react-msaview 4.4.6 → 4.6.0

package/dist/components/header/GappynessSlider.js

@@ -0,0 +1,19 @@
+import React from 'react';
+import { Slider, Typography } from '@mui/material';
+import { observer } from 'mobx-react';
+const GappynessSlider = observer(function GappynessSlider({ model, }) {
+    const { hideGaps, allowedGappyness } = model;
+    if (!hideGaps) {
+        return null;
+    }
+    return (React.createElement("div", { style: { display: 'flex', alignItems: 'center', gap: 8 } },
+        React.createElement(Typography, { style: { whiteSpace: 'nowrap' } },
+            "Hide columns w/ >",
+            allowedGappyness,
+            "% gaps"),
+        React.createElement(Slider, { style: { width: 100 }, min: 1, max: 100, value: allowedGappyness, onChange: (_, val) => {
+                model.setAllowedGappyness(val);
+            } })));
+});
+export default GappynessSlider;
+//# sourceMappingURL=GappynessSlider.js.map

package/dist/components/header/GappynessSlider.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"GappynessSlider.js","sourceRoot":"","sources":["../../../src/components/header/GappynessSlider.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,EAAE,MAAM,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAClD,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAIrC,MAAM,eAAe,GAAG,QAAQ,CAAC,SAAS,eAAe,CAAC,EACxD,KAAK,GAGN;IACC,MAAM,EAAE,QAAQ,EAAE,gBAAgB,EAAE,GAAG,KAAK,CAAA;IAC5C,IAAI,CAAC,QAAQ,EAAE,CAAC;QACd,OAAO,IAAI,CAAA;IACb,CAAC;IACD,OAAO,CACL,6BAAK,KAAK,EAAE,EAAE,OAAO,EAAE,MAAM,EAAE,UAAU,EAAE,QAAQ,EAAE,GAAG,EAAE,CAAC,EAAE;QAC3D,oBAAC,UAAU,IAAC,KAAK,EAAE,EAAE,UAAU,EAAE,QAAQ,EAAE;;YACpB,gBAAgB;qBAC1B;QACb,oBAAC,MAAM,IACL,KAAK,EAAE,EAAE,KAAK,EAAE,GAAG,EAAE,EACrB,GAAG,EAAE,CAAC,EACN,GAAG,EAAE,GAAG,EACR,KAAK,EAAE,gBAAgB,EACvB,QAAQ,EAAE,CAAC,CAAC,EAAE,GAAG,EAAE,EAAE;gBACnB,KAAK,CAAC,mBAAmB,CAAC,GAAG,CAAC,CAAA;YAChC,CAAC,GACD,CACE,CACP,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,eAAe,CAAA"}

package/dist/components/header/Header.js

@@ -3,6 +3,7 @@ import useMeasure from '@jbrowse/core/util/useMeasure';
 import Help from '@mui/icons-material/Help';
 import { IconButton } from '@mui/material';
 import { observer } from 'mobx-react';
+import GappynessSlider from './GappynessSlider';
 import HeaderInfoArea from './HeaderInfoArea';
 import HeaderMenu from './HeaderMenu';
 import HeaderStatusArea from './HeaderStatusArea';
@@ -23,7 +24,8 @@ const Header = observer(function ({ model }) {
         React.createElement(ZoomControls, { model: model }),
         model.showZoomStar ? React.createElement(ZoomStar, { model: model }) : null,
         React.createElement(ZoomMenu, { model: model }),
-        React.createElement("div", { style: { margin: 'auto' } },
+        React.createElement(GappynessSlider, { model: model }),
+        React.createElement("div", { style: { paddingLeft: 20, margin: 'auto' } },
             React.createElement(MultiAlignmentSelector, { model: model })),
         React.createElement(HeaderInfoArea, { model: model }),
         React.createElement(Spacer, null),

package/dist/components/header/Header.js.map

@@ -1 +1 @@
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+{"version":3,"file":"Header.js","sourceRoot":"","sources":["../../../src/components/header/Header.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,IAAI,EAAE,SAAS,EAAE,MAAM,OAAO,CAAA;AAE9C,OAAO,UAAU,MAAM,+BAA+B,CAAA;AACtD,OAAO,IAAI,MAAM,0BAA0B,CAAA;AAC3C,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAC1C,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAErC,OAAO,eAAe,MAAM,mBAAmB,CAAA;AAC/C,OAAO,cAAc,MAAM,kBAAkB,CAAA;AAC7C,OAAO,UAAU,MAAM,cAAc,CAAA;AACrC,OAAO,gBAAgB,MAAM,oBAAoB,CAAA;AACjD,OAAO,sBAAsB,MAAM,0BAA0B,CAAA;AAC7D,OAAO,YAAY,MAAM,gBAAgB,CAAA;AACzC,OAAO,YAAY,MAAM,gBAAgB,CAAA;AACzC,OAAO,QAAQ,MAAM,YAAY,CAAA;AACjC,OAAO,QAAQ,MAAM,YAAY,CAAA;AAIjC,MAAM,WAAW,GAAG,IAAI,CAAC,GAAG,EAAE,CAAC,MAAM,CAAC,wBAAwB,CAAC,CAAC,CAAA;AAEhE,MAAM,MAAM,GAAG,QAAQ,CAAC,UAAU,EAAE,KAAK,EAA2B;IAClE,MAAM,CAAC,GAAG,EAAE,EAAE,MAAM,EAAE,CAAC,GAAG,UAAU,EAAE,CAAA;IACtC,SAAS,CAAC,GAAG,EAAE;QACb,KAAK,CAAC,eAAe,CAAC,MAAM,IAAI,CAAC,CAAC,CAAA;IACpC,CAAC,EAAE,CAAC,KAAK,EAAE,MAAM,CAAC,CAAC,CAAA;IACnB,OAAO,CACL,6BAAK,GAAG,EAAE,GAAG,EAAE,KAAK,EAAE,EAAE,OAAO,EAAE,MAAM,EAAE;QACvC,oBAAC,UAAU,IAAC,KAAK,EAAE,KAAK,GAAI;QAC5B,oBAAC,YAAY,IAAC,KAAK,EAAE,KAAK,GAAI;QAC9B,oBAAC,YAAY,IAAC,KAAK,EAAE,KAAK,GAAI;QAC7B,KAAK,CAAC,YAAY,CAAC,CAAC,CAAC,oBAAC,QAAQ,IAAC,KAAK,EAAE,KAAK,GAAI,CAAC,CAAC,CAAC,IAAI;QACvD,oBAAC,QAAQ,IAAC,KAAK,EAAE,KAAK,GAAI;QAC1B,oBAAC,eAAe,IAAC,KAAK,EAAE,KAAK,GAAI;QACjC,6BAAK,KAAK,EAAE,EAAE,WAAW,EAAE,EAAE,EAAE,MAAM,EAAE,MAAM,EAAE;YAC7C,oBAAC,sBAAsB,IAAC,KAAK,EAAE,KAAK,GAAI,CACpC;QACN,oBAAC,cAAc,IAAC,KAAK,EAAE,KAAK,GAAI;QAChC,oBAAC,MAAM,OAAG;QACV,oBAAC,gBAAgB,IAAC,KAAK,EAAE,KAAK,GAAI;QAClC,oBAAC,UAAU,IACT,OAAO,EAAE,GAAG,EAAE;gBACZ,KAAK,CAAC,WAAW,CAAC,OAAO,CAAC,EAAE,CAAC,CAAC,WAAW,EAAE,EAAE,OAAO,EAAE,CAAC,CAAC,CAAA;YAC1D,CAAC;YAED,oBAAC,IAAI,OAAG,CACG,CACT,CACP,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,SAAS,MAAM;IACb,OAAO,6BAAK,KAAK,EAAE,EAAE,IAAI,EAAE,CAAC,EAAE,GAAI,CAAA;AACpC,CAAC;AAED,eAAe,MAAM,CAAA"}

