react-msaview 5.5.0 → 5.6.0

package/dist/components/msa/ColumnStats.js

@@ -0,0 +1,42 @@
+import React from 'react';
+import { observer } from 'mobx-react';
+const pct = (n) => `${Math.round(n * 100)}%`;
+const ColumnStats = observer(function ({ model }) {
+    const stats = model.mouseOverColumnStats;
+    if (!stats) {
+        return null;
+    }
+    const { col, total, conservation, propertyConservation, consensusLetter, consensusFraction, gapFraction, distribution, } = stats;
+    const top = distribution.slice(0, 6);
+    return (React.createElement("div", null,
+        React.createElement("b", null,
+            "Column ",
+            col + 1),
+        " (",
+        total,
+        " seqs)",
+        React.createElement("br", null),
+        "Consensus: ",
+        consensusLetter || '-',
+        " (",
+        pct(consensusFraction),
+        ")",
+        React.createElement("br", null),
+        "Conservation: ",
+        conservation.toFixed(2),
+        propertyConservation === undefined ? null : (React.createElement(React.Fragment, null,
+            React.createElement("br", null),
+            "Property conservation: ",
+            propertyConservation.toFixed(2))),
+        React.createElement("br", null),
+        "Gaps: ",
+        pct(gapFraction),
+        top.length > 0 ? (React.createElement(React.Fragment, null,
+            React.createElement("br", null),
+            top.map(([letter, count]) => (React.createElement("span", { key: letter, style: { marginRight: 8 } },
+                letter,
+                " ",
+                pct(count / total)))))) : null));
+});
+export default ColumnStats;
+//# sourceMappingURL=ColumnStats.js.map

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

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

@@ -5,7 +5,7 @@ import { IconButton, Paper, Typography } from '@mui/material';
 import { observer } from 'mobx-react';
 const DomainLegend = observer(function ({ model }) {
     const [expanded, setExpanded] = useState(true);
-    const { actuallyShowDomains, visibleDomainTypes: visible, fillPalette } = model;
+    const { actuallyShowDomains, visibleDomainTypes: visible, fillPalette, } = model;
     const ExpandIcon = expanded ? ExpandLess : ExpandMore;
     return actuallyShowDomains && visible.length > 0 ? (React.createElement(Paper, { elevation: 3, style: {
             position: 'absolute',

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

@@ -1 +1 @@
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+{"version":3,"file":"DomainLegend.js","sourceRoot":"","sources":["../../../src/components/msa/DomainLegend.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AAEvC,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,YAAY,GAAG,QAAQ,CAAC,UAAU,EAAE,KAAK,EAA2B;IACxE,MAAM,CAAC,QAAQ,EAAE,WAAW,CAAC,GAAG,QAAQ,CAAC,IAAI,CAAC,CAAA;IAC9C,MAAM,EACJ,mBAAmB,EACnB,kBAAkB,EAAE,OAAO,EAC3B,WAAW,GACZ,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,OAAO,EAAE,GAAG,EAAE;oBACZ,WAAW,CAAC,CAAC,QAAQ,CAAC,CAAA;gBACxB,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,YAAY,CAAA"}

