react-msaview 4.0.3 → 4.1.1

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

@@ -1 +1 @@
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package/dist/components/tree/TreeNodeMenu.js.map

@@ -1 +1 @@
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package/dist/components/tree/TreePanel.js.map

@@ -1 +1 @@
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+{"version":3,"file":"TreePanel.js","sourceRoot":"","sources":["../../../src/components/tree/TreePanel.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAErC,OAAO,UAAU,MAAM,cAAc,CAAA;AAIrC,MAAM,SAAS,GAAG,QAAQ,CAAC,UAAU,EAAE,KAAK,EAA2B;IACrE,MAAM,EAAE,aAAa,EAAE,GAAG,KAAK,CAAA;IAC/B,OAAO,CACL,6BAAK,KAAK,EAAE,EAAE,QAAQ,EAAE,QAAQ,EAAE,UAAU,EAAE,CAAC,EAAE,KAAK,EAAE,aAAa,EAAE;QACrE,oBAAC,UAAU,IAAC,KAAK,EAAE,KAAK,GAAI,CACxB,CACP,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,SAAS,CAAA"}

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

@@ -1 +1 @@
-{"version":3,"file":"TreeRuler.js","sourceRoot":"","sources":["../../../src/components/tree/TreeRuler.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AACzB,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAKrC,MAAM,SAAS,GAAG,QAAQ,CAAC,CAAC,EAAE,KAAK,EAA2B,EAAE,EAAE;IAChE,MAAM,EAAE,aAAa,EAAE,GAAG,KAAK,CAAA;IAC/B,OAAO,6BAAK,KAAK,EAAE,EAAE,UAAU,EAAE,CAAC,EAAE,KAAK,EAAE,aAAa,EAAE,GAAI,CAAA;AAChE,CAAC,CAAC,CAAA;AAEF,eAAe,SAAS,CAAA"}
+{"version":3,"file":"TreeRuler.js","sourceRoot":"","sources":["../../../src/components/tree/TreeRuler.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAIrC,MAAM,SAAS,GAAG,QAAQ,CAAC,CAAC,EAAE,KAAK,EAA2B,EAAE,EAAE;IAChE,MAAM,EAAE,aAAa,EAAE,GAAG,KAAK,CAAA;IAC/B,OAAO,6BAAK,KAAK,EAAE,EAAE,UAAU,EAAE,CAAC,EAAE,KAAK,EAAE,aAAa,EAAE,GAAI,CAAA;AAChE,CAAC,CAAC,CAAA;AAEF,eAAe,SAAS,CAAA"}

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

@@ -1,9 +1,9 @@
 import React from 'react';
+import Attributes from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/Attributes';
+import BaseCard from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/BaseCard';
 import { Dialog } from '@jbrowse/core/ui';
 import { DialogContent } from '@mui/material';
 import { observer } from 'mobx-react';
-import Attributes from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/Attributes';
-import BaseCard from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/BaseCard';
 import SequenceTextArea from '../../SequenceTextArea';
 const TreeNodeInfoDialog = observer(function ({ info, model, nodeName, onClose, }) {
     const { treeMetadata, rows } = model;

