make sure subsequences have a species name

copy species name from our source sequence

diff --git a/alg/sequence.cpp b/alg/sequence.cpp
index 7523ab679f3278ab9c2a9446dfb3497b8f1949c9..65ff57d2e326c42bea38346fabcdc2966d34e6a3 100644 (file)
--- a/alg/sequence.cpp
+++ b/alg/sequence.cpp
@@ -457,7 +457,7 @@ Sequence::subseq(int start, int count) const
   }
   Sequence new_seq(std::string::substr(start, count));
   new_seq.set_fasta_header(get_fasta_header());
-  //new_seq.set_species(get_species());
+  new_seq.set_species(get_species());
 
   new_seq.motif_list = motif_list;
   // attempt to copy & reannotate position based annotations 

diff --git a/alg/test/test_sequence.cpp b/alg/test/test_sequence.cpp
index c510739d43120e2706ba9e0b35d97bb0ca57c34b..b331bfaf49462f85e78a63f20a735e9bfcefe919 100644 (file)
--- a/alg/test/test_sequence.cpp
+++ b/alg/test/test_sequence.cpp
@@ -80,6 +80,17 @@ BOOST_AUTO_TEST_CASE( sequence_filter )
   BOOST_CHECK_EQUAL(s3, "AAGGNN");
 }
 
+BOOST_AUTO_TEST_CASE( subseq_names )
+{
+  Sequence s1("AAGGCCTT");
+  s1.set_species("species");
+  s1.set_fasta_header("a fasta header");
+  Sequence s2 = s1.subseq(2,2);
+  BOOST_CHECK_EQUAL(s2, "GG");
+  BOOST_CHECK_EQUAL(s2.get_species(), s1.get_species());
+  BOOST_CHECK_EQUAL(s2.get_fasta_header(), s1.get_fasta_header());
+}
+
 //! Can we load data from a file
 BOOST_AUTO_TEST_CASE( sequence_load )
 {