react-msaview 9.2.0 → 9.3.0

package/dist/constants.js.map

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

@@ -1,13 +1,17 @@
 /**
  * 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,
- * 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.
+ * theme, tree-area-width, reference-row and loading. Properties: msa, tree and
+ * gff text, features, colorScheme, highlights, columnTracks, residueMappings
+ * and selection. The colorScheme property takes a `{domain, range}` 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.
+ *
+ * `loading="lazy"` mounts the viewer once the element comes within 200 pixels
+ * of the viewport, as `<img loading="lazy">` loads its image. Until then the
+ * element shows its own children, such as an `<img>` of the first frame, and
+ * reserves the viewer's height.
  *
  * 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

@@ -1,4 +1,5 @@
 import { when } from 'mobx';
+import { defaultHeight, resizeHandleWidth } from './constants.js';
 import { mount } from './mount.js';
 const dataProperties = [
     'msa',
@@ -20,7 +21,11 @@ const ownAttributes = [
     'theme',
     'reference-row',
     'tree-area-width',
+    'loading',
 ];
+// how far outside the viewport a lazy element starts mounting, so the viewer
+// is drawing by the time the reader scrolls to it
+const lazyMargin = '200px';
 // the attributes a <nightingale-manager> writes on the elements it holds
 const nightingaleAttributes = ['display-start', 'display-end', 'highlight'];
 function numberAttribute(value) {
@@ -55,13 +60,17 @@ 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,
- * 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.
+ * theme, tree-area-width, reference-row and loading. Properties: msa, tree and
+ * gff text, features, colorScheme, highlights, columnTracks, residueMappings
+ * and selection. The colorScheme property takes a `{domain, range}` 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.
+ *
+ * `loading="lazy"` mounts the viewer once the element comes within 200 pixels
+ * of the viewport, as `<img loading="lazy">` loads its image. Until then the
+ * element shows its own children, such as an `<img>` of the first frame, and
+ * reserves the viewer's height.
  *
  * Inside a <nightingale-manager>, the element registers with it and speaks its
  * protocol: it follows the display-start, display-end and highlight attributes
@@ -76,6 +85,7 @@ export function defineMsaElement(tagName = 'jbrowse-msa') {
     class MsaElement extends HTMLElement {
         static observedAttributes = [...ownAttributes, ...nightingaleAttributes];
         #viewer;
+        #nearby;
         #model;
         #manager;
         #cancelRange;
@@ -224,7 +234,19 @@ export function defineMsaElement(tagName = 'jbrowse-msa') {
             if (!this.style.display) {
                 this.style.display = 'block';
             }
-            this.#viewer = mount(this, this.#props());
+            if (this.#lazy) {
+                const height = numberAttribute(this.getAttribute('height')) ?? defaultHeight;
+                this.style.minHeight = `${height + resizeHandleWidth}px`;
+                this.#nearby = new IntersectionObserver(entries => {
+                    if (entries.some(entry => entry.isIntersecting)) {
+                        this.#mount();
+                    }
+                }, { rootMargin: lazyMargin });
+                this.#nearby.observe(this);
+            }
+            else {
+                this.#mount();
+            }
             const manager = this.closest('nightingale-manager');
             if (manager) {
                 void customElements.whenDefined('nightingale-manager').then(() => {
@@ -235,7 +257,18 @@ export function defineMsaElement(tagName = 'jbrowse-msa') {
                 });
             }
         }
+        get #lazy() {
+            return (this.getAttribute('loading') === 'lazy' &&
+                typeof IntersectionObserver !== 'undefined');
+        }
+        #mount() {
+            this.#nearby?.disconnect();
+            this.#nearby = undefined;
+            this.#viewer ??= mount(this, this.#props());
+        }
         disconnectedCallback() {
+            this.#nearby?.disconnect();
+            this.#nearby = undefined;
             this.#manager?.unregister(this);
             this.#manager = undefined;
             this.#cancelRange?.();
@@ -258,6 +291,11 @@ export function defineMsaElement(tagName = 'jbrowse-msa') {
             else if (name === 'highlight') {
                 this.#followHighlight();
             }
+            else if (name === 'loading') {
+                if (this.#nearby && !this.#lazy) {
+                    this.#mount();
+                }
+            }
             else {
                 this.#viewer?.update(this.#props());
             }