package/dist/components/header/HeaderMenu.js

@@ -1,9 +1,9 @@
 import React, { lazy } from 'react';
 import CascadingMenuButton from '@jbrowse/core/ui/CascadingMenuButton';
+import AccountTree from '@mui/icons-material/AccountTree';
 import Assignment from '@mui/icons-material/Assignment';
 import FilterAlt from '@mui/icons-material/FilterAlt';
 import FolderOpen from '@mui/icons-material/FolderOpen';
-import List from '@mui/icons-material/List';
 import MoreVert from '@mui/icons-material/Menu';
 import PhotoCamera from '@mui/icons-material/PhotoCamera';
 import Search from '@mui/icons-material/Search';
@@ -12,14 +12,13 @@ import Visibility from '@mui/icons-material/Visibility';
 import { observer } from 'mobx-react';
 // lazies
 const MetadataDialog = lazy(() => import('../dialogs/MetadataDialog'));
-const TracklistDialog = lazy(() => import('../dialogs/TracklistDialog'));
 const ExportSVGDialog = lazy(() => import('../dialogs/ExportSVGDialog'));
 const FeatureFilterDialog = lazy(() => import('../dialogs/FeatureDialog'));
 const SettingsDialog = lazy(() => import('../dialogs/SettingsDialog'));
 const UserProvidedDomainsDialog = lazy(() => import('../dialogs/UserProvidedDomainsDialog'));
 const InterProScanDialog = lazy(() => import('../dialogs/InterProScanDialog'));
 const HeaderMenu = observer(({ model }) => {
-    const { showDomains, actuallyShowDomains, subFeatureRows, noDomains } = model;
+    const { showDomains, actuallyShowDomains, subFeatureRows, noDomains, tracks, turnedOffTracks, } = model;
     return (React.createElement(CascadingMenuButton, { menuItems: [
             {
                 label: 'Return to import form',
@@ -54,17 +53,17 @@ const HeaderMenu = observer(({ model }) => {
                 },
             },
             {
-                label: 'Extra tracks',
-                icon: List,
-                onClick: () => {
-                    model.queueDialog(onClose => [
-                        TracklistDialog,
-                        {
-                            model,
-                            onClose,
-                        },
-                    ]);
-                },
+                label: 'Tracks',
+                icon: Visibility,
+                type: 'subMenu',
+                subMenu: tracks.map(track => ({
+                    label: track.model.name,
+                    type: 'checkbox',
+                    checked: !turnedOffTracks.has(track.model.id),
+                    onClick: () => {
+                        model.toggleTrack(track.model.id);
+                    },
+                })),
             },
             {
                 label: 'Export SVG',
@@ -79,6 +78,23 @@ const HeaderMenu = observer(({ model }) => {
                     ]);
                 },
             },
+            ...(model.rows.length >= 2
+                ? [
+                    {
+                        label: 'Calculate neighbor joining tree (BLOSUM62)',
+                        icon: AccountTree,
+                        onClick: () => {
+                            try {
+                                model.calculateNeighborJoiningTreeFromMSA();
+                            }
+                            catch (e) {
+                                console.error('Failed to calculate NJ tree:', e);
+                                model.setError(e);
+                            }
+                        },
+                    },
+                ]
+                : []),
             {
                 label: 'Features/protein domains',
                 type: 'subMenu',

