react-msaview 2.1.5 → 3.0.0

package/src/model.ts

@@ -1,11 +1,12 @@
 import React from 'react'
+import { autorun } from 'mobx'
 import { Instance, cast, types, addDisposer, SnapshotIn } from 'mobx-state-tree'
 import { hierarchy, cluster, HierarchyNode } from 'd3-hierarchy'
 import { ascending } from 'd3-array'
 import { FileLocation, ElementId } from '@jbrowse/core/util/types/mst'
 import { FileLocation as FileLocationType } from '@jbrowse/core/util/types'
 import { openLocation } from '@jbrowse/core/util/io'
-import { autorun } from 'mobx'
+import { measureText, sum } from '@jbrowse/core/util'
 import BaseViewModel from '@jbrowse/core/pluggableElementTypes/models/BaseViewModel'
 import Stockholm from 'stockholm-js'
 
@@ -35,6 +36,7 @@ import parseNewick from './parseNewick'
 import colorSchemes from './colorSchemes'
 import { UniprotTrack } from './UniprotTrack'
 import { StructureModel } from './StructureModel'
+import { DialogQueueSessionMixin } from './DialogQueue'
 
 interface BasicTrackModel {
   id: string
@@ -74,9 +76,16 @@ type StructureSnap = SnapshotIn<typeof StructureModel>
  */
 function x() {} // eslint-disable-line @typescript-eslint/no-unused-vars
 
