react-msaview 5.0.7 → 5.0.13

package/dist/model.d.ts

@@ -1,10 +1,9 @@
-import { A3mMSA, ClustalMSA, EmfMSA, FastaMSA, StockholmMSA } from 'msa-parsers';
+import type { HierarchyNode } from './hierarchy.ts';
 import type { InterProScanResults } from './launchInterProScan.ts';
-import type { Accession, BasicTrack, NodeWithIds, NodeWithIdsAndLength } from './types.ts';
+import type { BasicTrack, NodeWithIds, NodeWithIdsAndLength } from './types.ts';
 import type { FileLocation as FileLocationType } from '@jbrowse/core/util/types';
 import type { Instance } from '@jbrowse/mobx-state-tree';
 import type { Theme } from '@mui/material';
-import type { HierarchyNode } from 'd3-hierarchy';
 /**
  * #stateModel MsaView
  * extends
@@ -17,7 +16,6 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
     labelsAlignRight: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
     treeAreaWidth: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
     treeWidth: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
-    treeWidthMatchesArea: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
     showBranchLen: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
     drawTree: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
     drawNodeBubbles: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
@@ -29,7 +27,6 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
     showDomains: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
     hideGaps: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
     allowedGappyness: import("@jbrowse/mobx-state-tree").IType<number | undefined, number, number>;
-    contrastLettering: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
     subFeatureRows: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
     type: import("@jbrowse/mobx-state-tree").ISimpleType<"MsaView">;
     drawMsaLetters: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
@@ -292,21 +289,23 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
     }>> & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject)>, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
     currentAlignment: import("@jbrowse/mobx-state-tree").IType<number | undefined, number, number>;
     collapsed: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
-    collapsedLeaves: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
     showOnly: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
     turnedOffTracks: import("@jbrowse/mobx-state-tree").IMapType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>>;
     data: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IModelType<{
         tree: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
         msa: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
         treeMetadata: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
+        gff: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
     }, {
         setTree(tree?: string): void;
         setMSA(msa?: string): void;
         setTreeMetadata(treeMetadata?: string): void;
+        setGFF(gff?: string): void;
     }, import("@jbrowse/mobx-state-tree")._NotCustomized, {
         tree: string | undefined;
         msa: string | undefined;
         treeMetadata: string | undefined;
+        gff: string | undefined;
     }>, [undefined]>;
     featureFilters: import("@jbrowse/mobx-state-tree").IMapType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>>;
     relativeTo: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
@@ -319,7 +318,6 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
     removeActiveDialog(): void;
     queueDialog(cb: (doneCallback: () => void) => [import("@jbrowse/core/util").DialogComponentType, unknown]): void;
 } & {
-    setTreeWidthMatchesArea(arg: boolean): void;
     setTreeAreaWidth(n: number): void;
     setTreeWidth(n: number): void;
     setLabelsAlignRight(arg: boolean): void;
@@ -348,11 +346,6 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
      * screens
      */
     highResScaleFactor: number;
-    /**
-     * #volatile
-     * obtained from localStorage
-     */
-    showZoomStar: boolean;
     /**
      * #volatile
      */
@@ -430,13 +423,6 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
      * #volatile
      */
     error: unknown;
-    /**
-     * #volatile
-     */
-    annotPos: {
-        left: number;
-        right: number;
-    } | undefined;
     /**
      * #volatile
      */
@@ -454,18 +440,10 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
      * #action
      */
     setAllowedGappyness(arg: number): void;
-    /**
-     * #action
-     */
-    setContrastLettering(arg: boolean): void;
     /**
      * #action
      */
     setLoadingMSA(arg: boolean): void;
-    /**
-     * #action
-     */
-    setShowZoomStar(arg: boolean): void;
     /**
      * #action
      */
@@ -536,10 +514,6 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
      * #action
      */
     toggleCollapsed(node: string): void;
-    /**
-     * #action
-     */
-    toggleCollapsedLeaf(node: string): void;
     /**
      * #action
      */
@@ -551,6 +525,7 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
         msa?: string;
         tree?: string;
         treeMetadata?: string;
+        gff?: string;
     }): void;
     /**
      * #action
@@ -590,9 +565,6 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
      * #getter
      */
     readonly actuallyShowDomains: boolean;
-    /**
-     * #getter
-     */
     readonly viewInitialized: boolean;
     /**
      * #getter
@@ -611,7 +583,7 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
     /**
      * #getter
      */
-    readonly header: {};
+    readonly header: Record<string, unknown>;
     /**
      * #getter
      */
@@ -620,13 +592,7 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
      * #getter
      */
     readonly noTree: boolean;
