generic-sequence-panel/esm/NCListFeature.js

read feature and sequence data and produce highlighted fasta

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 {
    constructor(ncFeature, parent, id) {
        this.ncFeature = ncFeature;
        this.uniqueId = id || ncFeature.id();
        this.parentHandle = parent;
    }
    set() {
        throw new Error("not implemented");
    }
    jb2TagToJb1Tag(tag) {
        // @ts-expect-error
        const mapped = jb2ToJb1[tag] || tag;
        return mapped.toLowerCase();
    }
    jb1TagToJb2Tag(tag) {
        const t = tag.toLowerCase();
        // @ts-expect-error
        const mapped = jb1ToJb2[t] || t;
        return mapped;
    }
    get(attrName) {
        const attr = this.ncFeature.get(this.jb2TagToJb1Tag(attrName));
        if (attr && attrName === "subfeatures") {
            return attr.map((subfeature) => new NCListFeature(subfeature, this));
        }
        return attr;
    }
    /**
     * Get an array listing which data keys are present in this feature.
     */
    tags() {
        return this.ncFeature.tags().map((t) => this.jb1TagToJb2Tag(t));
    }
    /**
     * Get the unique ID of this feature.
     */
    id() {
        return this.uniqueId;
    }
    /**
     * Get this feature's parent feature, or undefined if none.
     */
    parent() {
        return this.parentHandle;
    }
    /**
     * Get an array of child features, or undefined if none.
     */
    children() {
        return this.get("subfeatures");
    }
    toJSON() {
        const data = { uniqueId: this.id(), subfeatures: [] };
        this.ncFeature.tags().forEach((tag) => {
            const mappedTag = this.jb1TagToJb2Tag(tag);
            const value = this.ncFeature.get(tag);
            if (mappedTag === "subfeatures") {
                data.subfeatures = (value || []).map((f) => new NCListFeature(f, this).toJSON());
            }
            else {
                data[mappedTag] = value;
            }
        });
        return data;
    }
}