react-msaview 5.8.0 → 5.10.0

package/dist/parseAsn1.js

@@ -10,29 +10,38 @@ const remap = {
     'common-name': 'commonName',
     'leaf-count': 'leafCount',
 };
+// index just past the '}' closing the '{' at openIdx, or -1 when it never
+// closes. Braces nest (a node holds features, which hold values), so finding the
+// end of a block means counting depth rather than taking the next '}'.
+function afterMatchingBrace(str, openIdx) {
+    let depth = 1;
+    let pos = openIdx + 1;
+    while (pos < str.length && depth > 0) {
+        if (str[pos] === '{') {
+            depth++;
+        }
+        else if (str[pos] === '}') {
+            depth--;
+        }
+        pos++;
+    }
+    return depth === 0 ? pos : -1;
+}
+// the contents of each top-level {...} block in str, siblings only
 function extractBracedBlocks(str) {
     const blocks = [];
     let pos = 0;
     while (pos < str.length) {
-        pos = str.indexOf('{', pos);
-        if (pos === -1) {
+        const openIdx = str.indexOf('{', pos);
+        if (openIdx === -1) {
             break;
         }
-        let depth = 1;
-        const start = pos + 1;
-        pos++;
-        while (pos < str.length && depth > 0) {
-            if (str[pos] === '{') {
-                depth++;
-            }
-            else if (str[pos] === '}') {
-                depth--;
-            }
-            pos++;
-        }
-        if (depth === 0) {
-            blocks.push(str.slice(start, pos - 1).trim());
+        const end = afterMatchingBrace(str, openIdx);
+        if (end === -1) {
+            break;
         }
+        blocks.push(str.slice(openIdx + 1, end - 1).trim());
+        pos = end;
     }
     return blocks;
 }
@@ -41,18 +50,8 @@ function findBracedContent(str, after) {
     if (openIdx === -1) {
         return undefined;
     }
-    let depth = 1;
-    let pos = openIdx + 1;
-    while (pos < str.length && depth > 0) {
-        if (str[pos] === '{') {
-            depth++;
-        }
-        else if (str[pos] === '}') {
-            depth--;
-        }
-        pos++;
-    }
-    return depth === 0 ? str.slice(openIdx + 1, pos - 1).trim() : undefined;
+    const end = afterMatchingBrace(str, openIdx);
+    return end === -1 ? undefined : str.slice(openIdx + 1, end - 1).trim();
 }
 export function parseAsn1(asnString) {
     const normalized = asnString
@@ -120,22 +119,12 @@ function extractSections(asnString) {
             pos = pos === -1 ? content.length : pos + 1;
             continue;
         }
-        let depth = 1;
-        const start = pos + 1;
-        pos++;
-        while (pos < content.length && depth > 0) {
-            if (content[pos] === '{') {
-                depth++;
-            }
-            else if (content[pos] === '}') {
-                depth--;
-            }
-            pos++;
-        }
-        if (depth === 0) {
-            sections[name] = content.slice(start, pos - 1).trim();
+        const end = afterMatchingBrace(content, pos);
+        if (end === -1) {
+            break;
         }
-        pos = content.indexOf(',', pos);
+        sections[name] = content.slice(pos + 1, end - 1).trim();
+        pos = content.indexOf(',', end);
         pos = pos === -1 ? content.length : pos + 1;
     }
     return sections;

package/dist/parseAsn1.js.map

@@ -1 +1 @@
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package/dist/renderToSvg.js

@@ -111,6 +111,9 @@ function CoreRendering({ model, theme, layout, Context, }) {
         ctx: msaCtx,
         offsetX,
         offsetY,
+        // the overlay culls bands to this width; without it the export falls back
+        // to the on-screen 500px block size and drops every band past it
+        blockSizeXOverride: msaAreaWidth,
         blockSizeYOverride: contentHeight,
         highResScaleFactorOverride: 1,
     });

