README.rdoc in egor-0.0.2 vs README.rdoc in egor-0.0.3

@@ -1,69 +1,81 @@
 = egor
 
 * http://egor.rubyforge.org
 
+
 == DESCRIPTION:
 
 egor: Esst GeneratOR, a program for calculating environment-specific substitution tables
 
+
 == FEATURES/PROBLEMS:
 
 * No more segmentation fault
 * Fast enough not to leave your place
 * Slow enough to check your emails or have some chats with your colleagues next you
 * Full smoothing supported
 * In theory, infinite number of environment features can be handled
 
+
+== INSTALL:
+
+    $ sudo gem install egor
+
+
 == BASIC USAGE:
 
     $ egor -l TEMLIST-file -c classdef.dat
         or
     $ egor -f TEM-file -c classdef.dat
 
+
 == OPTIONS:
-    --tem-file (-f) STRING: a tem file
-    --tem-list (-l) STRING: a list for tem files
-    --classdef (-c) STRING: a file for the defintion of environments (default: 'classdef.dat')
-    --outfile (-o) STRING: output filename ("allmat.dat" if not specified)
-    --weight (-w) INTEGER: clustering level (PID) for the BLOSUM-like weighting (not supported yet)
+    --tem-file (-f) FILE: a tem file
+    --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)
     --smooth (-s) INTEGER:
         0 for parial smoothing (default)
         1 for full smoothing
     --nosmooth: perform no smoothing operation
-    --cys (-y) INTEGER: (!!!not implemented yet!!!)
-        0 for using C and J only for structure
-        1 for both structure and sequence (default)
+    --cys (-y) INTEGER:
+        0 for using C and J only for structure (default)
+        1 for both structure and sequence
+        2 for using only C for both
     --output INTEGER:
         0 for raw counts (no-smoothing performed)
         1 for probabilities
         2 for log-odds (default)
     --scale INTEGER: log-odds matrices in 1/n bit units (default 3)
     --sigma DOUBLE: change the sigma value for smoothing (default 5)
-    --add DOUBLE: add this value to raw counts when deriving log-odds without smoothing (default 1/#classes)
-    --penv: use environment-dependent frequencies for log-odds calculation (default false) (!!!not implemented yet!!!)
+    --add DOUBLE: add this value to raw counts when deriving log-odds without smoothing (default 1/=classes)
+    --penv: use environment-dependent frequencies for log-odds calculation (default false) (NOT implemented yet!!!)
     --pidmin DOUBLE: count substitutions only for pairs with PID equal to or greater than this value (default none)
     --pidmax DOUBLE: count substitutions only for pairs with PID smaller than this value (default none)
     --verbose (-v) INTEGER
         0 for ERROR level (default)
         1 for WARN or above level
         2 for INFO or above level
         3 for DEBUG or above level
     --version: print version
     --help (-h): show help
 
+
 == REQUIREMENTS:
 
 * ruby 1.8.6 or above (http://www.ruby-lang.org)
 * rubygems 1.2.0 or above (http://rubyforge.org/projects/rubygems/)
+
+Following RubyGems will be automatically installed if you have rubygems installed on your machine
+
 * narray (http://narray.rubyforge.org/)
 * facets (http://facets.rubyforge.org/)
 * bio (http://bioruby.open-bio.org/)
+* simple_memoize (http://github.com/JackDanger/simple_memoize/tree/master)
 
-== INSTALL:
-
-    $ sudo gem install egor
 
 == LICENSE:
 
 (The MIT License)