package/dist/components/msa/MSACanvasBlock.js

@@ -1,9 +1,10 @@
-import React, { useEffect, useRef, useState } from 'react';
+import React, { useState } from 'react';
 import { BaseTooltip } from '@jbrowse/core/ui';
-import { autorun } from 'mobx';
 import { observer } from 'mobx-react';
+import ColumnStats from "./ColumnStats.js";
 import { renderBoxFeatureCanvasBlock } from "./renderBoxFeatureCanvasBlock.js";
 import { renderMSABlock } from "./renderMSABlock.js";
+import { useCanvasAutorun } from "../../useCanvasAutorun.js";
 import { useColorContrast } from "../../useColorContrast.js";
 function eventToColRow(event, el, offsetX, offsetY, colWidth, rowHeight) {
     const { left, top } = el.getBoundingClientRect();
@@ -15,31 +16,24 @@ function eventToColRow(event, el, offsetX, offsetY, colWidth, rowHeight) {
 const MSACanvasBlock = observer(function ({ model, offsetX, offsetY, }) {
     const { colWidth, rowHeight, scrollY, scrollX, colorScheme, blockSize, mouseClickCol, mouseClickRow, highResScaleFactor, } = model;
     const { theme, contrastScheme } = useColorContrast(colorScheme);
-    const ref = useRef(null);
-    useEffect(() => {
-        const ctx = ref.current?.getContext('2d');
-        if (!ctx) {
-            return;
-        }
-        return autorun(() => {
-            ctx.resetTransform();
-            ctx.clearRect(0, 0, blockSize * highResScaleFactor, blockSize * highResScaleFactor);
-            if (model.actuallyShowDomains) {
-                renderBoxFeatureCanvasBlock({
-                    ctx,
-                    offsetX,
-                    offsetY,
-                    model,
-                });
-            }
-            renderMSABlock({
+    const ref = useCanvasAutorun(ctx => {
+        ctx.resetTransform();
+        ctx.clearRect(0, 0, blockSize * highResScaleFactor, blockSize * highResScaleFactor);
+        if (model.actuallyShowDomains) {
+            renderBoxFeatureCanvasBlock({
                 ctx,
-                theme,
                 offsetX,
                 offsetY,
-                contrastScheme,
                 model,
             });
+        }
+        renderMSABlock({
+            ctx,
+            theme,
+            offsetX,
+            offsetY,
+            contrastScheme,
+            model,
         });
     }, [
         model,
@@ -51,7 +45,7 @@ const MSACanvasBlock = observer(function ({ model, offsetX, offsetY, }) {
         contrastScheme,
     ]);
     const [mousePosition, setMousePosition] = useState();
-    const { hoveredInsertion, mouseOverDomains } = model;
+    const { hoveredInsertion, mouseOverDomains, showColumnStats } = model;
     return (React.createElement(React.Fragment, null,
         React.createElement("canvas", { ref: ref, onMouseMove: event => {
                 if (ref.current) {
@@ -67,11 +61,13 @@ const MSACanvasBlock = observer(function ({ model, offsetX, offsetY, }) {
                         model.setMousePos(undefined, undefined);
                     }
                     // only track client coords when there's something to show in the
-                    // tooltip (insertion or a domain under the cursor); avoids a
-                    // re-render on every move over plain alignment cells
-                    setMousePosition(model.hoveredInsertion || model.mouseOverDomains.length > 0
-                        ? { x: event.clientX, y: event.clientY }
-                        : undefined);
+                    // tooltip: an insertion, a domain under the cursor, or column stats
+                    // (when that option is enabled). avoids a re-render on every move
+                    // when nothing would be shown
+                    const hasTooltip = model.hoveredInsertion ||
+                        model.mouseOverDomains.length > 0 ||
+                        (model.showColumnStats && !!model.mouseOverColumnStats);
+                    setMousePosition(hasTooltip ? { x: event.clientX, y: event.clientY } : undefined);
                 }
             }, onClick: event => {
                 if (ref.current) {
@@ -102,17 +98,21 @@ const MSACanvasBlock = observer(function ({ model, offsetX, offsetY, }) {
             hoveredInsertion.letters.length > 20
                 ? `${hoveredInsertion.letters.slice(0, 20)}...`
                 : hoveredInsertion.letters)) : null,
-        !hoveredInsertion && mouseOverDomains.length > 0 && mousePosition ? (React.createElement(BaseTooltip, { clientPoint: { x: mousePosition.x, y: mousePosition.y + 15 } }, mouseOverDomains.map(d => (React.createElement("div", { key: `${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));
+        !hoveredInsertion &&
+            mousePosition &&
+            (mouseOverDomains.length > 0 || showColumnStats) ? (React.createElement(BaseTooltip, { clientPoint: { x: mousePosition.x, y: mousePosition.y + 15 } },
+            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));
 });
 export default MSACanvasBlock;
 //# sourceMappingURL=MSACanvasBlock.js.map

