react-msaview 8.2.0 → 8.4.0

package/dist/constants.js.map

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

@@ -1,9 +1,13 @@
 /**
  * Registers a custom element that renders MSAViewer, for pages with no React.
  * Attributes: msa-url, tree-url, gff-url, color-scheme, height, hide-header,
- * theme, tree-area-width and reference-row. Properties: msa, tree and gff text, highlights,
- * columnTracks and residueMappings. Events: cell-hover, cell-click and
- * viewport-change, each with the MSAViewer callback's value as detail.
+ * theme, tree-area-width and reference-row. Properties: msa, tree and gff text,
+ * features, colorScheme, highlights, columnTracks, residueMappings and
+ * selection. The
+ * colorScheme property takes a `{map}` the color-scheme attribute cannot hold,
+ * and wins over the attribute while set. Events: cell-hover, cell-click,
+ * viewport-change and selection-change, each with the MSAViewer callback's
+ * value as detail.
  *
  * Inside a <nightingale-manager>, the element registers with it and speaks its
  * protocol: it follows the display-start, display-end and highlight attributes

package/dist/element.js

@@ -48,9 +48,13 @@ function residueRange(model, row, viewport) {
 /**
  * Registers a custom element that renders MSAViewer, for pages with no React.
  * Attributes: msa-url, tree-url, gff-url, color-scheme, height, hide-header,
- * theme, tree-area-width and reference-row. Properties: msa, tree and gff text, highlights,
- * columnTracks and residueMappings. Events: cell-hover, cell-click and
- * viewport-change, each with the MSAViewer callback's value as detail.
+ * theme, tree-area-width and reference-row. Properties: msa, tree and gff text,
+ * features, colorScheme, highlights, columnTracks, residueMappings and
+ * selection. The
+ * colorScheme property takes a `{map}` the color-scheme attribute cannot hold,
+ * and wins over the attribute while set. Events: cell-hover, cell-click,
+ * viewport-change and selection-change, each with the MSAViewer callback's
+ * value as detail.
  *
  * Inside a <nightingale-manager>, the element registers with it and speaks its
  * protocol: it follows the display-start, display-end and highlight attributes
@@ -89,6 +93,18 @@ export function defineMsaElement(tagName = 'jbrowse-msa') {
         set gff(value) {
             this.#setData({ gff: value });
         }
+        get features() {
+            return this.#data.features;
+        }
+        set features(value) {
+            this.#setData({ features: value });
+        }
+        get colorScheme() {
+            return this.#data.colorScheme;
+        }
+        set colorScheme(value) {
+            this.#setData({ colorScheme: value });
+        }
         get highlights() {
             return this.#data.highlights;
         }
@@ -107,6 +123,13 @@ export function defineMsaElement(tagName = 'jbrowse-msa') {
         set residueMappings(value) {
             this.#setData({ residueMappings: value });
         }
+        // the viewer's selection, which the reader's drags change
+        get selection() {
+            return this.#model ? this.#model.selection : this.#data.selection;
+        }
+        set selection(value) {
+            this.#setData({ selection: value });
+        }
         get #referenceRow() {
             return this.getAttribute('reference-row') ?? undefined;
         }
@@ -121,7 +144,9 @@ export function defineMsaElement(tagName = 'jbrowse-msa') {
                 msaFilehandle: location(this.getAttribute('msa-url')),
                 treeFilehandle: location(this.getAttribute('tree-url')),
                 gffFilehandle: location(this.getAttribute('gff-url')),
-                colorScheme: this.getAttribute('color-scheme') ?? undefined,
+                colorScheme: this.#data.colorScheme ??
+                    this.getAttribute('color-scheme') ??
+                    undefined,
                 height: numberAttribute(this.getAttribute('height')),
                 treeAreaWidth: numberAttribute(this.getAttribute('tree-area-width')),
                 hideHeader: this.hasAttribute('hide-header'),
@@ -137,6 +162,9 @@ export function defineMsaElement(tagName = 'jbrowse-msa') {
                     this.#emit('viewport-change', viewport);
                     this.#reportRange(viewport);
                 },
+                onSelectionChange: selection => {
+                    this.#emit('selection-change', selection);
+                },
                 onModel: model => {
                     this.#model = model;
                     this.#followRange();

package/dist/element.js.map

@@ -1 +1 @@
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package/dist/expandSpec.js

