From: martinahansen <martinahansen@74ccb610-7750-0410-82ae-013aeee3265d>
Date: Tue, 22 Nov 2011 14:56:12 +0000 (+0000)
Subject: got rid of type in filesys.rb
X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=178225ead000ff26d6e76a654fceb10000bfc87d;p=biopieces.git

got rid of type in filesys.rb

git-svn-id: http://biopieces.googlecode.com/svn/trunk@1676 74ccb610-7750-0410-82ae-013aeee3265d
---

diff --git a/code_ruby/lib/maasha/fasta.rb b/code_ruby/lib/maasha/fasta.rb
index 05655f6..d4c443b 100644
--- a/code_ruby/lib/maasha/fasta.rb
+++ b/code_ruby/lib/maasha/fasta.rb
@@ -42,9 +42,9 @@ class Fasta < Filesys
     raise FastaError, "Bad FASTA format" if seq_name.nil? or seq.nil?
 
     entry          = Seq.new
-    entry.type     = @type.nil? ? nil : @type.downcase
     entry.seq      = seq.gsub(/\s/, '')
     entry.seq_name = seq_name.sub(/^>/, '').rstrip
+    entry.type     = nil
 
     raise FastaError, "Bad FASTA format" if entry.seq_name.empty?
     raise FastaError, "Bad FASTA format" if entry.seq.empty?
diff --git a/code_ruby/lib/maasha/fastq.rb b/code_ruby/lib/maasha/fastq.rb
index a6b3610..e2a96ea 100644
--- a/code_ruby/lib/maasha/fastq.rb
+++ b/code_ruby/lib/maasha/fastq.rb
@@ -39,10 +39,10 @@ class Fastq < Filesys
       qual           = @io.gets.chomp!
 
       entry          = Seq.new
-      entry.type     = @type.nil? ? nil : @type.downcase
       entry.seq      = seq
       entry.seq_name = seq_name[1 .. seq_name.length]
       entry.qual     = qual
+      entry.type     = nil
 
       entry
     rescue
diff --git a/code_ruby/lib/maasha/filesys.rb b/code_ruby/lib/maasha/filesys.rb
index 00530d6..bed11f0 100644
--- a/code_ruby/lib/maasha/filesys.rb
+++ b/code_ruby/lib/maasha/filesys.rb
@@ -65,10 +65,8 @@ class Filesys
     end
   end
 
-  # TODO figure out what type is for.
-  def initialize(io, type=nil)
-    @io   = io
-    @type = type
+  def initialize(io)
+    @io = io
   end
 
   # Method to close ios.
diff --git a/code_ruby/test/maasha/test_fasta.rb b/code_ruby/test/maasha/test_fasta.rb
index a8ba01c..e52440d 100755
--- a/code_ruby/test/maasha/test_fasta.rb
+++ b/code_ruby/test/maasha/test_fasta.rb
@@ -46,11 +46,6 @@ class FastaTest < Test::Unit::TestCase
     assert_equal("ATCG", fasta.get_entry.seq)
   end
 
-  def test_Fasta_get_entry_obtains_the_correct_type
-    fasta = Fasta.new(StringIO.new(">test\nATCG\n"), 'DNA')
-    assert_equal("dna", fasta.get_entry.type)
-  end
-
   def test_Fasta_get_entry_rstrips_whitespace_from_seq_name
     fasta = Fasta.new(StringIO.new(">test\n\r\t ATCG\n"))
     assert_equal("test", fasta.get_entry.seq_name)
diff --git a/code_ruby/test/maasha/test_fastq.rb b/code_ruby/test/maasha/test_fastq.rb
index 2316fc7..8432207 100755
--- a/code_ruby/test/maasha/test_fastq.rb
+++ b/code_ruby/test/maasha/test_fastq.rb
@@ -40,11 +40,6 @@ class FastqTest < Test::Unit::TestCase
     assert_equal("test1", @fastq.get_entry.seq_name)
   end
 
-  def test_Fasta_get_entry_obtains_the_correct_type
-    fastq = Fastq.new(@io, 'DNA')
-    assert_equal("dna", fastq.get_entry.type)
-  end
-
   def test_Fastq_get_entry_with_two_entries_obtain_correct
     assert_equal("ATCG", @fastq.get_entry.seq)
     assert_equal("atcg", @fastq.get_entry.seq)