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

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

@@ -1,21 +1,15 @@
-import React, { useEffect, useRef } from 'react';
+import React from 'react';
 import { isAlive } from '@jbrowse/mobx-state-tree';
-import { autorun } from 'mobx';
 import { observer } from 'mobx-react';
 import { renderMouseover } from "./renderMSAMouseover.js";
+import { useCanvasAutorun } from "../../useCanvasAutorun.js";
 const MSAMouseoverCanvas = observer(function ({ model, }) {
-    const ref = useRef(null);
     const { height, msaAreaWidth, verticalScrollbarWidth, highResScaleFactor } = model;
     const width = msaAreaWidth - verticalScrollbarWidth;
-    useEffect(() => {
-        const ctx = ref.current?.getContext('2d');
-        return ctx
-            ? autorun(() => {
-                if (isAlive(model)) {
-                    renderMouseover({ ctx, model });
-                }
-            })
-            : undefined;
+    const ref = useCanvasAutorun(ctx => {
+        if (isAlive(model)) {
+            renderMouseover({ ctx, model });
+        }
     }, [model]);
     return (React.createElement("canvas", { ref: ref, id: "mouseover", width: width * highResScaleFactor, height: height * highResScaleFactor, style: {
             position: 'absolute',

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,YAAY,CAAA;AAErC,OAAO,EAAE,eAAe,EAAE,MAAM,yBAAyB,CAAA;AACzD,OAAO,EAAE,gBAAgB,EAAE,MAAM,2BAA2B,CAAA;AAI5D,MAAM,kBAAkB,GAAG,QAAQ,CAAC,UAAU,EAC5C,KAAK,GAGN;IACC,MAAM,EAAE,MAAM,EAAE,YAAY,EAAE,sBAAsB,EAAE,kBAAkB,EAAE,GACxE,KAAK,CAAA;IACP,MAAM,KAAK,GAAG,YAAY,GAAG,sBAAsB,CAAA;IACnD,MAAM,GAAG,GAAG,gBAAgB,CAC1B,GAAG,CAAC,EAAE;QACJ,IAAI,OAAO,CAAC,KAAK,CAAC,EAAE,CAAC;YACnB,eAAe,CAAC,EAAE,GAAG,EAAE,KAAK,EAAE,CAAC,CAAA;QACjC,CAAC;IACH,CAAC,EACD,CAAC,KAAK,CAAC,CACR,CAAA;IAED,OAAO,CACL,gCACE,GAAG,EAAE,GAAG,EACR,EAAE,EAAC,WAAW,EACd,KAAK,EAAE,KAAK,GAAG,kBAAkB,EACjC,MAAM,EAAE,MAAM,GAAG,kBAAkB,EACnC,KAAK,EAAE;YACL,QAAQ,EAAE,UAAU;YACpB,GAAG,EAAE,CAAC;YACN,IAAI,EAAE,CAAC;YACP,KAAK;YACL,MAAM;YACN,MAAM,EAAE,IAAI;YACZ,aAAa,EAAE,MAAM;SACtB,GACD,CACH,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,kBAAkB,CAAA"}

package/dist/components/msa/renderBoxFeatureCanvasBlock.js

@@ -46,7 +46,9 @@ function drawTiles({ model, ctx, visibleLeaves, }) {
                         ctx.strokeRect(x, t, lw, h);
                         // segment (exon) number drawn once per band, on the top visible row,
                         // so it reads as a column header for the whole band
-                        const label = drawSegmentLabels ? segmentLabels.get(accession) : undefined;
+                        const label = drawSegmentLabels
+                            ? segmentLabels.get(accession)
+                            : undefined;
                         if (label !== undefined && i === 0) {
                             const fontSize = Math.min(h - 2, 11);
                             ctx.font = `${fontSize}px sans-serif`;