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

@@ -1 +1 @@
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+{"version":3,"file":"TreeNodeInfoDialog.js","sourceRoot":"","sources":["../../../../src/components/tree/dialogs/TreeNodeInfoDialog.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,UAAU,MAAM,8DAA8D,CAAA;AACrF,OAAO,QAAQ,MAAM,4DAA4D,CAAA;AACjF,OAAO,EAAE,MAAM,EAAE,MAAM,kBAAkB,CAAA;AACzC,OAAO,EAAE,aAAa,EAAE,MAAM,eAAe,CAAA;AAC7C,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAErC,OAAO,gBAAgB,MAAM,wBAAwB,CAAA;AAIrD,MAAM,kBAAkB,GAAG,QAAQ,CAAC,UAAU,EAC5C,IAAI,EACJ,KAAK,EACL,QAAQ,EACR,OAAO,GAMR;IACC,MAAM,EAAE,YAAY,EAAE,IAAI,EAAE,GAAG,KAAK,CAAA;IACpC,MAAM,QAAQ,GAAG,YAAY,CAAC,QAAQ,CAAC,CAAA;IACvC,MAAM,GAAG,GAAG,IAAI,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,KAAK,QAAQ,CAAC,CAAA;IAC7C,OAAO,CACL,oBAAC,MAAM,IACL,OAAO,EAAE,GAAG,EAAE;YACZ,OAAO,EAAE,CAAA;QACX,CAAC,EACD,IAAI,QACJ,KAAK,EAAC,gBAAgB,EACtB,QAAQ,EAAC,IAAI;QAEb,oBAAC,aAAa;YACZ,oBAAC,QAAQ,IAAC,KAAK,EAAC,YAAY;gBAC1B,oBAAC,UAAU,IAAC,UAAU,EAAE,EAAE,QAAQ,EAAE,GAAG,IAAI,EAAE,GAAI,CACxC;YACX,oBAAC,QAAQ,IAAC,KAAK,EAAC,UAAU,IACvB,GAAG,CAAC,CAAC,CAAC,CACL,oBAAC,gBAAgB,IAAC,GAAG,EAAE,CAAC,GAAG,CAAC,GAAI,CACjC,CAAC,CAAC,CAAC,CACF,sDAA6B,CAC9B,CACQ;YACV,QAAQ,CAAC,CAAC,CAAC,CACV,oBAAC,QAAQ,IAAC,KAAK,EAAC,gBAAgB;gBAC9B,oBAAC,UAAU,IAAC,UAAU,EAAE,QAAQ,GAAI,CAC3B,CACZ,CAAC,CAAC,CAAC,IAAI,CACM,CACT,CACV,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,kBAAkB,CAAA"}

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

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

package/dist/components/tree/renderTreeCanvas.js

@@ -130,22 +130,20 @@ export function renderTreeLabels({ theme, model, offsetY, ctx, clickMap, blockSi
 }
 export function renderTreeCanvas({ model, clickMap, ctx, offsetY, theme, highResScaleFactorOverride, blockSizeYOverride, }) {
     clickMap?.clear();
-    const { noTree, drawTree, drawNodeBubbles, treeWidth, highResScaleFactor, blockSize, fontSize, showTreeText, marginLeft, nref, 
+    const { noTree, drawTree, drawNodeBubbles, highResScaleFactor, fontSize, showTreeText, marginLeft, nref, 
     // eslint-disable-next-line  @typescript-eslint/no-unused-vars
     rowHeight: _rowHeight, // this is needed for redrawing after zoom change
      } = 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
-    // in this statement because otherwise it would be an unused variable, we
-    // 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
+    // this is a bogus use of nref, it is never less than 0. we just are using
+    // it in this statement because otherwise it would be an unused variable,
+    // we 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
         ? Number.NEGATIVE_INFINITY
         : highResScaleFactorOverride || highResScaleFactor;
     ctx.scale(k, k);
-    ctx.clearRect(0, 0, treeWidth + padding, by);
     ctx.translate(marginLeft, -offsetY);
     const font = ctx.font;
     ctx.font = font.replace(/\d+px/, `${fontSize}px`);

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

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

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

package/dist/index.js.map

@@ -1 +1 @@
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+{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,OAAO,IAAI,OAAO,EAAE,MAAM,sBAAsB,CAAA;AACzD,OAAO,EAAqB,OAAO,IAAI,SAAS,EAAE,MAAM,SAAS,CAAA"}

