react-msaview 5.10.0 → 6.0.0

package/dist/components/msa/domainBandCursor.d.ts

@@ -0,0 +1,17 @@
+import type { DomainBand } from '../../types.ts';
+/**
+ * Left-to-right cursor over one row's domain bands, answering "which band is
+ * drawn on top at this column" — the fill a letter there has to contrast
+ * against.
+ *
+ * Not simply the first band covering the column. The overlay paints in
+ * `domainBands` order, largest first, so where signatures nest — a family
+ * enclosing a domain, which InterProScan emits routinely — the box a reader
+ * actually sees is the last one painted over that column. `stackIndex` is that
+ * paint order.
+ *
+ * `bands` must be sorted by start column (`domainBandsByStart`), and columns
+ * must be visited in increasing order, which is what the block renderer does.
+ * Both keep this to one pass over the bands per row rather than a scan per cell.
+ */
+export declare function domainBandCursor(bands: DomainBand[] | undefined): (col: number) => DomainBand | undefined;

package/dist/components/msa/domainBandCursor.js

@@ -0,0 +1,39 @@
+/**
+ * Left-to-right cursor over one row's domain bands, answering "which band is
+ * drawn on top at this column" — the fill a letter there has to contrast
+ * against.
+ *
+ * Not simply the first band covering the column. The overlay paints in
+ * `domainBands` order, largest first, so where signatures nest — a family
+ * enclosing a domain, which InterProScan emits routinely — the box a reader
+ * actually sees is the last one painted over that column. `stackIndex` is that
+ * paint order.
+ *
+ * `bands` must be sorted by start column (`domainBandsByStart`), and columns
+ * must be visited in increasing order, which is what the block renderer does.
+ * Both keep this to one pass over the bands per row rather than a scan per cell.
+ */
+export function domainBandCursor(bands) {
+    let next = 0;
+    let active = [];
+    return (col) => {
+        if (!bands) {
+            return undefined;
+        }
+        while (next < bands.length && bands[next].startCol <= col) {
+            active.push(bands[next]);
+            next++;
+        }
+        if (active.some(band => band.endCol <= col)) {
+            active = active.filter(band => band.endCol > col);
+        }
+        let top;
+        for (const band of active) {
+            if (!top || band.stackIndex > top.stackIndex) {
+                top = band;
+            }
+        }
+        return top;
+    };
+}
+//# sourceMappingURL=domainBandCursor.js.map

package/dist/components/msa/domainBandCursor.js.map

@@ -0,0 +1 @@
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package/dist/components/msa/renderMSABlock.js

