react-msaview 3.1.5 → 3.1.6

package/dist/model.js

@@ -10,29 +10,45 @@ import { openLocation } from '@jbrowse/core/util/io';
 import { notEmpty, sum } from '@jbrowse/core/util';
 import BaseViewModel from '@jbrowse/core/pluggableElementTypes/models/BaseViewModel';
 // locals
-import { clamp, collapse, filterHiddenLeafNodes, generateNodeIds, maxLength, setBrLength, skipBlanks, } from './util';
+import { clamp, collapse, generateNodeIds, maxLength, setBrLength, skipBlanks, } from './util';
+import { blocksX, blocksY } from './calculateBlocks';
+import { measureTextCanvas } from './measureTextCanvas';
+// components
 import TextTrack from './components/TextTrack';
 import BoxTrack from './components/BoxTrack';
+// parsers
 import ClustalMSA from './parsers/ClustalMSA';
 import StockholmMSA from './parsers/StockholmMSA';
 import FastaMSA from './parsers/FastaMSA';
 import parseNewick from './parseNewick';
 import colorSchemes from './colorSchemes';
+// models
 import { UniprotTrack } from './UniprotTrack';
-import { StructureModel } from './StructureModel';
+import { DataModelF } from './DataModel';
 import { DialogQueueSessionMixin } from './DialogQueue';
-import { renderToSvg } from './renderToSvg';
-import { blocksX, blocksY } from './calculateBlocks';
-import measureTextCanvas from './measureTextCanvas';
+import { SelectedStructuresMixin } from './SelectedStructuresMixin';
 /**
  * #stateModel MsaView
  * extends
  * - BaseViewModel
  * - DialogQueueSessionMixin
+ * - SelectedStructuresMixin
  */
 function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+function reparseTree(tree) {
+    return {
+        ...tree,
+        branchset: tree.branchset.map(r => r.branchset.length
+            ? reparseTree(r)
+            : {
+                branchset: [r],
+                id: `${r.id}-leafnode`,
+                name: `${r.name}-hidden`,
+            }),
+    };
+}
 const model = types
-    .compose(BaseViewModel, DialogQueueSessionMixin(), types.model('MsaView', {
+    .compose(BaseViewModel, DialogQueueSessionMixin(), SelectedStructuresMixin(), types.model('MsaView', {
     /**
      * #property
      * id of view, randomly generated if not provided
@@ -78,11 +94,6 @@ const model = types
      * scroll position, X-offset, px
      */
     scrollX: 0,
-    /**
-     * #property
-     * currently "selected" structures, generally PDB 3-D protein structures
-     */
-    selectedStructures: types.array(StructureModel),
     /**
      * #property
      * right-align the labels
@@ -152,11 +163,7 @@ const model = types
      * array of tree nodes that are 'collapsed'
      */
     collapsed: types.array(types.string),
-    /**
-     * #property
-     * array of leaf nodes that are 'hidden', similar to collapsed but for leaf nodes
-     */
-    hidden: types.array(types.string),
+    collapsed2: types.array(types.string),
     /**
      * #property
      * focus on particular subtree
@@ -178,23 +185,7 @@ const model = types
      * data from the loaded tree/msa/treeMetadata, generally loaded by
      * autorun
      */
-    data: types.optional(types
-        .model({
-        tree: types.maybe(types.string),
-        msa: types.maybe(types.string),
-        treeMetadata: types.maybe(types.string),
-    })
-        .actions(self => ({
-        setTree(tree) {
-            self.tree = tree;
-        },
-        setMSA(msa) {
-            self.msa = msa;
-        },
-        setTreeMetadata(treeMetadata) {
-            self.treeMetadata = treeMetadata;
-        },
-    })), { tree: '', msa: '' }),
+    data: types.optional(DataModelF(), { tree: '', msa: '' }),
 }))
     .volatile(() => ({
     /**
@@ -217,6 +208,16 @@ const model = types
      * the currently mouse-hovered column
      */
     mouseCol: undefined,
+    /**
+     * #volatile
+     * the currently mouse-click row
+     */
+    mouseClickRow: undefined,
+    /**
+     * #volatile
+     * the currently mouse-click column
+     */
+    mouseClickCol: undefined,
     /**
      * #volatile
      * a dummy variable that is incremented when ref changes so autorun for
@@ -248,43 +249,6 @@ const model = types
     setHeight(height) {
         self.height = height;
     },
-    /**
-     * #action
-     * add to the selected structures
-     */
