0.9.9.1 26/08/2009¶ ↑
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Removed dependency on the Ruby Facets library
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Total -> total for compatibility with melody
0.9.9 09/08/2009¶ ↑
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Changed default value for –classdef option from 'classdef.dat' to nil When no definition file provided, –cys (-y) 2 and –nosmooth options are applied automatically
0.9.8 21/07/2009¶ ↑
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Fixed a bug in generating amino acids symbols when –cys 2 is set
0.9.7 30/05/2009¶ ↑
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Added –environment option to consider not only substituted amino acids' environments but also substituting amino acids' environments
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Changed the default pseudocount, (1 / # of environment classes) to 0, a pseudocount needs to be explicitly provided with –add option
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Changed the fixed column size (7) of raw count matrices to vary depending on the number of digits of a maximum amino acid count
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Fixed a bug in reading an environment feature definition file (empty line)
0.9.6 18/03/2009¶ ↑
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Warns if Rmagick is not properly installed or missing.
0.9.5 18/03/2009¶ ↑
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Fixed a bug in the order of requiring libraries
0.9.4 18/03/2009¶ ↑
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Fixed a bug for environment label and residue name when –cys 2 is set
0.9.3 23/2/2009¶ ↑
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Egor has been renamed to
Ulla
!
0.9.0 13/2/2009¶ ↑
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Added –heatmap option for heat map generation from substitution tables
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Added –heatmap-format option for heat map figure format (PNG, GIF, JPG, BMP, and PDF)
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Added –heatmap-stem option to set a file name of total heat maps figure when –heatmap 1 or 2 is set
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Added –heatmap-columns option to set the number of tables in a row when –heatmap 1 or 2 is set
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Added –heatmap-values option to print values in the cells of heat maps
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Renamed –noround option to –noroundoff
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'simple_memoize' RubyGem package is no longer required
0.0.5 23/1/2009¶ ↑
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Warns if your sigma value is too big for any amino acid count (minimum ratio of amino acid count to sigma value: 500.0)
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Added –augosigma option to avoid excessive influence of background frequencies
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Added –noround option was added to get original log odds ratios
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Added –p1smooth option was added to enable p1 probability smoothing when partial smoothing
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Fixed a bug in p2 probability calculation of the partial smoothing procedure
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Fixed a bug in total probability/log odds ratio calculation
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Changed default verbosity from ERROR to WARN
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Refactored codes to be more human readable and DRY
0.0.4 15/12/2008¶ ↑
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Fixed a bug to generated log-odds ratio matrices with –nosmooth option
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Copes with no observations or mutations
0.0.3 09/12/2008¶ ↑
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Added –cys (-j) 2 not to distinguish J from C, so 'disulphide bond' environment feature is not prerequisite
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Fixed a bug to make masking works for target amino acid, too
0.0.2 13/11/2008¶ ↑
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Supports user provided constrained environment features are properly handled
0.0.1 07/11/2008¶ ↑
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Initial release