react-msaview 9.0.0 → 9.1.1

package/dist/treeDisplay.js

@@ -0,0 +1,209 @@
+import { generateNodeIds, parseEmfTree, parseNewick } from 'msa-parsers';
+import { cladeHighlightAlpha, cladeHighlightColor } from './constants.js';
+import { flatToTree } from './flatToTree.js';
+import { collapse, find, forEachDescendant, hierarchy, leafIndex, leaves, mrca, sort, sum as hierarchySum, } from './hierarchy.js';
+import { parseAsn1 } from './parseAsn1.js';
+import { midpointRoot, preorder, rerootTree } from './rerootTree.js';
+import { withAlpha } from './util.js';
+export function parseTreeText(text) {
+    if (text.startsWith('BioTreeContainer')) {
+        return flatToTree(parseAsn1(text));
+    }
+    return parseNewick(text.startsWith('SEQ') ? parseEmfTree(text).tree : text);
+}
+// the marks that set tree state from a node rather than drawing
+const seedingMarks = new Set(['collapse', 'focus', 'rotate']);
+/**
+ * Each tip of the full tree in the order the tree draws it, with the on-screen
+ * row that shows it: its own, or the row of the collapsed node standing for it
+ */
+function tipRows(root) {
+    const rows = new Map();
+    let row = 0;
+    const pushReversed = (stack, nodes) => {
+        for (let i = nodes.length - 1; i >= 0; i--) {
+            stack.push(nodes[i]);
+        }
+    };
+    const stack = [root];
+    while (stack.length > 0) {
+        const node = stack.pop();
+        if (node.children?.length) {
+            pushReversed(stack, node.children);
+        }
+        else {
+            const hidden = [node];
+            while (hidden.length > 0) {
+                const tip = hidden.pop();
+                const kids = tip.children ?? tip._children;
+                if (kids?.length) {
+                    pushReversed(hidden, kids);
+                }
+                else {
+                    rows.set(tip.data.name, { order: rows.size, row });
+                }
+            }
+            row++;
+        }
+    }
+    return rows;
+}
+/**
+ * The rows a clade covers and the node an `mrca` names, or undefined when the
+ * clade does not resolve: a tip name the tree does not have or has twice, or a
+ * leaf count `tips` disagrees with. A `range` counts its tips in the order
+ * `tips` gives them, so a collapsed clade inside it counts every leaf it
+ * stands for. `index` is the memoized leaf pass over the tree.
+ */
+function cladeRows(clade, root, index, tips) {
+    if (clade.range) {
+        const [a, b] = clade.range.map(name => index.get(name) ? tips.get(name) : undefined);
+        if (a === undefined || b === undefined) {
+            return undefined;
+        }
+        const [first, last] = a.order <= b.order ? [a, b] : [b, a];
+        return last.order - first.order + 1 === clade.tips
+            ? { rows: [first.row, last.row] }
+            : undefined;
+    }
+    const node = clade.mrca ? mrca(root, clade.mrca, index) : undefined;
+    if (!node) {
+        return undefined;
+    }
+    const nodeTips = leaves(node);
+    if (nodeTips.length !== clade.tips) {
+        return undefined;
+    }
+    let first = Infinity;
+    let last = -Infinity;
+    for (const tip of nodeTips) {
+        const row = tips.get(tip.data.name)?.row;
+        if (row !== undefined) {
+            first = Math.min(first, row);
+            last = Math.max(last, row);
+        }
+    }
+    return first <= last
+        ? { rows: [first, last], nodeId: node.data.id }
+        : undefined;
+}
+/**
+ * Every clade that resolves, with its fill color settled, against the rows of
+ * `displayed`, the tree as drawn. The tree panel resolves against the
+ * displayed rows and the overview against its own, so both take the tree they
+ * draw. A `range` record names no node, so the seeding marks, which need one,
+ * drop it.
+ */
+export function resolveClades(clades, root, displayed) {
+    const index = leafIndex(root);
+    const tips = tipRows(displayed);
+    return clades.flatMap(clade => {
