react-msaview 2.1.5 → 3.0.1

package/dist/DialogQueue.d.ts

@@ -0,0 +1,25 @@
+import { DialogComponentType } from '@jbrowse/core/util';
+/**
+ * #stateModel DialogQueueSessionMixin
+ */
+export declare function DialogQueueSessionMixin(): import("mobx-state-tree").IModelType<{}, {
+    queueOfDialogs: [DialogComponentType, any][];
+} & {
+    /**
+     * #getter
+     */
+    readonly DialogComponent: DialogComponentType;
+    /**
+     * #getter
+     */
+    readonly DialogProps: any;
+} & {
+    /**
+     * #action
+     */
+    removeActiveDialog(): void;
+    /**
+     * #action
+     */
+    queueDialog(cb: (doneCallback: () => void) => [DialogComponentType, unknown]): void;
+}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;

package/dist/DialogQueue.js

@@ -0,0 +1,46 @@
+import { types } from 'mobx-state-tree';
+/**
+ * #stateModel DialogQueueSessionMixin
+ */
+export function DialogQueueSessionMixin() {
+    return types
+        .model('DialogQueueSessionMixin', {})
+        .volatile(() => ({
+        // eslint-disable-next-line @typescript-eslint/no-explicit-any
+        queueOfDialogs: [],
+    }))
+        .views(self => ({
+        /**
+         * #getter
+         */
+        get DialogComponent() {
+            var _a;
+            return (_a = self.queueOfDialogs[0]) === null || _a === void 0 ? void 0 : _a[0];
+        },
+        /**
+         * #getter
+         */
+        get DialogProps() {
+            var _a;
+            return (_a = self.queueOfDialogs[0]) === null || _a === void 0 ? void 0 : _a[1];
+        },
+    }))
+        .actions(self => ({
+        /**
+         * #action
+         */
+        removeActiveDialog() {
+            self.queueOfDialogs = self.queueOfDialogs.slice(1);
+        },
+        /**
+         * #action
+         */
+        queueDialog(cb) {
+            const [component, props] = cb(() => {
+                this.removeActiveDialog();
+            });
+            self.queueOfDialogs = [...self.queueOfDialogs, [component, props]];
+        },
+    }));
+}
+//# sourceMappingURL=DialogQueue.js.map

package/dist/DialogQueue.js.map

@@ -0,0 +1 @@
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package/dist/UniprotTrack.js.map

@@ -1 +1 @@
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package/dist/colorSchemes.js.map

@@ -1 +1 @@
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package/dist/components/BoxTrackBlock.js

@@ -3,7 +3,7 @@ import { observer } from 'mobx-react';
 import { getSnapshot, isStateTreeNode } from 'mobx-state-tree';
 import Layout from '../layout';
 const BoxTrackBlock = observer(function ({ track, model, offsetX, }) {
-    const { blockSize, colWidth, blanks, rowHeight, highResScaleFactor, scrollX, } = model;
+    const { blockSize, colWidth, blanks, rowHeight, highResScaleFactor, fontSize, scrollX, } = model;
     const { height, features, associatedRowName } = track.model;
     const feats = isStateTreeNode(features)
         ? // @ts-expect-error
@@ -44,7 +44,7 @@ const BoxTrackBlock = observer(function ({ track, model, offsetX, }) {
         ctx.clearRect(0, 0, blockSize, height);
         ctx.translate(-offsetX, 0);
         ctx.textAlign = 'center';
-        ctx.font = ctx.font.replace(/\d+px/, `${Math.max(8, rowHeight - 8)}px`);
+        ctx.font = ctx.font.replace(/\d+px/, `${fontSize}px`);
         const xStart = Math.max(0, Math.floor(offsetX / colWidth));
         ctx.fillStyle = 'goldenrod';
         layout.rectangles.forEach(value => {
@@ -57,6 +57,7 @@ const BoxTrackBlock = observer(function ({ track, model, offsetX, }) {
         });
     }, [
         associatedRowName,
+        fontSize,
         blockSize,
         colWidth,
         layout.rectangles,

