@apollo-annotation/jbrowse-plugin-apollo 0.3.5 → 0.3.7

package/src/makeDisplayComponent.tsx

@@ -1,6 +1,5 @@
 /* eslint-disable @typescript-eslint/unbound-method */
-import PluginManager from '@jbrowse/core/PluginManager'
-import type LinearGenomeViewPlugin from '@jbrowse/plugin-linear-genome-view'
+import { getSession } from '@jbrowse/core/util'
 import ExpandLessIcon from '@mui/icons-material/ExpandLess'
 import ExpandMoreIcon from '@mui/icons-material/ExpandMore'
 import { Alert, Typography, alpha } from '@mui/material'
@@ -9,13 +8,11 @@ import React, { useCallback, useEffect, useRef } from 'react'
 import { makeStyles } from 'tss-react/mui'
 
 import { LinearApolloDisplay } from './LinearApolloDisplay/components'
-import { LinearApolloDisplay as LinearApolloDisplayI } from './LinearApolloDisplay/stateModel'
-import { TrackLines } from './SixFrameFeatureDisplay/components'
-import { SixFrameFeatureDisplay } from './SixFrameFeatureDisplay/stateModel'
+import { type LinearApolloDisplay as LinearApolloDisplayI } from './LinearApolloDisplay/stateModel'
+import { LinearApolloSixFrameDisplay } from './LinearApolloSixFrameDisplay/components'
+import { type LinearApolloSixFrameDisplay as LinearApolloSixFrameDisplayI } from './LinearApolloSixFrameDisplay/stateModel'
 import { TabularEditorPane } from './TabularEditor'
-
-import { getSession } from '@jbrowse/core/util'
-import { ApolloSessionModel } from './session'
+import { type ApolloSessionModel } from './session'
 
 const accordionControlHeight = 12
 
@@ -63,7 +60,7 @@ const useStyles = makeStyles()((theme) => ({
 }))
 
 function scrollSelectedFeatureIntoView(
-  model: LinearApolloDisplayI,
+  model: LinearApolloDisplayI | LinearApolloSixFrameDisplayI,
   scrollContainerRef: React.RefObject<HTMLDivElement>,
 ) {
   const { apolloRowHeight, selectedFeature } = model
@@ -157,7 +154,7 @@ const AccordionControl = observer(function AccordionControl({
   )
 })
 
-export const DisplayComponent = observer(function DisplayComponent({
+export const LinearApolloDisplayComponent = observer(function DisplayComponent({
   model,
   ...other
 }: {
@@ -248,40 +245,96 @@ export const DisplayComponent = observer(function DisplayComponent({
   )
 })
 
