react-msaview 6.5.0 → 7.0.0

package/dist/components/Loading.js

@@ -26,9 +26,9 @@ const Reset = observer(function ({ model, error, }) {
             } }, "Return to import form")));
 });
 const Loading = observer(function ({ model }) {
-    const { isLoading, dataInitialized, error, msaFilehandle, treeFilehandle } = model;
+    const { isLoading, dataInitialized, error, resetCount, msaFilehandle, treeFilehandle, } = model;
     const hasPendingFilehandle = !!(msaFilehandle || treeFilehandle);
-    return (React.createElement("div", null, React.createElement(ErrorBoundary, { FallbackComponent: e => React.createElement(Reset, { model: model, error: e.error }) }, dataInitialized ? (isLoading ? (React.createElement(LoadingSpinner, { model: model })) : (React.createElement(MSAView, { model: model }))) : error ? (React.createElement(Reset, { model: model, error: error })) : hasPendingFilehandle || isLoading ? (React.createElement(LoadingSpinner, { model: model })) : (React.createElement(ImportForm, { model: model })))));
+    return (React.createElement("div", null, React.createElement(ErrorBoundary, { key: resetCount, FallbackComponent: e => React.createElement(Reset, { model: model, error: e.error }) }, dataInitialized ? (isLoading ? (React.createElement(LoadingSpinner, { model: model })) : (React.createElement(MSAView, { model: model }))) : error ? (React.createElement(Reset, { model: model, error: error })) : hasPendingFilehandle || isLoading ? (React.createElement(LoadingSpinner, { model: model })) : (React.createElement(ImportForm, { model: model })))));
 });
 export default Loading;
 //# sourceMappingURL=Loading.js.map

package/dist/components/Loading.js.map

@@ -1 +1 @@
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+{"version":3,"file":"Loading.js","sourceRoot":"","sources":["../../src/components/Loading.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,EAAE,YAAY,EAAE,MAAM,kBAAkB,CAAA;AAC/C,OAAO,EAAE,aAAa,EAAE,MAAM,gCAAgC,CAAA;AAC9D,OAAO,EAAE,MAAM,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAClD,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAErC,OAAO,OAAO,MAAM,cAAe,CAAA;AACnC,OAAO,UAAU,MAAM,wBAAyB,CAAA;AAIhD,MAAM,cAAc,GAAG,QAAQ,CAAC,UAAU,EAAE,KAAK,EAA2B;IAC1E,MAAM,EAAE,MAAM,EAAE,GAAG,KAAK,CAAA;IACxB,OAAO,CACL,6BACE,KAAK,EAAE,EAAE,OAAO,EAAE,MAAM,EAAE,UAAU,EAAE,QAAQ,EAAE,GAAG,EAAE,EAAE,EAAE,OAAO,EAAE,EAAE,EAAE;QAEtE,6BACE,KAAK,EAAC,IAAI,EACV,MAAM,EAAC,IAAI,EACX,OAAO,EAAC,WAAW,EACnB,KAAK,EAAC,4BAA4B;YAElC,mCACG,0DAA0D,CACrD;YACR,gCACE,EAAE,EAAC,IAAI,EACP,EAAE,EAAC,IAAI,EACP,CAAC,EAAC,IAAI,EACN,MAAM,EAAC,MAAM,EACb,WAAW,EAAC,GAAG,EACf,IAAI,EAAC,MAAM,GACX;YACF,8BACE,CAAC,EAAC,yBAAyB,EAC3B,MAAM,EAAC,SAAS,EAChB,WAAW,EAAC,GAAG,EACf,IAAI,EAAC,MAAM,EACX,aAAa,EAAC,OAAO,EACrB,KAAK,EAAE;oBACL,SAAS,EAAE,4BAA4B;oBACvC,eAAe,EAAE,QAAQ;iBAC1B,GACD,CACE;QACN,oBAAC,UAAU,IAAC,OAAO,EAAC,IAAI,IAAE,MAAM,EAAE,GAAG,IAAI,YAAY,CAAc;QAClE,MAAM,EAAE,QAAQ,CAAC,CAAC,CAAC,CAClB,oBAAC,MAAM,IACL,OAAO,EAAC,UAAU,EAClB,IAAI,EAAC,OAAO,EACZ,OAAO,EAAE,GAAG,EAAE,CAAC,MAAM,CAAC,QAAQ,EAAE,EAAE,aAG3B,CACV,CAAC,CAAC,CAAC,IAAI,CACJ,CACP,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,MAAM,KAAK,GAAG,QAAQ,CAAC,UAAU,EAC/B,KAAK,EACL,KAAK,GAIN;IACC,OAAO,CACL;QACE,oBAAC,YAAY,IAAC,KAAK,EAAE,KAAK,GAAI;QAC9B,oBAAC,MAAM,IACL,OAAO,EAAC,WAAW,EACnB,KAAK,EAAC,SAAS,EACf,OAAO,EAAE,GAAG,EAAE;gBACZ,KAAK,CAAC,KAAK,EAAE,CAAA;YACf,CAAC,4BAGM,CACL,CACP,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,MAAM,OAAO,GAAG,QAAQ,CAAC,UAAU,EAAE,KAAK,EAA2B;IACnE,MAAM,EACJ,SAAS,EACT,eAAe,EACf,KAAK,EACL,UAAU,EACV,aAAa,EACb,cAAc,GACf,GAAG,KAAK,CAAA;IACT,MAAM,oBAAoB,GAAG,CAAC,CAAC,CAAC,aAAa,IAAI,cAAc,CAAC,CAAA;IAEhE,OAAO,CACL,iCAIE,oBAAC,aAAa,IACZ,GAAG,EAAE,UAAU,EACf,iBAAiB,EAAE,CAAC,CAAC,EAAE,CAAC,oBAAC,KAAK,IAAC,KAAK,EAAE,KAAK,EAAE,KAAK,EAAE,CAAC,CAAC,KAAK,GAAI,IAE9D,eAAe,CAAC,CAAC,CAAC,CACjB,SAAS,CAAC,CAAC,CAAC,CACV,oBAAC,cAAc,IAAC,KAAK,EAAE,KAAK,GAAI,CACjC,CAAC,CAAC,CAAC,CACF,oBAAC,OAAO,IAAC,KAAK,EAAE,KAAK,GAAI,CAC1B,CACF,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,CAOV,oBAAC,KAAK,IAAC,KAAK,EAAE,KAAK,EAAE,KAAK,EAAE,KAAK,GAAI,CACtC,CAAC,CAAC,CAAC,oBAAoB,IAAI,SAAS,CAAC,CAAC,CAAC,CACtC,oBAAC,cAAc,IAAC,KAAK,EAAE,KAAK,GAAI,CACjC,CAAC,CAAC,CAAC,CACF,oBAAC,UAAU,IAAC,KAAK,EAAE,KAAK,GAAI,CAC7B,CACa,CACZ,CACP,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,OAAO,CAAA"}

