react-msaview 3.0.3 → 3.1.0

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 +21,7 @@ import colorSchemes from './colorSchemes';
 import { UniprotTrack } from './UniprotTrack';
 import { StructureModel } from './StructureModel';
 import { DialogQueueSessionMixin } from './DialogQueue';
+import { renderToSvg } from './renderToSvg';
 /**
  * #stateModel MsaView
  * extends
@@ -815,6 +817,7 @@ const model = types
      * #action
      */
     setScrollX(n) {
+        console.log({ n });
         self.scrollX = clamp(-(self.numColumns * self.colWidth) + (self.msaAreaWidth - 100), n, 0);
     },
     /**
@@ -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 +1,5 @@
+import { Theme } from '@mui/material';
+import { MsaViewModel } from './model';
+export declare function renderToSvg(model: MsaViewModel, opts: {
+    theme: Theme;
+}): Promise<string>;

package/dist/renderToSvg.js

@@ -0,0 +1,49 @@
+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 { renderBlock } from './components/MSAPanel/renderMSABlock';
+import { colorContrast } from './util';
+// 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 } = 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,
+    });
+    renderBlock({
+        model,
+        offsetY: scrollY,
+        offsetX: -scrollX,
+        contrastScheme,
+        ctx: ctx2,
+        blockSizeXOverride: width - treeAreaWidth,
+        blockSizeYOverride: height,
+        highResScaleFactorOverride: 1,
+    });
+    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("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);
+}
+//# sourceMappingURL=renderToSvg.js.map

package/dist/renderToSvg.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"renderToSvg.js","sourceRoot":"","sources":["../src/renderToSvg.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AACzB,OAAO,EAAE,UAAU,EAAE,MAAM,kBAAkB,CAAA;AAC7C,OAAO,EAAE,IAAI,EAAE,MAAM,MAAM,CAAA;AAC3B,OAAO,EAAE,oBAAoB,EAAE,MAAM,oBAAoB,CAAA;AAKzD,OAAO,EAAE,gBAAgB,EAAE,MAAM,yCAAyC,CAAA;AAC1E,OAAO,EAAE,WAAW,EAAE,MAAM,sCAAsC,CAAA;AAClE,OAAO,EAAE,aAAa,EAAE,MAAM,QAAQ,CAAA;AAEtC,oBAAoB;AACpB,MAAM,CAAC,KAAK,UAAU,WAAW,CAAC,KAAmB,EAAE,IAAsB;IAC3E,MAAM,IAAI,CAAC,GAAG,EAAE,CAAC,CAAC,CAAC,KAAK,CAAC,WAAW,CAAC,CAAA;IACrC,8DAA8D;IAC9D,MAAM,EAAE,KAAK,EAAE,MAAM,EAAE,OAAO,EAAE,OAAO,EAAE,WAAW,EAAE,aAAa,EAAE,GAAG,KAAK,CAAA;IAC7E,MAAM,EAAE,KAAK,EAAE,GAAG,IAAI,CAAA;IAEtB,MAAM,EAAE,OAAO,EAAE,GAAG,MAAM,MAAM,CAAC,WAAW,CAAC,CAAA;IAC7C,MAAM,IAAI,GAAG,OAAO,CAAC,KAAK,EAAE,MAAM,CAAC,CAAA;IACnC,MAAM,IAAI,GAAG,OAAO,CAAC,KAAK,EAAE,MAAM,CAAC,CAAA;IACnC,MAAM,cAAc,GAAG,aAAa,CAAC,WAAW,EAAE,KAAK,CAAC,CAAA;IACxD,gBAAgB,CAAC;QACf,KAAK;QACL,OAAO,EAAE,OAAO;QAChB,GAAG,EAAE,IAAI;QACT,KAAK;QACL,kBAAkB,EAAE,MAAM;QAC1B,0BAA0B,EAAE,CAAC;KAC9B,CAAC,CAAA;IACF,WAAW,CAAC;QACV,KAAK;QACL,OAAO,EAAE,OAAO;QAChB,OAAO,EAAE,CAAC,OAAO;QACjB,cAAc;QACd,GAAG,EAAE,IAAI;QACT,kBAAkB,EAAE,KAAK,GAAG,aAAa;QACzC,kBAAkB,EAAE,MAAM;QAC1B,0BAA0B,EAAE,CAAC;KAC9B,CAAC,CAAA;IAEF,MAAM,MAAM,GAAG,MAAM,CAAA;IACrB,wDAAwD;IACxD,OAAO,oBAAoB,CACzB,6BACE,KAAK,EAAE,KAAK,EACZ,MAAM,EAAE,MAAM,EACd,KAAK,EAAC,4BAA4B,EAClC,UAAU,EAAC,8BAA8B,EACzC,OAAO,EAAE,CAAC,CAAC,EAAE,CAAC,EAAE,KAAK,EAAE,MAAM,CAAC,CAAC,QAAQ,EAAE;QAEzC;YACE,kCAAU,EAAE,EAAE,MAAM;gBAClB,8BAAM,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,KAAK,EAAE,aAAa,EAAE,MAAM,EAAE,MAAM,GAAI,CACjD,CACN;QACP,2BACE,QAAQ,EAAE,QAAQ,MAAM,GAAG;YAC3B,8CAA8C;YAC9C,uBAAuB,EAAE,EAAE,MAAM,EAAE,IAAI,CAAC,MAAM,EAAE,CAAC,SAAS,EAAE,GAC5D;QACF,2BACE,SAAS,EAAE,aAAa,aAAa,KAAK;YAC1C,8CAA8C;YAC9C,uBAAuB,EAAE,EAAE,MAAM,EAAE,IAAI,CAAC,MAAM,EAAE,CAAC,SAAS,EAAE,GAC5D,CACE,EACN,UAAU,CACX,CAAA;AACH,CAAC"}

