CB_gene_v5b

function [Sequence] = CB_gene_v5(Segments)
NumTrials = 10;
Seq = {};
L = zeros(NumTrials,1);
for q = 1:NumTrials
	[Seq{q},L(q)] = CB_gene_v4b(Segments);
end
[value,Index]=min(L);
Sequence = Seq{Index(1)};
return;


function [Sequence,NewSeqLength] = CB_gene_v4b(Segments)
% Eliminate Duplicates
Segments = unique(Segments,'rows');
[rows,cols] = size(Segments);
[junk,remap] = sort(rand(rows,1));
Segments = Segments( remap,:);  % randomize
maxlength = rows*cols;
Sequence = zeros(1,maxlength);
Temp = zeros(cols,rows);
Temp = Segments';
Sequence = Temp(:)';  

SegPos = [1:cols:maxlength];

% Idea: Create a sparse matrix of dimension rows by rows*cols and an
% index variable that keeps track of where the Segs go.  
for k = 1:rows
	sparseM(k,[SegPos(k):(SegPos(k)+cols-1)]) = Segments(k,:);
end
sparseM = sparse( sparseM );

NumOverlapped = sum(sparseM>0);
SeqLength = sum(NumOverlapped>0);
NewSeqLength = SeqLength;

k = 0;

while (1)

	k = mod(k,rows)+1;

	indicies = [];
	indicies = findstr(Segments(k,:),Sequence);

	OrgPos = SegPos(k);
	useful = find(indicies~=OrgPos);

	if (length(indicies)>1)
		% Move it
		NewPos = indicies(useful(1));  % might want to try this with a random index??
												 % instead of the (1) first one
		TempSeg = sparseM(k,[OrgPos:(OrgPos+cols-1)]);
		sparseM(k,[OrgPos:(OrgPos+cols-1)]) = zeros(1,cols);
		sparseM(k,[NewPos:(NewPos+cols-1)]) = TempSeg;
		SegPos(k) = NewPos;

		[SegPos,MapIndex] = sort(SegPos); % sort according to placement
		Segments = Segments(MapIndex,:); % arrange rows
		sparseM = sparseM(MapIndex,:);

		% remove leading spaces
		if (SegPos(1)~=1)
			MoveBy = SegPos(1)-1;
			SegPos = SegPos - MoveBy;
			[A,B] = size(sparseM);
			sparseM = sparseM(:,[(SegPos(1)+MoveBy):B]); 
		end

		% remove spaces in the sequence
		Spacing = diff(SegPos);
		BadSpots = find(Spacing>cols);

		if ~isempty(BadSpots)
			SpaceSize = Spacing(BadSpots);
			MoveBy = SpaceSize - cols;

			for p = (BadSpots+1):rows
				% store info
				TempSeg = sparseM(p, [SegPos(p):(SegPos(p)+cols-1)]);
				% zero old position
				sparseM(p, [SegPos(p):(SegPos(p)+cols-1)]) = zeros(1,cols);
				% store in new position
				sparseM(p, ([SegPos(p):(SegPos(p)+cols-1)]-MoveBy)) = TempSeg;
			end			
			SegPos((BadSpots+1):rows) = SegPos((BadSpots+1):rows) - MoveBy;
		end
		
		sparseM = sparse(sparseM); % clean up

		NewNumOverlapped = sum(sparseM>0); % compute length
		NewSeqLength = sum(NewNumOverlapped>0);

		Sequence = sum(sparseM)./(NewNumOverlapped + ~(NewNumOverlapped));
		TempSequence = zeros(1,NewSeqLength);
		TempSequence = full(Sequence);
		Sequence = TempSequence; %Sequence( find(Sequence) );%TempSequence(1:NewSeqLength);
	end

	if (k==rows)  % Stop if there is minimal progress after trying all rows
		if (SeqLength-NewSeqLength<4) 
			break
		else
			SeqLength = NewSeqLength; % update to track progress
		end
	end

end

return;