-    addStructureToSelection(elt) {
-        self.selectedStructures.push(elt);
-    },
-    /**
-     * #action
-     * remove from the selected structures
-     */
-    removeStructureFromSelection(elt) {
-        const r = self.selectedStructures.find(node => node.id === elt.id);
-        if (r) {
-            self.selectedStructures.remove(r);
-        }
-    },
-    /**
-     * #action
-     * toggle a structure from the selected structures list
-     */
-    toggleStructureSelection(elt) {
-        const r = self.selectedStructures.find(node => node.id === elt.id);
-        if (r) {
-            self.selectedStructures.remove(r);
-        }
-        else {
-            self.selectedStructures.push(elt);
-        }
-    },
-    /**
-     * #action
-     * clear all selected structures
-     */
-    clearSelectedStructures() {
-        self.selectedStructures = cast([]);
-    },
     /**
      * #action
      * set error state
@@ -300,6 +264,14 @@ const model = types
         self.mouseCol = col;
         self.mouseRow = row;
     },
+    /**
+     * #action
+     * set mouse click position (row, column) in the MSA
+     */
+    setMouseClickPos(col, row) {
+        self.mouseClickCol = col;
+        self.mouseClickRow = row;
+    },
     /**
      * #action
      * set row height (px)
@@ -368,18 +340,6 @@ const model = types
     setDrawTree(arg) {
         self.drawTree = arg;
     },
-    /**
-     * #action
-     */
-    hideNode(arg) {
-        self.hidden.push(arg);
-    },
-    /**
-     * #action
-     */
-    clearHidden() {
-        self.hidden.clear();
-    },
     /**
      * #action
      */
@@ -391,6 +351,17 @@ const model = types
             self.collapsed.push(node);
         }
     },
+    /**
+     * #action
+     */
+    toggleCollapsed2(node) {
+        if (self.collapsed2.includes(node)) {
+            self.collapsed2.remove(node);
+        }
+        else {
+            self.collapsed2.push(node);
+        }
+    },
     /**
      * #action
      */
@@ -544,7 +515,7 @@ const model = types
      * #getter
      */
     get _tree() {
-        return self.data.tree
+        const ret = self.data.tree
             ? generateNodeIds(parseNewick(self.data.tree))
             : this.MSA?.getTree() || {
                 noTree: true,
@@ -552,6 +523,7 @@ const model = types
                 id: 'empty',
                 name: 'empty',
             };
+        return reparseTree(ret);
     },
     /**
      * #getter
@@ -586,18 +558,13 @@ const model = types
                 hier = res;
             }
         }
-        if (self.collapsed.length) {
-            self.collapsed
+        if (self.collapsed.length || self.collapsed2.length) {
+            ;
+            [...self.collapsed, ...self.collapsed2]
                 .map(collapsedId => hier.find(node => node.data.id === collapsedId))
                 .filter(notEmpty)
                 .map(node => collapse(node));
         }
-        if (self.hidden.length) {
-            self.hidden
-                .map(hiddenId => hier.find(node => node.data.id === hiddenId))
-                .filter(notEmpty)
-                .map(node => filterHiddenLeafNodes(node.parent, node.id));
-        }
         return hier;
     },
     /**
@@ -980,7 +947,7 @@ const model = types
     relativePxToBp(rowName, position) {
         const { rowNames, rows } = self;
         const index = rowNames.indexOf(rowName);
-        if (index !== -1) {
+        if (index !== -1 && rows[index]) {
             const row = rows[index][1];
             let k = 0;
             for (let i = 0; i < position; i++) {
@@ -1001,7 +968,7 @@ const model = types
     relativePxToBp2(rowName, position) {
         const { rowNames, rows } = self;
         const index = rowNames.indexOf(rowName);
-        if (index !== -1) {
+        if (index !== -1 && rows[index]) {
             const row = rows[index][1];
             let k = 0;
             let i = 0;
@@ -1045,6 +1012,7 @@ const model = types
      * #action
      */
     async exportSVG(opts) {
+        const { renderToSvg } = await import('./renderToSvg');
         const html = await renderToSvg(self, opts);
         const blob = new Blob([html], { type: 'image/svg+xml' });
         saveAs(blob, 'image.svg');

