react-msaview 5.4.0 → 5.5.0

package/dist/renderToSvg.js.map

@@ -1 +1 @@
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package/dist/{webpack.js → umd.js}

@@ -3,4 +3,4 @@ export { default as MSAView } from "./components/Loading.js";
 export { default as MSAModelF } from "./model.js";
 export * from 'react-dom/client';
 export { React };
-//# sourceMappingURL=webpack.js.map
+//# sourceMappingURL=umd.js.map

package/dist/umd.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"umd.js","sourceRoot":"","sources":["../src/umd.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,KAAK,MAAM,OAAO,CAAA;AAE9B,OAAO,EAAE,OAAO,IAAI,OAAO,EAAE,MAAM,yBAA0B,CAAA;AAC7D,OAAO,EAAqB,OAAO,IAAI,SAAS,EAAE,MAAM,YAAY,CAAA;AAEpE,cAAc,kBAAkB,CAAA;AAEhC,OAAO,EAAE,KAAK,EAAE,CAAA"}

package/dist/version.d.ts

@@ -1 +1 @@
-export declare const version = "5.4.0";
+export declare const version = "5.5.0";

package/dist/version.js

@@ -1,2 +1,2 @@
-export const version = '5.4.0';
+export const version = '5.5.0';
 //# sourceMappingURL=version.js.map

package/package.json

@@ -1,7 +1,7 @@
 {
   "name": "react-msaview",
   "author": "Colin",
-  "version": "5.4.0",
+  "version": "5.5.0",
   "license": "MIT",
   "type": "module",
   "repository": {
@@ -35,23 +35,24 @@
     "react-dom": ">=16.8.0"
   },
   "devDependencies": {
-    "@types/node": "^25.9.2"
+    "@types/node": "^26.0.1",
+    "esbuild": "^0.28.1"
   },
   "dependencies": {
     "@mui/icons-material": "^7.3.11",
     "@mui/material": "^7.3.11",
     "colord": "^2.9.3",
-    "flatbush": "^4.6.1",
-    "@jbrowse/svgcanvas": "5.4.0",
-    "msa-parsers": "5.4.0"
+    "flatbush": "^4.6.2",
+    "@jbrowse/svgcanvas": "5.5.0",
+    "msa-parsers": "5.5.0"
   },
   "scripts": {
     "clean": "rimraf dist bundle",
     "watch": "pnpm build:esm --watch",
     "format": "prettier --write .",
     "build:esm": "tsc --project tsconfig.build.json",
-    "build:bundle": "webpack",
-    "build": "pnpm clean && pnpm build:esm && pnpm build:bundle",
+    "build:umd": "node esbuild.mjs",
+    "build": "pnpm clean && pnpm build:esm && pnpm build:umd",
     "statedocs": "rm -rf apidocs && mkdir apidocs && node --experimental-strip-types docgen/generateStateModelDocs.ts",
     "poststatedocs": "pnpm format",
     "test": "vitest"

package/src/colorSchemes.ts

@@ -6,8 +6,19 @@ import { transform } from './util.ts'
 
 extend([namesPlugin])
 
+// standard A/C/G/T(/U) coloring, shared by the `jbrowse_dna` and `nucleotide`
+// scheme names
+const dna = {
+  A: green[500],
+  C: blue[500],
+  G: orange[500],
+  T: red[500],
+  U: red[500],
+}
+
 const colorSchemes = {
   none: {},
+  nucleotide: dna,
   clustal: {
     G: 'orange',
     P: 'orange',
@@ -135,13 +146,7 @@ const colorSchemes = {
     T: '#19cc19',
     U: '#19cc19',
   },
-  jbrowse_dna: {
-    A: green[500],
-    C: blue[500],
-    G: orange[500],
-    T: red[500],
-    U: red[500],
-  },
+  jbrowse_dna: dna,
   jalview_buried: {
     A: '#00a35c',
     R: '#00fc03',

package/src/components/Checkbox2.tsx

@@ -17,7 +17,13 @@ export default function Checkbox2({
     <div>
       <FormControlLabel
         control={
-          <Checkbox disabled={disabled} checked={checked} onChange={onChange} />
+          <Checkbox
+            disabled={disabled}
+            checked={checked}
+            onChange={() => {
+              onChange()
+            }}
+          />
         }
         label={label}
       />

package/src/components/MSAViewer.tsx

@@ -1,4 +1,4 @@
-import React, { useEffect, useMemo } from 'react'
+import React, { useEffect, useState } from 'react'
 
 import { createJBrowseTheme } from '@jbrowse/core/ui/theme'
 import useMeasure from '@jbrowse/core/util/useMeasure'
@@ -9,6 +9,8 @@ import Loading from './Loading.tsx'
 
 import type { FileLocation as FileLocationType } from '@jbrowse/core/util/types'
 
