react-msaview 9.1.1 → 9.3.0

package/dist/useWheelScroll.js

@@ -1,19 +1,65 @@
 import { useEffect, useRef, useState } from 'react';
 import { WheelZoomSmoother } from './wheelZoom.js';
 const zoomSettleMs = 150;
-export function useWheelScroll({ ref, onScrollX, onScrollY, onZoom, onZoomSettle, onWheelScroll, scrollZoom, }) {
+// a wheel event this soon after one the view took belongs to the same gesture,
+// so the view keeps it at an edge rather than handing the momentum to the page
+const wheelLatchMs = 150;
+/**
+ * Whether a vertical wheel `delta` moves a view at `scrollY`. At the top or
+ * bottom, or when every row fits, the page scrolls instead, so an embedded
+ * viewer never traps the reader scrolling past it.
+ */
+export function canScrollY(model, delta) {
+    const { scrollY, maxScrollY } = model;
+    return delta > 0 ? scrollY > maxScrollY : delta < 0 && scrollY < 0;
+}
+// Safari reads a touch-action holding pinch-zoom as invalid and falls back to
+// auto, which hands every swipe to the page
+const pinchZoom = typeof CSS !== 'undefined' && CSS.supports('touch-action', 'pinch-zoom')
+    ? 'pinch-zoom'
+    : undefined;
+function withPinch(pan) {
+    return pinchZoom ? `${pan} ${pinchZoom}` : pan;
+}
+/**
+ * The CSS touch-action for a pannable area: the browser keeps a touch pan
+ * along every axis the view cannot scroll, and pinch zoom on the page where it
+ * supports that value.
+ */
+export function panTouchAction(model, axes) {
+    const x = axes.includes('x') && model.maxScrollX < 0;
+    const y = axes.includes('y') && model.maxScrollY < 0;
+    return x && y
+        ? (pinchZoom ?? 'none')
+        : x
+            ? withPinch('pan-y')
+            : y
+                ? withPinch('pan-x')
+                : 'auto';
+}
+/**
+ * Wheel scrolling, wheel zoom and pointer-drag panning of `model` over `ref`,
+ * along `axes`. The returned `onPointerDown` starts a pan with a mouse, a pen
+ * or a finger; put `touchAction` on the same element.
+ */
+export function useWheelScroll({ ref, model, axes, zoom, onWheelScroll, }) {
     const scheduled = useRef(false);
     const zoomFrame = useRef(undefined);
     const zoomSettle = useRef(undefined);
     const deltaX = useRef(0);
     const deltaY = useRef(0);
+    const lastTaken = useRef(Number.NEGATIVE_INFINITY);
     const zoomSmoother = useRef(new WheelZoomSmoother());
     const zoomX = useRef(0);
     const zoomY = useRef(0);
     const lastZoomTime = useRef(null);
-    const prevX = useRef(0);
-    const prevY = useRef(0);
-    const [mouseDragging, setMouseDragging] = useState(false);
+    const prev = useRef({ x: 0, y: 0 });
+    const latest = useRef({ x: 0, y: 0 });
+    const panFrame = useRef(false);
+    // the pointer that started the pan; a second finger neither moves nor ends it
+    const [panPointer, setPanPointer] = useState();
+    const x = axes.includes('x');
+    const y = axes.includes('y');
     useEffect(() => {
         const curr = ref.current;
         if (!curr) {
@@ -24,11 +70,10 @@ export function useWheelScroll({ ref, onScrollX, onScrollY, onZoom, onZoomSettle
             // scrollZoom is on, a plain vertical-dominant wheel zooms too; holding
             // shift is the escape hatch to pan instead.
             const isCtrlZoom = event.ctrlKey || event.metaKey;
-            const isScrollZoom = scrollZoom &&
+            const isScrollZoom = model.scrollZoom &&
                 !event.shiftKey &&
                 Math.abs(event.deltaY) >= Math.abs(event.deltaX);
-            if (onZoom && (isCtrlZoom || isScrollZoom)) {
-                const zoom = onZoom;
+            if (zoom && (isCtrlZoom || isScrollZoom)) {
                 const rect = curr.getBoundingClientRect();
