react-msaview 9.5.0 → 9.7.0

package/dist/constants.d.ts

@@ -15,6 +15,14 @@ export declare const subFeatureRowHeight = 4;
 export declare const domainUnderlineHeight = 3;
 export declare const segmentFeatureTypes: Set<string>;
 export declare const segmentShades: string[];
+/**
+ * A site's feature type: CDD's GenPept `Site`, a Sequence Ontology `*_site`,
+ * InterPro's `Binding_site`, `Active_site` and `Conserved_site`, and UniProt's
+ * `Binding site`. A site is a set of scattered residues, often single columns
+ */
+export declare function isSiteType(featureType: string | undefined): boolean;
+export declare const domainFills: string[];
+export declare const siteFills: string[];
 export declare const defaultDrawMsaLetters = true;
 export declare const defaultScrollZoom = false;
 export declare const scrollZoomAxes: readonly ['both', 'horizontal', 'vertical'];

package/dist/constants.js

@@ -20,8 +20,8 @@ export const subFeatureRowHeight = 4;
 // 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.
+// alternates two shades across them and labels them by number, and every other
+// type gets its own color and legend row.
 export const segmentFeatureTypes = new Set([
     'exon',
     'CDS',
@@ -32,6 +32,30 @@ export const segmentFeatureTypes = new Set([
 ]);
 // the two shades alternated across adjacent segments (exons)
 export const segmentShades = ['#9fb6d4', '#d4dcea'];
+/**
+ * A site's feature type: CDD's GenPept `Site`, a Sequence Ontology `*_site`,
+ * InterPro's `Binding_site`, `Active_site` and `Conserved_site`, and UniProt's
+ * `Binding site`. A site is a set of scattered residues, often single columns
+ */
+export function isSiteType(featureType) {
+    return !!featureType && /(^|[_ ])site$/i.test(featureType);
+}
+// A domain fills a span the residue letters draw over, so it takes a mid-light
+// color, CIELAB L* 70 to 80, dark enough that its ends show against unfilled
+// cells. A site marks a few residues inside a domain, so it takes a dark one,
+// L* 45 or less: a thin mark needs lightness contrast to show on a fill, and
+// hue alone gives none. Neither list holds a grey or a magenta, which a
+// structure view draws for uncolored chains and for the hovered residue
+export const domainFills = [
+    '#8fb3d9',
+    '#f2b277',
+    '#9fd18f',
+    '#c3a5d9',
+    '#ee9f9f',
+    '#d4c08f',
+    '#8fd1cb',
+];
+export const siteFills = ['#0f6e52', '#a84a00', '#5a54a0', '#3f6b12', '#7a5514'];
 export const defaultDrawMsaLetters = true;
 export const defaultScrollZoom = false;
 // Which cell dimensions a wheel zoom scales. 'horizontal' holds the row height,

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package/dist/createPaletteMap.d.ts

@@ -3,9 +3,10 @@
  * 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.
+ * eight-color palette — every key gets an evenly spaced hue instead, so no
+ * two keys share a color. The hues sit at CIELAB `lightness` where one is
+ * given, else at HSL lightness 60.
  */
-export declare function createPaletteMap(keys: string[], palette?: readonly string[]): {
+export declare function createPaletteMap(keys: string[], palette?: readonly string[], lightness?: number): {
     [k: string]: string;
 };

package/dist/createPaletteMap.js

@@ -1,22 +1,30 @@
-import { colord } from 'colord';
+import { colord, extend } from 'colord';
+import lchPlugin from 'colord/plugins/lch';
 import palettes from './ggplotPalettes.js';
+extend([lchPlugin]);
 /**
  * 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.
+ * eight-color palette — every key gets an evenly spaced hue instead, so no
+ * two keys share a color. The hues sit at CIELAB `lightness` where one is
+ * given, else at HSL lightness 60.
  */
-export function createPaletteMap(keys, palette) {
+export function createPaletteMap(keys, palette, lightness) {
     const n = keys.length;
     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,
-        colord({ h: (i * 360) / n, s: 60, l: 60 }).toHex(),
-    ]));
+    return Object.fromEntries(keys.map((key, i) => {
+        const h = (i * 360) / n;
+        return [
+            key,
+            (lightness === undefined
+                ? colord({ h, s: 60, l: 60 })
+                : colord({ l: lightness, c: 40, h })).toHex(),
+        ];
+    }));
 }
 //# sourceMappingURL=createPaletteMap.js.map

