From c78dafd4289fb32d5c7e256b7d481866cd5f4a55 Mon Sep 17 00:00:00 2001
From: Shashank B R <shashank.b.r.gowda45587@gmail.com>
Date: Tue, 5 Nov 2024 16:05:40 +0000
Subject: [PATCH] Draw background on genes (#464)

* 1. Add backgroud color for topLevelFeature
2. Fix featureInThisRow not Iterable

* background for gene

* Lighten instead of darken background

* Fix strand fill for dark mode

---------

Co-authored-by: Garrett Stevens <stevens.garrett.j@gmail.com>
---
 .../LinearApolloDisplay/glyphs/GeneGlyph.ts   | 100 ++++++++++++------
 1 file changed, 70 insertions(+), 30 deletions(-)

diff --git a/packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/glyphs/GeneGlyph.ts b/packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/glyphs/GeneGlyph.ts
index 25b34b32..f8e01be7 100644
--- a/packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/glyphs/GeneGlyph.ts
+++ b/packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/glyphs/GeneGlyph.ts
@@ -13,35 +13,49 @@ import { Glyph } from './Glyph'
 import { boxGlyph } from './BoxGlyph'
 import { LinearApolloDisplayRendering } from '../stateModel/rendering'
 
-let forwardFill: CanvasPattern | null = null
-let backwardFill: CanvasPattern | null = null
+let forwardFillLight: CanvasPattern | null = null
+let backwardFillLight: CanvasPattern | null = null
+let forwardFillDark: CanvasPattern | null = null
+let backwardFillDark: CanvasPattern | null = null
 if ('document' in window) {
   for (const direction of ['forward', 'backward']) {
-    const canvas = document.createElement('canvas')
-    const canvasSize = 10
-    canvas.width = canvas.height = canvasSize
-    const ctx = canvas.getContext('2d')
-    if (ctx) {
-      const stripeColor1 = 'rgba(0,0,0,0)'
-      const stripeColor2 = 'rgba(255,255,255,0.25)'
-      const gradient =
-        direction === 'forward'
-          ? ctx.createLinearGradient(0, canvasSize, canvasSize, 0)
-          : ctx.createLinearGradient(0, 0, canvasSize, canvasSize)
-      gradient.addColorStop(0, stripeColor1)
-      gradient.addColorStop(0.25, stripeColor1)
-      gradient.addColorStop(0.25, stripeColor2)
-      gradient.addColorStop(0.5, stripeColor2)
-      gradient.addColorStop(0.5, stripeColor1)
-      gradient.addColorStop(0.75, stripeColor1)
-      gradient.addColorStop(0.75, stripeColor2)
-      gradient.addColorStop(1, stripeColor2)
-      ctx.fillStyle = gradient
-      ctx.fillRect(0, 0, 10, 10)
-      if (direction === 'forward') {
-        forwardFill = ctx.createPattern(canvas, 'repeat')
-      } else {
-        backwardFill = ctx.createPattern(canvas, 'repeat')
+    for (const themeMode of ['light', 'dark']) {
+      const canvas = document.createElement('canvas')
+      const canvasSize = 10
+      canvas.width = canvas.height = canvasSize
+      const ctx = canvas.getContext('2d')
+      if (ctx) {
+        const stripeColor1 =
+          themeMode === 'light' ? 'rgba(0,0,0,0)' : 'rgba(0,0,0,0.75)'
+        const stripeColor2 =
+          themeMode === 'light' ? 'rgba(255,255,255,0.25)' : 'rgba(0,0,0,0.50)'
+        const gradient =
+          direction === 'forward'
+            ? ctx.createLinearGradient(0, canvasSize, canvasSize, 0)
+            : ctx.createLinearGradient(0, 0, canvasSize, canvasSize)
+        gradient.addColorStop(0, stripeColor1)
+        gradient.addColorStop(0.25, stripeColor1)
+        gradient.addColorStop(0.25, stripeColor2)
+        gradient.addColorStop(0.5, stripeColor2)
+        gradient.addColorStop(0.5, stripeColor1)
+        gradient.addColorStop(0.75, stripeColor1)
+        gradient.addColorStop(0.75, stripeColor2)
+        gradient.addColorStop(1, stripeColor2)
+        ctx.fillStyle = gradient
+        ctx.fillRect(0, 0, 10, 10)
+        if (direction === 'forward') {
+          if (themeMode === 'light') {
+            forwardFillLight = ctx.createPattern(canvas, 'repeat')
+          } else {
+            forwardFillDark = ctx.createPattern(canvas, 'repeat')
+          }
+        } else {
+          if (themeMode === 'light') {
+            backwardFillLight = ctx.createPattern(canvas, 'repeat')
+          } else {
+            backwardFillDark = ctx.createPattern(canvas, 'repeat')
+          }
+        }
       }
     }
   }
@@ -61,13 +75,34 @@ function draw(
   const rowHeight = apolloRowHeight
   const exonHeight = Math.round(0.6 * rowHeight)
   const cdsHeight = Math.round(0.9 * rowHeight)
-  const { strand } = feature
-  const { children } = feature
+  const { children, min, strand } = feature
   if (!children) {
     return
   }
   const { apolloSelectedFeature } = session
 
+  // Draw background for gene
+  const topLevelFeatureMinX =
+    (lgv.bpToPx({
+      refName,
+      coord: min,
+      regionNumber: displayedRegionIndex,
+    })?.offsetPx ?? 0) - offsetPx
+  const topLevelFeatureWidthPx = feature.length / bpPerPx
+  const topLevelFeatureStartPx = reversed
+    ? topLevelFeatureMinX - topLevelFeatureWidthPx
+    : topLevelFeatureMinX
+  const topLevelFeatureTop = row * rowHeight
+  const topLevelFeatureHeight = getRowCount(feature) * rowHeight
+
+  ctx.fillStyle = alpha(theme?.palette.background.paper ?? '#ffffff', 0.6)
+  ctx.fillRect(
+    topLevelFeatureStartPx,
+    topLevelFeatureTop,
+    topLevelFeatureWidthPx,
+    topLevelFeatureHeight,
+  )
+
   // Draw lines on different rows for each mRNA
   let currentRow = 0
   for (const [, mrna] of children) {
@@ -102,6 +137,10 @@ function draw(
     }
   }
 
+  const forwardFill =
+    theme?.palette.mode === 'dark' ? forwardFillDark : forwardFillLight
+  const backwardFill =
+    theme?.palette.mode === 'dark' ? backwardFillDark : backwardFillLight
   // Draw exon and CDS for each mRNA
   currentRow = 0
   for (const [, child] of children) {
@@ -289,7 +328,8 @@ function getFeatureFromLayout(
   bp: number,
   row: number,
 ): AnnotationFeature | undefined {
-  const featureInThisRow: AnnotationFeature[] = featuresForRow(feature)[row]
+  const featureInThisRow: AnnotationFeature[] =
+    featuresForRow(feature)[row] || []
   for (const f of featureInThisRow) {
     let featureObj
     if (bp >= f.min && bp <= f.max && f.parent) {