStructure,le=O&&D?.userProvidedTranscriptSequence?{userProvidedTranscriptSequence:D.userProvidedTranscriptSequence,feature:D.feature,connectedViewId:D.connectedViewId}:{};e.addStructure({...x,...le}),W()}}catch(x){console.error(x),S(x)}};if(!ee)return null;let K=r!==""&&!ye(r),E=u==="url"&&d!==""||u==="file"&&t!==void 0||u==="pdb"&&ye(r)||u==="uniprot"&&s!=="";return c.default.createElement(p.Dialog,{open:!0,onClose:W,maxWidth:"sm",fullWidth:!0},c.default.createElement(p.DialogTitle,null,"Add structure"),c.default.createElement(p.DialogContent,null,v?c.default.createElement(Rt.ErrorMessage,{error:v}):null,c.default.createElement(p.Typography,{variant:"body2",color:"text.secondary",sx:{mb:2}},"Add another structure to superpose on the existing structure(s)."),c.default.createElement(p.FormControl,{component:"fieldset",sx:{mb:2}},c.default.createElement(p.RadioGroup,{value:u,onChange:x=>{y(x.target.value)}},c.default.createElement(p.FormControlLabel,{value:"pdb",control:c.default.createElement(p.Radio,null),label:"PDB ID"}),c.default.createElement(p.FormControlLabel,{value:"uniprot",control:c.default.createElement(p.Radio,null),label:"UniProt ID (AlphaFold)"}),c.default.createElement(p.FormControlLabel,{value:"url",control:c.default.createElement(p.Radio,null),label:"URL"}),c.default.createElement(p.FormControlLabel,{value:"file",control:c.default.createElement(p.Radio,null),label:"File"}))),u==="pdb"?c.default.createElement(p.TextField,{fullWidth:!0,value:r,onChange:x=>{i(x.target.value.trim().toUpperCase())},label:"PDB ID (e.g. 1CRN)",placeholder:"Enter PDB ID",error:K,helperText:K?"A PDB ID is four characters beginning with a digit":void 0,sx:{mb:2}}):null,u==="uniprot"?c.default.createElement(p.TextField,{fullWidth:!0,value:s,onChange:x=>{a(x.target.value.trim().toUpperCase())},label:"UniProt ID (e.g. P04637)",placeholder:"Enter UniProt ID",helperText:"Fetches the AlphaFold predicted structure",sx:{mb:2}}):null,u==="url"?c.default.createElement(p.TextField,{fullWidth:!0,label:"Structure URL",value:d,onChange:x=>{h(x.target.value.trim())},placeholder:"https://files.rcsb.org/download/1CRN.cif",sx:{mb:2}}):null,u==="file"?c.default.createElement("div",{style:{marginBottom:16}},c.default.createElement(p.Button,{variant:"outlined",component:"label"},t?t.name:"Choose file",c.default.createElement("input",{type:"file",hidden:!0,accept:pt,onChange:({target:x})=>{let D=x.files?.[0];D&&n(D)}})),t?c.default.createElement(p.Typography,{variant:"body2",sx:{mt:1}},"Selected: ",t.name):null):null,te?c.default.createElement(p.FormControlLabel,{control:c.default.createElement(p.Checkbox,{checked:O,onChange:x=>{Y(x.target.checked)}}),label:"Map to the same transcript as the first structure (alignment, hover and click linked to the genome)"}):null,c.default.createElement(p.Typography,{variant:"body2",color:"text.secondary",sx:{mt:1}},"Tip: Structures will be automatically superposed using TM-align. For manual control, use the Mol* controls (\u{1F527} wrench icon).")),c.default.createElement(p.DialogActions,null,c.default.createElement(p.Button,{onClick:()=>{W()}},"Cancel"),c.default.createElement(p.Button,{onClick:()=>{z()},variant:"contained",color:"primary",disabled:!E},"Add structure")))}),tr=Mo;var H=l(w()),or=l(Ce()),nr={width:8,height:8,border:"1px solid rgba(0,0,0,0.3)"};function ir({title:o,testId:e,color:t,children:n}){return H.default.createElement(or.default,{variant:"caption",color:t,component:"div","data-testid":e,style:{display:"flex",flexWrap:"wrap",alignItems:"center",gap:6,fontSize:9,paddingLeft:8}},H.default.createElement("span",null,o,":"),n)}function ke({title:o,entries:e,testId:t="track-legend",color:n="textSecondary"}){return H.default.createElement(ir,{title:o,testId:t,color:n},e.map(({label:r,color:i},s)=>H.default.createElement("span",{key:`${s}-${r}`,style:{display:"inline-flex",alignItems:"center",gap:3}},H.default.createElement("span",{style:{...nr,background:i}}),r)))}function Me({title:o,minLabel:e,maxLabel:t,colors:n,testId:r="track-legend",color:i="textSecondary"}){return H.default.createElement(ir,{title:o,testId:r,color:i},e,H.default.createElement("span",{style:{...nr,width:60,background:`linear-gradient(to right, ${n.join(", ")})`}}),t)}function Te(o){return`#${o.toString(16).padStart(6,"0")}`}function Io(o){return o.replaceAll(/([a-z])([A-Z])(?