+export type DialogComponentType =
+  // eslint-disable-next-line @typescript-eslint/no-explicit-any
+  | React.LazyExoticComponent<React.FC<any>>
+  // eslint-disable-next-line @typescript-eslint/no-explicit-any
+  | React.FC<any>
+
 const model = types
   .compose(
     BaseViewModel,
+    DialogQueueSessionMixin(),
     types.model('MsaView', {
       /**
        * #property
@@ -98,6 +107,10 @@ const model = types
        * #property
        */
       treeWidth: types.optional(types.number, 300),
+      /**
+       * #getter
+       */
+      treeWidthMatchesArea: true,
       /**
        * #property
        */
@@ -230,29 +243,33 @@ const model = types
     }),
   )
   .volatile(() => ({
-    rulerHeight: 20,
+    /**
+     * #volatile
+     * a dummy variable that is incremented when ref changes so autorun for
+     * drawing canvas commands will run
+     */
+    nref: 0,
+    /**
+     * #volatile
+     */
+    minimapHeight: 56,
+    /**
+     * #volatile
+     */
     error: undefined as unknown,
+    /**
+     * #volatile
+     */
     margin: {
       left: 20,
       top: 20,
     },
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any
-    DialogComponent: undefined as undefined | React.FC<any>,
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any
-    DialogProps: undefined as any,
-
-    // annotations
+    /**
+     * #volatile
+     */
     annotPos: undefined as { left: number; right: number } | undefined,
   }))
   .actions(self => ({
-    /**
-     * #action
-     */
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any
-    setDialogComponent(dlg?: React.FC<any>, props?: any) {
-      self.DialogComponent = dlg
-      self.DialogProps = props
-    },
     /**
      * #action
      */
@@ -328,15 +345,16 @@ const model = types
     /**
      * #action
      */
-    setScrollY(n: number) {
-      self.scrollY = n
+    setTreeWidthMatchesArea(arg: boolean) {
+      self.treeWidthMatchesArea = arg
     },
     /**
      * #action
      */
-    setScrollX(n: number) {
-      self.scrollX = n
+    setScrollY(n: number) {
+      self.scrollY = n
     },
+
     /**
      * #action
      */
@@ -358,14 +376,14 @@ const model = types
     /**
      * #action
      */
-    toggleLabelsAlignRight() {
-      self.labelsAlignRight = !self.labelsAlignRight
+    setLabelsAlignRight(arg: boolean) {
+      self.labelsAlignRight = arg
     },
     /**
      * #action
      */
-    toggleDrawTree() {
-      self.drawTree = !self.drawTree
+    setDrawTree(arg: boolean) {
+      self.drawTree = arg
     },
     /**
      * #action
@@ -386,20 +404,20 @@ const model = types
     /**
      * #action
      */
-    toggleBranchLen() {
-      self.showBranchLen = !self.showBranchLen
+    setShowBranchLen(arg: boolean) {
+      self.showBranchLen = arg
     },
     /**
      * #action
      */
-    toggleBgColor() {
-      self.bgColor = !self.bgColor
+    setBgColor(arg: boolean) {
+      self.bgColor = arg
     },
     /**
      * #action
      */
-    toggleNodeBubbles() {
-      self.drawNodeBubbles = !self.drawNodeBubbles
+    setDrawNodeBubbles(arg: boolean) {
+      self.drawNodeBubbles = arg
     },
     /**
      * #action
@@ -442,54 +460,8 @@ const model = types
     setTreeMetadata(result: string) {
       self.data.setTreeMetadata(result)
     },
-
-    afterCreate() {
-      addDisposer(
-        self,
-        autorun(async () => {
-          const { treeFilehandle } = self
-          if (treeFilehandle) {
-            try {
-              this.setTree(await openLocation(treeFilehandle).readFile('utf8'))
-            } catch (e) {
-              console.error(e)
-              this.setError(e)
-            }
-          }
-        }),
-      )
-      addDisposer(
-        self,
-        autorun(async () => {
-          const { treeMetadataFilehandle } = self
-          if (treeMetadataFilehandle) {
-            try {
-              this.setTreeMetadata(
-                await openLocation(treeMetadataFilehandle).readFile('utf8'),
-              )
-            } catch (e) {
-              console.error(e)
-              this.setError(e)
-            }
-          }
-        }),
-      )
-      addDisposer(
-        self,
-        autorun(async () => {
