react-msaview 4.0.3 → 4.1.1

package/dist/components/header/Header.js

@@ -1,15 +1,13 @@
 import React, { lazy, useEffect } from 'react';
-import { IconButton } from '@mui/material';
-import { observer } from 'mobx-react';
 import useMeasure from '@jbrowse/core/util/useMeasure';
-// icons
 import Help from '@mui/icons-material/Help';
-// locals
-import ZoomControls from './ZoomControls';
-import MultiAlignmentSelector from './MultiAlignmentSelector';
+import { IconButton } from '@mui/material';
+import { observer } from 'mobx-react';
 import HeaderInfoArea from './HeaderInfoArea';
-import HeaderStatusArea from './HeaderStatusArea';
 import HeaderMenuExtra from './HeaderMenuExtra';
+import HeaderStatusArea from './HeaderStatusArea';
+import MultiAlignmentSelector from './MultiAlignmentSelector';
+import ZoomControls from './ZoomControls';
 const AboutDialog = lazy(() => import('../dialogs/AboutDialog'));
 const Header = observer(function ({ model }) {
     const [ref, { height }] = useMeasure();

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

@@ -1 +1 @@
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package/dist/components/header/HeaderInfoArea.js.map

@@ -1 +1 @@
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+{"version":3,"file":"HeaderInfoArea.js","sourceRoot":"","sources":["../../../src/components/header/HeaderInfoArea.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAC1C,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAI1C,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC;IAC7B,MAAM,EAAE;QACN,MAAM,EAAE,MAAM;QACd,UAAU,EAAE,EAAE;KACf;CACF,CAAC,CAAA;AAEF,MAAM,cAAc,GAAG,QAAQ,CAAC,UAAU,EAAE,KAAK,EAA2B;IAC1E,MAAM,EAAE,gBAAgB,EAAE,QAAQ,EAAE,GAAG,KAAK,CAAA;IAC5C,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,OAAO,gBAAgB,IAAI,QAAQ,KAAK,SAAS,CAAC,CAAC,CAAC,CAClD,oBAAC,UAAU,IAAC,SAAS,EAAE,OAAO,CAAC,MAAM;QAClC,gBAAgB;;QAChB,KAAK,CAAC,kCAAkC,CAAC,gBAAgB,EAAE,QAAQ,CAAC;;QACpE,KAAK,CAAC,yBAAyB,CAAC,gBAAgB,EAAE,QAAQ,CAAC;YACjD,CACd,CAAC,CAAC,CAAC,IAAI,CAAA;AACV,CAAC,CAAC,CAAA;AAEF,eAAe,cAAc,CAAA"}

package/dist/components/header/HeaderMenu.js

@@ -1,12 +1,11 @@
 import React, { lazy } from 'react';
-import { observer } from 'mobx-react';
 import CascadingMenuButton from '@jbrowse/core/ui/CascadingMenuButton';
-// icons
-import FolderOpen from '@mui/icons-material/FolderOpen';
-import Settings from '@mui/icons-material/Settings';
 import Assignment from '@mui/icons-material/Assignment';
+import FolderOpen from '@mui/icons-material/FolderOpen';
 import List from '@mui/icons-material/List';
 import Menu from '@mui/icons-material/Menu';
+import Settings from '@mui/icons-material/Settings';
+import { observer } from 'mobx-react';
 // lazies
 const SettingsDialog = lazy(() => import('../dialogs/SettingsDialog'));
 const MetadataDialog = lazy(() => import('../dialogs/MetadataDialog'));

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,UAAU,MAAM,gCAAgC,CAAA;AACvD,OAAO,UAAU,MAAM,gCAAgC,CAAA;AACvD,OAAO,IAAI,MAAM,0BAA0B,CAAA;AAC3C,OAAO,IAAI,MAAM,0BAA0B,CAAA;AAC3C,OAAO,QAAQ,MAAM,8BAA8B,CAAA;AACnD,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,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;AAExE,MAAM,UAAU,GAAG,QAAQ,CAAC,UAAU,EAAE,KAAK,EAA2B;IACtE,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,OAAO,EAAE,GAAG,EAAE;oBACZ,KAAK,CAAC,WAAW,CAAC,OAAO,CAAC,EAAE,CAAC,CAAC,cAAc,EAAE,EAAE,KAAK,EAAE,OAAO,EAAE,CAAC,CAAC,CAAA;gBACpE,CAAC;gBACD,IAAI,EAAE,QAAQ;aACf;YACD;gBACE,KAAK,EAAE,UAAU;gBACjB,OAAO,EAAE,GAAG,EAAE;oBACZ,KAAK,CAAC,WAAW,CAAC,OAAO,CAAC,EAAE,CAAC,CAAC,cAAc,EAAE,EAAE,KAAK,EAAE,OAAO,EAAE,CAAC,CAAC,CAAA;gBACpE,CAAC;gBACD,IAAI,EAAE,UAAU;aACjB;YACD;gBACE,KAAK,EAAE,cAAc;gBACrB,OAAO,EAAE,GAAG,EAAE;oBACZ,KAAK,CAAC,WAAW,CAAC,OAAO,CAAC,EAAE,CAAC,CAAC,eAAe,EAAE,EAAE,KAAK,EAAE,OAAO,EAAE,CAAC,CAAC,CAAA;gBACrE,CAAC;gBACD,IAAI,EAAE,IAAI;aACX;SACF;QAED,oBAAC,IAAI,OAAG,CACY,CACvB,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,UAAU,CAAA"}

