jbrowse-plugin-msaview 5.1.1 → 5.2.0

package/dist/chunks/{MetadataDialog-QCUWTDBU.js → MetadataDialog-KZWQFRF7.js}

@@ -1,2 +1,2 @@
-import{a as n,b as m,c as l}from"./chunk-VJQWGQ4V.js";import"./chunk-NSKY4K4T.js";import"./chunk-OF4AZJER.js";import"./chunk-P7ZJCOIY.js";import"./chunk-73KAPCJ2.js";import"./chunk-VWM6IHF2.js";import"./chunk-IP2BEEIU.js";import{a as u}from"./chunk-CVLB4VFP.js";import{a as f}from"./chunk-DNFD5II2.js";import{a as d}from"./chunk-BX4Z274Q.js";import{a as s}from"./chunk-J6KYLXRD.js";import{b as a}from"./chunk-FY3BTKY4.js";var e=a(s(),1),i=a(f(),1),t=a(d(),1),c=a(u(),1);var E=(0,c.observer)(function({model:r,onClose:p}){let{header:o}=r;return e.default.createElement(i.Dialog,{onClose:()=>{p()},open:!0,title:"Metadata",maxWidth:"xl"},e.default.createElement(t.DialogContent,null,Object.values(o).every(n)?e.default.createElement(t.Typography,null,"This alignment has no metadata."):e.default.createElement(m,{record:o}),e.default.createElement(t.Typography,{variant:"h6"},"Sequences"),e.default.createElement(l,{str:r.rows})))}),v=E;export{v as default};
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+import{a as n,b as m,c as l}from"./chunk-H6IQBAW7.js";import"./chunk-YOTSFJMU.js";import"./chunk-F3EC6OCO.js";import"./chunk-QQ5LZUIO.js";import"./chunk-73KAPCJ2.js";import"./chunk-GDFVLZYX.js";import"./chunk-GIHMPOCO.js";import{a as u}from"./chunk-CVLB4VFP.js";import{a as f}from"./chunk-DNFD5II2.js";import{a as d}from"./chunk-BX4Z274Q.js";import{a as s}from"./chunk-J6KYLXRD.js";import{b as a}from"./chunk-FY3BTKY4.js";var e=a(s(),1),i=a(f(),1),t=a(d(),1),c=a(u(),1);var E=(0,c.observer)(function({model:r,onClose:p}){let{header:o}=r;return e.default.createElement(i.Dialog,{onClose:()=>{p()},open:!0,title:"Metadata",maxWidth:"xl"},e.default.createElement(t.DialogContent,null,Object.values(o).every(n)?e.default.createElement(t.Typography,null,"This alignment has no metadata."):e.default.createElement(m,{record:o}),e.default.createElement(t.Typography,{variant:"h6"},"Sequences"),e.default.createElement(l,{str:r.rows})))}),v=E;export{v as default};
+//# sourceMappingURL=MetadataDialog-KZWQFRF7.js.map

package/dist/chunks/{MetadataDialog-QCUWTDBU.js.map → MetadataDialog-KZWQFRF7.js.map}

@@ -1,6 +1,6 @@
 {
   "version": 3,
-  "sources": ["../../node_modules/.pnpm/react-msaview@8.4.1_3e54acfe76b6ad0d26e91cd532b7f775/node_modules/react-msaview/src/components/dialogs/MetadataDialog.tsx"],
+  "sources": ["../../node_modules/.pnpm/react-msaview@9.0.0_3e54acfe76b6ad0d26e91cd532b7f775/node_modules/react-msaview/src/components/dialogs/MetadataDialog.tsx"],
   "sourcesContent": ["import React from 'react'\n\nimport { Dialog } from '@jbrowse/core/ui'\nimport { DialogContent, Typography } from '@mui/material'\nimport { observer } from 'mobx-react'\n\nimport MetadataTable, { isEmpty } from '../MetadataTable.tsx'\nimport SequenceTextArea from '../SequenceTextArea.tsx'\n\nimport type { MsaViewModel } from '../../model.ts'\n\nconst MetadataDialog = observer(function ({\n  model,\n  onClose,\n}: {\n  model: MsaViewModel\n  onClose: () => void\n}) {\n  const { header } = model\n  return (\n    <Dialog\n      onClose={() => {\n        onClose()\n      }}\n      open\n      title=\"Metadata\"\n      maxWidth=\"xl\"\n    >\n      <DialogContent>\n        {Object.values(header).every(isEmpty) ? (\n          <Typography>This alignment has no metadata.</Typography>\n        ) : (\n          <MetadataTable record={header} />\n        )}\n        <Typography variant=\"h6\">Sequences</Typography>\n        <SequenceTextArea str={model.rows} />\n      </DialogContent>\n    </Dialog>\n  )\n})\n\nexport default MetadataDialog\n"],
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   "names": ["import_react", "import_ui", "import_material", "import_mobx_react", "MetadataDialog", "model", "onClose", "header", "React", "isEmpty", "MetadataTable", "SequenceTextArea", "MetadataDialog_default"]

