function [model, removedMets, removedRxns] = removeDeadEnds(model)
% Removes all dead end metabolites and reactions from the
% model
%
% USAGE:
%
%    [model, removedMets, removedRxns] = removeDeadEnds(model)
%
% INPUT:
%     model:          COBRA model structure
%
% OUTPUTS:
%    model:          COBRA model structure w/o dead end metabolites and
%                    reactions
%    removedMets:    List of removed metabolites
%    removedRxns:    List of removed reactions
%
% .. Author: - Markus Herrgard 8/29/06

removedMets = {};
removedRxns = {};

while (1)

    deadEnd = detectDeadEnds(model);

    if (length(deadEnd) == 0)
        break;
    end

    removedMets = union(removedMets,model.mets(deadEnd));
    if (length(deadEnd) > 1)
        deadRxns = model.rxns(find(sum(model.S(deadEnd,:) ~= 0) > 0));
    else
        deadRxns = model.rxns(find(model.S(deadEnd,:) ~= 0));
    end

    model = removeRxns(model,deadRxns);


    removedRxns = union(removedRxns,deadRxns);

end
