@jbrowse/plugin-sv-inspector 2.6.1 → 2.6.3

package/dist/LaunchSvInspectorView/index.js

@@ -24,4 +24,3 @@ exports.default = (pluginManager) => {
         await view.spreadsheetView.importWizard.import(assembly);
     });
 };
-//# sourceMappingURL=index.js.map

package/dist/SvInspectorView/components/CircularViewOptions.js

@@ -19,4 +19,3 @@ const CircularViewOptions = (0, mobx_react_1.observer)(function ({ svInspector,
             react_1.default.createElement(material_1.FormControlLabel, { control: react_1.default.createElement(material_1.Checkbox, { checked: svInspector.onlyDisplayRelevantRegionsInCircularView, onChange: e => svInspector.setOnlyDisplayRelevantRegionsInCircularView(e.target.checked) }), label: "show only regions with data" }))));
 });
 exports.default = CircularViewOptions;
-//# sourceMappingURL=CircularViewOptions.js.map

package/dist/SvInspectorView/components/SvInspectorView.js

@@ -48,4 +48,3 @@ exports.default = (0, mobx_react_1.observer)(function SvInspectorView({ model, }
                     react_1.default.createElement(CircularViewReactComponent, { model: model.circularView })))) : null),
         react_1.default.createElement(ui_1.ResizeHandle, { onDrag: model.resizeHeight, className: classes.resizeHandleHoriz })));
 });
-//# sourceMappingURL=SvInspectorView.js.map

package/dist/SvInspectorView/index.js

@@ -32,4 +32,3 @@ exports.default = (pluginManager) => {
         });
     });
 };
-//# sourceMappingURL=index.js.map

package/dist/SvInspectorView/models/SvInspectorView.js

@@ -314,4 +314,3 @@ function SvInspectorViewF(pluginManager) {
     }));
 }
 exports.default = SvInspectorViewF;
-//# sourceMappingURL=SvInspectorView.js.map

package/dist/SvInspectorView/models/adhocFeatureUtils.js

@@ -94,4 +94,3 @@ function makeAdHocSvFeature(sheet, rowNumber, row, isValidRefName) {
     return undefined;
 }
 exports.makeAdHocSvFeature = makeAdHocSvFeature;
-//# sourceMappingURL=adhocFeatureUtils.js.map

package/dist/SvInspectorView/models/breakpointSplitViewFromTableRow.js

@@ -46,4 +46,3 @@ function canOpenBreakpointSplitViewFromTableRow(svInspectorView, spreadsheetView
     }
 }
 exports.canOpenBreakpointSplitViewFromTableRow = canOpenBreakpointSplitViewFromTableRow;
-//# sourceMappingURL=breakpointSplitViewFromTableRow.js.map

package/dist/index.js

@@ -32,4 +32,3 @@ class SvInspectorViewPlugin extends Plugin_1.default {
     }
 }
 exports.default = SvInspectorViewPlugin;
-//# sourceMappingURL=index.js.map

package/esm/LaunchSvInspectorView/index.js

@@ -22,4 +22,3 @@ export default (pluginManager) => {
         await view.spreadsheetView.importWizard.import(assembly);
     });
 };
-//# sourceMappingURL=index.js.map

package/esm/SvInspectorView/components/CircularViewOptions.js

@@ -14,4 +14,3 @@ const CircularViewOptions = observer(function ({ svInspector, }) {
             React.createElement(FormControlLabel, { control: React.createElement(Checkbox, { checked: svInspector.onlyDisplayRelevantRegionsInCircularView, onChange: e => svInspector.setOnlyDisplayRelevantRegionsInCircularView(e.target.checked) }), label: "show only regions with data" }))));
 });
 export default CircularViewOptions;
-//# sourceMappingURL=CircularViewOptions.js.map

package/esm/SvInspectorView/components/SvInspectorView.js

@@ -43,4 +43,3 @@ export default observer(function SvInspectorView({ model, }) {
                     React.createElement(CircularViewReactComponent, { model: model.circularView })))) : null),
         React.createElement(ResizeHandle, { onDrag: model.resizeHeight, className: classes.resizeHandleHoriz })));
 });
-//# sourceMappingURL=SvInspectorView.js.map

package/esm/SvInspectorView/index.js

@@ -27,4 +27,3 @@ export default (pluginManager) => {
         });
     });
 };
-//# sourceMappingURL=index.js.map