                 zoomSmoother.current.add(event.deltaY, event.deltaMode, isCtrlZoom);
                 zoomX.current = event.clientX - rect.left;
@@ -38,10 +83,10 @@ export function useWheelScroll({ ref, onScrollX, onScrollY, onZoom, onZoomSettle
                     const frame = (now) => {
                         const elapsed = lastZoomTime.current === null ? 16.67 : now - lastZoomTime.current;
                         lastZoomTime.current = now;
-                        zoom(zoomSmoother.current.step(Math.min(100, elapsed)), zoomX.current, zoomY.current);
+                        model.wheelZoomToPos(zoomSmoother.current.step(Math.min(100, elapsed)), zoomX.current, zoomY.current);
                         clearTimeout(zoomSettle.current);
                         zoomSettle.current = setTimeout(() => {
-                            onZoomSettle?.();
+                            model.endWheelZoom();
                         }, zoomSettleMs);
                         zoomFrame.current = zoomSmoother.current.idle
                             ? undefined
@@ -53,29 +98,29 @@ export function useWheelScroll({ ref, onScrollX, onScrollY, onZoom, onZoomSettle
                 event.stopPropagation();
                 return;
             }
-            // only swallow the wheel event on an axis we actually handle, otherwise a
-            // vertical wheel over an x-only scroller (e.g. a Track) blocks page scroll
-            const consumeX = !!onScrollX && event.deltaX !== 0;
-            const consumeY = !!onScrollY && event.deltaY !== 0;
-            if (consumeX || consumeY) {
-                onWheelScroll?.(event);
-                if (onScrollX) {
-                    deltaX.current += event.deltaX;
-                }
-                if (onScrollY) {
-                    deltaY.current += event.deltaY;
+            // the dominant axis decides: a trackpad's vertical swipe carries a pixel
+            // or two of deltaX, which must not hold the page at the bottom row. A
+            // horizontal wheel stays taken at the edges, where the page would read
+            // it as a swipe back through history.
+            const { deltaX: dx, deltaY: dy } = event;
+            const vertical = Math.abs(dy) >= Math.abs(dx);
+            const latched = event.timeStamp - lastTaken.current < wheelLatchMs;
+            const takeY = y && dy !== 0 && (latched || canScrollY(model, dy) || !vertical);
+            const takeX = x && dx !== 0 && (!vertical || takeY);
+            if (takeX || takeY) {
+                if (takeY && vertical) {
+                    lastTaken.current = event.timeStamp;
                 }
+                onWheelScroll?.(event);
+                deltaX.current += takeX ? event.deltaX : 0;
+                deltaY.current += takeY ? event.deltaY : 0;
                 if (!scheduled.current) {
                     scheduled.current = true;
                     requestAnimationFrame(() => {
-                        if (onScrollX) {
-                            onScrollX(-deltaX.current);
-                            deltaX.current = 0;
-                        }
-                        if (onScrollY) {
-                            onScrollY(-deltaY.current);
-                            deltaY.current = 0;
-                        }
+                        model.doScrollX(-deltaX.current);
+                        model.doScrollY(-deltaY.current);
+                        deltaX.current = 0;
+                        deltaY.current = 0;
                         scheduled.current = false;
                     });
                 }
@@ -92,59 +137,51 @@ export function useWheelScroll({ ref, onScrollX, onScrollY, onZoom, onZoomSettle
             }
