react-msaview 4.0.2 → 4.1.0

package/dist/model.js

@@ -1,40 +1,35 @@
-import { autorun, transaction } from 'mobx';
-import { cast, types, addDisposer } from 'mobx-state-tree';
-import { hierarchy, cluster } from 'd3-hierarchy';
+import { groupBy, notEmpty, sum } from '@jbrowse/core/util';
+import { openLocation } from '@jbrowse/core/util/io';
+import { ElementId, FileLocation } from '@jbrowse/core/util/types/mst';
+import { colord } from 'colord';
 import { ascending } from 'd3-array';
-import Stockholm from 'stockholm-js';
+import { cluster, hierarchy } from 'd3-hierarchy';
 import { saveAs } from 'file-saver';
+import { autorun, transaction } from 'mobx';
+import { addDisposer, cast, types } from 'mobx-state-tree';
 import { ungzip } from 'pako';
-// jbrowse
-import { FileLocation, ElementId } from '@jbrowse/core/util/types/mst';
-import { openLocation } from '@jbrowse/core/util/io';
-import { groupBy, notEmpty, sum } from '@jbrowse/core/util';
-export function isGzip(buf) {
-    return buf[0] === 31 && buf[1] === 139 && buf[2] === 8;
-}
-// locals
-import { clamp, collapse, generateNodeIds, maxLength, setBrLength, skipBlanks, len, } from './util';
-import { colord } from 'colord';
-import { reparseTree } from './reparseTree';
+import Stockholm from 'stockholm-js';
 import { blocksX, blocksY } from './calculateBlocks';
-import { measureTextCanvas } from './measureTextCanvas';
-import palettes from './ggplotPalettes';
-// components
-import TextTrack from './components/TextTrack';
-// parsers
-import ClustalMSA from './parsers/ClustalMSA';
-import EmfMSA from './parsers/EmfMSA';
-import StockholmMSA from './parsers/StockholmMSA';
-import FastaMSA from './parsers/FastaMSA';
-import parseNewick from './parseNewick';
 import colorSchemes from './colorSchemes';
-// models
+import TextTrack from './components/TextTrack';
+import palettes from './ggplotPalettes';
+import { measureTextCanvas } from './measureTextCanvas';
 import { DataModelF } from './model/DataModel';
 import { DialogQueueSessionMixin } from './model/DialogQueue';
-import { TreeF } from './model/treeModel';
 import { MSAModelF } from './model/msaModel';
-import { mouseOverCoordToGlobalCoord, globalCoordToRowSpecificCoord, } from './rowCoordinateCalculations';
+import { TreeModelF } from './model/treeModel';
+import parseNewick from './parseNewick';
+import ClustalMSA from './parsers/ClustalMSA';
+import EmfMSA from './parsers/EmfMSA';
 import EmfTree from './parsers/EmfTree';
+import FastaMSA from './parsers/FastaMSA';
+import StockholmMSA from './parsers/StockholmMSA';
+import { reparseTree } from './reparseTree';
+import { globalCoordToRowSpecificCoord, mouseOverCoordToGlobalCoord, } from './rowCoordinateCalculations';
+import { clamp, collapse, generateNodeIds, len, maxLength, setBrLength, skipBlanks, } from './util';
+export function isGzip(buf) {
+    return buf[0] === 31 && buf[1] === 139 && buf[2] === 8;
+}
 /**
  * #stateModel MsaView
  * extends
@@ -44,7 +39,7 @@ import EmfTree from './parsers/EmfTree';
  */
 function stateModelFactory() {
     return types
-        .compose(DialogQueueSessionMixin(), TreeF(), MSAModelF(), types.model('MsaView', {
+        .compose(DialogQueueSessionMixin(), TreeModelF(), MSAModelF(), types.model('MsaView', {
         /**
          * #property
          * id of view, randomly generated if not provided
@@ -78,7 +73,7 @@ function stateModelFactory() {
         /**
          * #property
          */
-        hideGaps: true,
+        hideGaps: false,
         /**
          * #property
          */
@@ -165,6 +160,10 @@ function stateModelFactory() {
          * #property
          */
         featureFilters: types.map(types.boolean),
+        /**
+         * #property
+         */
+        relativeTo: types.maybe(types.string),
     }))
         .volatile(() => ({
         /**
