@jbrowse/plugin-wiggle 2.4.2 → 2.5.0

package/src/MultiLinearWiggleDisplay/components/SetColorDialog.tsx

@@ -129,6 +129,11 @@ export default function SetColorDialog({
   )
 }
 
+interface SortField {
+  idx: number
+  field: string | null
+}
+
 function SourcesGrid({
   rows,
   onChange,
@@ -143,53 +148,11 @@ function SourcesGrid({
 
   // @ts-expect-error
   const { name: _name, color: _color, baseUri: _baseUri, ...rest } = rows[0]
-
-  // similar to BaseFeatureDetail data-grid for auto-measuring columns
-  const columns = [
-    {
-      field: 'color',
-      headerName: 'Color',
-      renderCell: (params: GridCellParams) => {
-        const { value, id } = params
-        return (
-          <ColorPicker
-            color={value || 'blue'}
-            onChange={c => {
-              const elt = rows.find(f => f.name === id)
-              if (elt) {
-                elt.color = c
-              }
-              onChange([...rows])
-            }}
-          />
-        )
-      },
-    },
-    {
-      field: 'name',
-      sortingOrder: [null],
-      headerName: 'Name',
-      width: measureGridWidth(rows.map(r => r.name)),
-    },
-    ...Object.keys(rest).map(val => ({
-      field: val,
-      sortingOrder: [null],
-      renderCell: (params: GridCellParams) => {
-        const { value } = params
-        return isUriLocation(value) ? <UriLink value={value} /> : getStr(value)
-      },
-      // @ts-expect-error
-      width: measureGridWidth(rows.map(r => r[val])),
-    })),
-  ]
-
-  // this helps keep track of the selection, even though it is not used
-  // anywhere except inside the picker
   const [widgetColor, setWidgetColor] = useState('blue')
-  const [currSort, setCurrSort] = useState<{
-    idx: number
-    field: string | null
-  }>({ idx: 0, field: null })
+  const [currSort, setCurrSort] = useState<SortField>({
+    idx: 0,
+    field: null,
+  })
 
   return (
     <div>
@@ -247,12 +210,52 @@ function SourcesGrid({
         <DataGrid
           getRowId={row => row.name}
           checkboxSelection
-          disableSelectionOnClick
-          onSelectionModelChange={arg => setSelected(arg as string[])}
+          disableRowSelectionOnClick
+          onRowSelectionModelChange={arg => setSelected(arg as string[])}
           rows={rows}
           rowHeight={25}
-          headerHeight={33}
-          columns={columns}
+          columnHeaderHeight={33}
+          columns={[
+            {
+              field: 'color',
+              headerName: 'Color',
+              renderCell: params => {
+                const { value, id } = params
+                return (
+                  <ColorPicker
+                    color={value || 'blue'}
+                    onChange={c => {
+                      const elt = rows.find(f => f.name === id)
+                      if (elt) {
+                        elt.color = c
+                      }
+                      onChange([...rows])
+                    }}
+                  />
+                )
+              },
+            },
+            {
+              field: 'name',
+              sortingOrder: [null],
+              headerName: 'Name',
+              width: measureGridWidth(rows.map(r => r.name)),
+            },
+            ...Object.keys(rest).map(val => ({
+              field: val,
+              sortingOrder: [null],
+              renderCell: (params: GridCellParams) => {
+                const { value } = params
+                return isUriLocation(value) ? (
+                  <UriLink value={value} />
+                ) : (
+                  getStr(value)
+                )
+              },
+              // @ts-ignore
+              width: measureGridWidth(rows.map(r => r[val])),
+            })),
+          ]}
           sortModel={
             [
               /* we control the sort as a controlled component using onSortModelChange */

package/src/MultiLinearWiggleDisplay/models/model.tsx

@@ -30,8 +30,7 @@ import {
 import {
   getNiceDomain,
   getScale,
-  getStats,
-  statsAutorun,
+  quantitativeStatsAutorun,
   YSCALEBAR_LABEL_OFFSET,
 } from '../../util'
 
