react-msaview 8.4.1 → 9.1.0

package/dist/components/MSAViewer.js

@@ -1,25 +1,11 @@
-import React, { useEffect, useRef, useState } from 'react';
-import { createJBrowseTheme } from '@jbrowse/core/ui/theme';
+import React, { forwardRef, useEffect, useImperativeHandle, useRef, useState, } from 'react';
 import useMeasure from '@jbrowse/core/util/useMeasure';
 import { destroy, isAlive } from '@jbrowse/mobx-state-tree';
 import { ThemeProvider } from '@mui/material/styles';
 import { compareStructural, reaction, when } from 'mobx';
 import MSAModelF from '../model.js';
+import { fileLocations, resolveTheme, viewerHighlights, viewerSnapshot, } from '../viewerSnapshot.js';
 import Loading from './Loading.js';
-function resolveTheme(theme) {
-    return createJBrowseTheme(theme === 'dark'
-        ? { palette: { mode: 'dark' } }
-        : typeof theme === 'object'
-            ? theme
-            : undefined);
-}
-function colorSchemeSnapshot(scheme) {
-    return typeof scheme === 'string'
-        ? { colorSchemeName: scheme }
-        : scheme
-            ? { customColorScheme: scheme.map }
-            : {};
-}
 function sameSource(a, b) {
     return (a.msa === b.msa &&
         a.tree === b.tree &&
@@ -29,17 +15,19 @@ function sameSource(a, b) {
 /**
  * A new alignment or tree needs a new model, so the viewer remounts when one
  * of those props changes and keeps its model across every other change,
- * including a new annotation file.
+ * including a new annotation file. A `ref` holds the current model.
  */
-export default function MSAViewer(props) {
-    const { msa, tree, msaFilehandle, treeFilehandle } = props;
+const MSAViewer = forwardRef(function MSAViewer(props, ref) {
+    const resolved = { ...props, ...fileLocations(props) };
+    const { msa, tree, msaFilehandle, treeFilehandle } = resolved;
     const source = { msa, tree, msaFilehandle, treeFilehandle };
     const [shown, setShown] = useState({ source, generation: 0 });
     if (!sameSource(shown.source, source)) {
         setShown({ source, generation: shown.generation + 1 });
     }
-    return React.createElement(Viewer, { key: shown.generation, ...props });
-}
+    return React.createElement(Viewer, { key: shown.generation, modelRef: ref, ...resolved });
+});
+export default MSAViewer;
 function useModelReaction(model, key, handler) {
     const latest = useRef(handler);
     useEffect(() => {
@@ -52,49 +40,139 @@ function useModelReaction(model, key, handler) {
         }, { equals: compareStructural })
         : undefined, [model, key, listening]);
 }
-function Viewer({ msa, tree, gff, msaFilehandle, treeFilehandle, gffFilehandle, colorScheme, height, colWidth, rowHeight, allowedGappyness, highlightColumns, highlights, features, clades, relativeTo, columnTracks, residueMappings, rowData, encodings, rowPanels, drawTree, residueEncoding, treeAreaWidth, autoTreeAreaWidth, showBranchLen, treeOrder, treeRoot, region, selection, hideHeader, theme, onCellHover, onCellClick, onViewportChange, onSelectionChange, onModel, }) {
-    const [model] = useState(() => MSAModelF().create({
-        type: 'MsaView',
-        ...(msa || tree || gff || rowData
-            ? {
-                data: {
-                    msa: msa ?? '',
-                    tree: tree ?? '',
-                    gff,
-                    // the row table is stored as this JSON string, which is what a
-                    // shared URL and the size limit already cover
-                    ...(rowData ? { treeMetadata: JSON.stringify(rowData) } : {}),
-                },
+function synced(read, apply, { inSnapshot = false } = {}) {
+    return {
+        read,
+        apply: apply,
+        inSnapshot,
+    };
+}
+function ifSet(set) {
+    return (model, value) => {
+        if (value !== undefined) {
+            set(model, value);
+        }
+    };
+}
+/**
+ * How each prop reaches the mounted model. `inSnapshot` marks a prop the
+ * snapshot already applied, so only a later change reaches its setter.
+ */
+const syncedProps = [
+    synced(p => p.height, ifSet((m, v) => {
+        m.setHeight(v);
+    })),
+    synced(p => p.colWidth, ifSet((m, v) => {
+        m.setColWidth(v);
+    })),
+    synced(p => p.rowHeight, ifSet((m, v) => {
+        m.setRowHeight(v);
+    })),
+    synced(p => p.allowedGappyness, ifSet((m, v) => {
+        m.setAllowedGappyness(v);
+    })),
+    synced(p => p.drawTree, ifSet((m, v) => {
+        m.setDrawTree(v);
+    })),
+    synced(p => p.treeAreaWidth, ifSet((m, v) => {
+        m.setTreeAreaWidth(v);
+    })),
+    synced(p => p.showBranchLen, ifSet((m, v) => {
+        m.setShowBranchLen(v);
+    })),
+    synced(p => p.treeOrder, ifSet((m, v) => {
+        m.setTreeOrder(v);
+    })),
+    synced(p => p.residueEncoding, ifSet((m, v) => {
+        m.setBgColor(v === 'fill');
+    })),
