jbrowse-plugin-msaview 5.0.0 → 5.1.0

package/dist/chunks/{LaunchMsaViewDialog-LMZOJ7T6.js → LaunchMsaViewDialog-WBXEEHJL.js}

@@ -1,5 +1,5 @@
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-//# sourceMappingURL=LaunchMsaViewDialog-LMZOJ7T6.js.map
+//# sourceMappingURL=LaunchMsaViewDialog-WBXEEHJL.js.map

package/dist/chunks/chunk-DECSTFAT.js

@@ -0,0 +1,2 @@
+var w=["stack","splitRight","newTab"],i="splitRight",r="msaView-launchPlacement";function o(e,t){return t in e&&typeof e[t]=="function"}var a=!1;function M(e){return c(e)||o(e,"setUseWorkspaces")&&o(e,"setPendingMove")}function c(e){return o(e,"moveViewToNewTab")&&o(e,"moveViewToSplit")}function p(e){let t=o(e,"setUseWorkspaces"),s=o(e,"setPendingMove");return t!==s&&!a&&(a=!0,console.warn(`jbrowse-plugin-msaview: this session supports workspaces but not ${s?"setUseWorkspaces":"setPendingMove"}, so the MSA view was stacked instead of tiled: the session API moved and the plugin needs updating to match.`)),t&&s}function l(e,t,s){s!=="stack"&&(c(e)?s==="newTab"?e.moveViewToNewTab(t):e.moveViewToSplit(t,"row"):p(e)&&(e.setPendingMove({type:s,viewId:t}),e.setUseWorkspaces(!0)))}function u(e){return w.includes(e)}function m(){try{let e=globalThis.localStorage.getItem(r);return u(e)?e:i}catch(e){return console.error(e),i}}function d(e){try{globalThis.localStorage.setItem(r,e)}catch(t){console.error(t)}}async function P(e,{placement:t="stack",...s}){let n=await e.launchView("MsaView",{type:"MsaView",...s});return l(e,n.id,t),n}export{M as a,m as b,d as c,P as d};
+//# sourceMappingURL=chunk-DECSTFAT.js.map