@@ -110,7 +109,7 @@ const stateModelFactory = (
       clearLayout() {
         self.layout = []
       },
-      updateStats(stats: { scoreMin: number; scoreMax: number }) {
+      updateQuantitativeStats(stats: { scoreMin: number; scoreMax: number }) {
         const { scoreMin, scoreMax } = stats
         const EPSILON = 0.000001
         if (!self.stats) {
@@ -662,27 +661,12 @@ const stateModelFactory = (
       type ExportSvgOpts = Parameters<typeof superRenderSvg>[0]
 
       return {
-        // re-runs stats and refresh whole display on reload
         async reload() {
           self.setError()
-          const aborter = new AbortController()
-          let stats
-          try {
-            self.setLoading(aborter)
-            stats = await getStats(self, {
-              signal: aborter.signal,
-              ...self.renderProps(),
-            })
-            if (isAlive(self)) {
-              self.updateStats(stats)
-              superReload()
-            }
-          } catch (e) {
-            self.setError(e)
-          }
+          superReload()
         },
         afterAttach() {
-          statsAutorun(self)
+          quantitativeStatsAutorun(self)
           addDisposer(
             self,
             autorun(async () => {

package/src/MultiWiggleAdapter/MultiWiggleAdapter.ts

@@ -106,7 +106,7 @@ export default class MultiWiggleAdapter extends BaseFeatureDataAdapter {
   }
 
   // always render bigwig instead of calculating a feature density for it
-  async estimateRegionsStats(_regions: Region[]) {
+  async getMultiRegionFeatureDensityStats(_regions: Region[]) {
     return { featureDensity: 0 }
   }
 

package/src/WiggleRPC/MultiWiggleGetSources.ts

@@ -0,0 +1,68 @@
+import RpcMethodType from '@jbrowse/core/pluggableElementTypes/RpcMethodType'
+import SerializableFilterChain from '@jbrowse/core/pluggableElementTypes/renderers/util/serializableFilterChain'
+import { getAdapter } from '@jbrowse/core/data_adapters/dataAdapterCache'
+import { RenderArgs } from '@jbrowse/core/rpc/coreRpcMethods'
+import { renameRegionsIfNeeded, Region } from '@jbrowse/core/util'
+import { RemoteAbortSignal } from '@jbrowse/core/rpc/remoteAbortSignals'
+import { AnyConfigurationModel } from '@jbrowse/core/configuration'
+
+export class MultiWiggleGetSources extends RpcMethodType {
+  name = 'MultiWiggleGetSources'
+
+  // eslint-disable-next-line @typescript-eslint/no-explicit-any
+  async deserializeArguments(args: any, rpcDriverClassName: string) {
+    const l = await super.deserializeArguments(args, rpcDriverClassName)
+    return {
+      ...l,
+      filters: args.filters
+        ? new SerializableFilterChain({
+            filters: args.filters,
+          })
+        : undefined,
+    }
+  }
+
+  async serializeArguments(
+    args: RenderArgs & {
+      signal?: AbortSignal
+      statusCallback?: (arg: string) => void
+    },
+    rpcDriverClassName: string,
+  ) {
+    const pm = this.pluginManager
+    const assemblyManager = pm.rootModel?.session?.assemblyManager
+    if (!assemblyManager) {
+      return args
+    }
+
+    const renamedArgs = await renameRegionsIfNeeded(assemblyManager, {
+      ...args,
+      filters: args.filters?.toJSON().filters,
+    })
+
+    return super.serializeArguments(renamedArgs, rpcDriverClassName)
+  }
+
+  async execute(
+    args: {
+      adapterConfig: AnyConfigurationModel
+      signal?: RemoteAbortSignal
+      sessionId: string
+      headers?: Record<string, string>
+      regions: Region[]
+      bpPerPx: number
+    },
+    rpcDriverClassName: string,
+  ) {
+    const pm = this.pluginManager
+    const deserializedArgs = await this.deserializeArguments(
+      args,
+      rpcDriverClassName,
+    )
+    const { regions, adapterConfig, sessionId } = deserializedArgs
+    const { dataAdapter } = await getAdapter(pm, sessionId, adapterConfig)
+
+    // @ts-expect-error
+    return dataAdapter.getSources(regions, deserializedArgs)
+  }
+}