-          const { msaFilehandle } = self
-          if (msaFilehandle) {
-            try {
-              this.setMSA(await openLocation(msaFilehandle).readFile('utf8'))
-            } catch (e) {
-              console.error(e)
-              this.setError(e)
-            }
-          }
-        }),
-      )
-    },
   }))
+
   .views(self => {
     let oldBlocksX: number[] = []
     let oldBlocksY: number[] = []
@@ -573,6 +545,7 @@ const model = types
     get colorScheme() {
       return colorSchemes[self.colorSchemeName]
     },
+
     /**
      * #getter
      */
@@ -639,7 +612,7 @@ const model = types
      * #getter
      */
     get numColumns() {
-      return ((this.MSA?.getWidth() || 0) - this.blanks.length) * self.colWidth
+      return (this.MSA?.getWidth() || 0) - this.blanks.length
     },
     /**
      * #getter
@@ -772,6 +745,12 @@ const model = types
     get columns2d() {
       return this.rows.map(r => r[1]).map(str => skipBlanks(this.blanks, str))
     },
+    /**
+     * #getter
+     */
+    get fontSize() {
+      return Math.max(8, self.rowHeight - 8)
+    },
     /**
      * #getter
      */
@@ -842,11 +821,21 @@ const model = types
      */
     doScrollX(deltaX: number) {
       self.scrollX = clamp(
-        -self.numColumns + (self.msaAreaWidth - 100),
+        -(self.numColumns * self.colWidth) + (self.msaAreaWidth - 100),
         self.scrollX + deltaX,
         0,
       )
     },
+    /**
+     * #action
+     */
+    setScrollX(n: number) {
+      self.scrollX = clamp(
+        -(self.numColumns * self.colWidth) + (self.msaAreaWidth - 100),
+        n,
+        0,
+      )
+    },
     /**
      * #action
      */
@@ -879,6 +868,23 @@ const model = types
     },
   }))
   .views(self => ({
+    /**
+     * #getter
+     */
+    get labelsWidth() {
+      let x = 0
+      const { rowHeight, hierarchy, treeMetadata, fontSize } = self
+      if (rowHeight > 5) {
+        for (const node of hierarchy.leaves()) {
+          const {
+            data: { name },
+          } = node
+          const displayName = treeMetadata[name]?.genome || name
+          x = Math.max(measureText(displayName, fontSize), x)
+        }
+      }
+      return x
+    },
     /**
      * #getter
      */
@@ -1093,6 +1099,78 @@ const model = types
     clearAnnotationClickBoundaries() {
       self.annotPos = undefined
     },
+    /**
+     * #action
+     */
+    incrementRef() {
+      self.nref++
+    },
+  }))
+  .views(self => ({
+    /**
+     * #getter
+     */
+    get totalTrackAreaHeight() {
+      return sum(self.turnedOnTracks.map(r => r.model.height))
+    },
+  }))
+  .actions(self => ({
+    afterCreate() {
+      addDisposer(
+        self,
+        autorun(async () => {
+          const { treeFilehandle } = self
+          if (treeFilehandle) {
+            try {
+              self.setTree(await openLocation(treeFilehandle).readFile('utf8'))
+            } catch (e) {
+              console.error(e)
+              self.setError(e)
+            }
+          }
+        }),
+      )
+      addDisposer(
+        self,
+        autorun(async () => {
+          const { treeMetadataFilehandle } = self
+          if (treeMetadataFilehandle) {
+            try {
+              self.setTreeMetadata(
+                await openLocation(treeMetadataFilehandle).readFile('utf8'),
+              )
+            } catch (e) {
+              console.error(e)
+              self.setError(e)
+            }
+          }
+        }),
+      )
+      addDisposer(
+        self,
+        autorun(async () => {
+          const { msaFilehandle } = self
+          if (msaFilehandle) {
+            try {
+              self.setMSA(await openLocation(msaFilehandle).readFile('utf8'))
+            } catch (e) {
+              console.error(e)
+              self.setError(e)
+            }
+          }
+        }),
+      )
+      addDisposer(
+        self,
+        autorun(async () => {
+          if (self.treeWidthMatchesArea) {
+            self.setTreeWidth(
+              Math.max(50, self.treeAreaWidth - self.labelsWidth - 20),
+            )
+          }
+        }),
+      )
+    },
   }))
   .postProcessSnapshot(result => {
     const snap = result as Omit<typeof result, symbol>

