react-msaview 8.1.0 → 8.3.0

package/dist/expandSpec.js

@@ -0,0 +1,127 @@
+/**
+ * The label a single-residue shorthand highlight gets, filled in from the
+ * sequence when drawn: `175` on a row reading R there becomes "R175".
+ */
+export const residueLabel = '{residue}{position}';
+const span = /^(\d+)(?:-(\d+))?(?:\s+(.+))?$/;
+function parseSpan(text, what) {
+    const match = span.exec(text.trim());
+    if (!match) {
+        throw new Error(`${what} "${text}" is not "start", "start-end" or either followed by a label`);
+    }
+    const a = Number(match[1]);
+    const b = match[2] === undefined ? a : Number(match[2]);
+    return { start: Math.min(a, b), end: Math.max(a, b), label: match[3] };
+}
+function withRow(entry, query) {
+    const { row, ...rest } = entry;
+    const resolved = row === undefined ? query : (row ?? undefined);
+    return resolved === undefined ? rest : { ...rest, row: resolved };
+}
+function expandHighlight(entry, query) {
+    if (typeof entry === 'object') {
+        return (entry.rows
+            ? entry
+            : withRow(entry, entry.start === undefined ? undefined : query));
+    }
+    const { start, end, label } = parseSpan(String(entry), 'highlight');
+    const single = start === end && query !== undefined;
+    return {
+        ...(query === undefined ? {} : { row: query }),
+        start,
+        end,
+        ...(label ? { label } : single ? { label: residueLabel } : {}),
+    };
+}
+function expandRegion(region, query) {
+    if (typeof region === 'string') {
+        const { start, end } = parseSpan(region, 'region');
+        const parsed = { start, end };
+        return withRow(parsed, query);
+    }
+    return withRow(region, query);
+}
+function slug(name) {
+    return name
+        .toLowerCase()
+        .replaceAll(/[^a-z0-9]+/g, '-')
+        .replaceAll(/^-|-$/g, '');
+}
+function kindOf(track) {
+    if (track.kind) {
+        return track.kind;
+    }
+    if (track.values) {
+        return 'bar';
+    }
+    if (track.data !== undefined) {
+        return 'text';
+    }
+    if (track.arcs) {
+        return 'arc';
+    }
+    throw new Error(`column track "${track.name}" has no values, data or arcs to take its kind from`);
+}
+function expandTrack(track, query, ids) {
+    const { start, ...rest } = track;
+    const pad = start && start > 1 ? start - 1 : 0;
+    let id = track.id ?? (slug(track.name) || 'track');
+    for (let n = 2; !track.id && ids.has(id); n++) {
+        id = `${slug(track.name) || 'track'}-${n}`;
+    }
+    ids.add(id);
+    return {
+        ...withRow(rest, query),
+        id,
+        kind: kindOf(track),
+        ...(pad && track.values
+            ? { values: [...Array(pad).fill(0), ...track.values] }
+            : {}),
+        ...(pad && track.data !== undefined
+            ? { data: ' '.repeat(pad) + track.data }
+            : {}),
+    };
+}
+function isInlineMsa(msa) {
+    return msa.includes('\n');
+}
+function isInlineTree(tree) {
+    return tree.trimStart().startsWith('(');
+}
+function uri(location) {
+    return { uri: location, locationType: 'UriLocation' };
+}
+/**
+ * Expand the short forms of an MsaView spec into the snapshot the model takes.
+ * Idempotent, and a no-op on a spec that uses none of them.
+ */
+export function expandSpec(spec) {
+    const { query, msa, tree, highlights, region, columnTracks, ...rest } = spec;
+    const data = {
+        ...rest.data,
+        ...(msa !== undefined && isInlineMsa(msa) ? { msa } : {}),
+        ...(tree !== undefined && isInlineTree(tree) ? { tree } : {}),
+    };
+    const ids = new Set((columnTracks ?? []).map(t => t.id).filter(id => id !== undefined));
+    return {
+        ...rest,
+        ...(msa !== undefined && !isInlineMsa(msa)
+            ? { msaFilehandle: uri(msa) }
+            : {}),
+        ...(tree !== undefined && !isInlineTree(tree)
+            ? { treeFilehandle: uri(tree) }
+            : {}),
+        ...(Object.keys(data).length > 0 ? { data } : {}),
+        ...(query !== undefined && rest.relativeTo === undefined
+            ? { relativeTo: query }
+            : {}),
+        ...(highlights
+            ? { highlights: highlights.map(h => expandHighlight(h, query)) }
+            : {}),
+        ...(region === undefined ? {} : { region: expandRegion(region, query) }),
+        ...(columnTracks
+            ? { columnTracks: columnTracks.map(t => expandTrack(t, query, ids)) }
+            : {}),
+    };
+}
+//# sourceMappingURL=expandSpec.js.map