package/dist/components/BoxTrackBlock.js.map

@@ -1 +1 @@
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+{"version":3,"file":"BoxTrackBlock.js","sourceRoot":"","sources":["../../src/components/BoxTrackBlock.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,MAAM,EAAE,OAAO,EAAE,SAAS,EAAE,MAAM,OAAO,CAAA;AACzD,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,EAAE,WAAW,EAAE,eAAe,EAAE,MAAM,iBAAiB,CAAA;AAI9D,OAAO,MAAM,MAAM,WAAW,CAAA;AAO9B,MAAM,aAAa,GAAG,QAAQ,CAAC,UAAU,EACvC,KAAK,EACL,KAAK,EACL,OAAO,GAKR;IACC,MAAM,EACJ,SAAS,EACT,QAAQ,EACR,MAAM,EACN,SAAS,EACT,kBAAkB,EAClB,QAAQ,EACR,OAAO,GACR,GAAG,KAAK,CAAA;IACT,MAAM,EAAE,MAAM,EAAE,QAAQ,EAAE,iBAAiB,EAAE,GAAG,KAAK,CAAC,KAAK,CAAA;IAE3D,MAAM,KAAK,GAAW,eAAe,CAAC,QAAQ,CAAC;QAC7C,CAAC,CAAC,mBAAmB;YACnB,WAAW,CAAC,QAAQ,CAAC;QACvB,CAAC,CAAC,QAAQ,CAAA;IAEZ,MAAM,MAAM,GAAG,OAAO,CAAC,GAAG,EAAE;QAC1B,MAAM,IAAI,GAAG,IAAI,MAAM,EAAE,CAAA;QAEzB,KAAK,aAAL,KAAK,uBAAL,KAAK,CAAE,OAAO,CAAC,CAAC,OAAO,EAAE,KAAK,EAAE,EAAE;YAChC,MAAM,EAAE,KAAK,EAAE,GAAG,EAAE,GAAG,OAAO,CAAA;YAC9B,IAAI,iBAAiB,EAAE,CAAC;gBACtB,MAAM,CAAC,GAAG,KAAK,CAAC,iBAAiB,CAAC,iBAAiB,EAAE,KAAK,GAAG,CAAC,CAAC,CAAA;gBAC/D,MAAM,CAAC,GAAG,KAAK,CAAC,iBAAiB,CAAC,iBAAiB,EAAE,GAAG,CAAC,CAAA;gBACzD,IAAI,CAAC,OAAO,CAAC,GAAG,KAAK,EAAE,EAAE,CAAC,EAAE,CAAC,EAAE,SAAS,EAAE,OAAO,CAAC,CAAA;YACpD,CAAC;iBAAM,CAAC;gBACN,MAAM,CAAC,GAAG,KAAK,CAAC,YAAY,CAAC,KAAK,GAAG,CAAC,CAAC,CAAA;gBACvC,MAAM,CAAC,GAAG,KAAK,CAAC,YAAY,CAAC,GAAG,CAAC,CAAA;gBACjC,IAAI,CAAC,OAAO,CAAC,GAAG,KAAK,EAAE,EAAE,CAAC,EAAE,CAAC,EAAE,SAAS,EAAE,OAAO,CAAC,CAAA;YACpD,CAAC;QACH,CAAC,CAAC,CAAA;QACF,OAAO,IAAI,CAAA;QAEX,yCAAyC;QACzC,uDAAuD;IACzD,CAAC,EAAE,CAAC,SAAS,EAAE,KAAK,EAAE,iBAAiB,EAAE,KAAK,EAAE,MAAM,CAAC,CAAC,CAAA;IAExD,MAAM,GAAG,GAAG,MAAM,CAAoB,IAAI,CAAC,CAAA;IAC3C,MAAM,QAAQ,GAAG,MAAM,CAAoB,IAAI,CAAC,CAAA;IAChD,MAAM,YAAY,GAAG,MAAM,CAAoB,IAAI,CAAC,CAAA;IAEpD,SAAS,CAAC,GAAG,EAAE;QACb,IAAI,CAAC,GAAG,CAAC,OAAO,EAAE,CAAC;YACjB,OAAM;QACR,CAAC;QAED,MAAM,GAAG,GAAG,GAAG,CAAC,OAAO,CAAC,UAAU,CAAC,IAAI,CAAC,CAAA;QACxC,IAAI,CAAC,GAAG,EAAE,CAAC;YACT,OAAM;QACR,CAAC;QAED,GAAG,CAAC,cAAc,EAAE,CAAA;QACpB,GAAG,CAAC,KAAK,CAAC,kBAAkB,EAAE,kBAAkB,CAAC,CAAA;QACjD,GAAG,CAAC,SAAS,CAAC,CAAC,EAAE,CAAC,EAAE,SAAS,EAAE,MAAM,CAAC,CAAA;QACtC,GAAG,CAAC,SAAS,CAAC,CAAC,OAAO,EAAE,CAAC,CAAC,CAAA;QAC1B,GAAG,CAAC,SAAS,GAAG,QAAQ,CAAA;QACxB,GAAG,CAAC,IAAI,GAAG,GAAG,CAAC,IAAI,CAAC,OAAO,CAAC,OAAO,EAAE,GAAG,QAAQ,IAAI,CAAC,CAAA;QAErD,MAAM,MAAM,GAAG,IAAI,CAAC,GAAG,CAAC,CAAC,EAAE,IAAI,CAAC,KAAK,CAAC,OAAO,GAAG,QAAQ,CAAC,CAAC,CAAA;QAC1D,GAAG,CAAC,SAAS,GAAG,WAAW,CAAA;QAC3B,MAAM,CAAC,UAAU,CAAC,OAAO,CAAC,KAAK,CAAC,EAAE;YAChC,MAAM,EAAE,IAAI,EAAE,IAAI,EAAE,IAAI,EAAE,IAAI,EAAE,GAAG,KAAK,CAAA;YAExC,MAAM,EAAE,GAAG,CAAC,IAAI,GAAG,MAAM,CAAC,GAAG,QAAQ,GAAG,OAAO,GAAG,CAAC,OAAO,GAAG,QAAQ,CAAC,CAAA;YACtE,MAAM,EAAE,GAAG,CAAC,IAAI,GAAG,MAAM,CAAC,GAAG,QAAQ,GAAG,OAAO,GAAG,CAAC,OAAO,GAAG,QAAQ,CAAC,CAAA;YAEtE,IAAI,EAAE,GAAG,EAAE,GAAG,CAAC,EAAE,CAAC;gBAChB,GAAG,CAAC,QAAQ,CAAC,EAAE,EAAE,IAAI,EAAE,EAAE,GAAG,EAAE,EAAE,CAAC,IAAI,GAAG,IAAI,CAAC,GAAG,CAAC,CAAC,CAAA;YACpD,CAAC;QACH,CAAC,CAAC,CAAA;IACJ,CAAC,EAAE;QACD,iBAAiB;QACjB,QAAQ;QACR,SAAS;QACT,QAAQ;QACR,MAAM,CAAC,UAAU;QACjB,KAAK;QACL,SAAS;QACT,MAAM;QACN,OAAO;QACP,kBAAkB;QAClB,QAAQ;QACR,MAAM;KACP,CAAC,CAAA;IAEF,SAAS,CAAC,GAAG,EAAE;;QACb,IAAI,CAAC,QAAQ,CAAC,OAAO,EAAE,CAAC;YACtB,OAAM;QACR,CAAC;QAED,MAAM,GAAG,GAAG,QAAQ,CAAC,OAAO,CAAC,UAAU,CAAC,IAAI,CAAC,CAAA;QAC7C,IAAI,CAAC,GAAG,EAAE,CAAC;YACT,OAAM;QACR,CAAC;QAED,0CAA0C;QAC1C,GAAG,CAAC,cAAc,EAAE,CAAA;QACpB,GAAG,CAAC,KAAK,CAAC,kBAAkB,EAAE,kBAAkB,CAAC,CAAA;QACjD,GAAG,CAAC,SAAS,CAAC,CAAC,EAAE,CAAC,EAAE,SAAS,EAAE,MAAM,CAAC,CAAA;QACtC,GAAG,CAAC,SAAS,CAAC,CAAC,OAAO,EAAE,CAAC,CAAC,CAAA;QAC1B,GAAG,CAAC,SAAS,GAAG,QAAQ,CAAA;QACxB,GAAG,CAAC,IAAI,GAAG,GAAG,CAAC,IAAI,CAAC,OAAO,CAAC,OAAO,EAAE,GAAG,IAAI,CAAC,GAAG,CAAC,CAAC,EAAE,SAAS,GAAG,CAAC,CAAC,IAAI,CAAC,CAAA;QAEvE,GAAG,CAAC,SAAS,GAAG,OAAO,CAAA;QACvB,GAAG,CAAC,SAAS,GAAG,MAAM,CAAA;QACtB,KAAK,MAAM,KAAK,IAAI,MAAM,CAAC,UAAU,CAAC,MAAM,EAAE,EAAE,CAAC;YAC/C,MAAM,EAAE,IAAI,EAAE,IAAI,EAAE,IAAI,EAAE,IAAI,EAAE,IAAI,EAAE,GAAG,KAAK,CAAA;YAE9C,MAAM,EAAE,GAAG,IAAI,GAAG,QAAQ,CAAA;YAC1B,MAAM,EAAE,GAAG,IAAI,GAAG,QAAQ,CAAA;YAC1B,8DAA8D;YAC9D,MAAM,OAAO,GAAG,IAAW,CAAA;YAE3B,IAAI,EAAE,GAAG,EAAE,GAAG,CAAC,EAAE,CAAC;gBAChB,MAAM,IAAI,GAAG,MAAA,MAAA,OAAO,CAAC,UAAU,0CAAE,IAAI,0CAAG,CAAC,CAAC,CAAA;gBAC1C,MAAM,IAAI,GAAG,MAAA,MAAA,OAAO,CAAC,UAAU,0CAAE,IAAI,0CAAG,CAAC,CAAC,CAAA;gBAC1C,MAAM,IAAI,GAAG,OAAO,CAAC,IAAI,CAAA;gBACzB,GAAG,CAAC,QAAQ,CACV,CAAC,IAAI,EAAE,IAAI,EAAE,IAAI,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,KAAK,CAAC,EAC/C,IAAI,CAAC,GAAG,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,OAAO,EAAE,EAAE,CAAC,EAAE,EAAE,CAAC,EACpC,IAAI,GAAG,CAAC,IAAI,GAAG,IAAI,CAAC,CACrB,CAAA;YACH,CAAC;QACH,CAAC;IACH,CAAC,EAAE;QACD,SAAS;QACT,QAAQ;QACR,OAAO;QACP,kBAAkB;QAClB,MAAM;QACN,MAAM,CAAC,UAAU;QACjB,OAAO;QACP,QAAQ;QACR,KAAK;QACL,SAAS;QACT,MAAM;KACP,CAAC,CAAA;IAEF,OAAO,CAAC,QAAQ,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CACxB;QACE,gCACE,GAAG,EAAE,GAAG,EACR,MAAM,EAAE,MAAM,GAAG,kBAAkB,EACnC,KAAK,EAAE,SAAS,GAAG,kBAAkB,EACrC,KAAK,EAAE;gBACL,QAAQ,EAAE,UAAU;gBACpB,IAAI,EAAE,OAAO,GAAG,OAAO;gBACvB,KAAK,EAAE,SAAS;gBAChB,MAAM;aACP,GACD;QACF,gCACE,GAAG,EAAE,QA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package/dist/components/Header.js

