jbrowse-plugin-msaview 5.11.0 → 5.13.0

package/dist/MsaViewPanel/model.js

@@ -8,6 +8,7 @@ import { connectedDomains } from './connectedDomains';
 import { domainTrackConf } from './domainTrack';
 import { msaCoordToGenomeCoord, msaCoordToGenomeRegions, } from './msaCoordToGenomeCoord';
 import { resolveConnectedTranscriptIfNeeded } from './resolveConnectedTranscript';
+import { syncSessionHighlights } from './sessionHighlights';
 import { transcriptMap } from './transcriptMap';
 /**
  * Where the homolog set comes from. NCBI's ortholog sets cover vertebrates and
@@ -576,6 +577,7 @@ export default function stateModelFactory() {
             // so they're factories returning the autorun body rather than plain fns
             addDisposer(self, autorun(syncGenomeHoverToMsaColumn(self)));
             addDisposer(self, autorun(observeProteinHighlights(self)));
+            addDisposer(self, autorun(syncSessionHighlights(self)));
         },
     }));
 }

package/dist/MsaViewPanel/sessionHighlights.d.ts

@@ -0,0 +1,57 @@
+import type { JBrowsePluginMsaViewModel } from './model';
+import type { TranscriptMap } from './transcriptMap';
+/** The `transientHighlights` owner the session's highlights draw under */
+export declare const SESSION_HIGHLIGHT_OWNER = "session-highlights";
+/** A session highlight: a genome region, 0-based half-open */
+export interface GenomeHighlight {
+    assemblyName: string;
+    refName: string;
+    start: number;
+    end: number;
+    label?: string;
+    color?: string;
+}
+/** react-msaview's residue-span highlight: residues of `row`, 1-based */
+export interface RowHighlight {
+    row: string;
+    start: number;
+    end: number;
+    label?: string;
+    color?: string;
+}
+/**
+ * Where the query row sits on the genome: through a transcript, each coding
+ * base mapping to its residue, or as the bases of a MAF block
+ */
+export type QueryOnGenome = {
+    kind: 'transcript';
+    map: Pick<TranscriptMap, 'g2p' | 'refName'>;
+} | {
+    kind: 'maf';
+    refName: string;
+    start: number;
+    end: number;
+};
+/**
+ * The session's highlights on the query row, one residue span per run of
+ * consecutive residues a highlight covers, each keeping the highlight's label
+ * and color. A highlight on another assembly or chromosome, or off the
+ * transcript, draws nothing here.
+ */
+export declare function sessionHighlightsOnQueryRow({ highlights, onGenome, querySeqName, querySeqOffset, sameAssembly, sameRefName, labels, }: {
+    highlights: readonly GenomeHighlight[];
+    onGenome: QueryOnGenome;
+    querySeqName: string;
+    querySeqOffset: number;
+    sameAssembly: (assemblyName: string) => boolean;
+    sameRefName: (refName: string) => boolean;
+    /** whether the session writes labels on its highlights */
+    labels: boolean;
+}): RowHighlight[];
+/**
+ * Draw the session's highlights on the query row as react-msaview transient
+ * highlights, so a codon highlighted on the genome lights and labels its
+ * alignment column. They are derived, so the alignment's own snapshot never
+ * holds them.
+ */
+export declare function syncSessionHighlights(self: JBrowsePluginMsaViewModel): () => void;

package/dist/MsaViewPanel/sessionHighlights.js

@@ -0,0 +1,102 @@
+import { getSession } from '@jbrowse/core/util';
+import { hasQueryRow } from './util';
+/** The `transientHighlights` owner the session's highlights draw under */
+export const SESSION_HIGHLIGHT_OWNER = 'session-highlights';
+/**
+ * The 0-based query-row positions a genome region covers. A transcript's
+ * residues count from its start codon, so `querySeqOffset` moves them onto a
+ * query row that holds only part of the protein.
+ */
+function rowPositions({ start, end }, onGenome, querySeqOffset) {
+    const positions = new Set();
+    if (onGenome.kind === 'maf') {
+        for (let base = Math.max(start, onGenome.start); base < Math.min(end, onGenome.end); base++) {
+            positions.add(base - onGenome.start);
+        }
+    }
+    else {
+        for (let base = start; base < end; base++) {
+            const residue = onGenome.map.g2p[base];
+            if (residue !== undefined) {
+                positions.add(residue - querySeqOffset);
+            }
+        }
+    }
+    return [...positions].filter(p => p >= 0).sort((a, b) => a - b);
+}
+/**
+ * The session's highlights on the query row, one residue span per run of
+ * consecutive residues a highlight covers, each keeping the highlight's label
+ * and color. A highlight on another assembly or chromosome, or off the
+ * transcript, draws nothing here.
+ */
+export function sessionHighlightsOnQueryRow({ highlights, onGenome, querySeqName, querySeqOffset, sameAssembly, sameRefName, labels, }) {
+    return highlights.flatMap(h => {
+        if (!sameAssembly(h.assemblyName) || !sameRefName(h.refName)) {
+            return [];
+        }
+        const runs = [];
+        for (const pos of rowPositions(h, onGenome, querySeqOffset)) {
+            const last = runs.at(-1);
+            if (last?.end === pos) {
+                last.end = pos + 1;
+            }
+            else {
+                runs.push({
+                    row: querySeqName,
+                    start: pos + 1,
+                    end: pos + 1,
+                    ...(labels && h.label ? { label: h.label } : {}),
+                    ...(h.color ? { color: h.color } : {}),
+                });
+            }
+        }
+        return runs;
+    });
+}
+// `highlightLabelsVisible` arrived in core after the oldest host this plugin
+// supports, which writes every label
+function labelsVisible(session) {
+    return !('highlightLabelsVisible' in session &&
+        session.highlightLabelsVisible === false);
+}
+/**
+ * Draw the session's highlights on the query row as react-msaview transient
+ * highlights, so a codon highlighted on the genome lights and labels its
+ * alignment column. They are derived, so the alignment's own snapshot never
+ * holds them.
+ */
+export function syncSessionHighlights(self) {
+    return () => {
+        const session = getSession(self);
+        const { connectedView, transcriptToMsaMap, mafRegion } = self;
+        const assemblyName = mafRegion?.assemblyName ?? connectedView?.assemblyNames[0];
+        const { assemblyManager } = session;
+        const assembly = assemblyName
+            ? assemblyManager.get(assemblyName)
+            : undefined;
+        const onGenome = mafRegion
+            ? { kind: 'maf', ...mafRegion }
+            : transcriptToMsaMap
+                ? { kind: 'transcript', map: transcriptToMsaMap }
+                : undefined;
+        if (!session.highlightsVisible ||
+            !session.highlights.length ||
+            !onGenome ||
+            !assembly?.initialized ||
+            !hasQueryRow(self)) {
+            self.clearHighlight(SESSION_HIGHLIGHT_OWNER);
+            return;
+        }
+        const ownRefName = assembly.getCanonicalRefName(onGenome.kind === 'maf' ? onGenome.refName : onGenome.map.refName);
+        self.applyHighlight(SESSION_HIGHLIGHT_OWNER, sessionHighlightsOnQueryRow({
+            highlights: session.highlights,
+            onGenome,
+            querySeqName: self.querySeqName,
+            querySeqOffset: self.querySeqOffset,
+            sameAssembly: name => assemblyManager.get(name) === assembly,
+            sameRefName: refName => assembly.getCanonicalRefName(refName) === ownRefName,
+            labels: labelsVisible(session),
+        }));
+    };
+}

