react-msaview 2.1.0 → 2.1.2

package/dist/colorSchemes.js

@@ -1,5 +1,7 @@
-import Color from 'color';
+import { colord, extend } from 'colord';
+import namesPlugin from 'colord/plugins/names';
 import { transform } from './util';
+extend([namesPlugin]);
 const colorSchemes = {
     clustal: {
         G: 'orange',
@@ -325,7 +327,7 @@ const colorSchemes = {
 // requires
 export default transform(colorSchemes, ([key, val]) => [
     key,
-    transform(val, ([letter, color]) => [letter, Color(color).hex()]),
+    transform(val, ([letter, color]) => [letter, colord(color).toHex()]),
 ]);
 // info http://www.jalview.org/help/html/colourSchemes/clustal.html
 // modifications:

package/dist/colorSchemes.js.map

@@ -1 +1 @@
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package/dist/components/MSAView.js

@@ -34,10 +34,8 @@ export default observer(function ({ model }) {
                             React.createElement(MSAMouseoverCanvas, { model: model }))))),
             React.createElement(HorizontalResizeHandle, { model: model }))),
         model.DialogComponent ? (React.createElement(Suspense, { fallback: null },
-            React.createElement(model.DialogComponent, { ...(model.DialogProps || {}), onClose: () => {
-                    model.setDialogComponent(undefined, undefined);
-                } }))) : null,
+            React.createElement(model.DialogComponent, { ...(model.DialogProps || {}), onClose: () => model.setDialogComponent() }))) : null,
         model.annotPos ? (React.createElement(Suspense, { fallback: null },
-            React.createElement(AnnotationDialog, { data: model.annotPos, model: model, onClose: () => model.clearAnnotPos() }))) : null));
+            React.createElement(AnnotationDialog, { data: model.annotPos, model: model, onClose: () => model.clearAnnotationClickBoundaries() }))) : null));
 });
 //# sourceMappingURL=MSAView.js.map

