react-msaview 2.1.5 → 3.0.0

package/dist/model.js

@@ -1,9 +1,10 @@
+import { autorun } from 'mobx';
 import { cast, types, addDisposer } from 'mobx-state-tree';
 import { hierarchy, cluster } from 'd3-hierarchy';
 import { ascending } from 'd3-array';
 import { FileLocation, ElementId } from '@jbrowse/core/util/types/mst';
 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';
 // locals
@@ -17,12 +18,13 @@ import parseNewick from './parseNewick';
 import colorSchemes from './colorSchemes';
 import { UniprotTrack } from './UniprotTrack';
 import { StructureModel } from './StructureModel';
+import { DialogQueueSessionMixin } from './DialogQueue';
 /**
  * #stateModel MsaView
  */
 function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
 const model = types
-    .compose(BaseViewModel, types.model('MsaView', {
+    .compose(BaseViewModel, DialogQueueSessionMixin(), types.model('MsaView', {
     /**
      * #property
      */
@@ -43,6 +45,10 @@ const model = types
      * #property
      */
     treeWidth: types.optional(types.number, 300),
+    /**
+     * #getter
+     */
+    treeWidthMatchesArea: true,
     /**
      * #property
      */
@@ -169,28 +175,33 @@ const model = types
     })), { tree: '', msa: '' }),
 }))
     .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,
+    /**
+     * #volatile
+     */
     margin: {
         left: 20,
         top: 20,
     },
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any
-    DialogComponent: undefined,
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any
-    DialogProps: undefined,
-    // annotations
+    /**
+     * #volatile
+     */
     annotPos: undefined,
 }))
     .actions(self => ({
-    /**
-     * #action
-     */
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any
-    setDialogComponent(dlg, props) {
-        self.DialogComponent = dlg;
-        self.DialogProps = props;
-    },
     /**
      * #action
      */
@@ -264,14 +275,14 @@ const model = types
     /**
      * #action
      */
-    setScrollY(n) {
-        self.scrollY = n;
+    setTreeWidthMatchesArea(arg) {
+        self.treeWidthMatchesArea = arg;
     },
     /**
      * #action
      */
-    setScrollX(n) {
-        self.scrollX = n;
+    setScrollY(n) {
+        self.scrollY = n;
     },
     /**
      * #action
@@ -294,14 +305,14 @@ const model = types
     /**
      * #action
      */
-    toggleLabelsAlignRight() {
-        self.labelsAlignRight = !self.labelsAlignRight;
+    setLabelsAlignRight(arg) {
+        self.labelsAlignRight = arg;
     },
     /**
      * #action
      */
-    toggleDrawTree() {
-        self.drawTree = !self.drawTree;
+    setDrawTree(arg) {
+        self.drawTree = arg;
     },
     /**
      * #action
@@ -323,20 +334,20 @@ const model = types
     /**
      * #action
      */
-    toggleBranchLen() {
-        self.showBranchLen = !self.showBranchLen;
+    setShowBranchLen(arg) {
+        self.showBranchLen = arg;
     },
     /**
      * #action
      */
-    toggleBgColor() {
-        self.bgColor = !self.bgColor;
+    setBgColor(arg) {
+        self.bgColor = arg;
     },
     /**
      * #action
      */
-    toggleNodeBubbles() {
-        self.drawNodeBubbles = !self.drawNodeBubbles;
+    setDrawNodeBubbles(arg) {
+        self.drawNodeBubbles = arg;
     },
     /**
      * #action
@@ -380,44 +391,6 @@ const model = types
     setTreeMetadata(result) {
         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 = [];
@@ -566,7 +539,7 @@ const model = types
      */
     get numColumns() {
         var _a;
-        return ((((_a = this.MSA) === null || _a === void 0 ? void 0 : _a.getWidth()) || 0) - this.blanks.length) * self.colWidth;
+        return (((_a = this.MSA) === null || _a === void 0 ? void 0 : _a.getWidth()) || 0) - this.blanks.length;
     },
     /**
      * #getter
@@ -685,6 +658,12 @@ 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
      */
@@ -751,7 +730,13 @@ const model = types
      * #action
      */
     doScrollX(deltaX) {
-        self.scrollX = clamp(-self.numColumns + (self.msaAreaWidth - 100), self.scrollX + deltaX, 0);
+        self.scrollX = clamp(-(self.numColumns * self.colWidth) + (self.msaAreaWidth - 100), self.scrollX + deltaX, 0);
+    },
+    /**
+     * #action
+     */
+    setScrollX(n) {
+        self.scrollX = clamp(-(self.numColumns * self.colWidth) + (self.msaAreaWidth - 100), n, 0);
     },
     /**
      * #action
@@ -787,6 +772,22 @@ const model = types
     },
 }))
     .views(self => ({
+    /**
+     * #getter
+     */
+    get labelsWidth() {
+        var _a;
+        let x = 0;
+        const { rowHeight, hierarchy, treeMetadata, fontSize } = self;
+        if (rowHeight > 5) {
+            for (const node of hierarchy.leaves()) {
+                const { data: { name }, } = node;
+                const displayName = ((_a = treeMetadata[name]) === null || _a === void 0 ? void 0 : _a.genome) || name;
+                x = Math.max(measureText(displayName, fontSize), x);
+            }
+        }
+        return x;
+    },
     /**
      * #getter
      */
@@ -990,6 +991,65 @@ 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;

