/*************************************************************************
* *
* 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 java.util.Set;
import org.biopax.paxtools.model.level3.StepDirection;
public class BiochemicalPathwayStep extends BPElement {
StepDirection direction; // LEFT-TO-RIGHT
Resource conversion; // a Transport | BiochemicalReaction | both
Set<Resource> process; // a Catalysis
// while process.size() will usually be 1
// sometimes there are multiple proteins
// controlling a reaction, and so for the
// single conversion that is this step, there
// might be many options for catalysis
Set<Resource> nextSteps; // a ref to another BiochemicalPathwayStep:
// allows the specification of a branchout in
// the top to bottom graph, multiple nextSteps
// mean that they are alternative steps that
// can be followed. A single nextStep means
// in the pathway, if a subsequent rxn happens
// that is the one that happens.
public Resource getConversion() { return this.conversion; }
public Set<Resource> getProcess() { return this.process; }
public StepDirection getDirection() {
return this.direction;
}
public BiochemicalPathwayStep(BPElement basics, StepDirection dir, Resource conv, Set<Resource> process, Set<Resource> next) {
super(basics);
this.direction = dir;
this.conversion = conv;
this.process = process;
this.nextSteps = next;
}
}