react-msaview 3.1.3 → 3.1.4

package/dist/components/TreePanel/TreeNodeMenu.js

@@ -3,7 +3,6 @@ import { Menu, MenuItem } from '@mui/material';
 import { observer } from 'mobx-react';
 const TreeNodeInfoDialog = lazy(() => import('./dialogs/TreeNodeInfoDialog'));
 const TreeMenu = observer(function ({ node, onClose, model, }) {
-    var _a, _b;
     const { structures } = model;
     const nodeDetails = node ? model.getRowData(node.name) : undefined;
     return (React.createElement(React.Fragment, null,
@@ -27,8 +26,8 @@ const TreeMenu = observer(function ({ node, onClose, model, }) {
             React.createElement(MenuItem, { dense: true, onClick: () => {
                     model.hideNode(node.id);
                     onClose();
-                } }, "Hide node"), (_a = structures[node.name]) === null || _a === void 0 ? void 0 :
-            _a.map(entry => {
+                } }, "Hide node"),
+            structures[node.name]?.map(entry => {
                 return !model.selectedStructures.some(n => n.id === node.name) ? (React.createElement(MenuItem, { key: JSON.stringify(entry), dense: true, onClick: () => {
                         model.addStructureToSelection({
                             structure: entry,
@@ -49,11 +48,10 @@ const TreeMenu = observer(function ({ node, onClose, model, }) {
                     entry.pdb,
                     ")"));
             }), // @ts-expect-error
-        (_b = nodeDetails === null || nodeDetails === void 0 ? void 0 : nodeDetails.data.accession) === null || _b === void 0 ? void 0 :
-            _b.map(accession => (React.createElement(MenuItem, { dense: true, key: accession, onClick: () => {
+            nodeDetails?.data.accession?.map(accession => (React.createElement(MenuItem, { dense: true, key: accession, onClick: () => {
                     model.addUniprotTrack({
                         // @ts-expect-error
-                        name: nodeDetails === null || nodeDetails === void 0 ? void 0 : nodeDetails.data.name,
+                        name: nodeDetails?.data.name,
                         accession,
                     });
                     onClose();

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

@@ -1 +1 @@