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package/dist/parseNewick.js.map

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package/dist/parsers/StockholmMSA.js.map

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package/dist/util.js.map

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

@@ -1 +1 @@
-export declare const version = "2.1.5";
+export declare const version = "3.0.0";

package/dist/version.js

@@ -1,2 +1,2 @@
-export const version = '2.1.5';
+export const version = '3.0.0';
 //# sourceMappingURL=version.js.map

package/package.json

@@ -1,7 +1,7 @@
 {
   "name": "react-msaview",
   "author": "Colin",
-  "version": "2.1.5",
+  "version": "3.0.0",
   "license": "MIT",
   "main": "dist/index.js",
   "files": [
@@ -45,14 +45,16 @@
     "@types/d3": "^7.4.0",
     "@types/react": "^18.2.33",
     "@types/react-dom": "^18.2.1",
-    "eslint-plugin-unicorn": "^49.0.0",
-    "rollup": "^3.0.2",
-    "rollup-plugin-polyfill-node": "^0.12.0",
+    "eslint-plugin-unicorn": "^50.0.1",
+    "rollup": "^4.9.1",
+    "rollup-plugin-polyfill-node": "^0.13.0",
     "slugify": "^1.6.6",
     "tslib": "^2.1.0",
     "typescript": "^5.0.4"
   },
   "dependencies": {
+    "@typescript-eslint/eslint-plugin": "^6.7.2",
+    "@typescript-eslint/parser": "^6.7.2",
     "clustal-js": "^1.0.3",
     "colord": "^2.9.3",
     "copy-to-clipboard": "^3.3.1",

package/src/DialogQueue.ts

@@ -0,0 +1,47 @@
+import { DialogComponentType } from '@jbrowse/core/util'
+import { types } from 'mobx-state-tree'
+
+/**
+ * #stateModel DialogQueueSessionMixin
+ */
+export function DialogQueueSessionMixin() {
+  return types
+    .model('DialogQueueSessionMixin', {})
+    .volatile(() => ({
+      // eslint-disable-next-line @typescript-eslint/no-explicit-any
+      queueOfDialogs: [] as [DialogComponentType, any][],
+    }))
+    .views(self => ({
+      /**
+       * #getter
+       */
+      get DialogComponent() {
+        return self.queueOfDialogs[0]?.[0]
+      },
+      /**
+       * #getter
+       */
+      get DialogProps() {
+        return self.queueOfDialogs[0]?.[1]
+      },
+    }))
+    .actions(self => ({
+      /**
+       * #action
+       */
+      removeActiveDialog() {
+        self.queueOfDialogs = self.queueOfDialogs.slice(1)
+      },
+      /**
+       * #action
+       */
+      queueDialog(
+        cb: (doneCallback: () => void) => [DialogComponentType, unknown],
+      ) {
+        const [component, props] = cb(() => {
+          this.removeActiveDialog()
+        })
+        self.queueOfDialogs = [...self.queueOfDialogs, [component, props]]
+      },
+    }))
+}

