taxonium-component/dist/jb1ToJb2-DN9KH2A3.js

React component for exploring large phylogenetic trees in the browser

import { u as m, t as n } from "./JBrowsePanel-uJIA-L6s.js";
function F(e, c, y) {
  var u, p, l, d, s;
  const t = {
    trackId: m.objectHash(e),
    name: e.key || e.label
  }, U = e.metadata && (e.metadata.description || e.metadata.Description);
  U && (t.description = U);
  const T = e.category || ((u = e.metadata) === null || u === void 0 ? void 0 : u.category);
  t.category = T ? T.split(/\s*\/\s*/) : [];
  const { storeClass: r } = e;
  if (!e.urlTemplate) {
    if (!(r != null && r.endsWith("FromConfig"))) {
      const i = e.key || e.label;
      return console.warn(`Could not import JBrowse1 track "${i}" because it does not have a "urlTemplate" or is not a "FromConfig" track`), n.generateUnsupportedTrackConf(t.name, i, t.category);
    }
    return L(e, t);
  }
  const o = (i) => new URL(i, `${c}/`).href.replaceAll(/%7B/gi, "{").replaceAll(/%7D/gi, "}"), a = o(e.urlTemplate);
  if (r) {
    if (r === "JBrowse/Store/SeqFeature/BAM") {
      const i = {
        type: "BamAdapter",
        bamLocation: { uri: a, locationType: "UriLocation" }
      };
      return e.baiUrlTemplate ? i.index = {
        location: {
          uri: o(e.baiUrlTemplate),
          locationType: "UriLocation"
        }
      } : e.csiUrlTemplate ? i.index = {
        location: {
          uri: o(e.csiUrlTemplate),
          locationType: "UriLocation"
        },
        indexType: "CSI"
      } : i.index = {
        location: { uri: `${a}.bai`, locationType: "UriLocation" }
      }, {
        ...t,
        type: "AlignmentsTrack",
        adapter: i
      };
    }
    if (r === "JBrowse/Store/SeqFeature/CRAM") {
      const i = {
        type: "CramAdapter",
        cramLocation: { uri: a, locationType: "UriLocation" },
        sequenceAdapter: y
      };
      return i.craiLocation = e.craiUrlTemplate ? {
        uri: o(e.craiUrlTemplate),
        locationType: "UriLocation"
      } : {
        uri: `${a}.crai`,
        locationType: "UriLocation"
      }, {
        ...t,
        type: "AlignmentsTrack",
        adapter: i
      };
    }
    if (r === "JBrowse/Store/SeqFeature/NCList")
      return {
        ...t,
        type: "FeatureTrack",
        adapter: {
          type: "NCListAdapter",
          rootUrlTemplate: { uri: a, locationType: "UriLocation" }
        }
      };
    if (r === "JBrowse/Store/SeqFeature/BigWig" || r === "JBrowse/Store/BigWig")
      return !((p = e.type) === null || p === void 0) && p.endsWith("XYPlot") ? t.defaultRendering = "xyplot" : !((l = e.type) === null || l === void 0) && l.endsWith("Density") && (t.defaultRendering = "density"), {
        ...t,
        type: "QuantitativeTrack",
        adapter: {
          type: "BigWigAdapter",
          bigWigLocation: { uri: a, locationType: "UriLocation" }
        }
      };
    if (r === "JBrowse/Store/SeqFeature/VCFTabix") {
      const i = {
        type: "VcfTabixAdapter",
        vcfGzLocation: { uri: a, locationType: "UriLocation" }
      };
      return e.tbiUrlTemplate ? i.index = {
        location: {
          uri: o(e.tbiUrlTemplate),
          locationType: "UriLocation"
        }
      } : e.csiUrlTemplate ? i.index = {
        location: {
          uri: o(e.csiUrlTemplate),
          locationType: "UriLocation"
        },
        indexType: "CSI"
      } : i.index = {
        location: { uri: `${a}.tbi`, locationType: "UriLocation" }
      }, {
        ...t,
        type: "VariantTrack",
        adapter: i
      };
    }
    if (r === "JBrowse/Store/SeqFeature/VCFTribble")
      return n.generateUnsupportedTrackConf(t.name, `VCFTribble (${a})`, t.category);
    if (r === "JBrowse/Store/SeqFeature/GFF3")
      return {
        ...t,
        type: "FeatureTrack",
        adapter: {
          type: "Gff3Adapter",
          gffLocation: { uri: a, locationType: "UriLocation" }
        }
      };
    if (r === "JBrowse/Store/SeqFeature/BigBed")
      return {
        ...t,
        type: "FeatureTrack",
        adapter: {
          type: "BigBedAdapter",
          bigBedLocation: { uri: a, locationType: "UriLocation" }
        }
      };
    if (r === "JBrowse/Store/SeqFeature/GFF3Tabix") {
      const i = {
        type: "Gff3TabixAdapter",
