Package | Description |
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org.biopax.paxtools.io.sif |
This package contains methods and algorithms for reducing BioPAX to Simple Interaction Format.
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org.biopax.paxtools.io.sif.level2 | |
org.biopax.paxtools.io.sif.level3 |
This package contains the SIF rules for BioPAX Level 3.
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Modifier and Type | Method and Description |
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static List<InteractionRule> |
SimpleInteractionConverter.getRules(BioPAXLevel level)
Deprecated.
Gets all available interaction rules for the given level.
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Constructor and Description |
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SimpleInteractionConverter(InteractionRule... rules)
Deprecated.
Constructor with the mining rules to use.
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SimpleInteractionConverter(Map options,
InteractionRule... rules)
Deprecated.
Constructor with mining rules and options.
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SimpleInteractionConverter(Map options,
Set<String> blackList,
InteractionRule... rules)
Deprecated.
Constructor with mining rules, options, and black list.
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Modifier and Type | Interface and Description |
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interface |
InteractionRuleL2
This interface defines a rule which can be run on BioPAX model L2 to derive
simple interactions.
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Modifier and Type | Class and Description |
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class |
AffectsRule
This is an experimental rule that mines ACTIVATES and INHIBITS relations between molecules.
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class |
ComponentRule
Component.InSame: A and B are components of same flattened complex structure,
A and B are simple.
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class |
ConsecutiveCatalysisRule
This class creates an interaction between two entities if they are catalyzing
consecutive conversions.
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class |
ControlRule
A controls a conversion which B is at left or right or both.
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class |
ControlsTogetherRule
Implements Co-Control rule, which means A and B have a control over the same interaction.
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class |
InteractionRuleL2Adaptor
Base class for level 2 rules.
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class |
ParticipatesRule
Finds pairs of molecules that are participants of the same interaction.
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Modifier and Type | Interface and Description |
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interface |
InteractionRuleL3
This interface defines a rule which can be run on BioPAX model L2 to derive
simple interactions.
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Modifier and Type | Class and Description |
---|---|
class |
ExpressionRule
This rule mines the transctivation and transinhibition relations between entities.
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class |
InteractionRuleL3Adaptor
Base class for level 3 interactions rules.
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Copyright © 2015 BioPAX. All rights reserved.