fixed unit tests for seq.rb

git-svn-id: http://biopieces.googlecode.com/svn/trunk@1916 74ccb610-7750-0410-82ae-013aeee3265d

diff --git a/code_ruby/lib/maasha/seq.rb b/code_ruby/lib/maasha/seq.rb
index b919a7f31cff1a32555960e4fa60a03f4668eb34..d13cdaba9dde6cb68ff5c44f93a9759d5d6174d1 100644 (file)
--- a/code_ruby/lib/maasha/seq.rb
+++ b/code_ruby/lib/maasha/seq.rb
@@ -415,25 +415,18 @@ class Seq
       qual = self.qual[start .. stop] unless self.qual.nil?
     end
 
-    Seq.new(self.seq_name.dup, seq, self.type, qual)
+    Seq.new(self.seq_name, seq, self.type, qual)    # TODO changed self.seq_name.dup to self.seq_name -> consequence?
   end
 
   # Method that replaces a sequence with a subsequence from a given start position
   # and of a given length.
   def subseq!(start, length = self.length - start)
-    raise SeqError, "subsequence start: #{start} < 0"                                                if start  < 0
-    raise SeqError, "subsequence length: #{length} < 0"                                              if length < 0
-    raise SeqError, "subsequence start + length > Seq.length: #{start} + #{length} > #{self.length}" if start + length > self.length
-
-    if length == 0
-      self.seq  = ""
-      self.qual = "" unless self.qual.nil?
-    else
-      stop = start + length - 1
+    s = subseq(start, length)
 
-      self.seq  = self.seq[start .. stop]
-      self.qual = self.qual[start .. stop] unless self.qual.nil?
-    end
+    self.seq_name = s.seq_name
+    self.seq      = s.seq
+    self.type     = s.type
+    self.qual     = s.qual
 
     self
   end