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

@@ -1 +1 @@
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+{"version":3,"file":"renderBoxFeatureCanvasBlock.js","sourceRoot":"","sources":["../../../src/components/msa/renderBoxFeatureCanvasBlock.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,gBAAgB,EAAE,MAAM,uBAAuB,CAAA;AACxD,OAAO,EAAE,mBAAmB,EAAE,MAAM,oBAAoB,CAAA;AAOxD,MAAM,UAAU,2BAA2B,CAAC,EAC1C,KAAK,EACL,OAAO,EACP,OAAO,EACP,GAAG,EACH,0BAA0B,EAC1B,kBAAkB,GAQnB;IACC,MAAM,EAAE,SAAS,EAAE,SAAS,EAAE,kBAAkB,EAAE,WAAW,EAAE,GAAG,KAAK,CAAA;IACvE,IAAI,WAAW,EAAE,CAAC;QAChB,MAAM,CAAC,GAAG,0BAA0B,IAAI,kBAAkB,CAAA;QAC1D,MAAM,EAAE,GAAG,kBAAkB,IAAI,SAAS,CAAA;QAC1C,GAAG,CAAC,cAAc,EAAE,CAAA;QACpB,GAAG,CAAC,KAAK,CAAC,CAAC,EAAE,CAAC,CAAC,CAAA;QACf,GAAG,CAAC,SAAS,CAAC,CAAC,OAAO,EAAE,SAAS,GAAG,CAAC,GAAG,OAAO,CAAC,CAAA;QAEhD,MAAM,aAAa,GAAG,gBAAgB,CAAC,EAAE,KAAK,EAAE,OAAO,EAAE,UAAU,EAAE,EAAE,EAAE,CAAC,CAAA;QAE1E,SAAS,CAAC;YACR,KAAK;YACL,GAAG;YACH,aAAa;SACd,CAAC,CAAA;IACJ,CAAC;AACH,CAAC;AAED,SAAS,SAAS,CAAC,EACjB,KAAK,EACL,GAAG,EACH,aAAa,GAKd;IACC,MAAM,EACJ,cAAc,EACd,QAAQ,EACR,SAAS,EACT,WAAW,EACX,aAAa,EACb,aAAa,EACb,cAAc,EACd,uCAAuC,GACxC,GAAG,KAAK,CAAA;IACT,MAAM,CAAC,GAAG,cAAc,CAAC,CAAC,CAAC,mBAAmB,CAAC,CAAC,CAAC,SAAS,CAAA;IAC1D,8EAA8E;IAC9E,4EAA4E;IAC5E,+CAA+C;IAC/C,MAAM,iBAAiB,GAAG,CAAC,cAAc,IAAI,CAAC,cAAc,IAAI,CAAC,IAAI,CAAC,CAAA;IAEtE,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,EAAE,GAAG,aAAa,CAAC,MAAM,EAAE,CAAC,GAAG,EAAE,EAAE,CAAC,EAAE,EAAE,CAAC;QACvD,MAAM,IAAI,GAAG,aAAa,CAAC,CAAC,CAAE,CAAA;QAC9B,MAAM,EAAE,IAAI,EAAE,GAAG,IAAI,CAAC,IAAI,CAAA;QAC1B,MAAM,CAAC,GAAG,IAAI,CAAC,CAAE,CAAA;QACjB,MAAM,KAAK,GAAG,uCAAuC,CAAC,IAAI,CAAC,CAAA;QAE3D,IAAI,KAAK,EAAE,CAAC;YACV,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,EAAE,GAAG,KAAK,CAAC,MAAM,EAAE,CAAC,GAAG,EAAE,EAAE,CAAC,EAAE,EAAE,CAAC;gBAC/C,MAAM,EAAE,KAAK,EAAE,GAAG,EAAE,SAAS,EAAE,MAAM,EAAE,GAAG,KAAK,CAAC,CAAC,CAAE,CAAA;gBACnD,yDAAyD;gBACzD,6DAA6D;gBAC7D,MAAM,EAAE,GAAG,KAAK,CAAC,kBAAkB,CAAC,IAAI,EAAE,KAAK,GAAG,CAAC,CAAC,CAAA;gBACpD,MAAM,EAAE,GAAG,KAAK,CAAC,kBAAkB,CAAC,IAAI,EAAE,GAAG,CAAC,CAAA;gBAC9C,IAAI,EAAE,KAAK,SAAS,IAAI,EAAE,KAAK,SAAS,EAAE,CAAC;oBACzC,MAAM,CAAC,GAAG,EAAE,GAAG,QAAQ,CAAA;oBACvB,MAAM,CAAC,GAAG,CAAC,GAAG,SAAS,GAAG,CAAC,cAAc,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;oBACtD,MAAM,EAAE,GAAG,QAAQ,GAAG,CAAC,EAAE,GAAG,EAAE,CAAC,CAAA;oBAC/B,GAAG,CAAC,SAAS,GAAG,WAAW,CAAC,SAAS,CAAE,CAAA;oBACvC,GAAG,CAAC,WAAW,GAAG,aAAa,CAAC,SAAS,CAAE,CAAA;oBAC3C,IAAI,MAAM,KAAK,SAAS,EAAE,CAAC;wBACzB,GAAG,CAAC,QAAQ,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,EAAE,CAAC,CAAC,CAAA;wBACzB,GAAG,CAAC,UAAU,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,EAAE,CAAC,CAAC,CAAA;wBAC3B,qEAAqE;wBACrE,oDAAoD;wBACpD,MAAM,KAAK,GAAG,iBAAiB;4BAC7B,CAAC,CAAC,aAAa,CAAC,GAAG,CAAC,SAAS,CAAC;4BAC9B,CAAC,CAAC,SAAS,CAAA;wBACb,IAAI,KAAK,KAAK,SAAS,IAAI,CAAC,KAAK,CAAC,EAAE,CAAC;4BACnC,MAAM,QAAQ,GAAG,IAAI,CAAC,GAAG,CAAC,CAAC,GAAG,CAAC,EAAE,EAAE,CAAC,CAAA;4BACpC,GAAG,CAAC,IAAI,GAAG,GAAG,QAAQ,eAAe,CAAA;4BACrC,IAAI,GAAG,CAAC,WAAW,CAAC,KAAK,CAAC,CAAC,KAAK,GAAG,CAAC,IAAI,EAAE,EAAE,CAAC;gCAC3C,GAAG,CAAC,SAAS,GAAG,MAAM,CAAA;gCACtB,GAAG,CAAC,SAAS,GAAG,QAAQ,CAAA;gCACxB,GAAG,CAAC,YAAY,GAAG,QAAQ,CAAA;gCAC3B,GAAG,CAAC,QAAQ,CAAC,KAAK,EAAE,CAAC,GAAG,EAAE,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,GAAG,CAAC,CAAC,CAAA;4BAC5C,CAAC;wBACH,CAAC;oBACH,CAAC;yBAAM,CAAC;wBACN,aAAa,CAAC,EAAE,GAAG,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,EAAE,EAAE,CAAC,EAAE,MAAM,EAAE,CAAC,CAAA;oBAChD,CAAC;gBACH,CAAC;YACH,CAAC;QACH,CAAC;IACH,CAAC;AACH,CAAC;AAED,qEAAqE;AACrE,8EAA8E;AAC9E,8EAA8E;AAC9E,+EAA+E;AAC/E,6EAA6E;AAC7E,qEAAqE;AACrE,SAAS,aAAa,CAAC,EACrB,GAAG,EACH,CAAC,EACD,CAAC,EACD,CAAC,EACD,CAAC,EACD,MAAM,GAQP;IACC,0EAA0E;IAC1E,kDAAkD;IAClD,MAAM,GAAG,GAAG,MAAM,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;IAC/B,MAAM,SAAS,GAAG,MAAM,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAA;IACxC,MAAM,OAAO,GAAG,MAAM,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;IACtC,GAAG,CAAC,SAAS,EAAE,CAAA;IACf,GAAG,CAAC,MAAM,CAAC,SAAS,EAAE,CAAC,CAAC,CAAA;IACxB,GAAG,CAAC,MAAM,CAAC,OAAO,EAAE,CAAC,CAAC,CAAA;IACtB,GAAG,CAAC,MAAM,CAAC,OAAO,GAAG,GAAG,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,GAAG,CAAC,CAAC,CAAA;IACxC,GAAG,CAAC,MAAM,CAAC,OAAO,EAAE,CAAC,GAAG,CAAC,CAAC,CAAA;IAC1B,GAAG,CAAC,MAAM,CAAC,SAAS,EAAE,CAAC,GAAG,CAAC,CAAC,CAAA;IAC5B,GAAG,CAAC,SAAS,EAAE,CAAA;IACf,GAAG,CAAC,IAAI,EAAE,CAAA;IACV,GAAG,CAAC,MAAM,EAAE,CAAA;AACd,CAAC"}

