public class PatternBox extends Object
Constructor and Description |
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PatternBox() |
Modifier and Type | Method and Description |
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static Pattern |
actChange(boolean activating,
Map<EntityReference,Set<ModificationFeature>> activityFeat,
Map<EntityReference,Set<ModificationFeature>> inactivityFeat)
Pattern for the activity of an EntityReference is changed through a Conversion.
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static Pattern |
bindsTo()
Finds two Protein that appear together in a Complex.
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static Pattern |
catalysisPrecedes(Blacklist blacklist)
Pattern for detecting two EntityReferences are controlling consecutive reactions, where
output of one reaction is input to the other.
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static Pattern |
chemicalAffectsProteinThroughBinding(Blacklist blacklist)
A small molecule is in a complex with a protein.
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static Pattern |
chemicalAffectsProteinThroughControl()
A small molecule controls an interaction of which the protein is a participant.
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static Pattern |
controlsDegradationIndirectly()
Finds cases where protein A changes state of B, and B is then degraded.
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static Pattern |
controlsExpressionWithConversion()
Finds the cases where transcription relation is shown using a Conversion instead of a
TemplateReaction.
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static Pattern |
controlsExpressionWithTemplateReac()
Finds transcription factors that trans-activate or trans-inhibit an entity.
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static Pattern |
controlsMetabolicCatalysis(Blacklist blacklist,
boolean consumption)
Pattern for a Protein controlling a reaction whose participant is a small molecule.
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static Pattern |
controlsPhosphorylation() |
static Pattern |
controlsStateChange()
Pattern for a EntityReference has a member PhysicalEntity that is controlling a state change
reaction of another EntityReference.
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static Pattern |
controlsStateChangeBothControlAndPart()
Pattern for a EntityReference has a member PhysicalEntity that is controlling a state change
reaction of another EntityReference.
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static Pattern |
controlsStateChangeButIsParticipant()
Pattern for a EntityReference has a member PhysicalEntity that is controlling a state change
reaction of another EntityReference.
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static Pattern |
controlsStateChangeThroughBindingSmallMolecule(Blacklist blacklist)
Pattern for an entity is producing a small molecule, and the small molecule controls state
change of another molecule.
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static Pattern |
controlsStateChangeThroughControllerSmallMolecule(Blacklist blacklist)
Pattern for an entity is producing a small molecule, and the small molecule controls state
change of another molecule.
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static Pattern |
controlsStateChangeThroughDegradation()
Finds cases where proteins affect their degradation.
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static Pattern |
controlsTransport()
Pattern for a ProteinReference has a member PhysicalEntity that is controlling a
transportation of another ProteinReference.
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static Pattern |
controlsTransportOfChemical(Blacklist blacklist)
Pattern for a ProteinReference has a member PhysicalEntity that is controlling a reaction
that changes cellular location of a small molecule.
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static Pattern |
hasNonSelfEffect()
Pattern for detecting PhysicalEntity that controls a Conversion whose participants are not
associated with the EntityReference of the initial PhysicalEntity.
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static Pattern |
inComplexWith()
Two proteins have states that are members of the same complex.
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static Pattern |
inSameActiveComplex()
Pattern for two different EntityReference have member PhysicalEntity in the same Complex, and
the Complex has an activity.
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static Pattern |
inSameComplex()
Pattern for two different EntityReference have member PhysicalEntity in the same Complex.
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static Pattern |
inSameComplexEffectingConversion()
Pattern for two different EntityReference have member PhysicalEntity in the same Complex, and
the Complex is controlling a Conversion.
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static Pattern |
inSameComplexHavingTransActivity()
Pattern for two different EntityReference have member PhysicalEntity in the same Complex, and
the Complex has transcriptional activity.
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static Pattern |
modifiedPESimple()
Pattern for an EntityReference has distinct PhysicalEntities associated with both left and
right of a Conversion.
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static Pattern |
modifierConv()
Pattern for finding Conversions that an EntityReference is participating.
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static Pattern |
molecularInteraction()
Constructs a pattern where first and last molecules are participants of a
MolecularInteraction.
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static Pattern |
neighborOf()
Constructs a pattern where first and last proteins are related through an interaction.
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static Pattern |
peInOut() |
static Pattern |
reactsWith(Blacklist blacklist)
Constructs a pattern where first and last small molecules are substrates to the same
biochemical reaction.
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static Pattern |
relatedProteinRefOfInter(Class<? extends Interaction>... seedType)
Finds ProteinsReference related to an interaction.
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static Pattern |
stateChange(Pattern p,
String ctrlLabel)
Pattern for a Conversion has an input PhysicalEntity and another output PhysicalEntity that
belongs to the same EntityReference.
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static Pattern |
usedToProduce(Blacklist blacklist)
Constructs a pattern where first small molecule is an input a biochemical reaction that
produces the second small molecule.
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public PatternBox()
public static Pattern controlsStateChange()
public static Pattern controlsTransport()
public static Pattern controlsTransportOfChemical(Blacklist blacklist)
blacklist
- a skip-list of ubiquitous moleculespublic static Pattern controlsStateChangeBothControlAndPart()
public static Pattern controlsStateChangeButIsParticipant()
public static Pattern stateChange(Pattern p, String ctrlLabel)
p
- pattern to updatectrlLabel
- labelpublic static Pattern controlsStateChangeThroughControllerSmallMolecule(Blacklist blacklist)
blacklist
- a skip-list of ubiquitous moleculespublic static Pattern controlsStateChangeThroughBindingSmallMolecule(Blacklist blacklist)
blacklist
- a skip-list of ubiquitous moleculespublic static Pattern controlsStateChangeThroughDegradation()
public static Pattern controlsPhosphorylation()
public static Pattern controlsMetabolicCatalysis(Blacklist blacklist, boolean consumption)
blacklist
- a skip-list of ubiquitous moleculesconsumption
- true/false (TODO explain)public static Pattern catalysisPrecedes(Blacklist blacklist)
blacklist
- to detect ubiquitous small moleculespublic static Pattern controlsExpressionWithTemplateReac()
public static Pattern controlsExpressionWithConversion()
public static Pattern controlsDegradationIndirectly()
public static Pattern inComplexWith()
public static Pattern chemicalAffectsProteinThroughBinding(Blacklist blacklist)
blacklist
- a skip-list of ubiquitous moleculespublic static Pattern chemicalAffectsProteinThroughControl()
public static Pattern neighborOf()
public static Pattern reactsWith(Blacklist blacklist)
blacklist
- a skip-list of ubiquitous moleculespublic static Pattern usedToProduce(Blacklist blacklist)
blacklist
- a skip-list of ubiquitous moleculespublic static Pattern molecularInteraction()
public static Pattern relatedProteinRefOfInter(Class<? extends Interaction>... seedType)
seedType
- specific BioPAX interaction sub-types (interface classes)public static Pattern inSameComplex()
public static Pattern inSameActiveComplex()
public static Pattern inSameComplexHavingTransActivity()
public static Pattern inSameComplexEffectingConversion()
public static Pattern modifiedPESimple()
public static Pattern actChange(boolean activating, Map<EntityReference,Set<ModificationFeature>> activityFeat, Map<EntityReference,Set<ModificationFeature>> inactivityFeat)
activating
- desired changeactivityFeat
- modification features associated with activityinactivityFeat
- modification features associated with inactivitypublic static Pattern modifierConv()
public static Pattern hasNonSelfEffect()
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