package/dist/chunks/chunk-DECSTFAT.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../../src/utils/workspaces.ts", "../../src/utils/launchMsaView.ts"],
+  "sourcesContent": ["import type { AbstractSessionModel } from '@jbrowse/core/util'\n\n/**\n * Where a launched MSA view lands. Every launch names one of these and stops\n * there, so a host that arranges views differently is one function to teach.\n *\n *   stack       append below whatever is on screen\n *   splitRight  its own cell to the right, beside the view it is connected to\n *   newTab      its own tab in the current cell\n */\nexport type MsaViewPlacement = 'stack' | 'splitRight' | 'newTab'\n\nconst PLACEMENTS: MsaViewPlacement[] = ['stack', 'splitRight', 'newTab']\n\n/**\n * What the dialog does unasked. Side-by-side, because a launch from a gene\n * feature sets `connectedViewId`: the pair shares a hover and a highlight, and\n * reads as a split. A session spec defaults to `stack` instead.\n */\nexport const DEFAULT_LAUNCH_PLACEMENT: MsaViewPlacement = 'splitRight'\n\nexport const LAUNCH_PLACEMENT_KEY = 'msaView-launchPlacement'\n\n/**\n * The session actions that place a view in a tiled workspace. Only jbrowse-web\n * and desktop have them, so feature-detect rather than import.\n */\ninterface SessionWithMoves {\n  moveViewToNewTab: (viewId: string) => unknown\n  moveViewToSplit: (viewId: string, direction: 'row' | 'column') => unknown\n}\n\n// a host from before the workspace was always on\ninterface SessionWithWorkspaces {\n  setUseWorkspaces: (useWorkspaces: boolean) => void\n  setPendingMove: (move: {\n    type: 'newTab' | 'splitRight'\n    viewId: string\n  }) => void\n}\n\nfunction hasAction(session: AbstractSessionModel, name: string) {\n  return (\n    name in session &&\n    typeof (session as unknown as Record<string, unknown>)[name] === 'function'\n  )\n}\n\n// Warned at most once. This is a property of the host, so the answer is the\n// same on every launch and a dialog the user reopens should not stack up noise.\nlet warnedPartial = false\n\nexport function resetWorkspacesWarning() {\n  warnedPartial = false\n}\n\n/**\n * Whether this host can honor anything other than `stack`. Silent: the dialog\n * asks on every render, and only a launch is worth warning about.\n */\nexport function sessionSupportsPlacement(session: AbstractSessionModel) {\n  return (\n    isSessionWithMoves(session) ||\n    (hasAction(session, 'setUseWorkspaces') &&\n      hasAction(session, 'setPendingMove'))\n  )\n}\n\nfunction isSessionWithMoves(\n  session: AbstractSessionModel,\n): session is AbstractSessionModel & SessionWithMoves {\n  return (\n    hasAction(session, 'moveViewToNewTab') &&\n    hasAction(session, 'moveViewToSplit')\n  )\n}\n\nfunction isSessionWithWorkspaces(\n  session: AbstractSessionModel,\n): session is AbstractSessionModel & SessionWithWorkspaces {\n  const canEnable = hasAction(session, 'setUseWorkspaces')\n  const canPlace = hasAction(session, 'setPendingMove')\n\n  // Missing BOTH is an embedded session, with nothing to ask for. Missing ONE\n  // is a host that moved the action out from under us: protein3d once stopped\n  // tiling silently for weeks when jbrowse-web folded `setPendingMove` into its\n  // layout `init`.\n  if (canEnable !== canPlace && !warnedPartial) {\n    warnedPartial = true\n    console.warn(\n      `jbrowse-plugin-msaview: this session supports workspaces but not ` +\n        `${canPlace ? 'setUseWorkspaces' : 'setPendingMove'}, so the MSA view ` +\n        `was stacked instead of tiled: the session API moved and the plugin ` +\n        `needs updating to match.`,\n    )\n  }\n  return canEnable && canPlace\n}\n\n/**\n * Put a freshly added view where the launch said to. `stack` is a placement\n * rather than the absence of one, so no caller has to ask what host it is on.\n */\nexport function placeMsaView(\n  session: AbstractSessionModel,\n  viewId: string,\n  placement: MsaViewPlacement,\n) {\n  if (placement === 'stack') {\n    return\n  }\n  if (isSessionWithMoves(session)) {\n    if (placement === 'newTab') {\n      session.moveViewToNewTab(viewId)\n    } else {\n      session.moveViewToSplit(viewId, 'row')\n    }\n  } else if (isSessionWithWorkspaces(session)) {\n    session.setPendingMove({ type: placement, viewId })\n    session.setUseWorkspaces(true)\n  }\n}\n\nfunction isPlacement(value: unknown): value is MsaViewPlacement {\n  return PLACEMENTS.includes(value as MsaViewPlacement)\n}\n\n/**\n * The dialog's own remembered choice \u2014 not the host's preferences system, which\n * records whether the user likes workspaces and does not exist everywhere.\n */\nexport function readLaunchPlacement(): MsaViewPlacement {\n  try {\n    const stored = globalThis.localStorage.getItem(LAUNCH_PLACEMENT_KEY)\n    return isPlacement(stored) ? stored : DEFAULT_LAUNCH_PLACEMENT\n  } catch (error) {\n    console.error(error)\n    return DEFAULT_LAUNCH_PLACEMENT\n  }\n}\n\nexport function writeLaunchPlacement(placement: MsaViewPlacement) {\n  try {\n    globalThis.localStorage.setItem(LAUNCH_PLACEMENT_KEY, placement)\n  } catch (error) {\n    console.error(error)\n  }\n}\n", "import { placeMsaView } from './workspaces'\n\nimport type { MsaViewPlacement } from './workspaces'\nimport type { AbstractSessionModel } from '@jbrowse/core/util'\n\n/**\n * A launch, stated: what the view is, and where it goes. Everything but\n * `placement` is a react-msaview or plugin-model snapshot property, passed\n * through untouched so this never becomes a list that has to grow.\n */\nexport interface MsaViewLaunchSpec extends Record<string, unknown> {\n  /** default `stack`, the only thing an embedded session can do */\n  placement?: MsaViewPlacement\n}\n\n/**\n * The one place a launch adds an MSA view -- the dialog's four tabs, the Add\n * menu, and the `LaunchView-MsaView` extension point a session spec arrives on\n * all come through here. Each of them used to run its own `addView` and none\n * placed the result, which is how a launch from a gene feature landed stacked\n * under the very genome view it was connected to.\n */\nexport async function launchMsaView(\n  session: AbstractSessionModel,\n  { placement = 'stack', ...snapshot }: MsaViewLaunchSpec,\n) {\n  const view = await session.launchView('MsaView', {\n    type: 'MsaView',\n    ...snapshot,\n  })\n  placeMsaView(session, view.id, placement)\n  return view\n}\n"],
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+}

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

@@ -1,3 +1,3 @@
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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-ZMUARSUQ.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-WBXEEHJL.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-2T65ZS4E.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-YYP4CYYO.js"));function H(e){e.addViewType(()=>new ce.default({name:"MsaView",stateModel:()=>import("./chunks/model-7VBTOIJX.js").then(t=>t.default()),ReactComponent:je}))}var pe="5.1.0";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

@@ -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 = '5.0.0'\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 = '5.1.0'\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/utils/workspaces.js

@@ -21,8 +21,13 @@ export function resetWorkspacesWarning() {
  * asks on every render, and only a launch is worth warning about.
  */
 export function sessionSupportsPlacement(session) {
-    return (hasAction(session, 'setUseWorkspaces') &&
-        hasAction(session, 'setPendingMove'));
+    return (isSessionWithMoves(session) ||
+        (hasAction(session, 'setUseWorkspaces') &&
+            hasAction(session, 'setPendingMove')));
+}
+function isSessionWithMoves(session) {
+    return (hasAction(session, 'moveViewToNewTab') &&
+        hasAction(session, 'moveViewToSplit'));
 }
 function isSessionWithWorkspaces(session) {
     const canEnable = hasAction(session, 'setUseWorkspaces');
@@ -45,14 +50,21 @@ function isSessionWithWorkspaces(session) {
  * rather than the absence of one, so no caller has to ask what host it is on.
  */
 export function placeMsaView(session, viewId, placement) {
-    if (placement === 'stack' || !isSessionWithWorkspaces(session)) {
+    if (placement === 'stack') {
         return;
     }
-    session.setPendingMove({ type: placement, viewId });
-    // Session-scoped: turning workspaces on for this session leaves the user's
-    // own default alone, which is what `setUseWorkspaces` (as against
-    // `setUseWorkspacesPreference`) is for.
-    session.setUseWorkspaces(true);
+    if (isSessionWithMoves(session)) {
+        if (placement === 'newTab') {
+            session.moveViewToNewTab(viewId);
+        }
+        else {
+            session.moveViewToSplit(viewId, 'row');
+        }
+    }
+    else if (isSessionWithWorkspaces(session)) {
+        session.setPendingMove({ type: placement, viewId });
+        session.setUseWorkspaces(true);
+    }
 }
 function isPlacement(value) {
     return PLACEMENTS.includes(value);

package/dist/utils/workspaces.test.js

@@ -1,6 +1,17 @@
 import { afterEach, beforeEach, expect, test, vi } from 'vitest';
 import { launchMsaView } from './launchMsaView';
 import { DEFAULT_LAUNCH_PLACEMENT, LAUNCH_PLACEMENT_KEY, placeMsaView, readLaunchPlacement, resetWorkspacesWarning, sessionSupportsPlacement, writeLaunchPlacement, } from './workspaces';
+// a host whose workspace is always on, with the move actions the View menu uses
+function makeMovesSession() {
+    const recorded = { moves: [], workspaces: [], added: [] };
+    const session = {
+        moveViewToNewTab: (viewId) => recorded.moves.push({ to: 'tab', viewId }),
+        moveViewToSplit: (viewId, direction) => recorded.moves.push({ to: direction, viewId }),
+        setPendingMove: (move) => recorded.moves.push({ pending: move }),
+        setUseWorkspaces: (on) => recorded.workspaces.push(on),
+    };
+    return { session, recorded };
+}
 function makeSession({ canPlace = true, canEnable = true, } = {}) {
     const recorded = { moves: [], workspaces: [], added: [] };
     const session = {
@@ -34,6 +45,17 @@ afterEach(() => {
     vi.restoreAllMocks();
     vi.unstubAllGlobals();
 });
+test('a host with the move actions gets them, not setPendingMove', () => {
+    const { session, recorded } = makeMovesSession();
+    placeMsaView(session, 'view-1', 'splitRight');
+    placeMsaView(session, 'view-2', 'newTab');
+    expect(recorded.moves).toEqual([
+        { to: 'row', viewId: 'view-1' },
+        { to: 'tab', viewId: 'view-2' },
+    ]);
+    expect(recorded.workspaces).toEqual([]);
+    expect(sessionSupportsPlacement(session)).toBe(true);
+});
 test('stack places nothing, on a host that could tile', () => {
     const { session, recorded } = makeSession();
     placeMsaView(session, 'view-1', 'stack');

package/dist/version.d.ts

@@ -1 +1 @@
-export declare const version = "5.0.0";
+export declare const version = "5.1.0";

package/dist/version.js

@@ -1 +1 @@
-export const version = '5.0.0';
+export const version = '5.1.0';

package/package.json

@@ -1,5 +1,5 @@
 {
-  "version": "5.0.0",
+  "version": "5.1.0",
   "license": "MIT",
   "name": "jbrowse-plugin-msaview",
   "repository": {

package/src/utils/workspaces.test.ts

@@ -19,6 +19,20 @@ interface Recorded {
   added: { type: string; snapshot: Record<string, unknown> }[]
 }
 
+// a host whose workspace is always on, with the move actions the View menu uses
+function makeMovesSession() {
+  const recorded: Recorded = { moves: [], workspaces: [], added: [] }
+  const session = {
+    moveViewToNewTab: (viewId: string) =>
+      recorded.moves.push({ to: 'tab', viewId }),
+    moveViewToSplit: (viewId: string, direction: string) =>
+      recorded.moves.push({ to: direction, viewId }),
+    setPendingMove: (move: unknown) => recorded.moves.push({ pending: move }),
+    setUseWorkspaces: (on: boolean) => recorded.workspaces.push(on),
+  } as unknown as AbstractSessionModel
+  return { session, recorded }
+}
+
 function makeSession({
   canPlace = true,
   canEnable = true,
@@ -59,6 +73,18 @@ afterEach(() => {
   vi.unstubAllGlobals()
 })
 
+test('a host with the move actions gets them, not setPendingMove', () => {
+  const { session, recorded } = makeMovesSession()
+  placeMsaView(session, 'view-1', 'splitRight')
+  placeMsaView(session, 'view-2', 'newTab')
+  expect(recorded.moves).toEqual([
+    { to: 'row', viewId: 'view-1' },
+    { to: 'tab', viewId: 'view-2' },
+  ])
+  expect(recorded.workspaces).toEqual([])
+  expect(sessionSupportsPlacement(session)).toBe(true)
+})
+
 test('stack places nothing, on a host that could tile', () => {
   const { session, recorded } = makeSession()
   placeMsaView(session, 'view-1', 'stack')

package/src/utils/workspaces.ts

@@ -25,6 +25,12 @@ export const LAUNCH_PLACEMENT_KEY = 'msaView-launchPlacement'
  * The session actions that place a view in a tiled workspace. Only jbrowse-web
  * and desktop have them, so feature-detect rather than import.
  */
+interface SessionWithMoves {
+  moveViewToNewTab: (viewId: string) => unknown
+  moveViewToSplit: (viewId: string, direction: 'row' | 'column') => unknown
+}
+
+// a host from before the workspace was always on
 interface SessionWithWorkspaces {
   setUseWorkspaces: (useWorkspaces: boolean) => void
   setPendingMove: (move: {
@@ -54,8 +60,18 @@ export function resetWorkspacesWarning() {
  */
 export function sessionSupportsPlacement(session: AbstractSessionModel) {
   return (
-    hasAction(session, 'setUseWorkspaces') &&
-    hasAction(session, 'setPendingMove')
+    isSessionWithMoves(session) ||
+    (hasAction(session, 'setUseWorkspaces') &&
+      hasAction(session, 'setPendingMove'))
+  )
+}
+
+function isSessionWithMoves(
+  session: AbstractSessionModel,
+): session is AbstractSessionModel & SessionWithMoves {
+  return (
+    hasAction(session, 'moveViewToNewTab') &&
+    hasAction(session, 'moveViewToSplit')
   )
 }
 
@@ -90,14 +106,19 @@ export function placeMsaView(
   viewId: string,
   placement: MsaViewPlacement,
 ) {
-  if (placement === 'stack' || !isSessionWithWorkspaces(session)) {
+  if (placement === 'stack') {
     return
   }
-  session.setPendingMove({ type: placement, viewId })
-  // Session-scoped: turning workspaces on for this session leaves the user's
-  // own default alone, which is what `setUseWorkspaces` (as against
-  // `setUseWorkspacesPreference`) is for.
-  session.setUseWorkspaces(true)
+  if (isSessionWithMoves(session)) {
+    if (placement === 'newTab') {
+      session.moveViewToNewTab(viewId)
+    } else {
+      session.moveViewToSplit(viewId, 'row')
+    }
+  } else if (isSessionWithWorkspaces(session)) {
+    session.setPendingMove({ type: placement, viewId })
+    session.setUseWorkspaces(true)
+  }
 }
 
