react-msaview 1.3.1 → 2.0.0

package/dist/components/data/seq2.js

@@ -1,3 +1,33 @@
-export var smallMSA = "CLUSTAL O(1.2.3) multiple sequence alignment\nUniProt/Swiss-Prot|P26898|IL2RA_SHEEP      MEPSLLMWRFFVFIVVPGCVTEACHDDPPSLRNA----------MFKVLRYE----VGTM\nUniProt/Swiss-Prot|P01590|IL2RA_MOUSE      MEPRLLMLGFLSLTIVPSCRAELCLYDPPEVPNA----------TFKALSYK----NGTI\nUniProt/Swiss-Prot|P41690|IL2RA_FELCA      MEPSLLLWGILTFVVVHGHVTELCDENPPDIQHA----------TFKALTYK----TGTM\nUniProt/Swiss-Prot|P01589|IL2RA_HUMAN      MDSYLLMWGLLTFIMVPGCQAELCDDDPPEIPHA----------TFKAMAYK----EGTM\nUniProt/Swiss-Prot|Q5MNY4|IL2RA_MACMU      MDPYLLMWGLLTFITVPGCQAELCDDDPPKITHA----------TFKAVAYK----EGTM\nUniProt/Swiss-Prot|Q95118|IL2RG_BOVIN      -----------------------------------LLMWGLLT-----------------\nUniProt/Swiss-Prot|P40321|IL2RG_CANFA      MLKPPLPLRSLLFLQLSLLGVGLNSTVPMPNGNEDIT------PDFFLTATPSETLSVSS\nUniProt/Swiss-Prot|P26896|IL2RB_RAT        MATVDLSWRLPLYILLLLLATT--------------------------------WVSAAV\nUniProt/Swiss-Prot|Q8BZM1|GLMN_MOUSE       PLPLRSLLFLQLPLLGVGLNP------------------PLPLRSLLFLQLPLLGVGLNP\nUniProt/Swiss-Prot|P36835|IL2_CAPHI        -----------LLGVGLNPKFLTP------------------------------------\nUniProt/Swiss-Prot|Q7JFM4|IL2_AOTVO        MLKPPLPLRSLLFLQLPLLGVGLNPKFLTPSGNEDIGGKPGTGGDFFLTSTPAGTLDVST\nUniProt/Swiss-Prot|Q29416|IL2_CANFA        --------------LFLQLSLLG-------------------------------------\n";
-export var smallMSAOnly = "CLUSTAL O(1.2.4) multiple sequence alignment\n\n\nsp|P69905|HBA_HUMAN       MVLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHG\t60\nsp|P01942|HBA_MOUSE       MVLSGEDKSNIKAAWGKIGGHGAEYGAEALERMFASFPTTKTYFPHFDVSHGSAQVKGHG\t60\nsp|P13786|HBAZ_CAPHI      MSLTRTERTIILSLWSKISTQADVIGTETLERLFSCYPQAKTYFPHFDLHSGSAQLRAHG\t60\n                          * *:  ::: : : *.*:. :.   *:*:***:* .:* :********:  ****::.**\n\nsp|P69905|HBA_HUMAN       KKVADALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTP\t120\nsp|P01942|HBA_MOUSE       KKVADALASAAGHLDDLPGALSALSDLHAHKLRVDPVNFKLLSHCLLVTLASHHPADFTP\t120\nsp|P13786|HBAZ_CAPHI      SKVVAAVGDAVKSIDNVTSALSKLSELHAYVLRVDPVNFKFLSHCLLVTLASHFPADFTA\t120\n                          .**. *: .*.  :*:: .*** **:***: *********:**********:* **:**\n\nsp|P69905|HBA_HUMAN       AVHASLDKFLASVSTVLTSKYR\t142\nsp|P01942|HBA_MOUSE       AVHASLDKFLASVSTVLTSKYR\t142\nsp|P13786|HBAZ_CAPHI      DAHAAWDKFLSIVSGVLTEKYR\t142\n                           .**: ****: ** ***.***";
-export var smallTree = '(((UniProt/Swiss-Prot|P26898|IL2RA_SHEEP:0.24036,(UniProt/Swiss-Prot|P41690|IL2RA_FELCA:0.17737,(UniProt/Swiss-Prot|P01589|IL2RA_HUMAN:0.03906,UniProt/Swiss-Prot|Q5MNY4|IL2RA_MACMU:0.03787):0.13033):0.04964):0.02189,UniProt/Swiss-Prot|P01590|IL2RA_MOUSE:0.23072):0.06814,(((UniProt/Swiss-Prot|Q95118|IL2RG_BOVIN:0.09600,UniProt/Swiss-Prot|P40321|IL2RG_CANFA:0.09845):0.25333,UniProt/Swiss-Prot|Q29416|IL2_CANFA:-0.35055):0.10231,(UniProt/Swiss-Prot|P26896|IL2RB_RAT:0.33631,UniProt/Swiss-Prot|Q7JFM4|IL2_AOTVO:-0.33631):0.10166):0.01607,(UniProt/Swiss-Prot|Q8BZM1|GLMN_MOUSE:0.32378,UniProt/Swiss-Prot|P36835|IL2_CAPHI:-0.32378):0.09999)';