             clearTimeout(zoomSettle.current);
         };
-    }, [
-        ref,
-        onScrollX,
-        onScrollY,
-        onZoom,
-        onZoomSettle,
-        onWheelScroll,
-        scrollZoom,
-    ]);
+    }, [ref, model, x, y, zoom, onWheelScroll]);
     useEffect(() => {
-        if (!mouseDragging) {
+        if (panPointer === undefined) {
             return;
         }
-        function globalMouseMove(event) {
+        // a frame applies the distance from the last applied position to the
+        // newest one, so a move landing while a frame is pending is not dropped
+        function onMove(event) {
+            if (event.pointerId !== panPointer) {
+                return;
+            }
             event.preventDefault();
-            const distanceX = event.clientX - prevX.current;
-            const distanceY = event.clientY - prevY.current;
-            if ((distanceX && onScrollX) || (distanceY && onScrollY)) {
-                if (!scheduled.current) {
-                    scheduled.current = true;
-                    requestAnimationFrame(() => {
-                        onScrollX?.(distanceX);
-                        onScrollY?.(distanceY);
-                        scheduled.current = false;
-                        prevX.current = event.clientX;
-                        prevY.current = event.clientY;
-                    });
-                }
+            latest.current = { x: event.clientX, y: event.clientY };
+            if (!panFrame.current) {
+                panFrame.current = true;
+                requestAnimationFrame(() => {
+                    const to = latest.current;
+                    model.doScrollX(x ? to.x - prev.current.x : 0);
+                    model.doScrollY(y ? to.y - prev.current.y : 0);
+                    prev.current = to;
+                    panFrame.current = false;
+                });
             }
         }
-        function globalMouseUp() {
-            prevX.current = 0;
-            prevY.current = 0;
-            setMouseDragging(false);
+        function onUp(event) {
+            if (event.pointerId === panPointer) {
+                setPanPointer(undefined);
+            }
         }
-        window.addEventListener('mousemove', globalMouseMove, true);
-        window.addEventListener('mouseup', globalMouseUp, true);
+        window.addEventListener('pointermove', onMove, true);
+        window.addEventListener('pointerup', onUp, true);
+        window.addEventListener('pointercancel', onUp, true);
         return () => {
-            window.removeEventListener('mousemove', globalMouseMove, true);
-            window.removeEventListener('mouseup', globalMouseUp, true);
+            window.removeEventListener('pointermove', onMove, true);
+            window.removeEventListener('pointerup', onUp, true);
+            window.removeEventListener('pointercancel', onUp, true);
         };
-    }, [mouseDragging, onScrollX, onScrollY]);
-    function onMouseDown(event) {
-        if (event.button === 0) {
-            prevX.current = event.clientX;
-            prevY.current = event.clientY;
-            setMouseDragging(true);
+    }, [panPointer, model, x, y]);
+    function onPointerDown(event) {
+        if (event.button === 0 && event.isPrimary && panPointer === undefined) {
+            prev.current = { x: event.clientX, y: event.clientY };
+            latest.current = prev.current;
+            setPanPointer(event.pointerId);
         }
     }
-    function onMouseUp(event) {
-        event.preventDefault();
-        setMouseDragging(false);
-    }
-    return { onMouseDown, onMouseUp };
+    return { onPointerDown, touchAction: panTouchAction(model, axes) };
 }
 //# sourceMappingURL=useWheelScroll.js.map

