react-msaview 4.4.5 → 4.5.0

package/dist/components/tree/TreeNodeMenu.js

@@ -29,10 +29,10 @@ const TreeMenu = observer(function ({ node, onClose, model, }) {
                 }
                 else {
                     if (node.id.endsWith('-leafnode')) {
-                        model.toggleCollapsed2(node.id);
+                        model.toggleCollapsedLeaf(node.id);
                     }
                     else {
-                        model.toggleCollapsed2(`${node.id}-leafnode`);
+                        model.toggleCollapsedLeaf(`${node.id}-leafnode`);
                     }
                 }
                 onClose();

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

@@ -1 +1 @@
-{"version":3,"file":"TreeNodeMenu.js","sourceRoot":"","sources":["../../../src/components/tree/TreeNodeMenu.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,IAAI,EAAE,MAAM,OAAO,CAAA;AAEnC,OAAO,EAAE,IAAI,EAAE,QAAQ,EAAE,MAAM,eAAe,CAAA;AAC9C,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAIrC,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,GAUN;IACC,MAAM,EAAE,SAAS,EAAE,eAAe,EAAE,GAAG,KAAK,CAAA;IAC5C,MAAM,EAAE,IAAI,EAAE,GAAG,IAAI,CAAA;IACrB,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,CACI;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;wBAC5B,KAAK;wBACL,QAAQ,EAAE,IAAI;wBACd,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;QACX,oBAAC,QAAQ,IACP,KAAK,QACL,OAAO,EAAE,GAAG,EAAE;gBACZ,KAAK,CAAC,cAAc,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;gBAC/B,OAAO,EAAE,CAAA;YACX,CAAC,yCAGQ;QACV,KAAK,CAAC,UAAU,CAAC,CAAC,CAAC,CAClB,oBAAC,QAAQ,IACP,KAAK,QACL,OAAO,EAAE,GAAG,EAAE;gBACZ,KAAK,CAAC,cAAc,CAAC,SAAS,CAAC,CAAA;gBAC/B,OAAO,EAAE,CAAA;YACX,CAAC,0BAGQ,CACZ,CAAC,CAAC,CAAC,IAAI,CACH,CACR,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,QAAQ,CAAA"}
+{"version":3,"file":"TreeNodeMenu.js","sourceRoot":"","sources":["../../../src/components/tree/TreeNodeMenu.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,IAAI,EAAE,MAAM,OAAO,CAAA;AAEnC,OAAO,EAAE,IAAI,EAAE,QAAQ,EAAE,MAAM,eAAe,CAAA;AAC9C,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAIrC,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,GAUN;IACC,MAAM,EAAE,SAAS,EAAE,eAAe,EAAE,GAAG,KAAK,CAAA;IAC5C,MAAM,EAAE,IAAI,EAAE,GAAG,IAAI,CAAA;IACrB,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,CACI;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;wBAC5B,KAAK;wBACL,QAAQ,EAAE,IAAI;wBACd,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,mBAAmB,CAAC,IAAI,CAAC,EAAE,CAAC,CAAA;oBACpC,CAAC;yBAAM,CAAC;wBACN,KAAK,CAAC,mBAAmB,CAAC,GAAG,IAAI,CAAC,EAAE,WAAW,CAAC,CAAA;oBAClD,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;QACX,oBAAC,QAAQ,IACP,KAAK,QACL,OAAO,EAAE,GAAG,EAAE;gBACZ,KAAK,CAAC,cAAc,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;gBAC/B,OAAO,EAAE,CAAA;YACX,CAAC,yCAGQ;QACV,KAAK,CAAC,UAAU,CAAC,CAAC,CAAC,CAClB,oBAAC,QAAQ,IACP,KAAK,QACL,OAAO,EAAE,GAAG,EAAE;gBACZ,KAAK,CAAC,cAAc,CAAC,SAAS,CAAC,CAAA;gBAC/B,OAAO,EAAE,CAAA;YACX,CAAC,0BAGQ,CACZ,CAAC,CAAC,CAAC,IAAI,CACH,CACR,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,QAAQ,CAAA"}

package/dist/components/tree/renderTreeCanvas.js

@@ -41,7 +41,7 @@ export function renderNodeBubbles({ ctx, clickMap, offsetY, model, blockSizeYOve
         // @ts-expect-error
         const { [val]: x, data } = node;
         const y = node.x;
-        const { id = '', name = '' } = data;
+        const { id, name } = data;
         if (node.height > 1 &&
             y > offsetY - extendBounds &&
             y < offsetY + by + extendBounds) {

