react-msaview 5.6.1 → 5.6.2

package/dist/clustalX.d.ts

@@ -1,5 +1,6 @@
+import type { ColumnCounts } from './columnCounts.ts';
 /**
- * Computes the ClustalX letter->color map for a single alignment column given
- * its residue counts (`stats`) and total residue count (`total`).
+ * Computes the ClustalX letter->color map for a single alignment column, read
+ * out of the alignment-wide `ColumnCounts` tally.
  */
-export declare function clustalXColumnColors(stats: Record<string, number>, total: number): Record<string, string>;
+export declare function clustalXColumnColors(counts: ColumnCounts, col: number): Record<string, string>;

package/dist/clustalX.js

@@ -11,11 +11,32 @@ const ORANGE = 'rgb(240, 144, 72)';
 const YELLOW = 'rgb(204, 204, 0)';
 const CYAN = 'rgb(26, 179, 179)';
 /**
- * Computes the ClustalX letter->color map for a single alignment column given
- * its residue counts (`stats`) and total residue count (`total`).
+ * Computes the ClustalX letter->color map for a single alignment column, read
+ * out of the alignment-wide `ColumnCounts` tally.
  */
-export function clustalXColumnColors(stats, total) {
-    const { W = 0, L = 0, V = 0, I = 0, M = 0, A = 0, F = 0, C = 0, H = 0, P = 0, R = 0, K = 0, Q = 0, E = 0, D = 0, T = 0, S = 0, G = 0, Y = 0, N = 0, } = stats;
+export function clustalXColumnColors(counts, col) {
+    const total = counts.total(col);
+    const n = (letter) => counts.count(col, letter);
+    const W = n('W');
+    const L = n('L');
+    const V = n('V');
+    const I = n('I');
+    const M = n('M');
+    const A = n('A');
+    const F = n('F');
+    const C = n('C');
+    const H = n('H');
+    const P = n('P');
+    const R = n('R');
+    const K = n('K');
+    const Q = n('Q');
+    const E = n('E');
+    const D = n('D');
+    const T = n('T');
+    const S = n('S');
+    const G = n('G');
+    const Y = n('Y');
+    const N = n('N');
     const hydrophobic = W + L + V + I + M + A + F + C + H + P + Y;
     const KR = K + R;
     const QE = Q + E;

package/dist/clustalX.js.map

@@ -1 +1 @@
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package/dist/columnCounts.d.ts

@@ -0,0 +1,37 @@
+export declare function isGapSlot(slot: number): slot is 27 | 28;
+export declare class ColumnCounts {
+    readonly numColumns: number;
+    private readonly counts;
+    readonly totals: Uint32Array;
+    private readonly slotTotals;
+    constructor(numColumns: number);
+    addRow(row: string): void;
+    add(col: number, letter: string): void;
+    total(col: number): number;
+    count(col: number, letter: string): number;
+    gapCount(col: number): number;
+    /**
+     * Visits every non-gap residue present in a column. Slots with a zero count
+     * are skipped, so this is ~the number of distinct residues, not 32.
+     */
+    forEachResidue(col: number, cb: (slot: number, count: number) => void): void;
+    /** non-gap [letter, count] pairs for one column, for display */
+    residueEntries(col: number): [string, number][];
+    /** the distinct non-gap letters appearing anywhere in the alignment */
+    get lettersPresent(): Set<string>;
+}
+export declare function letterOfResidueSlot(slot: number): string;
+export declare function residueSlotOfLetter(letter: string): number;
+export declare const numResidueSlots = 32;
+/**
+ * Tally counts from alignment rows (gapped sequence strings, one per row). The
+ * column count follows the longest row, matching what a per-column tally of
+ * ragged input produces.
+ */
+export declare function columnCountsFromRows(rows: string[]): ColumnCounts;
+/**
+ * Tally counts from column strings (one string per column, listing that
+ * column's residues top to bottom). Convenient for tests and for callers that
+ * already think column-wise.
+ */
+export declare function columnCountsFromColumns(columns: string[]): ColumnCounts;