+    synced(p => !!p.hideHeader, (m, v) => {
+        m.setHideHeader(v);
+    }),
+    synced(p => p.relativeTo, (m, v) => {
+        m.drawRelativeTo(v);
+    }),
+    synced(p => p.gffFilehandle, (m, location, { gff }) => {
+        if (location) {
+            m.setGFFFilehandle(location);
+        }
+        else {
+            m.setGFF(gff);
+        }
+    }, { inSnapshot: true }),
+    synced(p => p.gff, (m, v) => {
+        m.setGFF(v);
+    }, { inSnapshot: true }),
+    synced(p => p.colorScheme, (m, scheme) => {
+        if (typeof scheme === 'string') {
+            m.setColorSchemeName(scheme);
+        }
+        else if (scheme) {
+            m.setCustomColorScheme(scheme.map);
+        }
+    }),
+    synced(viewerHighlights, (m, v) => {
+        m.setHighlights(v);
+    }),
+    synced(p => p.features ?? [], (m, v) => {
+        m.setFeatures(v);
+    }),
+    synced(p => p.selection, (m, v) => {
+        m.setSelection(v);
+    }),
+    synced(p => p.treeRoot, (m, v) => {
+        m.setTreeRoot(v);
+    }),
+    synced(p => p.clades ?? [], (m, v) => {
+        m.setClades(v);
+    }),
+    synced(p => p.columnTracks ?? [], (m, v) => {
+        m.setColumnTracks(v);
+    }),
+    synced(p => p.residueMappings ?? [], (m, v) => {
+        m.setResidueMappings(v);
+    }),
+    synced(p => p.rowData, (m, table) => {
+        if (table && Object.keys(table).length) {
+            m.setRowData(table);
+        }
+    }),
+    synced(p => p.encodings ?? [], (m, v) => {
+        m.setEncodings(v);
+    }),
+    synced(p => p.rowPanels ?? [], (m, v) => {
+        m.setRowPanels(v);
+    }),
+];
+/**
+ * Applies each prop whose content changed since the last render. Comparing
+ * JSON keys lets a host pass a freshly computed array every render, and
+ * applying only a changed prop keeps a change made inside the viewer across
+ * the host's next render. The model receives a parsed copy, never the host's
+ * own object.
+ */
+function useSyncedProps(model, props) {
+    const applied = useRef(undefined);
+    useEffect(() => {
+        const keys = syncedProps.map(({ read }) => JSON.stringify(read(props) ?? null));
+        applied.current ??= syncedProps.map(({ inSnapshot }, i) => inSnapshot ? keys[i] : '');
+        const last = applied.current;
+        syncedProps.forEach(({ apply }, i) => {
+            const key = keys[i];
+            if (last[i] !== key) {
+                last[i] = key;
+                apply(model, JSON.parse(key) ?? undefined, props);
             }
-            : {}),
-        ...(msaFilehandle ? { msaFilehandle } : {}),
-        ...(treeFilehandle ? { treeFilehandle } : {}),
-        ...(gffFilehandle ? { gffFilehandle } : {}),
-        ...colorSchemeSnapshot(colorScheme),
-        ...(height ? { height } : {}),
-        ...(colWidth ? { colWidth } : {}),
-        ...(rowHeight ? { rowHeight } : {}),
-        ...(allowedGappyness !== undefined ? { allowedGappyness } : {}),
-        ...(highlightColumns ? { highlightColumns } : {}),
-        ...(highlights ? { highlights } : {}),
-        ...(features ? { features } : {}),
-        ...(selection ? { selection } : {}),
-        ...(clades ? { clades } : {}),
-        ...(relativeTo ? { relativeTo } : {}),
-        ...(columnTracks ? { columnTracks } : {}),
-        ...(residueMappings ? { residueMappings } : {}),
-        ...(encodings ? { encodings } : {}),
-        ...(rowPanels ? { rowPanels } : {}),
-        ...(drawTree !== undefined ? { drawTree } : {}),
-        ...(treeAreaWidth ? { treeAreaWidth } : {}),
-        ...(autoTreeAreaWidth ? { autoTreeAreaWidth } : {}),
-        ...(showBranchLen !== undefined ? { showBranchLen } : {}),
-        ...(treeOrder ? { treeOrder } : {}),
-        ...(treeRoot ? { treeRoot } : {}),
-        ...(residueEncoding !== undefined
-            ? { bgColor: residueEncoding === 'fill' }
-            : {}),
-    }));
+        });
+    });
+}
+function Viewer({ modelRef, ...props }) {
+    const { region, theme, onCellHover, onCellClick, onViewportChange, onSelectionChange, onModel, } = props;
+    const [model] = useState(() => {
+        const model = MSAModelF().create(viewerSnapshot(props));
+        model.setImportForm(false);
+        return model;
+    });
     const destroyTimer = useRef(undefined);
     const [ref, { width }] = useMeasure();
     useEffect(() => {
@@ -102,150 +180,13 @@ function Viewer({ msa, tree, gff, msaFilehandle, treeFilehandle, gffFilehandle,
             model.setWidth(width);
         }
     }, [model, width]);
-    // Each effect depends only on its own prop, so a change made inside the
-    // viewer survives the host's next render.
-    useEffect(() => {
-        if (height !== undefined) {
-            model.setHeight(height);
-        }
-    }, [model, height]);
-    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]);
-    useEffect(() => {
