react-msaview 4.1.1 → 4.2.0

package/dist/parseAsn1.js

@@ -0,0 +1,385 @@
+/**
+ * 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
+ */
+// Parse the fdict section
+const remap = {
+    $NODE_COLLAPSED: 'collapsed',
+    $NODE_COLOR: 'color',
+    $LABEL_BG_COLOR: 'color',
+    'seq-id': 'seqId',
+    'seq-title': 'seqTitle',
+    'align-index': 'alignIndex',
+    'accession-nbr': 'accessionNbr',
+    'blast-name': 'blastName',
+    'common-name': 'commonName',
+    'leaf-count': 'leafCount',
+};
+/**
+ * Parse NCBI ASN.1 format string into a JavaScript object
+ * @param asnString The ASN.1 string to parse
+ * @returns Parsed BioTreeContainer object
+ */
+export function parseAsn1(asnString) {
+    const sections = extractSections(asnString
+        .replace(/\s+/g, ' ')
+        .replace(/\s*{\s*/g, '{')
+        .replace(/\s*}\s*/g, '}')
+        .replace(/\s*,\s*/g, ',')
+        .replace(/\s*::\s*=\s*/g, '::=')
+        .replace(/^.*?::=/, ''));
+    const dict = Object.fromEntries(parseFdict(sections.fdict).map(r => [
+        r.id,
+        remap[r.name] || r.name,
+    ]));
+    return parseNodes(sections.nodes).map(node => {
+        const { features, ...rest } = node;
+        return {
+            ...rest,
+            ...Object.fromEntries(features.map(f => [dict[f.featureid], f.value])),
+        };
+    });
+}
+/**
+ * Extract main sections from the ASN.1 string
+ * @param asnString The ASN.1 string without type definition
+ * @returns Object with extracted sections
+ */
+function extractSections(asnString) {
+    const sections = {};
+    // First, let's clean up the string by removing any leading/trailing whitespace
+    const cleanedString = asnString.trim();
+    // Remove the outer braces if they exist
+    const contentString = cleanedString.startsWith('{') && cleanedString.endsWith('}')
+        ? cleanedString.slice(1, -1).trim()
+        : cleanedString;
+    // Now we'll manually parse the top-level sections
+    let currentPos = 0;
+    while (currentPos < contentString.length) {
+        // Skip whitespace
+        while (currentPos < contentString.length &&
+            /\s/.test(contentString[currentPos])) {
+            currentPos++;
+        }
+        if (currentPos >= contentString.length) {
+            break;
+        }
+        // Read section name
+        const sectionNameStart = currentPos;
+        while (currentPos < contentString.length &&
+            /\w/.test(contentString[currentPos])) {
+            currentPos++;
+        }
+        if (currentPos >= contentString.length ||
+            (contentString[currentPos] !== ' ' && contentString[currentPos] !== '{')) {
+            // Not a valid section, skip to next comma or end
+            while (currentPos < contentString.length &&
+                contentString[currentPos] !== ',') {
+                currentPos++;
+            }
+            if (currentPos < contentString.length) {
+                currentPos++;
+            } // Skip the comma
+            continue;
+        }
+        const sectionName = contentString.slice(sectionNameStart, currentPos).trim();
+        // Skip whitespace
+        while (currentPos < contentString.length &&
+            /\s/.test(contentString[currentPos])) {
+            currentPos++;
+        }
+        if (currentPos >= contentString.length ||
+            contentString[currentPos] !== '{') {
+            // Not a valid section, skip to next comma or end
+            while (currentPos < contentString.length &&
+                contentString[currentPos] !== ',') {
+                currentPos++;
+            }
+            if (currentPos < contentString.length) {
+                currentPos++;
+            } // Skip the comma
+            continue;
+        }
+        // We found an opening brace, now we need to find the matching closing brace
+        const sectionContentStart = currentPos + 1;
+        let braceCount = 1;
+        currentPos++;
+        while (currentPos < contentString.length && braceCount > 0) {
+            if (contentString[currentPos] === '{') {
+                braceCount++;
+            }
+            else if (contentString[currentPos] === '}') {
+                braceCount--;
+            }
+            currentPos++;
+        }
+        if (braceCount === 0) {
+            // We found the matching closing brace
+            const sectionContent = contentString
+                .slice(sectionContentStart, currentPos - 1)
+                .trim();
