jbrowse-plugin-mafviewer 1.2.4 → 1.3.1

package/src/util/useSequences.ts

@@ -0,0 +1,90 @@
+import { useEffect, useState } from 'react'
+
+import { getContainingView, getSession } from '@jbrowse/core/util'
+import { getRpcSessionId } from '@jbrowse/core/util/tracks'
+
+import type { LinearMafDisplayModel } from '../LinearMafDisplay/stateModel'
+import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
+
+interface SelectionCoords {
+  dragStartX: number
+  dragEndX: number
+}
+
+interface UseSequencesOptions {
+  model: LinearMafDisplayModel
+  selectionCoords?: SelectionCoords
+  showAllLetters: boolean
+}
+
+/**
+ * React hook to fetch sequences for the given selection coordinates
+ * @param options - The options for fetching sequences
+ * @returns An object containing the sequence, loading state, and error
+ */
+export function useSequences({
+  model,
+  selectionCoords,
+  showAllLetters,
+}: UseSequencesOptions) {
+  const [sequence, setSequence] = useState<string>('')
+  const [loading, setLoading] = useState(true)
+  const [error, setError] = useState<unknown>()
+
+  useEffect(() => {
+    // If no selection coordinates, no need to fetch
+    if (!selectionCoords) {
+      return
+    }
+    // eslint-disable-next-line @typescript-eslint/no-floating-promises
+    ;(async () => {
+      try {
+        setLoading(true)
+        setError(undefined)
+
+        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,
+            showAllLetters,
+            regions: [
+              {
+                refName,
+                start: view.pxToBp(s).coord - 1,
+                end: view.pxToBp(e).coord,
+                assemblyName,
+              },
+            ],
+          },
+        )) as string[]
+
+        const formattedSequence = fastaSequence
+          .map((r, idx) => `>${samples![idx]!.label}\n${r}`)
+          .join('\n')
+
+        setSequence(formattedSequence)
+      } catch (e) {
+        console.error(e)
+        setError(e)
+      } finally {
+        setLoading(false)
+      }
+    })()
+  }, [model, selectionCoords, showAllLetters])
+
+  return { sequence, loading, error }
+}

package/dist/LinearMafDisplay/components/ColorLegend.js.map

@@ -1 +0,0 @@
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package/dist/LinearMafDisplay/components/RectBg.js.map

@@ -1 +0,0 @@
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package/dist/LinearMafDisplay/components/SetRowHeightDialog.js.map

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package/dist/LinearMafDisplay/components/SvgWrapper.js.map

@@ -1 +0,0 @@
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package/dist/LinearMafDisplay/components/Tree.js.map

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package/dist/LinearMafDisplay/components/YScaleBars.js.map

@@ -1 +0,0 @@
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package/dist/MafRPC/index.js.map

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