react-msaview 6.4.2 → 7.0.0

package/dist/components/dialogs/InterProScanDialog.js

@@ -1,137 +0,0 @@
-import React, { useState } from 'react';
-import { Dialog } from '@jbrowse/core/ui';
-import { getSession } from '@jbrowse/core/util';
-import { Button, DialogActions, DialogContent, Typography } from '@mui/material';
-import { observer } from 'mobx-react';
-import { getUngappedSequence } from 'msa-parsers';
-import { launchInterProScan } from '../../launchInterProScan.js';
-const FAMILIES = 'Families, domains, sites & repeats';
-const FEATURES = 'Other sequence features';
-const STRUCTURAL = 'Structural domains';
-const OTHER = 'Other category';
-// The analyses the EBI iprscan5 endpoint accepts, all on by default. Static, so
-// it lives out here rather than being rebuilt on every render of the dialog.
-const interProScanPrograms = [
-    {
-        name: 'NCBIfam',
-        category: FAMILIES,
-        description: 'NCBI RefSeq FAMs including TIGRFAMs',
-    },
-    {
-        name: 'SFLD',
-        category: FAMILIES,
-        description: 'Structure function linkage database',
-    },
-    {
-        name: 'Phobius',
-        category: FEATURES,
-        description: 'A combined transmembrane topology and signal peptide predictor',
-    },
-    { name: 'SignalP', category: FEATURES },
-    { name: 'SignalP_EUK', category: OTHER },
-    { name: 'SignalP_GRAM_POSITIVE', category: OTHER },
-    { name: 'SignalP_GRAM_NEGATIVE', category: OTHER },
-    { name: 'SuperFamily', category: STRUCTURAL },
-    { name: 'Panther', category: FAMILIES },
-    { name: 'Gene3d', category: STRUCTURAL },
-    { name: 'HAMAP', category: FAMILIES },
-    { name: 'PrositeProfiles', category: FAMILIES },
-    { name: 'PrositePatterns', category: FAMILIES },
-    { name: 'Coils', category: FEATURES },
-    { name: 'SMART', category: FAMILIES },
-    {
-        name: 'CDD',
-        category: FAMILIES,
-        description: 'Conserved Domains Database',
-    },
-    { name: 'PRINTS', category: FAMILIES },
-    { name: 'PfamA', category: FAMILIES },
-    { name: 'MobiDBLite', category: FEATURES },
-    { name: 'PIRSF', category: OTHER },
-    { name: 'TMHMM', category: FEATURES },
-    { name: 'AntiFam', category: OTHER },
-    { name: 'FunFam', category: OTHER },
-    { name: 'PIRSR', category: FAMILIES },
-].map(program => ({ ...program, checked: true }));
-const InterProScanDialog = observer(function ({ handleClose, model, }) {
-    const [vals, setVals] = useState(interProScanPrograms);
-    const programs = vals.filter(e => e.checked).map(e => e.name);
-    const [show, setShow] = useState(false);
-    return (React.createElement(Dialog, { maxWidth: "xl", title: "Query InterProScan API for domains", onClose: () => {
-            handleClose();
-        }, open: true },
-        React.createElement(DialogContent, null,
-            React.createElement(Typography, null, "This will run InterProScan via the InterProScan API on all rows of the current MSA"),
-            React.createElement(Button, { onClick: () => {
-                    setShow(!show);
-                } },
-                show ? 'Hide' : 'Show',
-                " advanced options"),
-            show ? (React.createElement("div", null,
-                React.createElement(Typography, null, "Select algorithms for InterProScan to run"),
-                React.createElement("div", null,
-                    React.createElement(Button, { variant: "contained", color: "secondary", onClick: () => {
-                            setVals(vals.map(v => ({ ...v, checked: false })));