package/dist/components/header/HeaderMenu.js.map

@@ -1 +1 @@
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+{"version":3,"file":"HeaderMenu.js","sourceRoot":"","sources":["../../../src/components/header/HeaderMenu.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,IAAI,EAAE,MAAM,OAAO,CAAA;AAEnC,OAAO,mBAAmB,MAAM,sCAAsC,CAAA;AACtE,OAAO,WAAW,MAAM,iCAAiC,CAAA;AACzD,OAAO,UAAU,MAAM,gCAAgC,CAAA;AACvD,OAAO,SAAS,MAAM,+BAA+B,CAAA;AACrD,OAAO,UAAU,MAAM,gCAAgC,CAAA;AACvD,OAAO,QAAQ,MAAM,0BAA0B,CAAA;AAC/C,OAAO,WAAW,MAAM,iCAAiC,CAAA;AACzD,OAAO,MAAM,MAAM,4BAA4B,CAAA;AAC/C,OAAO,IAAI,MAAM,0BAA0B,CAAA;AAC3C,OAAO,UAAU,MAAM,gCAAgC,CAAA;AACvD,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAIrC,SAAS;AACT,MAAM,cAAc,GAAG,IAAI,CAAC,GAAG,EAAE,CAAC,MAAM,CAAC,2BAA2B,CAAC,CAAC,CAAA;AACtE,MAAM,eAAe,GAAG,IAAI,CAAC,GAAG,EAAE,CAAC,MAAM,CAAC,4BAA4B,CAAC,CAAC,CAAA;AACxE,MAAM,mBAAmB,GAAG,IAAI,CAAC,GAAG,EAAE,CAAC,MAAM,CAAC,0BAA0B,CAAC,CAAC,CAAA;AAC1E,MAAM,cAAc,GAAG,IAAI,CAAC,GAAG,EAAE,CAAC,MAAM,CAAC,2BAA2B,CAAC,CAAC,CAAA;AACtE,MAAM,yBAAyB,GAAG,IAAI,CACpC,GAAG,EAAE,CAAC,MAAM,CAAC,sCAAsC,CAAC,CACrD,CAAA;AACD,MAAM,kBAAkB,GAAG,IAAI,CAAC,GAAG,EAAE,CAAC,MAAM,CAAC,+BAA+B,CAAC,CAAC,CAAA;AAE9E,MAAM,UAAU,GAAG,QAAQ,CAAC,CAAC,EAAE,KAAK,EAA2B,EAAE,EAAE;IACjE,MAAM,EACJ,WAAW,EACX,mBAAmB,EACnB,cAAc,EACd,SAAS,EACT,MAAM,EACN,eAAe,GAChB,GAAG,KAAK,CAAA;IACT,OAAO,CACL,oBAAC,mBAAmB,IAClB,SAAS,EAAE;YACT;gBACE,KAAK,EAAE,uBAAuB;gBAC9B,IAAI,EAAE,UAAU;gBAChB,OAAO,EAAE,GAAG,EAAE;oBACZ,KAAK,CAAC,KAAK,EAAE,CAAA;gBACf,CAAC;aACF;YACD;gBACE,KAAK,EAAE,UAAU;gBACjB,IAAI,EAAE,UAAU;gBAChB,OAAO,EAAE,GAAG,EAAE;oBACZ,KAAK,CAAC,WAAW,CAAC,OAAO,CAAC,EAAE,CAAC;wBAC3B,cAAc;wBACd;4BACE,KAAK;4BACL,OAAO;yBACR;qBACF,CAAC,CAAA;gBACJ,CAAC;aACF;YACD;gBACE,KAAK,EAAE,eAAe;gBACtB,OAAO,EAAE,GAAG,EAAE;oBACZ,KAAK,CAAC,WAAW,CAAC,OAAO,CAAC,EAAE,CAAC;wBAC3B,cAAc;wBACd;4BACE,KAAK;4BACL,OAAO;yBACR;qBACF,CAAC,CAAA;gBACJ,CAAC;aACF;YACD;gBACE,KAAK,EAAE,QAAQ;gBACf,IAAI,EAAE,UAAU;gBAChB,IAAI,EAAE,SAAS;gBACf,OAAO,EAAE,MAAM,CAAC,GAAG,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC;oBAC5B,KAAK,EAAE,KAAK,CAAC,KAAK,CAAC,IAAI;oBACvB,IAAI,EAAE,UAAmB;oBACzB,OAAO,EAAE,CAAC,eAAe,CAAC,GAAG,CAAC,KAAK,CAAC,KAAK,CAAC,EAAE,CAAC;oBAC7C,OAAO,EAAE,GAAG,EAAE;wBACZ,KAAK,CAAC,WAAW,CAAC,KAAK,CAAC,KAAK,CAAC,EAAE,CAAC,CAAA;oBACnC,CAAC;iBACF,CAAC,CAAC;aACJ;YACD;gBACE,KAAK,EAAE,YAAY;gBACnB,IAAI,EAAE,WAAW;gBACjB,OAAO,EAAE,GAAG,EAAE;oBACZ,KAAK,CAAC,WAAW,CAAC,OAAO,CAAC,EAAE,CAAC;wBAC3B,eAAe;wBACf;4BACE,OAAO;4BACP,KAAK;yBACN;qBACF,CAAC,CAAA;gBACJ,CAAC;aACF;YACD,GAAG,CAAC,KAAK,CAAC,IAAI,CAAC,MAAM,IAAI,CAAC;gBACxB,CAAC,CAAC;oBACE;wBACE,KAAK,EAAE,4CAA4C;wBACnD,IAAI,EAAE,WAAW;wBACjB,OAAO,EAAE,GAAG,EAAE;4BACZ,IAAI,CAAC;gCACH,KAAK,CAAC,mCAAmC,EAAE,CAAA;4BAC7C,CAAC;4BAAC,OAAO,CAAC,EAAE,CAAC;gCACX,OAAO,CAAC,KAAK,CAAC,8BAA8B,EAAE,CAAC,CAAC,CAAA;gCAChD,KAAK,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAA;4BACnB,CAAC;wBACH,CAAC;qBACF;iBACF;gBACH,CAAC,CAAC,EAAE,CAAC;YACP;gBACE,KAAK,EAAE,0BAA0B;gBACjC,IAAI,EAAE,SAAS;gBACf,OAAO,EAAE;oBACP;wBACE,KAAK,EAAE,iBAAiB;wBACxB,IAAI,EAAE,UAAU;wBAChB,OAAO,EAAE,GAAG,EAAE;4BACZ,KAAK,CAAC,WAAW,CAAC,WAAW,CAAC,EAAE,CAAC;gCAC/B,yBAAyB;gCACzB;oCACE,WAAW;oCACX,KAAK;iCACN;6BACF,CAAC,CAAA;wBACJ,CAAC;qBACF;oBACD;wBACE,KAAK,EAAE,mCAAmC;wBAC1C,IAAI,EAAE,MAAM;wBACZ,OAAO,EAAE,GAAG,EAAE;4BACZ,KAAK,CAAC,WAAW,CAAC,WAAW,CAAC,EAAE,CAAC;gCAC/B,kBAAkB;gCAClB;oCACE,WAAW;oCACX,KAAK;iCACN;6BACF,CAAC,CAAA;wBACJ,CAAC;qBACF;oBACD;wBACE,KAAK,EAAE,eAAe,SAAS,CAAC,CAAC,CAAC,sBAAsB,CAAC,CAAC,CAAC,EAAE,EAAE;wBAC/D,QAAQ,EAAE,SAAS;wBACnB,IAAI,EAAE,UAAU;wBAChB,OAAO,EAAE,mBAAmB,CAAC,CAAC,CAAC,WAAW,CAAC,CAAC,CAAC,KAAK;wBAClD,IAAI,EAAE,UAAU;wBAChB,OAAO,EAAE,GAAG,EAAE;4BACZ,KAAK,CAAC,cAAc,CAAC,CAAC,WAAW,CAAC,CAAA;wBACpC,CAAC;qBACF;oBACD;wBACE,KAAK,EAAE,qBAAqB,SAAS,CAAC,CAAC,CAAC,sBAAsB,CAAC,CAAC,CAAC,EAAE,EAAE;wBACrE,QAAQ,EAAE,SAAS;wBACnB,OAAO,EAAE,mBAAmB,CAAC,CAAC,CAAC,cAAc,CAAC,CAAC,CAAC,KAAK;wBACrD,IAAI,EAAE,IAAI;wBACV,IAAI,EAAE,UAAU;wBAChB,OAAO,EAAE,GAAG,EAAE;4BACZ,KAAK,CAAC,iBAAiB,CAAC,CAAC,cAAc,CAAC,CAAA;wBAC1C,CAAC;qBACF;oBACD;wBACE,KAAK,EAAE,iBAAiB,SAAS,CAAC,CAAC,CAAC,sBAAsB,CAAC,CAAC,CAAC,EAAE,EAAE;wBACjE,IAAI,EAAE,SAAS;wBACf,QAAQ,EAAE,SAAS;wBACnB,OAAO,EAAE,GAAG,EAAE;4BACZ,KAAK,CAAC,WAAW,CAAC,OAAO,CAAC,EAAE,CAAC;gCAC3B,mBAAmB;gCACnB;oCACE,OAAO;oCACP,KAAK;iCACN;6BACF,CAAC,CAAA;wBACJ,CAAC;qBACF;iBACF;aACF;YACD,GAAG,KAAK,CAAC,kBAAkB,EAAE;SAC9B;QAED,oBAAC,QAAQ,OAAG,CACQ,CACvB,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,UAAU,CAAA"}