package/dist/components/MSAView.js.map

@@ -1 +1 @@
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+{"version":3,"file":"MSAView.js","sourceRoot":"","sources":["../../src/components/MSAView.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,EAAE,IAAI,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAA;AAE7C,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAE1C,SAAS;AACT,OAAO,UAAU,MAAM,cAAc,CAAA;AACrC,OAAO,UAAU,MAAM,cAAc,CAAA;AACrC,OAAO,UAAU,MAAM,cAAc,CAAA;AACrC,OAAO,SAAS,MAAM,aAAa,CAAA;AACnC,OAAO,KAAK,MAAM,SAAS,CAAA;AAC3B,OAAO,SAAS,MAAM,aAAa,CAAA;AACnC,OAAO,MAAM,MAAM,UAAU,CAAA;AAC7B,OAAO,KAAK,MAAM,SAAS,CAAA;AAE3B,OAAO,EAAE,sBAAsB,EAAE,oBAAoB,EAAE,MAAM,iBAAiB,CAAA;AAE9E,OAAO,kBAAkB,MAAM,sBAAsB,CAAA;AAErD,MAAM,gBAAgB,GAAG,IAAI,CAAC,GAAG,EAAE,CAAC,MAAM,CAAC,yBAAyB,CAAC,CAAC,CAAA;AAEtE,eAAe,QAAQ,CAAC,UAAU,EAAE,KAAK,EAA2B;IAClE,MAAM,EAAE,IAAI,EAAE,WAAW,EAAE,aAAa,EAAE,MAAM,EAAE,cAAc,EAAE,GAAG,KAAK,CAAA;IAE1E,OAAO,CACL;QACG,CAAC,WAAW,CAAC,CAAC,CAAC,CACd,oBAAC,UAAU,IAAC,KAAK,EAAE,KAAK,GAAI,CAC7B,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CACV,oBAAC,UAAU,IAAC,OAAO,EAAC,IAAI,iBAAwB,CACjD,CAAC,CAAC,CAAC,CACF;YACE,6BAAK,KAAK,EAAE,EAAE,MAAM,EAAE,QAAQ,EAAE,QAAQ,EAAE;gBACxC,oBAAC,MAAM,IAAC,KAAK,EAAE,KAAK,GAAI;gBACxB;oBACE,6BAAK,KAAK,EAAE,EAAE,QAAQ,EAAE,UAAU,EAAE;wBAClC,6BAAK,KAAK,EAAE,EAAE,OAAO,EAAE,MAAM,EAAE;4BAC7B,6BAAK,KAAK,EAAE,EAAE,UAAU,EAAE,CAAC,EAAE,KAAK,EAAE,aAAa,EAAE;gCACjD,oBAAC,SAAS,IAAC,KAAK,EAAE,KAAK,GAAI,CACvB;4BAEN,oBAAC,UAAU,IACT,KAAK,EAAE,KAAK,EACZ,gBAAgB,EAAE,oBAAC,KAAK,IAAC,KAAK,EAAE,KAAK,GAAI,GACzC,CACE,EACL,cAAc,aAAd,cAAc;wBAAd,cAAc,CAAE,GAAG,CAAC,KAAK,CAAC,EAAE,CAAC,CAC5B,oBAAC,KAAK,IAAC,GAAG,EAAE,KAAK,CAAC,KAAK,CAAC,EAAE,EAAE,KAAK,EAAE,KAAK,EAAE,KAAK,EAAE,KAAK,GAAI,CAC3D,CAAC;wBAEF,6BAAK,KAAK,EAAE,EAAE,OAAO,EAAE,MAAM,EAAE;4BAC7B,6BAAK,KAAK,EAAE,EAAE,UAAU,EAAE,CAAC,EAAE,KAAK,EAAE,aAAa,EAAE;gCACjD,oBAAC,UAAU,IAAC,KAAK,EAAE,KAAK,GAAI,CACxB;4BACN,oBAAC,oBAAoB,IAAC,KAAK,EAAE,KAAK,GAAI;4BACtC,oBAAC,SAAS,IAAC,KAAK,EAAE,KAAK,GAAI;4BAC3B,oBAAC,kBAAkB,IAAC,KAAK,EAAE,KAAK,GAAI,CAChC,CACF,CACF,CACF;YACN,oBAAC,sBAAsB,IAAC,KAAK,EAAE,KAAK,GAAI,CACpC,CACP;QAEA,KAAK,CAAC,eAAe,CAAC,CAAC,CAAC,CACvB,oBAAC,QAAQ,IAAC,QAAQ,EAAE,IAAI;YACtB,oBAAC,KAAK,CAAC,eAAe,OAChB,CAAC,KAAK,CAAC,WAAW,IAAI,EAAE,CAAC,EAC7B,OAAO,EAAE,GAAG,EAAE,CAAC,KAAK,CAAC,kBAAkB,EAAE,GACzC,CACO,CACZ,CAAC,CAAC,CAAC,IAAI;QAEP,KAAK,CAAC,QAAQ,CAAC,CAAC,CAAC,CAChB,oBAAC,QAAQ,IAAC,QAAQ,EAAE,IAAI;YACtB,oBAAC,gBAAgB,IACf,IAAI,EAAE,KAAK,CAAC,QAAQ,EACpB,KAAK,EAAE,KAAK,EACZ,OAAO,EAAE,GAAG,EAAE,CAAC,KAAK,CAAC,8BAA8B,EAAE,GACrD,CACO,CACZ,CAAC,CAAC,CAAC,IAAI,CACJ,CACP,CAAA;AACH,CAAC,CAAC,CAAA"}

package/dist/components/Rubberband.js

@@ -105,7 +105,7 @@ function Rubberband({ model, ControlComponent = React.createElement("div", null)
     }
     function mouseOut() {
         setGuideX(undefined);
-        model.clearAnnotPos();
+        model.clearAnnotationClickBoundaries();
     }
     function handleClose() {
         setAnchorPosition(undefined);
@@ -132,7 +132,7 @@ function Rubberband({ model, ControlComponent = React.createElement("div", null)
             label: 'Create annotation',
             icon: AssignmentIcon,
             onClick: () => {
-                model.setOffsets(leftBpOffset, rightBpOffset);
+                model.setAnnotationClickBoundaries(leftBpOffset, rightBpOffset);
                 handleClose();
             },
         },

package/dist/components/Rubberband.js.map

@@ -1 +1 @@
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package/dist/model.d.ts

