jbrowse-plugin-protein3d 0.8.3 → 0.8.4
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.
- package/dist/LaunchProteinView/utils/sideBySide.js +26 -9
- package/dist/jbrowse-plugin-protein3d.umd.production.min.js +3 -3
- package/dist/jbrowse-plugin-protein3d.umd.production.min.js.map +3 -3
- package/dist/{molstar-chunk-UJIWPKE3.js → molstar-chunk-JDIZPSL3.js} +1 -1
- package/dist/{molstar-chunk-UJIWPKE3.js.map → molstar-chunk-JDIZPSL3.js.map} +1 -1
- package/dist/version.d.ts +1 -1
- package/dist/version.js +1 -1
- package/package.json +3 -2
- package/src/LaunchProteinView/utils/sideBySide.test.ts +6 -0
- package/src/LaunchProteinView/utils/sideBySide.ts +26 -9
- package/src/version.ts +1 -1
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@@ -23,19 +23,36 @@ function isSessionWithWorkspaces(session) {
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// Missing BOTH is an embedded session: it has no workspaces, there is nothing
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// to ask for, and silence is the right answer.
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//
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// Missing ONE is a host that has workspaces but
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//
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//
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//
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//
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//
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//
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// Missing ONE is a host that has workspaces but places views some other way —
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// and silence there is how this broke before. jbrowse-web folded
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// `setPendingMove` into its layout `init`, this guard went false, and the
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// plugin simply stopped asking for the split: no error, no missing feature,
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// just two views quietly stacking. Nobody noticed for weeks. Feature
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// detection cannot ask the host to announce a change, but it can tell "not
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// supported here" from "supported, and gone".
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//
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// Two very different hosts produce this one shape, and nothing on the session
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// tells them apart, so the message carries both rather than the guess:
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//
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// - Releases through v4.3.0, where placement is `setPendingMoveToSplitRight`,
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// a module function in @jbrowse/app-core's DockviewContext, not a session
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// action. Nothing is wrong and nothing needs fixing; this plugin targets v5+
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// and does not reach for v4's door. Measured 2026-08-17: v4.3.0 and latest
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// stack, main splits.
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// - A newer host that moved the action out from under us, which is the
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// regression this warning exists to catch.
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//
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// Do not quiet the first case by sniffing the version. The alarm is only worth
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// having if it fires on a shape it cannot explain, and these two shapes are
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// identical.
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if (canEnable !== canPlace && !warnedPartial) {
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warnedPartial = true;
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console.warn(`jbrowse-plugin-protein3d: this session supports workspaces but not ` +
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`${canPlace ? 'setUseWorkspaces' : 'setPendingMove'}, so the ` +
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`side-by-side launch was skipped and the views will stack.
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`
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`side-by-side launch was skipped and the views will stack. Expected on ` +
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`releases through v4.3.0, which place views through @jbrowse/app-core ` +
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`instead; on a newer host it means the session API moved and the plugin ` +
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`needs updating to match.`);
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}
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return canEnable && canPlace;
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}
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@@ -2,7 +2,7 @@
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The first sequence should be the transcript and the second should be the structure."),Ue.default.createElement(Ae.TextField,{multiline:!0,rows:12,fullWidth:!0,placeholder:`Example:
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transcript MKAAYLSMFGKEDHKPFGDDEVELFRAVPGLKLKIAG
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|||||||||||||||||||||||||||||||||||||
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structure MKAAYLSMFGKEDHKPFGDDEVELFRAVPGLKLKIAG`,value:n,onChange:u=>{o(u.target.value),i(void 0)},slotProps:{htmlInput:{style:{fontFamily:"monospace",fontSize:12}}}}),r?Ue.default.createElement(Ae.Typography,{color:"error",variant:"body2",sx:{mt:1}},r):null),Ue.default.createElement(Ae.DialogActions,null,Ue.default.createElement(Ae.Button,{onClick:()=>{a()}},"Cancel"),Ue.default.createElement(Ae.Button,{onClick:()=>{c()},variant:"contained",color:"primary",disabled:!n.trim()},"Apply alignment"))):null}),oc=Rf});var ic,sc,ac=T(()=>{"use client";nt();ic=p(ot(),1),sc=(0,se.createSvgIcon)((0,ic.jsx)("path",{d:"M3 17v2h6v-2zM3 5v2h10V5zm10 16v-2h8v-2h-8v-2h-2v6zM7 9v2H3v2h4v2h2V9zm14 4v-2H11v2zm-6-4h2V7h4V5h-4V3h-2z"}),"Tune")});var pc=z((u1,lc)=>{lc.exports=JBrowseExports["@mui/material/Checkbox"]});var cc=z((c1,uc)=>{uc.exports=JBrowseExports["@mui/material/IconButton"]});var dc=z((m1,mc)=>{mc.exports=JBrowseExports["@mui/material/ListItemIcon"]});var fc=z((d1,gc)=>{gc.exports=JBrowseExports["@mui/material/ListItemText"]});var bc=z((g1,hc)=>{hc.exports=JBrowseExports["@mui/material/Menu"]});var Sc=z((f1,yc)=>{yc.exports=JBrowseExports["@mui/material/MenuItem"]});var xc=z((h1,wc)=>{wc.exports=JBrowseExports["@mui/material/TextField"]});var Tc=z((b1,vc)=>{vc.exports=JBrowseExports["@mui/material/Tooltip"]});var H,Ac,B,Pc,Of,Cc,kc=T(()=>{"use strict";H=p(S()),Ac=p(_e()),B=p(V()),Pc=p($()),Of=(0,Pc.observer)(function({model:t}){let[n,o]=(0,H.useState)(),[r,i]=(0,H.useState)(""),[s,l]=(0,H.useState)(""),[a,c]=(0,H.useState)("pdb"),[u,m]=(0,H.useState)(""),[d,g]=(0,H.useState)(),{showAddStructureDialog:h}=t,b=()=>{o(void 0),i(""),l(""),m(""),g(void 0),t.setShowAddStructureDialog(!1)},x=async()=>{try{let y=a==="pdb"&&r?{pdbId:r}:a==="uniprot"&&s?{uniprotId:s}:a==="url"&&u?{url:u}:a==="file"&&n?{data:await n.text()}:void 0;y&&(t.addStructure(y),b())}catch(y){console.error(y),g(y)}};if(!h)return null;let w=a==="url"&&u!==""||a==="file"&&n!==void 0||a==="pdb"&&r!==""||a==="uniprot"&&s!