jbrowse-plugin-graphgenomeviewer 7.4.2 → 7.4.3

package/dist/chunks/{chunk-WY5W5X62.js → chunk-ZAYC5OMQ.js}

@@ -1,2 +1,2 @@
-import{h as B,k as M,n as F}from"./chunk-ZG2CQXOW.js";import{b as O,h as _}from"./chunk-2XZYJLCE.js";import{H as b,N as A}from"./chunk-Q3BXNKEL.js";import{e as R}from"./chunk-YU7T5WOQ.js";import{D as P,E,H as m,d as v,o as T,q as I,r as L,s as w,t as N,w as x,y as D,z as G}from"./chunk-UGCNPRKC.js";import{b as t,c as i,d as k}from"./chunk-JMBDTNUR.js";var S=[{value:0,label:"Fastest"},{value:1,label:"Fast"},{value:2,label:"Default"},{value:3,label:"Fine"},{value:4,label:"Best"}];function f({label:o,value:n,options:e,testId:s,size:c,sx:d,disabled:a,title:h,shown:g,onChange:Q}){let C=R();return i(w,{size:c,sx:d,disabled:a,title:h,children:[t(x,{id:C,shrink:!0,children:o}),t(P,{labelId:C,value:n,label:o,notched:!0,displayEmpty:!0,"data-testid":s,renderValue:l=>g??e.find(z=>z.value===l)?.label??l,onChange:l=>{Q(l.target.value)},children:e.map(l=>t(G,{value:l.value,disabled:l.disabled,title:l.disabled?void 0:l.description,children:t(D,{primary:l.label,secondary:l.disabled?l.description:void 0})},l.value))})]})}var u=F()({section:{marginBottom:24},group:{marginBottom:16},heading:{marginBottom:8}});function r({warn:o=!1,children:n}){return t(m,{variant:"caption",component:"div",color:o?"warning.main":"text.secondary",children:n})}function y({title:o,children:n}){let{classes:e}=u();return i("section",{className:e.group,children:[t(m,{variant:"subtitle1",className:e.heading,children:o}),n]})}function U({label:o,checked:n,onChange:e,children:s}){let{classes:c}=u();return i("div",{className:c.section,children:[t(N,{control:t(E,{checked:n,onChange:d=>{e(d.target.checked)}}),label:o}),s]})}function p({children:o,...n}){let{classes:e}=u();return i("div",{className:e.section,children:[t(f,{sx:{minWidth:200},...n}),o]})}var Y=[5e3,2e4,5e4,1e5];function H(o){return[...new Set([...Y,o])].sort((n,e)=>n-e).map(n=>({value:String(n),label:n.toLocaleString()}))}function W({label:o,choices:n,stored:e,auto:s,testId:c,onChange:d,children:a}){return n.length>0?t(p,{label:o,value:n.some(h=>h.trackId===e)?e:"",options:[{value:"",label:`Automatic (${s?.name??"none"})`},...n.map(({trackId:h,name:g})=>({value:h,label:g}))],testId:c,onChange:d,children:a}):null}var $=k(function(n){let{model:e,onClose:s,children:c}=n,{classes:d}=u();return i(v,{open:!0,onClose:s,title:"Graph settings",children:[i(L,{children:[i(y,{title:"Subgraph",children:[c,t(p,{label:"Node limit",value:String(e.maxGraphNodes),options:H(e.maxGraphNodes),testId:"graph-node-limit-select",onChange:a=>{e.setMaxGraphNodes(Number(a))},children:t(r,{children:"The most nodes a layout draws; past it the graph is declined. Walk rows take no limit."})})]}),i(y,{title:"Drawing",children:[e.anchorPaths.length>1?t(p,{label:"Reference path",value:e.activeReferencePath??"",options:e.anchorPaths.map(({name:a})=>({value:a,label:a})),testId:"graph-reference-path-select",onChange:a=>{e.setReferencePath(a),e.recomputeLayout()},children:t(r,{children:"The path the anchored layouts place x along"})}):null,t(p,{label:"Node width",value:e.nodeWidth,options:A,testId:"graph-node-width-select",onChange:a=>{e.setNodeWidth(a)},children:t(r,{children:"Depth as width. In a cut with walks, depth is how many haplotypes carry the node."})}),i(U,{label:"Draw paths",checked:e.drawPaths,onChange:a=>{e.setLayer("paths",a)},children:[t(r,{children:"Color each node by the paths through it, one lane per path"}),e.drawPaths&&!e.effectiveDrawPaths?t(r,{warn:!0,children:e.pathCount>b?`Off: ${e.pathCount.toLocaleString()} paths is past the ${b} this can tell apart`:"Off: this graph states no paths"}):null]}),t(W,{label:"Gene track",choices:e.geneTrackChoices,stored:e.geneTrackId,auto:M(e.geneTrackChoices,""),testId:"graph-gene-track-select",onChange:a=>{e.setGeneTrackId(a)},children:t(r,{children:"Where genes on the backbone come from"})}),t(W,{label:"Repeat track",choices:e.repeatTrackChoices,stored:e.repeatTrackId,auto:B(e.repeatTrackChoices,""),testId:"graph-repeat-track-select",onChange:a=>{e.setRepeatTrackId(a)},children:t(r,{children:"The tandem repeat annotation walk rows measure and tile by"})})]}),i(y,{title:"Force-directed layout",children:[e.hasGraph&&!e.usesLayoutEngine?t("div",{className:d.section,children:t(r,{warn:!0,children:"No effect on the current layout until Layout is Force-directed"})}):null,t(p,{label:"Engine",value:e.layoutEngine,options:O,testId:"graph-layout-engine-select",onChange:a=>{e.setLayoutEngine(a)},children:t(r,{children:"Stress keeps the reference straight, so a zoom keeps the picture; FMMM lets the whole graph settle."})}),t(p,{label:"Layout quality",value:String(e.layoutQuality),options:S.map(a=>({value:String(a.value),label:a.label})),testId:"graph-layout-quality-select",onChange:a=>{e.setLayoutQuality(Number(a))},children:t(r,{children:"The engine's iteration budget; higher is slower"})}),t(p,{label:"Bubble spread",value:e.bubbleSpread,options:_,testId:"graph-bubble-spread-select",onChange:a=>{e.setBubbleSpread(a)},children:t(r,{children:"How far the layout opens a bubble"})}),e.layoutEngine==="stress"?null:t(U,{label:"Linear layout",checked:e.linearLayout,onChange:a=>{e.setLinearLayout(a)},children:t(r,{children:"Keeps a chain of nodes on one line where it can"})})]})]}),t(I,{children:t(T,{variant:"contained",color:"primary",onClick:s,children:"Close"})})]})}),he=$;export{f as a,he as b};
-//# sourceMappingURL=chunk-WY5W5X62.js.map
+import{h as B,k as M,n as F}from"./chunk-TGSDXZXI.js";import{b as O,h as _}from"./chunk-CXOMX2I6.js";import{H as b,N as A}from"./chunk-WGTLNVST.js";import{e as R}from"./chunk-YU7T5WOQ.js";import{D as P,E,H as m,d as v,o as T,q as I,r as L,s as w,t as N,w as x,y as D,z as G}from"./chunk-UGCNPRKC.js";import{b as t,c as i,d as k}from"./chunk-JMBDTNUR.js";var S=[{value:0,label:"Fastest"},{value:1,label:"Fast"},{value:2,label:"Default"},{value:3,label:"Fine"},{value:4,label:"Best"}];function f({label:o,value:n,options:e,testId:s,size:c,sx:d,disabled:a,title:h,shown:g,onChange:Q}){let C=R();return i(w,{size:c,sx:d,disabled:a,title:h,children:[t(x,{id:C,shrink:!0,children:o}),t(P,{labelId:C,value:n,label:o,notched:!0,displayEmpty:!0,"data-testid":s,renderValue:l=>g??e.find(z=>z.value===l)?.label??l,onChange:l=>{Q(l.target.value)},children:e.map(l=>t(G,{value:l.value,disabled:l.disabled,title:l.disabled?void 0:l.description,children:t(D,{primary:l.label,secondary:l.disabled?l.description:void 0})},l.value))})]})}var u=F()({section:{marginBottom:24},group:{marginBottom:16},heading:{marginBottom:8}});function r({warn:o=!1,children:n}){return t(m,{variant:"caption",component:"div",color:o?"warning.main":"text.secondary",children:n})}function y({title:o,children:n}){let{classes:e}=u();return i("section",{className:e.group,children:[t(m,{variant:"subtitle1",className:e.heading,children:o}),n]})}function U({label:o,checked:n,onChange:e,children:s}){let{classes:c}=u();return i("div",{className:c.section,children:[t(N,{control:t(E,{checked:n,onChange:d=>{e(d.target.checked)}}),label:o}),s]})}function p({children:o,...n}){let{classes:e}=u();return i("div",{className:e.section,children:[t(f,{sx:{minWidth:200},...n}),o]})}var Y=[5e3,2e4,5e4,1e5];function H(o){return[...new Set([...Y,o])].sort((n,e)=>n-e).map(n=>({value:String(n),label:n.toLocaleString()}))}function W({label:o,choices:n,stored:e,auto:s,testId:c,onChange:d,children:a}){return n.length>0?t(p,{label:o,value:n.some(h=>h.trackId===e)?e:"",options:[{value:"",label:`Automatic (${s?.name??"none"})`},...n.map(({trackId:h,name:g})=>({value:h,label:g}))],testId:c,onChange:d,children:a}):null}var $=k(function(n){let{model:e,onClose:s,children:c}=n,{classes:d}=u();return i(v,{open:!0,onClose:s,title:"Graph settings",children:[i(L,{children:[i(y,{title:"Subgraph",children:[c,t(p,{label:"Node limit",value:String(e.maxGraphNodes),options:H(e.maxGraphNodes),testId:"graph-node-limit-select",onChange:a=>{e.setMaxGraphNodes(Number(a))},children:t(r,{children:"The most nodes a layout draws; past it the graph is declined. Walk rows take no limit."