react-msaview 3.1.0 → 3.1.2

package/dist/model.js

@@ -22,6 +22,7 @@ import { UniprotTrack } from './UniprotTrack';
 import { StructureModel } from './StructureModel';
 import { DialogQueueSessionMixin } from './DialogQueue';
 import { renderToSvg } from './renderToSvg';
+import { blocksX, blocksY } from './calculateBlocks';
 /**
  * #stateModel MsaView
  * extends
@@ -459,75 +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
      */
@@ -782,6 +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 => ({
     /**
@@ -811,14 +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) {
-        console.log({ n });
-        self.scrollX = clamp(-(self.numColumns * self.colWidth) + (self.msaAreaWidth - 100), n, 0);
+        self.scrollX = clamp(self.maxScrollX, n, 0);
     },
     /**
      * #action

package/dist/model.js.map

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

@@ -2,4 +2,5 @@ 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

@@ -3,14 +3,15 @@ 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 { 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 } = opts;
+    const { theme, includeMinimap } = opts;
     const { Context } = await import('svgcanvas');
     const ctx1 = Context(width, height);
     const ctx2 = Context(width, height);
@@ -23,7 +24,7 @@ export async function renderToSvg(model, opts) {
         blockSizeYOverride: height,
         highResScaleFactorOverride: 1,
     });
-    renderBlock({
+    renderMSABlock({
         model,
         offsetY: scrollY,
         offsetX: -scrollX,
@@ -33,17 +34,29 @@ export async function renderToSvg(model, opts) {
         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("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);
+        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

package/dist/renderToSvg.js.map

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

@@ -1 +1 @@
-export declare const version = "3.1.0";
+export declare const version = "3.1.2";

package/dist/version.js

@@ -1,2 +1,2 @@
-export const version = '3.1.0';
+export const version = '3.1.2';
 //# sourceMappingURL=version.js.map

package/package.json

@@ -1,7 +1,7 @@
 {
   "name": "react-msaview",
   "author": "Colin",
-  "version": "3.1.0",
+  "version": "3.1.2",
   "license": "MIT",
   "main": "dist/index.js",
   "files": [

package/src/calculateBlocks.ts

@@ -0,0 +1,58 @@
+export function blocksY({
+  mapHeight,
+  blockSize,
+  viewportY,
+  viewportHeight,
+}: {
+  mapHeight: number
+  blockSize: number
+  viewportY: number
+  viewportHeight: number
+}) {
+  const clampedViewportY = Math.max(
+    0,
+    Math.min(viewportY, mapHeight * blockSize - viewportHeight),
+  )
+
+  // Calculate visible tile ranges
+  const minTileY = Math.floor(clampedViewportY / blockSize)
+  const maxTileY = Math.floor(
+    (clampedViewportY + viewportHeight - 1) / blockSize,
+  )
+
+  // Generate list of visible tiles
+  const blocksY = []
+  for (let tileY = minTileY; tileY <= maxTileY; tileY++) {
+    blocksY.push(tileY * blockSize)
+  }
+
+  return blocksY
+}
+
+export function blocksX({
+  mapWidth,
+  blockSize,
+  viewportX,
+  viewportWidth,
+}: {
+  mapWidth: number
+  blockSize: number
+  viewportX: number
+  viewportWidth: number
+}) {
+  const clampedViewportX = Math.max(
+    0,
+    Math.min(viewportX, mapWidth - viewportWidth),
+  )
+
+  const minTileX = Math.floor(clampedViewportX / blockSize)
+  const maxTileX = Math.floor(
+    (clampedViewportX + viewportWidth - 1) / blockSize,
+  )
+  const blocksX = []
+  for (let tileX = minTileX; tileX <= maxTileX; tileX++) {
+    blocksX.push(tileX * blockSize)
+  }
+
+  return blocksX
+}