=="";return H.default.createElement(B.Dialog,{open:!0,onClose:b,maxWidth:"sm",fullWidth:!0},H.default.createElement(B.DialogTitle,null,"Add structure"),H.default.createElement(B.DialogContent,null,d?H.default.createElement(Ac.ErrorMessage,{error:d}):null,H.default.createElement(B.Typography,{variant:"body2",color:"text.secondary",sx:{mb:2}},"Add another structure to superpose on the existing structure(s)."),H.default.createElement(B.FormControl,{component:"fieldset",sx:{mb:2}},H.default.createElement(B.RadioGroup,{value:a,onChange:y=>{c(y.target.value)}},H.default.createElement(B.FormControlLabel,{value:"pdb",control:H.default.createElement(B.Radio,null),label:"PDB ID"}),H.default.createElement(B.FormControlLabel,{value:"uniprot",control:H.default.createElement(B.Radio,null),label:"UniProt ID (AlphaFold)"}),H.default.createElement(B.FormControlLabel,{value:"url",control:H.default.createElement(B.Radio,null),label:"URL"}),H.default.createElement(B.FormControlLabel,{value:"file",control:H.default.createElement(B.Radio,null),label:"File"}))),a==="pdb"?H.default.createElement(B.TextField,{fullWidth:!0,value:r,onChange:y=>{i(y.target.value.toUpperCase())},label:"PDB ID (e.g. 1CRN)",placeholder:"Enter PDB ID",sx:{mb:2}}):null,a==="uniprot"?H.default.createElement(B.TextField,{fullWidth:!0,value:s,onChange:y=>{l(y.target.value.toUpperCase())},label:"UniProt ID (e.g. P04637)",placeholder:"Enter UniProt ID",helperText:"Will fetch the AlphaFold v6 predicted structure",sx:{mb:2}}):null,a==="url"?H.default.createElement(B.TextField,{fullWidth:!0,label:"Structure URL",value:u,onChange:y=>{m(y.target.value)},placeholder:"https://files.rcsb.org/download/1CRN.cif",sx:{mb:2}}):null,a==="file"?H.default.createElement("div",{style:{marginBottom:16}},H.default.createElement(B.Button,{variant:"outlined",component:"label"},n?n.name:"Choose file",H.default.createElement("input",{type:"file",hidden:!0,accept:".pdb,.cif,.mmcif,.ent",onChange:({target:y})=>{let f=y.files?.[0];f&&o(f)}})),n?H.default.createElement(B.Typography,{variant:"body2",sx:{mt:1}},"Selected: ",n.name):null):null,H.default.createElement(B.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).")),H.default.createElement(B.DialogActions,null,H.default.createElement(B.Button,{onClick:()=>{b()}},"Cancel"),H.default.createElement(B.Button,{onClick:()=>{x()},variant:"contained",color:"primary",disabled:!w},"Add structure")))}),Cc=Of});var Mc,Ic,zf,Lc,Ec=T(()=>{"use strict";Mc=p(S()),Ic=p($()),zf=(0,Ic.observer)(function({model:t}){let{structures:n}=t,o=n.map(r=>r.hoverString).filter(Boolean).join(" ");return Mc.default.createElement("div",{style:{flex:1,minWidth:0,whiteSpace:"nowrap",overflow:"hidden",textOverflow:"ellipsis",fontSize:12},title:o},o?`Hover: ${o}`:"\xA0")}),Lc=zf});var Fc,qc,jf,Dc,Nc=T(()=>{"use strict";Fc=p(S()),qc=p($());st();jf=(0,qc.observer)(function({model:t}){let{alignmentHoverPos:n}=t;return n===void 0?null:Fc.default.createElement("div",{style:{position:"absolute",left:n*6,top:0,bottom:0,width:6,backgroundColor:Bu,pointerEvents:"none",zIndex:10}})}),Dc=jf});var Hc={};Qt(Hc,{default:()=>Gc});function ps({children:e}){return Pt.default.createElement(Ot.Typography,{style:{margin:4,marginBottom:12}},e)}function Gc({handleClose:e}){return Pt.default.createElement(Vc.Dialog,{open:!0,maxWidth:"lg",onClose:e,title:"Protein alignment"},Pt.default.createElement(Ot.DialogContent,null,Pt.default.createElement(ps,null,"This panel shows the computed pairwise alignment of the reference genome sequence to the structure sequence. The structure file (PDB file, mmCIF file, etc) has a stored representation of the e.g. amino acid sequence but the sequence in the structure file can differ from the sequence from the gene on the genome browser"),Pt.default.createElement(ps,null,"In order to resolve this, we align the two sequences together (using EMBOSS needle) to get pairwise alignment of the genome's representation of the protein and the structure file's representation of the protein."),Pt.default.createElement(ps,null,"If you need a 100% fidelity protein, you can do a folding with e.g. AlphaFold to make sure the structure you are using matches exactly the sequence of the transcript")),Pt.default.createElement(Ot.DialogActions,null,Pt.default.createElement(Ot.Button,{onClick:()=>{e()},variant:"contained",color:"primary"},"Close")))}var Pt,Vc,Ot,Bc=T(()=>{"use strict";Pt=p(S()),Vc=p(_e()),Ot=p(V())});function us({model:e}){return ao.default.createElement(Rc.IconButton,{style:{float:"right"},onClick:()=>{(0,Uc.getSession)(e).queueDialog(t=>[_f,{handleClose:t}])}},ao.default.createElement(or,null))}var ao,Uc,Rc,_f,Oc=T(()=>{"use strict";ao=p(S()),Uc=p(ie());Ui();Rc=p(V()),_f=(0,ao.lazy)(()=>Promise.resolve().then(()=>(Bc(),Hc)))});function zc(e){return Wf[e]??"#999999"}async function Kf(e){let t=await(await Jn(e)).text(),n=[];for(let o of t.split(`
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@@ -14,7 +14,7 @@ structure MKAAYLSMFGKEDHKPFGDDEVELFRAVPGLKLKIAG`,value:n,onChange:u=>{o(u.targ
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${t}`,...Object.values(s).map(({feature:u,seq:m})=>`>${je(u)}
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${m}`)].join(`
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`):[`${a.padEnd(c)}${l?"*":" "} ${t}`,l?`${je(l[1].feature).padEnd(c)}* ${l[1].seq}`:void 0,...Object.entries(s).filter(([u])=>u!==l?.[0]).map(([u,m])=>`${je(m.feature).padEnd(c)} ${m.seq}`)].filter(u=>!!u).join(`
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-
`),slotProps:{input:{readOnly:!0,classes:{input:o.textAreaFont}}}}))}function zn({structureSequence:e,structureName:t,isoformSequences:n}){let[o,r]=(0,vn.useState)(!1);return vn.default.createElement("div",{style:{margin:10}},vn.default.createElement(pl.Button,{variant:"contained",color:"primary",onClick:()=>{r(!o)}},o?"Hide all isoform protein sequences":"Show all isoform protein sequences"),o?vn.default.createElement(Nr,{structureSequence:e,structureName:t,isoformSequences:n}):null)}nn();Pe();function qd({uniprotId:e}){return De.default.createElement(_n.Typography,null,"No structure found for this UniProtID in AlphaFoldDB"," ",De.default.createElement(be,{href:`https://alphafold.ebi.ac.uk/search/text/${e}`},"(search for results)"))}function Br({uniprotId:e,selectedTranscript:t,structureSequence:n,isoformSequences:o,url:r}){return e?De.default.createElement(De.default.Fragment,null,De.default.createElement("div",null,De.default.createElement(_n.Typography,null,"UniProt link:"," ",De.default.createElement(be,{href:Tn(e)},e)),De.default.createElement(_n.Typography,null,"AlphaFoldDB link: ",De.default.createElement(be,{href:r},r))),n?De.default.createElement(zn,{structureSequence:n,structureName:e,isoformSequences:o}):De.default.createElement(qd,{uniprotId:e})):De.default.createElement(_n.Typography,null,"Searching"," ",t?je(t):"transcript"," ","for UniProt ID")}var Gt=p(S()),pt=p(V());function Ur({recognizedIds:e,geneName:t,selectedId:n,onSelectedIdChange:o}){let[r,i]=(0,Gt.useState)(!1),s=[{value:"auto",label:"Auto (try all)"},...e.map(l=>({value:l,label:ba(l)}))];return t&&s.push({value:`gene:${t}`,label:`${t} (gene name)`}),e.length===0&&!t?null:r?Gt.default.createElement(pt.FormControl,{size:"small"},Gt.default.createElement(pt.InputLabel,null,"Query UniProt by"),Gt.default.createElement(pt.Select,{value:n,label:"Query UniProt by",onChange:l=>{o(l.target.value)}},s.map(l=>Gt.default.createElement(pt.MenuItem,{key:l.value,value:l.value},l.label)))):Gt.default.createElement(pt.Button,{size:"small",variant:"text",onClick:()=>{i(!0)}},"Choose identifier to query...")}var me=p(S()),Wl=p(_e());nt();var wl=p(ot(),1),xl=(0,se.createSvgIcon)((0,wl.jsx)("path",{d:"m7 10 5 5 5-5z"}),"ArrowDropDown");nt();var vl=p(ot(),1),Pn=(0,se.createSvgIcon)((0,vl.jsx)("path",{d:"M19.14 12.94c.04-.3.06-.61.06-.94 0-.32-.02-.64-.07-.94l2.03-1.58c.18-.14.23-.41.12-.61l-1.92-3.32c-.12-.22-.37-.29-.59-.22l-2.39.96c-.5-.38-1.03-.7-1.62-.94l-.36-2.54c-.04-.24-.24-.41-.48-.41h-3.84c-.24 0-.43.17-.47.41l-.36 2.54c-.59.24-1.13.57-1.62.94l-2.39-.96c-.22-.08-.47 0-.59.22L2.74 8.87c-.12.21-.08.47.12.61l2.03 1.58c-.05.3-.09.63-.09.94s.02.64.07.94l-2.03 1.58c-.18.14-.23.41-.12.61l1.92 3.32c.12.22.37.29.59.22l2.39-.96c.5.38 1.03.7 1.62.94l.36 2.54c.05.24.24.41.48.41h3.84c.24 0 .44-.17.47-.41l.36-2.54c.59-.24 1.13-.56 1.62-.94l2.39.96c.22.08.47 0 .59-.22l1.92-3.32c.12-.22.07-.47-.12-.61zM12 15.6c-1.98 0-3.6-1.62-3.6-3.6s1.62-3.6 3.6-3.6 3.6 1.62 3.6 3.6-1.62 3.6-3.6 3.6"}),"Settings");var Ke=p(V());var vt=p(S()),Ne=p(V());function Rr({open:e,onClose:t,options:n}){return vt.default.createElement(Ne.Dialog,{open:e,onClose:t,"data-testid":"protein-launch-options-dialog"},vt.default.createElement(Ne.DialogTitle,null,"Launch options"),vt.default.createElement(Ne.DialogContent,null,vt.default.createElement(Ne.MenuList,null,n.map(o=>vt.default.createElement(Ne.MenuItem,{key:o.key,"data-testid":`protein-launch-option-${o.key}`,onClick:o.onClick},vt.default.createElement("div",null,vt.default.createElement(Ne.Typography,{variant:"body1"},o.title),vt.default.createElement(Ne.Typography,{variant:"body2",color:"text.secondary"},o.description)))))))}var We=p(S()),ge=p(V());var Pl="proteinView-launchSideBySide";function Or(){let e=localStorage.getItem(Pl);return e===null?!0:e==="true"}function Cl(e){localStorage.setItem(Pl,e?"true":"false")}var Tl=(e,t)=>t in e&&typeof e[t]=="function",Al=!1;function Dd(e){let t=Tl(e,"setUseWorkspaces"),n=Tl(e,"setPendingMove");return t!==n&&!Al&&(Al=!0,console.warn(`jbrowse-plugin-protein3d: this session supports workspaces but not ${n?"setUseWorkspaces":"setPendingMove"}, so the side-by-side launch was skipped and the views will stack.
