slib.sml.sm.core.measures.others.groupwise.indirect.experimental
Class Sim_groupwise_MAX_NORMALIZED_GOSIM

java.lang.Object
  extended by slib.sml.sm.core.measures.others.groupwise.indirect.experimental.Sim_groupwise_general_abstract
      extended by slib.sml.sm.core.measures.others.groupwise.indirect.experimental.Sim_groupwise_MAX_NORMALIZED_GOSIM
All Implemented Interfaces:
Sim_Groupwise, Sim_Groupwise_Indirect

public class Sim_groupwise_MAX_NORMALIZED_GOSIM
extends Sim_groupwise_general_abstract

 Frohlich H, Speer N, Poustka A, Beissbarth T: GOSim--an R-package for computation of information theoretic GO similarities between terms and gene products. BMC bioinformatics 2007, 8:166. Implementation as defined in equation 7 page 3/8

Author:
Sebastien Harispe

Constructor Summary
Sim_groupwise_MAX_NORMALIZED_GOSIM()
           
 
Method Summary
 double sim(double maxScore_sA_vs_sB, double maxScore_sA_vs_sA, double maxScore_sB_vs_sB)
           
 double sim(Set<org.openrdf.model.URI> setA, Set<org.openrdf.model.URI> setB, SM_Engine rc, SMconf groupwiseconf, SMconf paiwiseconf)
          Compute the similarity between the given sets of concepts considering a particular configuration.
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

Sim_groupwise_MAX_NORMALIZED_GOSIM

public Sim_groupwise_MAX_NORMALIZED_GOSIM()
Method Detail

sim

public double sim(double maxScore_sA_vs_sB,
                  double maxScore_sA_vs_sA,
                  double maxScore_sB_vs_sB)
Parameters:
maxScore_sA_vs_sB -
maxScore_sA_vs_sA -
maxScore_sB_vs_sB -
Returns:
See Also:
to compute max values

sim

public double sim(Set<org.openrdf.model.URI> setA,
                  Set<org.openrdf.model.URI> setB,
                  SM_Engine rc,
                  SMconf groupwiseconf,
                  SMconf paiwiseconf)
           throws slib.utils.ex.SLIB_Ex_Critic
Description copied from interface: Sim_Groupwise_Indirect
Compute the similarity between the given sets of concepts considering a particular configuration. Note that the specified pairwise configuration must override the pairwise configuration originally specified in the groupwise configuration (if any).

Parameters:
setA - the first set of vertices
setB - the second set of vertices
rc - the engine used to access specific information used by the measures
groupwiseconf - the groupwise configuration.
paiwiseconf - the pairwise configuration.
Returns:
the semantic similarity of the pair of groups of concepts
Throws:
slib.utils.ex.SLIB_Ex_Critic


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