package/dist/MsaViewPanel/sessionHighlights.test.d.ts

@@ -0,0 +1 @@
+export {};

package/dist/MsaViewPanel/sessionHighlights.test.js

@@ -0,0 +1,60 @@
+import { expect, test } from 'vitest';
+import { sessionHighlightsOnQueryRow } from './sessionHighlights';
+// minus strand: residue 0 on bases 109..107, residue 1 on 106..104, residue 2
+// on 103..101
+const g2p = {};
+for (let base = 101; base < 110; base++) {
+    g2p[base] = Math.floor((109 - base) / 3);
+}
+const transcript = {
+    kind: 'transcript',
+    map: { g2p, refName: 'chr12' },
+};
+function onRow(highlights, { onGenome = transcript, querySeqOffset = 0, labels = true } = {}) {
+    return sessionHighlightsOnQueryRow({
+        highlights,
+        onGenome,
+        querySeqName: 'human_query',
+        querySeqOffset,
+        sameAssembly: name => name === 'hg38',
+        sameRefName: refName => refName.replace(/^chr/, '') === '12',
+        labels,
+    });
+}
+const codon = (start, label) => ({
+    assemblyName: 'hg38',
+    refName: 'chr12',
+    start,
+    end: start + 3,
+    label,
+});
+test('a codon labels the residue it codes, 1-based on the query row', () => {
+    expect(onRow([codon(104, 'G12')])).toEqual([
+        { row: 'human_query', start: 2, end: 2, label: 'G12' },
+    ]);
+});
+test('a query row holding part of the protein shifts by its offset', () => {
+    expect(onRow([codon(101)], { querySeqOffset: 1 })).toEqual([
+        { row: 'human_query', start: 2, end: 2 },
+    ]);
+});
+test('a region over several residues is one span per consecutive run', () => {
+    expect(onRow([{ assemblyName: 'hg38', refName: '12', start: 101, end: 110 }])).toEqual([{ row: 'human_query', start: 1, end: 3 }]);
+});
+test('a highlight on another chromosome, assembly or off the CDS draws nothing', () => {
+    expect(onRow([
+        { ...codon(104), refName: 'chr7' },
+        { ...codon(104), assemblyName: 'mm39' },
+        codon(200),
+    ])).toEqual([]);
+});
+test('a MAF query row counts bases from the block start', () => {
+    expect(onRow([codon(1005, 'site')], {
+        onGenome: { kind: 'maf', refName: 'chr12', start: 1000, end: 1010 },
+    })).toEqual([{ row: 'human_query', start: 6, end: 8, label: 'site' }]);
+});
+test('labels turned off in the session keep the span and drop its text', () => {
+    expect(onRow([codon(104, 'G12')], { labels: false })).toEqual([
+        { row: 'human_query', start: 2, end: 2 },
+    ]);
+});

package/dist/chunks/{AboutDialog-QWBMKHTT.js → AboutDialog-HJKHE6X5.js}

@@ -1,2 +1,2 @@
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-//# sourceMappingURL=AboutDialog-QWBMKHTT.js.map
+import{a as l}from"./chunk-JYQQZRPF.js";import{a as i}from"./chunk-DNFD5II2.js";import{a as m}from"./chunk-BX4Z274Q.js";import{a}from"./chunk-J6KYLXRD.js";import{b as r}from"./chunk-FY3BTKY4.js";var e=r(a(),1),o=r(i(),1),t=r(m(),1);function c({onClose:n}){return e.default.createElement(o.Dialog,{open:!0,title:"About",onClose:()=>{n()}},e.default.createElement(t.DialogContent,null,e.default.createElement(t.Typography,null,"MSAView ",l," (",e.default.createElement(t.Link,{target:"_blank",rel:"noopener",href:"https://github.com/gmod/react-msaview"},"Github"),")"),e.default.createElement("ul",null,e.default.createElement("li",null,e.default.createElement(t.Typography,null,"We use some color schemes from the"," ",e.default.createElement(t.Link,{target:"_blank",rel:"noopener",href:"https://github.com/biotite-dev/biotite"},"biotite")," ","project, and their license is reproduced"," ",e.default.createElement(t.Link,{target:"_blank",rel:"noopener",href:"https://github.com/biotite-dev/biotite/blob/master/LICENSE.rst"},"here"))),e.default.createElement("li",null,e.default.createElement(t.Typography,null,"See this page for some information on jalview colorings"," ",e.default.createElement(t.Link,{target:"_blank",rel:"noopener",href:"https://www.jalview.org/help/html/colourSchemes/"},"here"))),e.default.createElement("li",null,e.default.createElement(t.Typography,null,"See this page for some info on the clustal, cinema, maeditor, and lesk color schemes"," ",e.default.createElement(t.Link,{target:"_blank",rel:"noopener",href:"http://www.bioinformatics.nl/~berndb/aacolour.html"},"here"))),e.default.createElement("li",null,e.default.createElement(t.Typography,null,"See this paper about the flower color scheme"," ",e.default.createElement(t.Link,{target:"_blank",rel:"noopener",href:"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7245768/"},"here"))))))}export{c as default};
+//# sourceMappingURL=AboutDialog-HJKHE6X5.js.map

package/dist/chunks/{AboutDialog-QWBMKHTT.js.map → AboutDialog-HJKHE6X5.js.map}

@@ -1,6 +1,6 @@
 {
   "version": 3,
-  "sources": ["../../node_modules/.pnpm/react-msaview@9.7.0_a4121c98828e538e8b3708814bbfe622/node_modules/react-msaview/src/components/dialogs/AboutDialog.tsx"],
+  "sources": ["../../node_modules/.pnpm/react-msaview@9.8.0_a4121c98828e538e8b3708814bbfe622/node_modules/react-msaview/src/components/dialogs/AboutDialog.tsx"],
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package/dist/chunks/{AnnotationFileDialog-M3VBMOKS.js → AnnotationFileDialog-MGUAGUEN.js}

@@ -1,2 +1,2 @@
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+//# sourceMappingURL=AnnotationFileDialog-MGUAGUEN.js.map

package/dist/chunks/{AnnotationFileDialog-M3VBMOKS.js.map → AnnotationFileDialog-MGUAGUEN.js.map}

@@ -1,6 +1,6 @@
 {
   "version": 3,
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+  "sources": ["../../node_modules/.pnpm/react-msaview@9.8.0_a4121c98828e538e8b3708814bbfe622/node_modules/react-msaview/src/components/dialogs/AnnotationFileDialog.tsx"],
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(\n            <div>\n              <Typography>Open an annotation file from a URL</Typography>\n              <TextField\n                label=\"URL\"\n                value={url}\n                onChange={event => {\n                  setUrl(event.target.value)\n                }}\n              />\n            </div>\n          ) : (\n            <div style={{ paddingTop: 20 }}>\n              <Typography>\n                Open an annotation file from your local drive\n              </Typography>\n              <Button variant=\"outlined\" component=\"label\">\n                Choose File\n                <input\n                  type=\"file\"\n                  hidden\n                  onChange={({ target }) => {\n                    const chosen = target.files?.[0]\n                    if (chosen) {\n                      setFile(chosen)\n                    }\n                  }}\n                />\n              </Button>\n              {file ? <Typography>{file.name}</Typography> : null}\n            </div>\n          )}\n        </div>\n      </DialogContent>\n      <DialogActions>\n        <Button\n          variant=\"contained\"\n          color=\"primary\"\n          disabled={loading || (choice === 'file' ? !file : !url.trim())}\n          onClick={() => {\n            // eslint-disable-next-line @typescript-eslint/no-floating-promises\n            ;(async () => {\n              setLoading(true)\n              setError(undefined)\n              try {\n                const text = await (choice === 'file' && file\n                  ? file.text()\n                  : fetchText(url))\n                // through the model's own GFF text, so the annotations travel\n                // in the snapshot and the shared URL like every other layer. A\n                // filehandle left set would make the snapshot drop that text\n                model.setGFFFilehandle(undefined)\n                model.setGFF(annotationTextToGFF(text))\n                model.setShowDomains(true)\n                model.setCellFill('domain')\n                handleClose()\n              } catch (e) {\n                console.error(e)\n                setError(e)\n              } finally {\n                setLoading(false)\n              }\n            })()\n          }}\n        >\n          Open annotations\n        </Button>\n        <Button\n          variant=\"contained\"\n          color=\"secondary\"\n          onClick={() => {\n            handleClose()\n          }}\n        >\n          Cancel\n        </Button>\n      </DialogActions>\n    </Dialog>\n  )\n})\n\nexport default AnnotationFileDialog\n"],
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   "names": ["import_react", "import_ui", "import_material", "import_mobx_react", "domainsTutorial", "fetchText", "url", "response", "AnnotationFileDialog", "handleClose", "model", "file", "setFile", "choice", "setChoice", "setUrl", "error", "setError", "loading", "setLoading", "React", "event", "target", "chosen", "text", "annotationTextToGFF", "e", "AnnotationFileDialog_default"]