package/src/WiggleRPC/WiggleGetGlobalQuantitativeStats.ts

@@ -0,0 +1,44 @@
+import RpcMethodType from '@jbrowse/core/pluggableElementTypes/RpcMethodType'
+import SerializableFilterChain from '@jbrowse/core/pluggableElementTypes/renderers/util/serializableFilterChain'
+import { getAdapter } from '@jbrowse/core/data_adapters/dataAdapterCache'
+import { RemoteAbortSignal } from '@jbrowse/core/rpc/remoteAbortSignals'
+import { QuantitativeStats } from '@jbrowse/core/util/stats'
+import { AnyConfigurationModel } from '@jbrowse/core/configuration'
+
+export class WiggleGetGlobalQuantitativeStats extends RpcMethodType {
+  name = 'WiggleGetGlobalQuantitativeStats'
+
+  // eslint-disable-next-line @typescript-eslint/no-explicit-any
+  async deserializeArguments(args: any, rpcDriverClassName: string) {
+    const l = await super.deserializeArguments(args, rpcDriverClassName)
+    return {
+      ...l,
+      filters: args.filters
+        ? new SerializableFilterChain({
+            filters: args.filters,
+          })
+        : undefined,
+    }
+  }
+
+  async execute(
+    args: {
+      adapterConfig: AnyConfigurationModel
+      signal?: RemoteAbortSignal
+      headers?: Record<string, string>
+      sessionId: string
+    },
+    rpcDriverClassName: string,
+  ): Promise<QuantitativeStats> {
+    const pm = this.pluginManager
+    const deserializedArgs = await this.deserializeArguments(
+      args,
+      rpcDriverClassName,
+    )
+    const { adapterConfig, sessionId } = deserializedArgs
+    const { dataAdapter } = await getAdapter(pm, sessionId, adapterConfig)
+
+    // @ts-expect-error
+    return dataAdapter.getGlobalStats(deserializedArgs)
+  }
+}

package/src/WiggleRPC/WiggleGetMultiRegionQuantitativeStats.ts

@@ -0,0 +1,73 @@
+import RpcMethodType from '@jbrowse/core/pluggableElementTypes/RpcMethodType'
+import SerializableFilterChain from '@jbrowse/core/pluggableElementTypes/renderers/util/serializableFilterChain'
+import { RenderArgs } from '@jbrowse/core/rpc/coreRpcMethods'
+import { getAdapter } from '@jbrowse/core/data_adapters/dataAdapterCache'
+import { RemoteAbortSignal } from '@jbrowse/core/rpc/remoteAbortSignals'
+import { Region, renameRegionsIfNeeded } from '@jbrowse/core/util'
+import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter'
+
+export class WiggleGetMultiRegionQuantitativeStats extends RpcMethodType {
+  name = 'WiggleGetMultiRegionQuantitativeStats'
+
+  // eslint-disable-next-line @typescript-eslint/no-explicit-any
+  async deserializeArguments(args: any, rpcDriverClassName: string) {
+    const l = await super.deserializeArguments(args, rpcDriverClassName)
+    return {
+      ...l,
+      filters: args.filters
+        ? new SerializableFilterChain({
+            filters: args.filters,
+          })
+        : undefined,
+    }
+  }
+
+  async serializeArguments(
+    args: RenderArgs & {
+      signal?: AbortSignal
+      statusCallback?: (arg: string) => void
+    },
+    rpcDriverClassName: string,
+  ) {
+    const pm = this.pluginManager
+    const assemblyManager = pm.rootModel?.session?.assemblyManager
+    if (!assemblyManager) {
+      return args
+    }
+
+    const renamedArgs = await renameRegionsIfNeeded(assemblyManager, {
+      ...args,
+      filters: args.filters?.toJSON().filters,
+    })
+
+    return super.serializeArguments(renamedArgs, rpcDriverClassName)
+  }
+
+  async execute(
+    args: {
+      adapterConfig: {}
+      signal?: RemoteAbortSignal
+      sessionId: string
+      headers?: Record<string, string>
+      regions: Region[]
+      bpPerPx: number
+    },
+    rpcDriverClassName: string,
+  ) {
+    const pm = this.pluginManager
+    const deserializedArgs = await this.deserializeArguments(
+      args,
+      rpcDriverClassName,
+    )
+    const { regions, adapterConfig, sessionId } = deserializedArgs
+    const { dataAdapter } = await getAdapter(pm, sessionId, adapterConfig)
+
+    if (dataAdapter instanceof BaseFeatureDataAdapter) {
+      return dataAdapter.getMultiRegionQuantitativeStats(
+        regions,
+        deserializedArgs,
+      )
+    }
+    throw new Error('Data adapter not found')
+  }
+}

