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.
- package/README.md +1 -1
- package/dist/chunks/AddTrackWorkflow-U3UNCVXJ.js +2 -0
- package/dist/chunks/{AddTrackWorkflow-F6FBBEJM.js.map → AddTrackWorkflow-U3UNCVXJ.js.map} +1 -1
- package/dist/chunks/{GbzBaseSyntenyAdapter-3BCUI2JI.js → GbzBaseSyntenyAdapter-AZBYMDIW.js} +5 -5
- package/dist/chunks/{GbzBaseSyntenyAdapter-3BCUI2JI.js.map → GbzBaseSyntenyAdapter-AZBYMDIW.js.map} +3 -3
- package/dist/chunks/{GraphGenomeView-QGJN2S27.js → GraphGenomeView-TJ667XWP.js} +2 -2
- package/dist/chunks/{GraphGenomeView-QGJN2S27.js.map → GraphGenomeView-TJ667XWP.js.map} +1 -1
- package/dist/chunks/GraphTrackSettingsDialog-JVPM25GV.js +4 -0
- package/dist/chunks/{GraphTrackSettingsDialog-LXYUYPZS.js.map → GraphTrackSettingsDialog-JVPM25GV.js.map} +1 -1
- package/dist/chunks/LinearGraphDisplay-ME3WCBV3.js +2 -0
- package/dist/chunks/{LinearGraphDisplay-WPXUCJNR.js.map → LinearGraphDisplay-ME3WCBV3.js.map} +1 -1
- package/dist/chunks/{MinigraphBubbleAdapter-CK7AE4QT.js → MinigraphBubbleAdapter-CZYQROL2.js} +2 -2
- package/dist/chunks/{RgfaTabixAdapter-QPKEJZXA.js → RgfaTabixAdapter-BBWH5IPF.js} +2 -2
- package/dist/chunks/TrackWarningsDialog-HPHM5S7U.js +2 -0
- package/dist/chunks/TrackWarningsDialog-HPHM5S7U.js.map +7 -0
- package/dist/chunks/{chunk-CNFN6EVE.js → chunk-BUXVOMDL.js} +2 -2
- package/dist/chunks/{chunk-LGKM2PZH.js → chunk-E7J6SB5P.js} +1 -1
- package/dist/chunks/{chunk-LGKM2PZH.js.map → chunk-E7J6SB5P.js.map} +1 -1
- package/dist/chunks/chunk-J6KYLXRD.js +2 -0
- package/dist/chunks/chunk-J6KYLXRD.js.map +7 -0
- package/dist/chunks/{chunk-EI5D5NAM.js → chunk-LXG44JKP.js} +2 -2
- package/dist/chunks/{chunk-EI5D5NAM.js.map → chunk-LXG44JKP.js.map} +3 -3
- package/dist/chunks/chunk-S3X3QFQD.js +2 -0
- package/dist/chunks/{chunk-KDIBFGZM.js.map → chunk-S3X3QFQD.js.map} +4 -4
- package/dist/chunks/chunk-TYJTJGPO.js +2 -0
- package/dist/chunks/chunk-TYJTJGPO.js.map +7 -0
- package/dist/chunks/chunk-WJ7SERCV.js +3 -0
- package/dist/chunks/{chunk-I2IONPCZ.js.map → chunk-WJ7SERCV.js.map} +2 -2
- package/dist/chunks/executeDiagonalize-DTKT5PPY.js +2 -0
- package/dist/chunks/{executeDiagonalize-XMPEDHVZ.js.map → executeDiagonalize-DTKT5PPY.js.map} +4 -4
- package/dist/jbrowse-plugin-graphgenomeviewer.esm.js +4 -4
- package/dist/jbrowse-plugin-graphgenomeviewer.esm.js.map +2 -2
- package/package.json +19 -19
- package/src/GetSubgraph.test.ts +1 -0
- package/src/GraphGenomeView/components/WalkStrip.tsx +1 -1
- package/src/GraphGenomeView/model.ts +3 -0
- package/src/panSNTabix.test.ts +1 -1
- package/src/panSNTabix.ts +2 -1
- package/src/synteny/ComparativeAdapterBase.ts +4 -6
- package/src/synteny/clipFeatureToRegion.test.ts +1 -2
- package/src/version.ts +1 -1
- package/dist/chunks/AddTrackWorkflow-F6FBBEJM.js +0 -2
- package/dist/chunks/GraphTrackSettingsDialog-LXYUYPZS.js +0 -4
- package/dist/chunks/LinearGraphDisplay-WPXUCJNR.js +0 -2
- package/dist/chunks/chunk-I2IONPCZ.js +0 -3
- package/dist/chunks/chunk-KDIBFGZM.js +0 -2
- package/dist/chunks/chunk-XEJ47DLD.js +0 -2
- package/dist/chunks/chunk-XEJ47DLD.js.map +0 -7
- package/dist/chunks/executeDiagonalize-XMPEDHVZ.js +0 -2
- /package/dist/chunks/{MinigraphBubbleAdapter-CK7AE4QT.js.map → MinigraphBubbleAdapter-CZYQROL2.js.map} +0 -0
- /package/dist/chunks/{RgfaTabixAdapter-QPKEJZXA.js.map → RgfaTabixAdapter-BBWH5IPF.js.map} +0 -0
- /package/dist/chunks/{chunk-CNFN6EVE.js.map → chunk-BUXVOMDL.js.map} +0 -0
package/README.md