package/dist/components/minimap/MinimapSVG.js

@@ -9,12 +9,13 @@ const MinimapSVG = observer(({ model }) => {
     const right = left + W;
     const s = left * unit;
     const e = right * unit;
-    const fill = 'rgba(66, 119, 127, 0.3)';
+    const fillColor = 'rgb(66, 119, 127)';
+    const fillOpacity = 0.3;
     return (React.createElement(React.Fragment, null,
         React.createElement("rect", { x: 0, y: 0, width: W, height: BAR_HEIGHT, stroke: "#555", fill: "none" }),
-        React.createElement("rect", { x: Math.max(0, s), y: 0, width: e - s, height: BAR_HEIGHT, fill: fill, stroke: "#555" }),
+        React.createElement("rect", { x: Math.max(0, s), y: 0, width: e - s, height: BAR_HEIGHT, fill: fillColor, fillOpacity: fillOpacity, stroke: "#555" }),
         React.createElement("g", { transform: `translate(0 ${BAR_HEIGHT})` },
-            React.createElement("polygon", { fill: fill, points: [
+            React.createElement("polygon", { fill: fillColor, fillOpacity: fillOpacity, points: [
                     [e, 0],
                     [s, 0],
                     [0, H2],

package/dist/components/minimap/MinimapSVG.js.map

@@ -1 +1 @@
-{"version":3,"file":"MinimapSVG.js","sourceRoot":"","sources":["../../../src/components/minimap/MinimapSVG.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAIrC,MAAM,UAAU,GAAG,QAAQ,CAAC,CAAC,EAAE,KAAK,EAA2B,EAAE,EAAE;IACjE,MAAM,EACJ,OAAO,EACP,YAAY,EAAE,CAAC,EACf,aAAa,EAAE,CAAC,EAChB,QAAQ,EACR,UAAU,GACX,GAAG,KAAK,CAAA;IAET,MAAM,UAAU,GAAG,EAAE,CAAA;IACrB,MAAM,EAAE,GAAG,CAAC,GAAG,EAAE,CAAA;IAEjB,MAAM,IAAI,GAAG,CAAC,GAAG,UAAU,GAAG,QAAQ,CAAA;IACtC,MAAM,IAAI,GAAG,CAAC,OAAO,CAAA;IACrB,MAAM,KAAK,GAAG,IAAI,GAAG,CAAC,CAAA;IACtB,MAAM,CAAC,GAAG,IAAI,GAAG,IAAI,CAAA;IACrB,MAAM,CAAC,GAAG,KAAK,GAAG,IAAI,CAAA;IACtB,MAAM,IAAI,GAAG,yBAAyB,CAAA;IAEtC,OAAO,CACL;QACE,8BACE,CAAC,EAAE,CAAC,EACJ,CAAC,EAAE,CAAC,EACJ,KAAK,EAAE,CAAC,EACR,MAAM,EAAE,UAAU,EAClB,MAAM,EAAC,MAAM,EACb,IAAI,EAAC,MAAM,GACX;QACF,8BACE,CAAC,EAAE,IAAI,CAAC,GAAG,CAAC,CAAC,EAAE,CAAC,CAAC,EACjB,CAAC,EAAE,CAAC,EACJ,KAAK,EAAE,CAAC,GAAG,CAAC,EACZ,MAAM,EAAE,UAAU,EAClB,IAAI,EAAE,IAAI,EACV,MAAM,EAAC,MAAM,GACb;QACF,2BAAG,SAAS,EAAE,eAAe,UAAU,GAAG;YACxC,iCACE,IAAI,EAAE,IAAI,EACV,MAAM,EAAE;oBACN,CAAC,CAAC,EAAE,CAAC,CAAC;oBACN,CAAC,CAAC,EAAE,CAAC,CAAC;oBACN,CAAC,CAAC,EAAE,EAAE,CAAC;oBACP,CAAC,CAAC,EAAE,EAAE,CAAC;iBACR,CAAC,QAAQ,EAAE,GACZ,CACA,CACH,CACJ,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,UAAU,CAAA"}
+{"version":3,"file":"MinimapSVG.js","sourceRoot":"","sources":["../../../src/components/minimap/MinimapSVG.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAIrC,MAAM,UAAU,GAAG,QAAQ,CAAC,CAAC,EAAE,KAAK,EAA2B,EAAE,EAAE;IACjE,MAAM,EACJ,OAAO,EACP,YAAY,EAAE,CAAC,EACf,aAAa,EAAE,CAAC,EAChB,QAAQ,EACR,UAAU,GACX,GAAG,KAAK,CAAA;IAET,MAAM,UAAU,GAAG,EAAE,CAAA;IACrB,MAAM,EAAE,GAAG,CAAC,GAAG,EAAE,CAAA;IAEjB,MAAM,IAAI,GAAG,CAAC,GAAG,UAAU,GAAG,QAAQ,CAAA;IACtC,MAAM,IAAI,GAAG,CAAC,OAAO,CAAA;IACrB,MAAM,KAAK,GAAG,IAAI,GAAG,CAAC,CAAA;IACtB,MAAM,CAAC,GAAG,IAAI,GAAG,IAAI,CAAA;IACrB,MAAM,CAAC,GAAG,KAAK,GAAG,IAAI,CAAA;IACtB,MAAM,SAAS,GAAG,mBAAmB,CAAA;IACrC,MAAM,WAAW,GAAG,GAAG,CAAA;IAEvB,OAAO,CACL;QACE,8BACE,CAAC,EAAE,CAAC,EACJ,CAAC,EAAE,CAAC,EACJ,KAAK,EAAE,CAAC,EACR,MAAM,EAAE,UAAU,EAClB,MAAM,EAAC,MAAM,EACb,IAAI,EAAC,MAAM,GACX;QACF,8BACE,CAAC,EAAE,IAAI,CAAC,GAAG,CAAC,CAAC,EAAE,CAAC,CAAC,EACjB,CAAC,EAAE,CAAC,EACJ,KAAK,EAAE,CAAC,GAAG,CAAC,EACZ,MAAM,EAAE,UAAU,EAClB,IAAI,EAAE,SAAS,EACf,WAAW,EAAE,WAAW,EACxB,MAAM,EAAC,MAAM,GACb;QACF,2BAAG,SAAS,EAAE,eAAe,UAAU,GAAG;YACxC,iCACE,IAAI,EAAE,SAAS,EACf,WAAW,EAAE,WAAW,EACxB,MAAM,EAAE;oBACN,CAAC,CAAC,EAAE,CAAC,CAAC;oBACN,CAAC,CAAC,EAAE,CAAC,CAAC;oBACN,CAAC,CAAC,EAAE,EAAE,CAAC;oBACP,CAAC,CAAC,EAAE,EAAE,CAAC;iBACR,CAAC,QAAQ,EAAE,GACZ,CACA,CACH,CACJ,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,UAAU,CAAA"}