package/dist/launchInterProScan.js.map

@@ -1 +1 @@
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+{"version":3,"file":"launchInterProScan.js","sourceRoot":"","sources":["../src/launchInterProScan.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,UAAU,EAAE,MAAM,oBAAoB,CAAA;AAE/C,OAAO,EAAE,SAAS,EAAE,SAAS,EAAE,OAAO,EAAE,MAAM,cAAc,CAAA;AAI5D,MAAM,IAAI,GAAG,2CAA2C,CAAA;AAmBxD,KAAK,UAAU,eAAe,CAAC,EAC7B,GAAG,EACH,UAAU,EACV,OAAO,EACP,QAAQ,EACR,KAAK,GAON;IACC,MAAM,KAAK,GAAG,MAAM,SAAS,CAAC,GAAG,IAAI,eAAe,EAAE;QACpD,MAAM,EAAE,MAAM;QACd,IAAI,EAAE,IAAI,eAAe,CAAC;YACxB,KAAK,EAAE,uBAAuB;YAC9B,QAAQ,EAAE,GAAG;YACb,QAAQ,EAAE,QAAQ,CAAC,IAAI,CAAC,GAAG,CAAC;SAC7B,CAAC;KACH,CAAC,CAAA;IACF,OAAO,EAAE,CAAC,KAAK,CAAC,CAAA;IAChB,MAAM,IAAI,CAAC;QACT,KAAK;QACL,UAAU;KACX,CAAC,CAAA;IACF,MAAM,iCAAiC,CAAC,EAAE,KAAK,EAAE,KAAK,EAAE,CAAC,CAAA;AAC3D,CAAC;AAED,MAAM,UAAU,uBAAuB,CAAC,KAAa;IACnD,OAAO,SAAS,CACd,GAAG,IAAI,oBAAoB,KAAK,OAAO,CACxC,CAAA;AACH,CAAC;AAED,KAAK,UAAU,IAAI,CAAC,EAClB,UAAU,EACV,KAAK,GAIN;IACC,MAAM,GAAG,GAAG,GAAG,IAAI,oBAAoB,KAAK,EAAE,CAAA;IAC9C,IAAI,CAAC;QACH,uEAAuE;QACvE,OAAO,IAAI,EAAE,CAAC;YACZ,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,EAAE,EAAE,CAAC,EAAE,EAAE,CAAC;gBAC5B,MAAM,OAAO,CAAC,IAAI,CAAC,CAAA;gBACnB,UAAU,CAAC,EAAE,GAAG,EAAE,mBAAmB,EAAE,GAAG,CAAC,EAAE,EAAE,GAAG,EAAE,CAAC,CAAA;YACvD,CAAC;YACD,MAAM,MAAM,GAAG,MAAM,SAAS,CAAC,GAAG,CAAC,CAAA;YACnC,IAAI,MAAM,CAAC,QAAQ,CAAC,UAAU,CAAC,EAAE,CAAC;gBAChC,MAAK;YACP,CAAC;YACD,IAAI,MAAM,CAAC,QAAQ,CAAC,SAAS,CAAC,EAAE,CAAC;gBAC/B,MAAM,IAAI,KAAK,CAAC,wBAAwB,KAAK,EAAE,CAAC,CAAA;YAClD,CAAC;QACH,CAAC;IACH,CAAC;YAAS,CAAC;QACT,UAAU,EAAE,CAAA;IACd,CAAC;AACH,CAAC;AAED,MAAM,CAAC,KAAK,UAAU,kBAAkB,CAAC,EACvC,SAAS,EACT,GAAG,EACH,QAAQ,EACR,OAAO,EACP,UAAU,EACV,KAAK,GAQN;IACC,IAAI,CAAC;QACH,UAAU,CAAC,EAAE,GAAG,EAAE,aAAa,SAAS,MAAM,EAAE,CAAC,CAAA;QACjD,IAAI,SAAS,KAAK,cAAc,EAAE,CAAC;YACjC,MAAM,eAAe,CAAC;gBACpB,GAAG;gBACH,OAAO;gBACP,UAAU;gBACV,QAAQ;gBACR,KAAK;aACN,CAAC,CAAA;QACJ,CAAC;QACD,MAAM,IAAI,KAAK,CAAC,mBAAmB,CAAC,CAAA;IACtC,CAAC;YAAS,CAAC;QACT,UAAU,EAAE,CAAA;IACd,CAAC;AACH,CAAC;AAED,MAAM,CAAC,KAAK,UAAU,iCAAiC,CAAC,EACtD,KAAK,EACL,KAAK,GAIN;IACC,IAAI,CAAC;QACH,KAAK,CAAC,SAAS,CAAC;YACd,GAAG,EAAE,0BAA0B,KAAK,iGAAiG;YACrI,GAAG,EAAE,6DAA6D,KAAK,OAAO;SAC/E,CAAC,CAAA;QACF,MAAM,GAAG,GAAG,MAAM,uBAAuB,CAAC,KAAK,CAAC,CAAA;QAChD,KAAK,CAAC,sBAAsB,CAC1B,MAAM,CAAC,WAAW,CAAC,GAAG,CAAC,OAAO,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAE,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC,CAC7D,CAAA;QACD,KAAK,CAAC,cAAc,CAAC,IAAI,CAAC,CAAA;QAC1B,UAAU,CAAC,KAAK,CAAC,CAAC,MAAM,CAAC,uBAAuB,KAAK,UAAU,EAAE,SAAS,CAAC,CAAA;IAC7E,CAAC;IAAC,OAAO,CAAC,EAAE,CAAC;QACX,OAAO,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;QAChB,UAAU,CAAC,KAAK,CAAC,CAAC,WAAW,CAAC,GAAG,CAAC,EAAE,EAAE,CAAC,CAAC,CAAA;IAC1C,CAAC;YAAS,CAAC;QACT,KAAK,CAAC,SAAS,EAAE,CAAA;IACnB,CAAC;AACH,CAAC"}

