egor 0.0.5 → 0.9.0

data/History.txt

@@ -1,36 +1,38 @@
-== 0.0.5 2009-1-23
+== 0.9.0 13/2/2009
 
-* 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
+* Added --heatmap option for heat map generation from substitution tables
+* Added --heatmap-format option for heat map figure format (PNG, GIF, JPG, BMP, and PDF)
+* Added --heatmap-stem option to set a file name of total heat maps figure when --heatmap 1 or 2 is set
+* Added --heatmap-columns option to set the number of tables in a row when --heatmap 1 or 2 is set
+* Added --heatmap-values option to print values in the cells of heat maps
+* Renamed --noround option to --noroundoff
+* 'simple_memoize' RubyGem package is no longer required
 
-* 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
+== 0.0.5 23/1/2009
 
-== 0.0.4 2008-12-15
+* Warns if your sigma value is too big for any amino acid count (minimum ratio of amino acid count to sigma value: 500.0)
+* Added --augosigma option to avoid excessive influence of background frequencies
+* Added --noround option was added to get original log odds ratios
+* Added --p1smooth option was added to enable p1 probability smoothing when partial smoothing
+* Fixed a bug in p2 probability calculation of the partial smoothing procedure
+* Fixed a bug in total probability/log odds ratio calculation
+* Changed default verbosity from ERROR to WARN
+* Refactored codes to be more human readable and DRY
 
-* 2 major enhancement:
-  * log-odds ratio matrices can be generated with --nosmooth option
-  * safe handling for zero observations or mutations of amino acids
+== 0.0.4 15/12/2008
 
-== 0.0.3 2008-12-09
+* Fixed a bug to generated log-odds ratio matrices with --nosmooth option
+* Copes with no observations or mutations
 
-* 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
+== 0.0.3 09/12/2008
 
-== 0.0.2 2008-11-13
+* Added --cys (-j) 2 not to distinguish J from C, so 'disulphide bond' environment feature is not prerequisite
+* Fixed a bug to make masking works for target amino acid, too
 
-* 2 major enhancement:
-  * Constrained environment features are properly handled
-  * Sane log-odds ratio matrices are produced
+== 0.0.2 13/11/2008
 
-== 0.0.1 2008-11-07
+* Supports user provided constrained environment features are properly handled
 
-* 1 major enhancement:
-  * Initial release
+== 0.0.1 07/11/2008
+
+* Initial release

data/Manifest.txt

@@ -9,24 +9,28 @@ config/website.yml.sample
 egor.gemspec
 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/egor/environment.rb
+lib/egor/environment_class_hash.rb
+lib/egor/environment_feature.rb
+lib/egor/environment_feature_array.rb
+lib/egor/heatmap_array.rb
 lib/math_extensions.rb
 lib/narray_extensions.rb
 lib/nmatrix_extensions.rb
+lib/string_extensions.rb
 script/console
 script/destroy
 script/generate
 script/txt2html
+test/egor/test_cli.rb
+test/egor/test_environment_class_hash.rb
+test/egor/test_environment_feature.rb
 test/test_egor.rb
-test/test_egor_cli.rb
-test/test_enumerable_extensions.rb
-test/test_environment_feature.rb
 test/test_helper.rb
+test/test_math_extensions.rb
+test/test_narray_extensions.rb
 test/test_nmatrix_extensions.rb
+test/test_string_extensions.rb
 website/index.html
 website/index.txt
 website/javascripts/rounded_corners_lite.inc.js

data/README.rdoc

@@ -1,102 +1,254 @@
 = egor
 
-* http://egor.rubyforge.org
+http://www-cryst.bioc.cam.ac.uk/egor
 
 
-== DESCRIPTION:
+== Description
 
-egor: Esst GeneratOR, a program for calculating environment-specific substitution tables
+'egor' is a program for calculating environment-specific substitution tables from user providing environmental class definitions and sequence alignments with the annotations of the environment classes.
 
