react-msaview 6.4.2 → 7.0.0

package/dist/types.d.ts

@@ -4,13 +4,14 @@ export interface Accession {
     name: string;
     description: string;
 }
-export type TrackKind = 'text' | 'bar' | 'logo';
+export type TrackKind = 'text' | 'bar' | 'logo' | 'arc' | 'ruler';
 export interface BasicTrackModel {
     id: string;
     name: string;
     associatedRowName?: string;
     height: number;
     kind: TrackKind;
+    defaultOff?: boolean;
 }
 export interface TextTrackModel extends BasicTrackModel {
     customColorScheme?: Record<string, string>;
@@ -19,22 +20,115 @@ export interface TextTrackModel extends BasicTrackModel {
 export interface BarTrackModel extends BasicTrackModel {
     barColor?: string;
 }
+export interface Arc {
+    start: number;
+    end: number;
+    color?: string;
+}
+export interface ArcTrackModel extends BasicTrackModel {
+    arcs?: Arc[];
+    arcColor?: string;
+}
 export interface BasicTrack {
     ReactComponent: React.FC<any>;
-    model: TextTrackModel & BarTrackModel;
+    model: TextTrackModel & BarTrackModel & ArcTrackModel;
+}
+export interface ArcSpec {
+    start: number;
+    end: number;
+    color?: string;
 }
 export interface ColumnTrackSpec {
     id: string;
     name: string;
-    kind: 'bar' | 'text';
+    kind: 'bar' | 'text' | 'arc';
     values?: number[];
     data?: string;
+    arcs?: ArcSpec[];
     max?: number;
     color?: string;
     colors?: Record<string, string>;
     row?: string;
     height?: number;
 }
+export interface ResidueSegment {
+    rowStart: number;
+    rowEnd: number;
+    structStart: number;
+    structEnd: number;
+}
+export interface MappedStructure {
+    id: string;
+    kind?: 'experimental' | 'predicted';
+    asymId?: string;
+    url?: string;
+}
+/**
+ * Which residue of which structure a row's residue is, as data. Computed by
+ * whatever knows how -- SIFTS, an AlphaFold model, a curator -- and carried in
+ * the snapshot, because the viewer cannot work it out: matching a row to a
+ * structure by sequence equality fails for a construct with an expression tag,
+ * a truncation, an engineered residue, or a row that is a subsequence of the
+ * entry, and it fails in the direction that looks like it worked.
+ *
+ * Positions are 1-based and inclusive on both sides, as GFF and `highlights`
+ * are. Structure positions are `label_seq_id`, the index into the entity's
+ * SEQRES; author numbering carries insertion codes and stays out.
+ *
+ * `unobserved` is in structure positions: present in SEQRES with no
+ * coordinates. Worth distinguishing from unmapped, because "the
+ * crystallographer could not see it" and "this protein does not have that
+ * residue" mean different things to a reader.
+ */
+export interface ResidueMapping {
+    row: string;
+    accession?: string;
+    structure: MappedStructure;
+    segments: ResidueSegment[];
+    unobserved?: [number, number][];
+    /**
+     * ungapped length of the row this was computed against. Optional, and worth
+     * setting: a mapping outlives the alignment it was made for, and pointing at
+     * residue 58 of a sequence that has since been re-aligned, revised or swapped
+     * is the failure this whole layer exists to avoid. Declared here, the viewer
+     * can notice and refuse instead of answering from stale arithmetic.
+     */
+    rowLength?: number;
+    generated?: {
+        by?: string;
+        date?: string;
+        sourceSha256?: string;
+    };
+}
+export interface ResidueMappingProblem {
+    row: string;
+    structureId: string;
+    /**
+     * `mapping` means the whole mapping is out: the evidence is about the row it
+     * claims, so nothing it says can be trusted. `segment` takes only that
+     * segment, since the rest of the mapping still describes residues that exist.
+     */
+    scope: 'mapping' | 'segment';
+    reason: string;
+}
+export interface StructureResidue {
+    structure: MappedStructure;
+    position: number;
+    observed: boolean;
+}
+export interface RowResidue {
+    rowName: string;
+    seqPos: number;
+}
+/**
+ * One loaded document that the snapshot leaves behind, and how big it is.
+ * `what` names it the way the import form does, since that is where the reader
+ * would go to load it differently.
+ */
+export interface UnshareableData {
+    what: 'alignment' | 'tree' | 'annotations' | 'row metadata' | 'data tracks';
+    bytes: number;
+}
 export type { Annotation };
 export type TidyDomainAnnotation = Annotation;
 export interface DomainBand {

