jbrowse-plugin-mafviewer 1.4.3 → 1.4.6

package/dist/util/useSequences.d.ts

@@ -1,21 +0,0 @@
-import type { LinearMafDisplayModel } from '../LinearMafDisplay/stateModel';
-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 declare function useSequences({ model, selectionCoords, showAllLetters, }: UseSequencesOptions): {
-    sequence: string;
-    loading: boolean;
-    error: unknown;
-};
-export {};

package/dist/util/useSequences.js

@@ -1,64 +0,0 @@
-import { useEffect, useState } from 'react';
-import { getContainingView, getSession } from '@jbrowse/core/util';
-import { getRpcSessionId } from '@jbrowse/core/util/tracks';
-/**
- * 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, }) {
-    const [sequence, setSequence] = useState('');
-    const [loading, setLoading] = useState(true);
-    const [error, setError] = useState();
-    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);
-                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,
-                        },
-                    ],
-                }));
-                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 };
-}
-//# sourceMappingURL=useSequences.js.map

package/dist/util/useSequences.js.map

@@ -1 +0,0 @@
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package/src/LinearMafDisplay/components/GetSequenceDialog/GetSequenceDialog.tsx

@@ -1,175 +0,0 @@
-import React, { useState } from 'react'
-
-import { Dialog, ErrorMessage, LoadingEllipses } from '@jbrowse/core/ui'
-import { getSession } from '@jbrowse/core/util'
-import {
-  Button,
-  DialogActions,
-  DialogContent,
-  TextField,
-  ToggleButton,
-  ToggleButtonGroup,
-} from '@mui/material'
-import { observer } from 'mobx-react'
-import { makeStyles } from 'tss-react/mui'
-
-import { useSequences } from '../../../util/useSequences'
-
-import type { LinearMafDisplayModel } from '../../stateModel'
-
-const useStyles = makeStyles()({
-  dialogContent: {
-    width: '80em',
-  },
-  textAreaInput: {
-    fontFamily: 'monospace',
-    whiteSpace: 'pre',
-    overflowX: 'auto',
-  },
-  ml: {
-    marginLeft: 10,
-  },
-})
-
-const GetSequenceDialog = observer(function ({
-  onClose,
-  model,
-  selectionCoords,
-}: {
-  onClose: () => void
-  model: LinearMafDisplayModel
-  selectionCoords?: {
-    dragStartX: number
-    dragEndX: number
-  }
-}) {
-  const [showAllLetters, setShowAllLetters] = useState(true)
-  const { classes } = useStyles()
-  const { sequence, loading, error } = useSequences({
-    model,
-    selectionCoords,
-    showAllLetters,
-  })
-  const sequenceTooLarge = sequence ? sequence.length > 1_000_000 : false
-
-  return (
-    <Dialog open onClose={onClose} title="Subsequence Data" maxWidth="xl">
-      <DialogContent>
-        <div
-          style={{
-            display: 'flex',
-            alignItems: 'center',
-            marginBottom: '16px',
-          }}
-        >
-          <ToggleButtonGroup
-            value={showAllLetters}
-            exclusive
-            size="small"
-            onChange={(_event, newDisplayMode) => {
-              if (newDisplayMode !== null) {
-                setShowAllLetters(newDisplayMode)
-              }
-            }}
-          >
-            <ToggleButton value={true}>Show All Letters</ToggleButton>
-            <ToggleButton value={false}>Show Only Differences</ToggleButton>
-          </ToggleButtonGroup>
-          <div style={{ flexGrow: 1 }} />
-          <Button
-            variant="contained"
-            color="primary"
-            disabled={loading || !sequence}
-            onClick={() => {
-              // eslint-disable-next-line @typescript-eslint/no-floating-promises
-              ;(async () => {
-                try {
-                  await navigator.clipboard.writeText(sequence)
-                  getSession(model).notify(
-                    'Sequence copied to clipboard',
-                    'info',
-                  )
-                } catch (e) {
-                  console.error(e)
-                  getSession(model).notifyError(`${e}`, e)
-                }
-              })()
-            }}
-          >
-            Copy to Clipboard
-          </Button>
-          <Button
-            variant="contained"
-            color="secondary"
-            disabled={loading || !sequence}
-            onClick={() => {
-              try {
-                const url = URL.createObjectURL(
-                  new Blob([sequence], { type: 'text/plain' }),
-                )
-
-                // Create a temporary anchor element
-                const a = document.createElement('a')
-                a.href = url
-                a.download = 'sequence.fasta'
-
-                // Trigger the download
-                document.body.append(a)
-                a.click()
-
-                // Clean up
-                a.remove()
-                URL.revokeObjectURL(url)
-                getSession(model).notify('Sequence downloaded', 'info')
-              } catch (e) {
-                console.error(e)
-                getSession(model).notifyError(`${e}`, e)
-              }
-            }}
-          >
-            Download
-          </Button>
-        </div>
-
-        {error ? (
-          <ErrorMessage error={error} />
-        ) : (
-          <>
-            {loading ? <LoadingEllipses /> : null}
-            <TextField
-              variant="outlined"
-              multiline
-              minRows={5}
-              maxRows={10}
-              disabled={sequenceTooLarge}
-              className={classes.dialogContent}
-              fullWidth
-              value={
-                loading
-                  ? 'Loading...'
-                  : sequenceTooLarge
-                    ? 'Reference sequence too large to display, use the download FASTA button'
-                    : sequence
-              }
-              slotProps={{
-                input: {
-                  readOnly: true,
-                  classes: {
-                    input: classes.textAreaInput,
-                  },
-                },
-              }}
-            />
-          </>
-        )}
-      </DialogContent>
-      <DialogActions>
-        <Button color="primary" variant="outlined" onClick={onClose}>
-          Close
-        </Button>
-      </DialogActions>
-    </Dialog>
-  )
-})
-
-export default GetSequenceDialog

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/LinearMafRenderer/components/util.ts

@@ -1,13 +0,0 @@
-export function minElt<T>(arr: Iterable<T>, cb: (arg: T) => number) {
-  let min = Infinity
-  let minElement: T | undefined
-  for (const entry of arr) {
-    const val = cb(entry)
-
-    if (val < min) {
-      min = val
-      minElement = entry
-    }
-  }
-  return minElement
-}

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 }
-}