sbrt.shell.proc.fba
Class BiggSbmlReader

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

public class BiggSbmlReader
extends java.lang.Object

This class is used to read SBML files downloaded directly from the BiGG Database.

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

Constructor Summary
BiggSbmlReader(java.lang.String sbmlFileName)
          Constructs a new SBML file reader.
 
Method Summary
 void writeFluxBounds(java.lang.String fluxBoundsFileName)
          Writes the flux bounds contained in the SBML file to a file with the provided name.
 void writeFluxVector(java.lang.String fluxVectorFileName)
          Writes the flux vector contained in the SBML file to a file with the provided name.
 void writeGenes(java.lang.String geneFileName)
          Writes the genes contained in the SBML file to a file with the provided name.
 void writeRxns(java.lang.String rxnFileName)
          Writes the reactions contained in the SBML file to a file with the provided name.
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

BiggSbmlReader

public BiggSbmlReader(java.lang.String sbmlFileName)
Constructs a new SBML file reader.

Parameters:
sbmlFileName - the canonical name of the SBML file to be read.
See Also:
AbstractSbrtFile.getCanonicalName(String)
Method Detail

writeRxns

public void writeRxns(java.lang.String rxnFileName)
Writes the reactions contained in the SBML file to a file with the provided name.

Parameters:
rxnFileName - the name of the file to generated.

writeGenes

public void writeGenes(java.lang.String geneFileName)
Writes the genes contained in the SBML file to a file with the provided name.

Parameters:
geneFileName - the name of the file to generated.

writeFluxVector

public void writeFluxVector(java.lang.String fluxVectorFileName)
Writes the flux vector contained in the SBML file to a file with the provided name.

Parameters:
fluxVectorFileName - the name of the file to generated.

writeFluxBounds

public void writeFluxBounds(java.lang.String fluxBoundsFileName)
Writes the flux bounds contained in the SBML file to a file with the provided name.

Parameters:
fluxBoundsFileName - the name of the file to generated.