package/dist/chunks/{ExportSVGDialog-GBJXLLOT.js → ExportSVGDialog-JNEIAPDD.js}

@@ -1,2 +1,2 @@
-import{a as p}from"./chunk-LTSMXRUM.js";import{aa as v,ba as y}from"./chunk-GS7LNBOS.js";import{a as L}from"./chunk-CVLB4VFP.js";import{a as D}from"./chunk-DNFD5II2.js";import{a as V}from"./chunk-BX4Z274Q.js";import{a as I}from"./chunk-J6KYLXRD.js";import{b as l}from"./chunk-FY3BTKY4.js";var t=l(I(),1),i=l(D(),1),e=l(V(),1),k=l(L(),1);function z(r){requestAnimationFrame(()=>{requestAnimationFrame(r)})}var P=(0,k.observer)(function({model:r,onClose:c}){let[s,C]=(0,t.useState)(!0),[n,T]=(0,t.useState)(!0),[o,b]=(0,t.useState)("viewport"),[E,w]=(0,t.useState)(),[m,h]=(0,t.useState)(!1),d=(0,e.useTheme)(),{turnedOnTracks:M,numColumns:S,leaves:A,showMsaLetters:F}=r,g=M.length>0,x=y(r,v(r,{theme:d,exportType:"entire",includeTracks:n})),f=F&&o==="entire"?S*A.length:0,G=f>1e5;return t.default.createElement(i.Dialog,{onClose:()=>{c()},open:!0,title:"Export SVG"},t.default.createElement(e.DialogContent,null,E?t.default.createElement(i.ErrorMessage,{error:E}):null,t.default.createElement(e.Typography,null,"Settings:"),t.default.createElement(p,{label:"Include minimap?",disabled:o==="entire",checked:s,onChange:()=>{C(!s)}}),g?t.default.createElement(p,{label:"Include tracks?",checked:n,onChange:()=>{T(!n)}}):null,t.default.createElement("div",null,t.default.createElement(e.FormControl,null,t.default.createElement(e.FormLabel,null,"Export type"),t.default.createElement(e.RadioGroup,{value:o,onChange:a=>{let{value:u}=a.target;(u==="entire"||u==="viewport")&&b(u)}},t.default.createElement(e.FormControlLabel,{value:"entire",control:t.default.createElement(e.Radio,null),label:"Entire MSA"}),t.default.createElement(e.FormControlLabel,{value:"viewport",control:t.default.createElement(e.Radio,null),label:"Current viewport only"})))),G?t.default.createElement(e.Alert,{severity:"warning",style:{marginTop:8}},"The entire MSA is ",Math.round(x.width),"x",Math.round(x.height)," pixels and draws"," ",Math.round(f/1e3),"k residue letters, each its own SVG element. Export may be slow or fail \u2014 zooming out far enough to hide the letters exports the same alignment as an image instead."):null),t.default.createElement(e.DialogActions,null,t.default.createElement(e.Button,{variant:"contained",color:"primary",disabled:m,startIcon:m?t.default.createElement(e.CircularProgress,{size:16,color:"inherit"}):null,onClick:()=>{h(!0),z(()=>{r.exportSVG({theme:d,includeMinimap:s,includeTracks:g&&n,exportType:o}).then(()=>{c()}).catch(a=>{console.error(a),w(a)}).finally(()=>{h(!1)})})}},m?"Exporting\u2026":"Export"),t.default.createElement(e.Button,{variant:"contained",color:"secondary",onClick:()=>{c()}},"Cancel")))}),B=P;export{B as default};
-//# sourceMappingURL=ExportSVGDialog-GBJXLLOT.js.map
+import{a as p}from"./chunk-NRAUA3EX.js";import{aa as v,ba as y}from"./chunk-4IRL4OLU.js";import{a as L}from"./chunk-CVLB4VFP.js";import{a as D}from"./chunk-DNFD5II2.js";import{a as V}from"./chunk-BX4Z274Q.js";import{a as I}from"./chunk-J6KYLXRD.js";import{b as l}from"./chunk-FY3BTKY4.js";var t=l(I(),1),i=l(D(),1),e=l(V(),1),k=l(L(),1);function z(r){requestAnimationFrame(()=>{requestAnimationFrame(r)})}var P=(0,k.observer)(function({model:r,onClose:c}){let[s,C]=(0,t.useState)(!0),[n,T]=(0,t.useState)(!0),[o,b]=(0,t.useState)("viewport"),[E,w]=(0,t.useState)(),[m,h]=(0,t.useState)(!1),d=(0,e.useTheme)(),{turnedOnTracks:M,numColumns:S,leaves:A,showMsaLetters:F}=r,g=M.length>0,x=y(r,v(r,{theme:d,exportType:"entire",includeTracks:n})),f=F&&o==="entire"?S*A.length:0,G=f>1e5;return t.default.createElement(i.Dialog,{onClose:()=>{c()},open:!0,title:"Export SVG"},t.default.createElement(e.DialogContent,null,E?t.default.createElement(i.ErrorMessage,{error:E}):null,t.default.createElement(e.Typography,null,"Settings:"),t.default.createElement(p,{label:"Include minimap?",disabled:o==="entire",checked:s,onChange:()=>{C(!s)}}),g?t.default.createElement(p,{label:"Include tracks?",checked:n,onChange:()=>{T(!n)}}):null,t.default.createElement("div",null,t.default.createElement(e.FormControl,null,t.default.createElement(e.FormLabel,null,"Export type"),t.default.createElement(e.RadioGroup,{value:o,onChange:a=>{let{value:u}=a.target;(u==="entire"||u==="viewport")&&b(u)}},t.default.createElement(e.FormControlLabel,{value:"entire",control:t.default.createElement(e.Radio,null),label:"Entire MSA"}),t.default.createElement(e.FormControlLabel,{value:"viewport",control:t.default.createElement(e.Radio,null),label:"Current viewport only"})))),G?t.default.createElement(e.Alert,{severity:"warning",style:{marginTop:8}},"The entire MSA is ",Math.round(x.width),"x",Math.round(x.height)," pixels and draws"," ",Math.round(f/1e3),"k residue letters, each its own SVG element. Export may be slow or fail \u2014 zooming out far enough to hide the letters exports the same alignment as an image instead."):null),t.default.createElement(e.DialogActions,null,t.default.createElement(e.Button,{variant:"contained",color:"primary",disabled:m,startIcon:m?t.default.createElement(e.CircularProgress,{size:16,color:"inherit"}):null,onClick:()=>{h(!0),z(()=>{r.exportSVG({theme:d,includeMinimap:s,includeTracks:g&&n,exportType:o}).then(()=>{c()}).catch(a=>{console.error(a),w(a)}).finally(()=>{h(!1)})})}},m?"Exporting\u2026":"Export"),t.default.createElement(e.Button,{variant:"contained",color:"secondary",onClick:()=>{c()}},"Cancel")))}),B=P;export{B as default};
+//# sourceMappingURL=ExportSVGDialog-JNEIAPDD.js.map

package/dist/chunks/{ExportSVGDialog-GBJXLLOT.js.map → ExportSVGDialog-JNEIAPDD.js.map}