package/dist/columnCounts.js

@@ -0,0 +1,148 @@
+// Per-column residue counts for an alignment, stored as a flat typed array
+// instead of one `Record<string, number>` per column. Column statistics are the
+// hottest computation in the viewer (they feed conservation, ClustalX coloring,
+// consensus and the hover tooltip), and the object-per-column form spent all of
+// its time on megamorphic string-keyed property increments: 1000x5000 residues
+// took ~1.6s to tally that way versus ~35ms here.
+//
+// Each column owns a fixed stride of counter slots. Slots 1-26 are A-Z (case
+// folded), plus a slot each for the two gap characters, '*', and anything else.
+const SLOTS = 32;
+const DASH = 27;
+const DOT = 28;
+const STAR = 29;
+const OTHER = 30;
+const A = 'A'.charCodeAt(0);
+const Z = 'Z'.charCodeAt(0);
+const a = 'a'.charCodeAt(0);
+const z = 'z'.charCodeAt(0);
+// charCode -> slot. A plain `code & 31` would fold digits and punctuation onto
+// letter slots ('0' onto 'P'), so the mapping is an explicit table.
+const slotOfCode = new Uint8Array(128).fill(OTHER);
+for (let c = A; c <= Z; c++) {
+    slotOfCode[c] = c - A + 1;
+}
+for (let c = a; c <= z; c++) {
+    slotOfCode[c] = c - a + 1;
+}
+slotOfCode['-'.charCodeAt(0)] = DASH;
+slotOfCode['.'.charCodeAt(0)] = DOT;
+slotOfCode['*'.charCodeAt(0)] = STAR;
+const letterOfSlot = Array.from({ length: SLOTS }, (_, slot) => slot >= 1 && slot <= 26 ? String.fromCharCode(A + slot - 1) : '');
+letterOfSlot[DASH] = '-';
+letterOfSlot[DOT] = '.';
+letterOfSlot[STAR] = '*';
+letterOfSlot[OTHER] = '?';
+function slotOf(code) {
+    return code < 128 ? slotOfCode[code] : OTHER;
+}
+export function isGapSlot(slot) {
+    return slot === DASH || slot === DOT;
+}
+export class ColumnCounts {
+    numColumns;
+    counts;
+    // per-column residue+gap totals
+    totals;
+    // whole-alignment totals per slot, so "which letters appear anywhere" is a
+    // 32-slot scan rather than a walk over every column
+    slotTotals = new Uint32Array(SLOTS);
+    constructor(numColumns) {
+        this.numColumns = numColumns;
+        this.counts = new Uint32Array(numColumns * SLOTS);
+        this.totals = new Uint32Array(numColumns);
+    }
+    addRow(row) {
+        const { counts, totals, slotTotals } = this;
+        const n = Math.min(row.length, this.numColumns);
+        for (let col = 0; col < n; col++) {
+            const slot = slotOf(row.charCodeAt(col));
+            counts[col * SLOTS + slot]++;
+            totals[col]++;
+            slotTotals[slot]++;
+        }
+    }
+    add(col, letter) {
+        const slot = slotOf(letter.charCodeAt(0));
+        this.counts[col * SLOTS + slot]++;
+        this.totals[col]++;
+        this.slotTotals[slot]++;
+    }
+    total(col) {
+        return this.totals[col] ?? 0;
+    }
+    count(col, letter) {
+        return this.counts[col * SLOTS + slotOf(letter.charCodeAt(0))] ?? 0;
+    }
+    gapCount(col) {
+        const base = col * SLOTS;
+        return (this.counts[base + DASH] ?? 0) + (this.counts[base + DOT] ?? 0);
+    }
+    /**
+     * Visits every non-gap residue present in a column. Slots with a zero count
+     * are skipped, so this is ~the number of distinct residues, not 32.
+     */
+    forEachResidue(col, cb) {
+        const { counts } = this;
+        const base = col * SLOTS;
+        for (let slot = 1; slot < SLOTS; slot++) {
+            const count = counts[base + slot];
+            if (count > 0 && !isGapSlot(slot)) {
+                cb(slot, count);
+            }
+        }
+    }
+    /** non-gap [letter, count] pairs for one column, for display */
+    residueEntries(col) {
+        const entries = [];
+        this.forEachResidue(col, (slot, count) => {
+            entries.push([letterOfSlot[slot], count]);
+        });
+        return entries;
+    }
+    /** the distinct non-gap letters appearing anywhere in the alignment */
+    get lettersPresent() {
+        const letters = new Set();
+        for (let slot = 1; slot < SLOTS; slot++) {
+            if (this.slotTotals[slot] > 0 && !isGapSlot(slot)) {
+                letters.add(letterOfSlot[slot]);
+            }
+        }
+        return letters;
+    }
+}
+export function letterOfResidueSlot(slot) {
+    return letterOfSlot[slot];
+}
+export function residueSlotOfLetter(letter) {
+    return slotOf(letter.charCodeAt(0));
+}
+export const numResidueSlots = SLOTS;
+/**
+ * Tally counts from alignment rows (gapped sequence strings, one per row). The
+ * column count follows the longest row, matching what a per-column tally of
+ * ragged input produces.
+ */
+export function columnCountsFromRows(rows) {
+    const numColumns = rows.reduce((max, row) => Math.max(max, row.length), 0);
+    const counts = new ColumnCounts(numColumns);
+    for (const row of rows) {
+        counts.addRow(row);
+    }
+    return counts;
+}
+/**
+ * Tally counts from column strings (one string per column, listing that
+ * column's residues top to bottom). Convenient for tests and for callers that
+ * already think column-wise.
+ */
+export function columnCountsFromColumns(columns) {
+    const counts = new ColumnCounts(columns.length);
+    for (const [col, column] of columns.entries()) {
+        for (const letter of column) {
+            counts.add(col, letter);
+        }
+    }
+    return counts;
+}
+//# sourceMappingURL=columnCounts.js.map

