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}