package/dist/components/header/HeaderMenuExtra.js

@@ -1,17 +1,16 @@
 import React, { lazy } from 'react';
-import { observer } from 'mobx-react';
 import CascadingMenuButton from '@jbrowse/core/ui/CascadingMenuButton';
-// icons
-import MoreVert from '@mui/icons-material/Menu';
-import Sort from '@mui/icons-material/Sort';
-import Visibility from '@mui/icons-material/Visibility';
+import Assignment from '@mui/icons-material/Assignment';
 import FilterAlt from '@mui/icons-material/FilterAlt';
-import Search from '@mui/icons-material/Search';
+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';
 import Settings from '@mui/icons-material/Settings';
-import Assignment from '@mui/icons-material/Assignment';
-import List from '@mui/icons-material/List';
-import FolderOpen from '@mui/icons-material/FolderOpen';
+import Sort from '@mui/icons-material/Sort';
+import Visibility from '@mui/icons-material/Visibility';
+import { observer } from 'mobx-react';
 // lazies
 const SettingsDialog = lazy(() => import('../dialogs/SettingsDialog'));
 const MetadataDialog = lazy(() => import('../dialogs/MetadataDialog'));

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

@@ -1 +1 @@
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package/dist/components/header/HeaderStatusArea.js

@@ -1,8 +1,8 @@
 import React from 'react';
+import { LoadingEllipses } from '@jbrowse/core/ui';
 import { Typography } from '@mui/material';
 import { observer } from 'mobx-react';
 import { makeStyles } from 'tss-react/mui';
-import { LoadingEllipses } from '@jbrowse/core/ui';
 const useStyles = makeStyles()({
     margin: {
         margin: 'auto',

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

@@ -1 +1 @@
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+{"version":3,"file":"HeaderStatusArea.js","sourceRoot":"","sources":["../../../src/components/header/HeaderStatusArea.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,EAAE,eAAe,EAAE,MAAM,kBAAkB,CAAA;AAClD,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAC1C,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAI1C,MAAM,SAAS,GAAG,UAAU,EAAE,CAAC;IAC7B,MAAM,EAAE;QACN,MAAM,EAAE,MAAM;QACd,UAAU,EAAE,EAAE;KACf;CACF,CAAC,CAAA;AAEF,MAAM,gBAAgB,GAAG,QAAQ,CAAC,CAAC,EAAE,KAAK,EAA2B,EAAE,EAAE;IACvE,MAAM,EAAE,MAAM,EAAE,GAAG,KAAK,CAAA;IACxB,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,OAAO,MAAM,CAAC,CAAC,CAAC,CACd,oBAAC,UAAU,IAAC,SAAS,EAAE,OAAO,CAAC,MAAM;QACnC,oBAAC,eAAe,IAAC,OAAO,EAAE,MAAM,CAAC,GAAG,EAAE,SAAS,EAAC,MAAM,GAAG;QAAC,GAAG;QAC5D,MAAM,CAAC,GAAG,CAAC,CAAC,CAAC,CACZ,2BAAG,IAAI,EAAE,MAAM,CAAC,GAAG,EAAE,MAAM,EAAC,QAAQ,EAAC,GAAG,EAAC,YAAY,eAEjD,CACL,CAAC,CAAC,CAAC,IAAI,CACG,CACd,CAAC,CAAC,CAAC,IAAI,CAAA;AACV,CAAC,CAAC,CAAA;AAEF,eAAe,gBAAgB,CAAA"}

package/dist/components/header/MultiAlignmentSelector.js

@@ -1,6 +1,6 @@
 import React from 'react';
-import { observer } from 'mobx-react';
 import { Select } from '@mui/material';
+import { observer } from 'mobx-react';
 const MultiAlignmentSelector = observer(function ({ model, }) {
     const { currentAlignment, alignmentNames } = model;
     return alignmentNames.length > 0 ? (React.createElement(Select, { native: true, value: currentAlignment, size: "small", onChange: event => {