+export const smallMSA = `CLUSTAL O(1.2.3) multiple sequence alignment
+UniProt/Swiss-Prot|P26898|IL2RA_SHEEP      MEPSLLMWRFFVFIVVPGCVTEACHDDPPSLRNA----------MFKVLRYE----VGTM
+UniProt/Swiss-Prot|P01590|IL2RA_MOUSE      MEPRLLMLGFLSLTIVPSCRAELCLYDPPEVPNA----------TFKALSYK----NGTI
+UniProt/Swiss-Prot|P41690|IL2RA_FELCA      MEPSLLLWGILTFVVVHGHVTELCDENPPDIQHA----------TFKALTYK----TGTM
+UniProt/Swiss-Prot|P01589|IL2RA_HUMAN      MDSYLLMWGLLTFIMVPGCQAELCDDDPPEIPHA----------TFKAMAYK----EGTM
+UniProt/Swiss-Prot|Q5MNY4|IL2RA_MACMU      MDPYLLMWGLLTFITVPGCQAELCDDDPPKITHA----------TFKAVAYK----EGTM
+UniProt/Swiss-Prot|Q95118|IL2RG_BOVIN      -----------------------------------LLMWGLLT-----------------
+UniProt/Swiss-Prot|P40321|IL2RG_CANFA      MLKPPLPLRSLLFLQLSLLGVGLNSTVPMPNGNEDIT------PDFFLTATPSETLSVSS
+UniProt/Swiss-Prot|P26896|IL2RB_RAT        MATVDLSWRLPLYILLLLLATT--------------------------------WVSAAV
+UniProt/Swiss-Prot|Q8BZM1|GLMN_MOUSE       PLPLRSLLFLQLPLLGVGLNP------------------PLPLRSLLFLQLPLLGVGLNP
+UniProt/Swiss-Prot|P36835|IL2_CAPHI        -----------LLGVGLNPKFLTP------------------------------------
+UniProt/Swiss-Prot|Q7JFM4|IL2_AOTVO        MLKPPLPLRSLLFLQLPLLGVGLNPKFLTPSGNEDIGGKPGTGGDFFLTSTPAGTLDVST
+UniProt/Swiss-Prot|Q29416|IL2_CANFA        --------------LFLQLSLLG-------------------------------------
+`;
+export const smallMSAOnly = `CLUSTAL O(1.2.4) multiple sequence alignment
+
+
+sp|P69905|HBA_HUMAN       MVLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHG	60
+sp|P01942|HBA_MOUSE       MVLSGEDKSNIKAAWGKIGGHGAEYGAEALERMFASFPTTKTYFPHFDVSHGSAQVKGHG	60
+sp|P13786|HBAZ_CAPHI      MSLTRTERTIILSLWSKISTQADVIGTETLERLFSCYPQAKTYFPHFDLHSGSAQLRAHG	60
+                          * *:  ::: : : *.*:. :.   *:*:***:* .:* :********:  ****::.**
+
+sp|P69905|HBA_HUMAN       KKVADALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTP	120
+sp|P01942|HBA_MOUSE       KKVADALASAAGHLDDLPGALSALSDLHAHKLRVDPVNFKLLSHCLLVTLASHHPADFTP	120
+sp|P13786|HBAZ_CAPHI      SKVVAAVGDAVKSIDNVTSALSKLSELHAYVLRVDPVNFKFLSHCLLVTLASHFPADFTA	120
+                          .**. *: .*.  :*:: .*** **:***: *********:**********:* **:**
+
+sp|P69905|HBA_HUMAN       AVHASLDKFLASVSTVLTSKYR	142
+sp|P01942|HBA_MOUSE       AVHASLDKFLASVSTVLTSKYR	142
+sp|P13786|HBAZ_CAPHI      DAHAAWDKFLSIVSGVLTEKYR	142
+                           .**: ****: ** ***.***`;
+export const smallTree = '(((UniProt/Swiss-Prot|P26898|IL2RA_SHEEP:0.24036,(UniProt/Swiss-Prot|P41690|IL2RA_FELCA:0.17737,(UniProt/Swiss-Prot|P01589|IL2RA_HUMAN:0.03906,UniProt/Swiss-Prot|Q5MNY4|IL2RA_MACMU:0.03787):0.13033):0.04964):0.02189,UniProt/Swiss-Prot|P01590|IL2RA_MOUSE:0.23072):0.06814,(((UniProt/Swiss-Prot|Q95118|IL2RG_BOVIN:0.09600,UniProt/Swiss-Prot|P40321|IL2RG_CANFA:0.09845):0.25333,UniProt/Swiss-Prot|Q29416|IL2_CANFA:-0.35055):0.10231,(UniProt/Swiss-Prot|P26896|IL2RB_RAT:0.33631,UniProt/Swiss-Prot|Q7JFM4|IL2_AOTVO:-0.33631):0.10166):0.01607,(UniProt/Swiss-Prot|Q8BZM1|GLMN_MOUSE:0.32378,UniProt/Swiss-Prot|P36835|IL2_CAPHI:-0.32378):0.09999)';
+//# sourceMappingURL=seq2.js.map