package/dist/model/DialogQueue.js.map

@@ -1 +1 @@
-{"version":3,"file":"DialogQueue.js","sourceRoot":"","sources":["../../src/model/DialogQueue.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,KAAK,EAAE,MAAM,iBAAiB,CAAA;AAEvC;;GAEG;AACH,MAAM,UAAU,uBAAuB;IACrC,OAAO,KAAK;SACT,KAAK,CAAC,yBAAyB,EAAE,EAAE,CAAC;SACpC,QAAQ,CAAC,GAAG,EAAE,CAAC,CAAC;QACf,cAAc,EAAE,EAAkC;KACnD,CAAC,CAAC;SACF,KAAK,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QACd;;WAEG;QACH,IAAI,eAAe;YACjB,OAAO,IAAI,CAAC,cAAc,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAA;QACpC,CAAC;QACD;;WAEG;QACH,IAAI,WAAW;YACb,OAAO,IAAI,CAAC,cAAc,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAA;QACpC,CAAC;KACF,CAAC,CAAC;SACF,OAAO,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QAChB;;WAEG;QACH,kBAAkB;YAChB,IAAI,CAAC,cAAc,GAAG,IAAI,CAAC,cAAc,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;QACpD,CAAC;QACD;;WAEG;QACH,WAAW,CACT,EAAgE;YAEhE,MAAM,CAAC,SAAS,EAAE,KAAK,CAAC,GAAG,EAAE,CAAC,GAAG,EAAE;gBACjC,IAAI,CAAC,kBAAkB,EAAE,CAAA;YAC3B,CAAC,CAAC,CAAA;YACF,IAAI,CAAC,cAAc,GAAG,CAAC,GAAG,IAAI,CAAC,cAAc,EAAE,CAAC,SAAS,EAAE,KAAK,CAAC,CAAC,CAAA;QACpE,CAAC;KACF,CAAC,CAAC,CAAA;AACP,CAAC"}
+{"version":3,"file":"DialogQueue.js","sourceRoot":"","sources":["../../src/model/DialogQueue.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,KAAK,EAAE,MAAM,iBAAiB,CAAA;AAIvC;;GAEG;AACH,MAAM,UAAU,uBAAuB;IACrC,OAAO,KAAK;SACT,KAAK,CAAC,yBAAyB,EAAE,EAAE,CAAC;SACpC,QAAQ,CAAC,GAAG,EAAE,CAAC,CAAC;QACf,cAAc,EAAE,EAAkC;KACnD,CAAC,CAAC;SACF,KAAK,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QACd;;WAEG;QACH,IAAI,eAAe;YACjB,OAAO,IAAI,CAAC,cAAc,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAA;QACpC,CAAC;QACD;;WAEG;QACH,IAAI,WAAW;YACb,OAAO,IAAI,CAAC,cAAc,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAA;QACpC,CAAC;KACF,CAAC,CAAC;SACF,OAAO,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QAChB;;WAEG;QACH,kBAAkB;YAChB,IAAI,CAAC,cAAc,GAAG,IAAI,CAAC,cAAc,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;QACpD,CAAC;QACD;;WAEG;QACH,WAAW,CACT,EAAgE;YAEhE,MAAM,CAAC,SAAS,EAAE,KAAK,CAAC,GAAG,EAAE,CAAC,GAAG,EAAE;gBACjC,IAAI,CAAC,kBAAkB,EAAE,CAAA;YAC3B,CAAC,CAAC,CAAA;YACF,IAAI,CAAC,cAAc,GAAG,CAAC,GAAG,IAAI,CAAC,cAAc,EAAE,CAAC,SAAS,EAAE,KAAK,CAAC,CAAC,CAAA;QACpE,CAAC;KACF,CAAC,CAAC,CAAA;AACP,CAAC"}