package/dist/components/msa/renderMSAMouseover.js

@@ -1,3 +1,4 @@
+import { multiRowHoverColor, referenceColor } from "../overlayColors.js";
 const hoverColor = 'rgba(0,0,0,0.15)';
 const highlightColor = 'rgba(128,128,0,0.2)';
 // the persistent highlightColumns overlay: a stronger fill plus a solid border
@@ -5,8 +6,6 @@ const highlightColor = 'rgba(128,128,0,0.2)';
 // faint hover-style wash alone is invisible against clustalx coloring)
 const highlightColumnsFill = 'rgba(255,140,0,0.28)';
 const highlightColumnsBorder = 'rgba(210,90,0,0.95)';
-const referenceColor = 'rgba(0,128,255,0.3)'; // Blue highlight for reference row
-const multiRowHoverColor = 'rgba(255,165,0,0.15)'; // Orange highlight for multi-row tree hover
 // Collapse sorted column indices into contiguous [start,end] runs so a run of
 // highlighted columns draws as one bordered band rather than per-column slices
 // (which would draw internal borders).

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

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

@@ -0,0 +1,3 @@
+export declare const referenceColor = "rgba(0,128,255,0.3)";
+export declare const treeHoverColor = "rgba(255,165,0,0.2)";
+export declare const multiRowHoverColor = "rgba(255,165,0,0.15)";

package/dist/components/overlayColors.js

@@ -0,0 +1,11 @@
+// Shared highlight colors for the MSA/tree hover and selection overlay canvases.
+// Kept in one place so the reference-row color (drawn identically over both the
+// tree and the alignment) can't drift between the two surfaces.
+// reference (relativeTo) row, drawn over both the tree and the alignment
+export const referenceColor = 'rgba(0,128,255,0.3)';
+// tree-node descendant rows highlighted on hover. The alpha differs by surface
+// intentionally: the tree background is plain so it can take a stronger wash,
+// while the alignment cells are already colored so a lighter wash reads better.
+export const treeHoverColor = 'rgba(255,165,0,0.2)';
+export const multiRowHoverColor = 'rgba(255,165,0,0.15)';
+//# sourceMappingURL=overlayColors.js.map

package/dist/components/overlayColors.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"overlayColors.js","sourceRoot":"","sources":["../../src/components/overlayColors.ts"],"names":[],"mappings":"AAAA,iFAAiF;AACjF,gFAAgF;AAChF,gEAAgE;AAEhE,yEAAyE;AACzE,MAAM,CAAC,MAAM,cAAc,GAAG,qBAAqB,CAAA;AAEnD,+EAA+E;AAC/E,8EAA8E;AAC9E,gFAAgF;AAChF,MAAM,CAAC,MAAM,cAAc,GAAG,qBAAqB,CAAA;AACnD,MAAM,CAAC,MAAM,kBAAkB,GAAG,sBAAsB,CAAA"}