package/dist/expandSpec.js.map

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

@@ -1,6 +1,6 @@
 import type { FileLocation } from '@jbrowse/core/util/types';
 /**
- * The name to save an export under: the loaded alignment's file name with the
- * extension swapped, or a plain default when the alignment was pasted in.
+ * The name to save an export under: the loaded file's name with the extension
+ * swapped, or `fallback` when the data was pasted in.
  */
-export declare function exportFileName(location: FileLocation | undefined, extension: string): string;
+export declare function exportFileName(location: FileLocation | undefined, extension: string, fallback?: string): string;

package/dist/exportFileName.js

@@ -1,8 +1,8 @@
 /**
- * The name to save an export under: the loaded alignment's file name with the
- * extension swapped, or a plain default when the alignment was pasted in.
+ * The name to save an export under: the loaded file's name with the extension
+ * swapped, or `fallback` when the data was pasted in.
  */
-export function exportFileName(location, extension) {
+export function exportFileName(location, extension, fallback = 'image') {
     const loc = location;
     const path = loc?.uri ?? loc?.localPath ?? loc?.name;
     const base = path
@@ -10,6 +10,6 @@ export function exportFileName(location, extension) {
         ?.split(/[/\\]/)
         .pop()
         ?.replace(/\.[^.]*$/, '');
-    return `${base || 'image'}.${extension}`;
+    return `${base || fallback}.${extension}`;
 }
 //# sourceMappingURL=exportFileName.js.map

package/dist/exportFileName.js.map

@@ -1 +1 @@
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+{"version":3,"file":"exportFileName.js","sourceRoot":"","sources":["../src/exportFileName.ts"],"names":[],"mappings":"AAEA;;;GAGG;AACH,MAAM,UAAU,cAAc,CAC5B,QAAkC,EAClC,SAAiB,EACjB,QAAQ,GAAG,OAAO;IAElB,MAAM,GAAG,GAAG,QAEC,CAAA;IACb,MAAM,IAAI,GAAG,GAAG,EAAE,GAAG,IAAI,GAAG,EAAE,SAAS,IAAI,GAAG,EAAE,IAAI,CAAA;IACpD,MAAM,IAAI,GAAG,IAAI;QACf,EAAE,KAAK,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC;QAClB,EAAE,KAAK,CAAC,OAAO,CAAC;SACf,GAAG,EAAE;QACN,EAAE,OAAO,CAAC,UAAU,EAAE,EAAE,CAAC,CAAA;IAC3B,OAAO,GAAG,IAAI,IAAI,QAAQ,IAAI,SAAS,EAAE,CAAA;AAC3C,CAAC"}