 function isPlacement(value: unknown): value is MsaViewPlacement {

package/src/version.ts

@@ -1 +1 @@
-export const version = '5.0.0'
+export const version = '5.1.0'

package/dist/chunks/chunk-VOBS7IVV.js

@@ -1,2 +0,0 @@
-var l=["stack","splitRight","newTab"],a="splitRight",i="msaView-launchPlacement";function n(e,t){return t in e&&typeof e[t]=="function"}var r=!1;function w(e){return n(e,"setUseWorkspaces")&&n(e,"setPendingMove")}function p(e){let t=n(e,"setUseWorkspaces"),s=n(e,"setPendingMove");return t!==s&&!r&&(r=!0,console.warn(`jbrowse-plugin-msaview: this session supports workspaces but not ${s?"setUseWorkspaces":"setPendingMove"}, so the MSA view was stacked instead of tiled: the session API moved and the plugin needs updating to match.`)),t&&s}function c(e,t,s){s==="stack"||!p(e)||(e.setPendingMove({type:s,viewId:t}),e.setUseWorkspaces(!0))}function u(e){return l.includes(e)}function M(){try{let e=globalThis.localStorage.getItem(i);return u(e)?e:a}catch(e){return console.error(e),a}}function d(e){try{globalThis.localStorage.setItem(i,e)}catch(t){console.error(t)}}async function h(e,{placement:t="stack",...s}){let o=await e.launchView("MsaView",{type:"MsaView",...s});return c(e,o.id,t),o}export{w as a,M as b,d as c,h as d};
-//# sourceMappingURL=chunk-VOBS7IVV.js.map

