react-msaview 5.0.1 → 5.0.3

package/dist/components/tree/TreePanel.d.ts

@@ -1,5 +1,5 @@
 import React from 'react';
-import type { MsaViewModel } from '../../model';
+import type { MsaViewModel } from '../../model.ts';
 declare const TreePanel: ({ model }: {
     model: MsaViewModel;
 }) => React.JSX.Element;

package/dist/components/tree/TreePanel.js

@@ -1,6 +1,6 @@
 import React from 'react';
 import { observer } from 'mobx-react';
-import TreeCanvas from './TreeCanvas';
+import TreeCanvas from "./TreeCanvas.js";
 const TreePanel = observer(function ({ model }) {
     const { treeAreaWidth } = model;
     return (React.createElement("div", { style: { overflow: 'hidden', flexShrink: 0, width: treeAreaWidth } },

package/dist/components/tree/TreePanel.js.map

@@ -1 +1 @@
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+{"version":3,"file":"TreePanel.js","sourceRoot":"","sources":["../../../src/components/tree/TreePanel.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAErC,OAAO,UAAU,MAAM,iBAAkB,CAAA;AAIzC,MAAM,SAAS,GAAG,QAAQ,CAAC,UAAU,EAAE,KAAK,EAA2B;IACrE,MAAM,EAAE,aAAa,EAAE,GAAG,KAAK,CAAA;IAC/B,OAAO,CACL,6BAAK,KAAK,EAAE,EAAE,QAAQ,EAAE,QAAQ,EAAE,UAAU,EAAE,CAAC,EAAE,KAAK,EAAE,aAAa,EAAE;QACrE,oBAAC,UAAU,IAAC,KAAK,EAAE,KAAK,GAAI,CACxB,CACP,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,eAAe,SAAS,CAAA"}

package/dist/components/tree/TreeRuler.d.ts

@@ -1,5 +1,5 @@
 import React from 'react';
-import type { MsaViewModel } from '../../model';
+import type { MsaViewModel } from '../../model.ts';
 declare const TreeRuler: ({ model }: {
     model: MsaViewModel;
 }) => React.JSX.Element;

package/dist/components/tree/dialogs/TreeNodeInfoDialog.d.ts

@@ -1,5 +1,5 @@
 import React from 'react';
-import type { MsaViewModel } from '../../../model';
+import type { MsaViewModel } from '../../../model.ts';
 declare const TreeNodeInfoDialog: ({ info, model, nodeName, onClose, }: {
     info: Record<string, unknown>;
     model: MsaViewModel;

package/dist/components/tree/dialogs/TreeNodeInfoDialog.js

@@ -4,7 +4,7 @@ import BaseCard from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/BaseCard
 import { Dialog } from '@jbrowse/core/ui';
 import { DialogContent } from '@mui/material';
 import { observer } from 'mobx-react';
-import SequenceTextArea from '../../SequenceTextArea';
+import SequenceTextArea from "../../SequenceTextArea.js";
 const TreeNodeInfoDialog = observer(function ({ info, model, nodeName, onClose, }) {
     const { treeMetadata, rows } = model;
     const metadata = treeMetadata[nodeName];

package/dist/components/tree/dialogs/TreeNodeInfoDialog.js.map

@@ -1 +1 @@
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package/dist/components/tree/renderTreeCanvas.d.ts

@@ -1,4 +1,4 @@
-import type { MsaViewModel } from '../../model';
+import type { MsaViewModel } from '../../model.ts';
 import type { Theme } from '@mui/material';
 export declare const padding = 600;
 interface ClickEntry {

package/dist/createPaletteMap.d.ts

@@ -0,0 +1,7 @@
+/**
+ * Creates a map from keys to colors using ggplot-style palettes.
+ * The palette is selected based on the number of keys.
+ */
+export declare function createPaletteMap(keys: string[]): {
+    [k: string]: string;
+};