package/dist/useWheelScroll.js.map

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package/dist/version.d.ts

@@ -1 +1 @@
-export declare const version = "9.1.1";
+export declare const version = "9.3.0";

package/dist/version.js

@@ -1,2 +1,2 @@
-export const version = '9.1.1';
+export const version = '9.3.0';
 //# sourceMappingURL=version.js.map

package/dist/viewerSnapshot.js

@@ -1,9 +1,10 @@
 import { createJBrowseTheme } from '@jbrowse/core/ui/theme';
+import { letterColors } from './scales.js';
 export function colorSchemeSnapshot(scheme) {
     return typeof scheme === 'string'
         ? { colorSchemeName: scheme }
         : scheme
-            ? { customColorScheme: scheme.map }
+            ? { customColorScheme: letterColors(scheme) }
             : {};
 }
 /**

package/dist/viewerSnapshot.js.map

@@ -1 +1 @@
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package/package.json

@@ -1,7 +1,7 @@
 {
   "name": "react-msaview",
   "author": "Colin",
-  "version": "9.1.1",
+  "version": "9.3.0",
   "license": "MIT",
   "type": "module",
   "repository": {
@@ -50,10 +50,10 @@
   },
   "dependencies": {
     "@gmod/newick": "^1.0.3",
-    "@jbrowse/svgcanvas": "9.1.1",
+    "@jbrowse/svgcanvas": "9.3.0",
     "colord": "^2.10.0",
     "flatbush": "^4.6.2",
-    "msa-parsers": "9.1.1"
+    "msa-parsers": "9.3.0"
   },
   "scripts": {
     "clean": "rimraf dist bundle",

package/src/components/DragHandle.tsx

@@ -85,11 +85,12 @@ export default function DragHandle({
       onMouseLeave={() => {
         setHovered(false)
       }}
-      onMouseDown={event => {
+      onPointerDown={event => {
         startDrag(event, getStart())
       }}
       style={{
         position,
+        touchAction: 'none',
         zIndex,
         cursor: cursor(axis),
         background: hovered ? fillHovered(theme) : fill(theme),

package/src/components/MSAViewer.tsx

@@ -12,6 +12,7 @@ import { ThemeProvider } from '@mui/material/styles'
 import { compareStructural, reaction, when } from 'mobx'
 
 import MSAModelF from '../model.ts'
+import { letterColors } from '../scales.ts'
 import {
   fileLocations,
   resolveTheme,
@@ -57,8 +58,9 @@ export interface MSAViewerProps {
   /** a URL the viewer fetches the GFF from; `gffFilehandle` wins */
   gffUrl?: string
   /**
-   * a scheme name from the built-in table, or `{map}`, a color per residue
-   * letter that leaves every other letter uncolored
+   * a scheme name from the built-in table, or `{domain, range}`, a color per
+   * residue letter that leaves every other letter uncolored. The earlier
+   * `{map}` still reads
    */
   colorScheme?: ColorScheme
   height?: number
@@ -103,15 +105,16 @@ export interface MSAViewerProps {
   /** extra fields per row name, such as a lineage or a host (see docs/layers.md) */
   rowData?: RowDataInput
   /**
-   * what the viewer's marks read from a table: `{channel, field, scale?}`,
-   * where `channel` is `tipLabel`, `rowTint` or `branch` over `rowData`, or
-   * `featureFill` or `featureLabel` over the annotations (see docs/layers.md)
+   * what the viewer's marks read from a table:
+   * `{channel, field, range?, domain?, title?}`, where `channel` is
+   * `tipLabel`, `rowTint` or `branch` over `rowData`, or `featureFill` or
+   * `featureLabel` over the annotations (see docs/layers.md)
    */
   encodings?: Encoding[]
   /**
    * panels between the tree and the alignment, one cell per row:
-   * `{kind: 'strip', field, scale?, width?, header?}` colors each row by a
-   * `rowData` field (see docs/layers.md)
+   * `{kind: 'strip', field, range?, domain?, title?, width?, header?}` colors
+   * each row by a `rowData` field (see docs/layers.md)
    */
   rowPanels?: RowPanelSpec[]
   /** draw the phylogenetic tree (default true); false leaves a labels-only gutter */
@@ -357,7 +360,7 @@ const syncedProps = [
       if (typeof scheme === 'string') {
         m.setColorSchemeName(scheme)
       } else if (scheme) {
-        m.setCustomColorScheme(scheme.map)
+        m.setCustomColorScheme(letterColors(scheme))
       }
     },
   ),

package/src/components/Track.tsx

@@ -1,4 +1,4 @@
-import React, { lazy, useCallback, useRef, useState } from 'react'
+import React, { lazy, useRef, useState } from 'react'
 
