charite.christo.metannogen
Class BraceExpansion

java.lang.Object
  charite.christo.metannogen.BraceExpansion

public class BraceExpansion
extends Object

HELP Some enzymes and transport carriers are unspecific. To avoid creation of many similar datasets, WIKI:Brace_expansion can be used. Brace expansion allows to define several similar biochemical conversions within one single text string. If the reaction string entered by the curator contains curly braces then Metannogen applies Brace expansion to determine the set of reactions resulting from the dataset. The result are several biochemical reactions each having a different metabolite from the group enclosed in curly braces. The number of resulting equations is the number of metabolites within braces. If there are several groups of metabolites enclosed in braces then every i-th metabolite within each group belongs together. If the number of elements is not the same in all groups then an error message is written out. Example for transport reaction

{ Alanine Proline Glutamine }@cyto  <=> { Alanine Proline Glutamine }@mito

is expanded to

Alanine@cyto  <=> Alanine@mito
Proline@cyto  <=> Proline@mito
Glutamine@cyto  <=> Glutamine@mito

Example for transaminase reaction

{Alanine Aspartate} + Alpha-Ketoglutarate   <=> { Pyruvate Oxalacetate} + Glutamate

is expanded to

Alanine   + Alpha-Ketoglutarate   <=>  Pyruvate    + Glutamate
Aspartate + Alpha-Ketoglutarate   <=>  Oxalacetate + Glutamate

If the second parenthetical group is identical to the first one as in the first example, then it can be abbreviated by "{}". There must not be space between both braces:

{ Alanine Proline Glutamine }@cyto  <=> {}@mito

Advanced: Double brace expansion: A second independent group of metabolites can be included in square brackets. The number of resulting reactions corresponds to the WIKI:Cartesian_product of the two sets.

Constructor Summary

BraceExpansion()

Method Summary

static byte[][]	expandReaction(byte[] T, List<String[]> returnID) Fro each element in braces a separate biochemical reaction is formed.
static void	main(String[] argv)

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

BraceExpansion

public BraceExpansion()

Method Detail

main

public static void main(String[] argv)
                 throws Exception

Throws:

Exception

expandReaction

public static byte[][] expandReaction(byte[] T,
                                      List<String[]> returnID)

Fro each element in braces a separate biochemical reaction is formed. First expand element list in curly brace than in square bracket. The element in braces is returned in the List.