+        const resolved = cladeRows(clade, root, index, tips);
+        const seeding = seedingMarks.has(clade.mark);
+        return resolved && !(seeding && resolved.nodeId === undefined)
+            ? [
+                {
+                    ...resolved,
+                    mark: clade.mark,
+                    color: withAlpha(clade.color ?? cladeHighlightColor, cladeHighlightAlpha),
+                    markColor: clade.color,
+                    label: clade.label,
+                },
+            ]
+            : [];
+    });
+}
+const childOrders = {
+    input: undefined,
+    branchLength: (a, b) => (a.data.length ?? 1) - (b.data.length ?? 1),
+    ladderize: (a, b) => a.value - b.value,
+    ladderizeReverse: (a, b) => b.value - a.value,
+};
+/**
+ * The tree with the display transforms applied: leaf counts summed, children
+ * put in `order` and each `rotated` node's reversed, `showOnly` taken as the
+ * new root, and each `collapsed` clade folded. The overview builds the same
+ * tree without the focus, so it shows the focused subtree inside the whole.
+ */
+export function buildTreeRoot(tree, { collapsed, rotated, order, showOnly, }) {
+    let hier = hierarchy(tree, d => d.children);
+    hierarchySum(hier, d => (d.children.length > 0 ? 0 : 1));
+    const compare = childOrders[order];
+    if (compare) {
+        sort(hier, compare);
+    }
+    if (rotated.length > 0) {
+        const flip = new Set(rotated);
+        forEachDescendant(hier, n => {
+            if (flip.has(n.data.id)) {
+                n.children?.reverse();
+            }
+        });
+    }
+    if (showOnly) {
+        const res = find(hier, n => n.data.id === showOnly);
+        if (res) {
+            hier = res;
+        }
+    }
+    for (const collapsedId of collapsed) {
+        const node = find(hier, n => n.data.id === collapsedId);
+        if (node) {
+            if (node.children) {
+                collapse(node);
+            }
+            else if (node.parent?.children) {
+                node.parent.children = node.parent.children.filter(c => c.data.id !== collapsedId);
+            }
+        }
+    }
+    return hier;
+}
+/**
+ * The node whose branch an outgroup roots the tree on: the outgroup's most
+ * recent common ancestor, or the rest of the tips' where that ancestor is the
+ * root, since the outgroup then straddles the root and the branch above the
+ * other side is the same branch of the unrooted tree.
+ */
+export function outgroupNode(root, outgroup) {
+    const index = leafIndex(root);
+    const node = mrca(root, outgroup, index);
+    if (node !== root) {
+        return node;
+    }
+    const out = new Set(outgroup);
+    const rest = leaves(root)
+        .map(n => n.data.name)
+        .filter(name => !out.has(name));
+    const other = mrca(root, rest, index);
+    return other === root ? undefined : other;
+}
+/**
+ * `tree` rerooted as `treeRoot` asks, with fresh path ids. The ids of the tree
+ * as written become names on unnamed nodes, and a rerooting would carry them
+ * along as labels, so they come off first.
+ */
+export function rootTree(tree, treeRoot) {
+    const plain = new Map();
+    for (const node of preorder(tree).reverse()) {
+        plain.set(node, {
+            name: node.name === node.id ? undefined : node.name,
+            length: node.length,
+            children: node.children.map(c => plain.get(c)),
+        });
+    }
+    const input = plain.get(tree);
+    if (treeRoot === 'midpoint') {
+        return generateNodeIds(midpointRoot(input));
+    }
+    const target = outgroupNode(hierarchy(tree, d => d.children), treeRoot.outgroup);
+    return target
+        ? generateNodeIds(rerootTree(input, plain.get(target.data)))
+        : tree;
+}
+// the inclusive tip indices a node covers, from its xMin/xMax in a layout one
+// row per tip
+export function tipRange(node) {
+    return [Math.round(node.xMin - 0.5), Math.round(node.xMax - 0.5)];
+}
+//# sourceMappingURL=treeDisplay.js.map

