react-msaview 6.2.3 → 6.3.0

package/dist/headlessRenderEnv.js

@@ -65,8 +65,11 @@ export class HeadlessDOMPoint {
  * average for layout and, more usefully, exactly predictable: a caller can
  * compute the width a renderer will see rather than hardcoding a number
  * measured from one machine's fonts.
+ *
+ * `contextExtras` adds to the context a test hands out -- the raster test
+ * supplies the ImageData methods that make the export take its image path.
  */
-export function installHeadlessRenderEnv(win = globalThis) {
+export function installHeadlessRenderEnv(win = globalThis, contextExtras = {}) {
     const g = globalThis;
     g.DOMMatrix = HeadlessDOMMatrix;
     g.DOMPoint = HeadlessDOMPoint;
@@ -74,7 +77,7 @@ export function installHeadlessRenderEnv(win = globalThis) {
         .HTMLCanvasElement;
     canvas.prototype.getContext = function () {
         let font = '10px sans-serif';
-        return {
+        return Object.assign({
             get font() {
                 return font;
             },
@@ -84,7 +87,7 @@ export function installHeadlessRenderEnv(win = globalThis) {
             measureText: (t) => ({
                 width: t.length * (Number.parseFloat(font) || 10) * CHAR_WIDTH_RATIO,
             }),
-        };
+        }, contextExtras);
     };
 }
 /** the per-character width factor `measureText` above reports */

package/dist/headlessRenderEnv.js.map

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package/dist/index.d.ts

@@ -1,4 +1,5 @@
 export { renderToSvg } from './renderToSvg.tsx';
+export type { ExportSvgOptions } from './renderToSvg.tsx';
 export { CHAR_WIDTH_RATIO, installHeadlessRenderEnv, } from './headlessRenderEnv.ts';
 export { default as MSAView } from './components/Loading.tsx';
 export { default as MSAViewer } from './components/MSAViewer.tsx';
@@ -7,4 +8,4 @@ export type { MSAFormat, MSAParserType } from 'msa-parsers';
 export type { HierarchyNode } from './hierarchy.ts';
 export type { InterProScanResults } from 'msa-parsers';
 export type { ColumnCounts } from './columnCounts.ts';
-export type { Accession, Annotation, BasicTrack, BasicTrackModel, DomainBand, Node, NodeWithIds, NodeWithIdsAndLength, TextTrackModel, TidyDomainAnnotation, } from './types.ts';
+export type { Accession, Annotation, BasicTrack, BasicTrackModel, ColumnTrackSpec, DomainBand, Highlight, Node, NodeWithIds, NodeWithIdsAndLength, ResolvedHighlight, TextTrackModel, TidyDomainAnnotation, } from './types.ts';

package/dist/index.js.map

@@ -1 +1 @@
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+{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,gFAAgF;AAChF,yDAAyD;AACzD,+EAA+E;AAC/E,6EAA6E;AAC7E,gFAAgF;AAChF,0EAA0E;AAC1E,yEAAyE;AACzE,OAAO,EAAE,WAAW,EAAE,MAAM,kBAAmB,CAAA;AAE/C,8EAA8E;AAC9E,yDAAyD;AACzD,OAAO,EACL,gBAAgB,EAChB,wBAAwB,GACzB,MAAM,wBAAwB,CAAA;AAC/B,OAAO,EAAE,OAAO,IAAI,OAAO,EAAE,MAAM,yBAA0B,CAAA;AAC7D,OAAO,EAAE,OAAO,IAAI,SAAS,EAAE,MAAM,2BAA4B,CAAA;AACjE,OAAO,EAAqB,OAAO,IAAI,SAAS,EAAE,MAAM,YAAY,CAAA"}

