react-msaview 4.1.0 → 4.2.0

package/dist/model.d.ts

@@ -1,35 +1,13 @@
-import React from 'react';
 import ClustalMSA from './parsers/ClustalMSA';
 import EmfMSA from './parsers/EmfMSA';
 import FastaMSA from './parsers/FastaMSA';
 import StockholmMSA from './parsers/StockholmMSA';
 import type { InterProScanResults } from './launchInterProScan';
-import type { NodeWithIds, NodeWithIdsAndLength } from './util';
+import type { Accession, BasicTrack, NodeWithIds, NodeWithIdsAndLength } from './types';
 import type { FileLocation as FileLocationType } from '@jbrowse/core/util/types';
 import type { Theme } from '@mui/material';
 import type { HierarchyNode } from 'd3-hierarchy';
 import type { Instance } from 'mobx-state-tree';
-export interface Accession {
-    accession: string;
-    name: string;
-    description: string;
-}
-export interface BasicTrackModel {
-    id: string;
-    name: string;
-    associatedRowName?: string;
-    height: number;
-}
-export interface TextTrackModel extends BasicTrackModel {
-    customColorScheme?: Record<string, string>;
-    data: string;
-}
-export interface ITextTrack {
-    ReactComponent: React.FC<any>;
-    model: TextTrackModel;
-}
-export type BasicTrack = ITextTrack;
-export declare function isGzip(buf: Uint8Array): boolean;
 /**
  * #stateModel MsaView
  * extends
@@ -275,6 +253,11 @@ declare function stateModelFactory(): import("mobx-state-tree").IModelType<{
      * screens
      */
     highResScaleFactor: number;
+    /**
+     * #volatile
+     * obtained from localStorage
+     */
+    showZoomStar: boolean;
     /**
      * #volatile
      */
@@ -367,6 +350,10 @@ declare function stateModelFactory(): import("mobx-state-tree").IModelType<{
      * #action
      */
     setLoadingMSA(arg: boolean): void;
+    /**
+     * #volatile
+     */
+    setShowZoomStar(arg: boolean): void;
     /**
      * #action
      */
@@ -604,6 +591,10 @@ declare function stateModelFactory(): import("mobx-state-tree").IModelType<{
      * #getter
      */
     readonly leaves: HierarchyNode<NodeWithIdsAndLength>[];
+    /**
+     * #getter
+     */
+    readonly allBranchesLength0: boolean;
 } & {
     /**
      * #getter
@@ -648,6 +639,10 @@ declare function stateModelFactory(): import("mobx-state-tree").IModelType<{
      * #action
      */
     setDrawMsaLetters(arg: boolean): void;
+    /**
+     * #action
+     */
+    resetZoom(): void;
     /**
      * #action
      */
@@ -727,7 +722,7 @@ declare function stateModelFactory(): import("mobx-state-tree").IModelType<{
     /**
      * #getter
      */
-    readonly turnedOnTracks: ITextTrack[];
+    readonly turnedOnTracks: import("./types").ITextTrack[];
     /**
      * #getter
      */

