react-msaview 5.0.7 → 5.0.13

package/dist/neighborJoining.js.map

@@ -1 +1 @@
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package/dist/parseAsn1.d.ts

@@ -1,10 +1,3 @@
-/**
- * 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;
@@ -22,11 +15,6 @@ 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;

package/dist/parseAsn1.js

@@ -1,11 +1,3 @@
-/**
- * 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',
@@ -18,368 +10,169 @@ const remap = {
     '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
- */
+function extractBracedBlocks(str) {
+    const blocks = [];
+    let pos = 0;
+    while (pos < str.length) {
+        pos = str.indexOf('{', pos);
+        if (pos === -1) {
+            break;
+        }
+        let depth = 1;
+        const start = pos + 1;
+        pos++;
+        while (pos < str.length && depth > 0) {
+            if (str[pos] === '{') {
+                depth++;
+            }
+            else if (str[pos] === '}') {
+                depth--;
+            }
+            pos++;
+        }
+        if (depth === 0) {
+            blocks.push(str.slice(start, pos - 1).trim());
+        }
+    }
+    return blocks;
+}
+function findBracedContent(str, after) {
+    const openIdx = str.indexOf('{', after);
+    if (openIdx === -1) {
+        return undefined;
+    }
+    let depth = 1;
+    let pos = openIdx + 1;
+    while (pos < str.length && depth > 0) {
+        if (str[pos] === '{') {
+            depth++;
+        }
+        else if (str[pos] === '}') {
+            depth--;
+        }
+        pos++;
+    }
+    return depth === 0 ? str.slice(openIdx + 1, pos - 1).trim() : undefined;
+}
 export function parseAsn1(asnString) {
-    const sections = extractSections(asnString
+    const normalized = 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])),
-        };
+        .replace(/^.*?::=/, '');
+    const sections = extractSections(normalized);
+    const dict = Object.fromEntries(extractBracedBlocks(sections.fdict).flatMap(block => {
+        const entry = parseDictEntry(block);
+        return entry ? [[entry.id, remap[entry.name] || entry.name]] : [];
+    }));
+    return extractBracedBlocks(sections.nodes).flatMap(block => {
+        const node = parseNode(block);
+        if (!node) {
+            return [];
+        }
+        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++;
+    let content = asnString.trim();
+    if (content.startsWith('{') && content.endsWith('}')) {
+        content = content.slice(1, -1).trim();
+    }
+    let pos = 0;
+    while (pos < content.length) {
+        while (pos < content.length && /\s/.test(content[pos])) {
+            pos++;
         }
-        if (currentPos >= contentString.length) {
+        if (pos >= content.length) {
             break;
         }
-        // Read section name
-        const sectionNameStart = currentPos;
-        while (currentPos < contentString.length &&
-            /\w/.test(contentString[currentPos])) {
-            currentPos++;
+        const nameStart = pos;
+        while (pos < content.length && /\w/.test(content[pos])) {
+            pos++;
         }
-        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
+        if (pos >= content.length ||
+            (content[pos] !== ' ' && content[pos] !== '{')) {
+            pos = content.indexOf(',', pos);
+            pos = pos === -1 ? content.length : pos + 1;
             continue;
         }
-        const sectionName = contentString.slice(sectionNameStart, currentPos).trim();
-        // Skip whitespace
-        while (currentPos < contentString.length &&
-            /\s/.test(contentString[currentPos])) {
-            currentPos++;
+        const name = content.slice(nameStart, pos).trim();
+        while (pos < content.length && /\s/.test(content[pos])) {
+            pos++;
         }
-        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
+        if (pos >= content.length || content[pos] !== '{') {
+            pos = content.indexOf(',', pos);
+            pos = pos === -1 ? content.length : pos + 1;
             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++;
+        let depth = 1;
+        const start = pos + 1;
+        pos++;
+        while (pos < content.length && depth > 0) {
+            if (content[pos] === '{') {
+                depth++;
             }
-            else if (contentString[currentPos] === '}') {
-                braceCount--;
+            else if (content[pos] === '}') {
+                depth--;
             }
-            currentPos++;
-        }
-        if (braceCount === 0) {
-            // We found the matching closing brace
-            const sectionContent = contentString
-                .slice(sectionContentStart, currentPos - 1)
-                .trim();
-            sections[sectionName] = sectionContent;
+            pos++;
         }
-        // Skip to next comma or end
-        while (currentPos < contentString.length &&
-            contentString[currentPos] !== ',') {
-            currentPos++;
+        if (depth === 0) {
+            sections[name] = content.slice(start, pos - 1).trim();
         }
-        if (currentPos < contentString.length) {
-            currentPos++;
-        } // Skip the comma
+        pos = content.indexOf(',', pos);
+        pos = pos === -1 ? content.length : pos + 1;
     }
     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,
-        };
+    if (!idMatch || !nameMatch) {
+        return null;
     }
-    return null;
+    return {
+        id: parseInt(idMatch[1], 10),
+        name: nameMatch[1].replace(/\\"/g, '"').replace(/\\\\/g, '\\'),
+    };
 }
-/**
- * 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;
+    if (!idMatch) {
+        return null;
     }
-    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;
+    const parentMatch = /parent\s+(\d+)/.exec(nodeString);
+    const featuresIdx = nodeString.indexOf('features');
+    const featuresContent = featuresIdx !== -1 ? findBracedContent(nodeString, featuresIdx) : undefined;
+    return {
+        id: parseInt(idMatch[1], 10),
+        ...(parentMatch ? { parent: parseInt(parentMatch[1], 10) } : {}),
+        features: featuresContent
+            ? extractBracedBlocks(featuresContent).flatMap(block => {
+                const f = parseFeature(block);
+                return f ? [f] : [];
+            })
+            : [],
+    };
 }
-/**
- * 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,
-        };
+    if (!featureidMatch || !valueMatch) {
+        return null;
     }
-    return null;
+    return {
+        featureid: parseInt(featureidMatch[1], 10),
+        value: valueMatch[1].replace(/\\"/g, '"').replace(/\\\\/g, '\\'),
+    };
 }
 //# sourceMappingURL=parseAsn1.js.map