react-msaview 9.0.0 → 9.1.1

package/dist/filehandleLoader.js.map

@@ -0,0 +1 @@
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package/dist/headlessRenderEnv.d.ts

@@ -1,48 +1,21 @@
-/**
- * DOM shims for driving `renderToSvg` outside a browser -- the SVG-export
- * tests, the README figure generator, and react-msaview-cli all need them.
- *
- * jsdom implements neither DOMMatrix nor a canvas 2D context, and
- * `@jbrowse/svgcanvas` needs both: it tracks the current transform as a real
- * matrix, and the renderers ask a throwaway canvas to measure text.
- *
- * The matrix stub has to accept the ARRAY constructor. svgcanvas normalizes
- * every transform through `new DOMMatrix([a, b, c, d, e, f])`, so a stub that
- * only takes six positional arguments silently binds the whole array to `a` and
- * leaves the rest undefined -- every emitted transform then carries `NaN` in its
- * x components, which no assertion on a drawn x-position can survive.
- */
-export declare class HeadlessDOMMatrix {
-    a: number;
-    b: number;
-    c: number;
-    d: number;
-    e: number;
-    f: number;
-    constructor(init?: number[]);
-    multiply(o: HeadlessDOMMatrix): HeadlessDOMMatrix;
-    translate(x: number, y?: number): HeadlessDOMMatrix;
-    scale(x: number, y?: number): HeadlessDOMMatrix;
-}
-export declare class HeadlessDOMPoint {
-    x: number;
-    y: number;
-    constructor(x?: number, y?: number);
-    matrixTransform(m: HeadlessDOMMatrix): HeadlessDOMPoint;
-}
 /**
  * Install the shims, into `globalThis` by default. A Node caller that builds
  * its own jsdom passes that window instead, because Node has no global
  * HTMLCanvasElement to patch.
  *
- * `measureText` reports 0.6em per character, close enough to a real sans-serif
- * average for layout and, more usefully, exactly predictable: a caller can
- * compute the width a renderer will see rather than hardcoding a number
- * measured from one machine's fonts.
+ * Without `measureContext`, `measureText` reports 0.6em per character, close
+ * enough to a real sans-serif average for layout and exactly predictable: a
+ * test can compute the width a renderer will see. A caller with a real canvas,
+ * such as react-msaview-cli with @napi-rs/canvas, passes one of its 2D
+ * contexts as `measureContext` to measure with the installed fonts.
  *
  * `contextExtras` adds to the context a test hands out -- the raster test
  * supplies the ImageData methods that make the export take its image path.
  */
-export declare function installHeadlessRenderEnv(win?: unknown, contextExtras?: Partial<CanvasRenderingContext2D>): void;
-/** the per-character width factor `measureText` above reports */
-export declare const CHAR_WIDTH_RATIO = 0.6;
+export declare function installHeadlessRenderEnv(win?: unknown, contextExtras?: Partial<CanvasRenderingContext2D>, measureContext?: MeasureContext): void;
+export interface MeasureContext {
+    font: string;
+    measureText(text: string): {
+        width: number;
+    };
+}

