react-msaview 4.1.1 → 4.3.0

package/src/parseAsn1.ts

@@ -0,0 +1,494 @@
+/**
+ * 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
+ */
+
+// Define types for our ASN structure
+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 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: string,
+): { id: number; parent: number; name: string }[] {
+  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 as keyof typeof remap] || r.name,
+    ]),
+  )
+
+  return parseNodes(sections.nodes!).map(node => {
+    const { features, ...rest } = node
+    return {
+      ...rest,
+      ...Object.fromEntries(
+        features!.map(f => [dict[f.featureid], f.value] as const),
+      ),
+    }
+  })
+}
+
+/**
+ * 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: string): Record<string, string> {
+  const sections: Record<string, string> = {}
+
+  // 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: string): ASNDictEntry[] {
+  const entries: ASNDictEntry[] = []
+
+  // 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: string): ASNDictEntry | null {
+  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: string): ASNNode[] {
+  const nodes: ASNNode[] = []
+
+  // 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: string): ASNNode | null {
+  const idMatch = /id\s+(\d+)/.exec(nodeString)
+  const parentMatch = /parent\s+(\d+)/.exec(nodeString)
+
+  if (idMatch) {
+    const node: ASNNode = {
+      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: string): ASNFeature[] {
+  const features: ASNFeature[] = []
+
+  // 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: string): ASNFeature | null {
+  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
+}

package/src/parsers/ClustalMSA.ts

@@ -1,6 +1,7 @@
 import { parse } from 'clustal-js'
 
-import type { NodeWithIds } from '../util'
+import type { NodeWithIds } from '../types'
+
 export default class ClustalMSA {
   private MSA: ReturnType<typeof parse>
 

package/src/parsers/EmfMSA.ts

@@ -1,6 +1,6 @@
 import { parseEmfAln } from 'emf-js'
 
-import type { NodeWithIds } from '../util'
+import type { NodeWithIds } from '../types'
 
 export default class EmfMSA {
   private MSA: ReturnType<typeof parseEmfAln>

package/src/parsers/FastaMSA.ts

@@ -1,4 +1,4 @@
-import type { NodeWithIds } from '../util'
+import type { NodeWithIds } from '../types'
 
 function parseSmallFasta(text: string) {
   return text

package/src/parsers/StockholmMSA.ts

@@ -1,7 +1,10 @@
 import Stockholm from 'stockholm-js'
 
 import parseNewick from '../parseNewick'
-import { type NodeWithIds, generateNodeIds } from '../util'
+import { generateNodeIds } from '../util'
+
+import type { NodeWithIds } from '../types'
+
 interface StockholmEntry {
   gf: {
     DE?: string[]

package/src/renderToSvg.tsx

@@ -13,10 +13,12 @@ import { colorContrast } from './util'
 import type { MsaViewModel } from './model'
 import type { Theme } from '@mui/material'
 
-export async function renderToSvg(
-  model: MsaViewModel,
-  opts: { theme: Theme; includeMinimap?: boolean; exportType: string },
-) {
+export interface ExportSvgOptions {
+  theme: Theme
+  includeMinimap?: boolean
+  exportType: string
+}
+export async function renderToSvg(model: MsaViewModel, opts: ExportSvgOptions) {
   await when(() => !!model.dataInitialized)
   const { width, height, scrollX, scrollY } = model
   const { exportType, theme, includeMinimap } = opts

package/src/reparseTree.ts

@@ -1,5 +1,7 @@
-import type { NodeWithIds } from './util'
+import type { NodeWithIds } from './types'
 
+// this reparse routine helps to allow the app to hide/collapse a single
+// leafnode
 export function reparseTree(tree: NodeWithIds): NodeWithIds {
   return {
     ...tree,

package/src/types.ts

@@ -0,0 +1,44 @@
+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/src/util.ts

@@ -2,6 +2,7 @@ import { colord, extend } from 'colord'
 import namesPlugin from 'colord/plugins/names'
 import { max } from 'd3-array'
 
+import type { Node, NodeWithIds } from './types'
 import type { Theme } from '@mui/material'
 import type { HierarchyNode } from 'd3-hierarchy'
 
@@ -14,28 +15,6 @@ export function transform<T>(
   return Object.fromEntries(Object.entries(obj).map(cb))
 }
 
-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 function generateNodeIds(
   tree: Node,
   parent = 'node',
@@ -118,3 +97,28 @@ export function clamp(min: number, num: number, max: number) {
 export function len(a: { end: number; start: number }) {
   return a.end - a.start
 }
+
+export function localStorageGetItem(item: string) {
+  return typeof localStorage !== 'undefined'
+    ? localStorage.getItem(item)
+    : undefined
+}
+
+export function localStorageGetBoolean(key: string, defaultVal: boolean) {
+  return Boolean(
+    JSON.parse(localStorageGetItem(key) || JSON.stringify(defaultVal)),
+  )
+}
+
+export function localStorageSetItem(str: string, item: string) {
+  if (typeof localStorage !== 'undefined') {
+    localStorage.setItem(str, item)
+  }
+}
+export function localStorageSetBoolean(key: string, value: boolean) {
+  localStorageSetItem(key, JSON.stringify(value))
+}
+
+export function isGzip(buf: Uint8Array) {
+  return buf[0] === 31 && buf[1] === 139 && buf[2] === 8
+}

package/src/version.ts

@@ -1 +1 @@
-export const version = '4.1.1'
+export const version = '4.3.0'

package/src/webpack.ts

@@ -0,0 +1,9 @@
+import * as React from 'react'
+
+export { default as MSAView } from './components/Loading'
+export { type MsaViewModel, default as MSAModelF } from './model'
+
+export * from 'react-dom/client'
+
+// eslint-disable-next-line unicorn/prefer-export-from
+export { React }