@Test public void testInSameComplex() throws Exception { List<Match> list = Searcher.search(model_P53.getByID("http: PatternBox.inSameComplex()); Assert.assertTrue(list.size() == 1); }
public static Pattern inSameComplex() { Pattern p = new Pattern(EntityReference.class, "first ER"); p.add(erToPE(), "first ER", "first simple PE"); p.add(linkToComplex(), "first simple PE", "Complex"); p.add(new Type(Complex.class), "Complex"); p.add(linkToSpecific(), "Complex", "second simple PE"); p.add(equal(false), "first simple PE", "second simple PE"); p.add(new PEChainsIntersect(false, true), "first simple PE", "Complex", "second simple PE", "Complex"); p.add(peToER(), "second simple PE", "second ER"); p.add(equal(false), "first ER", "second ER"); return p; }
PatternBox { public static Pattern inSameComplex() { Pattern p = new Pattern(EntityReference.class, "first ER"); p.add(erToPE(), "first ER", "first simple PE"); p.add(linkToComplex(), "first simple PE", "Complex"); p.add(new Type(Complex.class), "Complex"); p.add(linkToSpecific(), "Complex", "second simple PE"); p.add(equal(false), "first simple PE", "second simple PE"); p.add(new PEChainsIntersect(false, true), "first simple PE", "Complex", "second simple PE", "Complex"); p.add(peToER(), "second simple PE", "second ER"); p.add(equal(false), "first ER", "second ER"); return p; } }
PatternBox { public static Pattern inSameComplex() { Pattern p = new Pattern(EntityReference.class, "first ER"); p.add(erToPE(), "first ER", "first simple PE"); p.add(linkToComplex(), "first simple PE", "Complex"); p.add(new Type(Complex.class), "Complex"); p.add(linkToSpecific(), "Complex", "second simple PE"); p.add(equal(false), "first simple PE", "second simple PE"); p.add(new PEChainsIntersect(false, true), "first simple PE", "Complex", "second simple PE", "Complex"); p.add(peToER(), "second simple PE", "second ER"); p.add(equal(false), "first ER", "second ER"); return p; }  }
PatternBox { public static Pattern inSameComplex() { Pattern p = new Pattern(EntityReference.class, "first ER"); p.add(erToPE(), "first ER", "first simple PE"); p.add(linkToComplex(), "first simple PE", "Complex"); p.add(new Type(Complex.class), "Complex"); p.add(linkToSpecific(), "Complex", "second simple PE"); p.add(equal(false), "first simple PE", "second simple PE"); p.add(new PEChainsIntersect(false, true), "first simple PE", "Complex", "second simple PE", "Complex"); p.add(peToER(), "second simple PE", "second ER"); p.add(equal(false), "first ER", "second ER"); return p; }  static Pattern controlsStateChange(); static Pattern controlsTransport(); static Pattern controlsTransportOfChemical(Blacklist blacklist); static Pattern controlsStateChangeBothControlAndPart(); static Pattern controlsStateChangeButIsParticipant(); static Pattern stateChange(Pattern p, String ctrlLabel); static Pattern controlsStateChangeThroughControllerSmallMolecule(Blacklist blacklist); static Pattern controlsStateChangeThroughBindingSmallMolecule(Blacklist blacklist); static Pattern controlsStateChangeThroughDegradation(); static Pattern controlsPhosphorylation(); static Pattern controlsMetabolicCatalysis(Blacklist blacklist, boolean consumption); static Pattern catalysisPrecedes(Blacklist blacklist); static Pattern controlsExpressionWithTemplateReac(); static Pattern controlsExpressionWithConversion(); static Pattern controlsDegradationIndirectly(); static Pattern inComplexWith(); static Pattern chemicalAffectsProteinThroughBinding(Blacklist blacklist); static Pattern chemicalAffectsProteinThroughControl(); static Pattern neighborOf(); static Pattern reactsWith(Blacklist blacklist); static Pattern usedToProduce(Blacklist blacklist); static Pattern molecularInteraction(); static Pattern relatedProteinRefOfInter(Class<? extends Interaction>... seedType); static Pattern inSameComplex(); static Pattern inSameActiveComplex(); static Pattern inSameComplexHavingTransActivity(); static Pattern inSameComplexEffectingConversion(); static Pattern peInOut(); static Pattern modifiedPESimple(); static Pattern actChange(boolean activating,
		Map<EntityReference, Set<ModificationFeature>> activityFeat,
		Map<EntityReference, Set<ModificationFeature>> inactivityFeat); static Pattern modifierConv(); static Pattern hasNonSelfEffect(); static Pattern bindsTo(); }
PatternBox { public static Pattern inSameComplex() { Pattern p = new Pattern(EntityReference.class, "first ER"); p.add(erToPE(), "first ER", "first simple PE"); p.add(linkToComplex(), "first simple PE", "Complex"); p.add(new Type(Complex.class), "Complex"); p.add(linkToSpecific(), "Complex", "second simple PE"); p.add(equal(false), "first simple PE", "second simple PE"); p.add(new PEChainsIntersect(false, true), "first simple PE", "Complex", "second simple PE", "Complex"); p.add(peToER(), "second simple PE", "second ER"); p.add(equal(false), "first ER", "second ER"); return p; }  static Pattern controlsStateChange(); static Pattern controlsTransport(); static Pattern controlsTransportOfChemical(Blacklist blacklist); static Pattern controlsStateChangeBothControlAndPart(); static Pattern controlsStateChangeButIsParticipant(); static Pattern stateChange(Pattern p, String ctrlLabel); static Pattern controlsStateChangeThroughControllerSmallMolecule(Blacklist blacklist); static Pattern controlsStateChangeThroughBindingSmallMolecule(Blacklist blacklist); static Pattern controlsStateChangeThroughDegradation(); static Pattern controlsPhosphorylation(); static Pattern controlsMetabolicCatalysis(Blacklist blacklist, boolean consumption); static Pattern catalysisPrecedes(Blacklist blacklist); static Pattern controlsExpressionWithTemplateReac(); static Pattern controlsExpressionWithConversion(); static Pattern controlsDegradationIndirectly(); static Pattern inComplexWith(); static Pattern chemicalAffectsProteinThroughBinding(Blacklist blacklist); static Pattern chemicalAffectsProteinThroughControl(); static Pattern neighborOf(); static Pattern reactsWith(Blacklist blacklist); static Pattern usedToProduce(Blacklist blacklist); static Pattern molecularInteraction(); static Pattern relatedProteinRefOfInter(Class<? extends Interaction>... seedType); static Pattern inSameComplex(); static Pattern inSameActiveComplex(); static Pattern inSameComplexHavingTransActivity(); static Pattern inSameComplexEffectingConversion(); static Pattern peInOut(); static Pattern modifiedPESimple(); static Pattern actChange(boolean activating,
		Map<EntityReference, Set<ModificationFeature>> activityFeat,
		Map<EntityReference, Set<ModificationFeature>> inactivityFeat); static Pattern modifierConv(); static Pattern hasNonSelfEffect(); static Pattern bindsTo();  }