jbrowse-plugin-graphgenomeviewer 6.2.0 → 6.3.0

package/dist/chunks/{chunk-ZKLOV6MW.js → chunk-SYHZ5T54.js}

@@ -1,2 +1,2 @@
-import{N as u,T as w,W as S,ca as k,fa as D}from"./chunk-XWGKHQYO.js";import{a as y,b as A,c as N,d as R}from"./chunk-TYJTJGPO.js";import{b as c}from"./chunk-FY3BTKY4.js";var m=[{value:0,label:"Fastest"},{value:1,label:"Fast"},{value:2,label:"Default"},{value:3,label:"Fine"},{value:4,label:"Best"}];var L=c(A(),1),o=c(R(),1),b=c(N(),1),G=c(D(),1),e=c(y(),1),C=(0,G.makeStyles)()({section:{marginBottom:24},formControl:{minWidth:200}});function s({warn:l=!1,children:n}){return(0,e.jsx)(o.Typography,{variant:"caption",color:l?"warning.main":"text.secondary",children:n})}var T=(0,b.observer)(function({model:n}){return n.hasGraph&&!n.usesLayoutEngine?(0,e.jsx)(s,{warn:!0,children:"No effect on this layout: only the force-directed layout is drawn by the engine that reads this."}):null});function g({label:l,checked:n,onChange:t,children:p}){let{classes:i}=C();return(0,e.jsxs)("div",{className:i.section,children:[(0,e.jsx)(o.FormControlLabel,{control:(0,e.jsx)(o.Switch,{checked:n,onChange:d=>{t(d.target.checked)}}),label:l}),p]})}function h({label:l,value:n,options:t,testId:p,sx:i,onChange:d}){let{classes:r}=C();return(0,e.jsxs)(o.FormControl,{className:r.formControl,sx:i,children:[(0,e.jsx)(o.InputLabel,{children:l}),(0,e.jsx)(o.Select,{value:n,label:l,"data-testid":p,onChange:a=>{d(a.target.value)},children:t.map(({value:a,label:v,description:f})=>(0,e.jsx)(o.MenuItem,{value:a,children:f?(0,e.jsx)(o.Tooltip,{title:f,placement:"right",children:(0,e.jsx)("span",{children:v})}):v},a))})]})}var I=l=>l.map(({trackId:n,name:t})=>({value:n,label:t})),P=(0,b.observer)(function(n){let{model:t,open:p,onClose:i,children:d}=n,{classes:r}=C();return(0,e.jsxs)(L.Dialog,{open:p,onClose:i,title:"Graph settings",children:[(0,e.jsxs)(o.DialogContent,{children:[(0,e.jsx)("div",{className:r.section,children:(0,e.jsxs)(o.FormControl,{fullWidth:!0,children:[(0,e.jsx)(o.FormLabel,{component:"legend",children:"Layout quality"}),(0,e.jsx)(o.RadioGroup,{value:t.layoutQuality,onChange:a=>{t.setLayoutQuality(parseInt(a.target.value)),t.recomputeLayout()},children:m.map(a=>(0,e.jsx)(o.FormControlLabel,{value:a.value,control:(0,e.jsx)(o.Radio,{}),label:a.label},a.value))}),(0,e.jsx)(s,{children:"FMMM's iteration budget, the same scale Bandage exposes. 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-//# sourceMappingURL=chunk-ZKLOV6MW.js.map
+import{N as u,T as w,W as S,ca as k,fa as D}from"./chunk-CJ47OHWP.js";import{a as y,b as A,c as N,d as R}from"./chunk-TYJTJGPO.js";import{b as c}from"./chunk-FY3BTKY4.js";var m=[{value:0,label:"Fastest"},{value:1,label:"Fast"},{value:2,label:"Default"},{value:3,label:"Fine"},{value:4,label:"Best"}];var L=c(A(),1),o=c(R(),1),b=c(N(),1),G=c(D(),1),e=c(y(),1),C=(0,G.makeStyles)()({section:{marginBottom:24},formControl:{minWidth:200}});function s({warn:l=!1,children:n}){return(0,e.jsx)(o.Typography,{variant:"caption",color:l?"warning.main":"text.secondary",children:n})}var T=(0,b.observer)(function({model:n}){return n.hasGraph&&!n.usesLayoutEngine?(0,e.jsx)(s,{warn:!0,children:"No effect on this layout: only the force-directed layout is drawn by the engine that reads this."}):null});function g({label:l,checked:n,onChange:t,children:p}){let{classes:i}=C();return(0,e.jsxs)("div",{className:i.section,children:[(0,e.jsx)(o.FormControlLabel,{control:(0,e.jsx)(o.Switch,{checked:n,onChange:d=>{t(d.target.checked)}}),label:l}),p]})}function h({label:l,value:n,options:t,testId:p,sx:i,onChange:d}){let{classes:r}=C();return(0,e.jsxs)(o.FormControl,{className:r.formControl,sx:i,children:[(0,e.jsx)(o.InputLabel,{children:l}),(0,e.jsx)(o.Select,{value:n,label:l,"data-testid":p,onChange:a=>{d(a.target.value)},children:t.map(({value:a,label:v,description:f})=>(0,e.jsx)(o.MenuItem,{value:a,children:f?