Crazy

Author: cmdcolin

src/LinearMafDisplay/components/GetSequenceDialog/index.tsx

@@ -1,14 +1,13 @@
 import React, { useEffect, useState } from 'react'
 
 import { Dialog, ErrorMessage, LoadingEllipses } from '@jbrowse/core/ui'
-import { getContainingView, getSession } from '@jbrowse/core/util'
-import { getRpcSessionId } from '@jbrowse/core/util/tracks'
+import { getSession } from '@jbrowse/core/util'
 import { Button, DialogActions, DialogContent, TextField } from '@mui/material'
 import { observer } from 'mobx-react'
 import { makeStyles } from 'tss-react/mui'
 
+import { fetchSequences } from '../../../util/fetchSequences'
 import type { LinearMafDisplayModel } from '../../stateModel'
-import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
 
 const useStyles = makeStyles()({
   dialogContent: {
@@ -36,7 +35,6 @@ const SequenceDialog = observer(function ({
     dragEndX: number
   }
 }) {
-  const { samples } = model
   const [sequence, setSequence] = useState<string>('')
   const [loading, setLoading] = useState(true)
   const [error, setError] = useState<unknown>()
@@ -53,38 +51,9 @@ const SequenceDialog = observer(function ({
 
       try {
         setLoading(true)
-        setError(null)
+        setError(undefined)
 
-        const { rpcManager } = getSession(model)
-        const sessionId = getRpcSessionId(model)
-        const view = getContainingView(model) as LinearGenomeViewModel
-        const { refName, assemblyName } = view.displayedRegions[0]!
-        const { dragStartX, dragEndX } = selectionCoords
-        const [s, e] = [
-          Math.min(dragStartX, dragEndX),
-          Math.max(dragStartX, dragEndX),
-        ]
-
-        const fastaSequence = await rpcManager.call(
-          sessionId,
-          'MafGetSequences',
-          {
-            sessionId,
-            adapterConfig: model.adapterConfig,
-            samples,
-            regions: [
-              {
-                refName,
-                start: view.pxToBp(s).coord,
-                end: view.pxToBp(e).coord,
-                assemblyName,
-              },
-            ],
-          },
-        )
-
-        // Set the sequence data
-        setSequence(fastaSequence as string)
+        setSequence(await fetchSequences({ model, selectionCoords }))
       } catch (e) {
         console.error(e)
         setError(e)

src/util/fetchSequences.ts

@@ -0,0 +1,48 @@
+import { getContainingView, getSession } from '@jbrowse/core/util'
+import { getRpcSessionId } from '@jbrowse/core/util/tracks'
+import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
+import type { LinearMafDisplayModel } from '../LinearMafDisplay/stateModel'
+
+/**
+ * Fetch sequences for the given selection coordinates
+ * @param model - The LinearMafDisplayModel
+ * @param selectionCoords - The selection coordinates (dragStartX and dragEndX)
+ * @returns Promise that resolves to the FASTA sequence
+ */
+export async function fetchSequences({
+  model,
+  selectionCoords,
+}: {
+  model: LinearMafDisplayModel
+  selectionCoords: {
+    dragStartX: number
+    dragEndX: number
+  }
+}): Promise<string> {
+  const { samples, adapterConfig } = model
+  const { rpcManager } = getSession(model)
+  const sessionId = getRpcSessionId(model)
+  const view = getContainingView(model) as LinearGenomeViewModel
+  const { refName, assemblyName } = view.displayedRegions[0]!
+  const { dragStartX, dragEndX } = selectionCoords
+  const [s, e] = [
+    Math.min(dragStartX, dragEndX),
+    Math.max(dragStartX, dragEndX),
+  ]
+
+  const fastaSequence = await rpcManager.call(sessionId, 'MafGetSequences', {
+    sessionId,
+    adapterConfig,
+    samples,
+    regions: [
+      {
+        refName,
+        start: view.pxToBp(s).coord,
+        end: view.pxToBp(e).coord,
+        assemblyName,
+      },
+    ],
+  })
+
+  return fastaSequence as string
+}