package/dist/createPaletteMap.js

@@ -0,0 +1,11 @@
+import palettes from "./ggplotPalettes.js";
+/**
+ * Creates a map from keys to colors using ggplot-style palettes.
+ * The palette is selected based on the number of keys.
+ */
+export function createPaletteMap(keys) {
+    const k = Math.min(keys.length - 1, palettes.length - 1);
+    const palette = palettes[k];
+    return Object.fromEntries(keys.map((key, i) => [key, palette[i]]));
+}
+//# sourceMappingURL=createPaletteMap.js.map

package/dist/createPaletteMap.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"createPaletteMap.js","sourceRoot":"","sources":["../src/createPaletteMap.ts"],"names":[],"mappings":"AAAA,OAAO,QAAQ,MAAM,qBAAqB,CAAA;AAE1C;;;GAGG;AACH,MAAM,UAAU,gBAAgB,CAAC,IAAc;IAC7C,MAAM,CAAC,GAAG,IAAI,CAAC,GAAG,CAAC,IAAI,CAAC,MAAM,GAAG,CAAC,EAAE,QAAQ,CAAC,MAAM,GAAG,CAAC,CAAC,CAAA;IACxD,MAAM,OAAO,GAAG,QAAQ,CAAC,CAAC,CAAE,CAAA;IAC5B,OAAO,MAAM,CAAC,WAAW,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,GAAG,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,GAAG,EAAE,OAAO,CAAC,CAAC,CAAE,CAAC,CAAC,CAAC,CAAA;AACrE,CAAC"}

package/dist/createPaletteMap.test.d.ts

@@ -0,0 +1 @@
+export {};

package/dist/createPaletteMap.test.js

@@ -0,0 +1,49 @@
+import { expect, test } from 'vitest';
+import { createPaletteMap } from "./createPaletteMap.js";
+import palettes from "./ggplotPalettes.js";
+// Original implementation for comparison
+function originalFillPalette(keys) {
+    let i = 0;
+    const map = {};
+    for (const key of keys) {
+        const k = Math.min(keys.length - 1, palettes.length - 1);
+        map[key] = palettes[k][i];
+        i++;
+    }
+    return map;
+}
+test('createPaletteMap matches original implementation with 1 key', () => {
+    const keys = ['IPR001234'];
+    expect(createPaletteMap(keys)).toEqual(originalFillPalette(keys));
+});
+test('createPaletteMap matches original implementation with 3 keys', () => {
+    const keys = ['IPR001234', 'IPR005678', 'IPR009012'];
+    expect(createPaletteMap(keys)).toEqual(originalFillPalette(keys));
+});
+test('createPaletteMap matches original implementation with 8 keys (max palette size)', () => {
+    const keys = ['A', 'B', 'C', 'D', 'E', 'F', 'G', 'H'];
+    expect(createPaletteMap(keys)).toEqual(originalFillPalette(keys));
+});
+test('createPaletteMap matches original implementation with more keys than palette colors', () => {
+    const keys = ['A', 'B', 'C', 'D', 'E', 'F', 'G', 'H', 'I', 'J'];
+    expect(createPaletteMap(keys)).toEqual(originalFillPalette(keys));
+});
+test('createPaletteMap returns correct colors for 3 keys', () => {
+    const keys = ['X', 'Y', 'Z'];
+    const result = createPaletteMap(keys);
+    // With 3 keys, uses palette index 2 (0-indexed)
+    expect(result).toEqual({
+        X: '#F8766D',
+        Y: '#00BA38',
+        Z: '#619CFF',
+    });
+});
+test('createPaletteMap returns empty object for empty keys', () => {
+    expect(createPaletteMap([])).toEqual({});
+});
+test('createPaletteMap preserves key order', () => {
+    const keys = ['Z', 'A', 'M'];
+    const result = createPaletteMap(keys);
+    expect(Object.keys(result)).toEqual(['Z', 'A', 'M']);
+});
+//# sourceMappingURL=createPaletteMap.test.js.map

package/dist/createPaletteMap.test.js.map

@@ -0,0 +1 @@
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package/dist/index.d.ts