package/dist/columnCounts.js.map

@@ -0,0 +1 @@
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package/dist/components/MSAView.js

@@ -1,6 +1,5 @@
-import React, { Suspense, useEffect } from 'react';
+import React, { Suspense } from 'react';
 import { observer } from 'mobx-react';
-import { useDevicePixelRatio } from "../useDevicePixelRatio.js";
 import { HorizontalResizeHandle, VerticalResizeHandle, } from "./ResizeHandles.js";
 import Track from "./Track.js";
 import VerticalScrollbar from "./VerticalScrollbar.js";
@@ -72,12 +71,6 @@ const View = observer(function ({ model }) {
 });
 const MSAView = observer(function ({ model }) {
     const { height, viewInitialized, DialogComponent, DialogProps } = model;
-    // mirror the live device pixel ratio into the model so canvas backing stores
-    // re-scale when the window moves between monitors or the browser zooms
-    const devicePixelRatio = useDevicePixelRatio();
-    useEffect(() => {
-        model.setHighResScaleFactor(devicePixelRatio);
-    }, [model, devicePixelRatio]);
     return (React.createElement("div", null, viewInitialized ? (React.createElement(React.Fragment, null,
         React.createElement("div", { style: { height, overflow: 'hidden' } },
             React.createElement(Header, { model: model }),