package/dist/components/data/seq2.js.map

@@ -0,0 +1 @@
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package/{bundle/components/Ruler.d.ts → dist/components/util.d.ts}

@@ -1,5 +1,3 @@
-/// <reference types="react" />
-import { MsaViewModel } from '../model';
 /**
  * Given a scale ( bp/px ) and minimum distances (px) between major and minor
  * gridlines, return an object like `{ majorPitch: bp, minorPitch: bp }` giving
@@ -14,7 +12,4 @@ export declare function makeTicks(start: number, end: number, bpPerPx: number, e
     base: number;
     index: number;
 }[];
-declare const Ruler: ({ model }: {
-    model: MsaViewModel;
-}) => JSX.Element | null;
-export default Ruler;
+export declare function mathPower(num: number): string;

package/dist/components/util.js

@@ -0,0 +1,69 @@
+/**
+ * Given a scale ( bp/px ) and minimum distances (px) between major and minor
+ * gridlines, return an object like `{ majorPitch: bp, minorPitch: bp }` giving
+ * the gridline pitches to use.
+ */
+export function chooseGridPitch(scale, minMajorPitchPx, minMinorPitchPx) {
+    scale = Math.abs(scale);
+    const minMajorPitchBp = minMajorPitchPx * scale;
+    const majorMagnitude = parseInt(Number(minMajorPitchBp).toExponential().split(/e/i)[1], 10);
+    let majorPitch = 10 ** majorMagnitude;
+    while (majorPitch < minMajorPitchBp) {
+        majorPitch *= 2;
+        if (majorPitch >= minMajorPitchBp) {
+            break;
+        }
+        majorPitch *= 2.5;
+    }
+    majorPitch = Math.max(majorPitch, 5);
+    const majorPitchPx = majorPitch / scale;
+    let minorPitch = 0;
+    if (!(majorPitch % 10) && majorPitchPx / 10 >= minMinorPitchPx) {
+        minorPitch = majorPitch / 10;
+    }
+    else if (!(majorPitch % 5) && majorPitchPx / 5 >= minMinorPitchPx) {
+        minorPitch = majorPitch / 5;
+    }
+    else if (!(majorPitch % 2) && majorPitchPx / 2 >= minMinorPitchPx) {
+        minorPitch = majorPitch / 2;
+    }
+    return { majorPitch, minorPitch };
+}
+export function makeTicks(start, end, bpPerPx, emitMajor = true, emitMinor = true) {
+    const gridPitch = chooseGridPitch(bpPerPx, 60, 15);
+    let minBase = start;
+    let maxBase = end;
+    if (minBase === null || maxBase === null) {
+        return [];
+    }
+    if (bpPerPx < 0) {
+        // eslint-disable-next-line @typescript-eslint/no-extra-semi
+        ;
+        [minBase, maxBase] = [maxBase, minBase];
+    }
+    // add 20px additional on the right and left to allow us to draw the ends of
+    // labels that lie a little outside our region
+    minBase -= Math.abs(20 * bpPerPx);
+    maxBase += Math.abs(20 * bpPerPx) + 1;
+    const iterPitch = gridPitch.minorPitch || gridPitch.majorPitch;
+    let index = 0;
+    const ticks = [];
+    for (let base = Math.ceil(minBase / iterPitch) * iterPitch; base < maxBase; base += iterPitch) {
+        if (emitMinor && base % (gridPitch.majorPitch * 2)) {
+            ticks.push({ type: 'minor', base: base - 1, index });
+            index += 1;
+        }
+        else if (emitMajor && !(base % (gridPitch.majorPitch * 2))) {
+            ticks.push({ type: 'major', base: base - 1, index });
+            index += 1;
+        }
+    }
+    return ticks;
+}
+export function mathPower(num) {
+    if (num < 999) {
+        return String(num);
+    }
+    return `${mathPower(~~(num / 1000))},${`00${~~(num % 1000)}`.slice(-3, -3 + 3)}`;
+}
+//# sourceMappingURL=util.js.map