-        if (showBranchLen !== undefined) {
-            model.setShowBranchLen(showBranchLen);
-        }
-    }, [model, showBranchLen]);
-    useEffect(() => {
-        if (treeOrder !== undefined) {
-            model.setTreeOrder(treeOrder);
-        }
-    }, [model, treeOrder]);
-    useEffect(() => {
-        if (residueEncoding !== undefined) {
-            model.setBgColor(residueEncoding === 'fill');
-        }
-    }, [model, residueEncoding]);
-    useEffect(() => {
-        model.setHideHeader(!!hideHeader);
-    }, [model, hideHeader]);
-    // unguarded, so removing the prop turns the reference diff off
-    useEffect(() => {
-        model.drawRelativeTo(relativeTo);
-    }, [model, relativeTo]);
-    // The snapshot already holds the first gff and gffFilehandle, so these
-    // effects apply only a later change. Removing either one sets the text back
-    // to the gff prop, which clears the annotations when that is absent too.
-    const appliedGff = useRef(gff);
-    const gffFilehandleKey = JSON.stringify(gffFilehandle ?? null);
-    const appliedGffFilehandle = useRef(gffFilehandleKey);
-    useEffect(() => {
-        if (appliedGffFilehandle.current !== gffFilehandleKey) {
-            appliedGffFilehandle.current = gffFilehandleKey;
-            const location = JSON.parse(gffFilehandleKey);
-            if (location) {
-                model.setGFFFilehandle(location);
-            }
-            else {
-                model.setGFF(appliedGff.current);
-            }
-        }
-    }, [model, gffFilehandleKey]);
-    useEffect(() => {
-        if (appliedGff.current !== gff) {
-            appliedGff.current = gff;
-            model.setGFF(gff);
-        }
-    }, [model, gff]);
-    // keyed by content, since a host computing a layer inline passes a new array
-    // on every render
-    const colorSchemeKey = JSON.stringify(colorScheme ?? null);
-    useEffect(() => {
-        const scheme = JSON.parse(colorSchemeKey);
-        if (typeof scheme === 'string') {
-            model.setColorSchemeName(scheme);
-        }
-        else if (scheme) {
-            model.setCustomColorScheme(scheme.map);
-        }
-    }, [model, colorSchemeKey]);
-    const highlightsKey = JSON.stringify(highlights ?? []);
-    useEffect(() => {
-        model.setHighlights(JSON.parse(highlightsKey));
-    }, [model, highlightsKey]);
-    const featuresKey = JSON.stringify(features ?? []);
-    useEffect(() => {
-        model.setFeatures(JSON.parse(featuresKey));
-    }, [model, featuresKey]);
-    const selectionKey = JSON.stringify(selection ?? null);
-    useEffect(() => {
-        model.setSelection(JSON.parse(selectionKey) ?? undefined);
-    }, [model, selectionKey]);
-    const treeRootKey = JSON.stringify(treeRoot ?? null);
-    useEffect(() => {
-        model.setTreeRoot(JSON.parse(treeRootKey) ?? undefined);
-    }, [model, treeRootKey]);
-    const cladesKey = JSON.stringify(clades ?? []);
-    useEffect(() => {
-        model.setClades(JSON.parse(cladesKey));
-    }, [model, cladesKey]);
-    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 rowDataKey = JSON.stringify(rowData ?? {});
-    useEffect(() => {
-        const table = JSON.parse(rowDataKey);
-        // an empty table leaves whatever the snapshot or a filehandle loaded
-        if (Object.keys(table).length) {
-            model.setRowData(table);
-        }
-    }, [model, rowDataKey]);
-    const encodingsKey = JSON.stringify(encodings ?? []);
-    useEffect(() => {
-        model.setEncodings(JSON.parse(encodingsKey));
-    }, [model, encodingsKey]);
-    const rowPanelsKey = JSON.stringify(rowPanels ?? []);
-    useEffect(() => {
-        model.setRowPanels(JSON.parse(rowPanelsKey));
-    }, [model, rowPanelsKey]);
-    const highlightColumnsKey = JSON.stringify(highlightColumns ?? null);
-    useEffect(() => {
-        model.setHighlightedColumns(JSON.parse(highlightColumnsKey) ?? undefined);
-    }, [model, highlightColumnsKey]);
+    useSyncedProps(model, props);
     const regionKey = JSON.stringify(region ?? null);
     useEffect(() => {
         const target = JSON.parse(regionKey);
         return target
             ? when(() => model.viewInitialized && model.numColumns > 0, () => {
-                model.zoomToRegion(target);
+                model.revealRegion(target);
             })
             : undefined;
     }, [model, regionKey]);
@@ -253,6 +194,7 @@ function Viewer({ msa, tree, gff, msaFilehandle, treeFilehandle, gffFilehandle,
     useModelReaction(model, 'clickedCell', onCellClick);
     useModelReaction(model, 'viewport', onViewportChange);
     useModelReaction(model, 'selection', onSelectionChange);
+    useImperativeHandle(modelRef, () => model, [model]);
     const latestOnModel = useRef(onModel);
     useEffect(() => {
         latestOnModel.current = onModel;

