npm - jbrowse-plugin-msaview - Versions diffs - 5.2.0 → 5.3.0 - Mend

jbrowse-plugin-msaview 5.2.0 → 5.3.0

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Files changed (84) hide show

package/dist/chunks/renderToSvg-53FEV6IJ.js ADDED Viewed

	@@ -0,0 +1,2 @@
1	+ import{Z as a}from"./chunk-L6CBIH6H.js";import"./chunk-OVAXNTPN.js";import"./chunk-73KAPCJ2.js";import"./chunk-BX4Z274Q.js";import"./chunk-J6KYLXRD.js";import"./chunk-FY3BTKY4.js";export{a as renderToSvg};
2	+ //# sourceMappingURL=renderToSvg-53FEV6IJ.js.map

package/dist/jbrowse-plugin-msaview.esm.js CHANGED Viewed

@@ -1,3 +1,3 @@
-import{g as p,i as ye}from"./chunks/chunk-JFL3LJPO.js";import{a as Me}from"./chunks/chunk-FCWXYIFC.js";import{d as h}from"./chunks/chunk-DECSTFAT.js";import{a as we}from"./chunks/chunk-NSASZ5FM.js";import{a as u,c as f,d as B}from"./chunks/chunk-IBBQUV2I.js";import{a as q}from"./chunks/chunk-2IWD4OO4.js";import{a as P}from"./chunks/chunk-CVLB4VFP.js";import{a as c}from"./chunks/chunk-J6KYLXRD.js";import{a as z,b as i}from"./chunks/chunk-FY3BTKY4.js";var R=z((Ge,D)=>{D.exports=JBrowseExports["@jbrowse/core/Plugin"]});var le=z((pt,me)=>{me.exports=JBrowseExports["@jbrowse/core/pluggableElementTypes/ViewType"]});var de=i(R()),j=i(q()),ge=i(u()),G=i(Me());var $=i(B(),1),O=(0,f.createSvgIcon)((0,$.jsx)("path",{d:"M20 2H4c-1.1 0-2 .9-2 2v16c0 1.1.9 2 2 2h16c1.1 0 2-.9 2-2V4c0-1.1-.9-2-2-2M8 20H4v-4h4zm0-6H4v-4h4zm0-6H4V4h4zm6 12h-4v-4h4zm0-6h-4v-4h4zm0-6h-4V4h4zm6 12h-4v-4h4zm0-6h-4v-4h4zm0-6h-4V4h4z"}),"GridOn");var Z=i(c()),ee=i(u());function M(e){return e.type==="MsaView"}var g=i(c()),X=i(P());var V=i(c()),J=i(u()),v=i(P());var _=i(we()),w=(0,_.makeStyles)()({highlight:{height:"100%",background:"rgba(255,255,0,0.2)",border:"1px solid rgba(50,50,0,0.2)",position:"absolute",zIndex:99,textAlign:"center",pointerEvents:"none",overflow:"hidden"}});var be=(0,v.observer)(function({model:e}){let{hovered:t,views:r}=(0,J.getSession)(e);return r.some(o=>M(o)&&o.connectedViewId===e.id)&&p(t)?V.default.createElement(xe,{model:e,hovered:t}):null}),xe=(0,v.observer)(function({model:e,hovered:t}){let{classes:r}=w(),{offsetPx:n}=e,{coord:o,refName:s}=t.hoverPosition,a=e.bpToPx({refName:s,coord:o-1}),m=e.bpToPx({refName:s,coord:o});if(a&&m){let l=Math.max(Math.abs(m.offsetPx-a.offsetPx),4),b=Math.min(a.offsetPx,m.offsetPx)-n;return V.default.createElement("div",{className:r.highlight,style:{left:b,width:l}})}return null}),W=be;var d=i(c()),K=i(u()),T=i(P());function U(e,t,r){let n=e.filter(Pe).filter(o=>o.connectedViewId===t).flatMap(o=>[...o.connectedClickHighlights,...r?[]:o.connectedHoverHighlights]);return[...new Map(n.map(o=>[`${o.refName}:${o.start}-${o.end}`,o])).values()]}function Pe(e){return e.type==="MsaView"}var Ve=(0,T.observer)(function({model:t}){let{views:r,hovered:n}=(0,K.getSession)(t),o=U(r,t.id,p(n));return o.length?d.default.createElement(ve,{model:t,highlights:o}):null}),ve=(0,T.observer)(function({model:e,highlights:t}){let{classes:r}=w(),{offsetPx:n}=e;return d.default.createElement(d.default.Fragment,null,t.map(o=>{let s=e.bpToPx({refName:o.refName,coord:o.start}),a=e.bpToPx({refName:o.refName,coord:o.end});if(s&&a){let m=Math.max(Math.abs(a.offsetPx-s.offsetPx),4),l=Math.min(s.offsetPx,a.offsetPx)-n;return d.default.createElement("div",{key:`${o.refName}-${o.start}-${o.end}`,className:r.highlight,style:{left:l,width:m}})}return null}))}),Q=Ve;var Te=(0,X.observer)(function({model:t}){return g.default.createElement(g.default.Fragment,null,g.default.createElement(Q,{model:t}),g.default.createElement(W,{model:t}))}),Y=Te;function S(e){e.contributeToExtensionPoint("LinearGenomeView-TracksContainerComponent",({model:t})=>{let{views:r}=(0,ee.getSession)(t);return r.some(n=>M(n)&&n.connectedViewId===t.id)?Z.default.createElement(Y,{key:"highlight_protein_viewer_msaview",model:t}):void 0})}var oe=i(ye());var te=i(q());function F(e){let t=e.getAdapterType("BgzipFastaAdapter");return(0,te.ConfigurationSchema)("BgzipFastaMsaAdapter",{msaRegex:{type:"string",defaultValue:"_"}},{baseConfiguration:t.configSchema})}function L(e){return e.addAdapterType(()=>new oe.AdapterType({name:"BgzipFastaMsaAdapter",configSchema:F(e),adapterMetadata:{hiddenFromGUI:!0},getAdapterClass:()=>import("./chunks/BgzipFastaMsaAdapter-WWIGI57O.js").then(t=>t.default)}))}var se=i(c()),y=i(u());var re=i(B(),1),ne=(0,f.createSvgIcon)((0,re.jsx)("path",{d:"M19 13h-6v6h-2v-6H5v-2h6V5h2v6h6z"}),"Add");function Se(e){return e.get("type")?.toLowerCase()==="cds"}function I(e){return Se(e)||!!e.get("subfeatures")?.some(I)}var ie=i(u());function ae(e){let t=e.contextMenuInfo;return t&&(0,ie.isGeneLikeType)(t.item.type)?{fetchFeature:()=>e.fetchFullFeature(t.item.featureId,t.displayedRegionIndex),preferredTranscriptId:t.subfeature?.featureId}:void 0}var Fe=(0,se.lazy)(()=>import("./chunks/LaunchMsaViewDialog-GJAUPGFC.js"));function Le(e){return e.name==="LinearBasicDisplay"}function Ie(e){return e.get("name")??e.get("id")??"This feature"}function Ae(e,t){let r=(0,y.getContainingTrack)(e),n=(0,y.getSession)(r),{preferredTranscriptId:o}=t,s=a=>{n.queueDialog(m=>[Fe,{model:r,handleClose:m,feature:a,preferredTranscriptId:o}])};t.fetchFeature().then(a=>{a?I(a)?s(a):n.notify(`${Ie(a)} has no coding sequence, so there is no protein to align`,"info"):n.notify("Could not load feature for MSA view","warning")}).catch(a=>{n.notifyError(`${a}`,a)})}function Ce(e){return e.views(t=>{let r=t.contextMenuItems;return{contextMenuItems(){let n=ae(t);return[...r.call(t),...n?[{label:"Launch MSA view",icon:ne,onClick:()=>{Ae(t,n)}}]:[]]}}})}function A(e){e.addToExtensionPoint("Core-extendPluggableElement",t=>(Le(t)&&(t.stateModel=Ce(t.stateModel)),t))}function He({msa:e,tree:t,...r}){let n=e?.includes(`
-`)?e:void 0,o=t?.trimStart().startsWith("(")?t:void 0,s=n||o?{...r.data,...n?{msa:n}:{},...o?{tree:o}:{}}:r.data;return{...r,data:s,...e&&!n?{msaFileLocation:{uri:e}}:{},...t&&!o?{treeFileLocation:{uri:t}}:{},querySeqName:r.querySeqName??r.query}}function C(e){e.addToExtensionPoint("LaunchView-MsaView",async t=>{let{session:r,query:n,data:o,msaFileLocation:s,msaIndexedLocation:a,msaName:m,treeFileLocation:l,querySeqName:b,searchParams:x,...N}=He(t);if(!o&&!s&&!a&&!N.orthologParams&&!x)throw new Error("No MSA data, file location, orthologParams or searchParams provided when launching MSA view");let E={msaUrl:s?.uri,msaIndexedLocation:a,msaName:m,querySeqName:b},{expandSpec:fe}=await import("./chunks/dist-R73J3CC3.js");return await h(r,{...fe({...N,query:n}),...x?{blastParams:x}:{},data:o,...l?{treeFilehandle:{...l,locationType:"UriLocation"}}:{},...Object.values(E).some(he=>he!==void 0)?{init:E}:{}}),t})}var ue=i(c()),ce=i(le()),je=(0,ue.lazy)(()=>import("./chunks/MsaViewPanel-RUZAKFCB.js"));function H(e){e.addViewType(()=>new ce.default({name:"MsaView",stateModel:()=>import("./chunks/model-VE7IYWNU.js").then(t=>t.default()),ReactComponent:je}))}var pe="5.2.0";var k=class extends de.default{constructor(){super(...arguments);this.name="MsaViewPlugin";this.version=pe;this.rootConfigurationSchema=r=>({msa:(0,j.ConfigurationSchema)("MSA",{datasets:G.types.maybe(G.types.array((0,j.ConfigurationSchema)("MSAEntry",{datasetId:{type:"string",defaultValue:""},description:{type:"string",defaultValue:""},name:{type:"string",defaultValue:""},adapter:r.pluggableConfigSchemaType("adapter")})))})})}install(r){H(r),A(r),C(r),S(r),L(r)}configure(r){try{(0,ge.isAbstractMenuManager)(r.rootModel)&&r.rootModel.appendToSubMenu(["Add"],{label:"Multiple sequence alignment view",icon:O,onClick:n=>{h(n,{}).catch(o=>{console.error(o),n.notifyError(`${o}`,o)})}})}catch(n){console.error("jbrowse-plugin-msaview: could not add the Add menu item",n)}}};export{k as default};
+import{g as p,i as ye}from"./chunks/chunk-JFL3LJPO.js";import{a as Me}from"./chunks/chunk-FCWXYIFC.js";import{d as h}from"./chunks/chunk-DECSTFAT.js";import{a as we}from"./chunks/chunk-NSASZ5FM.js";import{a as u,c as f,d as B}from"./chunks/chunk-IBBQUV2I.js";import{a as q}from"./chunks/chunk-2IWD4OO4.js";import{a as P}from"./chunks/chunk-CVLB4VFP.js";import{a as c}from"./chunks/chunk-J6KYLXRD.js";import{a as z,b as i}from"./chunks/chunk-FY3BTKY4.js";var R=z((Ge,D)=>{D.exports=JBrowseExports["@jbrowse/core/Plugin"]});var le=z((pt,me)=>{me.exports=JBrowseExports["@jbrowse/core/pluggableElementTypes/ViewType"]});var de=i(R()),j=i(q()),ge=i(u()),G=i(Me());var $=i(B(),1),O=(0,f.createSvgIcon)((0,$.jsx)("path",{d:"M20 2H4c-1.1 0-2 .9-2 2v16c0 1.1.9 2 2 2h16c1.1 0 2-.9 2-2V4c0-1.1-.9-2-2-2M8 20H4v-4h4zm0-6H4v-4h4zm0-6H4V4h4zm6 12h-4v-4h4zm0-6h-4v-4h4zm0-6h-4V4h4zm6 12h-4v-4h4zm0-6h-4v-4h4zm0-6h-4V4h4z"}),"GridOn");var Z=i(c()),ee=i(u());function M(e){return e.type==="MsaView"}var g=i(c()),X=i(P());var V=i(c()),J=i(u()),v=i(P());var _=i(we()),w=(0,_.makeStyles)()({highlight:{height:"100%",background:"rgba(255,255,0,0.2)",border:"1px solid rgba(50,50,0,0.2)",position:"absolute",zIndex:99,textAlign:"center",pointerEvents:"none",overflow:"hidden"}});var be=(0,v.observer)(function({model:e}){let{hovered:t,views:r}=(0,J.getSession)(e);return r.some(o=>M(o)&&o.connectedViewId===e.id)&&p(t)?V.default.createElement(xe,{model:e,hovered:t}):null}),xe=(0,v.observer)(function({model:e,hovered:t}){let{classes:r}=w(),{offsetPx:n}=e,{coord:o,refName:s}=t.hoverPosition,a=e.bpToPx({refName:s,coord:o-1}),m=e.bpToPx({refName:s,coord:o});if(a&&m){let l=Math.max(Math.abs(m.offsetPx-a.offsetPx),4),b=Math.min(a.offsetPx,m.offsetPx)-n;return V.default.createElement("div",{className:r.highlight,style:{left:b,width:l}})}return null}),W=be;var d=i(c()),K=i(u()),T=i(P());function U(e,t,r){let n=e.filter(Pe).filter(o=>o.connectedViewId===t).flatMap(o=>[...o.connectedClickHighlights,...r?[]:o.connectedHoverHighlights]);return[...new Map(n.map(o=>[`${o.refName}:${o.start}-${o.end}`,o])).values()]}function Pe(e){return e.type==="MsaView"}var Ve=(0,T.observer)(function({model:t}){let{views:r,hovered:n}=(0,K.getSession)(t),o=U(r,t.id,p(n));return o.length?d.default.createElement(ve,{model:t,highlights:o}):null}),ve=(0,T.observer)(function({model:e,highlights:t}){let{classes:r}=w(),{offsetPx:n}=e;return d.default.createElement(d.default.Fragment,null,t.map(o=>{let s=e.bpToPx({refName:o.refName,coord:o.start}),a=e.bpToPx({refName:o.refName,coord:o.end});if(s&&a){let m=Math.max(Math.abs(a.offsetPx-s.offsetPx),4),l=Math.min(s.offsetPx,a.offsetPx)-n;return d.default.createElement("div",{key:`${o.refName}-${o.start}-${o.end}`,className:r.highlight,style:{left:l,width:m}})}return null}))}),Q=Ve;var Te=(0,X.observer)(function({model:t}){return g.default.createElement(g.default.Fragment,null,g.default.createElement(Q,{model:t}),g.default.createElement(W,{model:t}))}),Y=Te;function S(e){e.contributeToExtensionPoint("LinearGenomeView-TracksContainerComponent",({model:t})=>{let{views:r}=(0,ee.getSession)(t);return r.some(n=>M(n)&&n.connectedViewId===t.id)?Z.default.createElement(Y,{key:"highlight_protein_viewer_msaview",model:t}):void 0})}var oe=i(ye());var te=i(q());function F(e){let t=e.getAdapterType("BgzipFastaAdapter");return(0,te.ConfigurationSchema)("BgzipFastaMsaAdapter",{msaRegex:{type:"string",defaultValue:"_"}},{baseConfiguration:t.configSchema})}function L(e){return e.addAdapterType(()=>new oe.AdapterType({name:"BgzipFastaMsaAdapter",configSchema:F(e),adapterMetadata:{hiddenFromGUI:!0},getAdapterClass:()=>import("./chunks/BgzipFastaMsaAdapter-WWIGI57O.js").then(t=>t.default)}))}var se=i(c()),y=i(u());var re=i(B(),1),ne=(0,f.createSvgIcon)((0,re.jsx)("path",{d:"M19 13h-6v6h-2v-6H5v-2h6V5h2v6h6z"}),"Add");function Se(e){return e.get("type")?.toLowerCase()==="cds"}function I(e){return Se(e)||!!e.get("subfeatures")?.some(I)}var ie=i(u());function ae(e){let t=e.contextMenuInfo;return t&&(0,ie.isGeneLikeType)(t.item.type)?{fetchFeature:()=>e.fetchFullFeature(t.item.featureId,t.displayedRegionIndex),preferredTranscriptId:t.subfeature?.featureId}:void 0}var Fe=(0,se.lazy)(()=>import("./chunks/LaunchMsaViewDialog-R6CNRASN.js"));function Le(e){return e.name==="LinearBasicDisplay"}function Ie(e){return e.get("name")??e.get("id")??"This feature"}function Ae(e,t){let r=(0,y.getContainingTrack)(e),n=(0,y.getSession)(r),{preferredTranscriptId:o}=t,s=a=>{n.queueDialog(m=>[Fe,{model:r,handleClose:m,feature:a,preferredTranscriptId:o}])};t.fetchFeature().then(a=>{a?I(a)?s(a):n.notify(`${Ie(a)} has no coding sequence, so there is no protein to align`,"info"):n.notify("Could not load feature for MSA view","warning")}).catch(a=>{n.notifyError(`${a}`,a)})}function Ce(e){return e.views(t=>{let r=t.contextMenuItems;return{contextMenuItems(){let n=ae(t);return[...r.call(t),...n?[{label:"Launch MSA view",icon:ne,onClick:()=>{Ae(t,n)}}]:[]]}}})}function A(e){e.addToExtensionPoint("Core-extendPluggableElement",t=>(Le(t)&&(t.stateModel=Ce(t.stateModel)),t))}function He({msa:e,tree:t,...r}){let n=e?.includes(`
+`)?e:void 0,o=t?.trimStart().startsWith("(")?t:void 0,s=n||o?{...r.data,...n?{msa:n}:{},...o?{tree:o}:{}}:r.data;return{...r,data:s,...e&&!n?{msaFileLocation:{uri:e}}:{},...t&&!o?{treeFileLocation:{uri:t}}:{},querySeqName:r.querySeqName??r.query}}function C(e){e.addToExtensionPoint("LaunchView-MsaView",async t=>{let{session:r,query:n,data:o,msaFileLocation:s,msaIndexedLocation:a,msaName:m,treeFileLocation:l,querySeqName:b,searchParams:x,...N}=He(t);if(!o&&!s&&!a&&!N.orthologParams&&!x)throw new Error("No MSA data, file location, orthologParams or searchParams provided when launching MSA view");let E={msaUrl:s?.uri,msaIndexedLocation:a,msaName:m,querySeqName:b},{expandSpec:fe}=await import("./chunks/dist-N4ZJK63Q.js");return await h(r,{...fe({...N,query:n}),...x?{blastParams:x}:{},data:o,...l?{treeFilehandle:{...l,locationType:"UriLocation"}}:{},...Object.values(E).some(he=>he!==void 0)?{init:E}:{}}),t})}var ue=i(c()),ce=i(le()),je=(0,ue.lazy)(()=>import("./chunks/MsaViewPanel-R2WAER5O.js"));function H(e){e.addViewType(()=>new ce.default({name:"MsaView",stateModel:()=>import("./chunks/model-TCPB6WNJ.js").then(t=>t.default()),ReactComponent:je}))}var pe="5.3.0";var k=class extends de.default{constructor(){super(...arguments);this.name="MsaViewPlugin";this.version=pe;this.rootConfigurationSchema=r=>({msa:(0,j.ConfigurationSchema)("MSA",{datasets:G.types.maybe(G.types.array((0,j.ConfigurationSchema)("MSAEntry",{datasetId:{type:"string",defaultValue:""},description:{type:"string",defaultValue:""},name:{type:"string",defaultValue:""},adapter:r.pluggableConfigSchemaType("adapter")})))})})}install(r){H(r),A(r),C(r),S(r),L(r)}configure(r){try{(0,ge.isAbstractMenuManager)(r.rootModel)&&r.rootModel.appendToSubMenu(["Add"],{label:"Multiple sequence alignment view",icon:O,onClick:n=>{h(n,{}).catch(o=>{console.error(o),n.notifyError(`${o}`,o)})}})}catch(n){console.error("jbrowse-plugin-msaview: could not add the Add menu item",n)}}};export{k as default};
 //# sourceMappingURL=jbrowse-plugin-msaview.esm.js.map

