jbrowse-plugin-mafviewer 1.4.5 → 1.4.6

package/src/util/parseAssemblyName.ts

@@ -0,0 +1,106 @@
+export interface ParsedAssemblyName {
+  assemblyName: string
+  chr: string
+}
+
+/**
+ * Parses assembly name and chromosome from a combined string in MAF tabix format.
+ *
+ * Handles multiple formats:
+ * - Single string with no dots: assemblyName is the entire string, chr is empty
+ * - `assembly.chr`: Single dot separates assembly name from chromosome
+ * - `assembly.version.chr`: Two dots where middle part is numeric (version number)
+ *   - assemblyName includes the version (e.g., "hg38.1" from "hg38.1.chr1")
+ * - `assembly.chr.more`: Two dots where middle part is non-numeric
+ *   - assemblyName is first part, chr includes rest (e.g., "mm10" and "chr1.random")
+ */
+export function parseAssemblyAndChr(
+  assemblyAndChr: string,
+): ParsedAssemblyName {
+  const firstDotIndex = assemblyAndChr.indexOf('.')
+  if (firstDotIndex === -1) {
+    return {
+      assemblyName: assemblyAndChr,
+      chr: '',
+    }
+  }
+
+  const secondDotIndex = assemblyAndChr.indexOf('.', firstDotIndex + 1)
+  if (secondDotIndex === -1) {
+    return {
+      assemblyName: assemblyAndChr.slice(0, firstDotIndex),
+      chr: assemblyAndChr.slice(firstDotIndex + 1),
+    }
+  }
+
+  const secondPart = assemblyAndChr.slice(firstDotIndex + 1, secondDotIndex)
+  const isNumeric = secondPart.length > 0 && !Number.isNaN(+secondPart)
+
+  if (isNumeric) {
+    return {
+      assemblyName: assemblyAndChr.slice(0, secondDotIndex),
+      chr: assemblyAndChr.slice(secondDotIndex + 1),
+    }
+  }
+
+  return {
+    assemblyName: assemblyAndChr.slice(0, firstDotIndex),
+    chr: assemblyAndChr.slice(firstDotIndex + 1),
+  }
+}
+
+/**
+ * Parses assembly name and chromosome from a combined string in BigMaf format.
+ *
+ * Uses simple dot splitting: org.chr where org is before the first dot,
+ * chr is everything after the first dot.
+ */
+export function parseAssemblyAndChrSimple(
+  organismChr: string,
+): ParsedAssemblyName {
+  const dotIndex = organismChr.indexOf('.')
+  if (dotIndex === -1) {
+    return {
+      assemblyName: organismChr,
+      chr: '',
+    }
+  }
+  return {
+    assemblyName: organismChr.slice(0, dotIndex),
+    chr: organismChr.slice(dotIndex + 1),
+  }
+}
+
+/**
+ * Selects the appropriate sequence from alignments based on the lookup order:
+ * 1. refAssemblyName config value (if provided)
+ * 2. query.assemblyName (from the region being queried)
+ * 3. firstAssemblyNameFound (fallback to first assembly in data)
+ */
+export function selectReferenceSequence(
+  alignments: Record<string, { seq: string }>,
+  refAssemblyName: string | undefined,
+  queryAssemblyName: string | undefined,
+  firstAssemblyNameFound: string | undefined,
+): string | undefined {
+  let entry
+  if (refAssemblyName) {
+    entry = alignments[refAssemblyName]
+    if (entry) {
+      return entry.seq
+    }
+  }
+  if (queryAssemblyName) {
+    entry = alignments[queryAssemblyName]
+    if (entry) {
+      return entry.seq
+    }
+  }
+  if (firstAssemblyNameFound) {
+    entry = alignments[firstAssemblyNameFound]
+    if (entry) {
+      return entry.seq
+    }
+  }
+  return undefined
+}

package/dist/LinearMafDisplay/components/GetSequenceDialog/GetSequenceDialog.d.ts

@@ -1,11 +0,0 @@
-import React from 'react';
-import type { LinearMafDisplayModel } from '../../stateModel';
-declare const GetSequenceDialog: ({ onClose, model, selectionCoords, }: {
-    onClose: () => void;
-    model: LinearMafDisplayModel;
-    selectionCoords?: {
-        dragStartX: number;
-        dragEndX: number;
-    };
-}) => React.JSX.Element;
-export default GetSequenceDialog;