package/dist/components/MSAViewer.js.map

@@ -1 +1 @@
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+{"version":3,"file":"MSAViewer.js","sourceRoot":"","sources":["../../src/components/MSAViewer.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EACZ,UAAU,EACV,SAAS,EACT,mBAAmB,EACnB,MAAM,EACN,QAAQ,GACT,MAAM,OAAO,CAAA;AAEd,OAAO,UAAU,MAAM,+BAA+B,CAAA;AACtD,OAAO,EAAE,OAAO,EAAE,OAAO,EAAE,MAAM,0BAA0B,CAAA;AAC3D,OAAO,EAAE,aAAa,EAAE,MAAM,sBAAsB,CAAA;AACpD,OAAO,EAAE,iBAAiB,EAAE,QAAQ,EAAE,IAAI,EAAE,MAAM,MAAM,CAAA;AAExD,OAAO,SAAS,MAAM,aAAa,CAAA;AACnC,OAAO,EACL,aAAa,EACb,YAAY,EACZ,gBAAgB,EAChB,cAAc,GACf,MAAM,sBAAsB,CAAA;AAC7B,OAAO,OAAO,MAAM,cAAe,CAAA;AAkKnC,SAAS,UAAU,CAAC,CAAa,EAAE,CAAa;IAC9C,OAAO,CACL,CAAC,CAAC,GAAG,KAAK,CAAC,CAAC,GAAG;QACf,CAAC,CAAC,IAAI,KAAK,CAAC,CAAC,IAAI;QACjB,IAAI,CAAC,SAAS,CAAC,CAAC,CAAC,CAAC,aAAa,EAAE,CAAC,CAAC,cAAc,CAAC,CAAC;YACjD,IAAI,CAAC,SAAS,CAAC,CAAC,CAAC,CAAC,aAAa,EAAE,CAAC,CAAC,cAAc,CAAC,CAAC,CACtD,CAAA;AACH,CAAC;AAED;;;;GAIG;AACH,MAAM,SAAS,GAAG,UAAU,CAC1B,SAAS,SAAS,CAAC,KAAK,EAAE,GAAG;IAC3B,MAAM,QAAQ,GAAG,EAAE,GAAG,KAAK,EAAE,GAAG,aAAa,CAAC,KAAK,CAAC,EAAE,CAAA;IACtD,MAAM,EAAE,GAAG,EAAE,IAAI,EAAE,aAAa,EAAE,cAAc,EAAE,GAAG,QAAQ,CAAA;IAC7D,MAAM,MAAM,GAAG,EAAE,GAAG,EAAE,IAAI,EAAE,aAAa,EAAE,cAAc,EAAE,CAAA;IAC3D,MAAM,CAAC,KAAK,EAAE,QAAQ,CAAC,GAAG,QAAQ,CAAC,EAAE,MAAM,EAAE,UAAU,EAAE,CAAC,EAAE,CAAC,CAAA;IAC7D,IAAI,CAAC,UAAU,CAAC,KAAK,CAAC,MAAM,EAAE,MAAM,CAAC,EAAE,CAAC;QACtC,QAAQ,CAAC,EAAE,MAAM,EAAE,UAAU,EAAE,KAAK,CAAC,UAAU,GAAG,CAAC,EAAE,CAAC,CAAA;IACxD,CAAC;IACD,OAAO,oBAAC,MAAM,IAAC,GAAG,EAAE,KAAK,CAAC,UAAU,EAAE,QAAQ,EAAE,GAAG,KAAM,QAAQ,GAAI,CAAA;AACvE,CAAC,CACF,CAAA;AAED,eAAe,SAAS,CAAA;AAExB,SAAS,gBAAgB,CAGvB,KAAmB,EACnB,GAAM,EACN,OAAuD;IAEvD,MAAM,MAAM,GAAG,MAAM,CAAC,OAAO,CAAC,CAAA;IAC9B,SAAS,CAAC,GAAG,EAAE;QACb,MAAM,CAAC,OAAO,GAAG,OAAO,CAAA;IAC1B,CAAC,CAAC,CAAA;IACF,MAAM,SAAS,GAAG,CAAC,CAAC,OAAO,CAAA;IAC3B,SAAS,CACP,GAAG,EAAE,CACH,SAAS;QACP,CAAC,CAAC,QAAQ,CACN,GAAG,EAAE,CAAC,KAAK,CAAC,GAAG,CAAC,EAChB,KAAK,CAAC,EAAE;YACN,MAAM,CAAC,OAAO,EAAE,CAAC,KAAK,CAAC,CAAA;QACzB,CAAC,EACD,EAAE,MAAM,EAAE,iBAAiB,EAAE,CAC9B;QACH,CAAC,CAAC,SAAS,EACf,CAAC,KAAK,EAAE,GAAG,EAAE,SAAS,CAAC,CACxB,CAAA;AACH,CAAC;AAQD,SAAS,MAAM,CACb,IAAkC,EAClC,KAAqE,EACrE,EAAE,UAAU,GAAG,KAAK,EAAE,GAAG,EAAE;IAE3B,OAAO;QACL,IAAI;QACJ,KAAK,EAAE,KAA4B;QACnC,UAAU;KACX,CAAA;AACH,CAAC;AAED,SAAS,KAAK,CAAI,GAA4C;IAC5D,OAAO,CAAC,KAAmB,EAAE,KAAoB,EAAE,EAAE;QACnD,IAAI,KAAK,KAAK,SAAS,EAAE,CAAC;YACxB,GAAG,CAAC,KAAK,EAAE,KAAK,CAAC,CAAA;QACnB,CAAC;IACH,CAAC,CAAA;AACH,CAAC;AAED;;;GAGG;AACH,MAAM,WAAW,GAAG;IAClB,MAAM,CACJ,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,MAAM,EACb,KAAK,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE;QACb,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,CAAA;IAChB,CAAC,CAAC,CACH;IACD,MAAM,CACJ,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,QAAQ,EACf,KAAK,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE;QACb,CAAC,CAAC,WAAW,CAAC,CAAC,CAAC,CAAA;IAClB,CAAC,CAAC,CACH;IACD,MAAM,CACJ,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,SAAS,EAChB,KAAK,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE;QACb,CAAC,CAAC,YAAY,CAAC,CAAC,CAAC,CAAA;IACnB,CAAC,CAAC,CACH;IACD,MAAM,CACJ,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,gBAAgB,EACvB,KAAK,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE;QACb,CAAC,CAAC,mBAAmB,CAAC,CAAC,CAAC,CAAA;IAC1B,CAAC,CAAC,CACH;IACD,MAAM,CACJ,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,QAAQ,EACf,KAAK,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE;QACb,CAAC,CAAC,WAAW,CAAC,CAAC,CAAC,CAAA;IAClB,CAAC,CAAC,CACH;IACD,MAAM,CACJ,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,aAAa,EACpB,KAAK,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE;QACb,CAAC,CAAC,gBAAgB,CAAC,CAAC,CAAC,CAAA;IACvB,CAAC,CAAC,CACH;IACD,MAAM,CACJ,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,aAAa,EACpB,KAAK,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE;QACb,CAAC,CAAC,gBAAgB,CAAC,CAAC,CAAC,CAAA;IACvB,CAAC,CAAC,CACH;IACD,MAAM,CACJ,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,SAAS,EAChB,KAAK,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE;QACb,CAAC,CAAC,YAAY,CAAC,CAAC,CAAC,CAAA;IACnB,CAAC,CAAC,CACH;IACD,MAAM,CACJ,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,eAAe,EACtB,KAAK,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE;QACb,CAAC,CAAC,UAAU,CAAC,CAAC,KAAK,MAAM,CAAC,CAAA;IAC5B,CAAC,CAAC,CACH;IACD,MAAM,CACJ,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,UAAU,EACnB,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE;QACP,CAAC,CAAC,aAAa,CAAC,CAAC,CAAC,CAAA;IACpB,CAAC,CACF;IACD,MAAM,CACJ,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,UAAU,EACjB,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE;QACP,CAAC,CAAC,cAAc,CAAC,CAAC,CAAC,CAAA;IACrB,CAAC,CACF;IACD,MAAM,CACJ,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,aAAa,EACpB,CAAC,CAAC,EAAE,QAAQ,EAAE,EAAE,GAAG,EAAE,EAAE,EAAE;QACvB,IAAI,QAAQ,EAAE,CAAC;YACb,CAAC,CAAC,gBAAgB,CAAC,QAAQ,CAAC,CAAA;QAC9B,CAAC;aAAM,CAAC;YACN,CAAC,CAAC,MAAM,CAAC,GAAG,CAAC,CAAA;QACf,CAAC;IACH,CAAC,EACD,EAAE,UAAU,EAAE,IAAI,EAAE,CACrB;IACD,MAAM,CACJ,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,GAAG,EACV,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE;QACP,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,CAAA;IACb,CAAC,EACD,EAAE,UAAU,EAAE,IAAI,EAAE,CACrB;IACD,MAAM,CACJ,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,WAAW,EAClB,CAAC,CAAC,EAAE,MAAM,EAAE,EAAE;QACZ,IAAI,OAAO,MAAM,KAAK,QAAQ,EAAE,CAAC;YAC/B,CAAC,CAAC,kBAAkB,CAAC,MAAM,CAAC,CAAA;QAC9B,CAAC;aAAM,IAAI,MAAM,EAAE,CAAC;YAClB,CAAC,CAAC,oBAAoB,CAAC,MAAM,CAAC,GAAG,CAAC,CAAA;QACpC,CAAC;IACH,CAAC,CACF;IACD,MAAM,CAAC,gBAAgB,EAAE,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE;QAChC,CAAC,CAAC,aAAa,CAAC,CAAC,CAAC,CAAA;IACpB,CAAC,CAAC;IACF,MAAM,CACJ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package/dist/components/ResizeHandles.js

