add to_upper_case to some sequence unittests

forcing sequences to all uppercase (though useful for doing seqcomps and
rendering) does mean that I needed to update tests to deal with the
differences from .get_sequence()

diff --git a/alg/test/test_sequence.cpp b/alg/test/test_sequence.cpp
index f9634ce51f9958535f4b02264552c21c4681e33d..48492f79294fd9535a10210f3522a62f0a608d2f 100644 (file)
--- a/alg/test/test_sequence.cpp
+++ b/alg/test/test_sequence.cpp
@@ -3,6 +3,8 @@
 #include <boost/filesystem/operations.hpp>
 namespace fs=boost::filesystem;
 
+#include <boost/algorithm/string/case_conv.hpp>
+
 #include <list>
 #include <iostream>
 #include <sstream>
@@ -73,7 +75,8 @@ BOOST_AUTO_TEST_CASE( sequence_filter )
   BOOST_CHECK_EQUAL(s2.rev_comp(), "GGCCAATT");
   BOOST_CHECK_EQUAL(s2.rev_comp(), "ggccaatt"); // we should be case insensitive now
   BOOST_CHECK_EQUAL(s2.size(), s2.size());
-  BOOST_CHECK_EQUAL(s2.get_sequence(), "aattggcc");
+  //We're currently forcing sequences to uppercase
+  BOOST_CHECK_EQUAL(s2.get_sequence(), "AATTGGCC"); 
 
   Sequence s3("asdfg", Sequence::reduced_dna_alphabet);
   BOOST_CHECK_EQUAL(s3, "ANNNG");
@@ -100,7 +103,9 @@ BOOST_AUTO_TEST_CASE( sequence_nucleic_alphabet )
   std::string bdv("BDv");
   Sequence seq_bdv(bdv, Sequence::nucleic_alphabet);
   BOOST_CHECK_EQUAL(seq_bdv.size(), bdv.size());
-  BOOST_CHECK_EQUAL(seq_bdv.get_sequence(), bdv);
+  // forcing sequence to upper case
+  BOOST_CHECK_EQUAL(seq_bdv.get_sequence(), 
+                    boost::algorithm::to_upper_copy(bdv));
   
 }
 
@@ -261,7 +266,9 @@ BOOST_AUTO_TEST_CASE( sequence_reverse_complement )
   
   BOOST_CHECK( seq != seqr );
   BOOST_CHECK_EQUAL( seq, seqr.rev_comp() );
-  BOOST_CHECK_EQUAL( seq.get_sequence(), iupac_symbols );
+  // forcing sequence to upper case
+  BOOST_CHECK_EQUAL( seq.get_sequence(), 
+                     boost::algorithm::to_upper_copy(iupac_symbols) );
 }
 
 BOOST_AUTO_TEST_CASE( sequence_reverse_complement_dna )