(0,e.jsx)(o.Tooltip,{title:f,placement:"right",children:(0,e.jsx)("span",{children:v})}):v},a))})]})}var I=l=>l.map(({trackId:n,name:t})=>({value:n,label:t})),P=(0,b.observer)(function(n){let{model:t,open:p,onClose:i,children:d}=n,{classes:r}=C();return(0,e.jsxs)(L.Dialog,{open:p,onClose:i,title:"Graph settings",children:[(0,e.jsxs)(o.DialogContent,{children:[(0,e.jsx)("div",{className:r.section,children:(0,e.jsxs)(o.FormControl,{fullWidth:!0,children:[(0,e.jsx)(o.FormLabel,{component:"legend",children:"Layout quality"}),(0,e.jsx)(o.RadioGroup,{value:t.layoutQuality,onChange:a=>{t.setLayoutQuality(parseInt(a.target.value)),t.recomputeLayout()},children:m.map(a=>(0,e.jsx)(o.FormControlLabel,{value:a.value,control:(0,e.jsx)(o.Radio,{}),label:a.label},a.value))}),(0,e.jsx)(s,{children:"FMMM's iteration budget, the same scale Bandage exposes. 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In a cut with walks, depth is how many haplotypes carry the node."})]}),d,(0,e.jsxs)("div",{className:r.section,children:[(0,e.jsx)(h,{label:"Color scheme",value:t.chosenColorScheme,options:w,onChange:a=>{t.setColorScheme(a)}}),t.colorSchemeLock?(0,e.jsxs)(s,{warn:!0,children:["No effect now. ",t.colorSchemeLock.why]}):null]})]}),(0,e.jsx)(o.DialogActions,{children:(0,e.jsx)(o.Button,{variant:"contained",color:"primary",onClick:i,children:"Close"})})]})}),W=P;export{W as a};
+//# sourceMappingURL=chunk-SYHZ5T54.js.map

package/dist/chunks/{chunk-ZKLOV6MW.js.map → chunk-SYHZ5T54.js.map}

@@ -1,6 +1,6 @@
 {
   "version": 3,
-  "sources": ["../../node_modules/.pnpm/@jbrowse+bandage-core@7.5.1/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-K5SIJGAE.js", "../../src/GraphGenomeView/components/GraphSettingsDialog.tsx"],
+  "sources": ["../../node_modules/.pnpm/@jbrowse+bandage-core@8.0.0/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-K5SIJGAE.js", "../../src/GraphGenomeView/components/GraphSettingsDialog.tsx"],
   "sourcesContent": ["// src/layoutQualities.ts\nvar LAYOUT_QUALITIES = [\n  { value: 0, label: \"Fastest\" },\n  { value: 1, label: \"Fast\" },\n  { value: 2, label: \"Default\" },\n  { value: 3, label: \"Fine\" },\n  { value: 4, label: \"Best\" }\n];\n\nexport {\n  LAYOUT_QUALITIES\n};\n", "import type { ReactNode } from 'react'\n\nimport { BUBBLE_SPREADS } from '@jbrowse/bandage-core/bubbleSpreads'\nimport { COLOR_SCHEMES } from '@jbrowse/bandage-core/colorSchemes'\nimport { LAYOUT_QUALITIES } from '@jbrowse/bandage-core/layoutQualities'\nimport { NODE_WIDTHS } from '@jbrowse/bandage-core/nodeWidths'\nimport { MAX_PATH_COLORS } from '@jbrowse/bandage-core/pathColors'\nimport { Dialog } from '@jbrowse/core/ui'\nimport {\n  Button,\n  DialogActions,\n  DialogContent,\n  FormControl,\n  FormControlLabel,\n  FormLabel,\n  InputLabel,\n  MenuItem,\n  Radio,\n  RadioGroup,\n  Select,\n  Switch,\n  Tooltip,\n  Typography,\n} from '@mui/material'\nimport { observer } from 'mobx-react'\nimport { makeStyles } from 'tss-react/mui'\n\nimport type { GraphPaneModel } from '../model'\nimport type { SxProps } from '@mui/material'\n\nconst useStyles = makeStyles()({\n  section: {\n    marginBottom: 24,\n  },\n  formControl: {\n    minWidth: 200,\n  },\n})\n\nfunction Caption({\n  warn = false,\n  children,\n}: {\n  warn?: boolean\n  children: ReactNode\n}) {\n  return (\n    <Typography\n      variant=\"caption\"\n      color={warn ? 'warning.main' : 'text.secondary'}\n    >\n      {children}\n    </Typography>\n  )\n}\n\n// Layout quality and bubble spread are the engine's inputs, and an anchored\n// layout places a node from its coordinates without reaching it. Left enabled\n// so the force layout can be set up before switching to it.\nconst EngineOnly = observer(function EngineOnly({\n  model,\n}: {\n  model: GraphPaneModel\n}) {\n  return model.hasGraph && !model.usesLayoutEngine ? (\n    <Caption warn>\n      No effect on this layout: only the force-directed layout is drawn by the\n      engine that reads this.\n    </Caption>\n  ) : null\n})\n\nfunction SettingSwitch({\n  label,\n  checked,\n  onChange,\n  children,\n}: {\n  label: string\n  checked: boolean\n  onChange: (checked: boolean) => void\n  children?: ReactNode\n}) {\n  const { classes } = useStyles()\n  return (\n    <div className={classes.section}>\n      <FormControlLabel\n        control={\n          <Switch\n            checked={checked}\n            onChange={e => {\n              onChange(e.target.checked)\n            }}\n          />\n        }\n        label={label}\n      />\n      {children}\n    </div>\n  )\n}\n\n// One dropdown setting; an option's description is its tooltip\nfunction SettingSelect<T extends string>({\n  label,\n  value,\n  