@@ -9,9 +9,9 @@ function parseSpan(text, what) {
     if (!match) {
         throw new Error(`${what} "${text}" is not "start", "start-end" or either followed by a label`);
     }
-    const start = Number(match[1]);
-    const end = match[2] === undefined ? start : Number(match[2]);
-    return { start, end, label: match[3] };
+    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;

package/dist/expandSpec.js.map

@@ -1 +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/featuresLayer.d.ts

@@ -0,0 +1,8 @@
+import type { Annotation, Feature } from './types.ts';
+/**
+ * The `features` layer as the annotations a GFF would parse to. Every field
+ * but the placement is also an attribute, as a string like a GFF value, so an
+ * encoding reads `type` or a host's own field the way it reads a GFF column 9
+ * key.
+ */
+export declare function featuresToAnnotations(features: Feature[]): Annotation[];

package/dist/featuresLayer.js

@@ -0,0 +1,42 @@
+const placement = new Set(['row', 'start', 'end']);
+// The colors and labels are maps keyed by annotation, and a getter read
+// outside a reaction recomputes on every read. Caching on the frozen feature
+// gives it one annotation however often the layer converts.
+const converted = new WeakMap();
+/**
+ * The `features` layer as the annotations a GFF would parse to. Every field
+ * but the placement is also an attribute, as a string like a GFF value, so an
+ * encoding reads `type` or a host's own field the way it reads a GFF column 9
+ * key.
+ */
+export function featuresToAnnotations(features) {
+    return features.map(feature => {
+        const cached = converted.get(feature);
+        if (cached) {
+            return cached;
+        }
+        const annotation = featureAnnotation(feature);
+        converted.set(feature, annotation);
+        return annotation;
+    });
+}
+function featureAnnotation(feature) {
+    const { row, start, end, name, description, type, strand, color } = feature;
+    const accession = name ?? `${row}:${start}-${end}`;
+    const attributes = Object.fromEntries(Object.entries(feature)
+        .filter(([key, value]) => !placement.has(key) && value !== undefined)
+        .map(([key, value]) => [key, String(value)]));
+    return {
+        id: row,
+        accession,
+        name: name ?? accession,
+        description: description ?? name ?? accession,
+        featureType: type,
+        start,
+        end,
+        strand: strand === '+' ? 1 : strand === '-' ? -1 : undefined,
+        color,
+        attributes,
+    };
+}
+//# sourceMappingURL=featuresLayer.js.map

package/dist/featuresLayer.js.map

@@ -0,0 +1 @@
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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

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package/dist/index.d.ts

@@ -14,9 +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, ColorScheme, ColumnTrackSpec, DomainBand, Encoding, EncodingChannel, Feature, Highlight, Legend, LegendEntry, MsaSelection, Node, MappedStructure, NodeWithIds, NodeWithIdsAndLength, Region, ResidueEncoding, ResidueMapping, ResidueMappingProblem, ResidueSegment, ResolvedClade, ResolvedEncoding, ResolvedHighlight, ResolvedRowPanel, ResolvedSelection, RowDataInput, RowPanelSpec, RowResidue, StructureResidue, TextTrackModel, TidyDomainAnnotation, TrackKind, TreeOrder, TreeRoot, UnshareableData, Viewport, } from './types.ts';

package/dist/model/DataModel.d.ts

@@ -5,7 +5,7 @@
  * data will not be persisted in saved session snapshots, it will be fetched
  * from msaFilehandle at startup
  */
-export declare function DataModelF(): import("@jbrowse/mobx-state-tree").IModelType<{
+export declare function DataModelF(maxInlineBytes?: number): import("@jbrowse/mobx-state-tree").IModelType<{
     /**
      * #property
      */

package/dist/model/DataModel.js

@@ -7,7 +7,7 @@ import { maxInlineSnapshotBytes } from '../constants.js';
  * data will not be persisted in saved session snapshots, it will be fetched
  * from msaFilehandle at startup
  */
-export function DataModelF() {
+export function DataModelF(maxInlineBytes = maxInlineSnapshotBytes) {
     return types
         .model({
         /**
@@ -54,11 +54,11 @@ export function DataModelF() {
         },
     }))
         .postProcessSnapshot(snap => 
-    // drops any field over maxInlineSnapshotBytes; the parent model's
+    // drops any field over maxInlineBytes; the parent model's
     // `unshareableData` reports what was dropped
     Object.fromEntries(Object.entries(snap).map(([key, text]) => [
         key,
-        text && text.length > maxInlineSnapshotBytes ? undefined : text,
+        text && text.length > maxInlineBytes ? undefined : text,
     ])));
 }
 //# sourceMappingURL=DataModel.js.map