@@ -1,15 +1,16 @@
 import React, { useCallback } from 'react';
 import { observer } from 'mobx-react';
 import DragHandle from './DragHandle.js';
+const minViewHeight = 50;
 export const VerticalResizeHandle = observer(function ({ model, }) {
     const onDrag = useCallback((delta, startWidth) => {
-        model.setTreeAreaWidth(startWidth + delta);
+        model.setTreeAreaWidth(Math.min(Math.max(0, startWidth + delta), model.width - model.resizeHandleWidth));
     }, [model]);
-    return (React.createElement(DragHandle, { axis: "x", variant: "resizer", getStart: () => model.treeAreaWidth, onDrag: onDrag, style: { width: model.resizeHandleWidth } }));
+    return (React.createElement(DragHandle, { axis: "x", variant: "resizer", getStart: () => model.effectiveTreeAreaWidth, onDrag: onDrag, style: { width: model.resizeHandleWidth } }));
 });
 export const HorizontalResizeHandle = observer(function ({ model, }) {
     const onDrag = useCallback((delta, startHeight) => {
-        model.setHeight(startHeight + delta);
+        model.setHeight(Math.max(minViewHeight, startHeight + delta));
     }, [model]);
     return (React.createElement(DragHandle, { axis: "y", variant: "resizer", getStart: () => model.height, onDrag: onDrag, style: { width: '100%', height: model.resizeHandleWidth } }));
 });