package/dist/LinearMafDisplay/components/GetSequenceDialog/GetSequenceDialog.js

@@ -1,97 +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';
-const useStyles = makeStyles()({
-    dialogContent: {
-        width: '80em',
-    },
-    textAreaInput: {
-        fontFamily: 'monospace',
-        whiteSpace: 'pre',
-        overflowX: 'auto',
-    },
-    ml: {
-        marginLeft: 10,
-    },
-});
-const GetSequenceDialog = observer(function ({ onClose, model, selectionCoords, }) {
-    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 (React.createElement(Dialog, { open: true, onClose: onClose, title: "Subsequence Data", maxWidth: "xl" },
-        React.createElement(DialogContent, null,
-            React.createElement("div", { style: {
-                    display: 'flex',
-                    alignItems: 'center',
-                    marginBottom: '16px',
-                } },
-                React.createElement(ToggleButtonGroup, { value: showAllLetters, exclusive: true, size: "small", onChange: (_event, newDisplayMode) => {
-                        if (newDisplayMode !== null) {
-                            setShowAllLetters(newDisplayMode);
-                        }
-                    } },
-                    React.createElement(ToggleButton, { value: true }, "Show All Letters"),
-                    React.createElement(ToggleButton, { value: false }, "Show Only Differences")),
-                React.createElement("div", { style: { flexGrow: 1 } }),
-                React.createElement(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(`${e}`, e);
-                            }
-                        })();
-                    } }, "Copy to Clipboard"),
-                React.createElement(Button, { variant: "contained", color: "secondary", disabled: loading || !sequence, onClick: () => {
-                        try {
-                            const url = URL.createObjectURL(new Blob([sequence], { type: 'text/plain' }));
-                            // Create a temporary anchor element
-                            const a = document.createElement('a');
-                            a.href = url;
-                            a.download = 'sequence.fasta';
-                            // Trigger the download
-                            document.body.append(a);
-                            a.click();
-                            // Clean up
-                            a.remove();
-                            URL.revokeObjectURL(url);
-                            getSession(model).notify('Sequence downloaded', 'info');
-                        }
-                        catch (e) {
-                            console.error(e);
-                            getSession(model).notifyError(`${e}`, e);
-                        }
-                    } }, "Download")),
-            error ? (React.createElement(ErrorMessage, { error: error })) : (React.createElement(React.Fragment, null,
-                loading ? React.createElement(LoadingEllipses, null) : null,
-                React.createElement(TextField, { variant: "outlined", multiline: true, minRows: 5, maxRows: 10, disabled: sequenceTooLarge, className: classes.dialogContent, fullWidth: true, value: loading
-                        ? 'Loading...'
-                        : sequenceTooLarge
-                            ? 'Reference sequence too large to display, use the download FASTA button'
-                            : sequence, slotProps: {
-                        input: {
-                            readOnly: true,
-                            classes: {
-                                input: classes.textAreaInput,
-                            },
-                        },
-                    } })))),
-        React.createElement(DialogActions, null,
-            React.createElement(Button, { color: "primary", variant: "outlined", onClick: onClose }, "Close"))));
-});
-export default GetSequenceDialog;
-//# sourceMappingURL=GetSequenceDialog.js.map

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

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package/dist/LinearMafDisplay/components/InsertionSequenceDialog/InsertionSequenceDialog.d.ts

@@ -1,14 +0,0 @@
-import React from 'react';
-declare const InsertionSequenceDialog: ({ onClose, model, insertionData, }: {
-    onClose: () => void;
-    model: {
-        showAsUpperCase: boolean;
-    };
-    insertionData: {
-        sequence: string;
-        sampleLabel: string;
-        chr: string;
-        pos: number;
-    };
-}) => React.JSX.Element;
-export default InsertionSequenceDialog;

package/dist/LinearMafDisplay/components/InsertionSequenceDialog/InsertionSequenceDialog.js

@@ -1,69 +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, }) {
-    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 (React.createElement(Dialog, { open: true, onClose: onClose, title: `Insertion Sequence (${sequence.length}bp)`, maxWidth: "lg" },
-        React.createElement(DialogContent, null,
-            React.createElement("div", { style: { marginBottom: 16 } },
-                React.createElement("strong", null, "Sample:"),
-                " ",
-                sampleLabel,
-                React.createElement("br", null),
-                React.createElement("strong", null, "Position:"),
-                " ",
-                chr,
-                ":",
-                pos.toLocaleString('en-US'),
-                React.createElement("br", null),
-                React.createElement("strong", null, "Length:"),
-                " ",
-                sequence.length,
-                "bp"),
-            React.createElement(TextField, { variant: "outlined", multiline: true, minRows: 3, maxRows: 10, className: classes.dialogContent, fullWidth: true, value: displaySequence, slotProps: {
-                    input: {
-                        readOnly: true,
-                        classes: {
-                            input: classes.textAreaInput,
-                        },
-                    },
-                } })),
-        React.createElement(DialogActions, null,
-            React.createElement(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'),
-            React.createElement(Button, { color: "secondary", variant: "contained", onClick: onClose }, "Close"))));
-});
-export default InsertionSequenceDialog;
-//# sourceMappingURL=InsertionSequenceDialog.js.map

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package/dist/LinearMafDisplay/components/util.d.ts

@@ -1 +0,0 @@
-export declare function max(arr: number[], init?: number): number;

package/dist/LinearMafDisplay/components/util.js

@@ -1,8 +0,0 @@
-export function max(arr, init = Number.NEGATIVE_INFINITY) {
-    let max = init;
-    for (const entry of arr) {
-        max = Math.max(entry, max);
-    }
-    return max;
-}
-//# sourceMappingURL=util.js.map

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

@@ -1 +0,0 @@
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package/dist/util/fetchSequences.d.ts

@@ -1,18 +0,0 @@
-import type { LinearMafDisplayModel } from '../LinearMafDisplay/stateModel';
-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 declare function fetchSequences({ model, selectionCoords, showAllLetters, }: {
-    model: LinearMafDisplayModel;
-    selectionCoords: SelectionCoords;
-    showAllLetters: boolean;
-}): Promise<string>;
-export {};

package/dist/util/fetchSequences.js

@@ -1,39 +0,0 @@
-import { getContainingView, getSession } from '@jbrowse/core/util';
-import { getRpcSessionId } from '@jbrowse/core/util/tracks';
-/**
- * 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, }) {
-    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,
-            },
-        ],
-    }));
-    return fastaSequence
-        .map((r, idx) => `>${samples[idx].label}\n${r}`)
-        .join('\n');
-}
-//# sourceMappingURL=fetchSequences.js.map

package/dist/util/fetchSequences.js.map

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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