package/dist/model.d.ts

@@ -1,8 +1,8 @@
 import type { HierarchyNode } from './hierarchy.ts';
-import type { Annotation, BasicTrack, DomainBand, NodeWithIds, NodeWithIdsAndLength } from './types.ts';
+import type { ExportSvgOptions } from './renderToSvg.tsx';
+import type { Annotation, BasicTrack, ColumnTrackSpec, DomainBand, Highlight, NodeWithIds, NodeWithIdsAndLength, ResolvedHighlight } from './types.ts';
 import type { FileLocation as FileLocationType } from '@jbrowse/core/util/types';
 import type { Instance } from '@jbrowse/mobx-state-tree';
-import type { Theme } from '@mui/material';
 import type { InterProScanResults } from 'msa-parsers';
 /**
  * The snapshot properties reset() carries across a return to the import form:
@@ -55,7 +55,7 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
     colorSchemeName: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
     showColumnStats: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     msaFormat: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<import("msa-parsers").MSAFormat>>;
-}, "allowedGappyness" | "colWidth" | "collapsed" | "currentAlignment" | "data" | "drawMsaLetters" | "featureFilters" | "gffFilehandle" | "height" | "hideGaps" | "highlightColumns" | "id" | "msaFilehandle" | "relativeTo" | "rowHeight" | "scrollX" | "scrollY" | "scrollZoom" | "showDomainLegend" | "showDomains" | "showOnly" | "subFeatureRows" | "treeFilehandle" | "treeMetadataFilehandle" | "turnedOffTracks" | "type"> & {
+}, "allowedGappyness" | "colWidth" | "collapsed" | "columnTracks" | "currentAlignment" | "data" | "drawMsaLetters" | "featureFilters" | "gffFilehandle" | "height" | "hideGaps" | "highlightColumns" | "highlights" | "id" | "msaFilehandle" | "relativeTo" | "rowHeight" | "scrollX" | "scrollY" | "scrollZoom" | "showDomainLegend" | "showDomains" | "showOnly" | "subFeatureRows" | "treeFilehandle" | "treeMetadataFilehandle" | "turnedOffTracks" | "type"> & {
     /**
      * #property
      * id of view, randomly generated if not provided
@@ -541,6 +541,13 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
      * hidden-by-default track adds nothing to the shared URL.
      */
     turnedOffTracks: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IMapType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>>, [undefined]>;
+    /**
+     * #property
+     * tracks supplied as data rather than computed from the alignment:
+     * per-column values drawn as bars, or a per-column string drawn as a
+     * text track. See docs/layers.md
+     */
+    columnTracks: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IType<ColumnTrackSpec, ColumnTrackSpec, ColumnTrackSpec>>, [undefined]>;
     /**
      * #property
      * data from the loaded tree/msa/treeMetadata, generally loaded by
@@ -576,6 +583,14 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
      * in afterCreate.
      */
     highlightColumns: import("@jbrowse/mobx-state-tree").IType<number[] | undefined, number[] | undefined, number[] | undefined>;
+    /**
+     * #property
+     * labeled highlights in 1-based inclusive coordinates: a column span
+     * `{start, end}`, a residue span `{row, start, end}` of a named row,
+     * or a row set `{rows}`, each with an optional `label` and `color`.
+     * Persists in the snapshot, so a computed answer travels in the URL.
+     */
+    highlights: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IType<Highlight, Highlight, Highlight>>, [undefined]>;
 }, {
     queueOfDialogs: [import("@jbrowse/core/util").DialogComponentType, any][];
 } & {
@@ -766,6 +781,10 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
      * in-repo caller, so do not flag it as dead code — it is public API.
      */
     setHighlightedColumns(columns?: number[]): void;
+    /**
+     * #action
+     */
+    setHighlights(highlights: Highlight[]): void;
     /**
      * #action
      * toggle the annotation overlay on the alignment
@@ -1229,6 +1248,10 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
      * #action
      */
     setScrollX(n: number): void;
+    /**
+     * #action
+     */
+    setColumnTracks(tracks: ColumnTrackSpec[]): void;
     /**
      * #action