package/dist/components/tracks/renderTracksSvg.d.ts

@@ -1,14 +1,16 @@
 import type { MsaViewModel } from '../../model.ts';
 import type { BasicTrack } from '../../types.ts';
 import type { RenderCtx } from '../renderCtx.ts';
-export declare function drawConservationBars({ ctx, conservation, colWidth, trackHeight, offsetX, blockSize, }: {
+export declare function drawConservationBars({ ctx, values, color, colWidth, trackHeight, offsetX, blockSize, }: {
     ctx: RenderCtx;
-    conservation: number[];
+    values: number[];
+    color: string;
     colWidth: number;
     trackHeight: number;
     offsetX: number;
     blockSize: number;
 }): void;
+export declare function barTrackValues(model: MsaViewModel, trackId: string): number[];
 export declare function drawTextTrackContent({ ctx, data, colorScheme, contrastScheme, bgColor, colWidth, rowHeight, offsetX, blockSize, }: {
     ctx: RenderCtx;
     data: string | undefined;
@@ -20,9 +22,10 @@ export declare function drawTextTrackContent({ ctx, data, colorScheme, contrastS
     offsetX: number;
     blockSize: number;
 }): void;
-export declare function renderConservationTrack({ model, ctx, offsetX, offsetY, trackHeight, blockSizeXOverride, highResScaleFactorOverride, }: {
+export declare function renderConservationTrack({ model, ctx, track, offsetX, offsetY, trackHeight, blockSizeXOverride, highResScaleFactorOverride, }: {
     model: MsaViewModel;
     ctx: RenderCtx;
+    track: BasicTrack;
     offsetX: number;
     offsetY: number;
     trackHeight: number;

package/dist/components/tracks/renderTracksSvg.js

@@ -1,19 +1,26 @@
 import { setFontSize } from "../../setFontSize.js";
 import { visibleColRange } from "../msa/visibleColRange.js";
-export function drawConservationBars({ ctx, conservation, colWidth, trackHeight, offsetX, blockSize, }) {
+export function drawConservationBars({ ctx, values, color, colWidth, trackHeight, offsetX, blockSize, }) {
     const { xStart, xEnd } = visibleColRange({
         offsetX,
         blockWidth: blockSize,
         colWidth,
     });
-    ctx.fillStyle = 'gray';
-    for (let i = xStart; i < xEnd && i < conservation.length; i++) {
-        const value = conservation[i];
+    ctx.fillStyle = color;
+    for (let i = xStart; i < xEnd && i < values.length; i++) {
+        const value = values[i];
         const barHeight = value * trackHeight;
         const x = i * colWidth;
         ctx.fillRect(x, trackHeight - barHeight, colWidth, barHeight);
     }
 }
+// the bar-track values live on model getters (kept off the plain track object so
+// the live canvas autorun stays reactive); select the right one by track id
+export function barTrackValues(model, trackId) {
+    return trackId === 'property-conservation'
+        ? model.propertyConservation
+        : model.conservation;
+}
 export function drawTextTrackContent({ ctx, data, colorScheme, contrastScheme, bgColor, colWidth, rowHeight, offsetX, blockSize, }) {
     const { xStart, xEnd } = visibleColRange({
         offsetX,
@@ -35,8 +42,8 @@ export function drawTextTrackContent({ ctx, data, colorScheme, contrastScheme, b
         }
     }
 }
-export function renderConservationTrack({ model, ctx, offsetX, offsetY, trackHeight, blockSizeXOverride, highResScaleFactorOverride, }) {
-    const { blockSize, colWidth, highResScaleFactor, conservation } = model;
+export function renderConservationTrack({ model, ctx, track, offsetX, offsetY, trackHeight, blockSizeXOverride, highResScaleFactorOverride, }) {
+    const { blockSize, colWidth, highResScaleFactor } = model;
     const bx = blockSizeXOverride ?? blockSize;
     const k = highResScaleFactorOverride ?? highResScaleFactor;
     ctx.resetTransform();
@@ -44,7 +51,8 @@ export function renderConservationTrack({ model, ctx, offsetX, offsetY, trackHei
     ctx.translate(-offsetX, offsetY);
     drawConservationBars({
         ctx,
-        conservation,
+        values: barTrackValues(model, track.model.id),
+        color: track.model.barColor ?? 'gray',
         colWidth,
         trackHeight,
         offsetX,
@@ -81,10 +89,11 @@ export function renderAllTracks({ model, ctx, offsetX, contrastScheme, blockSize
     let currentY = 0;
     for (const track of turnedOnTracks) {
         const trackHeight = track.model.height;
-        if (track.model.id === 'conservation') {
+        if (track.model.barColor !== undefined) {
             renderConservationTrack({
                 model,
                 ctx,
+                track,
                 offsetX,
                 offsetY: currentY,
                 trackHeight,

