fr.umlv.gramofone.proteins
Class Homologies

java.lang.Object
  extended by fr.umlv.gramofone.proteins.Homologies

public class Homologies
extends java.lang.Object

Manage homologies of proteins

Author:
fsikora

Constructor Summary
Homologies(CyNetwork network, MyPattern pattern, GMTask task)
          Compute homologies between proteins Retrieve fasta from internet if no fasta file given
 
Method Summary
 java.util.Set<java.lang.String> computePatternProteinWithoutHomologs(java.util.Set<java.lang.String> set)
          Return the set of pattern proteins without homologous proteins in the network
 double h(java.lang.String n, java.lang.String q)
          get the hhomologie between the network node n and the query node q
 boolean multiH(java.lang.String n, java.util.Set<java.lang.String> qs)
          Homologie for multiset
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

Homologies

public Homologies(CyNetwork network,
                  MyPattern pattern,
                  GMTask task)
Compute homologies between proteins Retrieve fasta from internet if no fasta file given

Parameters:
network -
pattern -
task -
Method Detail

h

public double h(java.lang.String n,
                java.lang.String q)
get the hhomologie between the network node n and the query node q

Parameters:
n - a network node
q - a query node
Returns:
the homologie (or Double.MIN_VALUE if they are not homologous)

multiH

public boolean multiH(java.lang.String n,
                      java.util.Set<java.lang.String> qs)
Homologie for multiset

Parameters:
n -
qs -
Returns:

computePatternProteinWithoutHomologs

public java.util.Set<java.lang.String> computePatternProteinWithoutHomologs(java.util.Set<java.lang.String> set)
Return the set of pattern proteins without homologous proteins in the network

Parameters:
set -
Returns: