parseMetNames.m

function [baseMetNames,compSymbols,uniqueMetNames,uniqueCompSymbols] = parseMetNames(metNames)
%parseMetNames Figure out the base metabolite names and compartments for each metabolite
%
% [baseMetNames,compSymbols,uniqueMetNames,uniqueCompSymbols] = parseMetNames(metNames)
%
%INPUT
% metNames              List of metabolite names
%
%OUTPUTS
% baseMetNames          List of met names without compartment symbol
% compSymbols           Compartment symbols for each metabolite
% uniqueMetNames        Unique metabolite names (w/o comp symbol)
% uniqueCompSymbols     Unique compartment symbols
%
% Metabolite names should describe the compartment assignment in either the
% form "metName[compName]" or "metName(compName)"
%
% Markus Herrgard 10/4/06

uniqueCompSymbols = {};
uniqueMetNames = {};
for metNo = 1:length(metNames)
    metName = metNames{metNo};
    if (~isempty(regexp(metName,'\[')))
        [tokens,tmp] = regexp(metName,'(.+)\[(.+)\]','tokens','match');
    else
        [tokens,tmp] = regexp(metName,'(.+)\((.+)\)','tokens','match');
    end
    if ~isempty(tokens)
        compSymbol = tokens{1}{2};
        baseMetName = tokens{1}{1};
    else
        compSymbol = '';
        baseMetName = metName;
    end
    compSymbols{metNo} = compSymbol;
    baseMetNames{metNo} = baseMetName;
end

% Get the list of unique compartment symbols and unique metabolite base
% names
uniqueCompSymbols = columnVector(unique(compSymbols));
uniqueMetNames = columnVector(unique(baseMetNames));

compSymbols = columnVector(compSymbols);
baseMetNames = columnVector(baseMetNames);