react-msaview 6.5.0 → 8.0.0

package/dist/components/msa/AnnotationLegend.js

@@ -3,38 +3,46 @@ import ExpandLess from '@mui/icons-material/ExpandLess';
 import ExpandMore from '@mui/icons-material/ExpandMore';
 import { IconButton, Paper, Typography } from '@mui/material';
 import { observer } from 'mobx-react';
+import { legendZIndex } from '../../constants.js';
+import { legendRows } from './legendRows.js';
 const AnnotationLegend = observer(function ({ model, }) {
-    const { actuallyShowDomains, visibleDomainTypes: visible, fillPalette, showDomainLegend: expanded, } = model;
+    const { legends, showDomainLegend: expanded } = model;
+    const rows = legendRows(legends);
     const ExpandIcon = expanded ? ExpandLess : ExpandMore;
-    return actuallyShowDomains && visible.length > 0 ? (React.createElement(Paper, { elevation: 3, style: {
+    return rows.length > 0 ? (React.createElement(Paper, { elevation: 3, style: {
             position: 'absolute',
             top: 4,
             right: 4,
-            zIndex: 100,
-            maxWidth: 260,
+            zIndex: legendZIndex,
+            maxWidth: 220,
             maxHeight: '60%',
             display: 'flex',
             flexDirection: 'column',
             opacity: 0.95,
         } },
-        React.createElement("div", { style: {
+        React.createElement(IconButton, { size: "small", title: expanded ? 'Collapse key' : 'Expand key', style: expanded
+                ? { position: 'absolute', top: 0, right: 0, padding: 1 }
+                : { padding: 1 }, onClick: () => {
+                model.setShowDomainLegend(!expanded);
+            } },
+            React.createElement(ExpandIcon, { style: { fontSize: 14 } })),
+        expanded ? (React.createElement("div", { style: { overflow: 'auto', padding: '2px 6px 4px' } }, rows.map((row, i) => (React.createElement("div", { key: row.key, style: {
                 display: 'flex',
                 alignItems: 'center',
-                justifyContent: 'flex-end',
-                padding: '2px 4px 2px 8px',
-            } },
-            React.createElement(IconButton, { size: "small", title: expanded ? 'Collapse key' : 'Expand key', onClick: () => {
-                    model.setShowDomainLegend(!expanded);
-                } },
-                React.createElement(ExpandIcon, { fontSize: "small" }))),
-        expanded ? (React.createElement("div", { style: { overflow: 'auto', padding: '0 8px 6px' } }, visible.map(({ accession, name }) => (React.createElement("div", { key: accession, style: { display: 'flex', alignItems: 'center', gap: 6 }, title: accession },
-            React.createElement("div", { style: {
-                    width: 12,
-                    height: 12,
+                gap: 4,
+                marginRight: i === 0 ? 18 : 0,
+            }, title: row.hint },
+            row.color ? (React.createElement("div", { style: {
+                    width: 9,
+                    height: 9,
                     flexShrink: 0,
-                    background: fillPalette[accession],
-                } }),
-            React.createElement(Typography, { variant: "caption", noWrap: true }, name)))))) : null)) : null;
+                    background: row.color,
+                } })) : null,
+            React.createElement(Typography, { variant: "caption", noWrap: true, style: {
+                    fontSize: 10,
+                    lineHeight: 1.4,
+                    fontWeight: row.color ? undefined : 'bold',
+                } }, row.label)))))) : null)) : null;
 });
 export default AnnotationLegend;
 //# sourceMappingURL=AnnotationLegend.js.map

