18 files changed, 1280 insertions, 9 deletions
diff --git a/test/entropy/CalculateProteinEntropy.m b/test/entropy/CalculateProteinEntropy.m
new file mode 100644
index 0000000..41f06f5
--- a/dev/null
+++ b/test/entropy/CalculateProteinEntropy.m
@@ -0,0 +1,25 @@
+function OUT_DATA=CalculateProteinEntropy(Ref, ALIGN_CELL)
+OUT_DATA = cell(size(ALIGN_CELL));
+for i = 1:size(ALIGN_CELL,1)
+    
+    aligned_seqs = ALIGN_CELL{i};
+    
+    ref_seq = Ref.Sequence;
+    
+    ref_prof = seqprofile(ref_seq, 'alphabet', 'aa');
+    seqs_prof = seqprofile(aligned_seqs, 'alphabet', 'aa');
+    
+    [mp, H1, H2] = profalign(ref_prof, seqs_prof);
+    
+    merged_seqs = char(zeros(size(aligned_seqs,1)+1, size(mp,2)));
+    merged_seqs(2:end, H2) = aligned_seqs;
+    merged_seqs(1, H1) = ref_seq;
+    
+    entropy_vals = CalculateEntropy(merged_seqs);
+    
+    %only pull out the values that are in the reference positions
+    ref_entropy = entropy_vals(H1);
+    
+    OUT_DATA{i} = ref_entropy;
+end

diff --git a/test/entropy/CalculateProteinEntropy.m b/test/entropy/CalculateProteinEntropy.m new file mode 100644 index 0000000..41f06f5 --- a/dev/null +++ b/test/entropy/CalculateProteinEntropy.m
@@ -0,0 +1,25 @@
	1	function OUT_DATA=CalculateProteinEntropy(Ref, ALIGN_CELL)
	2
	3	OUT_DATA = cell(size(ALIGN_CELL));
	4	for i = 1:size(ALIGN_CELL,1)
	5
	6	aligned_seqs = ALIGN_CELL{i};
	7
	8	ref_seq = Ref.Sequence;
	9
	10	ref_prof = seqprofile(ref_seq, 'alphabet', 'aa');
	11	seqs_prof = seqprofile(aligned_seqs, 'alphabet', 'aa');
	12
	13	[mp, H1, H2] = profalign(ref_prof, seqs_prof);
	14
	15	merged_seqs = char(zeros(size(aligned_seqs,1)+1, size(mp,2)));
	16	merged_seqs(2:end, H2) = aligned_seqs;
	17	merged_seqs(1, H1) = ref_seq;
	18
	19	entropy_vals = CalculateEntropy(merged_seqs);
	20
	21	%only pull out the values that are in the reference positions
	22	ref_entropy = entropy_vals(H1);
	23
	24	OUT_DATA{i} = ref_entropy;
	25	end