package/dist/components/util.js.map

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

@@ -1,4 +1,2 @@
-import MSAView from './components/MSAView';
-import MSAModel, { MsaViewModel } from './model';
-export { MSAModel, MSAView };
-export type { MsaViewModel };
+export { default as MSAView } from './components/MSAView';
+export { default as MSAModel, type MsaViewModel } from './model';

package/dist/index.js

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

package/dist/index.js.map

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

@@ -1,7 +1,6 @@
 import RBush from 'rbush';
-var Layout = /** @class */ (function () {
-    function Layout(_a) {
-        var _b = _a === void 0 ? {} : _a, _c = _b.maxHeight, maxHeight = _c === void 0 ? 10000 : _c;
+export default class Layout {
+    constructor({ maxHeight = 10000, } = {}) {
         this.maxHeightReached = false;
         this.rbush = new RBush();
         this.rectangles = new Map();
@@ -12,13 +11,13 @@ var Layout = /** @class */ (function () {
      * @returns top position for the rect, or Null if laying
      *  out the rect would exceed maxHeighe
      */
-    Layout.prototype.addRect = function (id, left, right, height, data) {
+    addRect(id, left, right, height, data) {
         // add to rbush
-        var existingRecord = this.rectangles.get(id);
+        const existingRecord = this.rectangles.get(id);
         if (existingRecord) {
             return existingRecord.minY;
         }
-        var currHeight = 0;
+        let currHeight = 0;
         while (this.rbush.collides({
             minX: left,
             minY: currHeight,
@@ -28,26 +27,21 @@ var Layout = /** @class */ (function () {
             currHeight <= this.maxHeight) {
             currHeight += 1;
         }
-        var record = {
+        const record = {
             minX: left,
             minY: currHeight,
             maxX: right,
             maxY: currHeight + height,
-            id: id,
-            data: data,
+            id,
+            data,
         };
         this.rbush.insert(record);
         this.rectangles.set(id, record);
         this.pTotalHeight = Math.max(this.pTotalHeight, currHeight);
         return currHeight;
-    };
-    Object.defineProperty(Layout.prototype, "totalHeight", {
-        get: function () {
-            return this.pTotalHeight;
-        },
-        enumerable: false,
-        configurable: true
-    });
-    return Layout;
-}());
-export default Layout;
+    }
+    get totalHeight() {
+        return this.pTotalHeight;
+    }
+}
+//# sourceMappingURL=layout.js.map

package/dist/layout.js.map

@@ -0,0 +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;YAClB,OAAO,cAAc,CAAC,IAAI,CAAA;SAC3B;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;YACA,UAAU,IAAI,CAAC,CAAA;SAChB;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/model.d.ts

