exchanged subseq with seq[]

git-svn-id: http://biopieces.googlecode.com/svn/trunk@2285 74ccb610-7750-0410-82ae-013aeee3265d

diff --git a/code_ruby/lib/maasha/seq/trim.rb b/code_ruby/lib/maasha/seq/trim.rb
index 2be3e56800a518a25ce5da5665053b0951d4de8e..cc9b54938dedd8db3aa6bb5bba6ab21eb0be836e 100644 (file)
--- a/code_ruby/lib/maasha/seq/trim.rb
+++ b/code_ruby/lib/maasha/seq/trim.rb
@@ -40,7 +40,7 @@ module Trim
 
     pos = trim_right_pos_c(self.qual, self.length, min_qual, min_len, Seq::SCORE_BASE)
 
-    self.subseq(0, pos)
+    self[0, pos]
   end
 
   # Method to progressively trim a Seq object sequence from the right end until
@@ -50,7 +50,10 @@ module Trim
 
     pos = trim_right_pos_c(self.qual, self.length, min_qual, min_len, Seq::SCORE_BASE)
 
-    self.subseq!(0, pos)
+    self.seq  = self.seq[0, pos]
+    self.qual = self.qual[0, pos] if self.qual
+
+    self
   end
 
   # Method to progressively trim a Seq object sequence from the left end until
@@ -60,7 +63,7 @@ module Trim
 
     pos = trim_left_pos_c(self.qual, self.length, min_qual, min_len, Seq::SCORE_BASE)
 
-    self.subseq(pos)
+    self[pos .. -1]
   end
 
   # Method to progressively trim a Seq object sequence from the left end until
@@ -70,7 +73,10 @@ module Trim
 
     pos = trim_left_pos_c(self.qual, self.length, min_qual, min_len, Seq::SCORE_BASE)
 
-    self.subseq!(pos)
+    self.seq  = self.seq[pos .. -1]
+    self.qual = self.qual[pos .. -1] if self.qual
+
+    self
   end
 
   # Method to progressively trim a Seq object sequence from both ends until a
@@ -83,7 +89,7 @@ module Trim
 
     pos_left = pos_right if pos_left > pos_right
 
-    self.subseq(pos_left, pos_right - pos_left)
+    self[pos_left .. pos_right - 1]
   end
 
   # Method to progressively trim a Seq object sequence from both ends until a
@@ -96,7 +102,10 @@ module Trim
 
     pos_left = pos_right if pos_left > pos_right
 
-    self.subseq!(pos_left, pos_right - pos_left)
+    self.seq  = self.seq[pos_left .. pos_right - 1]
+    self.qual = self.qual[pos_left .. pos_right - 1] if self.qual
+
+    self
   end
 
   # Method to locate a pattern in a sequence and trim all sequence to the left