package/dist/renderToSvg.js.map

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

@@ -1,26 +1,13 @@
 /**
- * Convert a sequence position (ungapped, 0-based) to a global column index.
- * This finds the global column that contains the Nth non-gap character.
+ * The global column of every ungapped sequence position in a row, i.e.
+ * index[seqPos] is the column holding the seqPos-th non-gap character.
  *
- * @param row - The row's sequence string (including gaps)
- * @param seqPos - The sequence position (0-based count of non-gap characters)
- * @returns The global column index containing the seqPos-th non-gap character
+ * A row is indexed once and then answers seqPos -> column by lookup, which is
+ * what makes the domain overlay affordable: it resolves one position per feature
+ * per row on every redraw, and scanning the row for each would be quadratic.
  *
  * @example
  * // Row: "A-TG-C" (A at 0, T at 2, G at 3, C at 5)
- * seqPosToGlobalCol({ row: "A-TG-C", seqPos: 0 }) // → 0 (A)
- * seqPosToGlobalCol({ row: "A-TG-C", seqPos: 1 }) // → 2 (T)
- * seqPosToGlobalCol({ row: "A-TG-C", seqPos: 2 }) // → 3 (G)
- * seqPosToGlobalCol({ row: "A-TG-C", seqPos: 3 }) // → 5 (C)
- */
-/**
- * The global column of every ungapped sequence position in a row, i.e.
- * index[seqPos] is the column holding the seqPos-th non-gap character. Amortizes
- * repeated seqPosToGlobalCol lookups (the domain overlay does one per feature
- * per row) into a single pass per row.
+ * buildSeqPosIndex('A-TG-C') // → [0, 2, 3, 5]
  */
 export declare function buildSeqPosIndex(row: string): Int32Array<ArrayBuffer>;
-export declare function seqPosToGlobalCol({ row, seqPos, }: {
-    row: string;
-    seqPos: number;
-}): number;

package/dist/seqPosToGlobalCol.js

@@ -1,24 +1,14 @@
-import { isBlank } from './util.js';
 /**
- * Convert a sequence position (ungapped, 0-based) to a global column index.
- * This finds the global column that contains the Nth non-gap character.
+ * The global column of every ungapped sequence position in a row, i.e.
+ * index[seqPos] is the column holding the seqPos-th non-gap character.
  *
- * @param row - The row's sequence string (including gaps)
- * @param seqPos - The sequence position (0-based count of non-gap characters)
- * @returns The global column index containing the seqPos-th non-gap character
+ * A row is indexed once and then answers seqPos -> column by lookup, which is
+ * what makes the domain overlay affordable: it resolves one position per feature
+ * per row on every redraw, and scanning the row for each would be quadratic.
  *
  * @example
  * // Row: "A-TG-C" (A at 0, T at 2, G at 3, C at 5)
- * seqPosToGlobalCol({ row: "A-TG-C", seqPos: 0 }) // → 0 (A)
- * seqPosToGlobalCol({ row: "A-TG-C", seqPos: 1 }) // → 2 (T)
- * seqPosToGlobalCol({ row: "A-TG-C", seqPos: 2 }) // → 3 (G)
- * seqPosToGlobalCol({ row: "A-TG-C", seqPos: 3 }) // → 5 (C)
- */
-/**
- * The global column of every ungapped sequence position in a row, i.e.
- * index[seqPos] is the column holding the seqPos-th non-gap character. Amortizes
- * repeated seqPosToGlobalCol lookups (the domain overlay does one per feature
- * per row) into a single pass per row.
+ * buildSeqPosIndex('A-TG-C') // → [0, 2, 3, 5]
  */
 export function buildSeqPosIndex(row) {
     const index = new Int32Array(row.length);
@@ -31,21 +21,4 @@ export function buildSeqPosIndex(row) {
     }
     return index.subarray(0, n);
 }
-export function seqPosToGlobalCol({ row, seqPos, }) {
-    let nonGapCount = 0;
-    let globalCol = 0;
-    // Find the seqPos-th non-gap character
-    while (globalCol < row.length) {
-        if (!isBlank(row[globalCol])) {
-            if (nonGapCount === seqPos) {
-                return globalCol;
-            }
-            nonGapCount++;
-        }
-        globalCol++;
-    }
-    // If seqPos is 0 and we didn't find any non-gap character, return 0
-    // Otherwise return globalCol (which is row.length at this point)
-    return seqPos === 0 ? 0 : globalCol;
-}
 //# sourceMappingURL=seqPosToGlobalCol.js.map