package/esm/SvInspectorView/models/SvInspectorView.js

@@ -309,4 +309,3 @@ function SvInspectorViewF(pluginManager) {
     }));
 }
 export default SvInspectorViewF;
-//# sourceMappingURL=SvInspectorView.js.map

package/esm/SvInspectorView/models/adhocFeatureUtils.js

@@ -87,4 +87,3 @@ export function makeAdHocSvFeature(sheet, rowNumber, row, isValidRefName) {
     }
     return undefined;
 }
-//# sourceMappingURL=adhocFeatureUtils.js.map

package/esm/SvInspectorView/models/breakpointSplitViewFromTableRow.js

@@ -39,4 +39,3 @@ export function canOpenBreakpointSplitViewFromTableRow(svInspectorView, spreadsh
         return false;
     }
 }
-//# sourceMappingURL=breakpointSplitViewFromTableRow.js.map

package/esm/index.js

@@ -26,4 +26,3 @@ export default class SvInspectorViewPlugin extends Plugin {
         }
     }
 }
-//# sourceMappingURL=index.js.map

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-sv-inspector",
-  "version": "2.6.1",
+  "version": "2.6.3",
   "description": "JBrowse 2 SV inspector view",
   "keywords": [
     "jbrowse",
@@ -20,7 +20,6 @@
   "main": "dist/index.js",
   "files": [
     "dist",
-    "src",
     "esm"
   ],
   "scripts": {
@@ -33,7 +32,7 @@
     "useSrc": "node ../../scripts/useSrc.js",
     "prebuild": "npm run clean",
     "build:esm": "tsc --build tsconfig.build.esm.json",
-    "build:es5": "tsc --build tsconfig.build.es5.json",
+    "build:commonjs": "tsc --build tsconfig.build.commonjs.json",
     "clean": "rimraf dist esm *.tsbuildinfo"
   },
   "dependencies": {
@@ -58,5 +57,5 @@
   "publishConfig": {
     "access": "public"
   },
-  "gitHead": "1cbe7ba097fb2d2763c776e5e429e4670cdd583c"
+  "gitHead": "ed402c87efb0904858d602c363bd1757d5742129"
 }

package/dist/LaunchSvInspectorView/index.js.map

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package/dist/SvInspectorView/components/CircularViewOptions.js.map

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package/dist/SvInspectorView/components/SvInspectorView.js.map

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package/dist/SvInspectorView/index.js.map

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package/dist/SvInspectorView/models/SvInspectorView.js.map

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package/dist/SvInspectorView/models/adhocFeatureUtils.js.map

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package/esm/SvInspectorView/models/SvInspectorView.js.map

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package/esm/SvInspectorView/models/adhocFeatureUtils.js.map

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package/src/LaunchSvInspectorView/index.ts

@@ -1,41 +0,0 @@
-import PluginManager from '@jbrowse/core/PluginManager'
-import { AbstractSessionModel } from '@jbrowse/core/util'
-import { SvInspectorViewModel } from '../SvInspectorView/models/SvInspectorView'
-
-export default (pluginManager: PluginManager) => {
-  pluginManager.addToExtensionPoint(
-    'LaunchView-SvInspectorView',
-    // @ts-expect-error
-    async ({
-      session,
-      assembly,
-      uri,
-      fileType,
-    }: {
-      session: AbstractSessionModel
-      assembly: string
-      uri: string
-      fileType?: string
-    }) => {
-      // add view, make typescript happy with return type
-      const view = session.addView('SvInspectorView') as SvInspectorViewModel
-
-      if (!view) {
-        throw new Error('Failed to initialize view')
-      }
-      const exts = uri.split('.')
-      let ext = exts?.pop()?.toUpperCase()
-      if (ext === 'GZ') {
-        ext = exts?.pop()?.toUpperCase()
-      }
-
-      view.spreadsheetView.importWizard.setFileType(fileType || ext || '')
-      view.spreadsheetView.importWizard.setSelectedAssemblyName(assembly)
-      view.spreadsheetView.importWizard.setFileSource({
-        uri,
-        locationType: 'UriLocation',
-      })
-      await view.spreadsheetView.importWizard.import(assembly)
-    },
-  )
-}

