react-msaview 5.1.1 → 5.2.0

package/dist/components/tree/renderTreeCanvas.js

@@ -1,4 +1,4 @@
-import { calcDepthToLeaf, descendants, links } from "../../hierarchy.js";
+import { calcDepthToLeaf, forEachDescendant, forEachLink, } from "../../hierarchy.js";
 export const padding = 600;
 const extendBounds = 5;
 const radius = 2.5;
@@ -16,16 +16,15 @@ function getNodeX(node, showBranchLen, maxBranchLen, maxDepthToLeaf) {
 }
 export function renderTree({ offsetY, ctx, model, theme, maxBranchLen, maxDepthToLeaf, blockSizeYOverride, }) {
     const { hierarchy, showBranchLenEffective: showBranchLen, blockSize } = model;
-    const by = blockSizeYOverride || blockSize;
+    const by = blockSizeYOverride ?? blockSize;
     ctx.strokeStyle = theme.palette.text.primary;
-    for (const link of links(hierarchy)) {
-        const { source, target } = link;
+    forEachLink(hierarchy, (source, target) => {
         const sy = source.x;
         const ty = target.x;
         const tx = getNodeX(target, showBranchLen, maxBranchLen, maxDepthToLeaf);
         const sx = getNodeX(source, showBranchLen, maxBranchLen, maxDepthToLeaf);
         if (tx === undefined || sx === undefined) {
-            continue;
+            return;
         }
         const y1 = Math.min(sy, ty);
         const y2 = Math.max(sy, ty);
@@ -39,15 +38,15 @@ export function renderTree({ offsetY, ctx, model, theme, maxBranchLen, maxDepthT
             ctx.lineTo(tx, ty);
             ctx.stroke();
         }
-    }
+    });
 }
 export function renderNodeBubbles({ ctx, clickMap, offsetY, model, maxBranchLen, maxDepthToLeaf, blockSizeYOverride, }) {
     const { hierarchy, showBranchLenEffective: showBranchLen, collapsed, blockSize, marginLeft: ml, } = model;
-    const by = blockSizeYOverride || blockSize;
-    for (const node of descendants(hierarchy)) {
+    const by = blockSizeYOverride ?? blockSize;
+    forEachDescendant(hierarchy, node => {
         const x = getNodeX(node, showBranchLen, maxBranchLen, maxDepthToLeaf);
         if (x === undefined) {
-            continue;
+            return;
         }
         const { data } = node;
         const y = node.x;
@@ -71,11 +70,11 @@ export function renderNodeBubbles({ ctx, clickMap, offsetY, model, maxBranchLen,
                 name,
             });
         }
-    }
+    });
 }
 export function renderTreeLabels({ theme, model, offsetY, ctx, clickMap, maxBranchLen, maxDepthToLeaf, blockSizeYOverride, }) {
-    const { fontSize, showBranchLenEffective: showBranchLen, treeMetadata, blockSize, labelsAlignRight, drawTree, treeAreaWidth, treeAreaWidthMinusMargin, marginLeft, leaves, noTree, } = model;
-    const by = blockSizeYOverride || blockSize;
+    const { fontSize, showBranchLenEffective: showBranchLen, treeMetadata, blockSize, labelsAlignRight, drawTree, treeAreaWidth, treeAreaWidthMinusMargin, marginLeft, leaves, noTree, labelWidthMap, } = model;
+    const by = blockSizeYOverride ?? blockSize;
     const emHeight = ctx.measureText('M').width;
     if (labelsAlignRight) {
         ctx.textAlign = 'right';
@@ -93,9 +92,9 @@ export function renderTreeLabels({ theme, model, offsetY, ctx, clickMap, maxBran
             const yp = y + fontSize / 4;
             let xp = 0;
             if (!noTree) {
-                xp = getNodeX(node, showBranchLen, maxBranchLen, maxDepthToLeaf) || 0;
+                xp = getNodeX(node, showBranchLen, maxBranchLen, maxDepthToLeaf) ?? 0;
             }
-            const { width } = ctx.measureText(displayName);
+            const width = labelWidthMap.get(name) ?? ctx.measureText(displayName).width;
             ctx.fillStyle = theme.palette.text.primary;
             if (labelsAlignRight) {
                 const smallPadding = 2;
@@ -134,19 +133,12 @@ export function renderTreeLabels({ theme, model, offsetY, ctx, clickMap, maxBran
 export function renderTreeCanvas({ model, clickMap, ctx, offsetY, theme, highResScaleFactorOverride, blockSizeYOverride, }) {
     clickMap?.clear();
     // Defer the finish call until after all inserts are done
-    const { noTree, drawTree, drawNodeBubbles, highResScaleFactor, fontSize, showTreeText, marginLeft, nref, 
+    const { noTree, drawTree, drawNodeBubbles, highResScaleFactor, fontSize, showTreeText, marginLeft, 
     // eslint-disable-next-line  @typescript-eslint/no-unused-vars
-    rowHeight: _rowHeight, // this is needed for redrawing after zoom change
+    rowHeight: _rowHeight, // read so the draw autorun re-fires after a zoom change
      } = model;
     ctx.resetTransform();
-    // this is a bogus use of nref, it is never less than 0. we just are using
-    // it in this statement because otherwise it would be an unused variable,
-    // we just need to use nref to indicate a redraw in an autorun when canvas
-    // ref is updated and in order to convince bundlers like not to delete
-    // unused usage with propertyReadSideEffects
-    const k = nref < 0
-        ? Number.NEGATIVE_INFINITY
-        : highResScaleFactorOverride || highResScaleFactor;
+    const k = highResScaleFactorOverride ?? highResScaleFactor;
     ctx.scale(k, k);
     ctx.translate(marginLeft, -offsetY);
     const font = ctx.font;

