nct.networkblast
Class NetworkBlast
java.lang.Object
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.
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 |
options
protected static org.apache.commons.cli.Options options
VERSION
public static java.lang.String VERSION
FILEOUTPUT
public static boolean FILEOUTPUT
SILENT
public static boolean SILENT
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
defaultPathSize
public static int defaultPathSize
logLevel
public static java.util.logging.Level logLevel
expectation
protected double expectation
epsilon
protected double epsilon
numPathsPerNode
protected int numPathsPerNode
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
networkBlastRecord
protected static java.lang.StringBuffer networkBlastRecord
lineSep
protected static java.lang.String lineSep
NetworkBlast
public NetworkBlast(java.lang.String[] args)
- This is the main class that initializes and executes everything.
- Parameters:
args
- Command line args.
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.