@@ -1,3 +1,3 @@
-export { default as MSAView } from './components/Loading';
-export { type MsaViewModel, default as MSAModelF } from './model';
+export { default as MSAView } from './components/Loading.tsx';
+export { type MsaViewModel, default as MSAModelF } from './model.ts';
 export type { MSAParserType } from 'msa-parsers';

package/dist/index.js

@@ -1,3 +1,3 @@
-export { default as MSAView } from './components/Loading';
-export { default as MSAModelF } from './model';
+export { default as MSAView } from "./components/Loading.js";
+export { default as MSAModelF } from "./model.js";
 //# sourceMappingURL=index.js.map

package/dist/index.js.map

@@ -1 +1 @@
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+{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,OAAO,IAAI,OAAO,EAAE,MAAM,yBAA0B,CAAA;AAC7D,OAAO,EAAqB,OAAO,IAAI,SAAS,EAAE,MAAM,YAAY,CAAA"}

package/dist/launchInterProScan.d.ts

@@ -1,4 +1,4 @@
-import type { MsaViewModel } from './model';
+import type { MsaViewModel } from './model.ts';
 export interface InterProScanResults {
     matches: {
         signature: {

package/dist/launchInterProScan.js

@@ -1,5 +1,5 @@
 import { getSession } from '@jbrowse/core/util';
-import { jsonfetch, textfetch, timeout } from './fetchUtils';
+import { jsonfetch, textfetch, timeout } from "./fetchUtils.js";
 const base = 'https://www.ebi.ac.uk/Tools/services/rest';
 async function runInterProScan({ seq, onProgress, onJobId, programs, model, }) {
     const jobId = await textfetch(`${base}/iprscan5/run`, {

package/dist/launchInterProScan.js.map

@@ -1 +1 @@
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package/dist/model/msaModel.js

@@ -1,5 +1,5 @@
 import { types } from '@jbrowse/mobx-state-tree';
-import { defaultBgColor, defaultColorSchemeName } from '../constants';
+import { defaultBgColor, defaultColorSchemeName } from "../constants.js";
 /**
  * #stateModel MSAModel
  */

package/dist/model/msaModel.js.map

@@ -1 +1 @@
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package/dist/model/treeModel.js

@@ -1,5 +1,5 @@
 import { types } from '@jbrowse/mobx-state-tree';
-import { defaultDrawLabels, defaultDrawNodeBubbles, defaultDrawTree, defaultLabelsAlignRight, defaultShowBranchLen, defaultTreeAreaWidth, defaultTreeWidth, defaultTreeWidthMatchesArea, } from '../constants';
+import { defaultDrawLabels, defaultDrawNodeBubbles, defaultDrawTree, defaultLabelsAlignRight, defaultShowBranchLen, defaultTreeAreaWidth, defaultTreeWidth, defaultTreeWidthMatchesArea, } from "../constants.js";
 /**
  * #stateModel Tree
  */

package/dist/model/treeModel.js.map

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

@@ -1,6 +1,6 @@
 import { A3mMSA, ClustalMSA, EmfMSA, FastaMSA, StockholmMSA } from 'msa-parsers';
-import type { InterProScanResults } from './launchInterProScan';
-import type { Accession, BasicTrack, NodeWithIds, NodeWithIdsAndLength } from './types';
+import type { InterProScanResults } from './launchInterProScan.ts';
+import type { Accession, BasicTrack, NodeWithIds, NodeWithIdsAndLength } from './types.ts';
 import type { FileLocation as FileLocationType } from '@jbrowse/core/util/types';
 import type { Instance } from '@jbrowse/mobx-state-tree';
 import type { Theme } from '@mui/material';
@@ -720,6 +720,12 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
      * #getter
      */
     readonly colStatsSums: number[];
+    /**
+     * #getter
+     * Detects sequence type based on letters present in the alignment.
+     * Returns 'dna', 'rna', or 'amino'.
+     */
+    readonly sequenceType: "dna" | "rna" | "amino";
     /**
      * #getter
      * Pre-computed consensus letter and percent identity color per column.
@@ -1021,7 +1027,9 @@ declare function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelT
     /**
      * #getter
      */
-    readonly fillPalette: Record<string, string>;
+    readonly fillPalette: {
+        [k: string]: string;
+    };
     /**
      * #getter
      */