package/dist/chunks/{MsaViewPanel-DS4STM3W.js → MsaViewPanel-RUZAKFCB.js}

@@ -1,2 +1,2 @@
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-//# sourceMappingURL=MsaViewPanel-DS4STM3W.js.map
+import{a as b,c as k,d as C}from"./chunk-ZCT7RD24.js";import{e as M}from"./chunk-NMYD2GWF.js";import"./chunk-F3EC6OCO.js";import"./chunk-FCWXYIFC.js";import{a as B}from"./chunk-6YFCSBEE.js";import"./chunk-F726IWCW.js";import"./chunk-YUKJI2AH.js";import"./chunk-QQ5LZUIO.js";import{a as L}from"./chunk-NSASZ5FM.js";import"./chunk-IBBQUV2I.js";import"./chunk-QUWPHTZQ.js";import"./chunk-73KAPCJ2.js";import"./chunk-GIHMPOCO.js";import{a as y}from"./chunk-CVLB4VFP.js";import{a as P}from"./chunk-DNFD5II2.js";import{a as w}from"./chunk-BX4Z274Q.js";import{a as h}from"./chunk-J6KYLXRD.js";import{b as i}from"./chunk-FY3BTKY4.js";var e=i(h()),z=i(P()),E=i(y());var I=i(L());var o=i(h()),d=i(P()),n=i(w()),S=i(y()),x=i(L());var c=i(h()),J=i(w());function N({jobId:s}){let r=C(s)?k(s):b(s);return c.default.createElement(J.Typography,null,"Job ",s," (",c.default.createElement(B,{href:r},"see status"),")")}var v=N;var U=(0,x.makeStyles)()({margin:{padding:20},progressRow:{display:"flex",alignItems:"center",gap:12}}),D=(0,S.observer)(function({model:r}){let{progress:u,rid:a,error:m}=r,{classes:t}=U(),f=!r.launchCompleted,{blastParams:l,orthologParams:g}=r,p=l?`Running EBI ${l.searchProgram==="phmmer"?"phmmer":"BLAST"}`:g?g.source==="uniref"?"Building UniRef homolog alignment":"Building ortholog alignment":"Loading alignment";return o.default.createElement("div",{className:t.margin},m?o.default.createElement(o.default.Fragment,null,o.default.createElement(n.Typography,{variant:"h5"},f?`${p} failed`:"Alignment no longer available"),a?o.default.createElement(v,{jobId:a}):null,o.default.createElement(d.ErrorMessage,{error:m}),o.default.createElement("div",{className:t.progressRow},o.default.createElement(n.Button,{variant:"outlined",size:"small",onClick:()=>{r.retryLaunch()}},"Retry"),o.default.createElement(n.Button,{variant:"outlined",size:"small",onClick:()=>{r.cancelLaunch()}},"Dismiss"))):o.default.createElement(o.default.Fragment,null,o.default.createElement(d.LoadingEllipses,{message:p,variant:"h5"}),a?o.default.createElement(v,{jobId:a}):null,o.default.createElement("div",{className:t.progressRow},o.default.createElement(n.Typography,null,u||"Initializing"),o.default.createElement(n.Button,{variant:"outlined",size:"small",onClick:()=>{r.cancelLaunch()}},"Cancel"))))}),V=D;var $=(0,I.makeStyles)()({loadingContainer:{padding:20}}),q=(0,E.observer)(function({model:r}){let{classes:u}=$(),{blastParams:a,orthologParams:m,init:t,loadingStoredData:f}=r,l=a??m,g=!!l&&!r.launchCompleted,p=!!(r.data.msa||r.data.tree),T=!!l&&!!r.error&&!p,A=g||T||!!t&&!r.dataInitialized;return e.default.createElement("div",null,A?e.default.createElement(V,{model:r}):f&&!r.dataInitialized?e.default.createElement("div",{className:u.loadingContainer},e.default.createElement(z.LoadingEllipses,{message:"Loading MSA data",variant:"h6"})):e.default.createElement(M,{model:r}))}),X=q;export{X as default};
+//# sourceMappingURL=MsaViewPanel-RUZAKFCB.js.map