-                        } }, "Select none"),
-                    React.createElement(Button, { variant: "contained", color: "primary", onClick: () => {
-                            setVals(vals.map(v => ({ ...v, checked: true })));
-                        } }, "Select all")),
-                React.createElement("table", null,
-                    React.createElement("tbody", null, vals
-                        .toSorted((a, b) => a.category.localeCompare(b.category))
-                        .map(({ name, checked, category, description }) => (React.createElement("tr", { key: name },
-                        React.createElement("td", null,
-                            React.createElement("input", { type: "checkbox", checked: checked, onChange: () => {
-                                    setVals(vals.map(e => e.name === name
-                                        ? { ...e, checked: !e.checked }
-                                        : e));
-                                } })),
-                        React.createElement("td", { title: description }, name),
-                        React.createElement("td", null, category)))))))) : null),
-        React.createElement(DialogActions, null,
-            React.createElement(Button, { variant: "contained", color: "secondary", onClick: () => {
-                    handleClose();
-                } }, "Cancel"),
-            React.createElement(Button, { variant: "contained", color: "primary", onClick: () => {
-                    const controller = new AbortController();
-                    (async () => {
-                        try {
-                            const { rows } = model;
-                            if (rows.length > 140) {
-                                throw new Error('Too many sequences, please run InterProScan offline');
-                            }
-                            await launchInterProScan({
-                                algorithm: 'interproscan',
-                                programs: programs,
-                                seq: rows
-                                    .map(row => [row[0], getUngappedSequence(row[1])])
-                                    .filter(f => !!f[1])
-                                    .map(row => `>${row[0]}\n${row[1]}`)
-                                    .join('\n'),
-                                onProgress: arg => {
-                                    model.setStatus(arg
-                                        ? {
-                                            ...arg,
-                                            onCancel: () => {
-                                                controller.abort();
-                                            },
-                                        }
-                                        : undefined);
-                                },
-                                model,
-                                signal: controller.signal,
-                            });
-                        }
-                        catch (e) {
-                            console.error(e);
-                            getSession(model).notifyError(`${e}`, e);
-                        }
-                        finally {
-                            model.setStatus();
-                        }
-                    })();
-                    handleClose();
-                } }, "Send sequences to InterProScan"))));
-});
-export default InterProScanDialog;
-//# sourceMappingURL=InterProScanDialog.js.map

