@@ -1,15 +1,17 @@ require 'rubygems' require 'statarray' -class Gene < DataMapper::Base +class Gene + include DataMapper::Resource # Each of these defines a accessor method for the class # and each also corresponds to a column in the database - property :name, :string - property :sequence, :text + property :id, Integer, :serial => true + property :name, String + property :sequence, Text # Checks that the sequence has a start codon, a stop codon, and contains only ATGC - validates_format_of :sequence, :with => /^ATG[ATGC\n]+(TAG|TAA|TGA)$/im + validates_format :sequence, :with => /^ATG[ATGC\n]+(TAG|TAA|TGA)$/im def self.create_from_flatfile(entry) @@ -27,17 +29,15 @@ class Gene < DataMapper::Base end def self.mean_length - genes = Gene.find(:all) - genes.map{|gene| gene.sequence.length}.to_statarray.mean + Gene.all.map{|gene| gene.sequence.length}.to_statarray.mean end def self.sd_length - genes = Gene.find(:all) - genes.map{|gene| gene.sequence.length}.to_statarray.stddev + Gene.all.map{|gene| gene.sequence.length}.to_statarray.stddev end def self.bin_sequence_length(n_bins) - lengths = Gene.find(:all).map{|gene| gene.sequence.length} + lengths = Gene.all.map{|gene| gene.sequence.length} min = lengths.min max = lengths.max bin_size = (max - min) / n_bins models/gene.rb 47bfcfb397190e69caf3da26be03327edd4967e7 Michael Barton mail@michaelbarton.me.uk http://github.com/michaelbarton/organised_experiments/commit/d24cba1736eee9f5cdfe400eb16d83fba59d440f d24cba1736eee9f5cdfe400eb16d83fba59d440f 2008-07-25T10:11:31-07:00 2008-07-25T10:11:31-07:00 Updated gene model for new DataMapper compatability. 3f3f31caef00d69e96423b8f64bc1dd7b75b105d Michael Barton mail@michaelbarton.me.uk