react-msaview 3.0.3 → 3.1.1

package/dist/model.d.ts

@@ -7,6 +7,7 @@ import ClustalMSA from './parsers/ClustalMSA';
 import StockholmMSA from './parsers/StockholmMSA';
 import FastaMSA from './parsers/FastaMSA';
 import { StructureModel } from './StructureModel';
+import { Theme } from '@mui/material';
 export interface RowDetails {
     [key: string]: unknown;
     name: string;
@@ -79,22 +80,24 @@ declare const model: import("mobx-state-tree").IModelType<{
     highResScaleFactor: import("mobx-state-tree").IType<number | undefined, number, number>;
     colorSchemeName: import("mobx-state-tree").IType<string | undefined, string, string>;
     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<{
-        /**
-         * #property
-         * high resolution scale factor, helps make canvas look better on hi-dpi
-         * screens
-         */
         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").IModelType<{
             internetAccountType: import("mobx-state-tree").ISimpleType<string>;
-            authInfo: import("mobx-state-tree").IType<any, any, any>;
+            authInfo: import("mobx-state-tree").IType<any, any, any>; /**
+             * #property
+             * filehandle object for the MSA (which could contain a tree e.g. with
+             * stockholm files)
+             */
         }, {}, 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>; /**
+         * #property
+         *
+         */
         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">;
@@ -123,10 +126,7 @@ declare const model: import("mobx-state-tree").IModelType<{
         localPath: import("mobx-state-tree").ISimpleType<string>;
     }, {}> | ({
         locationType: "UriLocation";
-        uri: string; /**
-         * #volatile
-         * the currently mouse-hovered row
-         */
+        uri: string;
     } & Partial<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
         locationType: import("mobx-state-tree").ISimpleType<"UriLocation">;
         uri: import("mobx-state-tree").ISimpleType<string>;
@@ -135,28 +135,27 @@ declare const model: 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>>; /**
-         * #action
-         * set the height of the view in px
-         */
+        }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
     }>> & import("mobx-state-tree/dist/internal").NonEmptyObject)>, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
     msaFilehandle: 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<{
-        /**
-         * #property
-         * high resolution scale factor, helps make canvas look better on hi-dpi
-         * screens
-         */
         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").IModelType<{
             internetAccountType: import("mobx-state-tree").ISimpleType<string>;
-            authInfo: import("mobx-state-tree").IType<any, any, any>;
+            authInfo: import("mobx-state-tree").IType<any, any, any>; /**
+             * #property
+             * filehandle object for the MSA (which could contain a tree e.g. with
+             * stockholm files)
+             */
         }, {}, 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>; /**
+         * #property
+         *
+         */
         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">;
@@ -185,10 +184,7 @@ declare const model: import("mobx-state-tree").IModelType<{
         localPath: import("mobx-state-tree").ISimpleType<string>;
     }, {}> | ({
         locationType: "UriLocation";
-        uri: string; /**
-         * #volatile
-         * the currently mouse-hovered row
-         */
+        uri: string;
     } & Partial<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
         locationType: import("mobx-state-tree").ISimpleType<"UriLocation">;
         uri: import("mobx-state-tree").ISimpleType<string>;
@@ -197,28 +193,27 @@ declare const model: 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>>; /**
-         * #action
-         * set the height of the view in px
-         */
+        }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
     }>> & import("mobx-state-tree/dist/internal").NonEmptyObject)>, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
     treeMetadataFilehandle: 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<{
-        /**
-         * #property
-         * high resolution scale factor, helps make canvas look better on hi-dpi
-         * screens
-         */
         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").IModelType<{
             internetAccountType: import("mobx-state-tree").ISimpleType<string>;
-            authInfo: import("mobx-state-tree").IType<any, any, any>;
+            authInfo: import("mobx-state-tree").IType<any, any, any>; /**
+             * #property
+             * filehandle object for the MSA (which could contain a tree e.g. with
+             * stockholm files)
+             */
         }, {}, 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>; /**
+         * #property
+         *
+         */
         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">;
@@ -247,10 +242,7 @@ declare const model: import("mobx-state-tree").IModelType<{
         localPath: import("mobx-state-tree").ISimpleType<string>;
     }, {}> | ({
         locationType: "UriLocation";
-        uri: string; /**
-         * #volatile
-         * the currently mouse-hovered row
-         */
+        uri: string;
     } & Partial<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
         locationType: import("mobx-state-tree").ISimpleType<"UriLocation">;
         uri: import("mobx-state-tree").ISimpleType<string>;
@@ -259,10 +251,7 @@ declare const model: 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>>; /**
-         * #action
-         * set the height of the view in px
-         */
+        }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
     }>> & 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>>;
@@ -517,27 +506,6 @@ declare const model: import("mobx-state-tree").IModelType<{
      */
     setTreeMetadata(result: string): 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
      */
@@ -660,6 +628,37 @@ declare const model: import("mobx-state-tree").IModelType<{
      * #getter
      */
     readonly totalHeight: number;
+} & {
+    /**
+     * #getter
+     */
+    readonly totalWidth: number;
+} & {
+    /**
+     * #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 maxScrollX: number;
 } & {
     /**
      * #action
@@ -753,6 +752,13 @@ declare const model: import("mobx-state-tree").IModelType<{
      */
     readonly totalTrackAreaHeight: number;
 } & {
+    /**
+     * #action
+     */
+    exportSVG(opts: {
+        theme: Theme;
+        includeMinimap?: boolean;
+    }): Promise<void>;
     /**
      * #action
      * internal, used for drawing to canvas

package/dist/model.js

@@ -3,6 +3,7 @@ import { cast, types, addDisposer } from 'mobx-state-tree';
 import { hierarchy, cluster } from 'd3-hierarchy';
 import { ascending } from 'd3-array';
 import Stockholm from 'stockholm-js';
+import { saveAs } from 'file-saver';
 // jbrowse
 import { FileLocation, ElementId } from '@jbrowse/core/util/types/mst';
 import { openLocation } from '@jbrowse/core/util/io';
@@ -20,6 +21,8 @@ import colorSchemes from './colorSchemes';
 import { UniprotTrack } from './UniprotTrack';
 import { StructureModel } from './StructureModel';
 import { DialogQueueSessionMixin } from './DialogQueue';
+import { renderToSvg } from './renderToSvg';
+import { blocksX, blocksY } from './calculateBlocks';
 /**
  * #stateModel MsaView
  * extends
@@ -457,75 +460,7 @@ const model = types
         self.data.setTreeMetadata(result);
     },
 }))
-    .views(self => {
-    let oldBlocksX = [];
-    let oldBlocksY = [];
-    let oldValX = 0;
-    let oldValY = 0;
-    return {
-        /**
-         * #getter
-         */
-        get initialized() {
-            return ((self.data.msa ||
-                self.data.tree ||
-                self.msaFilehandle ||
-                self.treeFilehandle) &&
-                !self.error);
-        },
-        /**
-         * #getter
-         */
-        get blocksX() {
-            const { scrollX, blockSize: size, colWidth } = self;
-            const ret = -(size * Math.floor(scrollX / size)) - size;
-            const b = [];
-            for (let i = ret; i < ret + size * 3; i += size) {
-                if (i + size > 0) {
-                    b.push(i);
-                }
-            }
-            if (JSON.stringify(b) !== JSON.stringify(oldBlocksX) ||
-                colWidth !== oldValX) {
-                oldBlocksX = b;
-                oldValX = colWidth;
-            }
-            return oldBlocksX;
-        },
-        /**
-         * #getter
-         */
-        get blocksY() {
-            const { scrollY, blockSize: size, rowHeight } = self;
-            const ret = -(size * Math.floor(scrollY / size)) - 2 * size;
-            const b = [];
-            for (let i = ret; i < ret + size * 3; i += size) {
-                if (i + size > 0) {
-                    b.push(i);
-                }
-            }
-            if (JSON.stringify(b) !== JSON.stringify(oldBlocksY) ||
-                rowHeight !== oldValY) {
-                oldBlocksY = b;
-                oldValY = rowHeight;
-            }
-            return oldBlocksY;
-        },
-    };
-})
     .views(self => ({
-    /**
-     * #getter
-     */
-    get blocks2d() {
-        return self.blocksY.flatMap(by => self.blocksX.map(bx => [bx, by]));
-    },
-    /**
-     * #getter
-     */
-    get done() {
-        return self.initialized && (self.data.msa || self.data.tree);
-    },
     /**
      * #getter
      */
@@ -780,6 +715,74 @@ const model = types
     get totalHeight() {
         return this.root.leaves().length * self.rowHeight;
     },
+}))
+    .views(self => ({
+    /**
+     * #getter
+     */
+    get totalWidth() {
+        return self.numColumns * self.colWidth;
+    },
+}))
+    .views(self => ({
+    /**
+     * #getter
+     */
+    get initialized() {
+        return ((self.data.msa ||
+            self.data.tree ||
+            self.msaFilehandle ||
+            self.treeFilehandle) &&
+            !self.error);
+    },
+    /**
+     * #getter
+     */
+    get blocksX() {
+        return blocksX({
+            viewportWidth: self.msaAreaWidth,
+            viewportX: -self.scrollX,
+            blockSize: self.blockSize,
+            mapWidth: self.totalWidth,
+        });
+    },
+    /**
+     * #getter
+     */
+    get blocksY() {
+        return blocksY({
+            viewportHeight: self.height,
+            viewportY: -self.scrollY,
+            blockSize: self.blockSize,
+            mapHeight: self.totalHeight,
+        });
+    },
+}))
+    .views(self => ({
+    /**
+     * #getter
+     */
+    get blocks2d() {
+        const ret = [];
+        for (const by of self.blocksY) {
+            for (const bx of self.blocksX) {
+                ret.push([bx, by]);
+            }
+        }
+        return ret;
+    },
+    /**
+     * #getter
+     */
+    get done() {
+        return self.initialized && (self.data.msa || self.data.tree);
+    },
+    /**
+     * #getter
+     */
+    get maxScrollX() {
+        return -self.totalWidth + (self.msaAreaWidth - 100);
+    },
 }))
     .actions(self => ({
     /**
@@ -809,13 +812,13 @@ const model = types
      * #action
      */
     doScrollX(deltaX) {
-        self.scrollX = clamp(-(self.numColumns * self.colWidth) + (self.msaAreaWidth - 100), self.scrollX + deltaX, 0);
+        self.scrollX = clamp(self.maxScrollX, self.scrollX + deltaX, 0);
     },
     /**
      * #action
      */
     setScrollX(n) {
-        self.scrollX = clamp(-(self.numColumns * self.colWidth) + (self.msaAreaWidth - 100), n, 0);
+        self.scrollX = clamp(self.maxScrollX, n, 0);
     },
     /**
      * #action
@@ -1048,6 +1051,14 @@ const model = types
     },
 }))
     .actions(self => ({
+    /**
+     * #action
+     */
+    async exportSVG(opts) {
+        const html = await renderToSvg(self, opts);
+        const blob = new Blob([html], { type: 'image/svg+xml' });
+        saveAs(blob, 'image.svg');
+    },
     /**
      * #action
      * internal, used for drawing to canvas

package/dist/model.js.map

@@ -1 +1 @@
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package/dist/parsers/ClustalMSA.d.ts

