Refactorings

Author: cmdcolin

plugins/alignments/src/LinearAlignmentsDisplay/components/WebGLAlignmentsComponent.tsx

@@ -1,6 +1,4 @@
-import {
-  TooLargeMessage,
-} from '@jbrowse/plugin-linear-genome-view'
+import { TooLargeMessage } from '@jbrowse/plugin-linear-genome-view'
 import { observer } from 'mobx-react'
 
 import BlockMsg from './BlockMsg.tsx'

plugins/alignments/src/LinearAlignmentsDisplay/components/WebGLChainComponent.tsx

@@ -1,8 +1,6 @@
 import { useEffect } from 'react'
 
-import {
-  FloatingLegend,
-} from '@jbrowse/plugin-linear-genome-view'
+import { FloatingLegend } from '@jbrowse/plugin-linear-genome-view'
 import { observer } from 'mobx-react'
 
 import { YSCALEBAR_LABEL_OFFSET } from '../model.ts'

plugins/alignments/src/LinearAlignmentsDisplay/components/alignmentComponentUtils.ts

@@ -7,12 +7,16 @@
 
 import { colord } from '@jbrowse/core/util/colord'
 
+import { INTERBASE_TYPES } from './hitTesting.ts'
 import { fillColor } from '../../shared/color.ts'
 
 import type { ColorPalette, RGBColor, WebGLRenderer } from './WebGLRenderer'
-import { INTERBASE_TYPES } from './hitTesting.ts'
-
-import type { CigarHitResult, IndicatorHitResult, CoverageHitResult, SashimiArcHitResult } from './hitTesting'
+import type {
+  CigarHitResult,
+  CoverageHitResult,
+  IndicatorHitResult,
+  SashimiArcHitResult,
+} from './hitTesting'
 import type { WebGLPileupDataResult } from '../../RenderWebGLPileupDataRPC/types'
 import type { Theme } from '@mui/material'
 
@@ -252,8 +256,7 @@ export function formatIndicatorTooltip(
   blockRpcData: WebGLPileupDataResult | undefined,
   refName: string | undefined,
 ) {
-  const posOffset =
-    indicatorHit.position - (blockRpcData?.regionStart ?? 0)
+  const posOffset = indicatorHit.position - (blockRpcData?.regionStart ?? 0)
   const tooltipBin = blockRpcData?.tooltipData[posOffset]
 
   if (tooltipBin) {
@@ -296,8 +299,7 @@ export function formatCoverageTooltip(
   blockRpcData: WebGLPileupDataResult | undefined,
   refName: string | undefined,
 ) {
-  const posOffset =
-    coverageHit.position - (blockRpcData?.regionStart ?? 0)
+  const posOffset = coverageHit.position - (blockRpcData?.regionStart ?? 0)
   const tooltipBin = blockRpcData?.tooltipData[posOffset]
 
   if (tooltipBin || coverageHit.depth > 0) {
@@ -342,11 +344,7 @@ export function formatCoverageTooltip(
 
 export function formatSashimiTooltip(sashimiHit: SashimiArcHitResult) {
   const strandLabel =
-    sashimiHit.strand === 1
-      ? '+'
-      : sashimiHit.strand === -1
-        ? '-'
-        : 'unknown'
+    sashimiHit.strand === 1 ? '+' : sashimiHit.strand === -1 ? '-' : 'unknown'
   return JSON.stringify({
     type: 'sashimi',
     start: sashimiHit.start,
@@ -359,7 +357,18 @@ export function formatSashimiTooltip(sashimiHit: SashimiArcHitResult) {
 
 export function formatFeatureTooltip(
   featureId: string,
-  getFeatureInfoById: (id: string) => { id: string; name: string; start: number; end: number; strand: string; refName: string } | undefined,
+  getFeatureInfoById: (
+    id: string,
+  ) =>
+    | {
+        id: string
+        name: string
+        start: number
+        end: number
+        strand: string
+        refName: string
+      }
+    | undefined,
 ) {
   const info = getFeatureInfoById(featureId)
   if (info) {

