function [motifs] = enumerateMotifs(p,varargin)
% returns a string cell array that contains all motifs of length p.
% Optional argument 'fuzzy' contains the positions in motif that allow
% fuzzy letters (i.e. all IUPAC symbols).
% Note: a motif and its reverse complement only occurs in the list once.

%nargin
okargs   = {'fuzzy' 'keepcomplements'};
defaults = {[] false};
[eid,emsg,fuzzy,keepcomplements] = mygetargs(okargs,defaults,varargin{:});
fuzzyPositions = zeros(1,p);
fuzzyPositions(fuzzy) = 1;
nonfuzzy = find(fuzzyPositions==0);
numfuzzypos = sum(fuzzyPositions);

% --- n is the total number of such motifs.
Afuzzy = 15;
nonfuzzyn =1;
fuzzyn=1;
for i=1:p
    if fuzzyPositions(i)
        fuzzyn = fuzzyn*Afuzzy;
    else
        nonfuzzyn = nonfuzzyn*4;
    end
end
n = fuzzyn*nonfuzzyn;
motifs = cell(1,n);

ind=1;
for i=1:fuzzyn
    for j=1:nonfuzzyn
        fuzzys = dec2base(i-1,Afuzzy,numfuzzypos);
        nonfuzzys = dec2base(j-1,4,p-numfuzzypos);
        s = blanks(p);
        fcount = 1;
        count=1;
        for k=1:p
            if fuzzyPositions(k)
                s(k) = fuzzys(fcount);
                fcount=fcount+1;
            else
                s(k) = nonfuzzys(count);
                count=count+1;
            end
        end
        
        motifs{ind} = blanks(p);
        for k=1:length(s)
            if fuzzyPositions(k)
                base  = Afuzzy;
            else
                base=4;
            end
            motifs{ind}(k) = int2nt(base2dec(s(k),base)+1);
        end
        ind = ind+1;
    end
end

if ~keepcomplements
    % get rid of reverse complements.
    keep=zeros(1,n);
    for i=1:n
        temp = seqreverse(seqcomplement(motifs{i}));
        x1=0;
        for j=1:numfuzzypos
            b = mynt2int(temp(fuzzy(j)))-1;
            x1 = x1+b*(Afuzzy^(numfuzzypos-j));
        end
        x1=x1;
        numnonfuzzypos=p-numfuzzypos;
        x2=0;
        for j=1:(numnonfuzzypos)
            b = mynt2int(temp(nonfuzzy(j)))-1;
            x2 = x2+b*(4^(numnonfuzzypos-j));
        end
        x2=x2+1;
        tempind = x1*nonfuzzyn+x2;
        if tempind<=i
            keep(i) = 1;
        end
    %    fprintf('%s %s %d\n',motifs{i},motifs{tempind},keep(i));
    end
    motifs=motifs(find(keep));
end