package/dist/seqPosToGlobalCol.js.map

@@ -1 +1 @@
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+{"version":3,"file":"seqPosToGlobalCol.js","sourceRoot":"","sources":["../src/seqPosToGlobalCol.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;GAWG;AACH,MAAM,UAAU,gBAAgB,CAAC,GAAW;IAC1C,MAAM,KAAK,GAAG,IAAI,UAAU,CAAC,GAAG,CAAC,MAAM,CAAC,CAAA;IACxC,IAAI,CAAC,GAAG,CAAC,CAAA;IACT,KAAK,IAAI,GAAG,GAAG,CAAC,EAAE,GAAG,GAAG,GAAG,CAAC,MAAM,EAAE,GAAG,EAAE,EAAE,CAAC;QAC1C,oEAAoE;QACpE,IAAI,CAAC,CAAC,CAAC,GAAG,CAAC,UAAU,CAAC,GAAG,CAAC,GAAG,EAAE,CAAC,KAAK,CAAC,IAAI,CAAC,CAAC,EAAE,CAAC;YAC7C,KAAK,CAAC,CAAC,EAAE,CAAC,GAAG,GAAG,CAAA;QAClB,CAAC;IACH,CAAC;IACD,OAAO,KAAK,CAAC,QAAQ,CAAC,CAAC,EAAE,CAAC,CAAC,CAAA;AAC7B,CAAC"}

package/dist/useCanvasAutorun.d.ts

@@ -1,2 +1,24 @@
 import type React from 'react';
-export declare function useCanvasAutorun(draw: (ctx: CanvasRenderingContext2D) => void, deps: React.DependencyList): React.RefObject<HTMLCanvasElement | null>;
+/**
+ * Wires a canvas ref to a mobx autorun: grabs the 2d context once the canvas
+ * mounts and re-runs `draw` whenever any observable it reads changes. Collapses
+ * the getContext/null-guard/autorun-dispose boilerplate repeated by every canvas
+ * block host.
+ *
+ * `width`/`height` are the canvas *backing store* size the caller renders onto
+ * the element (logical size times the high-res scale factor), and they are load
+ * bearing rather than informational. Assigning either resets the canvas bitmap,
+ * and React assigns them on every commit where they changed -- which lands
+ * *after* the mobx reaction that already redrew at the old size. Without a redraw
+ * on the far side of that commit the canvas is left blank: it is what blanked the
+ * tree on a tree-area resize and the consensus tracks on a vertical zoom.
+ *
+ * `deps` covers everything else the effect should re-subscribe on, matching a
+ * normal useEffect dep array.
+ */
+export declare function useCanvasAutorun({ draw, width, height, deps, }: {
+    draw: (ctx: CanvasRenderingContext2D) => void;
+    width: number;
+    height: number;
+    deps: React.DependencyList;
+}): React.RefObject<HTMLCanvasElement | null>;

package/dist/useCanvasAutorun.js

@@ -1,14 +1,26 @@
 import { useEffect, useRef } from 'react';
 import { autorun } from 'mobx';
-// Wires a canvas ref to a mobx autorun: grabs the 2d context once the canvas
-// mounts and re-runs `draw` whenever any observable it reads changes. Collapses
-// the getContext/null-guard/autorun-dispose boilerplate repeated by every
-// canvas block host. `deps` controls when the effect (and thus the context
-// lookup) is torn down and re-created, matching a normal useEffect dep array.
-export function useCanvasAutorun(draw, deps) {
+/**
+ * Wires a canvas ref to a mobx autorun: grabs the 2d context once the canvas
+ * mounts and re-runs `draw` whenever any observable it reads changes. Collapses
+ * the getContext/null-guard/autorun-dispose boilerplate repeated by every canvas
+ * block host.
+ *
+ * `width`/`height` are the canvas *backing store* size the caller renders onto
+ * the element (logical size times the high-res scale factor), and they are load
+ * bearing rather than informational. Assigning either resets the canvas bitmap,
+ * and React assigns them on every commit where they changed -- which lands
+ * *after* the mobx reaction that already redrew at the old size. Without a redraw
+ * on the far side of that commit the canvas is left blank: it is what blanked the
+ * tree on a tree-area resize and the consensus tracks on a vertical zoom.
+ *
+ * `deps` covers everything else the effect should re-subscribe on, matching a
+ * normal useEffect dep array.
+ */
+export function useCanvasAutorun({ draw, width, height, deps, }) {
     const ref = useRef(null);
     // the autorun tracks its own observable reads, so `draw` is intentionally not
-    // a dependency; `deps` alone controls when the effect re-subscribes
+    // a dependency; `deps` plus the canvas size control when it re-subscribes
     useEffect(() => {
         const ctx = ref.current?.getContext('2d');
         return ctx
@@ -17,7 +29,7 @@ export function useCanvasAutorun(draw, deps) {
             })
             : undefined;
         // eslint-disable-next-line react-hooks/exhaustive-deps
-    }, deps);
+    }, [...deps, width, height]);
     return ref;
 }
 //# sourceMappingURL=useCanvasAutorun.js.map

