18 files changed, 1280 insertions, 9 deletions

diff --git a/test/entropy/don_anal.m b/test/entropy/don_anal.m
new file mode 100644
index 0000000..7d0a648
--- a/dev/null
+++ b/test/entropy/don_anal.m
@@ -0,0 +1,40 @@
+d = fastaread('C:\dondata\FASTA2.fa');

+lens = arrayfun(@(x)(numel(x.Sequence)), d);

+d(lens < 300) = [];

+rexp = '/Human/(\w*)/([\d\w]*)/(.*?)/(\d{4})/';

+headers = cell(length(d), 1);

+[headers{:}] = deal(d(:).Header);

+groups = regexp(headers, rexp, 'tokens', 'once');

+cgroups = cat(1,groups{:});

+dates = unique(cgroups(:,end));

+

+seqs = cell(length(d), 1);

+[seqs{:}] = deal(d(:).Sequence);

+

+ALIGN_CELL = cell(length(dates), 1);

+INDS_CELL = cell(length(dates), 1);

+PAIRWISE_CELL = cell(length(dates),1);

+for i = 1:length(dates)

+    display(dates{i})

+    tf = strcmp(cgroups(:,end), dates{i});

+    if isempty(PAIRWISE_CELL{i})

+        pairwise_dists = GenomePairwiseDist(d(tf), dates{i});

+        PAIRWISE_CELL{i} = pairwise_dists;

+    else

+        pairwise_dists = PAIRWISE_CELL{i};

+    end

+    if isempty(ALIGN_CELL{i}) || isempty(INDS_CELL{i})

+        [ALIGN_CELL{i}, INDS_CELL{i}] = GenomeAlignments(d(tf), ...

+                                        pairwise_dists);

+        save restore_data PAIRWISE_CELL ALIGN_CELL INDS_CELL

+    end

+end

+

+for i = 1:length(ALIGN_CELL)

+    [ALIGN_CELL{i}, ~]= RefineAlignments(ALIGN_CELL{i});

+end

+

+

+ents = CalculateProteinEntropy(d(1), ALIGN_CELL);

+

+dents = cat(1, ents{:});