package/dist/headlessRenderEnv.js

@@ -12,7 +12,8 @@
  * leaves the rest undefined -- every emitted transform then carries `NaN` in its
  * x components, which no assertion on a drawn x-position can survive.
  */
-export class HeadlessDOMMatrix {
+import { CHAR_WIDTH_RATIO } from './measureTextCanvas.js';
+class HeadlessDOMMatrix {
     a;
     b;
     c;
@@ -45,7 +46,7 @@ export class HeadlessDOMMatrix {
         return this.multiply(new HeadlessDOMMatrix([x, 0, 0, y, 0, 0]));
     }
 }
-export class HeadlessDOMPoint {
+class HeadlessDOMPoint {
     x;
     y;
     constructor(x = 0, y = 0) {
@@ -61,15 +62,16 @@ export class HeadlessDOMPoint {
  * its own jsdom passes that window instead, because Node has no global
  * HTMLCanvasElement to patch.
  *
- * `measureText` reports 0.6em per character, close enough to a real sans-serif
- * average for layout and, more usefully, exactly predictable: a caller can
- * compute the width a renderer will see rather than hardcoding a number
- * measured from one machine's fonts.
+ * Without `measureContext`, `measureText` reports 0.6em per character, close
+ * enough to a real sans-serif average for layout and exactly predictable: a
+ * test can compute the width a renderer will see. A caller with a real canvas,
+ * such as react-msaview-cli with @napi-rs/canvas, passes one of its 2D
+ * contexts as `measureContext` to measure with the installed fonts.
  *
  * `contextExtras` adds to the context a test hands out -- the raster test
  * supplies the ImageData methods that make the export take its image path.
  */
-export function installHeadlessRenderEnv(win = globalThis, contextExtras = {}) {
+export function installHeadlessRenderEnv(win = globalThis, contextExtras = {}, measureContext) {
     const g = globalThis;
     g.DOMMatrix = HeadlessDOMMatrix;
     g.DOMPoint = HeadlessDOMPoint;
@@ -84,12 +86,16 @@ export function installHeadlessRenderEnv(win = globalThis, contextExtras = {}) {
             set font(v) {
                 font = v;
             },
-            measureText: (t) => ({
-                width: t.length * (Number.parseFloat(font) || 10) * CHAR_WIDTH_RATIO,
-            }),
+            measureText: (t) => {
+                if (measureContext) {
+                    measureContext.font = font;
+                    return { width: measureContext.measureText(t).width };
+                }
+                return {
+                    width: t.length * (Number.parseFloat(font) || 10) * CHAR_WIDTH_RATIO,
+                };
+            },
         }, contextExtras);
     };
 }
-/** the per-character width factor `measureText` above reports */
-export const CHAR_WIDTH_RATIO = 0.6;
 //# sourceMappingURL=headlessRenderEnv.js.map

package/dist/headlessRenderEnv.js.map

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

@@ -23,7 +23,6 @@ export interface HierarchyNode<T = NodeWithIds> extends CoreHierarchyNode<T> {
 export { descendants, find, forEachDescendant, forEachLink, leaves, links, sort, sum, };
 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;
@@ -63,10 +62,10 @@ export declare class LaidOutNode<T> implements HierarchyNode<T> {
     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.
+ * The tree laid out 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;
@@ -80,8 +79,6 @@ export declare function collapsedSubtreeMaxLength<T extends {
     length?: number;
 }>(node: HierarchyNode<T>): number;
 export declare function calcDepthToLeaf<T>(node: HierarchyNode<T>): 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.
@@ -104,7 +101,7 @@ export declare function mrca<T extends {
 }>(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
+ * coordinates layoutTree 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.
  */

