react-msaview 6.5.0 → 8.0.0

package/src/useCanvasAutorun.ts

@@ -6,17 +6,12 @@ import type React from 'react'
 
 /**
  * Wires a canvas ref to a mobx autorun: grabs the 2d context once the canvas
- * mounts and re-runs `draw` whenever any observable it reads changes. Collapses
- * the getContext/null-guard/autorun-dispose boilerplate repeated by every canvas
- * block host.
+ * mounts and re-runs `draw` whenever any observable it reads changes.
  *
- * `width`/`height` are the canvas *backing store* size the caller renders onto
- * the element (logical size times the high-res scale factor), and they are load
- * bearing rather than informational. Assigning either resets the canvas bitmap,
- * and React assigns them on every commit where they changed -- which lands
- * *after* the mobx reaction that already redrew at the old size. Without a redraw
- * on the far side of that commit the canvas is left blank: it is what blanked the
- * tree on a tree-area resize and the consensus tracks on a vertical zoom.
+ * `width`/`height` are the canvas backing store size (logical size times the
+ * high-res scale factor). Assigning either clears the bitmap, and React assigns
+ * them after the mobx reaction has drawn at the old size, so the effect redraws
+ * when they change.
  *
  * `deps` covers everything else the effect should re-subscribe on, matching a
  * normal useEffect dep array.

package/src/useMsaSvgFigure.ts

@@ -0,0 +1,72 @@
+import { useEffect, useState } from 'react'
+
+import { createJBrowseTheme } from '@jbrowse/core/ui/theme'
+import { getSnapshot } from '@jbrowse/mobx-state-tree'
+import { compareStructural, reaction } from 'mobx'
+
+import { renderToSvg } from './renderToSvg.tsx'
+
+import type { MsaViewModel } from './model.ts'
+import type { Theme } from '@mui/material'
+
+export interface MsaSvgFigure {
+  /** the SVG document for what is on screen, once the first draw finishes */
+  svg?: string
+  error?: unknown
+}
+
+/**
+ * The viewer's SVG export of its viewport, as markup for the page to insert.
+ * It redraws after the view settles: `delay` ms after the last scroll, zoom,
+ * resize or change to the snapshot. A draw a later one overtakes is dropped.
+ *
+ * The figure's row names and letters are SVG text, so the browser's find
+ * locates them, a reader can select them, and print stylesheets apply.
+ */
+export function useMsaSvgFigure(
+  model: MsaViewModel,
+  {
+    theme,
+    includeTracks = false,
+    delay = 300,
+  }: { theme?: Theme; includeTracks?: boolean; delay?: number } = {},
+) {
+  const [figure, setFigure] = useState<MsaSvgFigure>({})
+  useEffect(() => {
+    let latest = 0
+    const dispose = reaction(
+      () =>
+        model.viewInitialized && model.dataInitialized
+          ? [getSnapshot(model), model.width, model.height]
+          : undefined,
+      key => {
+        if (!key) {
+          return
+        }
+        const draw = ++latest
+        renderToSvg(model, {
+          theme: theme ?? createJBrowseTheme(),
+          exportType: 'viewport',
+          includeTracks,
+        }).then(
+          svg => {
+            if (draw === latest) {
+              setFigure({ svg })
+            }
+          },
+          (error: unknown) => {
+            if (draw === latest) {
+              setFigure({ error })
+            }
+          },
+        )
+      },
+      { delay, fireImmediately: true, equals: compareStructural },
+    )
+    return () => {
+      latest = -1
+      dispose()
+    }
+  }, [model, theme, includeTracks, delay])
+  return figure
+}

package/src/util.ts

@@ -29,6 +29,18 @@ export function adjustColorForContrast(color: string, bg: string): string {
   return result
 }
 
+// a wash over the alignment or the tree: a color carrying its own alpha draws
+// at that alpha, and one with none takes `alpha` so the marks under it stay
+// readable
+export function withAlpha(color: string, alpha: number) {
+  const parsed = colord(color)
+  return parsed.alpha() === 1 ? parsed.alpha(alpha).toRgbString() : color
+}
+
+export function outlineColor(fill: string) {
+  return colord(fill).darken(0.1).toHex()
+}
+
 export function transform<T>(
   obj: Record<string, T>,
   cb: (arg0: [string, T]) => [string, T],
@@ -36,14 +48,34 @@ export function transform<T>(
   return Object.fromEntries(Object.entries(obj).map(cb))
 }
 