package/dist/element.js.map

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

@@ -1,4 +1,3 @@
-import type { ScaleSpec } from './scales.ts';
 import type { Annotation, DomainBand, RowFeaturesSpec, RowPanelSpan, RowPanelSpec } from './types.ts';
 export declare function rowPanelWidth(panel: RowPanelSpec, view: {
     rowHeight: number;
@@ -29,9 +28,3 @@ export declare function featurePanelSpans({ panel, width, colWidth, domainBands,
     annotationsByRow: Record<string, Annotation[]>;
     shifts: Map<string, number> | undefined;
 }): Map<string, RowPanelSpan[]>;
-export declare function resolveFeatureScale(field: string, scale: ScaleSpec | undefined, annotations: Annotation[], drawn: Annotation[]): {
-    kind: 'categorical';
-    colorOf: (value: string) => string | undefined;
-    field: string;
-    legend: import("./types.ts").LegendEntry[];
-};

package/dist/featurePanels.js

@@ -1,11 +1,9 @@
-import { notEmpty } from '@jbrowse/core/util';
 import { packDomainLanes } from './components/msa/packDomainLanes.js';
 import { defaultFeaturePanelWidth } from './constants.js';
 import { featureField } from './featureFields.js';
-import { resolveScale } from './scales.js';
 import { outlineColor } from './util.js';
 // the fill of a span under a scale that gives its value no color, such as a
-// gene a `map` over gene names leaves out
+// gene a `domain` of gene names leaves out
 const UNSCALED_FEATURE = '#d9d9d9';
 // the fraction of a span a following one may cover before it takes a lane of
 // its own in a `features` panel
@@ -171,17 +169,4 @@ export function featurePanelSpans({ panel, width, colWidth, domainBands, annotat
         })),
     ]));
 }
-// a scale over the values a field takes across every feature loaded, so hiding
-// a type in the filter dialog leaves the rest in their colors, and a legend of
-// the values the features drawn carry
-export function resolveFeatureScale(field, scale, annotations, drawn) {
-    const valuesOf = (list) => list.map(a => featureField(a, field)).filter(notEmpty);
-    const resolved = resolveScale(scale, valuesOf(annotations));
-    const shown = new Set(valuesOf(drawn));
-    return {
-        field,
-        ...resolved,
-        legend: resolved.legend.filter(entry => shown.has(entry.id)),
-    };
-}
 //# sourceMappingURL=featurePanels.js.map