package/dist/jbrowse-plugin-msaview.esm.js.map CHANGED Viewed

@@ -1,7 +1,7 @@
 {
   "version": 3,
   "sources": ["global-externals:@jbrowse/core/Plugin", "global-externals:@jbrowse/core/pluggableElementTypes/ViewType", "../src/index.ts", "../node_modules/.pnpm/@mui+icons-material@9.4.0_@mui+material@9.4.0_@emotion+react@11.14.0_@types+react@19.3._3766ec55733e6b150ee672ad270cc236/node_modules/@mui/icons-material/GridOn.mjs", "../src/AddHighlightModel/index.tsx", "../src/MsaViewPanel/isMsaView.ts", "../src/AddHighlightModel/HighlightComponents.tsx", "../src/AddHighlightModel/GenomeMouseoverHighlight.tsx", "../src/AddHighlightModel/util.ts", "../src/AddHighlightModel/MsaToGenomeHighlight.tsx", "../src/AddHighlightModel/connectedHighlights.ts", "../src/BgzipFastaMsaAdapter/index.ts", "../src/BgzipFastaMsaAdapter/configSchema.ts", "../src/LaunchMsaView/index.ts", "../node_modules/.pnpm/@mui+icons-material@9.4.0_@mui+material@9.4.0_@emotion+react@11.14.0_@types+react@19.3._3766ec55733e6b150ee672ad270cc236/node_modules/@mui/icons-material/Add.mjs", "../src/LaunchMsaView/codingFeature.ts", "../src/LaunchMsaView/launchTarget.ts", "../src/LaunchMsaViewExtensionPoint/index.ts", "../src/MsaViewPanel/index.ts", "../src/version.ts"],
-  "sourcesContent": ["module.exports = JBrowseExports[\"@jbrowse/core/Plugin\"];", "module.exports = JBrowseExports[\"@jbrowse/core/pluggableElementTypes/ViewType\"];", "import Plugin from '@jbrowse/core/Plugin'\nimport { ConfigurationSchema } from '@jbrowse/core/configuration'\nimport { isAbstractMenuManager } from '@jbrowse/core/util'\nimport { types } from '@jbrowse/mobx-state-tree'\nimport GridOn from '@mui/icons-material/GridOn'\n\nimport AddHighlightModelF from './AddHighlightModel'\nimport BgzipFastaMsaAdapterF from './BgzipFastaMsaAdapter'\nimport LaunchMsaViewF from './LaunchMsaView'\nimport LaunchMsaViewExtensionPointF from './LaunchMsaViewExtensionPoint'\nimport MsaViewF from './MsaViewPanel'\nimport { launchMsaView } from './utils/launchMsaView'\nimport { version } from './version'\n\nimport type PluginManager from '@jbrowse/core/PluginManager'\nimport type { AbstractSessionModel } from '@jbrowse/core/util'\n\nexport default class MsaViewPlugin extends Plugin {\n  name = 'MsaViewPlugin'\n  version = version\n\n  install(pluginManager: PluginManager) {\n    MsaViewF(pluginManager)\n    LaunchMsaViewF(pluginManager)\n    LaunchMsaViewExtensionPointF(pluginManager)\n    AddHighlightModelF(pluginManager)\n    BgzipFastaMsaAdapterF(pluginManager)\n  }\n\n  configure(pluginManager: PluginManager) {\n    // a throw here error-pages the whole app, and a menu entry is not worth a\n    // session\n    try {\n      if (isAbstractMenuManager(pluginManager.rootModel)) {\n        pluginManager.rootModel.appendToSubMenu(['Add'], {\n          label: 'Multiple sequence alignment view',\n          icon: GridOn,\n          onClick: (session: AbstractSessionModel) => {\n            // stacked, by default: nothing was launched from, so there is no\n            // connected view for it to sit beside\n            launchMsaView(session, {}).catch((e: unknown) => {\n              console.error(e)\n              session.notifyError(`${e}`, e)\n            })\n          },\n        })\n      }\n    } catch (e) {\n      console.error(\n        'jbrowse-plugin-msaview: could not add the Add menu item',\n        e,\n      )\n    }\n  }\n\n  rootConfigurationSchema = (pluginManager: PluginManager) => {\n    return {\n      msa: ConfigurationSchema('MSA', {\n        datasets: types.maybe(\n          types.array(\n            ConfigurationSchema('MSAEntry', {\n              datasetId: {\n                type: 'string',\n                defaultValue: '',\n              },\n              description: {\n                type: 'string',\n                defaultValue: '',\n              },\n              name: {\n                type: 'string',\n                defaultValue: '',\n              },\n              adapter: pluginManager.pluggableConfigSchemaType('adapter'),\n            }),\n          ),\n        ),\n      }),\n    }\n  }\n}\n", "\"use client\";\n\nimport createSvgIcon from \"./utils/createSvgIcon.mjs\";\nimport { jsx as _jsx } from \"react/jsx-runtime\";\nexport default createSvgIcon(/*#__PURE__*/_jsx(\"path\", {\n  d: \"M20 2H4c-1.1 0-2 .9-2 2v16c0 1.1.9 2 2 2h16c1.1 0 2-.9 2-2V4c0-1.1-.9-2-2-2M8 20H4v-4h4zm0-6H4v-4h4zm0-6H4V4h4zm6 12h-4v-4h4zm0-6h-4v-4h4zm0-6h-4V4h4zm6 12h-4v-4h4zm0-6h-4v-4h4zm0-6h-4V4h4z\"\n}), 'GridOn');", "import React from 'react'\n\nimport { getSession } from '@jbrowse/core/util'\n\nimport { isMsaView } from '../MsaViewPanel/isMsaView'\nimport HighlightComponents from './HighlightComponents'\n\nimport type PluginManager from '@jbrowse/core/PluginManager'\n\nexport default function AddHighlightComponentsModelF(\n  pluginManager: PluginManager,\n) {\n  pluginManager.contributeToExtensionPoint(\n    'LinearGenomeView-TracksContainerComponent',\n    ({ model }) => {\n      const { views } = getSession(model)\n      return views.some(v => isMsaView(v) && v.connectedViewId === model.id) ? (\n        <HighlightComponents\n          key=\"highlight_protein_viewer_msaview\"\n          model={model}\n        />\n      ) : undefined\n    },\n  )\n}\n", "import type { JBrowsePluginMsaViewModel } from './model'\n\nexport function isMsaView(view: {\n  type: string\n}): view is JBrowsePluginMsaViewModel {\n  return view.type === 'MsaView'\n}\n", "import React from 'react'\n\nimport { observer } from 'mobx-react'\n\nimport GenomeMouseoverHighlight from './GenomeMouseoverHighlight'\nimport MsaToGenomeHighlight from './MsaToGenomeHighlight'\n\nimport type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'\n\ntype LGV = LinearGenomeViewModel\n\nconst HighlightComponents = observer(function HighlightComponents2({\n  model,\n}: {\n  model: LGV\n}) {\n  return (\n    <>\n      <MsaToGenomeHighlight model={model} />\n      <GenomeMouseoverHighlight model={model} />\n    </>\n  )\n})\n\nexport default HighlightComponents\n", "import React from 'react'\n\nimport { getSession } from '@jbrowse/core/util'\nimport { observer } from 'mobx-react'\n\nimport { isMsaView } from '../MsaViewPanel/isMsaView'\nimport { hasHoverPosition, useStyles } from './util'\n\nimport type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'\n\nconst GenomeMouseoverHighlight = observer(function ({\n  model,\n}: {\n  model: LinearGenomeViewModel\n}) {\n  const { hovered, views } = getSession(model)\n  const hasMsaView = views.some(\n    s => isMsaView(s) && s.connectedViewId === model.id,\n  )\n  return hasMsaView && hasHoverPosition(hovered) ? (\n    <GenomeMouseoverHighlightRenderer model={model} hovered={hovered} />\n  ) : null\n})\n\nconst GenomeMouseoverHighlightRenderer = observer(function ({\n  model,\n  hovered,\n}: {\n  model: LinearGenomeViewModel\n  hovered: { hoverPosition: { coord: number; refName: string } }\n}) {\n  const { classes } = useStyles()\n  const { offsetPx } = model\n  const { coord, refName } = hovered.hoverPosition\n\n  const s = model.bpToPx({ refName, coord: coord - 1 })\n  const e = model.bpToPx({ refName, coord })\n\n  if (s && e) {\n    const width = Math.max(Math.abs(e.offsetPx - s.offsetPx), 4)\n    const left = Math.min(s.offsetPx, e.offsetPx) - offsetPx\n    return <div className={classes.highlight} style={{ left, width }} />\n  }\n\n  return null\n})\n\nexport default GenomeMouseoverHighlight\n", "import { makeStyles } from 'tss-react/mui'\n\nexport { hasHoverPosition } from '../MsaViewPanel/util'\n\nexport const useStyles = makeStyles()({\n  highlight: {\n    height: '100%',\n    background: 'rgba(255,255,0,0.2)',\n    border: '1px solid rgba(50,50,0,0.2)',\n    position: 'absolute',\n    zIndex: 99,\n    textAlign: 'center',\n    pointerEvents: 'none',\n    overflow: 'hidden',\n  },\n})\n", "import React from 'react'\n\nimport { getSession } from '@jbrowse/core/util'\nimport { observer } from 'mobx-react'\n\nimport { connectedHighlights } from './connectedHighlights'\nimport { hasHoverPosition, useStyles } from './util'\n\nimport type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'\n\ntype LGV = LinearGenomeViewModel\n\nconst MsaToGenomeHighlight = observer(function MsaToGenomeHighlight2({\n  model,\n}: {\n  model: LGV\n}) {\n  const { views, hovered } = getSession(model)\n  const highlights = connectedHighlights(\n    views,\n    model.id,\n    hasHoverPosition(hovered),\n  )\n\n  return highlights.length ? (\n    <MsaToGenomeHighlightRenderer model={model} highlights={highlights} />\n  ) : null\n})\n\nconst MsaToGenomeHighlightRenderer = observer(function ({\n  model,\n  highlights,\n}: {\n  model: LGV\n  highlights: { refName: string; start: number; end: number }[]\n}) {\n  const { classes } = useStyles()\n  const { offsetPx } = model\n\n  return (\n    <>\n      {highlights.map(r => {\n        // bpToPx matches refNames exactly, so canonicalizing \"chr17\" to \"17\"\n        // would miss a view whose regions say \"chr17\"\n        const s = model.bpToPx({ refName: r.refName, coord: r.start })\n        const e = model.bpToPx({ refName: r.refName, coord: r.end })\n        if (s && e) {\n          const width = Math.max(Math.abs(e.offsetPx - s.offsetPx), 4)\n          const left = Math.min(s.offsetPx, e.offsetPx) - offsetPx\n          return (\n            <div\n              key={`${r.refName}-${r.start}-${r.end}`}\n              className={classes.highlight}\n              style={{ left, width }}\n            />\n          )\n        }\n        return null\n      })}\n    </>\n  )\n})\n\nexport default MsaToGenomeHighlight\n", "interface Region {\n  refName: string\n  start: number\n  end: number\n}\n\ninterface LinkedView {\n  type: string\n  connectedViewId?: string\n  connectedClickHighlights: Region[]\n  connectedHoverHighlights: Region[]\n}\n\nexport function connectedHighlights(\n  views: readonly { type: string }[],\n  genomeViewId: string,\n  genomeHovered: boolean,\n) {\n  const regions = views\n    .filter(isLinkedMsaView)\n    .filter(v => v.connectedViewId === genomeViewId)\n    .flatMap(v => [\n      ...v.connectedClickHighlights,\n      ...(genomeHovered ? [] : v.connectedHoverHighlights),\n    ])\n  return [\n    ...new Map(\n      regions.map(r => [`${r.refName}:${r.start}-${r.end}`, r]),\n    ).values(),\n  ]\n}\n\nfunction isLinkedMsaView(view: { type: string }): view is LinkedView {\n  return view.type === 'MsaView'\n}\n", "import { AdapterType } from '@jbrowse/core/pluggableElementTypes'\n\nimport configSchemaF from './configSchema'\n\nimport type PluginManager from '@jbrowse/core/PluginManager'\n\nexport default function BgzipFastaMsaAdapterF(pluginManager: PluginManager) {\n  return pluginManager.addAdapterType(() => {\n    return new AdapterType({\n      name: 'BgzipFastaMsaAdapter',\n      configSchema: configSchemaF(pluginManager),\n      adapterMetadata: {\n        hiddenFromGUI: true,\n      },\n      getAdapterClass: () =>\n        import('./BgzipFastaMsaAdapter').then(t => t.default),\n    })\n  })\n}\n", "import { ConfigurationSchema } from '@jbrowse/core/configuration'\n\nimport type PluginManager from '@jbrowse/core/PluginManager'\n\nexport default function configSchemaF(pluginManager: PluginManager) {\n  const base = pluginManager.getAdapterType('BgzipFastaAdapter')\n  return ConfigurationSchema(\n    'BgzipFastaMsaAdapter',\n    {\n      msaRegex: {\n        type: 'string',\n        defaultValue: '_',\n      },\n    },\n    {\n      baseConfiguration: base.configSchema,\n    },\n  )\n}\n", "import { lazy } from 'react'\n\nimport { getContainingTrack, getSession } from '@jbrowse/core/util'\nimport AddIcon from '@mui/icons-material/Add'\n\nimport { isCodingFeature } from './codingFeature'\nimport { launchTarget } from './launchTarget'\n\nimport type { DisplayModel, MenuTarget } from './launchTarget'\nimport type PluginManager from '@jbrowse/core/PluginManager'\nimport type { PluggableElementType } from '@jbrowse/core/pluggableElementTypes'\nimport type DisplayType from '@jbrowse/core/pluggableElementTypes/DisplayType'\nimport type { Feature } from '@jbrowse/core/util'\nimport type { IAnyModelType } from '@jbrowse/mobx-state-tree'\n\nconst LaunchMsaViewDialog = lazy(\n  () => import('./components/LaunchMsaViewDialog'),\n)\n\nfunction isDisplay(elt: { name: string }): elt is DisplayType {\n  return elt.name === 'LinearBasicDisplay'\n}\n\n// Walking to the track and the session at click time, not while the menu is\n// built: contextMenuItems runs on every right-click and, on a host whose base\n// method reads `this`, is the one place a plugin can take the whole menu down.\n// Keeping it to a pure read of the display is also what lets a test call it.\nfunction featureName(feature: Feature) {\n  return feature.get('name') ?? feature.get('id') ?? 'This feature'\n}\n\nfunction openDialog(self: DisplayModel, target: MenuTarget) {\n  const track = getContainingTrack(self)\n  const session = getSession(track)\n  const { preferredTranscriptId } = target\n  const open = (feature: Feature) => {\n    session.queueDialog(handleClose => [\n      LaunchMsaViewDialog,\n      { model: track, handleClose, feature, preferredTranscriptId },\n    ])\n  }\n  target\n    .fetchFeature()\n    .then(feature => {\n      if (!feature) {\n        session.notify('Could not load feature for MSA view', 'warning')\n      } else if (!isCodingFeature(feature)) {\n        // the canvas hit test carries a type and nothing else, so this is the\n        // first point at which the CDS can be looked for. Saying so beats\n        // opening a dialog whose Submit never leaves grey.