package/dist/model.d.ts

@@ -1,16 +1,14 @@
 import React from 'react';
-import type { Buffer } from 'buffer';
-import { type Instance } from 'mobx-state-tree';
-import { type HierarchyNode } from 'd3-hierarchy';
-import type { Theme } from '@mui/material';
-import type { FileLocation as FileLocationType } from '@jbrowse/core/util/types';
-export declare function isGzip(buf: Buffer): boolean;
-import { type NodeWithIds, type NodeWithIdsAndLength } from './util';
 import ClustalMSA from './parsers/ClustalMSA';
 import EmfMSA from './parsers/EmfMSA';
-import StockholmMSA from './parsers/StockholmMSA';
 import FastaMSA from './parsers/FastaMSA';
+import StockholmMSA from './parsers/StockholmMSA';
 import type { InterProScanResults } from './launchInterProScan';
+import type { NodeWithIds, NodeWithIdsAndLength } from './util';
+import type { FileLocation as FileLocationType } from '@jbrowse/core/util/types';
+import type { Theme } from '@mui/material';
+import type { HierarchyNode } from 'd3-hierarchy';
+import type { Instance } from 'mobx-state-tree';
 export interface Accession {
     accession: string;
     name: string;
@@ -31,6 +29,7 @@ export interface ITextTrack {
     model: TextTrackModel;
 }
 export type BasicTrack = ITextTrack;
+export declare function isGzip(buf: Uint8Array): boolean;
 /**
  * #stateModel MsaView
  * extends
@@ -69,15 +68,8 @@ declare function stateModelFactory(): import("mobx-state-tree").IModelType<{
         locationType: import("mobx-state-tree").ISimpleType<"UriLocation">;
         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" /**
-         * #property
-         *
-         */).ISimpleType<string>>;
-        internetAccountPreAuthorization: import("mobx-state-tree" /**
-         * #property
-         * array of tree parent nodes that are 'collapsed' (all children are
-         * hidden)
-         */).IMaybe<import("mobx-state-tree").IModelType<{
+        internetAccountId: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+        internetAccountPreAuthorization: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IModelType<{
             internetAccountType: import("mobx-state-tree").ISimpleType<string>;
             authInfo: import("mobx-state-tree").IType<any, any, any>;
         }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
@@ -567,6 +559,10 @@ declare function stateModelFactory(): import("mobx-state-tree").IModelType<{
      * #getter
      */
     readonly rows: [string, string][];
+    /**
+     * #getter
+     */
+    readonly numRows: number;
     /**
      * #getter
      */
@@ -723,11 +719,11 @@ declare function stateModelFactory(): import("mobx-state-tree").IModelType<{
     /**
      * #getter
      */
-    readonly adapterTrackModels: ITextTrack[];
+    readonly adapterTrackModels: BasicTrack[];
     /**
      * #getter
      */
-    readonly tracks: ITextTrack[];
+    readonly tracks: BasicTrack[];
     /**
      * #getter
      */
@@ -866,9 +862,12 @@ declare function stateModelFactory(): import("mobx-state-tree").IModelType<{
      * #action
      */
     setFilter(arg: string, flag: boolean): void;
+    /**
+     * #action
+     */
+    showEntire(): void;
     afterCreate(): void;
 }, import("mobx-state-tree")._NotCustomized, {
-    height: number;
     drawLabels: boolean;
     labelsAlignRight: boolean;
     treeAreaWidth: number;
@@ -893,6 +892,7 @@ declare function stateModelFactory(): import("mobx-state-tree").IModelType<{
     colWidth: number;
     currentAlignment: number;
     type: "MsaView";
+    height: number;
     treeFilehandle: {
         locationType: "UriLocation";
         uri: string;

