Reduce re-rendering on quantitative and snpcoverage track height adjustments

packages/core/util/stats.test.ts

@@ -4,7 +4,6 @@ import {
   calcStdFromSums,
   rectifyStats,
   scoresToStats,
-  calcPerBaseStats,
   UnrectifiedQuantitativeStats,
 } from './stats'
 
@@ -55,34 +54,3 @@ test('scores to stats', async () => {
   expect(ret.scoreMin).toEqual(1)
   expect(ret.scoreStdDev).toEqual(1) // calculated from a webapp
 })
-
-// peter TODO: fix this test
-test('calc per base stats', () => {
-  // one score at start
-  expect(
-    calcPerBaseStats({ refName: 'ctgA', start: 0, end: 9 }, [
-      new SimpleFeature({ id: 1, data: { start: 0, end: 1, score: 10 } }),
-    ]),
-  ).toEqual([10, 0, 0, 0, 0, 0, 0, 0, 0])
-  // multiple features
-  expect(
-    calcPerBaseStats({ refName: 'ctgA', start: 0, end: 9 }, [
-      new SimpleFeature({ id: 1, data: { start: 0, end: 1, score: 10 } }),
-      new SimpleFeature({ id: 2, data: { start: 8, end: 9, score: 10 } }),
-    ]),
-  ).toEqual([10, 0, 0, 0, 0, 0, 0, 0, 10])
-  // multiple features
-  expect(
-    calcPerBaseStats({ refName: 'ctgA', start: 15, end: 30 }, [
-      new SimpleFeature({ id: 1, data: { start: 10, end: 20, score: 10 } }),
-      new SimpleFeature({ id: 2, data: { start: 25, end: 26, score: 10 } }),
-    ]),
-  ).toEqual([10, 10, 10, 10, 10, 0, 0, 0, 0, 0, 10, 0, 0, 0, 0])
-  // feature starts before region
-  expect(
-    calcPerBaseStats({ refName: 'ctgA', start: 10, end: 19 }, [
-      new SimpleFeature({ id: 1, data: { start: 5, end: 15, score: 10 } }),
-      new SimpleFeature({ id: 1, data: { start: 18, end: 26, score: 10 } }),
-    ]),
-  ).toEqual([10, 10, 10, 10, 10, 0, 0, 0, 10])
-})

packages/core/util/stats.ts

@@ -14,6 +14,7 @@ export interface UnrectifiedQuantitativeStats {
   basesCovered: number
 }
 export interface QuantitativeStats extends UnrectifiedQuantitativeStats {
+  currStatsBpPerPx: number
   featureDensity: number
   scoreMean: number
   scoreStdDev: number
@@ -71,45 +72,6 @@ export function rectifyStats(s: UnrectifiedQuantitativeStats) {
   } as QuantitativeStats
 }
 
-/**
- * calculates per-base scores for variable width features over a region
- *
- * @param region - object contains start, end
- * @param features - list of features with start, end, score
- * @returns array of numeric scores
- */
-export function calcPerBaseStats(
-  region: NoAssemblyRegion,
-  features: Feature[],
-): number[] {
-  const { start, end } = region
-  const scores = []
-  const feats = features.sort((a, b) => a.get('start') - b.get('start'))
-  let pos = start
-  let currentFeat = 0
-  let i = 0
-
-  while (pos < end) {
-    while (
-      currentFeat < feats.length &&
-      pos >= feats[currentFeat]!.get('end')
-    ) {
-      currentFeat += 1
-    }
-    const f = feats[currentFeat]
-    if (!f) {
-      scores[i] = 0
-    } else if (pos >= f.get('start') && pos < f.get('end')) {
-      scores[i] = f.get('score')
-    } else {
-      scores[i] = 0
-    }
-    i += 1
-    pos += 1
-  }
-  return scores
-}
-
 /**
  * transform a list of scores to summary statistics
  *

plugins/alignments/src/BamAdapter/BamAdapter.ts

@@ -207,7 +207,6 @@ export default class BamAdapter extends BaseFeatureDataAdapter {
           if (tagFilter) {
             const readVal = record.tags[tagFilter.tag]
             const filterVal = tagFilter.value
-            console.log({ readVal, filterVal })
             if (
               filterVal === '*'
                 ? readVal === undefined

plugins/alignments/src/LinearSNPCoverageDisplay/model.ts

@@ -135,7 +135,7 @@ function stateModelFactory(
       },
     }))
     .views(self => {
-      const { renderProps: superRenderProps } = self
+      const { adapterProps: superAdapterProps } = self
       return {
         /**
          * #getter
@@ -196,36 +196,16 @@ function stateModelFactory(
           )
         },
 