package/dist/components/tree/renderTreeCanvas.js.map

@@ -1 +1 @@
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package/dist/components/util.d.ts

@@ -1,15 +1 @@
-/**
- * Given a scale ( bp/px ) and minimum distances (px) between major and minor
- * gridlines, return an object like `{ majorPitch: bp, minorPitch: bp }` giving
- * the gridline pitches to use.
- */
-export declare function chooseGridPitch(scale: number, minMajorPitchPx: number, minMinorPitchPx: number): {
-    majorPitch: number;
-    minorPitch: number;
-};
-export declare function makeTicks(start: number, end: number, bpPerPx: number, emitMajor?: boolean, emitMinor?: boolean): {
-    type: string;
-    base: number;
-    index: number;
-}[];
 export declare function mathPower(num: number): string;

package/dist/components/util.js

@@ -1,61 +1,3 @@
-/**
- * Given a scale ( bp/px ) and minimum distances (px) between major and minor
- * gridlines, return an object like `{ majorPitch: bp, minorPitch: bp }` giving
- * the gridline pitches to use.
- */
-export function chooseGridPitch(scale, minMajorPitchPx, minMinorPitchPx) {
-    scale = Math.abs(scale);
-    const minMajorPitchBp = minMajorPitchPx * scale;
-    const majorMagnitude = Number.parseInt(minMajorPitchBp.toExponential().split(/e/i)[1], 10);
-    let majorPitch = 10 ** majorMagnitude;
-    while (majorPitch < minMajorPitchBp) {
-        majorPitch *= 2;
-        if (majorPitch >= minMajorPitchBp) {
-            break;
-        }
-        majorPitch *= 2.5;
-    }
-    majorPitch = Math.max(majorPitch, 5);
-    const majorPitchPx = majorPitch / scale;
-    let minorPitch = 0;
-    if (!(majorPitch % 10) && majorPitchPx / 10 >= minMinorPitchPx) {
-        minorPitch = majorPitch / 10;
-    }
-    else if (!(majorPitch % 5) && majorPitchPx / 5 >= minMinorPitchPx) {
-        minorPitch = majorPitch / 5;
-    }
-    else if (!(majorPitch % 2) && majorPitchPx / 2 >= minMinorPitchPx) {
-        minorPitch = majorPitch / 2;
-    }
-    return { majorPitch, minorPitch };
-}
-export function makeTicks(start, end, bpPerPx, emitMajor = true, emitMinor = true) {
-    const gridPitch = chooseGridPitch(bpPerPx, 60, 15);
-    let minBase = start;
-    let maxBase = end;
-    if (bpPerPx < 0) {
-        ;
-        [minBase, maxBase] = [maxBase, minBase];
-    }
-    // add 20px additional on the right and left to allow us to draw the ends of
-    // labels that lie a little outside our region
-    minBase -= Math.abs(20 * bpPerPx);
-    maxBase += Math.abs(20 * bpPerPx) + 1;
-    const iterPitch = gridPitch.minorPitch || gridPitch.majorPitch;
-    let index = 0;
-    const ticks = [];
-    for (let base = Math.ceil(minBase / iterPitch) * iterPitch; base < maxBase; base += iterPitch) {
-        if (emitMinor && base % (gridPitch.majorPitch * 2)) {
-            ticks.push({ type: 'minor', base: base - 1, index });
-            index += 1;
-        }
-        else if (emitMajor && !(base % (gridPitch.majorPitch * 2))) {
-            ticks.push({ type: 'major', base: base - 1, index });
-            index += 1;
-        }
-    }
-    return ticks;
-}
 export function mathPower(num) {
     if (num < 999) {
         return String(num);