\n        session.notify(\n          `${featureName(feature)} has no coding sequence, so there is no protein to align`,\n          'info',\n        )\n      } else {\n        open(feature)\n      }\n    })\n    .catch((e: unknown) => {\n      session.notifyError(`${e}`, e)\n    })\n}\n\nexport function extendStateModel(stateModel: IAnyModelType) {\n  return stateModel.views((self: DisplayModel) => {\n    const superContextMenuItems = self.contextMenuItems\n    return {\n      contextMenuItems() {\n        const target = launchTarget(self)\n        return [\n          // a detached call leaves `this` undefined for a host method that\n          // reads it, and the throw takes the host's own rows with it\n          ...superContextMenuItems.call(self),\n          ...(target\n            ? [\n                {\n                  label: 'Launch MSA view',\n                  icon: AddIcon,\n                  onClick: () => {\n                    openDialog(self, target)\n                  },\n                },\n              ]\n            : []),\n        ]\n      },\n    }\n  })\n}\n\nexport default function LaunchMsaViewF(pluginManager: PluginManager) {\n  pluginManager.addToExtensionPoint(\n    'Core-extendPluggableElement',\n    (elt: PluggableElementType) => {\n      if (isDisplay(elt)) {\n        elt.stateModel = extendStateModel(elt.stateModel)\n      }\n      return elt\n    },\n  )\n}\n", "\"use client\";\n\nimport createSvgIcon from \"./utils/createSvgIcon.mjs\";\nimport { jsx as _jsx } from \"react/jsx-runtime\";\nexport default createSvgIcon(/*#__PURE__*/_jsx(\"path\", {\n  d: \"M19 13h-6v6h-2v-6H5v-2h6V5h2v6h6z\"\n}), 'Add');", "import type { Feature } from '@jbrowse/core/util'\n\nfunction isCDS(feature: Feature) {\n  return feature.get('type')?.toLowerCase() === 'cds'\n}\n\n// The feature itself counts: a viral polyprotein hangs its cleavage products\n// off its CDS rather than off further CDSs.\nexport function isCodingFeature(feature: Feature): boolean {\n  return isCDS(feature) || !!feature.get('subfeatures')?.some(isCodingFeature)\n}\n", "import { isGeneLikeType } from '@jbrowse/core/util'\n\nimport type { MenuItem } from '@jbrowse/core/ui'\nimport type { Feature } from '@jbrowse/core/util'\n\nexport interface ContextMenuInfo {\n  item: { featureId: string; type?: string }\n  // the isoform under the pointer when the click landed on a gene's child\n  subfeature?: { featureId: string }\n  displayedRegionIndex: number\n}\n\nexport interface DisplayModel {\n  contextMenuItems: () => MenuItem[]\n  contextMenuInfo?: ContextMenuInfo\n  fetchFullFeature: (\n    featureId: string,\n    displayedRegionIndex: number,\n  ) => Promise<Feature | undefined>\n}\n\n/**\n * What the menu item launches on. The hit test carries a type and an id, so\n * whether the feature codes for anything can only be answered after the fetch,\n * and the caller answers it there.\n */\nexport interface MenuTarget {\n  fetchFeature: () => Promise<Feature | undefined>\n  /**\n   * The isoform the click actually landed on, when the dialog opens on its\n   * gene. Climbing to the gene is what puts every isoform in the picker, and it\n   * threw away which one the user pointed at: the picker then opened on the\n   * longest transcript.\n   */\n  preferredTranscriptId?: string\n}\n\n// Read off the clicked item rather than off the display: LinearBasicDisplay's\n// `isGeneLike` getter was inlined into its own `contextMenuItems`\n// (jbrowse-components 684142b3), and gating on it silently took the item off\n// every gene track.\nexport function launchTarget(self: DisplayModel): MenuTarget | undefined {\n  const info = self.contextMenuInfo\n  return info && isGeneLikeType(info.item.type)\n    ? {\n        fetchFeature: () =>\n          self.fetchFullFeature(info.item.featureId, info.displayedRegionIndex),\n        preferredTranscriptId: info.subfeature?.featureId,\n      }\n    : undefined\n}\n", "import { launchMsaView } from '../utils/launchMsaView'\n\nimport type { BlastParams, OrthologParams } from '../MsaViewPanel/model'\nimport type { MsaViewPlacement } from '../utils/workspaces'\nimport type PluginManager from '@jbrowse/core/PluginManager'\nimport type { AbstractSessionModel } from '@jbrowse/core/util'\nimport type {\n  Clade,\n  ColumnTrackShorthand,\n  Encoding,\n  HighlightShorthand,\n  RegionShorthand,\n  ResidueMapping,\n  RowPanelSpec,\n} from 'react-msaview'\n\ninterface LaunchMsaViewArgs {\n  session: AbstractSessionModel\n  /**\n   * Shorthand, see react-msaview's docs/layers.md: `msa` and `tree` take a\n   * url or the text itself, and `query` names the row the spec is about, the\n   * `querySeqName` and the `row` of every highlight, region and column track\n   * that names none\n   */\n  msa?: string\n  tree?: string\n  query?: string\n  data?: { msa: string; tree?: string }\n  msaFileLocation?: { uri: string }\n  msaIndexedLocation?: { uri: string }\n  msaName?: string\n  treeFileLocation?: { uri: string }\n  connectedViewId?: string\n  connectedFeature?: Record<string, unknown>\n  /**\n   * The short form of `connectedFeature`: a transcript id looked up in the\n   * connected genome view's open tracks at launch, and translated to become\n   * the query row of a `searchParams` or `orthologParams` launch that names\n   * no `proteinSequence` of its own.\n   */\n  connectedTranscript?: string\n  displayName?: string\n  colorSchemeName?: string\n  colWidth?: number\n  rowHeight?: number\n  treeAreaWidth?: number\n  treeWidth?: number\n  drawNodeBubbles?: boolean\n  labelsAlignRight?: boolean\n  showBranchLen?: boolean\n  querySeqName?: string\n  /**\n   * Transcript residues before the query row's first residue, for a row that\n   * carries only part of the protein -- what BLAST reports when it trims the\n   * query to the aligned region. Genome navigation is off by this much without\n   * it.\n   */\n  querySeqOffset?: number\n  highlightColumns?: number[]\n  /**\n   * Labeled highlights in 1-based inclusive coordinates: `{row, start, end}`\n   * for residues of that row, `{start, end}` for alignment columns, `{rows}`\n   * for whole rows. Prefer this over `highlightColumns`: a residue range stays\n   * put when `allowedGappyness` changes the visible columns.\n   */\n  highlights?: HighlightShorthand[]\n  /** per-column tracks supplied as data, see react-msaview's docs/layers.md */\n  columnTracks?: ColumnTrackShorthand[]\n  /**\n   * Where the view opens, in `highlights` coordinates: `{row, start, end}`\n   * zooms onto residues of that row, `{start, end}` onto alignment columns.\n   * Applied once the alignment has loaded, then dropped from the session.\n   */\n  region?: RegionShorthand\n  /**\n   * Passed through untouched as react-msaview snapshot properties; see its\n   * docs/layers.md. A bare `{ uri }` is enough for the two filehandles.\n   */\n  clades?: Clade[]\n  encodings?: Encoding[]\n  rowPanels?: RowPanelSpec[]\n  relativeTo?: string\n  residueMappings?: ResidueMapping[]\n  trackHeights?: Record<string, number>\n  turnedOffFeatures?: Record<string, boolean>\n  gffFilehandle?: { uri: string }\n  treeMetadataFilehandle?: { uri: string }\n  /**\n   * Build the alignment from NCBI orthologs at launch time instead of naming a\n   * file: `{ taxId, geneCandidates }` is enough, and `taxa` and\n   * `proteinSequence` both default (see OrthologParams). This is the launch\n   * dialog's Orthologs tab, reachable from a session spec \u2014 so a link can say\n   * \"NLRP1 across species\" and the view builds it.\n   */\n  orthologParams?: OrthologParams\n  /**\n   * Search for the alignment at launch: the dialog's BLAST tab reached\n   * declaratively. `{ searchProgram: 'phmmer', blastDatabase: 'rp15',\n   * accession: 'P04637' }` is a whole request. The query comes from\n   * `proteinSequence`, else fetched for `accession`, else translated from the\n   * view's `connectedTranscript`. Stored on the model as `blastParams`, the\n   * name the dialog has always used.\n   */\n  searchParams?: BlastParams\n  /**\n   * Hide any column gappier than this percentage, 100 being \"hide nothing\".\n   * A native react-msaview property, named here because it is the one setting\n   * that decides WHICH columns a freshly launched view opens on: proteins that\n   * differ in length put one row's private N-terminal extension at column 0,\n   * and everything else is gap there. Anything else react-msaview takes as a\n   * snapshot property passes through the same way.\n   */\n  allowedGappyness?: number\n  /**\n   * Where the view lands: `stack` (default), `splitRight` or `newTab`. The\n   * declarative half of the launch \u2014 a link states the arrangement it wants\n   * instead of the reader dragging the view into place.\n   *\n   * The default is `stack` and has to stay `stack`: it is what every link\n   * written before this key existed already does, and the only thing an\n   * embedded session can do. The launch DIALOG defaults to `splitRight`\n   * instead (see `DEFAULT_LAUNCH_PLACEMENT`), because a launch from a gene\n   * feature is a connected pair and reads as a split.\n   *\n   * A spec that arranges more than these two views should use the host's own\n   * `layout` key instead, which states the whole tree and is applied after\n   * every view in the spec has launched. Both may be given; `layout` wins,\n   * being the later and more specific statement.\n   */\n  placement?: MsaViewPlacement\n}\n\n/**\n * `msa` and `tree` onto the plugin's own sources, so a url still goes through\n * `init.msaUrl` and its format sniffing, and `query` onto `querySeqName`\n */\nfunction withLongSources({ msa, tree, ...args }: LaunchMsaViewArgs) {\n  const inlineMsa = msa?.includes('\\n') ? msa : undefined\n  const inlineTree = tree?.trimStart().startsWith('(') ? tree : undefined\n  const data =\n    inlineMsa || inlineTree\n      ? {\n          ...args.data,\n          ...(inlineMsa ? { msa: inlineMsa } : {}),\n          ...(inlineTree ? { tree: inlineTree } : {}),\n        }\n      : args.data\n  return {\n    ...args,\n    data: data as LaunchMsaViewArgs['data'],\n    ...(msa && !inlineMsa ? { msaFileLocation: { uri: msa } } : {}),\n    ...(tree && !inlineTree ? { treeFileLocation: { uri: tree } } : {}),\n    querySeqName: args.querySeqName ?? args.query,\n  }\n}\n\nexport default function LaunchMsaViewExtensionPointF(\n  pluginManager: PluginManager,\n) {\n  pluginManager.addToExtensionPoint(\n    'LaunchView-MsaView',\n    async (args: LaunchMsaViewArgs) => {\n      const {\n        session,\n        query,\n        data,\n        msaFileLocation,\n        msaIndexedLocation,\n        msaName,\n        treeFileLocation,\n        querySeqName,\n        searchParams,\n        ...rest\n      } = withLongSources(args)\n\n      // `orthologParams` and `searchParams` name no alignment at all \u2014 the\n      // view builds one at launch, which is the dialog's Orthologs and BLAST\n      // tabs reached declaratively.\n      if (\n        !data &&\n        !msaFileLocation &&\n        !msaIndexedLocation &&\n        !rest.orthologParams &&\n        !searchParams\n      ) {\n        throw new Error(\n          'No MSA data, file location, orthologParams or searchParams provided when launching MSA view',\n        )\n      }\n\n      // inline data and the tree URL are native react-msaview snapshot props, set\n      // directly, and so is orthologParams (the model's own autorun picks it up).\n      // Only sources needing launch-time resolution go through `init`: msaUrl\n      // (AlphaFold sniff) and the name-indexed bgzip block (no native loader).\n      //\n      // An init whose every field is undefined is still a truthy object, and\n      // MsaViewPanel reads any init as a launch in flight, so an inline-data\n      // launch flashed \"Loading alignment\" until processInit cleared it.\n      const init = {\n        msaUrl: msaFileLocation?.uri,\n        msaIndexedLocation,\n        msaName,\n        querySeqName,\n      }\n      const { expandSpec } = await import('react-msaview')\n      await launchMsaView(session, {\n        ...expandSpec({ ...rest, query }),\n        ...(searchParams ? { blastParams: searchParams } : {}),\n        data,\n        ...(treeFileLocation\n          ? {\n              treeFilehandle: {\n                ...treeFileLocation,\n                locationType: 'UriLocation',\n              },\n            }\n          : {}),\n        ...(Object.values(init).some(v => v !== undefined) ? { init } : {}),\n      })\n\n      return args\n    },\n  )\n}\n", "import { lazy } from 'react'\n\nimport ViewType from '@jbrowse/core/pluggableElementTypes/ViewType'\n\nimport type PluginManager from '@jbrowse/core/PluginManager'\n\nconst MsaViewPanel = lazy(() => import('./components/MsaViewPanel'))\n\nexport default function MsaViewF(pluginManager: PluginManager) {\n  pluginManager.addViewType(() => {\n    return new ViewType({\n      name: 'MsaView',\n      // a thunk, so react-msaview loads with the first view rather than with\n      // the plugin; addView refuses the type until then, hence launchView\n      stateModel: () => import('./model').then(m => m.default()),\n      ReactComponent: MsaViewPanel,\n    })\n  })\n}\n", "export const version = '5.2.0'\n"],