package/dist/hierarchy.d.ts

@@ -24,6 +24,57 @@ export { descendants, find, forEachDescendant, forEachLink, leaves, links, sort,
 export type { HierarchyLink } from '@gmod/newick';
 export declare function hierarchy<T>(data: T, childrenAccessor: (d: T) => T[] | undefined): HierarchyNode<T>;
 export declare function clusterLayout<T>(root: HierarchyNode<T>, sizeX: number, sizeY: number): void;
+export interface TreeScale {
+    readonly rowHeight: number;
+    readonly treeWidth: number;
+}
+interface LayoutFrame {
+    scale: TreeScale;
+    rootToTipLength: number;
+}
+/**
+ * A node of `layoutTree`: its source node's fields plus its place in unit
+ * space, rows down and branch length across. The pixel getters multiply by the
+ * scale on every read, so a zoom leaves the nodes valid, and an observer
+ * reading `x` observes whatever the scale reads.
+ */
+export declare class LaidOutNode<T> implements HierarchyNode<T> {
+    readonly parent: LaidOutNode<T> | null;
+    private readonly frame;
+    data: T;
+    depth: number;
+    height: number;
+    value?: number;
+    children: LaidOutNode<T>[] | null;
+    depthToLeaf: number;
+    row: number;
+    rowMin: number;
+    rowMax: number;
+    depthFraction: number;
+    branchLength: number;
+    collapsedBranchLength?: number;
+    constructor(source: HierarchyNode<T>, parent: LaidOutNode<T> | null, frame: LayoutFrame);
+    private get pxPerBranchLength();
+    get x(): number;
+    get xMin(): number;
+    get xMax(): number;
+    get y(): number;
+    get len(): number;
+    get collapsedTipXFar(): number | undefined;
+}
+/**
+ * The layout `clusterLayout` and `setBrLength` write, on new nodes: tips one
+ * row apart, a parent at the mean of its children, and branch length measured
+ * from the root, whose own branch is not drawn. A collapsed node records the
+ * farthest tip of its hidden subtree, where the base of its triangle goes.
+ */
+export declare function layoutTree<T extends {
+    length?: number;
+}>(root: HierarchyNode<T>, scale: TreeScale): {
+    root: LaidOutNode<T>;
+    leaves: LaidOutNode<T>[];
+    rootToTipLength: number;
+};
 export declare function collapse<T>(node: HierarchyNode<T>): void;
 export declare function collapsedSubtreeMaxLength<T extends {
     length?: number;

package/dist/hierarchy.js

@@ -50,6 +50,131 @@ export function clusterLayout(root, sizeX, sizeY) {
         }
     }
 }
+/**
+ * A node of `layoutTree`: its source node's fields plus its place in unit
+ * space, rows down and branch length across. The pixel getters multiply by the
+ * scale on every read, so a zoom leaves the nodes valid, and an observer
+ * reading `x` observes whatever the scale reads.
+ */
+export class LaidOutNode {
+    parent;
+    frame;
+    data;
+    depth;
+    height;
+    value;
+    children;
+    depthToLeaf = 0;
+    row = 0;
+    rowMin = 0;
+    rowMax = 0;
+    depthFraction = 0;
+    branchLength = 0;
+    collapsedBranchLength;
+    constructor(source, parent, frame) {
+        this.parent = parent;
+        this.frame = frame;
+        this.data = source.data;
+        this.depth = source.depth;
+        this.height = source.height;
+        this.value = source.value;
+        this.children = source.children ? [] : null;
+    }
+    get pxPerBranchLength() {
+        const { scale, rootToTipLength } = this.frame;
+        return rootToTipLength ? scale.treeWidth / rootToTipLength : 0;
+    }
+    get x() {
+        return this.row * this.frame.scale.rowHeight;
+    }
+    get xMin() {
+        return this.rowMin * this.frame.scale.rowHeight;
+    }
+    get xMax() {
+        return this.rowMax * this.frame.scale.rowHeight;
+    }
+    get y() {
+        return this.depthFraction * this.frame.scale.treeWidth;
+    }
+    get len() {
+        return this.branchLength * this.pxPerBranchLength;
+    }
+    get collapsedTipXFar() {
+        return this.collapsedBranchLength === undefined
+            ? undefined
+            : this.collapsedBranchLength * this.pxPerBranchLength;
+    }
+}
+/**
+ * The layout `clusterLayout` and `setBrLength` write, on new nodes: tips one
+ * row apart, a parent at the mean of its children, and branch length measured
+ * from the root, whose own branch is not drawn. A collapsed node records the
+ * farthest tip of its hidden subtree, where the base of its triangle goes.
+ */
+export function layoutTree(root, scale) {
+    const frame = { scale, rootToTipLength: 0 };
+    const nodes = [];
+    const leafNodes = [];
+    const rootHeight = root.height;
+    const stack = [
+        { source: root, parent: null },
+    ];
+    while (stack.length > 0) {
+        const { source, parent } = stack.pop();
+        const node = new LaidOutNode(source, parent, frame);
+        nodes.push(node);
+        node.depthFraction =
+            rootHeight === 0 ? 1 : (source.depth - root.depth) / rootHeight;
+        if (parent) {
+            parent.children.push(node);
+            node.branchLength =
+                parent.branchLength + Math.max(source.data.length || 0, 0);
+            frame.rootToTipLength = Math.max(frame.rootToTipLength, node.branchLength);
+        }
+        if (source._children) {
+            node.collapsedBranchLength =
+                node.branchLength + collapsedSubtreeMaxLength(source);
+        }
+        if (source.children) {
+            for (let i = source.children.length - 1; i >= 0; i--) {
+                stack.push({ source: source.children[i], parent: node });
+            }
+        }
+        else {
+            node.row = leafNodes.length + 0.5;
+            node.depthToLeaf = source.depthToLeaf ?? 0;
+            leafNodes.push(node);
+        }
+    }
+    for (let i = nodes.length - 1; i >= 0; i--) {
+        const node = nodes[i];
+        if (node.children) {
+            let sum = 0;
+            let min = Infinity;
+            let max = -Infinity;
+            let depthToLeaf = 0;
+            for (const child of node.children) {
+                sum += child.row;
+                min = Math.min(min, child.rowMin);
+                max = Math.max(max, child.rowMax);
+                depthToLeaf = Math.max(depthToLeaf, 1 + child.depthToLeaf);
+            }
+            node.row = sum / node.children.length;
+            node.rowMin = min;
+            node.rowMax = max;
+            node.depthToLeaf = depthToLeaf;
+        }
+        else {
+            node.rowMin = node.row;
+            node.rowMax = node.row;
+        }
+    }
+    return {
+        root: nodes[0],
+        leaves: leafNodes,
+        rootToTipLength: frame.rootToTipLength,
+    };
+}
 export function collapse(node) {
     if (node.children) {
         // memoize the real subtree depth onto the node before detaching its