package/dist/treeDisplay.js.map

@@ -0,0 +1 @@
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package/dist/types.d.ts

@@ -21,11 +21,9 @@ export type ColorScheme = string | Required<Pick<ScaleSpec, 'map'>>;
 export interface BasicTrackModel {
     id: string;
     name: string;
-    associatedRowName?: string;
     height: number;
     kind: TrackKind;
     heightKey?: string;
-    defaultOff?: boolean;
 }
 export interface TextTrackModel extends BasicTrackModel {
     customColorScheme?: Record<string, string>;
@@ -44,7 +42,6 @@ export interface ArcTrackModel extends BasicTrackModel {
     arcColor?: string;
 }
 export interface BasicTrack {
-    ReactComponent: React.FC<any>;
     model: TextTrackModel & BarTrackModel & ArcTrackModel;
 }
 export interface ArcSpec {
@@ -171,6 +168,12 @@ export interface MappedStructure {
     id: string;
     kind?: 'experimental' | 'predicted';
     asymId?: string;
+    /**
+     * which id `asymId` is, the file's `label_asym_id` or the author's
+     * `auth_asym_id`. Unset reads as either, label first, which is right for the
+     * common entry whose two ids agree and wrong where they collide.
+     */
+    asymIdKind?: 'label' | 'auth';
     url?: string;
 }
 /**

package/dist/useWheelScroll.d.ts

@@ -1,8 +1,10 @@
-export declare function useWheelScroll({ ref, onScrollX, onScrollY, onZoom, scrollZoom, }: {
+export declare function useWheelScroll({ ref, onScrollX, onScrollY, onZoom, onZoomSettle, onWheelScroll, scrollZoom, }: {
     ref: React.RefObject<HTMLDivElement | null>;
     onScrollX?: (delta: number) => void;
     onScrollY?: (delta: number) => void;
     onZoom?: (scaleFactor: number, offsetX: number, offsetY: number) => void;
+    onZoomSettle?: () => void;
+    onWheelScroll?: (event: WheelEvent) => void;
     scrollZoom?: boolean;
 }): {
     onMouseDown: (event: React.MouseEvent) => void;

