Package org.biopax.paxtools.pattern.miner

Class SIFInteraction

java.lang.Object
org.biopax.paxtools.pattern.miner.SIFInteraction
All Implemented Interfaces:
Comparable
public class SIFInteraction extends Object implements Comparable
Author:
Ozgun Babur

  • Field Details

  • Constructor Details

  • Method Details

    • hasIDs

      public boolean hasIDs()

    • hashCode

      public int hashCode()
      Overrides:
      hashCode in class Object

    • equals

      public boolean equals(Object obj)
      Overrides:
      equals in class Object

    • compareTo

      public int compareTo(Object o)
      Specified by:
      compareTo in interface Comparable

    • mergeWith

      public void mergeWith(SIFInteraction equivalent)
      Merges publications of the parameter equivalent sif with this one.
      Parameters:
      equivalent - the equivalent sif interaction to get its publications.

    • toString

      public String toString()
      Overrides:
      toString in class Object

    • getMediatorIDs

      public List<String> getMediatorIDs()
      Collects IDs of mediators.
      Returns:
      mediator IDs

    • getMediatorsInString

      public String getMediatorsInString()
      Gets the mediator IDs in a String with a space between each ID.
      Returns:
      mediator IDs joined with spaces.

    • getPublicationIDs

      public List<String> getPublicationIDs(boolean pubmed)
      Collects Pubmed or PMC ids
      Returns:
      publication IDs

    • getPathways

      public Set<Pathway> getPathways()
      Collects Pathway objects that the Interactions among the mediators are members.
      Returns:
      related pathways

    • getPathwayNames

      public List<String> getPathwayNames()
      Collects the names of the related pathways.
      Returns:
      pathway names

    • getPathwayUris

      public List<String> getPathwayUris()
      Collects the related pathway URIs.
      Returns:
      URIs

    • getDataSources

      public Set<String> getDataSources()
      Collects data source names (Provenance display names) of mediators.
      Returns:
      related data sources

    • getCellularLocationsOfTarget

      public Set<String> getCellularLocationsOfTarget()
      Collects cellular location terms of target objects.
      Returns:
      cellular locations

    • getCellularLocationsOfSource

      public Set<String> getCellularLocationsOfSource()
      Collects cellular location terms of source objects.
      Returns:
      cellular locations

    • getMediatorComments

      public Set<String> getMediatorComments()
      Collects comments strings of mediator objects.
      Returns:
      comments

    • getSortedGeneNames

      public static List<String> getSortedGeneNames(Collection<SIFInteraction> sifInts, SIFType... type)
      Collects and sorts sourceID and targetID of the given collection of sif interactions.
      Parameters:
      sifInts - interactions to consider
      type - types of interest, all types accepted if empty
      Returns:
      sorted source and target IDS

    • convertToAdjacencyMatrix

      public static boolean[][] convertToAdjacencyMatrix(Collection<SIFInteraction> sifInts, SIFType... type)
      Converts the given collection of interactions into an adjacency matrix.
      Parameters:
      sifInts - interactions to consider
      type - types of interest, all types accepted if empty
      Returns:
      the sif network as adjacency matrix