jbrowse-plugin-msaview 2.0.2 → 2.0.4

package/dist/MsaViewPanel/model.d.ts

@@ -28,7 +28,9 @@ export default function stateModelFactory(): import("mobx-state-tree").IModelTyp
     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]>;
+    treeWidth: import("mobx-state-tree" /**
+     * #property
+     */).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>;
@@ -39,21 +41,33 @@ 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" /**
+     * #getter
+     */).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<{
+    treeFilehandle: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISnapshotProcessor<import("mobx-state-tree" /**
+     * #action
+     */).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" /**
-         * #action
-         */).IMaybe<import("mobx-state-tree").IModelType<{
+        internetAccountPreAuthorization: import("mobx-state-tree").IMaybe<import(
+        /**
+         * #method
+         * overrides base
+         */
+        "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 +82,7 @@ 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 +217,7 @@ 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 +228,11 @@ 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>>;
@@ -239,7 +255,7 @@ export default function stateModelFactory(): import("mobx-state-tree").IModelTyp
 } & {
     queueOfDialogs: [import("@jbrowse/core/util").DialogComponentType, any][];
 } & {
-    readonly DialogComponent: import("@jbrowse/core/util").DialogComponentType;
+    readonly DialogComponent: import("@jbrowse/core/util").DialogComponentType | undefined;
     readonly DialogProps: any;
 } & {
     removeActiveDialog(): void;
@@ -257,6 +273,7 @@ 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 +281,7 @@ 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 +296,11 @@ 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;
@@ -300,12 +320,18 @@ export default function stateModelFactory(): import("mobx-state-tree").IModelTyp
     setData(data: {
         msa?: string;
         tree?: string;
+        treeMetadata?: string;
     }): void;
     setMSAFilehandle(msaFilehandle?: import("@jbrowse/core/util").FileLocation): void;
     setTreeFilehandle(treeFilehandle?: import("@jbrowse/core/util").FileLocation): void;
     setMSA(result: string): void;
     setTree(result: string): void;
     setTreeMetadata(result: string): void;
+} & {
+    readonly realAllowedGappyness: number;
+    readonly actuallyShowDomains: boolean;
+    readonly viewInitialized: boolean;
+    readonly width: number;
 } & {
     extraViewMenuItems(): never[];
     readonly colorScheme: Record<string, string>;
@@ -313,47 +339,60 @@ export default function stateModelFactory(): import("mobx-state-tree").IModelTyp
     getRowData(name: string): {
         data: {
             name: string;
-            accession: string;
-            dbxref: string;
+            accession: string | undefined;
+            dbxref: string | undefined;
         } | undefined;
     };
     readonly alignmentNames: string[];
     readonly noTree: boolean;
-    readonly noAnnotations: boolean;
-    readonly menuItems: never[];
+    readonly noDomains: boolean;
+    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 MSA: import("react-msaview/dist/parsers/StockholmMSA").default | import("react-msaview/dist/parsers/FastaMSA").default | import("react-msaview/dist/parsers/EmfMSA").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>;
     readonly msaAreaWidth: number;
     readonly treeAreaWidthMinusMargin: number;
     readonly blanks: number[];
+    readonly blanksSet: Set<number>;
     readonly rows: [string, string][];
+    readonly rowMap: Map<string, string>;
     readonly columns: {
         [k: string]: string;
     };
     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 blocks2d: (readonly [number, 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;
@@ -370,12 +409,16 @@ 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[];
-    globalCoordToRowSpecificSeqCoord(rowName: string, position: number): number;
+    readonly showHorizontalScrollbar: boolean;
+    readonly rowNamesSet: Map<string, number>;
+    mouseOverCoordToRowLetter(rowName: string, position: number): string | undefined;
+    mouseOverCoordToGapRemovedRowCoord(rowName: string, position: number): number | undefined;
     seqCoordToRowSpecificGlobalCoord(rowName: string, position: number): number;
 } & {
+    readonly msaAreaHeight: number;
     readonly totalTrackAreaHeight: number;
-    readonly tidyTypes: Map<string, import("react-msaview/dist/model").Accession>;
-    readonly tidyAnnotations: {
+    readonly tidyInterProAnnotationTypes: Map<string, import("react-msaview/dist/model").Accession>;
+    readonly tidyInterProAnnotations: {
         id: string;
         name: string;
         accession: string;
@@ -383,7 +426,7 @@ export default function stateModelFactory(): import("mobx-state-tree").IModelTyp
         start: number;
         end: number;
     }[];
-    readonly tidyFilteredAnnotations: {
+    readonly tidyFilteredInterProAnnotations: {
         id: string;
         name: string;
         accession: string;
@@ -391,20 +434,24 @@ export default function stateModelFactory(): import("mobx-state-tree").IModelTyp
         start: number;
         end: number;
     }[];
-    readonly tidyFilteredGatheredAnnotations: Record<string, {
+    readonly tidyFilteredGatheredInterProAnnotations: Record<string, {
         id: string;
         name: string;
         accession: string;
         description: string;
         start: number;
         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 +567,12 @@ 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 +628,7 @@ 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>;

