From b5a27ee6cfcd801325482ff0d1f4ccd8fbfb81db Mon Sep 17 00:00:00 2001
From: martinahansen <martinahansen@74ccb610-7750-0410-82ae-013aeee3265d>
Date: Fri, 3 Jul 2009 14:40:18 +0000
Subject: [PATCH] clearning ruby dir
git-svn-id: http://biopieces.googlecode.com/svn/trunk@552 74ccb610-7750-0410-82ae-013aeee3265d
---
code_ruby/Maasha/{ => lib}/biopieces.rb | 0
code_ruby/Maasha/lib/seq.rb | 5 +++++
code_ruby/Maasha/test/test_seq.rb | 30 +++++++++++++++----------
code_ruby/Maasha/test_module.rb | 7 ------
4 files changed, 23 insertions(+), 19 deletions(-)
rename code_ruby/Maasha/{ => lib}/biopieces.rb (100%)
delete mode 100755 code_ruby/Maasha/test_module.rb
diff --git a/code_ruby/Maasha/biopieces.rb b/code_ruby/Maasha/lib/biopieces.rb
similarity index 100%
rename from code_ruby/Maasha/biopieces.rb
rename to code_ruby/Maasha/lib/biopieces.rb
diff --git a/code_ruby/Maasha/lib/seq.rb b/code_ruby/Maasha/lib/seq.rb
index ba79c85..f80d397 100644
--- a/code_ruby/Maasha/lib/seq.rb
+++ b/code_ruby/Maasha/lib/seq.rb
@@ -8,6 +8,11 @@ class Seq < String
@seq_type = seq_type
end
+ # Method for outputting sequence as a String.
+ def to_s
+ @seq
+ end
+
# Guess the sequence type by analyzing the first 100 residues allowing for ambiguity codes.
def seq_type_guess
seq_beg = @seq[ 0, 100 ].upcase
diff --git a/code_ruby/Maasha/test/test_seq.rb b/code_ruby/Maasha/test/test_seq.rb
index 7e8c89d..4297720 100755
--- a/code_ruby/Maasha/test/test_seq.rb
+++ b/code_ruby/Maasha/test/test_seq.rb
@@ -28,6 +28,12 @@ class TestSeq < Test::Unit::TestCase
assert_equal( :DNA, s.seq_type )
end
+ # Testing Seq#to_s
+ def test_to_s
+ s = Seq.new( "ATCG" )
+ assert_equal( "ATCG", s.to_s )
+ end
+
# Testing Seq#seq_type_guess
def test_seq_type_guess_DNA_uppercase
@@ -150,19 +156,19 @@ class TestSeq < Test::Unit::TestCase
def test_wrap_with_0_args
s = Seq.new( "ACTGACTAGCATCGACTACGACTGACACGACGACGACGACCGAACGATCGATCGCAGACGACGCAGCATGACGACGTACGACTACGACT" )
- assert_equal( "ACTGACTAGCATCGACTACGACTGACACGACGACGACGACCGAACGATCGATCGCAGACGACGCAGCATGACGACGTACG\nACTACGACT", s.wrap )
+ assert_equal( "ACTGACTAGCATCGACTACGACTGACACGACGACGACGACCGAACGATCGATCGCAGACGACGCAGCATGACGACGTACG\nACTACGACT", s.wrap.to_s )
end
def test_wrap_with_1_args
s = Seq.new( "ATCG" )
- assert_equal( "AT\nCG", s.wrap( 2 ) )
+ assert_equal( "AT\nCG", s.wrap( 2 ).to_s )
end
def test_wrap_with_2_args
s = Seq.new( "ATCG" )
- assert_equal( "AT\rCG", s.wrap( 2, "\r" ) )
+ assert_equal( "AT\rCG", s.wrap( 2, "\r" ).to_s )
end
def test_wrap_dont_change_instance_var
@@ -170,7 +176,7 @@ class TestSeq < Test::Unit::TestCase
s.wrap( 2 )
- assert_equal( "ATCG", s.seq )
+ assert_equal( "ATCG", s.to_s )
end
# Testing Seq#wrap!
@@ -180,7 +186,7 @@ class TestSeq < Test::Unit::TestCase
s.wrap!
- assert_equal( "ACTGACTAGCATCGACTACGACTGACACGACGACGACGACCGAACGATCGATCGCAGACGACGCAGCATGACGACGTACG\nACTACGACT", s.seq )
+ assert_equal( "ACTGACTAGCATCGACTACGACTGACACGACGACGACGACCGAACGATCGATCGCAGACGACGCAGCATGACGACGTACG\nACTACGACT", s.to_s )
end
def test_wrap_with_1_args!
@@ -188,7 +194,7 @@ class TestSeq < Test::Unit::TestCase
s.wrap!( 2 )
- assert_equal( "AT\nCG", s.seq )
+ assert_equal( "AT\nCG", s.to_s )
end
def test_wrap_with_2_args!
@@ -196,7 +202,7 @@ class TestSeq < Test::Unit::TestCase
s.wrap!( 2, "\r" )
- assert_equal( "AT\rCG", s.seq )
+ assert_equal( "AT\rCG", s.to_s )
end
# Testing Seq#generate
@@ -227,7 +233,7 @@ class TestSeq < Test::Unit::TestCase
seq = s.generate( 40 )
- assert_equal( "", s.seq )
+ assert_equal( "", s.to_s )
end
# Testing Seq#generate!
@@ -235,11 +241,11 @@ class TestSeq < Test::Unit::TestCase
def test_generate!
s = Seq.new( "", :AA )
- gen_seq = s.generate!( 40 )
+ gen_seq = s.generate!( 40 ).to_s
assert_equal( 40, gen_seq.length )
assert_equal( 40, s.seq.length )
- assert_equal( gen_seq, s.seq )
+ assert_equal( gen_seq, s.to_s )
end
# Testing Seq::AA#initialize
@@ -247,14 +253,14 @@ class TestSeq < Test::Unit::TestCase
# test marked for deletion - too simple and not informative
def test_Seq_AA_initialize_with_0_args
s = Seq::AA.new
- assert_equal( "", s.seq )
+ assert_equal( "", s.to_s )
assert_equal( :AA, s.seq_type )
end
# test marked for deletion - too simple and not informative
def test_Seq_AA_initialize_with_1_args
s = Seq::AA.new( "SEQ" )
- assert_equal( "SEQ", s.seq )
+ assert_equal( "SEQ", s.to_s )
assert_equal( :AA, s.seq_type )
end
end
diff --git a/code_ruby/Maasha/test_module.rb b/code_ruby/Maasha/test_module.rb
deleted file mode 100755
index a94e234..0000000
--- a/code_ruby/Maasha/test_module.rb
+++ /dev/null
@@ -1,7 +0,0 @@
-class Test
- puts "Modules Test1 loaded"
-
- def greet_world
- puts "Hello"
- end
-end
--
2.39.5