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

@@ -1 +1 @@
-{"version":3,"file":"AnnotationLegend.js","sourceRoot":"","sources":["../../../src/components/msa/AnnotationLegend.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,UAAU,MAAM,gCAAgC,CAAA;AACvD,OAAO,UAAU,MAAM,gCAAgC,CAAA;AACvD,OAAO,EAAE,UAAU,EAAE,KAAK,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAC7D,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAIrC,MAAM,gBAAgB,GAAG,QAAQ,CAAC,UAAU,EAC1C,KAAK,GAGN;IACC,MAAM,EACJ,mBAAmB,EACnB,kBAAkB,EAAE,OAAO,EAC3B,WAAW,EACX,gBAAgB,EAAE,QAAQ,GAC3B,GAAG,KAAK,CAAA;IACT,MAAM,UAAU,GAAG,QAAQ,CAAC,CAAC,CAAC,UAAU,CAAC,CAAC,CAAC,UAAU,CAAA;IAErD,OAAO,mBAAmB,IAAI,OAAO,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,CAAC,CACjD,oBAAC,KAAK,IACJ,SAAS,EAAE,CAAC,EACZ,KAAK,EAAE;YACL,QAAQ,EAAE,UAAU;YACpB,GAAG,EAAE,CAAC;YACN,KAAK,EAAE,CAAC;YACR,MAAM,EAAE,GAAG;YACX,QAAQ,EAAE,GAAG;YACb,SAAS,EAAE,KAAK;YAChB,OAAO,EAAE,MAAM;YACf,aAAa,EAAE,QAAQ;YACvB,OAAO,EAAE,IAAI;SACd;QAED,6BACE,KAAK,EAAE;gBACL,OAAO,EAAE,MAAM;gBACf,UAAU,EAAE,QAAQ;gBACpB,cAAc,EAAE,UAAU;gBAC1B,OAAO,EAAE,iBAAiB;aAC3B;YAED,oBAAC,UAAU,IACT,IAAI,EAAC,OAAO,EACZ,KAAK,EAAE,QAAQ,CAAC,CAAC,CAAC,cAAc,CAAC,CAAC,CAAC,YAAY,EAC/C,OAAO,EAAE,GAAG,EAAE;oBACZ,KAAK,CAAC,mBAAmB,CAAC,CAAC,QAAQ,CAAC,CAAA;gBACtC,CAAC;gBAED,oBAAC,UAAU,IAAC,QAAQ,EAAC,OAAO,GAAG,CACpB,CACT;QACL,QAAQ,CAAC,CAAC,CAAC,CACV,6BAAK,KAAK,EAAE,EAAE,QAAQ,EAAE,MAAM,EAAE,OAAO,EAAE,WAAW,EAAE,IACnD,OAAO,CAAC,GAAG,CAAC,CAAC,EAAE,SAAS,EAAE,IAAI,EAAE,EAAE,EAAE,CAAC,CACpC,6BACE,GAAG,EAAE,SAAS,EACd,KAAK,EAAE,EAAE,OAAO,EAAE,MAAM,EAAE,UAAU,EAAE,QAAQ,EAAE,GAAG,EAAE,CAAC,EAAE,EACxD,KAAK,EAAE,SAAS;YAEhB,6BACE,KAAK,EAAE;oBACL,KAAK,EAAE,EAAE;oBACT,MAAM,EAAE,EAAE;oBACV,UAAU,EAAE,CAAC;oBACb,UAAU,EAAE,WAAW,CAAC,SAAS,CAAC;iBACnC,GACD;YACF,oBAAC,UAAU,IAAC,OAAO,EAAC,SAAS,EAAC,MAAM,UACjC,IAAI,CACM,CACT,CACP,CAAC,CACE,CACP,CAAC,CAAC,CAAC,IAAI,CACF,CACT,CAAC,CAAC,CAAC,IAAI,CAAA;AACV,CAAC,CAAC,CAAA;AAEF,eAAe,gBAAgB,CAAA"}
+{"version":3,"file":"AnnotationLegend.js","sourceRoot":"","sources":["../../../src/components/msa/AnnotationLegend.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,UAAU,MAAM,gCAAgC,CAAA;AACvD,OAAO,UAAU,MAAM,gCAAgC,CAAA;AACvD,OAAO,EAAE,UAAU,EAAE,KAAK,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAC7D,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAErC,OAAO,EAAE,YAAY,EAAE,MAAM,oBAAoB,CAAA;AACjD,OAAO,EAAE,UAAU,EAAE,MAAM,iBAAiB,CAAA;AAI5C,MAAM,gBAAgB,GAAG,QAAQ,CAAC,UAAU,EAC1C,KAAK,GAGN;IACC,MAAM,EAAE,OAAO,EAAE,gBAAgB,EAAE,QAAQ,EAAE,GAAG,KAAK,CAAA;IACrD,MAAM,IAAI,GAAG,UAAU,CAAC,OAAO,CAAC,CAAA;IAChC,MAAM,UAAU,GAAG,QAAQ,CAAC,CAAC,CAAC,UAAU,CAAC,CAAC,CAAC,UAAU,CAAA;IAErD,OAAO,IAAI,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,CAAC,CACvB,oBAAC,KAAK,IACJ,SAAS,EAAE,CAAC,EACZ,KAAK,EAAE;YACL,QAAQ,EAAE,UAAU;YACpB,GAAG,EAAE,CAAC;YACN,KAAK,EAAE,CAAC;YACR,MAAM,EAAE,YAAY;YACpB,QAAQ,EAAE,GAAG;YACb,SAAS,EAAE,KAAK;YAChB,OAAO,EAAE,MAAM;YACf,aAAa,EAAE,QAAQ;YACvB,OAAO,EAAE,IAAI;SACd;QAED,oBAAC,UAAU,IACT,IAAI,EAAC,OAAO,EACZ,KAAK,EAAE,QAAQ,CAAC,CAAC,CAAC,cAAc,CAAC,CAAC,CAAC,YAAY,EAC/C,KAAK,EACH,QAAQ;gBACN,CAAC,CAAC,EAAE,QAAQ,EAAE,UAAU,EAAE,GAAG,EAAE,CAAC,EAAE,KAAK,EAAE,CAAC,EAAE,OAAO,EAAE,CAAC,EAAE;gBACxD,CAAC,CAAC,EAAE,OAAO,EAAE,CAAC,EAAE,EAEpB,OAAO,EAAE,GAAG,EAAE;gBACZ,KAAK,CAAC,mBAAmB,CAAC,CAAC,QAAQ,CAAC,CAAA;YACtC,CAAC;YAED,oBAAC,UAAU,IAAC,KAAK,EAAE,EAAE,QAAQ,EAAE,EAAE,EAAE,GAAI,CAC5B;QACZ,QAAQ,CAAC,CAAC,CAAC,CACV,6BAAK,KAAK,EAAE,EAAE,QAAQ,EAAE,MAAM,EAAE,OAAO,EAAE,aAAa,EAAE,IACrD,IAAI,CAAC,GAAG,CAAC,CAAC,GAAG,EAAE,CAAC,EAAE,EAAE,CAAC,CACpB,6BACE,GAAG,EAAE,GAAG,CAAC,GAAG,EACZ,KAAK,EAAE;gBACL,OAAO,EAAE,MAAM;gBACf,UAAU,EAAE,QAAQ;gBACpB,GAAG,EAAE,CAAC;gBACN,WAAW,EAAE,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC;aAC9B,EACD,KAAK,EAAE,GAAG,CAAC,IAAI;YAEd,GAAG,CAAC,KAAK,CAAC,CAAC,CAAC,CACX,6BACE,KAAK,EAAE;oBACL,KAAK,EAAE,CAAC;oBACR,MAAM,EAAE,CAAC;oBACT,UAAU,EAAE,CAAC;oBACb,UAAU,EAAE,GAAG,CAAC,KAAK;iBACtB,GACD,CACH,CAAC,CAAC,CAAC,IAAI;YACR,oBAAC,UAAU,IACT,OAAO,EAAC,SAAS,EACjB,MAAM,QACN,KAAK,EAAE;oBACL,QAAQ,EAAE,EAAE;oBACZ,UAAU,EAAE,GAAG;oBACf,UAAU,EAAE,GAAG,CAAC,KAAK,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,MAAM;iBAC3C,IAEA,GAAG,CAAC,KAAK,CACC,CACT,CACP,CAAC,CACE,CACP,CAAC,CAAC,CAAC,IAAI,CACF,CACT,CAAC,CAAC,CAAC,IAAI,CAAA;AACV,CAAC,CAAC,CAAA;AAEF,eAAe,gBAAgB,CAAA"}

package/dist/components/msa/MSACanvas.js

@@ -13,7 +13,7 @@ const MSACanvas = observer(function ({ model }) {
         model.doScrollY(d);
     }, [model]);
     const onZoom = useCallback((scaleFactor, offsetX, offsetY) => {
-        model.zoomToPos(scaleFactor, offsetX, offsetY);
+        model.zoomToPos(scaleFactor, offsetX, offsetY, model.wheelZoomAxis);
     }, [model]);
     const { onMouseDown, onMouseUp } = useWheelScroll({
         ref,