 
-== FEATURES/PROBLEMS:
+== Features
 
-* 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
+* Environment-specific substitution table generation based on user providing environmental class definition
+* Entropy-based smoothing procedures to cope with sparse data problem
+* BLOSUM-like weighting procedures using PID threshold
+* Heat Map generation for substitution tables
 
 
-== INSTALL:
+== Requirements
 
-    $ sudo gem install egor
+* ruby 1.8.7 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)
+* RMagick (http://rmagick.rubyforge.org)
+
+
+== Installation
+
+    ~user $ sudo gem install egor
 
 
-== BASIC USAGE:
+== Basic Usage
 
-    $ egor -l TEMLIST-file -c classdef.dat
-        or
-    $ egor -f TEM-file -c classdef.dat
+It's pretty much the same as Kenji's subst (http://www-cryst.bioc.cam.ac.uk/~kenji/subst/), so in most cases, you can swap 'subst' with 'egor'.
 
+    ~user $ egor -l TEMLIST-file -c classdef.dat
+                or
+    ~user $ egor -f TEM-file -c classdef.dat
 
-== OPTIONS:
+
+== Options
     --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 (default: 60)
-    --noweight: calculate substitution counts with no weights
+    --noweight: calculate substitution count with no weights
     --smooth (-s) INTEGER:
-        0 for parial smoothing (default)
+        0 for partial smoothing (default)
         1 for full smoothing
+    --p1smooth: perform smoothing for p1 probability calculation when partial smoothing
     --nosmooth: perform no smoothing operation
     --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
+        2 for using only C for both (must be set when you have no 'disulphide' or 'disulfide' annotation in templates)
     --output INTEGER:
-        0 for raw counts (no-smoothing performed)
+        0 for raw count (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!!!)
+        2 for log odds ratios (default)
+    --noroundoff: do not round off log odds ratio
+    --scale INTEGER: log odds ratio matrices in 1/n bit units (default 3)
+    --sigma DOUBLE: change the sigma value for smoothing (default 5.0)
+    --autosigma: automatically adjust the sigma value for smoothing
+    --add DOUBLE: add this value to raw count when deriving log odds ratios without smoothing (default 1/#classes)
     --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)
+    --heatmap INTEGER:
+        0 create a heat map file for each substitution table
+        1 create one big file containing all heat maps from substitution tables
+        2 do both 0 and 1
+    --heatmap-format INTEGER:
+        0 for Portable Network Graphics (PNG) Format (default)
+        1 for Graphics Interchange Format (GIF)
+        2 for Joint Photographic Experts Group (JPEG) Format
+        3 for Microsoft Windows bitmap (BMP) Format
+        4 for Portable Document Format (PDF)
+    --heatmap-columns INTEGER: number of tables to print in a row when --heatmap 1 or 2 set (default: sqrt(no. of tables))
+    --heatmap-stem STRING: stem for a file name when --heatmap 1 or 2 set (default: 'heatmap')
+    --heatmap-values: print values in the cells when generating heat maps
     --verbose (-v) INTEGER
-        0 for ERROR level (default)
-        1 for WARN or above level
+        0 for ERROR level
+        1 for WARN or above level (default)
         2 for INFO or above level
         3 for DEBUG or above level
     --version: print version
     --help (-h): show help
 
 
-== REQUIREMENTS:
+== Usage
+
+1. Prepare an environmental class definition file. For more details, please check this notes (http://www-cryst.bioc.cam.ac.uk/~kenji/subst/NOTES).
+
+        ~user $ cat classdef.dat
+        #
+        # name of feature (string); values adopted in .tem file (string); class labels assigned for each value (string);
+        # constrained or not (T or F); silent (used as masks)? (T or F)
+        #
+        secondary structure and phi angle;HEPC;HEPC;T;F
+        solvent accessibility;TF;Aa;F;F
+
+2. Prepare structural alignments and their annotations of above environmental classes in PIR format.
+
+        ~user $ cat sample1.tem
+        >P1;1mnma
+        sequence
+        QKERRKIEIKFIENKTRRHVTFSKRKHGIMKKAFELSVLTGTQVLLLVVSETGLVYTFSTPKFEPIVTQQEGRNL
+        IQACLNAPDD*
+        >P1;1egwa
+        sequence
+        --GRKKIQITRIMDERNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNSSNKLFQYASTDMDKVLLKYTEY--
+        ----------*
+        >P1;1mnma
+        secondary structure and phi angle
+        CPCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHPCCCEEEEECCCPCEEEEECCCCCHHHHCHHHHHH
+        HHHHHCCCCP*
+        >P1;1egwa
+        secondary structure and phi angle
+        --CCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCPCCCEEEEECCCPCEEEEECCCHHHHHHHHHHC--
+        ----------*
+        >P1;1mnma
+        solvent accessibility
+        TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTFTTTTTTTTTTTTTTTT
+        TTTTTTTTTT*
+        >P1;1egwa
+        solvent accessibility
+        --TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTFTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT--
+        ----------*
+        ... 
+
+3. When you have two or more alignment files, you should make a separate file containing all the paths for the alignment files.
+
+        ~user $ ls -1 *.tem > TEMLIST
+        ~user $ cat TEMLIST
+        sample1.tem
+        sample2.tem
+        ...
+
+4. To produce substitution count matrices, type
+
+        ~user $ egor -l TEMLIST --output 0 -o substcount.mat
+
+5. To produce substitution probability matrices, type
+
+        ~user $ egor -l TEMLIST --output 1 -o substprob.mat
 