@@ -40,7 +40,8 @@ export interface IBoxTrack {
     model: BoxTrackModel;
 }
 type BasicTrack = IBoxTrack | ITextTrack;
-declare const model: import("mobx-state-tree").ISnapshotProcessor<import("mobx-state-tree").IModelType<{
+type StructureSnap = SnapshotIn<typeof StructureModel>;
+declare const model: 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>;
@@ -85,7 +86,9 @@ declare const model: import("mobx-state-tree").ISnapshotProcessor<import("mobx-s
         }, {}, 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<"BlobLocation">;
-        name: import("mobx-state-tree").ISimpleType<string>;
+        name: import("mobx-state-tree").ISimpleType<string>; /**
+         * #action
+         */
         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">;
@@ -104,13 +107,18 @@ declare const model: import("mobx-state-tree").ISnapshotProcessor<import("mobx-s
         blobId: import("mobx-state-tree").ISimpleType<string>;
     }> | import("mobx-state-tree").ModelSnapshotType<{
         locationType: import("mobx-state-tree").ISimpleType<"LocalPathLocation">;
+        /**
+         * #action
+         */
         localPath: import("mobx-state-tree").ISimpleType<string>;
     }>, 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").ModelInstanceType<{
-        locationType: import("mobx-state-tree").ISimpleType<"LocalPathLocation">;
+        locationType: import("mobx-state-tree").ISimpleType<"LocalPathLocation">; /**
+         * #action
+         */
         localPath: import("mobx-state-tree").ISimpleType<string>;
     }, {}> | ({
         locationType: "UriLocation";
@@ -136,7 +144,9 @@ declare const model: import("mobx-state-tree").ISnapshotProcessor<import("mobx-s
         }, {}, 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<"BlobLocation">;
-        name: import("mobx-state-tree").ISimpleType<string>;
+        name: import("mobx-state-tree").ISimpleType<string>; /**
+         * #action
+         */
         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">;
@@ -155,13 +165,18 @@ declare const model: import("mobx-state-tree").ISnapshotProcessor<import("mobx-s
         blobId: import("mobx-state-tree").ISimpleType<string>;
     }> | import("mobx-state-tree").ModelSnapshotType<{
         locationType: import("mobx-state-tree").ISimpleType<"LocalPathLocation">;
+        /**
+         * #action
+         */
         localPath: import("mobx-state-tree").ISimpleType<string>;
     }>, 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").ModelInstanceType<{
-        locationType: import("mobx-state-tree").ISimpleType<"LocalPathLocation">;
+        locationType: import("mobx-state-tree").ISimpleType<"LocalPathLocation">; /**
+         * #action
+         */
         localPath: import("mobx-state-tree").ISimpleType<string>;
     }, {}> | ({
         locationType: "UriLocation";
@@ -241,10 +256,25 @@ declare const model: import("mobx-state-tree").ISnapshotProcessor<import("mobx-s
         right: number;
     } | undefined;
 } & {
-    setDialogComponent(dlg: React.FC<any> | undefined, props: any): void;
+    /**
+     * #action
+     */
+    setDialogComponent(dlg?: React.FC<any>, props?: any): void;
+    /**
+     * #action
+     */
     setHeight(height: number): void;
-    addStructureToSelection(elt: SnapshotIn<typeof StructureModel>): void;
-    removeStructureFromSelection(elt: SnapshotIn<typeof StructureModel>): void;
+    /**
+     * #action
+     */
+    addStructureToSelection(elt: StructureSnap): void;
+    /**
+     * #action
+     */
+    removeStructureFromSelection(elt: StructureSnap): void;
+    /**
+     * #action
+     */
     toggleStructureSelection(elt: {
         id: string;
         structure: {
