main
Class FunSiP

java.lang.Object
  extended by main.FunSiP
All Implemented Interfaces:
java.lang.Runnable

public class FunSiP
extends java.lang.Object
implements java.lang.Runnable

This class is a Java implementation of the splicemachine code, used for splice site prediction in the annotation pipeline. The original code was written in C, but we thought it might be a good opportunity to re-implement the code in Java, so it can be used with other classifiers implemented in (among others) the WEKA machine learning library. The original SpliceMachine was written by Dr. Sven Degroeve The new SPR (formerly known as JSpliceMachine) was written by Michiel Van Bel We do not really think that it is necessary to make certain methods private or protected, since this application is not really to be used as a library type. Incorrect use of methods can however lead to inconsistency, since there are dependencies on the local class data.


Field Summary
static java.lang.String VERSION
          Version of the program.
 
Constructor Summary
FunSiP(java.lang.String[] args)
          The main launcher object for the project.
 
Method Summary
 org.apache.log4j.Logger getLogger()
           
static void main(java.lang.String[] args)
          Main method for FunSiP.
 void run()
          Method necessary to launch FunSiP as a different thread.
 
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

VERSION

public static final java.lang.String VERSION
Version of the program.

See Also:
Constant Field Values
Constructor Detail

FunSiP

public FunSiP(java.lang.String[] args)
The main launcher object for the project. This object just acts as an initializer for basic components. It is assumed that there is at least one commandline parameter (containing the name of the configuration file).

Parameters:
args - Array with commandline parameters.
Method Detail

main

public static void main(java.lang.String[] args)
Main method for FunSiP.

Parameters:
args - Possible commandline parameters (at least one : the name/location of the configuration file).

run

public void run()
Method necessary to launch FunSiP as a different thread. Implements the run-method from the Runnable-interface. This method calls the configuration file parser, and then launches the workflow that is built from this configuration file.

Specified by:
run in interface java.lang.Runnable

getLogger

public org.apache.log4j.Logger getLogger()
Returns:
The logging object that is used by this instance of FunSiP.