@@ -2,9 +2,19 @@
 import { Instance, SnapshotIn } from 'mobx-state-tree';
 import { HierarchyNode } from 'd3-hierarchy';
 import { FileLocation as FileLocationType } from '@jbrowse/core/util/types';
+export interface RowDetails {
+    [key: string]: unknown;
+    name: string;
+    range?: {
+        start: number;
+        end: number;
+    };
+}
+import { NodeWithIds, NodeWithIdsAndLength } from './util';
 import ClustalMSA from './parsers/ClustalMSA';
 import StockholmMSA from './parsers/StockholmMSA';
 import FastaMSA from './parsers/FastaMSA';
+import { StructureModel } from './StructureModel';
 interface BasicTrackModel {
     id: string;
     name: string;
@@ -23,27 +33,19 @@ export interface BoxTrackModel extends BasicTrackModel {
         end: number;
     }[];
 }
-export interface TextTrack {
+export interface ITextTrack {
     ReactComponent: React.FC<any>;
     model: TextTrackModel;
 }
-export interface BoxTrack {
+export interface IBoxTrack {
     ReactComponent: React.FC<any>;
     model: BoxTrackModel;
 }
-declare type BasicTrack = BoxTrack | TextTrack;
-declare const StructureModel: import("mobx-state-tree").IModelType<{
-    id: import("mobx-state-tree").ISimpleType<string>;
-    structure: import("mobx-state-tree").IModelType<{
-        pdb: import("mobx-state-tree").ISimpleType<string>;
-        startPos: import("mobx-state-tree").ISimpleType<number>;
-        endPos: import("mobx-state-tree").ISimpleType<number>;
-    }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
-    range: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
-}, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
+type BasicTrack = IBoxTrack | ITextTrack;
 declare const model: import("mobx-state-tree").ISnapshotProcessor<import("mobx-state-tree").IModelType<{
     id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
     displayName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+    minimized: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
 } & {
     id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
     type: import("mobx-state-tree").ISimpleType<"MsaView">;
@@ -83,13 +85,13 @@ declare const model: import("mobx-state-tree").ISnapshotProcessor<import("mobx-s
             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<"LocalPathLocation">;
-        localPath: import("mobx-state-tree").ISimpleType<string>;
     }>> | 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;
@@ -99,12 +101,12 @@ declare const model: import("mobx-state-tree").ISnapshotProcessor<import("mobx-s
             authInfo: import("mobx-state-tree").IType<any, any, any>;
         }> | undefined;
     } | import("mobx-state-tree").ModelSnapshotType<{
-        locationType: import("mobx-state-tree").ISimpleType<"LocalPathLocation">;
-        localPath: import("mobx-state-tree").ISimpleType<string>;
-    }> | 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").ModelCreationType<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
         locationType: import("mobx-state-tree").ISimpleType<"UriLocation">;
         uri: import("mobx-state-tree").ISimpleType<string>;
@@ -114,14 +116,14 @@ declare const model: import("mobx-state-tree").ISnapshotProcessor<import("mobx-s
             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").ModelInstanceTypeProps<{
-        locationType: import("mobx-state-tree").ISimpleType<"LocalPathLocation">;
-        localPath: import("mobx-state-tree").ISimpleType<string>;
-    }> | import("mobx-state-tree").ModelInstanceTypeProps<{
+    }>> | 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")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+    }, {}> | import("mobx-state-tree").ModelInstanceType<{
+        locationType: import("mobx-state-tree").ISimpleType<"LocalPathLocation">;
+        localPath: import("mobx-state-tree").ISimpleType<string>;
+    }, {}>>, 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>;
@@ -131,13 +133,13 @@ declare const model: import("mobx-state-tree").ISnapshotProcessor<import("mobx-s
             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<"LocalPathLocation">;
-        localPath: import("mobx-state-tree").ISimpleType<string>;
     }>> | 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;
@@ -147,12 +149,12 @@ declare const model: import("mobx-state-tree").ISnapshotProcessor<import("mobx-s
             authInfo: import("mobx-state-tree").IType<any, any, any>;
         }> | undefined;
     } | import("mobx-state-tree").ModelSnapshotType<{
-        locationType: import("mobx-state-tree").ISimpleType<"LocalPathLocation">;
-        localPath: import("mobx-state-tree").ISimpleType<string>;