package/dist/featurePanels.js.map

@@ -1 +1 @@
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+{"version":3,"file":"featurePanels.js","sourceRoot":"","sources":["../src/featurePanels.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,eAAe,EAAE,MAAM,qCAAqC,CAAA;AACrE,OAAO,EAAE,wBAAwB,EAAE,MAAM,gBAAgB,CAAA;AACzD,OAAO,EAAE,YAAY,EAAE,MAAM,oBAAoB,CAAA;AACjD,OAAO,EAAE,YAAY,EAAE,MAAM,WAAW,CAAA;AAUxC,4EAA4E;AAC5E,2CAA2C;AAC3C,MAAM,gBAAgB,GAAG,SAAS,CAAA;AAElC,6EAA6E;AAC7E,gCAAgC;AAChC,MAAM,WAAW,GAAG,GAAG,CAAA;AAEvB,6EAA6E;AAC7E,6EAA6E;AAC7E,6EAA6E;AAC7E,+BAA+B;AAC/B,MAAM,UAAU,aAAa,CAC3B,KAAmB,EACnB,IAA2B;IAE3B,OAAO,CACL,KAAK,CAAC,KAAK;QACX,CAAC,KAAK,CAAC,IAAI,KAAK,UAAU,CAAC,CAAC,CAAC,wBAAwB,CAAC,CAAC,CAAC,IAAI,CAAC,SAAS,CAAC,CACxE,CAAA;AACH,CAAC;AAED,0EAA0E;AAC1E,6EAA6E;AAC7E,MAAM,UAAU,YAAY,CAAC,GAAY;IACvC,IAAI,OAAO,GAAG,KAAK,QAAQ,IAAI,GAAG,KAAK,IAAI,EAAE,CAAC;QAC5C,OAAO,SAAS,CAAA;IAClB,CAAC;IACD,MAAM,MAAM,GAA2B,EAAE,CAAA;IACzC,KAAK,MAAM,CAAC,KAAK,EAAE,KAAK,CAAC,IAAI,MAAM,CAAC,OAAO,CAAC,GAAG,CAAC,EAAE,CAAC;QACjD,IAAI,OAAO,KAAK,KAAK,QAAQ,EAAE,CAAC;YAC9B,MAAM,CAAC,KAAK,CAAC,GAAG,KAAK,CAAA;QACvB,CAAC;aAAM,IAAI,OAAO,KAAK,KAAK,QAAQ,IAAI,OAAO,KAAK,KAAK,SAAS,EAAE,CAAC;YACnE,MAAM,CAAC,KAAK,CAAC,GAAG,MAAM,CAAC,KAAK,CAAC,CAAA;QAC/B,CAAC;IACH,CAAC;IACD,OAAO,MAAM,CAAA;AACf,CAAC;AAED,uEAAuE;AACvE,MAAM,UAAU,UAAU,CACxB,OAA2D,EAC3D,KAAa,EACb,OAA8C;IAE9C,MAAM,MAAM,GAAG,IAAI,GAAG,EAAkB,CAAA;IACxC,KAAK,MAAM,CAAC,IAAI,EAAE,GAAG,CAAC,IAAI,MAAM,CAAC,OAAO,CAAC,OAAO,CAAC,EAAE,CAAC;QAClD,MAAM,KAAK,GAAG,GAAG,EAAE,CAAC,KAAK,CAAC,CAAA;QAC1B,MAAM,KAAK,GAAG,KAAK,KAAK,SAAS,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,OAAO,CAAC,KAAK,CAAC,CAAA;QAC9D,IAAI,KAAK,EAAE,CAAC;YACV,MAAM,CAAC,GAAG,CAAC,IAAI,EAAE,KAAK,CAAC,CAAA;QACzB,CAAC;IACH,CAAC;IACD,OAAO,MAAM,CAAA;AACf,CAAC;AAED,+EAA+E;AAC/E,uEAAuE;AACvE,oBAAoB;AACpB,MAAM,UAAU,eAAe,CAC7B,WAAyB,EACzB,QAEa,EACb,WAAmC;IAEnC,MAAM,OAAO,GAAG,IAAI,GAAG,EAAkB,CAAA;IACzC,MAAM,QAAQ,GAAG,CAAC,IAAY,EAAE,EAAE;QAChC,MAAM,GAAG,GAAG,OAAO,CAAC,GAAG,CAAC,IAAI,CAAC,CAAA;QAC7B,IAAI,GAAG,KAAK,SAAS,EAAE,CAAC;YACtB,OAAO,GAAG,CAAA;QACZ,CAAC;QACD,MAAM,MAAM,GAAG,YAAY,CAAC,IAAI,CAAC,CAAA;QACjC,OAAO,CAAC,GAAG,CAAC,IAAI,EAAE,MAAM,CAAC,CAAA;QACzB,OAAO,MAAM,CAAA;IACf,CAAC,CAAA;IACD,OAAO,IAAI,GAAG,CACZ,WAAW,CAAC,GAAG,CAAC,UAAU,CAAC,EAAE;QAC3B,MAAM,KAAK,GAAG,QAAQ;YACpB,CAAC,CAAC,YAAY,CAAC,UAAU,EAAE,QAAQ,CAAC,KAAK,CAAC;YAC1C,CAAC,CAAC,SAAS,CAAA;QACb,MAAM,IAAI,GACR,UAAU,CAAC,KAAK;YAChB,CAAC,KAAK,KAAK,SAAS,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,QAAS,CAAC,OAAO,CAAC,KAAK,CAAC,CAAC;YAC5D,CAAC,QAAQ,CAAC,CAAC,CAAC,gBAAgB,CAAC,CAAC,CAAC,WAAW,CAAC,UAAU,CAAC,SAAS,CAAE,CAAC,CAAA;QACpE,OAAO,CAAC,UAAU,EAAE,EAAE,IAAI,EAAE,MAAM,EAAE,QAAQ,CAAC,IAAI,CAAC,EAAE,CAAC,CAAA;IACvD,CAAC,CAAC,CACH,CAAA;AACH,CAAC;AAED,6EAA6E;AAC7E,qBAAqB;AACrB,MAAM,UAAU,eAAe,CAAC,WAAyB,EAAE,KAAa;IACtE,MAAM,MAAM,GAAG,IAAI,GAAG,EAAsB,CAAA;IAC5C,KAAK,MAAM,UAAU,IAAI,WAAW,EAAE,CAAC;QACrC,MAAM,KAAK,GAAG,YAAY,CAAC,UAAU,EAAE,KAAK,CAAC,CAAA;QAC7C,IAAI,KAAK,KAAK,SAAS,EAAE,CAAC;YACxB,MAAM,CAAC,GAAG,CAAC,UAAU,EAAE,KAAK,CAAC,CAAA;QAC/B,CAAC;IACH,CAAC;IACD,OAAO,MAAM,CAAA;AACf,CAAC;AAQD;;;;;;GAMG;AACH,SAAS,eAAe,CACtB,IAA2B;IAE3B,MAAM,KAAK,GAAG,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,IAAI,EAAE,KAAK,CAAC,EAAE,EAAE;QACvC,MAAM,OAAO,GAAG,eAAe,CAC7B,KAAK,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,UAAU,CAAC,MAAM,KAAK,CAAC,CAAC,CAAC,CAC9C,CAAA;QACD,MAAM,OAAO,GAAG,eAAe,CAC7B,KAAK,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,UAAU,CAAC,MAAM,KAAK,CAAC,CAAC,CAAC,CAC9C,CAAA;QACD,OAAO,EAAE,IAAI,EAAE,OAAO,EAAE,OAAO,EAAE,CAAA;IACnC,CAAC,CAAC,CAAA;IACF,MAAM,EAAE,GAAG,IAAI,CAAC,GAAG,CAAC,CAAC,EAAE,GAAG,KAAK,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,EAAE,SAAS,IAAI,CAAC,CAAC,CAAC,CAAA;IACvE,MAAM,IAAI,GAAG,IAAI,CAAC,GAAG,CAAC,CAAC,EAAE,GAAG,KAAK,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,EAAE,SAAS,IAAI,CAAC,CAAC,CAAC,CAAA;IACzE,MAAM,SAAS,GAAG,EAAE,GAAG,IAAI,CAAA;IAC3B,OAAO,IAAI,GAAG,CACZ,KAAK,CAAC,GAAG,CAAC,CAAC,EAAE,IAAI,EAAE,OAAO,EAAE,OAAO,EAAE,EAAE,EAAE,CAAC;QACxC,IAAI;QACJ;YACE,mEAAmE;YACnE,GAAG,OAAO,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,GAAG,CAAC,EAAE,IAAI,EAAE,EAAE,GAAG,CAAC,GAAG,CAAC,CAAC,IAAI,EAAE,SAAS,EAAE,CAAC,CAAC;YACjE,GAAG,OAAO,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,GAAG,CAAC,EAAE,IAAI,EAAE,EAAE,GAAG,CAAC,CAAC,IAAI,EAAE,SAAS,EAAE,CAAC,CAAC;SAC9D;KACF,CAAC,CACH,CAAA;AACH,CAAC;AAED,yDAAyD;AACzD,SAAS,UAAU,CACjB,KAAsB,EACtB,IAA2B;IAE3B,OAAO,KAAK,CAAC,QAAQ,KAAK,YAAY;QACpC,CAAC,CAAC,eAAe,CAAC,IAAI,CAAC;QACvB,CAAC,CAAC,IAAI,GAAG,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,IAAI,EAAE,KAAK,CAAC,EAAE,EAAE,CAAC,CAAC,IAAI,EAAE,eAAe,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAA;AAC1E,CAAC;AAED;;;;;;;GAOG;AACH,MAAM,UAAU,iBAAiB,CAAC,EAChC,KAAK,EACL,KAAK,EACL,QAAQ,EACR,WAAW,EACX,gBAAgB,EAChB,MAAM,GAQP;IACC,IAAI,KAAK,CAAC,CAAC,KAAK,QAAQ,EAAE,CAAC;QACzB,OAAO,UAAU,CACf,KAAK,EACL,CAAC,GAAG,WAAW,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,IAAI,EAAE,KAAK,CAAC,EAAE,EAAE,CAAC;YACtC,IAAI;YACJ,KAAK,CAAC,GAAG,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;gBACjB,GAAG,IAAI;gBACP,MAAM,EAAE,IAAI,CAAC,QAAQ,GAAG,QAAQ;gBAChC,IAAI,EAAE,IAAI,CAAC,MAAM,GAAG,QAAQ;aAC7B,CAAC,CAAC;SACJ,CAAC,CACH,CAAA;IACH,CAAC;IACD,MAAM,OAAO,GAAG,MAAM,CAAC,OAAO,CAAC,gBAAgB,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package/dist/ggplotPalettes.js

