nct.service.homology
Class SIFHomologyReader
java.lang.Object
nct.service.homology.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. |
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 |
sifFile
protected java.lang.String sifFile
- The file that contains the blast output to be parsed.
SIFHomologyReader
public SIFHomologyReader(java.lang.String sifFile)
- Constructor.
- Parameters:
sifFile
- The SIF file used to specify the homology values.
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.