removed subseq and subseq! methods in favor of []

[biopieces.git] / code_ruby / lib / maasha / seq / trim.rb

diff --git a/code_ruby/lib/maasha/seq/trim.rb b/code_ruby/lib/maasha/seq/trim.rb
index e7e9bb1daf6b019e77e78b8eabf44cad1abc2ea5..2ca94542b65c3ed3e6d536b460095295b1f13181 100644 (file)
--- a/code_ruby/lib/maasha/seq/trim.rb
+++ b/code_ruby/lib/maasha/seq/trim.rb
@@ -23,6 +23,9 @@
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 require 'inline'
+require 'maasha/seq/backtrack'
+
+include BackTrack
 
 # Error class for all exceptions to do with Trim.
 class TrimError < StandardError; end
@@ -37,7 +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
@@ -47,7 +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
@@ -57,7 +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
@@ -67,7 +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
@@ -80,7 +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]
   end
 
   # Method to progressively trim a Seq object sequence from both ends until a
@@ -93,7 +102,42 @@ 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]
+    self.qual = self.qual[pos_left ... pos_right] if self.qual
+
+    self
+  end
+
+  # Method to locate a pattern in a sequence and trim all sequence to the left
+  # including the pattern.
+  def patmatch_trim_left!(pattern, options = {})
+    match = self.patmatch(pattern, options)
+
+    if match
+      stop = self.length
+
+      self.seq  = self.seq[match.pos + match.length .. stop]
+      self.qual = self.qual[match.pos + match.length .. stop] if self.qual
+
+      return self
+    end
+
+    nil
+  end
+
+  # Method to locate a pattern in a sequence and trim all sequence to the right
+  # including the pattern.
+  def patmatch_trim_right!(pattern, options = {})
+    match = self.patmatch(pattern, options)
+
+    if match
+      self.seq  = self.seq[0 ... match.pos]
+      self.qual = self.qual[0 ... match.pos] if self.qual
+
+      return self
+    end
+
+    nil
   end
 
   private