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+{"version":3,"file":"TreeNodeMenu.js","sourceRoot":"","sources":["../../../src/components/TreePanel/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,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,UAAU,EAAE,GAAG,KAAK,CAAA;IAC5B,MAAM,WAAW,GAAG,IAAI,CAAC,CAAC,CAAC,KAAK,CAAC,UAAU,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,SAAS,CAAA;IAElE,OAAO,CACL;QACE,oBAAC,IAAI,IACH,eAAe,EAAC,gBAAgB,EAChC,cAAc,EAAE;gBACd,GAAG,EAAE,IAAI,CAAC,CAAC;gBACX,IAAI,EAAE,IAAI,CAAC,CAAC;aACb,EACD,kBAAkB,EAAE,CAAC,EACrB,WAAW,QACX,IAAI,EAAE,OAAO,CAAC,IAAI,CAAC,EACnB,OAAO,EAAE,OAAO;YAEhB,oBAAC,QAAQ,IAAC,KAAK,QAAC,QAAQ,UACrB,IAAI,CAAC,IAAI,CACD;YAEX,oBAAC,QAAQ,IACP,KAAK,QACL,OAAO,EAAE,GAAG,EAAE;oBACZ,KAAK,CAAC,WAAW,CAAC,OAAO,CAAC,EAAE,CAAC;wBAC3B,kBAAkB;wBAClB;4BACE,IAAI,EAAE,KAAK,CAAC,UAAU,CAAC,IAAI,CAAC,IAAI,CAAC;4BACjC,KAAK;4BACL,QAAQ,EAAE,IAAI,CAAC,IAAI;4BACnB,OAAO;yBACR;qBACF,CAAC,CAAA;oBACF,OAAO,EAAE,CAAA;gBACX,CAAC,mBAGQ;YACX,oBAAC,QAAQ,IACP,KAAK,QACL,OAAO,EAAE,GAAG,EAAE;oBACZ,KAAK,CAAC,QAAQ,CAAC,IAAI,CAAC,EAAE,CAAC,CAAA;oBACvB,OAAO,EAAE,CAAA;gBACX,CAAC,gBAGQ;YAEV,UAAU,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,GAAG,CAAC,KAAK,CAAC,EAAE;gBAClC,OAAO,CAAC,KAAK,CAAC,kBAAkB,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,EAAE,KAAK,IAAI,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAC/D,oBAAC,QAAQ,IACP,GAAG,EAAE,IAAI,CAAC,SAAS,CAAC,KAAK,CAAC,EAC1B,KAAK,QACL,OAAO,EAAE,GAAG,EAAE;wBACZ,KAAK,CAAC,uBAAuB,CAAC;4BAC5B,SAAS,EAAE,KAAK;4BAChB,EAAE,EAAE,IAAI,CAAC,IAAI;yBACd,CAAC,CAAA;wBACF,OAAO,EAAE,CAAA;oBACX,CAAC;;oBAEsB,KAAK,CAAC,GAAG;wBACvB,CACZ,CAAC,CAAC,CAAC,CACF,oBAAC,QAAQ,IACP,GAAG,EAAE,IAAI,CAAC,SAAS,CAAC,KAAK,CAAC,EAC1B,KAAK,QACL,OAAO,EAAE,GAAG,EAAE;wBACZ,KAAK,CAAC,4BAA4B,CAAC;4BACjC,SAAS,EAAE,KAAK;4BAChB,EAAE,EAAE,IAAI,CAAC,IAAI;yBACd,CAAC,CAAA;wBACF,OAAO,EAAE,CAAA;oBACX,CAAC;;oBAE2B,KAAK,CAAC,GAAG;wBAC5B,CACZ,CAAA;YACH,CAAC,CAAC,EAED,mBAAmB;YACpB,WAAW,EAAE,IAAI,CAAC,SAAS,EAAE,GAAG,CAAC,SAAS,CAAC,EAAE,CAAC,CAC5C,oBAAC,QAAQ,IACP,KAAK,QACL,GAAG,EAAE,SAAS,EACd,OAAO,EAAE,GAAG,EAAE;oBACZ,KAAK,CAAC,eAAe,CAAC;wBACpB,mBAAmB;wBACnB,IAAI,EAAE,WAAW,EAAE,IAAI,CAAC,IAAI;wBAC5B,SAAS;qBACV,CAAC,CAAA;oBACF,OAAO,EAAE,CAAA;gBACX,CAAC;;gBAEoB,SAAS;oBACrB,CACZ,CAAC,CACG,CACN,CACJ,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,QAAQ,CAAA"}