package/dist/useCanvasAutorun.js.map

@@ -1 +1 @@
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+{"version":3,"file":"useCanvasAutorun.js","sourceRoot":"","sources":["../src/useCanvasAutorun.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,SAAS,EAAE,MAAM,EAAE,MAAM,OAAO,CAAA;AAEzC,OAAO,EAAE,OAAO,EAAE,MAAM,MAAM,CAAA;AAI9B;;;;;;;;;;;;;;;;GAgBG;AACH,MAAM,UAAU,gBAAgB,CAAC,EAC/B,IAAI,EACJ,KAAK,EACL,MAAM,EACN,IAAI,GAML;IACC,MAAM,GAAG,GAAG,MAAM,CAAoB,IAAI,CAAC,CAAA;IAC3C,8EAA8E;IAC9E,0EAA0E;IAC1E,SAAS,CAAC,GAAG,EAAE;QACb,MAAM,GAAG,GAAG,GAAG,CAAC,OAAO,EAAE,UAAU,CAAC,IAAI,CAAC,CAAA;QACzC,OAAO,GAAG;YACR,CAAC,CAAC,OAAO,CAAC,GAAG,EAAE;gBACX,IAAI,CAAC,GAAG,CAAC,CAAA;YACX,CAAC,CAAC;YACJ,CAAC,CAAC,SAAS,CAAA;QACb,uDAAuD;IACzD,CAAC,EAAE,CAAC,GAAG,IAAI,EAAE,KAAK,EAAE,MAAM,CAAC,CAAC,CAAA;IAC5B,OAAO,GAAG,CAAA;AACZ,CAAC"}

package/dist/version.d.ts

@@ -1 +1 @@
-export declare const version = "5.8.0";
+export declare const version = "5.10.0";

package/dist/version.js

@@ -1,2 +1,2 @@
-export const version = '5.8.0';
+export const version = '5.10.0';
 //# sourceMappingURL=version.js.map

package/dist/version.js.map

@@ -1 +1 @@
-{"version":3,"file":"version.js","sourceRoot":"","sources":["../src/version.ts"],"names":[],"mappings":"AAAA,MAAM,CAAC,MAAM,OAAO,GAAG,OAAO,CAAA"}
+{"version":3,"file":"version.js","sourceRoot":"","sources":["../src/version.ts"],"names":[],"mappings":"AAAA,MAAM,CAAC,MAAM,OAAO,GAAG,QAAQ,CAAA"}

package/package.json

@@ -1,7 +1,7 @@
 {
   "name": "react-msaview",
   "author": "Colin",
-  "version": "5.8.0",
+  "version": "5.10.0",
   "license": "MIT",
   "type": "module",
   "repository": {
@@ -43,8 +43,8 @@
     "@gmod/newick": "^1.0.0",
     "colord": "^2.9.3",
     "flatbush": "^4.6.2",
-    "@jbrowse/svgcanvas": "5.8.0",
-    "msa-parsers": "5.8.0"
+    "@jbrowse/svgcanvas": "5.10.0",
+    "msa-parsers": "5.10.0"
   },
   "scripts": {
     "clean": "rimraf dist bundle",

package/src/components/ConservationTrack.tsx

@@ -25,9 +25,9 @@ const ConservationBlock = observer(function ({
 }) {
   const { blockSize, scrollX, highResScaleFactor } = model
 