=[a-z])/g,(e,t,n)=>`${t} ${n.toLowerCase()}`)}function sr({title:o,legend:e}){return e.kind==="table-legend"?H.default.createElement(ke,{title:o,testId:"structure-legend",entries:e.table.map(([t,n])=>({label:Io(t),color:Te(n)}))}):H.default.createElement(Me,{title:o,testId:"structure-legend",minLabel:e.minLabel,maxLabel:e.maxLabel,colors:e.colors.map(t=>Array.isArray(t)?`${Te(t[0])} ${100*t[1]}%`:Te(t))})}var b=l(w());var lr=l($(),1),ar=(0,C.createSvgIcon)((0,lr.jsx)("path",{d:"M10 6 8.59 7.41 13.17 12l-4.58 4.59L10 18l6-6z"}),"ChevronRight");var ur=l($(),1),dr=(0,C.createSvgIcon)((0,ur.jsx)("path",{d:"M16.59 8.59 12 13.17 7.41 8.59 6 10l6 6 6-6z"}),"ExpandMore");var cr=l($(),1),pr=(0,C.createSvgIcon)((0,cr.jsx)("path",{d:"M12 4.5C7 4.5 2.73 7.61 1 12c1.73 4.39 6 7.5 11 7.5s9.27-3.11 11-7.5c-1.73-4.39-6-7.5-11-7.5M12 17c-2.76 0-5-2.24-5-5s2.24-5 5-5 5 2.24 5 5-2.24 5-5 5m0-8c-1.66 0-3 1.34-3 3s1.34 3 3 3 3-1.34 3-3-1.34-3-3-3"}),"Visibility");var mr=l($(),1),fr=(0,C.createSvgIcon)((0,mr.jsx)("path",{d:"M12 7c2.76 0 5 2.24 5 5 0 .65-.13 1.26-.36 1.83l2.92 2.92c1.51-1.26 2.7-2.89 3.43-4.75-1.73-4.39-6-7.5-11-7.5-1.4 0-2.74.25-3.98.7l2.16 2.16C10.74 7.13 11.35 7 12 7M2 4.27l2.28 2.28.46.46C3.08 8.3 1.78 10.02 1 12c1.73 4.39 6 7.5 11 7.5 1.55 0 3.03-.3 4.38-.84l.42.42L19.73 22 21 20.73 3.27 3zM7.53 9.8l1.55 1.55c-.05.21-.08.43-.08.65 0 1.66 1.34 3 3 3 .22 0 .44-.03.65-.08l1.55 1.55c-.67.33-1.41.53-2.2.53-2.76 0-5-2.24-5-5 0-.79.2-1.53.53-2.2m4.31-.78 3.15 3.15.02-.16c0-1.66-1.34-3-3-3z"}),"VisibilityOff");var wr=l(hr()),de=l(we()),Pr=l(br()),j=l(Pe()),re=l(Ce()),ce=l(k());var ue=l(w()),Z=l(U()),vr=l(k());var Lo=(0,vr.observer)(function({model:e}){let{entities:t,mappedEntity:n,userProvidedTranscriptSequence:r}=e;return!t||t.length<2?null:ue.default.createElement(Z.Tooltip,{title:r?"Mapped chain: the one the transcript maps to":"Chain: the one hovers read",placement:"left"},ue.default.createElement(Z.TextField,{select:!0,size:"small",variant:"standard","data-testid":"protein-mapped-chain",value:e.pendingEntityId??n?.entityId??"",onChange:i=>{e.chooseEntity(i.target.value)},slotProps:{input:{disableUnderline:!0,sx:{fontSize:12}},htmlInput:{"aria-label":"Mapped chain"}},sx:{minWidth:60}},t.map(i=>ue.default.createElement(Z.MenuItem,{key:i.entityId,value:i.entityId,dense:!0},tt(i)))))}),Sr=Lo;function xr(o){return o.aligned===0?"no residues aligned":[`${Math.round(o.identity*100)}% identity`,o.aligned===o.transcriptLength?"whole transcript":`transcript ${o.transcriptStart}\u2013${o.transcriptEnd} (${o.aligned} of ${o.transcriptLength})`,o.aligned<o.structureLength?`${o.aligned} of ${o.structureLength} structure residues`:void 0].filter(Boolean).join(" \xB7 ")}var Eo=`Under ${Math.round(je*100)}% of the shorter sequence is identical (${Math.round(Qe*100)}% for an alignment of fewer than ${Ye} residues): an alignment this weak is what two unrelated proteins produce, so the positions it maps may be unrelated. Check the mapped chain, the transcript isoform, or import a curated alignment.`,Bo=(0,ce.observer)(function({structure:e}){let{uniprotId:t,uniprotName:n}=e.uniProtEntry;return t?b.default.createElement(j.default,{title:`The mapped chain is UniProt ${t}${n?