@apollo-annotation/jbrowse-plugin-apollo 0.3.12 → 1.0.0

package/src/LinearApolloReferenceSequenceDisplay/drawSequenceOverlay.ts

@@ -67,7 +67,7 @@ function fillAndStrokeRect(
   ctx.strokeRect(left, top, width, height)
 }
 
-function drawHighlight(
+function drawHover(
   ctx: CanvasRenderingContext2D,
   feature: AnnotationFeature,
   bpPerPx: number,
@@ -78,7 +78,7 @@ function drawHighlight(
   selected = false,
 ) {
   const row = getSeqRow(feature.strand, bpPerPx, block.reversed)
-  if (!row) {
+  if (row === undefined) {
     return
   }
   const left = getLeftPx(feature, bpPerPx, offsetPx, block)
@@ -157,7 +157,7 @@ export function drawSequenceOverlay(
           feature._id === selectedFeature?._id,
         )
       } else {
-        drawHighlight(
+        drawHover(
           ctx,
           feature,
           bpPerPx,

package/src/LinearApolloReferenceSequenceDisplay/stateModel/base.ts

@@ -13,6 +13,7 @@ import {
 import { BaseDisplay } from '@jbrowse/core/pluggableElementTypes'
 import {
   type AbstractSessionModel,
+  type Region,
   getContainingView,
   getSession,
 } from '@jbrowse/core/util'
@@ -84,13 +85,30 @@ export function baseModelFactory(
         return regions
       },
       regionCannotBeRendered(/* region */) {
-        if (self.lgv && self.lgv.bpPerPx >= 3) {
+        if (self.lgv && self.lgv.bpPerPx > 3) {
           return 'Zoom in to see sequence'
         }
         return
       },
     }))
     .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 expandedStart = Math.round(
+            Math.max(start - 5, parentRegion.start),
+          )
+          const expandedEnd = Math.round(Math.min(end + 5, parentRegion.end))
+          return {
+            assemblyName,
+            refName,
+            start: expandedStart,
+            end: expandedEnd,
+          }
+        })
+        return regions
+      },
       get apolloInternetAccount() {
         const [region] = self.regions
         const { internetAccounts } = getRoot<ApolloRootModel>(self)
@@ -216,7 +234,7 @@ export function baseModelFactory(
               if (self.lgv.bpPerPx <= 3) {
                 void (
                   self.session as unknown as ApolloSessionModel
-                ).apolloDataStore.loadRefSeq(self.regions)
+                ).apolloDataStore.loadRefSeq(self.expandedRegions)
               }
             },
             {

package/src/LinearApolloSixFrameDisplay/components/LinearApolloSixFrameDisplay.tsx

@@ -22,6 +22,7 @@ import {
   clusterResultByMessage,
   useStyles,
 } from '../../util/displayUtils'
+import { looksLikeGene } from '../../util/glyphUtils'
 import type { LinearApolloSixFrameDisplay as LinearApolloSixFrameDisplayI } from '../stateModel'
 
 import { TrackLines } from './TrackLines'
@@ -185,7 +186,11 @@ export const LinearApolloSixFrameDisplay = observer(
                         regionNumber: idx,
                       })?.offsetPx ?? 0) - lgv.offsetPx
                     const [feature] = checkResult.featureIds
-                    if (!feature || !feature.parent?.looksLikeGene) {
+                    if (
+                      !feature ||
+                      !feature.parent ||
+                      !looksLikeGene(feature.parent, session)
+                    ) {
                       return null
                     }
 
@@ -202,7 +207,7 @@ export const LinearApolloSixFrameDisplay = observer(
                           ? [0, 5, 3, 1, 15, 13, 11]
                           : [0, 2, 1, 0, 8, 7, 6]
                         const rowNum = frameOffsets.at(frame)
-                        if (!rowNum) {
+                        if (rowNum === undefined) {
                           continue
                         }
                         if (

package/src/LinearApolloSixFrameDisplay/glyphs/GeneGlyph.ts

@@ -330,7 +330,7 @@ function draw(
       let prevCDSTop = 0
       let prevCDSEndPx = 0
       let counter = 1
-      for (const cds of cdsRow.sort((a, b) => a.max - b.max)) {
+      for (const cds of cdsRow.toSorted((a, b) => a.max - b.max)) {
         if (
           (selectedFeature &&
             isSelected &&
@@ -473,7 +473,7 @@ function drawDragPreview(
   overlayCtx.fillRect(rectX, rectY, rectWidth, rectHeight)
 }
 