package/dist/components/MSAViewer.d.ts

@@ -1,5 +1,5 @@
 import React from 'react';
-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';
 interface MSAViewerProps {
     msa?: string;
@@ -14,6 +14,12 @@ 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[];
     /**
@@ -26,6 +32,8 @@ 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 */
@@ -33,5 +41,5 @@ interface MSAViewerProps {
     /** auto-size the tree/label area to the labels (used when drawTree is false) */
     autoTreeAreaWidth?: boolean;
 }
-export default function MSAViewer({ msa, tree, gff, msaFilehandle, treeFilehandle, gffFilehandle, colorScheme, height, colWidth, rowHeight, highlightColumns, highlights, relativeTo, columnTracks, drawTree, treeAreaWidth, autoTreeAreaWidth, }: MSAViewerProps): React.JSX.Element;
+export default function MSAViewer({ msa, tree, gff, msaFilehandle, treeFilehandle, gffFilehandle, colorScheme, height, colWidth, rowHeight, allowedGappyness, highlightColumns, highlights, relativeTo, columnTracks, residueMappings, drawTree, treeAreaWidth, autoTreeAreaWidth, }: MSAViewerProps): React.JSX.Element;
 export {};

package/dist/components/MSAViewer.js

@@ -1,11 +1,12 @@
-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.js';
 import Loading from './Loading.js';
 const theme = createJBrowseTheme();
-export default function MSAViewer({ msa, tree, gff, msaFilehandle, treeFilehandle, gffFilehandle, colorScheme, height, colWidth, rowHeight, highlightColumns, highlights, relativeTo, columnTracks, drawTree, treeAreaWidth, autoTreeAreaWidth, }) {
+export default function MSAViewer({ msa, tree, gff, msaFilehandle, treeFilehandle, gffFilehandle, colorScheme, height, colWidth, rowHeight, allowedGappyness, highlightColumns, highlights, relativeTo, columnTracks, residueMappings, drawTree, treeAreaWidth, autoTreeAreaWidth, }) {
     // 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({
@@ -20,20 +21,107 @@ export default function MSAViewer({ msa, tree, gff, msaFilehandle, treeFilehandl
         ...(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(undefined);
     const [ref, { width }] = useMeasure();
     useEffect(() => {
         if (width) {
             model.setWidth(width);
         }
     }, [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 (React.createElement(ThemeProvider, { theme: theme },
         React.createElement("div", { ref: ref },
             React.createElement(Loading, { model: model }))));

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package/dist/components/ResizeHandles.d.ts

@@ -1,13 +1,13 @@
 import React from 'react';
 import type { MsaViewModel } from '../model.ts';
-import type { TrackKind } from '../types.ts';
+import type { BasicTrack } from '../types.ts';
 export declare const VerticalResizeHandle: ({ model, }: {
     model: MsaViewModel;
 }) => React.JSX.Element;
 export declare const HorizontalResizeHandle: ({ model, }: {
     model: MsaViewModel;
 }) => React.JSX.Element;
-export declare const TrackResizeHandle: ({ model, kind, }: {
+export declare const TrackResizeHandle: ({ model, track, }: {
     model: MsaViewModel;
-    kind: TrackKind;
+    track: BasicTrack;
 }) => React.JSX.Element | null;

package/dist/components/ResizeHandles.js

@@ -13,31 +13,38 @@ export const HorizontalResizeHandle = observer(function ({ model, }) {
     }, [model]);
     return (React.createElement(DragHandle, { axis: "y", variant: "resizer", getStart: () => model.height, onDrag: onDrag, style: { width: '100%', height: model.resizeHandleWidth } }));
 });
-// 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 = {
-    bar: {
-        get: model => model.conservationTrackHeight,
-        set: (model, height) => {
-            model.setConservationTrackHeight(height);
-        },
+// 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 = {
+    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, }) {
-    const height = trackHeights[kind];
+export const TrackResizeHandle = observer(function ({ model, track, }) {
+    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, startHeight) => {
-        height?.set(model, Math.max(10, startHeight + delta));
-    }, [model, height]);
-    return height ? (React.createElement(DragHandle, { axis: "y", variant: "resizer", getStart: () => height.get(model), onDrag: onDrag, style: {
+        const next = Math.max(10, startHeight + delta);
+        if (ownHeight) {
+            model.setColumnTrackHeight(id, next);
+        }
+        else {
+            setTrackHeight[kind]?.(model, next);
+        }
+    }, [model, id, kind, ownHeight]);
+    return setHeight ? (React.createElement(DragHandle, { axis: "y", variant: "resizer", getStart: () => height, onDrag: onDrag, style: {
             position: 'absolute',
             bottom: 0,
             left: 0,

