org.biopax.paxtools.pattern.miner.CSCOButIsParticipantMiner Maven / Gradle / Ivy

Go to download
package org.biopax.paxtools.pattern.miner;

import org.biopax.paxtools.model.level3.ProteinReference;
import org.biopax.paxtools.pattern.Pattern;
import org.biopax.paxtools.pattern.PatternBox;
import org.biopax.paxtools.pattern.constraint.Type;

/**
 * Miner for the controls-state-change pattern.
 * @author Ozgun Babur
 */
public class CSCOButIsParticipantMiner extends ControlsStateChangeOfMiner
{
	/**
	 * Constructor that sets name and description.
	 */
	public CSCOButIsParticipantMiner()
	{
		super("-but-a-participant", "The controller is modeled as a " +
			"participant of the Conversion. This is in fact a modeling error, but this pattern " +
			"exists in some resources. The controller PhysicalEntity appears at both left and " +
			"right of the Conversion.");
	}

	/**
	 * Constructs the pattern.
	 * @return pattern
	 */
	@Override
	public Pattern constructPattern()
	{
		Pattern p = PatternBox.controlsStateChangeButIsParticipant();
		p.add(new Type(ProteinReference.class), "controller ER");
		p.add(new Type(ProteinReference.class), "changed ER");
		return p;
	}

	@Override
	public String[] getMediatorLabels()
	{
		return new String[]{"Conversion"};
	}

	@Override
	public String getSourceLabel()
	{
		return "controller ER";
	}

	@Override
	public String getTargetLabel()
	{
		return "changed ER";
	}


	@Override
	public String[] getSourcePELabels()
	{
		return new String[]{"controller simple PE", "controller PE"};
	}

	@Override
	public String[] getTargetPELabels()
	{
		return new String[]{"input PE", "input simple PE", "output PE", "output simple PE"};
	}
}