})})]}),i(y,{title:"Drawing",children:[e.anchorPaths.length>1?t(p,{label:"Reference path",value:e.activeReferencePath??"",options:e.anchorPaths.map(({name:a})=>({value:a,label:a})),testId:"graph-reference-path-select",onChange:a=>{e.setReferencePath(a),e.recomputeLayout()},children:t(r,{children:"The path the anchored layouts place x along"})}):null,t(p,{label:"Node width",value:e.nodeWidth,options:A,testId:"graph-node-width-select",onChange:a=>{e.setNodeWidth(a)},children:t(r,{children:"Depth as width. In a cut with walks, depth is how many haplotypes carry the node."})}),i(U,{label:"Draw paths",checked:e.drawPaths,onChange:a=>{e.setLayer("paths",a)},children:[t(r,{children:"Color each node by the paths through it, one lane per path"}),e.drawPaths&&!e.effectiveDrawPaths?t(r,{warn:!0,children:e.pathCount>b?`Off: ${e.pathCount.toLocaleString()} paths is past the ${b} this can tell apart`:"Off: this graph states no paths"}):null]}),t(W,{label:"Gene track",choices:e.geneTrackChoices,stored:e.geneTrackId,auto:M(e.geneTrackChoices,""),testId:"graph-gene-track-select",onChange:a=>{e.setGeneTrackId(a)},children:t(r,{children:"Where genes on the backbone come from"})}),t(W,{label:"Repeat track",choices:e.repeatTrackChoices,stored:e.repeatTrackId,auto:B(e.repeatTrackChoices,""),testId:"graph-repeat-track-select",onChange:a=>{e.setRepeatTrackId(a)},children:t(r,{children:"The tandem repeat annotation walk rows measure and tile by"})})]}),i(y,{title:"Force-directed layout",children:[e.hasGraph&&!e.usesLayoutEngine?t("div",{className:d.section,children:t(r,{warn:!0,children:"No effect on the current layout until Layout is Force-directed"})}):null,t(p,{label:"Engine",value:e.layoutEngine,options:O,testId:"graph-layout-engine-select",onChange:a=>{e.setLayoutEngine(a)},children:t(r,{children:"Stress keeps the reference straight, so a zoom keeps the picture; FMMM lets the whole graph settle."})}),t(p,{label:"Layout quality",value:String(e.layoutQuality),options:S.map(a=>({value:String(a.value),label:a.label})),testId:"graph-layout-quality-select",onChange:a=>{e.setLayoutQuality(Number(a))},children:t(r,{children:"The engine's iteration budget; higher is slower"})}),t(p,{label:"Bubble spread",value:e.bubbleSpread,options:_,testId:"graph-bubble-spread-select",onChange:a=>{e.setBubbleSpread(a)},children:t(r,{children:"How far the layout opens a bubble"})}),e.layoutEngine==="stress"?null:t(U,{label:"Linear layout",checked:e.linearLayout,onChange:a=>{e.setLinearLayout(a)},children:t(r,{children:"Keeps a chain of nodes on one line where it can"})})]})]}),t(I,{children:t(T,{variant:"contained",color:"primary",onClick:s,children:"Close"})})]})}),he=$;export{f as a,he as b};
+//# sourceMappingURL=chunk-ZAYC5OMQ.js.map

package/dist/chunks/{chunk-WY5W5X62.js.map → chunk-ZAYC5OMQ.js.map}

@@ -1,6 +1,6 @@
 {
   "version": 3,
-  "sources": ["../../node_modules/.pnpm/@jbrowse+bandage-core@11.7.1/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-K5SIJGAE.js", "../../src/GraphGenomeView/components/LabelledSelect.tsx", "../../src/GraphGenomeView/components/GraphSettingsDialog.tsx"],
+  "sources": ["../../node_modules/.pnpm/@jbrowse+bandage-core@11.7.3/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-K5SIJGAE.js", "../../src/GraphGenomeView/components/LabelledSelect.tsx", "../../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 { useId } from 'react'\n\nimport {\n  FormControl,\n  InputLabel,\n  ListItemText,\n  MenuItem,\n  Select,\n} from '@mui/material'\n\nimport type { SxProps } from '@mui/material'\n\ninterface SelectOption<T extends string> {\n  value: T\n  label: string\n  // an option's tooltip, and the reason under a disabled one, whose tooltip\n  // cannot open\n  description?: string\n  disabled?: boolean\n}\n\n// One dropdown with its label tied to it, so a screen reader names the combobox\nexport default function LabelledSelect<T extends string>({\n  label,\n  value,\n  options,\n  testId,\n  size,\n  sx,\n  disabled,\n  title,\n  shown,\n  onChange,\n}: {\n  label: string\n  value: T\n  options: readonly SelectOption<T>[]\n  testId?: string\n  size?: 'small' | 'medium'\n  sx?: SxProps\n  disabled?: boolean\n  title?: string\n  // what the closed select reads, when not the picked option's label\n  shown?: string\n  onChange: (value: T) => void\n}) {\n  const labelId = useId()\n  return (\n    <FormControl size={size} sx={sx} disabled={disabled} title={title}>\n      <InputLabel id={labelId} shrink>\n        {label}\n      </InputLabel>\n      <Select\n        labelId={labelId}\n        value={value}\n        label={label}\n        notched\n        displayEmpty\n        data-testid={testId}\n        renderValue={picked =>\n          shown ?? options.find(o => o.value === picked)?.label ?? picked\n        }\n        onChange={e => {\n          onChange(e.target.value as T)\n        }}\n      >\n        {options.map(o => (\n          <MenuItem\n            key={o.value}\n            value={o.value}\n            disabled={o.disabled}\n            title={o.disabled ? undefined : o.description}\n          >\n            <ListItemText\n              primary={o.label}\n              secondary={o.disabled ? o.description : undefined}\n            />\n          </MenuItem>\n        ))}\n      </Select>\n    </FormControl>\n  )\n}\n", "import type { ReactNode } from 'react'\n\nimport { BUBBLE_SPREADS } from '@jbrowse/bandage-core/bubbleSpreads'\nimport { LAYOUT_ENGINES } from '@jbrowse/bandage-core/layoutEngines'\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  FormControlLabel,\n  Switch,\n  Typography,\n} from '@mui/material'\nimport { observer } from 'mobx-react'\nimport { makeStyles } from 'tss-react/mui'\n\nimport LabelledSelect from './LabelledSelect'\nimport { pickGeneTrack } from '../genes/geneFeatures'\nimport { pickRepeatTrack } from '../repeats/repeatFeatures'\n\nimport type { GraphPaneModel } from '../model'\n\nconst useStyles = makeStyles()({\n  section: {\n    marginBottom: 24,\n  },\n  group: {\n    marginBottom: 16,\n  },\n  heading: {\n    marginBottom: 8,\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      component=\"div\"\n      color={warn ? 'warning.main' : 'text.secondary'}\n    >\n      {children}\n    </Typography>\n  )\n}\n\nfunction Group({ title, children }: { title: string; children: ReactNode }) {\n  const { classes } = useStyles()\n  return (\n    <section className={classes.group}>\n      <Typography variant=\"subtitle1\" className={classes.heading}>\n        {title}\n      </Typography>\n      {children}\n    </section>\n  )\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, at the dialog's width, and its caption\nfunction SettingSelect<T extends string>({\n  children,\n  ...props\n}: Omit<Parameters<typeof LabelledSelect<T>>[0], 'size' | 'sx'> & {\n  children?: ReactNode\n}) {\n  const { classes } = useStyles()\n  return (\n    <div className={classes.section}>\n      <LabelledSelect sx={{ minWidth: 200 }} {...props} />\n      {children}\n    </div>\n  )\n}\n\nconst NODE_LIMITS = [5000, 20_000, 50_000, 100_000]\n\n// the presets, with a limit a session states among them\nfunction nodeLimitOptions(current: number) {\n  return [...new Set([...NODE_LIMITS, current])]\n    .sort((a, b) => a - b)\n    .map(limit => ({ value: String(limit), label: limit.toLocaleString() }))\n}\n\ninterface NamedTrack {\n  trackId: string\n  name: string\n}\n\n// '' leaves the pick to the heuristic, so a session can go back to it\nfunction TrackPickSetting({\n  label,\n  choices,\n  stored,\n  auto,\n  testId,\n  onChange,\n  children,\n}: {\n  label: string\n  choices: NamedTrack[]\n  stored: string\n  auto: NamedTrack | undefined\n  testId: string\n  onChange: (trackId: string) => void\n  children: ReactNode\n}) {\n  return choices.length > 0 ? (\n    <SettingSelect\n      label={label}\n      value={choices.some(t => t.trackId === stored) ? stored : ''}\n      options={[\n        { value: '', label: `Automatic (${auto?.name ?? 'none'})` },\n        ...choices.map(({ trackId, name }) => ({\n          value: trackId,\n          label: name,\n        })),\n      ]}\n      testId={testId}\n      onChange={onChange}\n    >\n      {children}\n    </SettingSelect>\n  ) : null\n}\n\n// Toggles the menus already offer (halos, genes, color) stay out of here.\n// `children` is the host's own part of the subgraph group.