package/dist/version.d.ts

@@ -1 +1 @@
-export declare const version = "3.0.3";
+export declare const version = "3.1.0";

package/dist/version.js

@@ -1,2 +1,2 @@
-export const version = '3.0.3';
+export const version = '3.1.0';
 //# sourceMappingURL=version.js.map

package/package.json

@@ -1,7 +1,7 @@
 {
   "name": "react-msaview",
   "author": "Colin",
-  "version": "3.0.3",
+  "version": "3.1.0",
   "license": "MIT",
   "main": "dist/index.js",
   "files": [
@@ -57,14 +57,17 @@
   "dependencies": {
     "@typescript-eslint/eslint-plugin": "^6.21.0",
     "@typescript-eslint/parser": "^6.21.0",
+    "canvas2svg": "^1.0.16",
     "clustal-js": "^2.0.0",
     "colord": "^2.9.3",
     "copy-to-clipboard": "^3.3.1",
     "d3-array": "^3.2.3",
     "d3-hierarchy": "^3.1.2",
+    "file-saver": "^2.0.5",
     "normalize-wheel": "^1.0.1",
     "rbush": "^3.0.1",
     "stockholm-js": "^1.0.10",
+    "svgcanvas": "^2.5.0",
     "tss-react": "^4.8.3"
   }
 }

package/src/components/MSAPanel/MSABlock.tsx

@@ -32,6 +32,7 @@ const MSABlock = observer(function ({
     () => colorContrast(colorScheme, theme),
     [colorScheme, theme],
   )
+  console.log({ offsetX, offsetY, scrollX, scrollY })
 