-export function makeSixFrameDisplayComponent(pluginManager: PluginManager) {
-  const LGVPlugin = pluginManager.getPlugin('LinearGenomeViewPlugin') as
-    | LinearGenomeViewPlugin
-    | undefined
-  if (!LGVPlugin) {
-    throw new Error('LinearGenomeView plugin not found')
-  }
-  const { BaseLinearDisplayComponent } = LGVPlugin.exports
-  function ApolloDisplayComponent({
+export const LinearApolloSixFrameDisplayComponent = observer(
+  function DisplayComponent({
     model,
     ...other
   }: {
-    model: SixFrameFeatureDisplay
+    model: LinearApolloSixFrameDisplayI
   }) {
+    const session = getSession(model) as unknown as ApolloSessionModel
+    const { ontologyManager } = session.apolloDataStore
+    const { featureTypeOntology } = ontologyManager
+    const ontologyStore = featureTypeOntology?.dataStore
+
     const { classes } = useStyles()
-    const { height, selectedFeature } = model
-    let { detailsHeight } = model
-    if (!selectedFeature) {
-      detailsHeight = 0
+
+    const {
+      detailsHeight,
+      graphical,
+      height: overallHeight,
+      isShown,
+      selectedFeature,
+      table,
+      tabularEditor,
+      toggleShown,
+    } = model
+
+    const canvasScrollContainerRef = useRef<HTMLDivElement>(null)
+    useEffect(() => {
+      scrollSelectedFeatureIntoView(model, canvasScrollContainerRef)
+    }, [model, selectedFeature])
+
+    const onDetailsResize = (delta: number) => {
+      model.setDetailsHeight(detailsHeight - delta)
     }
-    const featureAreaHeight = height - detailsHeight
-    return (
-      <div style={{ height: model.height }}>
-        <div className={classes.shading} style={{ height: featureAreaHeight }}>
-          <BaseLinearDisplayComponent model={model} {...other} />
+
+    if (!ontologyStore) {
+      return (
+        <div className={classes.alertContainer}>
+          <Alert severity="error">Could not load feature type ontology.</Alert>
+        </div>
+      )
+    }
+
+    if (graphical && table) {
+      const tabularHeight = tabularEditor.isShown ? detailsHeight : 0
+      const featureAreaHeight = isShown
+        ? overallHeight - detailsHeight - accordionControlHeight * 2
+        : 0
+      return (
+        <div style={{ height: overallHeight }}>
+          <AccordionControl
+            open={isShown}
+            title="Graphical"
+            onClick={toggleShown}
+          />
+          <div
+            className={classes.shading}
+            ref={canvasScrollContainerRef}
+            style={{ height: featureAreaHeight }}
+          >
+            <LinearApolloSixFrameDisplay model={model} {...other} />
+          </div>
+          <AccordionControl
+            title="Table"
+            open={tabularEditor.isShown}
+            onClick={tabularEditor.togglePane}
+            onResize={onDetailsResize}
+          />
+          <div className={classes.details} style={{ height: tabularHeight }}>
+            <TabularEditorPane model={model} />
+          </div>
         </div>
-        {/* <div className={classes.details} style={{ height: detailsHeight }}>
-          <ApolloDetails model={model} />
-        </div> */}
-        <div className="testTrackLines">
-          <TrackLines model={model} />
+      )
+    }
+
+    if (graphical) {
+      return (
+        <div
+          className={classes.shading}
+          ref={canvasScrollContainerRef}
+          style={{ height: overallHeight }}
+        >
+          <LinearApolloSixFrameDisplay model={model} {...other} />
         </div>
+      )
+    }
+
+    return (
+      <div className={classes.details} style={{ height: overallHeight }}>
+        <TabularEditorPane model={model} />
       </div>
     )
-  }
-  return observer(ApolloDisplayComponent)
-}
+  },
+)

package/src/session/ClientDataStore.ts

@@ -2,23 +2,27 @@
 /* eslint-disable @typescript-eslint/no-unsafe-assignment */
 /* eslint-disable @typescript-eslint/no-unnecessary-condition */
 /* eslint-disable @typescript-eslint/no-unsafe-argument */
-import { ClientDataStore as ClientDataStoreType } from '@apollo-annotation/common'
+import { type ClientDataStore as ClientDataStoreType } from '@apollo-annotation/common'
 import {
-  AnnotationFeatureModel,
-  AnnotationFeatureSnapshot,
+  type AnnotationFeatureModel,
+  type AnnotationFeatureSnapshot,
   ApolloAssembly,
-  ApolloAssemblySnapshot,
+  type ApolloAssemblySnapshot,
   ApolloRefSeq,
-  BackendDriverType,
+  type BackendDriverType,
   CheckResult,
-  CheckResultSnapshot,
+  type CheckResultSnapshot,
 } from '@apollo-annotation/mst'
 import { getConf, readConfObject } from '@jbrowse/core/configuration'
-import { ConfigurationModel } from '@jbrowse/core/configuration/types'
-import { Region, getSession, isElectron } from '@jbrowse/core/util'
-import { LocalPathLocation, UriLocation } from '@jbrowse/core/util/types/mst'
+import { type ConfigurationModel } from '@jbrowse/core/configuration/types'
+import { type Region, getSession, isElectron } from '@jbrowse/core/util'
 import {
-  Instance,
+  type LocalPathLocation,
+  type UriLocation,
+} from '@jbrowse/core/util/types/mst'
+import { autorun } from 'mobx'
+import {
+  type Instance,
   addDisposer,
   flow,
   getParentOfType,
@@ -28,21 +32,21 @@ import {
 } from 'mobx-state-tree'
 
 import {
-  ApolloInternetAccount,
+  type ApolloInternetAccount,
   CollaborationServerDriver,
   DesktopFileDriver,
   InMemoryFileDriver,
 } from '../BackendDrivers'
 import { ChangeManager } from '../ChangeManager'
-import ApolloPluginConfigurationSchema from '../config'
 import {
   OntologyManagerType,
-  OntologyRecordConfiguration,
-  TextIndexFieldDefinition,
+  type OntologyRecordConfiguration,
+  type TextIndexFieldDefinition,
 } from '../OntologyManager'
-import { ApolloRootModel } from '../types'
-import { autorun } from 'mobx'
-import { ApolloSessionModel } from './session'
+import type ApolloPluginConfigurationSchema from '../config'
+import { type ApolloRootModel } from '../types'
+
+import { type ApolloSessionModel } from './session'
 
