react-msaview 3.2.1 → 4.0.0

package/dist/components/msa/renderMSABlock.js

@@ -43,17 +43,19 @@ function drawTiles({ model, offsetX, ctx, visibleLeaves, theme, xStart, xEnd, })
     for (const node of visibleLeaves) {
         const { data: { name }, } = node;
         const y = node.x;
-        const str = columns[name].slice(xStart, xEnd);
-        for (let i = 0; i < str.length; i++) {
-            const letter = str[i];
-            const color = colorSchemeName === 'clustalx_protein_dynamic'
-                ? getClustalXColor(colStats[xStart + i], colStatsSums[xStart + i], model, name, xStart + i)
-                : colorSchemeName === 'percent_identity_dynamic'
-                    ? getPercentIdentityColor(colStats[xStart + i], colStatsSums[xStart + i], model, name, xStart + i)
-                    : colorScheme[letter.toUpperCase()];
-            if (bgColor) {
-                ctx.fillStyle = color || theme.palette.background.default;
-                ctx.fillRect(i * colWidth + offsetX - (offsetX % colWidth), y - rowHeight, colWidth, rowHeight);
+        const str = columns[name]?.slice(xStart, xEnd);
+        if (str) {
+            for (let i = 0; i < str.length; i++) {
+                const letter = str[i];
+                const color = colorSchemeName === 'clustalx_protein_dynamic'
+                    ? getClustalXColor(colStats[xStart + i], colStatsSums[xStart + i], model, name, xStart + i)
+                    : colorSchemeName === 'percent_identity_dynamic'
+                        ? getPercentIdentityColor(colStats[xStart + i], colStatsSums[xStart + i], model, name, xStart + i)
+                        : colorScheme[letter.toUpperCase()];
+                if (bgColor) {
+                    ctx.fillStyle = color || theme.palette.background.default;
+                    ctx.fillRect(i * colWidth + offsetX - (offsetX % colWidth), y - rowHeight, colWidth, rowHeight);
+                }
             }
         }
     }
@@ -64,21 +66,23 @@ function drawText({ model, offsetX, contrastScheme, ctx, visibleLeaves, xStart,
         for (const node of visibleLeaves) {
             const { data: { name }, } = node;
             const y = node.x;
-            const str = columns[name].slice(xStart, xEnd);
-            for (let i = 0; i < str.length; i++) {
-                const letter = str[i];
-                const color = colorScheme[letter.toUpperCase()];
-                const contrast = contrastLettering
-                    ? contrastScheme[letter.toUpperCase()] || 'black'
-                    : 'black';
-                const x = i * colWidth + offsetX - (offsetX % colWidth);
-                // note: -rowHeight/4 matches +rowHeight/4 in tree
-                ctx.fillStyle = actuallyShowDomains
-                    ? 'black'
-                    : bgColor
-                        ? contrast
-                        : color || 'black';
-                ctx.fillText(letter, x + colWidth / 2, y - rowHeight / 4);
+            const str = columns[name]?.slice(xStart, xEnd);
+            if (str) {
+                for (let i = 0; i < str.length; i++) {
+                    const letter = str[i];
+                    const color = colorScheme[letter.toUpperCase()];
+                    const contrast = contrastLettering
+                        ? contrastScheme[letter.toUpperCase()] || 'black'
+                        : 'black';
+                    const x = i * colWidth + offsetX - (offsetX % colWidth);
+                    // note: -rowHeight/4 matches +rowHeight/4 in tree
+                    ctx.fillStyle = actuallyShowDomains
+                        ? 'black'
+                        : bgColor
+                            ? contrast
+                            : color || 'black';
+                    ctx.fillText(letter, x + colWidth / 2, y - rowHeight / 4);
+                }
             }
         }
     }