-    }> | 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").ModelCreationType<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
         locationType: import("mobx-state-tree").ISimpleType<"UriLocation">;
         uri: import("mobx-state-tree").ISimpleType<string>;
@@ -162,14 +164,14 @@ declare const model: import("mobx-state-tree").ISnapshotProcessor<import("mobx-s
             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").ModelInstanceTypeProps<{
-        locationType: import("mobx-state-tree").ISimpleType<"LocalPathLocation">;
-        localPath: import("mobx-state-tree").ISimpleType<string>;
-    }> | import("mobx-state-tree").ModelInstanceTypeProps<{
+    }>> | 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")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+    }, {}> | import("mobx-state-tree").ModelInstanceType<{
+        locationType: import("mobx-state-tree").ISimpleType<"LocalPathLocation">;
+        localPath: import("mobx-state-tree").ISimpleType<string>;
+    }, {}>>, 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>>;
     showOnly: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
@@ -180,10 +182,10 @@ declare const model: import("mobx-state-tree").ISnapshotProcessor<import("mobx-s
         associatedRowName: import("mobx-state-tree").ISimpleType<string>;
         height: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
     }, {
-        error: Error | undefined;
-        data: any;
+        error: unknown;
+        data: string | undefined;
     } & {
-        setError(error: Error): void;
+        setError(error: unknown): void;
         setData(data: string): void;
     } & {
         afterCreate(): void;
@@ -210,8 +212,8 @@ declare const model: import("mobx-state-tree").ISnapshotProcessor<import("mobx-s
         tree: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
         msa: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
     }, {
-        setTree(tree?: string | undefined): void;
-        setMSA(msa?: string | undefined): void;
+        setTree(tree?: string): void;
+        setMSA(msa?: string): void;
     }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>;
 }, {
     width: number;
@@ -220,8 +222,9 @@ declare const model: import("mobx-state-tree").ISnapshotProcessor<import("mobx-s
 } & {
     setDisplayName(name: string): void;
     setWidth(newWidth: number): void;
+    setMinimized(flag: boolean): void;
 } & {
-    error: Error | undefined;
+    error: unknown;
     margin: {
         left: number;
         top: number;
@@ -246,8 +249,8 @@ declare const model: import("mobx-state-tree").ISnapshotProcessor<import("mobx-s
         };
     }): void;
     clearSelectedStructures(): void;
-    setError(error?: Error | undefined): void;
-    setMousePos(col?: number | undefined, row?: number | undefined): void;
+    setError(error?: unknown): void;
+    setMousePos(col?: number, row?: number): void;
     setRowHeight(n: number): void;
     setColWidth(n: number): void;
     setColorSchemeName(name: string): void;
@@ -259,7 +262,7 @@ declare const model: import("mobx-state-tree").ISnapshotProcessor<import("mobx-s
     toggleLabelsAlignRight(): void;
     toggleDrawTree(): void;
     toggleCollapsed(node: string): void;
-    setShowOnly(node: string | undefined): void;
+    setShowOnly(node?: string): void;
     toggleBranchLen(): void;
     toggleBgColor(): void;
     toggleNodeBubbles(): void;
@@ -267,8 +270,8 @@ declare const model: import("mobx-state-tree").ISnapshotProcessor<import("mobx-s
         msa?: string;
         tree?: string;
     }): void;
-    setMSAFilehandle(msaFilehandle?: FileLocationType | undefined): Promise<void>;
-    setTreeFilehandle(treeFilehandle?: FileLocationType | undefined): Promise<void>;
+    setMSAFilehandle(msaFilehandle?: FileLocationType): Promise<void>;
+    setTreeFilehandle(treeFilehandle?: FileLocationType): Promise<void>;
     setMSA(result: string): void;
     setTree(result: string): void;
     afterCreate(): void;
@@ -282,19 +285,29 @@ declare const model: import("mobx-state-tree").ISnapshotProcessor<import("mobx-s
     readonly colorScheme: {
         [key: string]: string;
     };
-    readonly alignmentDetails: Record<string, any>;
-    getRowDetails(name: string): any;
+    readonly header: {};
+    getRowData(name: string): {
+        range?: {
+            start: number;
+            end: number;
+        } | undefined;
+        data: {
+            name: string;
+            accession: string;
+            dbxref: string;
+        } | Record<string, unknown>;
+    };