package/src/components/ExportSVGDialog.tsx

@@ -0,0 +1,61 @@
+import React, { useState } from 'react'
+import { Dialog, ErrorMessage } from '@jbrowse/core/ui'
+import {
+  DialogContent,
+  DialogActions,
+  Button,
+  Checkbox,
+  FormControlLabel,
+  useTheme,
+  Typography,
+} from '@mui/material'
+import { MsaViewModel } from '../model'
+
+export default function ExportSVGDialog({
+  model,
+  onClose,
+}: {
+  model: MsaViewModel
+  onClose: () => void
+}) {
+  const [includeMinimap, setIncludeMinimap] = useState(true)
+  const [error, setError] = useState<unknown>()
+  const theme = useTheme()
+  return (
+    <Dialog onClose={() => onClose()} open title="Export SVG">
+      <DialogContent>
+        <Typography>Export SVG of current view</Typography>
+        {error ? <ErrorMessage error={error} /> : null}
+        <FormControlLabel
+          control={
+            <Checkbox
+              checked={includeMinimap}
+              onChange={event => setIncludeMinimap(event.target.checked)}
+            />
+          }
+          label="Include minimap?"
+        />
+      </DialogContent>
+      <DialogActions>
+        <Button
+          variant="contained"
+          color="primary"
+          onClick={async () => {
+            try {
+              await model.exportSVG({ theme, includeMinimap })
+            } catch (e) {
+              console.error(e)
+              setError(e)
+            }
+            onClose()
+          }}
+        >
+          Submit
+        </Button>
+        <Button variant="contained" color="secondary" onClick={() => onClose()}>
+          Cancel
+        </Button>
+      </DialogActions>
+    </Dialog>
+  )
+}

package/src/components/MSAPanel/MSABlock.tsx

@@ -4,7 +4,7 @@ import { useTheme } from '@mui/material'
 import { observer } from 'mobx-react'
 
 // locals
-import { renderBlock } from './renderMSABlock'
+import { renderMSABlock } from './renderMSABlock'
 import { MsaViewModel } from '../../model'
 import { colorContrast } from '../../util'
 
@@ -32,7 +32,6 @@ const MSABlock = observer(function ({
     () => colorContrast(colorScheme, theme),
     [colorScheme, theme],
   )
-  console.log({ offsetX, offsetY, scrollX, scrollY })
 
   const ref = useRef<HTMLCanvasElement>(null)
   useEffect(() => {
@@ -41,7 +40,7 @@ const MSABlock = observer(function ({
       return
     }
     return autorun(() => {
-      renderBlock({
+      renderMSABlock({
         ctx,
         offsetX,
         offsetY,

package/src/components/MSAPanel/renderMSABlock.ts

@@ -4,7 +4,7 @@ import { getClustalXColor, getPercentIdentityColor } from '../../colorSchemes'
 import { NodeWithIdsAndLength } from '../../util'
 import { HierarchyNode } from 'd3-hierarchy'
 
-export function renderBlock({
+export function renderMSABlock({
   model,
   offsetX,
   offsetY,

package/src/components/MinimapSVG.tsx

@@ -0,0 +1,57 @@
+import React from 'react'
+import { observer } from 'mobx-react'
+import { MsaViewModel } from '../model'
+
+const MinimapSVG = observer(function ({ model }: { model: MsaViewModel }) {
+  const {
+    scrollX,
+    msaAreaWidth: W,
+    minimapHeight: H,
+    colWidth,
+    numColumns,
+  } = model
+
+  const BAR_HEIGHT = 12
+  const H2 = H - 12
+
+  const unit = W / numColumns / colWidth
+  const left = -scrollX
+  const right = left + W
+  const s = left * unit
+  const e = right * unit
+  const fill = 'rgba(66, 119, 127, 0.3)'
+
+  return (
+    <>
+      <rect
+        x={0}
+        y={0}
+        width={W}
+        height={BAR_HEIGHT}
+        stroke="#555"
+        fill="none"
+      />
+      <rect
+        x={Math.max(0, s)}
+        y={0}
+        width={e - s}
+        height={BAR_HEIGHT}
+        fill={fill}
+        stroke="#555"
+      />
+      <g transform={`translate(0 ${BAR_HEIGHT})`}>
+        <polygon
+          fill={fill}
+          points={[
+            [e, 0],
+            [s, 0],
+            [0, H2],
+            [W, H2],
+          ].toString()}
+        />
+      </g>
+    </>
+  )
+})
+
+export default MinimapSVG

package/src/components/TreePanel/renderTreeCanvas.ts

@@ -239,20 +239,23 @@ export function renderTreeCanvas({
     blockSize,
     fontSize,
     rowHeight,
-    // nref has to be kept as a unused var or at least reference to force
-    // redraw after canvas ref change
-    // eslint-disable-next-line @typescript-eslint/no-unused-vars
     nref,
   } = model
   const by = blockSizeYOverride || blockSize
 
   ctx.resetTransform()
-  const k = highResScaleFactorOverride || highResScaleFactor
+
+  // this is a bogus use of nref, it is never less than 0. we just are using it
+  // in this statement because otherwise it would be an unused variable, we
+  // just need to use nref to indicate a redraw in an autorun when canvas ref
+  // is updated and in order to convince bundlers like not to delete unused
+  // usage with propertyReadSideEffects
+  const k =
+    nref < 0 ? -Infinity : 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`)