 export function clientDataStoreFactory(
   AnnotationFeatureExtended: typeof AnnotationFeatureModel,

package/src/session/session.ts

@@ -1,27 +1,31 @@
 /* eslint-disable @typescript-eslint/no-unsafe-return */
 /* eslint-disable @typescript-eslint/no-unnecessary-condition */
 /* eslint-disable @typescript-eslint/no-unsafe-assignment */
-import { ClientDataStore as ClientDataStoreType } from '@apollo-annotation/common'
+import { type ClientDataStore as ClientDataStoreType } from '@apollo-annotation/common'
 import {
-  AnnotationFeature,
+  type AnnotationFeature,
   AnnotationFeatureModel,
 } from '@apollo-annotation/mst'
 import {
-  filterJBrowseConfig,
   ImportJBrowseConfigChange,
-  JBrowseConfig,
-  UserLocation,
+  type JBrowseConfig,
+  type UserLocation,
+  filterJBrowseConfig,
 } from '@apollo-annotation/shared'
-import { readConfObject, getConf } from '@jbrowse/core/configuration'
-import { BaseTrackConfig } from '@jbrowse/core/pluggableElementTypes'
-import PluginManager from '@jbrowse/core/PluginManager'
-import { AbstractSessionModel, SessionWithAddTracks } from '@jbrowse/core/util'
-import { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
+import type PluginManager from '@jbrowse/core/PluginManager'
+import { type AssemblyModel } from '@jbrowse/core/assemblyManager/assembly'
+import { getConf, readConfObject } from '@jbrowse/core/configuration'
+import { type BaseTrackConfig } from '@jbrowse/core/pluggableElementTypes'
+import {
+  type AbstractSessionModel,
+  type SessionWithAddTracks,
+} from '@jbrowse/core/util'
+import { type LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
 import SaveIcon from '@mui/icons-material/Save'
 import { autorun, observable } from 'mobx'
 import {
-  Instance,
-  SnapshotOut,
+  type Instance,
+  type SnapshotOut,
   applySnapshot,
   flow,
   getRoot,
@@ -29,13 +33,14 @@ import {
   types,
 } from 'mobx-state-tree'
 
-import { ApolloInternetAccountModel } from '../ApolloInternetAccount/model'
+import { type ApolloInternetAccountModel } from '../ApolloInternetAccount/model'
 import { ApolloJobModel } from '../ApolloJobModel'
-import { ChangeManager } from '../ChangeManager'
-import { ApolloRootModel } from '../types'
+import { type ChangeManager } from '../ChangeManager'
+import type ApolloPluginConfigurationSchema from '../config'
+import { type ApolloRootModel } from '../types'
 import { createFetchErrorMessage } from '../util'
+
 import { clientDataStoreFactory } from './ClientDataStore'
-import { AssemblyModel } from '@jbrowse/core/assemblyManager/assembly'
 