@@ -253,42 +283,135 @@ declare const model: import("mobx-state-tree").ISnapshotProcessor<import("mobx-s
             pdb: string;
         };
     }): void;
+    /**
+     * #action
+     */
     clearSelectedStructures(): void;
+    /**
+     * #action
+     */
     setError(error?: unknown): void;
+    /**
+     * #action
+     */
     setMousePos(col?: number, row?: number): void;
+    /**
+     * #action
+     */
     setRowHeight(n: number): void;
+    /**
+     * #action
+     */
     setColWidth(n: number): void;
+    /**
+     * #action
+     */
     setColorSchemeName(name: string): void;
+    /**
+     * #action
+     */
     setScrollY(n: number): void;
+    /**
+     * #action
+     */
     setScrollX(n: number): void;
+    /**
+     * #action
+     */
     setTreeAreaWidth(n: number): void;
+    /**
+     * #action
+     */
     setTreeWidth(n: number): void;
+    /**
+     * #action
+     */
     setCurrentAlignment(n: number): void;
+    /**
+     * #action
+     */
     toggleLabelsAlignRight(): void;
+    /**
+     * #action
+     */
     toggleDrawTree(): void;
+    /**
+     * #action
+     */
     toggleCollapsed(node: string): void;
+    /**
+     * #action
+     */
     setShowOnly(node?: string): void;
+    /**
+     * #action
+     */
     toggleBranchLen(): void;
+    /**
+     * #action
+     */
     toggleBgColor(): void;
+    /**
+     * #action
+     */
     toggleNodeBubbles(): void;
+    /**
+     * #action
+     */
     setData(data: {
         msa?: string;
         tree?: string;
     }): void;
+    /**
+     * #action
+     */
     setMSAFilehandle(msaFilehandle?: FileLocationType): Promise<void>;
+    /**
+     * #action
+     */
     setTreeFilehandle(treeFilehandle?: FileLocationType): Promise<void>;
+    /**
+     * #action
+     */
     setMSA(result: string): void;
+    /**
+     * #action
+     */
     setTree(result: string): void;
     afterCreate(): void;
 } & {
+    /**
+     * #getter
+     */
     readonly initialized: boolean | "" | undefined;
+    /**
+     * #getter
+     */
     readonly blocksX: number[];
+    /**
+     * #getter
+     */
     readonly blocksY: number[];
 } & {
+    /**
+     * #getter
+     */
     readonly blocks2d: number[][];
+    /**
+     * #getter
+     */
     readonly done: string | false | undefined;
+    /**
+     * #getter
+     */
     readonly colorScheme: Record<string, string>;
+    /**
+     * #getter
+     */
     readonly header: {};
+    /**
+     * #method
+     */
     getRowData(name: string): {
         range?: {
             start: number;
@@ -300,62 +423,180 @@ declare const model: import("mobx-state-tree").ISnapshotProcessor<import("mobx-s
             dbxref: string;
         } | Record<string, unknown>;
     };
+    /**
+     * #getter
+     */
     readonly currentAlignmentName: string;
+    /**
+     * #getter
+     */
     readonly alignmentNames: string[];
+    /**
+     * #getter
+     */
     readonly noTree: boolean;
+    /**
+     * #getter
+     */
     readonly menuItems: never[];
+    /**
+     * #getter
+     */
     readonly MSA: StockholmMSA | FastaMSA | ClustalMSA | null;
+    /**
+     * #getter
+     */
     readonly numColumns: number;
+    /**
+     * #getter
+     */
     readonly tree: NodeWithIds;
+    /**
+     * #getter
+     */
     readonly rowNames: string[];
-    readonly mouseOverRowName: string | undefined;
+    /**
+     * #getter
+     */ readonly mouseOverRowName: string | undefined;
+    /**
+     * #method
+     */
     getMouseOverResidue(rowName: string): string;
+    /**
+     * #getter
+     */
     readonly root: HierarchyNode<NodeWithIds>;
+    /**
+     * #getter
+     */
     readonly structures: Record<string, {
         pdb: string;
         startPos: number;