-    /**
-     * #getter
-     */
     readonly noDomains: boolean;
-    /**
-     * #getter
-     */
     menuItems(): never[];
     /**
      * #getter
@@ -635,7 +601,7 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
     /**
      * #getter
      */
-    readonly MSA: StockholmMSA | A3mMSA | FastaMSA | EmfMSA | ClustalMSA | null;
+    readonly MSA: import("msa-parsers").MSAParserType | null;
     /**
      * #getter
      */
@@ -852,14 +818,12 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
      * #action
      */
     zoomOut(): void;
-    /**
-     * #action
-     */
-    setInterProAnnotations(data: Record<string, InterProScanResults>): void;
     /**
      * #action
      */
     doScrollY(deltaY: number): void;
+    setInterProAnnotations(data: Record<string, InterProScanResults>): void;
+    applyGFFText(gffText: string): void;
     /**
      * #action
      */
@@ -991,13 +955,14 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
      * total height of track area (px)
      */
     readonly totalTrackAreaHeight: number;
-    /**
-     * #getter
-     */
-    readonly tidyInterProAnnotationTypes: Map<string, Accession>;
-    /**
-     * #getter
-     */
+    readonly tidyInterProAnnotationTypes: Map<string, {
+        id: string;
+        name: string;
+        accession: string;
+        description: string;
+        start: number;
+        end: number;
+    }>;
     readonly tidyInterProAnnotations: {
         id: string;
         name: string;
@@ -1006,9 +971,6 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
         start: number;
         end: number;
     }[];
-    /**
-     * #getter
-     */
     readonly tidyFilteredInterProAnnotations: {
         id: string;
         name: string;
@@ -1017,9 +979,6 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
         start: number;
         end: number;
     }[];
-    /**
-     * #getter
-     */
     readonly tidyFilteredGatheredInterProAnnotations: Record<string, {
         id: string;
         name: string;
@@ -1038,15 +997,9 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
      * #getter
      */
     readonly verticalScrollbarWidth: 0 | 20;
-    /**
-     * #getter
-     */
     readonly fillPalette: {
         [k: string]: string;
     };
-    /**
-     * #getter
-     */
     readonly strokePalette: {
         [k: string]: string;
     };
@@ -1055,9 +1008,9 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
      */
     getRowData(name: string): {
         data: {
-            name: string;
-            accession: string | undefined;
-            dbxref: string | undefined;
+            name?: string;
+            accession?: string;
+            dbxref?: string;
         } | undefined;
         treeMetadata: any;
     };
@@ -1088,13 +1041,7 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
      * internal, used for drawing to canvas
      */
     incrementRef(): void;
-    /**
-     * #action
-     */
     initFilter(arg: string): void;
-    /**
-     * #action
-     */
     setFilter(arg: string, flag: boolean): void;
     /**
      * #action
@@ -1114,7 +1061,6 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
     labelsAlignRight: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
     treeAreaWidth: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
     treeWidth: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
-    treeWidthMatchesArea: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
     showBranchLen: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
     drawTree: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
     drawNodeBubbles: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
@@ -1126,7 +1072,6 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
     showDomains: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
     hideGaps: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
     allowedGappyness: import("@jbrowse/mobx-state-tree").IType<number | undefined, number, number>;
-    contrastLettering: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
     subFeatureRows: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
     type: import("@jbrowse/mobx-state-tree").ISimpleType<"MsaView">;
     drawMsaLetters: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
@@ -1389,21 +1334,23 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
     }>> & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject)>, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
     currentAlignment: import("@jbrowse/mobx-state-tree").IType<number | undefined, number, number>;
     collapsed: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
-    collapsedLeaves: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
     showOnly: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
     turnedOffTracks: import("@jbrowse/mobx-state-tree").IMapType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>>;
     data: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IModelType<{
         tree: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
         msa: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
         treeMetadata: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
+        gff: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
     }, {
         setTree(tree?: string): void;
         setMSA(msa?: string): void;
         setTreeMetadata(treeMetadata?: string): void;
+        setGFF(gff?: string): void;
     }, import("@jbrowse/mobx-state-tree")._NotCustomized, {
         tree: string | undefined;
         msa: string | undefined;
         treeMetadata: string | undefined;
+        gff: string | undefined;
     }>, [undefined]>;
     featureFilters: import("@jbrowse/mobx-state-tree").IMapType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>>;
     relativeTo: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;