      */
@@ -1265,6 +1288,19 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
      * #getter
      */
     readonly adapterTrackModels: BasicTrack[];
+    /**
+     * #getter
+     * a data track's values or string, projected from its row's residues
+     * onto alignment columns when it names a row
+     */
+    readonly columnTrackContent: Map<string, {
+        values?: number[];
+        data?: string;
+    }>;
+    /**
+     * #getter
+     */
+    readonly columnTrackModels: BasicTrack[];
     /**
      * #getter
      */
@@ -1454,6 +1490,14 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
         start: number;
         end: number;
     }[];
+    /**
+     * #getter
+     * `highlights` projected onto what is on screen: residue spans go
+     * through the named row's gap structure, column spans through the
+     * hidden-column list, and a span that lands entirely on hidden columns
+     * is dropped. Row names that match no row are ignored.
+     */
+    readonly resolvedHighlights: ResolvedHighlight[];
     /**
      * #getter
      * per-column summary statistics for the hovered column: consensus residue
@@ -1507,12 +1551,7 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
     /**
      * #action
      */
-    exportSVG(opts: {
-        theme: Theme;
-        includeMinimap?: boolean;
-        includeTracks?: boolean;
-        exportType: 'entire' | 'viewport';
-    }): Promise<void>;
+    exportSVG(opts: ExportSvgOptions): Promise<void>;
     initFilter(arg: string): void;
     setFilter(arg: string, flag: boolean): void;
     /**
@@ -1541,6 +1580,129 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
     drawTree: boolean;
     drawNodeBubbles: boolean;
     autoTreeAreaWidth: boolean;
+    columnTracks: ColumnTrackSpec[];
+    id: string;
+    showDomains: boolean;
+    showDomainLegend: boolean;
+    hideGaps: boolean;
+    allowedGappyness: number;
+    subFeatureRows: boolean;
+    type: "MsaView";
+    drawMsaLetters: boolean;
+    scrollZoom: boolean;
+    height: number;
+    rowHeight: number;
+    scrollY: number;
+    scrollX: number;
+    colWidth: number;
+    treeFilehandle: import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
+        locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"LocalPathLocation">;
+        localPath: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    }> | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
+        locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"BlobLocation">;
+        name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+        blobId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    }> | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
+        locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"FileHandleLocation">;
+        name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+        handleId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    }> | {
+        locationType: "UriLocation";
+        uri: string;
+        internetAccountId: string | undefined;
+        internetAccountPreAuthorization: import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
+            internetAccountType: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+            authInfo: import("@jbrowse/mobx-state-tree").IType<any, any, any>;
+        }> | undefined;
+    } | undefined;
+    msaFilehandle: import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
+        locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"LocalPathLocation">;
+        localPath: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    }> | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
+        locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"BlobLocation">;
+        name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+        blobId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    }> | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
+        locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"FileHandleLocation">;
+        name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+        handleId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    }> | {
