react-msaview 8.0.0 → 8.2.0

package/dist/components/msa/renderBoxFeatureCanvasBlock.js

@@ -22,15 +22,12 @@ export function renderBoxFeatureCanvasBlock({ model, theme, offsetX, offsetY, ct
     // out); when letters show, the alternating shades alone mark the boundaries
     // and a number would collide with the sequence. A featureLabel encoding names
     // what every span carries instead
-    const drawSegmentLabels = !featureLabels && !showMsaLetters && !subFeatureRows && barHeight >= 9;
+    const drawSegmentLabels = !featureLabels && !showMsaLetters && !subFeatureRows;
     // a segment (exon) number labels its band once per block, on the topmost
     // visible row carrying that segment, so it reads as a column header for the
     // whole band. Keyed by accession rather than drawn on row 0, because the rows
     // carrying the gene model are often not the first ones in the alignment
     const labelled = drawSegmentLabels ? new Set() : undefined;
-    // gene arrow heads stick out up to a row height past the band, so pad the
-    // cull window enough that a band just outside the block still draws its head
-    const cull = rowHeight + colWidth;
     drawFeatureSpans({
         ctx,
         rows: spanRows(getVisibleLeaves({ model, offsetY, blockSizeY: by }), domainBands),
@@ -43,9 +40,11 @@ export function renderBoxFeatureCanvasBlock({ model, theme, offsetX, offsetY, ct
             top: (y, lane, h) => y -
                 rowHeight +
                 (subFeatureRows ? lane * h : domainUnderline ? rowHeight - h : 0),
-            // the head keeps its full size on an underline bar, since a head as short
-            // as the bar reads as a nub rather than as a direction
             headLength: h => (domainUnderline ? rowHeight / 2 : h),
+            // a head only as tall as an underline bar tapers over ten pixels of
+            // three, which reads as nothing; it takes the lower two fifths of the
+            // row instead, leaving the letters above it
+            headRise: h => (domainUnderline ? Math.max(0, rowHeight * 0.4 - h) : 0),
         },
         xOf: band => [band.startCol * colWidth, band.endCol * colWidth],
         colors: featureColors,
@@ -55,8 +54,8 @@ export function renderBoxFeatureCanvasBlock({ model, theme, offsetX, offsetY, ct
                 : undefined),
         labelDrawn: band => labelled?.add(band.annotation.accession),
         contrastText: contrastTextFn(theme),
-        xMin: offsetX - cull,
-        xMax: offsetX + bx + cull,
+        xMin: offsetX,
+        xMax: offsetX + bx,
     });
 }
 //# sourceMappingURL=renderBoxFeatureCanvasBlock.js.map

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

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

@@ -50,13 +50,10 @@ export function renderMSABlock({ model, offsetX, offsetY, ctx, theme, highResSca
     ctx.resetTransform();
 }
 function drawTilesAndText({ model, ctx, theme, visibleLeaves, xStart, xEnd, referenceSeq, drawTiles, rasterTiles, }) {
-    const { bgColor, columns, colWidth, rowHeight, relativeTo, showMsaLetters, subFeatureRows, domainUnderline, domainBandsByStart, } = model;
+    const { bgColor, columns, colWidth, rowHeight, fontSize, relativeTo, showMsaLetters, subFeatureRows, domainUnderline, domainBandsByStart, featureColors, } = model;
     const tiles = drawTiles && bgColor;
     const paintTiles = tiles && !rasterTiles;
     if (paintTiles || showMsaLetters) {
-        // a letter takes its color from the cell it lands on, so the scheme lookup
-        // is only waste when nothing draws letters
-        const needsColor = paintTiles || showMsaLetters;
         const tileColor = tileColorFn(model);
         // Domain fills come from a categorical palette with no fixed lightness, and
         // a dynamic scheme colors a cell from its column, so a readable letter color
@@ -64,8 +61,10 @@ function drawTilesAndText({ model, ctx, theme, visibleLeaves, xStart, xEnd, refe
         const contrastText = contrastTextFn(theme);
         const offsetXAligned = xStart * colWidth;
         const halfColWidth = colWidth / 2;
-        // note: -rowHeight/4 matches +rowHeight/4 in tree
-        const quarterRowHeight = rowHeight / 4;
+        // the context is translated by rowHeight/2, so `y` is the row's bottom
+        // edge and the baseline lands fontSize/4 below the row center, where the
+        // tree puts its tip labels
+        const baselineOffset = rowHeight / 2 - fontSize / 4;
         // with the tiles coming from the domain overlay instead, letters sit either
         // on a domain box or on the plain background; sub-row layout stacks the boxes
         // above the letters and letter-color mode shrinks them to a bar under the
@@ -78,14 +77,14 @@ function drawTilesAndText({ model, ctx, theme, visibleLeaves, xStart, xEnd, refe
             const str = columns.get(name)?.slice(xStart, xEnd);
             if (str) {
                 const tileY = y - rowHeight;
-                const textY = y - quarterRowHeight;
+                const textY = y - baselineOffset;
                 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];
                     const x = j * colWidth + offsetXAligned;
                     const isMatchingReference = referenceSeq && name !== relativeTo && letter === referenceSeq[j];
-                    const color = needsColor ? tileColor(col, letter) : undefined;
+                    const color = tileColor(col, letter);
                     if (paintTiles) {
                         ctx.fillStyle = isMatchingReference
                             ? theme.palette.action.hover
@@ -96,7 +95,7 @@ function drawTilesAndText({ model, ctx, theme, visibleLeaves, xStart, xEnd, refe
                         const covering = bandAt(col);
                         ctx.fillStyle = covering
                             ? // on top of a domain box: contrast against the box fill
-                                contrastText(model.fillPalette[covering.annotation.accession])
+                                contrastText(featureColors.get(covering.annotation)?.fill)
                             : isMatchingReference
                                 ? // the dot sits on the faint reference-match wash, which is
                                     // the theme's background with a little of its text color in it