package/dist/util.d.ts

@@ -3,9 +3,17 @@ export declare function adjustColorForContrast(color: string, bg: string): strin
 export declare function transform<T>(obj: Record<string, T>, cb: (arg0: [string, T]) => [string, T]): {
     [k: string]: T;
 };
-export declare function colorContrast(colorScheme: Record<string, string>, theme: Theme): {
-    [k: string]: string;
-};
+/**
+ * Readable letter color over a given cell color, memoized per theme.
+ *
+ * A dynamic scheme colors a cell from its column, so there is no letter->color
+ * table to precompute a contrast table from; asking per cell color covers the
+ * dynamic schemes, the static ones and a track's own `colors` alike. An
+ * uncolored cell sits on the theme's background, where the theme's own text
+ * color is what stays readable -- `black` turned every gap and every uncolored
+ * cell invisible in the dark theme.
+ */
+export declare function contrastTextFn(theme: Theme): (color: string | undefined) => string;
 export declare function dropBlanks<T>(blanks: number[], arr: T[]): T[];
 export declare function skipBlanks(blanks: number[], str: string): string;
 export declare function computeRowInsertions(blanks: number[], seq: string): {
@@ -16,4 +24,3 @@ export declare function len(a: {
     end: number;
     start: number;
 }): number;
-export declare function isBlank(s?: string): s is "-" | ".";

package/dist/util.js

@@ -26,11 +26,36 @@ export function adjustColorForContrast(color, bg) {
 export function transform(obj, cb) {
     return Object.fromEntries(Object.entries(obj).map(cb));
 }
-export function colorContrast(colorScheme, theme) {
-    return transform(colorScheme, ([letter, color]) => [
-        letter,
-        theme.palette.getContrastText(colord(color).toHex()),
-    ]);
+const contrastTextCaches = new WeakMap();
+/**
+ * Readable letter color over a given cell color, memoized per theme.
+ *
+ * A dynamic scheme colors a cell from its column, so there is no letter->color
+ * table to precompute a contrast table from; asking per cell color covers the
+ * dynamic schemes, the static ones and a track's own `colors` alike. An
+ * uncolored cell sits on the theme's background, where the theme's own text
+ * color is what stays readable -- `black` turned every gap and every uncolored
+ * cell invisible in the dark theme.
+ */
+export function contrastTextFn(theme) {
+    let cache = contrastTextCaches.get(theme);
+    if (!cache) {
+        cache = new Map();
+        contrastTextCaches.set(theme, cache);
+    }
+    const fallback = theme.palette.text.primary;
+    return (color) => {
+        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(blanks, arr) {
     if (blanks.length === 0) {
@@ -95,9 +120,4 @@ export function computeRowInsertions(blanks, seq) {
 export function len(a) {
     return a.end - a.start;
 }
-// https://sonnhammer.sbc.su.se/Stockholm.html
-// gaps can be a . or - in stockholm
-export function isBlank(s) {
-    return s === '-' || s === '.';
-}
 //# sourceMappingURL=util.js.map

package/dist/util.js.map

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package/dist/version.d.ts

@@ -1 +1 @@
-export declare const version = "6.4.2";
+export declare const version = "7.0.0";

package/dist/version.js

@@ -1,2 +1,2 @@
-export const version = '6.4.2';
+export const version = '7.0.0';
 //# sourceMappingURL=version.js.map

package/dist/wuss.d.ts

@@ -0,0 +1,14 @@
+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 declare function parseWuss(ss: string): BasePair[];

package/dist/wuss.js

@@ -0,0 +1,55 @@
+// 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 = {
+    '>': '<',
+    ')': '(',
+    ']': '[',
+    '}': '{',
+};
+const opens = new Set(Object.values(closeToOpen));
+/**
+ * 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) {
+    const stacks = new Map();
+    const pairs = [];
+    const push = (key, col) => {
+        const stack = stacks.get(key);
+        if (stack) {
+            stack.push(col);
+        }
+        else {
+            stacks.set(key, [col]);
+        }
+    };
+    const pop = (key, col, pseudoknot) => {
+        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);
+}
+//# sourceMappingURL=wuss.js.map