\nconst GraphSettingsDialog = observer(function GraphSettingsDialog(props: {\n  model: GraphPaneModel\n  onClose: () => void\n  children?: ReactNode\n}) {\n  const { model, onClose, children } = props\n  const { classes } = useStyles()\n\n  return (\n    <Dialog open onClose={onClose} title=\"Graph settings\">\n      <DialogContent>\n        <Group title=\"Subgraph\">\n          {children}\n          <SettingSelect\n            label=\"Node limit\"\n            value={String(model.maxGraphNodes)}\n            options={nodeLimitOptions(model.maxGraphNodes)}\n            testId=\"graph-node-limit-select\"\n            onChange={limit => {\n              model.setMaxGraphNodes(Number(limit))\n            }}\n          >\n            <Caption>\n              The most nodes a layout draws; past it the graph is declined. Walk\n              rows take no limit.\n            </Caption>\n          </SettingSelect>\n        </Group>\n\n        <Group title=\"Drawing\">\n          {model.anchorPaths.length > 1 ? (\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>The path the anchored layouts place x along</Caption>\n            </SettingSelect>\n          ) : null}\n\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              Depth as width. In a cut with walks, depth is how many haplotypes\n              carry the node.\n            </Caption>\n          </SettingSelect>\n\n          <SettingSwitch\n            label=\"Draw paths\"\n            checked={model.drawPaths}\n            onChange={draw => {\n              model.setLayer('paths', draw)\n            }}\n          >\n            <Caption>\n              Color each node by the paths through it, one lane per path\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          <TrackPickSetting\n            label=\"Gene track\"\n            choices={model.geneTrackChoices}\n            stored={model.geneTrackId}\n            auto={pickGeneTrack(model.geneTrackChoices, '')}\n            testId=\"graph-gene-track-select\"\n            onChange={trackId => {\n              model.setGeneTrackId(trackId)\n            }}\n          >\n            <Caption>Where genes on the backbone come from</Caption>\n          </TrackPickSetting>\n\n          <TrackPickSetting\n            label=\"Repeat track\"\n            choices={model.repeatTrackChoices}\n            stored={model.repeatTrackId}\n            auto={pickRepeatTrack(model.repeatTrackChoices, '')}\n            testId=\"graph-repeat-track-select\"\n            onChange={trackId => {\n              model.setRepeatTrackId(trackId)\n            }}\n          >\n            <Caption>\n              The tandem repeat annotation walk rows measure and tile by\n            </Caption>\n          </TrackPickSetting>\n        </Group>\n\n        <Group title=\"Force-directed layout\">\n          {model.hasGraph && !model.usesLayoutEngine ? (\n            <div className={classes.section}>\n              <Caption warn>\n                No effect on the current layout until Layout is Force-directed\n              </Caption>\n            </div>\n          ) : null}\n\n          <SettingSelect\n            label=\"Engine\"\n            value={model.layoutEngine}\n            options={LAYOUT_ENGINES}\n            testId=\"graph-layout-engine-select\"\n            onChange={engine => {\n              model.setLayoutEngine(engine)\n            }}\n          >\n            <Caption>\n              Stress keeps the reference straight, so a zoom keeps the picture;\n              FMMM lets the whole graph settle.\n            </Caption>\n          </SettingSelect>\n\n          <SettingSelect\n            label=\"Layout quality\"\n            value={String(model.layoutQuality)}\n            options={LAYOUT_QUALITIES.map(q => ({\n              value: String(q.value),\n              label: q.label,\n            }))}\n            testId=\"graph-layout-quality-select\"\n            onChange={quality => {\n              model.setLayoutQuality(Number(quality))\n            }}\n          >\n            <Caption>\n              The engine&apos;s iteration budget; higher is slower\n            </Caption>\n          </SettingSelect>\n\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            }}\n          >\n            <Caption>How far the layout opens a bubble</Caption>\n          </SettingSelect>\n\n          {model.layoutEngine === 'stress' ? null : (\n            <SettingSwitch\n              label=\"Linear layout\"\n              checked={model.linearLayout}\n              onChange={linear => {\n                model.setLinearLayout(linear)\n              }}\n            >\n              <Caption>Keeps a chain of nodes on one line where it can</Caption>\n            </SettingSwitch>\n          )}\n        </Group>\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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package/dist/chunks/{renderSvg-Z7YIXVQ5.js → renderSvg-7G6NWBXF.js}

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

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r=this.tubeMapUnder(o);return(r?Dt(r.drawing,r.frame,t,o):null)??Rr(e.tubeMapConnectors,e.connectorZoneBottom,t,o)??null},tubeAt(t,o){let r=this.tubeMapUnder(o);if(!r)return null;let{picture:n,frame:a}=r,i=Nr(n,a,t,o),s=i?.readId??Ir(n,a,t,o);return s===void 0?null:{track:s,mismatch:i}},get hoveredTubeText(){let t=e.hoveredTube,o=e.layoutResult?.tubeMap?.layout,r=t&&o?.reads.find(i=>i.id===t.track);if(t&&r){let i=r.mapping_quality;return{label:r.name??"read",readout:[`MAPQ ${i??"unknown"}`,`${r.is_reverse?"reverse":"forward"} strand`,...t.mismatch?[Da(t.mismatch)]:[]].join(", ")}}let n=t?e.hoverGraph?.paths?.[t.track]:void 0,a=n?.members;return a?{label:`${a.length} haplotypes`,readout:`one route: ${Wa(a.map(i=>e.walkLabel(i)))}`}:n?{label:e.walkLabel(n.name),readout:"haplotype"}:void 0}}));var Vn=En.actions(()=>({writeGrammar(e){}})).actions(e=>({keepDrawingInView(){let t=e.layoutBounds,o=e.viewBox;if(!t||e.viewportOwner==="fit"||!e.paneMeasured||o.width<=0||o.height<=0)return;let r=Cn(t,e,o);e.viewportOwner!=="host"&&(e.translateX=r.translateX),e.translateY=r.translateY}})).actions(e=>{let t;return{setColorScheme(o){(e.statedColorDomain||e.chosenColorScheme==="reference-position")&&(t=e.statedColorDomain),e.writeGrammar({color:en(o,t)})}}}).actions(e=>({setError(t){e.error=t,e.isLoading=!1,e.statusMessage=""},finishLoading(){e.isLoading=!1,e.statusMessage=""},setStatusMessage(t){e.statusMessage=t},setFetchMs(t){e.lastFetchMs=t},setLayoutMs(t){e.lastLayoutMs=t},setGeometryMetrics(t,o,r){e.lastGeometryMs=t,e.lastGeometryStrokeCount=o.nodeStrokes.length,e.builtViewport={...r,viewportDirty:e.viewportDirty},e.drawnBatch=o},markPainted(){e.paintedViewport=e.builtViewport},setLayoutQuality(t){e.layoutQuality=t},setLayoutEngine(t){e.layoutEngine=t},setLinearLayout(t){e.linearLayout=t},setLayoutMode(t){e.writeGrammar({layoutMode:t})},setHover(t){e.writeGrammar({hover:t}),e.hoverLightsEverything||(e.hoveredEdge=null)},setReferencePath(t){e.referencePath=t;let 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t=e.getElementTypesInGroup("display"),o=n=>t.find(a=>a.name===n),r=n=>n&&Object.assign(Object.create(n),{adapterCapabilities:["headerLanes"]});return[o("LinearGraphDisplay"),o("LinearBasicDisplay"),...Yt.map(n=>r(o(n)))].filter(n=>n!==void 0)}function Ut(e){e.addTrackType(()=>{let t=j("GraphTrack",{},{baseConfiguration:hn(e),explicitIdentifier:"trackId"}),o=new gn({name:"GraphTrack",displayName:"Pangenome graph track",configSchema:t,stateModel:yn(e,"GraphTrack",t)});for(let r of ri(e))o.addDisplayType(r);return o})}function Xt(e){e.addToExtensionPoint("LaunchView-GraphGenomeView",t=>{let{session:o,...r}=t;return o.addView("GraphGenomeView",r),t})}var it=JBrowseExports["@jbrowse/core/pluggableElementTypes/DisplayType"];var qn=it&&it.__esModule?it.default:it;var ye=JBrowseExports["@jbrowse/display-kit/trackHeightConfigSchemaFields"],ni=e=>ye!=null&&e in Object(ye)?ye[e]:Object.assign(function(){throw new Error("This JBrowse does not provide '"+e+"' from 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JBrowse does not provide '"+e+"' from '@jbrowse/core/svg/svgReady' to plugins: GraphGenomeView was built for a different JBrowse version, so update the plugin or JBrowse")},{jbrowseHostMissing:e});var ea=ai("computeSvgReady");var pm=be&&be.__esModule?be.default:be;var st=JBrowseExports["@jbrowse/display-kit/TrackHeightMixin"];var ta=st&&st.__esModule?st.default:st;var we=JBrowseExports["@jbrowse/display-kit/plotMenu"],ii=e=>we!