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

@@ -1 +1 @@
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package/dist/components/tracks/drawTracks.js

@@ -178,7 +178,9 @@ export function drawSequenceLogo({ ctx, colStats, colorScheme, maxBits, textColo
  * `kind`, a draw function above, and a case here.
  */
 export function drawTrackBlock({ model, ctx, track, offsetX, offsetY = 0, theme, blockSizeXOverride, highResScaleFactorOverride, }) {
-    const { blockSize, bgColor, colWidth, colStats, colorScheme: modelColorScheme, fontSize, rowHeight, showMsaLetters, alphabetMaxBits, highResScaleFactor, } = model;
+    // an autorun tracks every model read here, so each kind reads only what it
+    // draws and a vertical zoom leaves the bar and arc canvases alone
+    const { blockSize, colWidth, highResScaleFactor } = model;
     const { id, kind, height: trackHeight, barColor, arcColor, arcs, customColorScheme, data, } = track.model;
     const blockSizeX = blockSizeXOverride ?? blockSize;
     const k = highResScaleFactorOverride ?? highResScaleFactor;
@@ -214,9 +216,9 @@ export function drawTrackBlock({ model, ctx, track, offsetX, offsetY = 0, theme,
         case 'logo': {
             drawSequenceLogo({
                 ctx,
-                colStats,
-                colorScheme: modelColorScheme,
-                maxBits: alphabetMaxBits,
+                colStats: model.colStats,
+                colorScheme: model.colorScheme,
+                maxBits: model.alphabetMaxBits,
                 textColor,
                 colWidth,
                 trackHeight,
@@ -246,13 +248,14 @@ export function drawTrackBlock({ model, ctx, track, offsetX, offsetY = 0, theme,
             break;
         }
         case 'text': {
+            const { bgColor, fontSize, rowHeight, showMsaLetters } = model;
             ctx.textAlign = 'center';
             ctx.textBaseline = 'middle';
             setFontSize(ctx, fontSize);
             drawTextTrackContent({
                 ctx,
                 data,
-                colorScheme: customColorScheme ?? modelColorScheme,
+                colorScheme: customColorScheme ?? model.colorScheme,
                 contrastText: contrastTextFn(theme),
                 bgColor,
                 drawLetters: showMsaLetters,

package/dist/components/tracks/drawTracks.js.map

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

@@ -5,7 +5,7 @@ const TreeBranchMenu = observer(function ({ node, model, onClose, }) {
     return (React.createElement(Menu, { anchorReference: "anchorPosition", anchorPosition: {
             left: node.x,
             top: node.y,
-        }, transitionDuration: 0, keepMounted: true, open: Boolean(node), onClose: onClose },
+        }, transitionDuration: 0, open: true, onClose: onClose },
         React.createElement(MenuItem, { dense: true, disabled: true }, node.name),
         React.createElement(MenuItem, { dense: true, onClick: () => {
                 model.toggleCollapsed(node.id);