package/dist/model.js.map

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package/dist/util.d.ts

@@ -40,6 +40,5 @@ export declare function skipBlanks(blanks: number[], arg: string | string[]): st
 export declare function setBrLength(d: HierarchyNode<NodeWithIds>, y0: number, k: number): void;
 export declare function maxLength(d: HierarchyNode<NodeWithIds>): number;
 export declare function collapse(d: HierarchyNode<NodeWithIds>): void;
-export declare function filterHiddenLeafNodes(d: HierarchyNode<NodeWithIds> | null, hiddenId?: string): void;
 export declare function clamp(min: number, num: number, max: number): number;
 export {};

package/dist/util.js

@@ -87,13 +87,6 @@ export function collapse(d) {
         d.children = null;
     }
 }
-// Collapse the node and all it's children, from
-// https://bl.ocks.org/d3noob/43a860bc0024792f8803bba8ca0d5ecd
-export function filterHiddenLeafNodes(d, hiddenId) {
-    if (d?.children) {
-        d.children = d.children.filter(f => f.id !== hiddenId);
-    }
-}
 export function clamp(min, num, max) {
     return Math.min(Math.max(num, min), max);
 }

package/dist/util.js.map

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

@@ -1 +1 @@
-export declare const version = "3.1.5";
+export declare const version = "3.1.6";

package/dist/version.js

@@ -1,2 +1,2 @@
-export const version = '3.1.5';
+export const version = '3.1.6';
 //# sourceMappingURL=version.js.map

package/package.json

@@ -1,7 +1,7 @@
 {
   "name": "react-msaview",
   "author": "Colin",
-  "version": "3.1.5",
+  "version": "3.1.6",
   "license": "MIT",
   "main": "dist/index.js",
   "files": [
@@ -35,7 +35,6 @@
     "react-dom": ">=16.8.0"
   },
   "dependencies": {
-    "canvas2svg": "^1.0.16",
     "clustal-js": "^2.0.0",
     "colord": "^2.9.3",
     "copy-to-clipboard": "^3.3.1",

package/src/DataModel.ts

@@ -0,0 +1,46 @@
+import { types } from 'mobx-state-tree'
+
+/**
+ * #stateModel DataModel
+ * the data stored for the model. this is sometimes temporary in the case that
+ * e.g. msaFilehandle is available on the parent model, because then the msa
+ * data will not be persisted in saved session snapshots, it will be fetched
+ * from msaFilehandle at startup
+ */
+export function DataModelF() {
+  return types
+    .model({
+      /**
+       * #property
+       */
+      tree: types.maybe(types.string),
+      /**
+       * #property
+       */
+      msa: types.maybe(types.string),
+      /**
+       * #property
+       */
+      treeMetadata: types.maybe(types.string),
+    })
+    .actions(self => ({
+      /**
+       * #action
+       */
+      setTree(tree?: string) {
+        self.tree = tree
+      },
+      /**
+       * #action
+       */
+      setMSA(msa?: string) {
+        self.msa = msa
+      },
+      /**
+       * #action
+       */
+      setTreeMetadata(treeMetadata?: string) {
+        self.treeMetadata = treeMetadata
+      },
+    }))
+}