package/dist/wuss.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"wuss.js","sourceRoot":"","sources":["../src/wuss.ts"],"names":[],"mappings":"AAAA,8EAA8E;AAC9E,4EAA4E;AAC5E,yEAAyE;AACzE,+EAA+E;AAC/E,6EAA6E;AAC7E,YAAY;AAEZ,MAAM,WAAW,GAA2B;IAC1C,GAAG,EAAE,GAAG;IACR,GAAG,EAAE,GAAG;IACR,GAAG,EAAE,GAAG;IACR,GAAG,EAAE,GAAG;CACT,CAAA;AACD,MAAM,KAAK,GAAG,IAAI,GAAG,CAAC,MAAM,CAAC,MAAM,CAAC,WAAW,CAAC,CAAC,CAAA;AAWjD;;;;GAIG;AACH,MAAM,UAAU,SAAS,CAAC,EAAU;IAClC,MAAM,MAAM,GAAG,IAAI,GAAG,EAAoB,CAAA;IAC1C,MAAM,KAAK,GAAe,EAAE,CAAA;IAC5B,MAAM,IAAI,GAAG,CAAC,GAAW,EAAE,GAAW,EAAE,EAAE;QACxC,MAAM,KAAK,GAAG,MAAM,CAAC,GAAG,CAAC,GAAG,CAAC,CAAA;QAC7B,IAAI,KAAK,EAAE,CAAC;YACV,KAAK,CAAC,IAAI,CAAC,GAAG,CAAC,CAAA;QACjB,CAAC;aAAM,CAAC;YACN,MAAM,CAAC,GAAG,CAAC,GAAG,EAAE,CAAC,GAAG,CAAC,CAAC,CAAA;QACxB,CAAC;IACH,CAAC,CAAA;IACD,MAAM,GAAG,GAAG,CAAC,GAAW,EAAE,GAAW,EAAE,UAAmB,EAAE,EAAE;QAC5D,MAAM,KAAK,GAAG,MAAM,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE,GAAG,EAAE,CAAA;QACpC,IAAI,KAAK,KAAK,SAAS,EAAE,CAAC;YACxB,KAAK,CAAC,IAAI,CAAC,EAAE,KAAK,EAAE,GAAG,EAAE,GAAG,EAAE,UAAU,EAAE,CAAC,CAAA;QAC7C,CAAC;IACH,CAAC,CAAA;IAED,KAAK,IAAI,GAAG,GAAG,CAAC,EAAE,GAAG,GAAG,EAAE,CAAC,MAAM,EAAE,GAAG,EAAE,EAAE,CAAC;QACzC,MAAM,EAAE,GAAG,EAAE,CAAC,GAAG,CAAE,CAAA;QACnB,MAAM,MAAM,GAAG,WAAW,CAAC,EAAE,CAAC,CAAA;QAC9B,IAAI,KAAK,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,CAAC;YAClB,IAAI,CAAC,EAAE,EAAE,GAAG,CAAC,CAAA;QACf,CAAC;aAAM,IAAI,MAAM,EAAE,CAAC;YAClB,GAAG,CAAC,MAAM,EAAE,GAAG,EAAE,KAAK,CAAC,CAAA;QACzB,CAAC;aAAM,IAAI,EAAE,IAAI,GAAG,IAAI,EAAE,IAAI,GAAG,EAAE,CAAC;YAClC,IAAI,CAAC,EAAE,EAAE,GAAG,CAAC,CAAA;QACf,CAAC;aAAM,IAAI,EAAE,IAAI,GAAG,IAAI,EAAE,IAAI,GAAG,EAAE,CAAC;YAClC,GAAG,CAAC,EAAE,CAAC,WAAW,EAAE,EAAE,GAAG,EAAE,IAAI,CAAC,CAAA;QAClC,CAAC;IACH,CAAC;IACD,OAAO,KAAK,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,KAAK,GAAG,CAAC,CAAC,KAAK,CAAC,CAAA;AAChD,CAAC"}