+            sections[sectionName] = sectionContent;
+        }
+        // Skip to next comma or end
+        while (currentPos < contentString.length &&
+            contentString[currentPos] !== ',') {
+            currentPos++;
+        }
+        if (currentPos < contentString.length) {
+            currentPos++;
+        } // Skip the comma
+    }
+    return sections;
+}
+/**
+ * Parse the fdict section
+ * @param fdictString The fdict section content
+ * @returns Array of ASNDictEntry objects
+ */
+function parseFdict(fdictString) {
+    const entries = [];
+    // We need to properly handle nested braces
+    let currentPos = 0;
+    while (currentPos < fdictString.length) {
+        // Skip whitespace
+        while (currentPos < fdictString.length &&
+            /\s/.test(fdictString[currentPos])) {
+            currentPos++;
+        }
+        if (currentPos >= fdictString.length) {
+            break;
+        }
+        // Look for opening brace
+        if (fdictString[currentPos] === '{') {
+            const entryContentStart = currentPos + 1;
+            let braceCount = 1;
+            currentPos++;
+            while (currentPos < fdictString.length && braceCount > 0) {
+                if (fdictString[currentPos] === '{') {
+                    braceCount++;
+                }
+                else if (fdictString[currentPos] === '}') {
+                    braceCount--;
+                }
+                currentPos++;
+            }
+            if (braceCount === 0) {
+                // We found the matching closing brace
+                const entryContent = fdictString
+                    .slice(entryContentStart, currentPos - 1)
+                    .trim();
+                const entry = parseDictEntry(entryContent);
+                if (entry) {
+                    entries.push(entry);
+                }
+            }
+        }
+        else {
+            // Skip to next opening brace
+            while (currentPos < fdictString.length &&
+                fdictString[currentPos] !== '{') {
+                currentPos++;
+            }
+        }
+    }
+    return entries;
+}
+/**
+ * Parse a single dictionary entry
+ * @param entryString The entry content
+ * @returns ASNDictEntry object or null if parsing fails
+ */
+function parseDictEntry(entryString) {
+    const idMatch = /id\s+(\d+)/.exec(entryString);
+    // Handle escaped quotes in strings
+    const nameMatch = /name\s+"((?:[^"\\]|\\.)*)"/s.exec(entryString);
+    if (idMatch && nameMatch) {
+        // Process escaped characters in the string
+        const processedName = nameMatch[1]
+            .replace(/\\"/g, '"')
+            .replace(/\\\\/g, '\\');
+        return {
+            id: parseInt(idMatch[1], 10),
+            name: processedName,
+        };
+    }
+    return null;
+}
+/**
+ * Parse the nodes section
+ * @param nodesString The nodes section content
+ * @returns Array of ASNNode objects
+ */
+function parseNodes(nodesString) {
+    const nodes = [];
+    // We need to properly handle nested braces
+    let currentPos = 0;
+    while (currentPos < nodesString.length) {
+        // Skip whitespace
+        while (currentPos < nodesString.length &&
+            /\s/.test(nodesString[currentPos])) {
+            currentPos++;
+        }
+        if (currentPos >= nodesString.length) {
+            break;
+        }
+        // Look for opening brace
+        if (nodesString[currentPos] === '{') {
+            const nodeContentStart = currentPos + 1;
+            let braceCount = 1;
+            currentPos++;
+            while (currentPos < nodesString.length && braceCount > 0) {
+                if (nodesString[currentPos] === '{') {
+                    braceCount++;
+                }
+                else if (nodesString[currentPos] === '}') {
+                    braceCount--;
+                }
+                currentPos++;
+            }
+            if (braceCount === 0) {
+                // We found the matching closing brace
+                const nodeContent = nodesString
+                    .slice(nodeContentStart, currentPos - 1)
+                    .trim();
+                const node = parseNode(nodeContent);
+                if (node) {
+                    nodes.push(node);
+                }
+            }
+        }
+        else {
+            // Skip to next opening brace
+            while (currentPos < nodesString.length &&
+                nodesString[currentPos] !== '{') {