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

@@ -1 +1 @@
-{"version":3,"file":"TreeBranchMenu.js","sourceRoot":"","sources":["../../../src/components/tree/TreeBranchMenu.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,EAAE,IAAI,EAAE,QAAQ,EAAE,MAAM,eAAe,CAAA;AAC9C,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAWrC,MAAM,cAAc,GAAG,QAAQ,CAAC,UAAU,EACxC,IAAI,EACJ,KAAK,EACL,OAAO,GAKR;IACC,OAAO,CACL,oBAAC,IAAI,IACH,eAAe,EAAC,gBAAgB,EAChC,cAAc,EAAE;YACd,IAAI,EAAE,IAAI,CAAC,CAAC;YACZ,GAAG,EAAE,IAAI,CAAC,CAAC;SACZ,EACD,kBAAkB,EAAE,CAAC,EACrB,WAAW,QACX,IAAI,EAAE,OAAO,CAAC,IAAI,CAAC,EACnB,OAAO,EAAE,OAAO;QAEhB,oBAAC,QAAQ,IAAC,KAAK,QAAC,QAAQ,UACrB,IAAI,CAAC,IAAI,CACD;QACX,oBAAC,QAAQ,IACP,KAAK,QACL,OAAO,EAAE,GAAG,EAAE;gBACZ,KAAK,CAAC,eAAe,CAAC,IAAI,CAAC,EAAE,CAAC,CAAA;gBAC9B,OAAO,EAAE,CAAA;YACX,CAAC,IAEA,KAAK,CAAC,SAAS,CAAC,QAAQ,CAAC,IAAI,CAAC,EAAE,CAAC;YAChC,CAAC,CAAC,kBAAkB;YACpB,CAAC,CAAC,oBAAoB,CACf;QACX,oBAAC,QAAQ,IACP,KAAK,QACL,OAAO,EAAE,GAAG,EAAE;gBACZ,IAAI,KAAK,CAAC,QAAQ,KAAK,IAAI,CAAC,EAAE,EAAE,CAAC;oBAC/B,KAAK,CAAC,WAAW,CAAC,SAAS,CAAC,CAAA;gBAC9B,CAAC;qBAAM,CAAC;oBACN,KAAK,CAAC,WAAW,CAAC,IAAI,CAAC,EAAE,CAAC,CAAA;gBAC5B,CAAC;gBACD,OAAO,EAAE,CAAA;YACX,CAAC,IAEA,KAAK,CAAC,QAAQ,KAAK,IAAI,CAAC,EAAE;YACzB,CAAC,CAAC,6BAA6B;YAC/B,CAAC,CAAC,qBAAqB,CAChB,CACN,CACR,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,cAAc,CAAA"}
+{"version":3,"file":"TreeBranchMenu.js","sourceRoot":"","sources":["../../../src/components/tree/TreeBranchMenu.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,EAAE,IAAI,EAAE,QAAQ,EAAE,MAAM,eAAe,CAAA;AAC9C,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAWrC,MAAM,cAAc,GAAG,QAAQ,CAAC,UAAU,EACxC,IAAI,EACJ,KAAK,EACL,OAAO,GAKR;IACC,OAAO,CACL,oBAAC,IAAI,IACH,eAAe,EAAC,gBAAgB,EAChC,cAAc,EAAE;YACd,IAAI,EAAE,IAAI,CAAC,CAAC;YACZ,GAAG,EAAE,IAAI,CAAC,CAAC;SACZ,EACD,kBAAkB,EAAE,CAAC,EACrB,IAAI,QACJ,OAAO,EAAE,OAAO;QAEhB,oBAAC,QAAQ,IAAC,KAAK,QAAC,QAAQ,UACrB,IAAI,CAAC,IAAI,CACD;QACX,oBAAC,QAAQ,IACP,KAAK,QACL,OAAO,EAAE,GAAG,EAAE;gBACZ,KAAK,CAAC,eAAe,CAAC,IAAI,CAAC,EAAE,CAAC,CAAA;gBAC9B,OAAO,EAAE,CAAA;YACX,CAAC,IAEA,KAAK,CAAC,SAAS,CAAC,QAAQ,CAAC,IAAI,CAAC,EAAE,CAAC;YAChC,CAAC,CAAC,kBAAkB;YACpB,CAAC,CAAC,oBAAoB,CACf;QACX,oBAAC,QAAQ,IACP,KAAK,QACL,OAAO,EAAE,GAAG,EAAE;gBACZ,IAAI,KAAK,CAAC,QAAQ,KAAK,IAAI,CAAC,EAAE,EAAE,CAAC;oBAC/B,KAAK,CAAC,WAAW,CAAC,SAAS,CAAC,CAAA;gBAC9B,CAAC;qBAAM,CAAC;oBACN,KAAK,CAAC,WAAW,CAAC,IAAI,CAAC,EAAE,CAAC,CAAA;gBAC5B,CAAC;gBACD,OAAO,EAAE,CAAA;YACX,CAAC,IAEA,KAAK,CAAC,QAAQ,KAAK,IAAI,CAAC,EAAE;YACzB,CAAC,CAAC,6BAA6B;YAC/B,CAAC,CAAC,qBAAqB,CAChB,CACN,CACR,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,cAAc,CAAA"}

package/dist/components/tree/TreeCanvas.js

@@ -43,9 +43,7 @@ const TreeCanvas = observer(function ({ model }) {
         height,
         deps: [model],
     });
-    return (React.createElement("div", { ref: ref, onMouseDown: onMouseDown, onMouseUp: onMouseUp, onMouseLeave: event => {
-            event.preventDefault();
-        }, style: {
+    return (React.createElement("div", { ref: ref, onMouseDown: onMouseDown, onMouseUp: onMouseUp, style: {
             height,
             position: 'relative',
             width: treeAreaWidth,

