jbrowse-plugin-msaview 5.6.0 → 5.7.0

package/dist/chunks/{FeatureDialog-NBDB5SWU.js.map → FeatureDialog-YEOUA5YS.js.map}

@@ -1,7 +1,7 @@
 {
   "version": 3,
-  "sources": ["../../node_modules/.pnpm/react-msaview@9.1.0_a4121c98828e538e8b3708814bbfe622/node_modules/react-msaview/src/components/dialogs/FeatureDialog.tsx"],
-  "sourcesContent": ["import React, { useState } from 'react'\n\nimport { Dialog } from '@jbrowse/core/ui'\nimport {\n  Button,\n  Checkbox,\n  DialogContent,\n  Table,\n  TableBody,\n  TableCell,\n  TableHead,\n  TableRow,\n  TextField,\n} from '@mui/material'\nimport { observer } from 'mobx-react'\n\nimport type { MsaViewModel } from '../../model.ts'\nimport type { Annotation } from '../../types.ts'\n\nfunction matches(type: Annotation, query: string) {\n  return [type.accession, type.name, type.description].some(field =>\n    field?.toLowerCase().includes(query),\n  )\n}\n\nconst Toggles = observer(function ({\n  model,\n  accessions,\n}: {\n  model: MsaViewModel\n  accessions: string[]\n}) {\n  const setAll = (shown: boolean) => {\n    for (const accession of accessions) {\n      model.setFilter(accession, shown)\n    }\n  }\n  return (\n    <div>\n      <Button\n        onClick={() => {\n          setAll(true)\n        }}\n      >\n        Toggle all on\n      </Button>\n\n      <Button\n        onClick={() => {\n          setAll(false)\n        }}\n      >\n        Toggle all off\n      </Button>\n    </div>\n  )\n})\n\nconst FeatureTable = observer(function ({ model }: { model: MsaViewModel }) {\n  const { annotationTypes, annotations, featureColors, fillPalette } = model\n  const [query, setQuery] = useState('')\n  const needle = query.trim().toLowerCase()\n  const types = [...annotationTypes.values()].filter(\n    type => !needle || matches(type, needle),\n  )\n  const counts = new Map<string, number>()\n  const swatches = new Map<string, string>()\n  for (const annot of annotations) {\n    const { accession } = annot\n    counts.set(accession, (counts.get(accession) ?? 0) + 1)\n    if (!swatches.has(accession)) {\n      swatches.set(\n        accession,\n        featureColors.get(annot)?.fill ?? fillPalette[accession]!,\n      )\n    }\n  }\n  return (\n    <>\n      <TextField\n        label=\"Filter\"\n        size=\"small\"\n        value={query}\n        onChange={event => {\n          setQuery(event.target.value)\n        }}\n      />\n      <Toggles model={model} accessions={types.map(t => t.accession)} />\n      <Table size=\"small\">\n        <TableHead>\n          <TableRow>\n            <TableCell padding=\"checkbox\" />\n            <TableCell>color</TableCell>\n            <TableCell>accession</TableCell>\n            <TableCell>name</TableCell>\n            <TableCell>count</TableCell>\n            <TableCell>description</TableCell>\n          </TableRow>\n        </TableHead>\n        <TableBody>\n          {types.map(({ accession, name, description }) => (\n            <TableRow key={accession}>\n              <TableCell padding=\"checkbox\">\n                <Checkbox\n                  checked={!model.turnedOffFeatures.get(accession)}\n                  onChange={() => {\n                    model.setFilter(\n                      accession,\n                      !!model.turnedOffFeatures.get(accession),\n                    )\n                  }}\n                />\n              </TableCell>\n              <TableCell>\n                <div\n                  style={{\n                    width: 20,\n                    height: 20,\n                    background: swatches.get(accession),\n                  }}\n                />\n              </TableCell>\n              <TableCell>{accession}</TableCell>\n              <TableCell>{name}</TableCell>\n              <TableCell>{counts.get(accession)}</TableCell>\n              <TableCell>{description}</TableCell>\n            </TableRow>\n          ))}\n        </TableBody>\n      </Table>\n    </>\n  )\n})\n\nconst FeatureTypeDialog = observer(function ({\n  onClose,\n  model,\n}: {\n  onClose: () => void\n  model: MsaViewModel\n}) {\n  return (\n    <Dialog\n      onClose={() => {\n        onClose()\n      }}\n      open\n      title=\"Feature filters\"\n      maxWidth=\"xl\"\n    >\n      <DialogContent>\n        <FeatureTable model={model} />\n      </DialogContent>\n    </Dialog>\n  )\n})\n\nexport default FeatureTypeDialog\n"],
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+  "sources": ["../../node_modules/.pnpm/react-msaview@9.3.0_a4121c98828e538e8b3708814bbfe622/node_modules/react-msaview/src/components/dialogs/FeatureDialog.tsx"],
