react-msaview 3.1.4 → 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
@@ -227,6 +228,10 @@ const model = types
      * #volatile
      */
     minimapHeight: 56,
+    /**
+     * #volatile
+     */
+    marginLeft: 20,
     /**
      * #volatile
      */
@@ -244,43 +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
@@ -296,6 +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)
@@ -364,18 +340,6 @@ const model = types
     setDrawTree(arg) {
         self.drawTree = arg;
     },
-    /**
-     * #action
-     */
-    hideNode(arg) {
-        self.hidden.push(arg);
-    },
-    /**
-     * #action
-     */
-    clearHidden() {
-        self.hidden.clear();
-    },
     /**
      * #action
      */
@@ -387,6 +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
      */
@@ -540,7 +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,
@@ -548,6 +523,7 @@ const model = types
                 id: 'empty',
                 name: 'empty',
             };
+        return reparseTree(ret);
     },
     /**
      * #getter
@@ -582,18 +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;
     },
     /**
@@ -615,6 +586,12 @@ const model = types
     get msaAreaWidth() {
         return self.width - self.treeAreaWidth;
     },
+    /**
+     * #getter
+     */
+    get treeAreaWidthMinusMargin() {
+        return self.treeAreaWidth - self.marginLeft;
+    },
     /**
      * #getter
      */
@@ -970,7 +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++) {
@@ -991,7 +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;
@@ -1035,6 +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');
@@ -1089,7 +1067,7 @@ const model = types
         // autorun synchronizes treeWidth with treeAreaWidth
         addDisposer(self, autorun(async () => {
             if (self.treeWidthMatchesArea) {
-                self.setTreeWidth(Math.max(50, self.treeAreaWidth - self.labelsWidth - 10));
+                self.setTreeWidth(Math.max(50, self.treeAreaWidth - self.labelsWidth - 10 - self.marginLeft));
             }
         }));
     },

package/dist/model.js.map

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package/dist/parsers/ClustalMSA.d.ts

@@ -26,15 +26,5 @@ export default class ClustalMSA {
     getTree(): NodeWithIds;
     get seqConsensus(): string;
     get secondaryStructureConsensus(): undefined;
-    get tracks(): {
-        id: string;
-        name: string;
-        data: string;
-        customColorScheme: {
-            '*': string;
-            ':': string;
-            '.': string;
-            ' ': string;
-        };
-    }[];
+    get tracks(): never[];
 }

package/dist/parsers/ClustalMSA.js

@@ -47,21 +47,7 @@ export default class ClustalMSA {
         return undefined;
     }
     get tracks() {
-        return this.seqConsensus?.trim()
-            ? [
-                {
-                    id: 'seqConsensus',
-                    name: 'Sequence consensus',
-                    data: this.seqConsensus,
-                    customColorScheme: {
-                        '*': 'white',
-                        ':': 'grey',
-                        '.': 'darkgrey',
-                        ' ': 'black',
-                    },
-                },
-            ]
-            : [];
+        return [];
     }
 }
 //# sourceMappingURL=ClustalMSA.js.map

