Contents

== 0.9.0 version

* 5 major enhancement:
    * --heatmap option has been added to generate heat maps from substitution tables
    * --heatmap-format option has been added for heat map figure format (PNG, GIF, JPG, BMP, and PDF)
    * --heatmap-stem option has been added to set a file name for total heat maps figure when --heatmap 1 or 2 is set
    * --heatmap-columns option has been added to set the number of tables in a row when --heatmap 1 or 2 is set
    * --heatmap-value option has been added to print values in the cells of heat maps

* 2 minor enhancement:
    * --noround option has been renamed to --noroundoff
    * 'simple_memoize' RubyGem package is no longer required

== 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 background frequencies
    * a bug in p2 probability 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:
    * log-odds ratio matrices can be generated with --nosmooth option
    * safe handling for zero observations or mutations of amino acids

== 0.0.3 2008-12-09

* 2 major enhancement:
    * An option '--cys (-j) 2' added not to distinguish J from C, so 'disulphide bond' environment feature is not prerequisite
    * Masking works for target amino acid, too

== 0.0.2 2008-11-13

* 2 major enhancement:
    * Constrained environment features are properly handled
    * Sane log-odds ratio matrices are produced

== 0.0.1 2008-11-07

* 1 major enhancement:
    * Initial release

Version data entries

3 entries across 3 versions & 1 rubygems

Version	Path
semin-egor-0.9.0	History.txt
semin-egor-0.9.1	History.txt
semin-egor-0.9.2	History.txt