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

@@ -1 +1 @@
-{"version":3,"file":"MSACanvas.js","sourceRoot":"","sources":["../../../src/components/msa/MSACanvas.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,WAAW,EAAE,MAAM,EAAE,MAAM,OAAO,CAAA;AAElD,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAErC,OAAO,EAAE,cAAc,EAAE,MAAM,yBAAyB,CAAA;AACxD,OAAO,OAAO,MAAM,cAAe,CAAA;AACnC,OAAO,cAAc,MAAM,qBAAsB,CAAA;AAIjD,MAAM,SAAS,GAAG,QAAQ,CAAC,UAAU,EAAE,KAAK,EAA2B;IACrE,MAAM,EACJ,GAAG,EACH,aAAa,EACb,MAAM,EACN,cAAc,EACd,QAAQ,EACR,UAAU,EACV,OAAO,EACP,OAAO,GACR,GAAG,KAAK,CAAA;IACT,MAAM,GAAG,GAAG,MAAM,CAAiB,IAAI,CAAC,CAAA;IACxC,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,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,MAAM,GAAG,WAAW,CACxB,CAAC,WAAmB,EAAE,OAAe,EAAE,OAAe,EAAE,EAAE;QACxD,KAAK,CAAC,SAAS,CAAC,WAAW,EAAE,OAAO,EAAE,OAAO,CAAC,CAAA;IAChD,CAAC,EACD,CAAC,KAAK,CAAC,CACR,CAAA;IACD,MAAM,EAAE,WAAW,EAAE,SAAS,EAAE,GAAG,cAAc,CAAC;QAChD,GAAG;QACH,SAAS;QACT,SAAS;QACT,MAAM;QACN,UAAU;KACX,CAAC,CAAA;IAEF,OAAO,CACL,6BACE,GAAG,EAAE,GAAG,iBAKI,YAAY,EACxB,WAAW,EAAE,WAAW,EACxB,SAAS,EAAE,SAAS,EACpB,YAAY,EAAE,KAAK,CAAC,EAAE;YACpB,KAAK,CAAC,cAAc,EAAE,CAAA;QACxB,CAAC,EACD,KAAK,EAAE;YACL,QAAQ,EAAE,UAAU;YACpB,MAAM;YACN,KAAK,EAAE,cAAc;YACrB,QAAQ,EAAE,QAAQ;SACnB,IAEA,CAAC,GAAG,IAAI,CAAC,aAAa,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,CAGrC,6BACE,KAAK,EAAE;YACL,QAAQ,EAAE,UAAU;YACpB,GAAG,EAAE,CAAC;YACN,IAAI,EAAE,CAAC;YACP,SAAS,EAAE,aAAa,OAAO,OAAO,OAAO,KAAK;YAClD,UAAU,EAAE,WAAW;SACxB,IAEA,QAAQ,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,EAAE,CAAC,EAAE,EAAE,CAAC,CAC1B,oBAAC,cAAc,IACb,GAAG,EAAE,GAAG,EAAE,IAAI,EAAE,EAAE,EAClB,KAAK,EAAE,KAAK,EACZ,OAAO,EAAE,EAAE,EACX,OAAO,EAAE,EAAE,GACX,CACH,CAAC,CACE,CACP,CAAC,CAAC,CAAC,CACF,oBAAC,OAAO,OAAG,CACZ,CACG,CACP,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,SAAS,CAAA"}
+{"version":3,"file":"MSACanvas.js","sourceRoot":"","sources":["../../../src/components/msa/MSACanvas.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,WAAW,EAAE,MAAM,EAAE,MAAM,OAAO,CAAA;AAElD,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAErC,OAAO,EAAE,cAAc,EAAE,MAAM,yBAAyB,CAAA;AACxD,OAAO,OAAO,MAAM,cAAe,CAAA;AACnC,OAAO,cAAc,MAAM,qBAAsB,CAAA;AAIjD,MAAM,SAAS,GAAG,QAAQ,CAAC,UAAU,EAAE,KAAK,EAA2B;IACrE,MAAM,EACJ,GAAG,EACH,aAAa,EACb,MAAM,EACN,cAAc,EACd,QAAQ,EACR,UAAU,EACV,OAAO,EACP,OAAO,GACR,GAAG,KAAK,CAAA;IACT,MAAM,GAAG,GAAG,MAAM,CAAiB,IAAI,CAAC,CAAA;IACxC,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,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,MAAM,GAAG,WAAW,CACxB,CAAC,WAAmB,EAAE,OAAe,EAAE,OAAe,EAAE,EAAE;QACxD,KAAK,CAAC,SAAS,CAAC,WAAW,EAAE,OAAO,EAAE,OAAO,EAAE,KAAK,CAAC,aAAa,CAAC,CAAA;IACrE,CAAC,EACD,CAAC,KAAK,CAAC,CACR,CAAA;IACD,MAAM,EAAE,WAAW,EAAE,SAAS,EAAE,GAAG,cAAc,CAAC;QAChD,GAAG;QACH,SAAS;QACT,SAAS;QACT,MAAM;QACN,UAAU;KACX,CAAC,CAAA;IAEF,OAAO,CACL,6BACE,GAAG,EAAE,GAAG,iBAGI,YAAY,EACxB,WAAW,EAAE,WAAW,EACxB,SAAS,EAAE,SAAS,EACpB,YAAY,EAAE,KAAK,CAAC,EAAE;YACpB,KAAK,CAAC,cAAc,EAAE,CAAA;QACxB,CAAC,EACD,KAAK,EAAE;YACL,QAAQ,EAAE,UAAU;YACpB,MAAM;YACN,KAAK,EAAE,cAAc;YACrB,QAAQ,EAAE,QAAQ;SACnB,IAEA,CAAC,GAAG,IAAI,CAAC,aAAa,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,CAGrC,6BACE,KAAK,EAAE;YACL,QAAQ,EAAE,UAAU;YACpB,GAAG,EAAE,CAAC;YACN,IAAI,EAAE,CAAC;YACP,SAAS,EAAE,aAAa,OAAO,OAAO,OAAO,KAAK;YAClD,UAAU,EAAE,WAAW;SACxB,IAEA,QAAQ,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,EAAE,CAAC,EAAE,EAAE,CAAC,CAC1B,oBAAC,cAAc,IACb,GAAG,EAAE,GAAG,EAAE,IAAI,EAAE,EAAE,EAClB,KAAK,EAAE,KAAK,EACZ,OAAO,EAAE,EAAE,EACX,OAAO,EAAE,EAAE,GACX,CACH,CAAC,CACE,CACP,CAAC,CAAC,CAAC,CACF,oBAAC,OAAO,OAAG,CACZ,CACG,CACP,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,SAAS,CAAA"}