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

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

@@ -0,0 +1,22 @@
+export declare const defaultRowHeight = 16;
+export declare const defaultColWidth = 12;
+export declare const defaultHeight = 550;
+export declare const defaultScrollX = 0;
+export declare const defaultScrollY = 0;
+export declare const defaultCurrentAlignment = 0;
+export declare const defaultShowDomains = false;
+export declare const defaultHideGaps = true;
+export declare const defaultAllowedGappyness = 100;
+export declare const defaultContrastLettering = true;
+export declare const defaultSubFeatureRows = false;
+export declare const defaultDrawMsaLetters = true;
+export declare const defaultBgColor = true;
+export declare const defaultColorSchemeName = "maeditor";
+export declare const defaultDrawLabels = true;
+export declare const defaultLabelsAlignRight = false;
+export declare const defaultTreeAreaWidth = 400;
+export declare const defaultTreeWidth = 300;
+export declare const defaultTreeWidthMatchesArea = true;
+export declare const defaultShowBranchLen = true;
+export declare const defaultDrawTree = true;
+export declare const defaultDrawNodeBubbles = true;

package/dist/constants.js

@@ -0,0 +1,26 @@
+// Main model defaults
+export const defaultRowHeight = 16;
+export const defaultColWidth = 12;
+export const defaultHeight = 550;
+export const defaultScrollX = 0;
+export const defaultScrollY = 0;
+export const defaultCurrentAlignment = 0;
+export const defaultShowDomains = false;
+export const defaultHideGaps = true;
+export const defaultAllowedGappyness = 100;
+export const defaultContrastLettering = true;
+export const defaultSubFeatureRows = false;
+export const defaultDrawMsaLetters = true;
+// MSA model defaults
+export const defaultBgColor = true;
+export const defaultColorSchemeName = 'maeditor';
+// Tree model defaults
+export const defaultDrawLabels = true;
+export const defaultLabelsAlignRight = false;
+export const defaultTreeAreaWidth = 400;
+export const defaultTreeWidth = 300;
+export const defaultTreeWidthMatchesArea = true;
+export const defaultShowBranchLen = true;
+export const defaultDrawTree = true;
+export const defaultDrawNodeBubbles = true;
+//# sourceMappingURL=constants.js.map

package/dist/constants.js.map

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

@@ -1 +1 @@
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package/dist/model/msaModel.js

@@ -1,4 +1,5 @@
 import { types } from 'mobx-state-tree';
+import { defaultBgColor, defaultColorSchemeName } from '../constants';
 /**
  * #stateModel MSAModel
  */
@@ -10,12 +11,12 @@ export function MSAModelF() {
          * #property
          * draw MSA tiles with a background color
          */
-        bgColor: true,
+        bgColor: defaultBgColor,
         /**
          * #property
          * default color scheme name
          */
-        colorSchemeName: 'maeditor',
+        colorSchemeName: defaultColorSchemeName,
     })
         .actions(self => ({
         /**

package/dist/model/msaModel.js.map

@@ -1 +1 @@
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+{"version":3,"file":"msaModel.js","sourceRoot":"","sources":["../../src/model/msaModel.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,KAAK,EAAE,MAAM,iBAAiB,CAAA;AAEvC,OAAO,EAAE,cAAc,EAAE,sBAAsB,EAAE,MAAM,cAAc,CAAA;AAErE;;GAEG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,MAAM,UAAU,SAAS;IACvB,OAAO,KAAK;SACT,KAAK,CAAC;QACL;;;WAGG;QACH,OAAO,EAAE,cAAc;QAEvB;;;WAGG;QACH,eAAe,EAAE,sBAAsB;KACxC,CAAC;SACD,OAAO,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QAChB;;;WAGG;QACH,kBAAkB,CAAC,IAAY;YAC7B,IAAI,CAAC,eAAe,GAAG,IAAI,CAAA;QAC7B,CAAC;QAED;;WAEG;QACH,UAAU,CAAC,GAAY;YACrB,IAAI,CAAC,OAAO,GAAG,GAAG,CAAA;QACpB,CAAC;KACF,CAAC,CAAC,CAAA;AACP,CAAC"}

