npm - jbrowse-plugin-graphgenomeviewer - Versions diffs - 4.4.1 → 4.5.0 - Mend

jbrowse-plugin-graphgenomeviewer 4.4.1 → 4.5.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

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package/dist/chunks/{GraphGenomeView-QGJN2S27.js → GraphGenomeView-TJ667XWP.js} RENAMED Viewed

@@ -1,4 +1,4 @@
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package/dist/chunks/{GraphGenomeView-QGJN2S27.js.map → GraphGenomeView-TJ667XWP.js.map} RENAMED Viewed

@@ -2,6 +2,6 @@
   "version": 3,
   "sources": ["../../src/GraphGenomeView/components/GraphGenomeView.tsx", "../../src/GraphGenomeView/components/GraphLoadStatus.tsx", "../../src/GraphGenomeView/components/ImportForm.tsx"],
   "sourcesContent": ["import { observer } from 'mobx-react'\n\nimport GraphCanvas from './GraphCanvas'\nimport GraphLoadStatus from './GraphLoadStatus'\nimport ImportForm from './ImportForm'\n\nimport type { GraphPaneModel } from '../model'\n\nconst GraphGenomeView = observer(function GraphGenomeView({\n  model,\n}: {\n  model: GraphPaneModel\n}) {\n  if (model.hasGraph) {\n    return <GraphCanvas model={model} />\n  }\n  // A launched or restored view has a source of its own, so the import form\n  // has nothing to offer it when that source fails\n  if (model.canRetryLoad && (model.error || model.loadCanceled)) {\n    return <GraphLoadStatus model={model} />\n  }\n  // Hidden rather than unmounted, so a typed URL survives a failed load\n  return (\n    <>\n      {model.isLoading ? <GraphLoadStatus model={model} /> : null}\n      <div hidden={model.isLoading}>\n        <ImportForm model={model} />\n      </div>\n    </>\n  )\n})\n\nexport default GraphGenomeView\n", "import { ErrorBanner, LoadingEllipses } from '@jbrowse/core/ui'\nimport { Button, LinearProgress, Paper, Typography } from '@mui/material'\nimport { observer } from 'mobx-react'\nimport { makeStyles } from 'tss-react/mui'\n\nimport type { GraphPaneModel } from '../model'\n\nconst useStyles = makeStyles()({\n  paper: {\n    padding: 16,\n    margin: 8,\n    maxWidth: 560,\n    marginInline: 'auto',\n    display: 'flex',\n    flexDirection: 'column',\n    gap: 12,\n  },\n  row: {\n    display: 'flex',\n    alignItems: 'center',\n    justifyContent: 'space-between',\n    gap: 8,\n  },\n})\n\n// What a view with no graph on screen shows while its load runs, and after a\n// load of a source it can retry was canceled or failed.\nconst GraphLoadStatus = observer(function GraphLoadStatus({\n  model,\n}: {\n  model: GraphPaneModel\n}) {\n  const { classes } = useStyles()\n  if (model.isLoading) {\n    return (\n      <Paper className={classes.paper} data-testid=\"graph-genome-loading\">\n        <div className={classes.row}>\n          <LoadingEllipses variant=\"h6\" message={model.statusMessage} />\n          <Button\n            size=\"small\"\n            data-testid=\"graph-genome-cancel\"\n            onClick={() => {\n              model.cancelLoad()\n            }}\n          >\n            Cancel\n          </Button>\n        </div>\n        <LinearProgress variant=\"indeterminate\" />\n      </Paper>\n    )\n  }\n  if (model.error) {\n    return (\n      <Paper className={classes.paper}>\n        <ErrorBanner\n          error={model.error}\n          onReset={() => {\n            model.retryLoad()\n          }}\n        />\n      </Paper>\n    )\n  }\n  return (\n    <Paper className={classes.paper} data-testid=\"graph-genome-load-canceled\">\n      <div className={classes.row}>\n        <Typography variant=\"h6\">Loading canceled</Typography>\n        <Button\n          variant=\"contained\"\n          size=\"small\"\n          data-testid=\"graph-genome-retry\"\n          