package/src/components/BoxTrackBlock.tsx

@@ -26,6 +26,7 @@ const BoxTrackBlock = observer(function ({
     blanks,
     rowHeight,
     highResScaleFactor,
+    fontSize,
     scrollX,
   } = model
   const { height, features, associatedRowName } = track.model
@@ -75,7 +76,7 @@ const BoxTrackBlock = observer(function ({
     ctx.clearRect(0, 0, blockSize, height)
     ctx.translate(-offsetX, 0)
     ctx.textAlign = 'center'
-    ctx.font = ctx.font.replace(/\d+px/, `${Math.max(8, rowHeight - 8)}px`)
+    ctx.font = ctx.font.replace(/\d+px/, `${fontSize}px`)
 
     const xStart = Math.max(0, Math.floor(offsetX / colWidth))
     ctx.fillStyle = 'goldenrod'
@@ -91,6 +92,7 @@ const BoxTrackBlock = observer(function ({
     })
   }, [
     associatedRowName,
+    fontSize,
     blockSize,
     colWidth,
     layout.rectangles,

package/src/components/Header.tsx

@@ -14,23 +14,21 @@ import List from '@mui/icons-material/List'
 import ZoomControls from './ZoomControls'
 import MultiAlignmentSelector from './MultiAlignmentSelector'
 
-const SettingsDialog = lazy(() => import('./dialogs/SettingsDlg'))
-const AboutDialog = lazy(() => import('./dialogs/AboutDlg'))
-const MetadataDialog = lazy(() => import('./dialogs/MetadataDlg'))
-const TracklistDialog = lazy(() => import('./dialogs/TracklistDlg'))
+const SettingsDialog = lazy(() => import('./dialogs/SettingsDialog'))
+const AboutDialog = lazy(() => import('./dialogs/AboutDialog'))
+const MetadataDialog = lazy(() => import('./dialogs/MetadataDialog'))
+const TracklistDialog = lazy(() => import('./dialogs/TracklistDialog'))
 
 const InfoArea = observer(({ model }: { model: MsaViewModel }) => {
-  const { mouseOverRowName, mouseCol } = model
+  const { mouseOverRowName } = model
   return (
     <div>
       <Typography display="inline">Row name: {mouseOverRowName}</Typography>
-      <span style={{ marginLeft: 10 }} />
-      <Typography display="inline">Position: {mouseCol}</Typography>
     </div>
   )
 })
 
-const Header = observer(({ model }: { model: MsaViewModel }) => {
+const Header = observer(function ({ model }: { model: MsaViewModel }) {
   const [settingsDialogViz, setSettingsDialogViz] = useState(false)
   const [aboutDialogViz, setAboutDialogViz] = useState(false)
   const [detailsDialogViz, setMetadataDialogViz] = useState(false)
@@ -42,11 +40,12 @@ const Header = observer(({ model }: { model: MsaViewModel }) => {
         onClick={async () => {
           try {
             model.setData({ tree: '', msa: '' })
-            await model.setTreeFilehandle(undefined)
-            await model.setMSAFilehandle(undefined)
+            model.clearSelectedStructures()
             model.setScrollY(0)
             model.setScrollX(0)
             model.setCurrentAlignment(0)
+            await model.setTreeFilehandle(undefined)
+            await model.setMSAFilehandle(undefined)
           } catch (e) {
             console.error(e)
             model.setError(e)