package/package.json

@@ -1,7 +1,7 @@
 {
   "name": "react-msaview",
   "author": "Colin",
-  "version": "6.4.2",
+  "version": "7.0.0",
   "license": "MIT",
   "type": "module",
   "repository": {
@@ -19,17 +19,19 @@
   "files": [
     "dist",
     "bundle",
-    "src"
+    "src",
+    "!src/**/*.test.ts",
+    "!src/**/*.test.tsx"
   ],
   "engines": {
-    "node": ">=10"
+    "node": ">=18"
   },
   "peerDependencies": {
     "@jbrowse/core": ">=2.0.0",
-    "@jbrowse/mobx-state-tree": "^6.0.0",
+    "@jbrowse/mobx-state-tree": ">=5.0.0",
     "@mui/icons-material": ">=5.0.0",
     "@mui/material": ">=5.0.0",
-    "mobx": ">=7.0.0",
+    "mobx": ">=6.0.0",
     "mobx-react": ">=9.0.0",
     "react": ">=16.8.0",
     "react-dom": ">=16.8.0"
@@ -40,11 +42,11 @@
     "esbuild": "^0.28.1"
   },
   "dependencies": {
-    "@gmod/newick": "^1.0.0",
-    "@jbrowse/svgcanvas": "6.4.2",
+    "@gmod/newick": "^1.0.3",
+    "@jbrowse/svgcanvas": "7.0.0",
     "colord": "^2.9.3",
     "flatbush": "^4.6.2",
-    "msa-parsers": "6.4.2"
+    "msa-parsers": "7.0.0"
   },
   "scripts": {
     "clean": "rimraf dist bundle",

package/src/components/Loading.tsx

@@ -83,13 +83,23 @@ const Reset = observer(function ({
 })
 
 const Loading = observer(function ({ model }: { model: MsaViewModel }) {
-  const { isLoading, dataInitialized, error, msaFilehandle, treeFilehandle } =
-    model
+  const {
+    isLoading,
+    dataInitialized,
+    error,
+    resetCount,
+    msaFilehandle,
+    treeFilehandle,
+  } = model
   const hasPendingFilehandle = !!(msaFilehandle || treeFilehandle)
 
   return (
     <div>
+      {/* keyed on the reset counter: the boundary holds the error it caught
+          until it is remounted, so without this "Return to import form" put
+          the model back and left the error screen up */}
       <ErrorBoundary
+        key={resetCount}
         FallbackComponent={e => <Reset model={model} error={e.error} />}
       >
         {dataInitialized ? (

package/src/components/MSAViewer.tsx

@@ -1,13 +1,14 @@
-import React, { useEffect, useState } from 'react'
+import React, { useEffect, useRef, useState } from 'react'
 
 import { createJBrowseTheme } from '@jbrowse/core/ui/theme'
 import useMeasure from '@jbrowse/core/util/useMeasure'
+import { destroy, isAlive } from '@jbrowse/mobx-state-tree'
 import { ThemeProvider } from '@mui/material/styles'
 
 import MSAModelF from '../model.ts'
 import Loading from './Loading.tsx'
 
-import type { ColumnTrackSpec, Highlight } from '../types.ts'
+import type { ColumnTrackSpec, Highlight, ResidueMapping } from '../types.ts'
 import type { FileLocation as FileLocationType } from '@jbrowse/core/util/types'
 