package/dist/components/MSAView.js.map

@@ -1 +1 @@
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+{"version":3,"file":"MSAView.js","sourceRoot":"","sources":["../../src/components/MSAView.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AAEvC,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAErC,OAAO,EACL,sBAAsB,EACtB,oBAAoB,GACrB,MAAM,oBAAqB,CAAA;AAC5B,OAAO,KAAK,MAAM,YAAa,CAAA;AAC/B,OAAO,iBAAiB,MAAM,wBAAyB,CAAA;AACvD,OAAO,MAAM,MAAM,oBAAqB,CAAA;AACxC,OAAO,OAAO,MAAM,sBAAuB,CAAA;AAC3C,OAAO,QAAQ,MAAM,mBAAoB,CAAA;AACzC,OAAO,SAAS,MAAM,qBAAsB,CAAA;AAC5C,OAAO,SAAS,MAAM,qBAAsB,CAAA;AAI5C,MAAM,OAAO,GAAG,QAAQ,CAAC,UAAU,EAAE,KAAK,EAA2B;IACnE,MAAM,EAAE,uBAAuB,EAAE,GAAG,KAAK,CAAA;IACzC,OAAO,CACL,6BAAK,KAAK,EAAE,EAAE,OAAO,EAAE,MAAM,EAAE;QAC7B,oBAAC,SAAS,IAAC,KAAK,EAAE,KAAK,GAAI;QAC1B,uBAAuB,CAAC,CAAC,CAAC,oBAAC,OAAO,IAAC,KAAK,EAAE,KAAK,GAAI,CAAC,CAAC,CAAC,IAAI,CACvD,CACP,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,MAAM,oBAAoB,GAAG,QAAQ,CAAC,UAAU,EAC9C,KAAK,GAGN;IACC,MAAM,EACJ,QAAQ,EACR,aAAa,EACb,QAAQ,EACR,OAAO,EACP,aAAa,EACb,iBAAiB,EACjB,oBAAoB,EACpB,YAAY,EACZ,sBAAsB,GACvB,GAAG,KAAK,CAAA;IAET,MAAM,IAAI,GAAG,aAAa,GAAG,iBAAiB,CAAA;IAC9C,MAAM,SAAS,GAAG,YAAY,GAAG,sBAAsB,CAAA;IAEvD,OAAO,CACL,6BACE,KAAK,EAAE;YACL,QAAQ,EAAE,UAAU;YACpB,IAAI;YACJ,GAAG,EAAE,CAAC;YACN,KAAK,EAAE,SAAS;YAChB,MAAM,EAAE,oBAAoB;YAC5B,QAAQ,EAAE,QAAQ;YAClB,aAAa,EAAE,MAAM;SACtB;QAEA,QAAQ,KAAK,SAAS,CAAC,CAAC,CAAC,CACxB,6BACE,KAAK,EAAE;gBACL,QAAQ,EAAE,UAAU;gBACpB,IAAI,EAAE,QAAQ,GAAG,QAAQ,GAAG,OAAO;gBACnC,GAAG,EAAE,CAAC;gBACN,KAAK,EAAE,QAAQ;gBACf,MAAM,EAAE,oBAAoB;gBAC5B,eAAe,EAAE,kBAAkB;gBACnC,MAAM,EAAE,GAAG;aACZ,GACD,CACH,CAAC,CAAC,CAAC,IAAI;QACP,aAAa,KAAK,SAAS,CAAC,CAAC,CAAC,CAC7B,6BACE,KAAK,EAAE;gBACL,QAAQ,EAAE,UAAU;gBACpB,IAAI,EAAE,aAAa,GAAG,QAAQ,GAAG,OAAO;gBACxC,GAAG,EAAE,CAAC;gBACN,KAAK,EAAE,QAAQ;gBACf,MAAM,EAAE,oBAAoB;gBAC5B,eAAe,EAAE,qBAAqB;gBACtC,MAAM,EAAE,GAAG;aACZ,GACD,CACH,CAAC,CAAC,CAAC,IAAI,CACJ,CACP,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,MAAM,SAAS,GAAG,QAAQ,CAAC,UAAU,EAAE,KAAK,EAA2B;IACrE,MAAM,EAAE,cAAc,EAAE,GAAG,KAAK,CAAA;IAChC,IAAI,cAAc,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;QAChC,OAAO,IAAI,CAAA;IACb,CAAC;IACD,OAAO,CACL,6BAAK,KAAK,EAAE,EAAE,QAAQ,EAAE,UAAU,EAAE;QAClC,oBAAC,oBAAoB,IAAC,KAAK,EAAE,KAAK,GAAI;QACrC,cAAc,CAAC,GAAG,CAAC,KAAK,CAAC,EAAE,CAAC,CAC3B,oBAAC,KAAK,IAAC,GAAG,EAAE,KAAK,CAAC,KAAK,CAAC,EAAE,EAAE,KAAK,EAAE,KAAK,EAAE,KAAK,EAAE,KAAK,GAAI,CAC3D,CAAC,CACE,CACP,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,MAAM,QAAQ,GAAG,QAAQ,CAAC,UAAU,EAAE,KAAK,EAA2B;IACpE,MAAM,EAAE,qBAAqB,EAAE,GAAG,KAAK,CAAA;IAEvC,OAAO,CACL,6BAAK,KAAK,EAAE,EAAE,OAAO,EAAE,MAAM,EAAE;QAC7B,oBAAC,SAAS,IAAC,KAAK,EAAE,KAAK,GAAI;QAC3B,oBAAC,oBAAoB,IAAC,KAAK,EAAE,KAAK,GAAI;QACtC,oBAAC,QAAQ,IAAC,KAAK,EAAE,KAAK,GAAI;QACzB,qBAAqB,CAAC,CAAC,CAAC,oBAAC,iBAAiB,IAAC,KAAK,EAAE,KAAK,GAAI,CAAC,CAAC,CAAC,IAAI,CAC/D,CACP,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,MAAM,IAAI,GAAG,QAAQ,CAAC,UAAU,EAAE,KAAK,EAA2B;IAChE,OAAO,CACL,6BAAK,KAAK,EAAE,EAAE,QAAQ,EAAE,UAAU,EAAE;QAClC,oBAAC,OAAO,IAAC,KAAK,EAAE,KAAK,GAAI;QACzB,oBAAC,SAAS,IAAC,KAAK,EAAE,KAAK,GAAI;QAC3B,oBAAC,QAAQ,IAAC,KAAK,EAAE,KAAK,GAAI,CACtB,CACP,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,MAAM,OAAO,GAAG,QAAQ,CAAC,UAAU,EAAE,KAAK,EAA2B;IACnE,MAAM,EAAE,MAAM,EAAE,eAAe,EAAE,eAAe,EAAE,WAAW,EAAE,GAAG,KAAK,CAAA;IAEvE,OAAO,CACL,iCACG,eAAe,CAAC,CAAC,CAAC,CACjB;QACE,6BAAK,KAAK,EAAE,EAAE,MAAM,EAAE,QAAQ,EAAE,QAAQ,EAAE;YACxC,oBAAC,MAAM,IAAC,KAAK,EAAE,KAAK,GAAI;YACxB,oBAAC,IAAI,IAAC,KAAK,EAAE,KAAK,GAAI,CAClB;QACN,oBAAC,sBAAsB,IAAC,KAAK,EAAE,KAAK,GAAI;QAEvC,eAAe,CAAC,CAAC,CAAC,CACjB,oBAAC,QAAQ,IAAC,QAAQ,EAAE,IAAI;YACtB,oBAAC,eAAe,OAAK,WAAW,GAAI,CAC3B,CACZ,CAAC,CAAC,CAAC,IAAI,CACP,CACJ,CAAC,CAAC,CAAC,IAAI,CACJ,CACP,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,OAAO,CAAA"}