package/dist/components/dialogs/InterProScanDialog.js.map

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package/dist/components/dialogs/InterProScanFileDialog.d.ts

@@ -1,7 +0,0 @@
-import React from 'react';
-import type { MsaViewModel } from '../../model.ts';
-declare const InterProScanFileDialog: ({ handleClose, model, }: {
-    handleClose: () => void;
-    model: MsaViewModel;
-}) => React.JSX.Element;
-export default InterProScanFileDialog;

package/dist/components/dialogs/InterProScanFileDialog.js

@@ -1,64 +0,0 @@
-import React, { useState } from 'react';
-import { Dialog } from '@jbrowse/core/ui';
-import { getSession } from '@jbrowse/core/util';
-import { Button, DialogActions, DialogContent, FormControl, FormControlLabel, Radio, RadioGroup, TextField, Typography, } from '@mui/material';
-import { observer } from 'mobx-react';
-import { interProScanResponseToAnnotations } from 'msa-parsers';
-import { jsonfetch } from '../../fetchUtils.js';
-const InterProScanFileDialog = observer(function ({ handleClose, model, }) {
-    const [file, setFile] = useState();
-    const [choice, setChoice] = useState('file');
-    const [interProURL, setInterProURL] = useState('');
-    return (React.createElement(Dialog, { maxWidth: "xl", title: "Open InterProScan results", onClose: () => {
-            handleClose();
-        }, open: true },
-        React.createElement(DialogContent, null,
-            React.createElement("div", null,
-                React.createElement(Typography, null, "Open a JSON file of InterProScan results that you run remotely on EBI servers or locally"),
-                React.createElement("div", { style: { display: 'flex', margin: 30 } },
-                    React.createElement(FormControl, { component: "fieldset" },
-                        React.createElement(RadioGroup, { value: choice, onChange: event => {
-                                setChoice(event.target.value);
-                            } },
-                            React.createElement(FormControlLabel, { value: "url", control: React.createElement(Radio, null), label: "URL" }),
-                            React.createElement(FormControlLabel, { value: "file", control: React.createElement(Radio, null), label: "File" }))),
-                    choice === 'url' ? (React.createElement("div", null,
-                        React.createElement(Typography, null, "Open a InterProScan JSON file remote URL"),
-                        React.createElement(TextField, { label: "URL", value: interProURL, onChange: event => {
-                                setInterProURL(event.target.value);
-                            } }))) : null,
-                    choice === 'file' ? (React.createElement("div", { style: { paddingTop: 20 } },
-                        React.createElement(Typography, null, "Open a InterProScan JSON file file from your local drive"),
-                        React.createElement(Button, { variant: "outlined", component: "label" },
-                            "Choose File",
-                            React.createElement("input", { type: "file", hidden: true, onChange: ({ target }) => {
-                                    const file = target.files?.[0];
-                                    if (file) {
-                                        setFile(file);
-                                    }
-                                } })))) : null))),
-        React.createElement(DialogActions, null,
-            React.createElement(Button, { variant: "contained", color: "primary", onClick: () => {
-                    // eslint-disable-next-line @typescript-eslint/no-floating-promises
-                    ;
-                    (async () => {
-                        try {
-                            const ret = file
-                                ? JSON.parse(await file.text())
-                                : await jsonfetch(interProURL);
-                            model.setAnnotations(interProScanResponseToAnnotations(ret));
-                            getSession(model).notify('Loaded interproscan results', 'success');
-                        }
-                        catch (e) {
-                            console.error(e);
-                            getSession(model).notifyError(`${e}`, e);
-                        }
-                        finally {
-                            model.setStatus();
-                        }
-                    })();
-                    handleClose();
-                } }, "Open results"))));
-});
-export default InterProScanFileDialog;
-//# sourceMappingURL=InterProScanFileDialog.js.map

package/dist/components/dialogs/InterProScanFileDialog.js.map

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

@@ -1,13 +0,0 @@
-import type { MsaViewModel } from './model.ts';
-export declare function launchInterProScan({ algorithm, seq, programs, onJobId, onProgress, model, signal, }: {
-    algorithm: string;
-    seq: string;
-    programs: string[];
-    onProgress: (arg?: {
-        msg: string;
-        url?: string;
-    }) => void;
-    onJobId?: (arg: string) => void;
-    model: MsaViewModel;
-    signal?: AbortSignal;
-}): Promise<void>;