` (${n})`:""}, which its feature tracks annotate`},b.default.createElement(Pr.default,{variant:"caption",href:nt(t),target:"_blank",rel:"noreferrer",noWrap:!0,sx:{minWidth:40}},"UniProt ",t)):null}),Ao=(0,ce.observer)(function({model:e,structure:t,readout:n}){let{label:r,alignmentQuality:i,statusMessage:s,hidden:a}=t,u=e.structures.length>1,y=e.showAlignment&&u,d=e.alignmentStructure===t,h=i?et(i):void 0;return b.default.createElement("div",{"data-testid":"structure-row","data-label":r,"data-open":y?d:void 0,"data-hidden":a||void 0,style:{opacity:a?.6:void 0,display:"flex",alignItems:"center",gap:8,minHeight:24,minWidth:0}},y?b.default.createElement(j.default,{title:d?"Alignment shown below":"Show alignment"},b.default.createElement("span",null,b.default.createElement(de.default,{size:"small","aria-label":`Show ${r} alignment`,"aria-expanded":d,disabled:d,onClick:()=>{e.openAlignmentOf(t)},sx:{p:0}},d?b.default.createElement(dr,{fontSize:"small"}):b.default.createElement(ar,{fontSize:"small"})))):null,b.default.createElement(re.default,{variant:"caption",sx:{fontWeight:"bold",flexShrink:0}},r),s?b.default.createElement(re.default,{variant:"caption",color:"error","data-testid":"structure-status"},s):null,n?b.default.createElement(re.default,{variant:"caption",noWrap:!0,title:n,"data-testid":"structure-hover"},n):i?b.default.createElement(j.default,{title:i.aligned===0?"":`${Re(i)}${h?`, ${h}`:""}; ${Ze(i)}`},b.default.createElement(re.default,{variant:"caption",color:"textSecondary",noWrap:!0,"data-testid":"header-alignment-quality"},xr(i))):null,b.default.createElement(Bo,{structure:t}),b.default.createElement("div",{style:{flex:1}}),d&&e.showAlignment||!t.userProvidedTranscriptSequence?b.default.createElement(Sr,{model:t}):null,i&&Xe(i)?b.default.createElement(j.default,{title:Eo},b.default.createElement(wr.default,{size:"small",color:"warning",variant:"outlined",label:"low similarity","data-testid":"header-low-similarity"})):null,u||a?b.default.createElement(j.default,{title:a?`Show ${r}`:`Hide ${r}`},b.default.createElement(de.default,{size:"small","aria-label":a?`Show ${r}`:`Hide ${r}`,"aria-pressed":a,onClick:()=>{t.setHidden(!a)},sx:{p:.25}},a?b.default.createElement(fr,{fontSize:"small"}):b.default.createElement(pr,{fontSize:"small"}))):null,b.default.createElement(j.default,{title:`Remove ${r}`},b.default.createElement(de.default,{size:"small","aria-label":`Remove ${r}`,onClick:()=>{e.removeStructure(t)},sx:{p:.25}},b.default.createElement(X,{fontSize:"small"}))))}),Fo=(0,ce.observer)(function({model:e}){let{structures:t}=e,n=t.some(r=>r.hoverPosition&&r.hoverPosition.source!=="structure");return b.default.createElement("div",{style:{flex:1,minWidth:0}},t.map((r,i)=>b.default.createElement(Ao,{key:i,model:e,structure:r,readout:r.hoverString||(n&&r.genomeToTranscriptSeqMapping?"not in structure":"")})))}),Cr=Fo;var g=l(w()),ro=l(U()),oo=l(mt()),no=l(k());var io=l(xo());var Ie=l(w()),Tr=l(k());function Do(o,e,t){let n=[];if(!o)return n;for(let r=0;r<e;r++){let i=o[r];if(i===void 0)continue;let s=t(i);s%10===0?n.push({col:r,label:`${s}`}):s%5===0&&n.push({col:r})}return n}var Ho=(0,Tr.observer)(function({model:e,columns:t}){let{columnWidth:n}=e,r=Do(e.pairwiseAlignmentToStructurePosition,t,i=>e.residueNumber(i));return Ie.default.createElement("div",{style:{position:"relative",height:"100%",color:"#888",fontSize:8}},r.map(({col:i,label:s})=>Ie.default.createElement("span",{key:i,style:{position:"absolute",left:i*n,top:0,bottom:0,borderLeft:"1px solid #aaa",paddingLeft:2,lineHeight:`${12}px`,whiteSpace:"nowrap"}},s)))}),kr=Ho;var F=l(w()),Le=l(k());function oe({start:o,end:e,columnWidth:t,background:n,border:r}){return F.default.createElement("div",{style:{position:"absolute",top:0,bottom:0,left:o*t,width:(e-o+1)*t,background:n,border:r,boxSizing:"border-box",pointerEvents:"none"}})}function Mr({zIndex:o,children:e}){return F.default.createElement("div",{style:{position:"absolute",inset:0,pointerEvents:"none",zIndex:o}},e)}var Ir=(0,Le.observer)(function({model:e,matchHeight:t}){let{clickAlignmentRanges:n,columnWidth:r,showHighlight:i,alignmentMatchSet:s}=e;return