@@ -1,5 +1,5 @@
 import React, { Suspense, lazy, useState } from 'react';
-import { IconButton, Typography } from '@mui/material';
+import { IconButton } from '@mui/material';
 import { observer } from 'mobx-react';
 // icons
 import FolderOpen from '@mui/icons-material/FolderOpen';
@@ -7,24 +7,15 @@ import Settings from '@mui/icons-material/Settings';
 import Help from '@mui/icons-material/Help';
 import Assignment from '@mui/icons-material/Assignment';
 import List from '@mui/icons-material/List';
+// locals
 import ZoomControls from './ZoomControls';
 import MultiAlignmentSelector from './MultiAlignmentSelector';
-const SettingsDialog = lazy(() => import('./dialogs/SettingsDlg'));
-const AboutDialog = lazy(() => import('./dialogs/AboutDlg'));
-const MetadataDialog = lazy(() => import('./dialogs/MetadataDlg'));
-const TracklistDialog = lazy(() => import('./dialogs/TracklistDlg'));
-const InfoArea = observer(({ model }) => {
-    const { mouseOverRowName, mouseCol } = model;
-    return (React.createElement("div", null,
-        React.createElement(Typography, { display: "inline" },
-            "Row name: ",
-            mouseOverRowName),
-        React.createElement("span", { style: { marginLeft: 10 } }),
-        React.createElement(Typography, { display: "inline" },
-            "Position: ",
-            mouseCol)));
-});
-const Header = observer(({ model }) => {
+import HeaderInfoArea from './HeaderInfoArea';
+const SettingsDialog = lazy(() => import('./dialogs/SettingsDialog'));
+const AboutDialog = lazy(() => import('./dialogs/AboutDialog'));
+const MetadataDialog = lazy(() => import('./dialogs/MetadataDialog'));
+const TracklistDialog = lazy(() => import('./dialogs/TracklistDialog'));
+const Header = observer(function ({ model }) {
     const [settingsDialogViz, setSettingsDialogViz] = useState(false);
     const [aboutDialogViz, setAboutDialogViz] = useState(false);
     const [detailsDialogViz, setMetadataDialogViz] = useState(false);
@@ -33,11 +24,12 @@ const Header = observer(({ model }) => {
         React.createElement(IconButton, { onClick: async () => {
                 try {
                     model.setData({ tree: '', msa: '' });
-                    await model.setTreeFilehandle(undefined);
-                    await model.setMSAFilehandle(undefined);
+                    model.clearSelectedStructures();
                     model.setScrollY(0);
                     model.setScrollX(0);
                     model.setCurrentAlignment(0);
+                    await model.setTreeFilehandle(undefined);
+                    await model.setMSAFilehandle(undefined);
                 }
                 catch (e) {
                     console.error(e);
@@ -58,7 +50,7 @@ const Header = observer(({ model }) => {
             tracklistDialogViz ? (React.createElement(TracklistDialog, { model: model, onClose: () => setTracklistDialogViz(false) })) : null),
         React.createElement(MultiAlignmentSelector, { model: model }),
         React.createElement(ZoomControls, { model: model }),
-        React.createElement(InfoArea, { model: model }),
+        React.createElement(HeaderInfoArea, { model: model }),
         React.createElement(Spacer, null),
         React.createElement(IconButton, { onClick: () => setAboutDialogViz(true) },
             React.createElement(Help, null))));