package/src/SelectedStructuresMixin.ts

@@ -0,0 +1,59 @@
+import { SnapshotIn, cast, types } from 'mobx-state-tree'
+import { StructureModel } from './StructureModel'
+
+export type StructureSnap = SnapshotIn<typeof StructureModel>
+
+export function SelectedStructuresMixin() {
+  return types
+    .model({
+      /**
+       * #property
+       * currently "selected" structures, generally PDB 3-D protein structures
+       */
+      selectedStructures: types.array(StructureModel),
+    })
+    .actions(self => ({
+      /**
+       * #action
+       * add to the selected structures
+       */
+      addStructureToSelection(elt: StructureSnap) {
+        self.selectedStructures.push(elt)
+      },
+
+      /**
+       * #action
+       * remove from the selected structures
+       */
+      removeStructureFromSelection(elt: StructureSnap) {
+        const r = self.selectedStructures.find(node => node.id === elt.id)
+        if (r) {
+          self.selectedStructures.remove(r)
+        }
+      },
+
+      /**
+       * #action
+       * toggle a structure from the selected structures list
+       */
+      toggleStructureSelection(elt: {
+        id: string
+        structure: { startPos: number; endPos: number; pdb: string }
+      }) {
+        const r = self.selectedStructures.find(node => node.id === elt.id)
+        if (r) {
+          self.selectedStructures.remove(r)
+        } else {
+          self.selectedStructures.push(elt)
+        }
+      },
+
+      /**
+       * #action
+       * clear all selected structures
+       */
+      clearSelectedStructures() {
+        self.selectedStructures = cast([])
+      },
+    }))
+}

package/src/components/MSAPanel/MSABlock.tsx

@@ -1,6 +1,6 @@
 import React, { useEffect, useRef, useMemo } from 'react'
-import { autorun } from 'mobx'
 import { useTheme } from '@mui/material'
+import { autorun } from 'mobx'
 import { observer } from 'mobx-react'
 
 // locals
@@ -24,6 +24,8 @@ const MSABlock = observer(function ({
     scrollX,
     colorScheme,
     blockSize,
+    mouseClickCol,
+    mouseClickRow,
     highResScaleFactor,
   } = model
   const theme = useTheme()
@@ -36,19 +38,18 @@ const MSABlock = observer(function ({
   const ref = useRef<HTMLCanvasElement>(null)
   useEffect(() => {
     const ctx = ref.current?.getContext('2d')
-    if (!ctx) {
-      return
-    }
-    return autorun(() => {
-      renderMSABlock({
-        ctx,
-        theme,
-        offsetX,
-        offsetY,
-        contrastScheme,
-        model,
-      })
-    })
+    return ctx
+      ? autorun(() => {
+          renderMSABlock({
+            ctx,
+            theme,
+            offsetX,
+            offsetY,
+            contrastScheme,
+            model,
+          })
+        })
+      : undefined
   }, [model, offsetX, offsetY, theme, contrastScheme])
   return (
     <canvas
@@ -60,10 +61,24 @@ const MSABlock = observer(function ({
         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),
-        )
+        const x = Math.floor(mouseX / colWidth) + 1
+        const y = Math.floor(mouseY / rowHeight)
+        model.setMousePos(x, y)
+      }}
+      onClick={event => {
+        if (!ref.current) {
+          return
+        }
+        const { left, top } = ref.current.getBoundingClientRect()
+        const mouseX = event.clientX - left + offsetX
+        const mouseY = event.clientY - top + offsetY
+        const x = Math.floor(mouseX / colWidth) + 1
+        const y = Math.floor(mouseY / rowHeight)
+        if (x === mouseClickCol && y === mouseClickRow) {
+          model.setMouseClickPos(undefined, undefined)
+        } else {
+          model.setMouseClickPos(x, y)
+        }
       }}
       onMouseLeave={() => model.setMousePos()}
       width={blockSize * highResScaleFactor}