F.default.createElement(Mr,{zIndex:0},i&&s?F.default.createElement("div",{style:{position:"relative",height:t}},kt(s).map(a=>F.default.createElement(oe,{key:a.start,start:a.start,end:a.end-1,columnWidth:r,background:bt}))):null,n.map(a=>F.default.createElement(oe,{key:a.start,start:a.start,end:a.end,columnWidth:r,background:ht})))}),$o=(0,Le.observer)(function({model:e}){let{clickAlignmentRanges:t,alignmentHoverRange:n,alignmentHoverPos:r,columnWidth:i}=e;return F.default.createElement(Mr,{zIndex:1},t.map(s=>F.default.createElement(oe,{key:s.start,start:s.start,end:s.end,columnWidth:i,background:"transparent",border:yt})),n?F.default.createElement(oe,{start:n.start,end:n.end,columnWidth:i,background:gt}):null,r===void 0?null:F.default.createElement(oe,{start:r,end:r,columnWidth:i,background:ft}))}),Lr=$o;var J=l(w());var Er=l($(),1),Br=(0,C.createSvgIcon)((0,Er.jsx)("path",{d:"M7.41 18.59 8.83 20 12 16.83 15.17 20l1.41-1.41L12 14zm9.18-13.18L15.17 4 12 7.17 8.83 4 7.41 5.41 12 10z"}),"UnfoldLess");var Ar=l($(),1),Fr=(0,C.createSvgIcon)((0,Ar.jsx)("path",{d:"M12 5.83 15.17 9l1.41-1.41L12 3 7.41 7.59 8.83 9zm0 12.34L8.83 15l-1.41 1.41L12 21l4.59-4.59L15.17 15z"}),"UnfoldMore");var ne=l(U()),Dr=l(k());var Uo=(0,Dr.observer)(function({type:e,laneCount:t,model:n}){let r=n.expandedFeatureTypes.has(e),i=n.trackHeight;return J.default.createElement(ne.Tooltip,{title:e,placement:"left"},J.default.createElement("div",{style:{height:"100%",whiteSpace:"nowrap",display:"flex",alignItems:r?"flex-start":"center",justifyContent:"flex-end",gap:2}},J.default.createElement(ne.IconButton,{onClick:()=>{n.hideFeatureType(e)},title:`Hide ${e} track`,sx:{p:0,color:xe}},J.default.createElement(X,{sx:{fontSize:i}})),t>1?J.default.createElement(ne.IconButton,{onClick:()=>{n.toggleFeatureTypeExpanded(e)},title:r?`Collapse ${e} track`:`Expand ${e} track (${t} overlapping rows)`,sx:{p:0,color:xe}},r?J.default.createElement(Br,{sx:{fontSize:i}}):J.default.createElement(Fr,{sx:{fontSize:i}})):null,J.default.createElement("span",null,e)))}),Hr=Uo;var Ur=l(w()),Jr=l(k());function Jo(o,e,t){if(!(!o||!e||o==="-"||e==="-"||o.toUpperCase()===e.toUpperCase()))return t===":"||t==="."?"similar":"different"}function $r(o){let e=o.alns[0]?.seq??"",t=o.alns[1]?.seq??"",n=[];for(let r=0;r<e.length;r++){let i=Jo(e[r],t[r],o.consensus[r]),s=n.at(-1);i&&s?.kind===i&&s.end===r?s.end=r+1:i&&n.push({start:r,end:r+1,kind:i})}return n}var Vo=(0,Jr.observer)(function({model:e}){let{alignment:t,columnWidth:n}=e;return t?$r(t).map(r=>Ur.default.createElement("div",{key:r.start,style:{position:"absolute",top:0,bottom:0,left:r.start*n,width:(r.end-r.start)*n,background:r.kind==="similar"?vt:St}})):null}),Vr=Vo;var Nr=l(w()),_r=l(k());var L=l(w()),Wr=l(U()),zr=l(k());var Oo={Domain:"#1f77b4","DNA binding":"#ff7f0e",Region:"#2ca02c","Zinc finger":"#d62728","Coiled coil":"#9467bd",Motif:"#8c564b","Compositional bias":"#e377c2",Repeat:"#7f7f7f",Transmembrane:"#bcbd22",Intramembrane:"#17becf","Topological domain":"#aec7e8",Signal:"#ffbb78","Signal peptide":"#ffbb78",Propeptide:"#98df8a","Transit peptide":"#ff9896",Chain:"#c5b0d5","Disulfide bond":"#c49c94","Active site":"#f7b6d2","Binding site":"#c7c7c7",Site:"#dbdb8d","Modified residue":"#9edae5",Glycosylation:"#393b79",Lipidation:"#637939","Cross-link":"#8c6d31","Alternative sequence":"#e7969c","Natural variant":"#de9ed6",Mutagenesis:"#ad494a","Sequence conflict":"#b5cf6b",Helix:"#e7ba52","Beta strand":"#6b6ecf",Turn:"#d6616b","Initiator methionine":"#ce6dbd",Peptide:"#6baed6","Calcium binding":"#fd8d3c","Nucleotide binding":"#74c476"};function Or(o){return Oo[o]??"#999999"}async function Wo(o){let e=await(await rt(o)).text(),t=[];for(let n of e.split(`