package/dist/model.js

@@ -5,27 +5,27 @@ import { addDisposer, cast, types } from '@jbrowse/mobx-state-tree';
 import { colord } from 'colord';
 import { ascending } from 'd3-array';
 import { cluster, hierarchy } from 'd3-hierarchy';
-import { saveAs } from 'file-saver';
 import { autorun, transaction } from 'mobx';
 import { A3mMSA, ClustalMSA, EmfMSA, FastaMSA, StockholmMSA, generateNodeIds, gffToInterProResults, parseEmfTree, parseGFF, parseNewick, stockholmSniff, } from 'msa-parsers';
-import { blocksX, blocksY } from './calculateBlocks';
-import colorSchemes from './colorSchemes';
-import ConservationTrack from './components/ConservationTrack';
-import TextTrack from './components/TextTrack';
-import { defaultAllowedGappyness, defaultBgColor, defaultColWidth, defaultColorSchemeName, defaultContrastLettering, defaultCurrentAlignment, defaultDrawLabels, defaultDrawMsaLetters, defaultDrawNodeBubbles, defaultDrawTree, defaultHeight, defaultHideGaps, defaultLabelsAlignRight, defaultRowHeight, defaultScrollX, defaultScrollY, defaultShowBranchLen, defaultShowDomains, defaultSubFeatureRows, defaultTreeAreaWidth, defaultTreeWidth, defaultTreeWidthMatchesArea, } from './constants';
-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 { calculateNeighborJoiningTree } from './neighborJoining';
-import { parseAsn1 } from './parseAsn1';
-import { reparseTree } from './reparseTree';
-import { globalColToVisibleCol, visibleColToGlobalCol, visibleColToSeqPosForRow, } from './rowCoordinateCalculations';
-import { seqPosToGlobalCol } from './seqPosToGlobalCol';
-import { collapse, len, maxLength, setBrLength, skipBlanks } from './util';
+import { blocksX, blocksY } from "./calculateBlocks.js";
+import colorSchemes from "./colorSchemes.js";
+import ConservationTrack from "./components/ConservationTrack.js";
+import TextTrack from "./components/TextTrack.js";
+import { defaultAllowedGappyness, defaultBgColor, defaultColWidth, defaultColorSchemeName, defaultContrastLettering, defaultCurrentAlignment, defaultDrawLabels, defaultDrawMsaLetters, defaultDrawNodeBubbles, defaultDrawTree, defaultHeight, defaultHideGaps, defaultLabelsAlignRight, defaultRowHeight, defaultScrollX, defaultScrollY, defaultShowBranchLen, defaultShowDomains, defaultSubFeatureRows, defaultTreeAreaWidth, defaultTreeWidth, defaultTreeWidthMatchesArea, } from "./constants.js";
+import { createPaletteMap } from "./createPaletteMap.js";
+import { flatToTree } from "./flatToTree.js";
+import { measureTextCanvas } from "./measureTextCanvas.js";
+import { DataModelF } from "./model/DataModel.js";
+import { DialogQueueSessionMixin } from "./model/DialogQueue.js";
+import { MSAModelF } from "./model/msaModel.js";
+import { TreeModelF } from "./model/treeModel.js";
+import { calculateNeighborJoiningTree } from "./neighborJoining.js";
+import { parseAsn1 } from "./parseAsn1.js";
+import { reparseTree } from "./reparseTree.js";
+import { globalColToVisibleCol, visibleColToGlobalCol, visibleColToSeqPosForRow, } from "./rowCoordinateCalculations.js";
+import { seqPosToGlobalCol } from "./seqPosToGlobalCol.js";
+import { collapse, len, maxLength, setBrLength, skipBlanks } from "./util.js";
+import { saveAs } from "./vendor/fileSaver.js";
 const showZoomStarKey = 'msa-showZoomStar';
 /**
  * #stateModel MsaView
@@ -349,7 +349,7 @@ function stateModelFactory() {
                 return;
             }
             // Get all descendant leaf names
-            const descendantNames = node.leaves().map((leaf) => leaf.data.name);
+            const descendantNames = node.leaves().map(leaf => leaf.data.name);