 const theme = createJBrowseTheme()
@@ -25,6 +26,12 @@ interface MSAViewerProps {
   colWidth?: number
   /** initial per-row pixel height */
   rowHeight?: number
+  /**
+   * hide columns at least this percent gaps (default 100, i.e. hide nothing).
+   * A deep family's alignment is mostly insertions carried by a few members;
+   * dropping those columns is what makes the rest readable
+   */
+  allowedGappyness?: number
   /** alignment columns (0-based) to highlight with a persistent overlay */
   highlightColumns?: number[]
   /**
@@ -37,6 +44,8 @@ interface MSAViewerProps {
   relativeTo?: string
   /** tracks supplied as data: per-column bar values or a text row (see docs/layers.md) */
   columnTracks?: ColumnTrackSpec[]
+  /** which residue of which structure each row's residues are (see docs/layers.md) */
+  residueMappings?: ResidueMapping[]
   /** draw the phylogenetic tree (default true); false leaves a labels-only gutter */
   drawTree?: boolean
   /** fixed width (px) of the tree/label area */
@@ -56,10 +65,12 @@ export default function MSAViewer({
   height,
   colWidth,
   rowHeight,
+  allowedGappyness,
   highlightColumns,
   highlights,
   relativeTo,
   columnTracks,
+  residueMappings,
   drawTree,
   treeAreaWidth,
   autoTreeAreaWidth,
@@ -79,16 +90,22 @@ export default function MSAViewer({
       ...(height ? { height } : {}),
       ...(colWidth ? { colWidth } : {}),
       ...(rowHeight ? { rowHeight } : {}),
+      ...(allowedGappyness !== undefined ? { allowedGappyness } : {}),
       ...(highlightColumns ? { highlightColumns } : {}),
       ...(highlights ? { highlights } : {}),
       ...(relativeTo ? { relativeTo } : {}),
       ...(columnTracks ? { columnTracks } : {}),
+      ...(residueMappings ? { residueMappings } : {}),
       ...(drawTree !== undefined ? { drawTree } : {}),
       ...(treeAreaWidth ? { treeAreaWidth } : {}),
       ...(autoTreeAreaWidth ? { autoTreeAreaWidth } : {}),
     }),
   )
 
+  const destroyTimer = useRef<ReturnType<typeof setTimeout> | undefined>(
+    undefined,
+  )
+
   const [ref, { width }] = useMeasure()
   useEffect(() => {
     if (width) {
@@ -96,6 +113,93 @@ export default function MSAViewer({
     }
   }, [model, width])
 
+  // The props below stay live after mount: change one and it drives the model,
+  // so a host can put a control on the viewer -- an expand button, a diff
+  // toggle, a color-scheme picker -- without remounting it and re-fetching its
+  // alignment. Each effect depends only on its own prop, so a change the user
+  // makes inside the viewer (picking a scheme from the menu, dragging a row
+  // taller) survives the host's next render rather than being snapped back.
+  // Data props are not among them: new msa/tree/gff is a different alignment,
+  // which is a new model, which React spells `key`.
+  useEffect(() => {
+    if (height !== undefined) {
+      model.setHeight(height)
+    }
+  }, [model, height])
+  useEffect(() => {
+    if (colorScheme !== undefined) {
+      model.setColorSchemeName(colorScheme)
+    }
+  }, [model, colorScheme])
+  useEffect(() => {
+    if (colWidth !== undefined) {
+      model.setColWidth(colWidth)
+    }
+  }, [model, colWidth])
+  useEffect(() => {
+    if (rowHeight !== undefined) {
+      model.setRowHeight(rowHeight)
+    }
+  }, [model, rowHeight])
+  useEffect(() => {
+    if (allowedGappyness !== undefined) {
+      model.setAllowedGappyness(allowedGappyness)
+    }
+  }, [model, allowedGappyness])
+  useEffect(() => {
+    if (drawTree !== undefined) {
+      model.setDrawTree(drawTree)
+    }
+  }, [model, drawTree])
+  useEffect(() => {
+    if (treeAreaWidth !== undefined) {
+      model.setTreeAreaWidth(treeAreaWidth)
+    }
+  }, [model, treeAreaWidth])
+  // unguarded: dropping the prop is how a host turns the reference diff back off
+  useEffect(() => {
+    model.drawRelativeTo(relativeTo)
+  }, [model, relativeTo])
+
+  // the data layers, keyed by content: a host that computes one inline hands a
+  // new array on every render, and replacing the model's copy each time would
+  // redraw the overlay for nothing
+  const highlightsKey = JSON.stringify(highlights ?? [])
+  useEffect(() => {
+    model.setHighlights(JSON.parse(highlightsKey))
+  }, [model, highlightsKey])
+  const columnTracksKey = JSON.stringify(columnTracks ?? [])
+  useEffect(() => {
+    model.setColumnTracks(JSON.parse(columnTracksKey))
+  }, [model, columnTracksKey])
+  const residueMappingsKey = JSON.stringify(residueMappings ?? [])
+  useEffect(() => {
+    model.setResidueMappings(JSON.parse(residueMappingsKey))
+  }, [model, residueMappingsKey])
+  const highlightColumnsKey = JSON.stringify(highlightColumns ?? null)
+  useEffect(() => {
+    model.setHighlightedColumns(JSON.parse(highlightColumnsKey) ?? undefined)
+  }, [model, highlightColumnsKey])
+
+  // the model owns a matchMedia listener and whatever fetches its filehandles
+  // started, so an unmounted viewer that keeps its model keeps those too. The
+  // destroy is deferred by a tick because React's StrictMode mounts, unmounts
+  // and remounts with the same state: the remount's effect cancels it
+  useEffect(() => {
+    if (destroyTimer.current !== undefined) {
+      clearTimeout(destroyTimer.current)
+      destroyTimer.current = undefined
+    }
+    return () => {
+      destroyTimer.current = setTimeout(() => {
+        destroyTimer.current = undefined
+        if (isAlive(model)) {
+          destroy(model)
+        }
+      })
+    }
+  }, [model])
+
   return (
     <ThemeProvider theme={theme}>
       <div ref={ref}>