@@ -1,6 +1,7 @@
 import { setFontSize } from '../../setFontSize.js';
 import { adjustColorForContrast } from '../../util.js';
 import { getVisibleLeaves } from '../getVisibleLeaves.js';
+import { domainBandCursor } from './domainBandCursor.js';
 import { visibleColRange } from './visibleColRange.js';
 export function renderMSABlock({ model, offsetX, offsetY, contrastScheme, ctx, theme, highResScaleFactorOverride, blockSizeXOverride, blockSizeYOverride, }) {
     const { colWidth, blockSize, rowHeight, fontSize, highResScaleFactor, actuallyShowDomains, bgColor, } = model;
@@ -94,8 +95,7 @@ function drawTilesAndText({ model, ctx, theme, contrastScheme, visibleLeaves, xS
             if (str) {
                 const tileY = y - rowHeight;
                 const textY = y - quarterRowHeight;
-                const bands = overDomains ? domainBandsByStart.get(name) : undefined;
-                let band = 0;
+                const bandAt = domainBandCursor(overDomains ? domainBandsByStart.get(name) : undefined);
                 for (let j = 0, l2 = str.length; j < l2; j++) {
                     const col = xStart + j;
                     const letter = str[j];
@@ -109,24 +109,18 @@ function drawTilesAndText({ model, ctx, theme, contrastScheme, visibleLeaves, xS
                         ctx.fillRect(x, tileY, colWidth, rowHeight);
                     }
                     if (showMsaLetters) {
-                        // bands are sorted by start column and the sweep is left to right,
-                        // so one forward-only cursor finds the band covering each column
-                        while (bands && band < bands.length && bands[band].endCol <= col) {
-                            band++;
-                        }
-                        const covering = bands?.[band];
-                        ctx.fillStyle =
-                            covering && covering.startCol <= col
-                                ? // on top of a domain box: contrast against the box fill
-                                    domainColors.get(covering.annotation.accession)
-                                : tiles
-                                    ? // on top of a colored tile
-                                        (contrastScheme[letter] ?? 'black')
-                                    : !drawTiles || !color
-                                        ? // plain background, uncolored letters
-                                            theme.palette.text.primary
-                                        : // letter-color mode: darken/lighten to stay readable
-                                            adjustColorForContrast(color, theme.palette.background.default);
+                        const covering = bandAt(col);
+                        ctx.fillStyle = covering
+                            ? // on top of a domain box: contrast against the box fill
+                                domainColors.get(covering.annotation.accession)
+                            : tiles
+                                ? // on top of a colored tile
+                                    (contrastScheme[letter] ?? 'black')
+                                : !drawTiles || !color
+                                    ? // plain background, uncolored letters
+                                        theme.palette.text.primary
+                                    : // letter-color mode: darken/lighten to stay readable
+                                        adjustColorForContrast(color, theme.palette.background.default);
                         ctx.fillText(isMatchingReference ? '.' : letter, x + halfColWidth, textY);
                     }
                 }

package/dist/components/msa/renderMSABlock.js.map

@@ -1 +1 @@
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package/dist/components/msa/renderMSAMouseover.js

@@ -5,8 +5,7 @@ import { clickColor, hoverColor, multiRowHoverColor, referenceColor, } from '../
 const highlightColumnsFill = 'rgba(255,140,0,0.28)';
 const highlightColumnsBorder = 'rgba(210,90,0,0.95)';
 export function renderMouseover({ ctx, model, }) {
-    const { mouseCol, colWidth, msaAreaWidth, verticalScrollbarWidth, height, rowHeight, scrollX, scrollY, mouseRow, mouseClickRow, mouseClickCol, highResScaleFactor, referenceRowIndex, hoveredRowIndices, highlightedColumnRuns, } = model;
-    const width = msaAreaWidth - verticalScrollbarWidth;
+    const { mouseCol, colWidth, msaCanvasWidth: width, height, rowHeight, scrollX, scrollY, mouseRow, mouseClickRow, mouseClickCol, highResScaleFactor, referenceRowIndex, hoveredRowIndices, highlightedColumnRuns, } = model;
     ctx.resetTransform();
     ctx.clearRect(0, 0, width * highResScaleFactor, height * highResScaleFactor);
     ctx.scale(highResScaleFactor, highResScaleFactor);

package/dist/components/msa/renderMSAMouseover.js.map

@@ -1 +1 @@
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package/dist/components/tree/TreeRuler.js

@@ -1,8 +1,11 @@
 import React from 'react';
 import { observer } from 'mobx-react';
+// The gutter above the tree panel. It spans the resize handle too, so whatever
+// follows it in the top row starts exactly where the alignment canvas does --
+// MainArea has TreePanel + VerticalResizeHandle before the alignment.
 const TreeRuler = observer(({ model }) => {
-    const { treeAreaWidth } = model;
-    return React.createElement("div", { style: { flexShrink: 0, width: treeAreaWidth } });
+    const { treeAreaWidth, resizeHandleWidth } = model;
+    return (React.createElement("div", { style: { flexShrink: 0, width: treeAreaWidth + resizeHandleWidth } }));
 });
 export default TreeRuler;
 //# sourceMappingURL=TreeRuler.js.map