@@ -69,11 +69,22 @@ export const namedPalettes = {
         '#bab0ac',
     ],
 };
+// the spellings jbrowse-components' `paletteFromSpec` takes for two of them
+const aliases = {
+    okabeIto: 'okabeito',
+    tableau10: 'tableau',
+};
 /**
  * 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];
+    return name === undefined
+        ? undefined
+        : Object.hasOwn(namedPalettes, name)
+            ? namedPalettes[name]
+            : Object.hasOwn(aliases, name)
+                ? namedPalettes[aliases[name]]
+                : undefined;
 }
 //# sourceMappingURL=ggplotPalettes.js.map

package/dist/ggplotPalettes.js.map

@@ -1 +1 @@
-{"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"}
+{"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,4EAA4E;AAC5E,MAAM,OAAO,GAA2B;IACtC,QAAQ,EAAE,UAAU;IACpB,SAAS,EAAE,SAAS;CACrB,CAAA;AAED;;;GAGG;AACH,MAAM,UAAU,YAAY,CAAC,IAAa;IACxC,OAAO,IAAI,KAAK,SAAS;QACvB,CAAC,CAAC,SAAS;QACX,CAAC,CAAC,MAAM,CAAC,MAAM,CAAC,aAAa,EAAE,IAAI,CAAC;YAClC,CAAC,CAAC,aAAa,CAAC,IAAI,CAAC;YACrB,CAAC,CAAC,MAAM,CAAC,MAAM,CAAC,OAAO,EAAE,IAAI,CAAC;gBAC5B,CAAC,CAAC,aAAa,CAAC,OAAO,CAAC,IAAI,CAAE,CAAC;gBAC/B,CAAC,CAAC,SAAS,CAAA;AACnB,CAAC"}

package/dist/groupKeys.d.ts

@@ -0,0 +1,6 @@
+/**
+ * Numbers first by value, then every other value run by run with digit runs
+ * by magnitude, so `2` before `10`, `chr2` before `chr10` and `2.3.2.1a`
+ * before `2.3.4.4b`. The empty value sorts last.
+ */
+export declare function compareGroupKeys(a: string, b: string): number;