package/dist/components/ResizeHandles.js.map

@@ -1 +1 @@
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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,aAAa,GAAG,EAAE,CAAA;AAExB,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,CACpB,IAAI,CAAC,GAAG,CACN,IAAI,CAAC,GAAG,CAAC,CAAC,EAAE,UAAU,GAAG,KAAK,CAAC,EAC/B,KAAK,CAAC,KAAK,GAAG,KAAK,CAAC,iBAAiB,CACtC,CACF,CAAA;IACH,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,sBAAsB,EAC5C,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,IAAI,CAAC,GAAG,CAAC,aAAa,EAAE,WAAW,GAAG,KAAK,CAAC,CAAC,CAAA;IAC/D,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,MAAM,CAAC,MAAM,iBAAiB,GAAG,QAAQ,CAAC,UAAU,EAClD,KAAK,EACL,KAAK,GAIN;IACC,MAAM,EAAE,EAAE,EAAE,SAAS,EAAE,MAAM,EAAE,GAAG,KAAK,CAAC,KAAK,CAAA;IAC7C,0EAA0E;IAC1E,uEAAuE;IACvE,4EAA4E;IAC5E,2EAA2E;IAC3E,MAAM,QAAQ,GAAG,KAAK,CAAC,cAAc,CAAC,MAAM,CAC1C,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,KAAK,CAAC,SAAS,KAAK,SAAS,CACrC,CAAA;IACD,MAAM,KAAK,GAAG,QAAQ,CAAC,MAAM,CAAA;IAC7B,MAAM,MAAM,GAAG,WAAW,CACxB,CAAC,KAAa,EAAE,WAAmB,EAAE,EAAE;QACrC,IAAI,SAAS,EAAE,CAAC;YACd,KAAK,CAAC,cAAc,CAClB,SAAS,EACT,IAAI,CAAC,GAAG,CAAC,EAAE,EAAE,WAAW,GAAG,KAAK,GAAG,KAAK,CAAC,CAC1C,CAAA;QACH,CAAC;IACH,CAAC,EACD,CAAC,KAAK,EAAE,SAAS,EAAE,KAAK,CAAC,CAC1B,CAAA;IACD,OAAO,SAAS,IAAI,QAAQ,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,EAAE,KAAK,CAAC,EAAE,KAAK,EAAE,CAAC,CAAC,CAAC,CACrD,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/Track.js

