nct.networkblast
Class NetworkBlast

java.lang.Object
  extended by nct.networkblast.NetworkBlast

public class NetworkBlast
extends java.lang.Object

The main program (NetworkBlast.java) will create all the objects needed to run the NetworkBlast algorithm.


Field Summary
protected  double backgroundProb
           
static double backgroundProbDefault
           
protected  java.lang.String compatFile
           
static int complexMaxSize
           
static int complexMinSeedSize
           
protected  double dupeThreshold
           
static double dupeThresholdDefault
           
protected  double expectation
           
static double expectationDefault
           
static boolean filterDuplicateComplexNodes
           
static boolean filterDuplicatePathNodes
           
protected  java.lang.String intGraph1
           
protected  java.lang.String intGraph2
           
static java.util.logging.Level logLevel
           
static java.util.logging.Level logLevelDefault
           
protected  double modelTruth
           
static double modelTruthDefault
           
protected  int numSimulations
           
protected static org.apache.commons.cli.Options options
           
protected  java.lang.String outFile
           
static java.lang.String outFileDefault
           
static int pathSize
           
protected  java.util.Random randomNG
           
static boolean SERIALIZE
           
static int simulationsDefault
           
protected  double truthFactor
           
static double truthFactorDefault
           
static boolean useZero
           
static java.lang.String VERSION
           
 
Constructor Summary
NetworkBlast(java.lang.String[] args)
          This is the main class that initializes and executes everything.
 
Method Summary
static void main(java.lang.String[] args)
          Main.
static void setUpLogging(java.util.logging.Level xlogLevel)
          Initializes the logger object according to user's wishes.
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

options

protected static org.apache.commons.cli.Options options

VERSION

public static java.lang.String VERSION

SERIALIZE

public static boolean SERIALIZE

useZero

public static boolean useZero

filterDuplicateComplexNodes

public static boolean filterDuplicateComplexNodes

filterDuplicatePathNodes

public static boolean filterDuplicatePathNodes

truthFactorDefault

public static double truthFactorDefault

modelTruthDefault

public static double modelTruthDefault

expectationDefault

public static double expectationDefault

backgroundProbDefault

public static double backgroundProbDefault

dupeThresholdDefault

public static double dupeThresholdDefault

outFileDefault

public static java.lang.String outFileDefault

logLevelDefault

public static java.util.logging.Level logLevelDefault

simulationsDefault

public static int simulationsDefault

complexMinSeedSize

public static int complexMinSeedSize

complexMaxSize

public static int complexMaxSize

pathSize

public static int pathSize

logLevel

public static java.util.logging.Level logLevel

expectation

protected double expectation

backgroundProb

protected double backgroundProb

truthFactor

protected double truthFactor

modelTruth

protected double modelTruth

dupeThreshold

protected double dupeThreshold

numSimulations

protected int numSimulations

randomNG

protected java.util.Random randomNG

compatFile

protected java.lang.String compatFile

intGraph1

protected java.lang.String intGraph1

intGraph2

protected java.lang.String intGraph2

outFile

protected java.lang.String outFile
Constructor Detail

NetworkBlast

public NetworkBlast(java.lang.String[] args)
This is the main class that initializes and executes everything.

Parameters:
args - Command line args.
Method Detail

main

public static void main(java.lang.String[] args)
Main. Duh.


setUpLogging

public static void setUpLogging(java.util.logging.Level xlogLevel)
Initializes the logger object according to user's wishes.