+  "sourcesContent": ["module.exports = JBrowseExports[\"@jbrowse/core/Plugin\"];", "module.exports = JBrowseExports[\"@jbrowse/core/pluggableElementTypes/ViewType\"];", "import Plugin from '@jbrowse/core/Plugin'\nimport { ConfigurationSchema } from '@jbrowse/core/configuration'\nimport { isAbstractMenuManager } from '@jbrowse/core/util'\nimport { types } from '@jbrowse/mobx-state-tree'\nimport GridOn from '@mui/icons-material/GridOn'\n\nimport AddHighlightModelF from './AddHighlightModel'\nimport BgzipFastaMsaAdapterF from './BgzipFastaMsaAdapter'\nimport LaunchMsaViewF from './LaunchMsaView'\nimport LaunchMsaViewExtensionPointF from './LaunchMsaViewExtensionPoint'\nimport MsaViewF from './MsaViewPanel'\nimport { launchMsaView } from './utils/launchMsaView'\nimport { version } from './version'\n\nimport type PluginManager from '@jbrowse/core/PluginManager'\nimport type { AbstractSessionModel } from '@jbrowse/core/util'\n\nexport default class MsaViewPlugin extends Plugin {\n  name = 'MsaViewPlugin'\n  version = version\n\n  install(pluginManager: PluginManager) {\n    MsaViewF(pluginManager)\n    LaunchMsaViewF(pluginManager)\n    LaunchMsaViewExtensionPointF(pluginManager)\n    AddHighlightModelF(pluginManager)\n    BgzipFastaMsaAdapterF(pluginManager)\n  }\n\n  configure(pluginManager: PluginManager) {\n    // a throw here error-pages the whole app, and a menu entry is not worth a\n    // session\n    try {\n      if (isAbstractMenuManager(pluginManager.rootModel)) {\n        pluginManager.rootModel.appendToSubMenu(['Add'], {\n          label: 'Multiple sequence alignment view',\n          icon: GridOn,\n          onClick: (session: AbstractSessionModel) => {\n            // stacked, by default: nothing was launched from, so there is no\n            // connected view for it to sit beside\n            launchMsaView(session, {}).catch((e: unknown) => {\n              console.error(e)\n              session.notifyError(`${e}`, e)\n            })\n          },\n        })\n      }\n    } catch (e) {\n      console.error(\n        'jbrowse-plugin-msaview: could not add the Add menu item',\n        e,\n      )\n    }\n  }\n\n  rootConfigurationSchema = (pluginManager: PluginManager) => {\n    return {\n      msa: ConfigurationSchema('MSA', {\n        datasets: types.maybe(\n          types.array(\n            ConfigurationSchema('MSAEntry', {\n              datasetId: {\n                type: 'string',\n                defaultValue: '',\n              },\n              description: {\n                type: 'string',\n                defaultValue: '',\n              },\n              name: {\n                type: 'string',\n                defaultValue: '',\n              },\n              adapter: pluginManager.pluggableConfigSchemaType('adapter'),\n            }),\n          ),\n        ),\n      }),\n    }\n  }\n}\n", "\"use client\";\n\nimport createSvgIcon from \"./utils/createSvgIcon.mjs\";\nimport { jsx as _jsx } from \"react/jsx-runtime\";\nexport default createSvgIcon(/*#__PURE__*/_jsx(\"path\", {\n  d: \"M20 2H4c-1.1 0-2 .9-2 2v16c0 1.1.9 2 2 2h16c1.1 0 2-.9 2-2V4c0-1.1-.9-2-2-2M8 20H4v-4h4zm0-6H4v-4h4zm0-6H4V4h4zm6 12h-4v-4h4zm0-6h-4v-4h4zm0-6h-4V4h4zm6 12h-4v-4h4zm0-6h-4v-4h4zm0-6h-4V4h4z\"\n}), 'GridOn');", "import React from 'react'\n\nimport { getSession } from '@jbrowse/core/util'\n\nimport { isMsaView } from '../MsaViewPanel/isMsaView'\nimport HighlightComponents from './HighlightComponents'\n\nimport type PluginManager from '@jbrowse/core/PluginManager'\n\nexport default function AddHighlightComponentsModelF(\n  pluginManager: PluginManager,\n) {\n  pluginManager.contributeToExtensionPoint(\n    'LinearGenomeView-TracksContainerComponent',\n    ({ model }) => {\n      const { views } = getSession(model)\n      return views.some(v => isMsaView(v) && v.connectedViewId === model.id) ? (\n        <HighlightComponents\n          key=\"highlight_protein_viewer_msaview\"\n          model={model}\n        />\n      ) : undefined\n    },\n  )\n}\n", "import type { JBrowsePluginMsaViewModel } from './model'\n\nexport function isMsaView(view: {\n  type: string\n}): view is JBrowsePluginMsaViewModel {\n  return view.type === 'MsaView'\n}\n", "import React from 'react'\n\nimport { observer } from 'mobx-react'\n\nimport GenomeMouseoverHighlight from './GenomeMouseoverHighlight'\nimport MsaToGenomeHighlight from './MsaToGenomeHighlight'\n\nimport type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'\n\ntype LGV = LinearGenomeViewModel\n\nconst HighlightComponents = observer(function HighlightComponents2({\n  model,\n}: {\n  model: LGV\n}) {\n  return (\n    <>\n      <MsaToGenomeHighlight model={model} />\n      <GenomeMouseoverHighlight model={model} />\n    </>\n  )\n})\n\nexport default HighlightComponents\n", "import React from 'react'\n\nimport { getSession } from '@jbrowse/core/util'\nimport { observer } from 'mobx-react'\n\nimport { isMsaView } from '../MsaViewPanel/isMsaView'\nimport { hasHoverPosition, useStyles } from './util'\n\nimport type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'\n\nconst GenomeMouseoverHighlight = observer(function ({\n  model,\n}: {\n  model: LinearGenomeViewModel\n}) {\n  const { hovered, views } = getSession(model)\n  const hasMsaView = views.some(\n    s => isMsaView(s) && s.connectedViewId === model.id,\n  )\n  return hasMsaView && hasHoverPosition(hovered) ? (\n    <GenomeMouseoverHighlightRenderer model={model} hovered={hovered} />\n  ) : null\n})\n\nconst GenomeMouseoverHighlightRenderer = observer(function ({\n  model,\n  hovered,\n}: {\n  model: LinearGenomeViewModel\n  hovered: { hoverPosition: { coord: number; refName: string } }\n}) {\n  const { classes } = useStyles()\n  const { offsetPx } = model\n  const { coord, refName } = hovered.hoverPosition\n\n  const s = model.bpToPx({ refName, coord: coord - 1 })\n  const e = model.bpToPx({ refName, coord })\n\n  if (s && e) {\n    const width = Math.max(Math.abs(e.offsetPx - s.offsetPx), 4)\n    const left = Math.min(s.offsetPx, e.offsetPx) - offsetPx\n    return <div className={classes.highlight} style={{ left, width }} />\n  }\n\n  return null\n})\n\nexport default GenomeMouseoverHighlight\n", "import { makeStyles } from 'tss-react/mui'\n\nexport { hasHoverPosition } from '../MsaViewPanel/util'\n\nexport const useStyles = makeStyles()({\n  highlight: {\n    height: '100%',\n    background: 'rgba(255,255,0,0.2)',\n    border: '1px solid rgba(50,50,0,0.2)',\n    position: 'absolute',\n    zIndex: 99,\n    textAlign: 'center',\n    pointerEvents: 'none',\n    overflow: 'hidden',\n  },\n})\n", "import React from 'react'\n\nimport { getSession } from '@jbrowse/core/util'\nimport { observer } from 'mobx-react'\n\nimport { connectedHighlights } from './connectedHighlights'\nimport { hasHoverPosition, useStyles } from './util'\n\nimport type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'\n\ntype LGV = LinearGenomeViewModel\n\nconst MsaToGenomeHighlight = observer(function MsaToGenomeHighlight2({\n  model,\n}: {\n  model: LGV\n}) {\n  const { views, hovered } = getSession(model)\n  const highlights = connectedHighlights(\n    views,\n    model.id,\n    hasHoverPosition(hovered),\n  )\n\n  return highlights.length ? (\n    <MsaToGenomeHighlightRenderer model={model} highlights={highlights} />\n  ) : null\n})\n\nconst MsaToGenomeHighlightRenderer = observer(function ({\n  model,\n  highlights,\n}: {\n  model: LGV\n  highlights: { refName: string; start: number; end: number }[]\n}) {\n  const { classes } = useStyles()\n  const { offsetPx } = model\n\n  return (\n    <>\n      {highlights.map(r => {\n        // bpToPx matches refNames exactly, so canonicalizing \"chr17\" to \"17\"\n        // would miss a view whose regions say \"chr17\"\n        const s = model.bpToPx({ refName: r.refName, coord: r.start })\n        const e = model.bpToPx({ refName: r.refName, coord: r.end })\n        if (s && e) {\n          const width = Math.max(Math.abs(e.offsetPx - s.offsetPx), 4)\n          const left = Math.min(s.offsetPx, e.offsetPx) - offsetPx\n          return (\n            <div\n              key={`${r.refName}-${r.start}-${r.end}`}\n              className={classes.highlight}\n              style={{ left, width }}\n            />\n          )\n        }\n        return null\n      })}\n    </>\n  )\n})\n\nexport default MsaToGenomeHighlight\n", "interface Region {\n  refName: string\n  start: number\n  end: number\n}\n\ninterface LinkedView {\n  type: string\n  connectedViewId?: string\n  connectedClickHighlights: Region[]\n  connectedHoverHighlights: Region[]\n}\n\nexport function connectedHighlights(\n  views: readonly { type: string }[],\n  genomeViewId: string,\n  genomeHovered: boolean,\n) {\n  const regions = views\n    .filter(isLinkedMsaView)\n    .filter(v => v.connectedViewId === genomeViewId)\n    .flatMap(v => [\n      ...v.connectedClickHighlights,\n      ...(genomeHovered ? [] : v.connectedHoverHighlights),\n    ])\n  return [\n    ...new Map(\n      regions.map(r => [`${r.refName}:${r.start}-${r.end}`, r]),\n    ).values(),\n  ]\n}\n\nfunction isLinkedMsaView(view: { type: string }): view is LinkedView {\n  return view.type === 'MsaView'\n}\n", "import { AdapterType } from '@jbrowse/core/pluggableElementTypes'\n\nimport configSchemaF from './configSchema'\n\nimport type PluginManager from '@jbrowse/core/PluginManager'\n\nexport default function BgzipFastaMsaAdapterF(pluginManager: PluginManager) {\n  return pluginManager.addAdapterType(() => {\n    return new AdapterType({\n      name: 'BgzipFastaMsaAdapter',\n      configSchema: configSchemaF(pluginManager),\n      adapterMetadata: {\n        hiddenFromGUI: true,\n      },\n      getAdapterClass: () =>\n        import('./BgzipFastaMsaAdapter').then(t => t.default),\n    })\n  })\n}\n", "import { ConfigurationSchema } from '@jbrowse/core/configuration'\n\nimport type PluginManager from '@jbrowse/core/PluginManager'\n\nexport default function configSchemaF(pluginManager: PluginManager) {\n  const base = pluginManager.getAdapterType('BgzipFastaAdapter')\n  return ConfigurationSchema(\n    'BgzipFastaMsaAdapter',\n    {\n      msaRegex: {\n        type: 'string',\n        defaultValue: '_',\n      },\n    },\n    {\n      baseConfiguration: base.configSchema,\n    },\n  )\n}\n", "import { lazy } from 'react'\n\nimport { getContainingTrack, getSession } from '@jbrowse/core/util'\nimport AddIcon from '@mui/icons-material/Add'\n\nimport { isCodingFeature } from './codingFeature'\nimport { launchTarget } from './launchTarget'\n\nimport type { DisplayModel, MenuTarget } from './launchTarget'\nimport type PluginManager from '@jbrowse/core/PluginManager'\nimport type { PluggableElementType } from '@jbrowse/core/pluggableElementTypes'\nimport type DisplayType from '@jbrowse/core/pluggableElementTypes/DisplayType'\nimport type { Feature } from '@jbrowse/core/util'\nimport type { IAnyModelType } from '@jbrowse/mobx-state-tree'\n\nconst LaunchMsaViewDialog = lazy(\n  () => import('./components/LaunchMsaViewDialog'),\n)\n\nfunction isDisplay(elt: { name: string }): elt is DisplayType {\n  return elt.name === 'LinearBasicDisplay'\n}\n\n// Walking to the track and the session at click time, not while the menu is\n// built: contextMenuItems runs on every right-click and, on a host whose base\n// method reads `this`, is the one place a plugin can take the whole menu down.\n// Keeping it to a pure read of the display is also what lets a test call it.\nfunction featureName(feature: Feature) {\n  return feature.get('name') ?? feature.get('id') ?? 'This feature'\n}\n\nfunction openDialog(self: DisplayModel, target: MenuTarget) {\n  const track = getContainingTrack(self)\n  const session = getSession(track)\n  const { preferredTranscriptId } = target\n  const open = (feature: Feature) => {\n    session.queueDialog(handleClose => [\n      LaunchMsaViewDialog,\n      { model: track, handleClose, feature, preferredTranscriptId },\n    ])\n  }\n  target\n    .fetchFeature()\n    .then(feature => {\n      if (!feature) {\n        session.notify('Could not load feature for MSA view', 'warning')\n      } else if (!isCodingFeature(feature)) {\n        // the canvas hit test carries a type and nothing else, so this is the\n        // first point at which the CDS can be looked for. Saying so beats\n        // opening a dialog whose Submit never leaves grey.\n        session.notify(\n          `${featureName(feature)} has no coding sequence, so there is no protein to align`,\n          'info',\n        )\n      } else {\n        open(feature)\n      }\n    })\n    .catch((e: unknown) => {\n      session.notifyError(`${e}`, e)\n    })\n}\n\nexport function extendStateModel(stateModel: IAnyModelType) {\n  return stateModel.views((self: DisplayModel) => {\n    const superContextMenuItems = self.contextMenuItems\n    return {\n      contextMenuItems() {\n        const target = launchTarget(self)\n        return [\n          // a detached call leaves `this` undefined for a host method that\n          // reads it, and the throw takes the host's own rows with it\n          ...superContextMenuItems.call(self),\n          ...(target\n            ? [\n                {\n                  label: 'Launch MSA view',\n                  icon: AddIcon,\n                  onClick: () => {\n                    openDialog(self, target)\n                  },\n                },\n              ]\n            : []),\n        ]\n      },\n    }\n  })\n}\n\nexport default function LaunchMsaViewF(pluginManager: PluginManager) {\n  pluginManager.addToExtensionPoint(\n    'Core-extendPluggableElement',\n    (elt: PluggableElementType) => {\n      if (isDisplay(elt)) {\n        elt.stateModel = extendStateModel(elt.stateModel)\n      }\n      return elt\n    },\n  )\n}\n", "\"use client\";\n\nimport createSvgIcon from \"./utils/createSvgIcon.mjs\";\nimport { jsx as _jsx } from \"react/jsx-runtime\";\nexport default createSvgIcon(/*#__PURE__*/_jsx(\"path\", {\n  d: \"M19 13h-6v6h-2v-6H5v-2h6V5h2v6h6z\"\n}), 'Add');", "import type { Feature } from '@jbrowse/core/util'\n\nfunction isCDS(feature: Feature) {\n  return feature.get('type')?.toLowerCase() === 'cds'\n}\n\n// The feature itself counts: a viral polyprotein hangs its cleavage products\n// off its CDS rather than off further CDSs.