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

@@ -1 +1 @@
-{"version":3,"file":"MultiAlignmentSelector.js","sourceRoot":"","sources":["../../../src/components/header/MultiAlignmentSelector.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AACzB,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,EAAE,MAAM,EAAE,MAAM,eAAe,CAAA;AAKtC,MAAM,sBAAsB,GAAG,QAAQ,CAAC,UAAU,EAChD,KAAK,GAGN;IACC,MAAM,EAAE,gBAAgB,EAAE,cAAc,EAAE,GAAG,KAAK,CAAA;IAClD,OAAO,cAAc,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,CAAC,CACjC,oBAAC,MAAM,IACL,MAAM,QACN,KAAK,EAAE,gBAAgB,EACvB,IAAI,EAAC,OAAO,EACZ,QAAQ,EAAE,KAAK,CAAC,EAAE;YAChB,KAAK,CAAC,mBAAmB,CAAC,CAAE,KAAK,CAAC,MAAM,CAAC,KAAgB,CAAC,CAAA;YAC1D,KAAK,CAAC,UAAU,CAAC,CAAC,CAAC,CAAA;YACnB,KAAK,CAAC,UAAU,CAAC,CAAC,CAAC,CAAA;QACrB,CAAC,IAEA,cAAc,CAAC,GAAG,CAAC,CAAC,MAAM,EAAE,KAAK,EAAE,EAAE,CAAC,CACrC,gCAAQ,GAAG,EAAE,GAAG,MAAM,IAAI,KAAK,EAAE,EAAE,KAAK,EAAE,KAAK,IAC5C,MAAM,CACA,CACV,CAAC,CACK,CACV,CAAC,CAAC,CAAC,IAAI,CAAA;AACV,CAAC,CAAC,CAAA;AACF,eAAe,sBAAsB,CAAA"}
+{"version":3,"file":"MultiAlignmentSelector.js","sourceRoot":"","sources":["../../../src/components/header/MultiAlignmentSelector.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,EAAE,MAAM,EAAE,MAAM,eAAe,CAAA;AACtC,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAIrC,MAAM,sBAAsB,GAAG,QAAQ,CAAC,UAAU,EAChD,KAAK,GAGN;IACC,MAAM,EAAE,gBAAgB,EAAE,cAAc,EAAE,GAAG,KAAK,CAAA;IAClD,OAAO,cAAc,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,CAAC,CACjC,oBAAC,MAAM,IACL,MAAM,QACN,KAAK,EAAE,gBAAgB,EACvB,IAAI,EAAC,OAAO,EACZ,QAAQ,EAAE,KAAK,CAAC,EAAE;YAChB,KAAK,CAAC,mBAAmB,CAAC,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC,CAAA;YAC9C,KAAK,CAAC,UAAU,CAAC,CAAC,CAAC,CAAA;YACnB,KAAK,CAAC,UAAU,CAAC,CAAC,CAAC,CAAA;QACrB,CAAC,IAEA,cAAc,CAAC,GAAG,CAAC,CAAC,MAAM,EAAE,KAAK,EAAE,EAAE,CAAC,CACrC,gCAAQ,GAAG,EAAE,GAAG,MAAM,IAAI,KAAK,EAAE,EAAE,KAAK,EAAE,KAAK,IAC5C,MAAM,CACA,CACV,CAAC,CACK,CACV,CAAC,CAAC,CAAC,IAAI,CAAA;AACV,CAAC,CAAC,CAAA;AACF,eAAe,sBAAsB,CAAA"}

package/dist/components/header/ZoomControls.js

@@ -1,12 +1,12 @@
 import React from 'react';
-import { IconButton } from '@mui/material';
-import { observer } from 'mobx-react';
 import CascadingMenuButton from '@jbrowse/core/ui/CascadingMenuButton';
-// icons
-import ZoomIn from '@mui/icons-material/ZoomIn';
-import ZoomOut from '@mui/icons-material/ZoomOut';
 import MoreVert from '@mui/icons-material/MoreVert';
 import RestartAlt from '@mui/icons-material/RestartAlt';
+import ZoomIn from '@mui/icons-material/ZoomIn';
+import ZoomOut from '@mui/icons-material/ZoomOut';
+import { IconButton } from '@mui/material';
+import { observer } from 'mobx-react';
+// icons
 const ZoomControls = observer(function ZoomControls({ model, }) {
     return (React.createElement(React.Fragment, null,
         React.createElement(IconButton, { onClick: () => {
@@ -42,6 +42,12 @@ const ZoomControls = observer(function ZoomControls({ model, }) {
                         model.zoomOutVertical();
                     },
                 },
+                {
+                    label: 'Show entire view',
+                    onClick: () => {
+                        model.showEntire();
+                    },
+                },
                 {
                     label: 'Reset zoom to default',
                     icon: RestartAlt,

