generic-sequence-panel/src/NCListFeature.ts

read feature and sequence data and produce highlighted fasta

/* eslint-disable @typescript-eslint/no-explicit-any,@typescript-eslint/no-unsafe-assignment,@typescript-eslint/prefer-nullish-coalescing,@typescript-eslint/no-unsafe-member-access,@typescript-eslint/no-unsafe-return,@typescript-eslint/no-unsafe-call */
import {
  Feature,
  SimpleFeatureSerialized,
} from "@jbrowse/core/util/simpleFeature";

const jb2ToJb1 = { refName: "seq_id" };

const jb1ToJb2 = { seq_id: "refName" };

/**
 * wrapper to adapt nclist features to act like jbrowse 2 features
 */
export default class NCListFeature implements Feature {
  private parentHandle?: Feature;

  private uniqueId: string;

  constructor(
    private ncFeature: any,
    parent?: Feature,
    id?: string,
  ) {
    this.uniqueId = id || ncFeature.id();
    this.parentHandle = parent;
  }

  set(): void {
    throw new Error("not implemented");
  }

  jb2TagToJb1Tag(tag: string): string {
    // @ts-expect-error
    const mapped = jb2ToJb1[tag] || tag;
    return mapped.toLowerCase();
  }

  jb1TagToJb2Tag(tag: string): string {
    const t = tag.toLowerCase();
    // @ts-expect-error
    const mapped = jb1ToJb2[t] || t;
    return mapped;
  }

  get(attrName: string): any {
    const attr = this.ncFeature.get(this.jb2TagToJb1Tag(attrName));
    if (attr && attrName === "subfeatures") {
      return attr.map((subfeature: any) => new NCListFeature(subfeature, this));
    }
    return attr;
  }

  /**
   * Get an array listing which data keys are present in this feature.
   */
  tags(): string[] {
    return this.ncFeature.tags().map((t: string) => this.jb1TagToJb2Tag(t));
  }

  /**
   * Get the unique ID of this feature.
   */
  id(): string {
    return this.uniqueId;
  }

  /**
   * Get this feature's parent feature, or undefined if none.
   */
  parent(): Feature | undefined {
    return this.parentHandle;
  }

  /**
   * Get an array of child features, or undefined if none.
   */
  children(): Feature[] | undefined {
    return this.get("subfeatures");
  }

  toJSON(): SimpleFeatureSerialized {
    const data = { uniqueId: this.id(), subfeatures: [] } as Record<
      string,
      unknown
    >;
    this.ncFeature.tags().forEach((tag: string) => {
      const mappedTag = this.jb1TagToJb2Tag(tag);
      const value = this.ncFeature.get(tag);
      if (mappedTag === "subfeatures") {
        data.subfeatures = (value || []).map((f: Feature) =>
          new NCListFeature(f, this).toJSON(),
        );
      } else {
        data[mappedTag] = value;
      }
    });
    return data as SimpleFeatureSerialized;
  }
}