Modularize helper function

GMOD · Nov 8, 2023 · 63a30d7 · 63a30d7
1 parent 7f5eba2
commit 63a30d7
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Showing 2 changed files with 71 additions and 70 deletions.
diff --git a/src/MsaView/model.ts b/src/MsaView/model.ts
@@ -3,12 +3,8 @@ 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'
+import { checkHovered, generateMap } from './util'
 
 type LGV = LinearGenomeViewModel
 type MaybeLGV = LGV | undefined
@@ -20,18 +16,6 @@ interface IRegion {
   end: number
 }
 
-function checkHovered(hovered: unknown): hovered is {
-  hoverFeature: Feature
-  hoverPosition: { coord: number; refName: string }
-} {
-  return (
-    !!hovered &&
-    typeof hovered == 'object' &&
-    'hoverFeature' in hovered &&
-    'hoverPosition' in hovered
-  )
-}
-
 export default function stateModelFactory() {
   return types
     .compose(
@@ -77,58 +61,7 @@ export default function stateModelFactory() {
        * #getter
        */
       get transcriptToMsaMap() {
-        const f = new SimpleFeature(self.connectedFeature)
-        let iter = 0
-
-        const strand = f.get('strand')
-        const subs = f.children() ?? []
-        return strand === -1
-          ? subs
-              .filter(f => f.get('type') === 'CDS')
-              .sort((a, b) => b.get('start') - a.get('start'))
-              .map(f => {
-                const refName = f.get('refName').replace('chr', '')
-                const featureStart = f.get('start')
-                const featureEnd = f.get('end')
-                const phase = f.get('phase')
-                const len = featureEnd - featureStart
-                const op = len / 3
-                const proteinStart = iter
-                const proteinEnd = iter + op
-                iter += op
-                return {
-                  refName,
-                  featureStart,
-                  featureEnd,
-                  proteinStart,
-                  proteinEnd,
-                  phase,
-                  strand,
-                } as const
-              })
-          : subs
-              .filter(f => f.get('type') === 'CDS')
-              .sort((a, b) => a.get('start') - b.get('start'))
-              .map(f => {
-                const refName = f.get('refName').replace('chr', '')
-                const featureStart = f.get('start')
-                const featureEnd = f.get('end')
-                const phase = f.get('phase')
-                const len = featureEnd - featureStart
-                const op = len / 3
-                const proteinStart = iter
-                const proteinEnd = iter + op
-                iter += op
-                return {
-                  refName,
-                  featureStart,
-                  featureEnd,
-                  proteinStart,
-                  proteinEnd,
-                  phase,
-                  strand,
-                } as const
-              })
+        return generateMap(new SimpleFeature(self.connectedFeature))
       },
 
       /**

diff --git a/src/MsaView/util.ts b/src/MsaView/util.ts
@@ -0,0 +1,68 @@
+import { Feature } from '@jbrowse/core/util'
+
+// see similar function in protein3d plugin
+export function generateMap(f: Feature) {
+  let iter = 0
+
+  const strand = f.get('strand')
+  const subs = f.children() ?? []
+  return strand === -1
+    ? subs
+        .filter(f => f.get('type') === 'CDS')
+        .sort((a, b) => b.get('start') - a.get('start'))
+        .map(f => {
+          const refName = f.get('refName').replace('chr', '')
+          const featureStart = f.get('start')
+          const featureEnd = f.get('end')
+          const phase = f.get('phase')
+          const len = featureEnd - featureStart
+          const op = len / 3
+          const proteinStart = iter
+          const proteinEnd = iter + op
+          iter += op
+          return {
+            refName,
+            featureStart,
+            featureEnd,
+            proteinStart,
+            proteinEnd,
+            phase,
+            strand,
+          } as const
+        })
+    : subs
+        .filter(f => f.get('type') === 'CDS')
+        .sort((a, b) => a.get('start') - b.get('start'))
+        .map(f => {
+          const refName = f.get('refName').replace('chr', '')
+          const featureStart = f.get('start')
+          const featureEnd = f.get('end')
+          const phase = f.get('phase')
+          const len = featureEnd - featureStart
+          const op = len / 3
+          const proteinStart = iter
+          const proteinEnd = iter + op
+          iter += op
+          return {
+            refName,
+            featureStart,
+            featureEnd,
+            proteinStart,
+            proteinEnd,
+            phase,
+            strand,
+          } as const
+        })
+}
+
+export function checkHovered(hovered: unknown): hovered is {
+  hoverFeature: Feature
+  hoverPosition: { coord: number; refName: string }
+} {
+  return (
+    !!hovered &&
+    typeof hovered == 'object' &&
+    'hoverFeature' in hovered &&
+    'hoverPosition' in hovered
+  )
+}