=null&&e in Object(we)?we[e]:Object.assign(function(){throw new Error("This JBrowse does not provide '"+e+"' from '@jbrowse/display-kit/plotMenu' to plugins: GraphGenomeView was built for a different JBrowse version, so update the plugin or JBrowse")},{jbrowseHostMissing:e}),oa=ii("editPlotMenuItems");var dm=we&&we.__esModule?we.default:we;var fe=JBrowseExports["@jbrowse/render-core/displayPhase"],ra=e=>fe!=null&&e in Object(fe)?fe[e]:Object.assign(function(){throw new Error("This JBrowse does not provide '"+e+"' from '@jbrowse/render-core/displayPhase' to plugins: GraphGenomeView was built for a different JBrowse version, so update the plugin or JBrowse")},{jbrowseHostMissing:e}),na=ra("computeActivityPhase");var aa=ra("computeDisplayStatusPhase"),lm=fe&&fe.__esModule?fe.default:fe;function Kt(e,t){if(e?.refName!==t.refName||e.assemblyName!==t.assemblyName)return!1;let o=e.end-e.start;return t.end-t.start>=o&&t.end>e.start-o&&t.start<e.end+o}var si=new Set(["scale","translateX","translateY"]);function pi(e){return Object.fromEntries(Object.keys(yr.properties).filter(t=>!si.has(t)).map(t=>[t,e[t]]))}var qt=10;function ci(e){let{aboveBpPerPx:t,foldBelowBp:o}=e??{};return typeof t=="number"?t:typeof o=="number"&&o>0?o/qt:void 0}var ui=ee(()=>import("./chunks/GraphTrackSettingsDialog-MR7X75EY.js"));function ia(e){return M.compose("LinearGraphDisplay",dn,ta(),at,M.model({type:M.literal("LinearGraphDisplay"),configuration:xo(e),layoutEngine:_o(Fo,"stress"),cutRegion:M.maybe(M.frozen()),coarseCut:M.optional(M.boolean,!1)})).volatile(()=>({recuts:0,settledWindow:void 0,dense:void 0,haplotypeNames:void 0,cutFoldBp:0})).views(t=>({get grammar(){return{layoutMode:Z(t,"layoutMode"),color:Z(t,"color"),size:Z(t,"size"),layers:Z(t,"layers"),facet:Z(t,"facet"),rows:Z(t,"rows"),hover:Z(t,"hover")}},get drawsGenomicCoordinates(){return t.layoutResult===void 0||t.hostPlacesX},get canvasHeight(){return t.height},get canRetryLoad(){return t.cutRegion!==void 0},get trackHaplotypes(){let o=t.sourceAdapter,r=t.sourceTrack;return(o&&Ae(o))??(r&&xt(r))},get coarseAboveBpPerPx(){return ci(t.sourceAdapter?.coarse)}})).views(t=>({tierAt(o){let r=t.coarseAboveBpPerPx;return r!==void 0&&o>r?"coarse":"fine"},capFor(o){return o==="coarse"?1/0:t.maxRegionBp},foldDrifted(o){let r=qt*o,n=t.cutFoldBp;return!t.graph?.paths?.length&&(r>=2*Math.max(n,1)||t.foldedBelowBp!==void 0&&r<=n/2)},get cutTier(){return t.coarseCut&&t.coarseAboveBpPerPx!==void 0?"coarse":"fine"}})).views(t=>({get settledCapBp(){let o=t.settledWindow;return o?t.capFor(t.tierAt(o.bpPerPx)):1/0}})).views(t=>({get regionTooLarge(){let o=t.settledWindow;return o!==void 0&&o.end-o.start>t.settledCapBp},get regionTooLargeReason(){let o=t.settledWindow;return o?`Region too large for a graph cut (${pe(o.end-o.start)}, max ${pe(t.settledCapBp)})`:""},get zoomCanReleaseGate(){return!0},get fetchCanceled(){return t.loadCanceled}})).views(t=>({get svgReady(){return ea({error:t.error,regionTooLarge:t.regionTooLarge,extraTerminal:!1,fetchCanceled:t.loadCanceled},()=>!t.isLoading&&t.hasGraph&&!!t.layoutResult)}})).views(t=>({get displayPhase(){return aa({regionTooLarge:t.regionTooLarge,error:t.error??t.renderError},()=>na({isMinimized:t.isMinimized,fetchInert:!1,viewportEmpty:t.host?.initialized===!0&&t.host.hasVisibleContent===!1,isLoading:t.isLoading||!t.hasGraph,fetchCanceled:t.loadCanceled,awaitingDependentData:!1,rendersCanvas:!0,canvasDrawn:t.painted&&t.geometryPainted},()=>!0,()=>t.host?.effectiveBodyMounted??!0))}})).actions(t=>({writeGrammar(o){for(let[r,n]of Object.entries(o))Ro(t,r,n)},setSubgraphContext(o){t.subgraphContext=o,t.dense=void 0},setSubgraphHaplotypes(o){t.subgraphHaplotypes=o,t.dense=void 0},setDense(o){t.dense=o},setHaplotypeNames(o){t.haplotypeNames=o},setMaxRegionBp(o){t.maxRegionBp=o},cut(){let o=t.cutRegion,r=t.sourceAdapter;if(!o||!r)return;let n=t.offReference(o);if(n){t.clearGraph(),t.setError(new Error(n));return}let a=t.cutTier==="coarse";return t.cutFoldBp=Math.round(qt*(t.settledWindow?.bpPerPx??t.host?.bpPerPx??0)),t.cutSubgraph(r,o,{...t.cutOptions,tier:a?"coarse":void 0},t.cutFoldBp)}})).actions(t=>({recutAt(o){let r=t.tierAt(o.bpPerPx);return t.coarseCut=r==="coarse",t.cutRegion=Yr(o,t.capFor(r),F(t.chosenLayoutMode).cutMargins),t.recuts++,t.cut()}})).actions(t=>({settleOn(o){t.settledWindow=o;let r=F(t.chosenLayoutMode).cutMargins;if(t.regionTooLarge||Kt(t.dense,o)||!t.loadCanceled&&t.tierAt(o.bpPerPx)===t.cutTier&&Ur(t.cutRegion,o,r)&&!t.foldDrifted(o.bpPerPx))return!1;let n=t.recutAt(o),a=t.recuts;return Promise.resolve(n).then(()=>{H(t)&&t.recuts===a&&wt(t.error)&&this.refuseDenseCut(o)}),!0},refuseDenseCut(o){t.setDense(o),t.cutRegion=void 0,this.settleOn(t.settledWindow??o)},recut(){t.cutRegion?t.cut():t.settledWindow&&this.settleOn(t.settledWindow)},relayoutFrom(o){let r=t.host?Xe(t.host):void 0;return r&&!t.regionTooLarge&&(t.cutChangedFrom(o)||F(o).cutMargins!==F(t.chosenLayoutMode).cutMargins)?t.recutAt(r):t.recomputeLayout()},retryLoad(){t.cut()},reload(){t.cut()},cancelFetchByUser(){t.stopLoad()}})).actions(t=>({async fetchHaplotypeNames(o,r){try{let n=await x(t).rpcManager.call(ae(t),"GetGraphHaplotypes",{adapterConfig:o,signal:r});H(t)&&!r?.aborted&&t.setHaplotypeNames(n)}catch(n){r?.aborted||console.warn("[LinearGraphDisplay] no haplotype names",n)}}})).actions(t=>({stretchWithHost(o,r){let n=t.layoutBounds;if(!n||!t.followsHostView)return;t.viewportOwner==="fit"&&(t.viewportOwner="user");let a=o.bpPerPx/r.bpPerPx,i=t.translateY+t.scaleY*(n.minY+n.h/2);t.scale*=a,t.translateX=a*(t.translateX+o.offsetPx)-r.offsetPx,t.translateY=i-a*(i-t.translateY)}})).actions(t=>({forceLoad(){let o=t.settledWindow;o&&(t.setMaxRegionBp(Math.ceil(o.end-o.start)),t.settleOn(o))},afterAttach(){t.cutRegion&&!t.graph&&t.cut();let o;G(t,()=>{o?.abort()}),G(t,C(()=>{let n=t.sourceAdapter;return n&&Jo(n)?n:void 0},n=>{o?.abort(),o=void 0,t.setHaplotypeNames(void 0),n&&(o=new AbortController,t.fetchHaplotypeNames(n,o.signal))},{fireImmediately:!0,equals:(n,a)=>JSON.stringify(n)===JSON.stringify(a),name:"GraphHaplotypeNames"})),G(t,C(()=>t.hostPlacesX,n=>{n||t.releaseHost()},{name:"GraphHostPlacesX"})),G(t,C(()=>t.hostFrame,n=>{n&&t.hostTransform(n.scale,n.translateX)},{equals:(n,a)=>n?.scale===a?.scale&&n?.translateX===a?.translateX,fireImmediately:!0,name:"GraphHostFrame"}));let r;G(t,C(()=>t.host&&!t.hostPlacesX?{bpPerPx:t.host.bpPerPx,offsetPx:t.host.offsetPx}:void 0,n=>{let a=r;r=n,n&&a&&n.bpPerPx>0&&t.stretchWithHost(a,n)},{equals:(n,a)=>n?.bpPerPx===a?.bpPerPx&&n?.offsetPx===a?.offsetPx,fireImmediately:!0,name:"GraphHostStretch"})),G(t,C(()=>`${t.facetSetting.field} ${t.facetPlacement?.count}`,()=>{let n=(t.facetGridIn(t.paneCeiling-qe)?.total??0)+qe;(t.facetGrid?.total??0)+qe>t.height&&t.setHeight(Math.max(t.height,Math.ceil(n)))},{name:"GraphFacetHeight"})),G(t,C(()=>t.host?.coarseDynamicBlocks,n=>{let{host:a}=t,i=n&&a?Xe(a):void 0;i&&t.settleOn(i)},{fireImmediately:!0,name:"GraphHostSettle"}))}})).views(t=>({get graphViewSpec(){let o=t.host?Xe(t.host):void 0,r=t.sourceTrackId;if(!o||!r||!t.hasGraph||t.coarseCut||t.regionTooLarge||Kt(t.dense,o))return;let n=Math.floor(o.start),a=Math.ceil(o.end);return{...pi(t),loadedTrackId:r,loadedRegion:{refName:o.refName,assemblyName:o.assemblyName,start:n,end:a},subgraphHaplotypes:t.cutHaplotypes,maxRegionBp:Math.max(t.maxRegionBp,a-n),...t.grammar,layoutMode:t.chosenLayoutMode,connectedViewId:t.host?.id}}})).actions(t=>({openGraphView(){let o=t.graphViewSpec;o&&x(t).addView("GraphGenomeView",o)}})).views(t=>({cutMenuItems(){let o=t.sourceAdapter,r=t.sourceTrack;if(!o||!r||!Yo(o))return[];let n=Ae(o),a=xt(r),i=t.haplotypeNames,s=t.subgraphHaplotypes,p=u=>{t.setSubgraphHaplotypes(u),t.recut()};return[{type:"subHeader",label:"Load"},{type:"radio",label:i?`Every haplotype in the graph (${i.length.toLocaleString()})`:"Every haplotype in the graph",checked:s?s.length===0:!n&&!a,onClick:()=>{p([])}},...n||a?[{type:"radio",label:n?"The track's default haplotypes":`The track's ${a?.length} assemblies`,checked:s===void 0,onClick:()=>{p(void 0)}}]:[],{type:"radio",label:"Chosen in Graph settings...",checked:(s?.length??0)>0,onClick:()=>{this.openSettings()}}]},openSettings(){x(t).queueDialog(o=>[ui,{model:t,onClose:o}])},async renderSvg(o){let{renderGraphTrackSvg:r}=await import("./chunks/renderSvg-Z7YIXVQ5.js");return r(t,o)},trackMenuItems(){let o=t.launchMenuItems();nt(o,{label:"Graph genome view",icon:Qe,disabled:!t.graphViewSpec,disabledHelpText:t.error&&!wt(t.error)?"The track could not cut a graph here":t.isLoading&&!t.hasGraph?"The track is still cutting its graph":"Zoom in until the track cuts a graph",onClick:()=>{t.openGraphView()}});let r=[...this.cutMenuItems(),...t.highlightMenuItems()];return[...r.length>0?