package/dist/model.js

@@ -4,6 +4,7 @@ import { ElementId, FileLocation } from '@jbrowse/core/util/types/mst';
 import { colord } from 'colord';
 import { ascending } from 'd3-array';
 import { cluster, hierarchy } from 'd3-hierarchy';
+import { parseEmfTree } from 'emf-js';
 import { saveAs } from 'file-saver';
 import { autorun, transaction } from 'mobx';
 import { addDisposer, cast, types } from 'mobx-state-tree';
@@ -12,24 +13,25 @@ import Stockholm from 'stockholm-js';
 import { blocksX, blocksY } from './calculateBlocks';
 import colorSchemes from './colorSchemes';
 import TextTrack from './components/TextTrack';
+import { flatToTree } from './flatToTree';
 import palettes from './ggplotPalettes';
 import { measureTextCanvas } from './measureTextCanvas';
 import { DataModelF } from './model/DataModel';
 import { DialogQueueSessionMixin } from './model/DialogQueue';
 import { MSAModelF } from './model/msaModel';
 import { TreeModelF } from './model/treeModel';
+import { parseAsn1 } from './parseAsn1';
 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;
-}
+import { clamp, collapse, generateNodeIds, isGzip, len, localStorageGetBoolean, localStorageSetBoolean, maxLength, setBrLength, skipBlanks, } from './util';
+const defaultRowHeight = 16;
+const defaultColWidth = 12;
+const showZoomStarKey = 'msa-showZoomStar';
 /**
  * #stateModel MsaView
  * extends
@@ -87,7 +89,7 @@ function stateModelFactory() {
          * #property
          * height of each row, px
          */
-        rowHeight: 18,
+        rowHeight: defaultRowHeight,
         /**
          * #property
          * scroll position, Y-offset, px
@@ -102,7 +104,7 @@ function stateModelFactory() {
          * #property
          * width of columns, px
          */
-        colWidth: 14,
+        colWidth: defaultColWidth,
         /**
          * #property
          * filehandle object for the tree
@@ -179,7 +181,12 @@ function stateModelFactory() {
          * high resolution scale factor, helps make canvas look better on hi-dpi
          * screens
          */
-        highResScaleFactor: 1,
+        highResScaleFactor: 2,
+        /**
+         * #volatile
+         * obtained from localStorage
+         */
+        showZoomStar: localStorageGetBoolean(showZoomStarKey, true),
         /**
          * #volatile
          */
@@ -280,6 +287,12 @@ function stateModelFactory() {
         setLoadingMSA(arg) {
             self.loadingMSA = arg;
         },
+        /**
+         * #volatile
+         */
+        setShowZoomStar(arg) {
+            self.showZoomStar = arg;
+        },
         /**
          * #action
          */
@@ -538,27 +551,19 @@ function stateModelFactory() {
          */
         get tree() {
             const text = self.data.tree;
-            let ret;
             if (text) {
-                let t;
-                if (text.startsWith('SEQ')) {
-                    const r = new EmfTree(text);
-                    t = r.data.tree;
-                }
-                else {
-                    t = text;
-                }
-                ret = generateNodeIds(parseNewick(t));
+                return reparseTree(generateNodeIds(text.startsWith('BioTreeContainer')
+                    ? flatToTree(parseAsn1(text))
+                    : parseNewick(text.startsWith('SEQ') ? parseEmfTree(text).tree : text)));
             }
             else {
-                ret = this.MSA?.getTree() || {
+                return reparseTree(this.MSA?.getTree() || {
                     noTree: true,
                     children: [],
                     id: 'empty',
                     name: 'empty',
-                };
+                });
             }
-            return reparseTree(ret);
         },
         /**
          * #getter
@@ -736,6 +741,12 @@ function stateModelFactory() {
         get leaves() {
             return this.hierarchy.leaves();
         },
+        /**
+         * #getter
+         */
+        get allBranchesLength0() {
+            return this.hierarchy.links().every(s => !s.source.data.length);
+        },
     }))
         .views(self => ({
         /**
@@ -822,6 +833,13 @@ function stateModelFactory() {
         setDrawMsaLetters(arg) {
             self.drawMsaLetters = arg;
         },
+        /**
+         * #action
+         */
+        resetZoom() {
+            self.setColWidth(defaultColWidth);
+            self.setRowHeight(defaultRowHeight);
+        },
         /**
          * #action
          */
@@ -1223,6 +1241,10 @@ function stateModelFactory() {
                     this.initFilter(key);
                 }
             }));
+            // autorun saves local settings
+            addDisposer(self, autorun(() => {
+                localStorageSetBoolean(showZoomStarKey, self.showZoomStar);
+            }));
             // autorun opens treeFilehandle
             addDisposer(self, autorun(async () => {
                 const { treeFilehandle } = self;

package/dist/model.js.map

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package/dist/parseAsn1.d.ts

@@ -0,0 +1,34 @@
+/**
+ * NCBI ASN.1 Parser
+ * A simple hand-made parser for NCBI ASN.1 format
+ * Was too lazy to figure out how ASN.1 actually worked, and use a dedicated
+ * ASN.1 parser (you have to generally pre-defined your schema)
+ * Written with help of Claude AI
+ */
+export interface ASNNode {
+    id: number;
+    parent?: number;
+    features?: ASNFeature[];
+}
+export interface ASNFeature {
+    featureid: number;
+    value: string;
+}
+export interface ASNDictEntry {
+    id: number;
+    name: string;
+}
+export interface BioTreeContainer {
+    fdict: ASNDictEntry[];
+    nodes: ASNNode[];
+}
+/**
+ * Parse NCBI ASN.1 format string into a JavaScript object
+ * @param asnString The ASN.1 string to parse
+ * @returns Parsed BioTreeContainer object
+ */
+export declare function parseAsn1(asnString: string): {
+    id: number;
+    parent: number;
+    name: string;
+}[];