package/src/version.ts

@@ -1 +1 @@
-export const version = '2.1.5'
+export const version = '3.0.0'

package/dist/components/ImportForm.js

@@ -1,84 +0,0 @@
-import React, { useState } from 'react';
-import { Button, Container, Grid, Typography, Link } from '@mui/material';
-import { observer } from 'mobx-react';
-import { FileSelector } from '@jbrowse/core/ui';
-import { smallTree, smallMSA, smallMSAOnly } from './data/seq2';
-async function load(model, msaFile, treeFile) {
-    model.setError(undefined);
-    try {
-        if (msaFile) {
-            await model.setMSAFilehandle(msaFile);
-        }
-        if (treeFile) {
-            await model.setTreeFilehandle(treeFile);
-        }
-    }
-    catch (e) {
-        model.setError(e);
-    }
-}
-const ListItem = ({ onClick, model, children, }) => (React.createElement("li", null,
-    React.createElement(Link, { onClick: event => {
-            model.setError(undefined);
-            event.preventDefault();
-            onClick();
-        }, href: "#" },
-        React.createElement(Typography, { display: "inline" }, children))));
-export default observer(({ model }) => {
-    const [msaFile, setMsaFile] = useState();
-    const [treeFile, setTreeFile] = useState();
-    const { error } = model;
-    return (React.createElement(Container, null,
-        React.createElement("div", { style: { width: '50%' } },
-            error ? (React.createElement("div", { style: { padding: 20 } },
-                React.createElement(Typography, { color: "error" },
-                    "Error: ",
-                    `${error}`))) : null,
-            React.createElement(Typography, null, "Open an MSA file (stockholm or clustal format) and/or a tree file (newick format)."),
-            React.createElement(Typography, { color: "error" }, "Note: you can open up just an MSA or just a tree, both are not required. Some MSA files e.g. stockholm format have an embedded tree also and this is fine, and opening a separate tree file is not required.")),
-        React.createElement(Grid, { container: true, spacing: 10, justifyContent: "center", alignItems: "center" },
-            React.createElement(Grid, { item: true },
-                React.createElement(Typography, null, "MSA file or URL"),
-                React.createElement(FileSelector, { location: msaFile, setLocation: setMsaFile }),
-                React.createElement(Typography, null, "Tree file or URL"),
-                React.createElement(FileSelector, { location: treeFile, setLocation: setTreeFile })),
-            React.createElement(Grid, { item: true },
-                React.createElement(Button, { onClick: () => load(model, msaFile, treeFile), variant: "contained", color: "primary", disabled: !msaFile && !treeFile }, "Open")),
-            React.createElement(Grid, { item: true },
-                React.createElement(Typography, null, "Examples"),
-                React.createElement("ul", null,
-                    React.createElement(ListItem, { model: model, onClick: () => load(model, undefined, {
-                            uri: 'https://jbrowse.org/genomes/newick_trees/sarscov2phylo.pub.ft.nh',
-                            locationType: 'UriLocation',
-                        }) }, "230k COVID-19 samples (tree only)"),
-                    React.createElement(ListItem, { model: model, onClick: () => {
-                            model.setData({ msa: smallMSA, tree: smallTree });
-                        } }, "Small protein MSA+tree"),
-                    React.createElement(ListItem, { model: model, onClick: () => {
-                            model.setData({ msa: smallMSAOnly });
-                        } }, "Small MSA only"),
-                    React.createElement(ListItem, { model: model, onClick: () => load(model, {
-                            uri: 'https://ihh.github.io/abrowse/build/pfam-cov2.stock',
-                            locationType: 'UriLocation',
-                        }) }, "PFAM SARS-CoV2 multi-stockholm"),
-                    React.createElement(ListItem, { model: model, onClick: () => load(model, {
-                            uri: 'https://jbrowse.org/genomes/multiple_sequence_alignments/Lysine.stock',
-                            locationType: 'UriLocation',
-                        }) }, "Lysine stockholm file"),
-                    React.createElement(ListItem, { model: model, onClick: () => load(model, {
-                            uri: 'https://jbrowse.org/genomes/multiple_sequence_alignments/PF01601_full.txt',
-                            locationType: 'UriLocation',
-                        }) }, "PF01601 stockholm file (SARS-CoV2 spike protein)"),
-                    React.createElement(ListItem, { model: model, onClick: () => load(model, {
-                            uri: 'https://jbrowse.org/genomes/multiple_sequence_alignments/europe_covid.fa',
-                            locationType: 'UriLocation',
-                        }) }, "Europe COVID full genomes (LR883044.1 and 199 other sequences)"),
-                    React.createElement(ListItem, { model: model, onClick: () => load(model, {
-                            uri: 'https://jbrowse.org/genomes/multiple_sequence_alignments/rhv_test-only.aligned_with_mafft_auto.fa',
-                            locationType: 'UriLocation',
-                        }, {
-                            uri: 'https://jbrowse.org/genomes/multiple_sequence_alignments/rhv_test-only.aligned_with_mafft_auto.nh',
-                            locationType: 'UriLocation',
-                        }) }, "MAFFT+VeryFastTree(17.9k samples)"))))));
-});
-//# sourceMappingURL=ImportForm.js.map

package/dist/components/ImportForm.js.map

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package/dist/components/MSABlock.js