plugins/alignments/src/LinearAlignmentsDisplay/components/hitTestPipeline.ts

@@ -26,7 +26,11 @@ export type HitTestResult =
       featureHit?: { id: string; index: number }
       resolved: ResolvedBlock
     }
-  | { type: 'feature'; hit: { id: string; index: number }; resolved: ResolvedBlock }
+  | {
+      type: 'feature'
+      hit: { id: string; index: number }
+      resolved: ResolvedBlock
+    }
   | { type: 'none' }
 
 interface HitTestOptions {

plugins/alignments/src/LinearAlignmentsDisplay/components/openFeatureWidget.ts

@@ -7,7 +7,11 @@ import {
 
 import { CIGAR_TYPE_LABELS } from './alignmentComponentUtils.ts'
 
-import type { CigarHitResult, IndicatorHitResult, CoverageHitResult } from './hitTesting.ts'
+import type {
+  CigarHitResult,
+  CoverageHitResult,
+  IndicatorHitResult,
+} from './hitTesting.ts'
 import type { WebGLPileupDataResult } from '../../RenderWebGLPileupDataRPC/types.ts'
 
 interface ModelForWidget {
@@ -39,8 +43,7 @@ export function openIndicatorWidget(
   refName: string,
   blockRpcData: WebGLPileupDataResult | undefined,
 ) {
-  const posOffset =
-    indicatorHit.position - (blockRpcData?.regionStart ?? 0)
+  const posOffset = indicatorHit.position - (blockRpcData?.regionStart ?? 0)
   const tooltipBin = blockRpcData?.tooltipData[posOffset]
 
   const featureData: Record<string, unknown> = {
@@ -53,8 +56,7 @@ export function openIndicatorWidget(
   }
 
   if (tooltipBin) {
-    const interbaseEntry =
-      tooltipBin.interbase[indicatorHit.indicatorType]
+    const interbaseEntry = tooltipBin.interbase[indicatorHit.indicatorType]
     if (interbaseEntry) {
       featureData.count = `${interbaseEntry.count}/${tooltipBin.depth}`
       featureData.size =
@@ -68,8 +70,7 @@ export function openIndicatorWidget(
     featureData.depth = tooltipBin.depth
   } else {
     const { counts } = indicatorHit
-    featureData.count =
-      counts.insertion + counts.softclip + counts.hardclip
+    featureData.count = counts.insertion + counts.softclip + counts.hardclip
   }
 
   showWidget(model, featureData)
@@ -81,22 +82,15 @@ export function openCoverageWidget(
   refName: string,
   blockRpcData: WebGLPileupDataResult | undefined,
 ) {
-  const posOffset =
-    coverageHit.position - (blockRpcData?.regionStart ?? 0)
+  const posOffset = coverageHit.position - (blockRpcData?.regionStart ?? 0)
   const tooltipBin = blockRpcData?.tooltipData[posOffset]
 
   const hasSNPs = coverageHit.snps.some(
-    s =>
-      s.base === 'A' ||
-      s.base === 'C' ||
-      s.base === 'G' ||
-      s.base === 'T',
+    s => s.base === 'A' || s.base === 'C' || s.base === 'G' || s.base === 'T',
   )
   const hasInterbase = coverageHit.snps.some(
     s =>
-      s.base === 'insertion' ||
-      s.base === 'softclip' ||
-      s.base === 'hardclip',
+      s.base === 'insertion' || s.base === 'softclip' || s.base === 'hardclip',
   )
   if (!hasSNPs && !hasInterbase && !tooltipBin) {
     return

plugins/alignments/src/LinearAlignmentsDisplay/components/useAlignmentsBase.ts

@@ -26,9 +26,9 @@ import {
   openIndicatorWidget,
 } from './openFeatureWidget.ts'
 
-import type { ResolvedBlock } from './hitTesting.ts'
 import type { CloudTicks } from './CloudYScaleBar.tsx'
 import type { CoverageTicks } from './CoverageYScaleBar.tsx'
+import type { ResolvedBlock } from './hitTesting.ts'
 import type { WebGLArcsDataResult } from '../../RenderWebGLArcsDataRPC/types.ts'
 import type { WebGLPileupDataResult } from '../../RenderWebGLPileupDataRPC/types.ts'
 import type {