package/dist/useWheelScroll.js

@@ -1,11 +1,13 @@
 import { useEffect, useRef, useState } from 'react';
-import { SCROLL_ZOOM_DIVISOR, getZoomNormalizer, normalizeWheelDelta, zoomFactorFromAccum, } from './wheelZoom.js';
-export function useWheelScroll({ ref, onScrollX, onScrollY, onZoom, scrollZoom, }) {
+import { WheelZoomSmoother } from './wheelZoom.js';
+const zoomSettleMs = 150;
+export function useWheelScroll({ ref, onScrollX, onScrollY, onZoom, onZoomSettle, onWheelScroll, scrollZoom, }) {
     const scheduled = useRef(false);
-    const zoomScheduled = useRef(false);
+    const zoomFrame = useRef(undefined);
+    const zoomSettle = useRef(undefined);
     const deltaX = useRef(0);
     const deltaY = useRef(0);
-    const zoomAccum = useRef(0);
+    const zoomSmoother = useRef(new WheelZoomSmoother());
     const zoomX = useRef(0);
     const zoomY = useRef(0);
     const lastZoomTime = useRef(null);
@@ -26,23 +28,26 @@ export function useWheelScroll({ ref, onScrollX, onScrollY, onZoom, scrollZoom,
                 !event.shiftKey &&
                 Math.abs(event.deltaY) >= Math.abs(event.deltaX);
             if (onZoom && (isCtrlZoom || isScrollZoom)) {
+                const zoom = onZoom;
                 const rect = curr.getBoundingClientRect();
-                // normalize away deltaMode (line/page), then divide by an adaptive
-                // factor so fine pinches and coarse notches feel consistent
-                const dY = normalizeWheelDelta(event.deltaY, event.deltaMode);
-                const divisor = isCtrlZoom ? getZoomNormalizer(dY) : SCROLL_ZOOM_DIVISOR;
-                zoomAccum.current += dY / divisor;
+                zoomSmoother.current.add(event.deltaY, event.deltaMode, isCtrlZoom);
                 zoomX.current = event.clientX - rect.left;
                 zoomY.current = event.clientY - rect.top;
-                if (!zoomScheduled.current) {
-                    zoomScheduled.current = true;
-                    requestAnimationFrame(now => {
+                if (zoomFrame.current === undefined) {
+                    lastZoomTime.current = null;
+                    const frame = (now) => {
                         const elapsed = lastZoomTime.current === null ? 16.67 : now - lastZoomTime.current;
                         lastZoomTime.current = now;
-                        onZoom(zoomFactorFromAccum(zoomAccum.current, Math.min(100, elapsed)), zoomX.current, zoomY.current);
-                        zoomAccum.current = 0;
-                        zoomScheduled.current = false;
-                    });
+                        zoom(zoomSmoother.current.step(Math.min(100, elapsed)), zoomX.current, zoomY.current);
+                        clearTimeout(zoomSettle.current);
+                        zoomSettle.current = setTimeout(() => {
+                            onZoomSettle?.();
+                        }, zoomSettleMs);
+                        zoomFrame.current = zoomSmoother.current.idle
+                            ? undefined
+                            : requestAnimationFrame(frame);
+                    };
+                    zoomFrame.current = requestAnimationFrame(frame);
                 }
                 event.preventDefault();
                 event.stopPropagation();
@@ -53,6 +58,7 @@ export function useWheelScroll({ ref, onScrollX, onScrollY, onZoom, scrollZoom,
             const consumeX = !!onScrollX && event.deltaX !== 0;
             const consumeY = !!onScrollY && event.deltaY !== 0;
             if (consumeX || consumeY) {
+                onWheelScroll?.(event);
                 if (onScrollX) {
                     deltaX.current += event.deltaX;
                 }
@@ -80,8 +86,21 @@ export function useWheelScroll({ ref, onScrollX, onScrollY, onZoom, scrollZoom,
         curr.addEventListener('wheel', onWheel, { passive: false });
         return () => {
             curr.removeEventListener('wheel', onWheel);
+            if (zoomFrame.current !== undefined) {
+                cancelAnimationFrame(zoomFrame.current);
+                zoomFrame.current = undefined;
+            }
+            clearTimeout(zoomSettle.current);
         };
-    }, [ref, onScrollX, onScrollY, onZoom, scrollZoom]);
+    }, [
+        ref,
+        onScrollX,
+        onScrollY,
+        onZoom,
+        onZoomSettle,
+        onWheelScroll,
+        scrollZoom,
+    ]);
     useEffect(() => {
         if (!mouseDragging) {
             return;

package/dist/useWheelScroll.js.map

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package/dist/util.d.ts

@@ -23,3 +23,5 @@ export declare function len(a: {
     end: number;
     start: number;
 }): number;
+/** reads computeds so a reaction observes them, which keeps them cached */
+export declare function readComputed(..._values: unknown[]): void;

package/dist/util.js

@@ -127,4 +127,6 @@ export function computeRowInsertions(blanks, seq) {
 export function len(a) {
     return a.end - a.start;
 }
+/** reads computeds so a reaction observes them, which keeps them cached */
+export function readComputed(..._values) { }
 //# sourceMappingURL=util.js.map

package/dist/util.js.map

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

@@ -1 +1 @@
-export declare const version = "9.0.0";
+export declare const version = "9.1.1";

package/dist/version.js

@@ -1,2 +1,2 @@
-export const version = '9.0.0';
+export const version = '9.1.1';
 //# sourceMappingURL=version.js.map

