react-msaview 7.0.0 → 8.1.0

package/dist/constants.js

@@ -5,21 +5,21 @@ export const defaultHeight = 550;
 export const defaultScrollX = 0;
 export const defaultScrollY = 0;
 export const defaultCurrentAlignment = 0;
-// Annotations are loaded on purpose -- a gff filehandle, a file picked in the
-// dialog -- so they are drawn unless the reader has said otherwise. Since only
-// the "no" is stored, a shared link with the overlay hidden reopens hidden, and
-// one that never mentions it opens showing whatever annotations it carries.
+// Only a hidden overlay is stored, so a link that never mentions it opens
+// showing its annotations.
 export const defaultShowDomains = true;
 export const defaultShowDomainLegend = true;
 export const defaultHideGaps = true;
 export const defaultAllowedGappyness = 100;
 export const defaultSubFeatureRows = false;
-// row height for each stacked feature when subFeatureRows is on
+// height of one sub-row when subFeatureRows is on, unless the row has more
+// lanes than fit at this height (see renderBoxFeatureCanvasBlock)
 export const subFeatureRowHeight = 4;
-// Feature types that are ordinal *segments* of a single transcript (exons and
-// the like) rather than categorical domains. Their identity is their position,
-// so the overlay alternates two shades to mark boundaries and labels them by
-// number, instead of assigning every one a distinct hue + legend row.
+// height of the bar the overlay draws under a row in letter-color mode
+export const domainUnderlineHeight = 3;
+// Feature types that are ordinal segments of one transcript. The overlay
+// alternates two shades across them and labels them by number, where a domain
+// type gets its own hue and legend row.
 export const segmentFeatureTypes = new Set([
     'exon',
     'CDS',
@@ -32,11 +32,20 @@ export const segmentFeatureTypes = new Set([
 export const segmentShades = ['#9fb6d4', '#d4dcea'];
 export const defaultDrawMsaLetters = true;
 export const defaultScrollZoom = false;
+// Which cell dimensions a wheel zoom scales. 'horizontal' holds the row height,
+// which fixes the label and letter font size while the columns compress.
+// 'vertical' does the reverse.
+export const scrollZoomAxes = ['both', 'horizontal', 'vertical'];
+export const defaultScrollZoomAxis = 'both';
 // Cell size floors for drawing residue letters and tree labels. Below these a
-// 500px block holds thousands of glyphs, and fillText -- which no sprite atlas
-// beats, measured -- dominates every zoom frame.
+// 500px block holds thousands of glyphs, and fillText dominates every zoom
+// frame. A sprite atlas measured slower.
 export const minLetterRowHeight = 8;
 export const minLetterColWidth = 5;
+// A feature span draws its label at two pixels under its height, capped at 11,
+// so a span shorter than this holds no readable text: an underline bar, a
+// sub-row band or a features panel over small rows
+export const minFeatureLabelHeight = 9;
 // Tree labels are measured once at this size and scaled to the current font
 // size, so a vertical zoom never re-measures the tree.
 export const labelReferenceFontSize = 16;
@@ -58,17 +67,38 @@ export const defaultTreeWidth = 300;
 export const defaultShowBranchLen = true;
 export const defaultDrawTree = true;
 export const defaultDrawNodeBubbles = true;
-// Neighbor joining refuses above this many rows. The distance matrix is O(n^2*L)
-// and the join loop O(n^3), both on the main thread with no progress and no
-// cancel: 400 rows measured 1.5s, 800 rows 10s, and 1600 would be about seventy.
-// See agent-docs/ideas/neighbor-joining-scaling.md for why the RapidNJ fix is a
-// real algorithm change rather than a port, and why capping is the honest answer
-// -- NJ on thousands of sequences is the wrong tool however fast it runs.
+export const defaultDrawNodeLabels = false;
+export const defaultShowTreeOverview = false;
+export const defaultOverviewHeight = 120;
+// Neighbor joining does not run above this many rows. The distance matrix is
+// O(n^2*L) and the join loop O(n^3), both on the main thread with no progress
+// and no cancel: 400 rows measured 1.5s, 800 rows 10s, and 1600 would be about
+// seventy. See agent-docs/ideas/neighbor-joining-scaling.md.
 export const maxNeighborJoiningRows = 500;
-// The largest inline document the snapshot carries. Past this a pasted or
-// locally-opened file stays in the live model and leaves the snapshot, since a
-// session or a shared URL holding megabytes of sequence is not a link anyone
-// can send. `unshareableData` reads the same number, so what the viewer warns
-// about and what the snapshot drops cannot drift apart.
+// The opacity a `rowTint` encoding draws its scale's color at, so the residues
+// under the wash stay readable. A color the producer already gave an alpha
+// keeps it.
+export const rowTintAlpha = 0.25;
+// The fill a `clades` record with the `highlight` mark draws behind its rows,
+// and the opacity a producer's own color takes when it carries none.
+export const cladeHighlightColor = '#fff3c4';
+export const cladeHighlightAlpha = 0.6;
+// The largest inline document the snapshot carries. A larger pasted or
+// locally-opened file stays in the live model and out of the snapshot, keeping
+// shared URLs sendable. `unshareableData` warns using the same number.
 export const maxInlineSnapshotBytes = 50_000;
+// Height of the band the `rowPanels` headers draw in, above the strips in the
+// top area beside the tree ruler and the minimap. A panel wider than the band
+// is tall writes its header across, where it has more room.
+export const rowPanelHeaderHeight = 56;
+// Height of the branch-length scale bar above the tree.
+export const treeScaleBarHeight = 22;
+// Width of a `features` row panel that names none, wide enough for a gene
+// neighborhood of a few arrows to read.
+export const defaultFeaturePanelWidth = 200;
+// The alignment's overlay canvas draws the mouseover, the persisted highlights
+// and the row tints over the residues, and the legend key floats above that,
+// so a tint reaching the top right corner leaves the key readable.
+export const msaOverlayZIndex = 1000;
+export const legendZIndex = msaOverlayZIndex + 1;
 //# sourceMappingURL=constants.js.map