-* ruby 1.8.7 or above (http://www.ruby-lang.org)
-* rubygems 1.2.0 or above (http://rubyforge.org/projects/rubygems/)
+6. To produce log odds ratio matrices, type
 
-Following RubyGems will be automatically installed if you have rubygems installed on your machine
+        ~user $ egor -l TEMLIST --output 2 -o substlogo.mat
+
+7. To produce substitution data only from the sequence pairs within a given PID range, type (if you don't provide any name for output, 'allmat.dat' will be used.)
+
+        ~user $ egor -l TEMLIST --pidmin 60 --pidmax 80 --output 1
+
+8. To change the clustering level (default 60), type
+
+        ~user $ egor -l TEMLIST --weight 80 --output 2
+
+9. In case any positions are masked with the character 'X' in any environmental features will be excluded from the calculation of substitution counts.
+
+10. Then, it will produce a file containing all the matrices, which will look like the one below. For more details, please check this notes (http://www-cryst.bioc.cam.ac.uk/~kenji/subst/NOTES).
+
+        # Environment-specific amino acid substitution matrices
+        # Creator: egor version 0.0.5
+        # Creation Date: 05/02/2009 17:29
+        #
+        # Definitions for structural environments:
+        # 2 features used
+        #
+        # secondary structure and phi angle;HEPC;HEPC;F;F
+        # solvent accessibility;TF;Aa;F;F
+        # (read in from classdef.dat)
+        #
+        # Number of alignments: 1187
+        # (list of .tem files read in from TEMLIST)
+        #
+        # Total number of environments: 8
+        #
+        # There are 21 amino acids considered.
+        # ACDEFGHIKLMNPQRSTVWYJ
+        # 
+        # C: Cystine (the disulfide-bonded form)
+        # J: Cysteine (the free thiol form)
+        #
+        # Weighting scheme: clustering at PID 60 level
+        # ...
+        #
+        >HA 0
+        #        A      C      D      E      F      G      H      I      K      L      M      N      P      Q      R      S      T      V      W      Y      J
+        A        3     -5      0      0     -1      2      0      0      1      0      0      0      1      1      0      1      1      1     -1      0      2
+        C      -16     19    -16    -18    -11    -14    -13    -13    -14    -14    -14    -11    -17    -16    -13    -16    -14    -12    -12    -10     -4
+        D        1     -7      6      3     -3      1      0     -3      1     -3     -2      2      1      2      0      1      0     -2     -3     -2     -2
+        E        3     -7      5      7     -1      2      2      0      3      0      0      3      2      4      3      3      2      1     -1      0     -1
+        F       -4     -4     -6     -6      7     -5     -1      0     -4      1      0     -5     -5     -4     -4     -4     -3     -1      3      3      0
+        G       -2     -6     -3     -4     -5      5     -4     -5     -4     -5     -4     -2     -3     -4     -4     -2     -3     -5     -6     -4     -3
+        H        0     -6      0      0      1      0      8     -1      0      0      0      1     -2      1      1      0      0      0      1      3      0
+        I       -3     -7     -6     -5      0     -5     -3      4     -4      1      1     -5     -4     -4     -3     -5     -2      2     -2     -1      0
+        K        2     -6      2      2     -1      1      2      0      5      1      1      2      0      3      4      2      2      0     -2      0     -1
+        L       -2     -6     -5     -4      1     -4     -2      2     -3      4      2     -3     -4     -3     -2     -4     -2      1      0      0      1
+        M       -2     -7     -4     -3      1     -2     -1      2     -2      2      6     -3     -4     -2     -1     -2     -1      1      0      0      1