@@ -247,11 +246,16 @@ function stateModelFactory() {
         annotPos: undefined,
         /**
          * #volatile
-         *
          */
         interProAnnotations: undefined,
     }))
         .actions(self => ({
+        /**
+         * #action
+         */
+        drawRelativeTo(id) {
+            self.relativeTo = id;
+        },
         /**
          * #action
          */
@@ -647,6 +651,12 @@ function stateModelFactory() {
                 .map(leaf => [leaf.data.name, MSA?.getRow(leaf.data.name)])
                 .filter((f) => !!f[1]);
         },
+        /**
+         * #getter
+         */
+        get numRows() {
+            return this.rows.length;
+        },
         /**
          * #getter
          */
@@ -663,7 +673,10 @@ function stateModelFactory() {
          * #getter
          */
         get columns2d() {
-            return this.rows.map(r => r[1]).map(str => skipBlanks(this.blanks, str));
+            const { hideGaps } = self;
+            return this.rows
+                .map(r => r[1])
+                .map(str => (hideGaps ? skipBlanks(this.blanks, str) : str));
         },
         /**
          * #getter
@@ -791,7 +804,9 @@ function stateModelFactory() {
          * #getter
          */
         get showMsaLetters() {
-            return self.drawMsaLetters && self.rowHeight >= 5;
+            return (self.drawMsaLetters &&
+                self.rowHeight >= 5 &&
+                self.colWidth > self.rowHeight / 2);
         },
         /**
          * #getter
@@ -939,11 +954,16 @@ function stateModelFactory() {
          * #getter
          */
         get adapterTrackModels() {
-            return (self.MSA?.tracks.map(t => ({
+            const { rowHeight, MSA, hideGaps, blanks } = self;
+            return (MSA?.tracks.map(t => ({
                 model: {
                     ...t,
-                    data: t.data ? skipBlanks(self.blanks, t.data) : undefined,
-                    height: self.rowHeight,
+                    data: t.data
+                        ? hideGaps
+                            ? skipBlanks(blanks, t.data)
+                            : t.data
+                        : undefined,
+                    height: rowHeight,
                 },
                 ReactComponent: TextTrack,
             })) || []);
@@ -1188,6 +1208,15 @@ function stateModelFactory() {
         setFilter(arg, flag) {
             self.featureFilters.set(arg, flag);
         },
+        /**
+         * #action
+         */
+        showEntire() {
+            self.rowHeight = self.msaAreaHeight / self.numRows;
+            self.colWidth = self.msaAreaWidth / self.numColumns;
+            self.scrollX = 0;
+            self.scrollY = 0;
+        },
         afterCreate() {
             addDisposer(self, autorun(() => {
                 for (const key of self.tidyInterProAnnotationTypes.keys()) {
@@ -1258,10 +1287,12 @@ function stateModelFactory() {
             // xref solution https://github.com/mobxjs/mobx/issues/266#issuecomment-222007278
             // xref problem https://github.com/GMOD/react-msaview/issues/75
             addDisposer(self, autorun(() => {
-                // eslint-disable-next-line  @typescript-eslint/no-unused-expressions
-                self.colStats;
-                // eslint-disable-next-line  @typescript-eslint/no-unused-expressions
-                self.colStatsSums;
+                if (self.colorSchemeName.includes('dynamic')) {
+                    // eslint-disable-next-line  @typescript-eslint/no-unused-expressions
+                    self.colStats;
+                    // eslint-disable-next-line  @typescript-eslint/no-unused-expressions
+                    self.colStatsSums;
+                }
                 // eslint-disable-next-line  @typescript-eslint/no-unused-expressions
                 self.columns;
             }));