package/src/SvInspectorView/components/CircularViewOptions.tsx

@@ -1,47 +0,0 @@
-import React from 'react'
-import { observer } from 'mobx-react'
-import { Grid, FormControlLabel, Checkbox } from '@mui/material'
-import { makeStyles } from 'tss-react/mui'
-
-// locals
-import { SvInspectorViewModel } from '../models/SvInspectorView'
-
-const useStyles = makeStyles()(theme => ({
-  circularViewOptions: {
-    padding: theme.spacing(1),
-  },
-}))
-
-const CircularViewOptions = observer(function ({
-  svInspector,
-}: {
-  svInspector: SvInspectorViewModel
-}) {
-  const { classes } = useStyles()
-
-  return (
-    <Grid
-      container
-      className={classes.circularViewOptions}
-      style={{ height: svInspector.circularViewOptionsBarHeight }}
-    >
-      <Grid item>
-        <FormControlLabel
-          control={
-            <Checkbox
-              checked={svInspector.onlyDisplayRelevantRegionsInCircularView}
-              onChange={e =>
-                svInspector.setOnlyDisplayRelevantRegionsInCircularView(
-                  e.target.checked,
-                )
-              }
-            />
-          }
-          label="show only regions with data"
-        />
-      </Grid>
-    </Grid>
-  )
-})
-
-export default CircularViewOptions

package/src/SvInspectorView/components/SvInspectorView.tsx

@@ -1,81 +0,0 @@
-import React from 'react'
-import { observer } from 'mobx-react'
-import { makeStyles } from 'tss-react/mui'
-import { ResizeHandle } from '@jbrowse/core/ui'
-
-// locals
-import { SvInspectorViewModel } from '../models/SvInspectorView'
-import CircularViewOptions from './CircularViewOptions'
-
-const useStyles = makeStyles()(theme => ({
-  resizeHandleVert: {
-    background: theme.palette.action.selected,
-    width: 4,
-    boxSizing: 'border-box',
-    borderTop: '1px solid #fafafa',
-  },
-  resizeHandleHoriz: {
-    background: theme.palette.action.selected,
-    height: 4,
-    boxSizing: 'border-box',
-    borderTop: '1px solid #fafafa',
-  },
-  viewControls: {
-    margin: 0,
-  },
-  viewsContainer: {
-    display: 'flex',
-  },
-  container: {
-    overflow: 'hidden',
-  },
-}))
-
-export default observer(function SvInspectorView({
-  model,
-}: {
-  model: SvInspectorViewModel
-}) {
-  const { classes } = useStyles()
-
-  const {
-    SpreadsheetViewReactComponent,
-    CircularViewReactComponent,
-    showCircularView,
-  } = model
-
-  return (
-    <div className={classes.container}>
-      <div className={classes.viewsContainer}>
-        <div
-          style={{ width: model.spreadsheetView.width }}
-          className={classes.container}
-        >
-          <SpreadsheetViewReactComponent model={model.spreadsheetView} />
-        </div>
-
-        {showCircularView ? (
-          <>
-            <ResizeHandle
-              onDrag={distance => {
-                const ret1 = model.circularView.resizeWidth(-distance)
-                return model.spreadsheetView.resizeWidth(-ret1)
-              }}
-              vertical
-              flexbox
-              className={classes.resizeHandleVert}
-            />
-            <div style={{ width: model.circularView.width }}>
-              <CircularViewOptions svInspector={model} />
-              <CircularViewReactComponent model={model.circularView} />
-            </div>
-          </>
-        ) : null}
-      </div>
-      <ResizeHandle
-        onDrag={model.resizeHeight}
-        className={classes.resizeHandleHoriz}
-      />
-    </div>
-  )
-})