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

@@ -1 +1 @@
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+{"version":3,"file":"ZoomControls.js","sourceRoot":"","sources":["../../../src/components/header/ZoomControls.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,mBAAmB,MAAM,sCAAsC,CAAA;AACtE,OAAO,QAAQ,MAAM,8BAA8B,CAAA;AACnD,OAAO,UAAU,MAAM,gCAAgC,CAAA;AACvD,OAAO,MAAM,MAAM,4BAA4B,CAAA;AAC/C,OAAO,OAAO,MAAM,6BAA6B,CAAA;AACjD,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAC1C,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAIrC,QAAQ;AAER,MAAM,YAAY,GAAG,QAAQ,CAAC,SAAS,YAAY,CAAC,EAClD,KAAK,GAGN;IACC,OAAO,CACL;QACE,oBAAC,UAAU,IACT,OAAO,EAAE,GAAG,EAAE;gBACZ,KAAK,CAAC,MAAM,EAAE,CAAA;YAChB,CAAC;YAED,oBAAC,MAAM,OAAG,CACC;QACb,oBAAC,UAAU,IACT,OAAO,EAAE,GAAG,EAAE;gBACZ,KAAK,CAAC,OAAO,EAAE,CAAA;YACjB,CAAC;YAED,oBAAC,OAAO,OAAG,CACA;QACb,oBAAC,mBAAmB,IAClB,SAAS,EAAE;gBACT;oBACE,KAAK,EAAE,oBAAoB;oBAC3B,OAAO,EAAE,GAAG,EAAE;wBACZ,KAAK,CAAC,gBAAgB,EAAE,CAAA;oBAC1B,CAAC;iBACF;gBACD;oBACE,KAAK,EAAE,kBAAkB;oBACzB,OAAO,EAAE,GAAG,EAAE;wBACZ,KAAK,CAAC,cAAc,EAAE,CAAA;oBACxB,CAAC;iBACF;gBACD;oBACE,KAAK,EAAE,qBAAqB;oBAC5B,OAAO,EAAE,GAAG,EAAE;wBACZ,KAAK,CAAC,iBAAiB,EAAE,CAAA;oBAC3B,CAAC;iBACF;gBAED;oBACE,KAAK,EAAE,mBAAmB;oBAC1B,OAAO,EAAE,GAAG,EAAE;wBACZ,KAAK,CAAC,eAAe,EAAE,CAAA;oBACzB,CAAC;iBACF;gBAED;oBACE,KAAK,EAAE,kBAAkB;oBACzB,OAAO,EAAE,GAAG,EAAE;wBACZ,KAAK,CAAC,UAAU,EAAE,CAAA;oBACpB,CAAC;iBACF;gBACD;oBACE,KAAK,EAAE,uBAAuB;oBAC9B,IAAI,EAAE,UAAU;oBAChB,OAAO,EAAE,GAAG,EAAE;wBACZ,KAAK,CAAC,WAAW,CAAC,EAAE,CAAC,CAAA;wBACrB,KAAK,CAAC,YAAY,CAAC,EAAE,CAAC,CAAA;oBACxB,CAAC;iBACF;aACF;YAED,oBAAC,QAAQ,OAAG,CACQ,CACrB,CACJ,CAAA;AACH,CAAC,CAAC,CAAA;AACF,eAAe,YAAY,CAAA"}