package/dist/components/ResizeHandles.js.map

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+{"version":3,"file":"ResizeHandles.js","sourceRoot":"","sources":["../../src/components/ResizeHandles.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,WAAW,EAAE,MAAM,OAAO,CAAA;AAE1C,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAErC,OAAO,UAAU,MAAM,iBAAkB,CAAA;AAKzC,MAAM,CAAC,MAAM,oBAAoB,GAAG,QAAQ,CAAC,UAAU,EACrD,KAAK,GAGN;IACC,MAAM,MAAM,GAAG,WAAW,CACxB,CAAC,KAAa,EAAE,UAAkB,EAAE,EAAE;QACpC,KAAK,CAAC,gBAAgB,CAAC,UAAU,GAAG,KAAK,CAAC,CAAA;IAC5C,CAAC,EACD,CAAC,KAAK,CAAC,CACR,CAAA;IACD,OAAO,CACL,oBAAC,UAAU,IACT,IAAI,EAAC,GAAG,EACR,OAAO,EAAC,SAAS,EACjB,QAAQ,EAAE,GAAG,EAAE,CAAC,KAAK,CAAC,aAAa,EACnC,MAAM,EAAE,MAAM,EACd,KAAK,EAAE,EAAE,KAAK,EAAE,KAAK,CAAC,iBAAiB,EAAE,GACzC,CACH,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,MAAM,CAAC,MAAM,sBAAsB,GAAG,QAAQ,CAAC,UAAU,EACvD,KAAK,GAGN;IACC,MAAM,MAAM,GAAG,WAAW,CACxB,CAAC,KAAa,EAAE,WAAmB,EAAE,EAAE;QACrC,KAAK,CAAC,SAAS,CAAC,WAAW,GAAG,KAAK,CAAC,CAAA;IACtC,CAAC,EACD,CAAC,KAAK,CAAC,CACR,CAAA;IACD,OAAO,CACL,oBAAC,UAAU,IACT,IAAI,EAAC,GAAG,EACR,OAAO,EAAC,SAAS,EACjB,QAAQ,EAAE,GAAG,EAAE,CAAC,KAAK,CAAC,MAAM,EAC5B,MAAM,EAAE,MAAM,EACd,KAAK,EAAE,EAAE,KAAK,EAAE,MAAM,EAAE,MAAM,EAAE,KAAK,CAAC,iBAAiB,EAAE,GACzD,CACH,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,6EAA6E;AAC7E,2EAA2E;AAC3E,+EAA+E;AAC/E,4EAA4E;AAC5E,8BAA8B;AAC9B,MAAM,cAAc,GAEhB;IACF,GAAG,EAAE,CAAC,KAAK,EAAE,MAAM,EAAE,EAAE;QACrB,KAAK,CAAC,0BAA0B,CAAC,MAAM,CAAC,CAAA;IAC1C,CAAC;IACD,IAAI,EAAE,CAAC,KAAK,EAAE,MAAM,EAAE,EAAE;QACtB,KAAK,CAAC,0BAA0B,CAAC,MAAM,CAAC,CAAA;IAC1C,CAAC;IACD,GAAG,EAAE,CAAC,KAAK,EAAE,MAAM,EAAE,EAAE;QACrB,KAAK,CAAC,iBAAiB,CAAC,MAAM,CAAC,CAAA;IACjC,CAAC;CACF,CAAA;AAED,MAAM,CAAC,MAAM,iBAAiB,GAAG,QAAQ,CAAC,UAAU,EAClD,KAAK,EACL,KAAK,GAIN;IACC,MAAM,EAAE,EAAE,EAAE,IAAI,EAAE,MAAM,EAAE,GAAG,KAAK,CAAC,KAAK,CAAA;IACxC,MAAM,SAAS,GAAG,cAAc,CAAC,IAAI,CAAC,CAAA;IACtC,2EAA2E;IAC3E,8DAA8D;IAC9D,MAAM,SAAS,GAAG,KAAK,CAAC,YAAY,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,EAAE,KAAK,EAAE,CAAC,CAAA;IAC3D,MAAM,MAAM,GAAG,WAAW,CACxB,CAAC,KAAa,EAAE,WAAmB,EAAE,EAAE;QACrC,MAAM,IAAI,GAAG,IAAI,CAAC,GAAG,CAAC,EAAE,EAAE,WAAW,GAAG,KAAK,CAAC,CAAA;QAC9C,IAAI,SAAS,EAAE,CAAC;YACd,KAAK,CAAC,oBAAoB,CAAC,EAAE,EAAE,IAAI,CAAC,CAAA;QACtC,CAAC;aAAM,CAAC;YACN,cAAc,CAAC,IAAI,CAAC,EAAE,CAAC,KAAK,EAAE,IAAI,CAAC,CAAA;QACrC,CAAC;IACH,CAAC,EACD,CAAC,KAAK,EAAE,EAAE,EAAE,IAAI,EAAE,SAAS,CAAC,CAC7B,CAAA;IACD,OAAO,SAAS,CAAC,CAAC,CAAC,CACjB,oBAAC,UAAU,IACT,IAAI,EAAC,GAAG,EACR,OAAO,EAAC,SAAS,EACjB,QAAQ,EAAE,GAAG,EAAE,CAAC,MAAM,EACtB,MAAM,EAAE,MAAM,EACd,KAAK,EAAE;YACL,QAAQ,EAAE,UAAU;YACpB,MAAM,EAAE,CAAC;YACT,IAAI,EAAE,CAAC;YACP,KAAK,EAAE,MAAM;YACb,MAAM,EAAE,KAAK,CAAC,iBAAiB;YAC/B,MAAM,EAAE,CAAC;SACV,GACD,CACH,CAAC,CAAC,CAAC,IAAI,CAAA;AACV,CAAC,CAAC,CAAA"}

package/dist/components/dialogs/{InterProScanDialog.d.ts → AnnotationFileDialog.d.ts}

@@ -1,7 +1,7 @@
 import React from 'react';
 import type { MsaViewModel } from '../../model.ts';
-declare const InterProScanDialog: ({ handleClose, model, }: {
+declare const AnnotationFileDialog: ({ handleClose, model, }: {
     handleClose: () => void;
     model: MsaViewModel;
 }) => React.JSX.Element;
-export default InterProScanDialog;
+export default AnnotationFileDialog;

package/dist/components/dialogs/AnnotationFileDialog.js

@@ -0,0 +1,92 @@
+import React, { useState } from 'react';
+import { Dialog, ErrorMessage } from '@jbrowse/core/ui';
+import { Button, DialogActions, DialogContent, FormControl, FormControlLabel, Radio, RadioGroup, TextField, Typography, } from '@mui/material';
+import { observer } from 'mobx-react';
+import { annotationsToGFF, interProScanResponseToAnnotations, } from 'msa-parsers';
+// GFF3 as the CLI writes it, or the JSON an InterProScan run returns. Both
+// arrive as text and the model keeps GFF, so the JSON is converted on the way
+// in rather than given a second path through the model
+function toGFF(text) {
+    const trimmed = text.trimStart();
+    if (!trimmed.startsWith('{')) {
+        return text;
+    }
+    const response = JSON.parse(trimmed);
+    return annotationsToGFF(interProScanResponseToAnnotations(response));
+}
+async function fetchText(url) {
+    const response = await fetch(url);
+    if (!response.ok) {
+        throw new Error(`HTTP ${response.status} fetching ${url} ${await response.text()}`);
+    }
+    return response.text();
+}
+const AnnotationFileDialog = observer(function ({ handleClose, model, }) {
+    const [file, setFile] = useState();
+    const [choice, setChoice] = useState('file');
+    const [url, setUrl] = useState('');
+    const [error, setError] = useState();
+    const [loading, setLoading] = useState(false);
+    // the error is shown here rather than notified: the standalone app and the
+    // MSAViewer component have no jbrowse session to notify, and asking one for
+    // its notify() threw out of the success path into the catch, which threw
+    // again on the same missing session
+    return (React.createElement(Dialog, { maxWidth: "xl", title: "Open annotation file", onClose: () => {
+            handleClose();
+        }, open: true },
+        React.createElement(DialogContent, null,
+            error ? React.createElement(ErrorMessage, { error: error }) : null,
+            React.createElement(Typography, null, "Open a GFF3 file of annotations, such as the one `react-msaview-cli interpro` writes, or the JSON an InterProScan run returns."),
+            React.createElement("div", { style: { display: 'flex', margin: 30 } },
+                React.createElement(FormControl, { component: "fieldset" },
+                    React.createElement(RadioGroup, { value: choice, onChange: event => {
+                            setChoice(event.target.value);
+                        } },
+                        React.createElement(FormControlLabel, { value: "url", control: React.createElement(Radio, null), label: "URL" }),
+                        React.createElement(FormControlLabel, { value: "file", control: React.createElement(Radio, null), label: "File" }))),
+                choice === 'url' ? (React.createElement("div", null,
+                    React.createElement(Typography, null, "Open an annotation file from a URL"),
+                    React.createElement(TextField, { label: "URL", value: url, onChange: event => {
+                            setUrl(event.target.value);
+                        } }))) : (React.createElement("div", { style: { paddingTop: 20 } },
+                    React.createElement(Typography, null, "Open an annotation file from your local drive"),
+                    React.createElement(Button, { variant: "outlined", component: "label" },
+                        "Choose File",
+                        React.createElement("input", { type: "file", hidden: true, onChange: ({ target }) => {
+                                const chosen = target.files?.[0];
+                                if (chosen) {
+                                    setFile(chosen);
+                                }
+                            } })),
+                    file ? React.createElement(Typography, null, file.name) : null)))),
+        React.createElement(DialogActions, null,
+            React.createElement(Button, { variant: "contained", color: "primary", disabled: loading, onClick: () => {
+                    // eslint-disable-next-line @typescript-eslint/no-floating-promises
+                    ;
+                    (async () => {
+                        setLoading(true);
+                        setError(undefined);
+                        try {
+                            const text = await (choice === 'file' && file
+                                ? file.text()
+                                : fetchText(url));
+                            // through the model's own GFF text, so the annotations travel
+                            // in the snapshot and the shared URL like every other layer.
+                            // Setting them straight onto the volatile left a view whose
+                            // link opened without them
+                            model.setGFF(toGFF(text));
+                            model.setShowDomains(true);
+                            handleClose();
+                        }
+                        catch (e) {
+                            console.error(e);
+                            setError(e);
+                        }
+                        finally {
+                            setLoading(false);
+                        }
+                    })();
+                } }, "Open annotations"))));
+});
+export default AnnotationFileDialog;
+//# sourceMappingURL=AnnotationFileDialog.js.map