package/dist/model/treeModel.js

@@ -1,4 +1,5 @@
 import { types } from 'mobx-state-tree';
+import { defaultDrawLabels, defaultDrawNodeBubbles, defaultDrawTree, defaultLabelsAlignRight, defaultShowBranchLen, defaultTreeAreaWidth, defaultTreeWidth, defaultTreeWidthMatchesArea, } from '../constants';
 /**
  * #stateModel Tree
  */
@@ -9,44 +10,44 @@ export function TreeModelF() {
         /**
          * #property
          */
-        drawLabels: true,
+        drawLabels: defaultDrawLabels,
         /**
          * #property
          * right-align the labels
          */
-        labelsAlignRight: false,
+        labelsAlignRight: defaultLabelsAlignRight,
         /**
          * #property
          * width of the area the tree is drawn in, px
          */
-        treeAreaWidth: types.optional(types.number, 400),
+        treeAreaWidth: types.optional(types.number, defaultTreeAreaWidth),
         /**
          * #property
          * width of the tree within the treeArea, px
          */
-        treeWidth: types.optional(types.number, 300),
+        treeWidth: types.optional(types.number, defaultTreeWidth),
         /**
          * #getter
          * synchronization that matches treeWidth to treeAreaWidth
          */
-        treeWidthMatchesArea: true,
+        treeWidthMatchesArea: defaultTreeWidthMatchesArea,
         /**
          * #property
          * use "branch length" e.g. evolutionary distance to draw tree branch
          * lengths. if false, the layout is a "cladogram" that does not take into
          * account evolutionary distances
          */
-        showBranchLen: true,
+        showBranchLen: defaultShowBranchLen,
         /**
          * #property
          * draw tree, boolean
          */
-        drawTree: true,
+        drawTree: defaultDrawTree,
         /**
          * #property
          * draw clickable node bubbles on the tree
          */
-        drawNodeBubbles: true,
+        drawNodeBubbles: defaultDrawNodeBubbles,
     })
         .actions(self => ({
         /**

