Clear selection

package.json

@@ -23,6 +23,7 @@
   "dependencies": {
     "@mui/icons-material": "^5.15.10",
     "clustal-js": "^2.0.1",
+    "g2p_mapper": "^1.0.3",
     "molstar": "^4.0.0",
     "pako": "^2.1.0"
   },

src/mappings.ts

@@ -1,4 +1,5 @@
 import { Feature } from '@jbrowse/core/util'
+import { genomeToTranscriptSeqMapping as g2p } from 'g2p_mapper'
 
 export interface Alignment {
   alns: {
@@ -83,45 +84,6 @@ export function transcriptPositionToAlignmentMap(alignment: Alignment) {
 
 // see similar function in msaview plugin
 export function genomeToTranscriptSeqMapping(feature: Feature) {
-  const strand = feature.get('strand') as number
-  const refName = feature.get('refName')
-  const subs = feature.children() ?? []
-  const cds = subs
-    .filter(f => f.get('type') === 'CDS')
-    .sort((a, b) => strand * (a.get('start') - b.get('start')))
-  const g2p = {} as Record<number, number | undefined>
-  const p2g = {} as Record<number, number | undefined>
-
-  let proteinCounter = 0
-  if (strand !== -1) {
-    for (const f of cds) {
-      for (
-        let genomePos = f.get('start');
-        genomePos < f.get('end');
-        genomePos++
-      ) {
-        const proteinPos = Math.floor(proteinCounter++ / 3)
-        g2p[genomePos] = proteinPos
-        if (!p2g[proteinPos]) {
-          p2g[proteinPos] = genomePos
-        }
-      }
-    }
-  } else {
-    for (const f of cds) {
-      for (
-        let genomePos = f.get('end');
-        genomePos > f.get('start');
-        genomePos--
-      ) {
-        const proteinPos = Math.floor(proteinCounter++ / 3)
-        g2p[genomePos] = proteinPos
-        if (!p2g[proteinPos]) {
-          p2g[proteinPos] = genomePos
-        }
-      }
-    }
-  }
-
-  return { g2p, p2g, refName, strand }
+  // @ts-expect-error
+  return g2p(feature.toJSON())
 }