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

@@ -1 +1 @@
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+{"version":3,"file":"renderMSABlock.js","sourceRoot":"","sources":["../../../src/components/msa/renderMSABlock.ts"],"names":[],"mappings":"AAKA,OAAO,EAAE,gBAAgB,EAAE,uBAAuB,EAAE,MAAM,oBAAoB,CAAA;AAG9E,MAAM,UAAU,cAAc,CAAC,EAC7B,KAAK,EACL,OAAO,EACP,OAAO,EACP,cAAc,EACd,GAAG,EACH,KAAK,EACL,0BAA0B,EAC1B,kBAAkB,EAClB,kBAAkB,GAWnB;IACC,MAAM,EACJ,QAAQ,EACR,SAAS,EACT,SAAS,EACT,QAAQ,EACR,kBAAkB,EAClB,mBAAmB,EACnB,MAAM,GACP,GAAG,KAAK,CAAA;IACT,MAAM,CAAC,GAAG,0BAA0B,IAAI,kBAAkB,CAAA;IAC1D,MAAM,EAAE,GAAG,kBAAkB,IAAI,SAAS,CAAA;IAC1C,MAAM,EAAE,GAAG,kBAAkB,IAAI,SAAS,CAAA;IAC1C,GAAG,CAAC,cAAc,EAAE,CAAA;IACpB,GAAG,CAAC,KAAK,CAAC,CAAC,EAAE,CAAC,CAAC,CAAA;IACf,GAAG,CAAC,SAAS,CAAC,CAAC,OAAO,EAAE,SAAS,GAAG,CAAC,GAAG,OAAO,CAAC,CAAA;IAChD,GAAG,CAAC,SAAS,GAAG,QAAQ,CAAA;IACxB,GAAG,CAAC,IAAI,GAAG,GAAG,CAAC,IAAI,CAAC,OAAO,CAAC,OAAO,EAAE,GAAG,QAAQ,IAAI,CAAC,CAAA;IAErD,MAAM,MAAM,GAAG,IAAI,CAAC,GAAG,CAAC,CAAC,EAAE,IAAI,CAAC,KAAK,CAAC,CAAC,OAAO,GAAG,SAAS,CAAC,GAAG,SAAS,CAAC,CAAC,CAAA;IACzE,MAAM,IAAI,GAAG,IAAI,CAAC,GAAG,CAAC,CAAC,EAAE,IAAI,CAAC,IAAI,CAAC,CAAC,OAAO,GAAG,EAAE,GAAG,SAAS,CAAC,GAAG,SAAS,CAAC,CAAC,CAAA;IAC3E,MAAM,MAAM,GAAG,IAAI,CAAC,GAAG,CAAC,CAAC,EAAE,IAAI,CAAC,KAAK,CAAC,OAAO,GAAG,QAAQ,CAAC,CAAC,CAAA;IAC1D,MAAM,IAAI,GAAG,IAAI,CAAC,GAAG,CAAC,CAAC,EAAE,IAAI,CAAC,IAAI,CAAC,CAAC,OAAO,GAAG,EAAE,CAAC,GAAG,QAAQ,CAAC,CAAC,CAAA;IAC9D,MAAM,aAAa,GAAG,MAAM,CAAC,KAAK,CAAC,MAAM,EAAE,IAAI,CAAC,CAAA;IAEhD,IAAI,CAAC,mBAAmB,EAAE,CAAC;QACzB,SAAS,CAAC;YACR,KAAK;YACL,GAAG;YACH,KAAK;YACL,OAAO;YACP,OAAO;YACP,MAAM;YACN,IAAI;YACJ,aAAa;SACd,CAAC,CAAA;IACJ,CAAC;IACD,QAAQ,CAAC;QACP,KAAK;QACL,GAAG;QACH,OAAO;QACP,cAAc;QACd,KAAK;QACL,MAAM;QACN,IAAI;QACJ,aAAa;KACd,CAAC,CAAA;IACF,GAAG,CAAC,cAAc,EAAE,CAAA;AACtB,CAAC;AAED,SAAS,SAAS,CAAC,EACjB,KAAK,EACL,OAAO,EACP,GAAG,EACH,aAAa,EACb,KAAK,EACL,MAAM,EACN,IAAI,GAUL;IACC,MAAM,EACJ,OAAO,EACP,eAAe,EACf,WAAW,EACX,QAAQ,EACR,YAAY,EACZ,OAAO,EACP,QAAQ,EACR,SAAS,GACV,GAAG,KAAK,CAAA;IAET,KAAK,MAAM,IAAI,IAAI,aAAa,EAAE,CAAC;QACjC,MAAM,EACJ,IAAI,EAAE,EAAE,IAAI,EAAE,GACf,GAAG,IAAI,CAAA;QACR,MAAM,CAAC,GAAG,IAAI,CAAC,CAAE,CAAA;QACjB,MAAM,GAAG,GAAG,