jbrowse-plugin-mafviewer 1.4.5 → 1.4.6

package/src/LinearMafDisplay/components/InsertionSequenceDialog/InsertionSequenceDialog.tsx

@@ -1,105 +0,0 @@
-import React, { useState } from 'react'
-
-import { Dialog } from '@jbrowse/core/ui'
-import { Button, DialogActions, DialogContent, TextField } from '@mui/material'
-import { observer } from 'mobx-react'
-import { makeStyles } from 'tss-react/mui'
-
-const useStyles = makeStyles()({
-  dialogContent: {
-    width: '60em',
-  },
-  textAreaInput: {
-    fontFamily: 'monospace',
-    whiteSpace: 'pre',
-    overflowX: 'auto',
-  },
-})
-
-const InsertionSequenceDialog = observer(function ({
-  onClose,
-  model,
-  insertionData,
-}: {
-  onClose: () => void
-  model: {
-    showAsUpperCase: boolean
-  }
-  insertionData: {
-    sequence: string
-    sampleLabel: string
-    chr: string
-    pos: number
-  }
-}) {
-  const { classes } = useStyles()
-  const [copied, setCopied] = useState(false)
-  const { sequence, sampleLabel, chr, pos } = insertionData
-  const { showAsUpperCase } = model
-  const displaySequence = showAsUpperCase
-    ? sequence.toUpperCase()
-    : sequence.toLowerCase()
-
-  return (
-    <Dialog
-      open
-      onClose={onClose}
-      title={`Insertion Sequence (${sequence.length}bp)`}
-      maxWidth="lg"
-    >
-      <DialogContent>
-        <div style={{ marginBottom: 16 }}>
-          <strong>Sample:</strong> {sampleLabel}
-          <br />
-          <strong>Position:</strong> {chr}:{pos.toLocaleString('en-US')}
-          <br />
-          <strong>Length:</strong> {sequence.length}bp
-        </div>
-        <TextField
-          variant="outlined"
-          multiline
-          minRows={3}
-          maxRows={10}
-          className={classes.dialogContent}
-          fullWidth
-          value={displaySequence}
-          slotProps={{
-            input: {
-              readOnly: true,
-              classes: {
-                input: classes.textAreaInput,
-              },
-            },
-          }}
-        />
-      </DialogContent>
-      <DialogActions>
-        <Button
-          variant="contained"
-          color="primary"
-          onClick={() => {
-            // eslint-disable-next-line @typescript-eslint/no-floating-promises
-            ;(async () => {
-              try {
-                await navigator.clipboard.writeText(displaySequence)
-                setCopied(true)
-                setTimeout(() => {
-                  setCopied(false)
-                }, 1000)
-              } catch (e) {
-                console.error(e)
-              }
-            })()
-          }}
-        >
-          {copied ? 'Copied!' : 'Copy to Clipboard'}
-        </Button>
-        <Button color="secondary" variant="contained" onClick={onClose}>
-          Close
-        </Button>
-      </DialogActions>
-    </Dialog>
-  )
-})
-
-export default InsertionSequenceDialog

package/src/LinearMafDisplay/components/util.ts

@@ -1,7 +0,0 @@
-export function max(arr: number[], init = Number.NEGATIVE_INFINITY) {
-  let max = init
-  for (const entry of arr) {
-    max = Math.max(entry, max)
-  }
-  return max
-}

package/src/util/fetchSequences.ts

@@ -1,57 +0,0 @@
-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
-}
-
-/**
- * Fetch sequences for the given selection coordinates
- * @param model - The LinearMafDisplayModel
- * @param selectionCoords - The selection coordinates (dragStartX and dragEndX)
- * @param showAllLetters - Whether to show all letters or just the differences
- * @returns Promise that resolves to the FASTA sequence
- */
-export async function fetchSequences({
-  model,
-  selectionCoords,
-  showAllLetters,
-}: {
-  model: LinearMafDisplayModel
-  selectionCoords: SelectionCoords
-  showAllLetters: boolean
-}) {
-  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[]
-
-  return fastaSequence
-    .map((r, idx) => `>${samples![idx]!.label}\n${r}`)
-    .join('\n')
-}

package/src/util/useSequences.ts

@@ -1,90 +0,0 @@
-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 }
-}