 `)){if(n.startsWith("#")||!n.trim())continue;let r=n.split("	");if(r.length<9)continue;let i=r[2],s=Number.parseInt(r[3]??"",10),a=Number.parseInt(r[4]??"",10),u=r[8]??"",y="",d;for(let h of u.split(";")){let[v,S]=h.split("=");v==="Note"?y=decodeURIComponent(S??""):v==="ID"&&(d=S)}if(i&&s>=1&&a>=s){let h=`${i}-${s}-${a}-${t.length}`;t.push({type:i,start:s,end:a,description:y,id:d,uniqueId:h})}}return t}function Ee(o){let{data:e,error:t,isLoading:n}=at(o?ot(o):null,Wo,ut);return{features:e,error:t,isLoading:n}}function zo({feature:o,layout:e,model:t}){let n=t.residueNumber(e.structureStart),r=t.residueNumber(e.structureEnd-1),i=n!==o.start||r!==o.end;return L.default.createElement("div",null,L.default.createElement("div",null,L.default.createElement("strong",null,o.type)),L.default.createElement("div",null,"UniProt position: ",o.start,"-",o.end),i?L.default.createElement("div",null,"Structure residue: ",n,"-",r):null,o.description?L.default.createElement("div",null,o.description):null)}var qo=(0,zr.observer)(function({layout:e,top:t,selected:n,model:r}){let[i,s]=(0,L.useState)(!1),{feature:a,alignmentStart:u,alignmentEnd:y}=e,{columnWidth:d,trackHeight:h}=r;return L.default.createElement(Wr.Tooltip,{title:L.default.createElement(zo,{feature:a,layout:e,model:r}),followCursor:!0},L.default.createElement("div",{"data-testid":`protein-feature-${a.type}`,"data-feature-id":a.uniqueId,"data-feature-start":a.start,"data-feature-end":a.end,onClick:()=>{n?(r.setSelectedFeatureId(void 0),r.setClickedStructureRanges([])):(r.setSelectedFeatureId(a.uniqueId),Tt({model:r,structureSeqPos:e.structureStart,structureSeqEndPos:e.structureEnd}).catch(v=>{console.error(v),r.setViewError(v)}))},onMouseEnter:()=>{s(!0),r.setAlignmentHoverRange({start:u,end:y})},onMouseLeave:()=>{s(!1),r.setAlignmentHoverRange(void 0)},style:{position:"absolute",left:u*d,top:t,width:(y-u+1)*d,height:h,backgroundColor:Or(a.type),opacity:i||n?.9:.6,cursor:"pointer",borderRadius:2,border:n?xt:i?wt:"none",boxSizing:"border-box"}}))}),qr=qo;function Kr(o,e){return(o.expandedFeatureTypes.has(e.type)?e.laneCount:1)*(o.trackHeight+o.trackGap)}var No=(0,_r.observer)(function({group:e,model:t}){let{selectedFeatureId:n,trackHeight:r,trackGap:i}=t,s=t.expandedFeatureTypes.has(e.type);return e.layouts.map(a=>Nr.default.createElement(qr,{key:a.feature.uniqueId,layout:a,top:(s?a.lane:0)*(r+i),selected:n===a.feature.uniqueId,model:t}))}),Gr=No;var N=l(w()),jr=l(U()),Be=l(k()),_o=(0,Be.observer)(function({cells:e,colorFor:t,model:n}){let{columnWidth:r,trackHeight:i}=n;return N.default.createElement("div",{style:{position:"relative",height:i}},e.map(s=>N.default.createElement("div",{key:s.col,style:{position:"absolute",left:s.col*r,width:r,height:i,backgroundColor:t(s.value)}})))}),Ko=(0,Be.observer)(function({cells:e,colorFor:t,formatValue:n,model:r}){let i=(0,N.useMemo)(()=>new Map(e.map(u=>[u.col,u.value])),[e]),{alignmentHoverPos:s}=r,a=s===void 0?void 0:i.get(s);return N.default.createElement(jr.Tooltip,{title:a===void 0?"":n(a),followCursor:!0},N.default.createElement("div",null,N.default.createElement(_o,{cells:e,colorFor:t,model:r})))}),Ae=Ko;var Yr=l(w()),Qr=l(k()),Go=(0,Qr.observer)(function({model:e,str:t}){let{columnWidth:n}=e;return t.split("").map((r,i)=>Yr.default.createElement("span",{key:i,style:{position:"absolute",left:i*n,width:n}},r===" "?"\xA0":r))}),Xr=Go;var Zr=l(mt());function jo({x:o,width:e,scrollLeft:t,clientWidth:n}){return o>=t&&o+e<=t+n?void 0:o+e/2-n/2}function Rr({start:o,end:e,scrollLeft:t,clientWidth:n}){let r=t+n;return e>=t&&o<=r?void 0:(o+e)/2-n/2}function eo(o,e){return(0,Zr.reaction)(()=>o.alignmentHoverPos,t=>{let n=e();if(t!==void 0&&n&&o.autoScrollAlignment&&!o.isMouseInAlignment){let r=jo({x:t*o.columnWidth,width:o.columnWidth,scrollLeft:n.scrollLeft,clientWidth:n.clientWidth});r!==void 0&&(n.scrollLeft=r)}})}var to=l(w());function Yo(o,e,t){let n=t(o.start),r=t(o.end);if(n===void 0||r===void 0)return;let i=e[n],s=e[r];return i===void 0||s===void 0?void 0:{feature:o,structureStart:n,structureEnd:r+1,alignmentStart:i,alignmentEnd:s,lane:0}}function Qo(o){let e=[],t=[...o].sort((n,r)=>n.alignmentStart-r.alignmentStart);for(let n of t){let r=e.findIndex(i=>i<n.alignmentStart);r===-1?