package/dist/components/msa/MSACanvasBlock.js

@@ -1,16 +1,15 @@
 import React from 'react';
 import BaseTooltip from '@jbrowse/core/ui/BaseTooltip';
+import { useTheme } from '@mui/material';
 import { observer } from 'mobx-react';
 import { useCanvasAutorun } from '../../useCanvasAutorun.js';
-import { useColorContrast } from '../../useColorContrast.js';
-import ColumnStats from './ColumnStats.js';
 import { drawMsaRaster, rasterSupported } from './msaRaster.js';
 import { renderBoxFeatureCanvasBlock } from './renderBoxFeatureCanvasBlock.js';
 import { renderMSABlock } from './renderMSABlock.js';
 import { useMsaBlockMouse } from './useMsaBlockMouse.js';
 const MSACanvasBlock = observer(function ({ model, offsetX, offsetY, }) {
-    const { colorScheme, blockSize, highResScaleFactor } = model;
-    const { theme, contrastScheme } = useColorContrast(colorScheme);
+    const { blockSize, highResScaleFactor } = model;
+    const theme = useTheme();
     const { tooltipPoint, onMouseMove, onClick, onMouseLeave } = useMsaBlockMouse({
         model,
         offsetX,
@@ -23,6 +22,7 @@ const MSACanvasBlock = observer(function ({ model, offsetX, offsetY, }) {
             ctx.clearRect(0, 0, canvasSize, canvasSize);
             renderBoxFeatureCanvasBlock({
                 ctx,
+                theme,
                 offsetX,
                 offsetY,
                 model,
@@ -39,16 +39,15 @@ const MSACanvasBlock = observer(function ({ model, offsetX, offsetY, }) {
                 theme,
                 offsetX,
                 offsetY,
-                contrastScheme,
                 model,
                 rasterTiles,
             });
         },
         width: canvasSize,
         height: canvasSize,
-        deps: [model, offsetX, offsetY, theme, contrastScheme],
+        deps: [model, offsetX, offsetY, theme],
     });
-    const { hoveredInsertion, mouseOverDomains, showColumnStats } = model;
+    const { hoveredInsertion, mouseOverDomains } = model;
     return (React.createElement(React.Fragment, null,
         React.createElement("canvas", { ref: ref, onMouseMove: event => {
                 if (ref.current) {
@@ -75,19 +74,17 @@ const MSACanvasBlock = observer(function ({ model, offsetX, offsetY, }) {
             ' ',
             hoveredInsertion.letters.length > 20
                 ? `${hoveredInsertion.letters.slice(0, 20)}...`
-                : hoveredInsertion.letters)) : (React.createElement(React.Fragment, null,
-            mouseOverDomains.map(d => (React.createElement("div", { key: `${d.accession}-${d.start}-${d.end}` },
-                React.createElement("b", null, d.name),
-                " (",
-                d.accession,
-                ") ",
-                d.start,
-                "-",
-                d.end,
-                d.description ? (React.createElement(React.Fragment, null,
-                    React.createElement("br", null),
-                    d.description)) : null))),
-            showColumnStats ? React.createElement(ColumnStats, { model: model }) : null)))) : null));
+                : hoveredInsertion.letters)) : (mouseOverDomains.map(d => (React.createElement("div", { key: `${d.accession}-${d.start}-${d.end}` },
+            React.createElement("b", null, d.name),
+            " (",
+            d.accession,
+            ") ",
+            d.start,
+            "-",
+            d.end,
+            d.description ? (React.createElement(React.Fragment, null,
+                React.createElement("br", null),
+                d.description)) : null)))))) : null));
 });
 export default MSACanvasBlock;
 //# sourceMappingURL=MSACanvasBlock.js.map