[{label:"Haplotypes",icon:an,subMenu:r}]:[],...t.graphMenuItems(),{label:"Graph settings...",icon:sn,helpText:"Subgraph, drawing and force-directed layout",onClick:()=>{this.openSettings()}},...o,...oa(t)]}}))}function Zt(e){e.addDisplayType(()=>{let t=Qn();return Object.assign(new qn({name:"LinearGraphDisplay",displayName:"Graph",configSchema:t,stateModel:ia(t),trackType:["GraphTrack","FeatureTrack","SyntenyTrack"],viewType:"LinearGenomeView",ReactComponent:ee(()=>import("./chunks/LinearGraphDisplay-AJ5OZN27.js"))}),{adapterCapabilities:["getSubgraph"]})})}function di(e){let{uri:t,baseUri:o,csi:r}=e;return typeof t=="string"?{...e,bubblesLocation:{uri:t,baseUri:o},index:Ge(t,o,r)}:e}var mi=j("MinigraphBubbleAdapter",{bubblesLocation:N("/path/to/graph.bb.bed.gz"),index:_("MinigraphBubbleIndex","/path/to/graph.bb.bed.gz.tbi"),assemblyNameToPanSN:{type:"frozen",defaultValue:{}}},{explicitlyTyped:!0,preProcessSnapshot:di}),sa=mi;function Qt(e){e.addAdapterType(()=>new te({name:"MinigraphBubbleAdapter",displayName:"Minigraph bubble BED adapter",configSchema:sa,adapterMetadata:{category:"Graph adapters"},getAdapterClass:()=>import("./chunks/MinigraphBubbleAdapter-PEQK5NII.js").then(t=>t.default)}))}function pa(e){let{uri:t,baseUri:o,csi:r}=e;return typeof t=="string"?{...e,segmentsLocation:{uri:`${t}.segs.bed.gz`,baseUri:o},segmentsIndex:Ge(`${t}.segs.bed.gz`,o,r),linksLocation:{uri:`${t}.links.bed.gz`,baseUri:o},linksIndex:Ge(`${t}.links.bed.gz`,o,r)}:e}function li(e){let{coarse:t,baseUri:o,csi:r}=e;return Oe(pa(typeof t=="object"&&t!==null?{...e,coarse:pa({baseUri:o,csi:r,...t})}:e))}var gi=j("RgfaTabixCoarseTier",{aboveBpPerPx:{type:"maybeNumber"},foldBelowBp:{type:"maybeNumber"},segmentsLocation:N("/path/to/graph.tier.segs.bed.gz"),segmentsIndex:_("RgfaCoarseSegmentsIndex","/path/to/graph.tier.segs.bed.gz.tbi"),linksLocation:N("/path/to/graph.tier.links.bed.gz"),linksIndex:_("RgfaCoarseLinksIndex","/path/to/graph.tier.links.bed.gz.tbi")}),hi=j("RgfaTabixAdapter",{segmentsLocation:N("/path/to/graph.segs.bed.gz"),segmentsIndex:_("RgfaSegmentsIndex","/path/to/graph.segs.bed.gz.tbi"),linksLocation:N("/path/to/graph.links.bed.gz"),linksIndex:_("RgfaLinksIndex","/path/to/graph.links.bed.gz.tbi"),walksLocation:N(""),walksIndex:_("RgfaWalksIndex"),walkStepBudget:{type:"integer",defaultValue:ke.stepBudget},walkByteBudget:{type:"integer",defaultValue:ke.byteBudget},defaultHaplotypes:{type:"stringArray",defaultValue:[]},assemblyNameToPanSN:{type:"frozen",defaultValue:{}},coarse:gi},{explicitlyTyped:!0,preProcessSnapshot:li}),ca=hi;function eo(e){e.addAdapterType(()=>new te({name:"RgfaTabixAdapter",displayName:"Indexed rGFA adapter",configSchema:ca,adapterCapabilities:["getSubgraph"],adapterMetadata:{category:"Graph adapters"},getAdapterClass:()=>import("./chunks/RgfaTabixAdapter-Q63YLPK4.js").then(t=>t.default)}))}var yi=j("WalkTabixSyntenyAdapter",{assemblyNames:{type:"stringArray",defaultValue:[]},walksLocation:N("/path/to/graph.walks.bed.gz"),walksIndex:_("WalkTabixWalksIndex"),walkStepBudget:{type:"integer",defaultValue:ke.stepBudget},walkByteBudget:{type:"integer",defaultValue:ke.byteBudget},defaultHaplotypes:{type:"stringArray",defaultValue:[]},samplesTsvLocation:N(""),assemblyNameToPanSN:{type:"frozen",defaultValue:{}}},{explicitlyTyped:!0,preProcessSnapshot:Oe}),ua=yi;function to(e){e.addAdapterType(()=>new te({name:"WalkTabixSyntenyAdapter",displayName:"Walk-indexed graph adapter",configSchema:ua,adapterCapabilities:["getSubgraph","headerLanes","lanePairsOnAnchor","lanePairBatches"],adapterMetadata:{category:"Synteny adapters"},getAdapterClass:()=>import("./chunks/WalkTabixSyntenyAdapter-N5PFI4LS.js").then(t=>t.default)}))}var bi=new Set(["RgfaTabixAdapter","GbzBaseSyntenyAdapter"]);function wi(e){return lt(e).toLowerCase().endsWith(".gbz.db")}function fi(e){let t=e.adapter;return t?.type!==void 0&&Xr.has(t.type)&&!t.assemblyNames?.length&&Array.isArray(e.assemblyNames)&&e.assemblyNames.length>0?{...e,adapter:{...t,assemblyNames:e.assemblyNames}}:e}function Mi(e){let t=e.adapter,[o]=Array.isArray(e.assemblyNames)?e.assemblyNames:[],r=t?.type==="RgfaTabixAdapter"&&t.walksLocation?Lo(t.walksLocation):void 0;return o&&r&&r!==o&&t?.assemblyNameToPanSN===void 0?{...e,adapter:{...t,assemblyNameToPanSN:{[o]:r}}}:e}function ki(e,t,o){let r=n=>Ho({choice:n,loc:e,indexLoc:t,assembly:"",sample:""});if((!o||o==="GbzBaseSyntenyAdapter")&&wi(e))return r("GbzBaseSyntenyAdapter");if(!o||o==="RgfaTabixAdapter"){if(Vo(e))return r("RgfaTabixAdapter");if(lt(e).endsWith(Go)&&(t!==void 0||Po(e)))return r("RgfaTabixWalks")}}function oo(e){e.addToExtensionPoint("Core-preProcessTrackConfig",fi),e.addToExtensionPoint("Core-preProcessTrackConfig",Mi),e.addToExtensionPoint("Core-guessAdapterForLocation",t=>(o,r,n)=>ki(o,r,n)??t(o,r,n)),e.addToExtensionPoint("Core-guessTrackTypeForLocation",t=>(o,r)=>bi.has(o)?"GraphTrack":t(o,r))}function da(e){let t;if(z(e)){let{refName:o,start:r,end:n,assemblyName:a}=e;typeof o=="string"&&typeof r=="number"&&typeof n=="number"&&(t={refName:o,start:r,end:n,assemblyName:typeof a=="string"?a:void 0})}return t}function Si(e,t,o){let r=e.connectedViewId;return r===void 0||r===t||!o.has(r)}function ma(e,t){return e.assemblyName===void 0||t===void 0||t.includes(e.assemblyName)}function xi(e){return(Array.isArray(e.tracks)?e.tracks:[]).flatMap(o=>z(o)&&Array.isArray(o.displays)?o.displays.filter(r=>z(r)&&r.type==="LinearGraphDisplay"):[])}function la(e,t,o){let r=[],n=$e(e),a=new Set(n.map(i=>z(i)?i.id:void 0));for(let i of n){if(z(i)&&i.id===t)for(let s of xi(i)){let p=da(s.hoverHighlight);p&&ma(p,o)&&r.push({key:typeof s.id=="string"?s.id:"graph-track",region:p})}if(z(i)&&i.type==="GraphGenomeView"&&Si(i,t,a)){let s=da(i.hoverHighlight);s&&ma(s,o)&&r.push({key:typeof i.id=="string"?i.id:"graph",region:s})}}return r}var Ri=nn()(e=>({highlight:{height:"100%",position:"absolute",background:De(e.palette.primary.main,.08),borderLeft:`1px solid ${De(e.palette.primary.main,.4)}`,borderRight:`1px solid ${De(e.palette.primary.main,.4)}`,pointerEvents:"none",zIndex:10}})),Ti=bt(function({model:t,region:o}){let{classes:r}=Ri(),n=t.getHighlightCoords(o);return n?A("div",{"data-testid":"graph-node-highlight",className:r.highlight,style:{left:n.left,width:n.width}}):null}),Gi=bt(function({model:t}){let{views:o}=x(t);return A(fo,{children:la([...o],t.id,t.assemblyNames).map(({key:r,region:n})=>A(Ti,{model:t,region:n},`graph-hover-${r}`))})}),ga=Gi;var Li="LinearGenomeView-TracksContainerComponent";function ro(e){e.contributeToExtensionPoint(Li,({model:t})=>A(ga,{model:t},"graphgenomeview-hover-highlight"))}function vi(e){return e.views(t=>({get adapterConfig(){return Kr(t,t.parentTrack.configuration)}}))}function no(e){e.addToExtensionPoint("Core-extendPluggableElement",t=>(t instanceof mn&&Yt.includes(t.name)&&t.extendStateModel(vi),t))}var ha="GraphGenomeView";var ya="7.4.2";var ao=class extends pn{constructor(){super(...arguments);this.name=ha;this.version=ya}install(o){Jt(o),Zt(o),Ut(o),Xt(o),ro(o),eo(o),Qt(o),Et(o),to(o),Ht(o),oo(o),no(o),o.addRpcMethod(()=>new Ve(o)),o.addRpcMethod(()=>new Ee(o)),o.addRpcMethod(()=>new Ne(o)),o.addRpcMethod(()=>new Ie(o))}configure(o){try{yo(o.rootModel)&&o.rootModel.appendToSubMenu(["Add"],{label:"Graph genome view",icon:Qe,onClick:r=>{r.addView("GraphGenomeView",{})}})}catch(r){console.warn("[GraphGenomeView] could not add the Add menu entry",r)}}};export{ao as default};