package/dist/components/import/ImportForm.js

@@ -1,28 +1,32 @@
 import React, { useState } from 'react';
+import { ErrorMessage, FileSelector } from '@jbrowse/core/ui';
+import { Button, Container, Typography } from '@mui/material';
 import { observer } from 'mobx-react';
-import { Button, Container, Grid, Typography } from '@mui/material';
-import { FileSelector } from '@jbrowse/core/ui';
-import { load } from './util';
 import ImportFormExamples from './ImportFormExamples';
+import { load } from './util';
 const ImportForm = observer(function ({ model }) {
     const [msaFile, setMsaFile] = useState();
     const [treeFile, setTreeFile] = useState();
     const { error } = model;
     return (React.createElement(Container, null,
         React.createElement("div", { style: { width: '50%' } },
-            error ? (React.createElement("div", { style: { padding: 20 } },
-                React.createElement(Typography, { color: "error" },
-                    "Error: ",
-                    `${error}`))) : null,
+            error ? React.createElement(ErrorMessage, { error: error }) : null,
             React.createElement(Typography, null, "Open an MSA file (stockholm or clustal format) and/or a tree file (newick format)."),
             React.createElement(Typography, { color: "error" }, "Note: you can open up just an MSA or just a tree, both are not required. Some MSA files e.g. stockholm format have an embedded tree also and this is fine, and opening a separate tree file is not required.")),
-        React.createElement(Grid, { container: true, spacing: 10, justifyContent: "center", alignItems: "center" },
-            React.createElement(Grid, { item: true },
-                React.createElement(Typography, null, "MSA file or URL"),
-                React.createElement(FileSelector, { location: msaFile, setLocation: setMsaFile }),
-                React.createElement(Typography, null, "Tree file or URL"),
-                React.createElement(FileSelector, { location: treeFile, setLocation: setTreeFile })),
-            React.createElement(Grid, { item: true },
+        React.createElement("div", { style: {
+                display: 'flex',
+                justifyContent: 'center',
+                alignItems: 'center',
+                gap: 40,
+            } },
+            React.createElement("div", null,
+                React.createElement("div", null,
+                    React.createElement(Typography, null, "MSA file or URL"),
+                    React.createElement(FileSelector, { location: msaFile, setLocation: setMsaFile })),
+                React.createElement("div", null,
+                    React.createElement(Typography, null, "Tree file or URL"),
+                    React.createElement(FileSelector, { location: treeFile, setLocation: setTreeFile }))),
+            React.createElement("div", null,
                 React.createElement(Button, { onClick: () => {
                         // eslint-disable-next-line @typescript-eslint/no-floating-promises
                         ;
@@ -36,7 +40,7 @@ const ImportForm = observer(function ({ model }) {
                             }
                         })();
                     }, variant: "contained", color: "primary", disabled: !msaFile && !treeFile }, "Open")),
-            React.createElement(Grid, { item: true },
+            React.createElement("div", null,
                 React.createElement(Typography, null, "Examples"),
                 React.createElement(ImportFormExamples, { model: model })))));
 });

package/dist/components/import/ImportForm.js.map

@@ -1 +1 @@
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package/dist/components/import/ImportFormExamples.js

@@ -1,7 +1,7 @@
 import React from 'react';
-import { Typography, Link } from '@mui/material';
+import { Link, Typography } from '@mui/material';
 import { observer } from 'mobx-react';
-import { smallTree, smallMSA, smallMSAOnly } from './data/seq2';
+import { smallMSA, smallMSAOnly, smallTree } from './data/seq2';
 import { load } from './util';
 function ListItem({ onClick, model, children, }) {
     return (React.createElement("li", null,

package/dist/components/import/ImportFormExamples.js.map

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package/dist/components/import/util.d.ts

@@ -1,3 +1,3 @@
-import type { FileLocation } from '@jbrowse/core/util';
 import type { MsaViewModel } from '../../model';
+import type { FileLocation } from '@jbrowse/core/util';
 export declare function load(model: MsaViewModel, msaFile?: FileLocation, treeFile?: FileLocation): Promise<void>;

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

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

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

@@ -1,5 +1,5 @@
-import { CircularProgress, Typography } from '@mui/material';
 import React from 'react';
+import { CircularProgress, Typography } from '@mui/material';
 export default function Loading() {
     return (React.createElement("div", { style: {
             position: 'absolute',

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

@@ -1 +1 @@
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+{"version":3,"file":"Loading.js","sourceRoot":"","sources":["../../../src/components/msa/Loading.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,EAAE,gBAAgB,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAC5D,MAAM,CAAC,OAAO,UAAU,OAAO;IAC7B,OAAO,CACL,6BACE,KAAK,EAAE;YACL,QAAQ,EAAE,UAAU;YACpB,IAAI,EAAE,KAAK;YACX,GAAG,EAAE,KAAK;SACX;QAED,oBAAC,gBAAgB,OAAG;QACpB,oBAAC,UAAU,qBAAwB,CAC/B,CACP,CAAA;AACH,CAAC"}

package/dist/components/msa/MSACanvas.js

@@ -1,7 +1,7 @@
-import React, { useEffect, useState, useRef } from 'react';
+import React, { useEffect, useRef, useState } from 'react';
 import { observer } from 'mobx-react';
-import MSACanvasBlock from './MSACanvasBlock';
 import Loading from './Loading';
+import MSACanvasBlock from './MSACanvasBlock';
 const MSACanvas = observer(function ({ model }) {
     const { MSA, verticalScrollbarWidth, msaFilehandle, height, msaAreaWidth, blocks2d, } = model;
     const ref = useRef(null);