package/dist/chunks/{TrackInfoDialog-BVZWIDEU.js → TrackInfoDialog-IFIG77WO.js}

@@ -1,2 +1,2 @@
-import{a as l}from"./chunk-VWM6IHF2.js";import{a as k}from"./chunk-IP2BEEIU.js";import{a as p}from"./chunk-CVLB4VFP.js";import{a as f}from"./chunk-DNFD5II2.js";import{a as g}from"./chunk-BX4Z274Q.js";import{a as d}from"./chunk-J6KYLXRD.js";import{b as o}from"./chunk-FY3BTKY4.js";var e=o(d(),1),c=o(f(),1),i=o(k(),1),t=o(g(),1),m=o(p(),1);var E=(0,i.makeStyles)()(a=>({textArea:{padding:a.spacing(2),overflow:"auto",background:a.palette.action.selected,wordBreak:"break-word"}})),x=(0,m.observer)(function({model:a,onClose:n}){let{name:s,data:r}=a,{classes:u}=E();return e.default.createElement(c.Dialog,{open:!0,onClose:n,fullWidth:!0,maxWidth:"lg",title:`Track info - ${s}`},e.default.createElement(t.DialogContent,null,r===void 0?e.default.createElement(t.Typography,null,"This track has no text data."):e.default.createElement(e.default.Fragment,null,e.default.createElement(l,{text:r}),e.default.createElement("pre",{className:u.textArea},r))),e.default.createElement(t.DialogActions,null,e.default.createElement(t.Button,{variant:"contained",onClick:n,color:"secondary"},"Close")))}),h=x;export{h as default};
-//# sourceMappingURL=TrackInfoDialog-BVZWIDEU.js.map
+import{a as l}from"./chunk-GDFVLZYX.js";import{a as k}from"./chunk-GIHMPOCO.js";import{a as p}from"./chunk-CVLB4VFP.js";import{a as f}from"./chunk-DNFD5II2.js";import{a as g}from"./chunk-BX4Z274Q.js";import{a as d}from"./chunk-J6KYLXRD.js";import{b as o}from"./chunk-FY3BTKY4.js";var e=o(d(),1),c=o(f(),1),i=o(k(),1),t=o(g(),1),m=o(p(),1);var E=(0,i.makeStyles)()(a=>({textArea:{padding:a.spacing(2),overflow:"auto",background:a.palette.action.selected,wordBreak:"break-word"}})),x=(0,m.observer)(function({model:a,onClose:n}){let{name:s,data:r}=a,{classes:u}=E();return e.default.createElement(c.Dialog,{open:!0,onClose:n,fullWidth:!0,maxWidth:"lg",title:`Track info - ${s}`},e.default.createElement(t.DialogContent,null,r===void 0?e.default.createElement(t.Typography,null,"This track has no text data."):e.default.createElement(e.default.Fragment,null,e.default.createElement(l,{text:r}),e.default.createElement("pre",{className:u.textArea},r))),e.default.createElement(t.DialogActions,null,e.default.createElement(t.Button,{variant:"contained",onClick:n,color:"secondary"},"Close")))}),h=x;export{h as default};
+//# sourceMappingURL=TrackInfoDialog-IFIG77WO.js.map

package/dist/chunks/{TrackInfoDialog-BVZWIDEU.js.map → TrackInfoDialog-IFIG77WO.js.map}

@@ -1,6 +1,6 @@
 {
   "version": 3,
-  "sources": ["../../node_modules/.pnpm/react-msaview@8.4.1_3e54acfe76b6ad0d26e91cd532b7f775/node_modules/react-msaview/src/components/dialogs/TrackInfoDialog.tsx"],
+  "sources": ["../../node_modules/.pnpm/react-msaview@9.0.0_3e54acfe76b6ad0d26e91cd532b7f775/node_modules/react-msaview/src/components/dialogs/TrackInfoDialog.tsx"],
   "sourcesContent": ["import React from 'react'\n\nimport { Dialog } from '@jbrowse/core/ui'\nimport { makeStyles } from '@jbrowse/core/util/tss-react'\nimport { Button, DialogActions, DialogContent, Typography } from '@mui/material'\nimport { observer } from 'mobx-react'\n\nimport CopyButton from '../CopyButton.tsx'\n\nimport type { BasicTrack } from '../../types.ts'\n\nconst useStyles = makeStyles()(theme => ({\n  textArea: {\n    padding: theme.spacing(2),\n    overflow: 'auto',\n    background: theme.palette.action.selected,\n    wordBreak: 'break-word',\n  },\n}))\n\nconst TrackInfoDialog = observer(function ({\n  model,\n  onClose,\n}: {\n  model: BasicTrack['model']\n  onClose: () => void\n}) {\n  const { name, data } = model\n  const { classes } = useStyles()\n  return (\n    <Dialog\n      open\n      onClose={onClose}\n      fullWidth\n      maxWidth=\"lg\"\n      title={`Track info - ${name}`}\n    >\n      <DialogContent>\n        {/* the bar tracks (conservation) are computed per column and carry no\n            text of their own, so there is nothing to show or copy for them */}\n        {data === undefined ? (\n          <Typography>This track has no text data.</Typography>\n        ) : (\n          <>\n            <CopyButton text={data} />\n            <pre className={classes.textArea}>{data}</pre>\n          </>\n        )}\n      </DialogContent>\n      <DialogActions>\n        <Button variant=\"contained\" onClick={onClose} color=\"secondary\">\n          Close\n        </Button>\n      </DialogActions>\n    </Dialog>\n  )\n})\n\nexport default TrackInfoDialog\n"],
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   "names": ["import_react", "import_ui", "import_tss_react", "import_material", "import_mobx_react", "useStyles", "theme", "TrackInfoDialog", "model", "onClose", "name", "data", "classes", "React", "CopyButton", "TrackInfoDialog_default"]

package/dist/chunks/{TreeNodeInfoDialog-LPLF6BA6.js → TreeNodeInfoDialog-VRCVIF26.js}

