From 85553b339acf3f9285a1c03b2fff342d9ddb9b6b Mon Sep 17 00:00:00 2001
From: Christoph Helma <helma@in-silico.ch>
Date: Wed, 11 Jan 2017 16:00:07 +0100
Subject: documentation for all classes

---
 lib/overwrite.rb | 57 +++++++++++++++++++++++++++++++++++++++++++++-----------
 1 file changed, 46 insertions(+), 11 deletions(-)

(limited to 'lib/overwrite.rb')

diff --git a/lib/overwrite.rb b/lib/overwrite.rb
index 31d30c9..91bc9e1 100644
--- a/lib/overwrite.rb
+++ b/lib/overwrite.rb
@@ -2,41 +2,51 @@ require "base64"
 class Object
   # An object is blank if it's false, empty, or a whitespace string.
   # For example, "", "   ", +nil+, [], and {} are all blank.
+  # @return [TrueClass,FalseClass]
   def blank?
     respond_to?(:empty?) ? empty? : !self
   end
 
+  # Is it a numeric object
+  # @return [TrueClass,FalseClass]
   def numeric?
     true if Float(self) rescue false
   end
 
   # Returns dimension of nested arrays
+  # @return [Fixnum]
   def dimension
     self.class == Array ? 1 + self[0].dimension : 0
   end
 end
 
 class Numeric
+  # Convert number to percent
+  # @return [Float]
   def percent_of(n)
     self.to_f / n.to_f * 100.0
   end
 end
 
 class Float
-  # round to n significant digits
-  # http://stackoverflow.com/questions/8382619/how-to-round-a-float-to-a-specified-number-of-significant-digits-in-ruby
+  # Round to n significant digits
+  #   http://stackoverflow.com/questions/8382619/how-to-round-a-float-to-a-specified-number-of-significant-digits-in-ruby
+  # @param [Fixnum]
+  # @return [Float]
   def signif(n)
     Float("%.#{n}g" % self)
   end
 
-  # converts -10 logarithmized values back
+  # Convert -10 log values to original values
+  # @return [Float]
   def delog10
     10**(-1*self)
   end
 end
 
 module Enumerable
-  # @return [Array] only the duplicates of an enumerable
+  # Get duplicates
+  # @return [Array] 
   def duplicates
     inject({}) {|h,v| h[v]=h[v].to_i+1; h}.reject{|k,v| v==1}.keys
   end
@@ -51,7 +61,10 @@ module Enumerable
 end
 
 class String
-  # @return [String] converts camel-case to underscore-case (OpenTox::SuperModel -> open_tox/super_model)
+  # Convert camel-case to underscore-case
+  # @example 
+  #   OpenTox::SuperModel -> open_tox/super_model
+  # @return [String]
   def underscore
     self.gsub(/::/, '/').
     gsub(/([A-Z]+)([A-Z][a-z])/,'\1_\2').
@@ -60,7 +73,7 @@ class String
     downcase
   end
 
-  # convert strings to boolean values
+  # Convert strings to boolean values
   # @return [TrueClass,FalseClass] true or false
   def to_boolean
     return true if self == true || self =~ (/(true|t|yes|y|1)$/i)
@@ -71,7 +84,8 @@ class String
 end
 
 class File
-  # @return [String] mime_type including charset using linux cmd command
+  # Get mime_type including charset using linux file command
+  # @return [String]
   def mime_type
     `file -ib '#{self.path}'`.chomp
   end
@@ -79,7 +93,7 @@ end
 
 class Array
 
-  # Sum up the size of single arrays in an array of arrays
+  # Sum the size of single arrays in an array of arrays
   # @param [Array] Array of arrays
   # @return [Integer] Sum of size of array elements
   def sum_size
@@ -92,33 +106,43 @@ class Array
     }
   end
 
-  # For symbolic features
+  # Check if the array has just one unique value.
   # @param [Array] Array to test.
-  # @return [Boolean] Whether the array has just one unique value.
+  # @return [TrueClass,FalseClass] 
   def zero_variance?
     return self.uniq.size == 1
   end
 
+  # Get the median of an array
+  # @return [Numeric]
   def median
     sorted = self.sort
     len = sorted.length
     (sorted[(len - 1) / 2] + sorted[len / 2]) / 2.0
   end
 
+  # Get the mean of an array
+  # @return [Numeric]
   def mean
     self.compact.inject{ |sum, el| sum + el }.to_f / self.compact.size
   end
 
+  # Get the variance of an array
+  # @return [Numeric]
   def sample_variance
     m = self.mean
     sum = self.compact.inject(0){|accum, i| accum +(i-m)**2 }
     sum/(self.compact.length - 1).to_f
   end
 
+  # Get the standard deviation of an array
+  # @return [Numeric]
   def standard_deviation
     Math.sqrt(self.sample_variance)
   end
 
+  # Convert array values for R
+  # @return [Array]
   def for_R
     if self.first.is_a?(String) 
       #"\"#{self.collect{|v| v.sub('[','').sub(']','')}.join(" ")}\"" # quote and remove square brackets
@@ -128,6 +152,8 @@ class Array
     end
   end
 
+  # Collect array with index
+  #   in analogy to each_with_index
   def collect_with_index
     result = []
     self.each_with_index do |elt, idx|
@@ -139,11 +165,15 @@ end
 
 module URI
 
+  # Is it a https connection
+  # @param [String]
+  # @return [TrueClass,FalseClass]
   def self.ssl? uri
     URI.parse(uri).instance_of? URI::HTTPS
   end
 
-  # @return [Boolean] checks if resource exists by making a HEAD-request
+  # Check if a http resource exists by making a HEAD-request
+  # @return [TrueClass,FalseClass]
   def self.accessible?(uri)
     parsed_uri = URI.parse(uri + (OpenTox::RestClientWrapper.subjectid ? "?subjectid=#{CGI.escape OpenTox::RestClientWrapper.subjectid}" : ""))
     http_code = URI.task?(uri) ? 600 : 400
@@ -163,6 +193,9 @@ module URI
     false
   end
 
+  # Is the URI valid
+  # @param [String]
+  # @return [TrueClass,FalseClass]
   def self.valid? uri
     u = URI.parse(uri)
     u.scheme!=nil and u.host!=nil
@@ -170,6 +203,8 @@ module URI
     false
   end
 
+  # Is the URI a task URI
+  # @param [String]
   def self.task? uri
     uri =~ /task/ and URI.valid? uri
   end
-- 
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