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

@@ -1 +1 @@
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+{"version":3,"file":"MSACanvasBlock.js","sourceRoot":"","sources":["../../../src/components/msa/MSACanvasBlock.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,WAAW,MAAM,8BAA8B,CAAA;AACtD,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,EAAE,aAAa,EAAE,eAAe,EAAE,MAAM,gBAAgB,CAAA;AAC/D,OAAO,EAAE,2BAA2B,EAAE,MAAM,kCAAkC,CAAA;AAC9E,OAAO,EAAE,cAAc,EAAE,MAAM,qBAAqB,CAAA;AACpD,OAAO,EAAE,gBAAgB,EAAE,MAAM,uBAAuB,CAAA;AAIxD,MAAM,cAAc,GAAG,QAAQ,CAAC,UAAU,EACxC,KAAK,EACL,OAAO,EACP,OAAO,GAKR;IACC,MAAM,EAAE,SAAS,EAAE,kBAAkB,EAAE,GAAG,KAAK,CAAA;IAC/C,MAAM,KAAK,GAAG,QAAQ,EAAE,CAAA;IACxB,MAAM,EAAE,YAAY,EAAE,WAAW,EAAE,OAAO,EAAE,YAAY,EAAE,GAAG,gBAAgB,CAC3E;QACE,KAAK;QACL,OAAO;QACP,OAAO;KACR,CACF,CAAA;IAED,MAAM,UAAU,GAAG,SAAS,GAAG,kBAAkB,CAAA;IACjD,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,UAAU,EAAE,UAAU,CAAC,CAAA;YAC3C,2BAA2B,CAAC;gBAC1B,GAAG;gBACH,KAAK;gBACL,OAAO;gBACP,OAAO;gBACP,KAAK;aACN,CAAC,CAAA;YACF,yEAAyE;YACzE,yEAAyE;YACzE,yBAAyB;YACzB,MAAM,WAAW,GACf,CAAC,KAAK,CAAC,mBAAmB,IAAI,KAAK,CAAC,OAAO,IAAI,eAAe,EAAE,CAAA;YAClE,IAAI,WAAW,EAAE,CAAC;gBAChB,aAAa,CAAC,EAAE,GAAG,EAAE,KAAK,EAAE,KAAK,EAAE,OAAO,EAAE,OAAO,EAAE,CAAC,CAAA;YACxD,CAAC;YACD,cAAc,CAAC;gBACb,GAAG;gBACH,KAAK;gBACL,OAAO;gBACP,OAAO;gBACP,KAAK;gBACL,WAAW;aACZ,CAAC,CAAA;QACJ,CAAC;QACD,KAAK,EAAE,UAAU;QACjB,MAAM,EAAE,UAAU;QAClB,IAAI,EAAE,CAAC,KAAK,EAAE,OAAO,EAAE,OAAO,EAAE,KAAK,CAAC;KACvC,CAAC,CAAA;IAEF,MAAM,EAAE,gBAAgB,EAAE,gBAAgB,EAAE,GAAG,KAAK,CAAA;IAEpD,OAAO,CACL;QACE,gCACE,GAAG,EAAE,GAAG,EACR,WAAW,EAAE,KAAK,CAAC,EAAE;gBACnB,IAAI,GAAG,CAAC,OAAO,EAAE,CAAC;oBAChB,WAAW,CAAC,KAAK,EAAE,GAAG,CAAC,OAAO,CAAC,CAAA;gBACjC,CAAC;YACH,CAAC,EACD,OAAO,EAAE,KAAK,CAAC,EAAE;gBACf,IAAI,GAAG,CAAC,OAAO,EAAE,CAAC;oBAChB,OAAO,CAAC,KAAK,EAAE,GAAG,CAAC,OAAO,CAAC,CAAA;gBAC7B,CAAC;YACH,CAAC,EACD,YAAY,EAAE,GAAG,EAAE;gBACjB,YAAY,EAAE,CAAA;YAChB,CAAC,EACD,KAAK,EAAE,UAAU,EACjB,MAAM,EAAE,UAAU,EAClB,KAAK,EAAE;gBACL,QAAQ,EAAE,UAAU;gBACpB,GAAG,EAAE,OAAO;gBACZ,IAAI,EAAE,OAAO;gBACb,KAAK,EAAE,SAAS;gBAChB,MAAM,EAAE,SAAS;aAClB,GACD;QACD,YAAY,CAAC,CAAC,CAAC,CACd,oBAAC,WAAW,IACV,WAAW,EAAE,EAAE,CAAC,EAAE,YAAY,CAAC,CAAC,EAAE,CAAC,EAAE,YAAY,CAAC,CAAC,GAAG,EAAE,EAAE,IAEzD,gBAAgB,CAAC,CAAC,CAAC,CAClB;;YACc,gBAAgB,CAAC,OAAO,CAAC,MAAM;YAC1C,KAAK,CAAC,YAAY,KAAK,OAAO,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,IAAI;;YAAI,GAAG;YACnD,gBAAgB,CAAC,OAAO,CAAC,MAAM,GAAG,EAAE;gBACnC,CAAC,CAAC,GAAG,gBAAgB,CAAC,OAAO,CAAC,KAAK,CAAC,CAAC,EAAE,EAAE,CAAC,KAAK;gBAC/C,CAAC,CAAC,gBAAgB,CAAC,OAAO,CAC3B,CACJ,CAAC,CAAC,CAAC,CACF,gBAAgB,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CACxB,6BAAK,GAAG,EAAE,GAAG,CAAC,CAAC,SAAS,IAAI,CAAC,CAAC,KAAK,IAAI,CAAC,CAAC,GAAG,EAAE;YAC5C,+BAAI,CAAC,CAAC,IAAI,CAAK;;YAAG,CAAC,CAAC,SAAS;;YAAI,CAAC,CAAC,KAAK;;YAAG,CAAC,CAAC,GAAG;YAC/C,CAAC,CAAC,WAAW,CAAC,CAAC,CAAC,CACf;gBACE,+BAAM;gBACL,CAAC,CAAC,WAAW,CACb,CACJ,CAAC,CAAC,CAAC,IAAI,CACJ,CACP,CAAC,CACH,CACW,CACf,CAAC,CAAC,CAAC,IAAI,CACP,CACJ,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,cAAc,CAAA"}

package/dist/components/msa/MSAMouseoverCanvas.js

@@ -2,6 +2,7 @@ import React from 'react';
 import { isAlive } from '@jbrowse/mobx-state-tree';
 import { useTheme } from '@mui/material';
 import { observer } from 'mobx-react';
+import { msaOverlayZIndex } from '../../constants.js';
 import { useCanvasAutorun } from '../../useCanvasAutorun.js';
 import { renderMouseover } from './renderMSAMouseover.js';
 const MSAMouseoverCanvas = observer(function ({ model, }) {
@@ -25,7 +26,7 @@ const MSAMouseoverCanvas = observer(function ({ model, }) {
             left: 0,
             width,
             height,
-            zIndex: 1000,
+            zIndex: msaOverlayZIndex,
             pointerEvents: 'none',
         } }));
 });