(n.lane=e.length,e.push(n.alignmentEnd)):(n.lane=r,e[r]=n.alignmentEnd)}return Math.max(e.length,1)}function Fe(o,e,t){let{features:n,isLoading:r,error:i}=Ee(e),{omittedFeatureTypes:s,structurePositionToAlignmentMap:a}=o;return{groups:(0,to.useMemo)(()=>{if(!n||!a)return;let y=new Map;for(let d of n)if(!s.has(d.type)){let h=Yo(d,a,t);if(h){let v=y.get(d.type);v?v.push(h):y.set(d.type,[h])}}return[...y].map(([d,h])=>({type:d,layouts:h,laneCount:Qo(h)}))},[n,s,a,t]),isLoading:r,error:i}}var Zo=(0,io.makeStyles)()(o=>({scroll:{overflow:"auto",whiteSpace:"nowrap",flex:1,paddingBottom:2,backgroundColor:o.palette.background.paper},trackMessage:{position:"sticky",left:0,lineHeight:`${12}px`,color:o.palette.text.secondary},trackError:{color:o.palette.error.main}}));function ie({label:o,title:e}){return g.default.createElement(ro.Tooltip,{title:e,placement:"left"},g.default.createElement("div",{style:{height:"100%",display:"flex",alignItems:"center",justifyContent:"flex-end"}},o))}var Ro=(0,no.observer)(function({model:e}){let{alignment:t,showProteinTracks:n,showAllFeatureTracks:r,label:i,confidenceCells:s,columnWidth:a,trackHeight:u,trackGap:y}=e,d=r?e.hydrophobicityCells:[],{classes:h,cx:v}=Zo(),S=(0,g.useRef)(null),O=(0,g.useRef)(void 0),{uniprotId:Y,mapUniProtPosition:ee,isLoading:te,error:W}=e.uniProtEntry,{groups:z,isLoading:K,error:E}=Fe(e,Y,ee),x=te||K,D=W??E,le=D?`${W?`Could not map ${i} to a UniProt entry through SIFTS`:`Could not load UniProt features for ${Y??i}`}: ${Ne(D)}`:void 0;if((0,g.useEffect)(()=>eo(e,()=>S.current),[e]),(0,g.useEffect)(()=>(0,oo.autorun)(()=>{let m=S.current,B=e.clickAlignmentRanges,I=B[0];if(m)if(I){let ae=B.map(G=>`${G.start}-${G.end}`).join(",");if(ae!==O.current){O.current=ae;let G=Rr({start:I.start*e.columnWidth,end:(I.end+1)*e.columnWidth,scrollLeft:m.scrollLeft,clientWidth:m.clientWidth});G!==void 0&&(m.scrollLeft=G)}}else O.current=void 0}),[e]),!t)return null;let fe=Ge(t),Oe=u+y,We=(m,B,I,ae,G)=>({key:m,height:12,label:g.default.createElement(ie,{label:B,title:I}),content:g.default.createElement("div",{style:{lineHeight:`${12}px`}},G,g.default.createElement(Xr,{model:e,str:ae})),selectsResidue:!0}),ge=le??(x?"Loading UniProt features...":""),ze=[We("transcript","GENOME","The protein as the reference genome's transcript translates",_e(t)),We("structure","STRUCT","The protein as the structure file spells it. Shaded where it differs from the transcript's: amber for a similar amino acid, red for a different one.",Ke(t),g.default.createElement(Vr,{model:e}))],Q=[...ze,{key:"ruler",height:12,label:g.default.createElement(ie,{label:"residue",title:"Residue numbers as the structure's authors assigned them, the numbering papers and the 3D view's hover label use"}),content:g.default.createElement(kr,{model:e,columns:fe}),selectsResidue:!0}],vo=ze.length*12;if(n){ge&&Q.push({key:"uniprot-status",height:12,label:g.default.createElement(ie,{label:"UniProt",title:ge}),content:g.default.createElement("span",{className:v(h.trackMessage,le&&h.trackError)},ge)});for(let m of z??[])Q.push({key:`feature-${m.type}`,height:Kr(e,m),label:g.default.createElement(Hr,{type:m.type,laneCount:m.laneCount,model:e}),content:g.default.createElement(Gr,{group:m,model:e})});s.length>0&&Q.push({key:"plddt",height:Oe,label:g.default.createElement(ie,{label:"pLDDT",title:g.default.createElement(ke,{title:"AlphaFold per-residue confidence (pLDDT)",entries:it,color:"inherit"})}),content:g.default.createElement(Ae,{cells:s,colorFor:st,formatValue:m=>`pLDDT ${m.toFixed(0)}`,model:e})}),d.length>0&&Q.push({key:"hydrophobicity",height:Oe,label:g.default.createElement(ie,{label:"hydro",title:g.default.createElement(Me,{title:"Kyte-Doolittle hydrophobicity",testId:"hydrophobicity-legend",minLabel:"hydrophilic",maxLabel:"hydrophobic",colors:lt.map(m=>be(m)),color:"inherit"})}),content:g.default.createElement(Ae,{cells:d,colorFor:be,formatValue:m=>`Kyte-Doolittle ${m.toFixed(1)}`,model:e})})}let