react-msaview 3.1.12 → 3.2.1

package/dist/model.d.ts

@@ -1,13 +1,15 @@
 import React from 'react';
-import { Instance } from 'mobx-state-tree';
-import { HierarchyNode } from 'd3-hierarchy';
-import { Theme } from '@mui/material';
-import { FileLocation as FileLocationType } from '@jbrowse/core/util/types';
-import { NodeWithIds, NodeWithIdsAndLength } from './util';
+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 StockholmMSA from './parsers/StockholmMSA';
 import FastaMSA from './parsers/FastaMSA';
-import { InterProScanResults } from './launchInterProScan';
+import type { InterProScanResults } from './launchInterProScan';
 export interface Accession {
     accession: string;
     name: string;
@@ -50,8 +52,13 @@ declare function stateModelFactory(): import("mobx-state-tree").IModelType<{
 } & {
     id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
     showDomains: 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>;
+    hideGaps: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    drawTreeText: 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>;
@@ -61,11 +68,17 @@ 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").ISimpleType<string>>;
-        internetAccountPreAuthorization: import("mobx-state-tree").IMaybe<import("mobx-state-tree" /**
-         * #volatile
-         */).IModelType<{
-            internetAccountType: 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>>;
+        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>;
             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<{
@@ -91,7 +104,12 @@ declare function stateModelFactory(): import("mobx-state-tree").IModelType<{
         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">;
+        locationType: import(
+        /**
+         * #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>;
     }, {}> | import("mobx-state-tree").ModelInstanceType<{
@@ -102,13 +120,16 @@ declare function stateModelFactory(): import("mobx-state-tree").IModelType<{
         uri: string;
     } & Partial<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
         locationType: import("mobx-state-tree" /**
-         * #action
-         * set mouse position (row, column) in the MSA
+         * #volatile
+         * a dummy variable that is incremented when ref changes so autorun for
+         * drawing canvas commands will run
          */).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<{
+        internetAccountPreAuthorization: import("mobx-state-tree").IMaybe<import("mobx-state-tree" /**
+         * #volatile
+         */).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>>;
@@ -217,7 +238,7 @@ declare function stateModelFactory(): import("mobx-state-tree").IModelType<{
     }>> & 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>>;
-    collapsed2: 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<{
@@ -228,7 +249,11 @@ declare function stateModelFactory(): import("mobx-state-tree").IModelType<{
         setTree(tree?: string): void;
         setMSA(msa?: string): void;
         setTreeMetadata(treeMetadata?: string): void;
-    }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>;
+    }, 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>>;
 }, {
     queueOfDialogs: [import("@jbrowse/core/util").DialogComponentType, any][];
@@ -251,6 +276,13 @@ declare function stateModelFactory(): import("mobx-state-tree").IModelType<{
     setColorSchemeName(name: string): void;
     setBgColor(arg: boolean): void;
 } & {
+    /**
+     * #volatile
+     */
+    headerHeight: number;
+    /**
+     * #volatile
+     */
     status: {
         msg: string;
         url?: string;
@@ -272,7 +304,7 @@ declare function stateModelFactory(): import("mobx-state-tree").IModelType<{
     /**
      * #volatile
      */
-    width: number;
+    volatileWidth: number | undefined;
     /**
      * #volatile
      * resize handle width between tree and msa area, px
@@ -332,8 +364,20 @@ declare function stateModelFactory(): import("mobx-state-tree").IModelType<{
      * #volatile
      *
      */
-    loadedInterProAnnotations: undefined | Record<string, InterProScanResults>;