package/dist/components/getVisibleLeaves.d.ts

@@ -0,0 +1,6 @@
+import type { MsaViewModel } from '../model.ts';
+export declare function getVisibleLeaves({ model, offsetY, blockSizeY, }: {
+    model: MsaViewModel;
+    offsetY: number;
+    blockSizeY: number;
+}): import("../hierarchy.ts").HierarchyNode<import("../types.ts").NodeWithIdsAndLength>[];

package/dist/components/getVisibleLeaves.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"getVisibleLeaves.js","sourceRoot":"","sources":["../../src/components/getVisibleLeaves.ts"],"names":[],"mappings":"AAEA,2EAA2E;AAC3E,2DAA2D;AAC3D,MAAM,UAAU,gBAAgB,CAAC,EAC/B,KAAK,EACL,OAAO,EACP,UAAU,GAKX;IACC,MAAM,EAAE,MAAM,EAAE,SAAS,EAAE,GAAG,KAAK,CAAA;IACnC,MAAM,MAAM,GAAG,IAAI,CAAC,GAAG,CAAC,CAAC,EAAE,IAAI,CAAC,KAAK,CAAC,CAAC,OAAO,GAAG,SAAS,CAAC,GAAG,SAAS,CAAC,CAAC,CAAA;IACzE,MAAM,IAAI,GAAG,IAAI,CAAC,GAAG,CACnB,CAAC,EACD,IAAI,CAAC,IAAI,CAAC,CAAC,OAAO,GAAG,UAAU,GAAG,SAAS,CAAC,GAAG,SAAS,CAAC,CAC1D,CAAA;IACD,OAAO,MAAM,CAAC,KAAK,CAAC,MAAM,EAAE,IAAI,CAAC,CAAA;AACnC,CAAC"}

