jbrowse-plugin-msaview 2.0.2 → 2.0.3

package/dist/MsaViewPanel/model.d.ts

@@ -25,10 +25,14 @@ export default function stateModelFactory(): import("mobx-state-tree").IModelTyp
     displayName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
     minimized: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
 } & {
-    drawLabels: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    drawLabels: import("mobx-state-tree" /**
+     * #property
+     */).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]>;
+    treeWidth: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree" /**
+     * #property
+     */).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>;
@@ -39,21 +43,28 @@ export default function stateModelFactory(): import("mobx-state-tree").IModelTyp
 } & {
     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>;
     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<{
+    colWidth: import("mobx-state-tree" /**
+     * #action
+     */).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" /**
+     * #action
+     */).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" /**
-         * #action
-         */).IMaybe<import("mobx-state-tree").IModelType<{
+        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>>;
@@ -68,9 +79,7 @@ export default function stateModelFactory(): import("mobx-state-tree").IModelTyp
         locationType: "UriLocation";
         uri: string;
         internetAccountId: string | undefined;
-        internetAccountPreAuthorization: import("mobx-state-tree" /**
-         * #getter
-         */).ModelSnapshotType<{
+        internetAccountPreAuthorization: import("mobx-state-tree").ModelSnapshotType<{
             internetAccountType: import("mobx-state-tree").ISimpleType<string>;
             authInfo: import("mobx-state-tree").IType<any, any, any>;
         }> | undefined;
@@ -205,7 +214,7 @@ export default function stateModelFactory(): import("mobx-state-tree").IModelTyp
     }>> & 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<{
@@ -216,7 +225,11 @@ export default function stateModelFactory(): import("mobx-state-tree").IModelTyp
         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>>;
 } & {
     connectedViewId: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
@@ -257,6 +270,7 @@ export default function stateModelFactory(): import("mobx-state-tree").IModelTyp
     setColorSchemeName(name: string): void;
     setBgColor(arg: boolean): void;
 } & {
+    headerHeight: number;
     status: {
         msg: string;
         url?: string;
@@ -264,7 +278,7 @@ export default function stateModelFactory(): import("mobx-state-tree").IModelTyp
     highResScaleFactor: number;
     loadingMSA: boolean;
     loadingTree: boolean;
-    width: number;
+    volatileWidth: number | undefined;
     resizeHandleWidth: number;
     blockSize: number;
     mouseRow: number | undefined;
@@ -279,8 +293,11 @@ export default function stateModelFactory(): import("mobx-state-tree").IModelTyp
         left: number;
         right: number;
     } | undefined;
-    loadedInterProAnnotations: undefined | Record<string, import("react-msaview/dist/launchInterProScan").InterProScanResults>;
+    interProAnnotations: undefined | Record<string, import("react-msaview/dist/launchInterProScan").InterProScanResults>;
 } & {
+    setHideGaps(arg: boolean): void;
+    setAllowedGappyness(arg: number): void;
+    setContrastLettering(arg: boolean): void;
     setLoadingMSA(arg: boolean): void;
     setLoadingTree(arg: boolean): void;
     setWidth(arg: number): void;
@@ -306,6 +323,10 @@ export default function stateModelFactory(): import("mobx-state-tree").IModelTyp
     setMSA(result: string): void;
     setTree(result: string): void;
     setTreeMetadata(result: string): void;
+} & {
+    readonly actuallyShowDomains: boolean;
+    readonly viewInitialized: boolean;
+    readonly width: number;
 } & {
     extraViewMenuItems(): never[];
     readonly colorScheme: Record<string, string>;
@@ -319,12 +340,12 @@ export default function stateModelFactory(): import("mobx-state-tree").IModelTyp