package/src/SvInspectorView/index.ts

@@ -1,41 +0,0 @@
-import PluginManager from '@jbrowse/core/PluginManager'
-import ViewType from '@jbrowse/core/pluggableElementTypes/ViewType'
-
-import ReactComponent from './components/SvInspectorView'
-import stateModelFactory from './models/SvInspectorView'
-import { Feature, getContainingView, getSession } from '@jbrowse/core/util'
-import { IAnyStateTreeNode } from 'mobx-state-tree'
-
-function defaultOnChordClick(
-  feature: Feature,
-  chordTrack: IAnyStateTreeNode,
-  pluginManager: PluginManager,
-) {
-  const session = getSession(chordTrack)
-  session.setSelection(feature)
-  const view = getContainingView(chordTrack)
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any
-  const viewType = pluginManager.getViewType('BreakpointSplitView') as any
-  const viewSnapshot = viewType.snapshotFromBreakendFeature(feature, view)
-
-  // try to center the offsetPx
-  viewSnapshot.views[0].offsetPx -= view.width / 2 + 100
-  viewSnapshot.views[1].offsetPx -= view.width / 2 + 100
-  viewSnapshot.featureData = feature.toJSON()
-
-  session.addView('BreakpointSplitView', viewSnapshot)
-}
-
-export default (pluginManager: PluginManager) => {
-  pluginManager.jexl.addFunction('defaultOnChordClick', defaultOnChordClick)
-
-  pluginManager.addViewType(() => {
-    const stateModel = stateModelFactory(pluginManager)
-    return new ViewType({
-      name: 'SvInspectorView',
-      displayName: 'SV inspector',
-      stateModel,
-      ReactComponent,
-    })
-  })
-}

