sbrt.shell.proc.fba
Class MetatoolOutputReader

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

public class MetatoolOutputReader
extends java.lang.Object

This class is used to parse Metatool output files for the purpose of creating SBRT compliant files.

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

Constructor Summary
MetatoolOutputReader()
          Creates a new Metatool output file reader.
 
Method Summary
 DoubleMatrix<java.lang.String,java.lang.String> getElementaryModes(InputFile<java.lang.String> file, java.util.List<java.lang.String> orderedRxnNames)
          Returns the elementary mode matrix contained in the provided Metatool output file.
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

MetatoolOutputReader

public MetatoolOutputReader()
Creates a new Metatool output file reader.

Method Detail

getElementaryModes

public DoubleMatrix<java.lang.String,java.lang.String> getElementaryModes(InputFile<java.lang.String> file,
                                                                          java.util.List<java.lang.String> orderedRxnNames)
Returns the elementary mode matrix contained in the provided Metatool output file.

Parameters:
file - a file produced by Metatool.
orderedRxnNames - the reactions corresponding to each matrix column.
Returns:
the elementary mode matrix contained in the provided Metatool output file.