@@ -1,2 +1,2 @@
-import{b as n,c}from"./chunk-VJQWGQ4V.js";import"./chunk-NSKY4K4T.js";import"./chunk-OF4AZJER.js";import"./chunk-P7ZJCOIY.js";import"./chunk-73KAPCJ2.js";import"./chunk-VWM6IHF2.js";import"./chunk-IP2BEEIU.js";import{a as g}from"./chunk-CVLB4VFP.js";import{a as h}from"./chunk-DNFD5II2.js";import{a as x}from"./chunk-BX4Z274Q.js";import{a as d}from"./chunk-J6KYLXRD.js";import{b as r}from"./chunk-FY3BTKY4.js";var e=r(d(),1),i=r(h(),1),t=r(x(),1),f=r(g(),1);var T=(0,f.observer)(function({info:u,model:o,nodeName:a,onClose:E}){let{rows:p}=o,l=o.rowDataOf(a),m=p.find(s=>s[0]===a);return e.default.createElement(i.Dialog,{onClose:()=>{E()},open:!0,title:"Tree node info",maxWidth:"xl"},e.default.createElement(t.DialogContent,null,e.default.createElement(t.Typography,{variant:"h6"},"Attributes"),e.default.createElement(n,{record:{nodeName:a,...u}}),e.default.createElement(t.Typography,{variant:"h6"},"Sequence"),m?e.default.createElement(c,{str:[m]}):e.default.createElement(t.Typography,null,"Sequence not found"),l?e.default.createElement(e.default.Fragment,null,e.default.createElement(t.Typography,{variant:"h6"},"Extra metadata"),e.default.createElement(n,{record:l})):null))}),b=T;export{b as default};
-//# sourceMappingURL=TreeNodeInfoDialog-LPLF6BA6.js.map
+import{b as n,c}from"./chunk-H6IQBAW7.js";import"./chunk-YOTSFJMU.js";import"./chunk-F3EC6OCO.js";import"./chunk-QQ5LZUIO.js";import"./chunk-73KAPCJ2.js";import"./chunk-GDFVLZYX.js";import"./chunk-GIHMPOCO.js";import{a as g}from"./chunk-CVLB4VFP.js";import{a as h}from"./chunk-DNFD5II2.js";import{a as x}from"./chunk-BX4Z274Q.js";import{a as d}from"./chunk-J6KYLXRD.js";import{b as r}from"./chunk-FY3BTKY4.js";var e=r(d(),1),i=r(h(),1),t=r(x(),1),f=r(g(),1);var T=(0,f.observer)(function({info:u,model:o,nodeName:a,onClose:E}){let{rows:p}=o,l=o.rowDataOf(a),m=p.find(s=>s[0]===a);return e.default.createElement(i.Dialog,{onClose:()=>{E()},open:!0,title:"Tree node info",maxWidth:"xl"},e.default.createElement(t.DialogContent,null,e.default.createElement(t.Typography,{variant:"h6"},"Attributes"),e.default.createElement(n,{record:{nodeName:a,...u}}),e.default.createElement(t.Typography,{variant:"h6"},"Sequence"),m?e.default.createElement(c,{str:[m]}):e.default.createElement(t.Typography,null,"Sequence not found"),l?e.default.createElement(e.default.Fragment,null,e.default.createElement(t.Typography,{variant:"h6"},"Extra metadata"),e.default.createElement(n,{record:l})):null))}),b=T;export{b as default};
+//# sourceMappingURL=TreeNodeInfoDialog-VRCVIF26.js.map

package/dist/chunks/{TreeNodeInfoDialog-LPLF6BA6.js.map → TreeNodeInfoDialog-VRCVIF26.js.map}

@@ -1,6 +1,6 @@
 {
   "version": 3,
-  "sources": ["../../node_modules/.pnpm/react-msaview@8.4.1_3e54acfe76b6ad0d26e91cd532b7f775/node_modules/react-msaview/src/components/tree/dialogs/TreeNodeInfoDialog.tsx"],
+  "sources": ["../../node_modules/.pnpm/react-msaview@9.0.0_3e54acfe76b6ad0d26e91cd532b7f775/node_modules/react-msaview/src/components/tree/dialogs/TreeNodeInfoDialog.tsx"],
   "sourcesContent": ["import React from 'react'\n\nimport { Dialog } from '@jbrowse/core/ui'\nimport { DialogContent, Typography } from '@mui/material'\nimport { observer } from 'mobx-react'\n\nimport MetadataTable from '../../MetadataTable.tsx'\nimport SequenceTextArea from '../../SequenceTextArea.tsx'\n\nimport type { MsaViewModel } from '../../../model.ts'\n\nconst TreeNodeInfoDialog = observer(function ({\n  info,\n  model,\n  nodeName,\n  onClose,\n}: {\n  info: Record<string, unknown>\n  model: MsaViewModel\n  nodeName: string\n  onClose: () => void\n}) {\n  const { rows } = model\n  const metadata = model.rowDataOf(nodeName)\n  const res = rows.find(f => f[0] === nodeName)\n  return (\n    <Dialog\n      onClose={() => {\n        onClose()\n      }}\n      open\n      title=\"Tree node info\"\n      maxWidth=\"xl\"\n    >\n      <DialogContent>\n        <Typography variant=\"h6\">Attributes</Typography>\n        <MetadataTable record={{ nodeName, ...info }} />\n        <Typography variant=\"h6\">Sequence</Typography>\n        {res ? (\n          <SequenceTextArea str={[res]} />\n        ) : (\n          <Typography>Sequence not found</Typography>\n        )}\n        {metadata ? (\n          <>\n            <Typography variant=\"h6\">Extra metadata</Typography>\n            <MetadataTable record={metadata} />\n          </>\n        ) : null}\n      </DialogContent>\n    </Dialog>\n  )\n})\n\nexport default TreeNodeInfoDialog\n"],
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package/dist/chunks/{chunk-OF4AZJER.js → chunk-F3EC6OCO.js}

