react-msaview 3.1.12 → 3.2.1

package/dist/components/tree/TreeCanvasBlock.js

@@ -1,4 +1,5 @@
-import React, { useCallback, useEffect, useRef, useState } from 'react';
+import React from 'react';
+import { useCallback, useEffect, useRef, useState } from 'react';
 import { autorun } from 'mobx';
 import { observer } from 'mobx-react';
 import { useTheme } from '@mui/material';
@@ -19,6 +20,7 @@ const TreeCanvasBlock = observer(function ({ model, offsetY, }) {
     const height = blockSize;
     const w2 = width * highResScaleFactor;
     const h2 = height * highResScaleFactor;
+    // biome-ignore lint/correctness/useExhaustiveDependencies:
     const vref = useCallback((arg) => {
         model.incrementRef();
         ref.current = arg;
@@ -88,8 +90,12 @@ const TreeCanvasBlock = observer(function ({ model, offsetY, }) {
         position: 'absolute',
     };
     return (React.createElement(React.Fragment, null,
-        branchMenu?.id ? (React.createElement(TreeBranchMenu, { node: branchMenu, model: model, onClose: () => setBranchMenu(undefined) })) : null,
-        toggleNodeMenu?.id ? (React.createElement(TreeNodeMenu, { node: toggleNodeMenu, model: model, onClose: () => setToggleNodeMenu(undefined) })) : null,
+        branchMenu?.id ? (React.createElement(TreeBranchMenu, { node: branchMenu, model: model, onClose: () => {
+                setBranchMenu(undefined);
+            } })) : null,
+        toggleNodeMenu?.id ? (React.createElement(TreeNodeMenu, { node: toggleNodeMenu, model: model, onClose: () => {
+                setToggleNodeMenu(undefined);
+            } })) : null,
         React.createElement("canvas", { width: w2, height: h2, style: style, onMouseMove: event => {
                 if (!ref.current) {
                     return;
@@ -101,13 +107,15 @@ const TreeCanvasBlock = observer(function ({ model, offsetY, }) {
                 const { clientX: x, clientY: y } = event;
                 const data = hoverBranchClickMap(event);
                 if (data?.id) {
-                    setBranchMenu({ ...data, x, y });
+                    setBranchMenu({ x, y, id: data.id, name: data.name });
                 }
                 const data2 = hoverNameClickMap(event);
                 if (data2?.id) {
                     setToggleNodeMenu({ ...data2, x, y });
                 }
-            }, onMouseLeave: () => setHoverElt(undefined), ref: vref }),
+            }, onMouseLeave: () => {
+                setHoverElt(undefined);
+            }, ref: vref }),
         React.createElement("canvas", { style: {
                 ...style,
                 pointerEvents: 'none',

