| -rw-r--r-- | src/Makefile.am | 2 | ||||
| -rw-r--r-- | src/controller/callbacks/reshape.c | 2 | ||||
| -rw-r--r-- | src/db/dbconnect.sqc | 12 | ||||
| -rw-r--r-- | src/model/data/base.sqc | 2 | ||||
| -rw-r--r-- | src/model/state/state.h | 3 | ||||
| -rw-r--r-- | src/util/check_error.c | 6 | ||||
| -rw-r--r-- | src/util/check_error_db.c | 13 | ||||
| -rw-r--r-- | src/util/check_error_db.h | 9 | ||||
| -rw-r--r-- | test/distance_sanity_check/gi_227977170_78032581.png | bin | 0 -> 51161 bytes | |||
| -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 |
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
|
