public class InterToPartER extends ConstraintAdapter
Modifier and Type | Class and Description |
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static class |
InterToPartER.Direction |
blacklist, size
Constructor and Description |
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InterToPartER()
Constructor without parameters.
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InterToPartER(int numOfTabooElements)
Constructor with parameters.
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InterToPartER(InterToPartER.Direction direction)
Constructor with direction.
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InterToPartER(InterToPartER.Direction direction,
int numOfTabooElements)
Constructor with parameters.
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Modifier and Type | Method and Description |
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boolean |
canGenerate()
This is a generative constraint.
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protected Collection<BioPAXElement> |
generate(Conversion conv,
InterToPartER.Direction direction,
Set<Entity> taboo)
Gets the related entity references of the given interaction,
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protected Collection<BioPAXElement> |
generate(Interaction inter,
Set<Entity> taboo)
Gets the related entity references of the given interaction.
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Collection<BioPAXElement> |
generate(Match match,
int... ind)
Iterated over non-taboo participants and collectes related ER.
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assertIndLength, convertStepDirection, findDirectionInCatalysis, findDirectionInPathways, getCatalysisDirection, getControlChain, getConvParticipants, getDirection, getDirection, getDirection, getDirection, getVariableSize, satisfies, setSize
public InterToPartER(int numOfTabooElements)
numOfTabooElements
- the number of entities to exclude from the analysispublic InterToPartER(InterToPartER.Direction direction, int numOfTabooElements)
direction
- ide(s) of an interaction to considernumOfTabooElements
- the number of entities to exclude from the analysispublic InterToPartER()
public InterToPartER(InterToPartER.Direction direction)
direction
- - side(s) of an interaction to consider;
see InterToPartER.Direction
public boolean canGenerate()
canGenerate
in interface Constraint
canGenerate
in class ConstraintAdapter
public Collection<BioPAXElement> generate(Match match, int... ind)
generate
in interface Constraint
generate
in class ConstraintAdapter
match
- current pattern matchind
- mapped indicesprotected Collection<BioPAXElement> generate(Interaction inter, Set<Entity> taboo)
inter
- interactiontaboo
- entities to ignore/skipprotected Collection<BioPAXElement> generate(Conversion conv, InterToPartER.Direction direction, Set<Entity> taboo)
conv
- conversion interactiondirection
- which side(s) participants of the conversion to considertaboo
- skip list of entitiesCopyright © 2015 BioPAX. All rights reserved.