+        locationType: "UriLocation";
+        uri: string;
+        internetAccountId: string | undefined;
+        internetAccountPreAuthorization: import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
+            internetAccountType: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+            authInfo: import("@jbrowse/mobx-state-tree").IType<any, any, any>;
+        }> | undefined;
+    } | undefined;
+    treeMetadataFilehandle: import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
+        locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"LocalPathLocation">;
+        localPath: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    }> | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
+        locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"BlobLocation">;
+        name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+        blobId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    }> | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
+        locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"FileHandleLocation">;
+        name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+        handleId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    }> | {
+        locationType: "UriLocation";
+        uri: string;
+        internetAccountId: string | undefined;
+        internetAccountPreAuthorization: import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
+            internetAccountType: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+            authInfo: import("@jbrowse/mobx-state-tree").IType<any, any, any>;
+        }> | undefined;
+    } | undefined;
+    gffFilehandle: import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
+        locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"LocalPathLocation">;
+        localPath: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    }> | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
+        locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"BlobLocation">;
+        name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+        blobId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    }> | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
+        locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"FileHandleLocation">;
+        name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+        handleId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    }> | {
+        locationType: "UriLocation";
+        uri: string;
+        internetAccountId: string | undefined;
+        internetAccountPreAuthorization: import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
+            internetAccountType: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+            authInfo: import("@jbrowse/mobx-state-tree").IType<any, any, any>;
+        }> | undefined;
+    } | undefined;
+    currentAlignment: number;
+    collapsed: string[];
+    showOnly: string | undefined;
+    turnedOffTracks: import("mobx").IKeyValueMap<boolean>;
+    featureFilters: import("mobx").IKeyValueMap<boolean>;
+    relativeTo: string | undefined;
+    highlightColumns: number[] | undefined;
+    highlights: Highlight[];
+    data: {
+        tree?: string | undefined;
+        msa?: string | undefined;
+        treeMetadata?: string | undefined;
+        gff?: string | undefined;
+    };
+} | {
+    bgColor: boolean;
+    colorSchemeName: string;
+    showColumnStats: boolean;
+    msaFormat: import("msa-parsers").MSAFormat | undefined;
+    drawLabels: boolean;
+    labelsAlignRight: boolean;
+    treeAreaWidth: number;
+    treeWidth: number;
+    showBranchLen: boolean;
+    drawTree: boolean;
+    drawNodeBubbles: boolean;
+    autoTreeAreaWidth: boolean;
+    columnTracks?: undefined;
     id: string;
     showDomains: boolean;
     showDomainLegend: boolean;
@@ -1642,6 +1804,7 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
     featureFilters: import("mobx").IKeyValueMap<boolean>;
     relativeTo: string | undefined;
     highlightColumns: number[] | undefined;
+    highlights: Highlight[];
     data: {
         tree?: string | undefined;
         msa?: string | undefined;