package/dist/components/Header.js.map

@@ -1 +1 @@
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+{"version":3,"file":"Header.js","sourceRoot":"","sources":["../../src/components/Header.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,QAAQ,EAAE,IAAI,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AACvD,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAC1C,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAKrC,QAAQ;AACR,OAAO,UAAU,MAAM,gCAAgC,CAAA;AACvD,OAAO,QAAQ,MAAM,8BAA8B,CAAA;AACnD,OAAO,IAAI,MAAM,0BAA0B,CAAA;AAC3C,OAAO,UAAU,MAAM,gCAAgC,CAAA;AACvD,OAAO,IAAI,MAAM,0BAA0B,CAAA;AAE3C,SAAS;AACT,OAAO,YAAY,MAAM,gBAAgB,CAAA;AACzC,OAAO,sBAAsB,MAAM,0BAA0B,CAAA;AAC7D,OAAO,cAAc,MAAM,kBAAkB,CAAA;AAE7C,MAAM,cAAc,GAAG,IAAI,CAAC,GAAG,EAAE,CAAC,MAAM,CAAC,0BAA0B,CAAC,CAAC,CAAA;AACrE,MAAM,WAAW,GAAG,IAAI,CAAC,GAAG,EAAE,CAAC,MAAM,CAAC,uBAAuB,CAAC,CAAC,CAAA;AAC/D,MAAM,cAAc,GAAG,IAAI,CAAC,GAAG,EAAE,CAAC,MAAM,CAAC,0BAA0B,CAAC,CAAC,CAAA;AACrE,MAAM,eAAe,GAAG,IAAI,CAAC,GAAG,EAAE,CAAC,MAAM,CAAC,2BAA2B,CAAC,CAAC,CAAA;AAEvE,MAAM,MAAM,GAAG,QAAQ,CAAC,UAAU,EAAE,KAAK,EAA2B;IAClE,MAAM,CAAC,iBAAiB,EAAE,oBAAoB,CAAC,GAAG,QAAQ,CAAC,KAAK,CAAC,CAAA;IACjE,MAAM,CAAC,cAAc,EAAE,iBAAiB,CAAC,GAAG,QAAQ,CAAC,KAAK,CAAC,CAAA;IAC3D,MAAM,CAAC,gBAAgB,EAAE,oBAAoB,CAAC,GAAG,QAAQ,CAAC,KAAK,CAAC,CAAA;IAChE,MAAM,CAAC,kBAAkB,EAAE,qBAAqB,CAAC,GAAG,QAAQ,CAAC,KAAK,CAAC,CAAA;IAEnE,OAAO,CACL,6BAAK,KAAK,EAAE,EAAE,OAAO,EAAE,MAAM,EAAE;QAC7B,oBAAC,UAAU,IACT,OAAO,EAAE,KAAK,IAAI,EAAE;gBAClB,IAAI,CAAC;oBACH,KAAK,CAAC,OAAO,CAAC,EAAE,IAAI,EAAE,EAAE,EAAE,GAAG,EAAE,EAAE,EAAE,CAAC,CAAA;oBACpC,KAAK,CAAC,uBAAuB,EAAE,CAAA;oBAC/B,KAAK,CAAC,UAAU,CAAC,CAAC,CAAC,CAAA;oBACnB,KAAK,CAAC,UAAU,CAAC,CAAC,CAAC,CAAA;oBACnB,KAAK,CAAC,mBAAmB,CAAC,CAAC,CAAC,CAAA;oBAC5B,MAAM,KAAK,CAAC,iBAAiB,CAAC,SAAS,CAAC,CAAA;oBACxC,MAAM,KAAK,CAAC,gBAAgB,CAAC,SAAS,CAAC,CAAA;gBACzC,CAAC;gBAAC,OAAO,CAAC,EAAE,CAAC;oBACX,OAAO,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;oBAChB,KAAK,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAA;gBACnB,CAAC;YACH,CAAC;YAED,oBAAC,UAAU,OAAG,CACH;QACb,oBAAC,UAAU,IAAC,OAAO,EAAE,GAAG,EAAE,CAAC,oBAAoB,CAAC,IAAI,CAAC;YACnD,oBAAC,QAAQ,OAAG,CACD;QACb,oBAAC,UAAU,IAAC,OAAO,EAAE,GAAG,EAAE,CAAC,oBAAoB,CAAC,IAAI,CAAC;YACnD,oBAAC,UAAU,OAAG,CACH;QACb,oBAAC,UAAU,IAAC,OAAO,EAAE,GAAG,EAAE,CAAC,qBAAqB,CAAC,IAAI,CAAC;YACpD,oBAAC,IAAI,OAAG,CACG;QACb,oBAAC,QAAQ,IAAC,QAAQ,EAAE,IAAI;YACrB,iBAAiB,CAAC,CAAC,CAAC,CACnB,oBAAC,cAAc,IACb,KAAK,EAAE,KAAK,EACZ,OAAO,EAAE,GAAG,EAAE,CAAC,oBAAoB,CAAC,KAAK,CAAC,GAC1C,CACH,CAAC,CAAC,CAAC,IAAI;YACP,cAAc,CAAC,CAAC,CAAC,CAChB,oBAAC,WAAW,IAAC,OAAO,EAAE,GAAG,EAAE,CAAC,iBAAiB,CAAC,KAAK,CAAC,GAAI,CACzD,CAAC,CAAC,CAAC,IAAI;YACP,gBAAgB,CAAC,CAAC,CAAC,CAClB,oBAAC,cAAc,IACb,KAAK,EAAE,KAAK,EACZ,OAAO,EAAE,GAAG,EAAE,CAAC,oBAAoB,CAAC,KAAK,CAAC,GAC1C,CACH,CAAC,CAAC,CAAC,IAAI;YAEP,kBAAkB,CAAC,CAAC,CAAC,CACpB,oBAAC,eAAe,IACd,KAAK,EAAE,KAAK,EACZ,OAAO,EAAE,GAAG,EAAE,CAAC,qBAAqB,CAAC,KAAK,CAAC,GAC3C,CACH,CAAC,CAAC,CAAC,IAAI,CACC;QACX,oBAAC,sBAAsB,IAAC,KAAK,EAAE,KAAK,GAAI;QACxC,oBAAC,YAAY,IAAC,KAAK,EAAE,KAAK,GAAI;QAC9B,oBAAC,cAAc,IAAC,KAAK,EAAE,KAAK,GAAI;QAChC,oBAAC,MAAM,OAAG;QACV,oBAAC,UAAU,IAAC,OAAO,EAAE,GAAG,EAAE,CAAC,iBAAiB,CAAC,IAAI,CAAC;YAChD,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/HeaderInfoArea.d.ts

@@ -0,0 +1,6 @@
+import React from 'react';
+import { MsaViewModel } from '../model';
+declare const HeaderInfoArea: ({ model }: {
+    model: MsaViewModel;
+}) => React.JSX.Element;
+export default HeaderInfoArea;

package/dist/components/HeaderInfoArea.js

@@ -0,0 +1,12 @@
+import React from 'react';
+import { Typography } from '@mui/material';
+import { observer } from 'mobx-react';
+const HeaderInfoArea = observer(({ model }) => {
+    const { mouseOverRowName, mouseCol } = model;
+    return (React.createElement("div", null, mouseOverRowName && mouseCol !== undefined ? (React.createElement(Typography, null,
+        mouseOverRowName,
+        ":",
+        model.relativePxToBp(mouseOverRowName, mouseCol))) : null));
+});
+export default HeaderInfoArea;
+//# sourceMappingURL=HeaderInfoArea.js.map

package/dist/components/HeaderInfoArea.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"HeaderInfoArea.js","sourceRoot":"","sources":["../../src/components/HeaderInfoArea.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AACzB,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAC1C,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAKrC,MAAM,cAAc,GAAG,QAAQ,CAAC,CAAC,EAAE,KAAK,EAA2B,EAAE,EAAE;IACrE,MAAM,EAAE,gBAAgB,EAAE,QAAQ,EAAE,GAAG,KAAK,CAAA;IAC5C,OAAO,CACL,iCACG,gBAAgB,IAAI,QAAQ,KAAK,SAAS,CAAC,CAAC,CAAC,CAC5C,oBAAC,UAAU;QACR,gBAAgB;;QAAG,KAAK,CAAC,cAAc,CAAC,gBAAgB,EAAE,QAAQ,CAAC,CACzD,CACd,CAAC,CAAC,CAAC,IAAI,CACJ,CACP,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,cAAc,CAAA"}