package/dist/components/msa/MSACanvasBlock.js

@@ -1,4 +1,5 @@
-import React, { useEffect, useMemo, useRef } from 'react';
+import React, { useEffect, useMemo, useRef, useState } from 'react';
+import { BaseTooltip } from '@jbrowse/core/ui';
 import { useTheme } from '@mui/material';
 import { autorun } from 'mobx';
 import { observer } from 'mobx-react';
@@ -45,47 +46,60 @@ const MSACanvasBlock = observer(function ({ model, offsetX, offsetY, }) {
         highResScaleFactor,
         contrastScheme,
     ]);
-    return (React.createElement("canvas", { ref: ref, onMouseMove: event => {
-            if (!ref.current) {
-                return;
-            }
-            const { left, top } = ref.current.getBoundingClientRect();
-            const mouseX = event.clientX - left + offsetX;
-            const mouseY = event.clientY - top + offsetY;
-            const x = Math.floor(mouseX / colWidth);
-            const y = Math.floor(mouseY / rowHeight);
-            // Only set mouse position if within valid MSA bounds
-            if (x >= 0 && x < model.numColumns && y >= 0 && y < model.numRows) {
-                model.setMousePos(x, y);
-            }
-            else {
-                // Clear mouse position when outside bounds
-                model.setMousePos(undefined, undefined);
-            }
-        }, onClick: event => {
-            if (!ref.current) {
-                return;
-            }
-            const { left, top } = ref.current.getBoundingClientRect();
-            const mouseX = event.clientX - left + offsetX;
-            const mouseY = event.clientY - top + offsetY;
-            const x = Math.floor(mouseX / colWidth);
-            const y = Math.floor(mouseY / rowHeight);
-            if (x === mouseClickCol && y === mouseClickRow) {
-                model.setMouseClickPos(undefined, undefined);
-            }
-            else {
-                model.setMouseClickPos(x, y);
-            }
-        }, onMouseLeave: () => {
-            model.setMousePos();
-        }, width: blockSize * highResScaleFactor, height: blockSize * highResScaleFactor, style: {
-            position: 'absolute',
-            top: scrollY + offsetY,
-            left: scrollX + offsetX,
-            width: blockSize,
-            height: blockSize,
-        } }));
+    const [mousePosition, setMousePosition] = useState();
+    const { hoveredInsertion } = model;
+    return (React.createElement(React.Fragment, null,
+        React.createElement("canvas", { ref: ref, onMouseMove: event => {
+                if (!ref.current) {
+                    return;
+                }
+                setMousePosition({ x: event.clientX, y: event.clientY });
+                const { left, top } = ref.current.getBoundingClientRect();
+                const mouseX = event.clientX - left + offsetX;
+                const mouseY = event.clientY - top + offsetY;
+                const x = Math.floor(mouseX / colWidth);
+                const y = Math.floor(mouseY / rowHeight);
+                // Only set mouse position if within valid MSA bounds
+                if (x >= 0 && x < model.numColumns && y >= 0 && y < model.numRows) {
+                    model.setMousePos(x, y);
+                }
+                else {
+                    // Clear mouse position when outside bounds
+                    model.setMousePos(undefined, undefined);
+                }
+            }, onClick: event => {
+                if (!ref.current) {
+                    return;
+                }
+                const { left, top } = ref.current.getBoundingClientRect();
+                const mouseX = event.clientX - left + offsetX;
+                const mouseY = event.clientY - top + offsetY;
+                const x = Math.floor(mouseX / colWidth);
+                const y = Math.floor(mouseY / rowHeight);
+                if (x === mouseClickCol && y === mouseClickRow) {
+                    model.setMouseClickPos(undefined, undefined);
+                }
+                else {
+                    model.setMouseClickPos(x, y);
+                }
+            }, onMouseLeave: () => {
+                model.setMousePos();
+                setMousePosition(undefined);
+            }, width: blockSize * highResScaleFactor, height: blockSize * highResScaleFactor, style: {
+                position: 'absolute',
+                top: scrollY + offsetY,