-function drawHover(
+function drawOverlay(
   stateModel: LinearApolloSixFrameDisplay,
   ctx: CanvasRenderingContext2D,
 ) {
@@ -520,7 +520,7 @@ function drawHover(
     let prevCDSTop = 0
     let prevCDSEndPx = 0
     let counter = 1
-    for (const cds of cdsRow.sort((a, b) => a.max - b.max)) {
+    for (const cds of cdsRow.toSorted((a, b) => a.max - b.max)) {
       const cdsWidthPx = (cds.max - cds.min) / bpPerPx
       const minX =
         (lgv.bpToPx({
@@ -859,7 +859,7 @@ function getContextMenuItems(
   const currentAssemblyId = display.getAssemblyId(region.assemblyName)
   const menuItems: MenuItem[] = []
   const role = internetAccount ? internetAccount.role : 'admin'
-  const admin = role === 'admin'
+  const readOnly = !(role && ['admin', 'user'].includes(role))
   if (!hoveredFeature) {
     return menuItems
   }
@@ -886,12 +886,7 @@ function getContextMenuItems(
         feature,
       )
       if (isExonFeature(feature, session)) {
-        const adjacentExons = getAdjacentExons(
-          feature,
-          display,
-          mousePosition,
-          session,
-        )
+        const adjacentExons = getAdjacentExons(feature, display)
         const lgv = getContainingView(
           display as BaseDisplayModel,
         ) as unknown as LinearGenomeViewModel
@@ -928,7 +923,7 @@ function getContextMenuItems(
         contextMenuItemsForFeature.push(
           {
             label: 'Merge exons',
-            disabled: !admin,
+            disabled: readOnly,
             onClick: () => {
               ;(session as unknown as AbstractSessionModel).queueDialog(
                 (doneCallback) => [
@@ -952,7 +947,7 @@ function getContextMenuItems(
           },
           {
             label: 'Split exon',
-            disabled: !admin,
+            disabled: readOnly,
             onClick: () => {
               ;(session as unknown as AbstractSessionModel).queueDialog(
                 (doneCallback) => [
@@ -1014,7 +1009,7 @@ function onMouseLeave(): void {
 export const geneGlyph: Glyph = {
   draw,
   drawDragPreview,
-  drawHover,
+  drawOverlay,
   drawTooltip,
   getContextMenuItems,
   getContextMenuItemsForFeature,

package/src/LinearApolloSixFrameDisplay/glyphs/Glyph.ts

@@ -16,7 +16,7 @@ export interface Glyph {
     displayedRegionIndex: number,
   ): void
 
-  drawHover(
+  drawOverlay(
     display: LinearApolloSixFrameDisplayMouseEvents,
     overlayCtx: CanvasRenderingContext2D,
   ): void

package/src/LinearApolloSixFrameDisplay/stateModel/layouts.ts

@@ -12,7 +12,8 @@ import { addDisposer, isAlive } from '@jbrowse/mobx-state-tree'
 import { autorun, observable } from 'mobx'
 
 import type { ApolloSessionModel } from '../../session'
-import { geneGlyph } from '../glyphs'
+import { looksLikeGene } from '../../util/glyphUtils'
+import { geneGlyph } from '../glyphs/GeneGlyph'
 
 import { baseModelFactory } from './base'
 
@@ -123,7 +124,7 @@ export function layoutsModelFactory(
             if (!featureTypeOntology) {
               throw new Error('featureTypeOntology is undefined')
             }
-            if (feature.looksLikeGene) {
+            if (looksLikeGene(feature, self.session)) {
               const rowNum =
                 feature.strand == 1
                   ? self.geneTrackRowNums[0]
@@ -169,7 +170,7 @@ export function layoutsModelFactory(
                         ? [0, 5, 3, 1, 15, 13, 11]
                         : [0, 2, 1, 0, 8, 7, 6]
                       const rowNum = frameOffsets.at(frame)
-                      if (!rowNum) {
+                      if (rowNum === undefined) {
                         continue
                       }
                       if (!featureLayout.get(rowNum)) {

package/src/LinearApolloSixFrameDisplay/stateModel/mouseEvents.ts

@@ -313,7 +313,7 @@ export function mouseEventsModelFactory(
               const glyph = self.getGlyph(hoveredFeature.feature)
 
               // draw mouseover hovers
-              glyph.drawHover(self, ctx)
+              glyph.drawOverlay(self, ctx)
 
               // draw tooltip on hover
               glyph.drawTooltip(self, ctx)

package/src/LinearApolloSixFrameDisplay/stateModel/rendering.ts

@@ -13,6 +13,7 @@ import { autorun } from 'mobx'
 
 import type { ApolloSessionModel } from '../../session'
 import { codonColorCode } from '../../util/displayUtils'
+import { looksLikeGene } from '../../util/glyphUtils'
 
 import { layoutsModelFactory } from './layouts'
 
@@ -209,7 +210,7 @@ export function renderingModelFactory(
                 const displayedRegion = displayedRegions[idx]
                 for (const [row, featureLayoutRow] of featureLayout.entries()) {
                   for (const { feature } of featureLayoutRow) {
-                    if (!feature.looksLikeGene) {
+                    if (!looksLikeGene(feature, self.session)) {
                       continue
                     }
                     if (