package/dist/components/TreePanel/renderTreeCanvas.js

@@ -46,7 +46,7 @@ export function renderNodeBubbles({ ctx, clickMap, offsetY, model, blockSizeYOve
             ctx.arc(x, y, radius, 0, 2 * Math.PI);
             ctx.fill();
             ctx.stroke();
-            clickMap === null || clickMap === void 0 ? void 0 : clickMap.insert({
+            clickMap?.insert({
                 minX: x - radius,
                 maxX: x - radius + d,
                 minY: y - radius,
@@ -59,8 +59,7 @@ export function renderNodeBubbles({ ctx, clickMap, offsetY, model, blockSizeYOve
     }
 }
 export function renderTreeLabels({ theme, model, offsetY, ctx, clickMap, blockSizeYOverride, }) {
-    var _a;
-    const { rowHeight, showBranchLen, treeMetadata, hierarchy, blockSize, labelsAlignRight, drawTree, structures, treeAreaWidth, margin, noTree, } = model;
+    const { rowHeight, showBranchLen, treeMetadata, hierarchy, blockSize, labelsAlignRight, drawTree, structures, treeAreaWidth, noTree, } = model;
     const by = blockSizeYOverride || blockSize;
     if (labelsAlignRight) {
         ctx.textAlign = 'right';
@@ -77,7 +76,7 @@ export function renderTreeLabels({ theme, model, offsetY, ctx, clickMap, blockSi
         y: x, data: { name, id }, 
         // @ts-expect-error
         len, } = node;
-        const displayName = ((_a = treeMetadata[name]) === null || _a === void 0 ? void 0 : _a.genome) || name;
+        const displayName = treeMetadata[name]?.genome || name;
         if (y > offsetY - extendBounds && y < offsetY + by + extendBounds) {
             // note: +rowHeight/4 matches with -rowHeight/4 in msa
             const yp = y + rowHeight / 4;
@@ -88,7 +87,7 @@ export function renderTreeLabels({ theme, model, offsetY, ctx, clickMap, blockSi
             ctx.fillStyle = hasStructure ? 'blue' : theme.palette.text.primary;
             if (!drawTree && !labelsAlignRight) {
                 ctx.fillText(displayName, 0, yp);
-                clickMap === null || clickMap === void 0 ? void 0 : clickMap.insert({
+                clickMap?.insert({
                     minX: 0,
                     maxX: width,
                     minY: yp - height,
@@ -99,7 +98,7 @@ export function renderTreeLabels({ theme, model, offsetY, ctx, clickMap, blockSi
             }
             else if (labelsAlignRight) {
                 const smallPadding = 2;
-                const offset = treeAreaWidth - smallPadding - margin.left;
+                const offset = treeAreaWidth - smallPadding;
                 if (drawTree && !noTree) {
                     const { width } = ctx.measureText(displayName);
                     ctx.moveTo(xp + radius + 2, y);
@@ -107,9 +106,9 @@ export function renderTreeLabels({ theme, model, offsetY, ctx, clickMap, blockSi
                     ctx.stroke();
                 }
                 ctx.fillText(displayName, offset, yp);
-                clickMap === null || clickMap === void 0 ? void 0 : clickMap.insert({
-                    minX: treeAreaWidth - margin.left - width,
-                    maxX: treeAreaWidth - margin.left,
+                clickMap?.insert({
+                    minX: treeAreaWidth - width,
+                    maxX: treeAreaWidth,
                     minY: yp - height,
                     maxY: yp,
                     name,
@@ -118,7 +117,7 @@ export function renderTreeLabels({ theme, model, offsetY, ctx, clickMap, blockSi
             }
             else {
                 ctx.fillText(displayName, xp + d, yp);
-                clickMap === null || clickMap === void 0 ? void 0 : clickMap.insert({
+                clickMap?.insert({
                     minX: xp + d,
                     maxX: xp + d + width,
                     minY: yp - height,
@@ -132,8 +131,8 @@ export function renderTreeLabels({ theme, model, offsetY, ctx, clickMap, blockSi
     ctx.setLineDash([]);
 }
 export function renderTreeCanvas({ model, clickMap, ctx, offsetY, theme, highResScaleFactorOverride, blockSizeYOverride, }) {
-    clickMap === null || clickMap === void 0 ? void 0 : clickMap.clear();
-    const { noTree, drawTree, drawNodeBubbles, treeWidth, highResScaleFactor, margin, blockSize, fontSize, rowHeight, nref, } = model;
+    clickMap?.clear();
+    const { noTree, drawTree, drawNodeBubbles, treeWidth, highResScaleFactor, blockSize, fontSize, rowHeight, 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
@@ -144,7 +143,7 @@ export function renderTreeCanvas({ model, clickMap, ctx, offsetY, theme, highRes
     const k = nref < 0 ? -Infinity : highResScaleFactorOverride || highResScaleFactor;
     ctx.scale(k, k);
     ctx.clearRect(0, 0, treeWidth + padding, by);
-    ctx.translate(margin.left, -offsetY);
+    ctx.translate(0, -offsetY);
     const font = ctx.font;
     ctx.font = font.replace(/\d+px/, `${fontSize}px`);
     if (!noTree && drawTree) {

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

@@ -1 +1 @@
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package/dist/index.d.ts

@@ -1,2 +1,2 @@
-export { default as MSAView } from './components/MSAView';
+export { default as MSAView } from './components/Loading';
 export { default as MSAModel, type MsaViewModel } from './model';

package/dist/index.js

@@ -1,3 +1,3 @@
-export { default as MSAView } from './components/MSAView';
+export { default as MSAView } from './components/Loading';
 export { default as MSAModel } from './model';
 //# sourceMappingURL=index.js.map

package/dist/layout.js

@@ -1,5 +1,10 @@
 import RBush from 'rbush';
 export default class Layout {
+    rectangles;
+    maxHeightReached;
+    maxHeight;
+    rbush;
+    pTotalHeight;
     constructor({ maxHeight = 10000, } = {}) {
         this.maxHeightReached = false;
         this.rbush = new RBush();

