Added source Matlab code for reference

matlab/linkage/i_encode_n.m

@@ -0,0 +1,61 @@
+function S=i_encode_n(Seq)
+%I_ENCODE_N - Convert a nucleotide sequence from a letter to an integer representation
+%Internal function encodes the nucleotide sequences by digits
+%
+% Syntax: S=i_encode_n(Seq)
+%
+% Inputs:
+%    Seq   - Letter representation of sequence
+%
+% Outputs:
+%    S     - Integer representation of sequence
+%
+%
+% See also: I_ENCODE_A
+
+% Molecular Biology & Evolution Toolbox, (C) 2005
+% Author: James J. Cai
+% Email: jamescai@hkusua.hku.hk
+% Website: http://web.hku.hk/~jamescai/
+% Last revision: 5/28/2005
+% seqcode = 'ACGTDI?-'
+method=1;
+Seq=upper(Seq); % Read lower case letters
+[NT,AA] = seqcode; % NT = 'ACGTDI?-'
+switch (method)
+    case (1)
+        [n,m]=size(Seq);
+        S = ones(n,m).*8;
+        Seq(find(Seq=='U'))='T';    %replace U with T
+        for (k=1:8),
+            S(find(Seq==NT(k)))=k;
+        end
+        S(find(Seq==NT(7))) = -999; % missing data denoted as -999.
+        S(find(Seq==NT(8))) = -999; % gap 
+    case (2)
+        [n,m]=size(Seq);
+        S = zeros(n,m);  i = 1; j = 1;
+        
+        code = zeros(256,1); 
+        for o = 1:256
+            code(o) = nan;
+        end
+        
+        % NT = 'ACGT-';
+        
+        for o = 1:5
+            code(abs(NT(o))) = o;  
+        end
+        
+        for i=1:n
+            for j=1:m
+                if Seq(i,j) == 'U' 
+                    S(i,j) = code(abs('T'));
+                else
+                    S(i,j) = code(abs(Seq(i,j)));
+                end;
+            end;
+        end;
+end
+
+% S=uint8(S);