+`);return[{type:"radio",label:"Every sample",checked:o===void 0,onClick:()=>{e.setWalkRowSamples(void 0)}},...t.length>0?[{type:"radio",label:"Where walk and call disagree",checked:r(t),onClick:()=>{e.setWalkRowSamples(t)}}]:[],{type:"radio",label:"Choose samples...",checked:o!==void 0&&!r(t),onClick:()=>{R(e).queueDialog(n=>[sr,{model:e,onClose:n}])}}]},walkRowGroupMenuItems(){let t=e.walkRowGroups?e.walkRowGroupBy?.field:void 0;return Z([{value:void 0,label:"None"},...e.walkRowGroupFields.map(o=>({value:o,label:o}))],t,o=>{e.setWalkRowGroupBy(o===void 0?void 0:{field:o})})},tubeMapPanelMenuItems(){let{graph:t,walkRowSampleTable:o}=e,{field:r}=e.facetSetting,n=r===""?e.walkRowGroupBy?.field:void 0,a=i=>!!t&&Xe(t,i).length>1;return[...Z(jr.map(i=>({value:i.field,label:i.label,disabled:i.field!==""&&!a({by:i.field})})),n?void 0:r,i=>{e.setFacet(i),i===""&&e.setWalkRowGroupBy(void 0)}),...Z(e.walkRowGroupFields.map(i=>({value:i,label:`By ${i}`,disabled:!o||!a({by:"column",field:i,table:o})})),n,i=>{e.setFacet(""),e.setWalkRowGroupBy({field:i})})]},layoutOptionMenuItems({repeat:t=!0}={}){return[...pe.has(e.chosenLayoutMode)?[{label:"Fold variants",subMenu:Z(dr.map(({bp:o,label:r})=>({value:o,label:r,disabled:o>0&&e.graph?.reads!==void 0})),e.graph?.reads?0:e.tubeMapFold,e.setTubeMapFold)},{label:"Panels",subMenu:this.tubeMapPanelMenuItems()},{label:"Routes",subMenu:Z(gr,e.tubeMapRoutes,e.setTubeMapRoutes)},...e.walkRowGroupFields.length>0?[{label:"Tube color",subMenu:Z(["",...e.walkRowGroupFields].map(o=>({value:o,label:o?`By ${o}`:"By role"})),e.tubeMapColorBy,e.setTubeMapColorBy)}]:[]]:[],...t&&e.chosenLayoutMode==="walkrows"&&e.repeatChoices.length>0?[{label:"Repeat",subMenu:Z(e.repeatOptions,e.selectedRepeat?.key??"",e.setRepeatKey)}]:[],...e.chosenLayoutMode==="walkrows"&&e.walkRowBars?[{label:"Samples",subMenu:this.walkRowSampleMenuItems()}]:[],...e.chosenLayoutMode==="walkrows"&&e.walkRowBars&&e.walkRowGroupFields.length>0?[{label:"Group by...",subMenu:this.walkRowGroupMenuItems()}]:[]]},showMenuItems(){let t=(o,r)=>({type:"checkbox",label:o,checked:e.layerSet.has(r),onClick:()=>{e.setLayer(r,!e.layerSet.has(r))}});return[t("Show bubble halos","bubbles"),t("Show deletion edges","deletions"),{label:"Hover highlight",subMenu:Z(Ge.map(o=>({value:o,label:o[0].toUpperCase()+o.slice(1)})),e.chosenHover,e.setHover)},t("Show genes on the backbone","genes"),...e.referenceStripApplies?[t("Show reference strip","referenceStrip")]:[]]},exportMenuItems(){return[{label:"Export SVG",icon:Tn,disabled:e.figureUnavailable!==void 0,disabledHelpText:e.figureUnavailable,onClick:()=>{let t=e.figure();t&&Un(t,`${(e.graph?.name??"graph").replaceAll(/[^\w.-]+/g,"_")}.svg`)}},{label:"Copy figure spec",icon:Sn,disabled:e.figureSpecUnavailable!==void 0,disabledHelpText:e.figureSpecUnavailable,onClick:()=>{let t=e.figureSpec(),o=R(e);navigator.clipboard.writeText(`${JSON.stringify(t,null,2)}
+`).then(()=>{o.notify("Figure spec copied. Save it as spec.json and run: npx -p @jbrowse/bandage-core bandage-figure spec.json -o figure.svg","info")}).catch(r=>{o.notify(`Could not copy the figure spec: ${String(r)}`)})}}]},highlightMenuItems({picks:t=!0}={}){let o=t?e.walkChoices:[];if(e.walkChoices.length===0||!e.liftsWalks||!t&&e.walkLayers.length===0)return[];let r=a=>e.walkLayers.some(i=>i.walk===a),n=o.length>ur;return[{type:"subHeader",label:"Highlight"},...n?[{label:"Choose haplotypes...",onClick:()=>{R(e).queueDialog(a=>[pr,{model:e,onClose:a}])}}]:[],...(n?o.filter(a=>r(a.name)):o).map(a=>({type:"checkbox",label:a.label,checked:r(a.name),onClick:()=>{e.toggleWalk(a.name)}})),{label:"Clear highlights",disabled:e.walkLayers.length===0,onClick:()=>{e.setWalkLayers([])}},...e.drawnWalks.length>0?[{label:"Color highlighted...",onClick:()=>{R(e).queueDialog(a=>[cr,{model:e,onClose:a}])}}]:[],...e.walkLayers.length>1&&e.modeDrawsNodes?[{type:"subHeader",label:"Arrange"},...Z(er.map(({value:a,label:i})=>({value:a,label:a==="walk"?"A panel per haplotype":i})),e.facetSetting.field,e.setFacet)]:[]]},colorSchemeLabel(t){let o=Lt.find(r=>r.value===t)?.label??t;return t==="auto"?`${o} (${this.colorSchemeLabel(e.effectiveColorScheme)})`:o},graphMenuItems(){let t=this.layoutOptionMenuItems(),o=O(e.chosenLayoutMode),r=Xn.find(([n])=>n===e.layoutEngine)[1];return[{label:`Layout: ${$t(o)}${o.value==="force"?` (${r})`:""}`,icon:xn,subMenu:[...Do.flatMap(n=>{let a={type:"radio",disabled:e.graph?!n.available(e.graph):!1,disabledHelpText:n.description};return n.value==="force"?Xn.map(([i,s])=>({...a,label:`${$t(n)} (${s})`,checked:e.chosenLayoutMode===n.value&&e.layoutEngine===i,onClick:()=>{e.switchForceEngine(i)}})):[{...a,label:$t(n),checked:e.chosenLayoutMode===n.value,onClick:()=>{e.switchLayout(n.value)}}]}),...t.length>0?[{type:"divider"},...t]:[],...e.hostPlacesX?[]:[{type:"divider"},{label:"Zoom to fit",onClick:()=>{e.refitView()}}]]},{label:`Color: ${e.colorSchemeLock?.value??this.colorSchemeLabel(e.chosenColorScheme)}`,icon:Rn,disabled:e.colorSchemeLock!==void 0,disabledHelpText:e.colorSchemeLock?.why,subMenu:Z(Lt.map(({value:n})=>({value:n,label:this.colorSchemeLabel(n)})),e.chosenColorScheme,e.setColorScheme)},{label:"Show...",icon:tr,subMenu:this.showMenuItems()}]},launchMenuItems(){let t=[],o=e.launchableAssemblies,r=e.graphRegion?.assemblyName;for(let n of rn({contributors:o,linearContributors:e.host?o.filter(a=>a.sample!==r):o,syntenyTracks:e.syntenyLaunchTracks,onShowLinear:a=>{e.showInLinearView(a)},onShowSynteny:a=>{e.showSyntenyView(a)}}))at(t,n);return t}}));var it=Kn.views(e=>({get trackHaplotypes(){let t=e.sourceAdapter;return t&&Ce(t)}})).views(e=>({get cutHaplotypes(){return e.subgraphHaplotypes??e.trackHaplotypes},offReference(t){let o=e.sourceTrack,r=o&&Uo(o),n=R(e);return r===void 0?void 0:Xo(Be(n,r),Be(n,t.assemblyName))},cutChangedFrom(t){let o=zo(O(t),{walkStrip:e.walkStrip,host:!!e.host});return e.cutsWholeWalks!==o||t==="walkrows"!=(e.chosenLayoutMode==="walkrows")}})).views(e=>({get cutOptions(){return{hops:e.subgraphContext,haplotypes:e.cutHaplotypes,...e.chosenLayoutMode==="walkrows"?{walkRows:!0}:{},...e.cutsWholeWalks?{snarls:"overlapping"}:{},...e.expandedWalks.length>0?{expand:e.expandedWalks}:{}}}}));function Jt(){return M.compose("GraphGenomeView",kn,it,M.model({type:M.literal("GraphGenomeView"),gfaLocation:M.maybe(M.frozen()),loadedRegion:M.maybe(M.frozen()),loadedTrackId:M.optional(M.string,""),layoutMode:xt($e),color:M.maybe(M.frozen()),size:M.maybe(M.frozen()),layers:M.maybe(M.frozen()),facet:M.maybe(M.frozen()),rows:M.maybe(M.frozen()),hover:xt(Ge)})).views(e=>({get grammar(){return{layoutMode:e.layoutMode,color:e.color,size:e.size,layers:e.layers,facet:e.facet,rows:e.rows,hover:e.hover}}})).actions(e=>({writeGrammar(t){Object.assign(e,t)}})).volatile(()=>({widthMeasured:!1})).actions(e=>{let t=e.setWidth;return{setWidth(o){t(o),e.widthMeasured=!0}}}).views(e=>({get rpcSessionId(){return e.id},get paneWidth(){return e.width},get paneMeasured(){return e.widthMeasured},get sourceGfaLocation(){return e.gfaLocation},get sourceTrack(){return e.loadedTrackId?e.sessionTrack(e.loadedTrackId):void 0},get canRetryLoad(){return e.gfaLocation!==void 0||e.loadedTrackId!==""&&e.loadedRegion!==void 0}})).views(e=>({get hasPendingSource(){return e.canRetryLoad&&!e.graph&&!e.loadCanceled},menuItems(){return[...e.exportMenuItems(),...e.launchMenuItems()]}})).actions(e=>{let t=e.clearGraph;function o(r){if(e.gfaLocation)return e.displayName||e.setDisplayName(ue(e.gfaLocation)),e.loadGFAFromLocation(e.gfaLocation,r);if(!e.loadedTrackId||!r)return;let n=e.sourceAdapter,a=r.end-r.start,i=e.offReference(r);if(!n)e.setError(new Error(`The track this graph was cut from, "${e.loadedTrackId}", is not in this session`));else if(i)e.setError(new Error(i));else if(a>e.maxRegionBp)e.setError(new Error(`Region too large (${ce(a)}) \u2014 zoom in to view graph (max ${ce(e.maxRegionBp)})`));else return e.cutSubgraph(n,r,e.cutOptions)}return{clearGraph(){t(),e.gfaLocation&&e.displayName===ue(e.gfaLocation)&&(e.displayName=void 0),e.gfaLocation=void 0,e.loadedRegion=void 0,e.loadedTrackId=""},load(){let r=e.loadedRegion,n=R(e),{assemblyManager:a}=n,i=r&&a.has(r.assemblyName)?a.get(r.assemblyName):void 0;return r&&i?.initialized===!1?a.waitForAssembly(r.assemblyName).catch(()=>{}).then(()=>e.loadedRegion===r?o(Gt(n,r)):void 0):o(r&&Gt(n,r))}}}).actions(e=>({retryLoad(){e.load()},setGfaLocation(t){e.gfaLocation=t},relayoutFrom(t){return e.loadedTrackId&&e.cutChangedFrom(t)?e.load():e.recomputeLayout()},async openGfaLocation(t){await e.loadGFAFromLocation(t),j(e)&&e.hasGraph&&(this.setGfaLocation(t),e.displayName||e.setDisplayName(ue(t)))},afterAttach(){e.graph||e.load(),A(e,I(()=>e.walkStrip,()=>{e.loadedTrackId&&!O(e.chosenLayoutMode).wholeWalks&&e.load()}))}}))}var ri=Mn()({});function Yt(e){e.addViewType(()=>new wn({name:"GraphGenomeView",displayName:"Graph genome view",stateModel:Jt(),launchKeys:ri,ReactComponent:te(()=>import("./chunks/GraphGenomeView-P3XMSKUQ.js"))}))}var Ut=["MultiWaySyntenyDisplay","LinearSyntenyDisplay","DotplotDisplay","ChordSyntenyDisplay"];function ni(e){let t=e.getElementTypesInGroup("display"),o=n=>t.find(a=>a.name===n),r=n=>n&&Object.assign(Object.create(n),{adapterCapabilities:["headerLanes"]});return[o("LinearGraphDisplay"),o("LinearBasicDisplay"),...Ut.map(n=>r(o(n)))].filter(n=>n!