@@ -6,6 +6,7 @@ import { IconButton, Menu, MenuItem } from '@mui/material';
 import { observer } from 'mobx-react';
 import { useWheelScroll } from '../useWheelScroll.js';
 import { onMsaKey } from './msa/msaKeys.js';
+import TrackBlocks from './tracks/TrackBlocks.js';
 import TrackTooltipContent from './tracks/TrackTooltipContent.js';
 import { useTrackHover } from './tracks/useTrackHover.js';
 const TrackInfoDialog = lazy(() => import('./dialogs/TrackInfoDialog.js'));
@@ -30,7 +31,7 @@ const TrackLabel = observer(function TrackLabel({ model, track, }) {
     const closeMenu = () => {
         setAnchorEl(undefined);
     };
-    const { drawLabels, fontSize, treeAreaWidth: width } = model;
+    const { drawLabels, fontSize, effectiveTreeAreaWidth: width } = model;
     const { model: { name, height }, } = track;
     const { classes } = useStyles();
     const trackLabelHeight = Math.min(height, fontSize);
@@ -103,7 +104,7 @@ const Track = observer(function ({ model, track, }) {
             }, onMouseLeave: () => {
                 onMouseLeave();
             } },
-            React.createElement(track.ReactComponent, { model: model, track: track }),
+            React.createElement(TrackBlocks, { model: model, track: track }),
             anchor ? (React.createElement(BaseTooltip, { clientPoint: anchor.clientPoint },
                 React.createElement(TrackTooltipContent, { model: model, track: track, col: anchor.value }))) : null)));
 });

package/dist/components/Track.js.map

@@ -1 +1 @@
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package/dist/components/controls.d.ts

@@ -0,0 +1,11 @@
+export interface Control {
+    label: string;
+    action: string;
+}
+export interface KeyControl extends Control {
+    keys: string[];
+    shiftKey?: boolean;
+}
+export declare const keyboardControls: KeyControl[];
+export declare const mouseControls: Control[];
+export declare const alignmentAriaLabel: string;

package/dist/components/controls.js

@@ -0,0 +1,48 @@
+const arrows = ['ArrowLeft', 'ArrowRight', 'ArrowUp', 'ArrowDown'];
+export const keyboardControls = [
+    { label: 'Arrow keys', action: 'Scroll one cell', keys: arrows },
+    {
+        label: 'Shift + arrow keys',
+        action: 'Scroll one page',
+        keys: arrows,
+        shiftKey: true,
+    },
+    { label: '+ and -', action: 'Zoom in and out', keys: ['+', '=', '-'] },
+    {
+        label: 'Home and End',
+        action: 'Jump to the first and last column',
+        keys: ['Home', 'End'],
+    },
+    { label: 'Escape', action: 'Clear the selection', keys: ['Escape'] },
+];
+const selectCells = {
+    label: 'Shift + drag',
+    action: 'Select a block of cells',
+};
+export const mouseControls = [
+    { label: 'Drag', action: 'Pan the alignment' },
+    {
+        label: 'Wheel',
+        action: 'Scroll, or zoom as set in Alignment settings → Mouse wheel',
+    },
+    { label: 'Ctrl + wheel', action: 'Zoom at the cursor' },
+    selectCells,
+    {
+        label: 'Drag along a track',
+        action: 'Select a range of columns across every row',
+    },
+    {
+        label: 'Click a tree node',
+        action: 'Collapse, rotate, reroot or show only that clade',
+    },
+    {
+        label: 'Click the tree overview',
+        action: 'Show only the clade under the pointer',
+    },
+    { label: 'Drag a divider', action: 'Resize the tree area or a track' },
+];
+export const alignmentAriaLabel = [
+    'Alignment',
+    ...[...keyboardControls, selectCells].map(c => `${c.label}: ${c.action}`),
+].join('. ');
+//# sourceMappingURL=controls.js.map

package/dist/components/controls.js.map

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

@@ -2,18 +2,7 @@ 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));
-}
+import { annotationTextToGFF } from 'msa-parsers';
 async function fetchText(url) {
     const response = await fetch(url);
     if (!response.ok) {
@@ -71,10 +60,10 @@ const AnnotationFileDialog = observer(function ({ handleClose, model, }) {
                                 ? 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));
+                            // in the snapshot and the shared URL like every other layer. A
+                            // filehandle left set would make the snapshot drop that text
+                            model.setGFFFilehandle(undefined);
+                            model.setGFF(annotationTextToGFF(text));
                             model.setShowDomains(true);
                             handleClose();
                         }

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

@@ -1 +1 @@
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