             self.hoveredTreeNode = { nodeId, descendantNames };
         },
         /**
@@ -855,6 +855,33 @@ function stateModelFactory() {
         get colStatsSums() {
             return this.colStats.map(val => sum(Object.values(val)));
         },
+        /**
+         * #getter
+         * Detects sequence type based on letters present in the alignment.
+         * Returns 'dna', 'rna', or 'amino'.
+         */
+        get sequenceType() {
+            const letters = new Set();
+            for (const stats of this.colStats) {
+                for (const letter of Object.keys(stats)) {
+                    const upper = letter.toUpperCase();
+                    if (upper !== '-' && upper !== '.') {
+                        letters.add(upper);
+                    }
+                }
+            }
+            const dna = new Set(['A', 'C', 'G', 'T', 'N']);
+            const rna = new Set(['A', 'C', 'G', 'U', 'N']);
+            const isDna = [...letters].every(l => dna.has(l));
+            const isRna = [...letters].every(l => rna.has(l));
+            if (isDna && !letters.has('U')) {
+                return 'dna';
+            }
+            if (isRna && !letters.has('T')) {
+                return 'rna';
+            }
+            return 'amino';
+        },
         /**
          * #getter
          * Pre-computed consensus letter and percent identity color per column.
@@ -1002,8 +1029,8 @@ function stateModelFactory() {
          * Returns values 0-1 where 1 = fully conserved, 0 = no conservation.
          */
         get conservation() {
-            const { colStats, colStatsSums } = this;
-            const alphabetSize = 20;
+            const { colStats, colStatsSums, sequenceType } = this;
+            const alphabetSize = sequenceType === 'amino' ? 20 : 4;
             const maxEntropy = Math.log2(alphabetSize);
             return colStats.map((stats, i) => {
                 const total = colStatsSums[i];
@@ -1406,9 +1433,9 @@ function stateModelFactory() {
          * @returns The global column index in the full MSA
          */
         seqPosToGlobalCol(rowName, seqPos) {
-            const { rowNames, rows } = self;
-            const index = rowNames.indexOf(rowName);
-            return index !== -1 && rows[index]
+            const { rows } = self;
+            const index = this.rowNamesSet.get(rowName);
+            return index !== undefined && rows[index]
                 ? seqPosToGlobalCol({
                     row: rows[index][1],
                     seqPos,
@@ -1516,15 +1543,7 @@ function stateModelFactory() {
          * #getter
          */
         get fillPalette() {
-            const arr = [...self.tidyInterProAnnotationTypes.keys()];
-            let i = 0;
-            const map = {};
-            for (const key of arr) {
-                const k = Math.min(arr.length - 1, palettes.length - 1);
-                map[key] = palettes[k][i];
-                i++;
-            }
-            return map;
+            return createPaletteMap([...self.tidyInterProAnnotationTypes.keys()]);
         },
         /**
          * #getter
@@ -1572,7 +1591,7 @@ function stateModelFactory() {
          * #action
          */
         async exportSVG(opts) {
-            const { renderToSvg } = await import('./renderToSvg');
+            const { renderToSvg } = await import("./renderToSvg.js");
             const html = await renderToSvg(self, opts);
             const blob = new Blob([html], { type: 'image/svg+xml' });
             saveAs(blob, 'image.svg');