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

@@ -1 +1 @@
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+{"version":3,"file":"TreeRuler.js","sourceRoot":"","sources":["../../../src/components/tree/TreeRuler.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAIrC,+EAA+E;AAC/E,8EAA8E;AAC9E,sEAAsE;AACtE,MAAM,SAAS,GAAG,QAAQ,CAAC,CAAC,EAAE,KAAK,EAA2B,EAAE,EAAE;IAChE,MAAM,EAAE,aAAa,EAAE,iBAAiB,EAAE,GAAG,KAAK,CAAA;IAClD,OAAO,CACL,6BAAK,KAAK,EAAE,EAAE,UAAU,EAAE,CAAC,EAAE,KAAK,EAAE,aAAa,GAAG,iBAAiB,EAAE,GAAI,CAC5E,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,SAAS,CAAA"}

package/dist/ggplotPalettes.d.ts

@@ -1,3 +1,2 @@
 declare const palettes: string[][];
-export declare function getPalette(l: number): string[];
 export default palettes;

package/dist/ggplotPalettes.js

@@ -17,8 +17,5 @@ const palettes = [
         '#FF61CC',
     ],
 ];
-export function getPalette(l) {
-    return palettes[Math.min(l, palettes.length - 1)];
-}
 export default palettes;
 //# sourceMappingURL=ggplotPalettes.js.map

package/dist/ggplotPalettes.js.map

@@ -1 +1 @@
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+{"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"}

package/dist/hierarchy.d.ts

@@ -16,7 +16,6 @@ export interface HierarchyNode<T = NodeWithIds> extends CoreHierarchyNode<T> {
     len?: number;
     depthToLeaf?: number;
     _children?: HierarchyNode<T>[] | null;
-    collapsedTipXNear?: number;
     collapsedTipXFar?: number;
 }
 export { descendants, find, forEachDescendant, forEachLink, leaves, links, sort, sum, };
@@ -24,12 +23,9 @@ 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 declare function collapse<T>(node: HierarchyNode<T>): void;
-export declare function collapsedSubtreeLengthExtent<T extends {
+export declare function collapsedSubtreeMaxLength<T extends {
     length?: number;
-}>(node: HierarchyNode<T>): {
-    min: number;
-    max: number;
-};
+}>(node: HierarchyNode<T>): number;
 export declare function calcDepthToLeaf<T>(node: HierarchyNode<T>): number;
 export declare function findMaxBranchLen(node: HierarchyNode): number;
 export declare function maxLength(d: HierarchyNode): number;

package/dist/hierarchy.js

@@ -56,12 +56,11 @@ export function collapse(node) {
         node.children = null;
     }
 }
-// Min/max cumulative raw branch length from a collapsed node down to the tips of
-// its detached subtree (excludes the node's own branch). Used to size the
+// Cumulative raw branch length from a collapsed node down to the farthest tip of
+// its detached subtree (excludes the node's own branch). Sizes the base of the
 // collapsed-clade triangle in phylogram mode.
-export function collapsedSubtreeLengthExtent(node) {
+export function collapsedSubtreeMaxLength(node) {
     const roots = node._children ?? node.children;
-    let min = Infinity;
     let max = 0;
     if (roots) {
         const stack = roots.map(child => ({
@@ -80,12 +79,11 @@ export function collapsedSubtreeLengthExtent(node) {
                 }
             }
             else {
-                min = Math.min(min, acc);
                 max = Math.max(max, acc);
             }
         }
     }
-    return { min: min === Infinity ? 0 : min, max };
+    return max;
 }
 // Cladogram positioning based on ape's plot.phylo: uses topological depth (max
 // steps to a tip) instead of branch length so all leaves align at the rightmost