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

@@ -1 +1 @@
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+{"version":3,"file":"TreeCanvas.js","sourceRoot":"","sources":["../../../src/components/tree/TreeCanvas.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,WAAW,EAAE,MAAM,EAAE,MAAM,OAAO,CAAA;AAElD,OAAO,EAAE,OAAO,EAAE,MAAM,0BAA0B,CAAA;AAClD,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAErC,OAAO,EAAE,gBAAgB,EAAE,MAAM,2BAA2B,CAAA;AAC5D,OAAO,EAAE,cAAc,EAAE,MAAM,yBAAyB,CAAA;AACxD,OAAO,EAAE,cAAc,EAAE,cAAc,EAAE,MAAM,qBAAqB,CAAA;AACpE,OAAO,WAAW,MAAM,kBAAmB,CAAA;AAC3C,OAAO,eAAe,MAAM,sBAAuB,CAAA;AAInD,MAAM,UAAU,GAAG,QAAQ,CAAC,UAAU,EAAE,KAAK,EAA2B;IACtE,MAAM,GAAG,GAAG,MAAM,CAAiB,IAAI,CAAC,CAAA;IACxC,MAAM,EAAE,MAAM,EAAE,OAAO,EAAE,aAAa,EAAE,OAAO,EAAE,GAAG,KAAK,CAAA;IACzD,MAAM,SAAS,GAAG,WAAW,CAC3B,CAAC,CAAS,EAAE,EAAE;QACZ,KAAK,CAAC,SAAS,CAAC,CAAC,CAAC,CAAA;IACpB,CAAC,EACD,CAAC,KAAK,CAAC,CACR,CAAA;IACD,MAAM,EAAE,WAAW,EAAE,SAAS,EAAE,GAAG,cAAc,CAAC,EAAE,GAAG,EAAE,SAAS,EAAE,CAAC,CAAA;IAErE,MAAM,YAAY,GAAG,gBAAgB,CAAC;QACpC,IAAI,EAAE,GAAG,CAAC,EAAE;YACV,IAAI,OAAO,CAAC,KAAK,CAAC,EAAE,CAAC;gBACnB,MAAM,EACJ,SAAS,EACT,aAAa,EAAE,CAAC,EAChB,MAAM,EAAE,CAAC,EACT,OAAO,EAAE,EAAE,EACX,QAAQ,EACR,iBAAiB,EACjB,iBAAiB,GAClB,GAAG,KAAK,CAAA;gBACT,GAAG,CAAC,cAAc,EAAE,CAAA;gBACpB,GAAG,CAAC,SAAS,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,CAAC,CAAA;gBAEzB,oEAAoE;gBACpE,6DAA6D;gBAC7D,MAAM,OAAO,GAAG,CAAC,KAAa,EAAE,EAAE;oBAChC,GAAG,CAAC,QAAQ,CAAC,CAAC,EAAE,KAAK,GAAG,SAAS,GAAG,EAAE,EAAE,CAAC,EAAE,SAAS,CAAC,CAAA;gBACvD,CAAC,CAAA;gBAED,IAAI,iBAAiB,KAAK,SAAS,EAAE,CAAC;oBACpC,GAAG,CAAC,SAAS,GAAG,cAAc,CAAA;oBAC9B,OAAO,CAAC,iBAAiB,CAAC,CAAA;gBAC5B,CAAC;gBAED,GAAG,CAAC,SAAS,GAAG,cAAc,CAAA;gBAC9B,KAAK,MAAM,KAAK,IAAI,iBAAiB,EAAE,CAAC;oBACtC,OAAO,CAAC,KAAK,CAAC,CAAA;gBAChB,CAAC;gBACD,IACE,QAAQ,KAAK,SAAS;oBACtB,QAAQ,KAAK,iBAAiB;oBAC9B,CAAC,iBAAiB,CAAC,QAAQ,CAAC,QAAQ,CAAC,EACrC,CAAC;oBACD,OAAO,CAAC,QAAQ,CAAC,CAAA;gBACnB,CAAC;YACH,CAAC;QACH,CAAC;QACD,KAAK,EAAE,aAAa;QACpB,MAAM;QACN,IAAI,EAAE,CAAC,KAAK,CAAC;KACd,CAAC,CAAA;IAEF,OAAO,CACL,6BACE,GAAG,EAAE,GAAG,EACR,WAAW,EAAE,WAAW,EACxB,SAAS,EAAE,SAAS,EACpB,KAAK,EAAE;YACL,MAAM;YACN,QAAQ,EAAE,UAAU;YACpB,KAAK,EAAE,aAAa;SACrB;QAID,6BACE,KAAK,EAAE;gBACL,QAAQ,EAAE,UAAU;gBACpB,GAAG,EAAE,CAAC;gBACN,IAAI,EAAE,CAAC;gBACP,SAAS,EAAE,cAAc,OAAO,KAAK;gBACrC,UAAU,EAAE,WAAW;aACxB;YAEA,OAAO,CAAC,GAAG,CAAC,KAAK,CAAC,EAAE,CAAC,CACpB,oBAAC,eAAe,IAAC,GAAG,EAAE,KAAK,EAAE,KAAK,EAAE,KAAK,EAAE,OAAO,EAAE,KAAK,GAAI,CAC9D,CAAC;YACF,oBAAC,WAAW,IAAC,KAAK,EAAE,KAAK,GAAI,CACzB;QACN,gCACE,GAAG,EAAE,YAAY,EACjB,KAAK,EAAE,aAAa,EACpB,MAAM,EAAE,MAAM,EACd,KAAK,EAAE;gBACL,QAAQ,EAAE,UAAU;gBACpB,GAAG,EAAE,CAAC;gBACN,IAAI,EAAE,CAAC;gBACP,KAAK,EAAE,aAAa;gBACpB,MAAM;gBACN,MAAM,EAAE,IAAI;gBACZ,aAAa,EAAE,MAAM;aACtB,GACD,CACE,CACP,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,UAAU,CAAA"}

