Minor refactoring

.travis.yml

@@ -68,4 +68,5 @@ matrix:
 branches:
   only:
     - master
+    - develop
 

lib/bio/alignment.rb

@@ -1475,22 +1475,21 @@ class SequenceHash < Hash
     module OriginalPrivate
 
       # Gets the sequence from given object.
+      # TODO Quite possibly could be shortened more,
+      # as the first condition appears to be a short circuit
+      # but since `seq` is really an identity, doesn't
+      # make sense.
       def extract_seq(obj)
-        seq = nil
         if obj.is_a?(Bio::Sequence::NA) or obj.is_a?(Bio::Sequence::AA) then
-          seq = obj
+          obj
         else
-          for m in [ :seq, :naseq, :aaseq ]
-            begin
-              seq = obj.send(m)
-            rescue NameError, ArgumentError
-              seq = nil
-            end
-            break if seq
-          end
-          seq = obj unless seq
+          m = [ :seq, :naseq, :aaseq ].find {|m|
+            obj.respond_to? m
+          }
+          m ?
+            obj.send(m) :
+            obj
         end
-        seq
       end
       module_function :extract_seq
 

lib/bio/data/aa.rb

@@ -108,23 +108,21 @@ module Data
     }
 
     def weight(x = nil)
-      if x
-        if x.length > 1
-          total = 0.0
-          x.each_byte do |byte|
-            aa = byte.chr.upcase
-            if WEIGHT[aa]
-              total += WEIGHT[aa]
-            else
-              raise "Error: invalid amino acid '#{aa}'"
-            end
+      return WEIGHT if x.nil?
+
+      if x.length > 1
+        total = 0.0
+        x.each_byte do |byte|
+          aa = byte.chr.upcase
+          if WEIGHT[aa]
+            total += WEIGHT[aa]
+          else
+            raise "Error: invalid amino acid '#{aa}'"
           end
-          total -= NucleicAcid.weight[:water] * (x.length - 1)
-        else
-          WEIGHT[x]
         end
+        total -= NucleicAcid.weight[:water] * (x.length - 1)
       else
-        WEIGHT
+        WEIGHT[x]
       end
     end
 
@@ -172,27 +170,18 @@ def to_3(x)
     alias three to_3
 
     def one2three(x)
-      if x and x.length != 1
-        raise ArgumentError
-      else
-        NAMES[x]
-      end
+      fail ArgumentError if x.nil? or x.length != 1
+      NAMES[x]
     end
 
     def three2one(x)
-      if x and x.length != 3
-        raise ArgumentError
-      else
-        reverse[x]
-      end
+      fail ArgumentError if x.nil? or x.length != 3
+      reverse[x]
     end
 
     def one2name(x)
-      if x and x.length != 1
-        raise ArgumentError
-      else
-        three2name(NAMES[x])
-      end
+      fail ArgumentError if x.nil? or x.length != 1
+      three2name(NAMES[x])
     end
 
     def name2one(x)
@@ -205,11 +194,8 @@ def name2one(x)
     end
 
     def three2name(x)
-      if x and x.length != 3
-        raise ArgumentError
-      else
-        NAMES[x]
-      end
+      fail ArgumentError if x.nil? or x.length != 3
+      NAMES[x]
     end
 
     def name2three(x)
@@ -237,11 +223,7 @@ def to_re(seq)
 
 
     def reverse
-      hash = Hash.new
-      NAMES.each do |k, v|
-        hash[v] = k
-      end
-      hash
+      @reverse ||= NAMES.invert
     end
 
   end
@@ -254,18 +236,6 @@ def reverse
   extend Data
 
 
-  private
-
-
-  # override when used as an instance method to improve performance
-  alias orig_reverse reverse
-  def reverse
-    unless @reverse
-      @reverse = orig_reverse
-    end
-    @reverse
-  end
-
 end
 
 end # module Bio

lib/bio/io/flatfile.rb

@@ -84,17 +84,15 @@ def self.open(*arg, &block)
         raise ArgumentError, 'wrong number of arguments (0 for 1)'
       end
       x = arg.shift
-      if x.is_a?(Module) then
-        # FlatFile.open(dbclass, filename_or_io, ...)
-        dbclass = x
-      elsif x.nil? then
-        # FlatFile.open(nil, filename_or_io, ...)
-        dbclass = nil
-      else
-        # FlatFile.open(filename, ...)
-        dbclass = nil
-        arg.unshift(x)
+
+      dbclass = case x
+        when Module then x # FlatFile.open(dbclass, filename_or_io, ...)
+        when nil then nil # FlatFile.open(nil, filename_or_io, ...)
+        else # FlatFile.open(filename, ...)
+          arg.unshift(x)
+          nil
       end
+
       if arg.size <= 0
         raise ArgumentError, 'wrong number of arguments (1 for 2)'
       end

lib/bio/sequence.rb

@@ -61,20 +61,17 @@ module Bio
 #   puts dna.gc_percent
 class Sequence
 
-  autoload :Common,  'bio/sequence/common'
-  autoload :NA,      'bio/sequence/na'
-  autoload :AA,      'bio/sequence/aa'
-  autoload :Generic, 'bio/sequence/generic'
-  autoload :Format,  'bio/sequence/format'
-  autoload :Adapter, 'bio/sequence/adapter'
-  autoload :QualityScore, 'bio/sequence/quality_score'
-  autoload :SequenceMasker, 'bio/sequence/sequence_masker'
-
-  #--
-  # require "bio/sequence/compat.rb" here to avoid circular require and
-  # possible superclass mismatch of AA class
-  #++
-  require 'bio/sequence/compat'
+  require File.expand_path(File.join File.dirname(__FILE__),"sequence/common.rb")
+  require File.expand_path(File.join File.dirname(__FILE__),"sequence/na.rb")
+  require File.expand_path(File.join File.dirname(__FILE__),"sequence/aa.rb")
+  require File.expand_path(File.join File.dirname(__FILE__),"sequence/generic.rb")
+  require File.expand_path(File.join File.dirname(__FILE__),"sequence/format.rb")
+  require File.expand_path(File.join File.dirname(__FILE__),"sequence/adapter.rb")
+  require File.expand_path(File.join File.dirname(__FILE__),"sequence/quality_score.rb")
+  require File.expand_path(File.join File.dirname(__FILE__),"sequence/sequence_masker.rb")
+
+
+  require File.expand_path(File.join File.dirname(__FILE__),"sequence/compat.rb")
 
   include Format
   include SequenceMasker

lib/bio/sequence/aa.rb

@@ -9,9 +9,10 @@
 
 module Bio
 
-  autoload :AminoAcid, 'bio/data/aa' unless const_defined?(:AminoAcid)
+  require File.expand_path(File.join File.dirname(__FILE__), '../sequence.rb')
+  require File.expand_path(File.join File.dirname(__FILE__), '../sequence/compat.rb')
 
-  require 'bio/sequence' unless const_defined?(:Sequence)
+  require File.expand_path(File.join File.dirname(__FILE__), '../data/aa.rb')
 
 class Sequence
 
@@ -30,9 +31,10 @@ class Sequence
 #
 #   # What is the molecular weight of this peptide?
 #   puts aa.molecular_weight
-class AA < String
+class AA < ::String
 
   include Bio::Sequence::Common
+  extend Bio::Sequence::Common::ClassMethods
 
   # Generate an amino acid sequence object from a string.
   #