@@ -1,6 +1,6 @@
 {
   "version": 3,
-  "sources": ["../../node_modules/.pnpm/react-msaview@9.7.0_a4121c98828e538e8b3708814bbfe622/node_modules/react-msaview/src/components/dialogs/ExportSVGDialog.tsx"],
+  "sources": ["../../node_modules/.pnpm/react-msaview@9.8.0_a4121c98828e538e8b3708814bbfe622/node_modules/react-msaview/src/components/dialogs/ExportSVGDialog.tsx"],
   "sourcesContent": ["import React, { useState } from 'react'\n\nimport { Dialog, ErrorMessage } from '@jbrowse/core/ui'\nimport {\n  Alert,\n  Button,\n  CircularProgress,\n  DialogActions,\n  DialogContent,\n  FormControl,\n  FormControlLabel,\n  FormLabel,\n  Radio,\n  RadioGroup,\n  Typography,\n  useTheme,\n} from '@mui/material'\nimport { observer } from 'mobx-react'\n\nimport { exportPageSize, getLayout } from '../../exportLayout.ts'\nimport Checkbox2 from '../Checkbox2.tsx'\n\nimport type { MsaViewModel } from '../../model.ts'\n\n// Run after the browser has painted. A requestAnimationFrame callback still\n// runs *before* the frame it was queued for, so one alone hands the main thread\n// to the render with the spinner not yet on screen; the second fires once that\n// frame is out.\nfunction afterPaint(fn: () => void) {\n  requestAnimationFrame(() => {\n    requestAnimationFrame(fn)\n  })\n}\n\nconst ExportSVGDialog = observer(function ({\n  model,\n  onClose,\n}: {\n  model: MsaViewModel\n  onClose: () => void\n}) {\n  const [includeMinimap, setIncludeMinimap] = useState(true)\n  const [includeTracks, setIncludeTracks] = useState(true)\n  const [exportType, setExportType] = useState<'entire' | 'viewport'>(\n    'viewport',\n  )\n  const [error, setError] = useState<unknown>()\n  const [exporting, setExporting] = useState(false)\n  const theme = useTheme()\n  const { turnedOnTracks, numColumns, leaves, showMsaLetters } = model\n  const hasTracks = turnedOnTracks.length > 0\n  const entire = exportPageSize(\n    model,\n    getLayout(model, { theme, exportType: 'entire', includeTracks }),\n  )\n  // the background is one raster image whatever its size, so what the figure\n  // actually costs is its residue letters: each is an svg element of its own.\n  // Past roughly this many the export runs to tens of seconds and can exhaust\n  // the tab's memory outright\n  const glyphs =\n    showMsaLetters && exportType === 'entire' ? numColumns * leaves.length : 0\n  const isLargeExport = glyphs > 100_000\n  return (\n    <Dialog\n      onClose={() => {\n        onClose()\n      }}\n      open\n      title=\"Export SVG\"\n    >\n      <DialogContent>\n        {error ? <ErrorMessage error={error} /> : null}\n        <Typography>Settings:</Typography>\n        <Checkbox2\n          label=\"Include minimap?\"\n          disabled={exportType === 'entire'}\n          checked={includeMinimap}\n          onChange={() => {\n            setIncludeMinimap(!includeMinimap)\n          }}\n        />\n        {hasTracks ? (\n          <Checkbox2\n            label=\"Include tracks?\"\n            checked={includeTracks}\n            onChange={() => {\n              setIncludeTracks(!includeTracks)\n            }}\n          />\n        ) : null}\n        <div>\n          <FormControl>\n            <FormLabel>Export type</FormLabel>\n            <RadioGroup\n              value={exportType}\n              onChange={event => {\n                const { value } = event.target\n                if (value === 'entire' || value === 'viewport') {\n                  setExportType(value)\n                }\n              }}\n            >\n              <FormControlLabel\n                value=\"entire\"\n                control={<Radio />}\n                label=\"Entire MSA\"\n              />\n              <FormControlLabel\n                value=\"viewport\"\n                control={<Radio />}\n                label=\"Current viewport only\"\n              />\n            </RadioGroup>\n          </FormControl>\n        </div>\n        {isLargeExport ? (\n          <Alert severity=\"warning\" style={{ marginTop: 8 }}>\n            The entire MSA is {Math.round(entire.width)}x\n            {Math.round(entire.height)} pixels and draws{' '}\n            {Math.round(glyphs / 1000)}k residue letters, each its own SVG\n            element. 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package/dist/chunks/{FeatureDialog-VYCJWC4A.js → FeatureDialog-36U3KHHS.js}

@@ -1,2 +1,2 @@
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-//# sourceMappingURL=FeatureDialog-VYCJWC4A.js.map
+//# sourceMappingURL=FeatureDialog-36U3KHHS.js.map

package/dist/chunks/{FeatureDialog-VYCJWC4A.js.map → FeatureDialog-36U3KHHS.js.map}