package/dist/model.js

@@ -12,6 +12,7 @@ import { columnCountsFromRows, letterOfResidueSlot } from './columnCounts.js';
 import TrackBlocks from './components/tracks/TrackBlocks.js';
 import { defaultAllowedGappyness, defaultColWidth, defaultColorSchemeName, defaultCurrentAlignment, defaultDrawMsaLetters, defaultHeight, defaultHideGaps, defaultRowHeight, defaultScrollX, defaultScrollY, defaultScrollZoom, defaultShowDomainLegend, defaultShowDomains, defaultSubFeatureRows, labelReferenceFontSize, maxCellSize, minColWidth, minLetterColWidth, minLetterRowHeight, minRowHeight, segmentFeatureTypes, segmentShades, } from './constants.js';
 import { createPaletteMap } from './createPaletteMap.js';
+import { exportFileName } from './exportFileName.js';
 import { fetchTextWithProgress, isAbortError } from './fetchUtils.js';
 import { flatToTree } from './flatToTree.js';
 import { calcDepthToLeaf, clusterLayout, collapse, collapsedSubtreeMaxLength, find, findMaxBranchLen, forEachDescendant, hierarchy, leaves, links, maxLength, setBrLength, sort, sum as hierarchySum, } from './hierarchy.js';
@@ -27,7 +28,7 @@ import { globalColToVisibleCol, visibleColToGlobalCol, visibleColToSeqPosForRow,
 import { buildSeqPosIndex } from './seqPosToGlobalCol.js';
 import { maxBitsFor } from './sequenceLogo.js';
 import { stripDefault } from './stripDefault.js';
-import { computeRowInsertions, len, skipBlanks, transform } from './util.js';
+import { computeRowInsertions, dropBlanks, len, skipBlanks, transform, } from './util.js';
 import { saveAs } from './vendor/fileSaver.js';
 function parseTreeText(text) {
     if (text.startsWith('BioTreeContainer')) {
@@ -39,6 +40,13 @@ function parseTreeText(text) {
 // conservation does and costs three times the vertical space, so it waits to be
 // asked for.
 const defaultOffTracks = new Set(['sequence-logo']);
+// a data track over this size stays in the live model but leaves the snapshot,
+// the same rule DataModel applies to an inline document
+const maxColumnTrackSnapshotBytes = 50_000;
+function smallColumnTracks(tracks) {
+    const kept = tracks?.filter(t => JSON.stringify(t).length <= maxColumnTrackSnapshotBytes);
+    return kept?.length ? { columnTracks: kept } : {};
+}
 /**
  * The snapshot properties reset() carries across a return to the import form:
  * display preferences and layout, nothing derived from the loaded file.
@@ -221,6 +229,13 @@ function stateModelFactory() {
          * hidden-by-default track adds nothing to the shared URL.
          */
         turnedOffTracks: stripDefault(types.map(types.boolean), {}),
+        /**
+         * #property
+         * tracks supplied as data rather than computed from the alignment:
+         * per-column values drawn as bars, or a per-column string drawn as a
+         * text track. See docs/layers.md
+         */
+        columnTracks: stripDefault(types.array(types.frozen()), []),
         /**
          * #property
          * data from the loaded tree/msa/treeMetadata, generally loaded by
@@ -248,6 +263,14 @@ function stateModelFactory() {
          * in afterCreate.
          */
         highlightColumns: types.frozen(),
+        /**
+         * #property
+         * labeled highlights in 1-based inclusive coordinates: a column span
+         * `{start, end}`, a residue span `{row, start, end}` of a named row,
+         * or a row set `{rows}`, each with an optional `label` and `color`.
+         * Persists in the snapshot, so a computed answer travels in the URL.
+         */
+        highlights: stripDefault(types.array(types.frozen()), []),
     }))
         .volatile(() => ({
         /**
@@ -435,6 +458,12 @@ function stateModelFactory() {
         setHighlightedColumns(columns) {
             self.highlightedColumns = columns;
         },
+        /**
+         * #action
+         */
+        setHighlights(highlights) {
+            self.highlights.replace(highlights);
+        },
         /**
          * #action
          * toggle the annotation overlay on the alignment
@@ -1305,6 +1334,12 @@ function stateModelFactory() {
         setScrollX(n) {
             self.scrollX = clamp(n, self.maxScrollX, 0);
         },
+        /**
+         * #action
+         */
+        setColumnTracks(tracks) {
+            self.columnTracks.replace(tracks);
+        },
         /**
          * #action
          */
@@ -1398,6 +1433,59 @@ function stateModelFactory() {
                 ReactComponent: TrackBlocks,
             }));
         },
+        /**
+         * #getter
+         * a data track's values or string, projected from its row's residues
+         * onto alignment columns when it names a row
+         */
+        get columnTrackContent() {
+            const { MSA, blanks, hideGapsEffective } = self;
+            const width = MSA?.getWidth() ?? 0;
+            const project = (track, items, fill) => {
+                if (!track.row) {
+                    return items;
+                }
+                const out = Array.from({ length: width }, () => fill);
+                const index = self.seqPosGlobalColIndex.get(track.row);
+                items.forEach((item, seqPos) => {
+                    const col = index?.[seqPos];