package/dist/model/DataModel.js.map

@@ -1 +1 @@
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+{"version":3,"file":"DataModel.js","sourceRoot":"","sources":["../../src/model/DataModel.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,KAAK,EAAE,MAAM,0BAA0B,CAAA;AAEhD,OAAO,EAAE,sBAAsB,EAAE,MAAM,iBAAiB,CAAA;AAExD;;;;;;GAMG;AACH,MAAM,UAAU,UAAU,CAAC,cAAc,GAAG,sBAAsB;IAChE,OAAO,KAAK;SACT,KAAK,CAAC;QACL;;WAEG;QACH,IAAI,EAAE,KAAK,CAAC,KAAK,CAAC,KAAK,CAAC,MAAM,CAAC;QAC/B;;WAEG;QACH,GAAG,EAAE,KAAK,CAAC,KAAK,CAAC,KAAK,CAAC,MAAM,CAAC;QAC9B;;WAEG;QACH,YAAY,EAAE,KAAK,CAAC,KAAK,CAAC,KAAK,CAAC,MAAM,CAAC;QACvC;;WAEG;QACH,GAAG,EAAE,KAAK,CAAC,KAAK,CAAC,KAAK,CAAC,MAAM,CAAC;KAC/B,CAAC;SACD,OAAO,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QAChB;;WAEG;QACH,OAAO,CAAC,IAAa;YACnB,IAAI,CAAC,IAAI,GAAG,IAAI,CAAA;QAClB,CAAC;QACD;;WAEG;QACH,MAAM,CAAC,GAAY;YACjB,IAAI,CAAC,GAAG,GAAG,GAAG,CAAA;QAChB,CAAC;QACD;;WAEG;QACH,eAAe,CAAC,YAAqB;YACnC,IAAI,CAAC,YAAY,GAAG,YAAY,CAAA;QAClC,CAAC;QACD;;WAEG;QACH,MAAM,CAAC,GAAY;YACjB,IAAI,CAAC,GAAG,GAAG,GAAG,CAAA;QAChB,CAAC;KACF,CAAC,CAAC;SACF,mBAAmB,CAAC,IAAI,CAAC,EAAE;IAC1B,0DAA0D;IAC1D,6CAA6C;IAC7C,MAAM,CAAC,WAAW,CAChB,MAAM,CAAC,OAAO,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,GAAG,EAAE,IAAI,CAAC,EAAE,EAAE,CAAC;QACxC,GAAG;QACH,IAAI,IAAI,IAAI,CAAC,MAAM,GAAG,cAAc,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI;KACxD,CAAC,CACH,CACF,CAAA;AACL,CAAC"}

package/dist/model/msaModel.d.ts

@@ -13,6 +13,12 @@ export declare function MSAModelF(): import("@jbrowse/mobx-state-tree").IModelTy
      * default color scheme name
      */
     colorSchemeName: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
+    /**
+     * #property
+     * a color per residue letter, which replaces the `colorSchemeName` table
+     * while set. A letter the map leaves out takes no color
+     */
+    customColorScheme: import("@jbrowse/mobx-state-tree").IType<Record<string, string> | undefined, Record<string, string> | undefined, Record<string, string> | undefined>;
     /**
      * #property
      * show a tooltip with the hovered column's value for a track while
@@ -29,9 +35,16 @@ export declare function MSAModelF(): import("@jbrowse/mobx-state-tree").IModelTy
 }, {
     /**
      * #action
-     * set color scheme name
+     * pick a scheme from the built-in table, which clears
+     * `customColorScheme`
      */
     setColorSchemeName(name: string): void;
+    /**
+     * #action
+     * color residues from a map of letter to color, or pass undefined to
+     * return to `colorSchemeName`
+     */
+    setCustomColorScheme(map?: Record<string, string>): void;
     /**
      * #action
      */