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

@@ -1 +1 @@
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+{"version":3,"file":"TreeCanvasBlock.js","sourceRoot":"","sources":["../../../src/components/tree/TreeCanvasBlock.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AACzB,OAAO,EAAE,WAAW,EAAE,SAAS,EAAE,MAAM,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AAChE,OAAO,EAAE,OAAO,EAAE,MAAM,MAAM,CAAA;AAC9B,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,EAAE,QAAQ,EAAE,MAAM,eAAe,CAAA;AACxC,OAAO,KAAK,MAAM,OAAO,CAAA;AAIzB,OAAO,YAAY,MAAM,gBAAgB,CAAA;AACzC,OAAO,cAAc,MAAM,kBAAkB,CAAA;AAC7C,OAAO,EAAE,OAAO,EAAE,gBAAgB,EAAE,MAAM,oBAAoB,CAAA;AAmB9D,MAAM,eAAe,GAAG,QAAQ,CAAC,UAAU,EACzC,KAAK,EACL,OAAO,GAIR;IACC,MAAM,KAAK,GAAG,QAAQ,EAAE,CAAA;IACxB,MAAM,GAAG,GAAG,MAAM,EAAqB,CAAA;IACvC,MAAM,QAAQ,GAAG,MAAM,CAAC,IAAI,KAAK,EAAc,CAAC,CAAA;IAChD,MAAM,YAAY,GAAG,MAAM,CAAoB,IAAI,CAAC,CAAA;IACpD,MAAM,CAAC,UAAU,EAAE,aAAa,CAAC,GAAG,QAAQ,EAAe,CAAA;IAC3D,MAAM,CAAC,cAAc,EAAE,iBAAiB,CAAC,GAAG,QAAQ,EAAe,CAAA;IACnE,MAAM,CAAC,QAAQ,EAAE,WAAW,CAAC,GAAG,QAAQ,EAAc,CAAA;IAEtD,MAAM,EAAE,OAAO,EAAE,aAAa,EAAE,SAAS,EAAE,kBAAkB,EAAE,GAAG,KAAK,CAAA;IAEvE,MAAM,KAAK,GAAG,aAAa,GAAG,OAAO,CAAA;IACrC,MAAM,MAAM,GAAG,SAAS,CAAA;IACxB,MAAM,EAAE,GAAG,KAAK,GAAG,kBAAkB,CAAA;IACrC,MAAM,EAAE,GAAG,MAAM,GAAG,kBAAkB,CAAA;IAEtC,2DAA2D;IAC3D,MAAM,IAAI,GAAG,WAAW,CACtB,CAAC,GAAsB,EAAE,EAAE;QACzB,KAAK,CAAC,YAAY,EAAE,CAAA;QACpB,GAAG,CAAC,OAAO,GAAG,GAAG,CAAA;IACnB,CAAC;IACD,uDAAuD;IACvD,CAAC,KAAK,EAAE,MAAM,EAAE,KAAK,CAAC,CACvB,CAAA;IACD,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;QAED,OAAO,OAAO,CAAC,GAAG,EAAE;YAClB,gBAAgB,CAAC;gBACf,GAAG;gBACH,KAAK;gBACL,OAAO;gBACP,QAAQ,EAAE,QAAQ,CAAC,OAAO;gBAC1B,KAAK;aACN,CAAC,CAAA;QACJ,CAAC,CAAC,CAAA;IACJ,CAAC,EAAE,CAAC,KAAK,EAAE,OAAO,EAAE,KAAK,CAAC,CAAC,CAAA;IAE3B,SAAS,CAAC,GAAG,EAAE;QACb,MAAM,GAAG,GAAG,YAAY,CAAC,OAAO,EAAE,UAAU,CAAC,IAAI,CAAC,CAAA;QAClD,IAAI,CAAC,GAAG,EAAE,CAAC;YACT,OAAM;QACR,CAAC;QAED,GAAG,CAAC,cAAc,EAAE,CAAA;QACpB,GAAG,CAAC,SAAS,CAAC,CAAC,EAAE,CAAC,EAAE,aAAa,GAAG,OAAO,EAAE,SAAS,CAAC,CAAA;QACvD,GAAG,CAAC,SAAS,CAAC,CAAC,EAAE,CAAC,OAAO,CAAC,CAAA;QAE1B,IAAI,QAAQ,EAAE,CAAC;YACb,MAAM,EAAE,IAAI,EAAE,IAAI,EAAE,IAAI,EAAE,IAAI,EAAE,GAAG,QAAQ,CAAA;YAE3C,GAAG,CAAC,SAAS,GAAG,iBAAiB,CAAA;YACjC,GAAG,CAAC,QAAQ,CAAC,IAAI,EAAE,IAAI,EAAE,IAAI,GAAG,IAAI,EAAE,IAAI,GAAG,IAAI,CAAC,CAAA;QACpD,CAAC;IACH,CAAC,EAAE,CAAC,QAAQ,EAAE,OAAO,EAAE,SAAS,EAAE,aAAa,CAAC,CAAC,CAAA;IAEjD,SAAS,mBAAmB,CAAC,KAAuB;QAClD,MAAM,CAAC,GAAG,KAAK,CAAC,WAAW,CAAC,OAAO,CAAA;QACnC,MAAM,CAAC,GAAG,KAAK,CAAC,WAAW,CAAC,OAAO,CAAA;QAEnC,MAAM,CAAC,KAAK,CAAC,GAAG,QAAQ,CAAC,OAAO,CAAC,MAAM,CAAC;YACtC,IAAI,EAAE,CAAC;YACP,IAAI,EAAE,CAAC,GAAG,CAAC;YACX,IAAI,EAAE,CAAC,GAAG,OAAO;YACjB,IAAI,EAAE,CAAC,GAAG,CAAC,GAAG,OAAO;SACtB,CAAC,CAAA;QAEF,OAAO,KAAK,EAAE,MAAM;YAClB,CAAC,CAAC,EAAE,GAAG,KAAK,EAAE,CAAC,EAAE,KAAK,CAAC,OAAO,EAAE,CAAC,EAAE,KAAK,CAAC,OAAO,EAAE;YAClD,CAAC,CAAC,SAAS,CAAA;IACf,CAAC;IAED,SAAS,iBAAiB,CAAC,KAAuB;QAChD,MAAM,CAAC,GAAG,KAAK,CAAC,WAAW,CAAC,OAAO,CAAA;QACnC,MAAM,CAAC,GAAG,KAAK,CAAC,WAAW,CAAC,OAAO,CAAA;QACnC,MAAM,CAAC,KAAK,CAAC,GAAG,QAAQ,CAAC,OAAO,CAAC,MAAM,CAAC;YACtC,IAAI,EAAE,CAAC;YACP,IAAI,EAAE,CAAC,GAAG,CAAC;YACX,IAAI,EAAE,CAAC,GAAG,OAAO;YACjB,IAAI,EAAE,CAAC,GAAG,CAAC,GAAG,OAAO;SACtB,CAAC,CAAA;QAEF,OAAO,KAAK,IAAI,CAAC,KAAK,CAAC,MAAM;YAC3B,CAAC,CAAC,EAAE,GAAG,KAAK,EAAE,CAAC,EAAE,KAAK,CAAC,OAAO,EAAE,CAAC,EAAE,KAAK,CAAC,OAAO,EAAE;YAClD,CAAC,CAAC,SAAS,CAAA;IACf,CAAC;IACD,MAAM,KAAK,GAAG;QACZ,KAAK;QACL,MAAM;QACN,GAAG,EAAE,OAAO,GAAG,OAAO;QACtB,IAAI,EAAE,CAAC;QACP,QAAQ,EAAE,UAAU;KACZ,CAAA;IACV,OAAO,CACL;QACG,UAAU,EAAE,EAAE,CAAC,CAAC,CAAC,CAChB,oBAAC,cAAc,IACb,IAAI,EAAE,UAAU,EAChB,KAAK,EAAE,KAAK,EACZ,OAAO,EAAE,GAAG,EAAE;gBACZ,aAAa,CAAC,SAAS,CAAC,CAAA;YAC1B,CAAC,GACD,CACH,CAAC,CAAC,CAAC,IAAI;QAEP,cAAc,EAAE,EAAE,CAAC,CAAC,CAAC,CACpB,oBAAC,YAAY,IACX,IAAI,EAAE,cAAc,EACpB,KAAK,EAAE,KAAK,EACZ,OAAO,EAAE,GAAG,EAAE;gBACZ,iBAAiB,CAAC,SAAS,CAAC,CAAA;YAC9B,CAAC,GACD,CACH,CAAC,CAAC,CAAC,IAAI;QAER,gCACE,KAAK,EAAE,EAAE,EACT,MAAM,EAAE,EAAE,EACV,KAAK,EAAE,KAAK,EACZ,WAAW,EAAE,KAAK,CAAC,EAAE;gBACnB,IAAI,CAAC,GAAG,CAAC,OAAO,EAAE,CAAC;oBACjB,OAAM;gBACR,CAAC;gBAED,MAAM,GAAG,GAAG,iBAAiB,CAAC,KAAK,CAAC,IAAI,mBAAmB,CAAC,KAAK,CAAC,CAAA;gBAClE,GAAG,CAAC,OAAO,CAAC,KAAK,CAAC,MAAM,GAAG,GAAG,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,SAAS,CAAA;gBACtD,WAAW,CAAC,iBAAiB,CAAC,KAAK,CAAC,CAAC,CAAA;YACvC,CAAC,EACD,OAAO,EAAE,KAAK,CAAC,EAAE;gBACf,MAAM,EAAE,OAAO,EAAE,CAAC,EAAE,OAAO,EAAE,CAAC,EAAE,GAAG,KAAK,CAAA;gBAExC,MAAM,IAAI,GAAG,mBAAmB,CAAC,KAAK,CAAC,CAAA;gBACvC,IAAI,IAAI,EAAE,EAAE,EAAE,CAAC;oBACb,aAAa,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,EAAE,EAAE,IAAI,CAAC,EAAE,EAAE,IAAI,EAAE,IAAI,CAAC,IAAI,EAAE,CAAC,CAAA;gBACvD,CAAC;gBAED,MAAM,KAAK,GAAG,iBAAiB,CAAC,KAAK,CAAC,CAAA;gBACtC,IAAI,KAAK,EAAE,EAAE,EAAE,CAAC;oBACd,iBAAiB,CAAC,EAAE,GAAG,KAAK,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,CAAA;gBACvC,CAAC;YACH,CAAC,EACD,YAAY,EAAE,GAAG,EAAE;gBACjB,WAAW,CAAC,SAAS,CAAC,CAAA;YACxB,CAAC,EACD,GAAG,EAAE,IAAI,GACT;QACF,gCACE,KAAK,EAAE;gBACL,GAAG,KAAK;gBACR,aAAa,EAAE,MAAM;gBACrB,MAAM,EAAE,GAAG;aACZ,EACD,KAAK,EAAE,KAAK,EACZ,MAAM,EAAE,MAAM,EACd,GAAG,EAAE,YAAY,GACjB,CACD,CACJ,CAAA;AACH,CAAC,CAAC,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package/dist/components/tree/TreeNodeMenu.d.ts