package/dist/components/ImportForm/ImportFormExamples.d.ts

@@ -0,0 +1,6 @@
+import React from 'react';
+import { MsaViewModel } from '../../model';
+declare const ImportFormExamples: ({ model, }: {
+    model: MsaViewModel;
+}) => React.JSX.Element;
+export default ImportFormExamples;

package/dist/components/ImportForm/ImportFormExamples.js

@@ -0,0 +1,50 @@
+import React from 'react';
+import { Typography, Link } from '@mui/material';
+import { observer } from 'mobx-react';
+import { smallTree, smallMSA, smallMSAOnly } from './data/seq2';
+import { load } from './util';
+const ListItem = ({ onClick, model, children, }) => (React.createElement("li", null,
+    React.createElement(Link, { onClick: event => {
+            model.setError(undefined);
+            event.preventDefault();
+            onClick();
+        }, href: "#" },
+        React.createElement(Typography, { display: "inline" }, children))));
+const ImportFormExamples = observer(function ({ model, }) {
+    return (React.createElement("ul", null,
+        React.createElement(ListItem, { model: model, onClick: () => load(model, undefined, {
+                uri: 'https://jbrowse.org/genomes/newick_trees/sarscov2phylo.pub.ft.nh',
+                locationType: 'UriLocation',
+            }) }, "230k COVID-19 samples (tree only)"),
+        React.createElement(ListItem, { model: model, onClick: () => {
+                model.setData({ msa: smallMSA, tree: smallTree });
+            } }, "Small protein MSA+tree"),
+        React.createElement(ListItem, { model: model, onClick: () => {
+                model.setData({ msa: smallMSAOnly });
+            } }, "Small MSA only"),
+        React.createElement(ListItem, { model: model, onClick: () => load(model, {
+                uri: 'https://jbrowse.org/genomes/multiple_sequence_alignments/pfam-cov2.stock',
+                locationType: 'UriLocation',
+            }) }, "PFAM SARS-CoV2 multi-stockholm"),
+        React.createElement(ListItem, { model: model, onClick: () => load(model, {
+                uri: 'https://jbrowse.org/genomes/multiple_sequence_alignments/Lysine.stock',
+                locationType: 'UriLocation',
+            }) }, "Lysine stockholm file"),
+        React.createElement(ListItem, { model: model, onClick: () => load(model, {
+                uri: 'https://jbrowse.org/genomes/multiple_sequence_alignments/PF01601_full.txt',
+                locationType: 'UriLocation',
+            }) }, "PF01601 stockholm file (SARS-CoV2 spike protein)"),
+        React.createElement(ListItem, { model: model, onClick: () => load(model, {
+                uri: 'https://jbrowse.org/genomes/multiple_sequence_alignments/europe_covid.fa',
+                locationType: 'UriLocation',
+            }) }, "Europe COVID full genomes (LR883044.1 and 199 other sequences)"),
+        React.createElement(ListItem, { model: model, onClick: () => load(model, {
+                uri: '/rhv_test-only.aligned_with_mafft_auto.fa',
+                locationType: 'UriLocation',
+            }, {
+                uri: 'https://jbrowse.org/genomes/multiple_sequence_alignments/rhv_test-only.aligned_with_mafft_auto.nh',
+                locationType: 'UriLocation',
+            }) }, "MAFFT+VeryFastTree(17.9k samples)")));
+});
+export default ImportFormExamples;
+//# sourceMappingURL=ImportFormExamples.js.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"ImportFormExamples.js","sourceRoot":"","sources":["../../../src/components/ImportForm/ImportFormExamples.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AACzB,OAAO,EAAE,UAAU,EAAE,IAAI,EAAE,MAAM,eAAe,CAAA;AAChD,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAIrC,OAAO,EAAE,SAAS,EAAE,QAAQ,EAAE,YAAY,EAAE,MAAM,aAAa,CAAA;AAC/D,OAAO,EAAE,IAAI,EAAE,MAAM,QAAQ,CAAA;AAE7B,MAAM,QAAQ,GAAG,CAAC,EAChB,OAAO,EACP,KAAK,EACL,QAAQ,GAKT,EAAE,EAAE,CAAC,CACJ;IACE,oBAAC,IAAI,IACH,OAAO,EAAE,KAAK,CAAC,EAAE;YACf,KAAK,CAAC,QAAQ,CAAC,SAAS,CAAC,CAAA;YACzB,KAAK,CAAC,cAAc,EAAE,CAAA;YACtB,OAAO,EAAE,CAAA;QACX,CAAC,EACD,IAAI,EAAC,GAAG;QAER,oBAAC,UAAU,IAAC,OAAO,EAAC,QAAQ,IAAE,QAAQ,CAAc,CAC/C,CACJ,CACN,CAAA;AAED,MAAM,kBAAkB,GAAG,QAAQ,CAAC,UAAU,EAC5C,KAAK,GAGN;IACC,OAAO,CACL;QACE,oBAAC,QAAQ,IACP,KAAK,EAAE,KAAK,EACZ,OAAO,EAAE,GAAG,EAAE,CACZ,IAAI,CAAC,KAAK,EAAE,SAAS,EAAE;gBACrB,GAAG,EAAE,kEAAkE;gBACvE,YAAY,EAAE,aAAa;aAC5B,CAAC,wCAIK;QACX,oBAAC,QAAQ,IACP,KAAK,EAAE,KAAK,EACZ,OAAO,EAAE,GAAG,EAAE;gBACZ,KAAK,CAAC,OAAO,CAAC,EAAE,GAAG,EAAE,QAAQ,EAAE,IAAI,EAAE,SAAS,EAAE,CAAC,CAAA;YACnD,CAAC,6BAGQ;QACX,oBAAC,QAAQ,IACP,KAAK,EAAE,KAAK,EACZ,OAAO,EAAE,GAAG,EAAE;gBACZ,KAAK,CAAC,OAAO,CAAC,EAAE,GAAG,EAAE,YAAY,EAAE,CAAC,CAAA;YACtC,CAAC,qBAGQ;QACX,oBAAC,QAAQ,IACP,KAAK,EAAE,KAAK,EACZ,OAAO,EAAE,GAAG,EAAE,CACZ,IAAI,CAAC,KAAK,EAAE;gBACV,GAAG,EAAE,0EAA0E;gBAC/E,YAAY,EAAE,aAAa;aAC5B,CAAC,qCAIK;QACX,oBAAC,QAAQ,IACP,KAAK,EAAE,KAAK,EACZ,OAAO,EAAE,GAAG,EAAE,CACZ,IAAI,CAAC,KAAK,EAAE;gBACV,GAAG,EAAE,uEAAuE;gBAC5E,YAAY,EAAE,aAAa;aAC5B,CAAC,4BAIK;QACX,oBAAC,QAAQ,IACP,KAAK,EAAE,KAAK,EACZ,OAAO,EAAE,GAAG,EAAE,CACZ,IAAI,CAAC,KAAK,EAAE;gBACV,GAAG,EAAE,2EAA2E;gBAChF,YAAY,EAAE,aAAa;aAC5B,CAAC,uDAIK;QACX,oBAAC,QAAQ,IACP,KAAK,EAAE,KAAK,EACZ,OAAO,EAAE,GAAG,EAAE,CACZ,IAAI,CAAC,KAAK,EAAE;gBACV,GAAG,EAAE,0EAA0E;gBAC/E,YAAY,EAAE,aAAa;aAC5B,CAAC,qEAIK;QACX,oBAAC,QAAQ,IACP,KAAK,EAAE,KAAK,EACZ,OAAO,EAAE,GAAG,EAAE,CACZ,IAAI,CACF,KAAK,EACL;gBACE,GAAG,EAAE,2CAA2C;gBAChD,YAAY,EAAE,aAAa;aAC5B,EACD;gBACE,GAAG,EAAE,mGAAmG;gBACxG,YAAY,EAAE,aAAa;aAC5B,CACF,wCAIM,CACR,CACN,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,kBAAkB,CAAA"}