@@ -1,103 +0,0 @@
-import React, { useEffect, useRef, useMemo } from 'react';
-import { useTheme } from '@mui/material';
-import { observer } from 'mobx-react';
-import { colorContrast } from '../util';
-import { getClustalXColor, getPercentIdentityColor } from '../colorSchemes';
-const MSABlock = observer(function ({ model, offsetX, offsetY, }) {
-    const { MSA, colWidth, bgColor, columns, rowHeight, scrollY, scrollX, hierarchy, colorScheme, colorSchemeName, blockSize, highResScaleFactor, colStats, } = model;
-    const theme = useTheme();
-    const contrastScheme = useMemo(() => colorContrast(colorScheme, theme), [colorScheme, theme]);
-    const ref = useRef(null);
-    useEffect(() => {
-        var _a, _b;
-        if (!ref.current) {
-            return;
-        }
-        const ctx = ref.current.getContext('2d');
-        if (!ctx) {
-            return;
-        }
-        ctx.resetTransform();
-        ctx.scale(highResScaleFactor, highResScaleFactor);
-        ctx.clearRect(0, 0, blockSize, blockSize);
-        ctx.translate(-offsetX, rowHeight / 2 - offsetY);
-        ctx.textAlign = 'center';
-        ctx.font = ctx.font.replace(/\d+px/, `${Math.max(8, rowHeight - 8)}px`);
-        const leaves = hierarchy.leaves();
-        const b = blockSize;
-        // slice vertical rows, e.g. tree leaves, avoid negative slice
-        const yStart = Math.max(0, Math.floor((offsetY - rowHeight) / rowHeight));
-        const yEnd = Math.max(0, Math.ceil((offsetY + b + rowHeight) / rowHeight));
-        // slice horizontal visible letters, avoid negative slice
-        const xStart = Math.max(0, Math.floor(offsetX / colWidth));
-        const xEnd = Math.max(0, Math.ceil((offsetX + b) / colWidth));
-        const visibleLeaves = leaves.slice(yStart, yEnd);
-        for (const node of visibleLeaves) {
-            const { 
-            // @ts-expect-error
-            x: y, data: { name }, } = node;
-            const str = (_a = columns[name]) === null || _a === void 0 ? void 0 : _a.slice(xStart, xEnd);
-            for (let i = 0; i < (str === null || str === void 0 ? void 0 : str.length); i++) {
-                const letter = str[i];
-                const color = colorSchemeName === 'clustalx_protein_dynamic'
-                    ? getClustalXColor(colStats[xStart + i], model, name, xStart + i)
-                    : colorSchemeName === 'percent_identity_dynamic'
-                        ? getPercentIdentityColor(colStats[xStart + i], model, name, xStart + i)
-                        : colorScheme[letter.toUpperCase()];
-                if (bgColor) {
-                    const x = i * colWidth + offsetX - (offsetX % colWidth);
-                    ctx.fillStyle = color || 'white';
-                    ctx.fillRect(x, y - rowHeight, colWidth, rowHeight);
-                }
-            }
-        }
-        if (rowHeight >= 5 && colWidth > rowHeight / 2) {
-            for (const node of visibleLeaves) {
-                const { 
-                // @ts-expect-error
-                x: y, data: { name }, } = node;
-                const str = (_b = columns[name]) === null || _b === void 0 ? void 0 : _b.slice(xStart, xEnd);
-                for (let i = 0; i < (str === null || str === void 0 ? void 0 : str.length); i++) {
-                    const letter = str[i];
-                    const color = colorScheme[letter.toUpperCase()];
-                    const contrast = contrastScheme[letter.toUpperCase()] || 'black';
-                    const x = i * colWidth + offsetX - (offsetX % colWidth);
-                    // note: -rowHeight/4 matches +rowHeight/4 in tree
-                    ctx.fillStyle = bgColor ? contrast : color || 'black';
-                    ctx.fillText(letter, x + colWidth / 2, y - rowHeight / 4);
-                }
-            }
-        }
-        // eslint-disable-next-line react-hooks/exhaustive-deps
-    }, [
-        MSA,
-        highResScaleFactor,
-        columns,
-        colorScheme,
-        contrastScheme,
-        bgColor,
-        rowHeight,
-        colWidth,
-        hierarchy,
-        offsetX,
-        offsetY,
-        blockSize,
-    ]);
-    return (React.createElement("canvas", { ref: ref, onMouseMove: event => {
-            if (!ref.current) {
-                return;
-            }
-            const { left, top } = ref.current.getBoundingClientRect();
-            const mouseX = event.clientX - left + offsetX;
-            const mouseY = event.clientY - top + offsetY;
-            model.setMousePos(Math.floor(mouseX / colWidth) + 1, Math.floor(mouseY / rowHeight));
-        }, onMouseLeave: () => model.setMousePos(), width: blockSize * highResScaleFactor, height: blockSize * highResScaleFactor, style: {
-            position: 'absolute',
-            top: scrollY + offsetY,
-            left: scrollX + offsetX,
-            width: blockSize,
-            height: blockSize,
-        } }));
-});
-export default MSABlock;
-//# sourceMappingURL=MSABlock.js.map