+  "sourcesContent": ["import React, { useState } from 'react'\n\nimport { Dialog } from '@jbrowse/core/ui'\nimport {\n  Button,\n  Checkbox,\n  DialogContent,\n  Table,\n  TableBody,\n  TableCell,\n  TableHead,\n  TableRow,\n  TextField,\n} from '@mui/material'\nimport { observer } from 'mobx-react'\n\nimport type { MsaViewModel } from '../../model.ts'\nimport type { Annotation } from '../../types.ts'\n\nfunction matches(type: Annotation, query: string) {\n  return [type.accession, type.name, type.description].some(field =>\n    field?.toLowerCase().includes(query),\n  )\n}\n\nconst Toggles = observer(function ({\n  model,\n  accessions,\n}: {\n  model: MsaViewModel\n  accessions: string[]\n}) {\n  const setAll = (shown: boolean) => {\n    for (const accession of accessions) {\n      model.setFilter(accession, shown)\n    }\n  }\n  return (\n    <div>\n      <Button\n        onClick={() => {\n          setAll(true)\n        }}\n      >\n        Toggle all on\n      </Button>\n\n      <Button\n        onClick={() => {\n          setAll(false)\n        }}\n      >\n        Toggle all off\n      </Button>\n    </div>\n  )\n})\n\nconst FeatureTable = observer(function ({ model }: { model: MsaViewModel }) {\n  const { annotationTypes, annotations, featureColors, fillPalette } = model\n  const [query, setQuery] = useState('')\n  const needle = query.trim().toLowerCase()\n  const types = [...annotationTypes.values()].filter(\n    type => !needle || matches(type, needle),\n  )\n  const counts = new Map<string, number>()\n  const swatches = new Map<string, string>()\n  for (const annot of annotations) {\n    const { accession } = annot\n    counts.set(accession, (counts.get(accession) ?? 0) + 1)\n    if (!swatches.has(accession)) {\n      swatches.set(\n        accession,\n        featureColors.get(annot)?.fill ?? fillPalette[accession]!,\n      )\n    }\n  }\n  return (\n    <>\n      <TextField\n        label=\"Filter\"\n        size=\"small\"\n        value={query}\n        onChange={event => {\n          setQuery(event.target.value)\n        }}\n      />\n      <Toggles model={model} accessions={types.map(t => t.accession)} />\n      <Table size=\"small\">\n        <TableHead>\n          <TableRow>\n            <TableCell padding=\"checkbox\" />\n            <TableCell>color</TableCell>\n            <TableCell>accession</TableCell>\n            <TableCell>name</TableCell>\n            <TableCell>count</TableCell>\n            <TableCell>description</TableCell>\n          </TableRow>\n        </TableHead>\n        <TableBody>\n          {types.map(({ accession, name, description }) => (\n            <TableRow key={accession}>\n              <TableCell padding=\"checkbox\">\n                <Checkbox\n                  checked={!model.featureOff(accession)}\n                  onChange={() => {\n                    model.setFilter(accession, model.featureOff(accession))\n                  }}\n                />\n              </TableCell>\n              <TableCell>\n                <div\n                  style={{\n                    width: 20,\n                    height: 20,\n                    background: swatches.get(accession),\n                  }}\n                />\n              </TableCell>\n              <TableCell>{accession}</TableCell>\n              <TableCell>{name}</TableCell>\n              <TableCell>{counts.get(accession)}</TableCell>\n              <TableCell>{description}</TableCell>\n            </TableRow>\n          ))}\n        </TableBody>\n      </Table>\n    </>\n  )\n})\n\nconst FeatureTypeDialog = observer(function ({\n  onClose,\n  model,\n}: {\n  onClose: () => void\n  model: MsaViewModel\n}) {\n  return (\n    <Dialog\n      onClose={() => {\n        onClose()\n      }}\n      open\n      title=\"Feature filters\"\n      maxWidth=\"xl\"\n    >\n      <DialogContent>\n        <FeatureTable model={model} />\n      </DialogContent>\n    </Dialog>\n  )\n})\n\nexport default FeatureTypeDialog\n"],
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   "names": ["import_react", "import_ui", "import_material", "import_mobx_react", "matches", "type", "query", "field", "Toggles", "model", "accessions", "setAll", "shown", "accession", "React", "FeatureTable", "annotationTypes", "annotations", "featureColors", "fillPalette", "setQuery", "needle", "types", "counts", "swatches", "annot", "event", "t", "name", "description", "FeatureTypeDialog", "onClose", "FeatureDialog_default"]
 }

