msa-parsers 1.0.3

package/src/types.ts

@@ -0,0 +1,68 @@
+export interface Node {
+  children?: Node[]
+  name?: string
+  length?: number
+}
+
+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 interface GFFRecord {
+  seq_id: string
+  source: string
+  type: string
+  start: number
+  end: number
+  score: number
+  strand: string
+  phase: string
+  [key: string]: string | number
+}
+
+export interface InterProScanMatch {
+  signature: {
+    entry?: {
+      name: string
+      description: string
+      accession: string
+    }
+  }
+  locations: { start: number; end: number }[]
+}
+
+export interface InterProScanResults {
+  matches: InterProScanMatch[]
+  xref: { id: string }[]
+}
+
+export interface InterProScanResponse {
+  results: InterProScanResults[]
+}
+
+export interface MSAParser {
+  getMSA(): unknown
+  getRow(name: string): string
+  getWidth(): number
+  getNames(): string[]
+  getTree(): NodeWithIds
+  getHeader(): unknown
+  getRowData(name: string): unknown
+  getStructures(): Record<string, unknown>
+  alignmentNames: string[]
+  seqConsensus: string | undefined
+  secondaryStructureConsensus: string | undefined
+  tracks: unknown[]
+}

package/src/util.ts

@@ -0,0 +1,19 @@
+import type { Node, NodeWithIds } from './types'
+
+export function generateNodeIds(
+  tree: Node,
+  parent = 'node',
+  depth = 0,
+): NodeWithIds {
+  const id = `${parent}-${depth}`
+
+  return {
+    ...tree,
+    id,
+    name: tree.name || id,
+    children:
+      tree.children?.map((b, i) =>
+        generateNodeIds(b, `${id}-${i}`, depth + 1),
+      ) || [],
+  }
+}