| -rw-r--r-- | test/entropy/Align2Ref.m | 24 | ||||
| -rw-r--r-- | test/entropy/CalculateEntropy.m | 15 | ||||
| -rw-r--r-- | test/entropy/CalculateProteinEntropy.m | 25 | ||||
| -rw-r--r-- | test/entropy/FastNWalign2.c | 94 | ||||
| -rw-r--r-- | test/entropy/GenomeAlignments.m | 31 | ||||
| -rw-r--r-- | test/entropy/GenomePairwiseDist.m | 98 | ||||
| -rw-r--r-- | test/entropy/RefineAlignments.m | 276 | ||||
| -rw-r--r-- | test/entropy/don_anal.m | 40 | ||||
| -rw-r--r-- | test/entropy/nwalign_mod.m | 637 |
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 |
