@jbrowse/plugin-linear-genome-view/esm/BaseLinearDisplay/util.js

JBrowse 2 linear genome view

import { SimpleFeature, mergeIntervals } from '@jbrowse/core/util';
export async function fetchFeatureByIdRpc({ rpcManager, sessionId, trackId, rendererType, featureId, parentFeatureId, }) {
    const lookupId = parentFeatureId || featureId;
    const { feature: featureData } = (await rpcManager.call(sessionId, 'CoreGetFeatureDetails', {
        featureId: lookupId,
        sessionId,
        trackInstanceId: trackId,
        rendererType,
    }));
    if (!featureData) {
        return undefined;
    }
    const feature = new SimpleFeature(featureData);
    if (parentFeatureId) {
        return findSubfeatureById(feature, featureId);
    }
    return feature;
}
export function findSubfeatureById(feature, targetId) {
    const subfeatures = feature.get('subfeatures');
    if (subfeatures) {
        for (const sub of subfeatures) {
            if (sub.id() === targetId) {
                return sub;
            }
            const found = findSubfeatureById(sub, targetId);
            if (found) {
                return found;
            }
        }
    }
    return undefined;
}
export function featureHasExonsOrCDS(feature) {
    const subs = feature.get('subfeatures') ?? [];
    return subs.some((f) => f.get('type') === 'exon' || f.get('type') === 'CDS');
}
export function hasExonsOrCDS(transcripts) {
    return transcripts.some(t => featureHasExonsOrCDS(t));
}
export function hasIntrons(transcripts) {
    const subs = transcripts.flatMap(transcript => transcript
        .get('subfeatures')
        ?.filter((f) => f.get('type') === 'exon' || f.get('type') === 'CDS') ?? []);
    if (subs.length < 2) {
        return false;
    }
    const merged = mergeIntervals(subs.map((f) => ({ start: f.get('start'), end: f.get('end') })), 0);
    return merged.length > 1;
}
export function getTranscripts(feature) {
    if (!feature) {
        return [];
    }
    return featureHasExonsOrCDS(feature)
        ? [feature]
        : (feature.get('subfeatures') ?? []);
}
export function drawCanvasImageData(canvas, imageData) {
    if (!canvas || !imageData) {
        return false;
    }
    const ctx = canvas.getContext('2d');
    if (!ctx) {
        return false;
    }
    ctx.resetTransform();
    ctx.clearRect(0, 0, canvas.width, canvas.height);
    ctx.drawImage(imageData, 0, 0);
    return true;
}