package/dist/components/dialogs/AnnotationFileDialog.js.map

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

@@ -3,17 +3,21 @@ import { Dialog } from '@jbrowse/core/ui';
 import { Button, Checkbox, DialogContent, Table, TableBody, TableCell, TableHead, TableRow, } from '@mui/material';
 import { observer } from 'mobx-react';
 const Toggles = observer(function ({ model }) {
-    const { featureFilters } = model;
+    // the accessions the file has, not the ones the filter map happens to hold:
+    // that map now carries only what the reader turned off, and before that it
+    // accumulated every accession of every file opened in this view
+    const { annotationTypes } = model;
+    const setAll = (shown) => {
+        for (const accession of annotationTypes.keys()) {
+            model.setFilter(accession, shown);
+        }
+    };
     return (React.createElement("div", null,
         React.createElement(Button, { onClick: () => {
-                for (const key of featureFilters.keys()) {
-                    model.setFilter(key, true);
-                }
+                setAll(true);
             } }, "Toggle all on"),
         React.createElement(Button, { onClick: () => {
-                for (const key of featureFilters.keys()) {
-                    model.setFilter(key, false);
-                }
+                setAll(false);
             } }, "Toggle all off")));
 });
 const FeatureTable = observer(function ({ model }) {
@@ -35,8 +39,8 @@ const FeatureTable = observer(function ({ model }) {
                     React.createElement(TableCell, null, "description"))),
             React.createElement(TableBody, null, [...annotationTypes.values()].map(({ accession, name, description }) => (React.createElement(TableRow, { key: accession },
                 React.createElement(TableCell, { padding: "checkbox" },
-                    React.createElement(Checkbox, { checked: model.featureFilters.get(accession) ?? false, onChange: () => {
-                            model.setFilter(accession, !model.featureFilters.get(accession));
+                    React.createElement(Checkbox, { checked: !model.turnedOffFeatures.get(accession), onChange: () => {
+                            model.setFilter(accession, !!model.turnedOffFeatures.get(accession));
                         } })),
                 React.createElement(TableCell, null,
                     React.createElement("div", { style: {

package/dist/components/dialogs/FeatureDialog.js.map

@@ -1 +1 @@
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+{"version":3,"file":"FeatureDialog.js","sourceRoot":"","sources":["../../../src/components/dialogs/FeatureDialog.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,EAAE,MAAM,EAAE,MAAM,kBAAkB,CAAA;AACzC,OAAO,EACL,MAAM,EACN,QAAQ,EACR,aAAa,EACb,KAAK,EACL,SAAS,EACT,SAAS,EACT,SAAS,EACT,QAAQ,GACT,MAAM,eAAe,CAAA;AACtB,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAIrC,MAAM,OAAO,GAAG,QAAQ,CAAC,UAAU,EAAE,KAAK,EAA2B;IACnE,4EAA4E;IAC5E,2EAA2E;IAC3E,gEAAgE;IAChE,MAAM,EAAE,eAAe,EAAE,GAAG,KAAK,CAAA;IACjC,MAAM,MAAM,GAAG,CAAC,KAAc,EAAE,EAAE;QAChC,KAAK,MAAM,SAAS,IAAI,eAAe,CAAC,IAAI,EAAE,EAAE,CAAC;YAC/C,KAAK,CAAC,SAAS,CAAC,SAAS,EAAE,KAAK,CAAC,CAAA;QACnC,CAAC;IACH,CAAC,CAAA;IACD,OAAO,CACL;QACE,oBAAC,MAAM,IACL,OAAO,EAAE,GAAG,EAAE;gBACZ,MAAM,CAAC,IAAI,CAAC,CAAA;YACd,CAAC,oBAGM;QAET,oBAAC,MAAM,IACL,OAAO,EAAE,GAAG,EAAE;gBACZ,MAAM,CAAC,KAAK,CAAC,CAAA;YACf,CAAC,qBAGM,CACL,CACP,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,MAAM,YAAY,GAAG,QAAQ,CAAC,UAAU,EAAE,KAAK,EAA2B;IACxE,MAAM,EAAE,eAAe,EAAE,WAAW,EAAE,WAAW,EAAE,GAAG,KAAK,CAAA;IAC3D,MAAM,MAAM,GAAG,IAAI,GAAG,EAAkB,CAAA;IACxC,KAAK,MAAM,KAAK,IAAI,WAAW,EAAE,CAAC;QAChC,MAAM,CAAC,GAAG,CAAC,KAAK,CAAC,SAAS,EAAE,CAAC,MAAM,CAAC,GAAG,CAAC,KAAK,CAAC,SAAS,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,CAAA;IACrE,CAAC;IACD,OAAO,CACL;QACE,oBAAC,OAAO,IAAC,KAAK,EAAE,KAAK,GAAI;QACzB,oBAAC,KAAK,IAAC,IAAI,EAAC,OAAO;YACjB,oBAAC,SAAS;gBACR,oBAAC,QAAQ;oBACP,oBAAC,SAAS,IAAC,OAAO,EAAC,UAAU,GAAG;oBAChC,oBAAC,SAAS,gBAAkB;oBAC5B,oBAAC,SAAS,oBAAsB;oBAChC,oBAAC,SAAS,eAAiB;oBAC3B,oBAAC,SAAS,gBAAkB;oBAC5B,oBAAC,SAAS,sBAAwB,CACzB,CACD;YACZ,oBAAC,SAAS,QACP,CAAC,GAAG,eAAe,CAAC,MAAM,EAAE,CAAC,CAAC,GAAG,CAChC,CAAC,EAAE,SAAS,EAAE,IAAI,EAAE,WAAW,EAAE,EAAE,EAAE,CAAC,CACpC,oBAAC,QAAQ,IAAC,GAAG,EAAE,SAAS;gBACtB,oBAAC,SAAS,IAAC,OAAO,EAAC,UAAU;oBAC3B,oBAAC,QAAQ,IACP,OAAO,EAAE,CAAC,KAAK,CAAC,iBAAiB,CAAC,GAAG,CAAC,SAAS,CAAC,EAChD,QAAQ,EAAE,GAAG,EAAE;4BACb,KAAK,CAAC,SAAS,CACb,SAAS,EACT,CAAC,CAAC,KAAK,CAAC,iBAAiB,CAAC,GAAG,CAAC,SAAS,CAAC,CACzC,CAAA;wBACH,CAAC,GACD,CACQ;gBACZ,oBAAC,SAAS;oBACR,6BACE,KAAK,EAAE;4BACL,KAAK,EAAE,EAAE;4BACT,MAAM,EAAE,EAAE;4BACV,UAAU,EAAE,WAAW,CAAC,SAAS,CAAC;yBACnC,GACD,CACQ;gBACZ,oBAAC,SAAS,QAAE,SAAS,CAAa;gBAClC,oBAAC,SAAS,QAAE,IAAI,CAAa;gBAC7B,oBAAC,SAAS,QAAE,MAAM,CAAC,GAAG,CAAC,SAAS,CAAC,CAAa;gBAC9C,oBAAC,SAAS,QAAE,WAAW,CAAa,CAC3B,CACZ,CACF,CACS,CACN,CACP,CACJ,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,MAAM,iBAAiB,GAAG,QAAQ,CAAC,UAAU,EAC3C,OAAO,EACP,KAAK,GAIN;IACC,OAAO,CACL,oBAAC,MAAM,IACL,OAAO,EAAE,GAAG,EAAE;YACZ,OAAO,EAAE,CAAA;QACX,CAAC,EACD,IAAI,QACJ,KAAK,EAAC,iBAAiB,EACvB,QAAQ,EAAC,IAAI;QAEb,oBAAC,aAAa;YACZ,oBAAC,YAAY,IAAC,KAAK,EAAE,KAAK,GAAI,CAChB,CACT,CACV,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,iBAAiB,CAAA"}