package/dist/chunks/GapThresholdDialog-3MOBT6NY.js

@@ -0,0 +1,2 @@
+import{a as c}from"./chunk-CVLB4VFP.js";import{a as v}from"./chunk-DNFD5II2.js";import{a as d}from"./chunk-BX4Z274Q.js";import{a as m}from"./chunk-J6KYLXRD.js";import{b as t}from"./chunk-FY3BTKY4.js";var a=t(m(),1),h=t(v(),1),e=t(d(),1),y=t(c(),1);var r=t(m(),1),o=t(d(),1),u=t(c(),1),w=(0,u.observer)(function({model:n}){let[f,s]=(0,r.useState)(),p=f??n.allowedGappyness;return r.default.createElement("div",{style:{display:"flex",alignItems:"center",gap:8}},r.default.createElement(o.Typography,{style:{whiteSpace:"nowrap"}},"\u2265",p,"% gaps"),r.default.createElement(o.Slider,{"data-testid":"gappyness_slider",style:{width:200,marginInline:10},min:1,max:100,value:p,onChange:(E,l)=>{s(l)},onChangeCommitted:(E,l)=>{n.setAllowedGappyness(l),s(void 0)}}))}),g=w;var C=(0,y.observer)(function({model:i,onClose:n}){return a.default.createElement(h.Dialog,{open:!0,onClose:n,title:"Hide gappy columns"},a.default.createElement(e.DialogContent,null,a.default.createElement(e.Typography,{variant:"body2",sx:{mb:2}},"The viewer hides each column where at least this share of the rows has a gap."),a.default.createElement(g,{model:i})),a.default.createElement(e.DialogActions,null,a.default.createElement(e.Button,{variant:"contained",onClick:n},"Close")))}),x=C;export{x as default};
+//# sourceMappingURL=GapThresholdDialog-3MOBT6NY.js.map