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`),slotProps:{input:{readOnly:!0,classes:{input:o.textAreaFont}}}}))}function zn({structureSequence:e,structureName:t,isoformSequences:n}){let[o,r]=(0,vn.useState)(!1);return vn.default.createElement("div",{style:{margin:10}},vn.default.createElement(pl.Button,{variant:"contained",color:"primary",onClick:()=>{r(!o)}},o?"Hide all isoform protein sequences":"Show all isoform protein sequences"),o?vn.default.createElement(Nr,{structureSequence:e,structureName:t,isoformSequences:n}):null)}nn();Pe();function qd({uniprotId:e}){return De.default.createElement(_n.Typography,null,"No structure found for this UniProtID in AlphaFoldDB"," ",De.default.createElement(be,{href:`https://alphafold.ebi.ac.uk/search/text/${e}`},"(search for results)"))}function Br({uniprotId:e,selectedTranscript:t,structureSequence:n,isoformSequences:o,url:r}){return e?De.default.createElement(De.default.Fragment,null,De.default.createElement("div",null,De.default.createElement(_n.Typography,null,"UniProt link:"," ",De.default.createElement(be,{href:Tn(e)},e)),De.default.createElement(_n.Typography,null,"AlphaFoldDB link: ",De.default.createElement(be,{href:r},r))),n?De.default.createElement(zn,{structureSequence:n,structureName:e,isoformSequences:o}):De.default.createElement(qd,{uniprotId:e})):De.default.createElement(_n.Typography,null,"Searching"," ",t?je(t):"transcript"," ","for UniProt ID")}var Gt=p(S()),pt=p(V());function Ur({recognizedIds:e,geneName:t,selectedId:n,onSelectedIdChange:o}){let[r,i]=(0,Gt.useState)(!1),s=[{value:"auto",label:"Auto (try all)"},...e.map(l=>({value:l,label:ba(l)}))];return t&&s.push({value:`gene:${t}`,label:`${t} (gene name)`}),e.length===0&&!t?null:r?Gt.default.createElement(pt.FormControl,{size:"small"},Gt.default.createElement(pt.InputLabel,null,"Query UniProt by"),Gt.default.createElement(pt.Select,{value:n,label:"Query UniProt by",onChange:l=>{o(l.target.value)}},s.map(l=>Gt.default.createElement(pt.MenuItem,{key:l.value,value:l.value},l.label)))):Gt.default.createElement(pt.Button,{size:"small",variant:"text",onClick:()=>{i(!0)}},"Choose identifier to query...")}var me=p(S()),Wl=p(_e());nt();var wl=p(ot(),1),xl=(0,se.createSvgIcon)((0,wl.jsx)("path",{d:"m7 10 5 5 5-5z"}),"ArrowDropDown");nt();var vl=p(ot(),1),Pn=(0,se.createSvgIcon)((0,vl.jsx)("path",{d:"M19.14 12.94c.04-.3.06-.61.06-.94 0-.32-.02-.64-.07-.94l2.03-1.58c.18-.14.23-.41.12-.61l-1.92-3.32c-.12-.22-.37-.29-.59-.22l-2.39.96c-.5-.38-1.03-.7-1.62-.94l-.36-2.54c-.04-.24-.24-.41-.48-.41h-3.84c-.24 0-.43.17-.47.41l-.36 2.54c-.59.24-1.13.57-1.62.94l-2.39-.96c-.22-.08-.47 0-.59.22L2.74 8.87c-.12.21-.08.47.12.61l2.03 1.58c-.05.3-.09.63-.09.94s.02.64.07.94l-2.03 1.58c-.18.14-.23.41-.12.61l1.92 3.32c.12.22.37.29.59.22l2.39-.96c.5.38 1.03.7 1.62.94l.36 2.54c.05.24.24.41.48.41h3.84c.24 0 .44-.17.47-.41l.36-2.54c.59-.24 1.13-.56 1.62-.94l2.39.96c.22.08.47 0 .59-.22l1.92-3.32c.12-.22.07-.47-.12-.61zM12 15.6c-1.98 0-3.6-1.62-3.6-3.6s1.62-3.6 3.6-3.6 3.6 1.62 3.6 3.6-1.62 3.6-3.6 3.6"}),"Settings");var Ke=p(V());var vt=p(S()),Ne=p(V());function Rr({open:e,onClose:t,options:n}){return vt.default.createElement(Ne.Dialog,{open:e,onClose:t,"data-testid":"protein-launch-options-dialog"},vt.default.createElement(Ne.DialogTitle,null,"Launch options"),vt.default.createElement(Ne.DialogContent,null,vt.default.createElement(Ne.MenuList,null,n.map(o=>vt.default.createElement(Ne.MenuItem,{key:o.key,"data-testid":`protein-launch-option-${o.key}`,onClick:o.onClick},vt.default.createElement("div",null,vt.default.createElement(Ne.Typography,{variant:"body1"},o.title),vt.default.createElement(Ne.Typography,{variant:"body2",color:"text.secondary"},o.description)))))))}var We=p(S()),ge=p(V());var Pl="proteinView-launchSideBySide";function Or(){let e=localStorage.getItem(Pl);return e===null?!0:e==="true"}function Cl(e){localStorage.setItem(Pl,e?"true":"false")}var Tl=(e,t)=>t in e&&typeof e[t]=="function",Al=!1;function Dd(e){let t=Tl(e,"setUseWorkspaces"),n=Tl(e,"setPendingMove");return t!==n&&!Al&&(Al=!0,console.warn(`jbrowse-plugin-protein3d: this session supports workspaces but not ${n?"setUseWorkspaces":"setPendingMove"}, so the side-by-side launch was skipped and the views will stack. Expected on releases through v4.3.0, which place views through @jbrowse/app-core instead; on a newer host it means the session API moved and the plugin needs updating to match.`)),t&&n}function Nd(e,t){Dd(e)&&(e.setPendingMove({type:"splitRight",viewId:t}),e.setUseWorkspaces(!0))}function Eo(e,t,n){(n??Or())&&Nd(e,t)}function zr({open:e,onClose:t}){let[n,o]=(0,We.useState)(()=>Or());return We.default.createElement(ge.Dialog,{open:e,onClose:()=>{t()}},We.default.createElement(ge.DialogTitle,null,"Launch settings"),We.default.createElement(ge.DialogContent,null,We.default.createElement(ge.FormGroup,null,We.default.createElement(ge.FormControlLabel,{control:We.default.createElement(ge.Checkbox,{checked:n}),label:"Open protein view side-by-side with the genome view",onChange:(r,i)=>{o(i),Cl(i)}})),We.default.createElement(ge.Typography,{variant:"body2",color:"text.secondary"},"When enabled, launching a protein view places it to the right of the connected genome view in a split layout instead of stacking it below.")),We.default.createElement(ge.DialogActions,null,We.default.createElement(ge.Button,{variant:"contained",onClick:()=>{t()}},"Close")))}var Jr=p(S()),Nl=p(V());var q=p(S());var F=p(V());jr();var _r={NEEDLEMAN_WUNSCH:"needleman_wunsch",SMITH_WATERMAN:"smith_waterman"},Wn="smith_waterman",Wr=["needleman_wunsch","smith_waterman"];function ql(e){return Wr.find(t=>t===e)??Wn}var Dl={needleman_wunsch:"Needleman-Wunsch",smith_waterman:"Smith-Waterman"};function Kr({value:e,onChange:t,onManualAlignment:n}){let[o,r]=(0,q.useState)(!1),[i,s]=(0,q.useState)(0),[l,a]=(0,q.useState)(e),[c,u]=(0,q.useState)(""),[m,d]=(0,q.useState)(),g=()=>{a(e),u(""),d(void 0),s(0),r(!0)},h=()=>{if(i===0)t(l);else if(i===1&&c.trim()&&n)try{let x=Fo(c.trim());n(x)}catch(x){d(`Failed to parse alignment: ${x}`);return}r(!1)},b=()=>{a(e),u(""),d(void 0),r(!1)};return q.default.createElement(q.default.Fragment,null,q.default.createElement(F.IconButton,{onClick:g,size:"small",title:"Alignment settings"},q.default.createElement(Pn,null)),q.default.createElement(F.Dialog,{open:o,onClose:b,maxWidth:"sm",fullWidth:!0},q.default.createElement(F.DialogTitle,null,"Alignment settings"),q.default.createElement(F.DialogContent,null,q.default.createElement(F.Tabs,{value:i,onChange:(x,w)=>{s(w)},sx:{mb:2}},q.default.createElement(F.Tab,{label:"Automatic"}),q.default.createElement(F.Tab,{label:"Manual",disabled:!n})),i===0?q.default.createElement(q.default.Fragment,null,q.default.createElement(F.Typography,{variant:"body2",color:"text.secondary",sx:{mb:2}},"Choose the algorithm for aligning transcript sequences to protein structures."),q.default.createElement(F.FormControl,{component:"fieldset"},q.default.createElement(F.FormLabel,{component:"legend"},"Algorithm"),q.default.createElement(F.RadioGroup,{value:l,onChange:x=>{a(x.target.value)}},q.default.createElement(F.FormControlLabel,{value:_r.SMITH_WATERMAN,control:q.default.createElement(F.Radio,null),label:"Smith-Waterman (local alignment)"}),q.default.createElement(F.Typography,{variant:"caption",color:"text.secondary",sx:{ml:4,mt:-1,mb:1}},"Finds best matching region. Recommended for most use cases."),q.default.createElement(F.FormControlLabel,{value:_r.NEEDLEMAN_WUNSCH,control:q.default.createElement(F.Radio,null),label:"Needleman-Wunsch (global alignment)"}),q.default.createElement(F.Typography,{variant:"caption",color:"text.secondary",sx:{ml:4,mt:-1,mb:1}},"End-to-end alignment. Use when sequences should align completely.")))):q.default.createElement(q.default.Fragment,null,q.default.createElement(F.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."),q.default.createElement(F.TextField,{multiline:!0,rows:10,fullWidth:!0,placeholder:`Example:
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b MKAAYLSMFGKEDHKPFGD`,value:c,onChange:x=>{u(x.target.value),d(void 0)},sx:{fontFamily:"monospace",fontSize:12}}),m?q.default.createElement(F.Typography,{color:"error",variant:"body2",sx:{mt:1}},m):null)),q.default.createElement(F.DialogActions,null,q.default.createElement(F.Button,{onClick:b},"Cancel"),q.default.createElement(F.Button,{onClick:h,variant:"contained",color:"primary",disabled:i===1&&!c.trim()},i===0?"Save":"Apply alignment"))))}function Kn({alignmentAlgorithm:e,onAlignmentAlgorithmChange:t}){return Jr.default.createElement(Nl.Typography,{variant:"body2",sx:{mr:2,display:"flex",alignItems:"center"}},"Transcript and structure sequences differ, will run"," ",Dl[e]," alignment",Jr.default.createElement(Kr,{value:e,onChange:t}))}var Hl=p(S());async function Vl(e,t,n){try{await e(),t?.()}catch(o){console.error(o),n?.(o)}}function Gl({uniprotId:e,userSelectedProteinSequence:t,selectedTranscript:n}){return[!e&&"No UniProt ID found",!t?.seq&&"Could not compute protein sequence (feature may be missing CDS subfeatures)",!n&&"No transcript selected"].filter(o=>typeof o=="string")}function Cn(e,t){let[n,o]=(0,Hl.useState)();return{runLaunch:i=>()=>{t?.(),Vl(i,e,o)},launchError:n}}var zl=p(ie());Pe();function qo(e){let{structures:t,...n}=e;return{type:"ProteinView",...n,structures:t.map(o=>({...o,userProvidedTranscriptSequence:o.userProvidedTranscriptSequence??""}))}}Pe();function Bl(e,t){e.addTemporaryAssembly?.({name:t,sequence:{type:"ReferenceSequenceTrack",trackId:`${t}-ReferenceSequenceTrack`,sequenceType:"pep",adapter:{type:"UnindexedFastaAdapter",rewriteRefNames:"jexl:split(refName,'|')[1]",fastaLocation:{uri:gl(t)}}}})}on();Pe();async function Bd(e){let t=await(await Jn(jn(e))).text();return[...new Set(t.split(`
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@@ -25,7 +25,7 @@ ${e}
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`,i=new URLSearchParams;i.append("q",r),i.append("mode","3diaa"),i.append("email","");for(let a of n)i.append("database[]",a);let s=await fetch("https://search.foldseek.com/api/ticket",{method:"POST",headers:{"Content-Type":"application/x-www-form-urlencoded"},body:i,signal:o}),l=await s.text();if(!s.ok)throw new Error(`Foldseek submission failed: ${s.status} ${l}`);return JSON.parse(l)}async function Qg({ticketId:e,signal:t}){let n=new URLSearchParams;n.append("tickets[]",e);let o=await fetch("https://search.foldseek.com/api/tickets",{method:"POST",headers:{"Content-Type":"application/x-www-form-urlencoded"},body:n,signal:t});if(!o.ok)throw new Error(`Failed to poll ticket status: ${o.status}`);let i=(await o.json())[0];if(!i)throw new Error("No ticket status returned");return i}async function $g({ticketId:e,signal:t}){return Ht(`https://search.foldseek.com/api/result/${e}/0`,{signal:t})}async function Op({ticketId:e,onStatusChange:t,signal:n}){let r=Date.now(),i=()=>Math.round((Date.now()-r)/1e3);for(;Date.now()-r<18e4;){if(n?.aborted)throw Do(n);let s=await Qg({ticketId:e,signal:n});if(s.status==="ERROR")throw console.error("[Foldseek] Search error:",s),new Error(`Foldseek search failed: ${s.error??"Unknown error"}`);if(s.status==="COMPLETE"){t?.("Fetching results...");let l=await $g({ticketId:e,signal:n});return{query:l.queries[0]??{header:"",sequence:""},results:l.results.map(c=>({db:c.db,alignments:c.alignments}))}}t?.(`Search ${s.status.toLowerCase()}... (${i()}s)`),await Ul(1e3,n)}throw new Error(`Foldseek search timed out after ${Math.round(18e4/1e3)}s`)}var Zg=(0,zp.makeStyles)()({root:{display:"flex",flexDirection:"column",gap:8},header:{display:"flex",alignItems:"center",gap:8},buttons:{display:"flex",gap:4},checkboxGroup:{display:"grid",gridTemplateColumns:"repeat(2, 1fr)",gap:0}});function Di({selected:e,onChange:t,disabled:n}){let{classes:o}=Zg();return mt.default.createElement("div",{className:o.root},mt.default.createElement("div",{className:o.header},mt.default.createElement(rt.Typography,{variant:"subtitle2"},"Databases to search:"),mt.default.createElement("div",{className:o.buttons},mt.default.createElement(rt.Button,{size:"small",onClick:()=>{t(qi.map(r=>r.id))},disabled:n},"Select all"),mt.default.createElement(rt.Button,{size:"small",onClick:()=>{t([])},disabled:n},"Clear"))),mt.default.createElement(rt.FormGroup,{className:o.checkboxGroup},qi.map(r=>mt.default.createElement(rt.FormControlLabel,{key:r.id,control:mt.default.createElement(rt.Checkbox,{size:"small",checked:e.includes(r.id),onChange:()=>{e.includes(r.id)?t(e.filter(i=>i!==r.id)):t([...e,r.id])},disabled:n}),label:r.label}))))}var j=p(S()),G=p(V()),Kp=p(tt());var $e=p(S()),Wp=p(_e()),Ut=p(V());var Xg={A:"ALA",C:"CYS",D:"ASP",E:"GLU",F:"PHE",G:"GLY",H:"HIS",I:"ILE",K:"LYS",L:"LEU",M:"MET",N:"ASN",P:"PRO",Q:"GLN",R:"ARG",S:"SER",T:"THR",V:"VAL",W:"TRP",Y:"TYR",X:"UNK"};function jp(e,t){return e.padStart(t," ")}function ef(e,t){return e.padEnd(t," ")}function Ni(e){return e.toFixed(3).padStart(8," ")}function _p(e,t,n="A",o){let r=e.split(",").map(Number),i=[];o&&i.push(`TITLE ${o}`),i.push("REMARK 1 Generated from Foldseek C\u03B1 coordinates");let s=1,l=1;for(let a=0;a<r.length-2;a+=3){let c=r[a],u=r[a+1],m=r[a+2],d=t[l-1]??"X",g=Xg[d]??"UNK";if(c===void 0||u===void 0||m===void 0)break;let h="ATOM "+jp(String(s),5)+" CA "+ef(g,3)+" "+n+jp(String(l),4)+" "+Ni(c)+Ni(u)+Ni(m)+" 1.00 0.00 C";i.push(h),s++,l++}return i.push("END"),i.join(`
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-
`)}function Vi(e){let{tCa:t,tSeq:n}=e;return!!t&&!!n&&t.split(",").length>=3}Pe();function Gi({hit:e,session:t,view:n,feature:o,selectedTranscript:r,userProvidedTranscriptSequence:i,onClose:s}){let[l,a]=(0,$e.useState)(null),c=!!l,u=An(e.target),m=A=>{a(A.currentTarget)},d=()=>{a(null)},{runLaunch:g,launchError:h}=Cn(s,d),b={session:t,view:n,feature:o,selectedTranscript:r,uniprotId:u},x=g(()=>{let A=!e.structureUrl&&Vi(e)?_p(e.tCa,e.tSeq,"A",e.target):void 0;rn({...b,url:e.structureUrl,data:A,userProvidedTranscriptSequence:i})}),{launch1D:w,launchMsa:y}=Vo({...b,confidenceUrl:Sl(e.target)});return!!e.structureUrl||Vi(e)?$e.default.createElement($e.default.Fragment,null,h?$e.default.createElement(Wp.ErrorMessage,{error:h}):null,$e.default.createElement(Ut.Button,{size:"small",variant:"outlined",onClick:m},"Load"),$e.default.createElement(Ut.Menu,{anchorEl:l,open:c,onClose:d},$e.default.createElement(Ut.MenuItem,{"data-testid":"protein-launch-option-3d",onClick:x},Tt["3d"]),w?$e.default.createElement(Ut.MenuItem,{"data-testid":"protein-launch-option-1d",onClick:g(w)},Tt["1d"]):null,y?$e.default.createElement(Ut.MenuItem,{"data-testid":"protein-launch-option-msa",onClick:g(y)},Tt.msa):null)):$e.default.createElement("span",null,"-")}Pe();var tf=(0,Kp.makeStyles)()(e=>({root:{display:"flex",flexDirection:"column",gap:16},tableContainer:{maxHeight:400},headerCell:{fontWeight:"bold",backgroundColor:e.palette.mode==="dark"?e.palette.grey[900]:e.palette.grey[100]},noResults:{padding:16,textAlign:"center"}})),nf=100;function of(e){let t=e.results.flatMap(n=>(n.alignments??[]).flat().map(o=>({...o,db:n.db,structureUrl:yl(o.target,n.db)})));return t.sort((n,o)=>(n.eval??1/0)-(o.eval??1/0)),t}function Hi({results:e,session:t,view:n,feature:o,selectedTranscript:r,userProvidedTranscriptSequence:i,onClose:s}){let{classes:l}=tf(),a=of(e),c=a.slice(0,nf);return c.length===0?j.default.createElement(G.Paper,{className:l.noResults},j.default.createElement(G.Typography,null,"No similar structures found")):j.default.createElement("div",{className:l.root},j.default.createElement(G.Typography,{variant:"subtitle2"},"Found ",a.length," similar structures",a.length>c.length?` (showing top ${c.length})`:""),j.default.createElement(G.TableContainer,{component:G.Paper,className:l.tableContainer},j.default.createElement(G.Table,{size:"small",stickyHeader:!0},j.default.createElement(G.TableHead,null,j.default.createElement(G.TableRow,null,j.default.createElement(G.TableCell,{className:l.headerCell},"Database"),j.default.createElement(G.TableCell,{className:l.headerCell},"Target"),j.default.createElement(G.TableCell,{className:l.headerCell},"Organism"),j.default.createElement(G.TableCell,{className:l.headerCell},"Prob"),j.default.createElement(G.TableCell,{className:l.headerCell},"Seq. 