package/dist/chunks/chunk-VOBS7IVV.js.map

@@ -1,7 +0,0 @@
-{
-  "version": 3,
-  "sources": ["../../src/utils/workspaces.ts", "../../src/utils/launchMsaView.ts"],
-  "sourcesContent": ["import type { AbstractSessionModel } from '@jbrowse/core/util'\n\n/**\n * Where a launched MSA view lands. Every launch names one of these and stops\n * there, so a host that arranges views differently is one function to teach.\n *\n *   stack       append below whatever is on screen\n *   splitRight  its own cell to the right, beside the view it is connected to\n *   newTab      its own tab in the current cell\n */\nexport type MsaViewPlacement = 'stack' | 'splitRight' | 'newTab'\n\nconst PLACEMENTS: MsaViewPlacement[] = ['stack', 'splitRight', 'newTab']\n\n/**\n * What the dialog does unasked. Side-by-side, because a launch from a gene\n * feature sets `connectedViewId`: the pair shares a hover and a highlight, and\n * reads as a split. A session spec defaults to `stack` instead.\n */\nexport const DEFAULT_LAUNCH_PLACEMENT: MsaViewPlacement = 'splitRight'\n\nexport const LAUNCH_PLACEMENT_KEY = 'msaView-launchPlacement'\n\n/**\n * The session actions that place a view in a tiled workspace. Only jbrowse-web\n * and desktop have them, so feature-detect rather than import.\n */\ninterface SessionWithWorkspaces {\n  setUseWorkspaces: (useWorkspaces: boolean) => void\n  setPendingMove: (move: {\n    type: 'newTab' | 'splitRight'\n    viewId: string\n  }) => void\n}\n\nfunction hasAction(session: AbstractSessionModel, name: string) {\n  return (\n    name in session &&\n    typeof (session as unknown as Record<string, unknown>)[name] === 'function'\n  )\n}\n\n// Warned at most once. This is a property of the host, so the answer is the\n// same on every launch and a dialog the user reopens should not stack up noise.\nlet warnedPartial = false\n\nexport function resetWorkspacesWarning() {\n  warnedPartial = false\n}\n\n/**\n * Whether this host can honor anything other than `stack`. Silent: the dialog\n * asks on every render, and only a launch is worth warning about.\n */\nexport function sessionSupportsPlacement(session: AbstractSessionModel) {\n  return (\n    hasAction(session, 'setUseWorkspaces') &&\n    hasAction(session, 'setPendingMove')\n  )\n}\n\nfunction isSessionWithWorkspaces(\n  session: AbstractSessionModel,\n): session is AbstractSessionModel & SessionWithWorkspaces {\n  const canEnable = hasAction(session, 'setUseWorkspaces')\n  const canPlace = hasAction(session, 'setPendingMove')\n\n  // Missing BOTH is an embedded session, with nothing to ask for. Missing ONE\n  // is a host that moved the action out from under us: protein3d once stopped\n  // tiling silently for weeks when jbrowse-web folded `setPendingMove` into its\n  // layout `init`.\n  if (canEnable !== canPlace && !warnedPartial) {\n    warnedPartial = true\n    console.warn(\n      `jbrowse-plugin-msaview: this session supports workspaces but not ` +\n        `${canPlace ? 'setUseWorkspaces' : 'setPendingMove'}, so the MSA view ` +\n        `was stacked instead of tiled: the session API moved and the plugin ` +\n        `needs updating to match.`,\n    )\n  }\n  return canEnable && canPlace\n}\n\n/**\n * Put a freshly added view where the launch said to. `stack` is a placement\n * rather than the absence of one, so no caller has to ask what host it is on.\n */\nexport function placeMsaView(\n  session: AbstractSessionModel,\n  viewId: string,\n  placement: MsaViewPlacement,\n) {\n  if (placement === 'stack' || !isSessionWithWorkspaces(session)) {\n    return\n  }\n  session.setPendingMove({ type: placement, viewId })\n  // Session-scoped: turning workspaces on for this session leaves the user's\n  // own default alone, which is what `setUseWorkspaces` (as against\n  // `setUseWorkspacesPreference`) is for.\n  session.setUseWorkspaces(true)\n}\n\nfunction isPlacement(value: unknown): value is MsaViewPlacement {\n  return PLACEMENTS.includes(value as MsaViewPlacement)\n}\n\n/**\n * The dialog's own remembered choice \u2014 not the host's preferences system, which\n * records whether the user likes workspaces and does not exist everywhere.\n */\nexport function readLaunchPlacement(): MsaViewPlacement {\n  try {\n    const stored = globalThis.localStorage.getItem(LAUNCH_PLACEMENT_KEY)\n    return isPlacement(stored) ? stored : DEFAULT_LAUNCH_PLACEMENT\n  } catch (error) {\n    console.error(error)\n    return DEFAULT_LAUNCH_PLACEMENT\n  }\n}\n\nexport function writeLaunchPlacement(placement: MsaViewPlacement) {\n  try {\n    globalThis.localStorage.setItem(LAUNCH_PLACEMENT_KEY, placement)\n  } catch (error) {\n    console.error(error)\n  }\n}\n", "import { placeMsaView } from './workspaces'\n\nimport type { MsaViewPlacement } from './workspaces'\nimport type { AbstractSessionModel } from '@jbrowse/core/util'\n\n/**\n * A launch, stated: what the view is, and where it goes. Everything but\n * `placement` is a react-msaview or plugin-model snapshot property, passed\n * through untouched so this never becomes a list that has to grow.\n */\nexport interface MsaViewLaunchSpec extends Record<string, unknown> {\n  /** default `stack`, the only thing an embedded session can do */\n  placement?: MsaViewPlacement\n}\n\n/**\n * The one place a launch adds an MSA view -- the dialog's four tabs, the Add\n * menu, and the `LaunchView-MsaView` extension point a session spec arrives on\n * all come through here. Each of them used to run its own `addView` and none\n * placed the result, which is how a launch from a gene feature landed stacked\n * under the very genome view it was connected to.\n */\nexport async function launchMsaView(\n  session: AbstractSessionModel,\n  { placement = 'stack', ...snapshot }: MsaViewLaunchSpec,\n) {\n  const view = await session.launchView('MsaView', {\n    type: 'MsaView',\n    ...snapshot,\n  })\n  placeMsaView(session, view.id, placement)\n  return view\n}\n"],
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-  "names": ["PLACEMENTS", "DEFAULT_LAUNCH_PLACEMENT", "LAUNCH_PLACEMENT_KEY", "hasAction", "session", "name", "warnedPartial", "sessionSupportsPlacement", "session", "hasAction", "isSessionWithWorkspaces", "canEnable", "canPlace", "warnedPartial", "placeMsaView", "viewId", "placement", "isPlacement", "value", "PLACEMENTS", "readLaunchPlacement", "stored", "LAUNCH_PLACEMENT_KEY", "DEFAULT_LAUNCH_PLACEMENT", "error", "writeLaunchPlacement", "launchMsaView", "session", "placement", "snapshot", "view", "placeMsaView"]
-}