package/dist/layout.js.map

@@ -1 +1 @@
-{"version":3,"file":"layout.js","sourceRoot":"","sources":["../src/layout.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,MAAM,CAAC,OAAO,OAAO,MAAM;IAqBzB,YAAY,EACV,SAAS,GAAG,KAAK,MAGf,EAAE;QACJ,IAAI,CAAC,gBAAgB,GAAG,KAAK,CAAA;QAC7B,IAAI,CAAC,KAAK,GAAG,IAAI,KAAK,EAAE,CAAA;QACxB,IAAI,CAAC,UAAU,GAAG,IAAI,GAAG,EAAE,CAAA;QAC3B,IAAI,CAAC,SAAS,GAAG,IAAI,CAAC,IAAI,CAAC,SAAS,CAAC,CAAA;QACrC,IAAI,CAAC,YAAY,GAAG,CAAC,CAAA,CAAC,uDAAuD;IAC/E,CAAC;IAED;;;OAGG;IACH,OAAO,CACL,EAAU,EACV,IAAY,EACZ,KAAa,EACb,MAAc,EACd,IAAa;QAEb,eAAe;QACf,MAAM,cAAc,GAAG,IAAI,CAAC,UAAU,CAAC,GAAG,CAAC,EAAE,CAAC,CAAA;QAC9C,IAAI,cAAc,EAAE,CAAC;YACnB,OAAO,cAAc,CAAC,IAAI,CAAA;QAC5B,CAAC;QAED,IAAI,UAAU,GAAG,CAAC,CAAA;QAClB,OACE,IAAI,CAAC,KAAK,CAAC,QAAQ,CAAC;YAClB,IAAI,EAAE,IAAI;YACV,IAAI,EAAE,UAAU;YAChB,IAAI,EAAE,KAAK;YACX,IAAI,EAAE,UAAU,GAAG,MAAM;SAC1B,CAAC;YACF,UAAU,IAAI,IAAI,CAAC,SAAS,EAC5B,CAAC;YACD,UAAU,IAAI,CAAC,CAAA;QACjB,CAAC;QAED,MAAM,MAAM,GAAG;YACb,IAAI,EAAE,IAAI;YACV,IAAI,EAAE,UAAU;YAChB,IAAI,EAAE,KAAK;YACX,IAAI,EAAE,UAAU,GAAG,MAAM;YACzB,EAAE;YACF,IAAI;SACL,CAAA;QACD,IAAI,CAAC,KAAK,CAAC,MAAM,CAAC,MAAM,CAAC,CAAA;QACzB,IAAI,CAAC,UAAU,CAAC,GAAG,CAAC,EAAE,EAAE,MAAM,CAAC,CAAA;QAC/B,IAAI,CAAC,YAAY,GAAG,IAAI,CAAC,GAAG,CAAC,IAAI,CAAC,YAAY,EAAE,UAAU,CAAC,CAAA;QAC3D,OAAO,UAAU,CAAA;IACnB,CAAC;IAED,IAAI,WAAW;QACb,OAAO,IAAI,CAAC,YAAY,CAAA;IAC1B,CAAC;CACF"}
+{"version":3,"file":"layout.js","sourceRoot":"","sources":["../src/layout.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,MAAM,CAAC,OAAO,OAAO,MAAM;IAClB,UAAU,CAUhB;IAEM,gBAAgB,CAAS;IAExB,SAAS,CAAQ;IAEjB,KAAK,CAAuB;IAE5B,YAAY,CAAQ;IAE5B,YAAY,EACV,SAAS,GAAG,KAAK,MAGf,EAAE;QACJ,IAAI,CAAC,gBAAgB,GAAG,KAAK,CAAA;QAC7B,IAAI,CAAC,KAAK,GAAG,IAAI,KAAK,EAAE,CAAA;QACxB,IAAI,CAAC,UAAU,GAAG,IAAI,GAAG,EAAE,CAAA;QAC3B,IAAI,CAAC,SAAS,GAAG,IAAI,CAAC,IAAI,CAAC,SAAS,CAAC,CAAA;QACrC,IAAI,CAAC,YAAY,GAAG,CAAC,CAAA,CAAC,uDAAuD;IAC/E,CAAC;IAED;;;OAGG;IACH,OAAO,CACL,EAAU,EACV,IAAY,EACZ,KAAa,EACb,MAAc,EACd,IAAa;QAEb,eAAe;QACf,MAAM,cAAc,GAAG,IAAI,CAAC,UAAU,CAAC,GAAG,CAAC,EAAE,CAAC,CAAA;QAC9C,IAAI,cAAc,EAAE,CAAC;YACnB,OAAO,cAAc,CAAC,IAAI,CAAA;QAC5B,CAAC;QAED,IAAI,UAAU,GAAG,CAAC,CAAA;QAClB,OACE,IAAI,CAAC,KAAK,CAAC,QAAQ,CAAC;YAClB,IAAI,EAAE,IAAI;YACV,IAAI,EAAE,UAAU;YAChB,IAAI,EAAE,KAAK;YACX,IAAI,EAAE,UAAU,GAAG,MAAM;SAC1B,CAAC;YACF,UAAU,IAAI,IAAI,CAAC,SAAS,EAC5B,CAAC;YACD,UAAU,IAAI,CAAC,CAAA;QACjB,CAAC;QAED,MAAM,MAAM,GAAG;YACb,IAAI,EAAE,IAAI;YACV,IAAI,EAAE,UAAU;YAChB,IAAI,EAAE,KAAK;YACX,IAAI,EAAE,UAAU,GAAG,MAAM;YACzB,EAAE;YACF,IAAI;SACL,CAAA;QACD,IAAI,CAAC,KAAK,CAAC,MAAM,CAAC,MAAM,CAAC,CAAA;QACzB,IAAI,CAAC,UAAU,CAAC,GAAG,CAAC,EAAE,EAAE,MAAM,CAAC,CAAA;QAC/B,IAAI,CAAC,YAAY,GAAG,IAAI,CAAC,GAAG,CAAC,IAAI,CAAC,YAAY,EAAE,UAAU,CAAC,CAAA;QAC3D,OAAO,UAAU,CAAA;IACnB,CAAC;IAED,IAAI,WAAW;QACb,OAAO,IAAI,CAAC,YAAY,CAAA;IAC1B,CAAC;CACF"}