@@ -1,5 +1,5 @@
 import React from 'react';
-import { MsaViewModel } from '../../model';
+import type { MsaViewModel } from '../../model';
 declare const TreeMenu: ({ node, onClose, model, }: {
     node: {
         x: number;

package/dist/components/tree/TreeNodeMenu.js

@@ -4,7 +4,7 @@ import { observer } from 'mobx-react';
 // lazies
 const TreeNodeInfoDialog = lazy(() => import('./dialogs/TreeNodeInfoDialog'));
 const TreeMenu = observer(function ({ node, onClose, model, }) {
-    const { collapsed, collapsed2 } = model;
+    const { collapsed, collapsedLeaves } = model;
     return (React.createElement(Menu, { anchorReference: "anchorPosition", anchorPosition: {
             top: node.y,
             left: node.x,
@@ -28,14 +28,14 @@ const TreeMenu = observer(function ({ node, onClose, model, }) {
                 }
                 else {
                     if (node.id.endsWith('-leafnode')) {
-                        model.toggleCollapsed2(`${node.id}`);
+                        model.toggleCollapsed2(node.id);
                     }
                     else {
                         model.toggleCollapsed2(`${node.id}-leafnode`);
                     }
                 }
                 onClose();
-            } }, collapsed.includes(node.id) || collapsed2.includes(node.id)
+            } }, collapsed.includes(node.id) || collapsedLeaves.includes(node.id)
             ? 'Show node'
             : 'Hide node')));
 });

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

@@ -1 +1 @@
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+{"version":3,"file":"TreeNodeMenu.js","sourceRoot":"","sources":["../../../src/components/tree/TreeNodeMenu.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,IAAI,EAAE,MAAM,OAAO,CAAA;AACnC,OAAO,EAAE,IAAI,EAAE,QAAQ,EAAE,MAAM,eAAe,CAAA;AAC9C,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAKrC,SAAS;AACT,MAAM,kBAAkB,GAAG,IAAI,CAAC,GAAG,EAAE,CAAC,MAAM,CAAC,8BAA8B,CAAC,CAAC,CAAA;AAE7E,MAAM,QAAQ,GAAG,QAAQ,CAAC,UAAU,EAClC,IAAI,EACJ,OAAO,EACP,KAAK,GAKN;IACC,MAAM,EAAE,SAAS,EAAE,eAAe,EAAE,GAAG,KAAK,CAAA;IAC5C,OAAO,CACL,oBAAC,IAAI,IACH,eAAe,EAAC,gBAAgB,EAChC,cAAc,EAAE;YACd,GAAG,EAAE,IAAI,CAAC,CAAC;YACX,IAAI,EAAE,IAAI,CAAC,CAAC;SACb,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;QAEX,oBAAC,QAAQ,IACP,KAAK,QACL,OAAO,EAAE,GAAG,EAAE;gBACZ,KAAK,CAAC,WAAW,CAAC,OAAO,CAAC,EAAE,CAAC;oBAC3B,kBAAkB;oBAClB;wBACE,IAAI,EAAE,KAAK,CAAC,UAAU,CAAC,IAAI,CAAC,IAAI,CAAC;wBACjC,KAAK;wBACL,QAAQ,EAAE,IAAI,CAAC,IAAI;wBACnB,OAAO;qBACR;iBACF,CAAC,CAAA;gBACF,OAAO,EAAE,CAAA;YACX,CAAC,mBAGQ;QACX,oBAAC,QAAQ,IACP,KAAK,QACL,OAAO,EAAE,GAAG,EAAE;gBACZ,IAAI,SAAS,CAAC,QAAQ,CAAC,IAAI,CAAC,EAAE,CAAC,EAAE,CAAC;oBAChC,KAAK,CAAC,eAAe,CAAC,IAAI,CAAC,EAAE,CAAC,CAAA;gBAChC,CAAC;qBAAM,CAAC;oBACN,IAAI,IAAI,CAAC,EAAE,CAAC,QAAQ,CAAC,WAAW,CAAC,EAAE,CAAC;wBAClC,KAAK,CAAC,gBAAgB,CAAC,IAAI,CAAC,EAAE,CAAC,CAAA;oBACjC,CAAC;yBAAM,CAAC;wBACN,KAAK,CAAC,gBAAgB,CAAC,GAAG,IAAI,CAAC,EAAE,WAAW,CAAC,CAAA;oBAC/C,CAAC;gBACH,CAAC;gBACD,OAAO,EAAE,CAAA;YACX,CAAC,IAEA,SAAS,CAAC,QAAQ,CAAC,IAAI,CAAC,EAAE,CAAC,IAAI,eAAe,CAAC,QAAQ,CAAC,IAAI,CAAC,EAAE,CAAC;YAC/D,CAAC,CAAC,WAAW;YACb,CAAC,CAAC,WAAW,CACN,CACN,CACR,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,QAAQ,CAAA"}

package/dist/components/tree/TreePanel.d.ts

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

package/dist/components/tree/TreeRuler.d.ts

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

package/dist/components/tree/dialogs/TreeNodeInfoDialog.d.ts

@@ -1,9 +1,9 @@
 import React from 'react';
-import { MsaViewModel } from '../../../model';
-declare const _default: ({ info, model, nodeName, onClose, }: {
+import type { MsaViewModel } from '../../../model';
+declare const TreeNodeInfoDialog: ({ info, model, nodeName, onClose, }: {
     info: Record<string, unknown>;
     model: MsaViewModel;
     nodeName: string;
     onClose: () => void;
 }) => React.JSX.Element;
-export default _default;
+export default TreeNodeInfoDialog;

