refactored SeqError/TrimError

git-svn-id: http://biopieces.googlecode.com/svn/trunk@1822 74ccb610-7750-0410-82ae-013aeee3265d

diff --git a/code_ruby/lib/maasha/seq/trim.rb b/code_ruby/lib/maasha/seq/trim.rb
index 09dff899d3727251bbf2c6ff4f8da72971c296fd..a322dc943c313c09840973e53c1f524027bb337d 100644 (file)
--- a/code_ruby/lib/maasha/seq/trim.rb
+++ b/code_ruby/lib/maasha/seq/trim.rb
@@ -23,6 +23,8 @@
 
 require 'inline'
 
+class TrimError < StandardError; end
+
 # Module containing methods for end trimming sequences with suboptimal quality
 # scores.
 module Trim
@@ -97,10 +99,10 @@ module Trim
   # Method to check the arguments for trimming and raise on bad sequence, qualities,
   # and min_qual.
   def check_trim_args(min_qual)
-    raise SeqError, "no sequence"      if self.seq.nil?
-    raise SeqError, "no quality score" if self.qual.nil?
+    raise TrimError, "no sequence"      if self.seq.nil?
+    raise TrimError, "no quality score" if self.qual.nil?
     unless (SCORE_MIN .. SCORE_MAX).include? min_qual
-      raise SeqError, "minimum quality value: #{min_qual} out of range #{SCORE_MIN} .. #{SCORE_MAX}"
+      raise TrimError, "minimum quality value: #{min_qual} out of range #{SCORE_MIN} .. #{SCORE_MAX}"
     end
   end
 

diff --git a/code_ruby/test/maasha/seq/test_trim.rb b/code_ruby/test/maasha/seq/test_trim.rb
index e9695bed953f73d588a7c3eafbd0083e2b40c76a..7c491bb5ba5ddce4a084d1771881446fa3da38cd 100755 (executable)
--- a/code_ruby/test/maasha/seq/test_trim.rb
+++ b/code_ruby/test/maasha/seq/test_trim.rb
@@ -11,22 +11,22 @@ class TestTrim < Test::Unit::TestCase
 
   def test_Trim_quality_trim_with_missing_seq_raises
     @entry.qual = "hhhh"
-    assert_raise(SeqError) { @entry.quality_trim_right(20) }
-    assert_raise(SeqError) { @entry.quality_trim_right!(20) }
-    assert_raise(SeqError) { @entry.quality_trim_left(20) }
-    assert_raise(SeqError) { @entry.quality_trim_left!(20) }
-    assert_raise(SeqError) { @entry.quality_trim(20) }
-    assert_raise(SeqError) { @entry.quality_trim!(20) }
+    assert_raise(TrimError) { @entry.quality_trim_right(20) }
+    assert_raise(TrimError) { @entry.quality_trim_right!(20) }
+    assert_raise(TrimError) { @entry.quality_trim_left(20) }
+    assert_raise(TrimError) { @entry.quality_trim_left!(20) }
+    assert_raise(TrimError) { @entry.quality_trim(20) }
+    assert_raise(TrimError) { @entry.quality_trim!(20) }
   end
 
   def test_Trim_quality_trim_with_missing_qual_raises
     @entry.seq = "ATCG"
-    assert_raise(SeqError) { @entry.quality_trim_right(20) }
-    assert_raise(SeqError) { @entry.quality_trim_right!(20) }
-    assert_raise(SeqError) { @entry.quality_trim_left(20) }
-    assert_raise(SeqError) { @entry.quality_trim_left!(20) }
-    assert_raise(SeqError) { @entry.quality_trim(20) }
-    assert_raise(SeqError) { @entry.quality_trim!(20) }
+    assert_raise(TrimError) { @entry.quality_trim_right(20) }
+    assert_raise(TrimError) { @entry.quality_trim_right!(20) }
+    assert_raise(TrimError) { @entry.quality_trim_left(20) }
+    assert_raise(TrimError) { @entry.quality_trim_left!(20) }
+    assert_raise(TrimError) { @entry.quality_trim(20) }
+    assert_raise(TrimError) { @entry.quality_trim!(20) }
   end
 
   def test_Trim_quality_trim_with_bad_min_raises
@@ -34,12 +34,12 @@ class TestTrim < Test::Unit::TestCase
     @entry.qual = "hhhh"
 
     [-1, 41].each do |min|
-      assert_raise(SeqError) { @entry.quality_trim_right(min) }
-      assert_raise(SeqError) { @entry.quality_trim_right!(min) }
-      assert_raise(SeqError) { @entry.quality_trim_left(min) }
-      assert_raise(SeqError) { @entry.quality_trim_left!(min) }
-      assert_raise(SeqError) { @entry.quality_trim(min) }
-      assert_raise(SeqError) { @entry.quality_trim!(min) }
+      assert_raise(TrimError) { @entry.quality_trim_right(min) }
+      assert_raise(TrimError) { @entry.quality_trim_right!(min) }
+      assert_raise(TrimError) { @entry.quality_trim_left(min) }
+      assert_raise(TrimError) { @entry.quality_trim_left!(min) }
+      assert_raise(TrimError) { @entry.quality_trim(min) }
+      assert_raise(TrimError) { @entry.quality_trim!(min) }
     end
   end