react-msaview 6.5.0 → 8.0.0

package/dist/element.js

@@ -0,0 +1,269 @@
+import { when } from 'mobx';
+import { mount } from './mount.js';
+const ownAttributes = [
+    'msa-url',
+    'tree-url',
+    'gff-url',
+    'color-scheme',
+    'height',
+    'hide-header',
+    'theme',
+    'reference-row',
+    'tree-area-width',
+];
+// the attributes a <nightingale-manager> writes on the elements it holds
+const nightingaleAttributes = ['display-start', 'display-end', 'highlight'];
+function location(uri) {
+    return uri ? { uri, locationType: 'UriLocation' } : undefined;
+}
+function numberAttribute(value) {
+    const n = value ? Number(value) : Number.NaN;
+    return Number.isFinite(n) ? n : undefined;
+}
+// Nightingale writes a highlight as "start:end,start:end", 1-based inclusive
+function parseHighlight(value, row) {
+    return (value ?? '').split(',').flatMap(span => {
+        const [start, end] = span.split(':').map(numberAttribute);
+        return start === undefined ? [] : [{ row, start, end: end ?? start }];
+    });
+}
+function residueAtColumn(model, row, column) {
+    const visible = model.globalColToVisibleCol(column - 1);
+    return visible === undefined
+        ? undefined
+        : model.visibleColToSeqPosOneBased(row, visible);
+}
+// the first and last residues of `row` inside the viewport's columns
+function residueRange(model, row, viewport) {
+    let start;
+    let end;
+    for (let c = viewport.startColumn; c <= viewport.endColumn && !start; c++) {
+        start = residueAtColumn(model, row, c);
+    }
+    for (let c = viewport.endColumn; c >= viewport.startColumn && !end; c--) {
+        end = residueAtColumn(model, row, c);
+    }
+    return start && end ? { start, end } : undefined;
+}
+/**
+ * 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.
+ *
+ * Inside a <nightingale-manager>, the element registers with it and speaks its
+ * protocol: it follows the display-start, display-end and highlight attributes
+ * the manager writes, and reports its own range and hovered residue as change
+ * events. Positions are residues of reference-row, or columns without one.
+ */
+export function defineMsaElement(tagName = 'jbrowse-msa') {
+    const existing = customElements.get(tagName);
+    if (existing) {
+        return existing;
+    }
+    class MsaElement extends HTMLElement {
+        static observedAttributes = [...ownAttributes, ...nightingaleAttributes];
+        #viewer;
+        #model;
+        #manager;
+        #cancelRange;
+        #rangePending = false;
+        #reported;
+        #data = {};
+        get msa() {
+            return this.#data.msa;
+        }
+        set msa(value) {
+            this.#setData({ msa: value });
+        }
+        get tree() {
+            return this.#data.tree;
+        }
+        set tree(value) {
+            this.#setData({ tree: value });
+        }
+        get gff() {
+            return this.#data.gff;
+        }
+        set gff(value) {
+            this.#setData({ gff: value });
+        }
+        get highlights() {
+            return this.#data.highlights;
+        }
+        set highlights(value) {
+            this.#setData({ highlights: value });
+        }
+        get columnTracks() {
+            return this.#data.columnTracks;
+        }
+        set columnTracks(value) {
+            this.#setData({ columnTracks: value });
+        }
+        get residueMappings() {
+            return this.#data.residueMappings;
+        }
+        set residueMappings(value) {
+            this.#setData({ residueMappings: value });
+        }
+        get #referenceRow() {
+            return this.getAttribute('reference-row') ?? undefined;
+        }
+        #setData(data) {
+            this.#data = { ...this.#data, ...data };
+            this.#viewer?.update(this.#props());
+        }
+        #props() {
+            const theme = this.getAttribute('theme');
+            return {
+                ...this.#data,
+                msaFilehandle: location(this.getAttribute('msa-url')),
+                treeFilehandle: location(this.getAttribute('tree-url')),
+                gffFilehandle: location(this.getAttribute('gff-url')),
+                colorScheme: this.getAttribute('color-scheme') ?? undefined,
+                height: numberAttribute(this.getAttribute('height')),
+                treeAreaWidth: numberAttribute(this.getAttribute('tree-area-width')),
+                hideHeader: this.hasAttribute('hide-header'),
+                theme: theme === 'dark' ? 'dark' : 'light',
+                onCellHover: cell => {
+                    this.#emit('cell-hover', cell);
+                    this.#reportHover(cell);
+                },
+                onCellClick: cell => {
+                    this.#emit('cell-click', cell);
+                },
+                onViewportChange: viewport => {
+                    this.#emit('viewport-change', viewport);
+                    this.#reportRange(viewport);
+                },
+                onModel: model => {
+                    this.#model = model;
+                    this.#followRange();
