sbrt.shell.proc.fba
Class PalssonSbmlTranslater

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

public class PalssonSbmlTranslater
extends java.lang.Object

This class is used to translate SBML files from Palsson's website 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
PalssonSbmlTranslater()
          Constructs a new SBML translater.
 
Method Summary
 void translate(java.lang.String sbmlFileName, java.lang.String rxnFileName, java.lang.String geneFileName, java.lang.String proteinFileName, java.io.PrintWriter out)
          Translates an SBML file into an FBA Reaction File and two FBA Catalyst Files.
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

PalssonSbmlTranslater

public PalssonSbmlTranslater()
Constructs a new SBML translater.

Method Detail

translate

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

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.
proteinFileName - the desired name of the FBA Catalyst File to which proteins will be written.
out - the print writer to which descriptive messages will be written.