package/dist/components/tree/dialogs/TreeNodeInfoDialog.js

@@ -4,11 +4,13 @@ import { DialogContent } from '@mui/material';
 import { observer } from 'mobx-react';
 import { Attributes, BaseCard, } from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail';
 import SequenceTextArea from '../../SequenceTextArea';
-export default observer(function ({ info, model, nodeName, onClose, }) {
+const TreeNodeInfoDialog = observer(function ({ info, model, nodeName, onClose, }) {
     const { treeMetadata, rows } = model;
     const metadata = treeMetadata[nodeName];
     const [name, sequence] = rows.find(f => f[0] === nodeName);
-    return (React.createElement(Dialog, { onClose: () => onClose(), open: true, title: "Tree node info", maxWidth: "xl" },
+    return (React.createElement(Dialog, { onClose: () => {
+            onClose();
+        }, open: true, title: "Tree node info", maxWidth: "xl" },
         React.createElement(DialogContent, null,
             React.createElement(BaseCard, { title: "Attributes" },
                 React.createElement(Attributes, { attributes: { nodeName, ...info } })),
@@ -17,4 +19,5 @@ export default observer(function ({ info, model, nodeName, onClose, }) {
             metadata ? (React.createElement(BaseCard, { title: "Extra metadata" },
                 React.createElement(Attributes, { attributes: metadata }))) : null)));
 });
+export default TreeNodeInfoDialog;
 //# sourceMappingURL=TreeNodeInfoDialog.js.map

package/dist/components/tree/dialogs/TreeNodeInfoDialog.js.map

@@ -1 +1 @@
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package/dist/components/tree/renderTreeCanvas.d.ts

@@ -1,6 +1,6 @@
-import RBush from 'rbush';
-import { Theme } from '@mui/material';
-import { MsaViewModel } from '../../model';
+import type RBush from 'rbush';
+import type { Theme } from '@mui/material';
+import type { MsaViewModel } from '../../model';
 export declare const padding = 600;
 interface ClickEntry {
     name: string;

package/dist/components/tree/renderTreeCanvas.js

@@ -8,6 +8,9 @@ export function renderTree({ offsetY, ctx, model, theme, blockSizeYOverride, })
     ctx.strokeStyle = theme.palette.text.primary;
     for (const link of hierarchy.links()) {
         const { source, target } = link;
+        if (target.height === 0 && !showBranchLen) {
+            continue;
+        }
         const sy = source.x;
         const ty = target.x;
         // @ts-expect-error
@@ -36,9 +39,8 @@ export function renderNodeBubbles({ ctx, clickMap, offsetY, model, blockSizeYOve
         // @ts-expect-error
         const { [val]: x, data } = node;
         const y = node.x;
-        const { branchset, id = '', name = '' } = data;
-        if (!id.endsWith('-leafnode') &&
-            branchset.length &&
+        const { id = '', name = '' } = data;
+        if (node.height > 1 &&
             y > offsetY - extendBounds &&
             y < offsetY + by + extendBounds) {
             ctx.strokeStyle = 'black';
@@ -60,7 +62,10 @@ export function renderNodeBubbles({ ctx, clickMap, offsetY, model, blockSizeYOve
     }
 }
 export function renderTreeLabels({ theme, model, offsetY, ctx, clickMap, blockSizeYOverride, }) {
-    const { fontSize, showBranchLen, treeMetadata, hierarchy, blockSize, labelsAlignRight, drawTree, treeAreaWidth, treeAreaWidthMinusMargin, marginLeft, noTree, } = model;
+    const { fontSize, showBranchLen, treeMetadata, hierarchy, collapsed, collapsedLeaves, blockSize, labelsAlignRight, drawTree, treeAreaWidth, treeWidth, treeAreaWidthMinusMargin, marginLeft, leaves, noTree, 
+    // eslint-disable-next-line  @typescript-eslint/no-unused-vars
+    rowHeight: _rowHeight, // this is needed for redrawing after zoom change
+     } = model;
     const by = blockSizeYOverride || blockSize;
     if (labelsAlignRight) {
         ctx.textAlign = 'right';
@@ -69,7 +74,7 @@ export function renderTreeLabels({ theme, model, offsetY, ctx, clickMap, blockSi
     else {
         ctx.textAlign = 'start';
     }
-    for (const node of hierarchy.leaves()) {
+    for (const node of leaves) {
         const { data: { name, id }, 
         // @ts-expect-error
         len, } = node;
@@ -79,7 +84,16 @@ export function renderTreeLabels({ theme, model, offsetY, ctx, clickMap, blockSi
         if (y > offsetY - extendBounds && y < offsetY + by + extendBounds) {
             // note: +rowHeight/4 matches with -rowHeight/4 in msa
             const yp = y + fontSize / 4;
-            const xp = (showBranchLen ? len : x) || 0;
+            let xp = (showBranchLen ? len : x) || 0;
+            if (!showBranchLen &&
+                !collapsed.includes(id) &&
+                !collapsedLeaves.includes(id)) {
+                // this subtraction is a hack to compensate for the leafnode rendering
+                // glitch (issue #71). the context is that an extra leaf node is added
+                // so that 'collapsing/hiding leaf nodes is possible' but this causes
+                // weird workarounds
+                xp -= treeWidth / hierarchy.height;
+            }
             const { width } = ctx.measureText(displayName);
             const height = ctx.measureText('M').width; // use an 'em' for height
             ctx.fillStyle = theme.palette.text.primary;
@@ -119,7 +133,7 @@ export function renderTreeLabels({ theme, model, offsetY, ctx, clickMap, blockSi
 }
 export function renderTreeCanvas({ model, clickMap, ctx, offsetY, theme, highResScaleFactorOverride, blockSizeYOverride, }) {
     clickMap?.clear();
-    const { noTree, drawTree, drawLabels, drawNodeBubbles, treeWidth, highResScaleFactor, blockSize, fontSize, rowHeight, marginLeft, nref, } = model;
+    const { noTree, drawTree, drawNodeBubbles, treeWidth, highResScaleFactor, blockSize, fontSize, showTreeText, marginLeft, nref, } = model;
     const by = blockSizeYOverride || blockSize;
     ctx.resetTransform();
     // this is a bogus use of nref, it is never less than 0. we just are using it
@@ -127,7 +141,9 @@ export function renderTreeCanvas({ model, clickMap, ctx, offsetY, theme, highRes
     // just need to use nref to indicate a redraw in an autorun when canvas ref
     // is updated and in order to convince bundlers like not to delete unused
     // usage with propertyReadSideEffects
-    const k = nref < 0 ? -Infinity : highResScaleFactorOverride || highResScaleFactor;
+    const k = nref < 0
+        ? Number.NEGATIVE_INFINITY
+        : highResScaleFactorOverride || highResScaleFactor;
     ctx.scale(k, k);
     ctx.clearRect(0, 0, treeWidth + padding, by);
     ctx.translate(marginLeft, -offsetY);
@@ -152,7 +168,7 @@ export function renderTreeCanvas({ model, clickMap, ctx, offsetY, theme, highRes
             });
         }
     }
-    if (rowHeight >= 5 && drawLabels) {
+    if (showTreeText) {
         renderTreeLabels({
             ctx,
             offsetY,