package/dist/components/util.js.map

@@ -1 +1 @@
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+{"version":3,"file":"util.js","sourceRoot":"","sources":["../../src/components/util.ts"],"names":[],"mappings":"AAAA,MAAM,UAAU,SAAS,CAAC,GAAW;IACnC,IAAI,GAAG,GAAG,GAAG,EAAE,CAAC;QACd,OAAO,MAAM,CAAC,GAAG,CAAC,CAAA;IACpB,CAAC;IACD,OAAO,GAAG,SAAS,CAAC,CAAC,CAAC,CAAC,GAAG,GAAG,IAAI,CAAC,CAAC,IAAI,KAAK,CAAC,CAAC,CAAC,GAAG,GAAG,IAAI,CAAC,EAAE,CAAC,KAAK,CAChE,CAAC,CAAC,EACF,CAAC,CAAC,GAAG,CAAC,CACP,EAAE,CAAA;AACL,CAAC"}

package/dist/hierarchy.d.ts

@@ -23,6 +23,8 @@ export declare function find<T>(node: HierarchyNode<T>, predicate: (n: Hierarchy
 export declare function leaves<T>(node: HierarchyNode<T>): HierarchyNode<T>[];
 export declare function descendants<T>(node: HierarchyNode<T>): HierarchyNode<T>[];
 export declare function links<T>(node: HierarchyNode<T>): HierarchyLink<T>[];
+export declare function forEachLink<T>(node: HierarchyNode<T>, cb: (source: HierarchyNode<T>, target: HierarchyNode<T>) => void): void;
+export declare function forEachDescendant<T>(node: HierarchyNode<T>, cb: (n: HierarchyNode<T>) => void): void;
 export declare function clusterLayout<T>(root: HierarchyNode<T>, sizeX: number, sizeY: number): void;
 export declare function collapse<T>(node: HierarchyNode<T>): void;
 export declare function calcDepthToLeaf(node: HierarchyNode): number;

package/dist/hierarchy.js

@@ -111,6 +111,25 @@ export function links(node) {
     visit(node);
     return result;
 }
+export function forEachLink(node, cb) {
+    function visit(n) {
+        if (n.children) {
+            for (const child of n.children) {
+                cb(n, child);
+                visit(child);
+            }
+        }
+    }
+    visit(node);
+}
+export function forEachDescendant(node, cb) {
+    cb(node);
+    if (node.children) {
+        for (const child of node.children) {
+            forEachDescendant(child, cb);
+        }
+    }
+}
 export function clusterLayout(root, sizeX, sizeY) {
     const leafNodes = leaves(root);
     const n = leafNodes.length;

package/dist/hierarchy.js.map

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package/dist/index.js

@@ -1,3 +1,10 @@
+// PUBLIC API — consumed by external JBrowse 2 plugins. Changing or removing any
+// export here is a breaking change for downstream repos:
+//   - jbrowse-plugin-msaview   (wraps MSAModelF + MSAView into a JBrowse view)
+//   - jbrowse-plugin-protein3d (drives MSA<->structure hover/highlight sync)
+// Those plugins also reach into the MsaViewModel instance at runtime; the model
+// members they rely on (e.g. mouseCol/setMousePos, setHighlightedColumns,
+// seqPosToVisibleCol/visibleColToSeqPos) are flagged inline in model.ts.
 export { default as MSAView } from "./components/Loading.js";
 export { default as MSAViewer } from "./components/MSAViewer.js";
 export { default as MSAModelF } from "./model.js";

package/dist/index.js.map

@@ -1 +1 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,OAAO,IAAI,OAAO,EAAE,MAAM,yBAA0B,CAAA;AAC7D,OAAO,EAAE,OAAO,IAAI,SAAS,EAAE,MAAM,2BAA4B,CAAA;AACjE,OAAO,EAAqB,OAAO,IAAI,SAAS,EAAE,MAAM,YAAY,CAAA"}
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,gFAAgF;AAChF,yDAAyD;AACzD,+EAA+E;AAC/E,6EAA6E;AAC7E,gFAAgF;AAChF,0EAA0E;AAC1E,yEAAyE;AACzE,OAAO,EAAE,OAAO,IAAI,OAAO,EAAE,MAAM,yBAA0B,CAAA;AAC7D,OAAO,EAAE,OAAO,IAAI,SAAS,EAAE,MAAM,2BAA4B,CAAA;AACjE,OAAO,EAAqB,OAAO,IAAI,SAAS,EAAE,MAAM,YAAY,CAAA"}