onClick={() => {\n            model.retryLoad()\n          }}\n        >\n          Retry\n        </Button>\n      </div>\n    </Paper>\n  )\n})\n\nexport default GraphLoadStatus\n", "import { useState } from 'react'\n\nimport { ErrorBanner } from '@jbrowse/core/ui'\nimport { Button, Paper, TextField, Typography } from '@mui/material'\nimport { observer } from 'mobx-react'\nimport { makeStyles } from 'tss-react/mui'\n\nimport type { GraphPaneModel } from '../model'\n\nconst EXAMPLE_GFA = `H\\tVN:Z:1.0\nS\\t1\\tACGT\nS\\t2\\tGGCC\nS\\t3\\tTTAA\nS\\t4\\tCCGG\nL\\t1\\t+\\t2\\t+\\t0M\nL\\t1\\t+\\t3\\t+\\t0M\nL\\t2\\t+\\t4\\t+\\t0M\nL\\t3\\t+\\t4\\t+\\t0M`\n\nconst useStyles = makeStyles()({\n  column: { display: 'flex', flexDirection: 'column', gap: 8 },\n  rowEnd: { display: 'flex', gap: 8, alignItems: 'flex-end' },\n  rowCenter: { display: 'flex', gap: 8, alignItems: 'center' },\n  flex1: { flex: 1 },\n  paper: { padding: 16, margin: 8, maxWidth: 560, marginInline: 'auto' },\n  header: { marginBottom: 12 },\n  footer: { marginTop: 12, display: 'flex', justifyContent: 'flex-end' },\n})\n\nconst ImportForm = observer(function ImportForm({\n  model,\n}: {\n  model: GraphPaneModel\n}) {\n  const { classes } = useStyles()\n  const [url, setUrl] = useState('')\n\n  function handleUrlLoad() {\n    if (url.trim()) {\n      void model.loadGFAFromLocation({ uri: url, locationType: 'UriLocation' })\n    }\n  }\n\n  function handleFileUpload(event: React.ChangeEvent<HTMLInputElement>) {\n    const file = event.target.files?.[0]\n    if (file) {\n      file\n        .text()\n        .then(text => model.loadGFA(text, file.name))\n        .catch((err: unknown) => {\n          model.setError(err)\n        })\n    }\n  }\n\n  return (\n    <Paper className={classes.paper}>\n      <div className={classes.header}>\n        <Typography variant=\"h6\">Load a GFA graph</Typography>\n      </div>\n\n      <div className={classes.column}>\n        <div className={classes.rowCenter}>\n          <Button variant=\"outlined\" component=\"label\" size=\"small\">\n            Choose file\n            <input\n              type=\"file\"\n              accept=\".gfa,.gfa1,.gfa2\"\n              hidden\n              onChange={event => {\n                handleFileUpload(event)\n              }}\n            />\n          </Button>\n          <Typography variant=\"caption\" color=\"text.secondary\">\n            Whole-file GFA; best for small/medium graphs.\n          </Typography>\n        </div>\n\n        <div className={classes.rowEnd}>\n          <TextField\n            size=\"small\"\n            label=\"URL\"\n            placeholder=\"https://example.com/graph.gfa\"\n            value={url}\n            onChange={e => {\n              setUrl(e.target.value)\n            }}\n            onKeyDown={e => {\n              if (e.key === 'Enter') {\n                handleUrlLoad()\n              }\n            }}\n            className={classes.flex1}\n          />\n          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   "names": ["import_mobx_react", "import_ui", "import_material", "import_mobx_react", "import_mui", "import_jsx_runtime", "useStyles", "GraphLoadStatus", "model", "classes", "GraphLoadStatus_default", "import_react", "import_ui", "import_material", "import_mobx_react", "import_mui", "import_jsx_runtime", "EXAMPLE_GFA", "useStyles", "ImportForm", "model", "classes", "url", "setUrl", "handleUrlLoad", "handleFileUpload", "event", "file", "text", "err", "e", "ImportForm_default", "import_jsx_runtime", "GraphGenomeView", "model", "GraphCanvas_default", "GraphLoadStatus_default", "ImportForm_default", "GraphGenomeView_default"]
 }