==void 0)}function Xt(e){e.addTrackType(()=>{let t=W("GraphTrack",{},{baseConfiguration:hn(e),explicitIdentifier:"trackId"}),o=new gn({name:"GraphTrack",displayName:"Pangenome graph track",configSchema:t,stateModel:yn(e,"GraphTrack",t)});for(let r of ni(e))o.addDisplayType(r);return o})}function Kt(e){e.addToExtensionPoint("LaunchView-GraphGenomeView",t=>{let{session:o,...r}=t;return o.addView("GraphGenomeView",r),t})}var st=JBrowseExports["@jbrowse/core/pluggableElementTypes/DisplayType"];var qn=st&&st.__esModule?st.default:st;var be=JBrowseExports["@jbrowse/display-kit/trackHeightConfigSchemaFields"],ai=e=>be!=null&&e in Object(be)?be[e]:Object.assign(function(){throw new Error("This JBrowse does not provide '"+e+"' from '@jbrowse/display-kit/trackHeightConfigSchemaFields' to plugins: GraphGenomeView was built for a different JBrowse version, so update the plugin or JBrowse")},{jbrowseHostMissing:e}),Zn=ai("trackHeightConfigSchemaFields"),tm=be&&be.__esModule?be.default:be;function Qn(){return W("LinearGraphDisplay",{layoutMode:{type:"stringEnum",model:M.enumeration("LayoutMode",$e),defaultValue:"auto"},color:{type:"frozen",defaultValue:{},plot:!0},size:{type:"frozen",defaultValue:{field:"depth",value:6},plot:!0},layers:{type:"frozen",defaultValue:{},plot:!0},facet:{type:"frozen",defaultValue:{},plot:!0},rows:{type:"frozen",defaultValue:{},plot:!0},hover:{type:"stringEnum",model:M.enumeration("HoverHighlight",Ge),defaultValue:"nodes"},...Zn({defaultHeight:300,height:"the height of the track the graph is drawn in"})},{explicitlyTyped:!0,explicitIdentifier:"displayId"})}var fe=JBrowseExports["@jbrowse/core/svg/svgReady"],ii=e=>fe!=null&&e in Object(fe)?fe[e]:Object.assign(function(){throw new Error("This JBrowse does not provide '"+e+"' from '@jbrowse/core/svg/svgReady' to plugins: GraphGenomeView was built for a different JBrowse version, so update the plugin or JBrowse")},{jbrowseHostMissing:e});var ea=ii("computeSvgReady");var cm=fe&&fe.__esModule?fe.default:fe;var pt=JBrowseExports["@jbrowse/display-kit/TrackHeightMixin"];var ta=pt&&pt.__esModule?pt.default:pt;var we=JBrowseExports["@jbrowse/display-kit/plotMenu"],si=e=>we!=null&&e in Object(we)?we[e]:Object.assign(function(){throw new Error("This JBrowse does not provide '"+e+"' from '@jbrowse/display-kit/plotMenu' to plugins: GraphGenomeView was built for a different JBrowse version, so update the plugin or JBrowse")},{jbrowseHostMissing:e}),oa=si("editPlotMenuItems");var mm=we&&we.__esModule?we.default:we;var Me=JBrowseExports["@jbrowse/render-core/displayPhase"],ra=e=>Me!=null&&e in Object(Me)?Me[e]:Object.assign(function(){throw new Error("This JBrowse does not provide '"+e+"' from '@jbrowse/render-core/displayPhase' to plugins: GraphGenomeView was built for a different JBrowse version, so update the plugin or JBrowse")},{jbrowseHostMissing:e}),na=ra("computeActivityPhase");var aa=ra("computeDisplayStatusPhase"),gm=Me&&Me.__esModule?Me.default:Me;function qt(e,t){if(e?.refName!==t.refName||e.assemblyName!==t.assemblyName)return!1;let o=e.end-e.start;return t.end-t.start>=o&&t.end>e.start-o&&t.start<e.end+o}var pi=new Set(["scale","translateX","translateY"]);function ci(e){return Object.fromEntries(Object.keys(yr.properties).filter(t=>!pi.has(t)).map(t=>[t,e[t]]))}var Zt=10;function ui(e){let{aboveBpPerPx:t,foldBelowBp:o}=e??{};return typeof t=="number"?t:typeof o=="number"&&o>0?o/Zt:void 0}var di=te(()=>import("./chunks/GraphTrackSettingsDialog-UTYH6HEC.js"));function ia(e){return M.compose("LinearGraphDisplay",dn,ta(),it,M.model({type:M.literal("LinearGraphDisplay"),configuration:xo(e),layoutEngine:_o(Fo,"stress"),cutRegion:M.maybe(M.frozen()),coarseCut:M.optional(M.boolean,!1)})).volatile(()=>({recuts:0,settledWindow:void 0,dense:void 0,haplotypeNames:void 0,cutFoldBp:0})).views(t=>({get grammar(){return{layoutMode:Q(t,"layoutMode"),color:Q(t,"color"),size:Q(t,"size"),layers:Q(t,"layers"),facet:Q(t,"facet"),rows:Q(t,"rows"),hover:Q(t,"hover")}},get drawsGenomicCoordinates(){return t.layoutResult===void 0||t.hostPlacesX},get canvasHeight(){return t.height},get canRetryLoad(){return t.cutRegion!==void 0},get trackHaplotypes(){let o=t.sourceAdapter,r=t.sourceTrack;return(o&&Ce(o))??(r&&Rt(r))},get coarseAboveBpPerPx(){return ui(t.sourceAdapter?.coarse)}})).views(t=>({tierAt(o){let r=t.coarseAboveBpPerPx;return r!==void 0&&o>r?"coarse":"fine"},capFor(o){return o==="coarse"?1/0:t.maxRegionBp},foldDrifted(o){let r=Zt*o,n=t.cutFoldBp;return!t.graph?.paths?.length&&(r>=2*Math.max(n,1)||t.foldedBelowBp!==void 0&&r<=n/2)},get cutTier(){return t.coarseCut&&t.coarseAboveBpPerPx!==void 0?"coarse":"fine"}})).views(t=>({get settledCapBp(){let o=t.settledWindow;return o?t.capFor(t.tierAt(o.bpPerPx)):1/0}})).views(t=>({get regionTooLarge(){let o=t.settledWindow;return o!==void 0&&o.end-o.start>t.settledCapBp},get regionTooLargeReason(){let o=t.settledWindow;return o?`Region too large for a graph cut (${ce(o.end-o.start)}, max ${ce(t.settledCapBp)})`:""},get zoomCanReleaseGate(){return!0},get fetchCanceled(){return t.loadCanceled}})).views(t=>({get svgReady(){return ea({error:t.error,regionTooLarge:t.regionTooLarge,extraTerminal:!1,fetchCanceled:t.loadCanceled},()=>!t.isLoading&&t.hasGraph&&!!t.layoutResult)}})).views(t=>({get displayPhase(){return aa({regionTooLarge:t.regionTooLarge,error:t.error??t.renderError},()=>na({isMinimized:t.isMinimized,fetchInert:!1,viewportEmpty:t.host?.initialized===!0&&t.host.hasVisibleContent===!1,isLoading:t.isLoading||!t.hasGraph,fetchCanceled:t.loadCanceled,awaitingDependentData:!1,rendersCanvas:!0,canvasDrawn:t.painted&&t.geometryPainted},()=>!0,()=>t.host?.effectiveBodyMounted??!0))}})).actions(t=>({writeGrammar(o){for(let[r,n]of Object.entries(o))Ro(t,r,n)},setSubgraphContext(o){t.subgraphContext=o,t.dense=void 0},setSubgraphHaplotypes(o){t.subgraphHaplotypes=o,t.dense=void 0},setDense(o){t.dense=o},setHaplotypeNames(o){t.haplotypeNames=o},setMaxRegionBp(o){t.maxRegionBp=o},cut(){let o=t.cutRegion,r=t.sourceAdapter;if(!o||!r)return;let n=t.offReference(o);if(n){t.clearGraph(),t.setError(new Error(n));return}let a=t.cutTier==="coarse";return t.cutFoldBp=Math.round(Zt*(t.settledWindow?.bpPerPx??t.host?.bpPerPx??0)),t.cutSubgraph(r,o,{...t.cutOptions,tier:a?"coarse":void 0},t.cutFoldBp)}})).actions(t=>({recutAt(o){let r=t.tierAt(o.bpPerPx);return t.coarseCut=r==="coarse",t.cutRegion=Yr(o,t.capFor(r),O(t.chosenLayoutMode).cutMargins),t.recuts++,t.cut()}})).actions(t=>({settleOn(o){t.settledWindow=o;let r=O(t.chosenLayoutMode).cutMargins;if(t.regionTooLarge||qt(t.dense,o)||!t.loadCanceled&&t.tierAt(o.bpPerPx)===t.cutTier&&Ur(t.cutRegion,o,r)&&!t.foldDrifted(o.bpPerPx))return!1;let n=t.recutAt(o),a=t.recuts;return Promise.resolve(n).then(()=>{j(t)&&t.recuts===a&&wt(t.error)&&this.refuseDenseCut(o)}),!0},refuseDenseCut(o){t.setDense(o),t.cutRegion=void 0,this.settleOn(t.settledWindow??o)},recut(){t.cutRegion?t.cut():t.settledWindow&&this.settleOn(t.settledWindow)},relayoutFrom(o){let r=t.host?Ke(t.host):void 0;return r&&!t.regionTooLarge&&(t.cutChangedFrom(o)||O(o).cutMargins!==O(t.chosenLayoutMode).cutMargins)?t.recutAt(r):t.recomputeLayout()},retryLoad(){t.cut()},reload(){t.cut()},cancelFetchByUser(){t.stopLoad()}})).actions(t=>({async fetchHaplotypeNames(o,r){try{let n=await R(t).rpcManager.call(ie(t),"GetGraphHaplotypes",{adapterConfig:o,signal:r});j(t)&&!r?.aborted&&t.setHaplotypeNames(n)}catch(n){r?.aborted||console.warn("[LinearGraphDisplay] no haplotype names",n)}}})).actions(t=>({stretchWithHost(o,r){let n=t.layoutBounds;if(!n||!t.followsHostView)return;t.viewportOwner==="fit"&&(t.viewportOwner="user");let a=o.bpPerPx/r.bpPerPx,i=t.translateY+t.scaleY*(n.minY+n.h/2);t.scale*=a,t.translateX=a*(t.translateX+o.offsetPx)-r.offsetPx,t.translateY=i-a*(i-t.translateY)}})).actions(t=>({forceLoad(){let o=t.settledWindow;o&&(t.setMaxRegionBp(Math.ceil(o.end-o.start)),t.settleOn(o))},afterAttach(){t.cutRegion&&!t.graph&&t.cut();let o;A(t,()=>{o?.abort()}),A(t,I(()=>{let n=t.sourceAdapter;return n&&Jo(n)?n:void 0},n=>{o?.abort(),o=void 0,t.setHaplotypeNames(void 0),n&&(o=new 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graph",checked:s?s.length===0:!n&&!a,onClick:()=>{p([])}},...n||a?