001package org.biopax.paxtools.pattern.miner; 002 003import org.biopax.paxtools.model.level3.Protein; 004import org.biopax.paxtools.model.level3.ProteinReference; 005import org.biopax.paxtools.pattern.Pattern; 006import org.biopax.paxtools.pattern.PatternBox; 007import org.biopax.paxtools.pattern.constraint.NOT; 008import org.biopax.paxtools.pattern.constraint.Type; 009 010import static org.biopax.paxtools.pattern.constraint.ConBox.*; 011 012/** 013 * Miner for the transcriptional regulation pattern. 014 * @author Ozgun Babur 015 */ 016public class ControlsExpressionMiner extends AbstractSIFMiner 017{ 018 /** 019 * Constructor that sets name and description. 020 */ 021 public ControlsExpressionMiner() 022 { 023 super(SIFEnum.CONTROLS_EXPRESSION_OF); 024 } 025 026 /** 027 * Constructor for extending this class. 028 * @param nameSuppl name 029 * @param descriptionSuppl description 030 */ 031 public ControlsExpressionMiner(String nameSuppl, String descriptionSuppl) 032 { 033 super(SIFEnum.CONTROLS_EXPRESSION_OF, nameSuppl, descriptionSuppl); 034 } 035 036 /** 037 * Constructs the pattern. 038 * @return pattern 039 */ 040 @Override 041 public Pattern constructPattern() 042 { 043 Pattern p = PatternBox.controlsExpressionWithTemplateReac(); 044 045 return p; 046 } 047 048 @Override 049 public String getSourceLabel() 050 { 051 return "TF ER"; 052 } 053 054 @Override 055 public String getTargetLabel() 056 { 057 return "product ER"; 058 } 059 060 @Override 061 public String[] getMediatorLabels() 062 { 063 return new String[]{"Control", "TempReac"}; 064 } 065 066 @Override 067 public String[] getSourcePELabels() 068 { 069 return new String[]{"TF SPE", "TF PE"}; 070 } 071 072 @Override 073 public String[] getTargetPELabels() 074 { 075 return new String[]{"product PE", "product SPE"}; 076 } 077}