OAAO,CAAC,IAAI,CAAC,EAAE,KAAK,CAAC,MAAM,EAAE,IAAI,CAAC,CAAA;QAC9C,IAAI,GAAG,EAAE,CAAC;YACR,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,GAAG,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE,CAAC;gBACpC,MAAM,MAAM,GAAG,GAAG,CAAC,CAAC,CAAE,CAAA;gBACtB,MAAM,KAAK,GACT,eAAe,KAAK,0BAA0B;oBAC5C,CAAC,CAAC,gBAAgB,CACd,QAAQ,CAAC,MAAM,GAAG,CAAC,CAAE,EACrB,YAAY,CAAC,MAAM,GAAG,CAAC,CAAE,EACzB,KAAK,EACL,IAAI,EACJ,MAAM,GAAG,CAAC,CACX;oBACH,CAAC,CAAC,eAAe,KAAK,0BAA0B;wBAC9C,CAAC,CAAC,uBAAuB,CACrB,QAAQ,CAAC,MAAM,GAAG,CAAC,CAAE,EACrB,YAAY,CAAC,MAAM,GAAG,CAAC,CAAE,EACzB,KAAK,EACL,IAAI,EACJ,MAAM,GAAG,CAAC,CACX;wBACH,CAAC,CAAC,WAAW,CAAC,MAAM,CAAC,WAAW,EAAE,CAAC,CAAA;gBACzC,IAAI,OAAO,EAAE,CAAC;oBACZ,GAAG,CAAC,SAAS,GAAG,KAAK,IAAI,KAAK,CAAC,OAAO,CAAC,UAAU,CAAC,OAAO,CAAA;oBACzD,GAAG,CAAC,QAAQ,CACV,CAAC,GAAG,QAAQ,GAAG,OAAO,GAAG,CAAC,OAAO,GAAG,QAAQ,CAAC,EAC7C,CAAC,GAAG,SAAS,EACb,QAAQ,EACR,SAAS,CACV,CAAA;gBACH,CAAC;YACH,CAAC;QACH,CAAC;IACH,CAAC;AACH,CAAC;AAED,SAAS,QAAQ,CAAC,EAChB,KAAK,EACL,OAAO,EACP,cAAc,EACd,GAAG,EACH,aAAa,EACb,MAAM,EACN,IAAI,GAUL;IACC,MAAM,EACJ,OAAO,EACP,mBAAmB,EACnB,cAAc,EACd,WAAW,EACX,OAAO,EACP,QAAQ,EACR,iBAAiB,EACjB,SAAS,GACV,GAAG,KAAK,CAAA;IACT,IAAI,cAAc,EAAE,CAAC;QACnB,KAAK,MAAM,IAAI,IAAI,aAAa,EAAE,CAAC;YACjC,MAAM,EACJ,IAAI,EAAE,EAAE,IAAI,EAAE,GACf,GAAG,IAAI,CAAA;YACR,MAAM,CAAC,GAAG,IAAI,CAAC,CAAE,CAAA;YACjB,MAAM,GAAG,GAAG,OAAO,CAAC,IAAI,CAAC,EAAE,KAAK,CAAC,MAAM,EAAE,IAAI,CAAC,CAAA;YAC9C,IAAI,GAAG,EAAE,CAAC;gBACR,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,GAAG,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE,CAAC;oBACpC,MAAM,MAAM,GAAG,GAAG,CAAC,CAAC,CAAE,CAAA;oBACtB,MAAM,KAAK,GAAG,WAAW,CAAC,MAAM,CAAC,WAAW,EAAE,CAAC,CAAA;oBAC/C,MAAM,QAAQ,GAAG,iBAAiB;wBAChC,CAAC,CAAC,cAAc,CAAC,MAAM,CAAC,WAAW,EAAE,CAAC,IAAI,OAAO;wBACjD,CAAC,CAAC,OAAO,CAAA;oBACX,MAAM,CAAC,GAAG,CAAC,GAAG,QAAQ,GAAG,OAAO,GAAG,CAAC,OAAO,GAAG,QAAQ,CAAC,CAAA;oBAEvD,kDAAkD;oBAClD,GAAG,CAAC,SAAS,GAAG,mBAAmB;wBACjC,CAAC,CAAC,OAAO;wBACT,CAAC,CAAC,OAAO;4BACP,CAAC,CAAC,QAAQ;4BACV,CAAC,CAAC,KAAK,IAAI,OAAO,CAAA;oBACtB,GAAG,CAAC,QAAQ,CAAC,MAAM,EAAE,CAAC,GAAG,QAAQ,GAAG,CAAC,EAAE,CAAC,GAAG,SAAS,GAAG,CAAC,CAAC,CAAA;gBAC3D,CAAC;YACH,CAAC;QACH,CAAC;IACH,CAAC;AACH,CAAC"}