package/dist/chunks/GraphTrackSettingsDialog-JVPM25GV.js ADDED Viewed

@@ -0,0 +1,4 @@
+import{a as g}from"./chunk-BUXVOMDL.js";import{Z as f}from"./chunk-UTWFU4X6.js";import"./chunk-7BKUWQE5.js";import"./chunk-KULNKXPT.js";import{a as x}from"./chunk-J6KYLXRD.js";import{a as l,c as m,d as y}from"./chunk-TYJTJGPO.js";import{b as o}from"./chunk-FY3BTKY4.js";var a=o(y(),1),b=o(m(),1),S=o(f(),1),n=o(l(),1),L=(0,S.makeStyles)()({section:{marginBottom:24},formControl:{minWidth:200}}),w=[{value:0,label:"None"},{value:1,label:"1 hop"},{value:2,label:"2 hops"}],k=(0,b.observer)(function({model:e}){let{classes:t}=L();return(0,n.jsxs)("div",{className:t.section,children:[(0,n.jsxs)(a.FormControl,{className:t.formControl,children:[(0,n.jsx)(a.InputLabel,{children:"Graph context"}),(0,n.jsx)(a.Select,{value:e.subgraphContext,label:"Graph context","data-testid":"graph-context-select",onChange:p=>{e.setSubgraphContext(p.target.value),e.cut()},children:w.map(({value:p,label:u})=>(0,n.jsx)(a.MenuItem,{value:p,children:u},p))})]}),(0,n.jsx)(a.Typography,{variant:"caption",color:"text.secondary",children:"How far the cut follows links out of the region, one hop by default. A detour that leaves the reference before the window and rejoins after it is indexed under its own sequence, so at none its middle is missing and the one bubble draws as two unrelated stubs. Each hop costs a query per off-reference segment already reached."})]})}),v=k;var C=o(x(),1),d=o(y(),1),c=o(m(),1),G=o(f(),1),i=o(l(),1),T=(0,G.makeStyles)()({section:{marginBottom:24}});function M(r){let e=r.split(/[\s,]+/).map(t=>t.trim()).filter(t=>t!=="");return e.length===0?void 0:e}var F=(0,c.observer)(function({model:e}){let[t,p]=(0,C.useState)(e.chosenHaplotypes?.join(", ")??""),u=()=>{let s=M(t)??[];s.join(`
+`)===(e.chosenHaplotypes??[]).join(`
+`)||(e.setSubgraphHaplotypes(s),e.cut())};return(0,i.jsx)(d.TextField,{fullWidth:!0,label:"Haplotypes",placeholder:"every haplotype",value:t,slotProps:{htmlInput:{"data-testid":"graph-haplotypes-field"}},onChange:s=>{p(s.target.value)},onBlur:()=>{u()},onKeyDown:s=>{s.key==="Enter"&&u()}})}),N=(0,c.observer)(function({model:e}){let{classes:t}=T();return e.adapterConfig.type==="GbzBaseSyntenyAdapter"?(0,i.jsxs)("div",{className:t.section,children:[(0,i.jsx)(F,{model:e},e.chosenHaplotypes?.join(",")??""),(0,i.jsx)(d.Typography,{variant:"caption",color:"text.secondary",children:"The haplotypes the cut is for, as lane assembly names or PanSN prefixes (HG002#1, or HG002 for both), separated by commas. The cut keeps their walks and the nodes those walks visit, with the reference. Empty is every haplotype."})]}):null}),H=N;var h=o(l(),1);function B({model:r,open:e,onClose:t}){return(0,h.jsxs)(g,{model:r,open:e,onClose:t,children:[(0,h.jsx)(v,{model:r}),(0,h.jsx)(H,{model:r})]})}export{B as default};
+//# sourceMappingURL=GraphTrackSettingsDialog-JVPM25GV.js.map

package/dist/chunks/{GraphTrackSettingsDialog-LXYUYPZS.js.map → GraphTrackSettingsDialog-JVPM25GV.js.map} RENAMED Viewed