package/src/WiggleRPC/rpcMethods.ts

@@ -1,170 +1,3 @@
-import RpcMethodType from '@jbrowse/core/pluggableElementTypes/RpcMethodType'
-import SerializableFilterChain from '@jbrowse/core/pluggableElementTypes/renderers/util/serializableFilterChain'
-import { getAdapter } from '@jbrowse/core/data_adapters/dataAdapterCache'
-import { RenderArgs } from '@jbrowse/core/rpc/coreRpcMethods'
-import { renameRegionsIfNeeded, Region } from '@jbrowse/core/util'
-import { RemoteAbortSignal } from '@jbrowse/core/rpc/remoteAbortSignals'
-import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter'
-import { FeatureStats } from '@jbrowse/core/util/stats'
-
-export class WiggleGetGlobalStats extends RpcMethodType {
-  name = 'WiggleGetGlobalStats'
-
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any
-  async deserializeArguments(args: any, rpcDriverClassName: string) {
-    const l = await super.deserializeArguments(args, rpcDriverClassName)
-    return {
-      ...l,
-      filters: args.filters
-        ? new SerializableFilterChain({
-            filters: args.filters,
-          })
-        : undefined,
-    }
-  }
-
-  async execute(
-    args: {
-      adapterConfig: {}
-      signal?: RemoteAbortSignal
-      headers?: Record<string, string>
-      sessionId: string
-    },
-    rpcDriverClassName: string,
-  ): Promise<FeatureStats> {
-    const pm = this.pluginManager
-    const deserializedArgs = await this.deserializeArguments(
-      args,
-      rpcDriverClassName,
-    )
-    const { adapterConfig, sessionId } = deserializedArgs
-    const { dataAdapter } = await getAdapter(pm, sessionId, adapterConfig)
-
-    // @ts-expect-error
-    return dataAdapter.getGlobalStats(deserializedArgs)
-  }
-}
-
-export class WiggleGetMultiRegionStats extends RpcMethodType {
-  name = 'WiggleGetMultiRegionStats'
-
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any
-  async deserializeArguments(args: any, rpcDriverClassName: string) {
-    const l = await super.deserializeArguments(args, rpcDriverClassName)
-    return {
-      ...l,
-      filters: args.filters
-        ? new SerializableFilterChain({
-            filters: args.filters,
-          })
-        : undefined,
-    }
-  }
-
-  async serializeArguments(
-    args: RenderArgs & {
-      signal?: AbortSignal
-      statusCallback?: (arg: string) => void
-    },
-    rpcDriverClassName: string,
-  ) {
-    const pm = this.pluginManager
-    const assemblyManager = pm.rootModel?.session?.assemblyManager
-    if (!assemblyManager) {
-      return args
-    }
-
-    const renamedArgs = await renameRegionsIfNeeded(assemblyManager, {
-      ...args,
-      filters: args.filters?.toJSON().filters,
-    })
-
-    return super.serializeArguments(renamedArgs, rpcDriverClassName)
-  }
-
-  async execute(
-    args: {
-      adapterConfig: {}
-      signal?: RemoteAbortSignal
-      sessionId: string
-      headers?: Record<string, string>
-      regions: Region[]
-      bpPerPx: number
-    },
-    rpcDriverClassName: string,
-  ) {
-    const pm = this.pluginManager
-    const deserializedArgs = await this.deserializeArguments(
-      args,
-      rpcDriverClassName,
-    )
-    const { regions, adapterConfig, sessionId } = deserializedArgs
-    const { dataAdapter } = await getAdapter(pm, sessionId, adapterConfig)
-
-    if (dataAdapter instanceof BaseFeatureDataAdapter) {
-      return dataAdapter.getMultiRegionStats(regions, deserializedArgs)
-    }
-    throw new Error('Data adapter not found')
-  }
-}
-
-export class MultiWiggleGetSources extends RpcMethodType {
-  name = 'MultiWiggleGetSources'
-
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any
-  async deserializeArguments(args: any, rpcDriverClassName: string) {
-    const l = await super.deserializeArguments(args, rpcDriverClassName)
-    return {
-      ...l,
-      filters: args.filters
-        ? new SerializableFilterChain({
-            filters: args.filters,
-          })
-        : undefined,
-    }
-  }
-
-  async serializeArguments(
-    args: RenderArgs & {
-      signal?: AbortSignal
-      statusCallback?: (arg: string) => void
-    },
-    rpcDriverClassName: string,
-  ) {
-    const pm = this.pluginManager
-    const assemblyManager = pm.rootModel?.session?.assemblyManager
-    if (!assemblyManager) {
-      return args
-    }
-
-    const renamedArgs = await renameRegionsIfNeeded(assemblyManager, {
-      ...args,
-      filters: args.filters?.toJSON().filters,
-    })
-
-    return super.serializeArguments(renamedArgs, rpcDriverClassName)
-  }
-
-  async execute(
-    args: {
-      adapterConfig: {}
-      signal?: RemoteAbortSignal
-      sessionId: string
-      headers?: Record<string, string>
-      regions: Region[]
-      bpPerPx: number
-    },
-    rpcDriverClassName: string,
-  ) {
-    const pm = this.pluginManager
-    const deserializedArgs = await this.deserializeArguments(
-      args,
-      rpcDriverClassName,
-    )
-    const { regions, adapterConfig, sessionId } = deserializedArgs
-    const { dataAdapter } = await getAdapter(pm, sessionId, adapterConfig)
-
-    // @ts-expect-error
-    return dataAdapter.getSources(regions, deserializedArgs)
-  }
-}
+export * from './MultiWiggleGetSources'
+export * from './WiggleGetMultiRegionQuantitativeStats'
+export * from './WiggleGetGlobalQuantitativeStats'