package/dist/model.js

@@ -1,40 +1,35 @@
-import { autorun, transaction } from 'mobx';
-import { cast, types, addDisposer } from 'mobx-state-tree';
-import { hierarchy, cluster } from 'd3-hierarchy';
+import { groupBy, notEmpty, sum } from '@jbrowse/core/util';
+import { openLocation } from '@jbrowse/core/util/io';
+import { ElementId, FileLocation } from '@jbrowse/core/util/types/mst';
+import { colord } from 'colord';
 import { ascending } from 'd3-array';
-import Stockholm from 'stockholm-js';
+import { cluster, hierarchy } from 'd3-hierarchy';
 import { saveAs } from 'file-saver';
+import { autorun, transaction } from 'mobx';
+import { addDisposer, cast, types } from 'mobx-state-tree';
 import { ungzip } from 'pako';
-// jbrowse
-import { FileLocation, ElementId } from '@jbrowse/core/util/types/mst';
-import { openLocation } from '@jbrowse/core/util/io';
-import { groupBy, notEmpty, sum } from '@jbrowse/core/util';
-export function isGzip(buf) {
-    return buf[0] === 31 && buf[1] === 139 && buf[2] === 8;
-}
-// locals
-import { clamp, collapse, generateNodeIds, maxLength, setBrLength, skipBlanks, len, } from './util';
-import { colord } from 'colord';
-import { reparseTree } from './reparseTree';
+import Stockholm from 'stockholm-js';
 import { blocksX, blocksY } from './calculateBlocks';
-import { measureTextCanvas } from './measureTextCanvas';
-import palettes from './ggplotPalettes';
-// components
-import TextTrack from './components/TextTrack';
-// parsers
-import ClustalMSA from './parsers/ClustalMSA';
-import EmfMSA from './parsers/EmfMSA';
-import StockholmMSA from './parsers/StockholmMSA';
-import FastaMSA from './parsers/FastaMSA';
-import parseNewick from './parseNewick';
 import colorSchemes from './colorSchemes';
-// models
+import TextTrack from './components/TextTrack';
+import palettes from './ggplotPalettes';
+import { measureTextCanvas } from './measureTextCanvas';
 import { DataModelF } from './model/DataModel';
 import { DialogQueueSessionMixin } from './model/DialogQueue';
-import { TreeModelF } from './model/treeModel';
 import { MSAModelF } from './model/msaModel';
-import { mouseOverCoordToGlobalCoord, globalCoordToRowSpecificCoord, } from './rowCoordinateCalculations';
+import { TreeModelF } from './model/treeModel';
+import parseNewick from './parseNewick';
+import ClustalMSA from './parsers/ClustalMSA';
+import EmfMSA from './parsers/EmfMSA';
 import EmfTree from './parsers/EmfTree';
+import FastaMSA from './parsers/FastaMSA';
+import StockholmMSA from './parsers/StockholmMSA';
+import { reparseTree } from './reparseTree';
+import { globalCoordToRowSpecificCoord, mouseOverCoordToGlobalCoord, } from './rowCoordinateCalculations';
+import { clamp, collapse, generateNodeIds, len, maxLength, setBrLength, skipBlanks, } from './util';
+export function isGzip(buf) {
+    return buf[0] === 31 && buf[1] === 139 && buf[2] === 8;
+}
 /**
  * #stateModel MsaView
  * extends
@@ -184,7 +179,7 @@ function stateModelFactory() {
          * high resolution scale factor, helps make canvas look better on hi-dpi
          * screens
          */
-        highResScaleFactor: 1,
+        highResScaleFactor: 2,
         /**
          * #volatile
          */
@@ -656,6 +651,12 @@ function stateModelFactory() {
                 .map(leaf => [leaf.data.name, MSA?.getRow(leaf.data.name)])
                 .filter((f) => !!f[1]);
         },
+        /**
+         * #getter
+         */
+        get numRows() {
+            return this.rows.length;
+        },
         /**
          * #getter
          */
@@ -803,7 +804,9 @@ function stateModelFactory() {
          * #getter
          */
         get showMsaLetters() {
-            return self.drawMsaLetters && self.rowHeight >= 5;
+            return (self.drawMsaLetters &&
+                self.rowHeight >= 5 &&
+                self.colWidth > self.rowHeight / 2);
         },
         /**
          * #getter
@@ -1205,6 +1208,15 @@ function stateModelFactory() {
         setFilter(arg, flag) {
             self.featureFilters.set(arg, flag);
         },
+        /**
+         * #action
+         */
+        showEntire() {
+            self.rowHeight = self.msaAreaHeight / self.numRows;
+            self.colWidth = self.msaAreaWidth / self.numColumns;
+            self.scrollX = 0;
+            self.scrollY = 0;
+        },
         afterCreate() {
             addDisposer(self, autorun(() => {
                 for (const key of self.tidyInterProAnnotationTypes.keys()) {

package/dist/model.js.map

@@ -1 +1 @@
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package/dist/parsers/ClustalMSA.js.map

@@ -1 +1 @@
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package/dist/parsers/EmfMSA.js.map

@@ -1 +1 @@
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package/dist/parsers/StockholmMSA.js.map