package/dist/groupKeys.js

@@ -0,0 +1,52 @@
+// copied from jbrowse-components packages/core/src/util/groupKeys.ts, which
+// @jbrowse/core 5.0.0-beta.9 ships but the hosts the plugin runs on do not
+const NUMERIC = /^-?\d+(\.\d+)?$/;
+const DIGIT_RUNS = /\d+|\D+/g;
+function compareRuns(a, b) {
+    const runsA = a.match(DIGIT_RUNS) ?? [];
+    const runsB = b.match(DIGIT_RUNS) ?? [];
+    const shared = Math.min(runsA.length, runsB.length);
+    for (let i = 0; i < shared; i++) {
+        const x = runsA[i];
+        const y = runsB[i];
+        if (x === y) {
+            continue;
+        }
+        if (/^\d/.test(x) && /^\d/.test(y)) {
+            const nx = Number(x);
+            const ny = Number(y);
+            if (nx !== ny) {
+                return nx < ny ? -1 : 1;
+            }
+            return x.length < y.length ? -1 : 1;
+        }
+        return x < y ? -1 : 1;
+    }
+    return runsA.length - runsB.length;
+}
+/**
+ * Numbers first by value, then every other value run by run with digit runs
+ * by magnitude, so `2` before `10`, `chr2` before `chr10` and `2.3.2.1a`
+ * before `2.3.4.4b`. The empty value sorts last.
+ */
+export function compareGroupKeys(a, b) {
+    if (a === b) {
+        return 0;
+    }
+    if (a === '' || b === '') {
+        return a === '' ? 1 : -1;
+    }
+    const numA = NUMERIC.test(a);
+    const numB = NUMERIC.test(b);
+    if (numA !== numB) {
+        return numA ? -1 : 1;
+    }
+    if (numA) {
+        const diff = Number(a) - Number(b);
+        if (diff !== 0) {
+            return diff < 0 ? -1 : 1;
+        }
+    }
+    return compareRuns(a, b);
+}
+//# sourceMappingURL=groupKeys.js.map

package/dist/groupKeys.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"groupKeys.js","sourceRoot":"","sources":["../src/groupKeys.ts"],"names":[],"mappings":"AAAA,4EAA4E;AAC5E,2EAA2E;AAE3E,MAAM,OAAO,GAAG,iBAAiB,CAAA;AACjC,MAAM,UAAU,GAAG,UAAU,CAAA;AAE7B,SAAS,WAAW,CAAC,CAAS,EAAE,CAAS;IACvC,MAAM,KAAK,GAAG,CAAC,CAAC,KAAK,CAAC,UAAU,CAAC,IAAI,EAAE,CAAA;IACvC,MAAM,KAAK,GAAG,CAAC,CAAC,KAAK,CAAC,UAAU,CAAC,IAAI,EAAE,CAAA;IACvC,MAAM,MAAM,GAAG,IAAI,CAAC,GAAG,CAAC,KAAK,CAAC,MAAM,EAAE,KAAK,CAAC,MAAM,CAAC,CAAA;IACnD,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,MAAM,EAAE,CAAC,EAAE,EAAE,CAAC;QAChC,MAAM,CAAC,GAAG,KAAK,CAAC,CAAC,CAAE,CAAA;QACnB,MAAM,CAAC,GAAG,KAAK,CAAC,CAAC,CAAE,CAAA;QACnB,IAAI,CAAC,KAAK,CAAC,EAAE,CAAC;YACZ,SAAQ;QACV,CAAC;QACD,IAAI,KAAK,CAAC,IAAI,CAAC,CAAC,CAAC,IAAI,KAAK,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC;YACnC,MAAM,EAAE,GAAG,MAAM,CAAC,CAAC,CAAC,CAAA;YACpB,MAAM,EAAE,GAAG,MAAM,CAAC,CAAC,CAAC,CAAA;YACpB,IAAI,EAAE,KAAK,EAAE,EAAE,CAAC;gBACd,OAAO,EAAE,GAAG,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;YACzB,CAAC;YACD,OAAO,CAAC,CAAC,MAAM,GAAG,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;QACrC,CAAC;QACD,OAAO,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;IACvB,CAAC;IACD,OAAO,KAAK,CAAC,MAAM,GAAG,KAAK,CAAC,MAAM,CAAA;AACpC,CAAC;AAED;;;;GAIG;AACH,MAAM,UAAU,gBAAgB,CAAC,CAAS,EAAE,CAAS;IACnD,IAAI,CAAC,KAAK,CAAC,EAAE,CAAC;QACZ,OAAO,CAAC,CAAA;IACV,CAAC;IACD,IAAI,CAAC,KAAK,EAAE,IAAI,CAAC,KAAK,EAAE,EAAE,CAAC;QACzB,OAAO,CAAC,KAAK,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;IAC1B,CAAC;IACD,MAAM,IAAI,GAAG,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;IAC5B,MAAM,IAAI,GAAG,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;IAC5B,IAAI,IAAI,KAAK,IAAI,EAAE,CAAC;QAClB,OAAO,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;IACtB,CAAC;IACD,IAAI,IAAI,EAAE,CAAC;QACT,MAAM,IAAI,GAAG,MAAM,CAAC,CAAC,CAAC,GAAG,MAAM,CAAC,CAAC,CAAC,CAAA;QAClC,IAAI,IAAI,KAAK,CAAC,EAAE,CAAC;YACf,OAAO,IAAI,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;QAC1B,CAAC;IACH,CAAC;IACD,OAAO,WAAW,CAAC,CAAC,EAAE,CAAC,CAAC,CAAA;AAC1B,CAAC"}