@@ -1,6 +1,6 @@
 {
   "version": 3,
-  "sources": ["../../node_modules/.pnpm/react-msaview@9.7.0_a4121c98828e538e8b3708814bbfe622/node_modules/react-msaview/src/components/dialogs/FeatureDialog.tsx"],
+  "sources": ["../../node_modules/.pnpm/react-msaview@9.8.0_a4121c98828e538e8b3708814bbfe622/node_modules/react-msaview/src/components/dialogs/FeatureDialog.tsx"],
   "sourcesContent": ["import React, { useState } from 'react'\n\nimport { Dialog } from '@jbrowse/core/ui'\nimport {\n  Button,\n  Checkbox,\n  DialogContent,\n  Table,\n  TableBody,\n  TableCell,\n  TableHead,\n  TableRow,\n  TextField,\n} from '@mui/material'\nimport { observer } from 'mobx-react'\n\nimport type { MsaViewModel } from '../../model.ts'\nimport type { Annotation } from '../../types.ts'\n\nfunction matches(type: Annotation, query: string) {\n  return [type.accession, type.name, type.description].some(field =>\n    field?.toLowerCase().includes(query),\n  )\n}\n\nconst Toggles = observer(function ({\n  model,\n  accessions,\n}: {\n  model: MsaViewModel\n  accessions: string[]\n}) {\n  const setAll = (shown: boolean) => {\n    for (const accession of accessions) {\n      model.setFilter(accession, shown)\n    }\n  }\n  return (\n    <div>\n      <Button\n        onClick={() => {\n          setAll(true)\n        }}\n      >\n        Toggle all on\n      </Button>\n\n      <Button\n        onClick={() => {\n          setAll(false)\n        }}\n      >\n        Toggle all off\n      </Button>\n    </div>\n  )\n})\n\nconst FeatureTable = observer(function ({ model }: { model: MsaViewModel }) {\n  const { annotationTypes, annotations, featureColors, fillPalette } = model\n  const [query, setQuery] = useState('')\n  const needle = query.trim().toLowerCase()\n  const types = [...annotationTypes.values()].filter(\n    type => !needle || matches(type, needle),\n  )\n  const counts = new Map<string, number>()\n  const swatches = new Map<string, string>()\n  for (const annot of annotations) {\n    const { accession } = annot\n    counts.set(accession, (counts.get(accession) ?? 0) + 1)\n    if (!swatches.has(accession)) {\n      swatches.set(\n        accession,\n        featureColors.get(annot)?.fill ?? fillPalette[accession]!,\n      )\n    }\n  }\n  return (\n    <>\n      <TextField\n        label=\"Filter\"\n        size=\"small\"\n        value={query}\n        onChange={event => {\n          setQuery(event.target.value)\n        }}\n      />\n      <Toggles model={model} accessions={types.map(t => t.accession)} />\n      <Table size=\"small\">\n        <TableHead>\n          <TableRow>\n            <TableCell padding=\"checkbox\" />\n            <TableCell>color</TableCell>\n            <TableCell>accession</TableCell>\n            <TableCell>name</TableCell>\n            <TableCell>count</TableCell>\n            <TableCell>description</TableCell>\n          </TableRow>\n        </TableHead>\n        <TableBody>\n          {types.map(({ accession, name, description }) => (\n            <TableRow key={accession}>\n              <TableCell padding=\"checkbox\">\n                <Checkbox\n                  checked={!model.featureOff(accession)}\n                  onChange={() => {\n                    model.setFilter(accession, model.featureOff(accession))\n                  }}\n                />\n              </TableCell>\n              <TableCell>\n                <div\n                  style={{\n                    width: 20,\n                    height: 20,\n                    background: swatches.get(accession),\n                  }}\n                />\n              </TableCell>\n              <TableCell>{accession}</TableCell>\n              <TableCell>{name}</TableCell>\n              <TableCell>{counts.get(accession)}</TableCell>\n              <TableCell>{description}</TableCell>\n            </TableRow>\n          ))}\n        </TableBody>\n      </Table>\n    </>\n  )\n})\n\nconst FeatureTypeDialog = observer(function ({\n  onClose,\n  model,\n}: {\n  onClose: () => void\n  model: MsaViewModel\n}) {\n  return (\n    <Dialog\n      onClose={() => {\n        onClose()\n      }}\n      open\n      title=\"Feature filters\"\n      maxWidth=\"xl\"\n    >\n      <DialogContent>\n        <FeatureTable model={model} />\n      </DialogContent>\n    </Dialog>\n  )\n})\n\nexport default FeatureTypeDialog\n"],
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   "names": ["import_react", "import_ui", "import_material", "import_mobx_react", "matches", "type", "query", "field", "Toggles", "model", "accessions", "setAll", "shown", "accession", "React", "FeatureTable", "annotationTypes", "annotations", "featureColors", "fillPalette", "setQuery", "needle", "types", "counts", "swatches", "annot", "event", "t", "name", "description", "FeatureTypeDialog", "onClose", "FeatureDialog_default"]

package/dist/chunks/{GapThresholdDialog-AXIDV62R.js → GapThresholdDialog-MMQTM2ZY.js}

@@ -1,2 +1,2 @@
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-//# sourceMappingURL=GapThresholdDialog-AXIDV62R.js.map
+//# sourceMappingURL=GapThresholdDialog-MMQTM2ZY.js.map

package/dist/chunks/{GapThresholdDialog-AXIDV62R.js.map → GapThresholdDialog-MMQTM2ZY.js.map}

