polished seq.rb

git-svn-id: http://biopieces.googlecode.com/svn/trunk@1279 74ccb610-7750-0410-82ae-013aeee3265d

diff --git a/code_ruby/Maasha/lib/seq.rb b/code_ruby/Maasha/lib/seq.rb
index 19cd1b1e9fbf6dfce1ad553567803c4626a4bfde..3bb65551d7be576d6ee3314345ff289ddba025b8 100644 (file)
--- a/code_ruby/Maasha/lib/seq.rb
+++ b/code_ruby/Maasha/lib/seq.rb
@@ -252,10 +252,10 @@ class Seq
   # Method that returns a subsequence of a given length
   # beginning at a random position.
   def subseq_rand(length)
-    if self.seq.length - length + 1 == 0
+    if self.length - length + 1 == 0
       start = 0
     else
-      start = rand(self.seq.length - length + 1)
+      start = rand(self.length - length + 1)
     end
 
     self.subseq(start, length)
@@ -308,10 +308,10 @@ class Seq
   # in the sequence that overlaps with the adaptor or -1 if the
   # adaptor was not found.
   def adaptor_locate_right(adaptor)
-    pos = self.seq.length - adaptor.length
+    pos = self.length - adaptor.length
 
-    while pos < self.seq.length
-      len        = self.seq.length - pos
+    while pos < self.length
+      len        = self.length - pos
       subseq     = self.seq[pos ... pos + len].upcase
       subadaptor = adaptor[0 ... len].upcase
 
@@ -361,7 +361,7 @@ class Seq
     pos = self.adaptor_locate_left(adaptor)
 
     if pos > 0
-      self.seq  = self.seq[pos + 1 ... self.seq.length]
+      self.seq  = self.seq[pos + 1 ... self.length]
       self.qual = self.qual[pos + 1 ... self.qual.length] unless self.qual.nil?
     end
   end
@@ -424,7 +424,7 @@ class Digest
     @seq.seq.upcase.scan @pattern do
       pos = $`.length + @cut_pos - 1
      
-      if pos >= 0 and pos < @seq.seq.length - 2
+      if pos >= 0 and pos < @seq.length - 2
         seq = Seq.new("#{@seq.seq_name}[#{@offset}-#{pos}]", @seq.seq[@offset .. pos], @seq.type)
 
         yield seq
@@ -435,11 +435,11 @@ class Digest
 
     if @offset < 0
       @offset = 0
-    elsif @offset > @seq.seq.length
+    elsif @offset > @seq.length
       @offset = 0
     end
 
-    seq = Seq.new("#{@seq.seq_name}[#{@offset}-#{@seq.seq.length - 1}]", @seq.seq[@offset .. @seq.seq.length], @seq.type)
+    seq = Seq.new("#{@seq.seq_name}[#{@offset}-#{@seq.length - 1}]", @seq.seq[@offset .. @seq.length], @seq.type)
 
     yield seq