+const theme = createJBrowseTheme()
+
 interface MSAViewerProps {
   msa?: string
   tree?: string
@@ -18,6 +20,12 @@ interface MSAViewerProps {
   gffFilehandle?: FileLocationType
   colorScheme?: string
   height?: number
+  /** initial per-column pixel width (zoom level) */
+  colWidth?: number
+  /** initial per-row pixel height */
+  rowHeight?: number
+  /** alignment columns (0-based) to highlight with a persistent overlay */
+  highlightColumns?: number[]
   /** row name to diff every other row against (matches render as ".") */
   relativeTo?: string
 }
@@ -31,33 +39,35 @@ export default function MSAViewer({
   gffFilehandle,
   colorScheme,
   height,
+  colWidth,
+  rowHeight,
+  highlightColumns,
   relativeTo,
 }: MSAViewerProps) {
-  const theme = useMemo(() => createJBrowseTheme(), [])
-  const model = useMemo(
-    () =>
-      MSAModelF().create({
-        type: 'MsaView',
-        ...(msa || tree || gff
-          ? { data: { msa: msa ?? '', tree: tree ?? '', gff } }
-          : {}),
-        ...(msaFilehandle ? { msaFilehandle } : {}),
-        ...(treeFilehandle ? { treeFilehandle } : {}),
-        ...(gffFilehandle ? { gffFilehandle } : {}),
-        ...(colorScheme ? { colorSchemeName: colorScheme } : {}),
-        ...(height ? { height } : {}),
-        ...(relativeTo ? { relativeTo } : {}),
-      }),
-    // eslint-disable-next-line react-hooks/exhaustive-deps
-    [],
+  // lazy initializer: the model is created exactly once from the initial props
+  // (a stable MST instance — not a value safe to recompute, so not useMemo)
+  const [model] = useState(() =>
+    MSAModelF().create({
+      type: 'MsaView',
+      ...(msa || tree || gff
+        ? { data: { msa: msa ?? '', tree: tree ?? '', gff } }
+        : {}),
+      ...(msaFilehandle ? { msaFilehandle } : {}),
+      ...(treeFilehandle ? { treeFilehandle } : {}),
+      ...(gffFilehandle ? { gffFilehandle } : {}),
+      ...(colorScheme ? { colorSchemeName: colorScheme } : {}),
+      ...(height ? { height } : {}),
+      ...(colWidth ? { colWidth } : {}),
+      ...(rowHeight ? { rowHeight } : {}),
+      ...(highlightColumns ? { highlightColumns } : {}),
+      ...(relativeTo ? { relativeTo } : {}),
+    }),
   )
 
   const [ref, { width }] = useMeasure()
   useEffect(() => {
     if (width) {
-      requestAnimationFrame(() => {
-        model.setWidth(width)
-      })
+      model.setWidth(width)
     }
   }, [model, width])
 

package/src/components/Track.tsx

@@ -26,12 +26,15 @@ const TrackLabel = observer(function TrackLabel({
   track: BasicTrack
 }) {
   const [anchorEl, setAnchorEl] = useState<HTMLButtonElement>()
-  const { drawLabels, rowHeight, treeAreaWidth: width } = model
+  const closeMenu = () => {
+    setAnchorEl(undefined)
+  }
+  const { drawLabels, fontSize, treeAreaWidth: width } = model
   const {
     model: { name, height },
   } = track
   const { classes } = useStyles()
-  const trackLabelHeight = Math.min(height, Math.max(8, rowHeight - 8))
+  const trackLabelHeight = Math.min(height, fontSize)
 
   return (
     <div
@@ -62,14 +65,14 @@ const TrackLabel = observer(function TrackLabel({
           transitionDuration={0}
           open
           onClose={() => {
-            setAnchorEl(undefined)
+            closeMenu()
           }}
         >
           <MenuItem
             dense
             onClick={() => {
               model.toggleTrack(track.model.id)
-              setAnchorEl(undefined)
+              closeMenu()
             }}
           >
             Close
@@ -81,7 +84,7 @@ const TrackLabel = observer(function TrackLabel({
                 TrackInfoDialog,
                 { onClose, model: track.model },
               ])
-              setAnchorEl(undefined)
+              closeMenu()
             }}
           >
             Get info

package/src/components/dialogs/FeatureDialog.tsx

@@ -1,11 +1,18 @@
 import React from 'react'
 
 import { Dialog } from '@jbrowse/core/ui'
-import { Button, DialogContent } from '@mui/material'
+import {
+  Button,
+  Checkbox,
+  DialogContent,
+  Table,
+  TableBody,
+  TableCell,
+  TableHead,
+  TableRow,
+} from '@mui/material'
 import { observer } from 'mobx-react'
 