package/dist/components/header/Header.js

@@ -8,9 +8,11 @@ import FileMenu from './FileMenu.js';
 import GappynessSlider from './GappynessSlider.js';
 import HeaderInfoArea from './HeaderInfoArea.js';
 import HeaderStatusArea from './HeaderStatusArea.js';
+import LoadWarnings from './LoadWarnings.js';
 import MSASettingsMenu from './MSASettingsMenu.js';
 import MultiAlignmentSelector from './MultiAlignmentSelector.js';
 import TreeSettingsMenu from './TreeSettingsMenu.js';
+import UnshareableDataWarning from './UnshareableDataWarning.js';
 import ZoomControls from './ZoomControls.js';
 import ZoomMenu from './ZoomMenu.js';
 const AboutDialog = lazy(() => import('../dialogs/AboutDialog.js'));
@@ -31,6 +33,8 @@ const Header = observer(function ({ model }) {
             React.createElement(MultiAlignmentSelector, { model: model })),
         React.createElement(HeaderInfoArea, { model: model }),
         React.createElement(Spacer, null),
+        React.createElement(LoadWarnings, { model: model }),
+        React.createElement(UnshareableDataWarning, { model: model }),
         React.createElement(HeaderStatusArea, { model: model }),
         React.createElement(Tooltip, { title: "About" },
             React.createElement(IconButton, { "aria-label": "About", onClick: () => {