-  const ref = useCanvasAutorun(
-    ctx => {
-      const { blockSize, colWidth, highResScaleFactor } = model
+  const ref = useCanvasAutorun({
+    draw: ctx => {
+      const { colWidth } = model
       ctx.resetTransform()
       ctx.scale(highResScaleFactor, highResScaleFactor)
       ctx.clearRect(0, 0, blockSize, trackHeight)
@@ -43,8 +43,10 @@ const ConservationBlock = observer(function ({
         blockSize,
       })
     },
-    [model, track, offsetX, trackHeight],
-  )
+    width: blockSize * highResScaleFactor,
+    height: trackHeight * highResScaleFactor,
+    deps: [model, track, offsetX, trackHeight],
+  })
 
   return (
     <canvas

package/src/components/MSAView.tsx

@@ -11,6 +11,7 @@ import VerticalScrollbar from './VerticalScrollbar.tsx'
 import Header from './header/Header.tsx'
 import Minimap from './minimap/Minimap.tsx'
 import MSAPanel from './msa/MSAPanel.tsx'
+import { clickColor, hoverColor } from './overlayColors.ts'
 import TreePanel from './tree/TreePanel.tsx'
 import TreeRuler from './tree/TreeRuler.tsx'
 
@@ -43,47 +44,40 @@ const TrackColumnIndicator = observer(function ({
     verticalScrollbarWidth,
   } = model
 
-  const left = treeAreaWidth + resizeHandleWidth
-  const clipWidth = msaAreaWidth - verticalScrollbarWidth
+  // hovered column, then the pinned one, matching the alignment's own overlay
+  const bands = [
+    { col: mouseCol, color: hoverColor },
+    { col: mouseClickCol, color: clickColor },
+  ]
 
   return (
     <div
       style={{
         position: 'absolute',
-        left,
+        left: treeAreaWidth + resizeHandleWidth,
         top: 0,
-        width: clipWidth,
+        width: msaAreaWidth - verticalScrollbarWidth,
         height: totalTrackAreaHeight,
         overflow: 'hidden',
         pointerEvents: 'none',
       }}
     >
-      {mouseCol !== undefined ? (
-        <div
-          style={{
-            position: 'absolute',
-            left: mouseCol * colWidth + scrollX,
-            top: 0,
-            width: colWidth,
-            height: totalTrackAreaHeight,
-            backgroundColor: 'rgba(0,0,0,0.15)',
-            zIndex: 100,
-          }}
-        />
-      ) : null}
-      {mouseClickCol !== undefined ? (
-        <div
-          style={{
-            position: 'absolute',
-            left: mouseClickCol * colWidth + scrollX,
-            top: 0,
-            width: colWidth,
-            height: totalTrackAreaHeight,
-            backgroundColor: 'rgba(128,128,0,0.2)',
-            zIndex: 100,
-          }}
-        />
-      ) : null}
+      {bands.map(({ col, color }) =>
+        col === undefined ? null : (
+          <div
+            key={color}
+            style={{
+              position: 'absolute',
+              left: col * colWidth + scrollX,
+              top: 0,
+              width: colWidth,
+              height: totalTrackAreaHeight,
+              backgroundColor: color,
+              zIndex: 100,
+            }}
+          />
+        ),
+      )}
     </div>
   )
 })

package/src/components/TextTrack.tsx

@@ -32,16 +32,9 @@ const AnnotationBlock = observer(function ({
 
   const colorScheme = customColorScheme ?? modelColorScheme
   const { theme, contrastScheme } = useColorContrast(colorScheme)
-  const ref = useCanvasAutorun(
-    ctx => {
-      const {
-        blockSize,
-        bgColor,
-        colWidth,
-        fontSize,
-        rowHeight,
-        highResScaleFactor,
-      } = model
+  const ref = useCanvasAutorun({
+    draw: ctx => {
+      const { bgColor, colWidth, fontSize } = model
       ctx.resetTransform()
       ctx.scale(highResScaleFactor, highResScaleFactor)
       ctx.clearRect(0, 0, blockSize, rowHeight)
@@ -62,8 +55,10 @@ const AnnotationBlock = observer(function ({
         blockSize,
       })
     },
-    [model, offsetX, theme, contrastScheme, colorScheme, data],
-  )
+    width: blockSize * highResScaleFactor,
+    height: rowHeight * highResScaleFactor,
+    deps: [model, offsetX, theme, contrastScheme, colorScheme, data],
+  })
   return (
     <canvas
       ref={ref}