package/dist/viewerSnapshot.d.ts

@@ -0,0 +1,169 @@
+import type { MSAViewerProps } from './components/MSAViewer.tsx';
+import type { ColorScheme, Highlight } from './types.ts';
+export declare function colorSchemeSnapshot(scheme: ColorScheme | undefined): {
+    colorSchemeName: string;
+    customColorScheme?: undefined;
+} | {
+    colorSchemeName?: undefined;
+    customColorScheme: Record<string, string>;
+} | {
+    colorSchemeName?: undefined;
+    customColorScheme?: undefined;
+};
+/**
+ * The `highlightColumns` prop as `highlights`: one `{start, end}` per run of
+ * adjacent 1-based alignment columns
+ */
+export declare function columnHighlights(columns?: number[]): {
+    start: number;
+    end: number;
+}[];
+export declare function viewerHighlights({ highlights, highlightColumns, }: Pick<MSAViewerProps, 'highlights' | 'highlightColumns'>): Highlight[];
+/** each filehandle prop, or the URL prop standing in for it */
+export declare function fileLocations({ msaFilehandle, treeFilehandle, gffFilehandle, msaUrl, treeUrl, gffUrl, }: MSAViewerProps): {
+    msaFilehandle: import("@jbrowse/core/util").BlobLocation | import("@jbrowse/core/util").FileHandleLocation | import("@jbrowse/core/util").LocalPathLocation | {
+        uri: string;
+        locationType: 'UriLocation';
+    } | undefined;
+    treeFilehandle: import("@jbrowse/core/util").BlobLocation | import("@jbrowse/core/util").FileHandleLocation | import("@jbrowse/core/util").LocalPathLocation | {
+        uri: string;
+        locationType: 'UriLocation';
+    } | undefined;
+    gffFilehandle: import("@jbrowse/core/util").BlobLocation | import("@jbrowse/core/util").FileHandleLocation | import("@jbrowse/core/util").LocalPathLocation | {
+        uri: string;
+        locationType: 'UriLocation';
+    } | undefined;
+};
+export declare function resolveTheme(theme: MSAViewerProps['theme']): import("@mui/material").Theme;
+/**
+ * The model snapshot `MSAViewer` creates from its props. The CLI's `--props`
+ * reads the same JSON the R and Python widgets send, so a figure exported
+ * headlessly draws what the widget drew.
+ */
+export declare function viewerSnapshot(props: MSAViewerProps): {
+    colorSchemeName: string;
+    customColorScheme?: undefined;
+    type: 'MsaView';
+    data?: {
+        msa: string;
+        tree: string;
+        gff: string | undefined;
+        treeMetadata?: string | undefined;
+    } | undefined;
+    msaFilehandle?: import("@jbrowse/core/util").BlobLocation | import("@jbrowse/core/util").FileHandleLocation | import("@jbrowse/core/util").LocalPathLocation | {
+        uri: string;
+        locationType: 'UriLocation';
+    } | undefined;
+    treeFilehandle?: import("@jbrowse/core/util").BlobLocation | import("@jbrowse/core/util").FileHandleLocation | import("@jbrowse/core/util").LocalPathLocation | {
+        uri: string;
+        locationType: 'UriLocation';
+    } | undefined;
+    gffFilehandle?: import("@jbrowse/core/util").BlobLocation | import("@jbrowse/core/util").FileHandleLocation | import("@jbrowse/core/util").LocalPathLocation | {
+        uri: string;
+        locationType: 'UriLocation';
+    } | undefined;
+    height?: number | undefined;
+    colWidth?: number | undefined;
+    rowHeight?: number | undefined;
+    allowedGappyness?: number | undefined;
+    highlights?: Highlight[] | undefined;
+    features?: import("./types.ts").Feature[] | undefined;
+    selection?: import("./types.ts").MsaSelection | undefined;
+    clades?: import("./types.ts").Clade[] | undefined;
+    relativeTo?: string | undefined;
+    columnTracks?: import("./types.ts").ColumnTrackSpec[] | undefined;
+    residueMappings?: import("./types.ts").ResidueMapping[] | undefined;
+    encodings?: import("./types.ts").Encoding[] | undefined;
+    rowPanels?: import("./types.ts").RowPanelSpec[] | undefined;
+    drawTree?: boolean | undefined;
+    treeAreaWidth?: number | undefined;
+    showBranchLen?: boolean | undefined;
+    treeOrder?: import("./types.ts").TreeOrder | undefined;
+    treeRoot?: import("./types.ts").TreeRoot | undefined;