qe=m=>{let{left:B}=m.currentTarget.getBoundingClientRect(),I=Math.floor((m.clientX-B)/a);return I>=0&&I<fe?I:void 0};return g.default.createElement("div",{"data-testid":"protein-alignment-panel","data-structure":i},g.default.createElement("div",{style:{display:"flex",fontSize:9,fontFamily:"monospace",margin:"2px 8px 4px"},onMouseEnter:()=>{e.setIsMouseInAlignment(!0)},onMouseLeave:()=>{e.leaveAlignment()}},g.default.createElement("div",{style:{flexShrink:0,minWidth:124,paddingRight:4,whiteSpace:"nowrap",lineHeight:1}},Q.map(m=>g.default.createElement("div",{key:m.key,"data-row-label":m.key,style:{height:m.height,overflow:"hidden"}},m.label))),g.default.createElement("div",{ref:S,className:h.scroll},g.default.createElement("div",{"data-testid":"alignment-rows",style:{position:"relative",width:fe*a},onMouseMove:m=>{let B=qe(m);B===void 0?e.setHoveredPosition(void 0):e.hoverAlignmentPosition(B)},onMouseLeave:()=>{e.setHoveredPosition(void 0)}},g.default.createElement(Ir,{model:e,matchHeight:vo}),Q.map(m=>g.default.createElement("div",{key:m.key,"data-row":m.key,style:{position:"relative",height:m.height,cursor:m.selectsResidue?"pointer":void 0},onClick:m.selectsResidue?B=>{let I=qe(B);I!==void 0&&e.clickAlignmentPosition(I)}:void 0},m.content)),g.default.createElement(Lr,{model:e})))))}),so=Ro;var R=l(w()),lo=l(So());var pe=l(U()),en=(0,R.lazy)(()=>import("./ProteinAlignmentHelpDialog-6VFZFN6X.js"));function De({model:o}){return R.default.createElement(pe.Tooltip,{title:"What the alignment panel shows"},R.default.createElement(pe.IconButton,{size:"small",onClick:()=>{(0,lo.getSession)(o).queueDialog(e=>[en,{handleClose:e}])}},R.default.createElement(dt,{fontSize:"small"})))}var tn=(0,me.observer)(function({model:e}){let[t,n]=(0,f.useState)(null),i=`Color scheme: ${Se.find(s=>s.value===e.colorScheme)?.label??e.colorScheme}`;return f.default.createElement(f.default.Fragment,null,f.default.createElement(Je.default,{title:i},f.default.createElement(He.default,{size:"small","aria-label":i,onClick:s=>{n(s.currentTarget)}},f.default.createElement($t,{fontSize:"small"}))),f.default.createElement($e.default,{anchorEl:t,open:!!t,onClose:()=>{n(null)}},Se.map(s=>f.default.createElement(Ue.default,{key:s.value,dense:!0,selected:s.value===e.colorScheme,onClick:()=>{e.setColorScheme(s.value),n(null)}},s.label))))});function ao({checked:o,label:e,onToggle:t}){return f.default.createElement(Ue.default,{onClick:()=>{t()},dense:!0},f.default.createElement(mo.default,null,f.default.createElement(co.default,{checked:o,size:"small",edge:"start",disableRipple:!0})),f.default.createElement(fo.default,null,e))}var rn=(0,me.observer)(function({model:e}){let[t,n]=(0,f.useState)(null);return f.default.createElement(f.default.Fragment,null,f.default.createElement(Je.default,{title:"Display settings"},f.default.createElement(He.default,{size:"small",onClick:r=>{n(r.currentTarget)}},f.default.createElement(Jt,{fontSize:"small"}))),f.default.createElement($e.default,{anchorEl:t,open:!!t,onClose:()=>{n(null)}},e.displayToggles.map(r=>f.default.createElement(ao,{key:r.label,checked:r.checked,label:r.label,onToggle:r.toggle})),f.default.createElement(po.default,null),e.behaviorToggles.map(r=>f.default.createElement(ao,{key:r.label,checked:r.checked,label:r.label,onToggle:r.toggle}))))}),on=(0,me.observer)(function({model:e}){let{alignmentStructure:t,showAlignment:n,colorLegend:r}=e;return f.default.createElement("div",null,f.default.createElement("div",{style:{display:"flex",alignItems:"flex-start",gap:8}},f.default.createElement(Cr,{model:e}),f.default.createElement("div",{style:{display:"flex",gap:4,alignItems:"center",flexShrink:0,minHeight:24}},f.default.createElement(tn,{model:e}),f.default.createElement(rn,{model:e}),f.default.createElement(De,{model:e}))),r?f.default.createElement(sr,{title:"Structure