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Pu=["A","R","N","D","C","Q","E","G","H","I","L","K","M","F","P","S","T","W","Y","V","B","Z","X","*"],xf=[[4,-1,-2,-2,0,-1,-1,0,-2,-1,-1,-1,-1,-2,-1,1,0,-3,-2,0,-2,-1,0,-4],[-1,5,0,-2,-3,1,0,-2,0,-3,-2,2,-1,-3,-2,-1,-1,-3,-2,-3,-1,0,-1,-4],[-2,0,6,1,-3,0,0,0,1,-3,-3,0,-2,-3,-2,1,0,-4,-2,-3,3,0,-1,-4],[-2,-2,1,6,-3,0,2,-1,-1,-3,-4,-1,-3,-3,-1,0,-1,-4,-3,-3,4,1,-1,-4],[0,-3,-3,-3,9,-3,-4,-3,-3,-1,-1,-3,-1,-2,-3,-1,-1,-2,-2,-1,-3,-3,-2,-4],[-1,1,0,0,-3,5,2,-2,0,-3,-2,1,0,-3,-1,0,-1,-2,-1,-2,0,3,-1,-4],[-1,0,0,2,-4,2,5,-2,0,-3,-3,1,-2,-3,-1,0,-1,-3,-2,-2,1,4,-1,-4],[0,-2,0,-1,-3,-2,-2,6,-2,-4,-4,-2,-3,-3,-2,0,-2,-2,-3,-3,-1,-2,-1,-4],[-2,0,1,-1,-3,0,0,-2,8,-3,-3,-1,-2,-1,-2,-1,-2,-2,2,-3,0,0,-1,-4],[-1,-3,-3,-3,-1,-3,-3,-4,-3,4,2,-3,1,0,-3,-2,-1,-3,-1,3,-3,-3,-1,-4],[-1,-2,-3,-4,-1,-2,-3,-4,-3,2,4,-2,2,0,-3,-2,-1,-2,-1,1,-4,-3,-1,-4],[-1,2,0,-1,-3,1,1,-2,-1,-3,-2,5,-1,-3,-1,0,-1,-3,-2,-2,0,1,-1,-4],[-1,-1,-2,-3,-1,0,-2,-3,-2,1,2,-1,5,0,-2,-1,-1,-1,-1,1,-3,-1,-1,-4],[-2,-3,-3,-3,-2,-3,-3,-3,-1,0,0,-3,0,6,-4,-2,-2,1,3,-1,-3,-3,-1,-4],[-1,-2,-2,-1,-3,-1,-1,-2,-2,-3,-3,-1,-2,-4,7,-1,-1,-4,-3,-2,-2,-1,-2,-4],[1,-1,1,0,-1,0,0,0,-1,-2,-2,0,-1,-2,-1,4,1,-3,-2,-2,0,0,0,-4],[0,-1,0,-1,-1,-1,-1,-2,-2,-1,-1,-1,-1,-2,-1,1,5,-2,-2,0,-1,-1,0,-4],[-3,-3,-4,-4,-2,-2,-3,-2,-2,-3,-2,-3,-1,1,-4,-3,-2,11,2,-3,-4,-3,-2,-4],[-2,-2,-2,-3,-2,-1,-2,-3,2,-1,-1,-2,-1,3,-3,-2,-2,2,7,-1,-3,-2,-1,-4],[0,-3,-3,-3,-1,-2,-2,-3,-3,3,1,-2,1,-1,-2,-2,0,-3,-1,4,-3,-2,-1,-4],[-2,-1,3,4,-3,0,1,-1,0,-3,-4,0,-3,-3,-2,0,-1,-4,-3,-3,4,1,-1,-4],[-1,0,0,1,-3,3,4,-2,0,-3,-3,1,-1,-3,-1,0,-1,-3,-2,-2,1,4,-1,-4],[0,-1,-1,-1,-2,-1,-1,-1,-1,-1,-1,-1,-1,-1,-2,0,0,-2,-1,-1,-1,-1,-1,-4],[-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,1]],Cu=-4,Rt=Pu.length,$i=new Int8Array(128).fill(-1);for(let e=0;e<Rt;e++){let t=Pu[e];$i[t.charCodeAt(0)]=e,$i[t.toLowerCase().charCodeAt(0)]=e}var Zi=new Int8Array(Rt*Rt);for(let e=0;e<Rt;e++)for(let t=0;t<Rt;t++)Zi[e*Rt+t]=xf[e][t];var lr=e=>{let t=e.charCodeAt(0);return t<128?$i[t]:-1};function vf(e,t){let n=lr(e),o=lr(t);return n<0||o<0?Cu:Zi[n*Rt+o]}var ku=-10,Mu=-.5,Iu=4e7;function Xi(e,t){return(e+1)*(t+1)>Iu}function Tf(e,t){if(Xi(e,t))throw new Error(`Sequences too long to align (${e} x ${t} residues exceeds the ${Iu} cell limit)`)}var mn=0,oo=1,ar=2,Lu=3,Eu=0,Fu=2,qu=4,Qi=(e,t,n)=>e[t]>>n&3;function Du(e,t,n,o,r){let i=e.length,s=t.length;Tf(i,s);let l=s+1,a=new Uint8Array((i+1)*l),c=new Float32Array(l),u=new Float32Array(l).fill(-1/0),m=new Float32Array(l).fill(-1/0),d=new Float32Array(l),g=new Float32Array(l),h=new Float32Array(l);if(!r){c.fill(-1/0),c[0]=0;for(let E=1;E<=s;E++)m[E]=n+(E-1)*o}let b=r?0:-1/0,x=0,w=0,y=mn,f=new Int8Array(s);for(let E=0;E<s;E++)f[E]=lr(t[E]);for(let E=1;E<=i;E++){d[0]=r?0:-1/0,g[0]=r?-1/0:n+(E-1)*o,h[0]=-1/0;let I=E*l,L=lr(e[E-1]),oe=L*Rt;for(let C=1;C<=s;C++){let O=f[C-1],pe=L<0||O<0?Cu:Zi[oe+O],Re=c[C-1],ke=u[C-1],Me=m[C-1],Ee=Math.max(Re,ke,Me),Oe=Ee===Re?mn:Ee===ke?oo:ar,Ie=Ee+pe,he=r&&Ie<=0;d[C]=he?0:Ie;let Wt=c[C]+n,It=u[C]+o;g[C]=Math.max(Wt,It);let Kt=d[C-1]+n,Xe=h[C-1]+o;if(h[C]=Math.max(Kt,Xe),a[I+C]=(he?Lu:Oe)<<Eu|(Wt>=It?mn:oo)<<Fu|(Kt>=Xe?mn:ar)<<qu,r){let Lt=Math.max(d[C],g[C],h[C]);Lt>b&&(b=Lt,x=E,w=C,y=Lt===d[C]?mn:Lt===g[C]?oo:ar)}}[c,d]=[d,c],[u,g]=[g,u],[m,h]=[h,m]}if(r)return{trace:a,width:l,score:b,startI:x,startJ:w,startMatrix:y};let A=c[s],P=u[s],v=m[s],D=Math.max(A,P,v);return{trace:a,width:l,score:D,startI:i,startJ:s,startMatrix:D===A?mn:D===P?oo:ar}}function Nu(e,t,n){let{trace:o,width:r,startI:i,startJ:s,score:l}=n,a=[],c=[];for(let g=e.length;g>i;g--)a.push(e[g-1]),c.push("-");for(let g=t.length;g>s;g--)a.push("-"),c.push(t[g-1]);let u=i,m=s,d=n.startMatrix;for(;u>0&&m>0;){let g=u*r+m;if(d===mn){let h=Qi(o,g,Eu);if(h===Lu)break;a.push(e[u-1]),c.push(t[m-1]),d=h,u--,m--}else d===oo?(a.push(e[u-1]),c.push("-"),d=Qi(o,g,Fu),u--):(a.push("-"),c.push(t[m-1]),d=Qi(o,g,qu),m--)}for(;u>0;)a.push(e[u-1]),c.push("-"),u--;for(;m>0;)a.push("-"),c.push(t[m-1]),m--;return{alignedSeq1:a.reverse().join(""),alignedSeq2:c.reverse().join(""),score:l}}function Af(e,t,n=ku,o=Mu){return Nu(e,t,Du(e,t,n,o,!1))}function Pf(e,t,n=ku,o=Mu){return Nu(e,t,Du(e,t,n,o,!0))}function Cf(e,t){let n=[];for(let o=0;o<e.length;o++){let r=e[o],i=t[o];r!=="-"&&i!=="-"&&r.toUpperCase()===i.toUpperCase()?n.push("|"):r!=="-"&&i!=="-"&&vf(r,i)>0?n.push(":"):n.push(" ")}return n.join("")}function Vu(e,t,n){let{alignedSeq1:o,alignedSeq2:r}=n==="smith_waterman"?Pf(e,t):Af(e,t);return{consensus:Cf(o,r),alns:[{id:"a",seq:o},{id:"b",seq:r}]}}lt();function Gu(e,t){return t===void 0||e===t}function kf(e){let t=Dt(e),n=$t(e),o=0;for(let r=0;r<t.length;r++){let i=t[r],s=n[r];i!=="-"&&s!=="-"&&i?.toUpperCase()===s?.toUpperCase()&&o++}return o}function Hu(e,t,n){let o=de(e);if(!o||t.length===0)return;let r=t.map(de),i=r.findIndex(a=>a.length>0&&a===o);if(i!==-1)return{index:i,alignment:{consensus:"|".repeat(o.length),alns:[{id:"seq1",seq:o},{id:"seq2",seq:r[i]}]},matches:o.length};let s=new Map,l;for(let a=0;a<r.length;a++){let c=r[a];if(c.length>0&&!Xi(o.length,c.length)){let u=s.get(c);if(!u){let m=Vu(o,c,n);u={alignment:m,matches:kf(m)},s.set(c,u)}(!l||u.matches>l.matches)&&(l={index:a,...u})}}return l}st();lt();var Ou=e=>e;var ts=e=>e;function zu(e){let{structureSeqToTranscriptSeqPosition:t,transcriptSeqToStructureSeqPosition:n}=Ys(e),o=$s(e),r=Zs(e),i=vr(o),s=vr(r);return{structureToTranscript:l=>t[l],transcriptToStructure:l=>n[l],structureToAlignment:l=>o[l],alignmentToStructure:l=>i[l],transcriptToAlignment:l=>r[l],alignmentToTranscript:l=>s[l],maps:{structureSeqToTranscriptSeqPosition:t,transcriptSeqToStructureSeqPosition:n,structurePositionToAlignmentMap:o,transcriptPositionToAlignmentMap:r,alignmentToStructurePosition:i,alignmentToTranscriptPosition:s}}}var ju=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]));os();is();Fn();function Ef(e,t){return{labelSeqId:e.StructureProperties.residue.label_seq_id(t),code:e.StructureProperties.atom.label_comp_id(t),chain:e.StructureProperties.chain.auth_asym_id(t),entityId:e.StructureProperties.entity.id(t)}}async function ss({plugin:e,kind:t,onUpdate:n}){let o=await He(),r=e.behaviors.interaction[t].subscribe(i=>{if(o.StructureElement.Loci.is(i.current.loci)){let s=o.StructureElement.Loci.getFirstLocation(i.current.loci);n(s?Ef(o,s):void 0)}else n(void 0)});return()=>{r.unsubscribe()}}Pe();lt();var Vf=ne.types.model({url:ne.types.maybe(ne.types.string),data:ne.types.maybe(ne.types.string),connectedViewId:ne.types.maybe(ne.types.string),pairwiseAlignment:ne.types.frozen(),feature:ne.types.frozen(),userProvidedTranscriptSequence:ne.types.optional(ne.types.string,""),initialSelection:ne.types.frozen()}).preProcessSnapshot(({uniprotId:e,pdbId:t,...n})=>({...n,url:Lo({...n,uniprotId:e,pdbId:t})})).volatile(()=>({clickedStructureRange:void 0,hoverPosition:void 0,entities:void 0,mappedEntityIndex:0,structureConfidence:void 0,isMouseInAlignment:!1,loadedToMolstar:!1,molstarStructure:void 0,alignmentHoverRange:void 0,selectedFeatureId:void 0,hiddenFeatureTypes:new Set,expandedFeatureTypes:new Set})).actions(e=>({setStructureData(t){e.entities=t.entities,e.structureConfidence=t.confidence,e.molstarStructure=t.molstarStructure},hideFeatureType(t){e.hiddenFeatureTypes=new Set([...e.hiddenFeatureTypes,t])},showFeatureType(t){let n=new Set(e.hiddenFeatureTypes);n.delete(t),e.hiddenFeatureTypes=n},showAllFeatureTypes(){e.hiddenFeatureTypes=new Set},toggleFeatureTypeExpanded(t){let n=new Set(e.expandedFeatureTypes);n.has(t)?n.delete(t):n.add(t),e.expandedFeatureTypes=n},setLoadedToMolstar(t){e.loadedToMolstar=t,t||(e.molstarStructure=void 0)}})).views(e=>({get connectedView(){let{views:t}=(0,so.getSession)(e);return t.find(n=>n.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},setMappedEntityIndex(t){e.mappedEntityIndex=t},setIsMouseInAlignment(t){e.isMouseInAlignment=t}})).views(e=>({get structureSequences(){return e.entities?.map(t=>t.seq)},get mappedEntity(){return e.entities?.[e.mappedEntityIndex]},get mappedStructureSeq(){return this.mappedEntity?.seq},get mappedEntityId(){return this.mappedEntity?.entityId},get uniprotId(){let{url:t}=e;if(t)return An(t)},get coordinateMapper(){return e.pairwiseAlignment?zu(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 t&&t.entityId===this.mappedEntityId&&xu(t.values)?rs(t.values,this.structurePositionToAlignmentMap):[]},get hydrophobicityCells(){let t=this.mappedStructureSeq;return t?rs(Ku(de(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 n=this.hoverStructureLetter,o=this.hoverGenomeLetter,r=[];return t.structureSeqPos!==void 0&&r.push(`${t.structureSeqPos+1}`),n&&r.push(`Structure: ${n}`),o&&n&&o!==n&&r.push(`Genome: ${o}`),t.chain&&r.push(`Chain: ${t.chain}`),r.join(", ")},get genomeToTranscriptSeqMapping(){return e.feature?wn(new so.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(Ou(t))},get hoverStructureRange(){let{alignmentHoverRange:t}=e,n=this.pairwiseAlignmentToStructurePosition;if(!t||!n)return;let o=n[t.start],r=n[t.end];return o===void 0||r===void 0?void 0:{start:o,end:r+1}},get hoverHighlightRange(){let t=this.structureSeqHoverPos;return this.hoverStructureRange??