package/src/SvInspectorView/models/SvInspectorView.ts

@@ -1,406 +0,0 @@
-import clone from 'clone'
-import { autorun, reaction } from 'mobx'
-import { types, getParent, addDisposer, Instance } from 'mobx-state-tree'
-
-import PluginManager from '@jbrowse/core/PluginManager'
-import { getSession, Region } from '@jbrowse/core/util'
-import { readConfObject } from '@jbrowse/core/configuration'
-import { ElementId } from '@jbrowse/core/util/types/mst'
-import { BaseViewModel } from '@jbrowse/core/pluggableElementTypes/models'
-import { SpreadsheetViewStateModel } from '@jbrowse/plugin-spreadsheet-view'
-import { CircularViewStateModel } from '@jbrowse/plugin-circular-view'
-
-// icons
-import OpenInNewIcon from '@mui/icons-material/OpenInNew'
-import FolderOpenIcon from '@mui/icons-material/FolderOpen'
-
-// locals
-import {
-  canOpenBreakpointSplitViewFromTableRow,
-  openBreakpointSplitViewFromTableRow,
-  getFeatureForRow,
-} from './breakpointSplitViewFromTableRow'
-
-/**
- * #stateModel SvInspectorView
- * #category view
- * combination of a spreadsheetview and a circularview
- */
-function SvInspectorViewF(pluginManager: PluginManager) {
-  const SpreadsheetViewType = pluginManager.getViewType('SpreadsheetView')
-  const CircularViewType = pluginManager.getViewType('CircularView')
-
-  const SpreadsheetModel =
-    SpreadsheetViewType.stateModel as SpreadsheetViewStateModel
-  const CircularModel = CircularViewType.stateModel as CircularViewStateModel
-
-  const minHeight = 400
-  const defaultHeight = 550
-  const headerHeight = 52
-  const circularViewOptionsBarHeight = 52
-  return types
-    .compose(
-      BaseViewModel,
-      types.model('SvInspectorView', {
-        /**
-         * #property
-         */
-        id: ElementId,
-        /**
-         * #property
-         */
-        type: types.literal('SvInspectorView'),
-
-        /**
-         * #property
-         */
-        height: types.optional(
-          types.refinement(
-            'SvInspectorViewHeight',
-            types.number,
-            n => n >= minHeight,
-          ),
-          defaultHeight,
-        ),
-        /**
-         * #property
-         */
-        onlyDisplayRelevantRegionsInCircularView: false,
-        /**
-         * #property
-         * switch specifying whether we are showing the import wizard or the
-         * spreadsheet in our viewing area
-         */
-        mode: types.optional(
-          types.enumeration('SvInspectorViewMode', ['import', 'display']),
-          'import',
-        ),
-        /**
-         * #property
-         */
-        spreadsheetView: types.optional(SpreadsheetModel, () =>
-          SpreadsheetModel.create({
-            type: 'SpreadsheetView',
-            hideVerticalResizeHandle: true,
-          }),
-        ),
-        /**
-         * #property
-         */
-        circularView: types.optional(CircularModel, () =>
-          CircularModel.create({
-            type: 'CircularView',
-            hideVerticalResizeHandle: true,
-            hideTrackSelectorButton: true,
-            disableImportForm: true,
-          }),
-        ),
-      }),
-    )
-    .volatile(() => ({
-      width: 800,
-    }))
-    .views(self => ({
-      /**
-       * #getter
-       */
-      get selectedRows() {
-        // @ts-expect-error
-        return self.spreadsheetView.rowSet.selectedRows
-      },
-      /**
-       * #getter
-       */
-      get assemblyName() {
-        const { assembly } = self.spreadsheetView
-        return assembly ? readConfObject(assembly, 'name') : undefined
-      },
-      /**
-       * #getter
-       */
-      get showCircularView() {
-        return self.spreadsheetView.mode === 'display'
-      },
-
-      /**
-       * #getter
-       */
-      get features() {
-        const session = getSession(self)
-        const { spreadsheetView } = self
-        const { outputRows = [] } = spreadsheetView
-        return outputRows
-          .map((r, i) => getFeatureForRow(session, spreadsheetView, r, i))
-          .filter(f => !!f)
-      },
-      /**
-       * #getter
-       */
-      get featuresAdapterConfigSnapshot() {
-        return {
-          type: 'FromConfigAdapter',
-          features: this.features,
-        }
-      },
-      /**
-       * #getter
-       */
-      get featureRefNames() {
-        const refs = this.features.map(r => r.refName)
-        const CHR2 = this.features.flatMap(r => r.INFO?.CHR2).filter(f => !!f)
-        return [...refs, ...CHR2]
-      },
-      /**
-       * #getter
-       */
-      get featuresCircularTrackConfiguration() {
-        return {
-          type: 'VariantTrack',
-          trackId: `sv-inspector-variant-track-${self.id}`,
-          name: 'features from tabular data',
-          adapter: this.featuresAdapterConfigSnapshot,
-          assemblyNames: [this.assemblyName],
-          displays: [
-            {
-              type: 'ChordVariantDisplay',
-              displayId: `sv-inspector-variant-track-chord-display-${self.id}`,
-              onChordClick: `jexl:defaultOnChordClick(feature, track, pluginManager)`,
-              renderer: { type: 'StructuralVariantChordRenderer' },
-            },
-          ],
-        }
-      },
-    }))
-    .volatile(() => ({
-      SpreadsheetViewReactComponent: SpreadsheetViewType.ReactComponent,
-      CircularViewReactComponent: CircularViewType.ReactComponent,
-      circularViewOptionsBarHeight,
-    }))
-    .actions(self => ({
-      /**
-       * #action
-       */
-      setWidth(newWidth: number) {
-        self.width = newWidth
-      },
-      /**
-       * #action
-       */
-      setHeight(newHeight: number) {
-        self.height = newHeight > minHeight ? newHeight : minHeight
-        return self.height
-      },
-      /**
-       * #action
-       */
-      setImportMode() {
-        self.spreadsheetView.setImportMode()
-      },
-      /**
-       * #action
-       */
-      setDisplayMode() {
-        self.spreadsheetView.setDisplayMode()
-      },
-      /**
-       * #action
-       */
-      closeView() {
-        // eslint-disable-next-line @typescript-eslint/no-explicit-any
-        getParent<any>(self, 2).removeView(self)
-      },
-      /**
-       * #action
-       */
-      setDisplayedRegions(regions: Region[]) {