-        /**
-         * #getter
-         */
-        get renderReady() {
-          const superProps = superRenderProps()
-          return !superProps.notReady && self.modificationsReady
-        },
-
-        /**
-         * #getter
-         */
-        get ready() {
-          return this.renderReady
-        },
-
         /**
          * #method
          */
-        renderProps() {
-          const superProps = superRenderProps()
-          const { filters, colorBy, filterBy, visibleModifications } = self
+        adapterProps() {
+          const superProps = superAdapterProps()
+          const { filters, filterBy } = self
           return {
             ...superProps,
-            notReady: !this.ready,
             filters,
-            colorBy,
             filterBy,
-            visibleModifications: Object.fromEntries(
-              visibleModifications.toJSON(),
-            ),
           }
         },
       }
@@ -288,8 +268,39 @@ function stateModelFactory(
     }))
 
     .views(self => {
-      const { trackMenuItems: superTrackMenuItems } = self
+      const {
+        renderProps: superRenderProps,
+        trackMenuItems: superTrackMenuItems,
+      } = self
       return {
+        /**
+         * #getter
+         */
+        get renderReady() {
+          const superProps = superRenderProps()
+          return !superProps.notReady && self.modificationsReady
+        },
+
+        /**
+         * #getter
+         */
+        get ready() {
+          return this.renderReady
+        },
+        /**
+         * #method
+         */
+        renderProps() {
+          const { colorBy, visibleModifications } = self
+          return {
+            ...superRenderProps(),
+            notReady: !this.ready,
+            colorBy,
+            visibleModifications: Object.fromEntries(
+              visibleModifications.toJSON(),
+            ),
+          }
+        },
         /**
          * #getter
          */

plugins/linear-genome-view/src/BaseLinearDisplay/models/TrackHeightMixin.tsx

@@ -23,7 +23,7 @@ export default function TrackHeightMixin() {
     })
     .volatile(() => ({
       /**
-       * #property
+       * #volatile
        */
       scrollTop: 0,
     }))

plugins/wiggle/src/LinearWiggleDisplay/components/WiggleDisplayComponent.tsx

@@ -12,7 +12,7 @@ import {
 } from '@jbrowse/plugin-linear-genome-view'
 
 // locals
-import { WiggleDisplayModel } from '../models/model'
+import { WiggleDisplayModel } from '../model'
 import YScaleBar from '../../shared/YScaleBar'
 
 type LGV = LinearGenomeViewModel

plugins/wiggle/src/LinearWiggleDisplay/models/configSchema.ts → plugins/wiggle/src/LinearWiggleDisplay/configSchema.ts

@@ -3,7 +3,7 @@ import { types } from 'mobx-state-tree'
 import PluginManager from '@jbrowse/core/PluginManager'
 
 // locals
-import sharedWiggleConfigFactory from '../../shared/configShared'
+import sharedWiggleConfigFactory from '../shared/SharedWiggleConfigSchema'
 
 /**
  * #config LinearWiggleDisplay

plugins/wiggle/src/LinearWiggleDisplay/index.ts

@@ -1,8 +1,8 @@
 import PluginManager from '@jbrowse/core/PluginManager'
 import DisplayType from '@jbrowse/core/pluggableElementTypes/DisplayType'
 
-import configSchemaFactory from './models/configSchema'
-import modelFactory from './models/model'
+import configSchemaFactory from './configSchema'
+import modelFactory from './model'
 import { lazy } from 'react'
 
 export default function LinearWiggleDisplayF(pluginManager: PluginManager) {
@@ -23,4 +23,4 @@ export default function LinearWiggleDisplayF(pluginManager: PluginManager) {
 
 export { default as Tooltip } from './components/Tooltip'
 export { default as ReactComponent } from './components/WiggleDisplayComponent'
-export { default as modelFactory } from './models/model'
+export { default as modelFactory } from './model'