package/dist/parsers/ClustalMSA.js.map

@@ -1 +1 @@
-{"version":3,"file":"ClustalMSA.js","sourceRoot":"","sources":["../../src/parsers/ClustalMSA.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,KAAK,EAAE,MAAM,YAAY,CAAA;AAElC,MAAM,CAAC,OAAO,OAAO,UAAU;IACrB,GAAG,CAA0B;IAErC,YAAY,IAAY;QACtB,IAAI,CAAC,GAAG,GAAG,KAAK,CAAC,IAAI,CAAC,CAAA;IACxB,CAAC;IAED,MAAM;QACJ,OAAO,IAAI,CAAC,GAAG,CAAA;IACjB,CAAC;IAED,MAAM,CAAC,IAAY;QACjB,OAAO,IAAI,CAAC,GAAG,CAAC,IAAI,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,EAAE,KAAK,IAAI,CAAC,EAAE,GAAG,IAAI,EAAE,CAAA;IAC9D,CAAC;IAED,QAAQ;QACN,OAAO,IAAI,CAAC,GAAG,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,MAAM,CAAA;IACpC,CAAC;IAED,UAAU;QACR,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,SAAS;QACP,OAAO,IAAI,CAAC,GAAG,CAAC,MAAM,CAAA;IACxB,CAAC;IAED,QAAQ;QACN,OAAO,IAAI,CAAC,GAAG,CAAC,IAAI,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC,CAAA;IACzC,CAAC;IAED,aAAa;QACX,OAAO,EAAE,CAAA;IACX,CAAC;IAED,IAAI,cAAc;QAChB,OAAO,EAAE,CAAA;IACX,CAAC;IAED,OAAO;QACL,OAAO;YACL,EAAE,EAAE,MAAM;YACV,IAAI,EAAE,MAAM;YACZ,MAAM,EAAE,IAAI;YACZ,SAAS,EAAE,IAAI,CAAC,QAAQ,EAAE,CAAC,GAAG,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;gBACtC,EAAE,EAAE,IAAI;gBACR,IAAI;gBACJ,SAAS,EAAE,EAAE;aACd,CAAC,CAAC;SACJ,CAAA;IACH,CAAC;IAED,IAAI,YAAY;QACd,OAAO,IAAI,CAAC,GAAG,CAAC,SAAS,CAAA;IAC3B,CAAC;IACD,IAAI,2BAA2B;QAC7B,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,IAAI,MAAM;QACR,OAAO,IAAI,CAAC,YAAY,EAAE,IAAI,EAAE;YAC9B,CAAC,CAAC;gBACE;oBACE,EAAE,EAAE,cAAc;oBAClB,IAAI,EAAE,oBAAoB;oBAC1B,IAAI,EAAE,IAAI,CAAC,YAAY;oBACvB,iBAAiB,EAAE;wBACjB,GAAG,EAAE,OAAO;wBACZ,GAAG,EAAE,MAAM;wBACX,GAAG,EAAE,UAAU;wBACf,GAAG,EAAE,OAAO;qBACb;iBACF;aACF;YACH,CAAC,CAAC,EAAE,CAAA;IACR,CAAC;CACF"}
+{"version":3,"file":"ClustalMSA.js","sourceRoot":"","sources":["../../src/parsers/ClustalMSA.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,KAAK,EAAE,MAAM,YAAY,CAAA;AAElC,MAAM,CAAC,OAAO,OAAO,UAAU;IACrB,GAAG,CAA0B;IAErC,YAAY,IAAY;QACtB,IAAI,CAAC,GAAG,GAAG,KAAK,CAAC,IAAI,CAAC,CAAA;IACxB,CAAC;IAED,MAAM;QACJ,OAAO,IAAI,CAAC,GAAG,CAAA;IACjB,CAAC;IAED,MAAM,CAAC,IAAY;QACjB,OAAO,IAAI,CAAC,GAAG,CAAC,IAAI,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,EAAE,KAAK,IAAI,CAAC,EAAE,GAAG,IAAI,EAAE,CAAA;IAC9D,CAAC;IAED,QAAQ;QACN,OAAO,IAAI,CAAC,GAAG,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,MAAM,CAAA;IACpC,CAAC;IAED,UAAU;QACR,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,SAAS;QACP,OAAO,IAAI,CAAC,GAAG,CAAC,MAAM,CAAA;IACxB,CAAC;IAED,QAAQ;QACN,OAAO,IAAI,CAAC,GAAG,CAAC,IAAI,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC,CAAA;IACzC,CAAC;IAED,aAAa;QACX,OAAO,EAAE,CAAA;IACX,CAAC;IAED,IAAI,cAAc;QAChB,OAAO,EAAE,CAAA;IACX,CAAC;IAED,OAAO;QACL,OAAO;YACL,EAAE,EAAE,MAAM;YACV,IAAI,EAAE,MAAM;YACZ,MAAM,EAAE,IAAI;YACZ,SAAS,EAAE,IAAI,CAAC,QAAQ,EAAE,CAAC,GAAG,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;gBACtC,EAAE,EAAE,IAAI;gBACR,IAAI;gBACJ,SAAS,EAAE,EAAE;aACd,CAAC,CAAC;SACJ,CAAA;IACH,CAAC;IAED,IAAI,YAAY;QACd,OAAO,IAAI,CAAC,GAAG,CAAC,SAAS,CAAA;IAC3B,CAAC;IACD,IAAI,2BAA2B;QAC7B,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,IAAI,MAAM;QACR,OAAO,EAAE,CAAA;IACX,CAAC;CACF"}