-        self.circularView.setDisplayedRegions(regions)
-      },
-      /**
-       * #action
-       */
-      setOnlyDisplayRelevantRegionsInCircularView(val: boolean) {
-        self.onlyDisplayRelevantRegionsInCircularView = Boolean(val)
-      },
-    }))
-    .views(self => ({
-      /**
-       * #method
-       */
-      menuItems() {
-        return [
-          {
-            label: 'Return to import form',
-            onClick: () => self.setImportMode(),
-            icon: FolderOpenIcon,
-          },
-        ]
-      },
-    }))
-    .actions(self => ({
-      /**
-       * #action
-       */
-      resizeHeight(distance: number) {
-        const oldHeight = self.height
-        const newHeight = self.setHeight(self.height + distance)
-        return newHeight - oldHeight
-      },
-      afterAttach() {
-        // synchronize subview widths
-        addDisposer(
-          self,
-          autorun(
-            () => {
-              const borderWidth = 1
-              if (self.showCircularView) {
-                const spreadsheetWidth = Math.round(self.width * 0.66)
-                const circularViewWidth = self.width - spreadsheetWidth
-                self.spreadsheetView.setWidth(spreadsheetWidth - borderWidth)
-                self.circularView.setWidth(circularViewWidth)
-              } else {
-                self.spreadsheetView.setWidth(self.width)
-              }
-            },
-            { name: 'SvInspectorView width binding' },
-          ),
-        )
-        // synchronize subview heights
-        addDisposer(
-          self,
-          autorun(
-            () => {
-              self.spreadsheetView.setHeight(self.height - headerHeight)
-              self.circularView.setHeight(
-                self.height - headerHeight - circularViewOptionsBarHeight,
-              )
-            },
-            { name: 'SvInspectorView height binding' },
-          ),
-        )
-
-        // bind circularview displayedRegions to spreadsheet assembly, mediated
-        // by the onlyRelevantRegions toggle
-        addDisposer(
-          self,
-          autorun(
-            async () => {
-              const {
-                assemblyName,
-                onlyDisplayRelevantRegionsInCircularView,
-                circularView,
-                featureRefNames,
-              } = self
-              const { tracks } = circularView
-              const { assemblyManager } = getSession(self)
-              if (!assemblyName) {
-                return
-              }
-              const asm = await assemblyManager.waitForAssembly(assemblyName)
-              if (!asm) {
-                return
-              }
-
-              const { getCanonicalRefName, regions = [] } = asm
-              if (onlyDisplayRelevantRegionsInCircularView) {
-                if (tracks.length === 1) {
-                  try {
-                    // canonicalize the store's ref names if necessary
-                    const refSet = new Set(
-                      featureRefNames.map(r => getCanonicalRefName(r) || r),
-                    )
-
-                    circularView.setDisplayedRegions(
-                      clone(regions.filter(r => refSet.has(r.refName))),
-                    )
-                  } catch (e) {
-                    circularView.setError(e)
-                  }
-                }
-              } else {
-                circularView.setDisplayedRegions(regions)
-              }
-            },
-            { name: 'SvInspectorView displayed regions bind' },
-          ),
-        )
-
-        // bind circularview tracks to our track snapshot view
-        addDisposer(
-          self,
-          reaction(
-            () => ({
-              generatedTrackConf: self?.featuresCircularTrackConfiguration,
-              assemblyName: self?.assemblyName,
-            }),
-            data => {
-              if (!data) {
-                return
-              }
-              const { assemblyName, generatedTrackConf } = data
-              const { circularView } = self
-              // hide any visible tracks
-              circularView.tracks.forEach(t =>
-                circularView.hideTrack(t.configuration.trackId),
-              )
-
-              // put our track in as the only track
-              if (assemblyName && generatedTrackConf) {
-                // @ts-expect-error
-                circularView.addTrackConf(generatedTrackConf, {
-                  assemblyName,
-                })
-              }
-            },
-            {
-              name: 'SvInspectorView track configuration binding',
-              fireImmediately: true,
-            },
-          ),
-        )
-
-        // bind spreadsheetView row menu actions to us
-        addDisposer(
-          self,
-          autorun(() => {
-            self.spreadsheetView.setRowMenuItems(
-              // these are the MenuItem entries for the row menu actions in the
-              // spreadsheet view.  these are installed into the child
-              // SpreadsheetView using an autorun below
-              [
-                {
-                  label: 'Open split detail view',
-                  icon: OpenInNewIcon,
-                  // @ts-expect-error
-                  disabled(spreadsheetView, spreadsheet, rowNumber, row) {
-                    return !canOpenBreakpointSplitViewFromTableRow(
-                      self,
-                      spreadsheetView,
-                      spreadsheet,
-                      row,
-                      rowNumber,
-                    )
-                  },
-
-                  // @ts-expect-error
-                  onClick(spreadsheetView, spreadsheet, rowNumber, row) {
-                    openBreakpointSplitViewFromTableRow(
-                      self,
-                      spreadsheetView,
-                      spreadsheet,
-                      row,
-                      rowNumber,
-                    )
-                  },
-                },
-              ],
-            )
-          }),
-        )
-      },
-    }))
-}
-
-export type SvInspectorViewStateModel = ReturnType<typeof SvInspectorViewF>
-export type SvInspectorViewModel = Instance<SvInspectorViewStateModel>
-
-export default SvInspectorViewF