package/dist/hierarchy.js

@@ -7,49 +7,6 @@ export { descendants, find, forEachDescendant, forEachLink, leaves, links, sort,
 export function hierarchy(data, childrenAccessor) {
     return coreHierarchy(data, childrenAccessor);
 }
-export function clusterLayout(root, sizeX, sizeY) {
-    const leafNodes = leaves(root);
-    const n = leafNodes.length;
-    const step = sizeX / n;
-    for (let i = 0; i < n; i++) {
-        leafNodes[i].x = (i + 0.5) * step;
-    }
-    // x of an internal node is the mean of its children's x, so process in
-    // post-order (children before parents). The subtree span comes from the same
-    // pass, for the block culls in the tree renderer.
-    const nodes = descendants(root);
-    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;
-            for (const child of node.children) {
-                sum += child.x;
-                min = Math.min(min, child.xMin);
-                max = Math.max(max, child.xMax);
-            }
-            node.x = sum / node.children.length;
-            node.xMin = min;
-            node.xMax = max;
-        }
-        else {
-            node.xMin = node.x;
-            node.xMax = node.x;
-        }
-    }
-    const rootHeight = root.height;
-    const stack = [{ node: root, depth: 0 }];
-    while (stack.length > 0) {
-        const { node, depth } = stack.pop();
-        node.y = rootHeight === 0 ? sizeY : (depth / rootHeight) * sizeY;
-        if (node.children) {
-            for (const child of node.children) {
-                stack.push({ node: child, depth: depth + 1 });
-            }
-        }
-    }
-}
 /**
  * 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
@@ -106,10 +63,10 @@ export class LaidOutNode {
     }
 }
 /**
- * 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.
+ * The tree laid out 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 };
@@ -242,37 +199,6 @@ export function calcDepthToLeaf(node) {
     }
     return node.depthToLeaf;
 }
-// Max root-to-leaf sum of branch lengths within the subtree at d. Negative
-// lengths are floored at zero, the same as setBrLength does when it lays the
-// tree out, so the extent this reports is the one that gets drawn
-export function maxLength(d) {
-    const nodes = descendants(d);
-    const pathLen = new Map();
-    for (let i = nodes.length - 1; i >= 0; i--) {
-        const n = nodes[i];
-        let childMax = 0;
-        if (n.children) {
-            for (const child of n.children) {
-                childMax = Math.max(childMax, pathLen.get(child));
-            }
-        }
-        pathLen.set(n, Math.max(n.data.length || 0, 0) + childMax);
-    }
-    return pathLen.get(d);
-}
-export function setBrLength(d, y0, k) {
-    const stack = [{ node: d, y0 }];
-    while (stack.length > 0) {
-        const { node, y0: acc } = stack.pop();
-        const next = acc + Math.max(node.data.length || 0, 0);
-        node.len = next * k;
-        if (node.children) {
-            for (const child of node.children) {
-                stack.push({ node: child, y0: next });
-            }
-        }
-    }
-}
 /**
  * Every leaf by name, with a name two leaves share mapping to undefined: a tip
  * set naming it cannot say which tip it means.
@@ -321,7 +247,7 @@ export function mrca(root, names, index = leafIndex(root)) {
 }
 /**
  * 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
+ * coordinates layoutTree 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.
  */

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package/dist/index.d.ts

@@ -1,12 +1,16 @@
 export { renderToSvg } from './renderToSvg.tsx';
 export type { ExportSvgOptions } from './renderToSvg.tsx';
-export { CHAR_WIDTH_RATIO, installHeadlessRenderEnv, } from './headlessRenderEnv.ts';
+export { installHeadlessRenderEnv } from './headlessRenderEnv.ts';
+export { CHAR_WIDTH_RATIO } from './measureTextCanvas.ts';
 export { 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';
+export type { ToolbarSlots } from './components/header/Header.tsx';
 export { default as MSAViewer } from './components/MSAViewer.tsx';
 export type { MSAViewerProps } from './components/MSAViewer.tsx';
+export { resolveTheme, viewerSnapshot } from './viewerSnapshot.ts';
+export { schemeResidueColor } from './schemeResidueColor.ts';
 export { mount } from './mount.tsx';
 export { defineMsaElement } from './element.ts';
 export { useMsaSvgFigure } from './useMsaSvgFigure.ts';
@@ -18,5 +22,6 @@ 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 { ZoomSnapshot } from './zoomSnapshot.ts';
 export type { ResolvedScale, ScaleSpec } 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/index.js

@@ -10,7 +10,8 @@
 export { renderToSvg } from './renderToSvg.js';
 // renderToSvg outside a browser needs DOM bits jsdom omits; react-msaview-cli
 // and the README figure generator both drive it that way
-export { CHAR_WIDTH_RATIO, installHeadlessRenderEnv, } from './headlessRenderEnv.js';
+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';
@@ -18,6 +19,10 @@ export { maxNeighborJoiningRows } from './constants.js';
 export { expandSpec, residueLabel } from './expandSpec.js';
 export { default as MSAView } from './components/Loading.js';
 export { default as MSAViewer } from './components/MSAViewer.js';
+// the snapshot MSAViewer builds from its props, for the CLI's --props
+export { resolveTheme, viewerSnapshot } from './viewerSnapshot.js';
+// the active scheme's hex color for a row residue, to paint a structure with
+export { schemeResidueColor } from './schemeResidueColor.js';
 export { mount } from './mount.js';
 export { defineMsaElement } from './element.js';
 export { useMsaSvgFigure } from './useMsaSvgFigure.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,sBAAsB,EAAE,MAAM,gBAAgB,CAAA;AACvD,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/measureTextCanvas.d.ts

