sbrt.shell.proc.fba
Class SimpleRxnFileReader

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

public class SimpleRxnFileReader
extends java.lang.Object

This class is used to translate simple reaction files from, say, spreadsheets into FBA Reaction Files.

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

Constructor Summary
SimpleRxnFileReader()
          Constructs a new simple reaction file reader.
 
Method Summary
 IrrevRxnFormatV2 getInputIrrevRxnFormat()
          Returns the parser used for irreversible reactions in the provided input file.
 RevRxnFormatV2 getInputRevRxnFormat()
          Returns the parser used for reversible reactions in the provided input file.
 EqualsMapEntryFormatV1<java.lang.String,java.lang.String> getLineFormat()
          Returns the format used for individual lines in the input and output files.
 RxnFormatV1 getOutputRxnFormat()
          Returns the formatter used for writing reactions to the output file.
 void translate(java.lang.String simpleRxnFileName, java.lang.String outputFileName)
          Translates a simple reaction file into an FBA Reaction File.
 void translate(java.lang.String simpleRxnFileName, java.lang.String outputFileName, java.io.PrintWriter out)
          Translates a simple reaction file into an FBA Reaction File.
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

SimpleRxnFileReader

public SimpleRxnFileReader()
Constructs a new simple reaction file reader.

Method Detail

getInputRevRxnFormat

public RevRxnFormatV2 getInputRevRxnFormat()
Returns the parser used for reversible reactions in the provided input file.

Returns:
the parser used for reversible reactions in the provided input file.

getInputIrrevRxnFormat

public IrrevRxnFormatV2 getInputIrrevRxnFormat()
Returns the parser used for irreversible reactions in the provided input file.

Returns:
the parser used for irreversible reactions in the provided input file.

getOutputRxnFormat

public RxnFormatV1 getOutputRxnFormat()
Returns the formatter used for writing reactions to the output file.

Returns:
the formatter used for writing reactions to the output file.

getLineFormat

public EqualsMapEntryFormatV1<java.lang.String,java.lang.String> getLineFormat()
Returns the format used for individual lines in the input and output files.

Returns:
the format used for individual lines in the input and output files.

translate

public void translate(java.lang.String simpleRxnFileName,
                      java.lang.String outputFileName)
Translates a simple reaction file into an FBA Reaction File.

Parameters:
simpleRxnFileName - the name of the simple reaction file.
outputFileName - the desired name of the FBA Reaction File.

translate

public void translate(java.lang.String simpleRxnFileName,
                      java.lang.String outputFileName,
                      java.io.PrintWriter out)
Translates a simple reaction file into an FBA Reaction File.

Parameters:
simpleRxnFileName - the name of the simple reaction file.
outputFileName - the desired name of the FBA Reaction File.
out - the print writer to which descriptive messages will be written.