/*************************************************************************
* *
* This file is part of the 20n/act project. *
* 20n/act enables DNA prediction for synthetic biology/bioengineering. *
* Copyright (C) 2017 20n Labs, Inc. *
* *
* Please direct all queries to act@20n.com. *
* *
* This program is free software: you can redistribute it and/or modify *
* it under the terms of the GNU General Public License as published by *
* the Free Software Foundation, either version 3 of the License, or *
* (at your option) any later version. *
* *
* This program is distributed in the hope that it will be useful, *
* but WITHOUT ANY WARRANTY; without even the implied warranty of *
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the *
* GNU General Public License for more details. *
* *
* You should have received a copy of the GNU General Public License *
* along with this program. If not, see <http://www.gnu.org/licenses/>. *
* *
*************************************************************************/
package act.installer.metacyc.annotations;
import act.installer.metacyc.Resource;
import act.installer.metacyc.BPElement;
import act.installer.metacyc.OrganismComposition;
import act.installer.metacyc.JsonHelper;
import org.json.JSONObject;
public class BioSource extends BPElement {
// contains only a xref and a name (both from BPElement)
// e.g., {
// ID: BioSource32423,
// xref: #UnificationXref32424,
// name: "Escherichia coli MS 124-1"
// }
// the xref points to a unification ref:
// { id: "679205", db: "NCBI Taxonomy" }
// which is great because we can then lookup the full lineage:
// cellular organisms; Bacteria; Proteobacteria;
// Gammaproteobacteria; Enterobacteriales;
// Enterobacteriaceae; Escherichia; Escherichia coli
// from http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=679205
public BioSource(BPElement basics) {
super(basics);
}
public JSONObject expandedJSON(OrganismComposition src) {
JsonHelper o = new JsonHelper(src);
if (name != null)
o.add("name", this.name);
return o.getJSON();
}
}