package/dist/model.js.map

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package/dist/parsers/ClustalMSA.js.map

@@ -1 +1 @@
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package/dist/parsers/EmfMSA.js.map

@@ -1 +1 @@
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package/dist/parsers/StockholmMSA.js.map

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

@@ -1,5 +1,5 @@
-import type { Theme } from '@mui/material';
 import type { MsaViewModel } from './model';
+import type { Theme } from '@mui/material';
 export declare function renderToSvg(model: MsaViewModel, opts: {
     theme: Theme;
     includeMinimap?: boolean;

package/dist/renderToSvg.js

@@ -1,13 +1,12 @@
 /* eslint-disable react-refresh/only-export-components */
 import React from 'react';
-import { createRoot } from 'react-dom/client';
-import { when } from 'mobx';
 import { renderToStaticMarkup } from '@jbrowse/core/util';
-import { renderTreeCanvas } from './components/tree/renderTreeCanvas';
-import { renderMSABlock } from './components/msa/renderMSABlock';
-import { colorContrast } from './util';
+import { when } from 'mobx';
 import MinimapSVG from './components/minimap/MinimapSVG';
 import { renderBoxFeatureCanvasBlock } from './components/msa/renderBoxFeatureCanvasBlock';
+import { renderMSABlock } from './components/msa/renderMSABlock';
+import { renderTreeCanvas } from './components/tree/renderTreeCanvas';
+import { colorContrast } from './util';
 export async function renderToSvg(model, opts) {
     await when(() => !!model.dataInitialized);
     const { width, height, scrollX, scrollY } = model;
@@ -41,7 +40,7 @@ async function render({ width, height, offsetX, offsetY, theme, model, includeMi
     const Wrapper = includeMinimap ? MinimapWrapper : NullWrapper;
     return renderToStaticMarkup(React.createElement(SvgWrapper, { width: width, height: height },
         React.createElement(Wrapper, { model: model },
-            React.createElement(CoreRendering, { Context: Context, model: model, theme: theme, offsetX: offsetX, offsetY: offsetY, width: width, height: height }))), createRoot);
+            React.createElement(CoreRendering, { Context: Context, model: model, theme: theme, offsetX: offsetX, offsetY: offsetY, width: width, height: height }))));
 }
 function CoreRendering({ model, theme, width, height, offsetX, offsetY, Context, }) {
     const clipId1 = 'tree';

package/dist/renderToSvg.js.map

@@ -1 +1 @@
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package/dist/rowCoordinateCalculations.test.js.map

@@ -1 +1 @@
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+{"version":3,"file":"rowCoordinateCalculations.test.js","sourceRoot":"","sources":["../src/rowCoordinateCalculations.test.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,MAAM,EAAE,IAAI,EAAE,MAAM,QAAQ,CAAA;AAErC,OAAO,EAAE,2BAA2B,EAAE,MAAM,6BAA6B,CAAA;AACzE,IAAI,CAAC,SAAS,EAAE,GAAG,EAAE;IACnB,MAAM,MAAM,GAAG,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,CAAC,CACvB;IACC;QACE,CAAC,CAAC,EAAE,CAAC,CAAC;QACN,CAAC,CAAC,EAAE,CAAC,CAAC;QACN,CAAC,CAAC,EAAE,CAAC,CAAC;QACN,CAAC,CAAC,EAAE,CAAC,CAAC;QACN,CAAC,CAAC,EAAE,CAAC,CAAC;QACN,CAAC,CAAC,EAAE,CAAC,CAAC;QACN,CAAC,CAAC,EAAE,CAAC,CAAC;QACN,CAAC,CAAC,EAAE,EAAE,CAAC;KAEV,CAAC,OAAO,CAAC,CAAC,CAAC,EAAE;QACZ,MAAM,CAAC,2BAA2B,CAAC,MAAM,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;IAC9D,CAAC,CAAC,CAAA;AACJ,CAAC,CAAC,CAAA"}

package/dist/util.d.ts

@@ -1,5 +1,5 @@
-import type { HierarchyNode } from 'd3-hierarchy';
 import type { Theme } from '@mui/material';
+import type { HierarchyNode } from 'd3-hierarchy';
 export declare function transform<T>(obj: Record<string, T>, cb: (arg0: [string, T]) => [string, T]): {
     [k: string]: T;
 };

package/dist/util.js

@@ -1,6 +1,6 @@
-import { max } from 'd3-array';
 import { colord, extend } from 'colord';
 import namesPlugin from 'colord/plugins/names';
+import { max } from 'd3-array';
 extend([namesPlugin]);
 export function transform(obj, cb) {
     return Object.fromEntries(Object.entries(obj).map(cb));

package/dist/util.js.map

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

@@ -1 +1 @@
-export declare const version = "4.0.2";
+export declare const version = "4.1.0";

package/dist/version.js

@@ -1,2 +1,2 @@
-export const version = '4.0.2';
+export const version = '4.1.0';
 //# sourceMappingURL=version.js.map

package/package.json

@@ -1,7 +1,7 @@
 {
   "name": "react-msaview",
   "author": "Colin",
-  "version": "4.0.2",
+  "version": "4.1.0",
   "license": "MIT",
   "main": "dist/index.js",
   "module": "dist/index.js",
@@ -23,7 +23,7 @@
     "build": "npm run build:esm && npm run build:bundle",
     "prepack": "npm run build",
     "postversion": "git push --follow-tags",
-    "statedocs": "rm -rf apidocs && mkdir apidocs && yarn tsx docgen/generateStateModelDocs.ts",
+    "statedocs": "rm -rf apidocs && mkdir apidocs && node --experimental-strip-types docgen/generateStateModelDocs.ts",
     "poststatedocs": "npm run format"
   },
   "peerDependencies": {
@@ -37,8 +37,8 @@
     "react-dom": ">=16.8.0"
   },
   "dependencies": {
-    "@mui/icons-material": "^6.0.2",
-    "@mui/material": "^6.0.2",
+    "@mui/icons-material": "^7.0.1",
+    "@mui/material": "^7.0.1",
     "clustal-js": "^2.0.0",
     "colord": "^2.9.3",
     "copy-to-clipboard": "^3.3.1",
@@ -48,7 +48,6 @@
     "file-saver": "^2.0.5",
     "pako": "^2.1.0",
     "rbush": "^3.0.1",
-    "react-error-boundary": "^4.0.13",
     "stockholm-js": "^1.0.10",
     "svgcanvas": "^2.5.0"
   }

