Fix LGV block API usage after upstream rename to displayedRegionIndex

packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/glyphs/util.ts

@@ -104,8 +104,16 @@ export function isMouseOnFeatureEdge(
   const { refName, regionNumber, x } = mousePosition
   const { lgv } = stateModel
   const { offsetPx } = lgv
-  const minPxInfo = lgv.bpToPx({ refName, coord: feature.min, regionNumber })
-  const maxPxInfo = lgv.bpToPx({ refName, coord: feature.max, regionNumber })
+  const minPxInfo = lgv.bpToPx({
+    refName,
+    coord: feature.min,
+    displayedRegionIndex: regionNumber,
+  })
+  const maxPxInfo = lgv.bpToPx({
+    refName,
+    coord: feature.max,
+    displayedRegionIndex: regionNumber,
+  })
   if (minPxInfo !== undefined && maxPxInfo !== undefined) {
     const minPx = minPxInfo.offsetPx - offsetPx
     const maxPx = maxPxInfo.offsetPx - offsetPx

packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/stateModel/rendering.ts

@@ -138,7 +138,7 @@ export function renderingModelFactory(
                     const locationStartPxInfo = self.lgv.bpToPx({
                       refName: refSeq,
                       coord: start,
-                      regionNumber: idx,
+                      displayedRegionIndex: idx,
                     })
                     if (!locationStartPxInfo) {
                       continue

packages/jbrowse-plugin-apollo/src/LinearApolloReferenceSequenceDisplay/stateModel/base.ts

@@ -14,7 +14,6 @@ import {
 import { BaseDisplay } from '@jbrowse/core/pluggableElementTypes'
 import {
   type AbstractSessionModel,
-  type Region,
   getContainingView,
   getSession,
 } from '@jbrowse/core/util'
@@ -95,8 +94,9 @@ export function baseModelFactory(
     .views((self) => ({
       get expandedRegions() {
         const regions = self.lgv.dynamicBlocks.contentBlocks.map((block) => {
-          const { assemblyName, end, refName, start } = block
-          const { parentRegion } = block as unknown as { parentRegion: Region }
+          const { assemblyName, displayedRegionIndex, end, refName, start } =
+            block
+          const parentRegion = self.lgv.displayedRegions[displayedRegionIndex]
           const expandedStart = Math.round(
             Math.max(start - 5, parentRegion.start),
           )

packages/jbrowse-plugin-apollo/src/LinearApolloSixFrameDisplay/components/LinearApolloSixFrameDisplay.tsx

@@ -186,7 +186,7 @@ export const LinearApolloSixFrameDisplay = observer(
                       (lgv.bpToPx({
                         refName: region.refName,
                         coord: checkResult.start,
-                        regionNumber: idx,
+                        displayedRegionIndex: idx,
                       })?.offsetPx ?? 0) - lgv.offsetPx
                     const [feature] = checkResult.featureIds
                     if (

packages/jbrowse-plugin-apollo/src/LinearApolloSixFrameDisplay/glyphs/GeneGlyph.ts

@@ -174,7 +174,7 @@ function draw(
     (lgv.bpToPx({
       refName,
       coord: min,
-      regionNumber: displayedRegionIndex,
+      displayedRegionIndex,
     })?.offsetPx ?? 0) - offsetPx
   const topLevelFeatureWidthPx = topLevelFeature.length / bpPerPx
   const topLevelFeatureStartPx = reversed
@@ -275,7 +275,7 @@ function draw(
         (lgv.bpToPx({
           refName,
           coord: exon.min,
-          regionNumber: displayedRegionIndex,
+          displayedRegionIndex,
         })?.offsetPx ?? 0) - offsetPx
       const widthPx = exon.length / bpPerPx
       const startPx = reversed ? minX - widthPx : minX
@@ -341,7 +341,7 @@ function draw(
             (lgv.bpToPx({
               refName,
               coord: cds.min,
-              regionNumber: displayedRegionIndex,
+              displayedRegionIndex,
             })?.offsetPx ?? 0) - offsetPx
           cdsStartPx = reversed ? minX - cdsWidthPx : minX
           ctx.fillStyle = theme.palette.text.primary
@@ -525,7 +525,7 @@ function drawOverlay(
         (lgv.bpToPx({
           refName,
           coord: cds.min,
-          regionNumber: layoutIndex,
+          displayedRegionIndex: layoutIndex,
         })?.offsetPx ?? 0) - offsetPx
       const cdsStartPx = reversed ? minX - cdsWidthPx : minX
       const frame = getFrame(cds.min, cds.max, strand ?? 1, cds.phase)
@@ -788,7 +788,7 @@ function drawTooltip(
     (lgv.bpToPx({
       refName,
       coord: reversed ? max : min,
-      regionNumber: layoutIndex,
+      displayedRegionIndex: layoutIndex,
     })?.offsetPx ?? 0) - offsetPx
   const frame = getFrame(min, max, strand ?? 1, phase)
   const frameOffsets = showFeatureLabels

packages/jbrowse-plugin-apollo/src/LinearApolloSixFrameDisplay/stateModel/rendering.ts

@@ -151,7 +151,7 @@ export function renderingModelFactory(
                     const locationStartPxInfo = self.lgv.bpToPx({
                       refName: refSeq,
                       coord: start,
-                      regionNumber: idx,
+                      displayedRegionIndex: idx,
                     })
                     if (!locationStartPxInfo) {
                       continue

packages/jbrowse-plugin-apollo/src/util/glyphUtils.ts

@@ -236,12 +236,12 @@ export function getMinAndMaxPx(
   const minPxInfo = lgv.bpToPx({
     refName,
     coord: feature.min,
-    regionNumber,
+    displayedRegionIndex: regionNumber,
   })
   const maxPxInfo = lgv.bpToPx({
     refName,
     coord: feature.max,
-    regionNumber,
+    displayedRegionIndex: regionNumber,
   })
   if (minPxInfo === undefined || maxPxInfo === undefined) {
     return