package/dist/components/tree/TreeCanvasBlock.js

@@ -8,12 +8,12 @@ import TreeBranchMenu from './TreeBranchMenu.js';
 import TreeNodeMenu from './TreeNodeMenu.js';
 import { renderTreeCanvas } from './renderTreeCanvas.js';
 import { useTreeHover } from './useTreeHover.js';
-const useStyles = makeStyles()(() => ({
+const useStyles = makeStyles()(theme => ({
     hover: {
         position: 'absolute',
         pointerEvents: 'none',
         zIndex: 100,
-        background: 'rgba(0,0,0,0.1)',
+        background: theme.palette.action.hover,
     },
 }));
 const TreeCanvasBlock = observer(function ({ model, offsetY, }) {

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

@@ -1 +1 @@
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+{"version":3,"file":"TreeCanvasBlock.js","sourceRoot":"","sources":["../../../src/components/tree/TreeCanvasBlock.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AAEvC,OAAO,EAAE,UAAU,EAAE,MAAM,8BAA8B,CAAA;AACzD,OAAO,EAAE,QAAQ,EAAE,MAAM,eAAe,CAAA;AACxC,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAErC,OAAO,EAAE,gBAAgB,EAAE,MAAM,2BAA2B,CAAA;AAC5D,OAAO,aAAa,MAAM,qBAAsB,CAAA;AAChD,OAAO,cAAc,MAAM,qBAAsB,CAAA;AACjD,OAAO,YAAY,MAAM,mBAAoB,CAAA;AAC7C,OAAO,EAAE,gBAAgB,EAAE,MAAM,uBAAuB,CAAA;AACxD,OAAO,EAAE,YAAY,EAAE,MAAM,mBAAmB,CAAA;AAIhD,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC;IACvC,KAAK,EAAE;QACL,QAAQ,EAAE,UAAU;QACpB,aAAa,EAAE,MAAM;QACrB,MAAM,EAAE,GAAG;QACX,UAAU,EAAE,KAAK,CAAC,OAAO,CAAC,MAAM,CAAC,KAAK;KACvC;CACF,CAAC,CAAC,CAAA;AASH,MAAM,eAAe,GAAG,QAAQ,CAAC,UAAU,EACzC,KAAK,EACL,OAAO,GAIR;IACC,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,KAAK,GAAG,QAAQ,EAAE,CAAA;IACxB,MAAM,CAAC,UAAU,EAAE,aAAa,CAAC,GAAG,QAAQ,EAAY,CAAA;IACxD,MAAM,CAAC,QAAQ,EAAE,WAAW,CAAC,GAAG,QAAQ,EAAY,CAAA;IACpD,MAAM,EAAE,QAAQ,EAAE,OAAO,EAAE,OAAO,EAAE,WAAW,EAAE,YAAY,EAAE,GAC7D,YAAY,CAAC,EAAE,KAAK,EAAE,OAAO,EAAE,CAAC,CAAA;IAElC,MAAM,EAAE,aAAa,EAAE,SAAS,EAAE,kBAAkB,EAAE,GAAG,KAAK,CAAA;IAC9D,8EAA8E;IAC9E,MAAM,KAAK,GAAG,aAAa,CAAA;IAC3B,MAAM,MAAM,GAAG,SAAS,CAAA;IAExB,MAAM,WAAW,GAAG,KAAK,GAAG,kBAAkB,CAAA;IAC9C,MAAM,YAAY,GAAG,MAAM,GAAG,kBAAkB,CAAA;IAChD,MAAM,GAAG,