@@ -1,2 +1,2 @@
 function n(c,o){let t=URL.createObjectURL(c),e=document.createElement("a");e.href=t,e.download=o,e.click(),setTimeout(()=>{URL.revokeObjectURL(t)},4e4)}export{n as a};
-//# sourceMappingURL=chunk-OF4AZJER.js.map
+//# sourceMappingURL=chunk-F3EC6OCO.js.map

package/dist/chunks/{chunk-OF4AZJER.js.map → chunk-F3EC6OCO.js.map}

@@ -1,6 +1,6 @@
 {
   "version": 3,
-  "sources": ["../../node_modules/.pnpm/react-msaview@8.4.1_3e54acfe76b6ad0d26e91cd532b7f775/node_modules/react-msaview/src/vendor/fileSaver.ts"],
+  "sources": ["../../node_modules/.pnpm/react-msaview@9.0.0_3e54acfe76b6ad0d26e91cd532b7f775/node_modules/react-msaview/src/vendor/fileSaver.ts"],
   "sourcesContent": ["export function saveAs(blob: Blob, name: string) {\n  const url = URL.createObjectURL(blob)\n  const a = document.createElement('a')\n  a.href = url\n  a.download = name\n  a.click()\n  setTimeout(() => {\n    URL.revokeObjectURL(url)\n  }, 40_000)\n}\n"],
   "mappings": "AAAM,SAAUA,EAAOC,EAAYC,EAAY,CAC7C,IAAMC,EAAM,IAAI,gBAAgBF,CAAI,EAC9BG,EAAI,SAAS,cAAc,GAAG,EACpCA,EAAE,KAAOD,EACTC,EAAE,SAAWF,EACbE,EAAE,MAAK,EACP,WAAW,IAAK,CACd,IAAI,gBAAgBD,CAAG,CACzB,EAAG,GAAM,CACX",
   "names": ["saveAs", "blob", "name", "url", "a"]

package/dist/chunks/{chunk-VWM6IHF2.js → chunk-GDFVLZYX.js}

@@ -1,2 +1,2 @@
-import{b as n}from"./chunk-IP2BEEIU.js";import{a as f}from"./chunk-BX4Z274Q.js";import{a as p}from"./chunk-J6KYLXRD.js";import{b as i}from"./chunk-FY3BTKY4.js";var e=i(p(),1),c=i(f(),1);function m({text:t,label:u="Copy to clipboard"}){let[a,r]=(0,e.useState)(!1),o=(0,e.useRef)(void 0);return(0,e.useEffect)(()=>()=>{clearTimeout(o.current)},[]),e.default.createElement(c.Button,{variant:"contained",color:"primary",onClick:()=>{n(typeof t=="string"?t:t()),r(!0),clearTimeout(o.current),o.current=setTimeout(()=>{r(!1)},500)}},a?"Copied!":u)}export{m as a};
-//# sourceMappingURL=chunk-VWM6IHF2.js.map
+import{b as n}from"./chunk-GIHMPOCO.js";import{a as f}from"./chunk-BX4Z274Q.js";import{a as p}from"./chunk-J6KYLXRD.js";import{b as i}from"./chunk-FY3BTKY4.js";var e=i(p(),1),c=i(f(),1);function m({text:t,label:u="Copy to clipboard"}){let[a,r]=(0,e.useState)(!1),o=(0,e.useRef)(void 0);return(0,e.useEffect)(()=>()=>{clearTimeout(o.current)},[]),e.default.createElement(c.Button,{variant:"contained",color:"primary",onClick:()=>{n(typeof t=="string"?t:t()),r(!0),clearTimeout(o.current),o.current=setTimeout(()=>{r(!1)},500)}},a?"Copied!":u)}export{m as a};
+//# sourceMappingURL=chunk-GDFVLZYX.js.map