package/dist/components/header/Header.js.map

@@ -1 +1 @@
-{"version":3,"file":"Header.js","sourceRoot":"","sources":["../../../src/components/header/Header.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,IAAI,EAAE,SAAS,EAAE,MAAM,OAAO,CAAA;AAE9C,OAAO,UAAU,MAAM,+BAA+B,CAAA;AACtD,OAAO,IAAI,MAAM,0BAA0B,CAAA;AAC3C,OAAO,EAAE,UAAU,EAAE,OAAO,EAAE,MAAM,eAAe,CAAA;AACnD,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAErC,OAAO,eAAe,MAAM,sBAAuB,CAAA;AACnD,OAAO,QAAQ,MAAM,eAAgB,CAAA;AACrC,OAAO,eAAe,MAAM,sBAAuB,CAAA;AACnD,OAAO,cAAc,MAAM,qBAAsB,CAAA;AACjD,OAAO,gBAAgB,MAAM,uBAAwB,CAAA;AACrD,OAAO,eAAe,MAAM,sBAAuB,CAAA;AACnD,OAAO,sBAAsB,MAAM,6BAA8B,CAAA;AACjE,OAAO,gBAAgB,MAAM,uBAAwB,CAAA;AACrD,OAAO,YAAY,MAAM,mBAAoB,CAAA;AAC7C,OAAO,QAAQ,MAAM,eAAgB,CAAA;AAIrC,MAAM,WAAW,GAAG,IAAI,CAAC,GAAG,EAAE,CAAC,MAAM,CAAC,2BAA4B,CAAC,CAAC,CAAA;AAEpE,MAAM,MAAM,GAAG,QAAQ,CAAC,UAAU,EAAE,KAAK,EAA2B;IAClE,MAAM,CAAC,GAAG,EAAE,EAAE,MAAM,EAAE,CAAC,GAAG,UAAU,EAAE,CAAA;IACtC,SAAS,CAAC,GAAG,EAAE;QACb,KAAK,CAAC,eAAe,CAAC,MAAM,IAAI,CAAC,CAAC,CAAA;IACpC,CAAC,EAAE,CAAC,KAAK,EAAE,MAAM,CAAC,CAAC,CAAA;IACnB,OAAO,CACL,6BAAK,GAAG,EAAE,GAAG,EAAE,KAAK,EAAE,EAAE,OAAO,EAAE,MAAM,EAAE;QACvC,oBAAC,QAAQ,IAAC,KAAK,EAAE,KAAK,GAAI;QAC1B,oBAAC,eAAe,IAAC,KAAK,EAAE,KAAK,GAAI;QACjC,oBAAC,gBAAgB,IAAC,KAAK,EAAE,KAAK,GAAI;QAClC,oBAAC,eAAe,IAAC,KAAK,EAAE,KAAK,GAAI;QACjC,oBAAC,YAAY,IAAC,KAAK,EAAE,KAAK,GAAI;QAC9B,oBAAC,QAAQ,IAAC,KAAK,EAAE,KAAK,GAAI;QAC1B,oBAAC,eAAe,IAAC,KAAK,EAAE,KAAK,GAAI;QACjC,6BAAK,KAAK,EAAE,EAAE,WAAW,EAAE,EAAE,EAAE,MAAM,EAAE,MAAM,EAAE;YAC7C,oBAAC,sBAAsB,IAAC,KAAK,EAAE,KAAK,GAAI,CACpC;QACN,oBAAC,cAAc,IAAC,KAAK,EAAE,KAAK,GAAI;QAChC,oBAAC,MAAM,OAAG;QACV,oBAAC,gBAAgB,IAAC,KAAK,EAAE,KAAK,GAAI;QAClC,oBAAC,OAAO,IAAC,KAAK,EAAC,OAAO;YACpB,oBAAC,UAAU,kBACE,OAAO,EAClB,OAAO,EAAE,GAAG,EAAE;oBACZ,KAAK,CAAC,WAAW,CAAC,OAAO,CAAC,EAAE,CAAC,CAAC,WAAW,EAAE,EAAE,OAAO,EAAE,CAAC,CAAC,CAAA;gBAC1D,CAAC;gBAED,oBAAC,IAAI,OAAG,CACG,CACL,CACN,CACP,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,SAAS,MAAM;IACb,OAAO,6BAAK,KAAK,EAAE,EAAE,IAAI,EAAE,CAAC,EAAE,GAAI,CAAA;AACpC,CAAC;AAED,eAAe,MAAM,CAAA"}
+{"version":3,"file":"Header.js","sourceRoot":"","sources":["../../../src/components/header/Header.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,IAAI,EAAE,SAAS,EAAE,MAAM,OAAO,CAAA;AAE9C,OAAO,UAAU,MAAM,+BAA+B,CAAA;AACtD,OAAO,IAAI,MAAM,0BAA0B,CAAA;AAC3C,OAAO,EAAE,UAAU,EAAE,OAAO,EAAE,MAAM,eAAe,CAAA;AACnD,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAErC,OAAO,eAAe,MAAM,sBAAuB,CAAA;AACnD,OAAO,QAAQ,MAAM,eAAgB,CAAA;AACrC,OAAO,eAAe,MAAM,sBAAuB,CAAA;AACnD,OAAO,cAAc,MAAM,qBAAsB,CAAA;AACjD,OAAO,gBAAgB,MAAM,uBAAwB,CAAA;AACrD,OAAO,YAAY,MAAM,mBAAoB,CAAA;AAC7C,OAAO,eAAe,MAAM,sBAAuB,CAAA;AACnD,OAAO,sBAAsB,MAAM,6BAA8B,CAAA;AACjE,OAAO,gBAAgB,MAAM,uBAAwB,CAAA;AACrD,OAAO,sBAAsB,MAAM,6BAA8B,CAAA;AACjE,OAAO,YAAY,MAAM,mBAAoB,CAAA;AAC7C,OAAO,QAAQ,MAAM,eAAgB,CAAA;AAIrC,MAAM,WAAW,GAAG,IAAI,CAAC,GAAG,EAAE,CAAC,MAAM,CAAC,2BAA4B,CAAC,CAAC,CAAA;AAEpE,MAAM,MAAM,GAAG,QAAQ,CAAC,UAAU,EAAE,KAAK,EAA2B;IAClE,MAAM,CAAC,GAAG,EAAE,EAAE,MAAM,EAAE,CAAC,GAAG,UAAU,EAAE,CAAA;IACtC,SAAS,CAAC,GAAG,EAAE;QACb,KAAK,CAAC,eAAe,CAAC,MAAM,IAAI,CAAC,CAAC,CAAA;IACpC,CAAC,EAAE,CAAC,KAAK,EAAE,MAAM,CAAC,CAAC,CAAA;IACnB,OAAO,CACL,6BAAK,GAAG,EAAE,GAAG,EAAE,KAAK,EAAE,EAAE,OAAO,EAAE,MAAM,EAAE;QACvC,oBAAC,QAAQ,IAAC,KAAK,EAAE,KAAK,GAAI;QAC1B,oBAAC,eAAe,IAAC,KAAK,EAAE,KAAK,GAAI;QACjC,oBAAC,gBAAgB,IAAC,KAAK,EAAE,KAAK,GAAI;QAClC,oBAAC,eAAe,IAAC,KAAK,EAAE,KAAK,GAAI;QACjC,oBAAC,YAAY,IAAC,KAAK,EAAE,KAAK,GAAI;QAC9B,oBAAC,QAAQ,IAAC,KAAK,EAAE,KAAK,GAAI;QAC1B,oBAAC,eAAe,IAAC,KAAK,EAAE,KAAK,GAAI;QACjC,6BAAK,KAAK,EAAE,EAAE,WAAW,EAAE,EAAE,EAAE,MAAM,EAAE,MAAM,EAAE;YAC7C,oBAAC,sBAAsB,IAAC,KAAK,EAAE,KAAK,GAAI,CACpC;QACN,oBAAC,cAAc,IAAC,KAAK,EAAE,KAAK,GAAI;QAChC,oBAAC,MAAM,OAAG;QACV,oBAAC,YAAY,IAAC,KAAK,EAAE,KAAK,GAAI;QAC9B,oBAAC,sBAAsB,IAAC,KAAK,EAAE,KAAK,GAAI;QACxC,oBAAC,gBAAgB,IAAC,KAAK,EAAE,KAAK,GAAI;QAClC,oBAAC,OAAO,IAAC,KAAK,EAAC,OAAO;YACpB,oBAAC,UAAU,kBACE,OAAO,EAClB,OAAO,EAAE,GAAG,EAAE;oBACZ,KAAK,CAAC,WAAW,CAAC,OAAO,CAAC,EAAE,CAAC,CAAC,WAAW,EAAE,EAAE,OAAO,EAAE,CAAC,CAAC,CAAA;gBAC1D,CAAC;gBAED,oBAAC,IAAI,OAAG,CACG,CACL,CACN,CACP,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,SAAS,MAAM;IACb,OAAO,6BAAK,KAAK,EAAE,EAAE,IAAI,EAAE,CAAC,EAAE,GAAI,CAAA;AACpC,CAAC;AAED,eAAe,MAAM,CAAA"}

package/dist/components/header/HeaderStatusArea.js

@@ -15,8 +15,6 @@ const HeaderStatusArea = observer(({ model }) => {
     return status ? (React.createElement(Typography, { className: classes.margin },
         React.createElement(LoadingEllipses, { message: status.msg, component: "span" }),
         ' ',
-        status.url ? (React.createElement("a", { href: status.url, target: "_blank", rel: "noreferrer" }, "(status)")) : null,
-        ' ',
         status.onCancel ? (React.createElement(Button, { size: "small", onClick: () => status.onCancel?.() }, "Cancel")) : null)) : null;
 });
 export default HeaderStatusArea;