\nexport function isCodingFeature(feature: Feature): boolean {\n  return isCDS(feature) || !!feature.get('subfeatures')?.some(isCodingFeature)\n}\n", "import { isGeneLikeType } from '@jbrowse/core/util'\n\nimport type { MenuItem } from '@jbrowse/core/ui'\nimport type { Feature } from '@jbrowse/core/util'\n\nexport interface ContextMenuInfo {\n  item: { featureId: string; type?: string }\n  // the isoform under the pointer when the click landed on a gene's child\n  subfeature?: { featureId: string }\n  displayedRegionIndex: number\n}\n\nexport interface DisplayModel {\n  contextMenuItems: () => MenuItem[]\n  contextMenuInfo?: ContextMenuInfo\n  fetchFullFeature: (\n    featureId: string,\n    displayedRegionIndex: number,\n  ) => Promise<Feature | undefined>\n}\n\n/**\n * What the menu item launches on. The hit test carries a type and an id, so\n * whether the feature codes for anything can only be answered after the fetch,\n * and the caller answers it there.\n */\nexport interface MenuTarget {\n  fetchFeature: () => Promise<Feature | undefined>\n  /**\n   * The isoform the click actually landed on, when the dialog opens on its\n   * gene. Climbing to the gene is what puts every isoform in the picker, and it\n   * threw away which one the user pointed at: the picker then opened on the\n   * longest transcript.\n   */\n  preferredTranscriptId?: string\n}\n\n// Read off the clicked item rather than off the display: LinearBasicDisplay's\n// `isGeneLike` getter was inlined into its own `contextMenuItems`\n// (jbrowse-components 684142b3), and gating on it silently took the item off\n// every gene track.\nexport function launchTarget(self: DisplayModel): MenuTarget | undefined {\n  const info = self.contextMenuInfo\n  return info && isGeneLikeType(info.item.type)\n    ? {\n        fetchFeature: () =>\n          self.fetchFullFeature(info.item.featureId, info.displayedRegionIndex),\n        preferredTranscriptId: info.subfeature?.featureId,\n      }\n    : undefined\n}\n", "import { launchMsaView } from '../utils/launchMsaView'\n\nimport type { BlastParams, OrthologParams } from '../MsaViewPanel/model'\nimport type { MsaViewPlacement } from '../utils/workspaces'\nimport type PluginManager from '@jbrowse/core/PluginManager'\nimport type { AbstractSessionModel } from '@jbrowse/core/util'\nimport type {\n  Clade,\n  ColumnTrackShorthand,\n  Encoding,\n  HighlightShorthand,\n  RegionShorthand,\n  ResidueMapping,\n  RowPanelSpec,\n} from 'react-msaview'\n\ninterface LaunchMsaViewArgs {\n  session: AbstractSessionModel\n  /**\n   * Shorthand, see react-msaview's docs/layers.md: `msa` and `tree` take a\n   * url or the text itself, and `query` names the row the spec is about, the\n   * `querySeqName` and the `row` of every highlight, region and column track\n   * that names none\n   */\n  msa?: string\n  tree?: string\n  query?: string\n  data?: { msa: string; tree?: string }\n  msaFileLocation?: { uri: string }\n  msaIndexedLocation?: { uri: string }\n  msaName?: string\n  treeFileLocation?: { uri: string }\n  connectedViewId?: string\n  connectedFeature?: Record<string, unknown>\n  /**\n   * The short form of `connectedFeature`: a transcript id looked up in the\n   * connected genome view's open tracks at launch, and translated to become\n   * the query row of a `searchParams` or `orthologParams` launch that names\n   * no `proteinSequence` of its own.\n   */\n  connectedTranscript?: string\n  displayName?: string\n  colorSchemeName?: string\n  colWidth?: number\n  rowHeight?: number\n  treeAreaWidth?: number\n  treeWidth?: number\n  drawNodeBubbles?: boolean\n  labelsAlignRight?: boolean\n  showBranchLen?: boolean\n  querySeqName?: string\n  /**\n   * Transcript residues before the query row's first residue, for a row that\n   * carries only part of the protein -- what BLAST reports when it trims the\n   * query to the aligned region. Genome navigation is off by this much without\n   * it.\n   */\n  querySeqOffset?: number\n  highlightColumns?: number[]\n  /**\n   * Labeled highlights in 1-based inclusive coordinates: `{row, start, end}`\n   * for residues of that row, `{start, end}` for alignment columns, `{rows}`\n   * for whole rows. Prefer this over `highlightColumns`: a residue range stays\n   * put when `allowedGappyness` changes the visible columns.\n   */\n  highlights?: HighlightShorthand[]\n  /** per-column tracks supplied as data, see react-msaview's docs/layers.md */\n  columnTracks?: ColumnTrackShorthand[]\n  /**\n   * Where the view opens, in `highlights` coordinates: `{row, start, end}`\n   * zooms onto residues of that row, `{start, end}` onto alignment columns.\n   * Applied once the alignment has loaded, then dropped from the session.\n   */\n  region?: RegionShorthand\n  /**\n   * Passed through untouched as react-msaview snapshot properties; see its\n   * docs/layers.md. A bare `{ uri }` is enough for the two filehandles.\n   */\n  clades?: Clade[]\n  encodings?: Encoding[]\n  rowPanels?: RowPanelSpec[]\n  relativeTo?: string\n  residueMappings?: ResidueMapping[]\n  trackHeights?: Record<string, number>\n  turnedOffFeatures?: Record<string, boolean>\n  gffFilehandle?: { uri: string }\n  treeMetadataFilehandle?: { uri: string }\n  /**\n   * Build the alignment from NCBI orthologs at launch time instead of naming a\n   * file: `{ taxId, geneCandidates }` is enough, and `taxa` and\n   * `proteinSequence` both default (see OrthologParams). This is the launch\n   * dialog's Orthologs tab, reachable from a session spec \u2014 so a link can say\n   * \"NLRP1 across species\" and the view builds it.\n   */\n  orthologParams?: OrthologParams\n  /**\n   * Search for the alignment at launch: the dialog's BLAST tab reached\n   * declaratively. `{ searchProgram: 'phmmer', blastDatabase: 'rp15',\n   * accession: 'P04637' }` is a whole request. The query comes from\n   * `proteinSequence`, else fetched for `accession`, else translated from the\n   * view's `connectedTranscript`. Stored on the model as `blastParams`, the\n   * name the dialog has always used.\n   */\n  searchParams?: BlastParams\n  /**\n   * Hide any column gappier than this percentage, 100 being \"hide nothing\".\n   * A native react-msaview property, named here because it is the one setting\n   * that decides WHICH columns a freshly launched view opens on: proteins that\n   * differ in length put one row's private N-terminal extension at column 0,\n   * and everything else is gap there. Anything else react-msaview takes as a\n   * snapshot property passes through the same way.\n   */\n  allowedGappyness?: number\n  /**\n   * Where the view lands: `stack` (default), `splitRight` or `newTab`. The\n   * declarative half of the launch \u2014 a link states the arrangement it wants\n   * instead of the reader dragging the view into place.\n   *\n   * The default is `stack` and has to stay `stack`: it is what every link\n   * written before this key existed already does, and the only thing an\n   * embedded session can do. The launch DIALOG defaults to `splitRight`\n   * instead (see `DEFAULT_LAUNCH_PLACEMENT`), because a launch from a gene\n   * feature is a connected pair and reads as a split.\n   *\n   * A spec that arranges more than these two views should use the host's own\n   * `layout` key instead, which states the whole tree and is applied after\n   * every view in the spec has launched. Both may be given; `layout` wins,\n   * being the later and more specific statement.\n   */\n  placement?: MsaViewPlacement\n}\n\n/**\n * `msa` and `tree` onto the plugin's own sources, so a url still goes through\n * `init.msaUrl` and its format sniffing, and `query` onto `querySeqName`\n */\nfunction withLongSources({ msa, tree, ...args }: LaunchMsaViewArgs) {\n  const inlineMsa = msa?.includes('\\n') ? msa : undefined\n  const inlineTree = tree?.trimStart().startsWith('(') ? tree : undefined\n  const data =\n    inlineMsa || inlineTree\n      ? {\n          ...args.data,\n          ...(inlineMsa ? { msa: inlineMsa } : {}),\n          ...(inlineTree ? { tree: inlineTree } : {}),\n        }\n      : args.data\n  return {\n    ...args,\n    data: data as LaunchMsaViewArgs['data'],\n    ...(msa && !inlineMsa ? { msaFileLocation: { uri: msa } } : {}),\n    ...(tree && !inlineTree ? { treeFileLocation: { uri: tree } } : {}),\n    querySeqName: args.querySeqName ?? args.query,\n  }\n}\n\nexport default function LaunchMsaViewExtensionPointF(\n  pluginManager: PluginManager,\n) {\n  pluginManager.addToExtensionPoint(\n    'LaunchView-MsaView',\n    async (args: LaunchMsaViewArgs) => {\n      const {\n        session,\n        query,\n        data,\n        msaFileLocation,\n        msaIndexedLocation,\n        msaName,\n        treeFileLocation,\n        querySeqName,\n        searchParams,\n        ...rest\n      } = withLongSources(args)\n\n      // `orthologParams` and `searchParams` name no alignment at all \u2014 the\n      // view builds one at launch, which is the dialog's Orthologs and BLAST\n      // tabs reached declaratively.\n      if (\n        !data &&\n        !msaFileLocation &&\n        !msaIndexedLocation &&\n        !rest.orthologParams &&\n        !searchParams\n      ) {\n        throw new Error(\n          'No MSA data, file location, orthologParams or searchParams provided when launching MSA view',\n        )\n      }\n\n      // inline data and the tree URL are native react-msaview snapshot props, set\n      // directly, and so is orthologParams (the model's own autorun picks it up).\n      // Only sources needing launch-time resolution go through `init`: msaUrl\n      // (AlphaFold sniff) and the name-indexed bgzip block (no native loader).\n      //\n      // An init whose every field is undefined is still a truthy object, and\n      // MsaViewPanel reads any init as a launch in flight, so an inline-data\n      // launch flashed \"Loading alignment\" until processInit cleared it.\n      const init = {\n        msaUrl: msaFileLocation?.uri,\n        msaIndexedLocation,\n        msaName,\n        querySeqName,\n      }\n      const { expandSpec } = await import('react-msaview')\n      await launchMsaView(session, {\n        ...expandSpec({ ...rest, query }),\n        ...(searchParams ? { blastParams: searchParams } : {}),\n        data,\n        ...(treeFileLocation\n          ? {\n              treeFilehandle: {\n                ...treeFileLocation,\n                locationType: 'UriLocation',\n              },\n            }\n          : {}),\n        ...(Object.values(init).some(v => v !== undefined) ? { init } : {}),\n      })\n\n      return args\n    },\n  )\n}\n", "import { lazy } from 'react'\n\nimport ViewType from '@jbrowse/core/pluggableElementTypes/ViewType'\n\nimport type PluginManager from '@jbrowse/core/PluginManager'\n\nconst MsaViewPanel = lazy(() => import('./components/MsaViewPanel'))\n\nexport default function MsaViewF(pluginManager: PluginManager) {\n  pluginManager.addViewType(() => {\n    return new ViewType({\n      name: 'MsaView',\n      // a thunk, so react-msaview loads with the first view rather than with\n      // the plugin; addView refuses the type until then, hence launchView\n      stateModel: () => import('./model').then(m => m.default()),\n      ReactComponent: MsaViewPanel,\n    })\n  })\n}\n", "export const version = '5.3.0'\n"],
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   "names": ["require_Plugin", "__commonJSMin", "exports", "module", "require_ViewType", "__commonJSMin", "exports", "module", "import_Plugin", "import_configuration", "import_util", "import_mobx_state_tree", "import_jsx_runtime", "GridOn_default", "_jsx", "import_react", "import_util", "isMsaView", "view", "import_react", "import_mobx_react", "import_react", "import_util", "import_mobx_react", "import_mui", "useStyles", "GenomeMouseoverHighlight", "model", "hovered", "views", "s", "isMsaView", "hasHoverPosition", "React", "GenomeMouseoverHighlightRenderer", "classes", "useStyles", "offsetPx", "coord", "refName", "e", "width", "left", "GenomeMouseoverHighlight_default", "import_react", "import_util", "import_mobx_react", "connectedHighlights", "views", "genomeViewId", "genomeHovered", "regions", "isLinkedMsaView", "v", "r", "view", "MsaToGenomeHighlight", "model", "views", "hovered", "highlights", "connectedHighlights", "hasHoverPosition", "React", "MsaToGenomeHighlightRenderer", "classes", "useStyles", "offsetPx", "r", "e", "width", "left", "MsaToGenomeHighlight_default", "HighlightComponents", "model", "React", "MsaToGenomeHighlight_default", "GenomeMouseoverHighlight_default", "HighlightComponents_default", "AddHighlightComponentsModelF", "pluginManager", "model", "views", "v", "isMsaView", "React", "HighlightComponents_default", "import_pluggableElementTypes", "import_configuration", "configSchemaF", "pluginManager", "base", "BgzipFastaMsaAdapterF", "pluginManager", "configSchemaF", "import_react", "import_util", "import_jsx_runtime", "Add_default", "_jsx", "isCDS", "feature", "isCodingFeature", "import_util", "launchTarget", "self", "info", "LaunchMsaViewDialog", "isDisplay", "elt", "featureName", "feature", "openDialog", "self", "target", "track", "session", "preferredTranscriptId", "open", "handleClose", "isCodingFeature", "e", "extendStateModel", "stateModel", "superContextMenuItems", "launchTarget", "Add_default", "LaunchMsaViewF", "pluginManager", "withLongSources", "msa", "tree", "args", "inlineMsa", "inlineTree", "data", "LaunchMsaViewExtensionPointF", "pluginManager", "session", "query", "msaFileLocation", "msaIndexedLocation", "msaName", "treeFileLocation", "querySeqName", "searchParams", "rest", "init", "expandSpec", "launchMsaView", "v", "import_react", "import_ViewType", "MsaViewPanel", "MsaViewF", "pluginManager", "ViewType", "m", "version", "MsaViewPlugin", "Plugin", "version", "pluginManager", "MsaViewF", "LaunchMsaViewF", "LaunchMsaViewExtensionPointF", "AddHighlightComponentsModelF", "BgzipFastaMsaAdapterF", "GridOn_default", "session", "launchMsaView", "e"]
 }