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

@@ -1 +1 @@
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+{"version":3,"file":"MSAMouseoverCanvas.js","sourceRoot":"","sources":["../../../src/components/msa/MSAMouseoverCanvas.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,EAAE,OAAO,EAAE,MAAM,0BAA0B,CAAA;AAClD,OAAO,EAAE,QAAQ,EAAE,MAAM,eAAe,CAAA;AACxC,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAErC,OAAO,EAAE,gBAAgB,EAAE,MAAM,oBAAoB,CAAA;AACrD,OAAO,EAAE,gBAAgB,EAAE,MAAM,2BAA2B,CAAA;AAC5D,OAAO,EAAE,eAAe,EAAE,MAAM,yBAAyB,CAAA;AAIzD,MAAM,kBAAkB,GAAG,QAAQ,CAAC,UAAU,EAC5C,KAAK,GAGN;IACC,MAAM,EAAE,MAAM,EAAE,cAAc,EAAE,KAAK,EAAE,kBAAkB,EAAE,GAAG,KAAK,CAAA;IACnE,MAAM,KAAK,GAAG,QAAQ,EAAE,CAAA;IACxB,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,IAAI,OAAO,CAAC,KAAK,CAAC,EAAE,CAAC;gBACnB,eAAe,CAAC,EAAE,GAAG,EAAE,KAAK,EAAE,KAAK,EAAE,CAAC,CAAA;YACxC,CAAC;QACH,CAAC;QACD,KAAK,EAAE,WAAW;QAClB,MAAM,EAAE,YAAY;QACpB,IAAI,EAAE,CAAC,KAAK,EAAE,KAAK,CAAC;KACrB,CAAC,CAAA;IAEF,OAAO,CACL,gCACE,GAAG,EAAE,GAAG,EACR,EAAE,EAAC,WAAW,EACd,KAAK,EAAE,WAAW,EAClB,MAAM,EAAE,YAAY,EACpB,KAAK,EAAE;YACL,QAAQ,EAAE,UAAU;YACpB,GAAG,EAAE,CAAC;YACN,IAAI,EAAE,CAAC;YACP,KAAK;YACL,MAAM;YACN,MAAM,EAAE,gBAAgB;YACxB,aAAa,EAAE,MAAM;SACtB,GACD,CACH,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,kBAAkB,CAAA"}

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

@@ -1,17 +1,13 @@
 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.
+ * Left-to-right cursor over one row's domain bands that returns the band drawn
+ * on top at a column, for a letter's contrast color.
  *
- * 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.
+ * The overlay paints in `domainBands` order, largest first, so where signatures
+ * nest (InterProScan often emits a family enclosing a domain) the visible band
+ * is the last one painted. `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.
+ * `bands` must be sorted by start column (`domainBandsByStart`) and columns
+ * visited in increasing order, which keeps this to one pass per row.
  */
 export declare function domainBandCursor(bands: DomainBand[] | undefined): (col: number) => DomainBand | undefined;

package/dist/components/msa/domainBandCursor.js

@@ -1,17 +1,13 @@
 /**
- * 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.
+ * Left-to-right cursor over one row's domain bands that returns the band drawn
+ * on top at a column, for a letter's contrast color.
  *
- * 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.
+ * The overlay paints in `domainBands` order, largest first, so where signatures
+ * nest (InterProScan often emits a family enclosing a domain) the visible band
+ * is the last one painted. `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.
+ * `bands` must be sorted by start column (`domainBandsByStart`) and columns
+ * visited in increasing order, which keeps this to one pass per row.
  */
 export function domainBandCursor(bands) {
     let next = 0;

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

@@ -1 +1 @@
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+{"version":3,"file":"domainBandCursor.js","sourceRoot":"","sources":["../../../src/components/msa/domainBandCursor.ts"],"names":[],"mappings":"AAEA;;;;;;;;;;GAUG;AACH,MAAM,UAAU,gBAAgB,CAAC,KAA+B;IAC9D,IAAI,IAAI,GAAG,CAAC,CAAA;IACZ,IAAI,MAAM,GAAiB,EAAE,CAAA;IAE7B,OAAO,CAAC,GAAW,EAAE,EAAE;QACrB,IAAI,CAAC,KAAK,EAAE,CAAC;YACX,OAAO,SAAS,CAAA;QAClB,CAAC;QACD,OAAO,IAAI,GAAG,KAAK,CAAC,MAAM,IAAI,KAAK,CAAC,IAAI,CAAE,CAAC,QAAQ,IAAI,GAAG,EAAE,CAAC;YAC3D,MAAM,CAAC,IAAI,CAAC,KAAK,CAAC,IAAI,CAAE,CAAC,CAAA;YACzB,IAAI,EAAE,CAAA;QACR,CAAC;QACD,IAAI,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC,IAAI,CAAC,MAAM,IAAI,GAAG,CAAC,EAAE,CAAC;YAC5C,MAAM,GAAG,MAAM,CAAC,MAAM,CAAC,IAAI,CAAC,EAAE,CAAC,IAAI,CAAC,MAAM,GAAG,GAAG,CAAC,CAAA;QACnD,CAAC;QACD,IAAI,GAA2B,CAAA;QAC/B,KAAK,MAAM,IAAI,IAAI,MAAM,EAAE,CAAC;YAC1B,IAAI,CAAC,GAAG,IAAI,IAAI,CAAC,UAAU,GAAG,GAAG,CAAC,UAAU,EAAE,CAAC;gBAC7C,GAAG,GAAG,IAAI,CAAA;YACZ,CAAC;QACH,CAAC;QACD,OAAO,GAAG,CAAA;IACZ,CAAC,CAAA;AACH,CAAC"}