package/dist/components/tree/TreeNodeMenu.js

@@ -5,18 +5,19 @@ import { observer } from 'mobx-react';
 const TreeNodeInfoDialog = lazy(() => import('./dialogs/TreeNodeInfoDialog'));
 const TreeMenu = observer(function ({ node, onClose, model, }) {
     const { collapsed, collapsedLeaves } = model;
+    const { name } = node;
     return (React.createElement(Menu, { anchorReference: "anchorPosition", anchorPosition: {
             top: node.y,
             left: node.x,
         }, transitionDuration: 0, keepMounted: true, open: Boolean(node), onClose: onClose },
-        React.createElement(MenuItem, { dense: true, disabled: true }, node.name),
+        React.createElement(MenuItem, { dense: true, disabled: true }, name),
         React.createElement(MenuItem, { dense: true, onClick: () => {
                 model.queueDialog(onClose => [
                     TreeNodeInfoDialog,
                     {
-                        info: model.getRowData(node.name),
+                        info: model.getRowData(name),
                         model,
-                        nodeName: node.name,
+                        nodeName: name,
                         onClose,
                     },
                 ]);

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

@@ -1 +1 @@
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package/dist/components/tree/dialogs/TreeNodeInfoDialog.js

@@ -7,15 +7,14 @@ import SequenceTextArea from '../../SequenceTextArea';
 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);
+    const res = rows.find(f => f[0] === nodeName);
     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 } })),
-            React.createElement(BaseCard, { title: "Sequence" },
-                React.createElement(SequenceTextArea, { str: [[name, sequence]] })),
+            React.createElement(BaseCard, { title: "Sequence" }, res ? (React.createElement(SequenceTextArea, { str: [res] })) : (React.createElement("div", null, "Sequence not found"))),
             metadata ? (React.createElement(BaseCard, { title: "Extra metadata" },
                 React.createElement(Attributes, { attributes: metadata }))) : null)));
 });

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

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package/dist/components/tree/renderTreeCanvas.js

@@ -62,10 +62,7 @@ export function renderNodeBubbles({ ctx, clickMap, offsetY, model, blockSizeYOve
     }
 }
 export function renderTreeLabels({ theme, model, offsetY, ctx, clickMap, blockSizeYOverride, }) {
-    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 { fontSize, showBranchLen, treeMetadata, hierarchy, collapsed, collapsedLeaves, blockSize, labelsAlignRight, drawTree, treeAreaWidth, treeWidth, treeAreaWidthMinusMargin, marginLeft, leaves, noTree, } = model;
     const by = blockSizeYOverride || blockSize;
     if (labelsAlignRight) {
         ctx.textAlign = 'right';
@@ -133,7 +130,10 @@ 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, } = model;
+    const { noTree, drawTree, drawNodeBubbles, treeWidth, highResScaleFactor, blockSize, 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

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

@@ -1 +1 @@
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package/dist/index.js

