001package org.biopax.paxtools.pattern.miner;
002
003import org.biopax.paxtools.model.level3.ProteinReference;
004import org.biopax.paxtools.pattern.Pattern;
005import org.biopax.paxtools.pattern.PatternBox;
006import org.biopax.paxtools.pattern.constraint.Type;
007
008/**
009 * Miner for the transcriptional regulation pattern, modeled using Conversion.
010 * @author Ozgun Babur
011 */
012public class ControlsExpressionWithConvMiner extends ControlsExpressionMiner
013{
014        /**
015         * Constructor that sets name and description.
016         */
017        public ControlsExpressionWithConvMiner()
018        {
019                super("-with-conversion", "Proper way to model this relation is to use a TemplateReaction" +
020                        ", however we see that Conversion is also used in resources. This miner find patterns" +
021                        " where a Conversion with a single participant at right is used instead of a " +
022                        "TemplateReaction.");
023        }
024
025        /**
026         * Constructs the pattern.
027         * @return pattern
028         */
029        @Override
030        public Pattern constructPattern()
031        {
032                Pattern p = PatternBox.controlsExpressionWithConversion();
033                return p;
034        }
035
036        @Override
037        public String[] getMediatorLabels()
038        {
039                return new String[]{"Control", "Conversion"};
040        }
041
042        @Override
043        public String[] getSourcePELabels()
044        {
045                return new String[]{"TF SPE", "TF PE"};
046        }
047
048        @Override
049        public String[] getTargetPELabels()
050        {
051                return new String[]{"right PE", "right SPE"};
052        }
053}