package/dist/chunks/GapThresholdDialog-3MOBT6NY.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../../node_modules/.pnpm/react-msaview@9.3.0_a4121c98828e538e8b3708814bbfe622/node_modules/react-msaview/src/components/dialogs/GapThresholdDialog.tsx", "../../node_modules/.pnpm/react-msaview@9.3.0_a4121c98828e538e8b3708814bbfe622/node_modules/react-msaview/src/components/dialogs/GappynessSlider.tsx"],
+  "sourcesContent": ["import React from 'react'\n\nimport { Dialog } from '@jbrowse/core/ui'\nimport { Button, DialogActions, DialogContent, Typography } from '@mui/material'\nimport { observer } from 'mobx-react'\n\nimport GappynessSlider from './GappynessSlider.tsx'\n\nimport type { MsaViewModel } from '../../model.ts'\n\nconst GapThresholdDialog = observer(function ({\n  model,\n  onClose,\n}: {\n  model: MsaViewModel\n  onClose: () => void\n}) {\n  return (\n    <Dialog open onClose={onClose} title=\"Hide gappy columns\">\n      <DialogContent>\n        <Typography variant=\"body2\" sx={{ mb: 2 }}>\n          The viewer hides each column where at least this share of the rows has\n          a gap.\n        </Typography>\n        <GappynessSlider model={model} />\n      </DialogContent>\n      <DialogActions>\n        <Button variant=\"contained\" onClick={onClose}>\n          Close\n        </Button>\n      </DialogActions>\n    </Dialog>\n  )\n})\n\nexport default GapThresholdDialog\n", "import React, { useState } from 'react'\n\nimport { Slider, Typography } from '@mui/material'\nimport { observer } from 'mobx-react'\n\nimport type { MsaViewModel } from '../../model.ts'\n\nconst GappynessSlider = observer(function GappynessSlider({\n  model,\n}: {\n  model: MsaViewModel\n}) {\n  const [dragValue, setDragValue] = useState<number>()\n  const value = dragValue ?? model.allowedGappyness\n  return (\n    <div style={{ display: 'flex', alignItems: 'center', gap: 8 }}>\n      {/* the threshold is inclusive: blanks are columns whose gap count is at\n          least ceil(allowedGappyness% of the rows), so at 100 it hides the\n          columns that are entirely gaps rather than nothing */}\n      <Typography style={{ whiteSpace: 'nowrap' }}>\n        &ge;{value}% gaps\n      </Typography>\n      <Slider\n        // In JBrowse other MUI Sliders share the page, so `.MuiSlider-thumb`\n        // can match the wrong one. Tests and screenshot specs target\n        // `[data-testid=\"gappyness_slider\"] input`, the hidden range input that\n        // takes focus and arrow/PageUp/PageDown.\n        //\n        // Not `slotProps={{ input: ... }}`: that widens `onChange`'s `val` to\n        // `number | number[]`, which setAllowedGappyness rejects.\n        //\n        // The thumb follows local state while dragging and the model takes the\n        // value on release, since each write recomputes the gap columns over\n        // the whole alignment.\n        data-testid=\"gappyness_slider\"\n        style={{ width: 200, marginInline: 10 }}\n        min={1}\n        max={100}\n        value={value}\n        onChange={(_, val) => {\n          setDragValue(val)\n        }}\n        onChangeCommitted={(_, val) => {\n          model.setAllowedGappyness(val)\n          setDragValue(undefined)\n        }}\n      />\n    </div>\n  )\n})\n\nexport default GappynessSlider\n"],
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+}

package/dist/chunks/GoToDialog-2L4KUO6R.js

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+import{b as r}from"./chunk-UVY5VU6U.js";import"./chunk-CVLB4VFP.js";import{a}from"./chunk-DNFD5II2.js";import{a as u}from"./chunk-BX4Z274Q.js";import{a as i}from"./chunk-J6KYLXRD.js";import{b as t}from"./chunk-FY3BTKY4.js";var o=t(i(),1),l=t(a(),1),m=t(u(),1);function f({model:n,onClose:e}){return o.default.createElement(l.Dialog,{open:!0,onClose:e,title:"Go to row or column",maxWidth:"xs",fullWidth:!0},o.default.createElement(m.DialogContent,null,o.default.createElement(r,{model:n,onFound:e})))}export{f as default};
+//# sourceMappingURL=GoToDialog-2L4KUO6R.js.map