-import { getPalette } from '../../ggplotPalettes.ts'
-
 import type { MsaViewModel } from '../../model.ts'
 
 const Toggles = observer(function ({ model }: { model: MsaViewModel }) {
@@ -35,53 +42,60 @@ const Toggles = observer(function ({ model }: { model: MsaViewModel }) {
   )
 })
 
-const Table = observer(function ({ model }: { model: MsaViewModel }) {
-  const { tidyInterProAnnotationTypes, featureFilters } = model
-  const values = [...tidyInterProAnnotationTypes.values()]
-  const palette = getPalette(values.length - 1)
+const FeatureTable = observer(function ({ model }: { model: MsaViewModel }) {
+  const { tidyInterProAnnotationTypes, tidyInterProAnnotations, fillPalette } =
+    model
+  const counts = new Map<string, number>()
+  for (const annot of tidyInterProAnnotations) {
+    counts.set(annot.accession, (counts.get(annot.accession) ?? 0) + 1)
+  }
   return (
     <>
       <Toggles model={model} />
-      <table>
-        <thead>
-          <tr>
-            <td />
-            <td>accession</td>
-            <td>name</td>
-            <td>description</td>
-          </tr>
-        </thead>
-        <tbody>
-          {values.map(({ accession, name, description }, idx) => (
-            <tr key={accession}>
-              <td>
-                <input
-                  type="checkbox"
-                  checked={featureFilters.get(accession) ?? false}
-                  onChange={() => {
-                    model.setFilter(
-                      accession,
-                      !model.featureFilters.get(accession),
-                    )
-                  }}
-                />
-              </td>
-              <td>{accession}</td>
-              <td>{name}</td>
-              <td>{description}</td>
-              <td>
-                <div
-                  style={{
-                    width: 20,
-                    height: 20,
-                    background: palette[idx] || 'black',
-                  }}
-                />
-              </td>
-            </tr>
-          ))}
-        </tbody>
-      </table>
+      <Table size="small">
+        <TableHead>
+          <TableRow>
+            <TableCell padding="checkbox" />
+            <TableCell>color</TableCell>
+            <TableCell>accession</TableCell>
+            <TableCell>name</TableCell>
+            <TableCell>count</TableCell>
+            <TableCell>description</TableCell>
+          </TableRow>
+        </TableHead>
+        <TableBody>
+          {[...tidyInterProAnnotationTypes.values()].map(
+            ({ accession, name, description }) => (
+              <TableRow key={accession}>
+                <TableCell padding="checkbox">
+                  <Checkbox
+                    checked={model.featureFilters.get(accession) ?? false}
+                    onChange={() => {
+                      model.setFilter(
+                        accession,
+                        !model.featureFilters.get(accession),
+                      )
+                    }}
+                  />
+                </TableCell>
+                <TableCell>
+                  <div
+                    style={{
+                      width: 20,
+                      height: 20,
+                      background: fillPalette[accession],
+                    }}
+                  />
+                </TableCell>
+                <TableCell>{accession}</TableCell>
+                <TableCell>{name}</TableCell>
+                <TableCell>{counts.get(accession)}</TableCell>
+                <TableCell>{description}</TableCell>
+              </TableRow>
+            ),
+          )}
+        </TableBody>
+      </Table>
     </>
   )
 })
@@ -103,7 +117,7 @@ const FeatureTypeDialog = observer(function ({
       maxWidth="xl"
     >
       <DialogContent>
-        <Table model={model} />
+        <FeatureTable model={model} />
       </DialogContent>
     </Dialog>
   )

package/src/components/dialogs/InterProScanDialog.tsx

@@ -4,6 +4,7 @@ import { Dialog } from '@jbrowse/core/ui'
 import { getSession } from '@jbrowse/core/util'
 import { Button, DialogActions, DialogContent, Typography } from '@mui/material'
 import { observer } from 'mobx-react'
+import { getUngappedSequence } from 'msa-parsers'
 
 import { launchInterProScan } from '../../launchInterProScan.ts'
 
