Misc

GMOD · Oct 31, 2023 · c0b7d70 · c0b7d70
1 parent 7d32376
commit c0b7d70
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Showing 4 changed files with 16 additions and 18 deletions.
diff --git a/config.json b/config.json
@@ -2,7 +2,7 @@
   "plugins": [
     {
       "name": "MsaView",
-      "url": "http://localhost:9000/out.js"
+      "url": "http://localhost:9000/dist/out.js"
     }
   ],
   "assemblies": [

diff --git a/esbuild.mjs b/esbuild.mjs
@@ -50,7 +50,7 @@ let ctx = await esbuild.context({
 })
 
 let { host, port } = await ctx.serve({
-  servedir: 'dist',
+  servedir: '.',
   port: 9000,
   host: 'localhost',
 })

diff --git a/package.json b/package.json
@@ -25,7 +25,6 @@
   },
   "scripts": {
     "clean": "rimraf dist",
-    "prestart": "mkdir dist; cp config.json dist",
     "start": "node esbuild.mjs",
     "prebuild": "npm run clean",
     "build": "rollup --config --bundleConfigAsCjs",

diff --git a/src/MsaView/model.ts b/src/MsaView/model.ts
@@ -3,12 +3,7 @@ import { Instance, addDisposer, cast, types } from 'mobx-state-tree'
 import { autorun } from 'mobx'
 import { Region } from '@jbrowse/core/util/types/mst'
 import { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
-import {
-  Feature,
-  SimpleFeature,
-  doesIntersect2,
-  getSession,
-} from '@jbrowse/core/util'
+import { SimpleFeature, doesIntersect2, getSession } from '@jbrowse/core/util'
 
 type LGV = LinearGenomeViewModel
 type MaybeLGV = LGV | undefined
@@ -44,19 +39,19 @@ export default function stateModelFactory() {
       /**
        * #action
        */
-      setHighlights(r: IRegion[]) {
+      setConnectedHighlights(r: IRegion[]) {
         self.connectedHighlights = cast(r)
       },
       /**
        * #action
        */
-      addToHighlights(r: IRegion) {
+      addToConnectedHighlights(r: IRegion) {
         self.connectedHighlights.push(r)
       },
       /**
        * #action
        */
-      clearHighlights() {
+      clearConnectedHighlights() {
         self.connectedHighlights = cast([])
       },
     }))
@@ -68,7 +63,10 @@ export default function stateModelFactory() {
         const f = new SimpleFeature(self.connectedFeature)
         let iter = 0
 
-        const subs: Feature[] = f.get('subfeatures') || []
+        const strand = f.get('strand')
+        const children = f.children() ?? []
+        const subs = strand === -1 ? children.reverse() : children
+
         return subs
           .filter(f => f.get('type') === 'CDS')
           .map(f => {
@@ -86,6 +84,7 @@ export default function stateModelFactory() {
               featureEnd,
               proteinStart,
               proteinEnd,
+              strand,
             } as const
           })
       },
@@ -150,11 +149,11 @@ export default function stateModelFactory() {
             }
             for (const entry of transcriptToMsaMap) {
               const { featureStart, refName, proteinStart, proteinEnd } = entry
-              if (
-                doesIntersect2(proteinStart, proteinEnd, mouseCol, mouseCol + 1)
-              ) {
-                const ret = (mouseCol - proteinStart) * 3
-                self.setHighlights([
+              const c = mouseCol - 1
+              console.log({ mouseCol })
+              if (doesIntersect2(proteinStart, proteinEnd, c, c + 1)) {
+                const ret = (c - proteinStart) * 3
+                self.setConnectedHighlights([
                   {
                     assemblyName: 'hg38',
                     refName,