egor 0.0.4 → 0.0.5

data/History.txt

@@ -1,3 +1,17 @@
+== 0.0.5 2009-1-23
+
+* 4 major enhancement:
+  * Egor warns if your sigma value is too big for any amino acid count (minimum ratio of amino acid count to sigma value: 500.0)
+  * --augosigma option was added to avoid excessive influence of backgournd frequencies
+  * a bug in p2 probabilty calculation of the partial smoothing procedure was fixed
+  * a bug in total probability/log odds ratio calculation was fixed
+
+* 4 minor enhancement:
+  * --noround option was added to get original log odds ratios
+  * --p1smooth option was added to enable p1 probability smoothing when partial smoothing
+  * default verbosity has been changed from ERROR to WARN
+  * codes were refactored to be more human readable and DRY
+
 == 0.0.4 2008-12-15
 
 * 2 major enhancement:

data/Manifest.txt

@@ -11,7 +11,9 @@ lib/egor.rb
 lib/egor/cli.rb
 lib/enumerable_extensions.rb
 lib/environment.rb
+lib/environment_class_hash.rb
 lib/environment_feature.rb
+lib/environment_feature_array.rb
 lib/math_extensions.rb
 lib/narray_extensions.rb
 lib/nmatrix_extensions.rb

data/README.rdoc

@@ -34,8 +34,8 @@ egor: Esst GeneratOR, a program for calculating environment-specific substitutio
     --tem-list (-l) FILE: a list for tem files
     --classdef (-c) FILE: a file for the defintion of environments (default: 'classdef.dat')
     --outfile (-o) FILE: output filename (default 'allmat.dat')
-    --weight (-w) INTEGER: clustering level (PID) for the BLOSUM-like weighting
-    --noweight: calculate substitution counts with no weights (default)
+    --weight (-w) INTEGER: clustering level (PID) for the BLOSUM-like weighting (default: 60)
+    --noweight: calculate substitution counts with no weights
     --smooth (-s) INTEGER:
         0 for parial smoothing (default)
         1 for full smoothing