 export interface ApolloSession extends AbstractSessionModel {
   apolloDataStore: ClientDataStoreType & { changeManager: ChangeManager }
@@ -119,16 +124,6 @@ export function extendSession(
                   : {}),
               },
             },
-            displays: [
-              {
-                type: 'LinearApolloDisplay',
-                displayId: `${trackId}-LinearApolloDisplay`,
-              },
-              {
-                type: 'SixFrameFeatureDisplay',
-                displayId: `${trackId}-SixFrameFeatureDisplay`,
-              },
-            ],
           })
         }
       },
@@ -191,15 +186,6 @@ export function extendSession(
     }))
     .actions((self) => ({
       afterCreate: flow(function* afterCreate() {
-        // When the initial config.json loads, it doesn't include the Apollo
-        // tracks, which would result in a potentially invalid session snapshot
-        // if any tracks are open. Here we copy the session snapshot, apply an
-        // empty session snapshot, and then restore the original session
-        // snapshot after the updated config.json loads.
-        const sessionSnapshot = getSnapshot(self)
-        const { id, name } = sessionSnapshot
-        applySnapshot(self, { name, id })
-        const { internetAccounts, jbrowse } = getRoot<ApolloRootModel>(self)
         autorun(
           () => {
             // broadcastLocations() // **** This is not working and therefore we need to duplicate broadcastLocations() -method code here because autorun() does not observe changes otherwise
@@ -260,7 +246,29 @@ export function extendSession(
           },
           { name: 'ApolloSession' },
         )
-        // END AUTORUN
+        // When the initial config.json loads, it doesn't include the Apollo
+        // tracks, which would result in a potentially invalid session snapshot
+        // if any tracks are open. Here we copy the session snapshot, apply an
+        // empty session snapshot, and then restore the original session
+        // snapshot after the updated config.json loads.
+        // @ts-expect-error type is missing on ApolloRootModel
+        const { internetAccounts, jbrowse, reloadPluginManagerCallback } =
+          getRoot<ApolloRootModel>(self)
+        const pluginConfiguration =
+          // eslint-disable-next-line @typescript-eslint/no-unsafe-member-access
+          jbrowse.configuration.ApolloPlugin as Instance<
+            typeof ApolloPluginConfigurationSchema
+          >
+        const hasRole = readConfObject(
+          pluginConfiguration,
+          'hasRole',
+        ) as boolean
+        if (hasRole) {
+          return
+        }
+        const sessionSnapshot = getSnapshot(self)
+        const { id, name } = sessionSnapshot
+        applySnapshot(self, { name, id })
 
         // fetch and initialize assemblies for each of our Apollo internet accounts
         for (const internetAccount of internetAccounts as ApolloInternetAccountModel[]) {
@@ -296,9 +304,8 @@ export function extendSession(
             console.error(error)
             continue
           }
-          applySnapshot(jbrowse, jbrowseConfig)
-          // @ts-expect-error snapshot seems to get wrong type?
-          applySnapshot(self, sessionSnapshot)
+          // eslint-disable-next-line @typescript-eslint/no-unsafe-call
+          reloadPluginManagerCallback(jbrowseConfig, sessionSnapshot)
         }
       }),
       beforeDestroy() {

package/src/types.ts

@@ -1,8 +1,8 @@
-import { BaseInternetAccountModel } from '@jbrowse/core/pluggableElementTypes'
-import { AppRootModel } from '@jbrowse/core/util'
+import { type BaseInternetAccountModel } from '@jbrowse/core/pluggableElementTypes'
+import { type AppRootModel } from '@jbrowse/core/util'
 
-import { ApolloInternetAccountModel } from './ApolloInternetAccount/model'
-import { ApolloSessionModel } from './session'
+import { type ApolloInternetAccountModel } from './ApolloInternetAccount/model'
+import { type ApolloSessionModel } from './session'
 
 export interface ApolloRootModel extends Omit<AppRootModel, 'session'> {
   session: ApolloSessionModel

package/src/util/annotationFeatureUtils.ts

@@ -1,4 +1,6 @@
-import { AnnotationFeature } from '@apollo-annotation/mst'
+import { type AnnotationFeature } from '@apollo-annotation/mst'
+
+import { type MousePosition } from '../LinearApolloDisplay/stateModel/mouseEvents'
 
 export function getFeatureName(feature: AnnotationFeature) {
   const { attributes } = feature
@@ -51,3 +53,66 @@ export function getStrand(strand: number | undefined) {
   }
   return ''
 }
+
+function getChildren(feature: AnnotationFeature): AnnotationFeature[] {
+  const children: AnnotationFeature[] = []
+  //
+  if (feature.children) {
+    for (const [, ff] of feature.children) {
+      children.push(ff)
+    }
+  }
+  return children
+}
+
+function getParents(feature: AnnotationFeature): AnnotationFeature[] {
+  const parents: AnnotationFeature[] = []
+  let { parent } = feature
+  while (parent) {
+    parents.push(parent)
+    ;({ parent } = parent)
+  }
+  return parents
+}
+
+export function getFeaturesUnderClick(
+  mousePosition: MousePosition,
+  includeSiblings = false,
+): AnnotationFeature[] {
+  const clickedFeatures: AnnotationFeature[] = []
+  if (!mousePosition.featureAndGlyphUnderMouse) {
+    return clickedFeatures
+  }
+  clickedFeatures.push(mousePosition.featureAndGlyphUnderMouse.feature)
+  for (const x of getParents(mousePosition.featureAndGlyphUnderMouse.feature)) {
+    clickedFeatures.push(x)
+  }
+  const { bp } = mousePosition
+  const children = getChildren(mousePosition.featureAndGlyphUnderMouse.feature)
+  for (const child of children) {
+    if (child.min < bp && child.max >= bp) {
+      clickedFeatures.push(child)
+    }
+  }
+  if (!includeSiblings) {
+    return clickedFeatures
+  }
+
+  // Also add siblings , i.e. features having the same parent as the clicked
+  // one and intersecting the click position
+  if (mousePosition.featureAndGlyphUnderMouse.feature.parent) {
+    const siblings =
+      mousePosition.featureAndGlyphUnderMouse.feature.parent.children
+    if (siblings) {
+      for (const [, sib] of siblings) {
+        if (sib._id == mousePosition.featureAndGlyphUnderMouse.feature._id) {
+          continue
+        }
+        if (sib.min < bp && sib.max >= bp) {
+          clickedFeatures.push(sib)
+        }
+      }
+    }
+  }
+  return clickedFeatures
+}

