/*************************************************************************
* *
* 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.entities;
import act.installer.metacyc.Resource;
import act.installer.metacyc.BPElement;
import act.installer.metacyc.NXT;
import java.util.Set;
import java.util.HashSet;
import act.installer.metacyc.OrganismComposition;
import act.installer.metacyc.JsonHelper;
import org.json.JSONObject;
public class Complex extends BPElement {
Set<Resource> componentStoichiometry;
Set<Resource> components;
public Complex(BPElement basics, Set<Resource> stoi, Set<Resource> comp) {
super(basics);
this.componentStoichiometry = stoi;
this.components = comp;
}
@Override
public Set<Resource> field(NXT typ) {
Set<Resource> s = new HashSet<Resource>();
if (typ == NXT.components) {
s.addAll(this.components);
}
return s;
}
public JSONObject expandedJSON(OrganismComposition src) {
JsonHelper o = new JsonHelper(src);
o.add("name", super.standardName); // from BPElement
if (components != null)
for (BPElement c : src.resolve(components))
o.add("component", c.expandedJSON(src));
if (componentStoichiometry != null) {
int pre = "R:http://biocyc.org/biopax/biopax-level3".length();
String str = "";
for (BPElement s : src.resolve(componentStoichiometry)) {
JSONObject st = s.expandedJSON(src);
str += (str.length()==0 ? "" : " + ") + st.get("c") + " x " + ((String)st.get("on")).substring(pre);
}
o.add("multiplicity", str);
}
return o.getJSON();
}
}