package/dist/model/treeModel.js.map

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

@@ -1,3 +1,4 @@
+import A3mMSA from './parsers/A3mMSA';
 import ClustalMSA from './parsers/ClustalMSA';
 import EmfMSA from './parsers/EmfMSA';
 import FastaMSA from './parsers/FastaMSA';
@@ -358,7 +359,7 @@ declare function stateModelFactory(): import("mobx-state-tree").IModelType<{
      */
     setLoadingMSA(arg: boolean): void;
     /**
-     * #volatile
+     * #action
      */
     setShowZoomStar(arg: boolean): void;
     /**
@@ -429,7 +430,7 @@ declare function stateModelFactory(): import("mobx-state-tree").IModelType<{
     /**
      * #action
      */
-    toggleCollapsed2(node: string): void;
+    toggleCollapsedLeaf(node: string): void;
     /**
      * #action
      */
@@ -463,6 +464,11 @@ declare function stateModelFactory(): import("mobx-state-tree").IModelType<{
      */
     setTreeMetadata(result: string): void;
 } & {
+    /**
+     * #getter
+     * hideGaps takes effect when there are collapsed rows or allowedGappyness < 100
+     */
+    readonly hideGapsEffective: boolean;
     /**
      * #getter
      */
@@ -516,7 +522,7 @@ declare function stateModelFactory(): import("mobx-state-tree").IModelType<{
     /**
      * #getter
      */
-    readonly MSA: StockholmMSA | FastaMSA | EmfMSA | ClustalMSA | null;
+    readonly MSA: StockholmMSA | A3mMSA | FastaMSA | EmfMSA | ClustalMSA | null;
     /**
      * #getter
      */
@@ -533,6 +539,15 @@ declare function stateModelFactory(): import("mobx-state-tree").IModelType<{
      * #getter
      */
     readonly mouseOverRowName: string | undefined;
+    /**
+     * #getter
+     * Returns insertion info if mouse is hovering over an insertion indicator
+     */
+    readonly hoveredInsertion: {
+        rowName: string;
+        col: number;
+        letters: string;
+    } | undefined;
     /**
      * #getter
      */
@@ -554,6 +569,14 @@ declare function stateModelFactory(): import("mobx-state-tree").IModelType<{
      * #getter
      */
     readonly blanksSet: Set<number>;
+    /**
+     * #getter
+     * Returns a map of row name to array of insertions with display position and letters
+     */
+    readonly insertionPositions: Map<string, {
+        pos: number;
+        letters: string;
+    }[]>;
     /**
      * #getter
      */
@@ -588,6 +611,29 @@ declare function stateModelFactory(): import("mobx-state-tree").IModelType<{
      * #getter
      */
     readonly colStatsSums: number[];
+    /**
+     * #getter
+     * Pre-computed consensus letter and percent identity color per column.
+     * Used by percent_identity_dynamic color scheme.
+     */
+    readonly colConsensus: {
+        letter: string;
+        color: string | undefined;
+    }[];
+    /**
+     * #getter
+     * Pre-computed ClustalX colors per column.
+     * Returns a map of letter -> color for each column.
+     * ref http://www.jalview.org/help/html/colourSchemes/clustal.html
+     */
+    readonly colClustalX: Record<string, string>[];
+    /**
+     * #getter
+     * Conservation score per column using Shannon entropy (biojs-msa style).
+     * Conservation = (1 - H/Hmax) * (1 - gapFraction)
+     * Returns values 0-1 where 1 = fully conserved, 0 = no conservation.
+     */
+    readonly conservation: number[];
     /**
      * #getter
      * generates a new tree that is clustered with x,y positions
@@ -649,6 +695,11 @@ declare function stateModelFactory(): import("mobx-state-tree").IModelType<{
      * #action
      */
     setDrawMsaLetters(arg: boolean): void;
+    /**
+     * #action
+     * Calculate a neighbor joining tree from the current MSA using BLOSUM62 distances
+     */
+    calculateNeighborJoiningTreeFromMSA(): void;
     /**
      * #action
      */
@@ -717,10 +768,6 @@ declare function stateModelFactory(): import("mobx-state-tree").IModelType<{
      * #getter
      */
     readonly seqConsensus: string | undefined;
-    /**
-     * #getter
-     */
-    readonly conservation: string[];
     /**
      * #getter
      */
@@ -732,7 +779,7 @@ declare function stateModelFactory(): import("mobx-state-tree").IModelType<{
     /**
      * #getter
      */
-    readonly turnedOnTracks: import("./types").ITextTrack[];
+    readonly turnedOnTracks: BasicTrack[];
     /**
      * #getter
      */
@@ -858,6 +905,7 @@ declare function stateModelFactory(): import("mobx-state-tree").IModelType<{
     exportSVG(opts: {
         theme: Theme;
         includeMinimap?: boolean;
+        includeTracks?: boolean;
         exportType: string;
     }): Promise<void>;
     /**
@@ -886,13 +934,206 @@ declare function stateModelFactory(): import("mobx-state-tree").IModelType<{
      */
     fitHorizontally(): void;
     afterCreate(): void;
-}, import("mobx-state-tree")._NotCustomized, {
-    data: {
-        treeMetadata?: string | undefined;
-        msa?: string | undefined;
-        tree?: string | undefined;
-    };
-}>;
+}, import("mobx-state-tree")._NotCustomized, Omit<import("mobx-state-tree").ModelSnapshotType<{
+    drawLabels: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    labelsAlignRight: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    treeAreaWidth: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
+    treeWidth: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
+    treeWidthMatchesArea: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    showBranchLen: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    drawTree: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    drawNodeBubbles: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+} & {
+    bgColor: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    colorSchemeName: import("mobx-state-tree").IType<string | undefined, string, string>;
+} & {
+    id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
+    showDomains: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    hideGaps: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    allowedGappyness: import("mobx-state-tree").IType<number | undefined, number, number>;
+    contrastLettering: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    subFeatureRows: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    type: import("mobx-state-tree").ISimpleType<"MsaView">;
+    drawMsaLetters: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    height: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
+    rowHeight: import("mobx-state-tree").IType<number | undefined, number, number>;
+    scrollY: import("mobx-state-tree").IType<number | undefined, number, number>;
+    scrollX: import("mobx-state-tree").IType<number | undefined, number, number>;
+    colWidth: import("mobx-state-tree").IType<number | undefined, number, number>;
