@Test public void testControlsStateChange() throws Exception { Map<BioPAXElement,List<Match>> map = Searcher.search( model_P53, PatternBox.controlsStateChange()); Assert.assertTrue(map.size() > 0); }
public static Pattern controlsStateChange() { Pattern p = new Pattern(SequenceEntityReference.class, "controller ER"); p.add(linkedER(true), "controller ER", "generic controller ER"); p.add(erToPE(), "generic controller ER", "controller simple PE"); p.add(linkToComplex(), "controller simple PE", "controller PE"); p.add(peToControl(), "controller PE", "Control"); p.add(controlToConv(), "Control", "Conversion"); p.add(new NOT(participantER()), "Conversion", "controller ER"); p.add(new Participant(RelType.INPUT, true), "Control", "Conversion", "input PE"); p.add(new NOT(new ConversionSide(ConversionSide.Type.OTHER_SIDE)), "input PE", "Conversion", "input PE"); p.add(linkToSpecific(), "input PE", "input simple PE"); p.add(new Type(SequenceEntity.class), "input simple PE"); p.add(peToER(), "input simple PE", "changed generic ER"); p.add(new ConversionSide(ConversionSide.Type.OTHER_SIDE), "input PE", "Conversion", "output PE"); p.add(new NOT(new ConversionSide(ConversionSide.Type.OTHER_SIDE)), "output PE", "Conversion", "output PE"); p.add(equal(false), "input PE", "output PE"); p.add(linkToSpecific(), "output PE", "output simple PE"); p.add(peToER(), "output simple PE", "changed generic ER"); p.add(linkedER(false), "changed generic ER", "changed ER"); return p; }
PatternBox { public static Pattern controlsStateChange() { Pattern p = new Pattern(SequenceEntityReference.class, "controller ER"); p.add(linkedER(true), "controller ER", "generic controller ER"); p.add(erToPE(), "generic controller ER", "controller simple PE"); p.add(linkToComplex(), "controller simple PE", "controller PE"); p.add(peToControl(), "controller PE", "Control"); p.add(controlToConv(), "Control", "Conversion"); p.add(new NOT(participantER()), "Conversion", "controller ER"); p.add(new Participant(RelType.INPUT, true), "Control", "Conversion", "input PE"); p.add(new NOT(new ConversionSide(ConversionSide.Type.OTHER_SIDE)), "input PE", "Conversion", "input PE"); p.add(linkToSpecific(), "input PE", "input simple PE"); p.add(new Type(SequenceEntity.class), "input simple PE"); p.add(peToER(), "input simple PE", "changed generic ER"); p.add(new ConversionSide(ConversionSide.Type.OTHER_SIDE), "input PE", "Conversion", "output PE"); p.add(new NOT(new ConversionSide(ConversionSide.Type.OTHER_SIDE)), "output PE", "Conversion", "output PE"); p.add(equal(false), "input PE", "output PE"); p.add(linkToSpecific(), "output PE", "output simple PE"); p.add(peToER(), "output simple PE", "changed generic ER"); p.add(linkedER(false), "changed generic ER", "changed ER"); return p; } }
PatternBox { public static Pattern controlsStateChange() { Pattern p = new Pattern(SequenceEntityReference.class, "controller ER"); p.add(linkedER(true), "controller ER", "generic controller ER"); p.add(erToPE(), "generic controller ER", "controller simple PE"); p.add(linkToComplex(), "controller simple PE", "controller PE"); p.add(peToControl(), "controller PE", "Control"); p.add(controlToConv(), "Control", "Conversion"); p.add(new NOT(participantER()), "Conversion", "controller ER"); p.add(new Participant(RelType.INPUT, true), "Control", "Conversion", "input PE"); p.add(new NOT(new ConversionSide(ConversionSide.Type.OTHER_SIDE)), "input PE", "Conversion", "input PE"); p.add(linkToSpecific(), "input PE", "input simple PE"); p.add(new Type(SequenceEntity.class), "input simple PE"); p.add(peToER(), "input simple PE", "changed generic ER"); p.add(new ConversionSide(ConversionSide.Type.OTHER_SIDE), "input PE", "Conversion", "output PE"); p.add(new NOT(new ConversionSide(ConversionSide.Type.OTHER_SIDE)), "output PE", "Conversion", "output PE"); p.add(equal(false), "input PE", "output PE"); p.add(linkToSpecific(), "output PE", "output simple PE"); p.add(peToER(), "output simple PE", "changed generic ER"); p.add(linkedER(false), "changed generic ER", "changed ER"); return p; }  }
PatternBox { public static Pattern controlsStateChange() { Pattern p = new Pattern(SequenceEntityReference.class, "controller ER"); p.add(linkedER(true), "controller ER", "generic controller ER"); p.add(erToPE(), "generic controller ER", "controller simple PE"); p.add(linkToComplex(), "controller simple PE", "controller PE"); p.add(peToControl(), "controller PE", "Control"); p.add(controlToConv(), "Control", "Conversion"); p.add(new NOT(participantER()), "Conversion", "controller ER"); p.add(new Participant(RelType.INPUT, true), "Control", "Conversion", "input PE"); p.add(new NOT(new ConversionSide(ConversionSide.Type.OTHER_SIDE)), "input PE", "Conversion", "input PE"); p.add(linkToSpecific(), "input PE", "input simple PE"); p.add(new Type(SequenceEntity.class), "input simple PE"); p.add(peToER(), "input simple PE", "changed generic ER"); p.add(new ConversionSide(ConversionSide.Type.OTHER_SIDE), "input PE", "Conversion", "output PE"); p.add(new NOT(new ConversionSide(ConversionSide.Type.OTHER_SIDE)), "output PE", "Conversion", "output PE"); p.add(equal(false), "input PE", "output PE"); p.add(linkToSpecific(), "output PE", "output simple PE"); p.add(peToER(), "output simple PE", "changed generic ER"); p.add(linkedER(false), "changed generic ER", "changed 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 controlsStateChange() { Pattern p = new Pattern(SequenceEntityReference.class, "controller ER"); p.add(linkedER(true), "controller ER", "generic controller ER"); p.add(erToPE(), "generic controller ER", "controller simple PE"); p.add(linkToComplex(), "controller simple PE", "controller PE"); p.add(peToControl(), "controller PE", "Control"); p.add(controlToConv(), "Control", "Conversion"); p.add(new NOT(participantER()), "Conversion", "controller ER"); p.add(new Participant(RelType.INPUT, true), "Control", "Conversion", "input PE"); p.add(new NOT(new ConversionSide(ConversionSide.Type.OTHER_SIDE)), "input PE", "Conversion", "input PE"); p.add(linkToSpecific(), "input PE", "input simple PE"); p.add(new Type(SequenceEntity.class), "input simple PE"); p.add(peToER(), "input simple PE", "changed generic ER"); p.add(new ConversionSide(ConversionSide.Type.OTHER_SIDE), "input PE", "Conversion", "output PE"); p.add(new NOT(new ConversionSide(ConversionSide.Type.OTHER_SIDE)), "output PE", "Conversion", "output PE"); p.add(equal(false), "input PE", "output PE"); p.add(linkToSpecific(), "output PE", "output simple PE"); p.add(peToER(), "output simple PE", "changed generic ER"); p.add(linkedER(false), "changed generic ER", "changed 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();  }