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

@@ -1 +1 @@
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+{"version":3,"file":"MSACanvas.js","sourceRoot":"","sources":["../../../src/components/msa/MSACanvas.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,SAAS,EAAE,MAAM,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AAE1D,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAErC,OAAO,OAAO,MAAM,WAAW,CAAA;AAC/B,OAAO,cAAc,MAAM,kBAAkB,CAAA;AAI7C,MAAM,SAAS,GAAG,QAAQ,CAAC,UAAU,EAAE,KAAK,EAA2B;IACrE,MAAM,EACJ,GAAG,EACH,sBAAsB,EACtB,aAAa,EACb,MAAM,EACN,YAAY,EACZ,QAAQ,GACT,GAAG,KAAK,CAAA;IACT,MAAM,GAAG,GAAG,MAAM,CAAiB,IAAI,CAAC,CAAA;IACxC,QAAQ;IACR,MAAM,SAAS,GAAG,MAAM,CAAC,KAAK,CAAC,CAAA;IAC/B,MAAM,MAAM,GAAG,MAAM,CAAC,CAAC,CAAC,CAAA;IACxB,MAAM,MAAM,GAAG,MAAM,CAAC,CAAC,CAAC,CAAA;IACxB,iCAAiC;IACjC,MAAM,KAAK,GAAG,MAAM,CAAS,CAAC,CAAC,CAAA;IAC/B,MAAM,KAAK,GAAG,MAAM,CAAS,CAAC,CAAC,CAAA;IAC/B,MAAM,CAAC,aAAa,EAAE,gBAAgB,CAAC,GAAG,QAAQ,CAAC,KAAK,CAAC,CAAA;IACzD,SAAS,CAAC,GAAG,EAAE;QACb,MAAM,IAAI,GAAG,GAAG,CAAC,OAAO,CAAA;QACxB,IAAI,CAAC,IAAI,EAAE,CAAC;YACV,OAAM;QACR,CAAC;QACD,SAAS,OAAO,CAAC,KAAiB;YAChC,MAAM,CAAC,OAAO,IAAI,KAAK,CAAC,MAAM,CAAA;YAC9B,MAAM,CAAC,OAAO,IAAI,KAAK,CAAC,MAAM,CAAA;YAE9B,IAAI,CAAC,SAAS,CAAC,OAAO,EAAE,CAAC;gBACvB,SAAS,CAAC,OAAO,GAAG,IAAI,CAAA;gBACxB,qBAAqB,CAAC,GAAG,EAAE;oBACzB,KAAK,CAAC,SAAS,CAAC,CAAC,MAAM,CAAC,OAAO,CAAC,CAAA;oBAChC,KAAK,CAAC,SAAS,CAAC,CAAC,MAAM,CAAC,OAAO,CAAC,CAAA;oBAChC,MAAM,CAAC,OAAO,GAAG,CAAC,CAAA;oBAClB,MAAM,CAAC,OAAO,GAAG,CAAC,CAAA;oBAClB,SAAS,CAAC,OAAO,GAAG,KAAK,CAAA;gBAC3B,CAAC,CAAC,CAAA;YACJ,CAAC;YACD,KAAK,CAAC,cAAc,EAAE,CAAA;YACtB,KAAK,CAAC,eAAe,EAAE,CAAA;QACzB,CAAC;QACD,IAAI,CAAC,gBAAgB,CAAC,OAAO,EAAE,OAAO,EAAE,EAAE,OAAO,EAAE,KAAK,EAAE,CAAC,CAAA;QAC3D,OAAO,GAAG,EAAE;YACV,IAAI,CAAC,mBAAmB,CAAC,OAAO,EAAE,OAAO,CAAC,CAAA;QAC5C,CAAC,CAAA;IACH,CAAC,EAAE,CAAC,KAAK,CAAC,CAAC,CAAA;IAEX,SAAS,CAAC,GAAG,EAAE;QACb,IAAI,OAAO,GAAG,GAAG,EAAE,GAAE,CAAC,CAAA;QAEtB,SAAS,eAAe,CAAC,KAAiB;YACxC,KAAK,CAAC,cAAc,EAAE,CAAA;YACtB,MAAM,KAAK,GAAG,KAAK,CAAC,OAAO,CAAA;YAC3B,MAAM,KAAK,GAAG,KAAK,CAAC,OAAO,CAAA;YAC3B,MAAM,SAAS,GAAG,KAAK,GAAG,KAAK,CAAC,OAAO,CAAA;YACvC,MAAM,SAAS,GAAG,KAAK,GAAG,KAAK,CAAC,OAAO,CAAA;YACvC,IAAI,SAAS,IAAI,SAAS,EAAE,CAAC;gBAC3B,uEAAuE;gBACvE,8EAA8E;gBAC9E,IAAI,CAAC,SAAS,CAAC,OAAO,EAAE,CAAC;oBACvB,SAAS,CAAC,OAAO,GAAG,IAAI,CAAA;oBACxB,MAAM,CAAC,qBAAqB,CAAC,GAAG,EAAE;wBAChC,KAAK,CAAC,SAAS,CAAC,SAAS,CAAC,CAAA;wBAC1B,KAAK,CAAC,SAAS,CAAC,SAAS,CAAC,CAAA;wBAC1B,SAAS,CAAC,OAAO,GAAG,KAAK,CAAA;wBACzB,KAAK,CAAC,OAAO,GAAG,KAAK,CAAC,OAAO,CAAA;wBAC7B,KAAK,CAAC,OAAO,GAAG,KAAK,CAAC,OAAO,CAAA;oBAC/B,CAAC,CAAC,CAAA;gBACJ,CAAC;YACH,CAAC;QACH,CAAC;QAED,SAAS,aAAa;YACpB,KAAK,CAAC,OAAO,GAAG,CAAC,CAAA;YACjB,IAAI,aAAa,EAAE,CAAC;gBAClB,gBAAgB,CAAC,KAAK,CAAC,CAAA;YACzB,CAAC;QACH,CAAC;QAED,IAAI,aAAa,EAAE,CAAC;YAClB,MAAM,CAAC,gBAAgB,CAAC,WAAW,EAAE,eAAe,EAAE,IAAI,CAAC,CAAA;YAC3D,MAAM,CAAC,gBAAgB,CAAC,SAAS,EAAE,aAAa,EAAE,IAAI,CAAC,CAAA;YACvD,OAAO,GAAG,GAAG,EAAE;gBACb,MAAM,CAAC,mBAAmB,CAAC,WAAW,EAAE,eAAe,EAAE,IAAI,CAAC,CAAA;gBAC9D,MAAM,CAAC,mBAAmB,CAAC,SAAS,EAAE,aAAa,EAAE,IAAI,CAAC,CAAA;YAC5D,CAAC,CAAA;QACH,CAAC;QACD,OAAO,OAAO,CAAA;IAChB,CAAC,EAAE,CAAC,KAAK,EAAE,aAAa,CAAC,CAAC,CAAA;IAE1B,OAAO,CACL,6BACE,GAAG,EAAE,GAAG,EACR,WAAW,EAAE,KAAK,CAAC,EAAE;YACnB,2DAA2D;YAC3D,MAAM,MAAM,GAAG,KAAK,CAAC,MAAqB,CAAA;YAC1C,IAAI,MAAM,CAAC,SAAS,IAAI,MAAM,CAAC,OAAO,CAAC,OAAO,EAAE,CAAC;gBAC/C,OAAM;YACR,CAAC;YAED,qCAAqC;YACrC,IAAI,KAAK,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;gBACvB,KAAK,CAAC,OAAO,GAAG,KAAK,CAAC,OAAO,CAAA;gBAC7B,KAAK,CAAC,OAAO,GAAG,KAAK,CAAC,OAAO,CAAA;gBAC7B,gBAAgB,CAAC,IAAI,CAAC,CAAA;YACxB,CAAC;QACH,CAAC,EACD,SAAS,EAAE,KAAK,CAAC,EAAE;YACjB,KAAK,CAAC,cAAc,EAAE,CAAA;YACtB,gBAAgB,CAAC,KAAK,CAAC,CAAA;QACzB,CAAC,EACD,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,YAAY,GAAG,sBAAsB;YAC5C,QAAQ,EAAE,QAAQ;SACnB,IAEA,CAAC,GAAG,IAAI,CAAC,aAAa,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,CACrC,QAAQ,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,EAAE,CAAC,EAAE,EAAE,CAAC,CACzB,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,CACH,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