+        N        0     -5      1      0     -3      1      1     -3      0     -2     -2      6     -2      0      0      1      1     -2     -3     -1     -1
+        P       -1     -7     -1     -2     -4     -1     -3     -3     -2     -3     -4     -2      9     -2     -3      0     -1     -2     -4     -4     -4
+        Q        2     -7      2      2     -1      1      2     -1      2      0      0      2      0      5      2      1      1      0     -2     -1      0
+        R        1     -6      1      1     -1      0      2      0      3      0      1      1     -1      2      6      1      1      0     -1      0      0
+        S        0     -6     -1     -1     -3      0     -2     -3     -1     -3     -3      0      0     -1     -1      3      1     -2     -4     -3      0
+        T       -1     -7     -2     -2     -3     -2     -2     -2     -2     -2     -2     -1     -2     -2     -2      0      3     -1     -3     -3      0
+        V       -3     -6     -6     -5     -1     -4     -3      1     -4      0      0     -5     -3     -4     -4     -4     -2      2     -2     -2      0
+        W       -4     -6     -6     -5      2     -6     -2     -2     -5     -1     -2     -5     -5     -4     -4     -5     -4     -2     12      2     -3
+        Y       -3     -5     -5     -5      3     -4      1     -1     -3     -1     -1     -3     -5     -3     -3     -4     -3     -2      3      7     -1
+        J       -2      0     -4     -5      0     -2     -1      0     -3      0      0     -3     -6     -2     -2     -1     -1      0     -1      0      9
+        U       -5     16     -7     -8     -3     -5     -4     -3     -6     -3     -3     -5     -9     -6     -5     -4     -4     -3     -4     -3      6
+        ...
+
+11. To generate a heat map for each table with values in it,
+
+        ~user $ egor -l TEMLIST --heatmap 0 --heatmap-values
+
+    which will look like this,
+
+    http://www-cryst.bioc.cam.ac.uk/~semin/images/0.HA.png
+
+12. To generate one big figure, 'myheatmaps.gif' containing all the heat maps (4 maps in a row),
+
+        ~user $ egor -l TEMLIST --heatmap 1 --heatmap-stem myheatmaps --heatmap-format 1 --heatmap-columns 4
+
+    which will look like this,
+
+    http://www-cryst.bioc.cam.ac.uk/~semin/images/myheatmaps.gif
+
+== Repository
+
+You can download a pre-built RubyGems package from
+
+* rubyforge: http://rubyforge.org/projects/egor
 
-* 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)
+or, You can fetch the source from
 
+* github: http://github.com/semin/egor/tree/master
 
-== LICENSE:
 
-(The MIT License)
+== Contact
 
-Copyright (c) 2008 Semin Lee
+Comments are welcome, please send an email to me (seminlee at gmail dot com). 
 
-Permission is hereby granted, free of charge, to any person obtaining
-a copy of this software and associated documentation files (the
-'Software'), to deal in the Software without restriction, including
-without limitation the rights to use, copy, modify, merge, publish,
-distribute, sublicense, and/or sell copies of the Software, and to
-permit persons to whom the Software is furnished to do so, subject to
-the following conditions:
 
-The above copyright notice and this permission notice shall be
-included in all copies or substantial portions of the Software.
+== License
 
-THE SOFTWARE IS PROVIDED 'AS IS', WITHOUT WARRANTY OF ANY KIND,
-EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
-MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
-IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY
-CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT,
-TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
-SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+http://i.creativecommons.org/l/by-nc/2.0/uk/88x31.png
+This work is licensed under a {Creative Commons Attribution-Noncommercial 2.0 UK: England & Wales License}[http://creativecommons.org/licenses/by-nc/2.0/uk/].