+                currentPos++;
+            }
+        }
+    }
+    return nodes;
+}
+/**
+ * Parse a single node
+ * @param nodeString The node content
+ * @returns ASNNode object or null if parsing fails
+ */
+function parseNode(nodeString) {
+    const idMatch = /id\s+(\d+)/.exec(nodeString);
+    const parentMatch = /parent\s+(\d+)/.exec(nodeString);
+    if (idMatch) {
+        const node = {
+            id: parseInt(idMatch[1], 10),
+        };
+        if (parentMatch) {
+            node.parent = parseInt(parentMatch[1], 10);
+        }
+        // Extract features if present
+        // First find the features section
+        const featuresIndex = nodeString.indexOf('features');
+        if (featuresIndex !== -1) {
+            // Find the opening brace after "features"
+            const openBraceIndex = nodeString.indexOf('{', featuresIndex);
+            if (openBraceIndex !== -1) {
+                // Now find the matching closing brace
+                let braceCount = 1;
+                let closeBraceIndex = openBraceIndex + 1;
+                while (closeBraceIndex < nodeString.length && braceCount > 0) {
+                    if (nodeString[closeBraceIndex] === '{') {
+                        braceCount++;
+                    }
+                    else if (nodeString[closeBraceIndex] === '}') {
+                        braceCount--;
+                    }
+                    closeBraceIndex++;
+                }
+                if (braceCount === 0) {
+                    // We found the matching closing brace
+                    const featuresContent = nodeString
+                        .slice(openBraceIndex + 1, closeBraceIndex - 1)
+                        .trim();
+                    node.features = parseFeatures(featuresContent);
+                }
+            }
+        }
+        return node;
+    }
+    return null;
+}
+/**
+ * Parse features section of a node
+ * @param featuresString The features section content
+ * @returns Array of ASNFeature objects
+ */
+function parseFeatures(featuresString) {
+    const features = [];
+    // We need to properly handle nested braces
+    let currentPos = 0;
+    while (currentPos < featuresString.length) {
+        // Skip whitespace
+        while (currentPos < featuresString.length &&
+            /\s/.test(featuresString[currentPos])) {
+            currentPos++;
+        }
+        if (currentPos >= featuresString.length) {
+            break;
+        }
+        // Look for opening brace
+        if (featuresString[currentPos] === '{') {
+            const featureContentStart = currentPos + 1;
+            let braceCount = 1;
+            currentPos++;
+            while (currentPos < featuresString.length && braceCount > 0) {
+                if (featuresString[currentPos] === '{') {
+                    braceCount++;
+                }
+                else if (featuresString[currentPos] === '}') {
+                    braceCount--;
+                }
+                currentPos++;
+            }
+            if (braceCount === 0) {
+                // We found the matching closing brace
+                const featureContent = featuresString
+                    .slice(featureContentStart, currentPos - 1)
+                    .trim();
+                const feature = parseFeature(featureContent);
+                if (feature) {
+                    features.push(feature);
+                }
+            }
+        }
+        else {
+            // Skip to next opening brace
+            while (currentPos < featuresString.length &&
+                featuresString[currentPos] !== '{') {
+                currentPos++;
+            }
+        }
+    }
+    return features;
+}
+/**
+ * Parse a single feature
+ * @param featureString The feature content
+ * @returns ASNFeature object or null if parsing fails
+ */
+function parseFeature(featureString) {
+    const featureidMatch = /featureid\s+(\d+)/.exec(featureString);
+    // Handle escaped quotes in strings
+    const valueMatch = /value\s+"((?:[^"\\]|\\.)*)"/s.exec(featureString);
+    if (featureidMatch && valueMatch) {
+        // Process escaped characters in the string
+        const processedValue = valueMatch[1]
+            .replace(/\\"/g, '"')
+            .replace(/\\\\/g, '\\');
+        return {
+            featureid: parseInt(featureidMatch[1], 10),
+            value: processedValue,
+        };
+    }
+    return null;
+}
+//# sourceMappingURL=parseAsn1.js.map