@@ -1,3 +1,4 @@
 export { default as MSAView } from './components/Loading';
 export { default as MSAModelF } from './model';
+console.log('wtf');
 //# sourceMappingURL=index.js.map

package/dist/index.js.map

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

package/dist/model/DialogQueue.d.ts

@@ -8,7 +8,7 @@ export declare function DialogQueueSessionMixin(): import("mobx-state-tree").IMo
     /**
      * #getter
      */
-    readonly DialogComponent: DialogComponentType;
+    readonly DialogComponent: DialogComponentType | undefined;
     /**
      * #getter
      */

package/dist/model.d.ts

@@ -7,6 +7,7 @@ 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 type { InterProScanResults } from './launchInterProScan';
@@ -68,22 +69,17 @@ 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
-         * array of tree parent nodes that are 'collapsed' (all children are
-         * hidden)
-         */).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<{
-            internetAccountType: import("mobx-state-tree" /**
-             * #property
-             * array of tree leaf nodes that are 'collapsed' (just that leaf node
-             * is hidden)
-             */).ISimpleType<string>;
+            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>>;
     }>> | import("mobx-state-tree").ModelCreationType<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
         locationType: import("mobx-state-tree").ISimpleType<"BlobLocation">;
-        name: import("mobx-state-tree").ISimpleType<string>;
+        name: import("mobx-state-tree" /**
+         * #property
+         * turned off tracks
+         */).ISimpleType<string>;
         blobId: import("mobx-state-tree").ISimpleType<string>;
     }>> | import("mobx-state-tree").ModelCreationType<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
         locationType: import("mobx-state-tree").ISimpleType<"LocalPathLocation">;
@@ -102,16 +98,17 @@ declare function stateModelFactory(): import("mobx-state-tree").IModelType<{
         blobId: import("mobx-state-tree").ISimpleType<string>;
     }> | import("mobx-state-tree").ModelSnapshotType<{
         locationType: import("mobx-state-tree").ISimpleType<"LocalPathLocation">;
-        localPath: import("mobx-state-tree").ISimpleType<string>;
+        localPath: import("mobx-state-tree" /**
+         * #volatile
+         * resize handle width between tree and msa area, px
+         */).ISimpleType<string>;
     }>, import("mobx-state-tree").ModelInstanceType<{
-        locationType: import(
-        /**
+        locationType: import("mobx-state-tree").ISimpleType<"BlobLocation">;
+        name: import("mobx-state-tree").ISimpleType<string>;
+        blobId: import("mobx-state-tree" /**
          * #volatile
          * the currently mouse-hovered row
-         */
-        "mobx-state-tree").ISimpleType<"BlobLocation">;
-        name: import("mobx-state-tree").ISimpleType<string>;
-        blobId: import("mobx-state-tree").ISimpleType<string>;
+         */).ISimpleType<string>;
     }, {}> | import("mobx-state-tree").ModelInstanceType<{
         locationType: import("mobx-state-tree").ISimpleType<"LocalPathLocation">;
         localPath: import("mobx-state-tree").ISimpleType<string>;
@@ -121,8 +118,7 @@ declare function stateModelFactory(): import("mobx-state-tree").IModelType<{
     } & Partial<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
         locationType: import("mobx-state-tree" /**
          * #volatile
-         * a dummy variable that is incremented when ref changes so autorun for
-         * drawing canvas commands will run
+         * the currently mouse-click column
          */).ISimpleType<"UriLocation">;
         uri: import("mobx-state-tree").ISimpleType<string>;
         baseUri: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
@@ -131,7 +127,9 @@ declare function stateModelFactory(): import("mobx-state-tree").IModelType<{
          * #volatile
          */).IModelType<{
             internetAccountType: import("mobx-state-tree").ISimpleType<string>;
-            authInfo: import("mobx-state-tree").IType<any, any, any>;
+            authInfo: import("mobx-state-tree" /**
+             * #volatile
+             */).IType<any, any, any>;
         }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
     }>> & 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<{
@@ -258,7 +256,7 @@ declare function stateModelFactory(): import("mobx-state-tree").IModelType<{
 }, {
     queueOfDialogs: [import("@jbrowse/core/util").DialogComponentType, any][];
 } & {
-    readonly DialogComponent: import("@jbrowse/core/util").DialogComponentType;
+    readonly DialogComponent: import("@jbrowse/core/util").DialogComponentType | undefined;
     readonly DialogProps: any;
 } & {
     removeActiveDialog(): void;
@@ -456,6 +454,7 @@ declare function stateModelFactory(): import("mobx-state-tree").IModelType<{
     setData(data: {
         msa?: string;
         tree?: string;
+        treeMetadata?: string;
     }): void;
     /**
      * #action
@@ -541,7 +540,7 @@ declare function stateModelFactory(): import("mobx-state-tree").IModelType<{
     /**
      * #getter
      */
-    readonly MSA: StockholmMSA | FastaMSA | ClustalMSA | null;
+    readonly MSA: StockholmMSA | FastaMSA | EmfMSA | ClustalMSA | null;
     /**
      * #getter
      */
@@ -820,7 +819,7 @@ declare function stateModelFactory(): import("mobx-state-tree").IModelType<{
         description: string;
         start: number;
         end: number;
-    }[] | undefined>;
+    }[]>;
 } & {
     /**
      * #getter