+                    if (col !== undefined) {
+                        out[col] = item;
+                    }
+                });
+                return out;
+            };
+            const skip = (items) => hideGapsEffective ? dropBlanks(blanks, items) : items;
+            return new Map(self.columnTracks.map(track => {
+                if (track.kind === 'bar') {
+                    const max = track.max ?? 1;
+                    const values = skip(project(track, track.values ?? [], 0)).map(v => Math.min(1, Math.max(0, v / max)));
+                    return [track.id, { values }];
+                }
+                const data = skip(project(track, (track.data ?? '').split(''), ' '));
+                return [track.id, { data: data.join('') }];
+            }));
+        },
+        /**
+         * #getter
+         */
+        get columnTrackModels() {
+            return self.columnTracks.map(track => ({
+                model: {
+                    id: track.id,
+                    name: track.name,
+                    kind: track.kind,
+                    height: track.height ??
+                        (track.kind === 'bar'
+                            ? self.conservationTrackHeight
+                            : self.rowHeight),
+                    barColor: track.color,
+                    customColorScheme: track.colors,
+                    data: this.columnTrackContent.get(track.id)?.data,
+                },
+                ReactComponent: TrackBlocks,
+            }));
+        },
         /**
          * #getter
          */
@@ -1424,6 +1512,7 @@ function stateModelFactory() {
             };
             return [
                 ...this.adapterTrackModels,
+                ...this.columnTrackModels,
                 ...[
                     conservationTrack,
                     ...(self.sequenceType === 'amino'
@@ -1771,6 +1860,47 @@ function stateModelFactory() {
             }
             return runs;
         },
+        /**
+         * #getter
+         * `highlights` projected onto what is on screen: residue spans go
+         * through the named row's gap structure, column spans through the
+         * hidden-column list, and a span that lands entirely on hidden columns
+         * is dropped. Row names that match no row are ignored.
+         */
+        get resolvedHighlights() {
+            const { blanks, rowNamesSet, rowMap } = self;
+            const toVisible = (globalCol) => {
+                const visible = self.globalColToVisibleCol(globalCol);
+                return visible ?? visibleColsBefore(blanks, globalCol);
+            };
+            return self.highlights.flatMap(({ row, rows, start, end, label, color }) => {
+                const base = { label, color };
+                if (rows) {
+                    const rowIndices = rows
+                        .map(name => rowNamesSet.get(name))
+                        .filter(notEmpty);
+                    return rowIndices.length ? [{ ...base, rowIndices }] : [];
+                }
+                if (start === undefined || end === undefined) {
+                    return [];
+                }
+                let startGlobal = start - 1;
+                let endGlobal = end - 1;
+                if (row !== undefined) {
+                    if (!rowMap.has(row)) {
+                        return [];
+                    }
+                    startGlobal = self.seqPosToGlobalCol(row, start - 1);
+                    endGlobal = self.seqPosToGlobalCol(row, end - 1);
+                }
+                const startCol = toVisible(startGlobal);
+                const endVisible = self.globalColToVisibleCol(endGlobal);
+                const endCol = endVisible ?? visibleColsBefore(blanks, endGlobal) - 1;
+                return startCol <= endCol
+                    ? [{ ...base, startCol, endCol, rowIndices: [] }]
+                    : [];
+            });
+        },
         /**
          * #getter
          * per-column summary statistics for the hovered column: consensus residue
@@ -1860,7 +1990,7 @@ function stateModelFactory() {
             const { renderToSvg } = await import('./renderToSvg.js');
             const html = await renderToSvg(self, opts);
             const blob = new Blob([html], { type: 'image/svg+xml' });
-            saveAs(blob, 'image.svg');
+            saveAs(blob, exportFileName(self.msaFilehandle, 'svg'));
         },
         initFilter(arg) {
             if (!self.featureFilters.has(arg)) {
@@ -2096,11 +2226,12 @@ function stateModelFactory() {
             }));
         },
     }))
-        .postProcessSnapshot(({ data, ...rest }) => ({
+        .postProcessSnapshot(({ data, columnTracks, ...rest }) => ({
         // per-property defaults are stripped by the stripDefault helper; the only thing
         // it can't express is this cross-field rule: drop inline tree/msa/metadata
         // when a sibling filehandle can refetch them, keeping sessions/URLs small
         ...rest,
+        ...smallColumnTracks(columnTracks),
         data: {
             ...(rest.treeFilehandle ? {} : { tree: data.tree }),
             ...(rest.msaFilehandle ? {} : { msa: data.msa }),