package/dist/index.d.ts

@@ -23,5 +23,5 @@ export type { InterProScanResults } from 'msa-parsers';
 export type { ColumnCounts } from './columnCounts.ts';
 export type { ColumnStats } from './columnStats.ts';
 export type { ZoomSnapshot } from './zoomSnapshot.ts';
-export type { ResolvedScale, ScaleSpec } from './scales.ts';
+export type { ColorChannel, ColorSpec, LegacyColumnTrack, LegacyEncoding, LegacyRowPanel, LegacyScale, ResolvedScale, ScaleTable, SharedScale, } from './scales.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.d.ts

@@ -2,6 +2,7 @@ import type { ColumnStats } from './columnStats.ts';
 import type { ScrollZoomAxis } from './constants.ts';
 import type { HierarchyNode } from './hierarchy.ts';
 import type { ExportSvgOptions } from './renderToSvg.tsx';
+import type { ColorChannel, LegacyColumnTrack, LegacyEncoding, LegacyRowPanel, ScaleTable, SharedScale } from './scales.ts';
 import type { Annotation, Arc, BasicTrack, Cell, Clade, ResidueMappingProblem, ColumnTrackSpec, DomainBand, Encoding, Feature, Highlight, Legend, MsaSelection, NodeWithIds, Region, ResidueMapping, ResolvedClade, ResolvedEncoding, ResolvedFeaturePanel, ResolvedStripPanel, ResolvedHighlight, ResolvedSelection, TreeRoot, ResolvedRowPanel, RowDataInput, RowPanelSpec, RowResidue, StructureResidue, TrackKind, UnshareableData, Viewport } from './types.ts';
 import type { ZoomSnapshot } from './zoomSnapshot.ts';
 import type { FileLocation as FileLocationType } from '@jbrowse/core/util/types';
@@ -542,7 +543,7 @@ declare function stateModelFactory({ maxInlineSnapshotBytes, }?: {
      * tracks supplied as data: per-column values drawn as bars, or a
      * per-column string drawn as a text track. See docs/layers.md
      */
-    columnTracks: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IType<ColumnTrackSpec, ColumnTrackSpec, ColumnTrackSpec>>, [undefined]>;
+    columnTracks: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").ISnapshotProcessor<import("@jbrowse/mobx-state-tree").IType<ColumnTrackSpec, ColumnTrackSpec, ColumnTrackSpec>, ColumnTrackSpec, import("@jbrowse/mobx-state-tree")._NotCustomized>>, [undefined]>;
     /**
      * #property
      * row-to-structure residue correspondence, computed outside the viewer
@@ -634,20 +635,21 @@ declare function stateModelFactory({ maxInlineSnapshotBytes, }?: {
     clades: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IType<Clade, Clade, Clade>>, [undefined]>;
     /**
      * #property
-     * what the viewer's own marks read from `rowData`:
-     * `{channel, field, scale?}` per channel, where `channel` is
-     * `tipLabel` or `rowTint`. See docs/layers.md
+     * what the viewer's own marks read from `rowData` or the feature
+     * table: `{channel, field, range?, domain?, title?}` per channel. The
+     * earlier `scale: {palette}` and `scale: {map}` read as `range` and
+     * `domain`. See docs/layers.md
      */
-    encodings: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IType<Encoding, Encoding, Encoding>>, [undefined]>;
+    encodings: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").ISnapshotProcessor<import("@jbrowse/mobx-state-tree").IType<Encoding, Encoding, Encoding>, Encoding | LegacyEncoding, import("@jbrowse/mobx-state-tree")._NotCustomized>>, [undefined]>;
     /**
      * #property
      * panels drawn between the tree and the alignment:
-     * `{kind: "strip", field, scale?, width?, header?}` colors one cell
-     * per row from a `rowData` field, and
+     * `{kind: "strip", field, range?, domain?, title?, width?, header?}`
+     * colors one cell per row from a `rowData` field, and
      * `{kind: "features", x, encoding?, transform?, width?, header?}`
      * draws the spans the GFF carries. See docs/layers.md
      */