@@ -1,11 +1,10 @@
-import React, { useEffect, useRef, useMemo } from 'react';
+import React, { useEffect, useMemo, useRef } from 'react';
 import { useTheme } from '@mui/material';
 import { autorun } from 'mobx';
 import { observer } from 'mobx-react';
-// locals
+import { renderBoxFeatureCanvasBlock } from './renderBoxFeatureCanvasBlock';
 import { renderMSABlock } from './renderMSABlock';
 import { colorContrast } from '../../util';
-import { renderBoxFeatureCanvasBlock } from './renderBoxFeatureCanvasBlock';
 const MSACanvasBlock = observer(function ({ model, offsetX, offsetY, }) {
     const { colWidth, rowHeight, scrollY, scrollX, colorScheme, blockSize, mouseClickCol, mouseClickRow, highResScaleFactor, } = model;
     const theme = useTheme();
@@ -18,7 +17,7 @@ const MSACanvasBlock = observer(function ({ model, offsetX, offsetY, }) {
         }
         return autorun(() => {
             ctx.resetTransform();
-            ctx.clearRect(0, 0, blockSize, blockSize);
+            ctx.clearRect(0, 0, blockSize * highResScaleFactor, blockSize * highResScaleFactor);
             const { actuallyShowDomains } = model;
             if (actuallyShowDomains) {
                 renderBoxFeatureCanvasBlock({
@@ -37,7 +36,15 @@ const MSACanvasBlock = observer(function ({ model, offsetX, offsetY, }) {
                 model,
             });
         });
-    }, [model, offsetX, offsetY, theme, blockSize, contrastScheme]);
+    }, [
+        model,
+        offsetX,
+        offsetY,
+        theme,
+        blockSize,
+        highResScaleFactor,
+        contrastScheme,
+    ]);
     return (React.createElement("canvas", { ref: ref, onMouseMove: event => {
             if (!ref.current) {
                 return;