+                    this.#followHighlight();
+                },
+            };
+        }
+        #emit(type, detail) {
+            this.dispatchEvent(new CustomEvent(type, { detail }));
+        }
+        #nightingaleChange(detail) {
+            if (this.#manager) {
+                this.dispatchEvent(new CustomEvent('change', {
+                    detail,
+                    bubbles: true,
+                    cancelable: true,
+                }));
+            }
+        }
+        #reportHover(cell) {
+            const model = this.#model;
+            const row = this.#referenceRow;
+            const position = cell && model && row
+                ? residueAtColumn(model, row, cell.column)
+                : cell?.column;
+            this.#nightingaleChange({
+                type: 'highlight',
+                value: position === undefined ? null : `${position}:${position}`,
+            });
+        }
+        #reportRange(viewport) {
+            const model = this.#model;
+            const row = this.#referenceRow;
+            if (!viewport || !model) {
+                return;
+            }
+            const range = row
+                ? residueRange(model, row, viewport)
+                : { start: viewport.startColumn, end: viewport.endColumn };
+            const shownStart = numberAttribute(this.getAttribute('display-start'));
+            const shownEnd = numberAttribute(this.getAttribute('display-end'));
+            // a range the manager just wrote comes back within a column of itself,
+            // since the viewer shows whole columns
+            const echo = range &&
+                shownStart !== undefined &&
+                shownEnd !== undefined &&
+                Math.abs(range.start - shownStart) <= 1 &&
+                Math.abs(range.end - shownEnd) <= 1;
+            if (range && !echo) {
+                this.#reported = range;
+                this.#nightingaleChange({
+                    'display-start': range.start,
+                    'display-end': range.end,
+                });
+            }
+        }
+        #followRange() {
+            const model = this.#model;
+            const start = numberAttribute(this.getAttribute('display-start'));
+            const end = numberAttribute(this.getAttribute('display-end'));
+            const reported = this.#reported;
+            // the manager writes the range this element reported back onto it, and
+            // zooming to it again would snap the reader's own zoom to whole residues
+            if (reported && reported.start === start && reported.end === end) {
+                return;
+            }
+            this.#cancelRange?.();
+            if (model && start !== undefined && end !== undefined) {
+                const row = this.#referenceRow;
+                this.#cancelRange = when(() => model.viewInitialized && model.numColumns > 0, () => {
+                    model.zoomToRegion({ row, start, end });
+                });
+            }
+        }
+        #followHighlight() {
+            const spans = parseHighlight(this.getAttribute('highlight'), this.#referenceRow);
+            if (spans.length) {
+                this.#model?.applyHighlight('nightingale', spans);
+            }
+            else {
+                this.#model?.clearHighlight('nightingale');
+            }
+        }
+        connectedCallback() {
+            if (!this.style.display) {
+                this.style.display = 'block';
+            }
+            this.#viewer = mount(this, this.#props());
+            const manager = this.closest('nightingale-manager');
+            if (manager) {
+                void customElements.whenDefined('nightingale-manager').then(() => {
+                    if (this.isConnected) {
+                        this.#manager = manager;
+                        manager.register(this);
+                    }
+                });
+            }
+        }
+        disconnectedCallback() {
+            this.#manager?.unregister(this);
+            this.#manager = undefined;
+            this.#cancelRange?.();
+            this.#viewer?.destroy();
+            this.#viewer = undefined;
+            this.#model = undefined;
+        }
+        attributeChangedCallback(name) {
+            if (name === 'display-start' || name === 'display-end') {
+                // the manager writes the two attributes one after the other, and a
+                // zoom between them reports a range that overwrites the second
+                if (!this.#rangePending) {
+                    this.#rangePending = true;
+                    queueMicrotask(() => {
+                        this.#rangePending = false;
+                        this.#followRange();
+                    });
+                }
+            }
+            else if (name === 'highlight') {
+                this.#followHighlight();
+            }
+            else {
+                this.#viewer?.update(this.#props());
+            }
+        }
+    }
+    customElements.define(tagName, MsaElement);
+    return MsaElement;
+}
+//# sourceMappingURL=element.js.map