package/dist/measureTextCanvas.d.ts

@@ -0,0 +1 @@
+export default function measureTextCanvas(text: string, fontSize: number): number;

package/dist/measureTextCanvas.js

@@ -0,0 +1,13 @@
+let canvasHandle;
+export default function measureTextCanvas(text, fontSize) {
+    if (!canvasHandle) {
+        canvasHandle = document.createElement('canvas');
+    }
+    const ctx = canvasHandle.getContext('2d');
+    if (!ctx) {
+        throw new Error('no canvas context');
+    }
+    ctx.font = ctx.font.replace(/\d+px/, `${fontSize}px`);
+    return ctx.measureText(text).width;
+}
+//# sourceMappingURL=measureTextCanvas.js.map

package/dist/measureTextCanvas.js.map

@@ -0,0 +1 @@
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package/dist/model.d.ts

@@ -81,7 +81,10 @@ declare const model: import("mobx-state-tree").IModelType<{
     colorSchemeName: import("mobx-state-tree").IType<string | undefined, string, string>;
     treeFilehandle: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISnapshotProcessor<import("mobx-state-tree").ITypeUnion<import("mobx-state-tree").ModelCreationType<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
         locationType: import("mobx-state-tree").ISimpleType<"UriLocation">;
-        uri: import("mobx-state-tree").ISimpleType<string>;
+        uri: import("mobx-state-tree").ISimpleType<string>; /**
+         * #property
+         * draw clickable node bubbles on the tree
+         */
         baseUri: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
         internetAccountId: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
         internetAccountPreAuthorization: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IModelType<{
@@ -98,12 +101,13 @@ declare const model: import("mobx-state-tree").IModelType<{
     }>>, {
         locationType: "UriLocation";
         uri: string;
-        internetAccountId: string | undefined; /**
-         * #property
-         * focus on particular subtree
-         */
+        internetAccountId: string | undefined;
         internetAccountPreAuthorization: import("mobx-state-tree").ModelSnapshotType<{
-            internetAccountType: import("mobx-state-tree").ISimpleType<string>;
+            internetAccountType: import("mobx-state-tree").ISimpleType<string>; /**
+             * #property
+             * a list of "tracks" to display, as box-like glyphs (e.g. protein
+             * domains)
+             */
             authInfo: import("mobx-state-tree").IType<any, any, any>;
         }> | undefined;
     } | import("mobx-state-tree").ModelSnapshotType<{
@@ -125,10 +129,7 @@ declare const model: import("mobx-state-tree").IModelType<{
         uri: string;
     } & Partial<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
         locationType: import("mobx-state-tree").ISimpleType<"UriLocation">;
-        uri: import("mobx-state-tree").ISimpleType<string>; /**
-         * #volatile
-         * the currently mouse-hovered row
-         */
+        uri: import("mobx-state-tree").ISimpleType<string>;
         baseUri: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
         internetAccountId: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
         internetAccountPreAuthorization: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IModelType<{
@@ -138,7 +139,10 @@ declare const model: import("mobx-state-tree").IModelType<{
     }>> & import("mobx-state-tree/dist/internal").NonEmptyObject)>, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
     msaFilehandle: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISnapshotProcessor<import("mobx-state-tree").ITypeUnion<import("mobx-state-tree").ModelCreationType<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
         locationType: import("mobx-state-tree").ISimpleType<"UriLocation">;
-        uri: import("mobx-state-tree").ISimpleType<string>;
+        uri: import("mobx-state-tree").ISimpleType<string>; /**
+         * #property
+         * draw clickable node bubbles on the tree
+         */
         baseUri: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
         internetAccountId: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
         internetAccountPreAuthorization: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IModelType<{
@@ -155,12 +159,13 @@ declare const model: import("mobx-state-tree").IModelType<{
     }>>, {
         locationType: "UriLocation";
         uri: string;
-        internetAccountId: string | undefined; /**
-         * #property
-         * focus on particular subtree
-         */
+        internetAccountId: string | undefined;
         internetAccountPreAuthorization: import("mobx-state-tree").ModelSnapshotType<{
-            internetAccountType: import("mobx-state-tree").ISimpleType<string>;
+            internetAccountType: import("mobx-state-tree").ISimpleType<string>; /**
+             * #property
+             * a list of "tracks" to display, as box-like glyphs (e.g. protein
+             * domains)
+             */
             authInfo: import("mobx-state-tree").IType<any, any, any>;
         }> | undefined;
     } | import("mobx-state-tree").ModelSnapshotType<{
@@ -182,10 +187,7 @@ declare const model: import("mobx-state-tree").IModelType<{
         uri: string;
     } & Partial<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
         locationType: import("mobx-state-tree").ISimpleType<"UriLocation">;
-        uri: import("mobx-state-tree").ISimpleType<string>; /**
-         * #volatile
-         * the currently mouse-hovered row
-         */
+        uri: import("mobx-state-tree").ISimpleType<string>;
         baseUri: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