   const ref = useRef<HTMLCanvasElement>(null)
   useEffect(() => {

package/src/components/MSAPanel/renderMSABlock.ts

@@ -10,12 +10,18 @@ export function renderBlock({
   offsetY,
   contrastScheme,
   ctx,
+  highResScaleFactorOverride,
+  blockSizeXOverride,
+  blockSizeYOverride,
 }: {
   offsetX: number
   offsetY: number
   model: MsaViewModel
   contrastScheme: Record<string, string>
   ctx: CanvasRenderingContext2D
+  highResScaleFactorOverride?: number
+  blockSizeXOverride?: number
+  blockSizeYOverride?: number
 }) {
   const {
     hierarchy,
@@ -25,20 +31,22 @@ export function renderBlock({
     fontSize,
     highResScaleFactor,
   } = model
+  const k = highResScaleFactorOverride || highResScaleFactor
+  const bx = blockSizeXOverride || blockSize
+  const by = blockSizeYOverride || blockSize
   ctx.resetTransform()
-  ctx.scale(highResScaleFactor, highResScaleFactor)
-  ctx.clearRect(0, 0, blockSize, blockSize)
+  ctx.scale(k, k)
+  ctx.clearRect(0, 0, bx, by)
   ctx.translate(-offsetX, rowHeight / 2 - offsetY)
   ctx.textAlign = 'center'
   ctx.font = ctx.font.replace(/\d+px/, `${fontSize}px`)
 
   const leaves = hierarchy.leaves()
-  const b = blockSize
 
   const yStart = Math.max(0, Math.floor((offsetY - rowHeight) / rowHeight))
-  const yEnd = Math.max(0, Math.ceil((offsetY + b + rowHeight) / rowHeight))
+  const yEnd = Math.max(0, Math.ceil((offsetY + by + rowHeight) / rowHeight))
   const xStart = Math.max(0, Math.floor(offsetX / colWidth))
-  const xEnd = Math.max(0, Math.ceil((offsetX + b) / colWidth))
+  const xEnd = Math.max(0, Math.ceil((offsetX + bx) / colWidth))
   const visibleLeaves = leaves.slice(yStart, yEnd)
 
   drawTiles({

package/src/components/MSAPanel/renderMSAMouseover.ts

@@ -25,7 +25,6 @@ export function renderMouseover({
   } = model
   ctx.resetTransform()
   ctx.clearRect(0, 0, width, height)
-  console.log({ mouseCol })
 
   if (mouseCol !== undefined) {
     ctx.fillStyle = 'rgba(0,0,0,0.15)'

package/src/components/TreePanel/TreeCanvasBlock.tsx

@@ -158,7 +158,6 @@ const TreeCanvasBlock = observer(function ({
           }
 
           const ret = hoverNameClickMap(event) || hoverBranchClickMap(event)
-          console.log({ ret })
           ref.current.style.cursor = ret ? 'pointer' : 'default'
           setHoverElt(hoverNameClickMap(event))
         }}

package/src/components/TreePanel/renderTreeCanvas.ts

@@ -1,8 +1,8 @@
 import RBush from 'rbush'
+import { Theme } from '@mui/material'
 
 // locals
 import { MsaViewModel } from '../../model'
-import { Theme } from '@mui/material'
 