     };
     readonly alignmentNames: string[];
     readonly noTree: boolean;
-    readonly noAnnotations: boolean;
+    readonly noDomains: boolean;
     readonly menuItems: never[];
     readonly treeMetadata: any;
     readonly MSA: import("react-msaview/dist/parsers/StockholmMSA").default | import("react-msaview/dist/parsers/FastaMSA").default | import("react-msaview/dist/parsers/ClustalMSA").default | null;
     readonly numColumns: number;
-    readonly _tree: import("react-msaview/dist/util").NodeWithIds;
+    readonly tree: import("react-msaview/dist/util").NodeWithIds;
     readonly rowNames: string[];
     readonly mouseOverRowName: string | undefined;
     readonly root: HierarchyNode<import("react-msaview/dist/util").NodeWithIds>;
@@ -338,22 +359,33 @@ export default function stateModelFactory(): import("mobx-state-tree").IModelTyp
     readonly columns2d: string[];
     readonly fontSize: number;
     readonly colStats: Record<string, number>[];
+    readonly colStatsSums: {
+        [k: string]: number;
+    };
     readonly hierarchy: HierarchyNode<import("react-msaview/dist/util").NodeWithIdsAndLength>;
     readonly totalHeight: number;
+    readonly leaves: HierarchyNode<import("react-msaview/dist/util").NodeWithIdsAndLength>[];
 } & {
     readonly totalWidth: number;
 } & {
-    readonly initialized: boolean | "" | undefined;
+    readonly dataInitialized: boolean | "" | undefined;
     readonly blocksX: number[];
     readonly blocksY: number[];
 } & {
     readonly blocks2d: number[][];
     readonly isLoading: boolean;
     readonly maxScrollX: number;
+    readonly showMsaLetters: boolean;
+    readonly showTreeText: boolean;
 } & {
+    setDrawMsaLetters(arg: boolean): void;
+    zoomOutHorizontal(): void;
+    zoomInHorizontal(): void;
+    zoomInVertical(): void;
+    zoomOutVertical(): void;
     zoomIn(): void;
     zoomOut(): void;
-    setLoadedInterProAnnotations(data: Record<string, import("react-msaview/dist/launchInterProScan").InterProScanResults>): void;
+    setInterProAnnotations(data: Record<string, import("react-msaview/dist/launchInterProScan").InterProScanResults>): void;
     doScrollY(deltaY: number): void;
     doScrollX(deltaX: number): void;
     setScrollX(n: number): void;
@@ -370,9 +402,11 @@ export default function stateModelFactory(): import("mobx-state-tree").IModelTyp
     readonly adapterTrackModels: import("react-msaview/dist/model").ITextTrack[];
     readonly tracks: import("react-msaview/dist/model").ITextTrack[];
     readonly turnedOnTracks: import("react-msaview/dist/model").ITextTrack[];
+    readonly showHorizontalScrollbar: boolean;
     globalCoordToRowSpecificSeqCoord(rowName: string, position: number): number;
     seqCoordToRowSpecificGlobalCoord(rowName: string, position: number): number;
 } & {
+    readonly msaAreaHeight: number;
     readonly totalTrackAreaHeight: number;
     readonly tidyTypes: Map<string, import("react-msaview/dist/model").Accession>;
     readonly tidyAnnotations: {
@@ -400,11 +434,15 @@ export default function stateModelFactory(): import("mobx-state-tree").IModelTyp
         end: number;
     }[] | undefined>;
 } & {
+    readonly showVerticalScrollbar: boolean;
+} & {
+    readonly verticalScrollbarWidth: 0 | 20;
     readonly fillPalette: Record<string, string>;
     readonly strokePalette: {
         [k: string]: string;
     };
 } & {
+    setHeaderHeight(arg: number): void;
     reset(): void;
     exportSVG(opts: {
         theme: import("@mui/material").Theme;
@@ -520,7 +558,12 @@ export default function stateModelFactory(): import("mobx-state-tree").IModelTyp
     colorSchemeName: string;
     id: string;
     showDomains: boolean;
+    allowedGappyness: number;
+    contrastLettering: boolean;
     subFeatureRows: boolean;
+    drawMsaLetters: boolean;
+    hideGaps: boolean;
+    drawTreeText: boolean;
     rowHeight: number;
     scrollY: number;
     scrollX: number;
@@ -576,7 +619,7 @@ export default function stateModelFactory(): import("mobx-state-tree").IModelTyp
         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>;