package/dist/version.d.ts CHANGED Viewed

	@@ -1 +1 @@
1	- export declare const version = "5.2.0";
1	+ export declare const version = "5.3.0";

package/dist/version.js CHANGED Viewed

	@@ -1 +1 @@
1	- export const version = '5.2.0';
1	+ export const version = '5.3.0';

package/package.json CHANGED Viewed

@@ -1,5 +1,5 @@
 {
-  "version": "5.2.0",
+  "version": "5.3.0",
   "license": "MIT",
   "name": "jbrowse-plugin-msaview",
   "repository": {
@@ -55,7 +55,7 @@
     "puppeteer": "^25.12.0",
     "react": "^19.3.0",
     "react-dom": "^19.3.0",
-    "react-msaview": "^9.0.0",
+    "react-msaview": "^9.1.0",
     "rimraf": "^6.1.3",
     "rxjs": "^7.8.2",
     "serve": "^14.2.6",

package/src/version.ts CHANGED Viewed

	@@ -1 +1 @@
1	- export const version = '5.2.0'
1	+ export const version = '5.3.0'

package/dist/chunks/AboutDialog-IRBPUPJK.js DELETED Viewed

	@@ -1,2 +0,0 @@
1	- import{a as i}from"./chunk-DNFD5II2.js";import{a as m}from"./chunk-BX4Z274Q.js";import{a}from"./chunk-J6KYLXRD.js";import{b as r}from"./chunk-FY3BTKY4.js";var e=r(a(),1),o=r(i(),1),t=r(m(),1);var l="9.0.0";function c({onClose:n}){return e.default.createElement(o.Dialog,{open:!0,title:"About",onClose:()=>{n()}},e.default.createElement(t.DialogContent,null,e.default.createElement(t.Typography,null,"MSAView ",l," (",e.default.createElement(t.Link,{target:"_blank",rel:"noopener",href:"https://github.com/gmod/react-msaview"},"Github"),")"),e.default.createElement("ul",null,e.default.createElement("li",null,e.default.createElement(t.Typography,null,"We use some color schemes from the"," ",e.default.createElement(t.Link,{target:"_blank",rel:"noopener",href:"https://github.com/biotite-dev/biotite"},"biotite")," ","project, and their license is reproduced"," ",e.default.createElement(t.Link,{target:"_blank",rel:"noopener",href:"https://github.com/biotite-dev/biotite/blob/master/LICENSE.rst"},"here"))),e.default.createElement("li",null,e.default.createElement(t.Typography,null,"See this page for some information on jalview colorings"," ",e.default.createElement(t.Link,{target:"_blank",rel:"noopener",href:"https://www.jalview.org/help/html/colourSchemes/"},"here"))),e.default.createElement("li",null,e.default.createElement(t.Typography,null,"See this page for some info on the clustal, cinema, maeditor, and lesk color schemes"," ",e.default.createElement(t.Link,{target:"_blank",rel:"noopener",href:"http://www.bioinformatics.nl/~berndb/aacolour.html"},"here"))),e.default.createElement("li",null,e.default.createElement(t.Typography,null,"See this paper about the flower color scheme"," ",e.default.createElement(t.Link,{target:"_blank",rel:"noopener",href:"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7245768/"},"here"))))))}export{c as default};
2	- //# sourceMappingURL=AboutDialog-IRBPUPJK.js.map

package/dist/chunks/AnnotationFileDialog-FCYYZ4JN.js DELETED Viewed

	@@ -1,2 +0,0 @@
1	- import{h as E,k as d}from"./chunk-QQ5LZUIO.js";import"./chunk-73KAPCJ2.js";import{a as x}from"./chunk-CVLB4VFP.js";import{a as w}from"./chunk-DNFD5II2.js";import{a as T}from"./chunk-BX4Z274Q.js";import{a as C}from"./chunk-J6KYLXRD.js";import{b as i}from"./chunk-FY3BTKY4.js";var e=i(C(),1),c=i(w(),1),t=i(T(),1),h=i(x(),1);function b(r){let n=r.trimStart();if(!n.startsWith("{"))return r;let a=JSON.parse(n);return d(E(a))}async function O(r){let n=await fetch(r);if(!n.ok)throw new Error(`HTTP ${n.status} fetching ${r} ${await n.text()}`);return n.text()}var R=(0,h.observer)(function({handleClose:r,model:n}){let[a,g]=(0,e.useState)(),[l,v]=(0,e.useState)("file"),[s,F]=(0,e.useState)(""),[m,u]=(0,e.useState)(),[y,f]=(0,e.useState)(!1);return e.default.createElement(c.Dialog,{maxWidth:"xl",title:"Open annotation file",onClose:()=>{r()},open:!0},e.default.createElement(t.DialogContent,null,m?e.default.createElement(c.ErrorMessage,{error:m}):null,e.default.createElement(t.Typography,null,"Open a GFF3 file of annotations, such as the one `react-msaview-cli interpro` writes, or the JSON an InterProScan run returns."),e.default.createElement("div",{style:{display:"flex",margin:30}},e.default.createElement(t.FormControl,{component:"fieldset"},e.default.createElement(t.RadioGroup,{value:l,onChange:o=>{v(o.target.value)}},e.default.createElement(t.FormControlLabel,{value:"url",control:e.default.createElement(t.Radio,null),label:"URL"}),e.default.createElement(t.FormControlLabel,{value:"file",control:e.default.createElement(t.Radio,null),label:"File"}))),l==="url"?e.default.createElement("div",null,e.default.createElement(t.Typography,null,"Open an annotation file from a URL"),e.default.createElement(t.TextField,{label:"URL",value:s,onChange:o=>{F(o.target.value)}})):e.default.createElement("div",{style:{paddingTop:20}},e.default.createElement(t.Typography,null,"Open an annotation file from your local drive"),e.default.createElement(t.Button,{variant:"outlined",component:"label"},"Choose File",e.default.createElement("input",{type:"file",hidden:!0,onChange:({target:o})=>{let p=o.files?.[0];p&&g(p)}})),a?e.default.createElement(t.Typography,null,a.name):null))),e.default.createElement(t.DialogActions,null,e.default.createElement(t.Button,{variant:"contained",color:"primary",disabled:y\|\|(l==="file"?!a:!s.trim()),onClick:()=>{(async()=>{f(!0),u(void 0);try{let o=await(l==="file"&&a?a.text():O(s));n.setGFF(b(o)),n.setShowDomains(!0),r()}catch(o){console.error(o),u(o)}finally{f(!1)}})()}},"Open annotations"),e.default.createElement(t.Button,{variant:"contained",color:"secondary",onClick:()=>{r()}},"Cancel")))}),D=R;export{D as default};
2	- //# sourceMappingURL=AnnotationFileDialog-FCYYZ4JN.js.map