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

@@ -0,0 +1,53 @@
+import type { HierarchyNode } from '../../hierarchy.ts';
+import type { Annotation, NodeWithIdsAndLength } from '../../types.ts';
+import type { RenderCtx } from '../renderCtx.ts';
+/** one drawn span: a feature, the lane it sits in, and its row's depth */
+export interface SpanBand {
+    annotation: Annotation;
+    lane: number;
+    laneCount: number;
+}
+/** one row's spans, at the row baseline `y` the tree layout gives it */
+export interface SpanRow<T extends SpanBand> {
+    y: number;
+    bands: T[];
+}
+/**
+ * Where a band lands inside its row. The alignment overlay fills the row, bars
+ * it along the bottom, or stacks thin sub-rows; a `features` row panel divides
+ * the row between its lanes.
+ */
+export interface SpanLayout {
+    /** the band height in a row needing `laneCount` lanes */
+    height: (laneCount: number) => number;
+    /** the band's top edge, from its row baseline, its lane and its height */
+    top: (y: number, lane: number, height: number) => number;
+    /** how far a strand head reaches past the body */
+    headLength: (height: number) => number;
+}
+/** the rows of `bandsByRow` that `leaves` covers, in display order */
+export declare function spanRows<T extends SpanBand>(leaves: HierarchyNode<NodeWithIdsAndLength>[], bandsByRow: Map<string, T[]>): SpanRow<T>[];
+/**
+ * The span mark, in whatever x space the caller maps its bands into: alignment
+ * columns for the domain overlay, panel pixels for a `features` row panel. A
+ * feature with a strand draws as an arrow, one without as a box, and a label
+ * draws inside the span wherever the text fits.
+ *
+ * `xOf` returns the span's `[xStart, xEnd]` in the context's coordinates, and
+ * the context is translated so that `y - rowHeight` is the row's top edge.
+ */
+export declare function drawFeatureSpans<T extends SpanBand>({ ctx, rows, layout, xOf, colors, labelOf, labelDrawn, contrastText, xMin, xMax, }: {
+    ctx: RenderCtx;
+    rows: SpanRow<T>[];
+    layout: SpanLayout;
+    xOf: (band: T) => [number, number];
+    colors: Map<Annotation, {
+        fill: string;
+        stroke: string;
+    }>;
+    labelOf?: (band: T) => string | undefined;
+    labelDrawn?: (band: T) => void;
+    contrastText: (color: string) => string;
+    xMin: number;
+    xMax: number;
+}): void;

package/dist/components/msa/drawFeatureSpans.js

@@ -0,0 +1,78 @@
+/** the rows of `bandsByRow` that `leaves` covers, in display order */
+export function spanRows(leaves, bandsByRow) {
+    const rows = [];
+    for (const leaf of leaves) {
+        const bands = bandsByRow.get(leaf.data.name);
+        if (bands && bands.length > 0) {
+            rows.push({ y: leaf.x, bands });
+        }
+    }
+    return rows;
+}
+/**
+ * The span mark, in whatever x space the caller maps its bands into: alignment
+ * columns for the domain overlay, panel pixels for a `features` row panel. A
+ * feature with a strand draws as an arrow, one without as a box, and a label
+ * draws inside the span wherever the text fits.
+ *
+ * `xOf` returns the span's `[xStart, xEnd]` in the context's coordinates, and
+ * the context is translated so that `y - rowHeight` is the row's top edge.
+ */
+export function drawFeatureSpans({ ctx, rows, layout, xOf, colors, labelOf, labelDrawn, contrastText, xMin, xMax, }) {
+    for (const { y, bands } of rows) {
+        const h = layout.height(bands[0].laneCount);
+        const headLen = layout.headLength(h);
+        for (const band of bands) {
+            const [xStart, xEnd] = xOf(band);
+            const w = xEnd - xStart;
+            if (xEnd < xMin || xStart > xMax) {
+                continue;
+            }
+            const t = layout.top(y, band.lane, h);
+            const { fill, stroke } = colors.get(band.annotation);
+            ctx.fillStyle = fill;
+            ctx.strokeStyle = stroke;
+            const { strand } = band.annotation;
+            if (strand === undefined) {
+                ctx.fillRect(xStart, t, w, h);
+                ctx.strokeRect(xStart, t, w, h);
+            }
+            else {
+                drawGeneArrow({ ctx, x: xStart, t, w, h, headLen, strand });
+            }
+            const label = labelOf?.(band);
+            if (label !== undefined) {
+                const fontSize = Math.min(h - 2, 11);
+                ctx.font = `${fontSize}px sans-serif`;
+                if (ctx.measureText(label).width + 2 <= w) {
+                    labelDrawn?.(band);
+                    ctx.fillStyle = contrastText(fill);
+                    ctx.textAlign = 'center';
+                    ctx.textBaseline = 'middle';
+                    ctx.fillText(label, xStart + w / 2, t + h / 2);
+                }
+            }
+        }
+    }
+}
+// A gene arrow: a full-width rectangular body spanning the feature's
+// start..end columns, plus a triangular head that points *beyond* that end in
+// the strand direction (right for +, left for -). Keeping the body aligned to
+// the exact start/end columns means + and - strand features read as having the
+// same boundaries; the arrow lives outside them purely to show transcription
+// direction, preserving the column-by-column homology down the rows.
+function drawGeneArrow({ ctx, x, t, w, h, headLen, strand, }) {
+    const dir = strand > 0 ? 1 : -1;
+    const bodyStart = strand > 0 ? x : x + w;
+    const bodyEnd = strand > 0 ? x + w : x;
+    ctx.beginPath();
+    ctx.moveTo(bodyStart, t);
+    ctx.lineTo(bodyEnd, t);
+    ctx.lineTo(bodyEnd + dir * headLen, t + h / 2);
+    ctx.lineTo(bodyEnd, t + h);
+    ctx.lineTo(bodyStart, t + h);
+    ctx.closePath();
+    ctx.fill();
+    ctx.stroke();
+}
+//# sourceMappingURL=drawFeatureSpans.js.map

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

@@ -0,0 +1 @@
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package/dist/components/msa/legendRows.d.ts