+    region?: import("./types.ts").Region | undefined;
+    bgColor?: boolean | undefined;
+} | {
+    colorSchemeName?: undefined;
+    customColorScheme: Record<string, string>;
+    type: 'MsaView';
+    data?: {
+        msa: string;
+        tree: string;
+        gff: string | undefined;
+        treeMetadata?: string | undefined;
+    } | undefined;
+    msaFilehandle?: import("@jbrowse/core/util").BlobLocation | import("@jbrowse/core/util").FileHandleLocation | import("@jbrowse/core/util").LocalPathLocation | {
+        uri: string;
+        locationType: 'UriLocation';
+    } | undefined;
+    treeFilehandle?: import("@jbrowse/core/util").BlobLocation | import("@jbrowse/core/util").FileHandleLocation | import("@jbrowse/core/util").LocalPathLocation | {
+        uri: string;
+        locationType: 'UriLocation';
+    } | undefined;
+    gffFilehandle?: import("@jbrowse/core/util").BlobLocation | import("@jbrowse/core/util").FileHandleLocation | import("@jbrowse/core/util").LocalPathLocation | {
+        uri: string;
+        locationType: 'UriLocation';
+    } | undefined;
+    height?: number | undefined;
+    colWidth?: number | undefined;
+    rowHeight?: number | undefined;
+    allowedGappyness?: number | undefined;
+    highlights?: Highlight[] | undefined;
+    features?: import("./types.ts").Feature[] | undefined;
+    selection?: import("./types.ts").MsaSelection | undefined;
+    clades?: import("./types.ts").Clade[] | undefined;
+    relativeTo?: string | undefined;
+    columnTracks?: import("./types.ts").ColumnTrackSpec[] | undefined;
+    residueMappings?: import("./types.ts").ResidueMapping[] | undefined;
+    encodings?: import("./types.ts").Encoding[] | undefined;
+    rowPanels?: import("./types.ts").RowPanelSpec[] | undefined;
+    drawTree?: boolean | undefined;
+    treeAreaWidth?: number | undefined;
+    showBranchLen?: boolean | undefined;
+    treeOrder?: import("./types.ts").TreeOrder | undefined;
+    treeRoot?: import("./types.ts").TreeRoot | undefined;
+    region?: import("./types.ts").Region | undefined;
+    bgColor?: boolean | undefined;
+} | {
+    colorSchemeName?: undefined;
+    customColorScheme?: undefined;
+    type: 'MsaView';
+    data?: {
+        msa: string;
+        tree: string;
+        gff: string | undefined;
+        treeMetadata?: string | undefined;
+    } | undefined;
+    msaFilehandle?: import("@jbrowse/core/util").BlobLocation | import("@jbrowse/core/util").FileHandleLocation | import("@jbrowse/core/util").LocalPathLocation | {
+        uri: string;
+        locationType: 'UriLocation';
+    } | undefined;
+    treeFilehandle?: import("@jbrowse/core/util").BlobLocation | import("@jbrowse/core/util").FileHandleLocation | import("@jbrowse/core/util").LocalPathLocation | {
+        uri: string;
+        locationType: 'UriLocation';
+    } | undefined;
+    gffFilehandle?: import("@jbrowse/core/util").BlobLocation | import("@jbrowse/core/util").FileHandleLocation | import("@jbrowse/core/util").LocalPathLocation | {
+        uri: string;
+        locationType: 'UriLocation';
+    } | undefined;
+    height?: number | undefined;
+    colWidth?: number | undefined;
+    rowHeight?: number | undefined;
+    allowedGappyness?: number | undefined;
+    highlights?: Highlight[] | undefined;
+    features?: import("./types.ts").Feature[] | undefined;
+    selection?: import("./types.ts").MsaSelection | undefined;
+    clades?: import("./types.ts").Clade[] | undefined;
+    relativeTo?: string | undefined;
+    columnTracks?: import("./types.ts").ColumnTrackSpec[] | undefined;
+    residueMappings?: import("./types.ts").ResidueMapping[] | undefined;
+    encodings?: import("./types.ts").Encoding[] | undefined;
+    rowPanels?: import("./types.ts").RowPanelSpec[] | undefined;
+    drawTree?: boolean | undefined;
+    treeAreaWidth?: number | undefined;
+    showBranchLen?: boolean | undefined;
+    treeOrder?: import("./types.ts").TreeOrder | undefined;
+    treeRoot?: import("./types.ts").TreeRoot | undefined;
+    region?: import("./types.ts").Region | undefined;
+    bgColor?: boolean | undefined;
+};