nct.service.homology.sif
Class SIFHomologyReader

java.lang.Object
  extended by nct.service.homology.sif.SIFHomologyReader
All Implemented Interfaces:
HomologyModel

public class SIFHomologyReader
extends java.lang.Object
implements HomologyModel

A class that implements the HomologyModel interface by reading a SIF file that contains nodes from two separate graphs. The format of the file is: "nodeA expectationValue nodeB" where nodeA and nodeB are from separate graphs.


Field Summary
protected  java.lang.String sifFile
          The file that contains the blast output to be parsed.
 
Constructor Summary
SIFHomologyReader(java.lang.String sifFile)
          Constructor.
 
Method Summary
 java.util.Map<java.lang.String,java.util.Map<java.lang.String,java.lang.Double>> expectationValues(SequenceGraph<java.lang.String,java.lang.Double> sg1, SequenceGraph<java.lang.String,java.lang.Double> sg2)
          Returns a map of expectation values between nodes of the specified graphs.
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

sifFile

protected java.lang.String sifFile
The file that contains the blast output to be parsed.

Constructor Detail

SIFHomologyReader

public SIFHomologyReader(java.lang.String sifFile)
Constructor.

Parameters:
sifFile - The SIF file used to specify the homology values.
Method Detail

expectationValues

public java.util.Map<java.lang.String,java.util.Map<java.lang.String,java.lang.Double>> expectationValues(SequenceGraph<java.lang.String,java.lang.Double> sg1,
                                                                                                          SequenceGraph<java.lang.String,java.lang.Double> sg2)
Returns a map of expectation values between nodes of the specified graphs.

Specified by:
expectationValues in interface HomologyModel
Parameters:
sg1 - The first graph containing nodes expected to be found in the SIF file.
sg2 - The second graph containing nodes expected to be found in the SIF file.
Returns:
A map of expectation values between nodes.