 export const padding = 600
 const extendBounds = 5
@@ -24,13 +24,16 @@ export function renderTree({
   ctx,
   model,
   theme,
+  blockSizeYOverride,
 }: {
   offsetY: number
   ctx: CanvasRenderingContext2D
   model: MsaViewModel
   theme: Theme
+  blockSizeYOverride?: number
 }) {
   const { hierarchy, showBranchLen, blockSize } = model
+  const by = blockSizeYOverride || blockSize
   ctx.strokeStyle = theme.palette.text.primary
   for (const { source, target } of hierarchy.links()) {
     const y = showBranchLen ? 'len' : 'y'
@@ -44,7 +47,7 @@ export function renderTree({
     // 1d line intersection to check if line crosses block at all, this is
     // an optimization that allows us to skip drawing most tree links
     // outside the block
-    if (offsetY + blockSize >= y1 && y2 >= offsetY) {
+    if (offsetY + by >= y1 && y2 >= offsetY) {
       ctx.beginPath()
       ctx.moveTo(sx, sy)
       ctx.lineTo(sx, ty)
@@ -59,14 +62,17 @@ export function renderNodeBubbles({
   clickMap,
   offsetY,
   model,
+  blockSizeYOverride,
 }: {
   ctx: CanvasRenderingContext2D
-  clickMap: RBush<ClickEntry>
+  clickMap?: RBush<ClickEntry>
   offsetY: number
   model: MsaViewModel
   theme: Theme
+  blockSizeYOverride?: number
 }) {
   const { hierarchy, showBranchLen, collapsed, blockSize } = model
+  const by = blockSizeYOverride || blockSize
   for (const node of hierarchy.descendants()) {
     const val = showBranchLen ? 'len' : 'y'
     const {
@@ -80,7 +86,7 @@ export function renderNodeBubbles({
     if (
       branchset.length &&
       y > offsetY - extendBounds &&
-      y < offsetY + blockSize + extendBounds
+      y < offsetY + by + extendBounds
     ) {
       ctx.strokeStyle = 'black'
       ctx.fillStyle = collapsed.includes(id) ? 'black' : 'white'
@@ -89,7 +95,7 @@ export function renderNodeBubbles({
       ctx.fill()
       ctx.stroke()
 
-      clickMap.insert({
+      clickMap?.insert({
         minX: x - radius,
         maxX: x - radius + d,
         minY: y - radius,
@@ -108,12 +114,14 @@ export function renderTreeLabels({
   offsetY,
   ctx,
   clickMap,
+  blockSizeYOverride,
 }: {
   model: MsaViewModel
   offsetY: number
   ctx: CanvasRenderingContext2D
-  clickMap: RBush<ClickEntry>
+  clickMap?: RBush<ClickEntry>
   theme: Theme
+  blockSizeYOverride?: number
 }) {
   const {
     rowHeight,
@@ -128,6 +136,7 @@ export function renderTreeLabels({
     margin,
     noTree,
   } = model
+  const by = blockSizeYOverride || blockSize
   if (labelsAlignRight) {
     ctx.textAlign = 'right'
     ctx.setLineDash([1, 3])
@@ -147,7 +156,7 @@ export function renderTreeLabels({
 
     const displayName = treeMetadata[name]?.genome || name
 
-    if (y > offsetY - extendBounds && y < offsetY + blockSize + extendBounds) {
+    if (y > offsetY - extendBounds && y < offsetY + by + extendBounds) {
       // note: +rowHeight/4 matches with -rowHeight/4 in msa
       const yp = y + rowHeight / 4
       const xp = showBranchLen ? len : x
@@ -160,7 +169,7 @@ export function renderTreeLabels({
 
       if (!drawTree && !labelsAlignRight) {
         ctx.fillText(displayName, 0, yp)
-        clickMap.insert({
+        clickMap?.insert({
           minX: 0,
           maxX: width,
           minY: yp - height,
@@ -178,7 +187,7 @@ export function renderTreeLabels({
           ctx.stroke()
         }
         ctx.fillText(displayName, offset, yp)
-        clickMap.insert({
+        clickMap?.insert({
           minX: treeAreaWidth - margin.left - width,
           maxX: treeAreaWidth - margin.left,
           minY: yp - height,
@@ -188,7 +197,7 @@ export function renderTreeLabels({
         })
       } else {
         ctx.fillText(displayName, xp + d, yp)
-        clickMap.insert({
+        clickMap?.insert({
           minX: xp + d,
           maxX: xp + d + width,
           minY: yp - height,
@@ -208,14 +217,18 @@ export function renderTreeCanvas({
   ctx,
   offsetY,
   theme,
+  highResScaleFactorOverride,
+  blockSizeYOverride,
 }: {
   model: MsaViewModel
   offsetY: number
   ctx: CanvasRenderingContext2D
-  clickMap: RBush<ClickEntry>
+  clickMap?: RBush<ClickEntry>
   theme: Theme
+  highResScaleFactorOverride?: number
+  blockSizeYOverride?: number
 }) {
-  clickMap.clear()
+  clickMap?.clear()
   const {
     noTree,
     drawTree,
@@ -231,24 +244,47 @@ export function renderTreeCanvas({
     // eslint-disable-next-line @typescript-eslint/no-unused-vars
     nref,
   } = model
+  const by = blockSizeYOverride || blockSize
 