+                left: scrollX + offsetX,
+                width: blockSize,
+                height: blockSize,
+            } }),
+        hoveredInsertion && mousePosition ? (React.createElement(BaseTooltip, { clientPoint: { x: mousePosition.x, y: mousePosition.y + 15 } },
+            "Insertion (",
+            hoveredInsertion.letters.length,
+            "bp):",
+            ' ',
+            hoveredInsertion.letters.length > 20
+                ? `${hoveredInsertion.letters.slice(0, 20)}...`
+                : hoveredInsertion.letters)) : 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,EAAE,EAAE,SAAS,EAAE,OAAO,EAAE,MAAM,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AAEnE,OAAO,EAAE,WAAW,EAAE,MAAM,kBAAkB,CAAA;AAC9C,OAAO,EAAE,QAAQ,EAAE,MAAM,eAAe,CAAA;AACxC,OAAO,EAAE,OAAO,EAAE,MAAM,MAAM,CAAA;AAC9B,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAErC,OAAO,EAAE,2BAA2B,EAAE,MAAM,+BAA+B,CAAA;AAC3E,OAAO,EAAE,cAAc,EAAE,MAAM,kBAAkB,CAAA;AACjD,OAAO,EAAE,aAAa,EAAE,MAAM,YAAY,CAAA;AAI1C,MAAM,cAAc,GAAG,QAAQ,CAAC,UAAU,EACxC,KAAK,EACL,OAAO,EACP,OAAO,GAKR;IACC,MAAM,EACJ,QAAQ,EACR,SAAS,EACT,OAAO,EACP,OAAO,EACP,WAAW,EACX,SAAS,EACT,aAAa,EACb,aAAa,EACb,kBAAkB,GACnB,GAAG,KAAK,CAAA;IACT,MAAM,KAAK,GAAG,QAAQ,EAAE,CAAA;IAExB,MAAM,cAAc,GAAG,OAAO,CAC5B,GAAG,EAAE,CAAC,aAAa,CAAC,WAAW,EAAE,KAAK,CAAC,EACvC,CAAC,WAAW,EAAE,KAAK,CAAC,CACrB,CAAA;IAED,MAAM,GAAG,GAAG,MAAM,CAAoB,IAAI,CAAC,CAAA;IAC3C,SAAS,CAAC,GAAG,EAAE;QACb,MAAM,GAAG,GAAG,GAAG,CAAC,OAAO,EAAE,UAAU,CAAC,IAAI,CAAC,CAAA;QACzC,IAAI,CAAC,GAAG,EAAE,CAAC;YACT,OAAM;QACR,CAAC;QACD,OAAO,OAAO,CAAC,GAAG,EAAE;YAClB,GAAG,CAAC,cAAc,EAAE,CAAA;YACpB,GAAG,CAAC,SAAS,CACX,CAAC,EACD,CAAC,EACD,SAAS,GAAG,kBAAkB,EAC9B,SAAS,GAAG,kBAAkB,CAC/B,CAAA;YACD,MAAM,EAAE,mBAAmB,EAAE,GAAG,KAAK,CAAA;YACrC,IAAI,mBAAmB,EAAE,CAAC;gBACxB,2BAA2B,CAAC;oBAC1B,GAAG;oBACH,OAAO;oBACP,OAAO;oBACP,KAAK;iBACN,CAAC,CAAA;YACJ,CAAC;YACD,cAAc,CAAC;gBACb,GAAG;gBACH,KAAK;gBACL,OAAO;gBACP,OAAO;gBACP,cAAc;gBACd,KAAK;aACN,CAAC,CAAA;QACJ,CAAC,CAAC,CAAA;IACJ,CAAC,EAAE;QACD,KAAK;QACL,OAAO;QACP,OAAO;QACP,KAAK;QACL,SAAS;QACT,kBAAkB;QAClB,cAAc;KACf,CAAC,CAAA;IAEF,MAAM,CAAC,aAAa,EAAE,gBAAgB,CAAC,GAAG,QAAQ,EAA4B,CAAA;IAC9E,MAAM,EAAE,gBAAgB,EAAE,GAAG,KAAK,CAAA;IAElC,OAAO,CACL;QACE,gCACE,GAAG,EAAE,GAAG,EACR,WAAW,EAAE,KAAK,CAAC,EAAE;gBACnB,IAAI,CAAC,GAAG,CAAC,OAAO,EAAE,CAAC;oBACjB,OAAM;gBACR,CAAC;gBACD,gBAAgB,CAAC,EAAE,CAAC,EAAE,KAAK,CAAC,OAAO,EAAE,CAAC,EAAE,KAAK,CAAC,OAAO,EAAE,CAAC,CAAA;gBACxD,MAAM,EAAE,IAAI,EAAE,GAAG,EAAE,GAAG,GAAG,CAAC,OAAO,CAAC,qBAAqB,EAAE,CAAA;gBACzD,MAAM,MAAM,GAAG,KAAK,CAAC,OAAO,GAAG,IAAI,GAAG,OAAO,CAAA;gBAC7C,MAAM,MAAM,GAAG,KAAK,CAAC,OAAO,GAAG,GAAG,GAAG,OAAO,CAAA;gBAC5C,MAAM,CAAC,GAAG,IAAI,CAAC,KAAK,CAAC,MAAM,GAAG,QAAQ,CAAC,CAAA;gBACvC,MAAM,CAAC,GAAG,IAAI,CAAC,KAAK,CAAC,MAAM,GAAG,SAAS,CAAC,CAAA;gBAExC,qDAAqD;gBACrD,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,GAAG,KAAK,CAAC,UAAU,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,GAAG,KAAK,CAAC,OAAO,EAAE,CAAC;oBAClE,KAAK,CAAC,WAAW,CAAC,CAAC,EAAE,CAAC,CAAC,CAAA;gBACzB,CAAC;qBAAM,CAAC;oBACN,2CAA2C;oBAC3C,KAAK,CAAC,WAAW,CAAC,SAAS,EAAE,SAAS,CAAC,CAAA;gBACzC,CAAC;YACH,CAAC,EACD,OAAO,EAAE,KAAK,CAAC,EAAE;gBACf,IAAI,CAAC,GAAG,CAAC,OAAO,EAAE,CAAC;oBACjB,OAAM;gBACR,CAAC;gBACD,MAAM,EAAE,IAAI,EAAE,GAAG,EAAE,GAAG,GAAG,CAAC,OAAO,CAAC,qBAAqB,EAAE,CAAA;gBACzD,MAAM,MAAM,GAAG,KAAK,CAAC,OAAO,GAAG,IAAI,GAAG,OAAO,CAAA;gBAC7C,MAAM,MAAM,GAAG,KAAK,CAAC,OAAO,GAAG,GAAG,GAAG,OAAO,CAAA;gBAC5C,MAAM,CAAC,GAAG,IAAI,CAAC,KAAK,CAAC,MAAM,GAAG,QAAQ,CAAC,CAAA;gBACvC,MAAM,CAAC,GAAG,IAAI,CAAC,KAAK,CAAC,MAAM,GAAG,SAAS,CAAC,CAAA;gBACxC,IAAI,CAAC,KAAK,aAAa,IAAI,CAAC,KAAK,aAAa,EAAE,CAAC;oBAC/C,KAAK,CAAC,gBAAgB,CAAC,SAAS,EAAE,SAAS,CAAC,CAAA;gBAC9C,CAAC;qBAAM,CAAC;oBACN,KAAK,CAAC,gBAAgB,CAAC,CAAC,EAAE,CAAC,CAAC,CAAA;gBAC9B,CAAC;YACH,CAAC,EACD,YAAY,EAAE,GAAG,EAAE;gBACjB,KAAK,CAAC,WAAW,EAAE,CAAA;gBACnB,gBAAgB,CAAC,SAAS,CAAC,CAAA;YAC7B,CAAC,EACD,KAAK,EAAE,SAAS,GAAG,kBAAkB,EACrC,MAAM,EAAE,SAAS,GAAG,kBAAkB,EACtC,KAAK,EAAE;gBACL,QAAQ,EAAE,UAAU;gBACpB,GAAG,EAAE,OAAO,GAAG,OAAO;gBACtB,IAAI,EAAE,OAAO,GAAG,OAAO;gBACvB,KAAK,EAAE,SAAS;gBAChB,MAAM,EAAE,SAAS;aAClB,GACD;QACD,gBAAgB,IAAI,aAAa,CAAC,CAAC,CAAC,CACnC,oBAAC,WAAW,IACV,WAAW,EAAE,EAAE,CAAC,EAAE,aAAa,CAAC,CAAC,EAAE,CAAC,EAAE,aAAa,CAAC,CAAC,GAAG,EAAE,EAAE;;YAEhD,gBAAgB,CAAC,OAAO,CAAC,MAAM;;YAAM,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,CAChB,CACf,CAAC,CAAC,CAAC,IAAI,CACP,CACJ,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,cAAc,CAAA"}