package/dist/components/msa/MSACanvasBlock.js

@@ -1,25 +1,25 @@
-import React, { useState } from 'react';
+import React from 'react';
 import { BaseTooltip } from '@jbrowse/core/ui';
 import { observer } from 'mobx-react';
 import ColumnStats from "./ColumnStats.js";
 import { renderBoxFeatureCanvasBlock } from "./renderBoxFeatureCanvasBlock.js";
 import { renderMSABlock } from "./renderMSABlock.js";
+import { useMsaBlockMouse } from "./useMsaBlockMouse.js";
 import { useCanvasAutorun } from "../../useCanvasAutorun.js";
 import { useColorContrast } from "../../useColorContrast.js";
-function eventToColRow(event, el, offsetX, offsetY, colWidth, rowHeight) {
-    const { left, top } = el.getBoundingClientRect();
-    return {
-        col: Math.floor((event.clientX - left + offsetX) / colWidth),
-        row: Math.floor((event.clientY - top + offsetY) / rowHeight),
-    };
-}
 const MSACanvasBlock = observer(function ({ model, offsetX, offsetY, }) {
-    const { colWidth, rowHeight, scrollY, scrollX, colorScheme, blockSize, mouseClickCol, mouseClickRow, highResScaleFactor, } = model;
+    const { scrollY, scrollX, colorScheme, blockSize, highResScaleFactor } = model;
     const { theme, contrastScheme } = useColorContrast(colorScheme);
+    const { tooltipPoint, onMouseMove, onClick, onMouseLeave } = useMsaBlockMouse({
+        model,
+        offsetX,
+        offsetY,
+    });
     const ref = useCanvasAutorun(ctx => {
+        const { blockSize, highResScaleFactor, actuallyShowDomains } = model;
         ctx.resetTransform();
         ctx.clearRect(0, 0, blockSize * highResScaleFactor, blockSize * highResScaleFactor);
-        if (model.actuallyShowDomains) {
+        if (actuallyShowDomains) {
             renderBoxFeatureCanvasBlock({
                 ctx,
                 offsetX,
@@ -35,53 +35,19 @@ const MSACanvasBlock = observer(function ({ model, offsetX, offsetY, }) {
             contrastScheme,
             model,
         });
-    }, [
-        model,
-        offsetX,
-        offsetY,
-        theme,
-        blockSize,
-        highResScaleFactor,
-        contrastScheme,
-    ]);
-    const [mousePosition, setMousePosition] = useState();
+    }, [model, offsetX, offsetY, theme, contrastScheme]);
     const { hoveredInsertion, mouseOverDomains, showColumnStats } = model;
     return (React.createElement(React.Fragment, null,
         React.createElement("canvas", { ref: ref, onMouseMove: event => {
                 if (ref.current) {
-                    const { col, row } = eventToColRow(event, ref.current, offsetX, offsetY, colWidth, rowHeight);
-                    // Only set mouse position if within valid MSA bounds
-                    if (col >= 0 &&
-                        col < model.numColumns &&
-                        row >= 0 &&
-                        row < model.numRows) {
-                        model.setMousePos(col, row);
-                    }
-                    else {
-                        model.setMousePos(undefined, undefined);
-                    }
-                    // only track client coords when there's something to show in the
-                    // tooltip: an insertion, a domain under the cursor, or column stats
-                    // (when that option is enabled). avoids a re-render on every move
-                    // when nothing would be shown
-                    const hasTooltip = model.hoveredInsertion ||
-                        model.mouseOverDomains.length > 0 ||
-                        (model.showColumnStats && !!model.mouseOverColumnStats);
-                    setMousePosition(hasTooltip ? { x: event.clientX, y: event.clientY } : undefined);
+                    onMouseMove(event, ref.current);
                 }
             }, onClick: event => {
                 if (ref.current) {
-                    const { col, row } = eventToColRow(event, ref.current, offsetX, offsetY, colWidth, rowHeight);
-                    if (col === mouseClickCol && row === mouseClickRow) {
-                        model.setMouseClickPos(undefined, undefined);
-                    }
-                    else {
-                        model.setMouseClickPos(col, row);
-                    }
+                    onClick(event, ref.current);
                 }
             }, onMouseLeave: () => {
-                model.setMousePos();
-                setMousePosition(undefined);
+                onMouseLeave();
             }, width: blockSize * highResScaleFactor, height: blockSize * highResScaleFactor, style: {
                 position: 'absolute',
                 top: scrollY + offsetY,
@@ -89,7 +55,7 @@ const MSACanvasBlock = observer(function ({ model, offsetX, offsetY, }) {
                 width: blockSize,
                 height: blockSize,
             } }),
-        hoveredInsertion && mousePosition ? (React.createElement(BaseTooltip, { clientPoint: { x: mousePosition.x, y: mousePosition.y + 15 } },
+        tooltipPoint ? (React.createElement(BaseTooltip, { clientPoint: { x: tooltipPoint.x, y: tooltipPoint.y + 15 } }, hoveredInsertion ? (React.createElement(React.Fragment, null,
             "Insertion (",
             hoveredInsertion.letters.length,
             model.sequenceType === 'amino' ? 'aa' : 'bp',
@@ -97,10 +63,7 @@ const MSACanvasBlock = observer(function ({ model, offsetX, offsetY, }) {
             ' ',
             hoveredInsertion.letters.length > 20
                 ? `${hoveredInsertion.letters.slice(0, 20)}...`
-                : hoveredInsertion.letters)) : null,
-        !hoveredInsertion &&
-            mousePosition &&
-            (mouseOverDomains.length > 0 || showColumnStats) ? (React.createElement(BaseTooltip, { clientPoint: { x: mousePosition.x, y: mousePosition.y + 15 } },
+                : hoveredInsertion.letters)) : (React.createElement(React.Fragment, null,
             mouseOverDomains.map(d => (React.createElement("div", { key: `${d.accession}-${d.start}-${d.end}` },
                 React.createElement("b", null, d.name),
                 " (",
@@ -112,7 +75,7 @@ const MSACanvasBlock = observer(function ({ model, offsetX, offsetY, }) {
                 d.description ? (React.createElement(React.Fragment, null,
                     React.createElement("br", null),
                     d.description)) : null))),
-            showColumnStats ? React.createElement(ColumnStats, { model: model }) : null)) : null));
+            showColumnStats ? React.createElement(ColumnStats, { model: model }) : null)))) : null));
 });
 export default MSACanvasBlock;
 //# sourceMappingURL=MSACanvasBlock.js.map

