public class SimpleInteractionConverter extends Object
Modifier and Type | Field and Description |
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static String |
REDUCE_COMPLEXES
Deprecated.
Option to reduce complexes or use them as they are in interactions.
|
static String |
REDUCE_GENERICS
Deprecated.
Option to reduce complexes or use them as they are in interactions.
|
Constructor and Description |
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SimpleInteractionConverter(InteractionRule... rules)
Deprecated.
Constructor with the mining rules to use.
|
SimpleInteractionConverter(Map options,
InteractionRule... rules)
Deprecated.
Constructor with mining rules and options.
|
SimpleInteractionConverter(Map options,
Set<String> blackList,
InteractionRule... rules)
Deprecated.
Constructor with mining rules, options, and black list.
|
Modifier and Type | Method and Description |
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static List<InteractionRule> |
getRules(BioPAXLevel level)
Deprecated.
Gets all available interaction rules for the given level.
|
Set<SimpleInteraction> |
inferInteractions(Model model)
Deprecated.
Infers simple interactions from the interactions found in the model for every
interaction rule given; and returns this inferred simple interactions.
|
protected void |
removeInteractionsWithBlackListMolecules(Set<SimpleInteraction> interactions,
Set<String> blackList)
Deprecated.
Filters out interactions whose source or target are in black list.
|
void |
writeInteractionsInSIF(Model model,
OutputStream out)
Deprecated.
Infers simple interactions from the model using
inferInteractions(org.biopax.paxtools.model.Model) and wrties them to an output stream. |
void |
writeInteractionsInSIFNX(Model model,
OutputStream edgeStream,
OutputStream nodeStream,
List<String> interactorPropertyPaths,
List<String> mediatorPropertyPaths,
boolean writeEntityTypes)
Deprecated.
This method outputs inferred interactions in SIF annotation extended format (Sifnx).
|
public static final String REDUCE_COMPLEXES
public static final String REDUCE_GENERICS
public SimpleInteractionConverter(InteractionRule... rules)
rules
- interaction rule set to be used in the conversionpublic SimpleInteractionConverter(Map options, InteractionRule... rules)
options
- options to be used during the conversion processrules
- interaction rule set to be used in the conversionpublic SimpleInteractionConverter(Map options, Set<String> blackList, InteractionRule... rules)
options
- options to be used during the conversion processblackList
- ids of molecules that we do not want them in SIFrules
- interaction rule set to be used in the conversionpublic Set<SimpleInteraction> inferInteractions(Model model)
model
- model from which simple interactions are going to be inferredprotected void removeInteractionsWithBlackListMolecules(Set<SimpleInteraction> interactions, Set<String> blackList)
interactions
- interactions to filterblackList
- IDs of unwanted elementspublic void writeInteractionsInSIF(Model model, OutputStream out) throws IOException
inferInteractions(org.biopax.paxtools.model.Model)
and wrties them to an output stream.model
- model from which simple interactions are going to be inferredout
- output stream to which simple interactions will be writtenIOException
- in case of problems with output.public void writeInteractionsInSIFNX(Model model, OutputStream edgeStream, OutputStream nodeStream, List<String> interactorPropertyPaths, List<String> mediatorPropertyPaths, boolean writeEntityTypes) throws IOException
model
- model to convertedgeStream
- output stream for interactions (edges)nodeStream
- output stream for nodes (second section)interactorPropertyPaths
- interactor property pathsmediatorPropertyPaths
- mediator property pathswriteEntityTypes
- whether to output participants' BioPAX typesIOException
- when there is an output stream errorpublic static List<InteractionRule> getRules(BioPAXLevel level)
level
- BioPAX levelCopyright © 2015 BioPAX. All rights reserved.