package/dist/launchInterProScan.js

@@ -1,110 +0,0 @@
-import { getSession } from '@jbrowse/core/util';
-import { interProScanResponseToAnnotations } from 'msa-parsers';
-import { isAbortError, jsonfetch, textfetch, timeout } from './fetchUtils.js';
-const base = 'https://www.ebi.ac.uk/Tools/services/rest';
-async function runInterProScan({ seq, onProgress, onJobId, programs, model, signal, }) {
-    const jobId = await textfetch(`${base}/iprscan5/run`, {
-        method: 'POST',
-        body: new URLSearchParams({
-            email: 'colin.diesh@gmail.com',
-            sequence: seq,
-            programs: programs.join(','),
-        }),
-        signal,
-    });
-    onJobId?.(jobId);
-    await wait({
-        jobId,
-        onProgress,
-        signal,
-    });
-    await loadInterProScanResultsWithStatus({ jobId, model, onProgress, signal });
-}
-function loadInterProScanResults(jobId, signal) {
-    return jsonfetch(`${base}/iprscan5/result/${jobId}/json`, { signal });
-}
-async function wait({ onProgress, jobId, signal, }) {
-    const url = `${base}/iprscan5/status/${jobId}`;
-    // EBI jobs run for minutes; cap polling so an unexpected/stuck status can't
-    // spin forever (the abort signal is the normal early exit). ~10s per check.
-    const maxChecks = 360;
-    try {
-        let finished = false;
-        for (let check = 0; check < maxChecks && !finished; check++) {
-            for (let i = 0; i < 10; i++) {
-                await timeout(1000, signal);
-                onProgress({ msg: `Checking status ${10 - i}`, url });
-            }
-            // status endpoint returns a bare status token; match exactly rather than
-            // substring so an error page mentioning "FINISHED" can't be a false hit
-            const status = (await textfetch(url, { signal })).trim();
-            if (status === 'FINISHED') {
-                finished = true;
-            }
-            else if (status === 'FAILURE' ||
-                status === 'ERROR' ||
-                status === 'NOT_FOUND') {
-                throw new Error(`InterProScan job ${jobId} ended with status: ${status}`);
-            }
-        }
-        if (!finished) {
-            throw new Error(`InterProScan job ${jobId} did not finish after ${maxChecks} status checks`);
-        }
-    }
-    finally {
-        onProgress();
-    }
-}
-export async function launchInterProScan({ algorithm, seq, programs, onJobId, onProgress, model, signal, }) {
-    try {
-        onProgress({ msg: `Launching ${algorithm} MSA` });
-        if (algorithm === 'interproscan') {
-            await runInterProScan({
-                seq,
-                onJobId,
-                onProgress,
-                programs,
-                model,
-                signal,
-            });
-        }
-        else {
-            throw new Error('unknown algorithm');
-        }
-    }
-    catch (e) {
-        if (isAbortError(e)) {
-            getSession(model).notify('Cancelled InterProScan query', 'info');
-        }
-        else {
-            throw e;
-        }
-    }
-    finally {
-        onProgress();
-    }
-}
-async function loadInterProScanResultsWithStatus({ jobId, model, onProgress, signal, }) {
-    try {
-        onProgress({
-            msg: `Downloading results of ${jobId} (for larger sequences this can be slow, click status to download and upload in the manual tab)`,
-            url: `https://www.ebi.ac.uk/Tools/services/rest/iprscan5/result/${jobId}/json`,
-        });
-        const ret = await loadInterProScanResults(jobId, signal);
-        model.setAnnotations(interProScanResponseToAnnotations(ret));
-        getSession(model).notify(`Loaded interproscan ${jobId} results`, 'success');
-    }
-    catch (e) {
-        if (isAbortError(e)) {
-            getSession(model).notify('Cancelled InterProScan query', 'info');
-        }
-        else {
-            console.error(e);
-            getSession(model).notifyError(`${e}`, e);
-        }
-    }
-    finally {
-        onProgress();
-    }
-}
-//# sourceMappingURL=launchInterProScan.js.map

package/dist/launchInterProScan.js.map

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package/dist/useColorContrast.d.ts

@@ -1,10 +0,0 @@
-/**
- * Resolves the current theme and a memoized contrast-color scheme for a given
- * color scheme. Shared by the MSA and text-track canvas blocks.
- */
-export declare function useColorContrast(colorScheme: Record<string, string>): {
-    theme: import("@mui/material").Theme;
-    contrastScheme: {
-        [k: string]: string;
-    };
-};

package/dist/useColorContrast.js

@@ -1,13 +0,0 @@
-import { useMemo } from 'react';
-import { useTheme } from '@mui/material';
-import { colorContrast } from './util.js';
-/**
- * Resolves the current theme and a memoized contrast-color scheme for a given
- * color scheme. Shared by the MSA and text-track canvas blocks.
- */
-export function useColorContrast(colorScheme) {
-    const theme = useTheme();
-    const contrastScheme = useMemo(() => colorContrast(colorScheme, theme), [colorScheme, theme]);
-    return { theme, contrastScheme };
-}
-//# sourceMappingURL=useColorContrast.js.map

package/dist/useColorContrast.js.map

@@ -1 +0,0 @@
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package/src/clustalX.test.ts