package/dist/hierarchy.js.map

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package/dist/index.d.ts

@@ -2,6 +2,8 @@ export { renderToSvg } from './renderToSvg.tsx';
 export type { ExportSvgOptions } from './renderToSvg.tsx';
 export { CHAR_WIDTH_RATIO, installHeadlessRenderEnv, } from './headlessRenderEnv.ts';
 export { maxNeighborJoiningRows } from './constants.ts';
+export { expandSpec, residueLabel } from './expandSpec.ts';
+export type { ColumnTrackShorthand, HighlightShorthand, MsaSpec, RegionShorthand, } from './expandSpec.ts';
 export { default as MSAView } from './components/Loading.tsx';
 export { default as MSAViewer } from './components/MSAViewer.tsx';
 export type { MSAViewerProps } from './components/MSAViewer.tsx';
@@ -12,9 +14,9 @@ export type { MsaSvgFigure } from './useMsaSvgFigure.ts';
 export type { MountedViewer } from './mount.tsx';
 export { type MsaViewModel, default as MSAModelF } from './model.ts';
 export type { MSAFormat, MSAParserType } from 'msa-parsers';
-export type { HierarchyNode } from './hierarchy.ts';
+export type { HierarchyNode, LaidOutNode, TreeScale } from './hierarchy.ts';
 export type { InterProScanResults } from 'msa-parsers';
 export type { ColumnCounts } from './columnCounts.ts';
 export type { ColumnStats } from './columnStats.ts';
 export type { ResolvedScale, ScaleSpec } from './scales.ts';
-export type { Accession, Annotation, Arc, ArcSpec, ArcTrackModel, BasicTrack, BasicTrackModel, Cell, Clade, CladeMark, ColumnTrackSpec, DomainBand, Encoding, EncodingChannel, Highlight, Legend, LegendEntry, Node, MappedStructure, NodeWithIds, NodeWithIdsAndLength, Region, ResidueEncoding, ResidueMapping, ResidueMappingProblem, ResidueSegment, ResolvedClade, ResolvedEncoding, ResolvedHighlight, ResolvedRowPanel, RowPanelSpec, RowResidue, StructureResidue, TextTrackModel, TidyDomainAnnotation, TrackKind, UnshareableData, Viewport, } from './types.ts';
+export type { Accession, Annotation, Arc, ArcSpec, ArcTrackModel, BasicTrack, BasicTrackModel, Cell, Clade, CladeMark, ColumnTrackSpec, DomainBand, Encoding, EncodingChannel, Highlight, Legend, LegendEntry, Node, MappedStructure, NodeWithIds, NodeWithIdsAndLength, Region, ResidueEncoding, ResidueMapping, ResidueMappingProblem, ResidueSegment, ResolvedClade, ResolvedEncoding, ResolvedHighlight, ResolvedRowPanel, RowPanelSpec, RowResidue, StructureResidue, TextTrackModel, TidyDomainAnnotation, TrackKind, TreeOrder, TreeRoot, UnshareableData, Viewport, } from './types.ts';