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

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

@@ -1,6 +1,6 @@
 import React, { useEffect, useRef } from 'react';
-import { observer } from 'mobx-react';
 import { autorun } from 'mobx';
+import { observer } from 'mobx-react';
 import { renderMouseover } from './renderMSAMouseover';
 const MSAMouseoverCanvas = observer(function ({ model, }) {
     const ref = useRef(null);

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

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

@@ -1,6 +1,5 @@
 import React from 'react';
 import { observer } from 'mobx-react';
-// locals
 import MSACanvas from './MSACanvas';
 import MSAMouseoverCanvas from './MSAMouseoverCanvas';
 const MSAPanel = observer(function ({ model }) {

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

@@ -1 +1 @@
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+{"version":3,"file":"MSAPanel.js","sourceRoot":"","sources":["../../../src/components/msa/MSAPanel.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAErC,OAAO,SAAS,MAAM,aAAa,CAAA;AACnC,OAAO,kBAAkB,MAAM,sBAAsB,CAAA;AAKrD,MAAM,QAAQ,GAAG,QAAQ,CAAC,UAAU,EAAE,KAAK,EAA2B;IACpE,OAAO,CACL,6BAAK,KAAK,EAAE,EAAE,QAAQ,EAAE,UAAU,EAAE;QAClC,oBAAC,SAAS,IAAC,KAAK,EAAE,KAAK,GAAI;QAC3B,oBAAC,kBAAkB,IAAC,KAAK,EAAE,KAAK,GAAI,CAChC,CACP,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,QAAQ,CAAA"}

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

@@ -1 +1 @@
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package/dist/components/msa/renderMSABlock.d.ts

@@ -1,5 +1,5 @@
-import type { Theme } from '@mui/material';
 import type { MsaViewModel } from '../../model';
+import type { Theme } from '@mui/material';
 export declare function renderMSABlock({ model, offsetX, offsetY, contrastScheme, ctx, theme, highResScaleFactorOverride, blockSizeXOverride, blockSizeYOverride, }: {
     offsetX: number;
     offsetY: number;

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

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

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

package/dist/components/tree/TreeCanvas.js

@@ -1,5 +1,4 @@
-import React from 'react';
-import { useEffect, useRef, useState } from 'react';
+import React, { useEffect, useRef, useState } from 'react';
 import { observer } from 'mobx-react';
 import TreeCanvasBlock from './TreeCanvasBlock';
 import { padding } from './renderTreeCanvas';

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

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

@@ -1,15 +1,14 @@
-import React from 'react';
-import { useCallback, useEffect, useRef, useState } from 'react';
+import React, { useCallback, useEffect, useRef, useState } from 'react';
+import { useTheme } from '@mui/material';
 import { autorun } from 'mobx';
 import { observer } from 'mobx-react';
-import { useTheme } from '@mui/material';
 import RBush from 'rbush';
-import TreeNodeMenu from './TreeNodeMenu';
 import TreeBranchMenu from './TreeBranchMenu';
+import TreeNodeMenu from './TreeNodeMenu';
 import { padding, renderTreeCanvas } from './renderTreeCanvas';
 const TreeCanvasBlock = observer(function ({ model, offsetY, }) {
     const theme = useTheme();
-    const ref = useRef();
+    const ref = useRef(null);
     const clickMap = useRef(new RBush());
     const mouseoverRef = useRef(null);
     const [branchMenu, setBranchMenu] = useState();
@@ -33,6 +32,8 @@ const TreeCanvasBlock = observer(function ({ model, offsetY, }) {
             return;
         }
         return autorun(() => {
+            ctx.resetTransform();
+            ctx.clearRect(0, 0, (treeAreaWidth + padding) * highResScaleFactor, blockSize * highResScaleFactor);
             renderTreeCanvas({
                 ctx,
                 model,
@@ -41,7 +42,7 @@ const TreeCanvasBlock = observer(function ({ model, offsetY, }) {
                 theme,
             });
         });
-    }, [model, offsetY, theme]);
+    }, [model, blockSize, highResScaleFactor, treeAreaWidth, offsetY, theme]);
     useEffect(() => {
         const ctx = mouseoverRef.current?.getContext('2d');
         if (!ctx) {