data/Rakefile

@@ -5,21 +5,21 @@ require File.dirname(__FILE__) + '/lib/egor'
 # Run 'rake -T' to see list of generated tasks (from gem root directory)
 $hoe = Hoe.new('egor', Egor::VERSION) do |p|
   p.developer('Semin Lee', 'seminlee@gmail.com')
-  p.changes              = p.paragraphs_of("History.txt", 0..1).join("\n\n")
-  p.post_install_message = 'PostInstall.txt' # TODO remove if post-install message not required
-  p.rubyforge_name       = p.name # TODO this is default value
-  p.extra_deps         = [
-    ['narray','>= 0.5.9.5'],
-    ['bio',   '>= 1.2.1'],
-    ['facets','>= 2.4.5'],
-    ['simple_memoize', '>= 1.0.0'],
+  p.changes               = p.paragraphs_of("History.txt", 0..1).join("\n\n")
+  p.post_install_message  = 'PostInstall.txt' # TODO remove if post-install message not required
+  p.rubyforge_name        = p.name # TODO this is default value
+  p.extra_deps            = [
+    ['narray',  '>= 0.5.9.5'],
+    ['bio',     '>= 1.2.1'],
+    ['facets',  '>= 2.4.5'],
+    ['rmagick', '>= 2.9.1'],
   ]
 
   p.extra_dev_deps = [
     ['newgem', ">= #{::Newgem::VERSION}"]
   ]
 
-  p.clean_globs |= %w[**/.DS_Store tmp *.log]
+  p.clean_globs |= %w[**/.DS_Store tmp *.log *.swp]
   path = (p.rubyforge_name == p.name) ? p.rubyforge_name : "\#{p.rubyforge_name}/\#{p.name}"
   p.remote_rdoc_dir = File.join(path.gsub(/^#{p.rubyforge_name}\/?/,''), 'rdoc')
   p.rsync_args = '-av --delete --ignore-errors'

data/egor.gemspec

@@ -2,28 +2,26 @@
 
 Gem::Specification.new do |s|
   s.name = %q{egor}
-  s.version = "0.0.4"
+  s.version = "0.9.0"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Semin Lee"]
-  s.cert_chain = ["/Users/semin/.gem/gem-public_cert.pem"]
-  s.date = %q{2008-12-15}
+  s.date = %q{2009-02-13}
   s.default_executable = %q{egor}
-  s.description = %q{egor: Esst GeneratOR, a program for calculating environment-specific substitution tables}
+  s.description = %q{'egor' is a program for calculating environment-specific substitution tables from user providing environmental class definitions and sequence alignments with the annotations of the environment classes.}
   s.email = ["seminlee@gmail.com"]
   s.executables = ["egor"]
   s.extra_rdoc_files = ["History.txt", "Manifest.txt", "PostInstall.txt", "README.rdoc", "website/index.txt"]
-  s.files = ["History.txt", "Manifest.txt", "PostInstall.txt", "README.rdoc", "Rakefile", "bin/egor", "config/website.yml", "config/website.yml.sample", "egor.gemspec", "lib/egor.rb", "lib/egor/cli.rb", "lib/enumerable_extensions.rb", "lib/environment.rb", "lib/environment_feature.rb", "lib/math_extensions.rb", "lib/narray_extensions.rb", "lib/nmatrix_extensions.rb", "script/console", "script/destroy", "script/generate", "script/txt2html", "test/test_egor.rb", "test/test_egor_cli.rb", "test/test_enumerable_extensions.rb", "test/test_environment_feature.rb", "test/test_helper.rb", "test/test_nmatrix_extensions.rb", "website/index.html", "website/index.txt", "website/javascripts/rounded_corners_lite.inc.js", "website/stylesheets/screen.css", "website/template.html.erb"]
+  s.files = ["History.txt", "Manifest.txt", "PostInstall.txt", "README.rdoc", "Rakefile", "bin/egor", "config/website.yml", "config/website.yml.sample", "egor.gemspec", "lib/egor.rb", "lib/egor/cli.rb", "lib/egor/environment.rb", "lib/egor/environment_class_hash.rb", "lib/egor/environment_feature.rb", "lib/egor/environment_feature_array.rb", "lib/egor/heatmap_array.rb", "lib/math_extensions.rb", "lib/narray_extensions.rb", "lib/nmatrix_extensions.rb", "lib/string_extensions.rb", "script/console", "script/destroy", "script/generate", "script/txt2html", "test/egor/test_cli.rb", "test/egor/test_environment_class_hash.rb", "test/egor/test_environment_feature.rb", "test/test_egor.rb", "test/test_helper.rb", "test/test_math_extensions.rb", "test/test_narray_extensions.rb", "test/test_nmatrix_extensions.rb", "test/test_string_extensions.rb", "website/index.html", "website/index.txt", "website/javascripts/rounded_corners_lite.inc.js", "website/stylesheets/screen.css", "website/template.html.erb"]
   s.has_rdoc = true
-  s.homepage = %q{http://egor.rubyforge.org}
+  s.homepage = %q{http://www-cryst.bioc.cam.ac.uk/egor}
   s.post_install_message = %q{PostInstall.txt}
   s.rdoc_options = ["--main", "README.rdoc"]
   s.require_paths = ["lib"]
   s.rubyforge_project = %q{egor}
   s.rubygems_version = %q{1.3.1}
-  s.signing_key = %q{/Users/semin/.gem/gem-private_key.pem}
-  s.summary = %q{egor: Esst GeneratOR, a program for calculating environment-specific substitution tables}
-  s.test_files = ["test/test_egor.rb", "test/test_egor_cli.rb", "test/test_enumerable_extensions.rb", "test/test_environment_feature.rb", "test/test_helper.rb", "test/test_nmatrix_extensions.rb"]
+  s.summary = %q{'egor' is a program for calculating environment-specific substitution tables from user providing environmental class definitions and sequence alignments with the annotations of the environment classes.}
+  s.test_files = ["test/test_string_extensions.rb", "test/test_nmatrix_extensions.rb", "test/test_math_extensions.rb", "test/test_helper.rb", "test/test_narray_extensions.rb", "test/egor/test_environment_feature.rb", "test/egor/test_cli.rb", "test/egor/test_environment_class_hash.rb", "test/test_egor.rb"]
 