package/dist/hierarchy.js.map

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

@@ -4,6 +4,6 @@ export { default as MSAViewer } from './components/MSAViewer.tsx';
 export { type MsaViewModel, default as MSAModelF } from './model.ts';
 export type { MSAFormat, MSAParserType } from 'msa-parsers';
 export type { HierarchyNode } from './hierarchy.ts';
-export type { InterProScanResults } from './launchInterProScan.ts';
+export type { InterProScanResults } from 'msa-parsers';
 export type { ColumnCounts } from './columnCounts.ts';
-export type { Accession, BasicTrack, BasicTrackModel, DomainBand, Node, NodeWithIds, NodeWithIdsAndLength, TextTrackModel, TidyDomainAnnotation, } from './types.ts';
+export type { Accession, Annotation, BasicTrack, BasicTrackModel, DomainBand, Node, NodeWithIds, NodeWithIdsAndLength, TextTrackModel, TidyDomainAnnotation, } from './types.ts';

package/dist/launchInterProScan.d.ts

@@ -1,27 +1,4 @@
 import type { MsaViewModel } from './model.ts';
-export interface InterProScanResults {
-    matches: {
-        signature: {
-            entry?: {
-                name: string;
-                description: string;
-                accession: string;
-                featureType?: string;
-            };
-        };
-        locations: {
-            start: number;
-            end: number;
-            strand?: number;
-        }[];
-    }[];
-    xref: {
-        id: string;
-    }[];
-}
-export interface InterProScanResponse {
-    results: InterProScanResults[];
-}
 export declare function launchInterProScan({ algorithm, seq, programs, onJobId, onProgress, model, signal, }: {
     algorithm: string;
     seq: string;

package/dist/launchInterProScan.js

@@ -1,4 +1,5 @@
 import { getSession } from '@jbrowse/core/util';
+import { interProScanResponseToAnnotations } from 'msa-parsers';
 import { isAbortError, jsonfetch, textfetch, timeout } from './fetchUtils.js';
 const base = 'https://www.ebi.ac.uk/Tools/services/rest';
 async function runInterProScan({ seq, onProgress, onJobId, programs, model, signal, }) {
@@ -90,11 +91,7 @@ async function loadInterProScanResultsWithStatus({ jobId, model, onProgress, sig
             url: `https://www.ebi.ac.uk/Tools/services/rest/iprscan5/result/${jobId}/json`,
         });
         const ret = await loadInterProScanResults(jobId, signal);
-        // key each result by its xref id; skip any result lacking an xref entry
-        // rather than crashing the whole load on one malformed result
-        model.setDomains(Object.fromEntries(ret.results
-            .map(r => [r.xref[0]?.id, r])
-            .filter((e) => e[0] !== undefined)));
+        model.setAnnotations(interProScanResponseToAnnotations(ret));
         getSession(model).notify(`Loaded interproscan ${jobId} results`, 'success');
     }
     catch (e) {

package/dist/launchInterProScan.js.map

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package/dist/measureTextCanvas.js

@@ -1,12 +1,27 @@
 import { setFontSize } from './setFontSize.js';
-let canvasHandle;
-export function measureTextCanvas(text, fontSize) {
-    if (!canvasHandle) {
-        canvasHandle = document.createElement('canvas');
+// Cached across calls: labelWidthMap measures every leaf label on every layout,
+// and both createElement and getContext are far more expensive than measureText.
+// `null` records that this environment has no 2d context, so the lookup is not
+// retried on every label.
+let ctxHandle;
+function getCtx() {
+    if (ctxHandle === undefined) {
+        ctxHandle =
+            typeof document === 'undefined'
+                ? null
+                : document.createElement('canvas').getContext('2d');
     }
-    const ctx = canvasHandle.getContext('2d');
+    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;
+export function measureTextCanvas(text, fontSize) {
+    const ctx = getCtx();
     if (!ctx) {
-        throw new Error('no canvas context');
+        return text.length * fontSize * fallbackGlyphWidthRatio;
     }
     setFontSize(ctx, fontSize);
     return ctx.measureText(text).width;

package/dist/measureTextCanvas.js.map

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