         internetAccountId: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
         internetAccountPreAuthorization: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IModelType<{
@@ -195,7 +197,10 @@ declare const model: import("mobx-state-tree").IModelType<{
     }>> & import("mobx-state-tree/dist/internal").NonEmptyObject)>, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
     treeMetadataFilehandle: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISnapshotProcessor<import("mobx-state-tree").ITypeUnion<import("mobx-state-tree").ModelCreationType<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
         locationType: import("mobx-state-tree").ISimpleType<"UriLocation">;
-        uri: import("mobx-state-tree").ISimpleType<string>;
+        uri: import("mobx-state-tree").ISimpleType<string>; /**
+         * #property
+         * draw clickable node bubbles on the tree
+         */
         baseUri: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
         internetAccountId: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
         internetAccountPreAuthorization: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IModelType<{
@@ -212,12 +217,13 @@ declare const model: import("mobx-state-tree").IModelType<{
     }>>, {
         locationType: "UriLocation";
         uri: string;
-        internetAccountId: string | undefined; /**
-         * #property
-         * focus on particular subtree
-         */
+        internetAccountId: string | undefined;
         internetAccountPreAuthorization: import("mobx-state-tree").ModelSnapshotType<{
-            internetAccountType: import("mobx-state-tree").ISimpleType<string>;
+            internetAccountType: import("mobx-state-tree").ISimpleType<string>; /**
+             * #property
+             * a list of "tracks" to display, as box-like glyphs (e.g. protein
+             * domains)
+             */
             authInfo: import("mobx-state-tree").IType<any, any, any>;
         }> | undefined;
     } | import("mobx-state-tree").ModelSnapshotType<{
@@ -239,10 +245,7 @@ declare const model: import("mobx-state-tree").IModelType<{
         uri: string;
     } & Partial<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
         locationType: import("mobx-state-tree").ISimpleType<"UriLocation">;
-        uri: import("mobx-state-tree").ISimpleType<string>; /**
-         * #volatile
-         * the currently mouse-hovered row
-         */
+        uri: import("mobx-state-tree").ISimpleType<string>;
         baseUri: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
         internetAccountId: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
         internetAccountPreAuthorization: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IModelType<{
@@ -342,13 +345,6 @@ declare const model: import("mobx-state-tree").IModelType<{
      * #volatile
      */
     error: unknown;
-    /**
-     * #volatile
-     */
-    margin: {
-        left: number;
-        top: number;
-    };
     /**
      * #volatile
      */
@@ -794,12 +790,13 @@ declare const model: import("mobx-state-tree").IModelType<{
     treeFilehandle: {
         locationType: "UriLocation";
         uri: string;
-        internetAccountId: string | undefined; /**
-         * #property
-         * focus on particular subtree
-         */
+        internetAccountId: string | undefined;
         internetAccountPreAuthorization: import("mobx-state-tree").ModelSnapshotType<{
-            internetAccountType: import("mobx-state-tree").ISimpleType<string>;
+            internetAccountType: import("mobx-state-tree").ISimpleType<string>; /**
+             * #property
+             * a list of "tracks" to display, as box-like glyphs (e.g. protein
+             * domains)
+             */
             authInfo: import("mobx-state-tree").IType<any, any, any>;
         }> | undefined;
     } | import("mobx-state-tree").ModelSnapshotType<{
@@ -813,12 +810,13 @@ declare const model: import("mobx-state-tree").IModelType<{
     msaFilehandle: {
         locationType: "UriLocation";
         uri: string;
-        internetAccountId: string | undefined; /**
-         * #property
-         * focus on particular subtree
-         */
+        internetAccountId: string | undefined;
         internetAccountPreAuthorization: import("mobx-state-tree").ModelSnapshotType<{
-            internetAccountType: import("mobx-state-tree").ISimpleType<string>;
+            internetAccountType: import("mobx-state-tree").ISimpleType<string>; /**
+             * #property
+             * a list of "tracks" to display, as box-like glyphs (e.g. protein
+             * domains)
+             */
             authInfo: import("mobx-state-tree").IType<any, any, any>;
         }> | undefined;
     } | import("mobx-state-tree").ModelSnapshotType<{
@@ -832,12 +830,13 @@ declare const model: import("mobx-state-tree").IModelType<{
     treeMetadataFilehandle: {
         locationType: "UriLocation";
         uri: string;
-        internetAccountId: string | undefined; /**
-         * #property
-         * focus on particular subtree
-         */
+        internetAccountId: string | undefined;
         internetAccountPreAuthorization: import("mobx-state-tree").ModelSnapshotType<{
-            internetAccountType: import("mobx-state-tree").ISimpleType<string>;
+            internetAccountType: import("mobx-state-tree").ISimpleType<string>; /**
+             * #property
+             * a list of "tracks" to display, as box-like glyphs (e.g. protein
+             * domains)
+             */
             authInfo: import("mobx-state-tree").IType<any, any, any>;
         }> | undefined;
     } | import("mobx-state-tree").ModelSnapshotType<{

