@jbrowse/core 3.6.5 → 3.7.0

package/BaseFeatureWidget/SequenceFeatureDetails/hooks.js

@@ -1,65 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.useFeatureSequence = useFeatureSequence;
-const react_1 = require("react");
-const configuration_1 = require("../../configuration");
-const util_1 = require("../../util");
-const BPLIMIT = 500000;
-function useFeatureSequence(model, feature, upDownBp, forceLoad) {
-    const [sequence, setSequence] = (0, react_1.useState)();
-    const [error, setError] = (0, react_1.useState)();
-    (0, react_1.useEffect)(() => {
-        var _a, _b;
-        if (!model) {
-            return;
-        }
-        const { assemblyManager, rpcManager } = (0, util_1.getSession)(model);
-        const assemblyName = ((_b = (_a = model.view) === null || _a === void 0 ? void 0 : _a.assemblyNames) === null || _b === void 0 ? void 0 : _b[0]) || '';
-        async function fetchSeq(start, end, refName) {
-            const assembly = await assemblyManager.waitForAssembly(assemblyName);
-            if (!assembly) {
-                throw new Error('assembly not found');
-            }
-            const sessionId = 'getSequence';
-            const feats = await rpcManager.call(sessionId, 'CoreGetFeatures', {
-                adapterConfig: (0, configuration_1.getConf)(assembly, ['sequence', 'adapter']),
-                sessionId,
-                regions: [
-                    {
-                        start,
-                        end,
-                        refName: assembly.getCanonicalRefName(refName),
-                        assemblyName,
-                    },
-                ],
-            });
-            const [feat] = feats;
-            return (feat === null || feat === void 0 ? void 0 : feat.get('seq')) || '';
-        }
-        ;
-        (async () => {
-            try {
-                setError(undefined);
-                const { start, end, refName } = feature;
-                if (!forceLoad && end - start > BPLIMIT) {
-                    setSequence({
-                        error: `Genomic sequence larger than ${BPLIMIT}bp, use "force load" button to display`,
-                    });
-                }
-                else {
-                    const b = start - upDownBp;
-                    const e = end + upDownBp;
-                    const seq = await fetchSeq(start, end, refName);
-                    const up = await fetchSeq(Math.max(0, b), start, refName);
-                    const down = await fetchSeq(end, e, refName);
-                    setSequence({ seq, upstream: up, downstream: down });
-                }
-            }
-            catch (e) {
-                console.error(e);
-                setError(e);
-            }
-        })();
-    }, [feature, model, upDownBp, forceLoad]);
-    return { sequence, error };
-}