@@ -1,74 +0,0 @@
-import { describe, expect, test } from 'vitest'
-
-import { clustalXColumnColors } from './clustalX.ts'
-import { columnCountsFromColumns } from './columnCounts.ts'
-
-// one alignment column, given top-to-bottom
-function column(letters: string) {
-  return clustalXColumnColors(columnCountsFromColumns([letters]), 0)
-}
-
-const BLUE = 'rgb(128,179,230)'
-const RED = '#d88'
-const GREEN = '#8f8'
-const GREEN_ST = 'rgb(26,204,26)'
-const ORANGE = 'rgb(240, 144, 72)'
-const YELLOW = 'rgb(204, 204, 0)'
-const CYAN = 'rgb(26, 179, 179)'
-
-describe('clustalXColumnColors', () => {
-  test('hydrophobic column (all L) colors the hydrophobic group', () => {
-    expect(column('LLLLLLLLLL')).toEqual({
-      W: BLUE,
-      L: BLUE,
-      V: BLUE,
-      A: BLUE,
-      I: BLUE,
-      M: BLUE,
-      F: BLUE,
-      C: BLUE,
-      S: GREEN_ST,
-      T: GREEN_ST,
-      H: CYAN,
-      Y: CYAN,
-    })
-  })
-
-  test('glycine is always colored when present', () => {
-    expect(column('GGGGGGGGGG')).toEqual({
-      G: ORANGE,
-    })
-  })
-
-  test('proline is always colored, and counts as hydrophobic', () => {
-    expect(column('PPPPPPPPPP')).toEqual({
-      W: BLUE,
-      L: BLUE,
-      V: BLUE,
-      A: BLUE,
-      I: BLUE,
-      M: BLUE,
-      F: BLUE,
-      C: BLUE,
-      S: GREEN_ST,
-      T: GREEN_ST,
-      P: YELLOW,
-      H: CYAN,
-      Y: CYAN,
-    })
-  })
-
-  test('positively charged column (all K)', () => {
-    expect(column('KKKKKKKKKK')).toEqual({
-      K: RED,
-      R: RED,
-      E: 'rgb(192, 72, 192)',
-      D: 'rgb(204, 77, 204)',
-      Q: GREEN,
-    })
-  })
-
-  test('unconserved column produces no colors', () => {
-    expect(column('XXXXXXXXXX')).toEqual({})
-  })
-})

package/src/colSpace.test.ts

@@ -1,67 +0,0 @@
-// @vitest-environment jsdom
-import { expect, test } from 'vitest'
-
-import MSAModelF from './model.ts'
-
-// a ragged alignment: row `a` stops early, so the alignment is as wide as `b`.
-// Column space has to follow the widest row -- the gap analysis already does --
-// or every column past the first row's end becomes unreachable: unscrollable,
-// unhoverable, and missing from the minimap.
-const msa = `>a
-ACGT
->b
-ACGTACGTAC`
-
-function makeModel() {
-  const model = MSAModelF().create({
-    id: 'col-space-test',
-    type: 'MsaView',
-    msaFormat: 'fasta',
-    data: { msa },
-  })
-  model.setWidth(800)
-  return model
-}
-
-test('column space spans the widest row', () => {
-  const model = makeModel()
-  expect(model.numColumns).toBe(10)
-  expect(model.totalWidth).toBe(10 * model.colWidth)
-})
-
-test('the last column agrees with the column statistics', () => {
-  const model = makeModel()
-  expect(model.colStats.numColumns).toBe(model.numColumns)
-  expect(model.conservation).toHaveLength(model.numColumns)
-
-  model.setMousePos(model.numColumns - 1, 1)
-  expect(model.mouseOverColumnStats?.col).toBe(9)
-  expect(model.visibleColToRowLetter('b', 9)).toBe('C')
-})
-
-// enough rows to force the vertical scrollbar, which eats into the width the
-// alignment canvas actually gets
-function makeTallModel() {
-  const names = Array.from({ length: 60 }, (_, i) => `seq${i}`)
-  const model = MSAModelF().create({
-    id: 'col-fit-test',
-    type: 'MsaView',
-    msaFormat: 'fasta',
-    height: 300,
-    data: { msa: names.map(n => `>${n}\n${'ACGT'.repeat(50)}`).join('\n') },
-  })
-  model.setWidth(800)
-  return model
-}
-
-test('fit horizontally leaves every column on screen', () => {
-  const model = makeTallModel()
-  expect(model.showVerticalScrollbar).toBe(true)
-
-  model.fitHorizontally()
-  // the canvas is the msa area minus the scrollbar; fitting to the msa area
-  // alone pushed the last columns past the right edge, with no minimap to
-  // show that anything was cut off
-  expect(model.totalWidth).toBeLessThanOrEqual(model.msaCanvasWidth)
-  expect(model.showHorizontalScrollbar).toBe(false)
-})

