sbrt.shell.proc.fba
Class BiggBracketParserV1

java.lang.Object
  extended by sbrt.shell.proc.fba.BiggBracketParserV1

public class BiggBracketParserV1
extends java.lang.Object

This class is used to parse bracketed expressions contained in SBML files from the BiGG Database. These expressions are used to represent gene-protein-reaction associations using boolean logic. An example would be:

((b3951 and b3952) or b3114 or (b0902 and b0903)).

All provided expressions are assumed to be formatted like the above example and free of errors. If this is not the case, the results of parsing are unpredictable.

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

Constructor Summary
BiggBracketParserV1()
           
 
Method Summary
static void main(java.lang.String[] args)
          Used for testing purposes.
 Or<And<java.lang.String>> parse(java.lang.String string)
          Parses the provided BiGG style bracketed expression.
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

BiggBracketParserV1

public BiggBracketParserV1()
Method Detail

main

public static void main(java.lang.String[] args)
Used for testing purposes.

Parameters:
args - ignored

parse

public Or<And<java.lang.String>> parse(java.lang.String string)
Parses the provided BiGG style bracketed expression.

Parameters:
string - a BiGG-type bracketed expressions with parantheses used as brackets.
Returns:
the boolean rules represented by the string.