GAAG,gBAAgB,CAAC;QAC3B,IAAI,EAAE,GAAG,CAAC,EAAE;YACV,GAAG,CAAC,cAAc,EAAE,CAAA;YACpB,GAAG,CAAC,SAAS,CAAC,CAAC,EAAE,CAAC,EAAE,WAAW,EAAE,YAAY,CAAC,CAAA;YAC9C,gBAAgB,CAAC;gBACf,GAAG;gBACH,KAAK;gBACL,OAAO;gBACP,QAAQ;gBACR,KAAK;aACN,CAAC,CAAA;QACJ,CAAC;QACD,KAAK,EAAE,WAAW;QAClB,MAAM,EAAE,YAAY;QACpB,IAAI,EAAE,CAAC,KAAK,EAAE,QAAQ,EAAE,OAAO,EAAE,KAAK,CAAC;KACxC,CAAC,CAAA;IAEF,MAAM,KAAK,GAAG;QACZ,KAAK;QACL,MAAM;QACN,GAAG,EAAE,OAAO;QACZ,IAAI,EAAE,CAAC;QACP,QAAQ,EAAE,UAAU;KACZ,CAAA;IAEV,OAAO,CACL;QACG,UAAU,CAAC,CAAC,CAAC,CACZ,oBAAC,cAAc,IACb,IAAI,EAAE,UAAU,EAChB,KAAK,EAAE,KAAK,EACZ,OAAO,EAAE,GAAG,EAAE;gBACZ,aAAa,CAAC,SAAS,CAAC,CAAA;YAC1B,CAAC,GACD,CACH,CAAC,CAAC,CAAC,IAAI;QAEP,QAAQ,CAAC,CAAC,CAAC,CACV,oBAAC,YAAY,IACX,IAAI,EAAE,QAAQ,EACd,KAAK,EAAE,KAAK,EACZ,OAAO,EAAE,GAAG,EAAE;gBACZ,WAAW,CAAC,SAAS,CAAC,CAAA;YACxB,CAAC,GACD,CACH,CAAC,CAAC,CAAC,IAAI;QAER,gCACE,GAAG,EAAE,GAAG,EACR,KAAK,EAAE,WAAW,EAClB,MAAM,EAAE,YAAY,EACpB,KAAK,EAAE,EAAE,GAAG,KAAK,EAAE,MAAM,EAAE,OAAO,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,SAAS,EAAE,EAC5D,WAAW,EAAE,KAAK,CAAC,EAAE;gBACnB,WAAW,CAAC,KAAK,CAAC,CAAA;YACpB,CAAC,EACD,YAAY,EAAE,GAAG,EAAE;gBACjB,YAAY,EAAE,CAAA;YAChB,CAAC,EACD,OAAO,EAAE,KAAK,CAAC,EAAE;gBACf,MAAM,KAAK,GAAG,OAAO,CAAC,KAAK,CAAC,CAAA;gBAC5B,IAAI,KAAK,EAAE,CAAC;oBACV,MAAM,IAAI,GAAG;wBACX,CAAC,EAAE,KAAK,CAAC,OAAO;wBAChB,CAAC,EAAE,KAAK,CAAC,OAAO;wBAChB,EAAE,EAAE,KAAK,CAAC,EAAE;wBACZ,IAAI,EAAE,KAAK,CAAC,IAAI;qBACjB,CAAA;oBACD,IAAI,KAAK,CAAC,MAAM,EAAE,CAAC;wBACjB,aAAa,CAAC,IAAI,CAAC,CAAA;oBACrB,CAAC;yBAAM,CAAC;wBACN,WAAW,CAAC,IAAI,CAAC,CAAA;oBACnB,CAAC;gBACH,CAAC;YACH,CAAC,GACD;QAGD,OAAO,IAAI,CAAC,OAAO,CAAC,MAAM,CAAC,CAAC,CAAC,CAC5B,6BACE,SAAS,EAAE,OAAO,CAAC,KAAK,EACxB,KAAK,EAAE;gBACL,IAAI,EAAE,OAAO,CAAC,IAAI;gBAClB,GAAG,EAAE,OAAO,CAAC,IAAI;gBACjB,KAAK,EAAE,OAAO,CAAC,IAAI,GAAG,OAAO,CAAC,IAAI;gBAClC,MAAM,EAAE,OAAO,CAAC,IAAI,GAAG,OAAO,CAAC,IAAI;aACpC,GACD,CACH,CAAC,CAAC,CAAC,IAAI;QAEP,OAAO,CAAC,CAAC,CAAC,CACT,oBAAC,aAAa,IAAC,OAAO,EAAE,OAAO,CAAC,OAAO,EAAE,OAAO,EAAE,OAAO,CAAC,OAAO,IAC9D,OAAO,CAAC,IAAI,CACC,CACjB,CAAC,CAAC,CAAC,IAAI,CACP,CACJ,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,eAAe,CAAA"}