         endPos: number;
     }[]>;
+    /**
+     * #getter
+     */
     readonly inverseStructures: {
         [k: string]: {
             id: string;
         };
     };
+    /**
+     * #getter
+     */
     readonly msaAreaWidth: number;
+    /**
+     * #getter
+     */
     readonly blanks: number[];
+    /**
+     * #getter
+     */
     readonly rows: [string, string[]][];
+    /**
+     * #getter
+     */
     readonly columns: {
         [k: string]: string;
     };
+    /**
+     * #getter
+     */
     readonly columns2d: string[];
+    /**
+     * #getter
+     */
     readonly colStats: Record<string, number>[];
+    /**
+     * #getter
+     * generates a new tree that is clustered with x,y positions
+     */
     readonly hierarchy: HierarchyNode<NodeWithIdsAndLength>;
+    /**
+     * #getter
+     */
     readonly totalHeight: number;
 } & {
+    /**
+     * #action
+     */
     addUniprotTrack(node: {
         name: string;
         accession: string;
     }): void;
+    /**
+     * #action
+     */
     doScrollY(deltaY: number): void;
+    /**
+     * #action
+     */
     doScrollX(deltaX: number): void;
+    /**
+     * #action
+     */
     setMouseoveredColumn(n: number, chain: string, file: string): void;
+    /**
+     * #action
+     */
     toggleTrack(id: string): void;
 } & {
+    /**
+     * #getter
+     */
     readonly secondaryStructureConsensus: string | undefined;
+    /**
+     * #getter
+     */
     readonly seqConsensus: string | undefined;
+    /**
+     * #getter
+     */
     readonly conservation: string[];
+    /**
+     * #getter
+     */
     readonly tracks: BasicTrack[];
+    /**
+     * #getter
+     */
     readonly turnedOnTracks: BasicTrack[];
+    /**
+     * #method
+     * returns coordinate in the current relative coordinate scheme
+     */
     pxToBp(coord: number): number;
+    /**
+     * #method
+     */
     rowSpecificBpToPx(rowName: string, position: number): number;
+    /**
+     * #method
+     */
     globalBpToPx(position: number): number;
+    /**
+     * #method
+     */
     relativePxToBp(rowName: string, position: number): number;
+    /**
+     * #method
+     */
     getPos(pos: number): number;
 } & {
+    /**
+     * #action
+     */
     addAnnotation(start: number, end: number, attributes: Record<string, string[]>): void;
-    setOffsets(left: number, right: number): void;
-    clearAnnotPos(): void;
-}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, import("mobx-state-tree")._NotCustomized, {
+    /**
+     * #action
+     */
+    setAnnotationClickBoundaries(left: number, right: number): void;
+    /**
+     * #action
+     */
+    clearAnnotationClickBoundaries(): void;
+}, import("mobx-state-tree")._NotCustomized, {
     id: string;
     type: "MsaView";
     height: number;
@@ -402,6 +643,9 @@ declare const model: import("mobx-state-tree").ISnapshotProcessor<import("mobx-s
         blobId: import("mobx-state-tree").ISimpleType<string>;
     }> | import("mobx-state-tree").ModelSnapshotType<{
         locationType: import("mobx-state-tree").ISimpleType<"LocalPathLocation">;
+        /**
+         * #action
+         */
         localPath: import("mobx-state-tree").ISimpleType<string>;
     }> | undefined;
     msaFilehandle: {
@@ -418,6 +662,9 @@ declare const model: import("mobx-state-tree").ISnapshotProcessor<import("mobx-s
         blobId: import("mobx-state-tree").ISimpleType<string>;
     }> | import("mobx-state-tree").ModelSnapshotType<{
         locationType: import("mobx-state-tree").ISimpleType<"LocalPathLocation">;
+        /**
+         * #action
+         */
         localPath: import("mobx-state-tree").ISimpleType<string>;
     }> | undefined;
     collapsed: string[];