package/dist/chunks/AnnotationFileDialog-FCYYZ4JN.js.map DELETED Viewed

@@ -1,7 +0,0 @@
-{
-  "version": 3,
-  "sources": ["../../node_modules/.pnpm/react-msaview@9.0.0_3e54acfe76b6ad0d26e91cd532b7f775/node_modules/react-msaview/src/components/dialogs/AnnotationFileDialog.tsx"],
-  "sourcesContent": ["import React, { useState } from 'react'\n\nimport { Dialog, ErrorMessage } from '@jbrowse/core/ui'\nimport {\n  Button,\n  DialogActions,\n  DialogContent,\n  FormControl,\n  FormControlLabel,\n  Radio,\n  RadioGroup,\n  TextField,\n  Typography,\n} from '@mui/material'\nimport { observer } from 'mobx-react'\nimport {\n  annotationsToGFF,\n  interProScanResponseToAnnotations,\n} from 'msa-parsers'\n\nimport type { MsaViewModel } from '../../model.ts'\nimport type { InterProScanResponse } from 'msa-parsers'\n\n// GFF3 as the CLI writes it, or the JSON an InterProScan run returns. Both\n// arrive as text and the model keeps GFF, so the JSON is converted on the way\n// in rather than given a second path through the model\nfunction toGFF(text: string) {\n  const trimmed = text.trimStart()\n  if (!trimmed.startsWith('{')) {\n    return text\n  }\n  const response: InterProScanResponse = JSON.parse(trimmed)\n  return annotationsToGFF(interProScanResponseToAnnotations(response))\n}\n\nasync function fetchText(url: string) {\n  const response = await fetch(url)\n  if (!response.ok) {\n    throw new Error(\n      `HTTP ${response.status} fetching ${url} ${await response.text()}`,\n    )\n  }\n  return response.text()\n}\n\nconst AnnotationFileDialog = observer(function ({\n  handleClose,\n  model,\n}: {\n  handleClose: () => void\n  model: MsaViewModel\n}) {\n  const [file, setFile] = useState<File>()\n  const [choice, setChoice] = useState('file')\n  const [url, setUrl] = useState('')\n  const [error, setError] = useState<unknown>()\n  const [loading, setLoading] = useState(false)\n\n  // the error is shown here rather than notified: the standalone app and the\n  // MSAViewer component have no jbrowse session to notify, and asking one for\n  // its notify() threw out of the success path into the catch, which threw\n  // again on the same missing session\n  return (\n    <Dialog\n      maxWidth=\"xl\"\n      title=\"Open annotation file\"\n      onClose={() => {\n        handleClose()\n      }}\n      open\n    >\n      <DialogContent>\n        {error ? <ErrorMessage error={error} /> : null}\n        <Typography>\n          Open a GFF3 file of annotations, such as the one `react-msaview-cli\n          interpro` writes, or the JSON an InterProScan run returns.\n        </Typography>\n\n        <div style={{ display: 'flex', margin: 30 }}>\n          <FormControl component=\"fieldset\">\n            <RadioGroup\n              value={choice}\n              onChange={event => {\n                setChoice(event.target.value)\n              }}\n            >\n              <FormControlLabel value=\"url\" control={<Radio />} label=\"URL\" />\n              <FormControlLabel value=\"file\" control={<Radio />} label=\"File\" />\n            </RadioGroup>\n          </FormControl>\n          {choice === 'url' ? (\n            <div>\n              <Typography>Open an annotation file from a URL</Typography>\n              <TextField\n                label=\"URL\"\n                value={url}\n                onChange={event => {\n                  setUrl(event.target.value)\n                }}\n              />\n            </div>\n          ) : (\n            <div style={{ paddingTop: 20 }}>\n              <Typography>\n                Open an annotation file from your local drive\n              </Typography>\n              <Button variant=\"outlined\" component=\"label\">\n                Choose File\n                <input\n                  type=\"file\"\n                  hidden\n                  onChange={({ target }) => {\n                    const chosen = target.files?.[0]\n                    if (chosen) {\n                      setFile(chosen)\n                    }\n                  }}\n                />\n              </Button>\n              {file ? <Typography>{file.name}</Typography> : null}\n            </div>\n          )}\n        </div>\n      </DialogContent>\n      <DialogActions>\n        <Button\n          variant=\"contained\"\n          color=\"primary\"\n          disabled={loading || (choice === 'file' ? !file : !url.trim())}\n          onClick={() => {\n            // eslint-disable-next-line @typescript-eslint/no-floating-promises\n            ;(async () => {\n              setLoading(true)\n              setError(undefined)\n              try {\n                const text = await (choice === 'file' && file\n                  ? file.text()\n                  : fetchText(url))\n                // through the model's own GFF text, so the annotations travel\n                // in the snapshot and the shared URL like every other layer.\n                // Setting them straight onto the volatile left a view whose\n                // link opened without them\n                model.setGFF(toGFF(text))\n                model.setShowDomains(true)\n                handleClose()\n              } catch (e) {\n                console.error(e)\n                setError(e)\n              } finally {\n                setLoading(false)\n              }\n            })()\n          }}\n        >\n          Open annotations\n        </Button>\n        <Button\n          variant=\"contained\"\n          color=\"secondary\"\n          onClick={() => {\n            handleClose()\n          }}\n        >\n          Cancel\n        </Button>\n      </DialogActions>\n    </Dialog>\n  )\n})\n\nexport default AnnotationFileDialog\n"],
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-  "names": ["import_react", "import_ui", "import_material", "import_mobx_react", "toGFF", "text", "trimmed", "response", "annotationsToGFF", "interProScanResponseToAnnotations", "fetchText", "url", "AnnotationFileDialog", "handleClose", "model", "file", "setFile", "choice", "setChoice", "setUrl", "error", "setError", "loading", "setLoading", "React", "event", "target", "chosen", "e", "AnnotationFileDialog_default"]
-}

package/dist/chunks/ExportSVGDialog-TYYPI6VB.js DELETED Viewed

	@@ -1,2 +0,0 @@
1	- import{a as p}from"./chunk-YOTSFJMU.js";import{a as P}from"./chunk-CVLB4VFP.js";import{a as R}from"./chunk-DNFD5II2.js";import{a as q}from"./chunk-BX4Z274Q.js";import{a as W}from"./chunk-J6KYLXRD.js";import{b as a}from"./chunk-FY3BTKY4.js";var t=a(W(),1),i=a(R(),1),e=a(q(),1),v=a(P(),1);function z(r){requestAnimationFrame(()=>{requestAnimationFrame(r)})}var O=(0,v.observer)(function({model:r,onClose:c}){let[s,f]=(0,t.useState)(!0),[n,x]=(0,t.useState)(!0),[o,k]=(0,t.useState)("viewport"),[h,y]=(0,t.useState)(),[m,d]=(0,t.useState)(!1),T=(0,e.useTheme)(),{totalWidth:C,totalHeight:b,effectiveTreeAreaWidth:w,rowPanelsWidth:M,turnedOnTracks:A,totalTrackAreaHeight:S,numColumns:F,leaves:G,showMsaLetters:I,treeOverviewHeight:D}=r,E=A.length>0,H=C+w+M,L=b+(n?S:0)+D,g=I&&o==="entire"?F*G.length:0,V=g>1e5;return t.default.createElement(i.Dialog,{onClose:()=>{c()},open:!0,title:"Export SVG"},t.default.createElement(e.DialogContent,null,h?t.default.createElement(i.ErrorMessage,{error:h}):null,t.default.createElement(e.Typography,null,"Settings:"),t.default.createElement(p,{label:"Include minimap?",disabled:o==="entire",checked:s,onChange:()=>{f(!s)}}),E?t.default.createElement(p,{label:"Include tracks?",checked:n,onChange:()=>{x(!n)}}):null,t.default.createElement("div",null,t.default.createElement(e.FormControl,null,t.default.createElement(e.FormLabel,null,"Export type"),t.default.createElement(e.RadioGroup,{value:o,onChange:l=>{let{value:u}=l.target;(u==="entire"\|\|u==="viewport")&&k(u)}},t.default.createElement(e.FormControlLabel,{value:"entire",control:t.default.createElement(e.Radio,null),label:"Entire MSA"}),t.default.createElement(e.FormControlLabel,{value:"viewport",control:t.default.createElement(e.Radio,null),label:"Current viewport only"})))),V?t.default.createElement(e.Alert,{severity:"warning",style:{marginTop:8}},"The entire MSA is ",Math.round(H),"x",Math.round(L)," pixels and draws"," ",Math.round(g/1e3),"k residue letters, each its own SVG element. Export may be slow or fail \u2014 zooming out far enough to hide the letters exports the same alignment as an image instead."):null),t.default.createElement(e.DialogActions,null,t.default.createElement(e.Button,{variant:"contained",color:"primary",disabled:m,startIcon:m?t.default.createElement(e.CircularProgress,{size:16,color:"inherit"}):null,onClick:()=>{d(!0),z(()=>{r.exportSVG({theme:T,includeMinimap:s,includeTracks:E&&n,exportType:o}).then(()=>{c()}).catch(l=>{console.error(l),y(l)}).finally(()=>{d(!1)})})}},m?"Exporting\u2026":"Export"),t.default.createElement(e.Button,{variant:"contained",color:"secondary",onClick:()=>{c()}},"Cancel")))}),_=O;export{_ as default};
2	- //# sourceMappingURL=ExportSVGDialog-TYYPI6VB.js.map

package/dist/chunks/ExportSVGDialog-TYYPI6VB.js.map DELETED Viewed

@@ -1,7 +0,0 @@
-{
-  "version": 3,
-  "sources": ["../../node_modules/.pnpm/react-msaview@9.0.0_3e54acfe76b6ad0d26e91cd532b7f775/node_modules/react-msaview/src/components/dialogs/ExportSVGDialog.tsx"],
-  "sourcesContent": ["import React, { useState } from 'react'\n\nimport { Dialog, ErrorMessage } from '@jbrowse/core/ui'\nimport {\n  Alert,\n  Button,\n  CircularProgress,\n  DialogActions,\n  DialogContent,\n  FormControl,\n  FormControlLabel,\n  FormLabel,\n  Radio,\n  RadioGroup,\n  Typography,\n  useTheme,\n} from '@mui/material'\nimport { observer } from 'mobx-react'\n\nimport Checkbox2 from '../Checkbox2.tsx'\n\nimport type { MsaViewModel } from '../../model.ts'\n\n// Run after the browser has painted. A requestAnimationFrame callback still\n// runs *before* the frame it was queued for, so one alone hands the main thread\n// to the render with the spinner not yet on screen; the second fires once that\n// frame is out.\nfunction afterPaint(fn: () => void) {\n  requestAnimationFrame(() => {\n    requestAnimationFrame(fn)\n  })\n}\n\nconst ExportSVGDialog = observer(function ({\n  model,\n  onClose,\n}: {\n  model: MsaViewModel\n  onClose: () => void\n}) {\n  const [includeMinimap, setIncludeMinimap] = useState(true)\n  const [includeTracks, setIncludeTracks] = useState(true)\n  const [exportType, setExportType] = useState<'entire' | 'viewport'>(\n    'viewport',\n  )\n  const [error, setError] = useState<unknown>()\n  const [exporting, setExporting] = useState(false)\n  const theme = useTheme()\n  const {\n    totalWidth,\n    totalHeight,\n    effectiveTreeAreaWidth,\n    rowPanelsWidth,\n    turnedOnTracks,\n    totalTrackAreaHeight,\n    numColumns,\n    leaves,\n    showMsaLetters,\n    treeOverviewHeight,\n  } = model\n  const hasTracks = turnedOnTracks.length > 0\n  const entireWidth = totalWidth + effectiveTreeAreaWidth + rowPanelsWidth\n  const entireHeight =\n    totalHeight +\n    (includeTracks ? totalTrackAreaHeight : 0) +\n    treeOverviewHeight\n  // the background is one raster image whatever its size, so what the figure\n  // actually costs is its residue letters: each is an svg element of its own.\n  // Past roughly this many the export runs to tens of seconds and can exhaust\n  // the tab's memory outright\n  const glyphs =\n    showMsaLetters && exportType === 'entire' ? numColumns * leaves.length : 0\n  const isLargeExport = glyphs > 100_000\n  return (\n    <Dialog\n      onClose={() => {\n        onClose()\n      }}\n      open\n      title=\"Export SVG\"\n    >\n      <DialogContent>\n        {error ? <ErrorMessage error={error} /> : null}\n        <Typography>Settings:</Typography>\n        <Checkbox2\n          label=\"Include minimap?\"\n          disabled={exportType === 'entire'}\n          checked={includeMinimap}\n          onChange={() => {\n            setIncludeMinimap(!includeMinimap)\n          }}\n        />\n        {hasTracks ? (\n          <Checkbox2\n            label=\"Include tracks?\"\n            checked={includeTracks}\n            onChange={() => {\n              setIncludeTracks(!includeTracks)\n            }}\n          />\n        ) : null}\n        <div>\n          <FormControl>\n            <FormLabel>Export type</FormLabel>\n            <RadioGroup\n              value={exportType}\n              onChange={event => {\n                const { value } = event.target\n                if (value === 'entire' || value === 'viewport') {\n                  setExportType(value)\n                }\n              }}\n            >\n              <FormControlLabel\n                value=\"entire\"\n                control={<Radio />}\n                label=\"Entire MSA\"\n              />\n              <FormControlLabel\n                value=\"viewport\"\n                control={<Radio />}\n                label=\"Current viewport only\"\n              />\n            </RadioGroup>\n          </FormControl>\n        </div>\n        {isLargeExport ? (\n          <Alert severity=\"warning\" style={{ marginTop: 8 }}>\n            The entire MSA is {Math.round(entireWidth)}x\n            {Math.round(entireHeight)} pixels and draws{' '}\n            {Math.round(glyphs / 1000)}k residue letters, each its own SVG\n            element. 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2	- //# sourceMappingURL=MetadataDialog-KZWQFRF7.js.map

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2	- //# sourceMappingURL=MsaViewPanel-RUZAKFCB.js.map

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package/dist/chunks/chunk-F726IWCW.js DELETED Viewed