(t===void 0?void 0:{start:t,end:t+1})},get labelSeqIdIndex(){return yp(this.mappedEntity)},get selectLabelSeqIds(){let t=this.mappedEntity,n=e.clickedStructureRange;if(n)return Ti(t,n);let o=this.structureSeqToTranscriptSeqPosition;return this.showHighlight&&o?bp(t,Object.keys(o).map(Number)):[]},get hoverLabelSeqIds(){return Ti(this.mappedEntity,this.hoverHighlightRange)},get clickAlignmentRange(){let t=e.clickedStructureRange,n=this.structurePositionToAlignmentMap;if(!t||!n)return;let o=n[t.start],r=n[t.end-1];return o===void 0||r===void 0?void 0:{start:o,end:r}},structureRangeToGenomeHighlight(t){let n=e.connectedView?.assemblyNames[0],o=this.genomeToTranscriptSeqMapping;if(!t||!n||!o)return[];let r={genomeToTranscriptSeqMapping:o,pairwiseAlignment:e.pairwiseAlignment,structureSeqToTranscriptSeqPosition:this.structureSeqToTranscriptSeqPosition},i=t.end>t.start+1?ns({model:r,structureSeqPos:t.start,structureSeqEndPos:t.end}):pr({model:r,structureSeqPos:t.start});if(!i)return[];let[s,l]=i;return[{assemblyName:n,refName:o.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 ju[t]?.singleLetterCode;let n=this.structureSeqHoverPos,o=this.mappedStructureSeq;if(n!==void 0&&o)return o[n]},get hoverGenomeLetter(){let t=this.structureSeqHoverPos;if(t===void 0)return;let n=this.structureSeqToTranscriptSeqPosition?.[t];if(n!==void 0)return e.userProvidedTranscriptSequence[n]},get alignmentMatchSet(){let t=e.pairwiseAlignment?.consensus;if(!t)return;let n=new Set;for(let o=0;o<t.length;o++)(t[o]==="|"||t[o]===":")&&n.add(o);return n},get alignmentPending(){return!e.pairwiseAlignment&&!!e.userProvidedTranscriptSequence&&!!this.structureSequences?.length},get exactMatch(){let t=de(e.userProvidedTranscriptSequence),n=this.mappedStructureSeq?de(this.mappedStructureSeq):void 0;return t===n},get parentView(){return(0,ne.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 this.parentView.alignmentAlgorithm},get molstarPluginContext(){return this.parentView.molstarPluginContext}})).actions(e=>({setError(t){e.parentView.setError(t)},hoverAlignmentPosition(t){if(!e.alignmentHoverRange){let n=e.coordinateMapper?.alignmentToStructure(ts(t));e.setHoveredPosition(n!==void 0?{structureSeqPos:n}:void 0)}},clickAlignmentPosition(t){let n=e.coordinateMapper?.alignmentToStructure(ts(t));e.setSelectedFeatureId(void 0),n!==void 0?ro({model:e,structureSeqPos:n}).catch(o=>{console.error(o),e.parentView.setError(o)}):e.setClickedStructureRange(void 0)}})).actions(e=>({afterAttach(){e.initialSelection&&e.setClickedStructureRange(e.initialSelection);let t=(r,i)=>{let s;(0,ne.addDisposer)(e,()=>{s?.()}),(0,ne.addDisposer)(e,(0,io.autorun)(async()=>{let{molstarPluginContext:l}=e;if(s?.(),s=void 0,l){let a=await ss({plugin:l,kind:r,onUpdate:i});(0,ne.isAlive)(e)&&e.molstarPluginContext===l?s=a:a()}}))};(0,ne.addDisposer)(e,(0,io.autorun)(async()=>{try{let{userProvidedTranscriptSequence:r,structureSequences:i,alignmentAlgorithm:s}=e;if(e.pairwiseAlignment||!r||!i?.length)return;let l=Hu(r,i,s);if(!l)return;e.setMappedEntityIndex(l.index),e.setAlignment(l.alignment),l.matches<go(l.alignment)&&e.parentView.setShowAlignment(!0)}catch(r){console.error(r),e.parentView.setError(r)}})),(0,ne.addDisposer)(e,(0,io.autorun)(()=>{let{hovered:r}=(0,so.getSession)(e),{transcriptSeqToStructureSeqPosition:i,genomeToTranscriptSeqMapping:s,connectedView:l}=e,a=l?.initialized?mo(r,s):void 0;a!==void 0?e.setGenomeHoveredPosition(i?.[a]):e.hoverPosition?.source==="genome"&&e.setGenomeHoveredPosition(void 0)}));let n=r=>{if(!r||!Gu(r.entityId,e.coordinateMapper?e.mappedEntityId:void 0))return;let i=e.labelSeqIdIndex.get(r.labelSeqId);return i===void 0?void 0:{...r,structureSeqPos:i}};t("click",r=>{let i=n(r);i&&(e.setHoveredPosition(i),e.setSelectedFeatureId(void 0),ro({model:e,structureSeqPos:i.structureSeqPos}).catch(s=>{console.error(s),e.parentView.setError(s)}))}),t("hover",r=>{e.setHoveredPosition(n(r))});let o=(r,i)=>{(0,ne.addDisposer)(e,(0,io.autorun)(async()=>{let{molstarStructure:s,molstarPluginContext:l}=e,a=i();s&&l&&await Au({structure:s,plugin:l,channel:r,entityId:e.mappedEntityId,labelSeqIds:a})}))};o("select",()=>e.selectLabelSeqIds),o("highlight",()=>e.hoverLabelSeqIds)}})),as=Vf;var Qu=p(Dn());Fn();var Gf="SuperpositionTransform";async function ur(e){let{QueryContext:t,StructureElement:n,StructureSelection:o,StructureSelectionQueries:r,PluginCommands:i,PluginStateObject:s,tmAlign:l}=await He(),a=e.managers.structure.hierarchy.current.structures;if(a.length<2)return;let{query:c}=r.trace,m=a.map(h=>{let b=h.cell.obj?.data;if(!b)return;let x=e.helpers.substructureParent.get(b);if(!x)return;let w=e.state.data.selectQ(f=>f.byValue(x).rootOfType(s.Molecule.Structure))[0]?.obj?.data;if(!w)return;let y=o.toLociWithSourceUnits(c(new t(b)));return n.Loci.remap(y,w)}).filter(h=>h!==void 0);if(m.length<2)return;let g=e.managers.structure.hierarchy.findStructure(m[0]?.structure)?.transform?.cell.obj?.data.coordinateSystem;for(let h=1;h<m.length;h++){let b=l(m[0],m[h]),{bTransform:x,tmScoreA:w,tmScoreB:y,rmsd:f,alignedLength:A}=b;await Hf(e,a[h].cell,x,g),e.log.info(`TM-align: TM-score=${w.toFixed(4)}/${y.toFixed(4)}, RMSD=${f.toFixed(2)} \xC5, aligned ${A} residues.`)}await new Promise(h=>requestAnimationFrame(h)),await i.Camera.Reset(e)}async function Hf(e,t,n,o){let{Mat4:r,StateObjectRef:i,StateTransforms:s}=await He(),l=i.resolveAndCheck(e.state.data,t);if(!l)return;let a=e.state.data.selectQ(d=>d.byRef(l.transform.ref).subtree().withTransformer(s.Model.TransformStructureConformation))[0],u={transform:{name:"matrix",params:{data:o&&!r.isIdentity(o.matrix)?r.mul(r(),o.matrix,n):n,transpose:!1}}},m=a?e.state.data.build().to(a).update(u):e.state.data.build().to(t).insert(s.Model.TransformStructureConformation,u,{tags:Gf});await e.runTask(e.state.data.updateTree(m))}function $u(e){let t=!1,n=0,o;function r(){let{molstarPluginContext:i,structures:s}=e,l=s.filter(a=>a.loadedToMolstar).length;i!==o&&(n=0),i&&!t&&l>=2&&l!==n&&(t=!0,ur(i).catch(a=>{(0,Qu.isAlive)(e)&&(e.setError(a),console.error(a))}).finally(()=>{t=!1,n=l,o=i,r()}))}return r}var Zu="proteinView-settings",ls=["showAlignment","showProteinTracks","showHighlight","zoomToBaseLevel","autoScrollAlignment","compactTracks"],Bf={showAlignment:!0,showProteinTracks:!0,showHighlight:!1,zoomToBaseLevel:!0,autoScrollAlignment:!1,compactTracks:!0};function Uf(){return fe.types.compose("ProteinView",Xu.BaseViewModel,fe.types.model({id:ec.ElementId,type:fe.types.literal("ProteinView"),structures:fe.types.array(as),showControls:!1,height:fe.types.optional(fe.types.number,650),showHighlight:!1,zoomToBaseLevel:!0,autoScrollAlignment:!1,colorScheme:fe.types.optional(fe.types.enumeration("ColorScheme",yu),"default"),showAlignment:!0,showProteinTracks:!0,compactTracks:!0,alignmentAlgorithm:fe.types.optional(fe.types.enumeration("AlignmentAlgorithm",Wr),Wn),connectedMsaViewId:fe.types.maybe(fe.types.string)})).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 n of e.structures)n.setLoadedToMolstar(!1);e.molstarPluginContext=t},setShowManualAlignmentDialog(t){e.showManualAlignmentDialog=t},setShowAddStructureDialog(t){e.showAddStructureDialog=t},setConnectedMsaViewId(t){e.connectedMsaViewId=t},addStructure(t){e.structures.push(as.create(t))}})).actions(e=>({afterAttach(){try{let t=localStorage.getItem(Zu);if(t){let n=JSON.parse(t);for(let o of ls)n[o]!==void 0&&e[o]===Bf[o]&&(e[o]=n[o])}}catch(t){console.error("Failed to restore protein view settings",t)}(0,fe.addDisposer)(e,(0,Vn.reaction)(()=>ls.map(t=>e[t]),()=>{try{let t={};for(let n of ls)t[n]=e[n];localStorage.setItem(Zu,JSON.stringify(t))}catch(t){console.error("Failed to save protein view settings",t)}})),(0,fe.addDisposer)(e,(0,Vn.autorun)(()=>{let{molstarPluginContext:t,colorScheme:n}=e,o=e.structures.filter(r=>r.structureSequences!==void 0).length;t&&o>0&&Su({plugin:t,colorScheme:n}).catch(r=>{console.error(r),e.setError(r)})})),(0,fe.addDisposer)(e,(0,Vn.autorun)(Tu(e))),(0,fe.addDisposer)(e,(0,Vn.autorun)($u(e)))}})).views(e=>({get primaryStructure(){return e.structures[0]},menuItems(){return[{label:"Pairwise alignment",icon:Ki,type:"checkbox",checked:e.showAlignment,onClick:()=>{e.setShowAlignment(!e.showAlignment)}},{label:"Protein feature tracks",icon:Ki,type:"checkbox",checked:e.showProteinTracks,onClick:()=>{e.setShowProteinTracks(!e.showProteinTracks)}},{label:"Color scheme...",subMenu:Nn.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:Pn,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&&ur(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 alignment to hovered position",type:"checkbox",checked:e.autoScrollAlignment,onClick:()=>{e.setAutoScrollAlignment(!e.autoScrollAlignment)}}]}]}}))}var tc=Uf;var Sh=(0,Qm.lazy)(()=>Promise.resolve().then(()=>(Ym(),Jm)));function Ts(e){e.addViewType(()=>new $m.ViewType({name:"ProteinView",displayName:"Protein view",stateModel:tc(),ReactComponent:Sh}))}var rd=p(xo());var Zm=p(en());var wh=(0,Zm.ConfigurationSchema)("UniProtVariationAdapter",{location:{type:"fileLocation",defaultValue:{uri:"/path/to/my.bed.gz",locationType:"UriLocation"}},scoreField:{type:"string",defaultValue:""}},{explicitlyTyped:!0}),Xm=wh;function As(e){e.addAdapterType(()=>new rd.default({name:"UniProtVariationAdapter",displayName:"UniProtVariation adapter",configSchema:Xm,getAdapterClass:()=>Promise.resolve().then(()=>(od(),nd)).then(t=>t.default)}))}var id="0.8.3";var br=class extends sd.default{name="ProteinViewer";version=id;install(t){Ts(t),zi(t),_i(t),Lr(t),Er(t),Fr(t),As(t)}configure(t){}};return gd(xh);})();