package/dist/components/header/HeaderStatusArea.js.map

@@ -1 +1 @@
-{"version":3,"file":"HeaderStatusArea.js","sourceRoot":"","sources":["../../../src/components/header/HeaderStatusArea.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,EAAE,eAAe,EAAE,MAAM,kBAAkB,CAAA;AAClD,OAAO,EAAE,UAAU,EAAE,MAAM,8BAA8B,CAAA;AACzD,OAAO,EAAE,MAAM,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAClD,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAIrC,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC;IAC7B,MAAM,EAAE;QACN,MAAM,EAAE,MAAM;QACd,UAAU,EAAE,EAAE;KACf;CACF,CAAC,CAAA;AAEF,MAAM,gBAAgB,GAAG,QAAQ,CAAC,CAAC,EAAE,KAAK,EAA2B,EAAE,EAAE;IACvE,MAAM,EAAE,MAAM,EAAE,GAAG,KAAK,CAAA;IACxB,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,OAAO,MAAM,CAAC,CAAC,CAAC,CACd,oBAAC,UAAU,IAAC,SAAS,EAAE,OAAO,CAAC,MAAM;QACnC,oBAAC,eAAe,IAAC,OAAO,EAAE,MAAM,CAAC,GAAG,EAAE,SAAS,EAAC,MAAM,GAAG;QAAC,GAAG;QAC5D,MAAM,CAAC,GAAG,CAAC,CAAC,CAAC,CACZ,2BAAG,IAAI,EAAE,MAAM,CAAC,GAAG,EAAE,MAAM,EAAC,QAAQ,EAAC,GAAG,EAAC,YAAY,eAEjD,CACL,CAAC,CAAC,CAAC,IAAI;QAAE,GAAG;QACZ,MAAM,CAAC,QAAQ,CAAC,CAAC,CAAC,CACjB,oBAAC,MAAM,IAAC,IAAI,EAAC,OAAO,EAAC,OAAO,EAAE,GAAG,EAAE,CAAC,MAAM,CAAC,QAAQ,EAAE,EAAE,aAE9C,CACV,CAAC,CAAC,CAAC,IAAI,CACG,CACd,CAAC,CAAC,CAAC,IAAI,CAAA;AACV,CAAC,CAAC,CAAA;AAEF,eAAe,gBAAgB,CAAA"}
+{"version":3,"file":"HeaderStatusArea.js","sourceRoot":"","sources":["../../../src/components/header/HeaderStatusArea.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,EAAE,eAAe,EAAE,MAAM,kBAAkB,CAAA;AAClD,OAAO,EAAE,UAAU,EAAE,MAAM,8BAA8B,CAAA;AACzD,OAAO,EAAE,MAAM,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAClD,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAIrC,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC;IAC7B,MAAM,EAAE;QACN,MAAM,EAAE,MAAM;QACd,UAAU,EAAE,EAAE;KACf;CACF,CAAC,CAAA;AAEF,MAAM,gBAAgB,GAAG,QAAQ,CAAC,CAAC,EAAE,KAAK,EAA2B,EAAE,EAAE;IACvE,MAAM,EAAE,MAAM,EAAE,GAAG,KAAK,CAAA;IACxB,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,OAAO,MAAM,CAAC,CAAC,CAAC,CACd,oBAAC,UAAU,IAAC,SAAS,EAAE,OAAO,CAAC,MAAM;QACnC,oBAAC,eAAe,IAAC,OAAO,EAAE,MAAM,CAAC,GAAG,EAAE,SAAS,EAAC,MAAM,GAAG;QAAC,GAAG;QAC5D,MAAM,CAAC,QAAQ,CAAC,CAAC,CAAC,CACjB,oBAAC,MAAM,IAAC,IAAI,EAAC,OAAO,EAAC,OAAO,EAAE,GAAG,EAAE,CAAC,MAAM,CAAC,QAAQ,EAAE,EAAE,aAE9C,CACV,CAAC,CAAC,CAAC,IAAI,CACG,CACd,CAAC,CAAC,CAAC,IAAI,CAAA;AACV,CAAC,CAAC,CAAA;AAEF,eAAe,gBAAgB,CAAA"}

package/dist/components/header/LoadWarnings.d.ts

@@ -0,0 +1,6 @@
+import React from 'react';
+import type { MsaViewModel } from '../../model.ts';
+declare const LoadWarnings: ({ model }: {
+    model: MsaViewModel;
+}) => React.JSX.Element | null;
+export default LoadWarnings;

package/dist/components/header/LoadWarnings.js

@@ -0,0 +1,36 @@
+import React from 'react';
+import { makeStyles } from '@jbrowse/core/util/tss-react';
+import Warning from '@mui/icons-material/Warning';
+import { Tooltip, Typography } from '@mui/material';
+import { observer } from 'mobx-react';
+const useStyles = makeStyles()(theme => ({
+    warning: {
+        display: 'flex',
+        alignItems: 'center',
+        gap: 4,
+        margin: 'auto',
+        marginLeft: 10,
+        whiteSpace: 'nowrap',
+        color: theme.palette.warning.main,
+        cursor: 'pointer',
+    },
+}));
+// An optional layer that failed -- a 404 on the annotations, a row-metadata
+// file that is not JSON -- used to go to `error`, which takes dataInitialized
+// down with it and replaces a perfectly good alignment with an error screen.
+// It says so here instead, and the reader dismisses it.
+const LoadWarnings = observer(function ({ model }) {
+    const { warnings } = model;
+    const { classes } = useStyles();
+    if (warnings.length === 0) {
+        return null;
+    }
+    return (React.createElement(Tooltip, { title: `${warnings.join(' ')} (click to dismiss)` },
+        React.createElement(Typography, { component: "div", className: classes.warning, onClick: () => {
+                model.clearWarnings();
+            } },
+            React.createElement(Warning, { fontSize: "small" }),
+            warnings.length > 1 ? `${warnings.length} warnings` : 'Warning')));
+});
+export default LoadWarnings;
+//# sourceMappingURL=LoadWarnings.js.map

package/dist/components/header/LoadWarnings.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"LoadWarnings.js","sourceRoot":"","sources":["../../../src/components/header/LoadWarnings.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,EAAE,UAAU,EAAE,MAAM,8BAA8B,CAAA;AACzD,OAAO,OAAO,MAAM,6BAA6B,CAAA;AACjD,OAAO,EAAE,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AACnD,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAIrC,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC;IACvC,OAAO,EAAE;QACP,OAAO,EAAE,MAAM;QACf,UAAU,EAAE,QAAQ;QACpB,GAAG,EAAE,CAAC;QACN,MAAM,EAAE,MAAM;QACd,UAAU,EAAE,EAAE;QACd,UAAU,EAAE,QAAQ;QACpB,KAAK,EAAE,KAAK,CAAC,OAAO,CAAC,OAAO,CAAC,IAAI;QACjC,MAAM,EAAE,SAAS;KAClB;CACF,CAAC,CAAC,CAAA;AAEH,4EAA4E;AAC5E,8EAA8E;AAC9E,6EAA6E;AAC7E,wDAAwD;AACxD,MAAM,YAAY,GAAG,QAAQ,CAAC,UAAU,EAAE,KAAK,EAA2B;IACxE,MAAM,EAAE,QAAQ,EAAE,GAAG,KAAK,CAAA;IAC1B,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,IAAI,QAAQ,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;QAC1B,OAAO,IAAI,CAAA;IACb,CAAC;IACD,OAAO,CACL,oBAAC,OAAO,IAAC,KAAK,EAAE,GAAG,QAAQ,CAAC,IAAI,CAAC,GAAG,CAAC,qBAAqB;QACxD,oBAAC,UAAU,IACT,SAAS,EAAC,KAAK,EACf,SAAS,EAAE,OAAO,CAAC,OAAO,EAC1B,OAAO,EAAE,GAAG,EAAE;gBACZ,KAAK,CAAC,aAAa,EAAE,CAAA;YACvB,CAAC;YAED,oBAAC,OAAO,IAAC,QAAQ,EAAC,OAAO,GAAG;YAC3B,QAAQ,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,CAAC,GAAG,QAAQ,CAAC,MAAM,WAAW,CAAC,CAAC,CAAC,SAAS,CACrD,CACL,CACX,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,YAAY,CAAA"}

