9 files changed, 1240 insertions, 0 deletions

diff --git a/test/entropy/Align2Ref.m b/test/entropy/Align2Ref.m
new file mode 100644
index 0000000..3021d4a
--- a/dev/null
+++ b/test/entropy/Align2Ref.m
@@ -0,0 +1,24 @@
+function NEW_INDS = Align2Ref(REF_SEQ, ALIGN, ALIGN_INDS, ALPHA)

+%   Align2Ref

+%       Uses a profile alignment to change a set of indicices in the

+%       "alignment space" to the "reference space".

+%

+%

+%   NEW_INDS = Align2Ref(REF_SEQ, ALIGN, ALIGN_INDS)

+%

+

+if nargin == 3

+    ALPHA = 'aa';

+end

+

+ref_prof = seqprofile(REF_SEQ, 'alphabet', ALPHA);

+align_prof = seqprofile(ALIGN, 'alphabet', ALPHA);

+

+[~, ind1, ind2] = profalign(ref_prof, align_prof);

+

+ninds = ind2(ALIGN_INDS);

+

+mask = sum(bsxfun(@le, ind1(:)', ninds(:)),2);

+mask(mask == 0) = 1;

+

+NEW_INDS = reshape(ind1(mask), size(ALIGN_INDS));
\ No newline at end of file