+    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>;
+        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<{
+            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>;
+        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">;
+        localPath: import("mobx-state-tree").ISimpleType<string>;
+    }>>, {
+        locationType: "UriLocation";
+        uri: string;
+        internetAccountId: string | undefined;
+        internetAccountPreAuthorization: import("mobx-state-tree").ModelSnapshotType<{
+            internetAccountType: import("mobx-state-tree").ISimpleType<string>;
+            authInfo: import("mobx-state-tree").IType<any, any, any>;
+        }> | undefined;
+    } | import("mobx-state-tree").ModelSnapshotType<{
+        locationType: import("mobx-state-tree").ISimpleType<"BlobLocation">;
+        name: import("mobx-state-tree").ISimpleType<string>;
+        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>;
+    }>, import("mobx-state-tree").ModelInstanceType<{
+        locationType: import("mobx-state-tree").ISimpleType<"BlobLocation">;
+        name: import("mobx-state-tree").ISimpleType<string>;
+        blobId: import("mobx-state-tree").ISimpleType<string>;
+    }, {}> | import("mobx-state-tree").ModelInstanceType<{
+        locationType: import("mobx-state-tree").ISimpleType<"LocalPathLocation">;
+        localPath: import("mobx-state-tree").ISimpleType<string>;
+    }, {}> | ({
+        locationType: "UriLocation";
+        uri: string;
+    } & Partial<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
+        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").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>>;
+    }>> & 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>;
+        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<{
+            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>;
+        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">;
+        localPath: import("mobx-state-tree").ISimpleType<string>;
+    }>>, {
+        locationType: "UriLocation";
+        uri: string;
+        internetAccountId: string | undefined;
+        internetAccountPreAuthorization: import("mobx-state-tree").ModelSnapshotType<{
+            internetAccountType: import("mobx-state-tree").ISimpleType<string>;
+            authInfo: import("mobx-state-tree").IType<any, any, any>;
+        }> | undefined;
+    } | import("mobx-state-tree").ModelSnapshotType<{
+        locationType: import("mobx-state-tree").ISimpleType<"BlobLocation">;
+        name: import("mobx-state-tree").ISimpleType<string>;
+        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>;
+    }>, import("mobx-state-tree").ModelInstanceType<{
+        locationType: import("mobx-state-tree").ISimpleType<"BlobLocation">;
+        name: import("mobx-state-tree").ISimpleType<string>;
+        blobId: import("mobx-state-tree").ISimpleType<string>;
+    }, {}> | import("mobx-state-tree").ModelInstanceType<{
+        locationType: import("mobx-state-tree").ISimpleType<"LocalPathLocation">;
+        localPath: import("mobx-state-tree").ISimpleType<string>;
+    }, {}> | ({
+        locationType: "UriLocation";
+        uri: string;
+    } & Partial<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
+        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").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>>;
+    }>> & 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>;
+        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<{
+            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>;
+        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">;
+        localPath: import("mobx-state-tree").ISimpleType<string>;
+    }>>, {
+        locationType: "UriLocation";
+        uri: string;
+        internetAccountId: string | undefined;
+        internetAccountPreAuthorization: import("mobx-state-tree").ModelSnapshotType<{
+            internetAccountType: import("mobx-state-tree").ISimpleType<string>;
+            authInfo: import("mobx-state-tree").IType<any, any, any>;
+        }> | undefined;
+    } | import("mobx-state-tree").ModelSnapshotType<{
+        locationType: import("mobx-state-tree").ISimpleType<"BlobLocation">;
+        name: import("mobx-state-tree").ISimpleType<string>;
+        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>;
+    }>, import("mobx-state-tree").ModelInstanceType<{
+        locationType: import("mobx-state-tree").ISimpleType<"BlobLocation">;
+        name: import("mobx-state-tree").ISimpleType<string>;
+        blobId: import("mobx-state-tree").ISimpleType<string>;
+    }, {}> | import("mobx-state-tree").ModelInstanceType<{
+        locationType: import("mobx-state-tree").ISimpleType<"LocalPathLocation">;
+        localPath: import("mobx-state-tree").ISimpleType<string>;
+    }, {}> | ({
+        locationType: "UriLocation";
+        uri: string;
+    } & Partial<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
+        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").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>>;
+    }>> & import("mobx-state-tree/dist/internal").NonEmptyObject)>, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+    currentAlignment: import("mobx-state-tree").IType<number | undefined, number, number>;
+    collapsed: import("mobx-state-tree").IArrayType<import("mobx-state-tree").ISimpleType<string>>;
+    collapsedLeaves: import("mobx-state-tree").IArrayType<import("mobx-state-tree").ISimpleType<string>>;
+    showOnly: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+    turnedOffTracks: import("mobx-state-tree").IMapType<import("mobx-state-tree").ISimpleType<boolean>>;
+    data: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{
+        tree: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+        msa: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+        treeMetadata: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+    }, {
+        setTree(tree?: string): void;
+        setMSA(msa?: string): void;
+        setTreeMetadata(treeMetadata?: string): void;
+    }, import("mobx-state-tree")._NotCustomized, {
+        tree: string | undefined;
+        msa: string | undefined;
+        treeMetadata: string | undefined;
+    }>, [undefined]>;
+    featureFilters: import("mobx-state-tree").IMapType<import("mobx-state-tree").ISimpleType<boolean>>;
+    relativeTo: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+}>, symbol>>;
 export default stateModelFactory;
 export type MsaViewStateModel = ReturnType<typeof stateModelFactory>;
 export type MsaViewModel = Instance<MsaViewStateModel>;