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+{"version":3,"file":"createPaletteMap.js","sourceRoot":"","sources":["../src/createPaletteMap.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,MAAM,EAAE,MAAM,EAAE,MAAM,QAAQ,CAAA;AACvC,OAAO,SAAS,MAAM,oBAAoB,CAAA;AAE1C,OAAO,QAAQ,MAAM,qBAAqB,CAAA;AAE1C,MAAM,CAAC,CAAC,SAAS,CAAC,CAAC,CAAA;AAEnB;;;;;;;;GAQG;AACH,MAAM,UAAU,gBAAgB,CAC9B,IAAc,EACd,OAA2B,EAC3B,SAAkB;IAElB,MAAM,CAAC,GAAG,IAAI,CAAC,MAAM,CAAA;IACrB,MAAM,MAAM,GAAG,OAAO,IAAI,QAAQ,CAAC,CAAC,GAAG,CAAC,CAAC,CAAA;IACzC,IAAI,MAAM,IAAI,CAAC,IAAI,MAAM,CAAC,MAAM,EAAE,CAAC;QACjC,OAAO,MAAM,CAAC,WAAW,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,GAAG,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,GAAG,EAAE,MAAM,CAAC,CAAC,CAAE,CAAC,CAAC,CAAC,CAAA;IACpE,CAAC;IACD,OAAO,MAAM,CAAC,WAAW,CACvB,IAAI,CAAC,GAAG,CAAC,CAAC,GAAG,EAAE,CAAC,EAAE,EAAE;QAClB,MAAM,CAAC,GAAG,CAAC,CAAC,GAAG,GAAG,CAAC,GAAG,CAAC,CAAA;QACvB,OAAO;YACL,GAAG;YACH,CAAC,SAAS,KAAK,SAAS;gBACtB,CAAC,CAAC,MAAM,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,EAAE,EAAE,CAAC,EAAE,EAAE,EAAE,CAAC;gBAC7B,CAAC,CAAC,MAAM,CAAC,EAAE,CAAC,EAAE,SAAS,EAAE,CAAC,EAAE,EAAE,EAAE,CAAC,EAAE,CAAC,CACrC,CAAC,KAAK,EAAE;SACV,CAAA;IACH,CAAC,CAAC,CACH,CAAA;AACH,CAAC"}

package/dist/index.d.ts

@@ -2,7 +2,7 @@ export { renderToSvg } from './renderToSvg.tsx';
 export type { ExportSvgOptions } from './renderToSvg.tsx';
 export { installHeadlessRenderEnv } from './headlessRenderEnv.ts';
 export { CHAR_WIDTH_RATIO } from './measureTextCanvas.ts';
-export { maxNeighborJoiningRows } from './constants.ts';
+export { isSiteType, 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';

package/dist/index.js

@@ -14,7 +14,7 @@ export { installHeadlessRenderEnv } from './headlessRenderEnv.js';
 export { CHAR_WIDTH_RATIO } from './measureTextCanvas.js';
 // the row count above which calculateNeighborJoiningTreeFromMSA throws, for
 // hosts gating their own menu item
-export { maxNeighborJoiningRows } from './constants.js';
+export { isSiteType, 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';

package/dist/index.js.map

@@ -1 +1 @@
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+{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,gFAAgF;AAChF,yDAAyD;AACzD,6EAA6E;AAC7E,+DAA+D;AAC/D,gFAAgF;AAChF,0EAA0E;AAC1E,yEAAyE;AACzE,8EAA8E;AAC9E,mEAAmE;AACnE,OAAO,EAAE,WAAW,EAAE,MAAM,kBAAmB,CAAA;AAE/C,8EAA8E;AAC9E,yDAAyD;AACzD,OAAO,EAAE,wBAAwB,EAAE,MAAM,wBAAwB,CAAA;AACjE,OAAO,EAAE,gBAAgB,EAAE,MAAM,wBAAwB,CAAA;AACzD,4EAA4E;AAC5E,mCAAmC;AACnC,OAAO,EAAE,UAAU,EAAE,sBAAsB,EAAE,MAAM,gBAAgB,CAAA;AACnE,6EAA6E;AAC7E,OAAO,EAAE,UAAU,EAAE,YAAY,EAAE,MAAM,iBAAiB,CAAA;AAO1D,OAAO,EAAE,OAAO,IAAI,OAAO,EAAE,MAAM,yBAA0B,CAAA;AAE7D,OAAO,EAAE,OAAO,IAAI,SAAS,EAAE,MAAM,2BAA4B,CAAA;AAEjE,sEAAsE;AACtE,OAAO,EAAE,YAAY,EAAE,cAAc,EAAE,MAAM,qBAAqB,CAAA;AAClE,6EAA6E;AAC7E,OAAO,EAAE,kBAAkB,EAAE,MAAM,yBAAyB,CAAA;AAC5D,OAAO,EAAE,KAAK,EAAE,MAAM,YAAa,CAAA;AACnC,OAAO,EAAE,gBAAgB,EAAE,MAAM,cAAc,CAAA;AAC/C,OAAO,EAAE,eAAe,EAAE,MAAM,sBAAsB,CAAA;AAGtD,OAAO,EAAqB,OAAO,IAAI,SAAS,EAAE,MAAM,YAAY,CAAA"}