package/dist/index.js

@@ -14,6 +14,8 @@ export { CHAR_WIDTH_RATIO, installHeadlessRenderEnv, } from './headlessRenderEnv
 // the row count above which calculateNeighborJoiningTreeFromMSA throws, for
 // hosts gating their own menu item
 export { maxNeighborJoiningRows } from './constants.js';
+// the short forms a link or a script can write a view in; see docs/layers.md
+export { expandSpec, residueLabel } from './expandSpec.js';
 export { default as MSAView } from './components/Loading.js';
 export { default as MSAViewer } from './components/MSAViewer.js';
 export { mount } from './mount.js';

package/dist/index.js.map

@@ -1 +1 @@
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package/dist/model/treeModel.d.ts

@@ -1,3 +1,4 @@
+import type { TreeOrder } from '../types.ts';
 /**
  * #stateModel Tree
  */
@@ -29,6 +30,13 @@ export declare function TreeModelF(): import("@jbrowse/mobx-state-tree").IModelT
      * account evolutionary distances
      */
     showBranchLen: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+    /**
+     * #property
+     * the order each node's children draw in: `branchLength` (shortest
+     * first), `input` (as the file gives them), `ladderize` (fewest tips
+     * first) or `ladderizeReverse` (most tips first)
+     */
+    treeOrder: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<TreeOrder>, [undefined]>;
     /**
      * #property
      * draw tree, boolean
@@ -90,6 +98,10 @@ export declare function TreeModelF(): import("@jbrowse/mobx-state-tree").IModelT
      * #action
      */
     setShowBranchLen(arg: boolean): void;
+    /**
+     * #action
+     */
+    setTreeOrder(order: TreeOrder): void;
     /**
      * #action
      */

package/dist/model/treeModel.js

@@ -1,5 +1,5 @@
 import { types } from '@jbrowse/mobx-state-tree';
-import { defaultDrawLabels, defaultDrawNodeBubbles, defaultDrawNodeLabels, defaultDrawTree, defaultLabelsAlignRight, defaultOverviewHeight, defaultShowBranchLen, defaultShowTreeOverview, defaultTreeAreaWidth, defaultTreeWidth, } from '../constants.js';
+import { defaultDrawLabels, defaultDrawNodeBubbles, defaultDrawNodeLabels, defaultDrawTree, defaultLabelsAlignRight, defaultOverviewHeight, defaultShowBranchLen, defaultTreeOrder, defaultShowTreeOverview, defaultTreeAreaWidth, defaultTreeWidth, treeOrders, } from '../constants.js';
 import { stripDefault } from '../stripDefault.js';
 /**
  * #stateModel Tree
@@ -34,6 +34,13 @@ export function TreeModelF() {
          * account evolutionary distances
          */
         showBranchLen: stripDefault(types.boolean, defaultShowBranchLen),
+        /**
+         * #property
+         * the order each node's children draw in: `branchLength` (shortest
+         * first), `input` (as the file gives them), `ladderize` (fewest tips
+         * first) or `ladderizeReverse` (most tips first)
+         */
+        treeOrder: stripDefault(types.enumeration('TreeOrder', [...treeOrders]), defaultTreeOrder),
         /**
          * #property
          * draw tree, boolean
@@ -108,6 +115,12 @@ export function TreeModelF() {
         setShowBranchLen(arg) {
             self.showBranchLen = arg;
         },
+        /**
+         * #action
+         */
+        setTreeOrder(order) {
+            self.treeOrder = order;
+        },
         /**
          * #action
          */

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