package/src/util/copyToClipboard.ts

@@ -0,0 +1,21 @@
+export async function copyToClipboard(element: HTMLElement) {
+  if (isSecureContext) {
+    const textBlob = new Blob([element.outerText], { type: 'text/plain' })
+    const htmlBlob = new Blob([element.outerHTML], { type: 'text/html' })
+    const clipboardItem = new ClipboardItem({
+      [textBlob.type]: textBlob,
+      [htmlBlob.type]: htmlBlob,
+    })
+    return navigator.clipboard.write([clipboardItem])
+  }
+  const copyCallback = (event: ClipboardEvent) => {
+    event.clipboardData?.setData('text/plain', element.outerText)
+    event.clipboardData?.setData('text/html', element.outerHTML)
+    event.preventDefault()
+  }
+  document.addEventListener('copy', copyCallback)
+  // fall back to deprecated only in non-secure contexts
+  // eslint-disable-next-line @typescript-eslint/no-deprecated
+  document.execCommand('copy')
+  document.removeEventListener('copy', copyCallback)
+}

package/src/util/glyphUtils.ts

@@ -0,0 +1,49 @@
+import {
+  type AnnotationFeature,
+  type TranscriptPartCoding,
+} from '@apollo-annotation/mst'
+import { type LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
+
+export function getMinAndMaxPx(
+  feature: AnnotationFeature | TranscriptPartCoding,
+  refName: string,
+  regionNumber: number,
+  lgv: LinearGenomeViewModel,
+): [number, number] | undefined {
+  const minPxInfo = lgv.bpToPx({
+    refName,
+    coord: feature.min,
+    regionNumber,
+  })
+  const maxPxInfo = lgv.bpToPx({
+    refName,
+    coord: feature.max,
+    regionNumber,
+  })
+  if (minPxInfo === undefined || maxPxInfo === undefined) {
+    return
+  }
+  const { offsetPx } = lgv
+  const minPx = minPxInfo.offsetPx - offsetPx
+  const maxPx = maxPxInfo.offsetPx - offsetPx
+  return [minPx, maxPx]
+}
+
+export function getOverlappingEdge(
+  feature: AnnotationFeature,
+  x: number,
+  minMax: [number, number],
+): { feature: AnnotationFeature; edge: 'min' | 'max' } | undefined {
+  const [minPx, maxPx] = minMax
+  // Feature is too small to tell if we're overlapping an edge
+  if (Math.abs(maxPx - minPx) < 8) {
+    return
+  }
+  if (Math.abs(minPx - x) < 4) {
+    return { feature, edge: 'min' }
+  }
+  if (Math.abs(maxPx - x) < 4) {
+    return { feature, edge: 'max' }
+  }
+  return
+}

package/src/util/index.ts

@@ -1,8 +1,8 @@
 import { getParent } from 'mobx-state-tree'
 
-import { ApolloInternetAccountModel } from '../ApolloInternetAccount/model'
-import { ApolloSessionModel } from '../session'
-import { ApolloRootModel } from '../types'
+import { type ApolloInternetAccountModel } from '../ApolloInternetAccount/model'
+import { type ApolloSessionModel } from '../session'
+import { type ApolloRootModel } from '../types'
 
 export async function createFetchErrorMessage(
   response: Response,
@@ -30,3 +30,5 @@ export function getApolloInternetAccount(session: ApolloSessionModel) {
 
 export * from './loadAssemblyIntoClient'
 export * from './annotationFeatureUtils'
+export * from './glyphUtils'
+export * from './mouseEventsUtils'