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-{
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-  "sources": ["../../src/utils/fetch.ts", "../../src/utils/useLocalStorage.ts", "../../src/utils/poll.ts", "../../src/utils/ebiJobDispatcher.ts", "../../src/LaunchMsaView/components/BlastQuery/consts.ts"],
-  "sourcesContent": ["function hostOf(url: string) {\n  try {\n    return new URL(url).host\n  } catch {\n    // a relative url, e.g. a same-origin proxy path\n    return url\n  }\n}\n\nexport class HttpError extends Error {\n  constructor(\n    message: string,\n    readonly status: number,\n  ) {\n    super(message)\n  }\n}\n\nexport async function handleFetch(url: string, args?: RequestInit) {\n  let response: Response\n  try {\n    response = await fetch(url, args)\n  } catch (e) {\n    // fetch rejects with a bare \"TypeError: Failed to fetch\" for every network\n    // level failure, including a cross-origin response the browser refused to\n    // hand over. That is not a hypothetical: NCBI's Blast.cgi stopped sending\n    // Access-Control-Allow-Origin to third-party origins, and the raw TypeError\n    // told users nothing at all about why. See docs/blast.md.\n    if (e instanceof TypeError) {\n      throw new Error(\n        `Could not reach ${hostOf(url)} \u2014 the request failed at the network level. This is usually a CORS restriction (the server refused to let this site read the response), an offline connection, or a blocked request.`,\n        { cause: e },\n      )\n    }\n    throw e\n  }\n\n  if (!response.ok) {\n    throw new HttpError(\n      `HTTP ${response.status} fetching ${url} ${(await response.text()).slice(0, 500)}`,\n      response.status,\n    )\n  }\n\n  return response\n}\n\nexport async function textfetch(url: string, args?: RequestInit) {\n  const response = await handleFetch(url, args)\n  return response.text()\n}\n\nexport async function jsonfetch<T>(url: string, args?: RequestInit) {\n  const response = await handleFetch(url, args)\n  return response.json() as Promise<T>\n}\n\nexport function timeout(time: number, signal?: AbortSignal) {\n  return new Promise<void>((resolve, reject) => {\n    if (signal?.aborted) {\n      reject(new DOMException('Aborted', 'AbortError'))\n      return\n    }\n    // the listener is removed on the natural path too: one signal serves every\n    // tick of a poll, and a 10-minute job is ~600 sleeps -- leaving each\n    // listener behind accumulates them all on that one signal\n    const onAbort = () => {\n      clearTimeout(id)\n      reject(new DOMException('Aborted', 'AbortError'))\n    }\n    const id = setTimeout(() => {\n      signal?.removeEventListener('abort', onAbort)\n      resolve()\n    }, time)\n    signal?.addEventListener('abort', onAbort, { once: true })\n  })\n}\n\n/**\n * A cancelled launch has to be told apart from a failed one: it must not render\n * the \"failed\" panel, and it must not touch a model that may already be gone.\n * `fetch` and the sleep above both reject with a DOMException named AbortError,\n * which subclasses Error.\n */\nexport function isAbortError(e: unknown) {\n  return e instanceof Error && e.name === 'AbortError'\n}\n", "import { useState } from 'react'\n\n// Vendored rather than imported from `@jbrowse/core/util`: that barrel is\n// host-provided, and a barrel split dropped this export, making the BLAST panel\n// throw \"(0, PR.useLocalStorage) is not a function\" on hosts built during that\n// window. Same failure mode as `defaultCodonTable`; keeping our own copy takes\n// this plugin out of the whack-a-mole.\nexport function readLocalStorage<T>(key: string, initialValue: T): T {\n  try {\n    const item = globalThis.localStorage.getItem(key)\n    return item === null ? initialValue : (JSON.parse(item) as T)\n  } catch (error) {\n    console.error(error)\n    return initialValue\n  }\n}\n\nexport function useLocalStorage<T>(key: string, initialValue: T) {\n  const [storedValue, setStoredValue] = useState<T>(() =>\n    readLocalStorage(key, initialValue),\n  )\n  const setValue = (value: T) => {\n    setStoredValue(value)\n    try {\n      globalThis.localStorage.setItem(key, JSON.stringify(value))\n    } catch (error) {\n      console.error(error)\n    }\n  }\n  return [storedValue, setValue] as const\n}\n", "import { timeout } from './fetch'\n\n/**\n * Poll a remote job until it reports done. `check` returns true when finished,\n * false when still pending, and throws on failure. Between checks it counts down\n * `intervalSeconds`, calling `onCountdown` each second so the UI can show\n * progress.\n *\n * `signal` ends the loop with an AbortError: the countdown rejects on the tick\n * it is aborted rather than at the end of the interval, so a cancelled launch\n * stops within a second instead of running for the job's lifetime.\n */\nexport async function pollLoop({\n  check,\n  intervalSeconds,\n  onCountdown,\n  signal,\n}: {\n  check: () => Promise<boolean>\n  intervalSeconds: number\n  onCountdown: (secondsRemaining: number) => void\n  signal?: AbortSignal\n}) {\n  // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition\n  while (true) {\n    signal?.throwIfAborted()\n    if (await check()) {\n      return\n    }\n    for (let i = intervalSeconds; i > 0; i--) {\n      onCountdown(i)\n      await timeout(1000, signal)\n    }\n  }\n}\n", "import { isAbortError, textfetch } from './fetch'\nimport { pollLoop } from './poll'\nimport { readLocalStorage } from './useLocalStorage'\n\n/**\n * EBI's Job Dispatcher REST services (clustalo, muscle, ncbiblast, ...) all\n * speak the same run/status/result protocol, so the transport lives here and\n * each tool only supplies its own parameters and result types.\n *\n * Unlike NCBI's Blast.cgi these endpoints send `Access-Control-Allow-Origin: *`,\n * which is why the BLAST backend moved here \u2014 see docs/blast.md.\n */\nexport const EBI_BASE = 'https://www.ebi.ac.uk/Tools/services/rest'\n\n/**\n * EBI asks for a contact address on every submission so they can reach whoever\n * is generating the load. The default is the project's mailbox; a deployment\n * that sends real volume should name its own maintainer in the BLAST settings\n * dialog.\n */\nexport const EBI_EMAIL_STORAGE_KEY = 'msa-ebiContactEmail'\nexport const DEFAULT_EBI_EMAIL = 'jbrowse2@berkeley.edu'\n\nexport function getEbiEmail() {\n  const configured = readLocalStorage(\n    EBI_EMAIL_STORAGE_KEY,\n    DEFAULT_EBI_EMAIL,\n  ).trim()\n  return configured || DEFAULT_EBI_EMAIL\n}\n\n/** Statuses that mean the job is over and produced no result. */\nconst FAILED_STATUSES = new Set(['ERROR', 'FAILURE', 'NOT_FOUND'])\n\nasync function submitEbiJob({\n  tool,\n  params,\n  signal,\n}: {\n  tool: string\n  params: Record<string, string>\n  signal?: AbortSignal\n}) {\n  const jobId = await textfetch(`${EBI_BASE}/${tool}/run`, {\n    method: 'POST',\n    body: new URLSearchParams({ email: getEbiEmail(), ...params }),\n    signal,\n  })\n  return jobId.trim()\n}\n\n/**\n * A status check that could not reach EBI at all says nothing about the job, so\n * it is not a reason to abandon one. A job the server has accepted keeps running\n * whatever happens to the poller's connection, and EBI's cluster has answered\n * status checks with a 502 for ten minutes on jobs that then finished (see\n * docs/blast.md).\n *\n * So the poll gives up only once checks have failed without a break for this\n * long: an endpoint that has genuinely gone away must not be polled forever.\n */\nexport const STATUS_FAILURE_BUDGET_MS = 15 * 60 * 1000\n\nexport async function waitForEbiJob({\n  tool,\n  jobId,\n  intervalSeconds = 10,\n  onCountdown,\n  signal,\n}: {\n  tool: string\n  jobId: string\n  intervalSeconds?: number\n  onCountdown: (secondsRemaining: number) => void\n  signal?: AbortSignal\n}) {\n  let failingSince: number | undefined\n  await pollLoop({\n    intervalSeconds,\n    onCountdown,\n    signal,\n    check: async () => {\n      let status: string\n      try {\n        status = (\n          await textfetch(`${EBI_BASE}/${tool}/status/${jobId}`, { signal })\n        ).trim()\n      } catch (e) {\n        // a cancelled request is the caller giving up, not EBI being\n        // unreachable, so it must end the poll rather than be retried\n        if (isAbortError(e)) {\n          throw e\n        }\n        failingSince ??= Date.now()\n        if (Date.now() - failingSince >= STATUS_FAILURE_BUDGET_MS) {\n          throw new Error(\n            `Could not reach EBI to check ${tool} job ${jobId} for ${Math.round(STATUS_FAILURE_BUDGET_MS / 60_000)} minutes`,\n            { cause: e },\n          )\n        }\n        console.warn('[msaview] EBI status check failed, retrying:', e)\n        return false\n      }\n      failingSince = undefined\n      // exact match, not includes(): a job whose status is ERROR must not be\n      // able to poll forever waiting for a FINISHED that will never arrive\n      if (status === 'FINISHED') {\n        return true\n      }\n      if (FAILED_STATUSES.has(status)) {\n        throw new Error(`EBI ${tool} job ${jobId} returned status ${status}`)\n      }\n      // RUNNING, QUEUED, PENDING and anything else EBI adds later\n      return false\n    },\n  })\n}\n\nexport async function runEbiJob({\n  tool,\n  label,\n  params,\n  onProgress,\n  onRid,\n  signal,\n}: {\n  tool: string\n  label: string\n  params: Record<string, string>\n  onProgress: (arg: string) => void\n  onRid?: (jobId: string) => void\n  signal?: AbortSignal\n}) {\n  onProgress(`Submitting ${label} to EBI...`)\n  const jobId = await submitEbiJob({ tool, params, signal })\n  onRid?.(jobId)\n  await waitForEbiJob({\n    tool,\n    jobId,\n    signal,\n    onCountdown: s => {\n      onProgress(`Re-checking ${label} status in... ${s}`)\n    },\n  })\n  return {\n    jobId,\n    result: (type: string) =>\n      textfetch(`${EBI_BASE}/${tool}/result/${jobId}/${type}`, { signal }),\n  }\n}\n", "/**\n * Only used to build the link-out on the manual panel, which sends the user to\n * NCBI's own site to run BLAST there. Nothing fetches this url: NCBI stopped\n * sending Access-Control-Allow-Origin to third-party origins, so a browser\n * cannot read a response from it at all. See docs/blast.md.\n */\nexport const BASE_BLAST_URL = 'https://blast.ncbi.nlm.nih.gov/Blast.cgi'\n\n/** The aligners EBI's Job Dispatcher runs, each a tool name at their REST api. */\nexport const ebiMsaAlgorithms = [\n  'clustalo',\n  'muscle',\n  'kalign',\n  'mafft',\n] as const\nexport type EbiMsaAlgorithm = (typeof ebiMsaAlgorithms)[number]\n\n/**\n * `browser` is no job at all: each sequence is aligned to the query in the\n * page and the rows merged on the query (utils/browserAlign.ts), with the tree\n * built by react-msaview's neighbour joining. It is the aligner for a launch\n * that must not depend on EBI, and for one that wants to be quick -- a\n * hundred 400-residue rows take under a second, and a hundred 1400-residue\n * rows eight, against a Job Dispatcher queue that has been measured at\n * anything from ten seconds to fifteen minutes. Past the per-sequence limit in\n * browserAlign.ts it refuses and names an EBI aligner instead.\n */\nexport const msaAlgorithms = [...ebiMsaAlgorithms, 'browser'] as const\nexport type MsaAlgorithm = (typeof msaAlgorithms)[number]\n\nexport const msaAlgorithmLabels: Record<MsaAlgorithm, string> = {\n  clustalo: 'Clustal Omega (EBI)',\n  muscle: 'MUSCLE (EBI)',\n  kalign: 'Kalign (EBI)',\n  mafft: 'MAFFT (EBI)',\n  browser: 'in browser, query-anchored',\n}\n\n/**\n * EBI rejects a submission naming a database outside its own list with a 400,\n * so every value here has to appear in\n * https://www.ebi.ac.uk/Tools/services/rest/ncbiblast/parameterdetails/database\n * -- `uniprotkb_reference_proteomes` did not, and 3.0.0 shipped it as a dead\n * menu entry.\n */\nexport const blastDatabaseOptions = [\n  'uniprotkb_swissprot',\n  'uniprotkb',\n  'pan_proteomes',\n  'uniprotkb_trembl',\n] as const\nexport type BlastDatabase = (typeof blastDatabaseOptions)[number]\n\n// curated, so it returns roughly one good sequence per species rather than the\n// many near-identical TrEMBL entries an alignment reads poorly\nconst defaultBlastDatabase: BlastDatabase = 'uniprotkb_swissprot'\n\nexport const searchPrograms = ['blastp', 'phmmer'] as const\nexport type SearchProgram = (typeof searchPrograms)[number]\n\nexport const searchProgramLabels: Record<SearchProgram, string> = {\n  blastp: 'blastp (sequence search)',\n  phmmer: 'phmmer (profile HMM search)',\n}\n\n/**\n * phmmer offers PDB, AlphaFold, Ensembl Genomes, MEROPS and ChEMBL too, but\n * targets outside UniProt carry no species in their description, so those rows\n * would lose their species and common name. Only the databases that label their\n * hits are offered.\n *\n * rp15..rp75 are the Representative Proteomes: UniProt's reference proteomes\n * thinned so that no two are more than 15% (35%, 55%, 75%) similar, which is\n * the widest taxonomic spread per hit that any of these databases gives. rp15\n * is the one to reach for when the question is \"what is this like across all\n * of life\"; swissprot when it is \"what is this like in the curated set\".\n */\nexport const phmmerDatabaseOptions = [\n  'swissprot',\n  'uniprotkb',\n  'uniprotrefprot',\n  'rp75',\n  'rp55',\n  'rp35',\n  'rp15',\n] as const\nexport type PhmmerDatabase = (typeof phmmerDatabaseOptions)[number]\n\nconst defaultPhmmerDatabase: PhmmerDatabase = 'swissprot'\n\n/**\n * The hit counts EBI's ncbiblast accepts for `alignments` and `scores`. A value\n * off this list is a 400 at submit time, so a request is rounded up to the next\n * one on it.\n */\nconst blastHitCounts = [5, 10, 20, 50, 100, 150, 200, 250, 500, 750, 1000]\n\nexport const defaultMaxHits = 100\n\nexport function snapBlastHitCount(maxHits: number) {\n  return blastHitCounts.find(n => n >= maxHits) ?? blastHitCounts.at(-1)!\n}\n\n/**\n * A program together with a database that program actually has.\n *\n * The pair travels as one value because neither service knows the other's\n * database names \u2014 `swissprot` is a phmmer database and `uniprotkb_swissprot` a\n * blastp one \u2014 so a program held apart from its database can drift into a\n * combination EBI answers with a 400, minutes after the user pressed Submit.\n */\nexport type SearchChoice =\n  | { program: 'blastp'; database: BlastDatabase }\n  | { program: 'phmmer'; database: PhmmerDatabase }\n\nexport function defaultSearchFor(program: SearchProgram): SearchChoice {\n  return program === 'phmmer'\n    ? { program, database: defaultPhmmerDatabase }\n    : { program, database: defaultBlastDatabase }\n}\n\nexport function databaseOptionsFor(program: SearchProgram) {\n  return program === 'phmmer' ? phmmerDatabaseOptions : blastDatabaseOptions\n}\n\n/**\n * What each database is called in the menu. The keys are what EBI is sent and\n * are not negotiable; `uniprotkb_swissprot` and `swissprot` are the same\n * collection under each service's own name, so they read the same here.\n */\nconst databaseLabels: Record<BlastDatabase | PhmmerDatabase, string> = {\n  uniprotkb_swissprot: 'UniProtKB/Swiss-Prot (curated)',\n  swissprot: 'UniProtKB/Swiss-Prot (curated)',\n  uniprotkb: 'UniProtKB (all entries)',\n  uniprotkb_trembl: 'UniProtKB/TrEMBL (unreviewed)',\n  pan_proteomes: 'Pan-proteomes',\n  uniprotrefprot: 'UniProt reference proteomes',\n  rp75: 'Representative proteomes, 75%',\n  rp55: 'Representative proteomes, 55%',\n  rp35: 'Representative proteomes, 35%',\n  rp15: 'Representative proteomes, 15% (widest spread)',\n}\n\nexport function databaseLabel(database: BlastDatabase | PhmmerDatabase) {\n  return databaseLabels[database]\n}\n"],
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