@@ -251,7 +252,7 @@ const InterProScanDialog = observer(function ({
                   algorithm: 'interproscan',
                   programs: programs,
                   seq: rows
-                    .map(row => [row[0], row[1].replaceAll('-', '')])
+                    .map(row => [row[0], getUngappedSequence(row[1])])
                     .filter(f => !!f[1])
                     .map(row => `>${row[0]}\n${row[1]}`)
                     .join('\n'),

package/src/components/msa/DomainLegend.tsx

@@ -0,0 +1,74 @@
+import React, { useState } from 'react'
+
+import ExpandLess from '@mui/icons-material/ExpandLess'
+import ExpandMore from '@mui/icons-material/ExpandMore'
+import { IconButton, Paper, Typography } from '@mui/material'
+import { observer } from 'mobx-react'
+
+import type { MsaViewModel } from '../../model.ts'
+
+const DomainLegend = observer(function ({ model }: { model: MsaViewModel }) {
+  const [expanded, setExpanded] = useState(true)
+  const { actuallyShowDomains, visibleDomainTypes: visible, fillPalette } = model
+  const ExpandIcon = expanded ? ExpandLess : ExpandMore
+
+  return actuallyShowDomains && visible.length > 0 ? (
+    <Paper
+      elevation={3}
+      style={{
+        position: 'absolute',
+        top: 4,
+        right: 4,
+        zIndex: 100,
+        maxWidth: 260,
+        maxHeight: '60%',
+        display: 'flex',
+        flexDirection: 'column',
+        opacity: 0.95,
+      }}
+    >
+      <div
+        style={{
+          display: 'flex',
+          alignItems: 'center',
+          justifyContent: 'flex-end',
+          padding: '2px 4px 2px 8px',
+        }}
+      >
+        <IconButton
+          size="small"
+          onClick={() => {
+            setExpanded(!expanded)
+          }}
+        >
+          <ExpandIcon fontSize="small" />
+        </IconButton>
+      </div>
+      {expanded ? (
+        <div style={{ overflow: 'auto', padding: '0 8px 6px' }}>
+          {visible.map(({ accession, name }) => (
+            <div
+              key={accession}
+              style={{ display: 'flex', alignItems: 'center', gap: 6 }}
+              title={accession}
+            >
+              <div
+                style={{
+                  width: 12,
+                  height: 12,
+                  flexShrink: 0,
+                  background: fillPalette[accession],
+                }}
+              />
+              <Typography variant="caption" noWrap>
+                {name}
+              </Typography>
+            </div>
+          ))}
+        </div>
+      ) : null}
+    </Paper>
+  ) : null
+})
+
+export default DomainLegend

package/src/components/msa/MSACanvasBlock.tsx

@@ -89,7 +89,7 @@ const MSACanvasBlock = observer(function ({
   ])
 
   const [mousePosition, setMousePosition] = useState<{ x: number; y: number }>()
-  const { hoveredInsertion } = model
+  const { hoveredInsertion, mouseOverDomains } = model
 
   return (
     <>
@@ -116,10 +116,11 @@ const MSACanvasBlock = observer(function ({
             } else {
               model.setMousePos(undefined, undefined)
             }
-            // only track client coords when an insertion is hovered (the only
-            // consumer is the tooltip below); avoids a re-render on every move
+            // only track client coords when there's something to show in the
+            // tooltip (insertion or a domain under the cursor); avoids a
+            // re-render on every move over plain alignment cells
             setMousePosition(
-              model.hoveredInsertion
+              model.hoveredInsertion || model.mouseOverDomains.length > 0
                 ? { x: event.clientX, y: event.clientY }
                 : undefined,
             )
@@ -167,6 +168,23 @@ const MSACanvasBlock = observer(function ({
             : hoveredInsertion.letters}
         </BaseTooltip>
       ) : null}
+      {!hoveredInsertion && mouseOverDomains.length > 0 && mousePosition ? (
+        <BaseTooltip
+          clientPoint={{ x: mousePosition.x, y: mousePosition.y + 15 }}
+        >
+          {mouseOverDomains.map(d => (
+            <div key={`${d.accession}-${d.start}-${d.end}`}>
+              <b>{d.name}</b> ({d.accession}) {d.start}-{d.end}
+              {d.description ? (
+                <>
+                  <br />
+                  {d.description}
+                </>
+              ) : null}
+            </div>
+          ))}
+        </BaseTooltip>
+      ) : null}
     </>
   )
 })

package/src/components/msa/MSAPanel.tsx

@@ -2,6 +2,7 @@ import React from 'react'
 
 import { observer } from 'mobx-react'
 
+import DomainLegend from './DomainLegend.tsx'
 import MSACanvas from './MSACanvas.tsx'
 import MSAMouseoverCanvas from './MSAMouseoverCanvas.tsx'
 
@@ -13,6 +14,7 @@ const MSAPanel = observer(function ({ model }: { model: MsaViewModel }) {
     <div style={{ position: 'relative' }}>
       <MSACanvas model={model} />
       <MSAMouseoverCanvas model={model} />
+      <DomainLegend model={model} />
     </div>
   )
 })