@@ -1 +1,8 @@
+/**
+ * Rough average glyph width as a fraction of the font size for the sans-serif
+ * stack the labels use. measureTextCanvas falls back on it where there is no
+ * canvas to measure with (jsdom, SSR), and the headless render environment's
+ * `measureText` reports it.
+ */
+export declare const CHAR_WIDTH_RATIO = 0.6;
 export declare function measureTextCanvas(text: string, fontSize: number): number;

package/dist/measureTextCanvas.js

@@ -13,15 +13,17 @@ function getCtx() {
     }
     return ctxHandle;
 }
-// Rough average glyph width as a fraction of the font size for the sans-serif
-// stack the tree labels use. Only reached where there is no canvas to measure
-// with (jsdom, SSR); estimating the label gutter beats throwing out of the
-// layout getters that read this on every render.
-const fallbackGlyphWidthRatio = 0.6;
+/**
+ * Rough average glyph width as a fraction of the font size for the sans-serif
+ * stack the labels use. measureTextCanvas falls back on it where there is no
+ * canvas to measure with (jsdom, SSR), and the headless render environment's
+ * `measureText` reports it.
+ */
+export const CHAR_WIDTH_RATIO = 0.6;
 export function measureTextCanvas(text, fontSize) {
     const ctx = getCtx();
     if (!ctx) {
-        return text.length * fontSize * fallbackGlyphWidthRatio;
+        return text.length * fontSize * CHAR_WIDTH_RATIO;
     }
     setFontSize(ctx, fontSize);
     return ctx.measureText(text).width;

package/dist/measureTextCanvas.js.map

@@ -1 +1 @@
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package/dist/model/treeModel.d.ts

@@ -62,6 +62,11 @@ export declare function TreeModelF(): import("@jbrowse/mobx-state-tree").IModelT
      * subtree boxed. A click on it focuses the subtree under the pointer
      */
     showTreeOverview: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+    /**
+     * #property
+     * draw the branch-length scale bar above the tree of a phylogram
+     */
+    showTreeScaleBar: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     /**
      * #property
      * height of the tree overview band, px
@@ -110,9 +115,8 @@ export declare function TreeModelF(): import("@jbrowse/mobx-state-tree").IModelT
     setShowTreeOverview(arg: boolean): void;
     /**
      * #action
-     * set the height of the tree overview band (px)
      */
-    setOverviewHeight(n: number): void;
+    setShowTreeScaleBar(arg: boolean): void;
     /**
      * #action
      */

package/dist/model/treeModel.js

@@ -1,5 +1,5 @@
 import { types } from '@jbrowse/mobx-state-tree';
-import { defaultDrawLabels, defaultDrawNodeBubbles, defaultDrawNodeLabels, defaultDrawTree, defaultLabelsAlignRight, defaultOverviewHeight, defaultShowBranchLen, defaultTreeOrder, defaultShowTreeOverview, treeOrders, } from '../constants.js';
+import { defaultDrawLabels, defaultDrawNodeBubbles, defaultDrawNodeLabels, defaultDrawTree, defaultLabelsAlignRight, defaultOverviewHeight, defaultShowBranchLen, defaultTreeOrder, defaultShowTreeOverview, defaultShowTreeScaleBar, treeOrders, } from '../constants.js';
 import { stripDefault } from '../stripDefault.js';
 /**
  * #stateModel Tree
@@ -66,6 +66,11 @@ export function TreeModelF() {
          * subtree boxed. A click on it focuses the subtree under the pointer
          */
         showTreeOverview: stripDefault(types.boolean, defaultShowTreeOverview),
+        /**
+         * #property
+         * draw the branch-length scale bar above the tree of a phylogram
+         */
+        showTreeScaleBar: stripDefault(types.boolean, defaultShowTreeScaleBar),
         /**
          * #property
          * height of the tree overview band, px
@@ -134,10 +139,9 @@ export function TreeModelF() {
         },
         /**
          * #action
-         * set the height of the tree overview band (px)
          */
-        setOverviewHeight(n) {
-            self.overviewHeight = Math.round(n);
+        setShowTreeScaleBar(arg) {
+            self.showTreeScaleBar = arg;
         },
         /**
          * #action

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