package/src/util/loadAssemblyIntoClient.ts

@@ -1,7 +1,14 @@
-import { ClientDataStore, checkRegistry } from '@apollo-annotation/common'
-import { ApolloAssemblyI, CheckResultSnapshot } from '@apollo-annotation/mst'
+import { type ClientDataStore, checkRegistry } from '@apollo-annotation/common'
+import {
+  type ApolloAssemblyI,
+  type CheckResultSnapshot,
+} from '@apollo-annotation/mst'
 import { gff3ToAnnotationFeature } from '@apollo-annotation/shared'
-import gff, { GFF3Comment, GFF3Feature, GFF3Sequence } from '@gmod/gff'
+import gff, {
+  type GFF3Comment,
+  type GFF3Feature,
+  type GFF3Sequence,
+} from '@gmod/gff'
 import { getSnapshot } from 'mobx-state-tree'
 
 export async function loadAssemblyIntoClient(

package/src/util/mouseEventsUtils.ts

@@ -0,0 +1,113 @@
+import { type AnnotationFeature } from '@apollo-annotation/mst'
+
+type MinEdge = 'min'
+type MaxEdge = 'max'
+export type Edge = MinEdge | MaxEdge
+
+interface LocationChange {
+  featureId: string
+  oldLocation: number
+  newLocation: number
+}
+
+function expandFeatures(
+  feature: AnnotationFeature,
+  newLocation: number,
+  edge: Edge,
+): LocationChange[] {
+  const featureId = feature._id
+  const oldLocation = feature[edge]
+  const changes: LocationChange[] = [{ featureId, oldLocation, newLocation }]
+  const { parent } = feature
+  if (
+    parent &&
+    ((edge === 'min' && parent[edge] > newLocation) ||
+      (edge === 'max' && parent[edge] < newLocation))
+  ) {
+    changes.push(...expandFeatures(parent, newLocation, edge))
+  }
+  return changes
+}
+
+function shrinkFeatures(
+  feature: AnnotationFeature,
+  newLocation: number,
+  edge: Edge,
+  shrinkParent: boolean,
+  childIdToSkip?: string,
+): LocationChange[] {
+  const featureId = feature._id
+  const oldLocation = feature[edge]
+  const changes: LocationChange[] = [{ featureId, oldLocation, newLocation }]
+  const { parent, children } = feature
+  if (children) {
+    for (const [, child] of children) {
+      if (child._id === childIdToSkip) {
+        continue
+      }
+      if (
+        (edge === 'min' && child[edge] < newLocation) ||
+        (edge === 'max' && child[edge] > newLocation)
+      ) {
+        changes.push(...shrinkFeatures(child, newLocation, edge, shrinkParent))
+      }
+    }
+  }
+  if (parent && shrinkParent) {
+    const siblings: AnnotationFeature[] = []
+    if (parent.children) {
+      for (const [, c] of parent.children) {
+        if (c._id === featureId) {
+          continue
+        }
+        siblings.push(c)
+      }
+    }
+    if (siblings.length === 0) {
+      changes.push(
+        ...shrinkFeatures(parent, newLocation, edge, shrinkParent, featureId),
+      )
+    } else {
+      const oldLocation = parent[edge]
+      const boundedLocation = Math[edge](
+        ...siblings.map((s) => s[edge]),
+        newLocation,
+      )
+      if (boundedLocation !== oldLocation) {
+        changes.push(
+          ...shrinkFeatures(
+            parent,
+            boundedLocation,
+            edge,
+            shrinkParent,
+            featureId,
+          ),
+        )
+      }
+    }
+  }
+  return changes
+}
+
+export function getPropagatedLocationChanges(
+  feature: AnnotationFeature,
+  newLocation: number,
+  edge: Edge,
+  shrinkParent = false,
+): LocationChange[] {
+  const oldLocation = feature[edge]
+  if (newLocation === oldLocation) {
+    throw new Error(`New and existing locations are the same: "${newLocation}"`)
+  }
+  if (edge === 'min') {
+    if (newLocation > oldLocation) {
+      // shrinking feature, may need to shrink children and/or parents
+      return shrinkFeatures(feature, newLocation, edge, shrinkParent)
+    }
+    return expandFeatures(feature, newLocation, edge)
+  }
+  if (newLocation < oldLocation) {
+    return shrinkFeatures(feature, newLocation, edge, shrinkParent)
+  }
+  return expandFeatures(feature, newLocation, edge)
+}