   ctx.resetTransform()
-  ctx.scale(highResScaleFactor, highResScaleFactor)
-  ctx.clearRect(0, 0, treeWidth + padding, blockSize)
+  const k = highResScaleFactorOverride || highResScaleFactor
+  ctx.scale(k, k)
+  ctx.clearRect(0, 0, treeWidth + padding, by)
   ctx.translate(margin.left, -offsetY)
 
+  // console.log(ctx.font)
   const font = ctx.font
   ctx.font = font.replace(/\d+px/, `${fontSize}px`)
 
   if (!noTree && drawTree) {
-    renderTree({ ctx, offsetY, model, theme })
+    renderTree({
+      ctx,
+      offsetY,
+      model,
+      theme,
+      blockSizeYOverride,
+    })
 
     if (drawNodeBubbles) {
-      renderNodeBubbles({ ctx, offsetY, clickMap, model, theme })
+      renderNodeBubbles({
+        ctx,
+        offsetY,
+        clickMap,
+        model,
+        theme,
+        blockSizeYOverride,
+      })
     }
   }
 
   if (rowHeight >= 5) {
-    renderTreeLabels({ ctx, offsetY, model, clickMap, theme })
+    renderTreeLabels({
+      ctx,
+      offsetY,
+      model,
+      clickMap,
+      theme,
+      blockSizeYOverride,
+    })
   }
 }

package/src/components/ZoomControls.tsx

@@ -1,5 +1,5 @@
 import React from 'react'
-import { IconButton } from '@mui/material'
+import { IconButton, useTheme } from '@mui/material'
 import { observer } from 'mobx-react'
 import CascadingMenuButton from '@jbrowse/core/ui/CascadingMenuButton'
 
@@ -17,6 +17,7 @@ const ZoomControls = observer(function ZoomControls({
   model: MsaViewModel
 }) {
   const { colWidth, rowHeight } = model
+  const theme = useTheme()
   return (
     <>
       <IconButton
@@ -39,27 +40,19 @@ const ZoomControls = observer(function ZoomControls({
         menuItems={[
           {
             label: 'Decrease row height',
-            onClick: () => {
-              model.setRowHeight(Math.max(1.5, rowHeight * 0.75))
-            },
+            onClick: () => model.setRowHeight(Math.max(1.5, rowHeight * 0.75)),
           },
           {
             label: 'Increase row height',
-            onClick: () => {
-              model.setRowHeight(rowHeight * 1.5)
-            },
+            onClick: () => model.setRowHeight(rowHeight * 1.5),
           },
           {
             label: 'Decrease col width',
-            onClick: () => {
-              model.setColWidth(Math.max(1, colWidth * 0.75))
-            },
+            onClick: () => model.setColWidth(Math.max(1, colWidth * 0.75)),
           },
           {
             label: 'Increase col width',
-            onClick: () => {
-              model.setColWidth(colWidth * 1.5)
-            },
+            onClick: () => model.setColWidth(colWidth * 1.5),
           },
           {
             label: 'Reset zoom to default',
@@ -68,6 +61,12 @@ const ZoomControls = observer(function ZoomControls({
               model.setRowHeight(20)
             },
           },
+          {
+            label: 'Export SVG',
+            onClick: () => {
+              model.exportSVG({ theme })
+            },
+          },
         ]}
       >
         <MoreVert />

package/src/declare.d.ts

@@ -1 +1,2 @@
 declare module 'stockholm-js'
+declare module 'svgcanvas'