@@ -2,6 +2,6 @@
   "version": 3,
   "sources": ["../../src/LinearGraphDisplay/components/SubgraphContextSelect.tsx", "../../src/LinearGraphDisplay/components/SubgraphHaplotypesField.tsx", "../../src/LinearGraphDisplay/components/GraphTrackSettingsDialog.tsx"],
   "sourcesContent": ["import {\n  FormControl,\n  InputLabel,\n  MenuItem,\n  Select,\n  Typography,\n} from '@mui/material'\nimport { observer } from 'mobx-react'\nimport { makeStyles } from 'tss-react/mui'\n\nimport type { LinearGraphCutModel } from '../model'\n\nconst useStyles = makeStyles()({\n  section: {\n    marginBottom: 24,\n  },\n  formControl: {\n    minWidth: 200,\n  },\n})\n\n// Hops past the region's own segments, each costing a tabix query per\n// off-reference segment already reached. One is the default: at none a single\n// detour draws as two unrelated stubs, which is a wrong picture of the graph\n// rather than a cheaper one. Two exists for a graph whose alleles have alleles\n// (HPRC's amylase window keeps growing at 2, the E. coli paa locus does not), and\n// it stops there because a frontier is still not a bubble decomposition. Cut an\n// exact slice with gfatools when that is what is wanted.\nconst SUBGRAPH_CONTEXTS = [\n  { value: 0, label: 'None' },\n  { value: 1, label: '1 hop' },\n  { value: 2, label: '2 hops' },\n]\n\nconst SubgraphContextSelect = observer(function SubgraphContextSelect({\n  model,\n}: {\n  model: LinearGraphCutModel\n}) {\n  const { classes } = useStyles()\n  return (\n    <div className={classes.section}>\n      <FormControl className={classes.formControl}>\n        <InputLabel>Graph context</InputLabel>\n        <Select\n          value={model.subgraphContext}\n          label=\"Graph context\"\n          data-testid=\"graph-context-select\"\n          onChange={e => {\n            model.setSubgraphContext(e.target.value)\n            void model.cut()\n          }}\n        >\n          {SUBGRAPH_CONTEXTS.map(({ value, label }) => (\n            <MenuItem key={value} value={value}>\n              {label}\n            </MenuItem>\n          ))}\n        </Select>\n      </FormControl>\n      <Typography variant=\"caption\" color=\"text.secondary\">\n        How far the cut follows links out of the region, one hop by default. A\n        detour that leaves the reference before the window and rejoins after it\n        is indexed under its own sequence, so at none its middle is missing and\n        the one bubble draws as two unrelated stubs. Each hop costs a query per\n        off-reference segment already reached.\n      </Typography>\n    </div>\n  )\n})\n\nexport default SubgraphContextSelect\n", "import { useState } from 'react'\n\nimport { TextField, Typography } from '@mui/material'\nimport { observer } from 'mobx-react'\nimport { makeStyles } from 'tss-react/mui'\n\nimport type { LinearGraphCutModel } from '../model'\n\nconst useStyles = makeStyles()({\n  section: {\n    marginBottom: 24,\n  },\n})\n\nexport function parseHaplotypeList(text: string) {\n  const names = text\n    .split(/[\\s,]+/)\n    .map(name => name.trim())\n    .filter(name => name !== '')\n  return names.length === 0 ? undefined : names\n}\n\nconst HaplotypeListField = observer(function HaplotypeListField({\n  model,\n}: {\n  model: LinearGraphCutModel\n}) {\n  const [draft, setDraft] = useState(model.chosenHaplotypes?.join(', ') ?? '')\n  const apply = () => {\n    const parsed = parseHaplotypeList(draft) ?? []\n    const unchanged =\n      parsed.join('\\n') === (model.chosenHaplotypes ?? []).join('\\n')\n    if (!unchanged) {\n      model.setSubgraphHaplotypes(parsed)\n      void model.cut()\n    }\n  }\n  return (\n    <TextField\n      fullWidth\n      label=\"Haplotypes\"\n      placeholder=\"every haplotype\"\n      value={draft}\n      slotProps={{ htmlInput: { 'data-testid': 'graph-haplotypes-field' } }}\n      onChange={e => {\n        setDraft(e.target.value)\n      }}\n      onBlur={() => {\n        apply()\n      }}\n      onKeyDown={e => {\n        if (e.key === 'Enter') {\n          apply()\n        }\n      }}\n    />\n  )\n})\n\n// Only a GBZ cut reads the set. The inner field is keyed on it so an outside\n// change (a restored session, a launch) resets the draft rather than fighting\n// it.\nconst SubgraphHaplotypesField = observer(function SubgraphHaplotypesField({\n  model,\n}: {\n  model: LinearGraphCutModel\n}) {\n  const { classes } = useStyles()\n  return model.adapterConfig.type === 'GbzBaseSyntenyAdapter' ? (\n    <div className={classes.section}>\n      <HaplotypeListField\n        key={model.chosenHaplotypes?.join(',') ?? ''}\n        model={model}\n      />\n      <Typography variant=\"caption\" color=\"text.secondary\">\n        The haplotypes the cut is for, as lane assembly names or PanSN prefixes\n        (HG002#1, or HG002 for both), separated by commas. The cut keeps their\n        walks and the nodes those walks visit, with the reference. Empty is\n        every haplotype.\n      </Typography>\n    </div>\n  ) : null\n})\n\nexport default SubgraphHaplotypesField\n", "import SubgraphContextSelect from './SubgraphContextSelect'\nimport SubgraphHaplotypesField from './SubgraphHaplotypesField'\nimport GraphSettingsDialog from '../../GraphGenomeView/components/GraphSettingsDialog'\n\nimport type { LinearGraphCutModel } from '../model'\n\nexport default function GraphTrackSettingsDialog({\n  model,\n  open,\n  onClose,\n}: {\n  model: LinearGraphCutModel\n  open: boolean\n  onClose: () => void\n}) {\n  return (\n    <GraphSettingsDialog model={model} open={open} onClose={onClose}>\n      <SubgraphContextSelect model={model} />\n      <SubgraphHaplotypesField model={model} />\n    </GraphSettingsDialog>\n  )\n}\n"],
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package/dist/chunks/LinearGraphDisplay-ME3WCBV3.js ADDED Viewed