package/dist/parseAsn1.js.map

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package/dist/parseAsn1.test.d.ts

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

package/dist/parseAsn1.test.js

@@ -0,0 +1,8 @@
+import fs from 'fs';
+import { expect, test } from 'vitest';
+import { parseAsn1 } from './parseAsn1';
+const r = fs.readFileSync(require.resolve('../test/data/tree.asn'), 'utf8');
+test('real data file', () => {
+    expect(parseAsn1(r)).toMatchSnapshot();
+});
+//# sourceMappingURL=parseAsn1.test.js.map

package/dist/parseAsn1.test.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"parseAsn1.test.js","sourceRoot":"","sources":["../src/parseAsn1.test.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,MAAM,IAAI,CAAA;AAEnB,OAAO,EAAE,MAAM,EAAE,IAAI,EAAE,MAAM,QAAQ,CAAA;AAErC,OAAO,EAAE,SAAS,EAAE,MAAM,aAAa,CAAA;AAEvC,MAAM,CAAC,GAAG,EAAE,CAAC,YAAY,CAAC,OAAO,CAAC,OAAO,CAAC,uBAAuB,CAAC,EAAE,MAAM,CAAC,CAAA;AAE3E,IAAI,CAAC,gBAAgB,EAAE,GAAG,EAAE;IAC1B,MAAM,CAAC,SAAS,CAAC,CAAC,CAAC,CAAC,CAAC,eAAe,EAAE,CAAA;AACxC,CAAC,CAAC,CAAA"}

package/dist/parsers/ClustalMSA.d.ts

@@ -1,4 +1,4 @@
-import type { NodeWithIds } from '../util';
+import type { NodeWithIds } from '../types';
 export default class ClustalMSA {
     private MSA;
     constructor(text: string);

package/dist/parsers/ClustalMSA.js.map

@@ -1 +1 @@
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package/dist/parsers/EmfMSA.d.ts

@@ -1,4 +1,4 @@
-import type { NodeWithIds } from '../util';
+import type { NodeWithIds } from '../types';
 export default class EmfMSA {
     private MSA;
     constructor(text: string);

package/dist/parsers/FastaMSA.d.ts

@@ -1,4 +1,4 @@
-import type { NodeWithIds } from '../util';
+import type { NodeWithIds } from '../types';
 export default class FastaMSA {
     private MSA;
     constructor(text: string);

package/dist/parsers/StockholmMSA.d.ts

@@ -1,4 +1,4 @@
-import { type NodeWithIds } from '../util';
+import type { NodeWithIds } from '../types';
 interface StockholmEntry {
     gf: {
         DE?: string[];

package/dist/parsers/StockholmMSA.js.map

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

@@ -1,7 +1,8 @@
 import type { MsaViewModel } from './model';
 import type { Theme } from '@mui/material';
-export declare function renderToSvg(model: MsaViewModel, opts: {
+export interface ExportSvgOptions {
     theme: Theme;
     includeMinimap?: boolean;
     exportType: string;
-}): Promise<string>;
+}
+export declare function renderToSvg(model: MsaViewModel, opts: ExportSvgOptions): Promise<string>;

package/dist/renderToSvg.js.map

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

@@ -1,2 +1,2 @@
-import type { NodeWithIds } from './util';
+import type { NodeWithIds } from './types';
 export declare function reparseTree(tree: NodeWithIds): NodeWithIds;

package/dist/reparseTree.js

@@ -1,3 +1,5 @@
+// this reparse routine helps to allow the app to hide/collapse a single
+// leafnode
 export function reparseTree(tree) {
     return {
         ...tree,

package/dist/reparseTree.js.map

@@ -1 +1 @@
-{"version":3,"file":"reparseTree.js","sourceRoot":"","sources":["../src/reparseTree.ts"],"names":[],"mappings":"AAEA,MAAM,UAAU,WAAW,CAAC,IAAiB;IAC3C,OAAO;QACL,GAAG,IAAI;QACP,QAAQ,EAAE,IAAI,CAAC,QAAQ,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAC9B,CAAC,CAAC,QAAQ,CAAC,MAAM;YACf,CAAC,CAAC,WAAW,CAAC,CAAC,CAAC;YAChB,CAAC,CAAC;gBACE,QAAQ,EAAE,CAAC,CAAC,CAAC;gBACb,EAAE,EAAE,GAAG,CAAC,CAAC,EAAE,WAAW;gBACtB,IAAI,EAAE,GAAG,CAAC,CAAC,IAAI,SAAS;aACzB,CACN;KACF,CAAA;AACH,CAAC"}
+{"version":3,"file":"reparseTree.js","sourceRoot":"","sources":["../src/reparseTree.ts"],"names":[],"mappings":"AAEA,wEAAwE;AACxE,WAAW;AACX,MAAM,UAAU,WAAW,CAAC,IAAiB;IAC3C,OAAO;QACL,GAAG,IAAI;QACP,QAAQ,EAAE,IAAI,CAAC,QAAQ,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAC9B,CAAC,CAAC,QAAQ,CAAC,MAAM;YACf,CAAC,CAAC,WAAW,CAAC,CAAC,CAAC;YAChB,CAAC,CAAC;gBACE,QAAQ,EAAE,CAAC,CAAC,CAAC;gBACb,EAAE,EAAE,GAAG,CAAC,CAAC,EAAE,WAAW;gBACtB,IAAI,EAAE,GAAG,CAAC,CAAC,IAAI,SAAS;aACzB,CACN;KACF,CAAA;AACH,CAAC"}