@@ -0,0 +1,8 @@
+import type { Legend } from '../../types.ts';
+export interface LegendRow {
+    key: string;
+    label: string;
+    color?: string;
+    hint?: string;
+}
+export declare function legendRows(legends: Legend[]): LegendRow[];

package/dist/components/msa/legendRows.js

@@ -0,0 +1,16 @@
+// the legends flattened into the rows both the overlay and the export stack
+// top to bottom. A title row separates one legend from the next, and a lone
+// legend needs no title.
+export function legendRows(legends) {
+    const titled = legends.length > 1;
+    return legends.flatMap(legend => [
+        ...(titled ? [{ key: legend.id, label: legend.title }] : []),
+        ...legend.entries.map(entry => ({
+            key: `${legend.id}:${entry.id}`,
+            label: entry.label,
+            color: entry.color,
+            hint: entry.id,
+        })),
+    ]);
+}
+//# sourceMappingURL=legendRows.js.map

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

@@ -0,0 +1 @@
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package/dist/components/msa/msaRaster.d.ts

@@ -12,21 +12,21 @@ export interface RasterSpec {
 }
 /**
  * CSS color string -> the packed pixel an ImageData holds for it. Painting a 1x1
- * canvas and reading it back handles every form a color scheme can produce --
- * hex, rgb(), hsl(), named -- without a parser of our own, and the cache means
- * each distinct color is resolved once per session rather than once per cell.
+ * canvas and reading it back parses hex, rgb(), hsl() and named colors; the
+ * cache resolves each distinct color once per session.
  */
 export declare function cssColorToPixel(css: string): number;
 /**
  * Packs a rectangle of the alignment into one pixel per cell, in `rowNames`
  * order, ready to hand to putImageData. Cells past the end of a row, and rows
- * with no sequence at all, stay transparent -- what the per-cell tile painter
- * also leaves behind.
+ * with no sequence, stay transparent, as in the per-cell painter.
  *
- * `colStep`/`rowStep` sample instead of covering, which is how the minimap fits
- * a whole alignment into a 12px bar.
+ * `colStep`/`rowStep` sample every nth cell, which fits a whole alignment into
+ * the minimap's 12px bar. `colSpan`/`rowSpan` average each block of that many
+ * cells into one pixel, so a zoom below a device pixel per column still shows
+ * every column's color without blending neighbouring rows.
  */
-export declare function rasterPixels({ spec, col0, row0, width, height, colStep, rowStep, toPixel, }: {
+export declare function rasterPixels({ spec, col0, row0, width, height, colStep, rowStep, colSpan, rowSpan, toPixel, out, }: {
     spec: RasterSpec;
     col0: number;
     row0: number;
@@ -34,14 +34,21 @@ export declare function rasterPixels({ spec, col0, row0, width, height, colStep,
     height: number;
     colStep?: number;
     rowStep?: number;
+    colSpan?: number;
+    rowSpan?: number;
     toPixel?: (css: string) => number;
-}): Uint32Array<ArrayBuffer>;
+    out?: Uint32Array;
+}): Uint32Array<ArrayBufferLike>;
 export declare function rasterSupported(): boolean;
 /**
  * Paints the alignment background of one MSA block from cached
  * one-pixel-per-cell tiles. The tiles do not depend on the zoom level, so a zoom
- * frame costs a handful of drawImage calls instead of a fillRect per visible
- * cell -- which ran to 885ms per block at the minimum column width.
+ * frame costs a handful of drawImage calls. A fillRect per visible cell measured
+ * 885ms per block at the minimum column width.
+ *
+ * Below a device pixel per cell the tiles average cells together, per axis.
+ * The browser's image smoothing blurs both axes, which turns every row
+ * boundary into a gradient at fit-to-width, where only the columns are narrow.
  */
 export declare function drawMsaRaster({ ctx, model, theme, offsetX, offsetY, }: {
     ctx: CanvasRenderingContext2D;
@@ -53,26 +60,23 @@ export declare function drawMsaRaster({ ctx, model, theme, offsetX, offsetY, }:
 /**
  * A raster canvas as a PNG data URI, for embedding in the SVG export.
  *
- * toDataURL is the synchronous read-back. The DOM canvas has it, and so does a
- * node canvas standing in for OffscreenCanvas headlessly; a browser
- * OffscreenCanvas -- which is what the tile and thumbnail caches hold wherever
- * it exists -- gets copied onto a DOM canvas first. Returns undefined wherever
- * the read-back is unavailable (jsdom) rather than throwing, which is the
- * signal to fall back to drawing the thing in vector.
+ * toDataURL is the synchronous read-back. The DOM canvas and a headless node
+ * canvas have it; a browser OffscreenCanvas, which the tile and thumbnail
+ * caches hold where it exists, is copied onto a DOM canvas first. Returns
+ * undefined where read-back is unavailable (jsdom), and the caller then draws
+ * in vector.
  */
 export declare function canvasHref(canvas: RasterCanvas | undefined): string | undefined;
 /**
  * The alignment rectangle [col0, col0+numCols) x [row0, row0+numRows) as a PNG
  * data URI, for the SVG export.
  *
- * SVG has no blit, so the export cannot reuse the tile cache the live canvas
- * draws from: one <image> is the whole background instead. That is the
- * difference between an export that scales and one that does not -- the vector
- * path emits a <rect> per cell, and a 200x500 alignment exhausts the heap
- * building them.
+ * SVG has no blit, so the export draws the whole background as one <image>. The
+ * vector path emits a <rect> per cell, and a 200x500 alignment exhausts the
+ * heap building them.
  *
- * Returns undefined wherever a canvas cannot be read back (jsdom, notably),
- * which is the signal to keep the per-cell path.
+ * Returns undefined where a canvas cannot be read back (jsdom), and the caller
+ * then keeps the per-cell path.
  */
 export declare function rasterImageHref({ model, theme, col0, row0, numCols, numRows, }: {
     model: MsaViewModel;
@@ -83,9 +87,8 @@ export declare function rasterImageHref({ model, theme, col0, row0, numCols, num
     numRows: number;
 }): string | undefined;
 /**
- * The whole alignment sampled down to a strip small enough to sit behind the
- * minimap thumb, cached alongside the block tiles because it goes stale under
- * exactly the same conditions.
+ * The whole alignment sampled down to a strip behind the minimap thumb, cached
+ * with the block tiles since the same keys invalidate both.
  */
 export declare function msaThumbnail({ model, theme, height, }: {
     model: MsaViewModel;