	@@ -0,0 +1,2 @@
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2	+ //# sourceMappingURL=LinearGraphDisplay-ME3WCBV3.js.map

package/dist/chunks/{LinearGraphDisplay-WPXUCJNR.js.map → LinearGraphDisplay-ME3WCBV3.js.map} RENAMED Viewed

@@ -2,6 +2,6 @@
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   "sourcesContent": ["module.exports = JBrowseExports[\"@jbrowse/display-kit/DisplayChrome\"];", "import { DisplayStatusChrome } from '@jbrowse/display-kit/DisplayChrome'\nimport { observer } from 'mobx-react'\n\nimport GraphCanvas from '../../GraphGenomeView/components/GraphCanvas'\n\nimport type { LinearGraphDisplayModel } from '../model'\n\nconst LinearGraphDisplay = observer(function LinearGraphDisplay({\n  model,\n}: {\n  model: LinearGraphDisplayModel\n}) {\n  return (\n    <DisplayStatusChrome\n      model={model}\n      phase={model.displayPhase}\n      drawn={model.painted && model.geometryPainted}\n      testid=\"linear-graph-display\"\n      data-layout={model.chosenLayoutMode}\n      data-cut-tier={model.cutTier}\n      data-recuts={model.recuts}\n      data-node-count={model.hasGraph ? model.nodeCount : undefined}\n      data-loading={model.isLoading ? '' : undefined}\n      style={{\n        width: model.paneWidth,\n        height: model.height,\n        overflow: 'hidden',\n      }}\n    >\n      <GraphCanvas model={model} ownChrome={false} />\n    </DisplayStatusChrome>\n  )\n})\n\nexport default LinearGraphDisplay\n"],
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package/dist/chunks/{MinigraphBubbleAdapter-CK7AE4QT.js → MinigraphBubbleAdapter-CZYQROL2.js} RENAMED Viewed