 import BaseTooltip from '@jbrowse/core/ui/BaseTooltip'
 import { makeStyles } from '@jbrowse/core/util/tss-react'
@@ -153,13 +153,7 @@ const Track = observer(function ({
     model: { height },
   } = track
   const ref = useRef<HTMLDivElement>(null)
-  const onScrollX = useCallback(
-    (d: number) => {
-      model.doScrollX(d)
-    },
-    [model],
-  )
-  useWheelScroll({ ref, onScrollX })
+  useWheelScroll({ ref, model, axes: 'x' })
   const { classes } = useStyles()
   const { anchor, onMouseMove, onMouseDown, onMouseLeave } = useTrackHover({
     model,

package/src/components/VerticalScrollbar.tsx

@@ -23,7 +23,7 @@ const VerticalScrollbar = observer(({ model }: { model: MsaViewModel }) => {
 
   return (
     <div
-      onMouseDown={event => {
+      onPointerDown={event => {
         if (event.button === 0 && event.target === event.currentTarget) {
           const y =
             event.clientY - event.currentTarget.getBoundingClientRect().top

package/src/components/header/Header.tsx

@@ -2,7 +2,8 @@ import React, { useEffect } from 'react'
 
 import useMeasure from '@jbrowse/core/util/useMeasure'
 import Tune from '@mui/icons-material/Tune'
-import { AppBar, Button, IconButton, Toolbar, Tooltip } from '@mui/material'
+import { Button, IconButton, Toolbar, Tooltip } from '@mui/material'
+import AppBar from '@mui/material/AppBar'
 import { observer } from 'mobx-react'
 
 import StatusMessage from '../StatusMessage.tsx'

package/src/components/minimap/Minimap.tsx

@@ -78,7 +78,7 @@ const Minimap = observer(function ({ model }: { model: MsaViewModel }) {
         ref={ref}
         width={barWidth}
         height={barHeight}
-        onMouseDown={event => {
+        onPointerDown={event => {
           if (event.button === 0 && unit > 0) {
             const x =
               event.clientX - event.currentTarget.getBoundingClientRect().left

package/src/components/msa/MSACanvas.tsx

@@ -1,4 +1,4 @@
-import React, { useCallback, useRef } from 'react'
+import React, { useRef } from 'react'
 
 import { observer } from 'mobx-react'
 
@@ -19,7 +19,6 @@ const MSACanvas = observer(function ({ model }: { model: MsaViewModel }) {
     height,
     msaCanvasWidth,
     blocks2d,
-    scrollZoom,
     scrollX,
     scrollY,
     zoomSnapshot,
@@ -33,36 +32,13 @@ const MSACanvas = observer(function ({ model }: { model: MsaViewModel }) {
     ? zoomSnapshotScale(model, zoomSnapshot)
     : undefined
   const ref = useRef<HTMLDivElement>(null)
-  const onScrollX = useCallback(
-    (d: number) => {
-      model.doScrollX(d)
-    },
-    [model],
-  )
-  const onScrollY = useCallback(
-    (d: number) => {
-      model.doScrollY(d)
-    },
-    [model],
-  )
-  const onZoom = useCallback(
-    (scaleFactor: number, offsetX: number, offsetY: number) => {
-      model.wheelZoomToPos(scaleFactor, offsetX, offsetY)
-    },
-    [model],
-  )
-  const onZoomSettle = useCallback(() => {
-    model.endWheelZoom()
-  }, [model])
   const hint = useWheelZoomHint(model)
-  const { onMouseDown, onMouseUp } = useWheelScroll({
+  const { onPointerDown, touchAction } = useWheelScroll({
     ref,
-    onScrollX,
-    onScrollY,
-    onZoom,
-    onZoomSettle,
+    model,
+    axes: 'xy',
+    zoom: true,
     onWheelScroll: hint.onWheelScroll,
-    scrollZoom,
   })
 
