TransferAA2Int( Sequence,Descend )

function IntMatrix = TransferAA2Int( Sequence,Descend )         
% transfer 20 amino acids to 1 to 20, for the rest, 21.
% if Descend exists, then just simply keep the most prevalent
[ Row,Col ]= size( Sequence );
IntCell = cell(1,Row);
parfor p = 1:Row
    IntMatrix = aa2int( Sequence(p,:) );
    Temp = find( IntMatrix > 20 );
    if isempty( Temp ) == 0  
       IntMatrix( Temp ) = 21*ones( 1,length(Temp) );
    end
    IntCell{ p } = IntMatrix;
end
IntMatrix = zeros(Row,Col);
   for p = 1:Row
       IntMatrix(p,:) = IntCell{p};
   end
if nargin == 2
   NewIntMatrix = zeros(Row,Col);
   for p = 1:Col
       Value = setdiff( unique( sort( IntMatrix(:,p) ) ),21 );
       for q = 1:Row
           Pos = find( Value == IntMatrix(q,p) );
           if isempty(Pos)==0 && Pos > 0.5
              NewIntMatrix(q,p) = Pos;
           end
       end
   end
   IntMatrix = NewIntMatrix;
end
end