@@ -1,6 +1,6 @@
 {
   "version": 3,
-  "sources": ["../../node_modules/.pnpm/react-msaview@9.7.0_a4121c98828e538e8b3708814bbfe622/node_modules/react-msaview/src/components/dialogs/GapThresholdDialog.tsx", "../../node_modules/.pnpm/react-msaview@9.7.0_a4121c98828e538e8b3708814bbfe622/node_modules/react-msaview/src/components/dialogs/GappynessSlider.tsx"],
+  "sources": ["../../node_modules/.pnpm/react-msaview@9.8.0_a4121c98828e538e8b3708814bbfe622/node_modules/react-msaview/src/components/dialogs/GapThresholdDialog.tsx", "../../node_modules/.pnpm/react-msaview@9.8.0_a4121c98828e538e8b3708814bbfe622/node_modules/react-msaview/src/components/dialogs/GappynessSlider.tsx"],
   "sourcesContent": ["import React from 'react'\n\nimport { Dialog } from '@jbrowse/core/ui'\nimport { Button, DialogActions, DialogContent, Typography } from '@mui/material'\nimport { observer } from 'mobx-react'\n\nimport GappynessSlider from './GappynessSlider.tsx'\n\nimport type { MsaViewModel } from '../../model.ts'\n\nconst GapThresholdDialog = observer(function ({\n  model,\n  onClose,\n}: {\n  model: MsaViewModel\n  onClose: () => void\n}) {\n  return (\n    <Dialog open onClose={onClose} title=\"Hide gappy columns\">\n      <DialogContent>\n        <Typography variant=\"body2\" sx={{ mb: 2 }}>\n          The viewer hides each column where at least this share of the rows has\n          a gap.\n        </Typography>\n        <GappynessSlider model={model} />\n      </DialogContent>\n      <DialogActions>\n        <Button variant=\"contained\" onClick={onClose}>\n          Close\n        </Button>\n      </DialogActions>\n    </Dialog>\n  )\n})\n\nexport default GapThresholdDialog\n", "import React, { useState } from 'react'\n\nimport { Slider, Typography } from '@mui/material'\nimport { observer } from 'mobx-react'\n\nimport type { MsaViewModel } from '../../model.ts'\n\nconst GappynessSlider = observer(function GappynessSlider({\n  model,\n}: {\n  model: MsaViewModel\n}) {\n  const [dragValue, setDragValue] = useState<number>()\n  const value = dragValue ?? model.allowedGappyness\n  return (\n    <div style={{ display: 'flex', alignItems: 'center', gap: 8 }}>\n      {/* the threshold is inclusive: blanks are columns whose gap count is at\n          least ceil(allowedGappyness% of the rows), so at 100 it hides the\n          columns that are entirely gaps rather than nothing */}\n      <Typography style={{ whiteSpace: 'nowrap' }}>\n        &ge;{value}% gaps\n      </Typography>\n      <Slider\n        // In JBrowse other MUI Sliders share the page, so `.MuiSlider-thumb`\n        // can match the wrong one. Tests and screenshot specs target\n        // `[data-testid=\"gappyness_slider\"] input`, the hidden range input that\n        // takes focus and arrow/PageUp/PageDown.\n        //\n        // Not `slotProps={{ input: ... }}`: that widens `onChange`'s `val` to\n        // `number | number[]`, which setAllowedGappyness rejects.\n        //\n        // The thumb follows local state while dragging and the model takes the\n        // value on release, since each write recomputes the gap columns over\n        // the whole alignment.\n        data-testid=\"gappyness_slider\"\n        style={{ width: 200, marginInline: 10 }}\n        min={1}\n        max={100}\n        value={value}\n        onChange={(_, val) => {\n          setDragValue(val)\n        }}\n        onChangeCommitted={(_, val) => {\n          model.setAllowedGappyness(val)\n          setDragValue(undefined)\n        }}\n      />\n    </div>\n  )\n})\n\nexport default GappynessSlider\n"],
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package/dist/chunks/{GoToDialog-7RZHEZXR.js → GoToDialog-HYG2ADFF.js}

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-import{b as r}from"./chunk-MUSD22PZ.js";import"./chunk-CVLB4VFP.js";import{a}from"./chunk-DNFD5II2.js";import{a as u}from"./chunk-BX4Z274Q.js";import{a as i}from"./chunk-J6KYLXRD.js";import{b as t}from"./chunk-FY3BTKY4.js";var o=t(i(),1),l=t(a(),1),m=t(u(),1);function f({model:n,onClose:e}){return o.default.createElement(l.Dialog,{open:!0,onClose:e,title:"Go to row or column",maxWidth:"xs",fullWidth:!0},o.default.createElement(m.DialogContent,null,o.default.createElement(r,{model:n,onFound:e})))}export{f as default};
-//# sourceMappingURL=GoToDialog-7RZHEZXR.js.map
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+//# sourceMappingURL=GoToDialog-HYG2ADFF.js.map

package/dist/chunks/{GoToDialog-7RZHEZXR.js.map → GoToDialog-HYG2ADFF.js.map}

@@ -1,6 +1,6 @@
 {
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-  "sources": ["../../node_modules/.pnpm/react-msaview@9.7.0_a4121c98828e538e8b3708814bbfe622/node_modules/react-msaview/src/components/dialogs/GoToDialog.tsx"],
+  "sources": ["../../node_modules/.pnpm/react-msaview@9.8.0_a4121c98828e538e8b3708814bbfe622/node_modules/react-msaview/src/components/dialogs/GoToDialog.tsx"],
   "sourcesContent": ["import React from 'react'\n\nimport { Dialog } from '@jbrowse/core/ui'\nimport { DialogContent } from '@mui/material'\n\nimport GoToBox from './GoToBox.tsx'\n\nimport type { MsaViewModel } from '../../model.ts'\n\nexport default function GoToDialog({\n  model,\n  onClose,\n}: {\n  model: MsaViewModel\n  onClose: () => void\n}) {\n  return (\n    <Dialog\n      open\n      onClose={onClose}\n      title=\"Go to row or column\"\n      maxWidth=\"xs\"\n      fullWidth\n    >\n      <DialogContent>\n        <GoToBox model={model} onFound={onClose} />\n      </DialogContent>\n    </Dialog>\n  )\n}\n"],
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package/dist/chunks/{HelpDialog-ELECZLPQ.js → HelpDialog-5WXA5QYK.js}