package/dist/model.js

@@ -23,6 +23,7 @@ import palettes from './ggplotPalettes';
 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';
@@ -33,6 +34,7 @@ import { DialogQueueSessionMixin } from './model/DialogQueue';
 import { TreeF } from './model/treeModel';
 import { MSAModelF } from './model/msaModel';
 import { mouseOverCoordToGlobalCoord, globalCoordToRowSpecificCoord, } from './rowCoordinateCalculations';
+import EmfTree from './parsers/EmfTree';
 /**
  * #stateModel MsaView
  * extends
@@ -90,7 +92,7 @@ function stateModelFactory() {
          * #property
          * height of each row, px
          */
-        rowHeight: 20,
+        rowHeight: 18,
         /**
          * #property
          * scroll position, Y-offset, px
@@ -105,7 +107,7 @@ function stateModelFactory() {
          * #property
          * width of columns, px
          */
-        colWidth: 16,
+        colWidth: 14,
         /**
          * #property
          * filehandle object for the tree
@@ -154,7 +156,11 @@ function stateModelFactory() {
          * data from the loaded tree/msa/treeMetadata, generally loaded by
          * autorun
          */
-        data: types.optional(DataModelF(), { tree: '', msa: '' }),
+        data: types.optional(DataModelF(), {
+            tree: '',
+            msa: '',
+            treeMetadata: '',
+        }),
         /**
          * #property
          */
@@ -513,10 +519,15 @@ function stateModelFactory() {
                 if (Stockholm.sniff(text)) {
                     return new StockholmMSA(text, self.currentAlignment);
                 }
-                if (text.startsWith('>')) {
+                else if (text.startsWith('>')) {
                     return new FastaMSA(text);
                 }
-                return new ClustalMSA(text);
+                else if (text.startsWith('SEQ')) {
+                    return new EmfMSA(text);
+                }
+                else {
+                    return new ClustalMSA(text);
+                }
             }
             return null;
         },
@@ -530,14 +541,27 @@ function stateModelFactory() {
          * #getter
          */
         get tree() {
-            const ret = self.data.tree
-                ? generateNodeIds(parseNewick(self.data.tree))
-                : this.MSA?.getTree() || {
+            const text = self.data.tree;
+            let ret;
+            if (text) {
+                let t;
+                if (text.startsWith('SEQ')) {
+                    const r = new EmfTree(text);
+                    t = r.data.tree;
+                }
+                else {
+                    t = text;
+                }
+                ret = generateNodeIds(parseNewick(t));
+            }
+            else {
+                ret = this.MSA?.getTree() || {
                     noTree: true,
-                    branchset: [],
+                    children: [],
                     id: 'empty',
                     name: 'empty',
                 };
+            }
             return reparseTree(ret);
         },
         /**
@@ -557,10 +581,10 @@ function stateModelFactory() {
          * #getter
          */
         get root() {
-            let hier = hierarchy(this.tree, d => d.branchset)
-                // todo: investigate whether needed, typescript says branchset always true
+            let hier = hierarchy(this.tree, d => d.children)
+                // todo: investigate whether needed, typescript says children always true
                 // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
-                .sum(d => (d.branchset ? 0 : 1))
+                .sum(d => (d.children ? 0 : 1))
                 .sort((a, b) => ascending(a.data.length || 1, b.data.length || 1));
             if (self.showOnly) {
                 const res = hier.find(n => n.data.id === self.showOnly);
@@ -653,7 +677,7 @@ function stateModelFactory() {
          * #getter
          */
         get fontSize() {
-            return Math.min(Math.max(6, self.rowHeight - 8), 18);
+            return Math.min(Math.max(6, self.rowHeight - 3), 18);
         },
         /**
          * #getter

package/dist/model.js.map

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