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

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

@@ -6,7 +6,7 @@
 export function chooseGridPitch(scale, minMajorPitchPx, minMinorPitchPx) {
     scale = Math.abs(scale);
     const minMajorPitchBp = minMajorPitchPx * scale;
-    const majorMagnitude = parseInt(Number(minMajorPitchBp).toExponential().split(/e/i)[1], 10);
+    const majorMagnitude = Number.parseInt(Number(minMajorPitchBp).toExponential().split(/e/i)[1], 10);
     let majorPitch = 10 ** majorMagnitude;
     while (majorPitch < minMajorPitchBp) {
         majorPitch *= 2;
@@ -33,9 +33,6 @@ export function makeTicks(start, end, bpPerPx, emitMajor = true, emitMinor = tru
     const gridPitch = chooseGridPitch(bpPerPx, 60, 15);
     let minBase = start;
     let maxBase = end;
-    if (minBase === null || maxBase === null) {
-        return [];
-    }
     if (bpPerPx < 0) {
         ;
         [minBase, maxBase] = [maxBase, minBase];

package/dist/components/util.js.map

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

@@ -1 +1 @@
-{"version":3,"file":"ggplotPalettes.js","sourceRoot":"","sources":["../src/ggplotPalettes.ts"],"names":[],"mappings":"AAAA,MAAM,QAAQ,GAAG;IACf,CAAC,SAAS,CAAC;IACX,CAAC,SAAS,EAAE,SAAS,CAAC;IACtB,CAAC,SAAS,EAAE,SAAS,EAAE,SAAS,CAAC;IACjC,CAAC,SAAS,EAAE,SAAS,EAAE,SAAS,EAAE,SAAS,CAAC;IAC5C,CAAC,SAAS,EAAE,SAAS,EAAE,SAAS,EAAE,SAAS,EAAE,SAAS,CAAC;IACvD,CAAC,SAAS,EAAE,SAAS,EAAE,SAAS,EAAE,SAAS,EAAE,SAAS,EAAE,SAAS,CAAC;IAClE,CAAC,SAAS,EAAE,SAAS,EAAE,SAAS,EAAE,SAAS,EAAE,SAAS,EAAE,SAAS,EAAE,SAAS,CAAC;IAC7E;QACE,SAAS;QACT,SAAS;QACT,SAAS;QACT,SAAS;QACT,SAAS;QACT,SAAS;QACT,SAAS;QACT,SAAS;KACV;CACF,CAAA;AAED,MAAM,UAAU,UAAU,CAAC,CAAS;IAClC,OAAO,QAAQ,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,EAAE,QAAQ,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,CAAA;AACnD,CAAC;AAED,eAAe,QAAQ,CAAA"}
+{"version":3,"file":"ggplotPalettes.js","sourceRoot":"","sources":["../src/ggplotPalettes.ts"],"names":[],"mappings":"AAAA,MAAM,QAAQ,GAAG;IACf,CAAC,SAAS,CAAC;IACX,CAAC,SAAS,EAAE,SAAS,CAAC;IACtB,CAAC,SAAS,EAAE,SAAS,EAAE,SAAS,CAAC;IACjC,CAAC,SAAS,EAAE,SAAS,EAAE,SAAS,EAAE,SAAS,CAAC;IAC5C,CAAC,SAAS,EAAE,SAAS,EAAE,SAAS,EAAE,SAAS,EAAE,SAAS,CAAC;IACvD,CAAC,SAAS,EAAE,SAAS,EAAE,SAAS,EAAE,SAAS,EAAE,SAAS,EAAE,SAAS,CAAC;IAClE,CAAC,SAAS,EAAE,SAAS,EAAE,SAAS,EAAE,SAAS,EAAE,SAAS,EAAE,SAAS,EAAE,SAAS,CAAC;IAC7E;QACE,SAAS;QACT,SAAS;QACT,SAAS;QACT,SAAS;QACT,SAAS;QACT,SAAS;QACT,SAAS;QACT,SAAS;KACV;CACF,CAAA;AAED,MAAM,UAAU,UAAU,CAAC,CAAS;IAClC,OAAO,QAAQ,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,EAAE,QAAQ,CAAC,MAAM,GAAG,CAAC,CAAC,CAAE,CAAA;AACpD,CAAC;AAED,eAAe,QAAQ,CAAA"}

package/dist/launchInterProScan.d.ts

@@ -1,4 +1,4 @@
-import { MsaViewModel } from './model';
+import type { MsaViewModel } from './model';
 export interface InterProScanResults {
     matches: {
         signature: {

package/dist/launchInterProScan.js

@@ -1,12 +1,12 @@
 import { getSession } from '@jbrowse/core/util';
 import { jsonfetch, textfetch, timeout } from './fetchUtils';
-const base = `https://www.ebi.ac.uk/Tools/services/rest`;
+const base = 'https://www.ebi.ac.uk/Tools/services/rest';