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28
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+
`)}function Vi(e){let{tCa:t,tSeq:n}=e;return!!t&&!!n&&t.split(",").length>=3}Pe();function Gi({hit:e,session:t,view:n,feature:o,selectedTranscript:r,userProvidedTranscriptSequence:i,onClose:s}){let[l,a]=(0,$e.useState)(null),c=!!l,u=An(e.target),m=A=>{a(A.currentTarget)},d=()=>{a(null)},{runLaunch:g,launchError:h}=Cn(s,d),b={session:t,view:n,feature:o,selectedTranscript:r,uniprotId:u},x=g(()=>{let A=!e.structureUrl&&Vi(e)?_p(e.tCa,e.tSeq,"A",e.target):void 0;rn({...b,url:e.structureUrl,data:A,userProvidedTranscriptSequence:i})}),{launch1D:w,launchMsa:y}=Vo({...b,confidenceUrl:Sl(e.target)});return!!e.structureUrl||Vi(e)?$e.default.createElement($e.default.Fragment,null,h?$e.default.createElement(Wp.ErrorMessage,{error:h}):null,$e.default.createElement(Ut.Button,{size:"small",variant:"outlined",onClick:m},"Load"),$e.default.createElement(Ut.Menu,{anchorEl:l,open:c,onClose:d},$e.default.createElement(Ut.MenuItem,{"data-testid":"protein-launch-option-3d",onClick:x},Tt["3d"]),w?$e.default.createElement(Ut.MenuItem,{"data-testid":"protein-launch-option-1d",onClick:g(w)},Tt["1d"]):null,y?$e.default.createElement(Ut.MenuItem,{"data-testid":"protein-launch-option-msa",onClick:g(y)},Tt.msa):null)):$e.default.createElement("span",null,"-")}Pe();var tf=(0,Kp.makeStyles)()(e=>({root:{display:"flex",flexDirection:"column",gap:16},tableContainer:{maxHeight:400},headerCell:{fontWeight:"bold",backgroundColor:e.palette.mode==="dark"?e.palette.grey[900]:e.palette.grey[100]},noResults:{padding:16,textAlign:"center"}})),nf=100;function of(e){let t=e.results.flatMap(n=>(n.alignments??[]).flat().map(o=>({...o,db:n.db,structureUrl:yl(o.target,n.db)})));return t.sort((n,o)=>(n.eval??1/0)-(o.eval??1/0)),t}function Hi({results:e,session:t,view:n,feature:o,selectedTranscript:r,userProvidedTranscriptSequence:i,onClose:s}){let{classes:l}=tf(),a=of(e),c=a.slice(0,nf);return c.length===0?j.default.createElement(G.Paper,{className:l.noResults},j.default.createElement(G.Typography,null,"No similar structures found")):j.default.createElement("div",{className:l.root},j.default.createElement(G.Typography,{variant:"subtitle2"},"Found ",a.length," similar structures",a.length>c.length?` (showing top ${c.length})`:""),j.default.createElement(G.TableContainer,{component:G.Paper,className:l.tableContainer},j.default.createElement(G.Table,{size:"small",stickyHeader:!0},j.default.createElement(G.TableHead,null,j.default.createElement(G.TableRow,null,j.default.createElement(G.TableCell,{className:l.headerCell},"Database"),j.default.createElement(G.TableCell,{className:l.headerCell},"Target"),j.default.createElement(G.TableCell,{className:l.headerCell},"Organism"),j.default.createElement(G.TableCell,{className:l.headerCell},"Prob"),j.default.createElement(G.TableCell,{className:l.headerCell},"Seq. 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it=p(S());function Bi(){let[e,t]=(0,it.useState)(),[n,o]=(0,it.useState)(),[r,i]=(0,it.useState)(!1),[s,l]=(0,it.useState)(!1),[a,c]=(0,it.useState)(),[u,m]=(0,it.useState)(""),d=(0,it.useRef)(null);(0,it.useEffect)(()=>()=>{d.current?.abort()},[]);let g=()=>{d.current?.abort();let w=new AbortController;return d.current=w,w.signal},h=async w=>{let y=g();l(!0),c(void 0),m("Predicting 3Di structure...");try{let f=await Up({aaSequence:w,signal:y});return o(f),f}catch(f){y.aborted||(console.error(f),c(f));return}finally{y.aborted||(l(!1),m(""))}},b=async(w,y,f=nr)=>{let A=g();i(!0),c(void 0),m("Submitting search...");try{let P=await Rp({aaSequence:w,di3Sequence:y,databases:f,signal:A}),v=await Op({ticketId:P.id,onStatusChange:m,signal:A});return t(v),v}catch(P){A.aborted||(console.error(P),c(P));return}finally{A.aborted||(i(!1),m(""))}},x=()=>{d.current?.abort(),t(void 0),o(void 0),c(void 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0,mappedEntityIndex:0,structureConfidence:void 0,isMouseInAlignment:!1,loadedToMolstar:!1,molstarStructure:void 0,alignmentHoverRange:void 0,selectedFeatureId:void 0,hiddenFeatureTypes:new Set,expandedFeatureTypes:new Set})).actions(e=>({setStructureData(t){e.entities=t.entities,e.structureConfidence=t.confidence,e.molstarStructure=t.molstarStructure},hideFeatureType(t){e.hiddenFeatureTypes=new Set([...e.hiddenFeatureTypes,t])},showFeatureType(t){let n=new Set(e.hiddenFeatureTypes);n.delete(t),e.hiddenFeatureTypes=n},showAllFeatureTypes(){e.hiddenFeatureTypes=new Set},toggleFeatureTypeExpanded(t){let n=new Set(e.expandedFeatureTypes);n.has(t)?n.delete(t):n.add(t),e.expandedFeatureTypes=n},setLoadedToMolstar(t){e.loadedToMolstar=t,t||(e.molstarStructure=void 0)}})).views(e=>({get connectedView(){let{views:t}=(0,so.getSession)(e);return t.find(n=>n.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},setMappedEntityIndex(t){e.mappedEntityIndex=t},setIsMouseInAlignment(t){e.isMouseInAlignment=t}})).views(e=>({get structureSequences(){return e.entities?.map(t=>t.seq)},get mappedEntity(){return e.entities?.[e.mappedEntityIndex]},get mappedStructureSeq(){return this.mappedEntity?.seq},get mappedEntityId(){return this.mappedEntity?.entityId},get uniprotId(){let{url:t}=e;if(t)return An(t)},get coordinateMapper(){return e.pairwiseAlignment?zu(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 t&&t.entityId===this.mappedEntityId&&xu(t.values)?rs(t.values,this.structurePositionToAlignmentMap):[]},get hydrophobicityCells(){let t=this.mappedStructureSeq;return t?rs(Ku(de(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 n=this.hoverStructureLetter,o=this.hoverGenomeLetter,r=[];return t.structureSeqPos!==void 0&&r.push(`${t.structureSeqPos+1}`),n&&r.push(`Structure: ${n}`),o&&n&&o!==n&&r.push(`Genome: ${o}`),t.chain&&r.push(`Chain: ${t.chain}`),r.join(", ")},get genomeToTranscriptSeqMapping(){return e.feature?wn(new so.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(Ou(t))},get hoverStructureRange(){let{alignmentHoverRange:t}=e,n=this.pairwiseAlignmentToStructurePosition;if(!t||!n)return;let o=n[t.start],r=n[t.end];return o===void 0||r===void 0?void 0:{start:o,end:r+1}},get hoverHighlightRange(){let t=this.structureSeqHoverPos;return this.hoverStructureRange??(t===void 0?void 0:{start:t,end:t+1})},get labelSeqIdIndex(){return yp(this.mappedEntity)},get selectLabelSeqIds(){let t=this.mappedEntity,n=e.clickedStructureRange;if(n)return Ti(t,n);let o=this.structureSeqToTranscriptSeqPosition;return this.showHighlight&&o?bp(t,Object.keys(o).map(Number)):[]},get hoverLabelSeqIds(){return Ti(this.mappedEntity,this.hoverHighlightRange)},get clickAlignmentRange(){let t=e.clickedStructureRange,n=this.structurePositionToAlignmentMap;if(!t||!n)return;let o=n[t.start],r=n[t.end-1];return o===void 0||r===void 0?void 0:{start:o,end:r}},structureRangeToGenomeHighlight(t){let n=e.connectedView?.assemblyNames[0],o=this.genomeToTranscriptSeqMapping;if(!t||!n||!o)return[];let r={genomeToTranscriptSeqMapping:o,pairwiseAlignment:e.pairwiseAlignment,structureSeqToTranscriptSeqPosition:this.structureSeqToTranscriptSeqPosition},i=t.end>t.start+1?ns({model:r,structureSeqPos:t.start,structureSeqEndPos:t.end}):pr({model:r,structureSeqPos:t.start});if(!i)return[];let[s,l]=i;return[{assemblyName:n,refName:o.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 ju[t]?.singleLetterCode;let n=this.structureSeqHoverPos,o=this.mappedStructureSeq;if(n!