options,\n  testId,\n  sx,\n  onChange,\n}: {\n  label: string\n  value: T\n  options: readonly { value: T; label: string; description?: string }[]\n  testId?: string\n  sx?: SxProps\n  onChange: (value: T) => void\n}) {\n  const { classes } = useStyles()\n  return (\n    <FormControl className={classes.formControl} sx={sx}>\n      <InputLabel>{label}</InputLabel>\n      <Select\n        value={value}\n        label={label}\n        data-testid={testId}\n        onChange={e => {\n          onChange(e.target.value as T)\n        }}\n      >\n        {options.map(({ value, label, description }) => (\n          <MenuItem key={value} value={value}>\n            {description ? (\n              <Tooltip title={description} placement=\"right\">\n                <span>{label}</span>\n              </Tooltip>\n            ) : (\n              label\n            )}\n          </MenuItem>\n        ))}\n      </Select>\n    </FormControl>\n  )\n}\n\nconst trackOptions = (tracks: { trackId: string; name: string }[]) =>\n  tracks.map(({ trackId, name }) => ({ value: trackId, label: name }))\n\n// `children` is the host's own section, between node width and colour\nconst GraphSettingsDialog = observer(function GraphSettingsDialog(props: {\n  model: GraphPaneModel\n  open: boolean\n  onClose: () => void\n  children?: ReactNode\n}) {\n  const { model, open, onClose, children } = props\n  const { classes } = useStyles()\n\n  return (\n    <Dialog open={open} onClose={onClose} title=\"Graph settings\">\n      <DialogContent>\n        <div className={classes.section}>\n          <FormControl fullWidth>\n            <FormLabel component=\"legend\">Layout quality</FormLabel>\n            <RadioGroup\n              value={model.layoutQuality}\n              onChange={e => {\n                model.setLayoutQuality(parseInt(e.target.value))\n                void model.recomputeLayout()\n              }}\n            >\n              {LAYOUT_QUALITIES.map(q => (\n                <FormControlLabel\n                  key={q.value}\n                  value={q.value}\n                  control={<Radio />}\n                  label={q.label}\n                />\n              ))}\n            </RadioGroup>\n            <Caption>\n              FMMM&apos;s iteration budget, the same scale Bandage exposes.\n              Higher is slower: on a thousand-node cut the top setting is\n              seconds rather than tenths.\n            </Caption>\n            <EngineOnly model={model} />\n          </FormControl>\n        </div>\n\n        <SettingSwitch\n          label=\"Draw paths\"\n          checked={model.drawPaths}\n          onChange={draw => {\n            model.setDrawPaths(draw)\n          }}\n        >\n          <Caption>\n            Color each node and connector by the paths through it, one lane per\n            path in legend order, so a path that skips a node leaves its lane\n            empty\n          </Caption>\n          {model.drawPaths && !model.effectiveDrawPaths ? (\n            <Caption warn>\n              {model.pathCount > MAX_PATH_COLORS\n                ? `Off: ${model.pathCount.toLocaleString()} paths is past the ${MAX_PATH_COLORS} this can tell apart`\n                : 'Off: this graph states no paths'}\n            </Caption>\n          ) : null}\n        </SettingSwitch>\n\n        <SettingSwitch\n          label=\"Mark bubbles\"\n          checked={model.showBubbles}\n          onChange={show => {\n            model.setShowBubbles(show)\n          }}\n        >\n          <Caption>\n            A halo along the nodes of each bubble, labelled by what it is, with\n            the label opening the bubble on its own\n          </Caption>\n        </SettingSwitch>\n\n        <SettingSwitch\n          label=\"Genes on the backbone\"\n          checked={model.showGenes}\n          onChange={show => {\n            model.setShowGenes(show)\n          }}\n        >\n          <Caption>\n            Exons along the reference nodes that carry them and each gene's name\n            at its midpoint, from the assembly's annotation track\n          </Caption>\n          {model.geneTrackChoices.length > 1 ? (\n            <SettingSelect\n              label=\"Gene track\"\n              value={model.geneTrack?.trackId ?? ''}\n              options={trackOptions(model.geneTrackChoices)}\n              testId=\"graph-gene-track-select\"\n              sx={{ mt: 1 }}\n              onChange={trackId => {\n                model.setGeneTrackId(trackId)\n                void model.reloadGenes()\n              }}\n            />\n          ) : null}\n          {model.repeatTrackChoices.length > 1 ? (\n            <SettingSelect\n              label=\"Repeat track\"\n              value={model.repeatTrack?.trackId ?? ''}\n              options={trackOptions(model.repeatTrackChoices)}\n              testId=\"graph-repeat-track-select\"\n              sx={{ mt: 1 }}\n              onChange={trackId => {\n                model.setRepeatTrackId(trackId)\n                void model.reloadRepeats()\n              }}\n            />\n          ) : null}\n        </SettingSwitch>\n\n        {model.anchorPaths.length > 1 ? (\n          <div className={classes.section}>\n            <SettingSelect\n              label=\"Reference path\"\n              value={model.activeReferencePath ?? ''}\n              options={model.anchorPaths.map(({ name }) => ({\n                value: name,\n                label: name,\n              }))}\n              testId=\"graph-reference-path-select\"\n              onChange={name => {\n                model.setReferencePath(name)\n                void model.recomputeLayout()\n              }}\n            />\n            <Caption>\n              Which path the anchored layouts draw x against. A GFA with no rGFA\n              tags states its coordinates only in its paths, and marks none of\n              them as the reference.\n            </Caption>\n          </div>\n        ) : null}\n\n        <div className={classes.section}>\n          <SettingSelect\n            label=\"Bubble spread\"\n            value={model.bubbleSpread}\n            options={BUBBLE_SPREADS}\n            testId=\"graph-bubble-spread-select\"\n            onChange={spread => {\n              model.setBubbleSpread(spread)\n              void model.recomputeLayout()\n            }}\n          />\n          <Caption>\n            How far the force layout opens a bubble. A pangenome allele is a few\n            bp, so at Bandage&apos;s own scale both arms land inside one node\n            thickness and the graph draws as a rope.\n          </Caption>\n          <EngineOnly model={model} />\n        </div>\n\n        <div className={classes.section}>\n          <SettingSelect\n            label=\"Node width\"\n            value={model.nodeWidth}\n            options={NODE_WIDTHS}\n            testId=\"graph-node-width-select\"\n            onChange={width => {\n              model.setNodeWidth(width)\n            }}\n          />\n          <Caption>\n            Bandage&apos;s depth as width. In a cut with walks, depth is how\n            many haplotypes carry the node.\n          </Caption>\n        </div>\n\n        {children}\n\n        <div className={classes.section}>\n          <SettingSelect\n            label=\"Color scheme\"\n            value={model.chosenColorScheme}\n            options={COLOR_SCHEMES}\n            onChange={scheme => {\n              model.setColorScheme(scheme)\n            }}\n          />\n          {model.colorSchemeLock ? (\n            <Caption warn>No effect now. {model.colorSchemeLock.why}</Caption>\n          ) : null}\n        </div>\n      </DialogContent>\n\n      <DialogActions>\n        <Button variant=\"contained\" color=\"primary\" onClick={onClose}>\n          Close\n        </Button>\n      </DialogActions>\n    </Dialog>\n  )\n})\n\nexport default GraphSettingsDialog\n"],
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   "names": ["LAYOUT_QUALITIES", "import_ui", "import_material", "import_mobx_react", "import_mui", "import_jsx_runtime", "useStyles", "Caption", "warn", "children", "EngineOnly", "model", "SettingSwitch", "label", "checked", "onChange", "classes", "e", "SettingSelect", "value", "options", "testId", "sx", "description", "trackOptions", "tracks", "trackId", "name", "GraphSettingsDialog", "props", "open", "onClose", "LAYOUT_QUALITIES", "q", "draw", "MAX_PATH_COLORS", "show", "BUBBLE_SPREADS", "spread", "NODE_WIDTHS", "width", "COLOR_SCHEMES", "scheme", "GraphSettingsDialog_default"]