package/dist/chunks/{chunk-VWM6IHF2.js.map → chunk-GDFVLZYX.js.map}

@@ -1,6 +1,6 @@
 {
   "version": 3,
-  "sources": ["../../node_modules/.pnpm/react-msaview@8.4.1_3e54acfe76b6ad0d26e91cd532b7f775/node_modules/react-msaview/src/components/CopyButton.tsx"],
+  "sources": ["../../node_modules/.pnpm/react-msaview@9.0.0_3e54acfe76b6ad0d26e91cd532b7f775/node_modules/react-msaview/src/components/CopyButton.tsx"],
   "sourcesContent": ["import React, { useEffect, useRef, useState } from 'react'\n\nimport { Button } from '@mui/material'\n\nimport copy from '../vendor/copyToClipboard.ts'\n\n/**\n * Copy-to-clipboard button that confirms on the label for a moment. The timer is\n * cleared on unmount, since these live in dialogs the copy itself often closes.\n */\nexport default function CopyButton({\n  text,\n  label = 'Copy to clipboard',\n}: {\n  text: string | (() => string)\n  label?: string\n}) {\n  const [copied, setCopied] = useState(false)\n  const timer = useRef<ReturnType<typeof setTimeout>>(undefined)\n\n  useEffect(\n    () => () => {\n      clearTimeout(timer.current)\n    },\n    [],\n  )\n\n  return (\n    <Button\n      variant=\"contained\"\n      color=\"primary\"\n      onClick={() => {\n        copy(typeof text === 'string' ? text : text())\n        setCopied(true)\n        clearTimeout(timer.current)\n        timer.current = setTimeout(() => {\n          setCopied(false)\n        }, 500)\n      }}\n    >\n      {copied ? 'Copied!' : label}\n    </Button>\n  )\n}\n"],
   "mappings": "gKAAA,IAAAA,EAAmD,SAEnDC,EAAuB,SAQT,SAAPC,EAA4B,CACjC,KAAAC,EACA,MAAAC,EAAQ,mBAAmB,EAI5B,CACC,GAAM,CAACC,EAAQC,CAAS,KAAI,YAAS,EAAK,EACpCC,KAAQ,UAAsC,MAAS,EAE7D,sBACE,IAAM,IAAK,CACT,aAAaA,EAAM,OAAO,CAC5B,EACA,CAAA,CAAE,EAIF,EAAAC,QAAA,cAAC,SAAM,CACL,QAAQ,YACR,MAAM,UACN,QAAS,IAAK,CACZC,EAAK,OAAON,GAAS,SAAWA,EAAOA,EAAI,CAAE,EAC7CG,EAAU,EAAI,EACd,aAAaC,EAAM,OAAO,EAC1BA,EAAM,QAAU,WAAW,IAAK,CAC9BD,EAAU,EAAK,CACjB,EAAG,GAAG,CACR,CAAC,EAEAD,EAAS,UAAYD,CAAK,CAGjC",
   "names": ["import_react", "import_material", "CopyButton", "text", "label", "copied", "setCopied", "timer", "React", "copy"]

package/dist/chunks/{chunk-IP2BEEIU.js → chunk-GIHMPOCO.js}

@@ -1,2 +1,2 @@
 import{a}from"./chunk-FY3BTKY4.js";var i=a((p,c)=>{c.exports=JBrowseExports["@jbrowse/core/util/tss-react"]});function n(t){let o=navigator.clipboard;if(o?.writeText){o.writeText(t).catch(r=>{console.error("Failed to copy to clipboard:",r)});return}let e=document.createElement("textarea");e.value=t,e.style.position="fixed",e.style.opacity="0",document.body.append(e),e.select(),document.execCommand("copy"),e.remove()}export{i as a,n as b};
-//# sourceMappingURL=chunk-IP2BEEIU.js.map
+//# sourceMappingURL=chunk-GIHMPOCO.js.map

package/dist/chunks/{chunk-IP2BEEIU.js.map → chunk-GIHMPOCO.js.map}

@@ -1,6 +1,6 @@
 {
   "version": 3,
-  "sources": ["global-externals:@jbrowse/core/util/tss-react", "../../node_modules/.pnpm/react-msaview@8.4.1_3e54acfe76b6ad0d26e91cd532b7f775/node_modules/react-msaview/src/vendor/copyToClipboard.ts"],
+  "sources": ["global-externals:@jbrowse/core/util/tss-react", "../../node_modules/.pnpm/react-msaview@9.0.0_3e54acfe76b6ad0d26e91cd532b7f775/node_modules/react-msaview/src/vendor/copyToClipboard.ts"],
   "sourcesContent": ["module.exports = JBrowseExports[\"@jbrowse/core/util/tss-react\"];", "export default function copy(text: string) {\n  const clip = navigator.clipboard as Clipboard | undefined\n  if (clip?.writeText) {\n    clip.writeText(text).catch((e: unknown) => {\n      console.error('Failed to copy to clipboard:', e)\n    })\n    return\n  }\n  const textarea = document.createElement('textarea')\n  textarea.value = text\n  textarea.style.position = 'fixed'\n  textarea.style.opacity = '0'\n  document.body.append(textarea)\n  textarea.select()\n  document.execCommand('copy')\n  textarea.remove()\n}\n"],
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   "names": ["require_tss_react", "__commonJSMin", "exports", "module", "copy", "text", "clip", "e", "textarea"]

