function [ cdavg ncdavg comboavg ] = evcdsplot( seq, cds, deg, step )
% Takes a gene sequence, degree for window, degree for step size, and a 
% vector specifying coding and noncoding regions and produces a plot of 
% the cumulative evolutionary slope with plotted averages for coding, 
% noncoding, and combination regions.
% Makes sequence divisible by 2^step.
% Makes sure cds values are not outside of the possible indices.

% correct the length of seq
a = floor(length(seq)/(2^step));
seq = seq(1:a*2^step);

% delete any coding sections outside of new sequence range
cds = cds(cds < length(seq)); 
if mod(length(cds),2) == 1
    seq = seq(1:(cds(end)-1));
    a = floor(length(seq)/(2^step));
    seq = seq(1:a*2^step);
    cds = cds(1:(end-1));
end

% if sequence only has noncoding
if length(cds) == 0
    [seq_s seq_r] = evdnaslopec(seq,deg,step);
    avgn = mean(seq_s);
    plot([1,length(seq)],[avgn,avgn], 'g-', 'LineWidth', 3)
    cdavg = [];
    ncdavg = [avgn];
    comboavg = [];
    
    titl = strjoin({'Evolutionary DNA Slopes: Mean(introns)= ',num2str(avgn)},'');

    title(titl)
    xlabel('Number in Gene Sequence')
    ylabel('Slope')
    
% if sequence has coding and noncoding
else
    % plot evolutionary slopes, saving slope and range
    [seq_s seq_r] = evdnaslopec(seq,deg,step);

    % plot separations between introns, exons, and combo
    starts = cds(1:2:end);
    ends = cds(2:2:end);
    cdind = [];
    for i = 1:length(starts)
        cdind = [cdind starts(i):ends(i)];
    end
    
    cdlabel = [];
    for k=seq_r
        windowind = (k-(2^deg)/2):(k+(2^deg)/2-1);
        common = intersect(windowind,cdind);
        if length(common) == 0
            cdlabel = [cdlabel 0];  % introns
        elseif length(common) == length(windowind)
            cdlabel = [cdlabel 1];  % exons
        else
            cdlabel = [cdlabel 2];  % combo
        end
    end
    
    % plot vertical separations
    findchanges = find(logical(diff(cdlabel)));
    avglabel = cdlabel([1,diff(cdlabel)]~=0);
    for f = 1:length(findchanges)
        plot([seq_r(findchanges(f))+(2^deg)/2-1 ...
              seq_r(findchanges(f))+(2^deg)/2-1], ...
              [min(seq_s),max(seq_s(seq_s < Inf))], 'r--')
    end
    
    % plot average slopes for each region
    % first region
    firstavg = mean(seq_s(1:findchanges(1)));
    averages = [firstavg];
    if avglabel(1) == 0
        color = 'g-';
    elseif avglabel(1) == 1
        color = 'r-';
    else
        color = 'b-';
    end
    plot([1,seq_r(findchanges(1))+(2^deg)/2-1],[firstavg,firstavg], ...
        color, 'LineWidth', 3)
    
    % middle regions
    for j = 1:(length(findchanges)-1)
        avg = mean(seq_s(findchanges(j)+1:findchanges(j+1)));
        averages = [averages avg];
        if avglabel(j+1) == 0
            color = 'g-';
        elseif avglabel(j+1) == 1
            color = 'r-';
        else
            color = 'b-';
        end
        plot([seq_r(findchanges(j))+(2^deg)/2-1,seq_r(findchanges(j+1))+(2^deg)/2-1], ...
             [avg,avg],color,'LineWidth',3)
    end
    
    % last region
    lastavg = mean(seq_s(findchanges(j+1):length(seq_s)));
    averages = [averages lastavg];
    if avglabel(end) == 0
        color = 'g-';
    elseif avglabel(end) == 1
        color = 'r-';
    else
        color = 'b-';
    end
    plot([seq_r(findchanges(end))+(2^deg)/2-1,length(seq)],[lastavg,lastavg], ...
        color, 'LineWidth', 3)
    
    % find overall average slopes for introns, exons, combo
    ncdavg = averages(find(avglabel == 0));
    cdavg = averages(find(avglabel == 1));
    comboavg = averages(find(avglabel == 2));
    
    ncdavgplot = mean(ncdavg);
    cdavgplot = mean(cdavg);
    comboavgplot = mean(comboavg);
    
    titl = strjoin({'Evolutionary DNA Slopes: Mean(exons)= ',num2str(cdavgplot), ...
        ', Mean(introns)= ',num2str(ncdavgplot),', Mean(combo)= ', ...
        num2str(comboavgplot)},'');

    title(titl)
    xlabel('Number in Gene Sequence')
    ylabel('Slope')



end

end