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

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

@@ -1,54 +1,47 @@
-import React, { useCallback, useEffect, useRef } from 'react';
+import React, { useCallback, useRef } from 'react';
 import { isAlive } from '@jbrowse/mobx-state-tree';
-import { autorun } from 'mobx';
 import { observer } from 'mobx-react';
 import TreeCanvasBlock from "./TreeCanvasBlock.js";
 import { padding } from "./renderTreeCanvas.js";
+import { useCanvasAutorun } from "../../useCanvasAutorun.js";
 import { useWheelScroll } from "../../useWheelScroll.js";
-const referenceColor = 'rgba(0,128,255,0.3)';
-const treeHoverColor = 'rgba(255,165,0,0.2)';
+import { referenceColor, treeHoverColor } from "../overlayColors.js";
 const TreeCanvas = observer(function ({ model }) {
     const ref = useRef(null);
-    const mouseoverRef = useRef(null);
     const { treeWidth, height, blocksY, treeAreaWidth } = model;
     const onScrollY = useCallback((d) => {
         model.doScrollY(d);
     }, [model]);
     const { onMouseDown, onMouseUp } = useWheelScroll({ ref, onScrollY });
-    useEffect(() => {
-        const ctx = mouseoverRef.current?.getContext('2d');
-        return ctx
-            ? autorun(() => {
-                if (isAlive(model)) {
-                    const { relativeTo, leaves, rowHeight, hoveredTreeNode, treeAreaWidth: w, height: h, scrollY: sy, mouseOverRowName, } = model;
-                    ctx.resetTransform();
-                    ctx.clearRect(0, 0, w, h);
-                    const leafByName = new Map(leaves.map(leaf => [leaf.data.name, leaf]));
-                    const fillRow = (name) => {
-                        const leaf = leafByName.get(name);
-                        if (leaf) {
-                            ctx.fillRect(0, leaf.x + sy - rowHeight / 2, w, rowHeight);
-                        }
-                    };
-                    if (relativeTo) {
-                        ctx.fillStyle = referenceColor;
-                        fillRow(relativeTo);
-                    }
-                    if (hoveredTreeNode) {
-                        ctx.fillStyle = treeHoverColor;
-                        for (const descendantName of hoveredTreeNode.descendantNames) {
-                            fillRow(descendantName);
-                        }
-                    }
-                    if (mouseOverRowName &&
-                        mouseOverRowName !== relativeTo &&
-                        !hoveredTreeNode?.descendantNames.includes(mouseOverRowName)) {
-                        ctx.fillStyle = treeHoverColor;
-                        fillRow(mouseOverRowName);
-                    }
+    const mouseoverRef = useCanvasAutorun(ctx => {
+        if (isAlive(model)) {
+            const { relativeTo, leaves, rowHeight, hoveredTreeNode, treeAreaWidth: w, height: h, scrollY: sy, mouseOverRowName, } = model;
+            ctx.resetTransform();
+            ctx.clearRect(0, 0, w, h);
+            const leafByName = new Map(leaves.map(leaf => [leaf.data.name, leaf]));
+            const fillRow = (name) => {
+                const leaf = leafByName.get(name);
+                if (leaf) {
+                    ctx.fillRect(0, leaf.x + sy - rowHeight / 2, w, rowHeight);
                 }
-            })
-            : undefined;
+            };
+            if (relativeTo) {
+                ctx.fillStyle = referenceColor;
+                fillRow(relativeTo);
+            }
+            if (hoveredTreeNode) {
+                ctx.fillStyle = treeHoverColor;
+                for (const descendantName of hoveredTreeNode.descendantNames) {
+                    fillRow(descendantName);
+                }
+            }
+            if (mouseOverRowName &&
+                mouseOverRowName !== relativeTo &&
+                !hoveredTreeNode?.descendantNames.includes(mouseOverRowName)) {
+                ctx.fillStyle = treeHoverColor;
+                fillRow(mouseOverRowName);
+            }
+        }
     }, [model]);
     return (React.createElement("div", { ref: ref, onMouseDown: onMouseDown, onMouseUp: onMouseUp, onMouseLeave: event => {
             event.preventDefault();

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

@@ -1 +1 @@
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