sbrt.shell.proc.fba
Class PalssonSbmlReader

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

public class PalssonSbmlReader
extends java.lang.Object

This class is used to read SBML files downloaded directly from Dr. Bernhard Palsson's website.

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

Field Summary
static java.lang.String NOT_PROVIDED
          The string used to denote that a particular value was not provided in an SBML input file.
 
Constructor Summary
PalssonSbmlReader(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 writeProteins(java.lang.String proteinFileName)
          Writes the proteins 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
 

Field Detail

NOT_PROVIDED

public static final java.lang.String NOT_PROVIDED
The string used to denote that a particular value was not provided in an SBML input file.

See Also:
Constant Field Values
Constructor Detail

PalssonSbmlReader

public PalssonSbmlReader(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.

writeProteins

public void writeProteins(java.lang.String proteinFileName)
Writes the proteins contained in the SBML file to a file with the provided name.

Parameters:
proteinFileName - 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.