package/src/index.ts

@@ -30,8 +30,8 @@ import MultiWiggleAddTrackWidgetF from './MultiWiggleAddTrackWidget'
 import * as utils from './util'
 
 import {
-  WiggleGetGlobalStats,
-  WiggleGetMultiRegionStats,
+  WiggleGetGlobalQuantitativeStats,
+  WiggleGetMultiRegionQuantitativeStats,
   MultiWiggleGetSources,
 } from './WiggleRPC/rpcMethods'
 
@@ -101,8 +101,8 @@ export default class WigglePlugin extends Plugin {
       },
     )
 
-    pm.addRpcMethod(() => new WiggleGetGlobalStats(pm))
-    pm.addRpcMethod(() => new WiggleGetMultiRegionStats(pm))
+    pm.addRpcMethod(() => new WiggleGetGlobalQuantitativeStats(pm))
+    pm.addRpcMethod(() => new WiggleGetMultiRegionQuantitativeStats(pm))
     pm.addRpcMethod(() => new MultiWiggleGetSources(pm))
   }
 

package/src/util.ts

@@ -5,7 +5,7 @@ import {
   getSession,
   getContainingView,
 } from '@jbrowse/core/util'
-import { FeatureStats } from '@jbrowse/core/util/stats'
+import { QuantitativeStats } from '@jbrowse/core/util/stats'
 import { getRpcSessionId } from '@jbrowse/core/util/tracks'
 import { addDisposer, isAlive } from 'mobx-state-tree'
 