package/src/collapseLogic.test.ts

@@ -1,115 +0,0 @@
-import { describe, expect, test } from 'vitest'
-
-import { collapse, find, hierarchy, leaves, sort, sum } from './hierarchy.ts'
-
-import type { NodeWithIds } from './types.ts'
-
-function buildRoot(tree: NodeWithIds, collapsed: string[], showOnly?: string) {
-  let hier = hierarchy(tree, d => d.children)
-  sum(hier, d => (d.children.length > 0 ? 0 : 1))
-  sort(hier, (a, b) => (a.data.length ?? 1) - (b.data.length ?? 1))
-
-  if (showOnly) {
-    const res = find(hier, n => n.data.id === showOnly)
-    if (res) {
-      hier = res
-    }
-  }
-
-  for (const collapsedId of collapsed) {
-    const node = find(hier, n => n.data.id === collapsedId)
-    if (!node) {
-      continue
-    }
-    if (node.children) {
-      collapse(node)
-    } else if (node.parent?.children) {
-      node.parent.children = node.parent.children.filter(
-        c => c.data.id !== collapsedId,
-      )
-    }
-  }
-
-  return hier
-}
-
-function simpleTree(): NodeWithIds {
-  return {
-    id: 'root',
-    name: 'root',
-    children: [
-      {
-        id: 'clade1',
-        name: 'clade1',
-        children: [
-          { id: 'seq1', name: 'seq1', children: [] },
-          { id: 'seq2', name: 'seq2', children: [] },
-        ],
-      },
-      {
-        id: 'clade2',
-        name: 'clade2',
-        children: [
-          { id: 'seq3', name: 'seq3', children: [] },
-          { id: 'seq4', name: 'seq4', children: [] },
-        ],
-      },
-    ],
-  }
-}
-
-describe('collapse logic (mirrors model.root getter)', () => {
-  test('no collapsed nodes returns all leaves', () => {
-    const root = buildRoot(simpleTree(), [])
-    expect(leaves(root).map(n => n.data.name)).toEqual([
-      'seq1',
-      'seq2',
-      'seq3',
-      'seq4',
-    ])
-  })
-
-  test('collapsing a branch hides its children', () => {
-    const root = buildRoot(simpleTree(), ['clade1'])
-    const l = leaves(root).map(n => n.data.name)
-    expect(l).toEqual(['clade1', 'seq3', 'seq4'])
-  })
-
-  test('collapsing a leaf node removes it', () => {
-    const root = buildRoot(simpleTree(), ['seq2'])
-    const l = leaves(root).map(n => n.data.name)
-    expect(l).toEqual(['seq1', 'seq3', 'seq4'])
-  })
-
-  test('collapsing multiple leaves', () => {
-    const root = buildRoot(simpleTree(), ['seq1', 'seq4'])
-    const l = leaves(root).map(n => n.data.name)
-    expect(l).toEqual(['seq2', 'seq3'])
-  })
-
-  test('collapsing a branch and a leaf in another branch', () => {
-    const root = buildRoot(simpleTree(), ['clade1', 'seq3'])
-    const l = leaves(root).map(n => n.data.name)
-    expect(l).toEqual(['clade1', 'seq4'])
-  })
-
-  test('collapsing nonexistent id is a no-op', () => {
-    const root = buildRoot(simpleTree(), ['doesnotexist'])
-    expect(leaves(root).map(n => n.data.name)).toEqual([
-      'seq1',
-      'seq2',
-      'seq3',
-      'seq4',
-    ])
-  })
-
-  test('showOnly focuses on a subtree', () => {
-    const root = buildRoot(simpleTree(), [], 'clade2')
-    expect(leaves(root).map(n => n.data.name)).toEqual(['seq3', 'seq4'])
-  })
-
-  test('showOnly + collapse within subtree', () => {
-    const root = buildRoot(simpleTree(), ['seq3'], 'clade2')
-    expect(leaves(root).map(n => n.data.name)).toEqual(['seq4'])
-  })
-})