package/dist/components/msa/MSACanvasBlock.js.map

@@ -1 +1 @@
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package/dist/components/msa/renderBoxFeatureCanvasBlock.d.ts

@@ -1,10 +1,11 @@
 import type { MsaViewModel } from '../../model.ts';
 import type { RenderCtx } from '../renderCtx.ts';
-export declare function renderBoxFeatureCanvasBlock({ model, offsetX, offsetY, ctx, highResScaleFactorOverride, blockSizeYOverride, }: {
+export declare function renderBoxFeatureCanvasBlock({ model, offsetX, offsetY, ctx, highResScaleFactorOverride, blockSizeXOverride, blockSizeYOverride, }: {
     offsetX: number;
     offsetY: number;
     model: MsaViewModel;
     ctx: RenderCtx;
     highResScaleFactorOverride?: number;
+    blockSizeXOverride?: number;
     blockSizeYOverride?: number;
 }): void;

package/dist/components/msa/renderBoxFeatureCanvasBlock.js

@@ -1,44 +1,46 @@
-import { getVisibleLeaves } from "./getVisibleLeaves.js";
 import { subFeatureRowHeight } from "../../constants.js";
-export function renderBoxFeatureCanvasBlock({ model, offsetX, offsetY, ctx, highResScaleFactorOverride, blockSizeYOverride, }) {
+import { getVisibleLeaves } from "../getVisibleLeaves.js";
+export function renderBoxFeatureCanvasBlock({ model, offsetX, offsetY, ctx, highResScaleFactorOverride, blockSizeXOverride, blockSizeYOverride, }) {
     const { blockSize, rowHeight, highResScaleFactor, showDomains } = model;
     if (showDomains) {
         const k = highResScaleFactorOverride ?? highResScaleFactor;
+        const bx = blockSizeXOverride ?? blockSize;
         const by = blockSizeYOverride ?? blockSize;
         ctx.resetTransform();
         ctx.scale(k, k);
         ctx.translate(-offsetX, rowHeight / 2 - offsetY);
-        const visibleLeaves = getVisibleLeaves({ model, offsetY, blockSizeY: by });
         drawTiles({
             model,
             ctx,
-            visibleLeaves,
+            visibleLeaves: getVisibleLeaves({ model, offsetY, blockSizeY: by }),
+            offsetX,
+            blockWidth: bx,
         });
     }
 }
-function drawTiles({ model, ctx, visibleLeaves, }) {
-    const { subFeatureRows, colWidth, rowHeight, fillPalette, strokePalette, segmentLabels, showMsaLetters, tidyFilteredGatheredInterProAnnotations, } = model;
+function drawTiles({ model, ctx, visibleLeaves, offsetX, blockWidth, }) {
+    const { subFeatureRows, colWidth, rowHeight, fillPalette, strokePalette, segmentLabels, showMsaLetters, domainBands, } = model;
     const h = subFeatureRows ? subFeatureRowHeight : rowHeight;
     // exon numbers label the bands only when residue letters aren't drawn (zoomed
     // out); when letters show, the alternating shades alone mark the boundaries
     // and a number would collide with the sequence
     const drawSegmentLabels = !showMsaLetters && !subFeatureRows && h >= 9;
+    // gene arrow heads stick out one row-height past the band, so pad the cull
+    // window enough that a band just outside the block still draws its head
+    const cull = h + colWidth;
+    const xMin = offsetX - cull;
+    const xMax = offsetX + blockWidth + cull;
     for (let i = 0, l1 = visibleLeaves.length; i < l1; i++) {
         const node = visibleLeaves[i];
-        const { name } = node.data;
         const y = node.x;
-        const entry = tidyFilteredGatheredInterProAnnotations[name];
-        if (entry) {
-            for (let j = 0, l2 = entry.length; j < l2; j++) {
-                const { start, end, accession, strand } = entry[j];
-                // Convert sequence positions to visible column positions
-                // seqPos is 1-based from InterPro, so subtract 1 for 0-based
-                const m1 = model.seqPosToVisibleCol(name, start - 1);
-                const m2 = model.seqPosToVisibleCol(name, end);
-                if (m1 !== undefined && m2 !== undefined) {
-                    const x = m1 * colWidth;
-                    const t = y - rowHeight + (subFeatureRows ? j * h : 0);
-                    const lw = colWidth * (m2 - m1);
+        const bands = domainBands.get(node.data.name);
+        if (bands) {
+            for (const { annotation, startCol, endCol, stackIndex } of bands) {
+                const { accession, strand } = annotation;
+                const x = startCol * colWidth;
+                const lw = colWidth * (endCol - startCol);
+                if (x + lw >= xMin && x <= xMax) {
+                    const t = y - rowHeight + (subFeatureRows ? stackIndex * h : 0);
                     ctx.fillStyle = fillPalette[accession];
                     ctx.strokeStyle = strokePalette[accession];
                     if (strand === undefined) {

package/dist/components/msa/renderBoxFeatureCanvasBlock.js.map

@@ -1 +1 @@
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