   if s.respond_to? :specification_version then
     current_version = Gem::Specification::CURRENT_SPECIFICATION_VERSION
@@ -33,23 +31,23 @@ Gem::Specification.new do |s|
       s.add_runtime_dependency(%q<narray>, [">= 0.5.9.5"])
       s.add_runtime_dependency(%q<bio>, [">= 1.2.1"])
       s.add_runtime_dependency(%q<facets>, [">= 2.4.5"])
-      s.add_runtime_dependency(%q<simple_memoize>, [">= 1.0.0"])
-      s.add_development_dependency(%q<newgem>, [">= 1.2.1"])
+      s.add_runtime_dependency(%q<rmagick>, [">= 2.9.1"])
+      s.add_development_dependency(%q<newgem>, [">= 1.2.3"])
       s.add_development_dependency(%q<hoe>, [">= 1.8.0"])
     else
       s.add_dependency(%q<narray>, [">= 0.5.9.5"])
       s.add_dependency(%q<bio>, [">= 1.2.1"])
       s.add_dependency(%q<facets>, [">= 2.4.5"])
-      s.add_dependency(%q<simple_memoize>, [">= 1.0.0"])
-      s.add_dependency(%q<newgem>, [">= 1.2.1"])
+      s.add_dependency(%q<rmagick>, [">= 2.9.1"])
+      s.add_dependency(%q<newgem>, [">= 1.2.3"])
       s.add_dependency(%q<hoe>, [">= 1.8.0"])
     end
   else
     s.add_dependency(%q<narray>, [">= 0.5.9.5"])
     s.add_dependency(%q<bio>, [">= 1.2.1"])
     s.add_dependency(%q<facets>, [">= 2.4.5"])
-    s.add_dependency(%q<simple_memoize>, [">= 1.0.0"])
-    s.add_dependency(%q<newgem>, [">= 1.2.1"])
+    s.add_dependency(%q<rmagick>, [">= 2.9.1"])
+    s.add_dependency(%q<newgem>, [">= 1.2.3"])
     s.add_dependency(%q<hoe>, [">= 1.8.0"])
   end
 end