   return (
@@ -78,20 +54,23 @@ const MSACanvas = observer(function ({ model }: { model: MsaViewModel }) {
           event.preventDefault()
         }
       }}
+      // a shifted press selects cells (useMsaBlockMouse), so it takes the
+      // focus Escape clears from, and leaves out the pan and the page's own
+      // text selection
       onMouseDown={event => {
-        // a shifted press selects cells (useMsaBlockMouse), so it takes the
-        // focus Escape clears from, and leaves out the pan and the page's own
-        // text selection
         if (event.shiftKey) {
           event.preventDefault()
           ref.current?.focus({ preventScroll: true })
-        } else {
-          onMouseDown(event)
         }
       }}
-      onMouseUp={onMouseUp}
+      onPointerDown={event => {
+        if (!event.shiftKey) {
+          onPointerDown(event)
+        }
+      }}
       style={{
         position: 'relative',
+        touchAction,
         height,
         width: msaCanvasWidth,
         overflow: 'hidden',

package/src/components/rowpanels/RowPanels.tsx

@@ -1,4 +1,4 @@
-import React, { useCallback, useRef } from 'react'
+import React, { useRef } from 'react'
 
 import { observer } from 'mobx-react'
 
@@ -17,21 +17,19 @@ const RowPanel = observer(function ({
 }) {
   const ref = useRef<HTMLDivElement>(null)
   const { height, blocksY, scrollY } = model
-  const onScrollY = useCallback(
-    (d: number) => {
-      model.doScrollY(d)
-    },
-    [model],
-  )
-  const { onMouseDown, onMouseUp } = useWheelScroll({ ref, onScrollY })
+  const { onPointerDown, touchAction } = useWheelScroll({
+    ref,
+    model,
+    axes: 'y',
+  })
 
   return (
     <div
       ref={ref}
       data-testid={`rowpanel_${panel.id}`}
-      onMouseDown={onMouseDown}
-      onMouseUp={onMouseUp}
+      onPointerDown={onPointerDown}
       style={{
+        touchAction,
         height,
         width: panel.width,
         flexShrink: 0,

package/src/components/settings/SettingsPanel.tsx

@@ -3,7 +3,8 @@ import React, { useState } from 'react'
 import ArrowDropDown from '@mui/icons-material/ArrowDropDown'
 import ArrowRight from '@mui/icons-material/ArrowRight'
 import Close from '@mui/icons-material/Close'
-import { Box, ButtonBase, IconButton, Typography } from '@mui/material'
+import { Box, IconButton, Typography } from '@mui/material'
+import ButtonBase from '@mui/material/ButtonBase'
 import { observer } from 'mobx-react'
 
 import { settingsPanelWidth } from '../../constants.ts'

package/src/components/settings/TrackList.tsx

@@ -21,15 +21,20 @@ function trackGroups(model: MsaViewModel) {
   const computed = new Set(model.computedTrackModels.map(t => t.model.id))
   const computedEntries: Entry[] = []
   const alignmentEntries: Entry[] = []
+  const referenceEntries: Entry[] = []
   for (const { model: t } of model.tracks) {
-    ;(computed.has(t.id) ? computedEntries : alignmentEntries).push({
-      id: t.id,
-      label: t.name,
-    })
+    const entries =
+      t.kind === 'reference'
+        ? referenceEntries
+        : computed.has(t.id)
+          ? computedEntries
+          : alignmentEntries
+    entries.push({ id: t.id, label: t.name })
   }
   return [
     { title: 'Computed from the alignment', entries: computedEntries },
     { title: 'Alignment annotations', entries: alignmentEntries },
+    { title: 'Reference row', entries: referenceEntries },
   ].filter(g => g.entries.length > 0)
 }
 

package/src/components/tracks/TrackTooltipContent.tsx

@@ -137,7 +137,8 @@ const TrackTooltipContent = observer(function ({
     case 'logo': {
       return <LogoTooltip model={model} col={col} />
     }
-    case 'text': {
+    case 'text':
+    case 'reference': {
       return <TextTooltip model={model} track={track} col={col} />
     }
     case 'arc': {