package/dist/chunks/{chunk-VJQWGQ4V.js → chunk-H6IQBAW7.js}

@@ -1,6 +1,6 @@
-import{a as d}from"./chunk-NSKY4K4T.js";import{a as b}from"./chunk-OF4AZJER.js";import{f as y}from"./chunk-P7ZJCOIY.js";import{a as S}from"./chunk-VWM6IHF2.js";import{a as x}from"./chunk-IP2BEEIU.js";import{a as g}from"./chunk-BX4Z274Q.js";import{a as w}from"./chunk-J6KYLXRD.js";import{b as s}from"./chunk-FY3BTKY4.js";var l=s(w(),1),E=s(x(),1),a=s(g(),1),j=(0,E.makeStyles)()({key:{fontWeight:"bold",verticalAlign:"top"},value:{whiteSpace:"pre-wrap",wordBreak:"break-word"}});function k(e){return typeof e=="object"&&e!==null&&!Array.isArray(e)}function B(e){return k(e)&&Object.keys(e).length===0}function A({record:e}){let{classes:o}=j();return l.default.createElement(a.Table,{size:"small"},l.default.createElement(a.TableBody,null,Object.entries(e).filter(([,t])=>t!=null&&!B(t)).map(([t,r])=>l.default.createElement(a.TableRow,{key:t},l.default.createElement(a.TableCell,{component:"th",className:o.key},t),l.default.createElement(a.TableCell,{className:o.value},k(r)?l.default.createElement(A,{record:r}):Array.isArray(r)?r.join(`
+import{a as d}from"./chunk-YOTSFJMU.js";import{a as b}from"./chunk-F3EC6OCO.js";import{f as y}from"./chunk-QQ5LZUIO.js";import{a as S}from"./chunk-GDFVLZYX.js";import{a as x}from"./chunk-GIHMPOCO.js";import{a as g}from"./chunk-BX4Z274Q.js";import{a as w}from"./chunk-J6KYLXRD.js";import{b as s}from"./chunk-FY3BTKY4.js";var l=s(w(),1),E=s(x(),1),a=s(g(),1),j=(0,E.makeStyles)()({key:{fontWeight:"bold",verticalAlign:"top"},value:{whiteSpace:"pre-wrap",wordBreak:"break-word"}});function k(e){return typeof e=="object"&&e!==null&&!Array.isArray(e)}function B(e){return k(e)&&Object.keys(e).length===0}function A({record:e}){let{classes:o}=j();return l.default.createElement(a.Table,{size:"small"},l.default.createElement(a.TableBody,null,Object.entries(e).filter(([,t])=>t!=null&&!B(t)).map(([t,r])=>l.default.createElement(a.TableRow,{key:t},l.default.createElement(a.TableCell,{component:"th",className:o.key},t),l.default.createElement(a.TableCell,{className:o.value},k(r)?l.default.createElement(A,{record:r}):Array.isArray(r)?r.join(`
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 ${t?o:y(o)}`}function G(e){return!/[^.-]/.test(e)}function O(e,o){let t=[],r=0;for(let c of e){if(t.length>=N||r>=$)break;let i=T(c,o);t.push(i),r+=i.length+1}return{text:t.join(`
 `),hidden:e.length-t.length}}function W({str:e}){let{classes:o}=F(),[t,r]=(0,n.useState)(!1),[c,i]=(0,n.useState)(!1),m=c?e:e.filter(([,p])=>t?!!p:!G(p)),{text:R,hidden:u}=O(m,t),h=()=>m.map(p=>T(p,t)).join(`
 `);return n.default.createElement(n.default.Fragment,null,n.default.createElement(S,{text:h}),n.default.createElement(f.Button,{onClick:()=>{b(new Blob([h()],{type:"text/plain"}),"sequences.fasta")}},"Download"),n.default.createElement(d,{label:"Show gaps",checked:t,onChange:()=>{r(!t)}}),n.default.createElement(d,{label:"Show empty",checked:c,onChange:()=>{i(!c)}}),n.default.createElement(f.TextField,{variant:"outlined",multiline:!0,className:o.dialogContent,minRows:5,maxRows:10,fullWidth:!0,value:R,helperText:u>0?`Showing ${m.length-u} of ${m.length.toLocaleString()} sequences. ${u.toLocaleString()} more are in the copy and the download.`:void 0,slotProps:{input:{readOnly:!0,className:o.textAreaFont}}}))}export{B as a,A as b,W as c};
-//# sourceMappingURL=chunk-VJQWGQ4V.js.map
+//# sourceMappingURL=chunk-H6IQBAW7.js.map