package/src/SvInspectorView/models/adhocFeatureUtils.js

@@ -1,152 +0,0 @@
-// this file contains the rather verbose functions for
-// creating features from CSV/TSV lines
-import { parseLocString } from '@jbrowse/core/util'
-
-export function makeAdHocFeature(
-  columns,
-  columnsAlreadyUsedInLocations,
-  row,
-  loc1,
-  loc2,
-  rowNumber,
-) {
-  // load all the other data in the row into an `otherData` object
-  const otherData = {}
-  columns.forEach((column, columnNumber) => {
-    if (columnsAlreadyUsedInLocations.includes(columnNumber)) {
-      return
-    }
-    let { text } = row.cells[columnNumber]
-    if (column.dataType.type === 'Number') {
-      text = parseFloat(text)
-    }
-    otherData[column.name] = text
-  })
-
-  // make the final feature data out of otherData + the parsed locations
-  return {
-    ...otherData,
-    uniqueId: `sv-inspector-adhoc-${rowNumber}`,
-    refName: loc1.refName,
-    start: loc1.start,
-    end: loc1.end,
-    mate: {
-      refName: loc2.refName,
-      start: loc2.start,
-      end: loc2.end,
-    },
-  }
-}
-
-export function makeAdHocSvFeatureFromTwoLocations(
-  columns,
-  locationColumnNumbers,
-  row,
-  rowNumber,
-  isValidRefName,
-) {
-  // use the first two locations we found (first according to *displayed* order)
-  const loc1 = parseLocString(
-    row.cells[locationColumnNumbers[0]].text,
-    isValidRefName,
-  )
-  const loc2 = parseLocString(
-    row.cells[locationColumnNumbers[1]].text,
-    isValidRefName,
-  )
-
-  const columnsAlreadyUsedInLocations = [
-    locationColumnNumbers[0],
-    locationColumnNumbers[1],
-  ]
-
-  return makeAdHocFeature(
-    columns,
-    columnsAlreadyUsedInLocations,
-    row,
-    loc1,
-    loc2,
-    rowNumber,
-  )
-}
-
-export function makeAdHocSvFeatureFromTwoRefStartEndSets(
-  columns,
-  locRefColumnNumbers,
-  locStartColumnNumbers,
-  locEndColumnNumbers,
-  row,
-  rowNumber,
-) {
-  const textOf = colno => row.cells[colno].text
-  const loc1 = {
-    refName: textOf(locRefColumnNumbers[0]),
-    start: parseInt(textOf(locStartColumnNumbers[0]), 10) - 1,
-    end: parseInt(textOf(locEndColumnNumbers[0]), 10),
-  }
-  const loc2 = {
-    refName: textOf(locRefColumnNumbers[1]),
-    start: parseInt(textOf(locStartColumnNumbers[1]), 10) - 1,
-    end: parseInt(textOf(locEndColumnNumbers[1]), 10),
-  }
-  const columnsAlreadyUsedInLocations = [
-    locRefColumnNumbers[0],
-    locStartColumnNumbers[0],
-    locEndColumnNumbers[0],
-    locRefColumnNumbers[1],
-    locStartColumnNumbers[1],
-    locEndColumnNumbers[1],
-  ]
-  return makeAdHocFeature(
-    columns,
-    columnsAlreadyUsedInLocations,
-    row,
-    loc1,
-    loc2,
-    rowNumber,
-  )
-}
-
-// makes a feature data object (passed as `data` to a SimpleFeature constructor)
-// out of table row if the row has 2 location columns. undefined if not
-export function makeAdHocSvFeature(sheet, rowNumber, row, isValidRefName) {
-  const { columns, columnDisplayOrder } = sheet
-  const columnTypes = {}
-  columnDisplayOrder.forEach(columnNumber => {
-    const columnDefinition = columns[columnNumber]
-    if (!columnTypes[columnDefinition.dataType.type]) {
-      columnTypes[columnDefinition.dataType.type] = []
-    }
-    columnTypes[columnDefinition.dataType.type].push(columnNumber)
-  })
-  const locationColumnNumbers = columnTypes.LocString || []
-  const locStartColumnNumbers = columnTypes.LocStart || []
-  const locEndColumnNumbers = columnTypes.LocEnd || []
-  const locRefColumnNumbers = columnTypes.LocRef || []
-
-  // if we have 2 or more columns of type location, make a feature from them
-  if (locationColumnNumbers.length >= 2) {
-    return makeAdHocSvFeatureFromTwoLocations(
-      columns,
-      locationColumnNumbers,
-      row,
-      rowNumber,
-      isValidRefName,
-    )
-  }
-  if (
-    locRefColumnNumbers.length >= 2 &&
-    locStartColumnNumbers.length >= 2 &&
-    locEndColumnNumbers.length >= 2
-  ) {
-    return makeAdHocSvFeatureFromTwoRefStartEndSets(
-      columns,
-      locRefColumnNumbers,
-      locStartColumnNumbers,
-      locEndColumnNumbers,
-      row,
-      rowNumber,
-    )
-  }
-  return undefined
-}