@@ -176,9 +176,10 @@ export function groupBy<T>(array: T[], predicate: (v: T) => string) {
   return result
 }
 
-export async function getStats(
+export async function getQuantitativeStats(
   self: {
     adapterConfig: AnyConfigurationModel
+    configuration: AnyConfigurationModel
     autoscaleType: string
     setMessage: (str: string) => void
   },
@@ -187,7 +188,7 @@ export async function getStats(
     signal?: AbortSignal
     filters?: string[]
   },
-): Promise<FeatureStats> {
+): Promise<QuantitativeStats> {
   const { rpcManager } = getSession(self)
   const nd = getConf(self, 'numStdDev') || 3
   const { adapterConfig, autoscaleType } = self
@@ -204,11 +205,11 @@ export async function getStats(
   }
 
   if (autoscaleType === 'global' || autoscaleType === 'globalsd') {
-    const results: FeatureStats = (await rpcManager.call(
+    const results: QuantitativeStats = (await rpcManager.call(
       sessionId,
-      'WiggleGetGlobalStats',
+      'WiggleGetGlobalQuantitativeStats',
       params,
-    )) as FeatureStats
+    )) as QuantitativeStats
     const { scoreMin, scoreMean, scoreStdDev } = results
     // globalsd uses heuristic to avoid unnecessary scoreMin<0
     // if the scoreMin is never less than 0
@@ -225,7 +226,7 @@ export async function getStats(
     const { dynamicBlocks, bpPerPx } = getContainingView(self) as LGV
     const results = (await rpcManager.call(
       sessionId,
-      'WiggleGetMultiRegionStats',
+      'WiggleGetMultiRegionQuantitativeStats',
       {
         ...params,
         regions: dynamicBlocks.contentBlocks.map(region => {
@@ -238,7 +239,7 @@ export async function getStats(
         }),
         bpPerPx,
       },
-    )) as FeatureStats
+    )) as QuantitativeStats
     const { scoreMin, scoreMean, scoreStdDev } = results
 
     // localsd uses heuristic to avoid unnecessary scoreMin<0 if the
@@ -255,20 +256,25 @@ export async function getStats(
   if (autoscaleType === 'zscale') {
     return rpcManager.call(
       sessionId,
-      'WiggleGetGlobalStats',
+      'WiggleGetGlobalQuantitativeStats',
       params,
-    ) as Promise<FeatureStats>
+    ) as Promise<QuantitativeStats>
   }
   throw new Error(`invalid autoscaleType '${autoscaleType}'`)
 }
 
-export function statsAutorun(self: {
-  estimatedStatsReady: boolean
+export function quantitativeStatsAutorun(self: {
+  featureDensityStatsReady: boolean
   regionTooLarge: boolean
+  error: unknown
   setLoading: (aborter: AbortController) => void
   setError: (error: unknown) => void
-  updateStats: (stats: FeatureStats, statsRegion: string) => void
+  updateQuantitativeStats: (
+    stats: QuantitativeStats,
+    statsRegion: string,
+  ) => void
   renderProps: () => Record<string, unknown>
+  configuration: AnyConfigurationModel
   adapterConfig: AnyConfigurationModel
   autoscaleType: string
   setMessage: (str: string) => void
@@ -284,20 +290,21 @@ export function statsAutorun(self: {
 
           if (
             !view.initialized ||
-            !self.estimatedStatsReady ||
-            self.regionTooLarge
+            !self.featureDensityStatsReady ||
+            self.regionTooLarge ||
+            self.error
           ) {
             return
           }
           const statsRegion = JSON.stringify(view.dynamicBlocks)
 
-          const wiggleStats = await getStats(self, {
+          const wiggleStats = await getQuantitativeStats(self, {
             signal: aborter.signal,
             ...self.renderProps(),
           })
 
           if (isAlive(self)) {
-            self.updateStats(wiggleStats, statsRegion)
+            self.updateQuantitativeStats(wiggleStats, statsRegion)
           }
         } catch (e) {
           if (!isAbortException(e) && isAlive(self)) {