From: Diane Trout <diane@caltech.edu>
Date: Sat, 1 Jul 2006 06:18:07 +0000 (+0000)
Subject: make sure subsequences have a species name
X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=mussa.git;a=commitdiff_plain;h=2235a6e6326a93f261cfd01fb85f7c832b45935f

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 7523ab6..65ff57d 100644
--- 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 c510739..b331bfa 100644
--- 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 )
 {