package/dist/components/msa/renderMSABlock.js

@@ -1,4 +1,3 @@
-import { getClustalXColor, getPercentIdentityColor } from '../../colorSchemes';
 export function renderMSABlock({ model, offsetX, offsetY, contrastScheme, ctx, theme, highResScaleFactorOverride, blockSizeXOverride, blockSizeYOverride, }) {
     const { colWidth, blockSize, rowHeight, fontSize, highResScaleFactor, actuallyShowDomains, leaves, bgColor, } = model;
     const k = highResScaleFactorOverride || highResScaleFactor;
@@ -20,7 +19,6 @@ export function renderMSABlock({ model, offsetX, offsetY, contrastScheme, ctx, t
             ctx,
             theme,
             offsetX,
-            offsetY,
             xStart,
             xEnd,
             visibleLeaves,
@@ -31,7 +29,13 @@ export function renderMSABlock({ model, offsetX, offsetY, contrastScheme, ctx, t
         ctx,
         offsetX,
         contrastScheme,
-        theme,
+        xStart,
+        xEnd,
+        visibleLeaves,
+    });
+    drawInsertionIndicators({
+        model,
+        ctx,
         xStart,
         xEnd,
         visibleLeaves,
@@ -44,36 +48,34 @@ function drawTiles({ model, offsetX, ctx, visibleLeaves, theme, xStart, xEnd, })
     const referenceSeq = relativeTo
         ? columns[relativeTo]?.slice(xStart, xEnd)
         : null;
+    const isClustalX = colorSchemeName === 'clustalx_protein_dynamic';
+    const isPercentIdentity = colorSchemeName === 'percent_identity_dynamic';
+    const offsetXAligned = offsetX - (offsetX % colWidth);
     for (let i = 0, l1 = visibleLeaves.length; i < l1; i++) {
         const node = visibleLeaves[i];
         const { data: { name }, } = node;
         const y = node.x;
         const str = columns[name]?.slice(xStart, xEnd);
         if (str) {
-            for (let i = 0, l2 = str.length; i < l2; i++) {
-                const letter = str[i];
+            for (let j = 0, l2 = str.length; j < l2; j++) {
+                const letter = str[j];
                 // Use a muted background for positions that match reference
-                const isMatchingReference = referenceSeq && name !== relativeTo && letter === referenceSeq[i];
-                const r1 = colorSchemeName === 'clustalx_protein_dynamic';
-                const r2 = colorSchemeName === 'percent_identity_dynamic';
-                const color = r1
-                    ? getClustalXColor(
-                    // use model.colStats dot notation here: delay use of colStats
-                    // until absolutely needed
-                    model.colStats[xStart + i], model.colStatsSums[xStart + i], model, name, xStart + i)
-                    : r2
-                        ? getPercentIdentityColor(
-                        // use model.colStats dot notation here: delay use of
-                        // colStats until absolutely needed
-                        model.colStats[xStart + i], model.colStatsSums[xStart + i], model, name, xStart + i)
+                const isMatchingReference = referenceSeq && name !== relativeTo && letter === referenceSeq[j];
+                const color = isClustalX
+                    ? model.colClustalX[xStart + j][letter]
+                    : isPercentIdentity
+                        ? (() => {
+                            const consensus = model.colConsensus[xStart + j];
+                            return letter === consensus.letter ? consensus.color : undefined;
+                        })()
                         : colorScheme[letter.toUpperCase()];
-                if (bgColor || r1 || r2) {
+                if (bgColor || isClustalX || isPercentIdentity) {
                     // Use a very light background for matching positions in relative mode
                     const finalColor = isMatchingReference
                         ? theme.palette.action.hover
                         : color || theme.palette.background.default;
                     ctx.fillStyle = finalColor;
-                    ctx.fillRect(i * colWidth + offsetX - (offsetX % colWidth), y - rowHeight, colWidth, rowHeight);
+                    ctx.fillRect(j * colWidth + offsetXAligned, y - rowHeight, colWidth, rowHeight);
                 }
             }
         }
@@ -86,30 +88,73 @@ function drawText({ model, offsetX, contrastScheme, ctx, visibleLeaves, xStart,
         ? columns[relativeTo]?.slice(xStart, xEnd)
         : null;
     if (showMsaLetters) {
+        const offsetXAligned = offsetX - (offsetX % colWidth);
+        const halfColWidth = colWidth / 2;
+        const quarterRowHeight = rowHeight / 4;
         for (let i = 0, l1 = visibleLeaves.length; i < l1; i++) {
             const node = visibleLeaves[i];
             const { data: { name }, } = node;
-            const y = node.x;
+            const y = node.x - quarterRowHeight;
             const str = columns[name]?.slice(xStart, xEnd);
             if (str) {
-                for (let i = 0, l2 = str.length; i < l2; i++) {
-                    const letter = str[i];
+                for (let j = 0, l2 = str.length; j < l2; j++) {
+                    const letter = str[j];
                     // Check if this position matches the reference
-                    const isMatchingReference = referenceSeq && name !== relativeTo && letter === referenceSeq[i];
+                    const isMatchingReference = referenceSeq && name !== relativeTo && letter === referenceSeq[j];
                     // Show dot for matching positions, original letter for differences
                     const displayLetter = isMatchingReference ? '.' : letter;
                     const color = colorScheme[letter.toUpperCase()];
                     const contrast = contrastLettering
                         ? contrastScheme[letter.toUpperCase()] || 'black'
                         : 'black';
-                    const x = i * colWidth + offsetX - (offsetX % colWidth);
                     // note: -rowHeight/4 matches +rowHeight/4 in tree
                     ctx.fillStyle = actuallyShowDomains
                         ? 'black'
                         : bgColor
                             ? contrast
                             : color || 'black';
-                    ctx.fillText(displayLetter, x + colWidth / 2, y - rowHeight / 4);
+                    ctx.fillText(displayLetter, j * colWidth + offsetXAligned + halfColWidth, y);
+                }
+            }
+        }
+    }
+}
+function drawInsertionIndicators({ model, ctx, visibleLeaves, xStart, xEnd, }) {
+    const { bgColor, hideGapsEffective } = model;
+    if (!hideGapsEffective) {
+        return;
+    }
+    ctx.lineWidth = 1;
+    ctx.strokeStyle = '#f0f';
+    drawZigZag({ visibleLeaves, xStart, ctx, model, xEnd, offset: 0 });
+    ctx.strokeStyle = !bgColor ? '#000' : '#fff';
+    drawZigZag({ visibleLeaves, xStart, ctx, model, xEnd, offset: -1 });
+}
+function drawZigZag({ model, ctx, visibleLeaves, xStart, xEnd, offset, }) {
+    const zigSize = 1;
+    const { colWidth, rowHeight, insertionPositions } = model;
+    for (const node of visibleLeaves) {
+        const { name } = node.data;
+        const insertions = insertionPositions.get(name);
+        if (insertions) {
+            const y = node.x;
+            for (const { pos } of insertions) {
+                if (pos >= xStart && pos < xEnd) {
+                    const x = pos * colWidth;
+                    const top = y - rowHeight;
+                    const bottom = y;
+                    ctx.beginPath();
+                    ctx.moveTo(x + offset, top + offset);
+                    let currentY = top;
+                    let goRight = true;
+                    while (currentY < bottom) {
+                        const nextY = Math.min(currentY + zigSize * 2, bottom);
+                        const nextX = goRight ? x + zigSize : x - zigSize;
+                        ctx.lineTo(nextX + offset, nextY + offset);
+                        currentY = nextY;
+                        goRight = !goRight;
+                    }
+                    ctx.stroke();
                 }
             }
         }