package/dist/model.d.ts

@@ -2074,12 +2074,15 @@ declare function stateModelFactory({ maxInlineSnapshotBytes, }?: {
     /**
      * #getter
      * categorical feature types (InterPro domains and the like) that each get
-     * their own color and a legend entry, in palette order: grouped by
-     * feature type, types in the order they first appear. A GenPept
-     * record's CDD Sites follow every Region, so the palette spends the
-     * colors after the domains' on the sites inside them
+     * their own color and a legend entry
      */
     readonly categoricalDomainTypes: Annotation[];
+    /**
+     * #getter
+     * accession -> fill: segments alternate two shades, a domain takes a
+     * mid-light color and a site a dark one, so a site's residues stand out on
+     * the domain around them
+     */
     readonly fillPalette: {
         [x: string]: string;
     };

package/dist/model.js

@@ -13,7 +13,7 @@ import { packDomainLanes } from './components/msa/packDomainLanes.js';
 import { visibleColRange } from './components/msa/visibleColRange.js';
 import { cladeGutterWidth } from './components/tree/cladeBrackets.js';
 import { scaleBarLength } from './components/tree/scaleBar.js';
-import { defaultAllowedGappyness, defaultColWidth, defaultColorSchemeName, defaultCurrentAlignment, defaultDrawMsaLetters, defaultHeight, defaultHideGaps, defaultRowHeight, defaultScrollX, defaultScrollY, defaultScrollZoom, defaultScrollZoomAxis, defaultShowDomainLegend, defaultShowDomains, defaultSubFeatureRows, fontSizeFor, labelFitFontSize, maxCellSize, maxFitTreeWidth, maxTreeAreaShare, maxInlineSnapshotBytes as defaultMaxInlineSnapshotBytes, maxNeighborJoiningRows, minColWidth, minLetterColWidth, minLetterRowHeight, minRowHeight, minTreeWidth, pxPerTreeDepth, resizeHandleWidth, rowPanelHeaderHeight, rowTintAlpha, scrollZoomAxes, segmentFeatureTypes, segmentShades, settingsPanelWidth, treeScaleBarHeight, } from './constants.js';
+import { defaultAllowedGappyness, defaultColWidth, defaultColorSchemeName, defaultCurrentAlignment, defaultDrawMsaLetters, defaultHeight, defaultHideGaps, defaultRowHeight, defaultScrollX, defaultScrollY, defaultScrollZoom, defaultScrollZoomAxis, defaultShowDomainLegend, defaultShowDomains, domainFills, defaultSubFeatureRows, fontSizeFor, labelFitFontSize, maxCellSize, maxFitTreeWidth, maxTreeAreaShare, maxInlineSnapshotBytes as defaultMaxInlineSnapshotBytes, maxNeighborJoiningRows, minColWidth, minLetterColWidth, minLetterRowHeight, isSiteType, minRowHeight, minTreeWidth, pxPerTreeDepth, resizeHandleWidth, rowPanelHeaderHeight, rowTintAlpha, scrollZoomAxes, segmentFeatureTypes, segmentShades, settingsPanelWidth, siteFills, treeScaleBarHeight, } from './constants.js';
 import { createPaletteMap } from './createPaletteMap.js';
 import { exportFileName } from './exportFileName.js';
 import { featureField, featureName } from './featureFields.js';
@@ -3055,23 +3055,30 @@ function stateModelFactory({ maxInlineSnapshotBytes = defaultMaxInlineSnapshotBy
         /**
          * #getter
          * categorical feature types (InterPro domains and the like) that each get
-         * their own color and a legend entry, in palette order: grouped by
-         * feature type, types in the order they first appear. A GenPept
-         * record's CDD Sites follow every Region, so the palette spends the
-         * colors after the domains' on the sites inside them
+         * their own color and a legend entry
          */
         get categoricalDomainTypes() {
-            const types = [...self.annotationTypes.values()].filter(d => !segmentFeatureTypes.has(d.featureType ?? ''));
-            const typeOrder = [...new Set(types.map(d => d.featureType))];
-            return types.toSorted((a, b) => typeOrder.indexOf(a.featureType) - typeOrder.indexOf(b.featureType));
+            return [...self.annotationTypes.values()].filter(d => !segmentFeatureTypes.has(d.featureType ?? ''));
         },
+        /**
+         * #getter
+         * accession -> fill: segments alternate two shades, a domain takes a
+         * mid-light color and a site a dark one, so a site's residues stand out on
+         * the domain around them
+         */
         get fillPalette() {
             const segments = Object.fromEntries(this.segmentDomainTypes.map((d, i) => [
                 d.accession,
                 segmentShades[i % segmentShades.length],
             ]));
-            const categorical = createPaletteMap(this.categoricalDomainTypes.map(d => d.accession));
-            return { ...segments, ...categorical };
+            const accessions = (site) => this.categoricalDomainTypes
+                .filter(d => isSiteType(d.featureType) === site)
+                .map(d => d.accession);
+            return {
+                ...segments,
+                ...createPaletteMap(accessions(false), domainFills, 75),
+                ...createPaletteMap(accessions(true), siteFills, 40),
+            };
         },
         /**
          * #getter