package/dist/model.js

@@ -7,7 +7,7 @@ import { saveAs } from 'file-saver';
 // jbrowse
 import { FileLocation, ElementId } from '@jbrowse/core/util/types/mst';
 import { openLocation } from '@jbrowse/core/util/io';
-import { measureText, notEmpty, sum } from '@jbrowse/core/util';
+import { notEmpty, sum } from '@jbrowse/core/util';
 import BaseViewModel from '@jbrowse/core/pluggableElementTypes/models/BaseViewModel';
 // locals
 import { clamp, collapse, filterHiddenLeafNodes, generateNodeIds, maxLength, setBrLength, skipBlanks, } from './util';
@@ -23,6 +23,7 @@ import { StructureModel } from './StructureModel';
 import { DialogQueueSessionMixin } from './DialogQueue';
 import { renderToSvg } from './renderToSvg';
 import { blocksX, blocksY } from './calculateBlocks';
+import measureTextCanvas from './measureTextCanvas';
 /**
  * #stateModel MsaView
  * extends
@@ -230,13 +231,6 @@ const model = types
      * #volatile
      */
     error: undefined,
-    /**
-     * #volatile
-     */
-    margin: {
-        left: 20,
-        top: 20,
-    },
     /**
      * #volatile
      */
@@ -471,17 +465,15 @@ const model = types
      * #getter
      */
     get header() {
-        var _a;
-        return ((_a = this.MSA) === null || _a === void 0 ? void 0 : _a.getHeader()) || {};
+        return this.MSA?.getHeader() || {};
     },
     /**
      * #method
      */
     getRowData(name) {
-        var _a;
         const matches = name.match(/\S+\/(\d+)-(\d+)/);
         return {
-            data: ((_a = this.MSA) === null || _a === void 0 ? void 0 : _a.getRowData(name)) || {},
+            data: this.MSA?.getRowData(name) || {},
             ...(matches && {
                 range: {
                     start: +matches[1],
@@ -500,8 +492,7 @@ const model = types
      * #getter
      */
     get alignmentNames() {
-        var _a;
-        return ((_a = this.MSA) === null || _a === void 0 ? void 0 : _a.alignmentNames) || [];
+        return this.MSA?.alignmentNames || [];
     },
     /**
      * #getter
@@ -543,17 +534,15 @@ const model = types
      * #getter
      */
     get numColumns() {
-        var _a;
-        return (((_a = this.MSA) === null || _a === void 0 ? void 0 : _a.getWidth()) || 0) - this.blanks.length;
+        return (this.MSA?.getWidth() || 0) - this.blanks.length;
     },
     /**
      * #getter
      */
     get _tree() {
-        var _a;
         return self.data.tree
             ? generateNodeIds(parseNewick(self.data.tree))
-            : ((_a = this.MSA) === null || _a === void 0 ? void 0 : _a.getTree()) || {
+            : this.MSA?.getTree() || {
                 noTree: true,
                 branchset: [],
                 id: 'empty',
@@ -611,8 +600,7 @@ const model = types
      * #getter
      */
     get structures() {
-        var _a;
-        return ((_a = this.MSA) === null || _a === void 0 ? void 0 : _a.getStructures()) || {};
+        return this.MSA?.getStructures() || {};
     },
     /**
      * #getter
@@ -631,13 +619,12 @@ const model = types
      * #getter
      */
     get blanks() {
-        var _a;
         const blanks = [];
         const strs = this.hierarchy
             .leaves()
-            .map(leaf => { var _a; return (_a = this.MSA) === null || _a === void 0 ? void 0 : _a.getRow(leaf.data.name); })
+            .map(leaf => this.MSA?.getRow(leaf.data.name))
             .filter((item) => !!item);
-        for (let i = 0; i < ((_a = strs[0]) === null || _a === void 0 ? void 0 : _a.length); i++) {
+        for (let i = 0; i < strs[0]?.length; i++) {
             let counter = 0;
             for (const str of strs) {
                 if (str[i] === '-') {
@@ -657,7 +644,7 @@ const model = types
         const MSA = this.MSA;
         return this.hierarchy
             .leaves()