        gffGzLocation: { uri: a, locationType: "UriLocation" }
      };
      return e.tbiUrlTemplate ? i.index = {
        location: {
          uri: o(e.tbiUrlTemplate),
          locationType: "UriLocation"
        }
      } : e.csiUrlTemplate ? i.index = {
        location: {
          uri: o(e.csiUrlTemplate),
          locationType: "UriLocation"
        },
        indexType: "CSI"
      } : i.index = {
        location: { uri: `${a}.tbi`, locationType: "UriLocation" }
      }, {
        ...t,
        type: "FeatureTrack",
        adapter: i
      };
    }
    if (r === "JBrowse/Store/SeqFeature/BED")
      return n.generateUnsupportedTrackConf(t.name, `BED (${a})`, t.category);
    if (r === "JBrowse/Store/SeqFeature/BEDTabix") {
      const i = {
        type: "BedTabixAdapter",
        bedGzLocation: { uri: a, locationType: "UriLocation" }
      };
      return e.tbiUrlTemplate ? i.index = {
        location: {
          uri: o(e.tbiUrlTemplate),
          locationType: "UriLocation"
        }
      } : e.csiUrlTemplate ? i.index = {
        location: {
          uri: o(e.csiUrlTemplate),
          locationType: "UriLocation"
        },
        indexType: "CSI"
      } : i.index = {
        location: { uri: `${a}.tbi`, locationType: "UriLocation" }
      }, {
        ...t,
        type: "FeatureTrack",
        adapter: i
      };
    }
    if (r === "JBrowse/Store/SeqFeature/GTF")
      return {
        ...t,
        type: "FeatureTrack",
        adapter: {
          type: "GtfAdapter",
          gtfLocation: { uri: a, locationType: "UriLocation" }
        }
      };
    if (r === "JBrowse/Store/SeqFeature/StaticChunked" || r === "JBrowse/Store/Sequence/StaticChunked")
      return n.generateUnsupportedTrackConf(t.name, `StaticChunked (${a})`, t.category);
    if (r === "JBrowse/Store/SeqFeature/UnindexedFasta")
      return n.generateUnsupportedTrackConf(t.name, `UnindexedFasta (${a})`, t.category);
    if (r === "JBrowse/Store/SeqFeature/IndexedFasta") {
      const i = {
        type: "IndexedFastaAdapter",
        fastaLocation: { uri: a, locationType: "UriLocation" }
      };
      return i.faiLocation = e.faiUrlTemplate ? {
        uri: o(e.faiUrlTemplate),
        locationType: "UriLocation"
      } : {
        uri: `${a}.fai`,
        locationType: "UriLocation"
      }, {
        ...t,
        type: "SequenceTrack",
        adapter: i
      };
    }
    if (r === "JBrowse/Store/SeqFeature/BgzipIndexedFasta") {
      const i = {
        type: "BgzipFastaAdapter",
        fastaLocation: { uri: a, locationType: "UriLocation" }
      };
      return i.faiLocation = e.faiUrlTemplate ? {
        uri: o(e.faiUrlTemplate),
        locationType: "UriLocation"
      } : {
        uri: `${a}.fai`,
        locationType: "UriLocation"
      }, i.gziLocation = e.gziUrlTemplate ? {
        uri: o(e.gziUrlTemplate),
        locationType: "UriLocation"
      } : {
        uri: `${a}.gzi`,
        locationType: "UriLocation"
      }, {
        ...t,
        type: "ReferenceSequenceTrack",
        adapter: i
      };
    }
    if (r === "JBrowse/Store/SeqFeature/TwoBit")
      return {
        ...t,
        type: "ReferenceSequenceTrack",
        adapter: {
          type: "TwoBitAdapter",
          twoBitLocation: { uri: a, locationType: "UriLocation" }
        }
      };
  }
  return t.adapter = n.guessAdapter({ uri: a, locationType: "UriLocation" }, void 0, a), t.adapter.type === n.UNSUPPORTED ? n.generateUnsupportedTrackConf(t.name, a, t.category) : t.adapter.type === n.UNKNOWN ? n.generateUnknownTrackConf(t.name, a, t.category) : (t.type = n.guessTrackType(t.adapter.type), t.type === "QuantitativeTrack" && (!((d = e.type) === null || d === void 0) && d.endsWith("XYPlot") ? t.defaultRendering = "xyplot" : !((s = e.type) === null || s === void 0) && s.endsWith("Density") && (t.defaultRendering = "density")), t);
}
function L(e, c) {
  const u = (e.features || []).map((p) => {
    const l = JSON.parse(JSON.stringify(p));
    return l.refName = p.seq_id, l.uniqueId = `${p.seq_id}:${p.start}-${p.end}:${p.name || ""}`, l;
  });
  return c.adapter = {
    type: "FromConfigAdapter",
    features: u
  }, c.type = "FeatureTrack", c;
}
export {
  F as convertTrackConfig
};
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