package/dist/chunks/GoToDialog-2L4KUO6R.js.map

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+{
+  "version": 3,
+  "sources": ["../../node_modules/.pnpm/react-msaview@9.3.0_a4121c98828e538e8b3708814bbfe622/node_modules/react-msaview/src/components/dialogs/GoToDialog.tsx"],
+  "sourcesContent": ["import React from 'react'\n\nimport { Dialog } from '@jbrowse/core/ui'\nimport { DialogContent } from '@mui/material'\n\nimport GoToBox from './GoToBox.tsx'\n\nimport type { MsaViewModel } from '../../model.ts'\n\nexport default function GoToDialog({\n  model,\n  onClose,\n}: {\n  model: MsaViewModel\n  onClose: () => void\n}) {\n  return (\n    <Dialog\n      open\n      onClose={onClose}\n      title=\"Go to row or column\"\n      maxWidth=\"xs\"\n      fullWidth\n    >\n      <DialogContent>\n        <GoToBox model={model} onFound={onClose} />\n      </DialogContent>\n    </Dialog>\n  )\n}\n"],
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+  "names": ["import_react", "import_ui", "import_material", "GoToDialog", "model", "onClose", "React", "GoToBox_default"]
+}

package/dist/chunks/{HelpDialog-UCUYPCOI.js → HelpDialog-3KGMHUYG.js}

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-//# sourceMappingURL=HelpDialog-UCUYPCOI.js.map
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+//# sourceMappingURL=HelpDialog-3KGMHUYG.js.map

package/dist/chunks/{HelpDialog-UCUYPCOI.js.map → HelpDialog-3KGMHUYG.js.map}

@@ -1,6 +1,6 @@
 {
   "version": 3,
-  "sources": ["../../node_modules/.pnpm/react-msaview@9.1.0_a4121c98828e538e8b3708814bbfe622/node_modules/react-msaview/src/components/dialogs/HelpDialog.tsx"],
+  "sources": ["../../node_modules/.pnpm/react-msaview@9.3.0_a4121c98828e538e8b3708814bbfe622/node_modules/react-msaview/src/components/dialogs/HelpDialog.tsx"],
   "sourcesContent": ["import React, { lazy } from 'react'\n\nimport { Dialog } from '@jbrowse/core/ui'\nimport {\n  Button,\n  DialogActions,\n  DialogContent,\n  Table,\n  TableBody,\n  TableCell,\n  TableRow,\n  Typography,\n} from '@mui/material'\n\nimport { version } from '../../version.ts'\nimport { keyboardControls, mouseControls } from '../controls.ts'\n\nimport type { MsaViewModel } from '../../model.ts'\nimport type { Control } from '../controls.ts'\n\nconst AboutDialog = lazy(() => import('./AboutDialog.tsx'))\n\nfunction ControlTable({ title, rows }: { title: string; rows: Control[] }) {\n  return (\n    <>\n      <Typography variant=\"subtitle2\" sx={{ mt: 1 }}>\n        {title}\n      </Typography>\n      <Table size=\"small\" aria-label={title}>\n        <TableBody>\n          {rows.map(({ label, action }) => (\n            <TableRow key={label}>\n              <TableCell sx={{ whiteSpace: 'nowrap', fontWeight: 500 }}>\n                {label}\n              </TableCell>\n              <TableCell>{action}</TableCell>\n            </TableRow>\n          ))}\n        </TableBody>\n      </Table>\n    </>\n  )\n}\n\nexport default function HelpDialog({\n  model,\n  onClose,\n}: {\n  model: MsaViewModel\n  onClose: () => void\n}) {\n  return (\n    <Dialog open title=\"Mouse & keyboard\" onClose={onClose}>\n      <DialogContent>\n        <ControlTable title=\"Mouse\" rows={mouseControls} />\n        <ControlTable\n          title=\"Keyboard (click the alignment first)\"\n          rows={keyboardControls}\n        />\n      </DialogContent>\n      <DialogActions>\n        <Typography variant=\"caption\" sx={{ mr: 'auto', pl: 1 }}>\n          MSAView {version}\n        </Typography>\n        <Button\n          onClick={() => {\n            model.queueDialog(done => [AboutDialog, { onClose: done }])\n            onClose()\n          }}\n        >\n          About & credits\n        </Button>\n        <Button variant=\"contained\" onClick={onClose}>\n          Close\n        </Button>\n      </DialogActions>\n    </Dialog>\n  )\n}\n"],
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package/dist/chunks/{LaunchMsaViewDialog-BG4MX2BW.js → LaunchMsaViewDialog-GR4BB3W2.js}

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