package/dist/components/ImportForm/data/seq2.js.map

@@ -0,0 +1 @@
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package/dist/components/{ImportForm.d.ts → ImportForm/index.d.ts}

@@ -1,5 +1,5 @@
 import React from 'react';
-import { MsaViewModel } from '../model';
+import { MsaViewModel } from '../../model';
 declare const _default: ({ model }: {
     model: MsaViewModel;
 }) => React.JSX.Element;

package/dist/components/ImportForm/index.js

@@ -0,0 +1,31 @@
+import React, { useState } from 'react';
+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';
+export default observer(({ 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,
+            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(Button, { onClick: () => load(model, msaFile, treeFile), variant: "contained", color: "primary", disabled: !msaFile && !treeFile }, "Open")),
+            React.createElement(Grid, { item: true },
+                React.createElement(Typography, null, "Examples"),
+                React.createElement(ImportFormExamples, { model: model })))));
+});
+//# sourceMappingURL=index.js.map

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

@@ -0,0 +1 @@
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package/dist/components/ImportForm/util.d.ts

@@ -0,0 +1,3 @@
+import { FileLocation } from '@jbrowse/core/util';
+import { MsaViewModel } from '../../model';
+export declare function load(model: MsaViewModel, msaFile?: FileLocation, treeFile?: FileLocation): Promise<void>;

package/dist/components/ImportForm/util.js

@@ -0,0 +1,15 @@
+export async function load(model, msaFile, treeFile) {
+    model.setError(undefined);
+    try {
+        if (msaFile) {
+            await model.setMSAFilehandle(msaFile);
+        }
+        if (treeFile) {
+            await model.setTreeFilehandle(treeFile);
+        }
+    }
+    catch (e) {
+        model.setError(e);
+    }
+}
+//# sourceMappingURL=util.js.map

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

@@ -0,0 +1 @@
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package/dist/components/MSAPanel/Loading.d.ts

@@ -0,0 +1,2 @@
+import React from 'react';
+export default function Loading(): React.JSX.Element;

package/dist/components/MSAPanel/Loading.js

@@ -0,0 +1,12 @@
+import { CircularProgress, Typography } from '@mui/material';
+import React from 'react';
+export default function Loading() {
+    return (React.createElement("div", { style: {
+            position: 'absolute',
+            left: '50%',
+            top: '50%',
+        } },
+        React.createElement(CircularProgress, null),
+        React.createElement(Typography, null, "Loading...")));
+}
+//# sourceMappingURL=Loading.js.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"Loading.js","sourceRoot":"","sources":["../../../src/components/MSAPanel/Loading.tsx"],"names":[],"mappings":"AAAA,OAAO,EAAE,gBAAgB,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAC5D,OAAO,KAAK,MAAM,OAAO,CAAA;AACzB,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/{MSABlock.d.ts → MSAPanel/MSABlock.d.ts}