@@ -1 +1 @@
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+{"version":3,"file":"StockholmMSA.js","sourceRoot":"","sources":["../../src/parsers/StockholmMSA.ts"],"names":[],"mappings":"AAAA,OAAO,SAAS,MAAM,cAAc,CAAA;AAEpC,OAAO,WAAW,MAAM,gBAAgB,CAAA;AACxC,OAAO,EAAoB,eAAe,EAAE,MAAM,SAAS,CAAA;AAiB3D,MAAM,CAAC,OAAO,OAAO,YAAY;IACvB,IAAI,CAAkB;IACtB,GAAG,CAAgB;IAE3B,YAAY,IAAY,EAAE,gBAAwB;QAChD,MAAM,GAAG,GAAG,SAAS,CAAC,QAAQ,CAAC,IAAI,CAAC,CAAA;QACpC,IAAI,CAAC,IAAI,GAAG,GAAG,CAAA;QACf,IAAI,CAAC,GAAG,GAAG,GAAG,CAAC,gBAAgB,CAAC,CAAA;IAClC,CAAC;IAED,MAAM;QACJ,OAAO,IAAI,CAAC,GAAG,CAAA;IACjB,CAAC;IAED,MAAM,CAAC,IAAY;QACjB,OAAO,IAAI,CAAC,GAAG,CAAC,OAAO,CAAC,IAAI,CAAC,IAAI,EAAE,CAAA;IACrC,CAAC;IAED,QAAQ;QACN,MAAM,IAAI,GAAG,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC,CAAC,CAAE,CAAA;QAC9C,OAAO,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,CAAC,MAAM,CAAA;IACjC,CAAC;IAED,IAAI,cAAc;QAChB,OAAO,IAAI,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,GAAG,EAAE,GAAG,EAAE,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,IAAI,aAAa,GAAG,GAAG,CAAC,EAAE,CAAC,CAAA;IAC9E,CAAC;IAED,SAAS;QACP,OAAO;YACL,OAAO,EAAE,IAAI,CAAC,GAAG,CAAC,EAAE;YACpB,UAAU,EAAE,IAAI,CAAC,GAAG,CAAC,EAAE,EAAE,EAAE;YAC3B,MAAM,EAAE,IAAI,CAAC,GAAG,CAAC,EAAE,EAAE,EAAE;SACxB,CAAA;IACH,CAAC;IAED,UAAU,CAAC,OAAe;QACxB,OAAO;YACL,IAAI,EAAE,OAAO;YACb,SAAS,EAAE,IAAI,CAAC,GAAG,CAAC,EAAE,EAAE,EAAE,CAAC,OAAO,CAAC;YACnC,MAAM,EAAE,IAAI,CAAC,GAAG,CAAC,EAAE,EAAE,EAAE,EAAE,CAAC,OAAO,CAAC;SACnC,CAAA;IACH,CAAC;IAED,QAAQ;QACN,OAAO,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,GAAG,CAAC,OAAO,CAAC,CAAA;IACtC,CAAC;IAED,YAAY,KAAI,CAAC;IAEjB,aAAa;QACX,MAAM,QAAQ,GAAG,sCAAsC,CAAA;QACvD,MAAM,GAAG,GAAG,IAAI,CAAC,GAAG,CAAA;QACpB,MAAM,IAAI,GAAG,MAAM,CAAC,OAAO,CAAC,GAAG,CAAC,EAAE,EAAE,EAAE,IAAI,EAAE,CAAC;aAC1C,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,EAAE,EAAE,QAAQ,CAAC,IAAI,CAAC,EAAE,CAAC,CAAU,CAAC;aACnD,MAAM,CAAC,CAAC,IAAI,EAAqC,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;aAC9D,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,KAAK,CAAC,EAAE,EAAE;YACnB,MAAM,GAAG,GAAG,KAAK,CAAC,CAAC,CAAE,CAAC,WAAW,EAAE,CAAA;YACnC,MAAM,KAAK,GAAG,KAAK,CAAC,CAAC,CAAE,CAAA;YACvB,MAAM,QAAQ,GAAG,CAAC,KAAK,CAAC,CAAC,CAAE,CAAA;YAC3B,MAAM,MAAM,GAAG,CAAC,KAAK,CAAC,CAAC,CAAE,CAAA;YACzB,OAAO,EAAE,EAAE,EAAE,GAAG,EAAE,KAAK,EAAE,QAAQ,EAAE,MAAM,EAAE,CAAA;QAC7C,CAAC,CAAC,CAAA;QAEJ,MAAM,GAAG,GAAG,EAAoD,CAAA;QAChE,KAAK,MAAM,KAAK,IAAI,IAAI,EAAE,CAAC;YACzB,MAAM,EAAE,EAAE,EAAE,GAAG,IAAI,EAAE,GAAG,KAAK,CAAA;YAC7B,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,CAAC;gBACb,GAAG,CAAC,EAAE,CAAC,GAAG,EAAE,CAAA;YACd,CAAC;YACD,GAAG,CAAC,EAAE,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;QACpB,CAAC;QACD,OAAO,GAAG,CAAA;IACZ,CAAC;IAED,OAAO;QACL,MAAM,IAAI,GAAG,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,CAAA;QAChC,OAAO,IAAI;YACT,CAAC,CAAC,eAAe,CAAC,WAAW,CAAC,IAAI,CAAC,CAAC;YACpC,CAAC,CAAC;gBACE,EAAE,EAAE,MAAM;gBACV,IAAI,EAAE,MAAM;gBACZ,MAAM,EAAE,IAAI;gBACZ,QAAQ,EAAE,IAAI,CAAC,QAAQ,EAAE,CAAC,GAAG,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;oBACrC,EAAE,EAAE,IAAI;oBACR,QAAQ,EAAE,EAAE;oBACZ,IAAI;iBACL,CAAC,CAAC;aACJ,CAAA;IACP,CAAC;IAED,IAAI,YAAY;QACd,OAAO,IAAI,CAAC,GAAG,CAAC,EAAE,EAAE,QAAQ,CAAA;IAC9B,CAAC;IACD,IAAI,2BAA2B;QAC7B,OAAO,IAAI,CAAC,GAAG,CAAC,EAAE,EAAE,OAAO,CAAA;IAC7B,CAAC;IAED,IAAI,MAAM;QACR,OAAO;YACL;gBACE,EAAE,EAAE,cAAc;gBAClB,IAAI,EAAE,oBAAoB;gBAC1B,IAAI,EAAE,IAAI,CAAC,YAAY;gBACvB,iBAAiB,EAAE,EAAE;aACtB;YACD;gBACE,EAAE,EAAE,iBAAiB;gBACrB,IAAI,EAAE,qBAAqB;gBAC3B,IAAI,EAAE,IAAI,CAAC,2BAA2B;gBACtC,iBAAiB,EAAE;oBACjB,GAAG,EAAE,MAAM;oBACX,GAAG,EAAE,WAAW;iBACjB;aACF;SACF,CAAA;IACH,CAAC;CACF"}