colors",legend:r}):null,n&&t?.pairwiseAlignment?f.default.createElement(so,{model:t}):n&&t?.alignmentPending?f.default.createElement(uo.LoadingEllipses,{message:"Loading pairwise alignment"}):null,f.default.createElement(tr,{model:e}))}),go=on;var V=l(w()),yo=l(wo());var ho=!1;function nn(o){if(!ho){ho=!0;let e=document.createElement("style");e.append(o),document.head.append(e)}}function Ve({showControls:o,model:e}){let t=(0,V.useRef)(null),n=(0,V.useRef)(null),[r,i]=(0,V.useState)(),[s,a]=(0,V.useState)(!0);return(0,V.useEffect)(()=>{let u={cancelled:!1};return(async()=>{try{if(!t.current)return;let{Color:y,GeometryExport:d,MAQualityAssessment:h,PluginConfig:v,PluginSpec:S,DefaultPluginUISpec:O,createPluginUI:Y,registerColorThemes:ee,renderReact18:te,css:W}=await ve();nn(W);let z=document.createElement("div");t.current.append(z),u.host=z;let K=O(),E=await Y({target:z,render:te,spec:{...K,behaviors:[...K.behaviors,S.Behavior(d),S.Behavior(h)],layout:{initial:{controlsDisplay:"reactive",showControls:o}},config:[[v.Viewport.ShowExpand,!1]]}});await E.initialized,ee(E),E.canvas3d?.setProps({renderer:{selectColor:y(16711935),selectStrength:1},marking:{selectEdgeColor:y(16711935)}}),u.cancelled?(E.dispose(),z.remove()):(u.plugin=E,n.current=E,e?.setMolstarPluginContext(E))}catch(y){console.error(y),i(y)}finally{a(!1)}})(),()=>{u.cancelled=!0,n.current=null,e&&(0,yo.isAlive)(e)&&e.setMolstarPluginContext(void 0),u.plugin?.dispose(),u.host?.remove()}},[]),(0,V.useEffect)(()=>{let u={cancelled:!1};return(async()=>{let y=n.current;if(y){let{PluginCommands:d}=await ve();u.cancelled||await d.Layout.Update(y,{state:{showControls:o}})}})(),()=>{u.cancelled=!0}},[o]),{parentRef:t,error:r,loading:s}}var sn=(0,se.observer)(function({model:e}){let{showControls:t}=e,{parentRef:n,error:r,loading:i}=Ve({showControls:t,model:e});return r?P.default.createElement(_.ErrorMessage,{error:r}):P.default.createElement(un,{model:e,parentRef:n,loading:i})}),ln=(0,se.observer)(function({model:e}){let{error:t}=e;return t?P.default.createElement("div",{style:{display:"flex",alignItems:"flex-start"}},P.default.createElement("div",{style:{flex:1}},P.default.createElement(_.ErrorMessage,{error:t})),P.default.createElement(bo.IconButton,{size:"small","aria-label":"Dismiss error",onClick:()=>{e.setError(void 0)}},P.default.createElement(X,{fontSize:"small"}))):null}),an=(0,se.observer)(function({model:e}){let{loadingMessages:t}=e;return t.length>0?P.default.createElement("div",{"data-testid":"protein-view-loading-overlay",style:{position:"absolute",top:8,left:8,maxWidth:"calc(100% - 16px)",padding:"2px 8px",borderRadius:4,background:"rgba(255,255,255,0.85)",color:"#000",pointerEvents:"none"}},t.map(({id:n,message:r})=>P.default.createElement(_.LoadingEllipses,{key:n,message:r}))):null}),un=(0,se.observer)(function({model:e,parentRef:t,loading:n}){let{width:r,height:i}=e,s=!n&&!e.showLoading;return P.default.createElement("div",{style:{background:"#ccc"},"data-testid":s?"protein-view-ready":"protein-view-loading"},P.default.createElement(ln,{model:e}),n?P.default.createElement(_.LoadingEllipses,{message:"Loading protein viewer"}):P.default.createElement(go,{model:e}),P.default.createElement("div",{style:{position:"relative",width:r,height:i}},P.default.createElement("div",{ref:t,"data-testid":"protein-view-molstar",style:{position:"relative",width:r,height:i}}),P.default.createElement(an,{model:e})),P.default.createElement(_.ResizeHandle,{style:{height:4,background:"grey"},onDrag:a=>e.setHeight(e.height+a)}),P.default.createElement(Dt,{model:e}))}),hs=sn;export{hs as default};
-//# sourceMappingURL=ProteinView-B57QOH3K.js.map
+//# sourceMappingURL=ProteinView-MG7N24DJ.js.map

package/dist/chunks/{chunk-UTUOAPWU.js → chunk-252AFZJZ.js}

@@ -13,4 +13,4 @@ use-sync-external-store/cjs/use-sync-external-store-shim.production.js:
    * LICENSE file in the root directory of this source tree.
    *)
 */
-//# sourceMappingURL=chunk-UTUOAPWU.js.map
+//# sourceMappingURL=chunk-252AFZJZ.js.map