-            .map(leaf => [leaf.data.name, MSA === null || MSA === void 0 ? void 0 : MSA.getRow(leaf.data.name)])
+            .map(leaf => [leaf.data.name, MSA?.getRow(leaf.data.name)])
             .filter((f) => !!f[1]);
     },
     /**
@@ -824,11 +811,10 @@ const model = types
      * #action
      */
     setMouseoveredColumn(n, chain, file) {
-        var _a;
         let j = 0;
         let i = 0;
         const { id } = self.inverseStructures[file.slice(0, -4)] || {};
-        const row = (_a = self.MSA) === null || _a === void 0 ? void 0 : _a.getRow(id);
+        const row = self.MSA?.getRow(id);
         if (row) {
             for (i = 0; i < row.length && j < n; i++) {
                 if (row[i] !== '-') {
@@ -858,12 +844,11 @@ const model = types
      * #getter
      */
     get labelsWidth() {
-        var _a;
         let x = 0;
         const { rowHeight, hierarchy, treeMetadata, fontSize } = self;
         if (rowHeight > 5) {
             for (const node of hierarchy.leaves()) {
-                x = Math.max(measureText(((_a = treeMetadata[node.data.name]) === null || _a === void 0 ? void 0 : _a.genome) || node.data.name, fontSize), x);
+                x = Math.max(measureTextCanvas(treeMetadata[node.data.name]?.genome || node.data.name, fontSize), x);
             }
         }
         return x;
@@ -872,15 +857,13 @@ const model = types
      * #getter
      */
     get secondaryStructureConsensus() {
-        var _a;
-        return (_a = self.MSA) === null || _a === void 0 ? void 0 : _a.secondaryStructureConsensus;
+        return self.MSA?.secondaryStructureConsensus;
     },
     /**
      * #getter
      */
     get seqConsensus() {
-        var _a;
-        return (_a = self.MSA) === null || _a === void 0 ? void 0 : _a.seqConsensus;
+        return self.MSA?.seqConsensus;
     },
     /**
      * #getter
@@ -900,15 +883,14 @@ const model = types
      * #getter
      */
     get adapterTrackModels() {
-        var _a;
-        return (((_a = self.MSA) === null || _a === void 0 ? void 0 : _a.tracks.map(t => ({
+        return (self.MSA?.tracks.map(t => ({
             model: {
                 ...t,
                 data: t.data ? skipBlanks(self.blanks, t.data) : undefined,
                 height: self.rowHeight,
             },
             ReactComponent: TextTrack,
-        }))) || []);
+        })) || []);
     },
     /**
      * #getter
@@ -944,12 +926,11 @@ const model = types
      * #method
      */
     rowSpecificBpToPx(rowName, position) {
-        var _a;
         const { rowNames, rows } = self;
         const index = rowNames.indexOf(rowName);
         const row = rows[index][1];
         const details = self.getRowData(rowName);
-        const offset = ((_a = details.range) === null || _a === void 0 ? void 0 : _a.start) || 0;
+        const offset = details.range?.start || 0;
         const current = position - offset;
         const s = new Set(self.blanks);
         if (current < 0) {
@@ -974,10 +955,9 @@ const model = types
      * #method
      */
     globalBpToPx(position) {
-        var _a;
         let count = 0;
         const s = new Set(self.blanks);
-        for (let k = 0; k < ((_a = self.rows[0]) === null || _a === void 0 ? void 0 : _a[1].length); k++) {
+        for (let k = 0; k < self.rows[0]?.[1].length; k++) {
             if (s.has(k) && k < position + 1) {
                 count++;
             }
@@ -1109,7 +1089,7 @@ const model = types
         // autorun synchronizes treeWidth with treeAreaWidth
         addDisposer(self, autorun(async () => {
             if (self.treeWidthMatchesArea) {
-                self.setTreeWidth(Math.max(50, self.treeAreaWidth - self.labelsWidth - 20));
+                self.setTreeWidth(Math.max(50, self.treeAreaWidth - self.labelsWidth - 10));
             }
         }));
     },