 async function runInterProScan({ seq, onProgress, onJobId, programs, model, }) {
     const jobId = await textfetch(`${base}/iprscan5/run`, {
         method: 'POST',
         body: new URLSearchParams({
             email: 'colin.diesh@gmail.com',
-            sequence: `${seq}`,
+            sequence: seq,
             programs: programs.join(','),
         }),
     });
@@ -15,7 +15,7 @@ async function runInterProScan({ seq, onProgress, onJobId, programs, model, }) {
         jobId,
         onProgress,
     });
-    return loadInterProScanResultsWithStatus({ jobId, model });
+    await loadInterProScanResultsWithStatus({ jobId, model });
 }
 export function loadInterProScanResults(jobId) {
     return jsonfetch(`${base}/iprscan5/result/${jobId}/json`);
@@ -23,7 +23,7 @@ export function loadInterProScanResults(jobId) {
 async function wait({ onProgress, jobId, }) {
     const url = `${base}/iprscan5/status/${jobId}`;
     try {
-        // eslint-disable-next-line no-constant-condition
+        // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
         while (true) {
             for (let i = 0; i < 10; i++) {
                 await timeout(1000);
@@ -33,6 +33,9 @@ async function wait({ onProgress, jobId, }) {
             if (result.includes('FINISHED')) {
                 break;
             }
+            if (result.includes('FAILURE')) {
+                throw new Error(`Failed to run: jobId ${jobId}`);
+            }
         }
     }
     finally {
@@ -43,18 +46,15 @@ export async function launchInterProScan({ algorithm, seq, programs, onJobId, on
     try {
         onProgress({ msg: `Launching ${algorithm} MSA` });
         if (algorithm === 'interproscan') {
-            const result = await runInterProScan({
+            await runInterProScan({
                 seq,
                 onJobId,
                 onProgress,
                 programs,
                 model,
             });
-            return result;
-        }
-        else {
-            throw new Error('unknown algorithm');
         }
+        throw new Error('unknown algorithm');
     }
     finally {
         onProgress();
@@ -63,13 +63,11 @@ export async function launchInterProScan({ algorithm, seq, programs, onJobId, on
 export async function loadInterProScanResultsWithStatus({ jobId, model, }) {
     try {
         model.setStatus({
-            msg: 'Downloading results of ' +
-                jobId +
-                ' (for larger sequences this can be slow, click status to download and upload in the manual tab)',
+            msg: `Downloading results of ${jobId} (for larger sequences this can be slow, click status to download and upload in the manual tab)`,
             url: `https://www.ebi.ac.uk/Tools/services/rest/iprscan5/result/${jobId}/json`,
         });
         const ret = await loadInterProScanResults(jobId);
-        model.setLoadedInterProAnnotations(Object.fromEntries(ret.results.map(r => [r.xref[0].id, r])));
+        model.setInterProAnnotations(Object.fromEntries(ret.results.map(r => [r.xref[0].id, r])));
         model.setShowDomains(true);
         getSession(model).notify(`Loaded interproscan ${jobId} results`, 'success');
     }