     readonly currentAlignmentName: string;
     readonly alignmentNames: string[];
     readonly noTree: boolean;
     readonly menuItems: never[];
-    readonly MSA: ClustalMSA | StockholmMSA | FastaMSA | null;
+    readonly MSA: StockholmMSA | FastaMSA | ClustalMSA | null;
     readonly numColumns: number;
-    readonly tree: any;
+    readonly tree: NodeWithIds;
     readonly rowNames: string[];
     readonly mouseOverRowName: string | undefined;
     getMouseOverResidue(rowName: string): string;
-    readonly root: HierarchyNode<any>;
+    readonly root: HierarchyNode<NodeWithIds>;
     readonly structures: {
         [key: string]: {
             pdb: string;
@@ -302,16 +315,22 @@ declare const model: import("mobx-state-tree").ISnapshotProcessor<import("mobx-s
             endPos: number;
         }[];
     };
-    readonly inverseStructures: any;
+    readonly inverseStructures: {
+        [k: string]: {
+            id: string;
+        };
+    };
     readonly msaAreaWidth: number;
     readonly blanks: number[];
-    readonly rows: string[][];
-    readonly columns: Record<string, string>;
+    readonly rows: [string, string[]][];
+    readonly columns: {
+        [k: string]: string;
+    };
     readonly columns2d: string[];
     readonly colStats: {
         [key: string]: number;
     }[];
-    readonly hierarchy: HierarchyNode<any>;
+    readonly hierarchy: HierarchyNode<NodeWithIdsAndLength>;
     readonly totalHeight: number;
 } & {
     addUniprotTrack(node: {
@@ -341,16 +360,26 @@ declare const model: import("mobx-state-tree").ISnapshotProcessor<import("mobx-s
     clearAnnotPos(): void;
 }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, import("mobx-state-tree")._NotCustomized, {
     id: string;
-    displayName: string | undefined;
     type: "MsaView";
     height: number;
-    treeAreaWidth: number;
-    treeWidth: number;
+    displayName: string | undefined;
+    minimized: boolean;
     rowHeight: number;
     scrollY: number;
     scrollX: number;
     resizeHandleWidth: number;
     blockSize: number;
+    labelsAlignRight: boolean;
+    colWidth: number;
+    showBranchLen: boolean;
+    bgColor: boolean;
+    drawTree: boolean;
+    drawNodeBubbles: boolean;
+    highResScaleFactor: number;
+    colorSchemeName: string;
+    currentAlignment: number;
+    treeAreaWidth: number;
+    treeWidth: number;
     mouseRow: number | undefined;
     mouseCol: number | undefined;
     selectedStructures: import("mobx-state-tree").ModelSnapshotType<{
@@ -362,14 +391,6 @@ declare const model: import("mobx-state-tree").ISnapshotProcessor<import("mobx-s
         }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
         range: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
     }>[];
-    labelsAlignRight: boolean;
-    colWidth: number;
-    showBranchLen: boolean;
-    bgColor: boolean;
-    drawTree: boolean;
-    drawNodeBubbles: boolean;
-    highResScaleFactor: number;
-    colorSchemeName: string;
     treeFilehandle: {
         locationType: "UriLocation";
         uri: string;
@@ -379,12 +400,12 @@ declare const model: import("mobx-state-tree").ISnapshotProcessor<import("mobx-s
             authInfo: import("mobx-state-tree").IType<any, any, any>;
         }> | undefined;
     } | import("mobx-state-tree").ModelSnapshotType<{
-        locationType: import("mobx-state-tree").ISimpleType<"LocalPathLocation">;
-        localPath: import("mobx-state-tree").ISimpleType<string>;
-    }> | 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>;
     }> | undefined;
     msaFilehandle: {
         locationType: "UriLocation";
@@ -395,14 +416,13 @@ declare const model: import("mobx-state-tree").ISnapshotProcessor<import("mobx-s
             authInfo: import("mobx-state-tree").IType<any, any, any>;
         }> | undefined;
     } | import("mobx-state-tree").ModelSnapshotType<{
-        locationType: import("mobx-state-tree").ISimpleType<"LocalPathLocation">;
-        localPath: import("mobx-state-tree").ISimpleType<string>;
-    }> | 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>;
     }> | undefined;
-    currentAlignment: number;
     collapsed: string[];
     showOnly: string | undefined;
     boxTracks: import("mobx-state-tree").ModelSnapshotType<{
@@ -424,5 +444,5 @@ declare const model: import("mobx-state-tree").ISnapshotProcessor<import("mobx-s
     };
 }>;
 export default model;
-export declare type MsaViewStateModel = typeof model;
-export declare type MsaViewModel = Instance<MsaViewStateModel>;
+export type MsaViewStateModel = typeof model;
+export type MsaViewModel = Instance<MsaViewStateModel>;