@@ -1,2 +1,2 @@
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+  "sources": ["../../node_modules/.pnpm/@jbrowse+synteny-core@5.0.0-beta.11_@emotion+react@11.14.0_@types+react@19.3.0_react@19_62128aa7a8a5629affa9cb1a58afadc3/node_modules/@jbrowse/synteny-core/esm/TrackWarningsDialog.js"],
+  "sourcesContent": ["import { jsxs as _jsxs } from \"react/jsx-runtime\";\nimport { InfoDialog } from '@jbrowse/core/ui';\nimport { Alert, Typography } from '@mui/material';\nimport { observer } from 'mobx-react';\n/**\n * The render-warnings report both comparative views open, over the rows\n * `collectTrackWarnings` builds for them. Reads them off the view rather than\n * taking a copy, so a refetch that raises or clears a warning while the dialog\n * is open shows in it.\n *\n * Grouped by track, with the track name leading each row: a stacked view's\n * levels raise the same swapped-assemblies warning verbatim, and so does every\n * overlaid track that hits it, so an ungrouped list repeated one sentence N\n * times without ever naming the file to go fix.\n *\n * Keyed by position \u2014 the message is not an identity, and neither is the track\n * name once one track raises two warnings.\n */\nconst TrackWarningsDialog = observer(function TrackWarningsDialog({ model, title, children, handleClose, }) {\n    return (_jsxs(InfoDialog, { open: true, title: title, onClose: () => {\n            handleClose();\n        }, children: [children, model.trackWarnings.flatMap(({ name, warnings }, i) => warnings.map((w, j) => (_jsxs(Alert\n            // eslint-disable-next-line @eslint-react/no-array-index-key -- see above\n            , { severity: \"warning\", style: { marginBottom: 8 }, children: [_jsxs(Typography, { variant: \"subtitle2\", children: [name, \": \", w.message] }), w.effect] }, `${i}_${j}`))))] }));\n});\nexport default TrackWarningsDialog;\n"],
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package/dist/chunks/{chunk-CNFN6EVE.js → chunk-BUXVOMDL.js} RENAMED Viewed

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package/dist/chunks/{chunk-LGKM2PZH.js → chunk-E7J6SB5P.js} RENAMED Viewed

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package/dist/chunks/{chunk-LGKM2PZH.js.map → chunk-E7J6SB5P.js.map} RENAMED Viewed

@@ -1,6 +1,6 @@
 {
   "version": 3,
-  "sources": ["../../node_modules/.pnpm/@jbrowse+synteny-core@5.0.0-beta.9_@emotion+react@11.14.0_@types+react@19.3.0_react@19._e0d3f2cd9fb3ca518fba8dcf7794837f/node_modules/@jbrowse/synteny-core/esm/extractAlignmentData.js"],
+  "sources": ["../../node_modules/.pnpm/@jbrowse+synteny-core@5.0.0-beta.11_@emotion+react@11.14.0_@types+react@19.3.0_react@19_62128aa7a8a5629affa9cb1a58afadc3/node_modules/@jbrowse/synteny-core/esm/extractAlignmentData.js"],
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package/dist/chunks/chunk-J6KYLXRD.js ADDED Viewed

	@@ -0,0 +1,2 @@
1	+ import{a as e}from"./chunk-FY3BTKY4.js";var o=e((s,r)=>{r.exports=JBrowseExports.react});export{o as a};
2	+ //# sourceMappingURL=chunk-J6KYLXRD.js.map

package/dist/chunks/chunk-J6KYLXRD.js.map ADDED Viewed

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["global-externals:react"],
+  "sourcesContent": ["module.exports = JBrowseExports[\"react\"];"],
+  "mappings": "wCAAA,IAAAA,EAAAC,EAAA,CAAAC,EAAAC,IAAA,CAAAA,EAAO,QAAU,eAAe",
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+}