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

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

@@ -5,7 +5,7 @@ const multiRowHoverColor = 'rgba(255,165,0,0.15)'; // Orange highlight for multi
 export function renderMouseover({ ctx, model, }) {
     const { mouseCol, colWidth, width, height, rowHeight, scrollX, scrollY, mouseRow, 
     // @ts-expect-error
-    mouseCol2, mouseClickRow, mouseClickCol, relativeTo, rowNamesSet, hoveredTreeNode, } = model;
+    mouseCol2, mouseClickRow, mouseClickCol, relativeTo, rowNamesSet, hoveredTreeNode, highlightedColumns, } = model;
     ctx.resetTransform();
     ctx.clearRect(0, 0, width, height);
     // Highlight reference row (relativeTo) persistently
@@ -26,6 +26,13 @@ export function renderMouseover({ ctx, model, }) {
             }
         }
     }
+    // Highlight multiple columns
+    if (highlightedColumns?.length) {
+        ctx.fillStyle = highlightColor;
+        for (const col of highlightedColumns) {
+            ctx.fillRect(col * colWidth + scrollX, 0, colWidth, height);
+        }
+    }
     if (mouseCol !== undefined) {
         ctx.fillStyle = hoverColor;
         ctx.fillRect(mouseCol * colWidth + scrollX, 0, colWidth, height);

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

@@ -1 +1 @@
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package/dist/components/tracks/renderTracksSvg.d.ts

@@ -0,0 +1,29 @@
+import type { MsaViewModel } from '../../model';
+import type { BasicTrack } from '../../types';
+export declare function renderConservationTrack({ model, ctx, offsetX, offsetY, trackHeight, blockSizeXOverride, highResScaleFactorOverride, }: {
+    model: MsaViewModel;
+    ctx: CanvasRenderingContext2D;
+    offsetX: number;
+    offsetY: number;
+    trackHeight: number;
+    blockSizeXOverride?: number;
+    highResScaleFactorOverride?: number;
+}): void;
+export declare function renderTextTrack({ model, ctx, track, offsetX, offsetY, contrastScheme, blockSizeXOverride, highResScaleFactorOverride, }: {
+    model: MsaViewModel;
+    ctx: CanvasRenderingContext2D;
+    track: BasicTrack;
+    offsetX: number;
+    offsetY: number;
+    contrastScheme: Record<string, string>;
+    blockSizeXOverride?: number;
+    highResScaleFactorOverride?: number;
+}): void;
+export declare function renderAllTracks({ model, ctx, offsetX, contrastScheme, blockSizeXOverride, highResScaleFactorOverride, }: {
+    model: MsaViewModel;
+    ctx: CanvasRenderingContext2D;
+    offsetX: number;
+    contrastScheme: Record<string, string>;
+    blockSizeXOverride?: number;
+    highResScaleFactorOverride?: number;
+}): void;