package/src/SvInspectorView/models/breakpointSplitViewFromTableRow.js

@@ -1,84 +0,0 @@
-import { SimpleFeature, getEnv, getSession } from '@jbrowse/core/util'
-import { makeAdHocSvFeature } from './adhocFeatureUtils'
-
-export function getFeatureForRow(session, spreadsheetView, row, rowNumber) {
-  return (
-    row.extendedData?.vcfFeature ||
-    row.extendedData?.feature ||
-    makeAdHocSvFeature(
-      spreadsheetView.spreadsheet,
-      rowNumber,
-      row,
-      session.assemblyManager.isValidRefName,
-    )
-  )
-}
-
-export function breakpointSplitViewSnapshotFromTableRow(
-  svInspectorView,
-  spreadsheetView,
-  spreadsheet,
-  row,
-  rowNumber,
-) {
-  const { pluginManager } = getEnv(svInspectorView)
-  const session = getSession(spreadsheetView)
-  const featureData = getFeatureForRow(session, spreadsheet, row, rowNumber)
-
-  if (featureData) {
-    const feature = new SimpleFeature(featureData)
-    session.setSelection(feature)
-    return pluginManager
-      .getViewType('BreakpointSplitView')
-      .snapshotFromBreakendFeature(feature, svInspectorView.circularView)
-  }
-  return undefined
-}
-
-export function openBreakpointSplitViewFromTableRow(
-  svInspectorView,
-  spreadsheetView,
-  spreadsheet,
-  row,
-  rowNumber,
-) {
-  const viewSnapshot = breakpointSplitViewSnapshotFromTableRow(
-    svInspectorView,
-    spreadsheetView,
-    spreadsheet,
-    row,
-    rowNumber,
-  )
-  if (viewSnapshot) {
-    // try to center the offsetPx
-    const { circularView } = svInspectorView
-    viewSnapshot.views[0].offsetPx -= circularView.width / 2 + 100
-    viewSnapshot.views[1].offsetPx -= circularView.width / 2 + 100
-
-    const session = getSession(spreadsheetView)
-    session.addView('BreakpointSplitView', viewSnapshot)
-  }
-}
-
-export function canOpenBreakpointSplitViewFromTableRow(
-  svInspectorView,
-  spreadsheetView,
-  spreadsheet,
-  row,
-  rowNumber,
-) {
-  try {
-    return Boolean(
-      breakpointSplitViewSnapshotFromTableRow(
-        svInspectorView,
-        spreadsheetView,
-        spreadsheet,
-        row,
-        rowNumber,
-      ),
-    )
-  } catch (e) {
-    console.error('Unable to open breakpoint split view from table row', e)
-    return false
-  }
-}

package/src/index.ts

@@ -1,34 +0,0 @@
-import PluginManager from '@jbrowse/core/PluginManager'
-import Plugin from '@jbrowse/core/Plugin'
-import {
-  AbstractSessionModel,
-  isAbstractMenuManager,
-} from '@jbrowse/core/util/types'
-
-// icons
-import TableChartIcon from '@mui/icons-material/TableChart'
-
-// locals
-import SvInspectorViewF from './SvInspectorView'
-import LaunchSvInspectorViewF from './LaunchSvInspectorView'
-
-export default class SvInspectorViewPlugin extends Plugin {
-  name = 'SvInspectorViewPlugin'
-
-  install(pluginManager: PluginManager) {
-    SvInspectorViewF(pluginManager)
-    LaunchSvInspectorViewF(pluginManager)
-  }
-
-  configure(pluginManager: PluginManager) {
-    if (isAbstractMenuManager(pluginManager.rootModel)) {
-      pluginManager.rootModel.appendToSubMenu(['Add'], {
-        label: 'SV inspector',
-        icon: TableChartIcon,
-        onClick: (session: AbstractSessionModel) => {
-          session.addView('SvInspectorView', {})
-        },
-      })
-    }
-  }
-}