sbrt.shell.proc.fba
Class BiggSbmlTranslater

java.lang.Object
  extended by sbrt.shell.proc.fba.BiggSbmlTranslater

public class BiggSbmlTranslater
extends java.lang.Object

This class is used to translate SBML files from the BiGG Database into the Systems Biology Research Tool's FBA Reaction Files and FBA Catalyst Files.

Author:
This class was written and documented by Jeremiah Wright while in the Wagner lab.

Constructor Summary
BiggSbmlTranslater()
          Constructs a new SBML translater.
 
Method Summary
 void translate(java.lang.String sbmlFileName, java.lang.String rxnFileName, java.lang.String geneFileName, java.io.PrintWriter out)
          Translates an SBML file into an FBA Reaction File and an FBA Catalyst File.
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

BiggSbmlTranslater

public BiggSbmlTranslater()
Constructs a new SBML translater.

Method Detail

translate

public void translate(java.lang.String sbmlFileName,
                      java.lang.String rxnFileName,
                      java.lang.String geneFileName,
                      java.io.PrintWriter out)
Translates an SBML file into an FBA Reaction File and an FBA Catalyst File.

Parameters:
sbmlFileName - the name of the SBML file.
rxnFileName - the desired name of the FBA Reaction File.
geneFileName - the desired name of the FBA Catalyst File to which genes will be written.
out - the print writer to which descriptive messages will be written.