Lint

Author: cmdcolin

plugins/linear-comparative-view/src/LinearComparativeView/components/MinLengthSlider.tsx

@@ -4,8 +4,8 @@ import { Box, Slider, Tooltip, Typography } from '@mui/material'
 import { observer } from 'mobx-react'
 import { makeStyles } from 'tss-react/mui'
 
-import type { LinearComparativeViewModel } from '../model'
 import type { LinearSyntenyDisplayModel } from '../../LinearSyntenyDisplay/model'
+import type { LinearComparativeViewModel } from '../model'
 import type { SliderValueLabelProps } from '@mui/material'
 
 const useStyles = makeStyles()({
@@ -65,17 +65,17 @@ const MinLengthSlider = observer(function ({
       <Slider
         value={minLengthValue}
         onChange={(_, val) => {
-          setMinLengthValue(val as number)
+          setMinLengthValue(val)
         }}
         onChangeCommitted={() => {
           const newMinLength = Math.round(2 ** (minLengthValue / 100))
           // Set minAlignmentLength for all synteny displays across all levels
           for (const level of levels) {
             for (const track of level.tracks) {
               for (const display of track.displays) {
-                ;(
-                  display as LinearSyntenyDisplayModel
-                ).setMinAlignmentLength(newMinLength)
+                ;(display as LinearSyntenyDisplayModel).setMinAlignmentLength(
+                  newMinLength,
+                )
               }
             }
           }

plugins/linear-comparative-view/src/LinearComparativeView/components/OpacitySlider.tsx

@@ -2,8 +2,8 @@ import { Box, Slider, Tooltip, Typography } from '@mui/material'
 import { observer } from 'mobx-react'
 import { makeStyles } from 'tss-react/mui'
 
-import type { LinearComparativeViewModel } from '../model'
 import type { LinearSyntenyDisplayModel } from '../../LinearSyntenyDisplay/model'
+import type { LinearComparativeViewModel } from '../model'
 import type { SliderValueLabelProps } from '@mui/material'
 
 const useStyles = makeStyles()({

plugins/linear-comparative-view/src/LinearSyntenyDisplay/afterAttach.ts

@@ -66,6 +66,7 @@ export function doAfterAttach(self: LinearSyntenyDisplayModel) {
       }
 
       // Access alpha to make autorun react to alpha changes
+      // eslint-disable-next-line @typescript-eslint/no-unused-vars
       const { alpha } = self
       const height = self.height
       const width = view.width
@@ -90,6 +91,7 @@ export function doAfterAttach(self: LinearSyntenyDisplayModel) {
         return
       }
       // Access reactive properties so autorun is triggered when they change
+      // eslint-disable-next-line @typescript-eslint/no-unused-vars
       const { clickId, mouseoverId } = self
       // Draw mouseover with light debounce for performance
       debouncedDrawMouseoverClickMap(self)

plugins/linear-comparative-view/src/LinearSyntenyDisplay/drawSynteny.ts

@@ -97,8 +97,6 @@ export function drawCigarClickMap(
         const unitMultiplier2 = Math.floor(MAX_COLOR_RANGE / cigar.length)
 
         for (let j = 0; j < cigar.length; j += 2) {
-          const idx = j * unitMultiplier2 + 1
-
           const len = +cigar[j]!
           const op = cigar[j + 1] as keyof typeof colorMap
 
@@ -146,8 +144,19 @@ export function drawCigarClickMap(
                   Math.abs(cx2 - px2) > 1)
 
               if (shouldDraw) {
+                const idx = j * unitMultiplier2 + 1
                 cigarClickMapCanvas.fillStyle = makeColor(idx)
-                draw(cigarClickMapCanvas, px1, cx1, y1, cx2, px2, y2, mid, drawCurves)
+                draw(
+                  cigarClickMapCanvas,
+                  px1,
+                  cx1,
+                  y1,
+                  cx2,
+                  px2,
+                  y2,
+                  mid,
+                  drawCurves,
+                )
                 cigarClickMapCanvas.fill()
               }
             }
@@ -283,8 +292,6 @@ export function drawRef(
         const unitMultiplier2 = Math.floor(MAX_COLOR_RANGE / cigar.length)
 
         for (let j = 0; j < cigar.length; j += 2) {
-          const idx = j * unitMultiplier2 + 1
-
           const len = +cigar[j]!
           const op = cigar[j + 1] as keyof typeof colorMap
 
@@ -398,7 +405,8 @@ export function drawRef(
 
     // Filter by total alignment length for this query sequence
     if (minAlignmentLength > 0) {
-      const queryName = feature.f.get('name') || feature.f.get('id') || feature.f.id()
+      const queryName =
+        feature.f.get('name') || feature.f.get('id') || feature.f.id()
       const totalLength = queryTotalLengths.get(queryName) || 0
       if (totalLength < minAlignmentLength) {
         continue

plugins/linear-comparative-view/src/LinearSyntenyView/components/DiagonalizationProgressDialog.tsx

@@ -14,8 +14,8 @@ import { observer } from 'mobx-react'
 
 import { diagonalizeRegions } from '../util/diagonalize'
 
-import type { AlignmentData } from '../util/diagonalize'
 import type { LinearSyntenyViewModel } from '../model'
+import type { AlignmentData } from '../util/diagonalize'
 
 const DiagonalizationProgressDialog = observer(function ({
   handleClose,

plugins/linear-comparative-view/src/LinearSyntenyView/util/diagonalize.ts

@@ -31,9 +31,10 @@ export interface DiagonalizationResult {
   }
 }
 
-export interface ProgressCallback {
-  (progress: number, message: string): void | Promise<void>
-}
+export type ProgressCallback = (
+  progress: number,
+  message: string,
+) => void | Promise<void>
 
 /**
  * Diagonalize a set of regions based on alignment data.
@@ -159,15 +160,6 @@ export async function diagonalizeRegions(
   const newQueryRegions: Region[] = []
   let regionsReversed = 0
 
-  console.log('Query ordering:', queryOrdering)
-  console.log(
-    'Current query regions:',
-    currentRegions.map(r => ({
-      refName: r.refName,
-      assemblyName: r.assemblyName,
-    })),
-  )
-
   for (const { refName, shouldReverse } of queryOrdering) {
     const region = currentRegions.find(r => r.refName === refName)
     if (region) {
@@ -183,8 +175,6 @@ export async function diagonalizeRegions(
     }
   }
 
-  console.log('New query regions count:', newQueryRegions.length)
-
   await updateProgress(100, 'Diagonalization complete!')
 
   return {