@@ -2,12 +2,25 @@ import { NodeWithIds } from '../util';
 export default class ClustalMSA {
     private MSA;
     constructor(text: string);
-    getMSA(): import("clustal-js/dist/types").Results;
-    getRow(name: string): string;
-    getWidth(): number;
+    getMSA(): {
+        consensus: string;
+        alns: {
+            id: any;
+            seq: any;
+        }[];
+        header: {
+            info: string;
+            version: string;
+        };
+    };
+    getRow(name: string): any;
+    getWidth(): any;
     getRowData(): undefined;
-    getHeader(): import("clustal-js/dist/types").Header;
-    getNames(): string[];
+    getHeader(): {
+        info: string;
+        version: string;
+    };
+    getNames(): any[];
     getStructures(): {};
     get alignmentNames(): never[];
     getTree(): NodeWithIds;

package/dist/renderToSvg.d.ts

@@ -0,0 +1,6 @@
+import { Theme } from '@mui/material';
+import { MsaViewModel } from './model';
+export declare function renderToSvg(model: MsaViewModel, opts: {
+    theme: Theme;
+    includeMinimap?: boolean;
+}): Promise<string>;

package/dist/renderToSvg.js

@@ -0,0 +1,62 @@
+import React from 'react';
+import { createRoot } from 'react-dom/client';
+import { when } from 'mobx';
+import { renderToStaticMarkup } from '@jbrowse/core/util';
+import { renderTreeCanvas } from './components/TreePanel/renderTreeCanvas';
+import { renderMSABlock } from './components/MSAPanel/renderMSABlock';
+import { colorContrast } from './util';
+import MinimapSVG from './components/MinimapSVG';
+// render LGV to SVG
+export async function renderToSvg(model, opts) {
+    await when(() => !!model.initialized);
+    // eslint-disable-next-line @typescript-eslint/no-explicit-any
+    const { width, height, scrollX, scrollY, colorScheme, treeAreaWidth } = model;
+    const { theme, includeMinimap } = opts;
+    const { Context } = await import('svgcanvas');
+    const ctx1 = Context(width, height);
+    const ctx2 = Context(width, height);
+    const contrastScheme = colorContrast(colorScheme, theme);
+    renderTreeCanvas({
+        model,
+        offsetY: scrollY,
+        ctx: ctx1,
+        theme,
+        blockSizeYOverride: height,
+        highResScaleFactorOverride: 1,
+    });
+    renderMSABlock({
+        model,
+        offsetY: scrollY,
+        offsetX: -scrollX,
+        contrastScheme,
+        ctx: ctx2,
+        blockSizeXOverride: width - treeAreaWidth,
+        blockSizeYOverride: height,
+        highResScaleFactorOverride: 1,
+    });
+    const Wrapper = includeMinimap ? MinimapWrapper : NullWrapper;
+    const clipId = 'tree';
+    // the xlink namespace is used for rendering <image> tag
+    return renderToStaticMarkup(React.createElement("svg", { width: width, height: height, xmlns: "http://www.w3.org/2000/svg", xmlnsXlink: "http://www.w3.org/1999/xlink", viewBox: [0, 0, width, height].toString() },
+        React.createElement(Wrapper, { model: model },
+            React.createElement("defs", null,
+                React.createElement("clipPath", { id: clipId },
+                    React.createElement("rect", { x: 0, y: 0, width: treeAreaWidth, height: height }))),
+            React.createElement("g", { clipPath: `url(#${clipId})`, 
+                /* eslint-disable-next-line react/no-danger */
+                dangerouslySetInnerHTML: { __html: ctx1.getSvg().innerHTML } }),
+            React.createElement("g", { transform: `translate(${treeAreaWidth} 0)`, 
+                /* eslint-disable-next-line react/no-danger */
+                dangerouslySetInnerHTML: { __html: ctx2.getSvg().innerHTML } }))), createRoot);
+}
+function MinimapWrapper({ model, children, }) {
+    const { minimapHeight, treeAreaWidth } = model;
+    return (React.createElement(React.Fragment, null,
+        React.createElement("g", { transform: `translate(${treeAreaWidth} 0)` },
+            React.createElement(MinimapSVG, { model: model })),
+        React.createElement("g", { transform: `translate(0 ${minimapHeight})` }, children)));
+}
+function NullWrapper({ children }) {
+    return React.createElement(React.Fragment, null, children);
+}
+//# sourceMappingURL=renderToSvg.js.map