001package org.biopax.paxtools.pattern.miner; 002 003import org.biopax.paxtools.pattern.Pattern; 004import org.biopax.paxtools.pattern.PatternBox; 005 006/** 007 * Miner for the chemical-affects-protein pattern. 008 * @author Ozgun Babur 009 */ 010public class ChemicalAffectsThroughBindingMiner extends AbstractSIFMiner 011{ 012 /** 013 * Constructor that sets name and description. 014 */ 015 public ChemicalAffectsThroughBindingMiner() 016 { 017 super(SIFEnum.CHEMICAL_AFFECTS, "-through-binding", "In this case the chemical appears in" + 018 " the same complex with the protein."); 019 } 020 021 /** 022 * Constructs the pattern. 023 * @return pattern 024 */ 025 @Override 026 public Pattern constructPattern() 027 { 028 return PatternBox.chemicalAffectsProteinThroughBinding(blacklist); 029 } 030 031 @Override 032 public String getSourceLabel() 033 { 034 return "SMR"; 035 } 036 037 @Override 038 public String getTargetLabel() 039 { 040 return "ER"; 041 } 042 043 @Override 044 public String[] getMediatorLabels() 045 { 046 return new String[]{"Complex"}; 047 } 048 049 @Override 050 public String[] getSourcePELabels() 051 { 052 return new String[]{"SPE1", "PE1", "Complex"}; 053 } 054 055 @Override 056 public String[] getTargetPELabels() 057 { 058 return new String[]{"SPE2", "PE2", "Complex"}; 059 } 060}