/*************************************************************************
* *
* 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.processes;
import act.installer.metacyc.Resource;
import act.installer.metacyc.BPElement;
import act.installer.metacyc.OrganismComposition;
import act.installer.metacyc.JsonHelper;
import act.installer.metacyc.NXT;
import org.biopax.paxtools.model.level3.CatalysisDirectionType;
import org.biopax.paxtools.model.level3.ControlType;
import java.util.Set;
import java.util.HashSet;
import org.json.JSONObject;
public class Catalysis extends BPElement {
CatalysisDirectionType direction; // RIGHT-TO-LEFT or LEFT-TO-RIGHT
ControlType controlType; // only ACTIVATION seen, but many more exist in Enum.values(ControlType)
Set<Resource> controller;
Set<Resource> controlled;
Set<Resource> cofactors;
public CatalysisDirectionType getDirection() { return this.direction; }
public ControlType getControlType() { return this.controlType; }
public Catalysis(BPElement basics, CatalysisDirectionType dir, ControlType ctrlt, Set<Resource> controller, Set<Resource> controlled, Set<Resource> cofactors) {
super(basics);
this.direction = dir;
this.controlType = ctrlt;
this.controller = controller;
this.controlled = controlled;
this.cofactors = cofactors;
}
@Override
public Set<Resource> field(NXT typ) {
Set<Resource> s = new HashSet<Resource>();
if (typ == NXT.controller) {
s.addAll(this.controller);
} else if (typ == NXT.controlled) {
s.addAll(this.controlled);
} else if (typ == NXT.cofactors) {
s.addAll(this.cofactors);
}
return s;
}
public JSONObject expandedJSON(OrganismComposition src) {
JsonHelper o = new JsonHelper(src);
if (controlType != null) o.add("type", controlType.toString());
if (direction != null) o.add("dir", direction.toString());
if (controller != null)
for (BPElement c : src.resolve(controller))
o.add("controller", c.expandedJSON(src));
if (controlled != null)
for (BPElement c : src.resolve(controlled))
o.add("controlled", c.expandedJSON(src));
if (cofactors != null)
for (BPElement c : src.resolve(cofactors))
o.add("cofactors", c.expandedJSON(src));
return o.getJSON();
}
}