package/dist/types.d.ts

@@ -0,0 +1,38 @@
+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 interface Node {
+    children?: Node[];
+    name?: string;
+}
+export interface NodeWithIds {
+    id: string;
+    name: string;
+    children: NodeWithIds[];
+    length?: number;
+    noTree?: boolean;
+}
+export interface NodeWithIdsAndLength {
+    id: string;
+    name: string;
+    children: NodeWithIdsAndLength[];
+    noTree?: boolean;
+    length: number;
+}

package/dist/types.js

@@ -0,0 +1,2 @@
+export {};
+//# sourceMappingURL=types.js.map

package/dist/types.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"types.js","sourceRoot":"","sources":["../src/types.ts"],"names":[],"mappings":""}

package/dist/util.d.ts

@@ -1,27 +1,9 @@
+import type { Node, NodeWithIds } from './types';
 import type { Theme } from '@mui/material';
 import type { HierarchyNode } from 'd3-hierarchy';
 export declare function transform<T>(obj: Record<string, T>, cb: (arg0: [string, T]) => [string, T]): {
     [k: string]: T;
 };
-interface Node {
-    children?: Node[];
-    name?: string;
-    [key: string]: unknown;
-}
-export interface NodeWithIds {
-    id: string;
-    name: string;
-    children: NodeWithIds[];
-    length?: number;
-    noTree?: boolean;
-}
-export interface NodeWithIdsAndLength {
-    id: string;
-    name: string;
-    children: NodeWithIdsAndLength[];
-    noTree?: boolean;
-    length: number;
-}
 export declare function generateNodeIds(tree: Node, parent?: string, depth?: number): NodeWithIds;
 export declare function colorContrast(colorScheme: Record<string, string>, theme: Theme): {
     [k: string]: string;
@@ -35,4 +17,8 @@ export declare function len(a: {
     end: number;
     start: number;
 }): number;
-export {};
+export declare function localStorageGetItem(item: string): string | null | undefined;
+export declare function localStorageGetBoolean(key: string, defaultVal: boolean): boolean;
+export declare function localStorageSetItem(str: string, item: string): void;
+export declare function localStorageSetBoolean(key: string, value: boolean): void;
+export declare function isGzip(buf: Uint8Array): boolean;

package/dist/util.js

@@ -63,4 +63,23 @@ export function clamp(min, num, max) {
 export function len(a) {
     return a.end - a.start;
 }
+export function localStorageGetItem(item) {
+    return typeof localStorage !== 'undefined'
+        ? localStorage.getItem(item)
+        : undefined;
+}
+export function localStorageGetBoolean(key, defaultVal) {
+    return Boolean(JSON.parse(localStorageGetItem(key) || JSON.stringify(defaultVal)));
+}
+export function localStorageSetItem(str, item) {
+    if (typeof localStorage !== 'undefined') {
+        localStorage.setItem(str, item);
+    }
+}
+export function localStorageSetBoolean(key, value) {
+    localStorageSetItem(key, JSON.stringify(value));
+}
+export function isGzip(buf) {
+    return buf[0] === 31 && buf[1] === 139 && buf[2] === 8;
+}
 //# sourceMappingURL=util.js.map

package/dist/util.js.map

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

@@ -1 +1 @@
-export declare const version = "4.1.1";
+export declare const version = "4.2.0";