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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+{"version":3,"file":"util.js","sourceRoot":"","sources":["../src/util.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,GAAG,EAAE,MAAM,UAAU,CAAA;AAE9B,OAAO,EAAE,MAAM,EAAE,MAAM,EAAE,MAAM,QAAQ,CAAA;AACvC,OAAO,WAAW,MAAM,sBAAsB,CAAA;AAE9C,MAAM,CAAC,CAAC,WAAW,CAAC,CAAC,CAAA;AAErB,MAAM,UAAU,SAAS,CACvB,GAAsB,EACtB,EAAsC;IAEtC,OAAO,MAAM,CAAC,WAAW,CAAC,MAAM,CAAC,OAAO,CAAC,GAAG,CAAC,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC,CAAA;AACxD,CAAC;AAwBD,MAAM,UAAU,eAAe,CAC7B,IAAU,EACV,MAAM,GAAG,MAAM,EACf,KAAK,GAAG,CAAC;IAET,MAAM,EAAE,GAAG,GAAG,MAAM,IAAI,KAAK,EAAE,CAAA;IAE/B,OAAO;QACL,GAAG,IAAI;QACP,EAAE;QACF,IAAI,EAAE,IAAI,CAAC,IAAI,IAAI,EAAE;QACrB,SAAS,EACP,IAAI,CAAC,SAAS,EAAE,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAC3B,eAAe,CAAC,CAAC,EAAE,GAAG,EAAE,IAAI,CAAC,EAAE,EAAE,KAAK,GAAG,CAAC,CAAC,CAC5C,IAAI,EAAE;KACV,CAAA;AACH,CAAC;AAED,MAAM,UAAU,aAAa,CAC3B,WAAmC,EACnC,KAAY;IAEZ,OAAO,SAAS,CAAC,WAAW,EAAE,CAAC,CAAC,MAAM,EAAE,KAAK,CAAC,EAAE,EAAE,CAAC;QACjD,MAAM;QACN,KAAK,CAAC,OAAO,CAAC,eAAe,CAAC,MAAM,CAAC,KAAK,CAAC,CAAC,KAAK,EAAE,CAAC;KACrD,CAAC,CAAA;AACJ,CAAC;AAED,MAAM,UAAU,QAAQ,CAAC,GAAY;IACnC,OAAO,GAAG;QACR,EAAE,KAAK,CAAC,IAAI,CAAC;SACZ,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,EAAE,CAAC;SAClB,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,UAAU,CAAC,GAAG,CAAC,CAAC;SACtC,GAAG,CAAC,CAAC,CAAC,EAAE;QACP,MAAM,CAAC,MAAM,EAAE,MAAM,EAAE,IAAI,EAAE,KAAK,EAAE,GAAG,EAAE,KAAK,EAAE,MAAM,EAAE,KAAK,EAAE,IAAI,CAAC,GAClE,CAAC,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QAEf,OAAO;YACL,MAAM;YACN,MAAM;YACN,IAAI;YACJ,KAAK,EAAE,CAAC,KAAK;YACb,GAAG,EAAE,CAAC,GAAG;YACT,KAAK,EAAE,CAAC,KAAK;YACb,MAAM;YACN,KAAK;YACL,GAAG,MAAM,CAAC,WAAW,CACnB,IAAI;iBACD,KAAK,CAAC,GAAG,CAAC;iBACV,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,EAAE,CAAC;iBAClB,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC;iBAChB,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC;iBACtB,GAAG,CAAC,CAAC,CAAC,GAAG,EAAE,GAAG,CAAC,EAAE,EAAE,CAAC;gBACnB,GAAG,CAAC,IAAI,EAAE;gBACV,kBAAkB,CAAC,GAAG,CAAC,CAAC,IAAI,EAAE,