+    interProAnnotations: undefined | Record<string, InterProScanResults>;
 } & {
+    /**
+     * #action
+     */
+    setHideGaps(arg: boolean): void;
+    /**
+     * #action
+     */
+    setAllowedGappyness(arg: number): void;
+    /**
+     * #action
+     */
+    setContrastLettering(arg: boolean): void;
     /**
      * #action
      */
@@ -433,6 +477,23 @@ declare function stateModelFactory(): import("mobx-state-tree").IModelType<{
      * #action
      */
     setTreeMetadata(result: string): void;
+} & {
+    /**
+     * #getter
+     */
+    readonly realAllowedGappyness: number;
+    /**
+     * #getter
+     */
+    readonly actuallyShowDomains: boolean;
+    /**
+     * #getter
+     */
+    readonly viewInitialized: boolean;
+    /**
+     * #getter
+     */
+    readonly width: number;
 } & {
     /**
      * #method
@@ -453,8 +514,8 @@ declare function stateModelFactory(): import("mobx-state-tree").IModelType<{
     getRowData(name: string): {
         data: {
             name: string;
-            accession: string;
-            dbxref: string;
+            accession: string | undefined;
+            dbxref: string | undefined;
         } | undefined;
     };
     /**
@@ -468,11 +529,11 @@ declare function stateModelFactory(): import("mobx-state-tree").IModelType<{
     /**
      * #getter
      */
-    readonly noAnnotations: boolean;
+    readonly noDomains: boolean;
     /**
      * #getter
      */
-    readonly menuItems: never[];
+    menuItems(): never[];
     /**
      * #getter
      */
@@ -488,7 +549,7 @@ declare function stateModelFactory(): import("mobx-state-tree").IModelType<{
     /**
      * #getter
      */
-    readonly _tree: NodeWithIds;
+    readonly tree: NodeWithIds;
     /**
      * #getter
      */
@@ -514,10 +575,18 @@ declare function stateModelFactory(): import("mobx-state-tree").IModelType<{
      * #getter
      */
     readonly blanks: number[];
+    /**
+     * #getter
+     */
+    readonly blanksSet: Set<number>;
     /**
      * #getter
      */
     readonly rows: [string, string][];
+    /**
+     * #getter
+     */
+    readonly rowMap: Map<string, string>;
     /**
      * #getter
      */
@@ -536,6 +605,12 @@ declare function stateModelFactory(): import("mobx-state-tree").IModelType<{
      * #getter
      */
     readonly colStats: Record<string, number>[];
+    /**
+     * #getter
+     */
+    readonly colStatsSums: {
+        [k: string]: number;
+    };
     /**
      * #getter
      * generates a new tree that is clustered with x,y positions
@@ -545,6 +620,10 @@ declare function stateModelFactory(): import("mobx-state-tree").IModelType<{
      * #getter
      */
     readonly totalHeight: number;
+    /**
+     * #getter
+     */
+    readonly leaves: HierarchyNode<NodeWithIdsAndLength>[];
 } & {
     /**
      * #getter
@@ -554,7 +633,7 @@ declare function stateModelFactory(): import("mobx-state-tree").IModelType<{
     /**
      * #getter
      */
-    readonly initialized: boolean | "" | undefined;
+    readonly dataInitialized: boolean | "" | undefined;
     /**
      * #getter
      */
@@ -567,7 +646,7 @@ declare function stateModelFactory(): import("mobx-state-tree").IModelType<{
     /**
      * #getter
      */
-    readonly blocks2d: number[][];
+    readonly blocks2d: (readonly [number, number])[];
     /**
      * #getter
      */
@@ -576,7 +655,35 @@ declare function stateModelFactory(): import("mobx-state-tree").IModelType<{
      * #getter
      */
     readonly maxScrollX: number;
+    /**
+     * #getter
+     */
+    readonly showMsaLetters: boolean;
+    /**
+     * #getter
+     */
+    readonly showTreeText: boolean;
 } & {
+    /**
+     * #action
+     */
+    setDrawMsaLetters(arg: boolean): void;
+    /**
+     * #action
+     */
+    zoomOutHorizontal(): void;
+    /**
+     * #action
+     */
+    zoomInHorizontal(): void;
+    /**
+     * #action
+     */
+    zoomInVertical(): void;
+    /**
+     * #action
+     */
+    zoomOutVertical(): void;
     /**
      * #action
      */
@@ -588,7 +695,7 @@ declare function stateModelFactory(): import("mobx-state-tree").IModelType<{
     /**