package/dist/element.js.map

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package/dist/featureFields.d.ts

@@ -0,0 +1,11 @@
+import type { Annotation } from './types.ts';
+/**
+ * The value a feature gives an encoded field: an Annotation property, else one
+ * of the GFF attributes the parser kept.
+ */
+export declare function featureField(annotation: Annotation, field: string): string | undefined;
+/**
+ * The name a feature answers to in a transform: its GFF `Name` attribute, else
+ * the name the parser gave it.
+ */
+export declare function featureName(annotation: Annotation): string | undefined;

package/dist/featureFields.js

@@ -0,0 +1,17 @@
+/**
+ * The value a feature gives an encoded field: an Annotation property, else one
+ * of the GFF attributes the parser kept.
+ */
+export function featureField(annotation, field) {
+    const own = annotation[field];
+    const value = own ?? annotation.attributes?.[field];
+    return typeof value === 'string' ? value : undefined;
+}
+/**
+ * The name a feature answers to in a transform: its GFF `Name` attribute, else
+ * the name the parser gave it.
+ */
+export function featureName(annotation) {
+    return featureField(annotation, 'Name') ?? featureField(annotation, 'name');
+}
+//# sourceMappingURL=featureFields.js.map

package/dist/featureFields.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"featureFields.js","sourceRoot":"","sources":["../src/featureFields.ts"],"names":[],"mappings":"AAEA;;;GAGG;AACH,MAAM,UAAU,YAAY,CAAC,UAAsB,EAAE,KAAa;IAChE,MAAM,GAAG,GAAI,UAAiD,CAAC,KAAK,CAAC,CAAA;IACrE,MAAM,KAAK,GAAG,GAAG,IAAI,UAAU,CAAC,UAAU,EAAE,CAAC,KAAK,CAAC,CAAA;IACnD,OAAO,OAAO,KAAK,KAAK,QAAQ,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,SAAS,CAAA;AACtD,CAAC;AAED;;;GAGG;AACH,MAAM,UAAU,WAAW,CAAC,UAAsB;IAChD,OAAO,YAAY,CAAC,UAAU,EAAE,MAAM,CAAC,IAAI,YAAY,CAAC,UAAU,EAAE,MAAM,CAAC,CAAA;AAC7E,CAAC"}

package/dist/fetchUtils.d.ts

@@ -2,7 +2,6 @@ import { fetchAndMaybeUnzipText } from '@jbrowse/core/util';
 import type { RpcStatus } from '@jbrowse/core/util';
 export interface FetchStatus {
     msg: string;
-    url?: string;
     onCancel?: () => void;
 }
 type Filehandle = Parameters<typeof fetchAndMaybeUnzipText>[0];
@@ -14,12 +13,13 @@ type ProgressFetcher = (loc: Filehandle, opts: {
  * Fetch text from a filehandle while reporting download/unzip progress through
  * setStatus, and wiring a Cancel handler that aborts the underlying request.
  * The status is always cleared once the fetch settles. The fetcher is injectable
- * for testing.
+ * for testing, and so is the AbortController: a caller that can supersede its
+ * own request -- the model's loaders, when the filehandle changes under them --
+ * holds one and aborts the download it no longer wants.
  */
-export declare function fetchTextWithProgress(loc: Filehandle, setStatus: (status?: FetchStatus) => void, fetcher?: ProgressFetcher): Promise<string>;
-export declare function myfetch(url: string, args?: RequestInit): Promise<Response>;
-export declare function textfetch(url: string, args?: RequestInit): Promise<string>;
-export declare function jsonfetch<T>(url: string, args?: RequestInit): Promise<T>;
-export declare function timeout(time: number, signal?: AbortSignal): Promise<void>;
+export declare function fetchTextWithProgress(loc: Filehandle, setStatus: (status?: FetchStatus) => void, { fetcher, controller, }?: {
+    fetcher?: ProgressFetcher;
+    controller?: AbortController;
+}): Promise<string>;
 export declare function isAbortError(e: unknown): boolean;
 export {};