package/dist/chunks/{chunk-VJQWGQ4V.js.map → chunk-H6IQBAW7.js.map}

@@ -1,6 +1,6 @@
 {
   "version": 3,
-  "sources": ["../../node_modules/.pnpm/react-msaview@8.4.1_3e54acfe76b6ad0d26e91cd532b7f775/node_modules/react-msaview/src/components/MetadataTable.tsx", "../../node_modules/.pnpm/react-msaview@8.4.1_3e54acfe76b6ad0d26e91cd532b7f775/node_modules/react-msaview/src/components/SequenceTextArea.tsx"],
+  "sources": ["../../node_modules/.pnpm/react-msaview@9.0.0_3e54acfe76b6ad0d26e91cd532b7f775/node_modules/react-msaview/src/components/MetadataTable.tsx", "../../node_modules/.pnpm/react-msaview@9.0.0_3e54acfe76b6ad0d26e91cd532b7f775/node_modules/react-msaview/src/components/SequenceTextArea.tsx"],
   "sourcesContent": ["import React from 'react'\n\nimport { makeStyles } from '@jbrowse/core/util/tss-react'\nimport { Table, TableBody, TableCell, TableRow } from '@mui/material'\n\nconst useStyles = makeStyles()({\n  key: {\n    fontWeight: 'bold',\n    verticalAlign: 'top',\n  },\n  value: {\n    whiteSpace: 'pre-wrap',\n    wordBreak: 'break-word',\n  },\n})\n\nfunction isRecord(value: unknown): value is Record<string, unknown> {\n  return typeof value === 'object' && value !== null && !Array.isArray(value)\n}\n\nexport function isEmpty(value: unknown) {\n  return isRecord(value) && Object.keys(value).length === 0\n}\n\nexport default function MetadataTable({\n  record,\n}: {\n  record: Record<string, unknown>\n}) {\n  const { classes } = useStyles()\n  return (\n    <Table size=\"small\">\n      <TableBody>\n        {Object.entries(record)\n          .filter(([, value]) => value != null && !isEmpty(value))\n          .map(([key, value]) => (\n            <TableRow key={key}>\n              <TableCell component=\"th\" className={classes.key}>\n                {key}\n              </TableCell>\n              <TableCell className={classes.value}>\n                {isRecord(value) ? (\n                  <MetadataTable record={value} />\n                ) : Array.isArray(value) ? (\n                  value.join('\\n')\n                ) : (\n                  String(value)\n                )}\n              </TableCell>\n            </TableRow>\n          ))}\n      </TableBody>\n    </Table>\n  )\n}\n", "import React, { useState } from 'react'\n\nimport { makeStyles } from '@jbrowse/core/util/tss-react'\nimport { Button, TextField } from '@mui/material'\nimport { getUngappedSequence } from 'msa-parsers'\n\nimport { saveAs } from '../vendor/fileSaver.ts'\nimport Checkbox2 from './Checkbox2.tsx'\nimport CopyButton from './CopyButton.tsx'\n\nconst useStyles = makeStyles()(theme => ({\n  textAreaFont: {\n    fontFamily: 'Courier New',\n    wordWrap: 'break-word',\n  },\n  dialogContent: {\n    background: theme.palette.action.selected,\n    margin: 4,\n  },\n}))\n\nexport const maxShownRecords = 100\nexport const maxShownChars = 200_000\n\nfunction fastaRecord([name, seq]: [string, string], showGaps: boolean) {\n  return `>${name}\\n${showGaps ? seq : getUngappedSequence(seq)}`\n}\n\nfunction isAllGaps(seq: string) {\n  return !/[^.-]/.test(seq)\n}\n\n/**\n * The first records of `rows` as FASTA, up to `maxShownRecords` records or\n * `maxShownChars` characters, whichever comes first. A textarea holding every\n * row of a large alignment freezes the page.\n */\nexport function fastaPreview(rows: [string, string][], showGaps: boolean) {\n  const shown: string[] = []\n  let chars = 0\n  for (const row of rows) {\n    if (shown.length >= maxShownRecords || chars >= maxShownChars) {\n      break\n    }\n    const record = fastaRecord(row, showGaps)\n    shown.push(record)\n    chars += record.length + 1\n  }\n  return { text: shown.join('\\n'), hidden: rows.length - shown.length }\n}\n\nexport default function SequenceTextArea({ str }: { str: [string, string][] }) {\n  const { classes } = useStyles()\n  const [showGaps, setShowGaps] = useState(false)\n  const [showEmpty, setShowEmpty] = useState(false)\n\n  const rows = showEmpty\n    ? str\n    : str.filter(([, seq]) => (showGaps ? !!seq : !isAllGaps(seq)))\n  const { text, hidden } = fastaPreview(rows, showGaps)\n  const fullText = () => rows.map(row => fastaRecord(row, showGaps)).join('\\n')\n  return (\n    <>\n      <CopyButton text={fullText} />\n      <Button\n        onClick={() => {\n          saveAs(\n            new Blob([fullText()], { type: 'text/plain' }),\n            'sequences.fasta',\n          )\n        }}\n      >\n        Download\n      </Button>\n      <Checkbox2\n        label=\"Show gaps\"\n        checked={showGaps}\n        onChange={() => {\n          setShowGaps(!showGaps)\n        }}\n      />\n      <Checkbox2\n        label=\"Show empty\"\n        checked={showEmpty}\n        onChange={() => {\n          setShowEmpty(!showEmpty)\n        }}\n      />\n      <TextField\n        variant=\"outlined\"\n        multiline\n        className={classes.dialogContent}\n        minRows={5}\n        maxRows={10}\n        fullWidth\n        value={text}\n        helperText={\n          hidden > 0\n            ? `Showing ${rows.length - hidden} of ${rows.length.toLocaleString()} sequences. ${hidden.toLocaleString()} more are in the copy and the download.`\n            : undefined\n        }\n        slotProps={{\n          input: {\n            readOnly: true,\n            className: classes.textAreaFont,\n          },\n        }}\n      />\n    </>\n  )\n}\n"],
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   "names": ["import_react", "import_tss_react", "import_material", "useStyles", "isRecord", "value", "isEmpty", "MetadataTable", "record", "classes", "React", "key", "import_react", "import_tss_react", "import_material", "useStyles", "theme", "maxShownRecords", "maxShownChars", "fastaRecord", "name", "seq", "showGaps", "getUngappedSequence", "isAllGaps", "fastaPreview", "rows", "shown", "chars", "row", "record", "SequenceTextArea", "str", "classes", "setShowGaps", "showEmpty", "setShowEmpty", "text", "hidden", "fullText", "React", "CopyButton", "saveAs", "Checkbox2"]