function [count, loc, comploc] = motifCount(motif, seq, countOverlap)
% Inputs:
%   motif: a string (e.g. 'TTGAC') for the motif.
%   seq: a string for the promoter sequence, 5'-3' coding.
%   countOverlap: true if overlapping motifs are counted twice.
%                 false if we want to discount overlapping.
% Returns:
%   count: number of times 'motif' appears in 'seq'.
%   loc:   locations of the motif in seq.  should have
%           seq(loc(i):loc(i+len-1))==motif.
%   comploc: locations of m'=seqreverse(seqcomplement(motif)) in the
%   complementary sequence.  comploc(i) is the _start_ position of m' in
%   the 3'-5' direction in complementary sequence.
%
% To try it out:
%   seq='AAAATTTTCCCCGGGGAAAATTTTCCCCGGGG';
%   [c,loc,rloc]=motifCount('TTCC',seq,false);
% Or for degenerate motif:
%   [c,loc,rloc]=motifCount('YCCS',seq,false)
%
% Also, as an independent check, can use the function:
%   seqshowwords(seq,'YCCS');
%   seqshowwords(seqcomplement(seq),'SCCY');

seqlen = length(seq);

if strcmp(motif, 'TSS START')==1
    count=1;
    loc=[seqlen];
    comploc=[seqlen];
    return
end

    
motifset = reduceFuzzyMotif(motif,false);
nm=length(motifset);

seqrc=seqreverse(seqcomplement(seq));
loc=[];
comploc=[];
for i=1:nm
    loc= [loc strfind(seq, motifset{i})];
    comploc= [comploc strfind(seqrc, motifset{i})];
end
loc=sort(loc);
comploc = seqlen+1-comploc;
comploc = sort(comploc);

codingOccupancy = zeros(1,seqlen); % =1 if those indices of the coding strand belongs to a _counted_ motif., 0 if otherwise.
count=0;
len=length(motif);
if countOverlap
    count= length(loc)+length(comploc);
else
    if length(loc)<=1
        count =count+length(loc);
        if length(loc)==1
            codingOccupancy(loc(1):(loc(1)+len-1))=1;
        end
    else
        count=count+1; %count the first one.
        codingOccupancy(loc(1):(loc(1)+len-1))=1;
        for i=1:length(loc)-1
            if loc(i+1)-loc(i)>=len
                count = count+1; %for each next one, count if no overlap.
                codingOccupancy(loc(i+1):(loc(i+1)+len-1))=1;
            end
        end
    end

    if length(comploc)<=1
        if length(comploc)==1
            % check that it does not overlap with complementary strand.
            if sum(codingOccupancy(comploc(1):(-1):(comploc(1)-len+1)))==0
                count =count+1;
            end
        end
    else
        if sum(codingOccupancy(comploc(1):(-1):(comploc(1)-len+1)))==0
                count =count+1;
        end
        for i=1:(length(comploc)-1)
            if comploc(i+1)-comploc(i)>=len
                if sum(codingOccupancy(comploc(i+1):(-1):(comploc(i+1)-len+1)))==0
                    count =count+1;
                end
            end
        end
    end
end

comploc = comploc-len+1;