package/dist/fetchUtils.js

@@ -17,10 +17,11 @@ function statusMessageText(status) {
  * Fetch text from a filehandle while reporting download/unzip progress through
  * setStatus, and wiring a Cancel handler that aborts the underlying request.
  * The status is always cleared once the fetch settles. The fetcher is injectable
- * for testing.
+ * for testing, and so is the AbortController: a caller that can supersede its
+ * own request -- the model's loaders, when the filehandle changes under them --
+ * holds one and aborts the download it no longer wants.
  */
-export async function fetchTextWithProgress(loc, setStatus, fetcher = fetchAndMaybeUnzipText) {
-    const controller = new AbortController();
+export async function fetchTextWithProgress(loc, setStatus, { fetcher = fetchAndMaybeUnzipText, controller = new AbortController(), } = {}) {
     try {
         return await fetcher(loc, {
             signal: controller.signal,
@@ -41,35 +42,6 @@ export async function fetchTextWithProgress(loc, setStatus, fetcher = fetchAndMa
         setStatus(undefined);
     }
 }
-export async function myfetch(url, args) {
-    const response = await fetch(url, args);
-    if (!response.ok) {
-        throw new Error(`HTTP ${response.status} fetching ${url} ${await response.text()}`);
-    }
-    return response;
-}
-export async function textfetch(url, args) {
-    const response = await myfetch(url, args);
-    return response.text();
-}
-export async function jsonfetch(url, args) {
-    const response = await myfetch(url, args);
-    return response.json();
-}
-export function timeout(time, signal) {
-    return new Promise((resolve, reject) => {
-        if (signal?.aborted) {
-            reject(new DOMException('Aborted', 'AbortError'));
-        }
-        else {
-            const id = setTimeout(resolve, time);
-            signal?.addEventListener('abort', () => {
-                clearTimeout(id);
-                reject(new DOMException('Aborted', 'AbortError'));
-            });
-        }
-    });
-}
 export function isAbortError(e) {
     return e instanceof DOMException && e.name === 'AbortError';
 }

package/dist/fetchUtils.js.map

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

@@ -5,8 +5,7 @@ export function flatToTree(items) {
             item.id,
             {
                 id: `${item.id}`,
-                // the label is what NCBI's own tree viewer shows; falling back to the
-                // node id would render a tree of bare numbers
+                // NCBI's tree viewer shows the label
                 name: item.label || `${item.id}`,
                 ...(length !== undefined && Number.isFinite(length)
                     ? { length }

package/dist/flatToTree.js.map

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

@@ -1,2 +1,12 @@
 declare const palettes: string[][];
 export default palettes;
+/**
+ * Fixed categorical palettes a scale names. `ggplot` is not one of them: it is
+ * the ramp above, which picks its colors from the number of keys.
+ */
+export declare const namedPalettes: Record<string, readonly string[]>;
+/**
+ * The colors a palette name asks for. `ggplot`, an unknown name, and no name at
+ * all give undefined, which `createPaletteMap` answers with the hue ramp.
+ */
+export declare function paletteNamed(name?: string): readonly string[] | undefined;

package/dist/ggplotPalettes.js

@@ -18,4 +18,62 @@ const palettes = [
     ],
 ];
 export default palettes;
+/**
+ * Fixed categorical palettes a scale names. `ggplot` is not one of them: it is
+ * the ramp above, which picks its colors from the number of keys.
+ */
+export const namedPalettes = {
+    set1: [
+        '#e41a1c',
+        '#377eb8',
+        '#4daf4a',
+        '#984ea3',
+        '#ff7f00',
+        '#ffff33',
+        '#a65628',
+        '#f781bf',
+        '#999999',
+    ],
+    dark2: [
+        '#1b9e77',
+        '#d95f02',
+        '#7570b3',
+        '#e7298a',
+        '#66a61e',
+        '#e6ab02',
+        '#a6761d',
+        '#666666',
+    ],
+    // Okabe-Ito, which stays distinguishable under the common forms of color
+    // blindness
+    okabeito: [
+        '#e69f00',
+        '#56b4e9',
+        '#009e73',
+        '#f0e442',
+        '#0072b2',
+        '#d55e00',
+        '#cc79a7',
+        '#000000',
+    ],
+    tableau: [
+        '#4e79a7',
+        '#f28e2b',
+        '#e15759',
+        '#76b7b2',
+        '#59a14f',
+        '#edc948',
+        '#b07aa1',
+        '#ff9da7',
+        '#9c755f',
+        '#bab0ac',
+    ],
+};
+/**
+ * The colors a palette name asks for. `ggplot`, an unknown name, and no name at
+ * all give undefined, which `createPaletteMap` answers with the hue ramp.
+ */
+export function paletteNamed(name) {
+    return name === undefined ? undefined : namedPalettes[name];
+}
 //# sourceMappingURL=ggplotPalettes.js.map