-    rowPanels: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IType<RowPanelSpec, RowPanelSpec, RowPanelSpec>>, [undefined]>;
+    rowPanels: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").ISnapshotProcessor<import("@jbrowse/mobx-state-tree").IType<RowPanelSpec, RowPanelSpec, RowPanelSpec>, LegacyRowPanel | RowPanelSpec, import("@jbrowse/mobx-state-tree")._NotCustomized>>, [undefined]>;
 }, {
     queueOfDialogs: [import("@jbrowse/core/util").DialogComponentType, any][];
 } & {
@@ -739,7 +741,8 @@ declare function stateModelFactory({ maxInlineSnapshotBytes, }?: {
     volatileWidth: number | undefined;
     /**
      * #volatile
-     * resize handle width between tree and msa area, px
+     * thickness of the dividers, between the tree and the alignment and under
+     * the view, px
      */
     resizeHandleWidth: number;
     /**
@@ -1998,7 +2001,7 @@ declare function stateModelFactory({ maxInlineSnapshotBytes, }?: {
     /**
      * #action
      */
-    setColumnTracks(tracks: ColumnTrackSpec[]): void;
+    setColumnTracks(tracks: (ColumnTrackSpec | LegacyColumnTrack)[]): void;
     /**
      * #action
      * replace the row table, which the model keeps as the JSON string
@@ -2009,12 +2012,12 @@ declare function stateModelFactory({ maxInlineSnapshotBytes, }?: {
      * #action
      * replace what the viewer's marks read from the row table
      */
-    setEncodings(encodings: Encoding[]): void;
+    setEncodings(encodings: (Encoding | LegacyEncoding)[]): void;
     /**
      * #action
      * replace the panels drawn between the tree and the alignment
      */
-    setRowPanels(panels: RowPanelSpec[]): void;
+    setRowPanels(panels: (RowPanelSpec | LegacyRowPanel)[]): void;
     /**
      * #action
      * replace the alignment<->structure correspondence (see docs/layers.md)
@@ -2121,11 +2124,10 @@ declare function stateModelFactory({ maxInlineSnapshotBytes, }?: {
      * the categorical color keys drawn for this view, shared by the on-screen
      * legend overlay and the SVG export's reserved column. The domain overlay
      * produces the first, listing the `featureFill` scale where an encoding
-     * names one. Every field a row-table encoding or a row panel reads
-     * produces one more, so two channels over one field, or two strips over
-     * it, list that field once. A strip's `legend` names the title it lists
-     * under, so strips over eight fields with one set of colors list one
-     * legend between them
+     * names one. Every scale a row-table encoding or a row panel reads
+     * produces one more, keyed by its declaration, so two channels or two
+     * strips declaring one scale list it once, and strips over eight fields
+     * naming one `title` list one legend between them
      */
     readonly legends: Legend[];
     /**
@@ -2256,6 +2258,21 @@ declare function stateModelFactory({ maxInlineSnapshotBytes, }?: {
      * table or the encodings, never per row per frame.
      */
     readonly resolvedEncodings: ResolvedEncoding[];
+    /**
+     * #getter
+     * every color object the encodings and the row panels declare, keyed
+     * by declaration (`declarationKey`) and resolved once over the union
+     * of the values its records' fields take, so a value two strips share
+     * takes one color in both. A feature field reads every feature loaded,
+     * so hiding a type in the filter dialog leaves the rest in their
+     * colors, and its legend lists the values of the drawn features.
+     */
+    readonly resolvedScales: Map<string, SharedScale>;
+    /**
+     * #method
+     * the shared scale a record's color object resolves to
+     */
+    scaleOf(channel: ColorChannel, table: ScaleTable): SharedScale;
     /**
      * #getter
      * each row panel's scale resolved against the values its field takes,