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+//# sourceMappingURL=HelpDialog-5WXA5QYK.js.map

package/dist/chunks/{HelpDialog-ELECZLPQ.js.map → HelpDialog-5WXA5QYK.js.map}

@@ -1,6 +1,6 @@
 {
   "version": 3,
-  "sources": ["../../node_modules/.pnpm/react-msaview@9.7.0_a4121c98828e538e8b3708814bbfe622/node_modules/react-msaview/src/components/dialogs/HelpDialog.tsx"],
+  "sources": ["../../node_modules/.pnpm/react-msaview@9.8.0_a4121c98828e538e8b3708814bbfe622/node_modules/react-msaview/src/components/dialogs/HelpDialog.tsx"],
   "sourcesContent": ["import React, { lazy } from 'react'\n\nimport { Dialog } from '@jbrowse/core/ui'\nimport {\n  Button,\n  DialogActions,\n  DialogContent,\n  Table,\n  TableBody,\n  TableCell,\n  TableRow,\n  Typography,\n} from '@mui/material'\n\nimport { version } from '../../version.ts'\nimport { keyboardControls, mouseControls } from '../controls.ts'\n\nimport type { MsaViewModel } from '../../model.ts'\nimport type { Control } from '../controls.ts'\n\nconst AboutDialog = lazy(() => import('./AboutDialog.tsx'))\n\nfunction ControlTable({ title, rows }: { title: string; rows: Control[] }) {\n  return (\n    <>\n      <Typography variant=\"subtitle2\" sx={{ mt: 1 }}>\n        {title}\n      </Typography>\n      <Table size=\"small\" aria-label={title}>\n        <TableBody>\n          {rows.map(({ label, action }) => (\n            <TableRow key={label}>\n              <TableCell sx={{ whiteSpace: 'nowrap', fontWeight: 500 }}>\n                {label}\n              </TableCell>\n              <TableCell>{action}</TableCell>\n            </TableRow>\n          ))}\n        </TableBody>\n      </Table>\n    </>\n  )\n}\n\nexport default function HelpDialog({\n  model,\n  onClose,\n}: {\n  model: MsaViewModel\n  onClose: () => void\n}) {\n  return (\n    <Dialog open title=\"Mouse & keyboard\" onClose={onClose}>\n      <DialogContent>\n        <ControlTable title=\"Mouse\" rows={mouseControls} />\n        <ControlTable\n          title=\"Keyboard (click the alignment first)\"\n          rows={keyboardControls}\n        />\n      </DialogContent>\n      <DialogActions>\n        <Typography variant=\"caption\" sx={{ mr: 'auto', pl: 1 }}>\n          MSAView {version}\n        </Typography>\n        <Button\n          onClick={() => {\n            model.queueDialog(done => [AboutDialog, { onClose: done }])\n            onClose()\n          }}\n        >\n          About & credits\n        </Button>\n        <Button variant=\"contained\" onClick={onClose}>\n          Close\n        </Button>\n      </DialogActions>\n    </Dialog>\n  )\n}\n"],
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package/dist/chunks/{MetadataDialog-Z6Z5PJJI.js → MetadataDialog-QQNNQELM.js}

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package/dist/chunks/{MsaViewPanel-TWWHZCKE.js → MsaViewPanel-4PHVMXIL.js}

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package/dist/chunks/{TrackInfoDialog-KBMR6BIS.js → TrackInfoDialog-WJAJNV5S.js}

@@ -1,2 +1,2 @@
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package/dist/chunks/{TrackInfoDialog-KBMR6BIS.js.map → TrackInfoDialog-WJAJNV5S.js.map}

@@ -1,6 +1,6 @@
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+  "sources": ["../../node_modules/.pnpm/react-msaview@9.8.0_a4121c98828e538e8b3708814bbfe622/node_modules/react-msaview/src/components/dialogs/TrackInfoDialog.tsx"],
   "sourcesContent": ["import React from 'react'\n\nimport { Dialog } from '@jbrowse/core/ui'\nimport { makeStyles } from '@jbrowse/core/util/tss-react'\nimport { Button, DialogActions, DialogContent, Typography } from '@mui/material'\nimport { observer } from 'mobx-react'\n\nimport CopyButton from '../CopyButton.tsx'\n\nimport type { BasicTrack } from '../../types.ts'\n\nconst useStyles = makeStyles()(theme => ({\n  textArea: {\n    padding: theme.spacing(2),\n    overflow: 'auto',\n    background: theme.palette.action.selected,\n    wordBreak: 'break-word',\n  },\n}))\n\nconst TrackInfoDialog = observer(function ({\n  model,\n  onClose,\n}: {\n  model: BasicTrack['model']\n  onClose: () => void\n}) {\n  const { name, data } = model\n  const { classes } = useStyles()\n  return (\n    <Dialog\n      open\n      onClose={onClose}\n      fullWidth\n      maxWidth=\"lg\"\n      title={`Track info - ${name}`}\n    >\n      <DialogContent>\n        {/* the bar tracks (conservation) are computed per column and carry no\n            text of their own, so there is nothing to show or copy for them */}\n        {data === undefined ? (\n          <Typography>This track has no text data.</Typography>\n        ) : (\n          <>\n            <CopyButton text={data} />\n            <pre className={classes.textArea}>{data}</pre>\n          </>\n        )}\n      </DialogContent>\n      <DialogActions>\n        <Button variant=\"contained\" onClick={onClose} color=\"secondary\">\n          Close\n        </Button>\n      </DialogActions>\n    </Dialog>\n  )\n})\n\nexport default TrackInfoDialog\n"],
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   "names": ["import_react", "import_ui", "import_tss_react", "import_material", "import_mobx_react", "useStyles", "theme", "TrackInfoDialog", "model", "onClose", "name", "data", "classes", "React", "CopyButton", "TrackInfoDialog_default"]