@@ -1,5 +1,5 @@
 import React from 'react';
-import { MsaViewModel } from '../model';
+import { MsaViewModel } from '../../model';
 declare const MSABlock: ({ model, offsetX, offsetY, }: {
     model: MsaViewModel;
     offsetX: number;

package/dist/components/MSAPanel/MSABlock.js

@@ -0,0 +1,46 @@
+import React, { useEffect, useRef, useMemo } from 'react';
+import { autorun } from 'mobx';
+import { useTheme } from '@mui/material';
+import { observer } from 'mobx-react';
+// locals
+import { renderBlock } from './renderMSABlock';
+import { colorContrast } from '../../util';
+const MSABlock = observer(function ({ model, offsetX, offsetY, }) {
+    const { colWidth, rowHeight, scrollY, scrollX, colorScheme, blockSize, highResScaleFactor, } = model;
+    const theme = useTheme();
+    const contrastScheme = useMemo(() => colorContrast(colorScheme, theme), [colorScheme, theme]);
+    const ref = useRef(null);
+    useEffect(() => {
+        var _a;
+        const ctx = (_a = ref.current) === null || _a === void 0 ? void 0 : _a.getContext('2d');
+        if (!ctx) {
+            return;
+        }
+        return autorun(() => {
+            renderBlock({
+                ctx,
+                offsetX,
+                offsetY,
+                contrastScheme,
+                model,
+            });
+        });
+    }, [model, offsetX, offsetY, 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;
+            model.setMousePos(Math.floor(mouseX / colWidth) + 1, Math.floor(mouseY / rowHeight));
+        }, onMouseLeave: () => model.setMousePos(), width: blockSize * highResScaleFactor, height: blockSize * highResScaleFactor, style: {
+            position: 'absolute',
+            top: scrollY + offsetY,
+            left: scrollX + offsetX,
+            width: blockSize,
+            height: blockSize,
+        } }));
+});
+export default MSABlock;
+//# sourceMappingURL=MSABlock.js.map

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

@@ -0,0 +1 @@
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package/dist/components/{MSACanvas.d.ts → MSAPanel/MSACanvas.d.ts}

@@ -1,5 +1,5 @@
 import React from 'react';
-import { MsaViewModel } from '../model';
+import { MsaViewModel } from '../../model';
 declare const MSACanvas: ({ model }: {
     model: MsaViewModel;
 }) => React.JSX.Element;

package/dist/components/{MSACanvas.js → MSAPanel/MSACanvas.js}

@@ -1,8 +1,8 @@
 import React, { useEffect, useState, useRef } from 'react';
-import { Typography, CircularProgress } from '@mui/material';
 import { observer } from 'mobx-react';
 import normalizeWheel from 'normalize-wheel';
 import MSABlock from './MSABlock';
+import Loading from './Loading';
 const MSACanvas = observer(function ({ model }) {
     const { MSA, msaFilehandle, height, msaAreaWidth, blocks2d } = model;
     const ref = useRef(null);
@@ -101,9 +101,7 @@ const MSACanvas = observer(function ({ model }) {
             height,
             width: msaAreaWidth,
             overflow: 'hidden',
-        } }, !MSA && !msaFilehandle ? null : !MSA ? (React.createElement("div", { style: { position: 'absolute', left: '50%', top: '50%' } },
-        React.createElement(CircularProgress, null),
-        React.createElement(Typography, null, "Loading..."))) : (blocks2d.map(([bx, by]) => (React.createElement(MSABlock, { key: `${bx}_${by}`, model: model, offsetX: bx, offsetY: by }))))));
+        } }, !MSA && !msaFilehandle ? null : !MSA ? (React.createElement(Loading, null)) : (blocks2d.map(([bx, by]) => (React.createElement(MSABlock, { key: `${bx}_${by}`, model: model, offsetX: bx, offsetY: by }))))));
 });
 export default MSACanvas;
 //# sourceMappingURL=MSACanvas.js.map

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

@@ -0,0 +1 @@
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package/dist/components/{MSAMouseoverCanvas.d.ts → MSAPanel/MSAMouseoverCanvas.d.ts}

@@ -1,5 +1,5 @@
 import React from 'react';
-import { MsaViewModel } from '../model';
+import { MsaViewModel } from '../../model';
 declare const MSAMouseoverCanvas: ({ model, }: {
     model: MsaViewModel;
 }) => React.JSX.Element;

package/dist/components/MSAPanel/MSAMouseoverCanvas.js

@@ -0,0 +1,29 @@
+import React, { useEffect, useRef } from 'react';
+import { observer } from 'mobx-react';
+import { autorun } from 'mobx';
+import { renderMouseover } from './renderMSAMouseover';
+const MSAMouseoverCanvas = observer(function ({ model, }) {
+    const ref = useRef(null);
+    const { height, width } = model;
+    useEffect(() => {
+        var _a;
+        const ctx = (_a = ref.current) === null || _a === void 0 ? void 0 : _a.getContext('2d');
+        if (!ctx) {
+            return;
+        }
+        return autorun(() => {
+            renderMouseover({ ctx, model });
+        });
+    }, [model]);
+    return (React.createElement("canvas", { ref: ref, width: width, height: height, style: {
+            position: 'absolute',
+            top: 0,
+            left: 0,
+            width,
+            height,
+            zIndex: 1000,
+            pointerEvents: 'none',
+        } }));
+});
+export default MSAMouseoverCanvas;
+//# sourceMappingURL=MSAMouseoverCanvas.js.map