      * #action
      */
-    setLoadedInterProAnnotations(data: Record<string, InterProScanResults>): void;
+    setInterProAnnotations(data: Record<string, InterProScanResults>): void;
     /**
      * #action
      */
@@ -641,12 +748,25 @@ declare function stateModelFactory(): import("mobx-state-tree").IModelType<{
      * #getter
      */
     readonly turnedOnTracks: ITextTrack[];
+    /**
+     * #getter
+     */
+    readonly showHorizontalScrollbar: boolean;
+    /**
+     * #getter
+     */
+    readonly rowNamesSet: Map<string, number>;
     /**
      * #method
-     * return a row-specific sequence coordinate, skipping gaps, given a global
-     * coordinate
+     * return a row-specific letter, or undefined if gap
      */
-    globalCoordToRowSpecificSeqCoord(rowName: string, position: number): number;
+    mouseOverCoordToRowLetter(rowName: string, position: number): string | undefined;
+    /**
+     * #method
+     * return a row-specific sequence coordinate, skipping gaps, given a
+     * global coordinate
+     */
+    mouseOverCoordToGapRemovedRowCoord(rowName: string, position: number): number | undefined;
     /**
      * #method
      * return a global coordinate given a row-specific sequence coordinate
@@ -654,6 +774,11 @@ declare function stateModelFactory(): import("mobx-state-tree").IModelType<{
      */
     seqCoordToRowSpecificGlobalCoord(rowName: string, position: number): number;
 } & {
+    /**
+     * #getter
+     * widget width minus the tree area gives the space for the MSA
+     */
+    readonly msaAreaHeight: number;
     /**
      * #getter
      * total height of track area (px)
@@ -662,8 +787,11 @@ declare function stateModelFactory(): import("mobx-state-tree").IModelType<{
     /**
      * #getter
      */
-    readonly tidyTypes: Map<string, Accession>;
-    readonly tidyAnnotations: {
+    readonly tidyInterProAnnotationTypes: Map<string, Accession>;
+    /**
+     * #getter
+     */
+    readonly tidyInterProAnnotations: {
         id: string;
         name: string;
         accession: string;
@@ -674,7 +802,7 @@ declare function stateModelFactory(): import("mobx-state-tree").IModelType<{
     /**
      * #getter
      */
-    readonly tidyFilteredAnnotations: {
+    readonly tidyFilteredInterProAnnotations: {
         id: string;
         name: string;
         accession: string;
@@ -685,7 +813,7 @@ declare function stateModelFactory(): import("mobx-state-tree").IModelType<{
     /**
      * #getter
      */
-    readonly tidyFilteredGatheredAnnotations: Record<string, {
+    readonly tidyFilteredGatheredInterProAnnotations: Record<string, {
         id: string;
         name: string;
         accession: string;
@@ -694,11 +822,30 @@ declare function stateModelFactory(): import("mobx-state-tree").IModelType<{
         end: number;
     }[] | undefined>;
 } & {
+    /**
+     * #getter
+     */
+    readonly showVerticalScrollbar: boolean;
+} & {
+    /**
+     * #getter
+     */
+    readonly verticalScrollbarWidth: 0 | 20;
+    /**
+     * #getter
+     */
     readonly fillPalette: Record<string, string>;
+    /**
+     * #getter
+     */
     readonly strokePalette: {
         [k: string]: string;
     };
 } & {
+    /**
+     * #action
+     */
+    setHeaderHeight(arg: number): void;
     /**
      * #action
      */
@@ -739,7 +886,12 @@ declare function stateModelFactory(): import("mobx-state-tree").IModelType<{
     colorSchemeName: string;
     id: string;
     showDomains: boolean;
+    allowedGappyness: number;
+    contrastLettering: boolean;
     subFeatureRows: boolean;
+    drawMsaLetters: boolean;
+    hideGaps: boolean;
+    drawTreeText: boolean;
     rowHeight: number;
     scrollY: number;
     scrollX: number;
@@ -795,7 +947,7 @@ declare function stateModelFactory(): import("mobx-state-tree").IModelType<{
         localPath: import("mobx-state-tree").ISimpleType<string>;
     }> | undefined;
     collapsed: string[];
-    collapsed2: string[];
+    collapsedLeaves: string[];
     showOnly: string | undefined;
     turnedOffTracks: import("mobx").IKeyValueMap<boolean>;
     featureFilters: import("mobx").IKeyValueMap<boolean>;