package/src/components/ResizeHandles.tsx

@@ -5,7 +5,7 @@ import { observer } from 'mobx-react'
 import DragHandle from './DragHandle.tsx'
 
 import type { MsaViewModel } from '../model.ts'
-import type { TrackKind } from '../types.ts'
+import type { BasicTrack, TrackKind } from '../types.ts'
 
 export const VerticalResizeHandle = observer(function ({
   model,
@@ -51,53 +51,53 @@ export const HorizontalResizeHandle = observer(function ({
   )
 })
 
-// The height behind each resizable track kind. Both bar tracks read one height
-// so conservation and property conservation stay directly comparable; the logo
-// keeps its own, being taller by default. Text tracks are absent: they are one
-// alignment row tall and follow rowHeight, so the zoom controls already size
-// them.
-const trackHeights: Partial<
-  Record<
-    TrackKind,
-    {
-      get: (model: MsaViewModel) => number
-      set: (model: MsaViewModel, height: number) => void
-    }
-  >
+// The volatile behind each resizable kind of computed track. Both bar tracks
+// write one height so conservation and property conservation stay directly
+// comparable; the logo keeps its own, being taller by default. Text tracks are
+// absent: they are one alignment row tall and follow rowHeight, so the zoom
+// controls already size them.
+const setTrackHeight: Partial<
+  Record<TrackKind, (model: MsaViewModel, height: number) => void>
 > = {
-  bar: {
-    get: model => model.conservationTrackHeight,
-    set: (model, height) => {
-      model.setConservationTrackHeight(height)
-    },
+  bar: (model, height) => {
+    model.setConservationTrackHeight(height)
   },
-  logo: {
-    get: model => model.sequenceLogoTrackHeight,
-    set: (model, height) => {
-      model.setSequenceLogoTrackHeight(height)
-    },
+  logo: (model, height) => {
+    model.setSequenceLogoTrackHeight(height)
+  },
+  arc: (model, height) => {
+    model.setArcTrackHeight(height)
   },
 }
 
 export const TrackResizeHandle = observer(function ({
   model,
-  kind,
+  track,
 }: {
   model: MsaViewModel
-  kind: TrackKind
+  track: BasicTrack
 }) {
-  const height = trackHeights[kind]
+  const { id, kind, height } = track.model
+  const setHeight = setTrackHeight[kind]
+  // a data track carries its own height, so its handle resizes that track --
+  // dragging one used to resize every track of its kind instead
+  const ownHeight = model.columnTracks.some(t => t.id === id)
   const onDrag = useCallback(
     (delta: number, startHeight: number) => {
-      height?.set(model, Math.max(10, startHeight + delta))
+      const next = Math.max(10, startHeight + delta)
+      if (ownHeight) {
+        model.setColumnTrackHeight(id, next)
+      } else {
+        setTrackHeight[kind]?.(model, next)
+      }
     },
-    [model, height],
+    [model, id, kind, ownHeight],
   )
-  return height ? (
+  return setHeight ? (
     <DragHandle
       axis="y"
       variant="resizer"
-      getStart={() => height.get(model)}
+      getStart={() => height}
       onDrag={onDrag}
       style={{
         position: 'absolute',