package/dist/renderToSvg.d.ts

@@ -1,5 +1,5 @@
-import type { Theme } from '@mui/material';
 import type { MsaViewModel } from './model';
+import type { Theme } from '@mui/material';
 export declare function renderToSvg(model: MsaViewModel, opts: {
     theme: Theme;
     includeMinimap?: boolean;

package/dist/renderToSvg.js

@@ -1,13 +1,12 @@
 /* eslint-disable react-refresh/only-export-components */
 import React from 'react';
-import { createRoot } from 'react-dom/client';
-import { when } from 'mobx';
 import { renderToStaticMarkup } from '@jbrowse/core/util';
-import { renderTreeCanvas } from './components/tree/renderTreeCanvas';
-import { renderMSABlock } from './components/msa/renderMSABlock';
-import { colorContrast } from './util';
+import { when } from 'mobx';
 import MinimapSVG from './components/minimap/MinimapSVG';
 import { renderBoxFeatureCanvasBlock } from './components/msa/renderBoxFeatureCanvasBlock';
+import { renderMSABlock } from './components/msa/renderMSABlock';
+import { renderTreeCanvas } from './components/tree/renderTreeCanvas';
+import { colorContrast } from './util';
 export async function renderToSvg(model, opts) {
     await when(() => !!model.dataInitialized);
     const { width, height, scrollX, scrollY } = model;
@@ -41,7 +40,7 @@ async function render({ width, height, offsetX, offsetY, theme, model, includeMi
     const Wrapper = includeMinimap ? MinimapWrapper : NullWrapper;
     return renderToStaticMarkup(React.createElement(SvgWrapper, { width: width, height: height },
         React.createElement(Wrapper, { model: model },
-            React.createElement(CoreRendering, { Context: Context, model: model, theme: theme, offsetX: offsetX, offsetY: offsetY, width: width, height: height }))), createRoot);
+            React.createElement(CoreRendering, { Context: Context, model: model, theme: theme, offsetX: offsetX, offsetY: offsetY, width: width, height: height }))));
 }
 function CoreRendering({ model, theme, width, height, offsetX, offsetY, Context, }) {
     const clipId1 = 'tree';