package/dist/ggplotPalettes.js.map

@@ -1 +1 @@
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+{"version":3,"file":"ggplotPalettes.js","sourceRoot":"","sources":["../src/ggplotPalettes.ts"],"names":[],"mappings":"AAAA,MAAM,QAAQ,GAAG;IACf,CAAC,SAAS,CAAC;IACX,CAAC,SAAS,EAAE,SAAS,CAAC;IACtB,CAAC,SAAS,EAAE,SAAS,EAAE,SAAS,CAAC;IACjC,CAAC,SAAS,EAAE,SAAS,EAAE,SAAS,EAAE,SAAS,CAAC;IAC5C,CAAC,SAAS,EAAE,SAAS,EAAE,SAAS,EAAE,SAAS,EAAE,SAAS,CAAC;IACvD,CAAC,SAAS,EAAE,SAAS,EAAE,SAAS,EAAE,SAAS,EAAE,SAAS,EAAE,SAAS,CAAC;IAClE,CAAC,SAAS,EAAE,SAAS,EAAE,SAAS,EAAE,SAAS,EAAE,SAAS,EAAE,SAAS,EAAE,SAAS,CAAC;IAC7E;QACE,SAAS;QACT,SAAS;QACT,SAAS;QACT,SAAS;QACT,SAAS;QACT,SAAS;QACT,SAAS;QACT,SAAS;KACV;CACF,CAAA;AAED,eAAe,QAAQ,CAAA;AAEvB;;;GAGG;AACH,MAAM,CAAC,MAAM,aAAa,GAAsC;IAC9D,IAAI,EAAE;QACJ,SAAS;QACT,SAAS;QACT,SAAS;QACT,SAAS;QACT,SAAS;QACT,SAAS;QACT,SAAS;QACT,SAAS;QACT,SAAS;KACV;IACD,KAAK,EAAE;QACL,SAAS;QACT,SAAS;QACT,SAAS;QACT,SAAS;QACT,SAAS;QACT,SAAS;QACT,SAAS;QACT,SAAS;KACV;IACD,yEAAyE;IACzE,YAAY;IACZ,QAAQ,EAAE;QACR,SAAS;QACT,SAAS;QACT,SAAS;QACT,SAAS;QACT,SAAS;QACT,SAAS;QACT,SAAS;QACT,SAAS;KACV;IACD,OAAO,EAAE;QACP,SAAS;QACT,SAAS;QACT,SAAS;QACT,SAAS;QACT,SAAS;QACT,SAAS;QACT,SAAS;QACT,SAAS;QACT,SAAS;QACT,SAAS;KACV;CACF,CAAA;AAED;;;GAGG;AACH,MAAM,UAAU,YAAY,CAAC,IAAa;IACxC,OAAO,IAAI,KAAK,SAAS,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,aAAa,CAAC,IAAI,CAAC,CAAA;AAC7D,CAAC"}

package/dist/hierarchy.d.ts

@@ -13,6 +13,8 @@ export interface HierarchyNode<T = NodeWithIds> extends CoreHierarchyNode<T> {
     parent: HierarchyNode<T> | null;
     x?: number;
     y?: number;
+    xMin?: number;
+    xMax?: number;
     len?: number;
     depthToLeaf?: number;
     _children?: HierarchyNode<T>[] | null;
@@ -27,6 +29,32 @@ export declare function collapsedSubtreeMaxLength<T extends {
     length?: number;
 }>(node: HierarchyNode<T>): number;
 export declare function calcDepthToLeaf<T>(node: HierarchyNode<T>): number;
-export declare function findMaxBranchLen(node: HierarchyNode): number;
 export declare function maxLength(d: HierarchyNode): number;
 export declare function setBrLength(d: HierarchyNode, y0: number, k: number): void;
+/**
+ * Every leaf by name, with a name two leaves share mapping to undefined: a tip
+ * set naming it cannot say which tip it means.
+ */
+export declare function leafIndex<T extends {
+    name: string;
+}>(root: HierarchyNode<T>): Map<string, HierarchyNode<T> | undefined>;
+/**
+ * The most recent common ancestor of a set of tip names, or undefined when a
+ * name is not a tip of this tree or names two of them.
+ *
+ * Each name lifts through `parent` to the ancestor the names before it share,
+ * so the walk holds two nodes. Recording a root-to-tip path per name instead
+ * costs the depth in memory per name, and a caterpillar tree's depth is its tip
+ * count. `index` is `leafIndex(root)`, which a caller resolving several tip
+ * sets against one tree builds once.
+ */
+export declare function mrca<T extends {
+    name: string;
+}>(root: HierarchyNode<T>, names: string[], index?: Map<string, HierarchyNode<T> | undefined>): HierarchyNode<T> | undefined;
+/**
+ * The deepest node whose subtree covers a run of rows, given in the row-space
+ * coordinates clusterLayout writes to xMin/xMax. A subtree's leaves are one
+ * contiguous run, so at most one child per level covers the run and the descent
+ * visits the tree's depth rather than its nodes.
+ */
+export declare function nodeCoveringRows<T>(root: HierarchyNode<T>, top: number, bottom: number): HierarchyNode<T>;