package/dist/components/header/MultiAlignmentSelector.js.map

@@ -1 +1 @@
-{"version":3,"file":"MultiAlignmentSelector.js","sourceRoot":"","sources":["../../../src/components/header/MultiAlignmentSelector.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,EAAE,QAAQ,EAAE,SAAS,EAAE,MAAM,eAAe,CAAA;AACnD,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAIrC,MAAM,sBAAsB,GAAG,QAAQ,CAAC,UAAU,EAChD,KAAK,GAGN;IACC,MAAM,EAAE,gBAAgB,EAAE,cAAc,EAAE,GAAG,KAAK,CAAA;IAClD,8EAA8E;IAC9E,6EAA6E;IAC7E,2EAA2E;IAC3E,sEAAsE;IACtE,MAAM,IAAI,GAAG,IAAI,GAAG,EAAkB,CAAA;IACtC,OAAO,cAAc,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,CAAC,CACjC,oBAAC,SAAS,IACR,MAAM,QACN,OAAO,EAAC,UAAU,EAClB,KAAK,EAAE,gBAAgB,EACvB,IAAI,EAAC,OAAO,EACZ,QAAQ,EAAE,KAAK,CAAC,EAAE;YAChB,KAAK,CAAC,mBAAmB,CAAC,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC,CAAA;YAC9C,KAAK,CAAC,UAAU,CAAC,CAAC,CAAC,CAAA;YACnB,KAAK,CAAC,UAAU,CAAC,CAAC,CAAC,CAAA;QACrB,CAAC,IAEA,cAAc,CAAC,GAAG,CAAC,CAAC,MAAM,EAAE,KAAK,EAAE,EAAE;QACpC,MAAM,CAAC,GAAG,IAAI,CAAC,GAAG,CAAC,MAAM,CAAC,IAAI,CAAC,CAAA;QAC/B,IAAI,CAAC,GAAG,CAAC,MAAM,EAAE,CAAC,GAAG,CAAC,CAAC,CAAA;QACvB,OAAO,CACL,oBAAC,QAAQ,IAAC,GAAG,EAAE,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,GAAG,MAAM,IAAI,CAAC,EAAE,EAAE,KAAK,EAAE,KAAK,IAC7D,MAAM,CACE,CACZ,CAAA;IACH,CAAC,CAAC,CACQ,CACb,CAAC,CAAC,CAAC,IAAI,CAAA;AACV,CAAC,CAAC,CAAA;AACF,eAAe,sBAAsB,CAAA"}
+{"version":3,"file":"MultiAlignmentSelector.js","sourceRoot":"","sources":["../../../src/components/header/MultiAlignmentSelector.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,EAAE,QAAQ,EAAE,SAAS,EAAE,MAAM,eAAe,CAAA;AACnD,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAIrC,MAAM,sBAAsB,GAAG,QAAQ,CAAC,UAAU,EAChD,KAAK,GAGN;IACC,MAAM,EAAE,gBAAgB,EAAE,cAAc,EAAE,GAAG,KAAK,CAAA;IAClD,8EAA8E;IAC9E,6EAA6E;IAC7E,2EAA2E;IAC3E,sEAAsE;IACtE,MAAM,IAAI,GAAG,IAAI,GAAG,EAAkB,CAAA;IACtC,OAAO,cAAc,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,CAAC,CACjC,oBAAC,SAAS,IACR,MAAM,QACN,OAAO,EAAC,UAAU,EAClB,KAAK,EAAE,gBAAgB,EACvB,IAAI,EAAC,OAAO,EACZ,QAAQ,EAAE,KAAK,CAAC,EAAE;YAChB,KAAK,CAAC,mBAAmB,CAAC,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC,CAAA;QAChD,CAAC,IAEA,cAAc,CAAC,GAAG,CAAC,CAAC,MAAM,EAAE,KAAK,EAAE,EAAE;QACpC,MAAM,CAAC,GAAG,IAAI,CAAC,GAAG,CAAC,MAAM,CAAC,IAAI,CAAC,CAAA;QAC/B,IAAI,CAAC,GAAG,CAAC,MAAM,EAAE,CAAC,GAAG,CAAC,CAAC,CAAA;QACvB,OAAO,CACL,oBAAC,QAAQ,IAAC,GAAG,EAAE,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,GAAG,MAAM,IAAI,CAAC,EAAE,EAAE,KAAK,EAAE,KAAK,IAC7D,MAAM,CACE,CACZ,CAAA;IACH,CAAC,CAAC,CACQ,CACb,CAAC,CAAC,CAAC,IAAI,CAAA;AACV,CAAC,CAAC,CAAA;AACF,eAAe,sBAAsB,CAAA"}

package/dist/components/header/TreeSettingsMenu.js

@@ -2,9 +2,11 @@ import React from 'react';
 import CascadingMenuButton from '@jbrowse/core/ui/CascadingMenuButton';
 import AccountTree from '@mui/icons-material/AccountTree';
 import { observer } from 'mobx-react';
+import { maxNeighborJoiningRows } from '../../constants.js';
 import { treeSettingsMenuItems } from './settingsMenuItems.js';
 const TreeSettingsMenu = observer(function ({ model, }) {
     const { rows } = model;
+    const tooManyRows = rows.length > maxNeighborJoiningRows;
     return (React.createElement(CascadingMenuButton, { "data-testid": "tree_settings_menu", tooltip: "Tree settings", closeAfterItemClick: false, anchorOrigin: { vertical: 'bottom', horizontal: 'left' }, transformOrigin: { vertical: 'top', horizontal: 'left' }, menuItems: [
             ...treeSettingsMenuItems(model),
             ...(rows.length >= 2
@@ -14,7 +16,13 @@ const TreeSettingsMenu = observer(function ({ model, }) {
                         type: 'subMenu',
                         subMenu: [
                             {
-                                label: 'Calculate neighbor joining tree (BLOSUM62)',
+                                // the cap shows in the label rather than arriving as an
+                                // error after the click, since the click is what would
+                                // freeze the tab
+                                label: tooManyRows
+                                    ? `Calculate neighbor joining tree (over ${maxNeighborJoiningRows} rows, use FastTree)`
+                                    : 'Calculate neighbor joining tree (BLOSUM62)',
+                                disabled: tooManyRows,
                                 onClick: () => {
                                     try {
                                         model.calculateNeighborJoiningTreeFromMSA();