-export function colorContrast(
-  colorScheme: Record<string, string>,
-  theme: Theme,
-) {
-  return transform(colorScheme, ([letter, color]) => [
-    letter,
-    theme.palette.getContrastText(colord(color).toHex()),
-  ])
+const contrastTextCaches = new WeakMap<Theme, Map<string, string>>()
+
+/**
+ * Readable letter color over a given cell color, memoized per theme.
+ *
+ * Keyed by cell color, since a dynamic scheme has no letter->color table; this
+ * covers static schemes and a track's own `colors` too. An uncolored cell gets
+ * the theme's text color, which stays readable in the dark theme.
+ */
+export function contrastTextFn(theme: Theme) {
+  let cache = contrastTextCaches.get(theme)
+  if (!cache) {
+    cache = new Map()
+    contrastTextCaches.set(theme, cache)
+  }
+  const fallback = theme.palette.text.primary
+  return (color: string | undefined) => {
+    if (!color) {
+      return fallback
+    }
+    const hit = cache.get(color)
+    if (hit !== undefined) {
+      return hit
+    }
+    const out = theme.palette.getContrastText(colord(color).toHex())
+    cache.set(color, out)
+    return out
+  }
 }
 
 export function dropBlanks<T>(blanks: number[], arr: T[]) {
@@ -110,9 +142,3 @@ export function computeRowInsertions(blanks: number[], seq: string) {
 export function len(a: { end: number; start: number }) {
   return a.end - a.start
 }
-
-// https://sonnhammer.sbc.su.se/Stockholm.html
-// gaps can be a . or - in stockholm
-export function isBlank(s?: string) {
-  return s === '-' || s === '.'
-}

package/src/version.ts

@@ -1 +1 @@
-export const version = '6.5.0'
+export const version = '8.0.0'

package/src/wuss.ts

@@ -0,0 +1,62 @@
+// WUSS notation (Rfam's `#=GC SS_cons`) names a consensus secondary structure
+// by pairing columns. Nested helices use bracket pairs -- <>, (), [], {} --
+// each type kept on its own stack, and a pseudoknot, which by definition
+// crosses a helix it cannot nest inside, uses a letter pair instead: `A` opens
+// and `a` closes, `B`/`b` for a second one. Everything else (. , _ - : ~) is
+// unpaired.
+
+const closeToOpen: Record<string, string> = {
+  '>': '<',
+  ')': '(',
+  ']': '[',
+  '}': '{',
+}
+const opens = new Set(Object.values(closeToOpen))
+
+export interface BasePair {
+  /** 0-based column */
+  start: number
+  /** 0-based column */
+  end: number
+  /** the pair crosses a helix rather than nesting inside one */
+  pseudoknot: boolean
+}
+
+/**
+ * The base pairs a WUSS string encodes, as 0-based column indexes. Unmatched
+ * brackets are dropped rather than throwing: a hand-edited or truncated
+ * alignment should still draw the helices it does close.
+ */
+export function parseWuss(ss: string): BasePair[] {
+  const stacks = new Map<string, number[]>()
+  const pairs: BasePair[] = []
+  const push = (key: string, col: number) => {
+    const stack = stacks.get(key)
+    if (stack) {
+      stack.push(col)
+    } else {
+      stacks.set(key, [col])
+    }
+  }
+  const pop = (key: string, col: number, pseudoknot: boolean) => {
+    const start = stacks.get(key)?.pop()
+    if (start !== undefined) {
+      pairs.push({ start, end: col, pseudoknot })
+    }
+  }
+
+  for (let col = 0; col < ss.length; col++) {
+    const ch = ss[col]!
+    const opener = closeToOpen[ch]
+    if (opens.has(ch)) {
+      push(ch, col)
+    } else if (opener) {
+      pop(opener, col, false)
+    } else if (ch >= 'A' && ch <= 'Z') {
+      push(ch, col)
+    } else if (ch >= 'a' && ch <= 'z') {
+      pop(ch.toUpperCase(), col, true)
+    }
+  }
+  return pairs.sort((a, b) => a.start - b.start)
+}

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

@@ -1 +0,0 @@
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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/components/msa/ColumnStats.js

@@ -1,42 +0,0 @@
-import React from 'react';
-import { observer } from 'mobx-react';
-const pct = (n) => `${Math.round(n * 100)}%`;
-const ColumnStats = observer(function ({ model }) {
-    const stats = model.mouseOverColumnStats;
-    if (!stats) {
-        return null;
-    }
-    const { col, total, conservation, propertyConservation, consensusLetter, consensusFraction, gapFraction, distribution, } = stats;
-    const top = distribution.slice(0, 6);
-    return (React.createElement("div", null,
-        React.createElement("b", null,
-            "Column ",
-            col + 1),
-        " (",
-        total,
-        " seqs)",
-        React.createElement("br", null),
-        "Consensus: ",
-        consensusLetter || '-',
-        " (",
-        pct(consensusFraction),
-        ")",
-        React.createElement("br", null),
-        "Conservation: ",
-        conservation.toFixed(2),
-        propertyConservation === undefined ? null : (React.createElement(React.Fragment, null,
-            React.createElement("br", null),
-            "Property conservation: ",
-            propertyConservation.toFixed(2))),
-        React.createElement("br", null),
-        "Gaps: ",
-        pct(gapFraction),
-        top.length > 0 ? (React.createElement(React.Fragment, null,
-            React.createElement("br", null),
-            top.map(([letter, count]) => (React.createElement("span", { key: letter, style: { marginRight: 8 } },
-                letter,
-                " ",
-                pct(count / total)))))) : null));
-});
-export default ColumnStats;
-//# sourceMappingURL=ColumnStats.js.map

package/dist/components/msa/ColumnStats.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;
-    };
-};