public class SIFInteraction extends Object implements Comparable
Modifier and Type | Field and Description |
---|---|
Set<BioPAXElement> |
mediators |
Set<BioPAXElement> |
sourceERs |
String |
sourceID |
Set<BioPAXElement> |
sourcePEs |
Set<BioPAXElement> |
targetERs |
String |
targetID |
Set<BioPAXElement> |
targetPEs |
SIFType |
type |
Constructor and Description |
---|
SIFInteraction(String sourceID,
String targetID,
BioPAXElement sourceER,
BioPAXElement targetER,
SIFType type,
Set<BioPAXElement> mediators,
Set<BioPAXElement> sourcePEs,
Set<BioPAXElement> targetPEs) |
Modifier and Type | Method and Description |
---|---|
int |
compareTo(Object o) |
static boolean[][] |
convertToAdjacencyMatrix(Collection<SIFInteraction> sifInts,
SIFType... type)
Converts the given collection of interactions into an adjacency matrix.
|
boolean |
equals(Object obj) |
Set<String> |
getCellularLocationsOfSource()
Collects cellular location terms of source objects.
|
Set<String> |
getCellularLocationsOfTarget()
Collects cellular location terms of target objects.
|
Set<String> |
getDataSources()
Collects data source names (Provenance display names) of mediators.
|
List<String> |
getMediatorIDs()
Collects IDs of mediators.
|
String |
getMediatorsInString()
Gets the mediator IDs in a String with a space between each ID.
|
List<String> |
getPathwayNames()
Collects the names of the related pathways.
|
Set<Pathway> |
getPathways()
Collects Pathway objects that the Interactions among the mediators are members.
|
List<String> |
getPubmedIDs()
Collects PMIDs from mediators.
|
static List<String> |
getSortedGeneNames(Collection<SIFInteraction> sifInts,
SIFType... type)
Collects and sorts sourceID and targetID of the given collection of sif interactions.
|
int |
hashCode() |
boolean |
hasIDs() |
void |
mergeWith(SIFInteraction equivalent)
Merges publications of the parameter equivalent sif with this one.
|
String |
toString() |
String |
toString(boolean withMediators) |
public Set<BioPAXElement> sourceERs
public Set<BioPAXElement> targetERs
public Set<BioPAXElement> sourcePEs
public Set<BioPAXElement> targetPEs
public Set<BioPAXElement> mediators
public SIFInteraction(String sourceID, String targetID, BioPAXElement sourceER, BioPAXElement targetER, SIFType type, Set<BioPAXElement> mediators, Set<BioPAXElement> sourcePEs, Set<BioPAXElement> targetPEs)
public boolean hasIDs()
public int compareTo(Object o)
compareTo
in interface Comparable
public void mergeWith(SIFInteraction equivalent)
equivalent
- the equivalent sif interaction to get its publications.public List<String> getMediatorIDs()
public String getMediatorsInString()
public List<String> getPubmedIDs()
public Set<Pathway> getPathways()
public List<String> getPathwayNames()
public Set<String> getDataSources()
public Set<String> getCellularLocationsOfTarget()
public Set<String> getCellularLocationsOfSource()
public static List<String> getSortedGeneNames(Collection<SIFInteraction> sifInts, SIFType... type)
sifInts
- interactions to considertype
- types of interest, all types accepted if emptypublic static boolean[][] convertToAdjacencyMatrix(Collection<SIFInteraction> sifInts, SIFType... type)
sifInts
- interactions to considertype
- types of interest, all types accepted if emptyCopyright © 2015 BioPAX. All rights reserved.