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC;aACpD,CAAC,CACL;SACF,CAAA;IACH,CAAC,CAAC,CAAA;AACN,CAAC;AAED,MAAM,UAAU,UAAU,CAAC,MAAgB,EAAE,GAAsB;IACjE,IAAI,CAAC,GAAG,EAAE,CAAA;IACV,IAAI,CAAC,GAAG,CAAC,CAAA;IACT,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,GAAG,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE,CAAC;QACpC,IAAI,CAAC,KAAK,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC;YACpB,CAAC,EAAE,CAAA;QACL,CAAC;aAAM,CAAC;YACN,CAAC,IAAI,GAAG,CAAC,CAAC,CAAC,CAAA;QACb,CAAC;IACH,CAAC;IACD,OAAO,CAAC,CAAA;AACV,CAAC;AAED,6EAA6E;AAC7E,MAAM,UAAU,WAAW,CACzB,CAA6B,EAC7B,EAAU,EACV,CAAS;IAET,mBAAmB;IACnB,CAAC,CAAC,GAAG,GAAG,CAAC,EAAE,IAAI,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,MAAM,IAAI,CAAC,EAAE,CAAC,CAAC,CAAC,GAAG,CAAC,CAAA;IAEnD,IAAI,CAAC,CAAC,QAAQ,EAAE,CAAC;QACf,CAAC,CAAC,QAAQ,CAAC,OAAO,CAAC,CAAC,CAAC,EAAE;YACrB,WAAW,CAAC,CAAC,EAAE,EAAE,EAAE,CAAC,CAAC,CAAA;QACvB,CAAC,CAAC,CAAA;IACJ,CAAC;AACH,CAAC;AAED,6EAA6E;AAC7E,MAAM,UAAU,SAAS,CAAC,CAA6B;IACrD,OAAO,CACL,CAAC,CAAC,CAAC,IAAI,CAAC,MAAM,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,QAAQ,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,QAAQ,EAAE,SAAS,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAC1E,CAAA;AACH,CAAC;AAED,gDAAgD;AAChD,8DAA8D;AAC9D,MAAM,UAAU,QAAQ,CAAC,CAA6B;IACpD,IAAI,CAAC,CAAC,QAAQ,EAAE,CAAC;QACf,mBAAmB;QACnB,CAAC,CAAC,SAAS,GAAG,CAAC,CAAC,QAAQ,CAAA;QACxB,mBAAmB;QACnB,CAAC,CAAC,SAAS,CAAC,OAAO,CAAC,QAAQ,CAAC,CAAA;QAC7B,mBAAmB;QACnB,CAAC,CAAC,QAAQ,GAAG,IAAI,CAAA;IACnB,CAAC;AACH,CAAC;AAED,MAAM,UAAU,KAAK,CAAC,GAAW,EAAE,GAAW,EAAE,GAAW;IACzD,OAAO,IAAI,CAAC,GAAG,CAAC,IAAI,CAAC,GAAG,CAAC,GAAG,EAAE,GAAG,CAAC,EAAE,GAAG,CAAC,CAAA;AAC1C,CAAC"}

package/dist/version.d.ts

@@ -1 +1 @@
-export declare const version = "3.1.4";
+export declare const version = "3.1.6";

package/dist/version.js

@@ -1,2 +1,2 @@
-export const version = '3.1.4';
+export const version = '3.1.6';
 //# sourceMappingURL=version.js.map

package/package.json

@@ -1,7 +1,7 @@
 {
   "name": "react-msaview",
   "author": "Colin",
-  "version": "3.1.4",
+  "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([])
+      },
+    }))
+}