package/src/colorSchemes.ts

@@ -1,6 +1,7 @@
+import { blue, green, orange, red } from '@mui/material/colors'
 import { colord, extend } from 'colord'
 import namesPlugin from 'colord/plugins/names'
-import { blue, green, red, grey, orange } from '@mui/material/colors'
+
 import { transform } from './util'
 
 extend([namesPlugin])

package/src/components/Checkbox2.tsx

@@ -1,4 +1,5 @@
 import React from 'react'
+
 import {
   Checkbox,
   FormControlLabel,

package/src/components/Loading.tsx

@@ -1,12 +1,13 @@
 import React from 'react'
-import { observer } from 'mobx-react'
-import { Button, Typography } from '@mui/material'
-import { ErrorBoundary } from 'react-error-boundary'
+
 import { ErrorMessage } from '@jbrowse/core/ui'
+import { ErrorBoundary } from '@jbrowse/core/ui/ErrorBoundary'
+import { Button, Typography } from '@mui/material'
+import { observer } from 'mobx-react'
 
-// locals
-import ImportForm from './import/ImportForm'
 import MSAView from './MSAView'
+import ImportForm from './import/ImportForm'
+
 import type { MsaViewModel } from '../model'
 
 const Reset = observer(function ({
@@ -38,7 +39,7 @@ const Loading = observer(function ({ model }: { model: MsaViewModel }) {
   return (
     <div>
       <ErrorBoundary
-        fallbackRender={props => <Reset model={model} error={props.error} />}
+        FallbackComponent={e => <Reset model={model} error={e.error} />}
       >
         {dataInitialized ? (
           isLoading ? (

package/src/components/MSAView.tsx

@@ -1,15 +1,16 @@
 import React, { Suspense } from 'react'
+
 import { observer } from 'mobx-react'
 
-// locals
 import { HorizontalResizeHandle, VerticalResizeHandle } from './ResizeHandles'
-import type { MsaViewModel } from '../model'
-import TreeRuler from './tree/TreeRuler'
+import VerticalScrollbar from './VerticalScrollbar'
 import Header from './header/Header'
+import Minimap from './minimap/Minimap'
 import MSAPanel from './msa/MSAPanel'
 import TreePanel from './tree/TreePanel'
-import Minimap from './minimap/Minimap'
-import VerticalScrollbar from './VerticalScrollbar'
+import TreeRuler from './tree/TreeRuler'
+
+import type { MsaViewModel } from '../model'
 
 const TopArea = observer(function ({ model }: { model: MsaViewModel }) {
   const { showHorizontalScrollbar } = model

package/src/components/ResizeHandles.tsx

@@ -1,7 +1,7 @@
 import React, { useEffect, useRef, useState } from 'react'
+
 import { observer } from 'mobx-react'
 
-// locals
 import type { MsaViewModel } from '../model'
 
 export const VerticalResizeHandle = observer(function ({

package/src/components/SequenceTextArea.tsx

@@ -1,9 +1,9 @@
 import React, { useState } from 'react'
+
 import { Button, TextField } from '@mui/material'
-import { makeStyles } from 'tss-react/mui'
 import copy from 'copy-to-clipboard'
+import { makeStyles } from 'tss-react/mui'
 
-// locals
 import Checkbox2 from './Checkbox2'
 
 const useStyles = makeStyles()({

package/src/components/TextTrack.tsx

@@ -1,10 +1,12 @@
-import React, { useRef, useMemo, useEffect } from 'react'
+import React, { useEffect, useMemo, useRef } from 'react'
+
 import { useTheme } from '@mui/material'
 import { observer } from 'mobx-react'
-// locals
-import type { MsaViewModel, ITextTrack } from '../model'
+
 import { colorContrast } from '../util'
 
+import type { ITextTrack, MsaViewModel } from '../model'
+
 const AnnotationBlock = observer(function ({
   track,
   model,