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import{b as F,c as T,i as y}from"./chunk-4T7DPQTR.js";import{a as N}from"./chunk-J4OLMLS5.js";import{a as W}from"./chunk-FCWXYIFC.js";import{a as O}from"./chunk-J6KYLXRD.js";import{a as C,b as B,c as H,d as _}from"./chunk-TYJTJGPO.js";import{a as w,b as t}from"./chunk-FY3BTKY4.js";var S=w((q,L)=>{L.exports=JBrowseExports["@jbrowse/core/util/tss-react"]});var s=t(O(),1),i=t(B(),1),l=t(N(),1),A=t(S(),1),R=t(W(),1),e=t(_(),1),x=t(H(),1);var o=t(C(),1),j=(0,A.makeStyles)()(n=>({paper:{margin:n.spacing(),padding:n.spacing()},field:{marginTop:n.spacing(2)},submit:{marginTop:25,marginBottom:100,display:"block"}})),D=["RgfaTabixAdapter","MinigraphBubbleAdapter"],J=(0,x.observer)(function({model:r}){let{classes:c}=j(),h=(0,l.getSession)(r),b=(0,R.getRoot)(r),[m,G]=(0,s.useState)("RgfaTabixAdapter"),[p,v]=(0,s.useState)(),[g,P]=(0,s.useState)(),[u,I]=(0,s.useState)(""),[d,M]=(0,s.useState)("Pangenome graph"),[f,k]=(0,s.useState)();function E(){if(!(!p||!r.assembly))try{k(void 0);let a=d.trim();(0,l.addTrackFromWidget)({model:r,session:h,conf:y({choice:m,loc:p,indexLoc:g,assembly:r.assembly,sample:u,trackId:(0,l.makeTrackId)({name:a}),name:a})})}catch(a){k(a)}}return(0,o.jsxs)(e.Paper,{className:c.paper,children:[f?(0,o.jsx)(i.ErrorMessage,{error:f}):null,(0,o.jsxs)(e.FormControl,{children:[(0,o.jsx)(e.FormLabel,{children:"File type"}),(0,o.jsx)(e.RadioGroup,{value:m,onChange:a=>{G(a.target.value)},children:D.map(a=>(0,o.jsx)(e.FormControlLabel,{value:a,control:(0,o.jsx)(e.Radio,{}),label:F[a]},a))})]}),(0,o.jsx)(i.FileSelector,{location:p,name:T[m],rootModel:b,setLocation:v}),(0,o.jsx)(i.FileSelector,{location:g,name:"Path to tabix index (optional; the sibling .tbi is assumed, a .csi is recognised by name)",rootModel:b,setLocation:P}),(0,o.jsx)(e.TextField,{className:c.field,value:u,onChange:a=>{I(a.target.value)},label:"Sample name in the graph",slotProps:{htmlInput:{"data-testid":"graph-sample-input"}},helperText:"Optional. The PanSN prefix the graph gives this assembly, e.g. GRCh38 for HPRC's GRCh38#0#chr1; leave blank when the graph's stable names are bare",placeholder:"GRCh38",fullWidth:!0}),(0,o.jsx)(e.TextField,{className:c.field,value:d,helperText:"Track name",slotProps:{htmlInput:{"data-testid":"graph-track-name-input"}},onChange:a=>{M(a.target.value)}}),(0,o.jsx)(i.AssemblySelector,{session:h,helperText:"Select assembly to add track to",selected:r.assembly,onChange:a=>{r.setAssembly(a)},fullWidth:!0}),(0,o.jsx)(e.Button,{variant:"contained",className:c.submit,disabled:!p||!d.trim()||!r.assembly,onClick:E,children:"Submit"})]})}),K=J;export{K as default};
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//# sourceMappingURL=AddTrackWorkflow-U3UNCVXJ.js.map
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"sources": ["global-externals:@jbrowse/core/util/tss-react", "../../src/GraphAddTrackWorkflow/AddTrackWorkflow.tsx"],
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"sourcesContent": ["module.exports = JBrowseExports[\"@jbrowse/core/util/tss-react\"];", "import { useState } from 'react'\n\nimport { AssemblySelector, ErrorMessage, FileSelector } from '@jbrowse/core/ui'\nimport { addTrackFromWidget, getSession, makeTrackId } from '@jbrowse/core/util'\nimport { makeStyles } from '@jbrowse/core/util/tss-react'\nimport { getRoot } from '@jbrowse/mobx-state-tree'\nimport {\n Button,\n FormControl,\n FormControlLabel,\n FormLabel,\n Paper,\n Radio,\n RadioGroup,\n TextField,\n} from '@mui/material'\nimport { observer } from 'mobx-react'\n\nimport {\n GRAPH_FILE_FIELDS,\n GRAPH_FILE_LABELS,\n buildTrackConfig,\n} from './buildTrackConfig'\n\nimport type { GraphFileChoice } from './buildTrackConfig'\nimport type {\n AbstractRootModel,\n AddTrackWorkflowModel,\n FileLocation,\n} from '@jbrowse/core/util'\n\nconst useStyles = makeStyles()(theme => ({\n paper: {\n margin: theme.spacing(),\n padding: theme.spacing(),\n },\n field: {\n marginTop: theme.spacing(2),\n },\n submit: {\n marginTop: 25,\n marginBottom: 100,\n display: 'block',\n },\n}))\n\nconst CHOICES: GraphFileChoice[] = [\n 'RgfaTabixAdapter',\n 'MinigraphBubbleAdapter',\n]\n\nconst GraphAddTrackWidget = observer(function GraphAddTrackWidget({\n model,\n}: {\n model: AddTrackWorkflowModel\n}) {\n const { classes } = useStyles()\n const session = getSession(model)\n const rootModel = getRoot<AbstractRootModel>(model)\n const [choice, setChoice] = useState<GraphFileChoice>('RgfaTabixAdapter')\n const [loc, setLoc] = useState<FileLocation>()\n const [indexLoc, setIndexLoc] = useState<FileLocation>()\n const [sample, setSample] = useState('')\n const [trackName, setTrackName] = useState('Pangenome graph')\n const [error, setError] = useState<unknown>()\n\n function handleSubmit() {\n if (!loc || !model.assembly) {\n return\n }\n try {\n setError(undefined)\n const name = trackName.trim()\n addTrackFromWidget({\n model,\n session,\n conf: buildTrackConfig({\n choice,\n loc,\n indexLoc,\n assembly: model.assembly,\n sample,\n trackId: makeTrackId({ name }),\n name,\n }),\n })\n } catch (e) {\n setError(e)\n }\n }\n\n return (\n <Paper className={classes.paper}>\n {error ? <ErrorMessage error={error} /> : null}\n <FormControl>\n <FormLabel>File type</FormLabel>\n <RadioGroup\n value={choice}\n onChange={event => {\n setChoice(event.target.value as GraphFileChoice)\n }}\n >\n {CHOICES.map(option => (\n <FormControlLabel\n key={option}\n value={option}\n control={<Radio />}\n label={GRAPH_FILE_LABELS[option]}\n />\n ))}\n </RadioGroup>\n </FormControl>\n <FileSelector\n location={loc}\n name={GRAPH_FILE_FIELDS[choice]}\n rootModel={rootModel}\n setLocation={setLoc}\n />\n <FileSelector\n location={indexLoc}\n name=\"Path to tabix index (optional; the sibling .tbi is assumed, a .csi is recognised by name)\"\n rootModel={rootModel}\n setLocation={setIndexLoc}\n />\n <TextField\n className={classes.field}\n value={sample}\n onChange={event => {\n setSample(event.target.value)\n }}\n label=\"Sample name in the graph\"\n slotProps={{ htmlInput: { 'data-testid': 'graph-sample-input' } }}\n helperText=\"Optional. The PanSN prefix the graph gives this assembly, e.g. GRCh38 for HPRC's GRCh38#0#chr1; leave blank when the graph's stable names are bare\"\n placeholder=\"GRCh38\"\n fullWidth\n />\n <TextField\n className={classes.field}\n value={trackName}\n helperText=\"Track name\"\n slotProps={{ htmlInput: { 'data-testid': 'graph-track-name-input' } }}\n onChange={event => {\n setTrackName(event.target.value)\n }}\n />\n <AssemblySelector\n session={session}\n helperText=\"Select assembly to add track to\"\n selected={model.assembly}\n onChange={arg => {\n model.setAssembly(arg)\n }}\n fullWidth\n />\n <Button\n variant=\"contained\"\n className={classes.submit}\n disabled={!loc || !trackName.trim() || !model.assembly}\n onClick={handleSubmit}\n >\n Submit\n </Button>\n </Paper>\n )\n})\n\nexport default GraphAddTrackWidget\n"],
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"names": ["require_tss_react", "__commonJSMin", "exports", "module", "import_react", "import_ui", "import_util", "import_tss_react", "import_mobx_state_tree", "import_material", "import_mobx_react", "import_jsx_runtime", "useStyles", "theme", "CHOICES", "GraphAddTrackWidget", "model", "classes", "session", "rootModel", "choice", "setChoice", "loc", "setLoc", "indexLoc", "setIndexLoc", "sample", "setSample", "trackName", "setTrackName", "error", "setError", "handleSubmit", "name", "buildTrackConfig", "e", "event", "option", "GRAPH_FILE_LABELS", "GRAPH_FILE_FIELDS", "arg", "AddTrackWorkflow_default"]
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}
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