==void 0&&o)return o[n]},get hoverGenomeLetter(){let t=this.structureSeqHoverPos;if(t===void 0)return;let n=this.structureSeqToTranscriptSeqPosition?.[t];if(n!==void 0)return e.userProvidedTranscriptSequence[n]},get alignmentMatchSet(){let t=e.pairwiseAlignment?.consensus;if(!t)return;let n=new Set;for(let o=0;o<t.length;o++)(t[o]==="|"||t[o]===":")&&n.add(o);return n},get alignmentPending(){return!e.pairwiseAlignment&&!!e.userProvidedTranscriptSequence&&!!this.structureSequences?.length},get exactMatch(){let t=de(e.userProvidedTranscriptSequence),n=this.mappedStructureSeq?de(this.mappedStructureSeq):void 0;return t===n},get parentView(){return(0,ne.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 this.parentView.alignmentAlgorithm},get molstarPluginContext(){return this.parentView.molstarPluginContext}})).actions(e=>({setError(t){e.parentView.setError(t)},hoverAlignmentPosition(t){if(!e.alignmentHoverRange){let n=e.coordinateMapper?.alignmentToStructure(ts(t));e.setHoveredPosition(n!==void 0?{structureSeqPos:n}:void 0)}},clickAlignmentPosition(t){let n=e.coordinateMapper?.alignmentToStructure(ts(t));e.setSelectedFeatureId(void 0),n!==void 0?ro({model:e,structureSeqPos:n}).catch(o=>{console.error(o),e.parentView.setError(o)}):e.setClickedStructureRange(void 0)}})).actions(e=>({afterAttach(){e.initialSelection&&e.setClickedStructureRange(e.initialSelection);let t=(r,i)=>{let s;(0,ne.addDisposer)(e,()=>{s?.()}),(0,ne.addDisposer)(e,(0,io.autorun)(async()=>{let{molstarPluginContext:l}=e;if(s?.(),s=void 0,l){let a=await ss({plugin:l,kind:r,onUpdate:i});(0,ne.isAlive)(e)&&e.molstarPluginContext===l?s=a:a()}}))};(0,ne.addDisposer)(e,(0,io.autorun)(async()=>{try{let{userProvidedTranscriptSequence:r,structureSequences:i,alignmentAlgorithm:s}=e;if(e.pairwiseAlignment||!r||!i?.length)return;let l=Hu(r,i,s);if(!l)return;e.setMappedEntityIndex(l.index),e.setAlignment(l.alignment),l.matches<go(l.alignment)&&e.parentView.setShowAlignment(!0)}catch(r){console.error(r),e.parentView.setError(r)}})),(0,ne.addDisposer)(e,(0,io.autorun)(()=>{let{hovered:r}=(0,so.getSession)(e),{transcriptSeqToStructureSeqPosition:i,genomeToTranscriptSeqMapping:s,connectedView:l}=e,a=l?.initialized?mo(r,s):void 0;a!==void 0?e.setGenomeHoveredPosition(i?.[a]):e.hoverPosition?.source==="genome"&&e.setGenomeHoveredPosition(void 0)}));let n=r=>{if(!r||!Gu(r.entityId,e.coordinateMapper?e.mappedEntityId:void 0))return;let i=e.labelSeqIdIndex.get(r.labelSeqId);return i===void 0?void 0:{...r,structureSeqPos:i}};t("click",r=>{let i=n(r);i&&(e.setHoveredPosition(i),e.setSelectedFeatureId(void 0),ro({model:e,structureSeqPos:i.structureSeqPos}).catch(s=>{console.error(s),e.parentView.setError(s)}))}),t("hover",r=>{e.setHoveredPosition(n(r))});let o=(r,i)=>{(0,ne.addDisposer)(e,(0,io.autorun)(async()=>{let{molstarStructure:s,molstarPluginContext:l}=e,a=i();s&&l&&await Au({structure:s,plugin:l,channel:r,entityId:e.mappedEntityId,labelSeqIds:a})}))};o("select",()=>e.selectLabelSeqIds),o("highlight",()=>e.hoverLabelSeqIds)}})),as=Vf;var Qu=p(Dn());Fn();var Gf="SuperpositionTransform";async function ur(e){let{QueryContext:t,StructureElement:n,StructureSelection:o,StructureSelectionQueries:r,PluginCommands:i,PluginStateObject:s,tmAlign:l}=await He(),a=e.managers.structure.hierarchy.current.structures;if(a.length<2)return;let{query:c}=r.trace,m=a.map(h=>{let b=h.cell.obj?.data;if(!b)return;let x=e.helpers.substructureParent.get(b);if(!x)return;let w=e.state.data.selectQ(f=>f.byValue(x).rootOfType(s.Molecule.Structure))[0]?.obj?.data;if(!w)return;let y=o.toLociWithSourceUnits(c(new t(b)));return n.Loci.remap(y,w)}).filter(h=>h!==void 0);if(m.length<2)return;let g=e.managers.structure.hierarchy.findStructure(m[0]?.structure)?.transform?.cell.obj?.data.coordinateSystem;for(let h=1;h<m.length;h++){let b=l(m[0],m[h]),{bTransform:x,tmScoreA:w,tmScoreB:y,rmsd:f,alignedLength:A}=b;await Hf(e,a[h].cell,x,g),e.log.info(`TM-align: TM-score=${w.toFixed(4)}/${y.toFixed(4)}, RMSD=${f.toFixed(2)} \xC5, aligned ${A} residues.`)}await new Promise(h=>requestAnimationFrame(h)),await i.Camera.Reset(e)}async function Hf(e,t,n,o){let{Mat4:r,StateObjectRef:i,StateTransforms:s}=await He(),l=i.resolveAndCheck(e.state.data,t);if(!l)return;let a=e.state.data.selectQ(d=>d.byRef(l.transform.ref).subtree().withTransformer(s.Model.TransformStructureConformation))[0],u={transform:{name:"matrix",params:{data:o&&!r.isIdentity(o.matrix)?r.mul(r(),o.matrix,n):n,transpose:!1}}},m=a?e.state.data.build().to(a).update(u):e.state.data.build().to(t).insert(s.Model.TransformStructureConformation,u,{tags:Gf});await e.runTask(e.state.data.updateTree(m))}function $u(e){let t=!1,n=0,o;function r(){let{molstarPluginContext:i,structures:s}=e,l=s.filter(a=>a.loadedToMolstar).length;i!==o&&(n=0),i&&!t&&l>=2&&l!==n&&(t=!0,ur(i).catch(a=>{(0,Qu.isAlive)(e)&&(e.setError(a),console.error(a))}).finally(()=>{t=!1,n=l,o=i,r()}))}return r}var Zu="proteinView-settings",ls=["showAlignment","showProteinTracks","showHighlight","zoomToBaseLevel","autoScrollAlignment","compactTracks"],Bf={showAlignment:!0,showProteinTracks:!0,showHighlight:!1,zoomToBaseLevel:!0,autoScrollAlignment:!1,compactTracks:!0};function Uf(){return fe.types.compose("ProteinView",Xu.BaseViewModel,fe.types.model({id:ec.ElementId,type:fe.types.literal("ProteinView"),structures:fe.types.array(as),showControls:!1,height:fe.types.optional(fe.types.number,650),showHighlight:!1,zoomToBaseLevel:!0,autoScrollAlignment:!1,colorScheme:fe.types.optional(fe.types.enumeration("ColorScheme",yu),"default"),showAlignment:!0,showProteinTracks:!0,compactTracks:!0,alignmentAlgorithm:fe.types.optional(fe.types.enumeration("AlignmentAlgorithm",Wr),Wn),connectedMsaViewId:fe.types.maybe(fe.types.string)})).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 n of e.structures)n.setLoadedToMolstar(!1);e.molstarPluginContext=t},setShowManualAlignmentDialog(t){e.showManualAlignmentDialog=t},setShowAddStructureDialog(t){e.showAddStructureDialog=t},setConnectedMsaViewId(t){e.connectedMsaViewId=t},addStructure(t){e.structures.push(as.create(t))}})).actions(e=>({afterAttach(){try{let t=localStorage.getItem(Zu);if(t){let n=JSON.parse(t);for(let o of ls)n[o]!==void 0&&e[o]===Bf[o]&&(e[o]=n[o])}}catch(t){console.error("Failed to restore protein view settings",t)}(0,fe.addDisposer)(e,(0,Vn.reaction)(()=>ls.map(t=>e[t]),()=>{try{let t={};for(let n of ls)t[n]=e[n];localStorage.setItem(Zu,JSON.stringify(t))}catch(t){console.error("Failed to save protein view settings",t)}})),(0,fe.addDisposer)(e,(0,Vn.autorun)(()=>{let{molstarPluginContext:t,colorScheme:n}=e,o=e.structures.filter(r=>r.structureSequences!==void 0).length;t&&o>0&&Su({plugin:t,colorScheme:n}).catch(r=>{console.error(r),e.setError(r)})})),(0,fe.addDisposer)(e,(0,Vn.autorun)(Tu(e))),(0,fe.addDisposer)(e,(0,Vn.autorun)($u(e)))}})).views(e=>({get primaryStructure(){return e.structures[0]},menuItems(){return[{label:"Pairwise alignment",icon:Ki,type:"checkbox",checked:e.showAlignment,onClick:()=>{e.setShowAlignment(!e.showAlignment)}},{label:"Protein feature tracks",icon:Ki,type:"checkbox",checked:e.showProteinTracks,onClick:()=>{e.setShowProteinTracks(!e.showProteinTracks)}},{label:"Color scheme...",subMenu:Nn.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:Pn,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&&ur(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 alignment to hovered position",type:"checkbox",checked:e.autoScrollAlignment,onClick:()=>{e.setAutoScrollAlignment(!e.autoScrollAlignment)}}]}]}}))}var tc=Uf;var Sh=(0,Qm.lazy)(()=>Promise.resolve().then(()=>(Ym(),Jm)));function Ts(e){e.addViewType(()=>new $m.ViewType({name:"ProteinView",displayName:"Protein view",stateModel:tc(),ReactComponent:Sh}))}var rd=p(xo());var Zm=p(en());var wh=(0,Zm.ConfigurationSchema)("UniProtVariationAdapter",{location:{type:"fileLocation",defaultValue:{uri:"/path/to/my.bed.gz",locationType:"UriLocation"}},scoreField:{type:"string",defaultValue:""}},{explicitlyTyped:!0}),Xm=wh;function As(e){e.addAdapterType(()=>new rd.default({name:"UniProtVariationAdapter",displayName:"UniProtVariation adapter",configSchema:Xm,getAdapterClass:()=>Promise.resolve().then(()=>(od(),nd)).then(t=>t.default)}))}var id="0.8.4";var br=class extends sd.default{name="ProteinViewer";version=id;install(t){Ts(t),zi(t),_i(t),Lr(t),Er(t),Fr(t),As(t)}configure(t){}};return gd(xh);})();
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use-sync-external-store/cjs/use-sync-external-store-shim.production.js:
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