package/dist/components/tree/TreeNodeMenu.js

@@ -10,7 +10,7 @@ const TreeMenu = observer(function ({ node, onClose, model, }) {
     return (React.createElement(Menu, { anchorReference: "anchorPosition", anchorPosition: {
             top: node.y,
             left: node.x,
-        }, transitionDuration: 0, keepMounted: true, open: Boolean(node), onClose: onClose },
+        }, transitionDuration: 0, open: true, onClose: onClose },
         React.createElement(MenuItem, { dense: true, disabled: true }, name),
         React.createElement(MenuItem, { dense: true, onClick: () => {
                 model.queueDialog(onClose => [

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

@@ -1 +1 @@
-{"version":3,"file":"TreeNodeMenu.js","sourceRoot":"","sources":["../../../src/components/tree/TreeNodeMenu.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,IAAI,EAAE,MAAM,OAAO,CAAA;AAEnC,OAAO,EAAE,IAAI,EAAE,QAAQ,EAAE,MAAM,eAAe,CAAA;AAC9C,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAIrC,SAAS;AACT,MAAM,kBAAkB,GAAG,IAAI,CAC7B,GAAG,EAAE,CAAC,MAAM,CAAC,iCAAkC,CAAC,CACjD,CAAA;AAED,MAAM,QAAQ,GAAG,QAAQ,CAAC,UAAU,EAClC,IAAI,EACJ,OAAO,EACP,KAAK,GAUN;IACC,MAAM,EAAE,SAAS,EAAE,GAAG,KAAK,CAAA;IAC3B,MAAM,EAAE,IAAI,EAAE,EAAE,EAAE,GAAG,IAAI,CAAA;IACzB,MAAM,WAAW,GAAG,SAAS,CAAC,QAAQ,CAAC,EAAE,CAAC,CAAA;IAC1C,OAAO,CACL,oBAAC,IAAI,IACH,eAAe,EAAC,gBAAgB,EAChC,cAAc,EAAE;YACd,GAAG,EAAE,IAAI,CAAC,CAAC;YACX,IAAI,EAAE,IAAI,CAAC,CAAC;SACb,EACD,kBAAkB,EAAE,CAAC,EACrB,WAAW,QACX,IAAI,EAAE,OAAO,CAAC,IAAI,CAAC,EACnB,OAAO,EAAE,OAAO;QAEhB,oBAAC,QAAQ,IAAC,KAAK,QAAC,QAAQ,UACrB,IAAI,CACI;QAEX,oBAAC,QAAQ,IACP,KAAK,QACL,OAAO,EAAE,GAAG,EAAE;gBACZ,KAAK,CAAC,WAAW,CAAC,OAAO,CAAC,EAAE,CAAC;oBAC3B,kBAAkB;oBAClB;wBACE,IAAI,EAAE,KAAK,CAAC,UAAU,CAAC,IAAI,CAAC;wBAC5B,KAAK;wBACL,QAAQ,EAAE,IAAI;wBACd,OAAO;qBACR;iBACF,CAAC,CAAA;gBACF,OAAO,EAAE,CAAA;YACX,CAAC,mBAGQ;QACX,oBAAC,QAAQ,IACP,KAAK,QACL,OAAO,EAAE,GAAG,EAAE;gBACZ,KAAK,CAAC,eAAe,CAAC,EAAE,CAAC,CAAA;gBACzB,OAAO,EAAE,CAAA;YACX,CAAC,IAEA,WAAW,CAAC,CAAC,CAAC,gBAAgB,CAAC,CAAC,CAAC,kBAAkB,CAC3C;QACX,oBAAC,QAAQ,IACP,KAAK,QACL,OAAO,EAAE,GAAG,EAAE;gBACZ,KAAK,CAAC,cAAc,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;gBAC/B,OAAO,EAAE,CAAA;YACX,CAAC,yCAGQ;QACV,KAAK,CAAC,UAAU,CAAC,CAAC,CAAC,CAClB,oBAAC,QAAQ,IACP,KAAK,QACL,OAAO,EAAE,GAAG,EAAE;gBACZ,KAAK,CAAC,cAAc,CAAC,SAAS,CAAC,CAAA;gBAC/B,OAAO,EAAE,CAAA;YACX,CAAC,0BAGQ,CACZ,CAAC,CAAC,CAAC,IAAI,CACH,CACR,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,QAAQ,CAAA"}
+{"version":3,"file":"TreeNodeMenu.js","sourceRoot":"","sources":["../../../src/components/tree/TreeNodeMenu.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,IAAI,EAAE,MAAM,OAAO,CAAA;AAEnC,OAAO,EAAE,IAAI,EAAE,QAAQ,EAAE,MAAM,eAAe,CAAA;AAC9C,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAIrC,SAAS;AACT,MAAM,kBAAkB,GAAG,IAAI,CAC7B,GAAG,EAAE,CAAC,MAAM,CAAC,iCAAkC,CAAC,CACjD,CAAA;AAED,MAAM,QAAQ,GAAG,QAAQ,CAAC,UAAU,EAClC,IAAI,EACJ,OAAO,EACP,KAAK,GAUN;IACC,MAAM,EAAE,SAAS,EAAE,GAAG,KAAK,CAAA;IAC3B,MAAM,EAAE,IAAI,EAAE,EAAE,EAAE,GAAG,IAAI,CAAA;IACzB,MAAM,WAAW,GAAG,SAAS,CAAC,QAAQ,CAAC,EAAE,CAAC,CAAA;IAC1C,OAAO,CACL,oBAAC,IAAI,IACH,eAAe,EAAC,gBAAgB,EAChC,cAAc,EAAE;YACd,GAAG,EAAE,IAAI,CAAC,CAAC;YACX,IAAI,EAAE,IAAI,CAAC,CAAC;SACb,EACD,kBAAkB,EAAE,CAAC,EACrB,IAAI,QACJ,OAAO,EAAE,OAAO;QAEhB,oBAAC,QAAQ,IAAC,KAAK,QAAC,QAAQ,UACrB,IAAI,CACI;QAEX,oBAAC,QAAQ,IACP,KAAK,QACL,OAAO,EAAE,GAAG,EAAE;gBACZ,KAAK,CAAC,WAAW,CAAC,OAAO,CAAC,EAAE,CAAC;oBAC3B,kBAAkB;oBAClB;wBACE,IAAI,EAAE,KAAK,CAAC,UAAU,CAAC,IAAI,CAAC;wBAC5B,KAAK;wBACL,QAAQ,EAAE,IAAI;wBACd,OAAO;qBACR;iBACF,CAAC,CAAA;gBACF,OAAO,EAAE,CAAA;YACX,CAAC,mBAGQ;QACX,oBAAC,QAAQ,IACP,KAAK,QACL,OAAO,EAAE,GAAG,EAAE;gBACZ,KAAK,CAAC,eAAe,CAAC,EAAE,CAAC,CAAA;gBACzB,OAAO,EAAE,CAAA;YACX,CAAC,IAEA,WAAW,CAAC,CAAC,CAAC,gBAAgB,CAAC,CAAC,CAAC,kBAAkB,CAC3C;QACX,oBAAC,QAAQ,IACP,KAAK,QACL,OAAO,EAAE,GAAG,EAAE;gBACZ,KAAK,CAAC,cAAc,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;gBAC/B,OAAO,EAAE,CAAA;YACX,CAAC,yCAGQ;QACV,KAAK,CAAC,UAAU,CAAC,CAAC,CAAC,CAClB,oBAAC,QAAQ,IACP,KAAK,QACL,OAAO,EAAE,GAAG,EAAE;gBACZ,KAAK,CAAC,cAAc,CAAC,SAAS,CAAC,CAAA;gBAC/B,OAAO,EAAE,CAAA;YACX,CAAC,0BAGQ,CACZ,CAAC,CAAC,CAAC,IAAI,CACH,CACR,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,QAAQ,CAAA"}