package/dist/launchInterProScan.js.map

@@ -1 +1 @@
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package/dist/model/DataModel.d.ts

@@ -31,4 +31,8 @@ export declare function DataModelF(): import("mobx-state-tree").IModelType<{
      * #action
      */
     setTreeMetadata(treeMetadata?: string): void;
-}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
+}, import("mobx-state-tree")._NotCustomized, {
+    tree: string | undefined;
+    msa: string | undefined;
+    treeMetadata: string | undefined;
+}>;

package/dist/model/DataModel.js

@@ -41,6 +41,15 @@ export function DataModelF() {
         setTreeMetadata(treeMetadata) {
             self.treeMetadata = treeMetadata;
         },
-    }));
+    }))
+        .postProcessSnapshot(snap => {
+        const { tree, msa, treeMetadata } = snap;
+        const max = 50_000;
+        return {
+            tree: tree && tree.length > max ? undefined : tree,
+            msa: msa && msa.length > max ? undefined : msa,
+            treeMetadata: treeMetadata && treeMetadata.length > max ? undefined : treeMetadata,
+        };
+    });
 }
 //# sourceMappingURL=DataModel.js.map

package/dist/model/DataModel.js.map

@@ -1 +1 @@
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+{"version":3,"file":"DataModel.js","sourceRoot":"","sources":["../../src/model/DataModel.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,KAAK,EAAE,MAAM,iBAAiB,CAAA;AAEvC;;;;;;GAMG;AACH,MAAM,UAAU,UAAU;IACxB,OAAO,KAAK;SACT,KAAK,CAAC;QACL;;WAEG;QACH,IAAI,EAAE,KAAK,CAAC,KAAK,CAAC,KAAK,CAAC,MAAM,CAAC;QAC/B;;WAEG;QACH,GAAG,EAAE,KAAK,CAAC,KAAK,CAAC,KAAK,CAAC,MAAM,CAAC;QAC9B;;WAEG;QACH,YAAY,EAAE,KAAK,CAAC,KAAK,CAAC,KAAK,CAAC,MAAM,CAAC;KACxC,CAAC;SACD,OAAO,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QAChB;;WAEG;QACH,OAAO,CAAC,IAAa;YACnB,IAAI,CAAC,IAAI,GAAG,IAAI,CAAA;QAClB,CAAC;QACD;;WAEG;QACH,MAAM,CAAC,GAAY;YACjB,IAAI,CAAC,GAAG,GAAG,GAAG,CAAA;QAChB,CAAC;QACD;;WAEG;QACH,eAAe,CAAC,YAAqB;YACnC,IAAI,CAAC,YAAY,GAAG,YAAY,CAAA;QAClC,CAAC;KACF,CAAC,CAAC;SACF,mBAAmB,CAAC,IAAI,CAAC,EAAE;QAC1B,MAAM,EAAE,IAAI,EAAE,GAAG,EAAE,YAAY,EAAE,GAAG,IAAI,CAAA;QACxC,MAAM,GAAG,GAAG,MAAM,CAAA;QAClB,OAAO;YACL,IAAI,EAAE,IAAI,IAAI,IAAI,CAAC,MAAM,GAAG,GAAG,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI;YAClD,GAAG,EAAE,GAAG,IAAI,GAAG,CAAC,MAAM,GAAG,GAAG,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,GAAG;YAC9C,YAAY,EACV,YAAY,IAAI,YAAY,CAAC,MAAM,GAAG,GAAG,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,YAAY;SACvE,CAAA;IACH,CAAC,CAAC,CAAA;AACN,CAAC"}

package/dist/model/DialogQueue.d.ts

@@ -1,4 +1,4 @@
-import { DialogComponentType } from '@jbrowse/core/util';
+import type { DialogComponentType } from '@jbrowse/core/util';
 /**
  * #stateModel DialogQueueSessionMixin
  */

package/dist/model/DialogQueue.js

@@ -6,7 +6,6 @@ export function DialogQueueSessionMixin() {
     return types
         .model('DialogQueueSessionMixin', {})
         .volatile(() => ({
-        // eslint-disable-next-line @typescript-eslint/no-explicit-any
         queueOfDialogs: [],
     }))
         .views(self => ({

package/dist/model/DialogQueue.js.map

@@ -1 +1 @@
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