[{type:"radio",label:n?"The track's default haplotypes":`The track's ${a?.length} assemblies`,checked:s===void 0,onClick:()=>{p(void 0)}}]:[],{type:"radio",label:"Chosen in Graph settings...",checked:(s?.length??0)>0,onClick:()=>{this.openSettings()}}]},openSettings(){R(t).queueDialog(o=>[di,{model:t,onClose:o}])},async renderSvg(o){let{renderGraphTrackSvg:r}=await import("./chunks/renderSvg-7G6NWBXF.js");return r(t,o)},trackMenuItems(){let o=t.launchMenuItems();at(o,{label:"Graph genome view",icon:et,disabled:!t.graphViewSpec,disabledHelpText:t.error&&!wt(t.error)?"The track could not cut a graph here":t.isLoading&&!t.hasGraph?"The track is still cutting its graph":"Zoom in until the track cuts a graph",onClick:()=>{t.openGraphView()}});let r=[...this.cutMenuItems(),...t.highlightMenuItems()];return[...r.length>0?[{label:"Haplotypes",icon:an,subMenu:r}]:[],...t.graphMenuItems(),{label:"Graph settings...",icon:sn,helpText:"Subgraph, drawing and force-directed layout",onClick:()=>{this.openSettings()}},...o,...oa(t)]}}))}function Qt(e){e.addDisplayType(()=>{let t=Qn();return Object.assign(new qn({name:"LinearGraphDisplay",displayName:"Graph",configSchema:t,stateModel:ia(t),trackType:["GraphTrack","FeatureTrack","SyntenyTrack"],viewType:"LinearGenomeView",ReactComponent:te(()=>import("./chunks/LinearGraphDisplay-O4SQSXJJ.js"))}),{adapterCapabilities:["getSubgraph"]})})}function mi(e){let{uri:t,baseUri:o,csi:r}=e;return typeof t=="string"?{...e,bubblesLocation:{uri:t,baseUri:o},index:ve(t,o,r)}:e}var li=W("MinigraphBubbleAdapter",{bubblesLocation:E("/path/to/graph.bb.bed.gz"),index:$("MinigraphBubbleIndex","/path/to/graph.bb.bed.gz.tbi"),assemblyNameToPanSN:{type:"frozen",defaultValue:{}}},{explicitlyTyped:!0,preProcessSnapshot:mi}),sa=li;function eo(e){e.addAdapterType(()=>new oe({name:"MinigraphBubbleAdapter",displayName:"Minigraph bubble BED adapter",configSchema:sa,adapterMetadata:{category:"Graph adapters"},getAdapterClass:()=>import("./chunks/MinigraphBubbleAdapter-3NJ2VLN2.js").then(t=>t.default)}))}function pa(e){let{uri:t,baseUri:o,csi:r}=e;return typeof t=="string"?{...e,segmentsLocation:{uri:`${t}.segs.bed.gz`,baseUri:o},segmentsIndex:ve(`${t}.segs.bed.gz`,o,r),linksLocation:{uri:`${t}.links.bed.gz`,baseUri:o},linksIndex:ve(`${t}.links.bed.gz`,o,r)}:e}function gi(e){let{coarse:t,baseUri:o,csi:r}=e;return We(pa(typeof t=="object"&&t!==null?{...e,coarse:pa({baseUri:o,csi:r,...t})}:e))}var hi=W("RgfaTabixCoarseTier",{aboveBpPerPx:{type:"maybeNumber"},foldBelowBp:{type:"maybeNumber"},segmentsLocation:E("/path/to/graph.tier.segs.bed.gz"),segmentsIndex:$("RgfaCoarseSegmentsIndex","/path/to/graph.tier.segs.bed.gz.tbi"),linksLocation:E("/path/to/graph.tier.links.bed.gz"),linksIndex:$("RgfaCoarseLinksIndex","/path/to/graph.tier.links.bed.gz.tbi")}),yi=W("RgfaTabixAdapter",{segmentsLocation:E("/path/to/graph.segs.bed.gz"),segmentsIndex:$("RgfaSegmentsIndex","/path/to/graph.segs.bed.gz.tbi"),linksLocation:E("/path/to/graph.links.bed.gz"),linksIndex:$("RgfaLinksIndex","/path/to/graph.links.bed.gz.tbi"),walksLocation:E(""),walksIndex:$("RgfaWalksIndex"),walkStepBudget:{type:"integer",defaultValue:xe.stepBudget},walkByteBudget:{type:"integer",defaultValue:xe.byteBudget},defaultHaplotypes:{type:"stringArray",defaultValue:[]},assemblyNameToPanSN:{type:"frozen",defaultValue:{}},coarse:hi},{explicitlyTyped:!0,preProcessSnapshot:gi}),ca=yi;function to(e){e.addAdapterType(()=>new oe({name:"RgfaTabixAdapter",displayName:"Indexed rGFA adapter",configSchema:ca,adapterCapabilities:["getSubgraph"],adapterMetadata:{category:"Graph adapters"},getAdapterClass:()=>import("./chunks/RgfaTabixAdapter-55DGDID2.js").then(t=>t.default)}))}var bi=W("WalkTabixSyntenyAdapter",{assemblyNames:{type:"stringArray",defaultValue:[]},walksLocation:E("/path/to/graph.walks.bed.gz"),walksIndex:$("WalkTabixWalksIndex"),walkStepBudget:{type:"integer",defaultValue:xe.stepBudget},walkByteBudget:{type:"integer",defaultValue:xe.byteBudget},defaultHaplotypes:{type:"stringArray",defaultValue:[]},samplesTsvLocation:E(""),assemblyNameToPanSN:{type:"frozen",defaultValue:{}}},{explicitlyTyped:!0,preProcessSnapshot:We}),ua=bi;function oo(e){e.addAdapterType(()=>new oe({name:"WalkTabixSyntenyAdapter",displayName:"Walk-indexed graph adapter",configSchema:ua,adapterCapabilities:["getSubgraph","headerLanes","lanePairsOnAnchor","lanePairBatches"],adapterMetadata:{category:"Synteny adapters"},getAdapterClass:()=>import("./chunks/WalkTabixSyntenyAdapter-NHNSZZBX.js").then(t=>t.default)}))}var fi=new Set(["RgfaTabixAdapter","GbzBaseSyntenyAdapter"]);function wi(e){return gt(e).toLowerCase().endsWith(".gbz.db")}function Mi(e){let t=e.adapter;return t?.type!==void 0&&Xr.has(t.type)&&!t.assemblyNames?.length&&Array.isArray(e.assemblyNames)&&e.assemblyNames.length>0?{...e,adapter:{...t,assemblyNames:e.assemblyNames}}:e}function ki(e){let t=e.adapter,[o]=Array.isArray(e.assemblyNames)?e.assemblyNames:[],r=t?.type==="RgfaTabixAdapter"&&t.walksLocation?Lo(t.walksLocation):void 0;return o&&r&&r!==o&&t?.assemblyNameToPanSN===void 0?{...e,adapter:{...t,assemblyNameToPanSN:{[o]:r}}}:e}function Si(e,t,o){let r=n=>Ho({choice:n,loc:e,indexLoc:t,assembly:"",sample:""});if((!o||o==="GbzBaseSyntenyAdapter")&&wi(e))return r("GbzBaseSyntenyAdapter");if(!o||o==="RgfaTabixAdapter"){if(Vo(e))return r("RgfaTabixAdapter");if(gt(e).endsWith(Go)&&(t!==void 0||Po(e)))return r("RgfaTabixWalks")}}function ro(e){e.addToExtensionPoint("Core-preProcessTrackConfig",Mi),e.addToExtensionPoint("Core-preProcessTrackConfig",ki),e.addToExtensionPoint("Core-guessAdapterForLocation",t=>(o,r,n)=>Si(o,r,n)??t(o,r,n)),e.addToExtensionPoint("Core-guessTrackTypeForLocation",t=>(o,r)=>fi.has(o)?"GraphTrack":t(o,r))}function da(e){let t;if(J(e)){let{refName:o,start:r,end:n,assemblyName:a}=e;typeof o=="string"&&typeof r=="number"&&typeof n=="number"&&(t={refName:o,start:r,end:n,assemblyName:typeof a=="string"?a:void 0})}return t}function xi(e,t,o){let r=e.connectedViewId;return r===void 0||r===t||!o.has(r)}function ma(e,t){return e.assemblyName===void 0||t===void 0||t.includes(e.assemblyName)}function Ri(e){return(Array.isArray(e.tracks)?e.tracks:[]).flatMap(o=>J(o)&&Array.isArray(o.displays)?o.displays.filter(r=>J(r)&&r.type==="LinearGraphDisplay"):[])}function la(e,t,o){let r=[],n=Je(e),a=new Set(n.map(i=>J(i)?i.id:void 0));for(let i of n){if(J(i)&&i.id===t)for(let s of Ri(i)){let p=da(s.hoverHighlight);p&&ma(p,o)&&r.push({key:typeof s.id=="string"?s.id:"graph-track",region:p})}if(J(i)&&i.type==="GraphGenomeView"&&xi(i,t,a)){let s=da(i.hoverHighlight);s&&ma(s,o)&&r.push({key:typeof i.id=="string"?i.id:"graph",region:s})}}return r}var Ti=nn()(e=>({highlight:{height:"100%",position:"absolute",background:_e(e.palette.primary.main,.08),borderLeft:`1px solid ${_e(e.palette.primary.main,.4)}`,borderRight:`1px solid ${_e(e.palette.primary.main,.4)}`,pointerEvents:"none",zIndex:10}})),Gi=ft(function({model:t,region:o}){let{classes:r}=Ti(),n=t.getHighlightCoords(o);return n?C("div",{"data-testid":"graph-node-highlight",className:r.highlight,style:{left:n.left,width:n.width}}):null}),Li=ft(function({model:t}){let{views:o}=R(t);return C(wo,{children:la([...o],t.id,t.assemblyNames).map(({key:r,region:n})=>C(Gi,{model:t,region:n},`graph-hover-${r}`))})}),ga=Li;var vi="LinearGenomeView-TracksContainerComponent";function no(e){e.contributeToExtensionPoint(vi,({model:t})=>C(ga,{model:t},"graphgenomeview-hover-highlight"))}function Ai(e){return e.views(t=>({get adapterConfig(){return Kr(t,t.parentTrack.configuration)}}))}function ao(e){e.addToExtensionPoint("Core-extendPluggableElement",t=>(t instanceof mn&&Ut.includes(t.name)&&t.extendStateModel(Ai),t))}var ha="GraphGenomeView";var ya="7.4.3";var io=class extends pn{constructor(){super(...arguments);this.name=ha;this.version=ya}install(o){Yt(o),Qt(o),Xt(o),Kt(o),no(o),to(o),eo(o),Vt(o),oo(o),Ft(o),ro(o),ao(o),o.addRpcMethod(()=>new Fe(o)),o.addRpcMethod(()=>new He(o)),o.addRpcMethod(()=>new Ve(o)),o.addRpcMethod(()=>new Ee(o))}configure(o){try{yo(o.rootModel)&&o.rootModel.appendToSubMenu(["Add"],{label:"Graph genome view",icon:et,onClick:r=>{r.addView("GraphGenomeView",{})}})}catch(r){console.warn("[GraphGenomeView] could not add the Add menu entry",r)}}};export{io as default};
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