package/dist/components/tree/renderTreeCanvas.js

@@ -236,7 +236,8 @@ function renderTreeLabels({ theme, model, offsetY, ctx, clickMap, tipX, maxDepth
         // label when the "name" is just the auto-generated internal-node id
         const isAnonymousCollapsed = collapsedSet.has(id) && name === id;
         if (!isAnonymousCollapsed && inYBlock(y, offsetY, by, pad)) {
-            // note: +rowHeight/4 matches with -rowHeight/4 in msa
+            // fontSize/4 below the row center, the baseline the alignment letters
+            // share
             const yp = y + fontSize / 4;
             let xp = 0;
             if (!noTree) {

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

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

@@ -20,6 +20,7 @@ export type ScrollZoomAxis = (typeof scrollZoomAxes)[number];
 export declare const defaultScrollZoomAxis: ScrollZoomAxis;
 export declare const minLetterRowHeight = 8;
 export declare const minLetterColWidth = 5;
+export declare const minFeatureLabelHeight = 9;
 export declare const labelReferenceFontSize = 16;
 export declare const minColWidth = 0.2;
 export declare const minRowHeight = 1;

package/dist/constants.js

@@ -42,6 +42,10 @@ export const defaultScrollZoomAxis = 'both';
 // frame. A sprite atlas measured slower.
 export const minLetterRowHeight = 8;
 export const minLetterColWidth = 5;
+// A feature span draws its label at two pixels under its height, capped at 11,
+// so a span shorter than this holds no readable text: an underline bar, a
+// sub-row band or a features panel over small rows
+export const minFeatureLabelHeight = 9;
 // Tree labels are measured once at this size and scaled to the current font
 // size, so a vertical zoom never re-measures the tree.
 export const labelReferenceFontSize = 16;

package/dist/constants.js.map

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package/dist/expandSpec.d.ts

@@ -0,0 +1,46 @@
+import type { ColumnTrackSpec, Highlight, Region } from './types.ts';
+/**
+ * `row: null` opts one entry out of the spec's `query` row, back to alignment
+ * columns.
+ */
+type RowChoice = {
+    row?: string | null;
+};
+export type HighlightShorthand = number | string | (Omit<Highlight, 'row'> & RowChoice);
+export type RegionShorthand = string | (Omit<Region, 'row'> & RowChoice);
+export type ColumnTrackShorthand = Omit<ColumnTrackSpec, 'id' | 'kind' | 'row'> & RowChoice & {
+    id?: string;
+    kind?: ColumnTrackSpec['kind'];
+    /** the 1-based position `values` or `data` begins at */
+    start?: number;
+};
+/**
+ * The short forms a hand-written or generated link can use. Every long form
+ * passes through unchanged, so a snapshot is also a valid spec.
+ */
+export interface MsaSpec {
+    /**
+     * The row the spec is about: sets `relativeTo`, and is the `row` of every
+     * highlight, region and column track that names none
+     */
+    query?: string;
+    /** a url, or the alignment itself when it spans more than one line */
+    msa?: string;
+    /** a url, or a newick string when it starts with "(" */
+    tree?: string;
+    highlights?: HighlightShorthand[];
+    region?: RegionShorthand;
+    columnTracks?: ColumnTrackShorthand[];
+    [key: string]: unknown;
+}
+/**
+ * The label a single-residue shorthand highlight gets, filled in from the
+ * sequence when drawn: `175` on a row reading R there becomes "R175".
+ */
+export declare const residueLabel = "{residue}{position}";
+/**
+ * Expand the short forms of an MsaView spec into the snapshot the model takes.
+ * Idempotent, and a no-op on a spec that uses none of them.
+ */
+export declare function expandSpec(spec: MsaSpec): Record<string, unknown>;
+export {};