package/dist/components/MSABlock.js.map

@@ -1 +0,0 @@
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package/dist/components/MSACanvas.js.map

@@ -1 +0,0 @@
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package/dist/components/MSAMouseoverCanvas.js

@@ -1,61 +0,0 @@
-import React, { useEffect, useRef } from 'react';
-import { observer } from 'mobx-react';
-import { sum } from '@jbrowse/core/util';
-const MSAMouseoverCanvas = observer(function ({ model, }) {
-    const ref = useRef(null);
-    const { height, width, treeAreaWidth, resizeHandleWidth, rulerHeight, turnedOnTracks, scrollX, scrollY, mouseCol, 
-    // @ts-expect-error
-    mouseCol2, mouseRow, rowHeight, colWidth, } = model;
-    const totalTrackAreaHeight = sum(turnedOnTracks.map(r => r.model.height));
-    useEffect(() => {
-        if (!ref.current) {
-            return;
-        }
-        const ctx = ref.current.getContext('2d');
-        if (!ctx) {
-            return;
-        }
-        ctx.resetTransform();
-        ctx.clearRect(0, 0, width, height);
-        if (mouseCol !== undefined) {
-            ctx.fillStyle = 'rgba(0,0,0,0.15)';
-            const x = (mouseCol - 1) * colWidth + scrollX + treeAreaWidth + resizeHandleWidth;
-            ctx.fillRect(x, 0, colWidth, height);
-        }
-        if (mouseRow !== undefined) {
-            ctx.fillStyle = 'rgba(0,0,0,0.15)';
-            const y = mouseRow * rowHeight + scrollY + rulerHeight + totalTrackAreaHeight;
-            ctx.fillRect(treeAreaWidth + resizeHandleWidth, y, width, rowHeight);
-        }
-        if (mouseCol2 !== undefined) {
-            ctx.fillStyle = 'rgba(255,255,0,0.2)';
-            const x = (mouseCol2 - 1) * colWidth + scrollX + treeAreaWidth + resizeHandleWidth;
-            ctx.fillRect(x, 0, colWidth, height);
-        }
-    }, [
-        mouseCol,
-        mouseCol2,
-        colWidth,
-        scrollY,
-        totalTrackAreaHeight,
-        mouseRow,
-        rowHeight,
-        rulerHeight,
-        scrollX,
-        height,
-        resizeHandleWidth,
-        treeAreaWidth,
-        width,
-    ]);
-    return (React.createElement("canvas", { ref: ref, width: width, height: height, style: {
-            position: 'absolute',
-            top: 0,
-            left: 0,
-            width,
-            height,
-            zIndex: 1000,
-            pointerEvents: 'none',
-        } }));
-});
-export default MSAMouseoverCanvas;
-//# sourceMappingURL=MSAMouseoverCanvas.js.map

package/dist/components/MSAMouseoverCanvas.js.map

@@ -1 +0,0 @@
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package/dist/components/Ruler.d.ts

@@ -1,6 +0,0 @@
-import React from 'react';
-import { MsaViewModel } from '../model';
-declare const Ruler: ({ model }: {
-    model: MsaViewModel;
-}) => React.JSX.Element | null;
-export default Ruler;