package/dist/constants.js.map

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

@@ -1,10 +1,11 @@
 /**
- * Creates a map from keys to colors. Up to the largest ggplot palette (8 keys)
- * we use the hand-picked ggplot colors; beyond that — e.g. a gene-structure
- * overlay with one feature per exon — we generate evenly spaced HSL hues so
- * every key still gets a distinct, stable color instead of running off the end
- * of the palette.
+ * Creates a map from keys to colors. `palette` names the colors to take in
+ * order, such as the list a scale asked for by name; without it the keys take
+ * the ggplot palette of their own size. Beyond the colors available — a
+ * gene-structure overlay with one feature per exon, or nine keys on an
+ * eight-color palette — every key gets an evenly spaced HSL hue instead, so no
+ * two keys share a color.
  */
-export declare function createPaletteMap(keys: string[]): {
+export declare function createPaletteMap(keys: string[], palette?: readonly string[]): {
     [k: string]: string;
 };

package/dist/createPaletteMap.js

@@ -1,17 +1,18 @@
 import { colord } from 'colord';
 import palettes from './ggplotPalettes.js';
 /**
- * Creates a map from keys to colors. Up to the largest ggplot palette (8 keys)
- * we use the hand-picked ggplot colors; beyond that — e.g. a gene-structure
- * overlay with one feature per exon — we generate evenly spaced HSL hues so
- * every key still gets a distinct, stable color instead of running off the end
- * of the palette.
+ * Creates a map from keys to colors. `palette` names the colors to take in
+ * order, such as the list a scale asked for by name; without it the keys take
+ * the ggplot palette of their own size. Beyond the colors available — a
+ * gene-structure overlay with one feature per exon, or nine keys on an
+ * eight-color palette — every key gets an evenly spaced HSL hue instead, so no
+ * two keys share a color.
  */
-export function createPaletteMap(keys) {
+export function createPaletteMap(keys, palette) {
     const n = keys.length;
-    if (n <= palettes.length) {
-        const palette = palettes[n - 1];
-        return Object.fromEntries(keys.map((key, i) => [key, palette[i]]));
+    const colors = palette ?? palettes[n - 1];
+    if (colors && n <= colors.length) {
+        return Object.fromEntries(keys.map((key, i) => [key, colors[i]]));
     }
     return Object.fromEntries(keys.map((key, i) => [
         key,

package/dist/createPaletteMap.js.map

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package/dist/element.d.ts

@@ -0,0 +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.
+ *
+ * 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 declare function defineMsaElement(tagName?: string): CustomElementConstructor;

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/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

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