Convert displayedRegions from MST array of Region[] into a types.froz…

…en<IRegion[]> to speed up large displayedRegions sets (#4423)
GMOD · Jun 14, 2024 · 9cffada · 9cffada
1 parent c9cc868
commit 9cffada
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Showing 5 changed files with 21 additions and 27 deletions.
diff --git a/packages/core/util/Base1DUtils.ts b/packages/core/util/Base1DUtils.ts
@@ -1,4 +1,3 @@
-import { getSnapshot } from 'mobx-state-tree'
 import { Region, ViewSnap } from './index'
 
 export interface BpOffset {
@@ -100,7 +99,7 @@ export function pxToBp(
   offset: number
   start: number
   end: number
-  reversed: boolean
+  reversed?: boolean
 } {
   let bpSoFar = 0
   const {
@@ -114,8 +113,7 @@ export function pxToBp(
   const bp = (offsetPx + px) * bpPerPx
   if (bp < 0) {
     const r = displayedRegions[0]
-    const snap = getSnapshot(r)
-    // @ts-expect-error
+    const snap = r
     return {
       // xref https://github.com/mobxjs/mobx-state-tree/issues/1524 for Omit
       ...(snap as Omit<typeof snap, symbol>),
@@ -133,8 +131,7 @@ export function pxToBp(
     const len = r.end - r.start
     const offset = bp - bpSoFar
     if (len + bpSoFar > bp && bpSoFar <= bp) {
-      const snap = getSnapshot(r)
-      // @ts-expect-error
+      const snap = r
       return {
         // xref https://github.com/mobxjs/mobx-state-tree/issues/1524 for Omit
         ...(snap as Omit<typeof snap, symbol>),
@@ -160,8 +157,7 @@ export function pxToBp(
     const len = r.end - r.start
     const offset = bp - bpSoFar + len
 
-    const snap = getSnapshot(r)
-    // @ts-expect-error
+    const snap = r
     return {
       // xref https://github.com/mobxjs/mobx-state-tree/issues/1524 for Omit
       ...(snap as Omit<typeof snap, symbol>),

diff --git a/packages/core/util/Base1DViewModel.ts b/packages/core/util/Base1DViewModel.ts
@@ -1,7 +1,7 @@
 import { types, cast, Instance } from 'mobx-state-tree'
-import { clamp } from './index'
+import { clamp, sum } from './index'
 import { Feature } from './simpleFeature'
-import { Region, ElementId } from './types/mst'
+import { ElementId } from './types/mst'
 import { Region as IRegion } from './types'
 import calculateDynamicBlocks from './calculateDynamicBlocks'
 import calculateStaticBlocks from './calculateStaticBlocks'
@@ -23,7 +23,7 @@ const Base1DView = types
     /**
      * #property
      */
-    displayedRegions: types.array(Region),
+    displayedRegions: types.optional(types.frozen<IRegion[]>(), []),
     /**
      * #property
      */
@@ -76,9 +76,7 @@ const Base1DView = types
      * #getter
      */
     get assemblyNames() {
-      return [
-        ...new Set(self.displayedRegions.map(region => region.assemblyName)),
-      ]
+      return [...new Set(self.displayedRegions.map(r => r.assemblyName))]
     },
     /**
      * #getter
@@ -109,9 +107,7 @@ const Base1DView = types
      * #getter
      */
     get totalBp() {
-      return self.displayedRegions
-        .map(a => a.end - a.start)
-        .reduce((a, b) => a + b, 0)
+      return sum(self.displayedRegions.map(a => a.end - a.start))
     },
   }))
   .views(self => ({
@@ -133,9 +129,7 @@ const Base1DView = types
      * #getter
      */
     get currBp() {
-      return this.dynamicBlocks
-        .map(a => a.end - a.start)
-        .reduce((a, b) => a + b, 0)
+      return sum(this.dynamicBlocks.map(a => a.end - a.start))
     },
   }))
   .views(self => ({
@@ -265,8 +259,8 @@ const Base1DView = types
   .actions(self => ({
     /**
      * #action
-     * offset is the base-pair-offset in the displayed region, index is the index of the
-     * displayed region in the linear genome view
+     * offset is the base-pair-offset in the displayed region, index is the
+     * index of the displayed region in the linear genome view
      *
      * @param start - object as `{start, end, offset, index}`
      * @param end - object as `{start, end, offset, index}`

diff --git a/packages/core/util/index.ts b/packages/core/util/index.ts
@@ -1126,7 +1126,7 @@ export interface ViewSnap {
     start: number
     end: number
     refName: string
-    reversed: boolean
+    reversed?: boolean
     assemblyName: string
   })[]
 }

diff --git a/packages/core/util/types/index.ts b/packages/core/util/types/index.ts
@@ -416,7 +416,10 @@ export function isAbstractMenuManager(
 export interface NoAssemblyRegion
   extends SnapshotIn<typeof MUNoAssemblyRegion> {}
 
-/** a description of a specific genomic region. assemblyName, refName, start, end, and reversed */
+/**
+ * a description of a specific genomic region. assemblyName, refName, start,
+ * end, and reversed
+ */
 export interface Region extends SnapshotIn<typeof MUIRegion> {}
 
 export interface AugmentedRegion extends Region {

diff --git a/plugins/linear-genome-view/src/LinearGenomeView/model.ts b/plugins/linear-genome-view/src/LinearGenomeView/model.ts
@@ -2,7 +2,8 @@ import React, { lazy } from 'react'
 import { getConf, AnyConfigurationModel } from '@jbrowse/core/configuration'
 import { BaseViewModel } from '@jbrowse/core/pluggableElementTypes/models'
 import { Region } from '@jbrowse/core/util/types'
-import { ElementId, Region as MUIRegion } from '@jbrowse/core/util/types/mst'
+import { ElementId } from '@jbrowse/core/util/types/mst'
+import { Region as IRegion } from '@jbrowse/core/util/types'
 import { MenuItem } from '@jbrowse/core/ui'
 import {
   assembleLocString,
@@ -175,7 +176,7 @@ export function stateModelFactory(pluginManager: PluginManager) {
          * advised to use the entire set of chromosomes if your assembly is very
          * fragmented
          */
-        displayedRegions: types.array(MUIRegion),
+        displayedRegions: types.optional(types.frozen<IRegion[]>(), []),
 
         /**
          * #property
@@ -421,7 +422,7 @@ export function stateModelFactory(pluginManager: PluginManager) {
        * #getter
        */
       get totalBp() {
-        return self.displayedRegions.reduce((a, b) => a + b.end - b.start, 0)
+        return sum(self.displayedRegions.map(r => r.end - r.start))
       },
 
       /**