package/dist/MsaViewPanel/model.js

@@ -166,7 +166,9 @@ export default function stateModelFactory() {
                     label: 'Zoom to base level on click?',
                     checked: self.zoomToBaseLevel,
                     type: 'checkbox',
-                    onClick: () => self.setZoomToBaseLevel(!self.zoomToBaseLevel),
+                    onClick: () => {
+                        self.setZoomToBaseLevel(!self.zoomToBaseLevel);
+                    },
                 },
             ];
         },

package/dist/MsaViewPanel/model.js.map

@@ -1 +1 @@
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package/dist/MsaViewPanel/msaCoordToGenomeCoord.js

@@ -1,11 +1,11 @@
 export function msaCoordToGenomeCoord({ model, coord: mouseCol, }) {
     const { transcriptToMsaMap } = model;
-    if (mouseCol === undefined || transcriptToMsaMap === undefined) {
+    if (transcriptToMsaMap === undefined) {
         return;
     }
-    const c = mouseCol - 1;
-    const k1 = model.globalCoordToRowSpecificSeqCoord('QUERY', c) || 0;
-    const k2 = model.globalCoordToRowSpecificSeqCoord('QUERY', c + 1) || 0;
+    const c = mouseCol;
+    const k1 = model.seqCoordToRowSpecificGlobalCoord('QUERY', c) || 0;
+    const k2 = model.seqCoordToRowSpecificGlobalCoord('QUERY', c + 1) || 0;
     const { refName, p2g } = transcriptToMsaMap;
     const s = p2g[k1];
     const e = p2g[k2];

package/dist/MsaViewPanel/msaCoordToGenomeCoord.js.map

@@ -1 +1 @@
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+{"version":3,"file":"msaCoordToGenomeCoord.js","sourceRoot":"","sources":["../../src/MsaViewPanel/msaCoordToGenomeCoord.ts"],"names":[],"mappings":"AAGA,MAAM,UAAU,qBAAqB,CAAC,EACpC,KAAK,EACL,KAAK,EAAE,QAAQ,GAIhB;IACC,MAAM,EAAE,kBAAkB,EAAE,GAAG,KAAK,CAAA;IACpC,IAAI,kBAAkB,KAAK,SAAS,EAAE,CAAC;QACrC,OAAM;IACR,CAAC;IAED,MAAM,CAAC,GAAG,QAAQ,CAAA;IAClB,MAAM,EAAE,GAAG,KAAK,CAAC,gCAAgC,CAAC,OAAO,EAAE,CAAC,CAAC,IAAI,CAAC,CAAA;IAClE,MAAM,EAAE,GAAG,KAAK,CAAC,gCAAgC,CAAC,OAAO,EAAE,CAAC,GAAG,CAAC,CAAC,IAAI,CAAC,CAAA;IACtE,MAAM,EAAE,OAAO,EAAE,GAAG,EAAE,GAAG,kBAAkB,CAAA;IAC3C,MAAM,CAAC,GAAG,GAAG,CAAC,EAAE,CAAC,CAAA;IACjB,MAAM,CAAC,GAAG,GAAG,CAAC,EAAE,CAAC,CAAA;IACjB,OAAO,CAAC,KAAK,SAAS,IAAI,CAAC,KAAK,SAAS;QACvC,CAAC,CAAC;YACE,OAAO;YACP,KAAK,EAAE,IAAI,CAAC,GAAG,CAAC,CAAC,EAAE,CAAC,CAAC;YACrB,GAAG,EAAE,IAAI,CAAC,GAAG,CAAC,CAAC,EAAE,CAAC,CAAC;SACpB;QACH,CAAC,CAAC,SAAS,CAAA;AACf,CAAC"}