package/dist/model.d.ts

@@ -230,12 +230,6 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
      * array of column indices to highlight
      */
     highlightedColumns: number[] | undefined;
-    /**
-     * #volatile
-     * a dummy variable that is incremented when ref changes so autorun for
-     * drawing canvas commands will run
-     */
-    nref: number;
     /**
      * #volatile
      */
@@ -294,6 +288,10 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
     /**
      * #action
      * set mouse position (row, column) in the MSA
+     *
+     * CROSS-REPO CONTRACT: jbrowse-plugin-protein3d calls this (and reads the
+     * `mouseCol` volatile) to sync MSA<->3D-structure hover. Keep the name and
+     * signature stable; see that repo's ProteinToMsaHoverSync.tsx.
      */
     setMousePos(col?: number, row?: number): void;
     /**
@@ -304,6 +302,10 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
     /**
      * #action
      * set highlighted columns
+     *
+     * CROSS-REPO CONTRACT: called by jbrowse-plugin-msaview
+     * (afterCreateAutoruns.ts) to highlight alignment columns. It has no
+     * in-repo caller, so do not flag it as dead code — it is public API.
      */
     setHighlightedColumns(columns?: number[]): void;
     /**
@@ -442,7 +444,16 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
     /**
      * #getter
      */
+    /**
+     * #getter
+     * Returns the list of row (sequence) names in display order.
+     * Part of the public API used by downstream consumers (e.g. jbrowse plugins).
+     */
     readonly rowNames: string[];
+    /**
+     * #getter
+     */
+    readonly rowNamesSet: Map<string, number>;
     /**
      * #getter
      */
@@ -500,9 +511,7 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
     /**
      * #getter
      */
-    readonly columns: {
-        [k: string]: string;
-    };
+    readonly columns: Map<string, string>;
     /**
      * #getter
      */
@@ -661,7 +670,7 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
      * #action
      */
     doScrollY(deltaY: number): void;
-    setInterProAnnotations(data: Record<string, InterProScanResults>): void;
+    setInterProAnnotations(data?: Record<string, InterProScanResults>): void;
     applyGFFText(gffText: string): void;
     /**
      * #action
@@ -687,6 +696,7 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
     /**
      * #getter
      */
+    readonly labelWidthMap: Map<string, number>;
     readonly labelsWidth: number;
     /**
      * #getter
@@ -712,10 +722,6 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
      * #getter
      */
     readonly showHorizontalScrollbar: boolean;
-    /**
-     * #getter
-     */
-    readonly rowNamesSet: Map<string, number>;
     /**
      * #method
      * Return a row-specific letter at a visible column, or undefined if gap.
@@ -730,6 +736,11 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
      * Convert a visible column to a row-specific sequence position (0-based).
      * Returns undefined if the position is a gap in the sequence.
      *
+     * CROSS-REPO CONTRACT: this and the sibling coordinate converters
+     * (seqPosToVisibleCol, globalColToVisibleCol, seqPosToGlobalCol) are used
+     * by jbrowse-plugin-protein3d to translate between alignment columns and
+     * structure/sequence residue positions across gaps. Keep them stable.
+     *
      * @param rowName - The name of the row
      * @param visibleCol - The visible column index
      * @returns The sequence position (0-based), or undefined if it's a gap
@@ -775,16 +786,6 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
      */
     seqPosToVisibleCol(rowName: string, seqPos: number): number | undefined;
 } & {
-    /**
-     * #getter
-     * Returns information about the currently hovered cell
-     */
-    readonly hoveredCell: {
-        rowName: string;
-        col: number;
-        base: string | undefined;
-        seqPos: number | undefined;
-    } | undefined;
     /**
      * #getter
      * widget width minus the tree area gives the space for the MSA
@@ -874,13 +875,8 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
         theme: Theme;
         includeMinimap?: boolean;
         includeTracks?: boolean;
-        exportType: string;
+        exportType: "entire" | "viewport";
     }): Promise<void>;
-    /**
-     * #action
-     * internal, used for drawing to canvas
-     */
-    incrementRef(): void;
     initFilter(arg: string): void;
     setFilter(arg: string, flag: boolean): void;
     /**